Molecules for controlling allergic diseases
Molecules targeting IgE antibodies through enhanced FcγRIIB binding degrade these antibodies, addressing the inadequacies of current treatments by effectively reducing allergic responses.
Patent Information
- Application Number
- PCT/US2025/040205
- Authority / Receiving Office
- WO · WO
- Patent Type
- Applications
- Current Assignee / Owner
- Priority Date
- 2025-04-22
- Filing Date
- 2025-07-31
- Publication Date
- 2026-02-05
AI Technical Summary
Current treatments for allergic diseases involving immunoglobulin E (IgE) antibodies are inadequate in selectively targeting and neutralizing these antibodies, leading to ineffective symptom management.
Development of molecules comprising a first polypeptide with an antibody variable domain and a first Fc domain, and a second polypeptide with a second Fc domain, designed to target and degrade IgE antibodies by forming immune complexes that enhance binding to FcγRIIB, thereby depleting these antibodies.
The molecules effectively neutralize and deplete IgE antibodies, reducing allergic responses by inhibiting B cells and minimizing immune cell activation, thus providing targeted treatment for allergic diseases such as food allergy and asthma.
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Figure US2025040205_05022026_PF_FP_ABST
Abstract
Description
Attorney Docket No.: 2017420-0028 MOLECULES FOR CONTROLLING ALLERGIC DISEASES CROSS REFERENCE TO RELATED APPLICATIONS
[0001] This application claims the benefit of U.S. Provisional Applications 63 / 792,842, filed April 22, 2025 and 63 / 678,205, filed August 1, 2024. The contents of the aforementioned applications are hereby incorporated by reference in their entirety. BACKGROUND
[0002] Allergic diseases encompass various conditions caused by hypersensitivity of the immune system to typically harmless substances in the environment called allergens. Certain allergic diseases involve immunoglobulin E (IgE) antibodies, binding to an allergen and to a receptor on mast cells or basophils where it triggers the release of inflammatory chemicals such as histamine. IgE has been shown to play a role in type I hypersensitivity, which manifests in various allergic diseases, such as allergic asthma, most types of sinusitis, allergic rhinitis, food allergies, specific types of chronic urticaria, and atopic dermatitis (see, e.g., Gould et al., Annual Review of Immunology.21: 579–628 (2003), which is herein incorporated by reference in its entirety). Current treatments for allergic diseases include avoiding the allergy trigger and anti-allergic medications to improve symptoms. Allergen immunotherapies have been developed and tested for certain inhalant allergens such as pollen, food allergies, and venoms (see, e.g., Gueguen et al., J. Allergy Clin. Immunol.137, 545–558 (2016); Yu et al., Nat. Rev. Immunol.16, 751–765 (2016); Stock et al., World Allergy Organ. J.14, 100496 (2021), each of which is herein incorporated by reference in their entirety). In recent years, there have been attempts to improve the safety and convenience for patients while retaining efficacy of allergen immunotherapy (see, e.g., Durham et al., Nat Rev Immunol.23, 317–328 (2023), which is herein incorporated by reference in its entirety). Despite this progress there remains a need in the art for methods for controlling allergic diseases including those that involve immunoglobulin E (IgE) antibodies. SUMMARY
[0003] Among other things, in some embodiments, the present disclosure provides a molecule that selectively targets and neutralizes and / or depletes target antibodies (i.e., IgE Page 1 of 203 12904890v1Attorney Docket No.: 2017420-0028 antibodies), to treat, e.g., allergic disease such as food allergy, allergic asthma and chronic hives in a subject.
[0004] Molecules described herein comprise a first polypeptide and a second polypeptide, wherein the first polypeptide comprises an antibody variable domain and a first Fc domain and the second polypeptide comprises a second Fc domain. As described herein, such molecules neutralize and deplete target antibodies (i.e., IgE antibodies). In some embodiments, targeting and depletion of target antibodies (i.e., IgE antibodies) is through a mechanism of targeting immune complexes including the target antibodies (i.e., IgE antibodies) to the lysosome of a cell for degradation.
[0005] Molecules described herein may be used for treatment of allergic disease (e.g., an allergic disease caused by IgE antibodies). In some embodiments, a molecule comprises an antibody variable domain that binds specifically to target antibodies (i.e., IgE antibodies).
[0006] In addition to including an antibody variable domain that binds specifically to target antibodies (i.e., IgE antibodies), a molecule described herein may also include modifications to target specific internalizing receptors. In some embodiments, a molecule described herein includes an Fc domain that binds to a receptor on a cell that causes internalization of the bound molecule. Such molecules allow for binding of IgE antibodies through the antibody variable domain and targeting to the lysosome for degradation through binding of an internalizing receptor. In some embodiments, a molecule may include in its first and / or second Fc domains, a modification that increases its binding affinity to the Fc- gamma–RIIB (FcγRIIB). In some embodiments, a first and / or second Fc domain of a molecule may include a modification that increases its binding affinity to the human neonatal Fc receptor (FcRn).
[0007] In some embodiments, molecules described herein include an additional antibody variable domain, wherein the additional antibody variable domain binds to a receptor on a cell that internalizes the bound molecule. In some embodiments, an additional antibody variable domain binds to an internalizing receptor such as FcγRIIB, ASPGR and / or FcRn. A molecule that targets an internalizing receptor such as FcγRIIB may inhibit / deplete antibody-specific B cells on which the target antibody is expressed on the cell surface (e.g., Page 2 of 203 12904890v1Attorney Docket No.: 2017420-0028 as described in Chu et al., Mol Immunol 45:3926-3933 (2008), which is herein incorporated by reference in its entirety).
[0008] All of such strategies aim to deplete certain target antibodies (i.e., IgE antibodies) implicated in allergic diseases. In some embodiments, a target antibody is an IgE antibody and the allergic disease is an allergic disease caused byMolecules may include an antibody variable domain that targets an IgE antibody and an Fc domain and / or an additional antibody variable domain that targets the complex (molecule and autoantibody) to the lysosome of a cell for selective degradation.
[0009] In one aspect, the present disclosure provides, a molecule comprising: a first polypeptide comprising a first Fc domain and an antibody variable domain that binds to IgE antibodies; and a second polypeptide comprising a second Fc domain; wherein the first Fc domain and the second Fc domain form a homodimer or heterodimer of the first polypeptide and the second polypeptide. In some embodiments, the second polypeptide further comprises an antibody variable domain that binds to IgE antibodies and the molecule is a homodimer. In some embodiments, the second polypeptide further comprises an antibody variable domain that binds to IgE antibodies and the molecule is a heterodimer. In some embodiments, the second polypeptide does not comprise an antibody variable domain that binds to IgE antibodies and the molecule is a heterodimer.
[0010] In some embodiments, the antibody variable domain is covalently linked to the first Fc domain. In some embodiments, the C-terminus of the antibody variable domain is covalently linked to the N-terminus of the first Fc domain. In some embodiments, the N- terminus of the antibody variable domain is covalently linked to the C-terminus of the first Fc domain.
[0011] In some embodiments, the first and second Fc domains form a heterodimer as a result of knobs-in-holes (KIH) mutations. In some embodiments, the KIH mutations comprise Y349T and T394F, according to EU numbering scheme. In some embodiments, the first Fc domain comprises the Y349T mutation and the second Fc domain comprises the T394F mutation. In some embodiments, the KIH mutations comprise T366W, S354C, T366S, L368A, Y407V, and Y349C, according to the EU numbering scheme. In some embodiments, the first Fc domain comprises the T366W, and S354C mutations and the Page 3 of 203 12904890v1Attorney Docket No.: 2017420-0028 second Fc domain comprises the T366S, L368A, Y407V, and Y349C mutations, according to the EU numbering scheme.
[0012] In some embodiments, the first and / or second Fc domains comprise an IgG1 isotype. In some embodiments, the first and / or second Fc domains comprise a human IgG1 isotype.
[0013] In some embodiments, the first and / or second Fc domain comprises one or more mutated amino acid residues that increase half-life. In some embodiments, the first and / or second Fc domain comprises one of the following mutated amino acid residues: M252Y, S254T, and T256E, according to the EU numbering scheme. In some embodiments, the first and / or second Fc domain comprises a combination of the following mutated amino acid residues: M252Y, S254T, and T256E, according to the EU numbering scheme. In some embodiments, the first and / or second Fc domain comprises one of the following mutated amino acid residues: M428L and N434S, according to the EU numbering scheme. In some embodiments, the first and / or second Fc domain comprises a combination of the following mutated amino acid residues: M428L and N434S, according to the EU numbering scheme.
[0014] In some embodiments, the first and / or second Fc domain comprises one or more mutated amino acid residues that increases binding to FcγRIIB relative to a corresponding wildtype Fc domain.
[0015] In some embodiments, the first and / or second Fc domain comprising one or more mutated amino acid residues does not have increased binding affinity to FcγRI, FcγRIIA167H, FcγRIIA167R, FcγRIIIA176F, FcγRIIIA176V, FcγRIIIB, and / or FcRn relative to the corresponding wild-type Fc domain. In some embodiments, the first and / or second Fc domain comprising one or more mutated amino acid residues has decreased binding affinity to FcγRI, FcγRIIA167H, FcγRIIA167R, FcγRIIIA176F, FcγRIIIA176V, FcγRIIIB, and / or FcRn relative to the corresponding wild-type Fc domain. In some embodiments, the first and / or second Fc domain comprising one or more mutated amino acid residues has substantially no binding affinity to FcγRI, FcγRIIA167H, FcγRIIA167R, FcγRIIIA176F, FcγRIIIA176V, FcγRIIIB, and / or FcRn relative to the corresponding wild- type Fc domain. Page 4 of 203 12904890v1Attorney Docket No.: 2017420-0028
[0016] In some embodiments, upon binding of two molecules to an IgE antibody, an immune complex is formed that has enhanced binding kinetics with FcγRIIB relative to an immune complex that comprises the IgE antibody and two corresponding molecules with wild-type Fc domains. In some embodiments, upon binding of two molecules to an IgE antibody, an immune complex is formed that has enhanced binding kinetics with FcγRIIB relative to an immune complex that comprises the IgE antibody bound to only a single molecule. In some embodiments, upon binding of two molecules to an IgE antibody, an immune complex is formed that has enhanced binding kinetics with FcγRIIB relative to the IgE antibody alone. In some embodiments, the enhanced binding kinetics comprise an increase in the rate of association, a decrease in the rate of disassociation, and / or a change in the equilibrium dissociation constant. In some embodiments, the enhanced binding kinetics produce an increase in avidity, stability, strength, frequency, and / or duration of binding between the immune complex and FcγRIIB.
[0017] In some embodiments, the enhanced binding kinetics comprises at least 10% greater binding affinity of the immune complex to FcγRIIB. In some embodiments, the at least 10% greater binding affinity comprises at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, or at least 50% or greater binding affinity. In some embodiments, the molecule binds to FcγRIIB with an affinity within the range of about 1 µM to 0.001 µM. In some embodiments, the molecule binds to FcγRIIB with an affinity within the range of about 1 µM to 0.001 µM. In some embodiments, the molecule binds to FcγRIIB with an affinity within the range of about 0.1 µM to 0.01 µM. In some embodiments, the binding affinity comprises binding affinity to a cell line (e.g., a CHO cell line) overexpressing FcγRIIB measured by flow cytometry.
[0018] In some embodiments, the molecule does not bind to complement component C1q.
[0019] In some embodiments, the molecule preferentially binds to immune cells expressing FcγRIIB over immune cells expressing FcγRIIA. In some embodiments, the molecule comprises substantially no binding affinity for cells that do not express FcγRIIB. In some embodiments, the immune cells expressing FcγRIIB comprise B cells, monocytes and / or basophils. In some embodiments, the immune cells that do not express FcγRIIB comprise T cells, NK cells, neutrophils, and / or eosinophils. Page 5 of 203 12904890v1Attorney Docket No.: 2017420-0028
[0020] In some embodiments, the molecule does not activate immune cells (e.g., does not activate immune cells to secrete pro-inflammatory cytokines, e.g., IL-6).
[0021] In some embodiments, the molecule inhibits B cells by cross-linking FcγRIIB with a B cell receptor. In some embodiments, the molecule cross-links FcγRIIB with a B cell receptor. In some embodiments, an immune complex of one or two molecules with an anti- TSHR autoantibody cross-links FcγRIIB with a B cell receptor.
[0022] In some embodiments, the one or more mutated amino acid residues that increases binding to FcγRIIB comprises one or more of the following amino acid mutations, according to the EU numbering scheme: E233V, L234D, L235F, G236R, G237D, S239L, S267D, H268P, S298G, T299A, A327L, L328A, A330H, E333I, R292Q, E233P, P238D, H268D, P271G, A330R, L234Y, T250V, V264I, T307P, Q311R, A330K, P343R, M428L, N434A, Y436T, Q438R, S440E, G236N, S267E, L235R, D270E, E233D, and G237D.
[0023] In some embodiments, the one or more mutated amino acid residues that increases binding to FcγRIIB comprises one or more of the following sets of amino acid mutations, according to the EU numbering scheme: (i) E233V, L234D, L235F, G236R, G237D, S239L, S267D, H268P, S298G, T299A, A327L, L328A, A330H, and E333I; (ii) E233V, L234D, L235F, G236R, G237D, S239L, S267D, R292Q, H268P, S298G, T299A, A327L, L328A, A330H, and E333I; (iii) E233V, L234D, L235F, G236R, G237D, S239L, H268P, R292Q, S298G, T299A, A327L, L328A, A330H, and E333I; (iv) E233P, G237D, P238D, H268D, P271G, and A330R; (v) L234Y, P238D, T250V, V264I, T307P, Q311R, A330K, P343R, M428L, N434A, Y436T, Q438R, and S440E; (vi) L234D, G236N, and S267E; (vii) L235R; (viii) G236N and S267E; (ix) P238D and D270E; (x) P238D and P271G; (xi) P238D, D270E, and P271G; (xii) G237D, P238D, P271G, and A330R; (xiii) G237D, P238D, D270E, P271G, and A330R; (xiv) E233D, G237D, P238D, H268D, P271G, and A330R; and (xv) P238D.
[0024] In some embodiments, the one or more mutated amino acid residues comprises the mutated amino acid residue P238D, according to the EU numbering scheme. In some embodiments, the one or more mutated amino acid residues comprises the following mutated amino acid residues: P238D and P271G, according to the EU numbering scheme. In some embodiments, the one or more mutated amino acid residues comprises the Page 6 of 203 12904890v1Attorney Docket No.: 2017420-0028 following mutated amino acid residues: G237D, P238D, P271G, and A330R, according to the EU numbering scheme. In some embodiments, the one or more mutated amino acid residues comprises the following mutated amino acid residues: G237D, P238D, D270E, P271G, and A330R, according to the EU numbering scheme. In some embodiments, the one or more mutated amino acid residues does not comprise the following mutated amino acid residues: S267E and L328F, according to the EU numbering scheme.
[0025] In some embodiments, the first and / or second Fc domain comprises the following mutated amino acid residues: L234A, L235A, and P238D, according to the EU numbering scheme. In some embodiments, the first and / or second Fc domain comprises the following mutated amino acid residues: L234A, L235A, P238D and P329G, according to the EU numbering scheme.
[0026] In some embodiments, the first and / or second Fc domain comprises the following mutated amino acid residues: M428L, N434S, and P238D, according to the EU numbering scheme. wherein the first and / or second Fc domain comprises the following mutated amino acid residues: M428L, N434S, P238D, and P271G, according to the EU numbering scheme. In some embodiments, the first and / or second Fc domain comprises the following mutated amino acid residues: M428L, N434S, G237D, P238D, P271G, A330R, according to the EU numbering scheme. In some embodiments, the first and / or second Fc domain comprises the following mutated amino acid residues: M428L, N434S, G237D, P238D, D270E, P271G, A330R, according to the EU numbering scheme.
[0027] In some embodiments, the first and / or second Fc domain comprises the following mutated amino acid residues: P238D, M252Y, S254T, and T256E according to the EU numbering scheme. In some embodiments, the first and / or second Fc domain comprises the following mutated amino acid residues: P238D, M252Y, S254T, T256E and P271G, according to the EU numbering scheme. In some embodiments, the first and / or second Fc domain comprises the following mutated amino acid residues: M252Y, S254T, T256E, G237D, P238D, P271G, A330R, according to the EU numbering scheme. In some embodiments, the first and / or second Fc domain comprises the following mutated amino acid residues: M252Y, S254T, T256E, G237D, P238D, D270E, P271G, A330R, according to the EU numbering scheme. Page 7 of 203 12904890v1Attorney Docket No.: 2017420-0028
[0028] In some embodiments, the first and / or second Fc domain comprises at least one of the following mutated amino acid residues: S267E and L328F, according to the EU numbering scheme. In some embodiments, the first and / or second Fc domain comprise a combination of the following mutated amino acid residues: S267E and L328F, according to the EU numbering scheme.
[0029] In some embodiments, the first and / or second Fc domain comprises one or more mutated amino acid residues that increase binding to FcRn. In some embodiments, the first and / or second Fc domain comprises one or more mutated amino acid residues that increase binding to FcRn at a neutral or near-neutral pH (e.g., pH between about 6.8 and 7.5).
[0030] In some embodiments, the first and second Fc domain comprises a human IgG1 isotype and remains bound to FcRn upon entry into an environment having an acidic pH and / or having low calcium concentration (e.g., into an endosome of a cell). In some embodiments, the first and / or second Fc domain comprises at least one of the following mutated amino acid residues: M252Y, S254T, T256E, H433K, and N434F, according to the EU numbering scheme. In some embodiments, the first and / or second Fc domain comprises a combination of the following mutated amino acid residues: M252Y, S254T, T256E, H433K, and N434F, according to the EU numbering scheme.
[0031] In some embodiments, the first and / or second Fc domain comprises at least one mutated amino acid sequence that decreases binding to one or more Fc-gamma receptors (FcγRs). In some embodiments, the first and / or second Fc domain comprises at least one of the following mutated amino acid residues: G236R and L328R, according to the EU numbering scheme. In some embodiments, the first and / or second Fc domain comprises the following mutated amino acid residues: G236R and L328R, according to the EU numbering scheme.
[0032] In some embodiments, the first Fc domain comprises a sequence selected from SEQ ID NOs: 90, 92, 94, 103, 105, 107, 109, 111-113, 115, 117, 119, 121, 123, 125, 127, 129, 131, 133, 135, 137, 139-149, 163-164, 374-376, 378, 392-407, or 514-534 or a fragment or variant thereof (e.g., a sequence selected from SEQ ID NOs: 107, 109, 113, 115, 119, 131, 139, 140, 142, 148, 374, 378, 533, or 534). Page 8 of 203 12904890v1Attorney Docket No.: 2017420-0028
[0033] In some embodiments, wherein the second Fc domain comprises a sequence selected from SEQ ID NOs: 91, 93, 95, 104, 106, 108, 110, 111, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 139-149, 163-164, 374-375, 377, 379 , 392- 407, or 514-534 or a fragment or variant thereof (e.g., a sequence selected from SEQ ID NOs: 108, 110, 114, 116, 120, 132, 139, 140, 142, 148, 374, 379, 533 or 534).
[0034] In some embodiments, the first antibody variable domain is covalently linked to the first Fc domain through a linker and / or the second antibody variable domain is covalently linked to the second Fc domain through a linker. In some embodiments, the linker comprises the amino acid sequence of SEQ ID NO: 150 (GGGGS), SEQ ID NO: 151 (GGGGSGGGGS), SEQ ID NO: 152 (GGGGSGGGGSGGGGS), SEQ ID NO: 153 (VDGGGGSGGGGSGGGGSG), SEQ ID NO: 154 (GGGGSGGGGSGGGGSGGGGS), SEQ ID NO: 155 (GGGGSGGGGSGGGGSGGGGSSGGGGS), SEQ ID NO: 156 (GSGGS), SEQ ID NO: 157 (GGSG), SEQ ID NO: 158 (GGSGG), SEQ ID NO: 159 (GSGSG), SEQ ID NO: 160 (GSGGG), SEQ ID NO: 161 (GGGSG), or SEQ ID NO: 162 (GSSSG).
[0035] In some embodiments, first and / or second antibody variable domain comprises a Fab, Fab’, Fab’2, Fab2, Fab3, F(ab’)2, Fd, Fv, sdAb, scFv, SMIP, diabody, triabody, tetrabody, minibody, nanobody, maxibody, tandab, DVD, BiTe, TandAb, VHH, or any combination thereof. In some embodiments, the first and / or second antibody variable domain that binds to the IgE antibody comprises a Fab.
[0036] In some embodiments, the first and / or second antibody variable domain that binds to the IgE antibody comprises: (i) an HCDR1 comprising an amino acid sequence of SEQ ID NO: 3, an HCDR2 comprising an amino acid sequence of SEQ ID NO: 4, an HCDR3 comprising an amino acid sequence of SEQ ID NO: 5, an LCDR1 comprising an amino acid sequence of SEQ ID NO: 6, an LCDR2 comprising an amino acid sequence of SEQ ID NO: 7, and an LCDR3 comprising an amino acid sequence of SEQ ID NO: 8; (ii) an HCDR1 comprising an amino acid sequence of SEQ ID NO: 15, an HCDR2 comprising an amino acid sequence of SEQ ID NO: 16, an HCDR3 comprising an amino acid sequence of SEQ ID NO: 17, an LCDR1 comprising an amino acid sequence of SEQ ID NO: 18, an LCDR2 comprising an amino acid sequence of SEQ ID NO: 19, and an LCDR3 comprising an amino acid sequence of SEQ ID NO: 20; (iii) an HCDR1 comprising an amino acid Page 9 of 203 12904890v1Attorney Docket No.: 2017420-0028 sequence of SEQ ID NO: 25, an HCDR2 comprising an amino acid sequence of SEQ ID NO: 26, an HCDR3 comprising an amino acid sequence of SEQ ID NO: 27, an LCDR1 comprising an amino acid sequence of SEQ ID NO: 28, an LCDR2 comprising an amino acid sequence of SEQ ID NO: 29, and an LCDR3 comprising an amino acid sequence of SEQ ID NO: 30; (iv) an HCDR1 comprising an amino acid sequence of SEQ ID NO: 35, an HCDR2 comprising an amino acid sequence of SEQ ID NO: 36, an HCDR3 comprising an amino acid sequence of SEQ ID NO: 37, an LCDR1 comprising an amino acid sequence of SEQ ID NO: 38, an LCDR2 comprising an amino acid sequence of SEQ ID NO: 39, and an LCDR3 comprising an amino acid sequence of SEQ ID NO: 40; (v) an HCDR1 comprising an amino acid sequence of SEQ ID NO: 45, an HCDR2 comprising an amino acid sequence of SEQ ID NO: 46, an HCDR3 comprising an amino acid sequence of SEQ ID NO: 47, an LCDR1 comprising an amino acid sequence of SEQ ID NO: 48, an LCDR2 comprising an amino acid sequence of SEQ ID NO: 49, and an LCDR3 comprising an amino acid sequence of SEQ ID NO: 50; or (vi) an HCDR1 comprising an amino acid sequence of SEQ ID NO: 55, an HCDR2 comprising an amino acid sequence of SEQ ID NO: 56, an HCDR3 comprising an amino acid sequence of SEQ ID NO: 57, an LCDR1 comprising an amino acid sequence of SEQ ID NO: 58, an LCDR2 comprising an amino acid sequence of SEQ ID NO: 59, and an LCDR3 comprising an amino acid sequence of SEQ ID NO: 60.
[0037] In some embodiments, the first and / or second antibody variable domain that binds to the IgE antibody comprises a VH comprising an amino acid sequence having at least 90% identity to any one of SEQ ID NOs: 9, 21, 31, 41, 51, and 61. In some embodiments, the first and / or second antibody variable domain that binds to the IgE antibody comprises a VH comprising an amino acid sequence of any one of SEQ ID NOs: 9, 21, 31, 41, 51, and 61.
[0038] In some embodiments, the first and / or second antibody variable domain that binds to the IgE antibody comprises a VL comprising an amino acid sequence having at least 90% identity to any one of SEQ ID NOs: 10, 22, 32, 42, 52, and 62. In some embodiments, the first and / or second antibody variable domain that binds to the IgE antibody comprises a VL comprising an amino acid sequence of any one of SEQ ID NOs: 10, 22, 32, 42, 52, and 62. Page 10 of 203 12904890v1Attorney Docket No.: 2017420-0028
[0039] In some embodiments, the first polypeptide comprises: (i) an amino acid sequence that is at least 90% identical to SEQ ID NO: 1 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 2; (ii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 11 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 12; (iii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 13 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 14; (iv) an amino acid sequence that is at least 90% identical to SEQ ID NO: 23 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 24; (v) an amino acid sequence that is at least 90% identical to SEQ ID NO: 33 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 34; (vi) an amino acid sequence that is at least 90% identical to SEQ ID NO: 43 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 44; (vii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 53 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 54; (viii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 63 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 65; (ix) an amino acid sequence that is at least 90% identical to SEQ ID NO: 66 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 67; (x) an amino acid sequence that is at least 90% identical to SEQ ID NO: 68 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 69; (xi) an amino acid sequence that is at least 90% identical to SEQ ID NO: 70 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 72; (xii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 73 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 75; (xiii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 76 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 78; (xiv) an amino acid sequence that is at least 90% identical to SEQ ID NO: 79 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 80; (xv) an amino acid sequence that is at least 90% identical to SEQ ID NO: 81 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 182; (xvi) an amino acid sequence that is at least 90% identical to SEQ ID NO: 83 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 84; (xvii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 97 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 98; (xviii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 99 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 100; (xix) an amino acid sequence that is at least 90% identical to SEQ ID NO: 101 and an amino acid sequence that is at least 90% identical to Page 11 of 203 12904890v1Attorney Docket No.: 2017420-0028 SEQ ID NO: 102; (xx) an amino acid sequence that is at least 90% identical to SEQ ID NO: 165 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 166; (xxi) an amino acid sequence that is at least 90% identical to SEQ ID NO: 167 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 168; (xxii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 169 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 170; (xxiii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 171 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 172; (xxiv) an amino acid sequence that is at least 90% identical to SEQ ID NO: 173 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 174; (xxv) an amino acid sequence that is at least 90% identical to SEQ ID NO: 175 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 176; (xxvi) an amino acid sequence that is at least 90% identical to SEQ ID NO: 177 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 178; (xxvii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 179 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 180; (xxviii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 181 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 172; or (xxix) an amino acid sequence that is at least 90% identical to SEQ ID NO: 182 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 174.
[0040] In some embodiments, the first polypeptide comprises: (i) the amino acid sequence of SEQ ID NO: 1 and the amino acid sequence of SEQ ID NO: 2; (ii) the amino acid sequence of SEQ ID NO: 11 and the amino acid sequence of SEQ ID NO: 12; (iii) the amino acid sequence of SEQ ID NO: 13 and the amino acid sequence of SEQ ID NO: 14; (iv) the amino acid sequence of SEQ ID NO: 23 and the amino acid sequence of SEQ ID NO: 24; (v) the amino acid sequence of SEQ ID NO: 33 and the amino acid sequence of SEQ ID NO: 34; (vi) the amino acid sequence of SEQ ID NO: 43 and the amino acid sequence of SEQ ID NO: 44; (vii) the amino acid sequence of SEQ ID NO: 53 and the amino acid sequence of SEQ ID NO: 54; (viii) the amino acid sequence of SEQ ID NO: 63 and the amino acid sequence of SEQ ID NO: 65; (ix) the amino acid sequence of SEQ ID NO: 66 and the amino acid sequence of SEQ ID NO: 67; (x) the amino acid sequence of SEQ ID NO: 68 and the amino acid sequence of SEQ ID NO: 69; (xi) the amino acid sequence of SEQ ID NO: 70 and the amino acid sequence of SEQ ID NO: 72; (xii) the amino acid sequence of SEQ ID NO: 73 and the amino acid sequence of SEQ ID NO: 75; Page 12 of 203 12904890v1Attorney Docket No.: 2017420-0028 (xiii) the amino acid sequence of SEQ ID NO: 76 and the amino acid sequence of SEQ ID NO: 78; (xiv) the amino acid sequence of SEQ ID NO: 79 and the amino acid sequence of SEQ ID NO: 80; (xv) the amino acid sequence of SEQ ID NO: 81 and the amino acid sequence of SEQ ID NO: 182; (xvi): the amino acid sequence of SEQ ID NO: 83 and the amino acid sequence of SEQ ID NO: 84; (xvii) the amino acid sequence of SEQ ID NO: 97 and the amino acid sequence of SEQ ID NO: 98; (xviii) the amino acid sequence of SEQ ID NO: 99 and the amino acid sequence of SEQ ID NO: 100; (xix) the amino acid sequence of SEQ ID NO: 101 and the amino acid sequence of SEQ ID NO: 102; (xx) the amino acid sequence of SEQ ID NO: 165 and the amino acid sequence of SEQ ID NO: 166; (xxi) the amino acid sequence of SEQ ID NO: 167 and the amino acid of SEQ ID NO: 168; (xxii) the amino acid sequence of SEQ ID NO: 169 and the amino acid sequence of SEQ ID NO: 170; (xxiii) the amino acid sequence of SEQ ID NO: 171 and the amino acid sequence of SEQ ID NO: 172; (xxiv) the amino acid sequence of SEQ ID NO: 173 and the amino acid sequence of SEQ ID NO: 174; (xxv) the amino acid sequence of SEQ ID NO: 175 and the amino acid sequence of SEQ ID NO: 176; (xxvi) the amino acid sequence of SEQ ID NO: 177 and the amino acid sequence of SEQ ID NO: 178; (xxvii) the amino acid sequence of SEQ ID NO: 179 and the amino acid sequence of SEQ ID NO: 180; (xxviii) the amino acid sequence of SEQ ID NO: 181 and the amino acid sequence of SEQ ID NO: 172; or (xxix) the amino acid sequence of SEQ ID NO: 182 and the amino acid sequence of SEQ ID NO: 174.
[0041] In some embodiments, the second polypeptide comprises: (i) an amino acid sequence that is at least 90% identical to SEQ ID NO: 1 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 2; (ii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 11 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 12; (iii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 13 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 14; (iv) an amino acid sequence that is at least 90% identical to SEQ ID NO: 23 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 24; (v) an amino acid sequence that is at least 90% identical to SEQ ID NO: 33 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 34; (vi) an amino acid sequence that is at least 90% identical to SEQ ID NO: 43 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 44; (vii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 53 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 54; (viii) an amino acid Page 13 of 203 12904890v1Attorney Docket No.: 2017420-0028 sequence that is at least 90% identical to SEQ ID NO: 64; (ix) an amino acid sequence that is at least 90% identical to SEQ ID NO: 66 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 67; (x) an amino acid sequence that is at least 90% identical to SEQ ID NO: 68 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 69; (xi) an amino acid sequence that is at least 90% identical to SEQ ID NO: 71; (xii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 74; (xiii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 77; (xiv) an amino acid sequence that is at least 90% identical to SEQ ID NO: 79 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 80; (xv) an amino acid sequence that is at least 90% identical to SEQ ID NO: 81 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 182; (xvi): an amino acid sequence that is at least 90% identical to SEQ ID NO: 83 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 84; (xvii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 97 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 98; (xviii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 99 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 100; ; (xix) an amino acid sequence that is at least 90% identical to SEQ ID NO: 101 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 102; (xx) an amino acid sequence that is at least 90% identical to SEQ ID NO: 165 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 166; (xxi) an amino acid sequence that is at least 90% identical to SEQ ID NO: 167 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 168; (xxii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 169 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 170; (xxiii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 171 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 172; (xxiv) an amino acid sequence that is at least 90% identical to SEQ ID NO: 173 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 174; (xxv) an amino acid sequence that is at least 90% identical to SEQ ID NO: 175 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 176; (xxvi) an amino acid sequence that is at least 90% identical to SEQ ID NO: 177 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 178; (xxvii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 179 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 180; (xxviii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 181 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 172; or (xxix) an amino Page 14 of 203 12904890v1Attorney Docket No.: 2017420-0028 acid sequence that is at least 90% identical to SEQ ID NO: 182 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 174.
[0042] In some embodiments, the second polypeptide comprises: (i) an amino acid sequence that is at least 90% identical to SEQ ID NO: 1 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 2; (ii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 11 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 12; (iii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 13 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 14; (iv) an amino acid sequence that is at least 90% identical to SEQ ID NO: 23 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 24; (v) an amino acid sequence that is at least 90% identical to SEQ ID NO: 33 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 34; (vi) an amino acid sequence that is at least 90% identical to SEQ ID NO: 43 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 44; (vii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 53 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 54; (viii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 64; (ix) an amino acid sequence that is at least 90% identical to SEQ ID NO: 66 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 67; (x) an amino acid sequence that is at least 90% identical to SEQ ID NO: 68 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 69; (xi) an amino acid sequence that is at least 90% identical to SEQ ID NO: 71; (xii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 74; (xiii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 77; (xiv) an amino acid sequence that is at least 90% identical to SEQ ID NO: 79 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 80; (xv) an amino acid sequence that is at least 90% identical to SEQ ID NO: 81 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 182; (xvi): an amino acid sequence that is at least 90% identical to SEQ ID NO: 83 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 84; (xvii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 97 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 98; (xviii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 99 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 100; (xix) the amino acid sequence of SEQ ID NO: 101 and the amino acid sequence of SEQ ID NO: 102; (xx) the amino acid sequence of SEQ ID NO: 165 and the Page 15 of 203 12904890v1Attorney Docket No.: 2017420-0028 amino acid sequence of SEQ ID NO: 166; (xxi) the amino acid sequence of SEQ ID NO: 167 and the amino acid of SEQ ID NO: 168; (xxii) the amino acid sequence of SEQ ID NO: 169 and the amino acid sequence of SEQ ID NO: 170; (xxiii) the amino acid sequence of SEQ ID NO: 171 and the amino acid sequence of SEQ ID NO: 172; (xxiv) the amino acid sequence of SEQ ID NO: 173 and the amino acid sequence of SEQ ID NO: 174; (xxv) the amino acid sequence of SEQ ID NO: 175 and the amino acid sequence of SEQ ID NO: 176; (xxvi) the amino acid sequence of SEQ ID NO: 177 and the amino acid sequence of SEQ ID NO: 178; (xxvii) the amino acid sequence of SEQ ID NO: 179 and the amino acid sequence of SEQ ID NO: 180; (xxviii) SEQ ID NO: 181 and SEQ ID NO: 172; or (xxix) SEQ ID NO: 182 and SEQ ID NO: 174.
[0043] In some embodiments, the first polypeptide comprises the amino acid sequence of SEQ ID NO: 1 and SEQ ID NO: 2, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 1 and SEQ ID NO: 2. In some embodiments, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 11 and SEQ ID NO: 12, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 11 and SEQ ID NO: 12. In some embodiments, the first polypeptide comprises the amino acid sequence of SEQ ID NO: 13 and SEQ ID NO: 14, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 13 and SEQ ID NO: 14. In some embodiments, the first polypeptide comprises the amino acid sequence of SEQ ID NO: 23 and SEQ ID NO: 24, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 23 and SEQ ID NO: 24. In some embodiments, the first polypeptide comprises the amino acid sequence of SEQ ID NO: 33 and SEQ ID NO: 34, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 33 and SEQ ID NO: 34. In some embodiments, the first polypeptide comprises the amino acid sequence of SEQ ID NO: 43 and SEQ ID NO: 44, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 43 and SEQ ID NO: 44. In some embodiments, the first polypeptide comprises the amino acid sequence of SEQ ID NO: 53 and SEQ ID NO: 53, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 53 and SEQ ID NO: 54. In some embodiments, the first polypeptide comprises the amino acid sequence of SEQ ID NO: 63 and SEQ ID NO: 65, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 64. In some embodiments, the first polypeptide comprises the amino acid sequence of SEQ ID NO: 66 and SEQ ID NO: 67, and the second polypeptide comprises the amino acid sequence of SEQ Page 16 of 203 12904890v1Attorney Docket No.: 2017420-0028 ID NO: 66 and SEQ ID NO: 67. In some embodiments, the first polypeptide comprises the amino acid sequence of SEQ ID NO: 68 and SEQ ID NO: 69, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 68 and SEQ ID NO: 69. In some embodiments, the first polypeptide comprises the amino acid sequence of SEQ ID NO: 70 and SEQ ID NO: 72, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 71. In some embodiments, the first polypeptide comprises the amino acid sequence of SEQ ID NO: 73 and SEQ ID NO: 75, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 74. In some embodiments, the first polypeptide comprises the amino acid sequence of SEQ ID NO: 76 and SEQ ID NO: 78, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 77. In some embodiments, the first polypeptide comprises the amino acid sequence of SEQ ID NO: 79 and SEQ ID NO: 80, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 79 and SEQ ID NO: 80. In some embodiments, the first polypeptide comprises the amino acid sequence of SEQ ID NO: 81 and SEQ ID NO: 82, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 81 and SEQ ID NO: 82. In some embodiments, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 83 and SEQ ID NO: 84, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 83 and SEQ ID NO: 84. In some embodiments, the first polypeptide comprises the amino acid sequence of SEQ ID NO: 97 and SEQ ID NO: 98, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 97 and SEQ ID NO: 98. In some embodiments, the first polypeptide comprises the amino acid sequence of SEQ ID NO: 99 and SEQ ID NO: 100, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 99 and SEQ ID NO: 100.
[0044] In some embodiments, the first polypeptide comprises the amino acid sequence of SEQ ID NO: 101 and SEQ ID NO: 102, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 101 and SEQ ID NO: 102. In some embodiments, the first polypeptide comprises the amino acid sequence of SEQ ID NO: 165 and SEQ ID NO: 166, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 165 and SEQ ID NO: 166. In some embodiments, the first polypeptide comprises the amino acid sequence of SEQ ID NO: 167 and SEQ ID NO: 168, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 167 and SEQ ID NO: 168. In some embodiments, the first polypeptide comprises the amino acid sequence of SEQ ID NO: 169 and SEQ ID Page 17 of 203 12904890v1Attorney Docket No.: 2017420-0028 NO: 170, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 169 and SEQ ID NO: 170. In some embodiments, the first polypeptide comprises the amino acid sequence of SEQ ID NO: 171 and SEQ ID NO: 172, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 171 and SEQ ID NO: 172. In some embodiments, the first polypeptide comprises the amino acid sequence of SEQ ID NO: 173 and SEQ ID NO: 174, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 173 and SEQ ID NO: 174. In some embodiments, the first polypeptide comprises the amino acid sequence of SEQ ID NO: 175 and SEQ ID NO: 176, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 175 and SEQ ID NO: 176. In some embodiments, the first polypeptide comprises the amino acid sequence of SEQ ID NO: 177 and SEQ ID NO: 178, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 177 and SEQ ID NO: 178. In some embodiments, the first polypeptide comprises the amino acid sequence of SEQ ID NO: 179 and SEQ ID NO: 180, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 179 and SEQ ID NO: 180. In some embodiments, the first polypeptide comprises the amino acid sequence of SEQ ID NO: 181 and SEQ ID NO: 172, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 181 and SEQ ID NO: 172. In some embodiments, the first polypeptide comprises the amino acid sequence of SEQ ID NO: 182 and SEQ ID NO: 174, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 182 and SEQ ID NO: 174.
[0045] In some embodiments, the second Fc domain further comprises a second autoantibody-binding domain. In some embodiments, the N-terminus of the second Fc domain is covalently linked to the C-terminus of the second autoantibody-binding domain. In some embodiments, the C-terminus of the second Fc domain is covalently linked to the N-terminus of the second autoantibody-binding domain.
[0046] In some embodiments, the autoantibody-binding domain binds to an anti- IgE antibody. In some embodiments, the first and second antibody variable domains are the same. In some embodiments, the first and second antibody variable domains are different. In some embodiments, the first and second antibody variable domains bind to different epitopes on an IgE antibody. In some embodiments, the second antibody variable domain binds to a constant domain of the IgE antibody. Page 18 of 203 12904890v1Attorney Docket No.: 2017420-0028
[0047] In some embodiments, the molecule is capable of selectively depleting IgE antibodies that bind to the binding domain when administered to a subject. In some embodiments, the IgE antibodies that bind to the binding domain are selectively depleted by uptake into cells and shuttling of the autoantibodies to the lysosome for degradation.
[0048] In some embodiments, the second polypeptide does not comprise an antibody variable domain that binds to an IgE antibody.
[0049] In another aspect, the present disclosure provides a nucleic acid comprising a nucleotide sequence encoding a molecule of the present disclosure.
[0050] In another aspect, the present disclosure provides a host cell containing a nucleic acid comprising a nucleotide sequence encoding a molecule of the present disclosure.
[0051] In another aspect, the present disclosure provides a vector comprising a nucleic acid comprising a nucleotide sequence encoding a molecule of the present disclosure. In some embodiments, the vector comprises a viral vector. In some embodiments, the viral vector comprises a retroviral vector, a lentiviral vector, an adeno-associated viral (AAV) vector, or an adenoviral vector.
[0052] In another aspect, the present disclosure provides a pharmaceutical composition comprising a molecule of the present disclosure or a nucleic acid encoding a molecule and a pharmaceutically acceptable carrier.
[0053] In another aspect, the present disclosure provides a pharmaceutical composition comprising: a molecule of the present disclosure or a nucleic acid encoding the molecule; a molecule that selectively depletes plasma cells producing the autoantibodies that are targeted by the autoantibody-binding domain, or a nucleic acid encoding the same; and a pharmaceutically acceptable carrier.
[0054] In another aspect, the present disclosure provides a method of making a molecule of the present disclosure, the method comprising expressing a nucleic acid comprising a nucleotide sequence encoding a molecule in a host cell, and recovering the molecule. Page 19 of 203 12904890v1Attorney Docket No.: 2017420-0028
[0055] In another aspect, the present disclosure provides a method of treating a subject suffering from or susceptible to an allergic disease, the method comprising: administering to the subject a pharmaceutical composition comprising a molecule of the present disclosure or a nucleic acid encoding the molecule.
[0056] In another aspect, the present disclosure provides a method of treating a subject suffering from or susceptible to an allergic disease, the method comprising: administering to the subject a first pharmaceutical composition comprising a molecule of the present disclosure or a nucleic acid encoding the molecule; and administering to the subject a second pharmaceutical composition that selectively depletes plasma cells producing autoantibodies that are targeted by the antibody variable domain.
[0057] In some embodiments, the allergic disease is associated with an elevated level of IgE antibodies that is targeted by the antibody variable domain of the molecule.
[0058] In some embodiments, the first pharmaceutical composition is administered before the second pharmaceutical composition. In some embodiments, the first pharmaceutical composition is administered after the second pharmaceutical composition. In some embodiments, the first pharmaceutical composition and the second pharmaceutical composition are co-administered.
[0059] In some embodiments, the level of circulating IgE antibodies is reduced within less than 12 hours of administering the pharmaceutical composition to the subject. In some embodiments, the level of IgE antibodies in the subject or in a biological sample from the subject is reduced after administration relative to a level before administration. In some embodiments, In some embodiments, the level of autoantibodies in the subject or in a biological sample from the subject after administration is reduced relative to a level before administration. In some embodiments, the level of autoantibodies is reduced by at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% relative to a level before the administration. In some embodiments, the reduced level of autoantibodies is sustained over time. In some embodiments, a sustained period of time comprises at least 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 Page 20 of 203 12904890v1Attorney Docket No.: 2017420-0028 weeks, 7 weeks, 8 weeks, 10 weeks, 12 weeks, or longer. In some embodiments, the pharmaceutical composition is administered intravenously, intramuscularly, or subcutaneously to the subject. In some embodiments, the subject is a human.
[0060] In another aspect, the present disclosure provides a method of reducing the level of circulating IgE antibodies in a subject suffering from an allergic disease, the method comprising administering to the subject a pharmaceutical composition of the present disclosure.
[0061] In some embodiments, the level of circulating IgE antibodies is reduced within less than 12 hours of administering the pharmaceutical composition. In some embodiments, the level of IgE antibodies in the subject or in a biological sample from the subject is reduced after administration relative to a level before administration. In some embodiments, reduction of the IgE antibodies occurs within 30 minutes of administering the pharmaceutical composition to the subject.
[0062] In another aspect, the present disclosure provides a composition for decreasing the titer of IgE antibody in the blood serum of a subject in need thereof, the composition comprising: a plurality of molecules, each molecule comprising (a) a first polypeptide comprising a first Fc domain and a first antibody variable domain that binds specifically to an IgE antibody; and (b) a second polypeptide comprising a second Fc domain, wherein the first Fc domain and the second Fc domain form a homodimer or heterodimer of the first polypeptide and the second polypeptide; wherein the first and / or second Fc domain comprises one or more mutated amino acid residues and has increased binding affinity to FcγRIIB relative to a corresponding wild-type Fc domain, and wherein, upon administration of the plurality of molecules, the molecules bind to IgE antibodies to form immune complexes comprising two molecules bound to an IgE antibody, and wherein the immune complex binds with higher avidity to FcγRIIB expressed on the surface of liver sinusoidal endothelial cells (LSECs) and are endocytosed thereby decreasing the titer of the IgE antibodies in the subject’s blood serum, wherein the higher avidity is relative to an immune complex comprising two molecules with wild-type Fc domains.
[0063] In another aspect, the present disclosure provides an immune complex comprising an IgE antibody and two molecules of the present disclosure, wherein the Page 21 of 203 12904890v1Attorney Docket No.: 2017420-0028 immune complex has enhanced binding kinetics with FcγRIIB relative to an immune complex that comprises the IgE antibody bound to two corresponding molecules with wild- type Fc domains.
[0064] In another aspect, the present disclosure provides an immune complex comprising: (i) an IgE antibody; and (ii) two molecules, wherein each molecule comprises: a first polypeptide comprising a first Fc domain and a first antibody variable domain that binds to a constant domain of an IgE antibody; and a second polypeptide comprising a second Fc domain; wherein the first Fc domain and the second Fc domain form a homodimer or heterodimer of the first polypeptide and the second polypeptide, wherein the first and / or second Fc domain comprises one or more mutated amino acid residues and has increased binding affinity to FcγRIIB relative to a corresponding wild-type Fc domain; and wherein the immune complex has enhanced binding kinetics with FcγRIIB relative to an immune complex that comprises the IgE antibody bound to two corresponding molecules with wild-type Fc domains.
[0065] In some embodiments, the enhanced binding kinetics comprise an increase in the rate of association, a decrease in the rate of disassociation, and / or a change in the equilibrium dissociation constant.
[0066] In some embodiments, the enhanced binding kinetics produce an increase in avidity, stability, strength, frequency, and / or duration of the binding between the immune complex and FcγRIIB.
[0067] In some embodiments, the first and / or second Fc domain comprising one or more mutated amino acid residues does not have increased binding affinity to FcγRI, FcγRIIA167H, FcγRIIA167R, FcγRIIIA176F, FcγRIIIA176V, FcγRIIIB, and / or FcRn relative to the corresponding wild-type Fc domain. In some embodiments, the first and / or second Fc domain comprising one or more mutated amino acid residues has decreased binding affinity to FcγRI, FcγRIIA167H, FcγRIIA167R, FcγRIIIA176F, FcγRIIIA176V, FcγRIIIB, and / or FcRn relative to the corresponding wild-type Fc domain. In some embodiments, the first and / or second Fc domain comprising one or more mutated amino acid residues has negligible or no binding affinity to FcγRI, FcγRIIA167H, FcγRIIA167R, Page 22 of 203 12904890v1Attorney Docket No.: 2017420-0028 FcγRIIIA176F, FcγRIIIA176V, FcγRIIIB, and / or FcRn relative to the corresponding wild- type Fc domain.
[0068] In some embodiments, the enhanced binding kinetics comprises at least 10% greater binding affinity of the immune complex to FcγRIIB. In some embodiments, the at least 10% greater binding affinity comprises at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, or at least 50% or greater binding affinity.
[0069] In some embodiments, the binding affinity comprises binding affinity to a cell line (e.g., a CHO cell line) overexpressing FcγRIIB measured by flow cytometry. In some embodiments, the immune complex preferentially binds to immune cells expressing FcγRIIB over immune cells expressing FcγRIIA. In some embodiments, the immune complex cross-links FcγRIIB with a B cell receptor on a B cell. BRIEF DESCRIPTION OF THE DRAWING
[0070] FIG.1A shows a schematic of an exemplary mechanism of action of molecules described herein, wherein Fc mutations are introduced (e.g., P238D) into a bivalent molecule format described herein to facilitate FcγRIIB-mediated clearance of IgE antibodies.
[0071] FIG.1B shows a schematic of an exemplary mechanism of action of molecules described herein, wherein Fc mutations are introduced (e.g., P238D) into a monovalent molecule format described herein to facilitate FcγRIIB-mediated clearance of IgE antibodies.
[0072] FIG.2A shows an exemplary bivalent molecule format described herein.
[0073] FIG.2B shows an exemplary monovalent molecule format described herein.
[0074] FIG.3 shows a representative HPLC-SEC profile of an exemplary bivalent molecule described herein (Variant A3, bivalent omalizumab hIgG1 with P238D mutations).
[0075] FIG.4 shows a representative HPLC-SEC profile of an exemplary monovalent molecule described herein (Variant A5, monovalent omalizumab hIgG1 with P238D mutations). Page 23 of 203 12904890v1Attorney Docket No.: 2017420-0028
[0076] FIG.5 shows exemplary levels of binding affinity and specificity of various exemplary molecules complexed with IgE antibodies for FcγRIIB. Complexes of molecule / IgE bound to FcγRIIB-expressing CHO cells were detected via flow cytometry. Results comparing the following groups: cells incubated with Variant A8 / IgE, Variant A2 / IgE, Variant A3 / IgE, Variant A1 / IgE, and Variant A4 / IgE are shown with resulting MFIs in a bar graph format.
[0077] FIG.6 shows exemplary levels of binding affinity and specificity of various exemplary molecules complexed with IgE antibodies for FcγRIIB. Complexes of molecule / IgE bound to FcγRIIB-expressing CHO cells were detected via flow cytometry. Results comparing the following groups: cells incubated with Variant A8 / IgE, Variant A2 / IgE, Variant A3 / IgE, Variant A1 / IgE, Variant A4 / IgE, Variant B2 / IgE, Variant B1 / IgE, and Variant C4 / IgE are shown with resulting MFIs in a bar graph format.
[0078] FIG.7 shows the pharmacokinetic profile of exemplary molecule Variant A3 when injected intravenously into hFcgR / hFcRn mice. Variant A3 exhibits an antibody-like half-life of 224 ± 2.75 hours.
[0079] FIG.8 shows results from binding assays measuring binding activity of Trastuzumab control, Variant G1, Variant G2, Variant G3, Variant G6, Variant G7, and Variant G8 to activating receptor FcγRIIA167R when molecules were captured onto an SPR sensor chip and FcγR used as the analyte.
[0080] FIG.9 shows results from binding assays measuring binding activity of Variant G9, Variant G10, Variant G11, Variant G12, Variant G13, Variant G14, and Variant G4 to activating receptor FcγRIIA167R when molecules were captured onto an SPR sensor chip and FcγR used as the analyte.
[0081] FIG.10 shows results from binding assays measuring binding activity of Trastuzumab control, Variant G1, Variant G2, Variant G3, Variant G6, Variant G7, and Variant G8 to activating receptor FcγRIIA167H when molecules were captured onto an SPR sensor chip and FcγR used as the analyte.
[0082] FIG.11 shows results from binding assays measuring binding activity of Variant G9, Variant G10, Variant G11, Variant G12, Variant G13, Variant G14, and Variant Page 24 of 203 12904890v1Attorney Docket No.: 2017420-0028 G4 to activating receptor FcγRIIA167H when molecules were captured onto an SPR sensor chip and FcγR used as the analyte.
[0083] FIG.12 shows results from binding assays measuring binding activity of Trastuzumab control, Variant G1, Variant G2, Variant G3, Variant G6, Variant G7, and Variant G8 to inhibitory receptor FcγRIIB when molecules were captured onto an SPR sensor chip and FcγR used as the analyte.
[0084] FIG.13 shows results from binding assays measuring binding activity of Variant G9, Variant G10, Variant G11, Variant G12, Variant G13, Variant G14, and Variant G4 to inhibitory receptor FcγRIIB when molecules were captured onto an SPR sensor chip and FcγR used as the analyte.
[0085] FIG.14 shows a bar graph of mean fluorescence intensities (MFI) of Alexa Fluor 647-labeled autoantibody detecting, by flow cytometry, binding of free molecules at increasing concentrations to FcγRIIB ectopically expressed in a genetically-engineered CHO-K1 cell line (CHO-FcγRIIB). Pre-treatment of CHO-FcγRIIB cells with anti-FcγRIIB blocking antibody clone 2B6 at 10 µg / mL was used to evaluate FcγRIIB-dependent binding of exemplary molecules. MFI values were calculated from live single cells. Each condition was assessed in singlicate.
[0086] FIG.15 shows flow cytometry half-offset histograms of Alexa Fluor 647- labeled autoantibody fluorescence signal representing detection of free molecule binding at increasing concentrations to FcγRIIB ectopically expressed in a genetically-engineered CHO-K1 cell line (CHO-FcγRIIB). Pre-treatment of CHO-FcγRIIB cells with anti-FcγRIIB blocking antibody clone 2B6 at 10 µg / mL was used to evaluate FcγRIIB-dependent binding of exemplary molecules. Signal was calculated from live cell singlets. Each condition was assessed in singlicate.
[0087] FIG.16 shows a bar graph of mean fluorescence intensities (MFI) of Alexa Fluor 647-labeled autoantibody detecting, by flow cytometry, binding of free molecules at increasing concentrations to FcγRIIA167R ectopically expressed in a genetically-engineered CHO-K1 cell line (CHO-FcγRIIA167R). Pre-treatment of CHO-FcγRIIA167R cells with anti-FcγRIIA blocking antibody clone IV.3 at 10 µg / mL was used to evaluate FcγRIIA- dependent binding of molecules. MFI values were calculated from live single cells. Each Page 25 of 203 12904890v1Attorney Docket No.: 2017420-0028 condition was assessed in singlicate. Data represent n=2 biological replicates and mean ± s.d.
[0088] FIG.17 shows flow cytometry half-offset histograms of Alexa Fluor 647- labeled autoantibody fluorescence signal representing detection of free molecule binding at increasing concentrations to FcγRIIA167R ectopically expressed in a genetically-engineered CHO-K1 cell line (CHO-FcγRIIA167R). Pre-treatment of CHO-FcγRIIA167R cells with anti-FcγRIIA blocking antibody clone IV.3 at 10 µg / mL was used to evaluate FcγRIIA- dependent binding of molecules. Signal was calculated from live cell singlets. Representative data from 1 of two independent experiments.
[0089] FIG.18 shows clearance of IgE antibodies by exemplary anti-IgE molecules in serum from humanized FcγR / FcRn mice injected with human IgE (3mg / kg) and later injected with exemplary anti-IgE molecules at 5X molar excess (12mg / kg).
[0090] FIG.19 shows a pharmacokinetic profile of exemplary anti-IgE molecules in serum of humanized FcγR / FcRn mice injected with exemplary anti-IgE molecules at 2.5mg / kg.
[0091] FIG.20 shows surface expression (by mean fluorescent intensity “MFI”) of membrane-bound IgE in Raji cells transduced with lentiviral constructs containing the long (“mIgE L”) and short (“mIgE S”) isoforms of membrane-bound IgE against the bet v1 allergen.
[0092] FIG.21 shows results from western blot measuring phosphorylated FcγRIIB (CD32B) levels in Raji B cells that overexpress either the long isoform (“mIgE L”) or short isoform (“mIgE S”) of membrane-bound IgE against the bet v1 allergen as compared to a control (“Raptor”).
[0093] FIGs.22A-E show binding of exemplary anti-IgE molecules to PBMCs. Specifically, binding was measured between exemplary anti-IgE molecules to CD19+ B cells (FIG.22A), CD14+ monocytes (FIG.22B), CD56+ NK cells (FIG.22C), CD123+CD193+ basophils (FIG.22D), and CD3+ T cells (FIG.22E) with increasing concentrations of exemplary anti-IgE molecules. Page 26 of 203 12904890v1Attorney Docket No.: 2017420-0028
[0094] FIG.23 shows binding of exemplary anti-IgE molecules to complement factor, C1q, measured by ELISA.
[0095] FIG.24 shows percent aggregation of human platelets when incubated with an exemplary molecule alone or pre-complexed with IgE measured by human washed platelet aggregation assay. Anti-CD9 antibody was used as a positive control for aggregation, and human IgE alone was used as a negative control. Omalizumab control and XmAb7195 were also used as controls.
[0096] FIG.25 shows internal body temperature measurements of humanized FcγR / FcRn mice prior to, 30 mins after, and 2 hours after injection with human IgE and an exemplary anti-IgE molecule.
[0097] FIGs.26A-E show binding of exemplary anti-IgE molecules to various subpopulations of isolated PBMCs. Specifically, binding was measured between exemplary anti-IgE molecules to different subpopulations of the PBMCs, including CD19+ B cells (FIG.26A), CD14+ monocytes (FIG.26B), CD3+ T cells (FIG.26C), CD123+CD193+ basophils (FIG.26D), and CD56+ NK cells (FIG.26E), after incubation of the PMBCs with 250nM of exemplary anti-IgE molecules alone or in the presence of an anti-FcγRIIB antibody “2B6”.
[0098] FIGs.27A-E show selective binding of exemplary anti-IgE molecules pre- complexed with IgE antibodies (denoted as “molecule:IgE” or “immune complexes” or “IC”) to various subpopulations of PBMCs. Specifically, binding of the immune complexes was measured in subpopulations of the PBMCs, including CD19+ B cells (FIG.27A), CD14+ monocytes (FIG.27B), CD3+ T cells (FIG.27C), CD123+CD193+ basophils (FIG.27D), and CD56+ NK cells (FIG.27E), after incubation of the PMBCs with 50nM or 250nM of immune complex alone or in the presence of anti-FcγRIIB antibody 2B6.
[0099] FIG.28 shows binding of exemplary anti-IgE molecules to complement factor, C1q, measured by ELISA.
[0100] FIG.29 shows IgE antibody concentration in serum of humanized FcγR / FcRn mice injected with human IgE antibodies (3mg / kg) and later injected with exemplary anti-IgE molecules at 5X molar excess (12mg / kg). Page 27 of 203 12904890v1Attorney Docket No.: 2017420-0028
[0101] FIG.30 shows pharmacokinetic profile and half-life of exemplary anti-IgE molecules, and anti-IgE antibodies omalizumab and XmAb7195 (controls), in serum of humanized FcγR / FcRn mice injected with molecules at 2.5mg / kg.
[0102] FIG.31 shows IgE antibody concentration in serum of humanized FcγR / FcRn mice injected with human IgE antibodies (3mg / kg) and later injected with exemplary anti-IgE molecule (Variant A12, Variant A13, and Variant A14) at 4X molar excess (12mg / kg, denoted as “4:1”) or at equimolar dosing (denoted as “1:1”).
[0103] FIGs 32A-D show pharmacokinetic profiles and bioavailability of exemplary anti-IgE molecules after administration to humanized FcγR / FcRn mice via intravenous (IV) or subcutaneous (SC) injection. Specifically, pharmacokinetic profiles and bioavailability after IV or SC administration are shown for Variant A12 (FIG.32A), Variant A14 (FIG. 32B), Variant A13 (FIG.32C), and control anti-IgE antibody omalizumab (FIG.32D).
[0104] FIG.33 shows concentration of IgE antibodies (ng / mL) in serum of hFcγR / FcRn mice injected with multiple doses of human IgE (3mg / kg) after a single dose of anti-IgE molecule Variant A12 or control IgE antibodies omalizumab and XmAb at various timepoints.
[0105] FIGs.34A-F show results from binding assays measuring binding activity of exemplary anti-IgE molecules Variant A12 (FIG.34A and FIG.34B), Variant A14 (FIG. 34C and FIG.34D), and Variant A13 (FIG.34E and FIG.34F) to inhibitory receptor FcγRIIB when molecules were captured onto an SPR sensor chip and human FcγRIIB used as the analyte. Each exemplary anti-IgE molecule was expressed from two different vector backbones “Config1” and “Config2”.
[0106] FIGs.35A-F show results from binding assays measuring binding activity of exemplary anti-IgE molecules Variant A12 (FIG.35A and FIG.35B), Variant A14 (FIG. 35C and FIG.35D), and Variant A13 (FIG.35E and FIG.35F) to IgE when molecules were captured onto an SPR sensor chip and anti-Betv1 IgE used as the analyte. Each exemplary anti-IgE molecule was expressed from two different vector backbones “Config1” and “Config2”. Page 28 of 203 12904890v1Attorney Docket No.: 2017420-0028 DEFINITIONS
[0107] In order for the present disclosure to be more readily understood, certain terms are first defined below. Additional definitions for the following terms and other terms are set forth throughout the specification. The publications and other reference materials referenced herein to describe the background and to provide additional detail regarding its practice are hereby incorporated by reference.
[0108] The articles “a” and “an” are used herein to refer to one or to more than one (i.e., to at least one) of the grammatical object of the article. By way of example, “an element” means one element or more than one element.
[0109] Administration: As used herein, typically refers to the administration of a composition to a subject or system. Those of ordinary skill in the art will be aware of a variety of routes that may, in appropriate circumstances, be utilized for administration to a subject, for example a human. For example, in some embodiments, administration may be ocular, oral, parenteral, topical, etc.. In some particular embodiments, administration may be bronchial (e.g., by bronchial instillation), buccal, dermal (which may be or comprise, for example, one or more of topical to the dermis, intradermal, interdermal, transdermal, etc.), enteral, intra-arterial, intradermal, intragastric, intramedullary, intramuscular, intranasal, intraperitoneal, intrathecal, intravenous, intraventricular, within a specific organ (e.g., intrahepatic), mucosal, nasal, oral, rectal, subcutaneous, sublingual, topical, tracheal (e.g., by intratracheal instillation), vaginal, vitreal, etc. In some particular embodiments, administration may be parenteral (e.g., by intravenous injection). In some embodiments, administration may involve dosing that is intermittent (e.g., a plurality of doses separated in time) and / or periodic (e.g., individual doses separated by a common period of time) dosing. In some embodiments, administration may involve continuous dosing (e.g., perfusion) for at least a selected period of time.
[0110] Affinity: As is known in the art, “affinity” is a measure of the tightness with which two or more binding partners associate with one another (e.g., an antibody and target antigen). Those skilled in the art are aware of a variety of assays that can be used to assess affinity, and will furthermore be aware of appropriate controls for such assays. In some embodiments, affinity is assessed in a quantitative assay. In some embodiments, affinity is Page 29 of 203 12904890v1Attorney Docket No.: 2017420-0028 assessed over a plurality of concentrations (e.g., of one binding partner at a time). In some embodiments, affinity is assessed in the presence of one or more potential competitor entities (e.g., that might be present in a relevant – e.g., physiological – setting). In some embodiments, affinity is assessed relative to a reference (e.g., that has a known affinity above a particular threshold – a “positive control” reference – or that has a known affinity below a particular threshold – a “negative control” reference”). In some embodiments, affinity may be assessed relative to a contemporaneous reference. In some embodiments, affinity may be assessed relative to a historical reference. Typically, when affinity is assessed relative to a reference, it is assessed under comparable conditions.
[0111] Approximately or about: As used herein and as applied to one or more values of interest, refers to a value that is similar to a stated reference value. In some embodiments, the term “approximately” or “about” refers to a range of values that fall within 20% in either direction (greater than or less than) of the stated reference value unless otherwise stated or otherwise evident from the context (except where such number would exceed 100% of a possible reference value).
[0112] Antibody: As used herein, refers to a polypeptide that includes canonical immunoglobulin sequence elements sufficient to confer specific binding to a particular target antigen. As is known in the art, intact antibodies as produced in nature are tetrameric agents comprising two identical heavy chain polypeptides and two identical light chain polypeptides that associate with each other into what is commonly referred to as a “Y- shaped” structure. Each heavy chain comprises at least four domains – an amino-terminal variable (VH) domain (located at the tips of the Y structure), followed by three constant domains: CH1, CH2, and the carboxy-terminal CH3 (located at the base of the Y’s stem). A short region, known as the “switch”, connects the heavy chain variable and constant regions. The “hinge” connects CH2 and CH3 domains to the rest of the antibody. Two disulfide bonds in this hinge region connect the two heavy chain polypeptides to one another in an intact antibody. Each light chain comprises two domains – an amino-terminal variable (VL) domain, followed by a carboxy-terminal constant (CL) domain, separated from one another by another “switch”. Intact antibody tetramers comprise two heavy chain-light chain dimers in which the heavy and light chains are linked to one another by a single disulfide bond; two other disulfide bonds connect the heavy chain hinge regions to one another, so that the dimers are connected to one another and a tetramer is formed. Naturally produced Page 30 of 203 12904890v1Attorney Docket No.: 2017420-0028 antibodies are also glycosylated, typically on the CH2 domain. Each domain in a natural antibody has a structure characterized by an “immunoglobulin fold” formed from two beta sheets (e.g., 3-, 4-, or 5-stranded sheets) packed against each other in a compressed antiparallel beta barrel. Each variable domain contains three hypervariable loops known as “complementarity determining regions” or “CDRs” (CDR1, CDR2, and CDR3) and four somewhat invariant “framework” regions (FR1, FR2, FR3, and FR4). When natural antibodies fold, the FR regions form the beta sheets that provide the structural framework for the domains, and the CDR loop regions from both the heavy and light chains are brought together in three-dimensional space so that they create a single hypervariable antibody variable domain site located at the tip of the Y structure. The Fc region of naturally occurring antibodies is located at the bottom of the Y structure and binds to elements of the complement system, and also to receptors on effector cells, including, for example, effector cells that mediate cytotoxicity. Affinity and / or other binding attributes of Fc regions for Fc receptors can be modulated through glycosylation or other modification. In some embodiments, antibodies produced and / or utilized in accordance with the present disclosure include glycosylated Fc domains, including Fc domains with modified or engineered glycosylation. In some embodiments, any polypeptide or complex of polypeptides that includes sufficient immunoglobulin domain sequences as found in natural antibodies can be referred to and / or used as an “antibody”, whether such polypeptide is naturally produced (e.g., generated by an organism reacting to an antigen), or produced by recombinant engineering, chemical synthesis, or other artificial system or methodology. In some embodiments, an antibody is polyclonal. In some embodiments, an antibody is monoclonal. In some embodiments, an antibody has constant region sequences that are characteristic of mouse, rabbit, primate, or human antibodies. In some embodiments, antibody sequence elements are humanized, primatized, chimeric, etc., as is known in the art. Moreover, the term “antibody”, as used herein, can refer in appropriate embodiments (unless otherwise stated or clear from context) to any of the art-known or developed constructs or formats for utilizing antibody structural and functional features in alternative presentation. For example, in some embodiments, an antibody utilized in accordance with the present disclosure is in a format selected from, but not limited to, intact IgA, IgG, IgE or IgM antibodies; bi- or multi- specific antibodies; antibody fragments such as is used herein in the broadest sense and encompasses various antibody structures (preferably those fragments that exhibit the desired binding activity). For example, an antibody described herein can be an immunoglobulin, Page 31 of 203 12904890v1Attorney Docket No.: 2017420-0028 heavy chain antibody, light chain antibody, LRR-based antibody, or other protein scaffold with antibody-like properties, as well as any other immunological binding moiety known in the art, including, e.g., a Fab, Fab’, Fab’2, Fab2, Fab3, F(ab’)2, Fd, Fv, sdAb, scFv, SMIP, diabody, triabody, tetrabody, minibody, nanobody, maxibody, tandab, DVD, BiTe, TandAb, or the like, or any combination thereof. The subunit structures and three-dimensional configurations of different classes of antibodies are known in the art. In some embodiments, an antibody may lack a covalent modification (e.g., attachment of a glycan) that it would have if produced naturally. In some embodiments, an antibody may contain a covalent modification, e.g., attachment of a glycan, a cargo moiety (e.g., a detectable moiety, a therapeutic moiety, a catalytic moiety, etc.), or other pendant group (e.g., polyethylene glycol, etc.).
[0113] Antibody variable domain: An “antibody variable domain” refers to a portion of an antibody that binds the antigen to which the intact antibody binds. An antibody variable domain of an antibody includes any naturally occurring, enzymatically obtainable, synthetic, or genetically engineered polypeptide or glycoprotein that specifically binds an antigen to form a complex. Exemplary antibody variable domains include, but are not limited to, a Fab, Fab’, Fab’2, Fab2, Fab3, F(ab’)2, Fd, Fv, sdAb, scFv, SMIP, diabody, triabody, tetrabody, minibody, nanobody, maxibody, tandab, DVD, BiTe, TandAb, or the like, or any combination thereof. In some embodiments, the antibody variable domain of the antibodies described herein are scFvs. In some embodiments, the antibody variable domains of the antibodies described herein are VHH domains only. As with full antibody molecules, antibody variable domains may be mono-specific or multispecific (e.g., bispecific). A multispecific antibody variable domain of an antibody may comprise at least two different variable domains, wherein each variable domain is capable of specifically binding to a separate antigen or to a different epitope of the same antigen.
[0114] Antibody heavy chain: As used herein, refers to the larger of the two types of polypeptide chains present in intact antibodies as produced in nature.
[0115] Antibody light chain: As used herein, refers to the smaller of the two types of polypeptide chains present in intact antibodies as produced in nature. Page 32 of 203 12904890v1Attorney Docket No.: 2017420-0028
[0116] Synthetic antibody: As used herein, refers to an antibody that is generated using recombinant DNA technology. The term should also be construed to mean an antibody which has been generated by the synthesis of a DNA molecule encoding the antibody and which DNA molecule expresses an antibody protein, or an amino acid sequence specifying the antibody, wherein the DNA or amino acid sequence has been obtained using synthetic DNA or amino acid sequence technology which is available and well known in the art.
[0117] Antigen: The term “antigen”, as used herein, refers to a molecule (e.g., a peptide, a polypeptide or a polysaccharide) that elicits a specific immune response. Antigen- specific immunological responses, also known as adaptive immune responses, are mediated by lymphocytes (e.g., T cells, B cells, NK cells) that express antigen receptors (e.g., T cell receptors, B cell receptors). In some embodiments, an antigen is a T cell antigen, and elicits a cellular immune response. In some embodiments, an antigen is a B cell antigen, and elicits a humoral (i.e., antibody) response. In some embodiments, an antigen is both a T cell antigen and a B cell antigen. As used herein, the term “antigen” encompasses both a full- length polypeptide as well as a portion or immunogenic fragment of the polypeptide, and a peptide epitope within the polypeptides (e.g., a peptide epitope bound by a Major Histocompatibility Complex (MHC) molecule (e.g., MHC class I, or MHC class II)). In some embodiments, an antigen is an autoantigen. In some embodiments, an antigen is tissue-specific or non-specific, e.g., identified from a cell or tissue that is a target of an autoimmune response, or from a healthy cell or tissue.
[0118] Associated: Two events or entities are “associated” with one another, as that term is used herein, if the presence, level, degree, type and / or form of one is correlated with that of the other. For example, a particular entity (e.g., polypeptide, genetic signature, metabolite, microbe, etc.) is considered to be associated with a particular disease, disorder, or condition, if its presence, level and / or form correlates with incidence of, susceptibility to, severity of, stage of, etc. the disease, disorder, or condition (e.g., across a relevant population).
[0119] Binding domain: As used herein, refers to a moiety or entity that specifically binds to a target moiety or entity. Typically, the interaction between a binding domain and its target is non-covalent. In some embodiments, a binding domain may be or comprise a Page 33 of 203 12904890v1Attorney Docket No.: 2017420-0028 moiety or entity of any chemical class including, for example, a carbohydrate, a lipid, a nucleic acid, a metal, a polypeptide, a small molecule. In some embodiments, a binding domain may be or comprise a polypeptide (or complex thereof). In some embodiments, a binding domain may be or comprise a target-binding portion of an antibody agent, a cytokine, a ligand (e.g., a receptor ligand), a receptor, a toxin, etc. In some embodiments, a binding domain may be or comprise an aptamer. In some embodiments, a binding domain may be or comprise a peptide nucleic acid (PNA). In some embodiments, a binding domain binds an antibody (i.e., a “target antibody”).
[0120] Effective amount: As used herein with reference to a dose of an agent, refers to a dose that is adequate to prevent or treat a target disease or disorder in a subject. Amounts effective for a therapeutic or prophylactic use will depend on, for example, the stage and severity of the disease or disorder being treated, the age, weight, and general state of health of the subject, and the judgment of the prescribing physician. The size of the dose will also be determined by the agent selected, method of administration, timing and frequency of administration, the existence, nature, and extent of any adverse side effects that might accompany the administration of a particular agent, and the desired physiological effect. It will be appreciated by one of skill in the art that various diseases or disorders could require prolonged treatment involving multiple administrations, perhaps using the inventive molecules in each or various rounds of administration.
[0121] Encoding: As used herein, “encoding” refers to the inherent property of specific sequences of nucleotides in a polynucleotide, such as a gene, a cDNA, or an mRNA, to serve as templates for synthesis of other polymers and macromolecules in biological processes having either a defined sequence of nucleotides (i.e., rRNA, tRNA and mRNA) or a defined sequence of amino acids and the biological properties resulting therefrom. Thus, a gene encodes a protein if transcription and translation of mRNA corresponding to that gene produces the protein in a cell or other biological system. Both the coding strand, the nucleotide sequence of which is identical to the mRNA sequence and is usually provided in sequence listings, and the non-coding strand, used as the template for transcription of a gene or cDNA, can be referred to as encoding the protein or other product of that gene or cDNA.
[0122] Epitope: as used herein, refers to a moiety that is specifically recognized by an immunoglobulin (e.g., antibody) binding component. In some embodiments, an epitope Page 34 of 203 12904890v1Attorney Docket No.: 2017420-0028 is comprised of a plurality of chemical atoms or groups on an antigen. In some embodiments, such chemical atoms or groups are surface-exposed when the antigen adopts a relevant three-dimensional conformation. In some embodiments, such chemical atoms or groups are physically near to each other in space when the antigen adopts such a conformation. In some embodiments, at least some such chemical atoms are groups are physically separated from one another when the antigen adopts an alternative conformation (e.g., is linearized or denatured).
[0123] Expression: As used herein, the term “expression” of a nucleic acid sequence refers to generation of any gene product from a nucleic acid sequence. In some embodiments, a gene product can be a transcript. In some embodiments, a gene product can be a polypeptide. In some embodiments, expression of a nucleic acid sequence involves one or more of the following: (1) production of an RNA template from a DNA sequence (e.g., by transcription); (2) processing of an RNA transcript (e.g., by splicing, editing, 5’ cap formation, and / or 3’ end formation); (3) translation of an RNA into a polypeptide or protein; and (4) post-translational modification of a polypeptide or protein.
[0124] Fragment: As used herein, the terms “fragment” or “portion” refers to a structure that includes a discrete portion of the whole, but lacks one or more moieties found in the whole structure. In some embodiments, a fragment consists of such a discrete portion. In some embodiments, a fragment consists of or comprises a characteristic structural element or moiety found in the whole. In some embodiments, a nucleotide fragment comprises or consists of at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, or more monomeric units (e.g., nucleic acids) as found in the whole nucleotide. In some embodiments, a nucleotide fragment comprises or consists of at least about 5%, 10%, 15%, 20%, 25%, 30%, 25%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or more of the monomeric units (e.g., nucleic acids) found in the whole nucleotide. In some embodiments, a polypeptide or protein fragment comprises or consists of at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, or more monomeric units (e.g., amino acids) as found in the whole polypeptide or protein. In some Page 35 of 203 12904890v1Attorney Docket No.: 2017420-0028 embodiments, a polypeptide or protein fragment comprises or consists of at least about 5%, 10%, 15%, 20%, 25%, 30%, 25%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or more of the monomeric units (e.g., amino acids) found in the whole polypeptide or protein. The whole material or entity may, in some embodiments, be referred to as the “parent” of the fragment.
[0125] Identity: As used herein, the term “identity” refers to the overall relatedness between polymeric molecules, e.g., between nucleic acid molecules (e.g., DNA molecules and / or RNA molecules) and / or between polypeptide molecules. In some embodiments, polymeric molecules are considered to be “substantially identical” to one another if their sequences are at least 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% identical. Calculation of the percent identity of two nucleic acid or polypeptide sequences, for example, can be performed by aligning the two sequences for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second sequences for optimal alignment and non-identical sequences can be disregarded for comparison purposes). In some embodiments, the length of a sequence aligned for comparison purposes is at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or substantially 100% of the length of a reference sequence. The nucleotides at corresponding positions are then compared. When a position in the first sequence is occupied by the same residue (e.g., nucleotide or amino acid) as the corresponding position in the second sequence, then the molecules are identical at that position. The percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which needs to be introduced for optimal alignment of the two sequences. The comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm. For example, the percent identity between two nucleotide sequences can be determined using the algorithm of Meyers and Miller (CABIOS, 1989, 4: 11-17), which has been incorporated into the ALIGN program (version 2.0). In some exemplary embodiments, nucleic acid sequence comparisons made with the ALIGN program use a PAM120 weight residue table, a gap length penalty of 12 and a gap penalty of 4. The percent identity between two nucleotide sequences can, alternatively, be determined using the GAP program in the GCG software package using an NWSgapdna.CMP matrix. Page 36 of 203 12904890v1Attorney Docket No.: 2017420-0028
[0126] Human antibody: As used herein, is intended to include antibodies having variable and constant regions generated (or assembled) from human immunoglobulin sequences. In some embodiments, antibodies (or antibody components) may be considered to be “human” even though their amino acid sequences include residues or elements not encoded by human germline immunoglobulin sequences (e.g., include sequence variations, for example that may (originally) have been introduced by random or site-specific mutagenesis in vitro or by somatic mutation in vivo), for example in one or more CDRs and in particular CDR3.
[0127] Immune cell: As used herein, refers to a cell that is involved in an immune response, e.g., promotion of an immune response. Examples of immune cells include, but are not limited to, T-lymphocytes, natural killer (NK) cells, macrophages, monocytes, dendritic cells, neutrophils, eosinophils, mast cells, platelets, large granular lymphocytes, Langerhans’ cells, plasma cells, or B-lymphocytes. A source of immune cells (e.g., T lymphocytes) can be obtained from a subject.
[0128] Immune mediator: As used herein, the term “immune mediator” refers to any molecule that affects the cells and processes involved in immune responses. Immune mediators include cytokines, chemokines, soluble proteins, enzymes, and cell surface markers.
[0129] Immune response: As used herein, refers to a cellular and / or systemic response to an antigen that occurs when an immune cell identifies an antigenic molecule as foreign and induces the formation of antibodies and / or activates itself or other immune cells to remove the antigen.
[0130] Immunoglobulin or Ig: As used herein, refers to a class of proteins that function as antibodies. Antibodies expressed by B cells are sometimes referred to as a BCR (B cell receptor) or antigen receptor. The five members included in this class of proteins are IgA, IgG, IgM, IgD, and IgE. IgA is the primary antibody that is present in body secretions, such as saliva, tears, breast milk, gastrointestinal secretions and mucus secretions of the respiratory and genitourinary tracts. IgG is the most common circulating antibody. IgM is the main immunoglobulin produced in the primary immune response in most subjects. It is the most efficient immunoglobulin in agglutination, complement fixation, and other Page 37 of 203 12904890v1Attorney Docket No.: 2017420-0028 antibody responses, and is important in defense against bacteria and viruses. IgD is an immunoglobulin that has no known antibody function, but may serve as an antigen receptor. IgE is an immunoglobulin that mediates immediate hypersensitivity by causing release of mediators from mast cells and basophils upon exposure to allergen.
[0131] Improved, increased or reduced: As used herein, the terms “improved”, “increased” or “reduced”, or grammatically comparable comparative terms, indicate values that are relative to a comparable reference measurement. For example, in some embodiments, an assessed value achieved with an agent of interest may be “improved” relative to that obtained with a comparable reference agent. Alternatively or additionally, in some embodiments, an assessed value achieved in a subject or system of interest may be “improved” relative to that obtained in the same subject or system under different conditions (e.g., prior to or after an event such as administration of an agent of interest), or in a different, comparable subject (e.g., in a comparable subject or system that differs from the subject or system of interest in presence of one or more indicators of a particular disease, disorder or condition of interest, or in prior exposure to a condition or agent, etc.). In some embodiments, comparative terms refer to statistically relevant differences (e.g., that are of a prevalence and / or magnitude sufficient to achieve statistical relevance). Those skilled in the art will be aware, or will readily be able to determine, in a given context, a degree and / or prevalence of difference that is required or sufficient to achieve such statistical significance.
[0132] Isolated: As used herein, refers to something altered or removed from the natural state. For example, a nucleic acid or a polypeptide naturally present in a living animal is not “isolated,” but the same nucleic acid or polypeptide partially or completely separated from the coexisting materials of its natural state is “isolated.” An isolated nucleic acid or polypeptide can exist in substantially purified form, or can exist in a non-native environment such as, for example, a host cell.
[0133] KD: As used herein, refers to the dissociation constant of a binding agent (e.g., an antibody or binding component thereof) from a complex with its partner (e.g., the epitope to which the antibody or binding component thereof binds). Page 38 of 203 12904890v1Attorney Docket No.: 2017420-0028
[0134] Koff: As used herein, refers to the off rate constant for dissociation of a binding agent (e.g., an antibody or binding component thereof) from a complex with its partner (e.g., the epitope to which the antibody or binding component thereof binds).
[0135] Kon: As used herein, refers to the on rate constant for association of a binding agent (e.g., an antibody or binding component thereof) with its partner (e.g., the epitope to which the antibody or binding component thereof binds).
[0136] Modulating: As used herein the term “modulating,” refers to mediating a detectable increase or decrease in the level of a response and / or a change in the nature of a response in a subject compared with the level and / or nature of a response in the subject in the absence of a treatment, and / or compared with the level and / or nature of a response in an otherwise identical but untreated subject. The term encompasses perturbing and / or affecting a native signal or response thereby mediating a beneficial therapeutic response in a subject, preferably, a human.
[0137] Nucleic acid: As used herein, refers to a polymer of at least three nucleotides. In some embodiments, a nucleic acid comprises DNA. In some embodiments, a nucleic acid comprises RNA. In some embodiments, a nucleic acid is single stranded. In some embodiments, a nucleic acid is double stranded. In some embodiments, a nucleic acid comprises both single and double stranded portions. In some embodiments, a nucleic acid comprises a backbone that comprises one or more phosphodiester linkages. In some embodiments, a nucleic acid comprises a backbone that comprises both phosphodiester and non-phosphodiester linkages. For example, in some embodiments, a nucleic acid may comprise a backbone that comprises one or more phosphorothioate or 5’-N-phosphoramidite linkages and / or one or more peptide bonds, e.g., as in a “peptide nucleic acid”. In some embodiments, a nucleic acid comprises one or more, or all, natural residues (e.g., adenine, cytosine, deoxyadenosine, deoxycytidine, deoxyguanosine, deoxythymidine, guanine, thymine, uracil). In some embodiments, a nucleic acid comprises one or more, or all, non- natural residues. In some embodiments, a non-natural residue comprises a nucleoside analog (e.g., 2-aminoadenosine, 2-thiothymidine, inosine, pyrrolo-pyrimidine, 3 -methyl adenosine, 5-methylcytidine, C-5 propynyl-cytidine, C-5 propynyl-uridine, 2- aminoadenosine, C5-bromouridine, C5-fluorouridine, C5-iodouridine, C5-propynyl-uridine, C5 -propynyl-cytidine, C5-methylcytidine, 2-aminoadenosine, 7-deazaadenosine, 7- Page 39 of 203 12904890v1Attorney Docket No.: 2017420-0028 deazaguanosine, 8-oxoadenosine, 8-oxoguanosine, 0(6)-methylguanine, 2-thiocytidine, methylated bases, intercalated bases, and combinations thereof). In some embodiments, a non-natural residue comprises one or more modified sugars (e.g., 2’-fluororibose, ribose, 2’- deoxyribose, arabinose, and hexose) as compared to those in natural residues. In some embodiments, a nucleic acid has a nucleotide sequence that encodes a functional gene product such as an RNA or polypeptide. In some embodiments, a nucleic acid has a nucleotide sequence that comprises one or more introns. In some embodiments, a nucleic acid may be prepared by isolation from a natural source, enzymatic synthesis (e.g., by polymerization based on a complementary template, e.g., in vivo or in vitro, reproduction in a recombinant cell or system, or chemical synthesis. In some embodiments, a nucleic acid is at least 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 20, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 600, 700, 800, 900, 1000, 1500, 2000, 2500, 3000, 3500, 4000, 4500, 5000 or more residues long.
[0138] Operably linked: As used herein, refers to functional linkage between, for example, a regulatory sequence and a heterologous nucleic acid sequence resulting in expression of the latter. For example, a first nucleic acid sequence is operably linked with a second nucleic acid sequence when the first nucleic acid sequence is placed in a functional relationship with the second nucleic acid sequence. For instance, a promoter is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence. Generally, operably linked DNA sequences are contiguous and, where necessary to join two protein coding regions, in the same reading frame.
[0139] Pharmaceutical composition: As used herein, refers to an active agent, formulated together with one or more pharmaceutically acceptable carriers. In some embodiments, an active agent of interest is present in unit dose amount appropriate for administration in a therapeutic regimen that shows a statistically significant probability of achieving a predetermined therapeutic effect when administered to a relevant population. In some embodiments, pharmaceutical compositions may be specially formulated for administration in solid or liquid form, including those adapted for the following: oral administration, for example, drenches (aqueous or non-aqueous solutions or suspensions), tablets, e.g., those targeted for buccal, sublingual, and systemic absorption, boluses, powders, granules, pastes for application to the tongue; parenteral administration, for Page 40 of 203 12904890v1Attorney Docket No.: 2017420-0028 example, by subcutaneous, intramuscular, intravenous or epidural injection as, for example, a sterile solution or suspension, or sustained-release formulation; topical application, for example, as a cream, ointment, or a controlled-release patch or spray applied to the skin, lungs, or oral cavity; intravaginally or intrarectally, for example, as a pessary, cream, or foam; sublingually; ocularly; transdermally; or nasally, pulmonary, and to other mucosal surfaces.
[0140] Polynucleotide: As used herein, refers to a chain of nucleotides. Furthermore, nucleic acids are polymers of nucleotides. Thus, nucleic acids and polynucleotides as used herein are interchangeable. One skilled in the art has the general knowledge that nucleic acids are polynucleotides, which can be hydrolyzed into the monomeric “nucleotides.” The monomeric nucleotides can be hydrolyzed into nucleosides. As used herein polynucleotides include, but are not limited to, all nucleic acid sequences which are obtained by any means available in the art, including, without limitation, recombinant means, i.e., the cloning of nucleic acid sequences from a recombinant library or a cell genome, using ordinary cloning technology and PCR, and the like, and by synthetic means.
[0141] Protein: As used herein, refers to a polypeptide (i.e., a string of at least two amino acids linked to one another by peptide bonds). Thus, proteins and polypeptides as used herein are interchangeable. Proteins may include moieties other than amino acids (e.g., may be glycoproteins, proteoglycans, etc.) and / or may be otherwise processed or modified. Those of ordinary skill in the art will appreciate that a “protein” can be a complete polypeptide as produced by a cell (with or without a signal sequence), or can be a characteristic portion thereof. Those of ordinary skill will appreciate that a protein can sometimes include more than one polypeptide, for example linked by one or more disulfide bonds or associated by other covalent or non-covalent means. Polypeptides may contain L- amino acids, D-amino acids, or both and may contain any of a variety of amino acid modifications or analogs known in the art. Useful modifications include, e.g., terminal acetylation, amidation, methylation, etc. In some embodiments, proteins may comprise natural amino acids, non-natural amino acids, synthetic amino acids, and combinations thereof. The term “peptide” is generally used to refer to a polypeptide having a length of less than about 100 amino acids, less than about 50 amino acids, less than 20 amino acids, or Page 41 of 203 12904890v1Attorney Docket No.: 2017420-0028 less than 10 amino acids. In some embodiments, proteins are antibodies, antibody fragments, biologically active portions thereof, and / or characteristic portions thereof.
[0142] Specifically binds: As used herein, the term “specifically binds,” with respect to an antibody variable domain, such as those found in an antibody, refers to an antibody variable domain which recognizes a specific antigen, but does not substantially recognize or bind other molecules in a sample. For example, an antibody variable domain that specifically binds to an antigen from one species may also bind to that antigen from one or more other species. But, such cross-species reactivity does not itself alter the classification of an antibody variable domain as specific. In another example, an antibody variable domain that specifically binds to an antigen may also bind to different allelic forms of the antigen. However, such cross reactivity does not itself alter the classification of an antibody variable domain as specific. In some instances, the terms “specific binding” or “specifically binding,” can be used in reference to the interaction of an antibody variable domain with a second chemical species, to mean that the interaction is dependent upon the presence of a particular structure (e.g., an antigenic determinant or epitope) on the chemical species; for example, an antibody variable domain recognizes and binds to a specific protein structure rather than to proteins generally. If an antibody variable domain is specific for epitope “A”, the presence of a molecule containing epitope A (or free, unlabeled A), in a reaction containing labeled “A” and the antibody variable domain, will reduce the amount of labeled A bound to the antibody variable domain.
[0143] Subject: As used herein, refers to an organism, for example, a mammal (e.g., a human, a non-human mammal, a non-human primate, a primate, a laboratory animal, a mouse, a rat, a hamster, a gerbil, a cat, or a dog). In some embodiments a human subject is an adult, adolescent, or pediatric subject. In some embodiments, a subject is suffering from a disease, disorder or condition, e.g., a disease, disorder, or condition that can be treated as provided herein, e.g., a an autoimmune disease. In some embodiments, a subject is susceptible to a disease, disorder, or condition; in some embodiments, a susceptible subject is predisposed to and / or shows an increased risk (as compared to the average risk observed in a reference subject or population) of developing the disease, disorder, or condition. In some embodiments, a subject displays one or more symptoms of a disease, disorder, or condition. In some embodiments, a subject does not display a particular symptom (e.g., clinical manifestation of disease) or characteristic of a disease, disorder, or condition. In Page 42 of 203 12904890v1Attorney Docket No.: 2017420-0028 some embodiments, a subject does not display any symptom or characteristic of a disease, disorder, or condition. In some embodiments, a subject is a patient. In some embodiments, a subject is an individual to whom diagnosis and / or therapy is and / or has been administered.
[0144] Target: As used herein, refers to a cell, tissue, organ, or site within the body that is the subject of provided methods, systems, and / or compositions, for example, a cell, tissue, organ or site within a body that is in need of treatment or is preferentially bound by, for example, a molecule described herein.
[0145] Treat: As used herein, the term “treat,” “treatment,” or “treating” refers to partial or complete alleviation, amelioration, delay of onset of, inhibition, prevention, relief, and / or reduction in incidence and / or severity of one or more symptoms or features of a disease, disorder, and / or condition. In some embodiments, treatment may be administered to a subject who does not exhibit signs or features of a disease, disorder, and / or condition (e.g., may be prophylactic). In some embodiments, treatment may be administered to a subject who exhibits only early or mild signs or features of the disease, disorder, and / or condition, for example for the purpose of decreasing the risk of developing pathology associated with the disease, disorder, and / or condition. In some embodiments, treatment may be administered to a subject who exhibits established, severe, and / or late-stage signs of the disease, disorder, or condition. As used herein, a “therapeutic” is any agent used to treat a subject.
[0146] Vector: As used herein, the term “vector” refers to a composition of matter that comprises an isolated nucleic acid and which can be used to deliver the isolated nucleic acid to the interior of a cell. Numerous vectors are known in the art including, but not limited to, linear polynucleotides, polynucleotides associated with ionic or amphiphilic compounds, plasmids, and viruses. Thus, the term “vector” includes an autonomously replicating plasmid or a virus. The term should also be construed to include non-plasmid and non-viral components which facilitate transfer of nucleic acid into cells, such as, for example, polylysine compounds, liposomes, and the like. Examples of viral vectors include, but are not limited to, adenoviral vectors, adeno-associated virus vectors, retroviral vectors, lentiviral vectors, and the like. Page 43 of 203 12904890v1Attorney Docket No.: 2017420-0028
[0147] Throughout this disclosure, various aspects can be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on scope. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 2.7, 3, 4, 5, 5.3, and 6. This applies regardless of the breadth of the range. DETAILED DESCRIPTION Allergic Disease
[0148] In some embodiments, molecules described herein may be used for the treatment of, e.g., allergic diseases such as food allergy, allergic asthma, and chronic hives. Allergic diseases encompass various conditions caused by hypersensitivity of the immune system to typically harmless substances in the environment. Current treatments for allergic disease include avoiding the allergy trigger and anti-allergic medications to improve symptoms. Allergen immunotherapies have been developed and tested for certain inhalant allergens such as pollen, food allergies, and venoms (see, e.g., Gueguen et al., J. Allergy Clin. Immunol.137, 545–558 (2016); Yu et al., Nat. Rev. Immunol.16, 751–765 (2016); Stock et al., World Allergy Organ. J.14, 100496 (2021), each of which is herein incorporated by reference in their entirety). In recent years, there have been attempts to improve the safety and convenience for patients while retaining efficacy of allergen immunotherapy (see, e.g., Durham et al., Nat Rev Immunol.23, 317–328 (2023), which is herein incorporated by reference in its entirety).
[0149] The present disclosure encompasses molecules for selectively depleting IgE antibodies, to treat allergic diseases. Molecules described herein in some embodiments include a first polypeptide comprising a first Fc domain and a first antibody variable domain that binds to a constant domain of an IgE antibody; and a second polypeptide comprising a second Fc domain; wherein the first Fc domain and the second Fc domain form a homodimer or heterodimer of the first polypeptide and the second polypeptide, wherein the Page 44 of 203 12904890v1Attorney Docket No.: 2017420-0028 first and / or second Fc domain comprises one or more mutated amino acid residues that increases binding affinity to FcγRIIB relative to a corresponding wild-type Fc domain; and wherein upon binding of two molecules to the IgE antibody, an immune complex is formed that has enhanced binding kinetics with FcγRIIB relative to an immune complex that comprises the IgE antibody bound to two corresponding molecules with wild-type Fc domains. In some embodiments, the second polypeptide further comprises a second antibody variable domain that binds to a constant domain of an IgE antibody (i.e., the molecule is bivalent). In some such embodiments, the first and second antibody variable domains are identical. In some embodiments, the second polypeptide does not further comprise a second antibody variable domain that binds to a constant domain of an IgE antibody (i.e., the molecule is monovalent).
[0150] The disclosure provides, among other things, molecules that selectively target and deplete IgE antibodies, for example, by targeting them to FcγRIIB receptors which bind to and internalize the complex into a cell for lysosomal degradation. In addition to including an antibody variable domain that binds to a constant domain of an IgE antibody, a molecule may also include in its first and / or second Fc domains, a modification that increases its binding to FcγRIIB. Allergic Disease and IgE
[0151] In some embodiments, molecules described herein may be used for the treatment of allergic disease (e.g., an allergic disease caused by IgE antibodies), by including an antibody variable domain that binds specifically to target antibodies (i.e., IgE antibodies).
[0152] Allergic disease occurs when a subject’s immune system exhibits a hypersensitive response to a foreign protein or antigen. In some embodiments, an allergic disease is rhinitis, sinusitis, eczema, hives, asthma, allergic dermatitis, atopic dermatitis, a drug allergy, or a food allergy. Symptoms of allergic disease may include, for example, rash, runny nose, itchy eyes, watery eyes, sneezing, coughing, rash, vomiting, shortness of breath, and swelling.
[0153] Without wishing to be bound to any theory, in some embodiments, an underlying mechanism of allergic diseases involves immunoglobulin E (IgE) antibodies, Page 45 of 203 12904890v1Attorney Docket No.: 2017420-0028 binding to an allergen and to a receptor on mast cells or basophils where it triggers the release of inflammatory chemicals such as histamine. IgE has been shown to play a role in type I hypersensitivity, which manifests in various allergic diseases, such as allergic asthma, most types of sinusitis, allergic rhinitis, food allergies, specific types of chronic urticaria, and atopic dermatitis (see, e.g., Gould et al., Annual Review of Immunology.21: 579–628 (2003), which is herein incorporated by reference in its entirety).
[0154] IgE antibodies have a high affinity cell surface receptor, FcεRI, and a low affinity receptor FcεRII (e.g., CD23) (see, e.g., Gould et al., Nat Rev Immunol.8:205–217 (2008), which is herein incorporated by reference in its entirety). Each Fcε receptor recognizes a distinct epitope located on opposite sites of the Cε3 domain of the IgE constant region, and binding of one receptor to this domain prevents binding of the other to IgE. In some embodiments, IgE that can specifically recognize an allergen (e.g., dust mite, pollen, food protein, etc.) has a unique long-lived interaction with its high-affinity receptor FcεRI such that basophils and mast cells become “primed”, ready to release chemicals involved in immune response, such as histamine, leukotrienes, and certain interleukins.
[0155] Molecules described herein include a further selectivity to target IgE antibodies that implicate allergic disease. This strategy includes, in some embodiments, utilizing an antibody variable domain that binds to a constant region of an IgE antibody, for targeted destruction of IgE antibodies, thus removing the immune response that implicates allergic disease. Exemplary Molecules
[0156] The present disclosure provides molecules for selectively depleting and neutralizing target antibodies (i.e., IgE antibodies), to treat, e.g., allergic disease such as food allergy, allergic asthma, and chronic hives. Molecules described herein in some embodiments include a first polypeptide comprising a first Fc domain and an antibody variable domain that binds specifically to target antibodies (i.e., IgE antibodies); and a second polypeptide comprising a second Fc domain; wherein the first Fc domain and the second Fc domain form a homodimer or heterodimer of the first polypeptide and the second polypeptide. In some embodiments, the molecule is bivalent and the second polypeptide further comprises an antibody variable domain that binds to target antibodies (i.e., IgE Page 46 of 203 12904890v1Attorney Docket No.: 2017420-0028 antibodies). In some embodiments, the molecule is monovalent and the second polypeptide does not comprise an antibody variable domain that binds to target antibodies (i.e., IgE antibodies).
[0157] In some embodiments, the first and / or second polypeptide further comprises an additional antibody variable domain that binds to an internalizing receptor expressed on the surface of a cell.
[0158] In some embodiments, a first and second polypeptide of a molecule described herein can be in the form of a fusion protein. In some embodiments, a first and second polypeptide of a molecule described herein can be in the form of a chemically conjugated molecule.
[0159] In some embodiments, the first and / or second Fc domain comprises one or more mutated amino acid residues and has increased binding affinity to an internalizing receptor (e.g., FcγRIIB) relative to a corresponding wild-type Fc domain.
[0160] In some embodiments, upon binding of one or two molecules to an IgE antibody, an immune complex is formed. In some embodiments, immune complexes formed with one molecule described herein and an IgE antibody, have enhanced binding kinetics with FcγRIIB relative to an immune complex that comprises the IgE antibody bound to one corresponding molecule with wild-type Fc domains. In some embodiments, immune complexes formed with two molecules described herein and an IgE antibody have enhanced binding kinetics with FcγRIIB relative to an immune complex that comprises the IgE antibody bound to two corresponding molecules with wild-type Fc domains. Such enhanced binding kinetics increases clearance of the immune complex. Antibody variable domains that bind IgE
[0161] The present disclosure provides molecules that include an antibody variable domain that specifically binds to an IgE antibody. An antibody variable domain may include any domain that binds to an IgE antibody. In some embodiments, an antibody variable domain targets any portion or region or epitope on an IgE antibody. In some embodiments, an antibody variable comprises a Fab, Fab’, Fab’2, Fab2, Fab3, F(ab’)2, Fd, Fv, sdAb, scFv, Page 47 of 203 12904890v1Attorney Docket No.: 2017420-0028 SMIP, diabody, triabody, tetrabody, minibody, nanobody, maxibody, tandab, DVD, BiTe, TandAb, VHH, or any combination thereof.
[0162] In some embodiments, a molecule provided herein includes two or more antibody variable domains that bind to an IgE antibody, e.g., a first antibody variable domain comprised in the first polypeptide and a second antibody variable domain comprised in the second polypeptide. In some embodiments, an antibody variable domain binds to a constant domain of an IgE antibody. In some embodiments, a first and / or second antibody variable domain that binds to an IgE antibody comprises a Fab.
[0163] In some embodiments, an antibody variable domain described herein blocks engagement of the IgE antibody with FcεRIA and / or FcεRII.
[0164] In some embodiments, a first and / or second antibody variable domain that binds to an IgE antibody comprises sequences that are at least 90% identical to any one of SEQ ID NOs: 3-10, 15-22, 25-32, 35-42, 45-52, or 55-62 (shown below in Table 1). In some embodiments, a first and / or second antibody variable domain that binds to an IgE antibody comprises sequences selected from any one of SEQ ID NOs: 3-10, 15-22, 25-32, 35-42, 45-52, or 55-62 (shown below in Table 1).
[0165] In some embodiments, a first and / or second antibody variable domain that binds to an IgE antibody comprises sequences that are at least 90% identical to SEQ ID NOs: 9 and 10, SEQ ID NOs: 21 and 22, SEQ ID NOs: 31 and 32, SEQ ID NOs: 41 and 42, SEQ ID NOs: 51 and 52, or SEQ ID NOs: 61 and 62 (shown below in Table 1). In some embodiments, a first and / or second antibody variable domain that binds to an IgE antibody comprises sequences selected from SEQ ID NOs: 9 and 10, SEQ ID NOs: 21 and 22, SEQ ID NOs: 31 and 32, SEQ ID NOs: 41 and 42, SEQ ID NOs: 51 and 52, or SEQ ID NOs: 61 and 62 (shown below in Table 1).
[0166] In some embodiments, a first and / or second antibody variable domain that binds to an IgE antibody comprises sequences selected from SEQ ID NOs: 3-8, SEQ ID NOs: 15-20, SEQ ID NOs: 25-30, SEQ ID NOs: 35-40, SEQ ID NOs: 45-50, or SEQ ID NOs: 55-60 (shown below in Table 1). Page 48 of 203 12904890v1Attorney Docket No.: 2017420-0028 Table 1: Exemplary Antibody Variable Domain Sequences Name Targeted Descripti SEQ ID Sequence Domain on NO:12904890v1Attorney Docket No.: 2017420-0028 LCDR3 20QQSWSWPTTPage 50 of 203 12904890v1Attorney Docket No.: 2017420-0028 MEDI4212b Cε3 / Cε4 VH 51EVQLVQSGAEVKKPGATVKISCKVYGYIFTDYNIYWVQQAPGKGLEWMGLIDPDNGETPage 51 of 203 12904890v1Attorney Docket No.: 2017420-0028 Antibody variable domains that bind an internalizing receptor
[0167] In some embodiments, a molecule provided herein includes an additional antibody variable domain that targets an internalizing receptor (e.g., FcγRIIB, FcRn, ASGPR, BCMA, CD38, SLAMF7, GPCR5D, and / or CD138).
[0168] An antibody variable domain can include, but is not limited to, a monoclonal antibody, a synthetic antibody, a human antibody, a humanized antibody, a non-human antibody, and any fragment thereof. Thus, in one embodiment, the antibody variable domain comprises a mammalian antibody or a fragment thereof. In some embodiments, the additional antibody variable domain included in a molecule can be any binding polypeptide such as, but not limited protein scaffold with antibody-like properties (e.g., an antibody variable domain), as well as any other immunological binding moiety known in the art, including, e.g., a Fab, Fab’, Fab’2, Fab2, Fab3, F(ab’)2, Fd, Fv, sdAb, scFv, SMIP, diabody, triabody, tetrabody, minibody, nanobody, maxibody, tandab, DVD, BiTe, TandAb, VHH, or any combination thereof.
[0169] In some embodiments, a molecule described herein includes an additional antibody variable domain that targets two or more targets. In some embodiments, the additional antibody variable domain is a bispecific antibody variable domain. In some embodiments, the additional antibody variable domain comprises a trispecific antibody variable domain. In some embodiments, the additional antibody variable domain targets two non-overlapping epitopes on the same target (e.g., two non-overlapping epitopes on FcγRIIB, FcRn, ASGPR, BCMA, CD38, SLAMF7, GPCR5D, and / or CD138).
[0170] In some embodiments, the additional antibody variable domain comprises a Fab comprising a heavy chain and light chain antibody component. In some embodiments, the additional antibody variable domain comprises a Fab that comprises any of the following particular heavy chain and light chain antibody sequences shown in Table 2.
[0171] In some embodiments, the additional antibody variable domain is a Fab that comprises an antibody heavy chain sequence that is at least 90% identical to SEQ ID NO: 209, and / or an antibody light chain sequence that is at least 90% identical to SEQ ID NO: 210. In some embodiments, an antibody variable domain is a Fab that comprises an Page 52 of 203 12904890v1Attorney Docket No.: 2017420-0028 antibody heavy chain sequence SEQ ID NO: 209 and / or an antibody light chain sequence SEQ ID NO: 210. Table 2: Exemplary Additional Antibody Variable Domain Sequences Fab Targeting Arm Sequences SEQ ID NO
[0172] In some embodiments, a molecule described herein includes a first polypeptide comprising a first Fc domain and a first antibody variable domain that binds to a constant domain of an IgE antibody and a second polypeptide comprising a second Fc domain. An antibody variable domain thereof targets IgE antibodies and upon binding, the complexes are targeted to an internalizing receptor and shuttled to the lysosome for degradation of the IgE antibodies.
[0173] In some embodiments, an Fc domain described herein includes one or more mutations that alter its binding affinity to certain Fc receptors (e.g., FcγRIIB, FcγRI, FcγRIIA167H, FcγRIIA167R, FcγRIIIA176F, FcγRIIIA176V, FcγRIIIB, and / or FcRn).
[0174] In some embodiments, a first Fc domain and a second Fc domain are the same (e.g., in a homodimeric molecule or in a bivalent molecule). In some embodiments, a first Fc domain and a second Fc domain are different (e.g., in a heterodimeric molecule or in a monovalent molecule).
[0175] In some embodiments, an Fc domain includes one or more mutated amino acid residues and has decreased binding affinity to FcγRI, FcγRIIA167H, FcγRIIA167R, Page 53 of 203 12904890v1Attorney Docket No.: 2017420-0028 FcγRIIIA176F, FcγRIIIA176V, FcγRIIIB, and / or FcRn relative to the corresponding wild- type Fc domain. In some embodiments, an Fc domain includes one or more mutated amino acid residues and has substantially no binding affinity to FcγRI, FcγRIIA167H, FcγRIIA167R, FcγRIIIA176F, FcγRIIIA176V, FcγRIIIB, and / or FcRn relative to the corresponding wild-type Fc domain.
[0176] In some embodiments, a first and / or second Fc domain of a molecule comprise a modification (e.g., one or more mutations) that enhances binding to an internalizing receptor. In some embodiments, a first and / or second Fc domain of a molecule comprise a modification (e.g., one or more mutations) that decrease binding to certain Fc- receptors. In some embodiments, a first and / or second Fc domain of a molecule comprise a modification (e.g., one or more mutations) that enhances other characteristics of a molecule described herein (e.g., increased half-life, heterodimerization, etc.).
[0177] An Fc domain included in a molecule may comprise any one of the five major classes of antibodies: IgA, IgD, IgE, IgG, and IgM. In some embodiments, a conventional antibody comprises an IgG antibody. In some embodiments, an Fc domain described herein comprises a particular isotype selected from the group of IgG isotypes: IgG1, IgG2, IgG3, IgG4. In some embodiments, a molecule comprises first and / or second Fc domains that are an IgG1 isotype. In some embodiments, a molecule comprises first and / or second Fc domains that are a human IgG1 isotype. Additionally, in some embodiments, an Fc domain may include any particular heavy chain constant domains that correspond to the different classes of immunoglobulins which include α, δ, ε, γ, and μ, respectively. In some embodiments, a conventional antibody is an intact IgG1 antibody or other antibody class or isotype as described herein (see, e.g., Hudson et al., Nat. Med.9:129 (2003); Pluckthun, The Pharmacology of Monoclonal Antibodies, 113:269 (1994); Hollinger et al., Proc. Natl. Acad. Sci. USA 90: 6444 (1993); WO 1993 / 01161; and U.S. Pat. Nos. 5,571,894, 5,869,046, 6,248,516, and 5,587,458, each of which are herein incorporated by reference).
[0178] The Fc region of an antibody and included in molecules described herein may bind to elements of the complement system, and also to receptors on effector cells, including for example effector cells that mediate cytotoxicity. As is known in the art, affinity and / or other binding attributes of Fc regions for Fc receptors can be modulated through Page 54 of 203 12904890v1Attorney Docket No.: 2017420-0028 glycosylation or other modification. In some embodiments, a molecule described herein includes glycosylated Fc domains, including Fc domains with modified or engineered glycosylation. In some embodiments, a molecule is naturally produced (e.g., generated by an organism reacting to an antigen), or produced by recombinant engineering, chemical synthesis, or other artificial system or methodology.
[0179] In some embodiments, one or more modifications made to an Fc domain increases clearance of an immune complex formed by one or more molecules described herein bound to an IgE antibody. In some embodiments, one or more modifications made to an Fc domain may induce selective targeting and / or clearance of an immune complex formed by one or more molecules described herein bound to an IgE antibody. For example, in some embodiments, wherein upon binding of two molecules to an IgE antibody, an immune complex is formed that has enhanced binding kinetics with one or more Fc receptors (e.g., FcγRIIB) relative to an immune complex that comprises the IgE antibody bound to two corresponding molecules with wild-type Fc domains. Binding kinetics may be characterized by, e.g., an increase rate of association, a decrease in the rate of disassociation, and / or a change in the equilibrium dissociation constant. In some embodiments, an Fc domain preferentially binds to immune cells expressing FcγRIIB over immune cells expressing FcγRIIA. In some embodiments, an Fc domain comprises substantially no binding affinity for cells that do not express FcγRIIB (e.g., T cells, NK cells, neutrophils, and / or eosinophils). In some embodiment, cells that express FcγRIIB are B cells, monocytes and / or basophils.
[0180] In some embodiments, enhanced binding kinetics comprises at least 10% greater binding affinity of the immune complex to one or more Fc receptors (e.g., FcγRIIB). In some embodiments, enhanced binding kinetics comprises at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, or at least 50% or greater binding affinity.
[0181] In some embodiments, a molecule binds to FcγRIIB with an affinity within the range of about 1 µM to 0.001 µM. In some embodiments, a molecule binds to FcγRIIB with an affinity within the range of about 1 µM to 0.01 µM. In some embodiments, a molecule binds to FcγRIIB with an affinity within the range of about 0.1 µM to 0.01 µM. Page 55 of 203 12904890v1Attorney Docket No.: 2017420-0028
[0182] In some embodiments, an Fc domain described herein comprises one or more modifications such that a molecule described herein does not activate immune cells (e.g., does not activate immune cells to secrete pro-inflammatory cytokines, e.g., IL-6).
[0183] Exemplary Fc domain sequences for use in accordance with the present disclosure are shown below in Table 3. It will be understood that any of these Fc domain sequences can be used in a first or second polypeptide of a molecule of the present disclosure. It will also be understood that any of the exemplary Fc domain sequences with knob mutations (identified with a “Knob” reference) can be used with any of the exemplary Fc domain sequences with hole mutations (identified with a “Hole” reference) in preparing a heterodimeric molecule (e.g., a monovalent molecule). In some embodiments, Fc domain sequences shown in Table 3 can be used in pairs for preparing a heterodimeric molecule, e.g., without limitation based on the numerical references found in Table 3 (e.g., Human IgG1 Fc 1.1 Knob can be used with Human IgG1 Fc 1.1 Hole, Human IgG1 Fc 1.2 Knob can be used with Human IgG1 Fc 1.2 Hole, etc.). In addition, the present disclosure encompasses corresponding pairs of Fc domain sequences where the “Knob” mutations (e.g., S354C / T366W) are located on a “Free arm for IgE Depletion” (e.g., in a second polypeptide that does not include an antibody variable domain that binds to a constant domain of an IgE antibody) and the “Hole” mutations (e.g., T366S / L368A / Y407V / Y349C) are located on a “Binding Arm for IgE Depletion” (e.g., in a first polypeptide that also includes an antibody variable domain that binds to a constant domain of an IgE antibody).
[0184] It is also to be understood that the present disclosure encompasses the use of variants of any of these Fc domain sequences, including for example, Fc domain sequences with allotypic variations, including the variations found in G1m17, also known as G1m(z), with Lys (K) at position 214 in the CH1 domain (EU numbering); G1m3, also known as G1m(f), with Arg (R) at position 214 in the CH1 domain; G1m1, also known as G1m(a), with Asp (D) and Leu (L) at positions 356 and 358 in the CH3 domain (EU numbering); nG1m1, also known as nG1m(a), with Glu (E) and Met (M) at positions 356 and 358; G1m2, also known as G1m(x), with Gly (G) at position 431 in the CH3 domain (EU numbering); or nG1m2, also known as nG1m(x), with Ala (A) at position 431 in the CH3 domain. Page 56 of 203 12904890v1Attorney Docket No.: 2017420-0028 Table 3: Exemplary Fc Domain Sequences (with hinge sequences in italics and mutations in bold underlined) Fc Sequences Sequences SEQ ID NOPage 57 of 203 12904890v1Attorney Docket No.: 2017420-0028 Fc Sequences Sequences SEQ ID NO12904890v1Attorney Docket No.: 2017420-0028 Fc Sequences Sequences SEQ ID NOPage 59 of 203 12904890v1Attorney Docket No.: 2017420-0028 Fc Sequences Sequences SEQ ID NO12904890v1Attorney Docket No.: 2017420-0028 Fc Sequences Sequences SEQ ID NO12904890v1Attorney Docket No.: 2017420-0028 Fc Sequences Sequences SEQ ID NOg 12904890v1Attorney Docket No.: 2017420-0028 Fc Sequences Sequences SEQ ID NOPage 63 of 203 12904890v1Attorney Docket No.: 2017420-0028 Fc Sequences Sequences SEQ ID NO12904890v1Attorney Docket No.: 2017420-0028 Fc Sequences Sequences SEQ ID NO12904890v1Attorney Docket No.: 2017420-0028 Fc Sequences Sequences SEQ ID NO12904890v1Attorney Docket No.: 2017420-0028 Fc Sequences Sequences SEQ ID NO12904890v1Attorney Docket No.: 2017420-0028 Fc Sequences Sequences SEQ ID NOPage 68 of 203 12904890v1Attorney Docket No.: 2017420-0028 Fc Sequences Sequences SEQ ID NO12904890v1Attorney Docket No.: 2017420-0028 Fc Sequences Sequences SEQ ID NO12904890v1Attorney Docket No.: 2017420-0028 Fc Sequences Sequences SEQ ID NO12904890v1Attorney Docket No.: 2017420-0028 Fc Sequences Sequences SEQ ID NO12904890v1Attorney Docket No.: 2017420-0028 Fc Sequences Sequences SEQ ID NOPage 73 of 203 12904890v1Attorney Docket No.: 2017420-0028 Fc Sequences Sequences SEQ ID NO12904890v1Attorney Docket No.: 2017420-0028 Fc Sequences Sequences SEQ ID NOPage 75 of 203 12904890v1Attorney Docket No.: 2017420-0028 Fc Sequences Sequences SEQ ID NO12904890v1Attorney Docket No.: 2017420-0028 Fc Sequences Sequences SEQ ID NOSEQ ID NO: 90, SEQ ID NO: 92, SEQ ID NO: 94, SEQ ID NO: 103, SEQ ID NO: 105, SEQ ID NO: 107, SEQ ID NO: 109, SEQ ID NO: 113, SEQ ID NO: 115, SEQ ID NO: 117, SEQ ID NO: 119, SEQ ID NO: 121, SEQ ID NO: 123, SEQ ID NO: 125, SEQ ID NO: 127, SEQ ID NO: 129, SEQ ID NO: 131, SEQ ID NO: 133, SEQ ID NO: 135, SEQ ID NO: 137, SED ID NO: 376, SEQ ID NO: 378, SEQ ID NO: 392, SEQ ID NO: 394, SEQ ID NO: 396, SEQ ID NO: 398, SEQ ID NO: 400, SEQ ID NO: 402, SEQ ID NO: 404, SEQ ID NO: 406, SEQ ID NO: 514, SEQ ID NO: 516, SEQ ID NO: 518, SEQ ID NO: 520, SEQ ID NO: 521, SEQ ID NO: 522, SEQ ID NO: 523, SEQ ID NO: 524, SEQ ID NO: 525, SEQ ID NO: 526, SEQ ID NO: 527, SEQ ID NO: 528, SEQ ID NO: 529, SEQ ID NO: 530, SEQ ID NO: 531, SEQ ID NO: 532, SEQ ID NO: 533, and SEQ ID NO: 534 and a second Fc domain comprises a sequence selected from SEQ ID NO: 91, SEQ ID NO: 93, SEQ ID NO: 95, SEQ ID NO: 104, SEQ ID NO: 106, SEQ ID NO: 108, SEQ ID NO: 110, SEQ ID NO: 114, SEQ ID NO: 116, SEQ ID NO: 118, SEQ ID NO: 120, SEQ ID NO: 122, SEQ ID NO: 124, SEQ ID NO: 126, SEQ ID NO: 128, SEQ ID NO: 130, SEQ ID NO: 132, SEQ ID NO: 134, SEQ ID NO: 136, SEQ ID NO: 138, SEQ ID NO: 377, SEQ ID NO: 379, SEQ ID NO: 392, SEQ ID NO: 394, SEQ ID NO: 396, SEQ ID NO: 398, SEQ ID NO: 401, SEQ ID NO: 403,12904890v1Attorney Docket No.: 2017420-0028 SEQ ID NO: 405, SEQ ID NO: 407, SEQ ID NO: 515, SEQ ID NO: 517, SEQ ID NO: 519, SEQ ID NO: 520, SEQ ID NO: 521, SEQ ID NO: 522, SEQ ID NO: 523, SEQ ID NO: 524, SEQ ID NO: 525, SEQ ID NO: 526, SEQ ID NO: 527, SEQ ID NO: 528, SEQ ID NO: 529, SEQ ID NO: 530, SEQ ID NO: 531, SEQ ID NO: 532, SEQ ID NO: 533, and SEQ ID NO: 534.
[0186] In some embodiments, a first Fc domain comprises a sequence selected from SEQ ID NO: 103, SEQ ID NO: 105, SEQ ID NO: 113, SEQ ID NO: 115, SEQ ID NO: 117, SEQ ID NO: 121, SEQ ID NO: 123, SEQ ID NO:125, and SEQ ID NO: 376, and a second Fc domain comprises a sequence selected from SEQ ID NO: 104, SEQ ID NO: 106, SEQ ID NO: 114, SEQ ID NO: 116, SEQ ID NO: 118, SEQ ID NO: 122, SEQ ID NO: 124, SEQ ID NO: 126, and SEQ ID NO: 377.
[0187] In some embodiments, a first Fc domain comprises a sequence selected from SEQ ID NO: 90, SEQ ID NO: 92, SEQ ID NO: 94, SEQ ID NO: 107, SEQ ID NO: 109, SEQ ID NO: 119, SEQ ID NO: 127, SEQ ID NO: 129, SEQ ID NO: 131, SEQ ID NO: 133, SEQ ID NO: 135, and SEQ ID NO: 137, and a second Fc domain comprises a sequence selected from SEQ ID NO: 91, SEQ ID NO: 93, SEQ ID NO: 95, SEQ ID NO: 108, SEQ ID NO: 110, SEQ ID NO: 120, SEQ ID NO: 128, SEQ ID NO: 130, SEQ ID NO: 132, SEQ ID NO: 134, SEQ ID NO: 136, and SEQ ID NO: 138.
[0188] In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 103 and a second Fc domain comprises a sequence of SEQ ID NO: 104. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 105 and a second Fc domain comprises a sequence of SEQ ID NO: 106. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 107 and a second Fc domain comprises a sequence of SEQ ID NO: 108. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 109 and a second Fc domain comprises a sequence of SEQ ID NO: 110. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 113 and a second Fc domain comprises a sequence of SEQ ID NO: 114. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 115 and a second Fc domain comprises a sequence of SEQ ID NO: 116. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 117 and a second Fc domain comprises a sequence of SEQ ID NO: 118. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 119 and a second Fc Page 78 of 203 12904890v1Attorney Docket No.: 2017420-0028 domain comprises a sequence of SEQ ID NO: 120. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 121 and a second Fc domain comprises a sequence of SEQ ID NO: 122. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 123 and a second Fc domain comprises a sequence of SEQ ID NO: 124. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 125 and a second Fc domain comprises a sequence of SEQ ID NO: 126. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 127 and a second Fc domain comprises a sequence of SEQ ID NO: 128. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 129 and a second Fc domain comprises a sequence of SEQ ID NO: 130. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 131 and a second Fc domain comprises a sequence of SEQ ID NO: 132. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 133 and a second Fc domain comprises a sequence of SEQ ID NO: 134. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 135 and a second Fc domain comprises a sequence of SEQ ID NO: 136. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 137 and a second Fc domain comprises a sequence of SEQ ID NO: 138. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 376 and a second Fc domain comprises a sequence of SEQ ID NO: 377. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 111 and a second Fc domain comprises a sequence of SEQ ID NO: 111. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 139 and a second Fc domain comprises a sequence of SEQ ID NO: 139. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 140 and a second Fc domain comprises a sequence of SEQ ID NO: 140. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 141 and a second Fc domain comprises a sequence of SEQ ID NO: 141. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 142 and a second Fc domain comprises a sequence of SEQ ID NO: 142. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 143 and a second Fc domain comprises a sequence of SEQ ID NO: 143. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 144 and a second Fc domain comprises a sequence of SEQ ID NO: 144. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 145 and a second Fc domain comprises a sequence of SEQ ID NO: 145. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 146 and a second Fc domain comprises a sequence of SEQ ID NO: 146. In some embodiments, a first Fc domain comprises a sequence of SEQ Page 79 of 203 12904890v1Attorney Docket No.: 2017420-0028 ID NO: 147 and a second Fc domain comprises a sequence of SEQ ID NO: 147. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 148 and a second Fc domain comprises a sequence of SEQ ID NO: 148. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 149 and a second Fc domain comprises a sequence of SEQ ID NO: 149. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 163 and a second Fc domain comprises a sequence of SEQ ID NO: 163. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 164 and a second Fc domain comprises a sequence of SEQ ID NO: 164. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 374 and a second Fc domain comprises a sequence of SEQ ID NO: 374. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 375 and a second Fc domain comprises a sequence of SEQ ID NO: 375. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 85 and a second Fc domain comprises a sequence of SEQ ID NO: 85. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 86 and a second Fc domain comprises a sequence of SEQ ID NO: 86. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 89 and a second Fc domain comprises a sequence of SEQ ID NO: 89. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 90 and a second Fc domain comprises a sequence of SEQ ID NO: 91. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 92 and a second Fc domain comprises a sequence of SEQ ID NO: 93. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 94 and a second Fc domain comprises a sequence of SEQ ID NO: 95.
[0189] In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 378 and a second Fc domain comprises a sequence of SEQ ID NO: 379. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 392 and a second Fc domain comprises a sequence of SEQ ID NO: 393. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 394 and a second Fc domain comprises a sequence of SEQ ID NO: 395. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 396 and a second Fc domain comprises a sequence of SEQ ID NO: 397. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 398 and a second Fc domain comprises a sequence of SEQ ID NO: 399. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 400 and a second Fc domain comprises a sequence of SEQ ID NO: 401. In some embodiments, a first Fc domain comprises a sequence of SEQ ID Page 80 of 203 12904890v1Attorney Docket No.: 2017420-0028 NO: 402 and a second Fc domain comprises a sequence of SEQ ID NO: 403. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 404 and a second Fc domain comprises a sequence of SEQ ID NO: 405. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 406 and a second Fc domain comprises a sequence of SEQ ID NO: 407. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 514 and a second Fc domain comprises a sequence of SEQ ID NO: 515. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 516 and a second Fc domain comprises a sequence of SEQ ID NO: 517. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 518 and a second Fc domain comprises a sequence of SEQ ID NO: 519. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 520 and a second Fc domain comprises a sequence of SEQ ID NO: 520. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 521 and a second Fc domain comprises a sequence of SEQ ID NO: 521. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 522 and a second Fc domain comprises a sequence of SEQ ID NO: 522. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 523 and a second Fc domain comprises a sequence of SEQ ID NO: 523. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 524 and a second Fc domain comprises a sequence of SEQ ID NO: 524. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 525 and a second Fc domain comprises a sequence of SEQ ID NO: 525. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 526 and a second Fc domain comprises a sequence of SEQ ID NO: 526. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 527 and a second Fc domain comprises a sequence of SEQ ID NO: 527. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 528 and a second Fc domain comprises a sequence of SEQ ID NO: 528. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 529 and a second Fc domain comprises a sequence of SEQ ID NO: 529. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 530 and a second Fc domain comprises a sequence of SEQ ID NO: 530. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 531 and a second Fc domain comprises a sequence of SEQ ID NO: 531. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 532 and a second Fc domain comprises a sequence of SEQ ID NO: 532. In some embodiments, a first Fc domain comprises a sequence of SEQ ID NO: 533 and a second Fc domain comprises a sequence of SEQ ID NO: 533. In some embodiments, a first Fc domain Page 81 of 203 12904890v1Attorney Docket No.: 2017420-0028 comprises a sequence of SEQ ID NO: 534 and a second Fc domain comprises a sequence of SEQ ID NO: 534. Hinge sequences
[0190] In some embodiments, an Fc domain comprises a hinge sequence. In some embodiments, an Fc domain comprises the amino acid sequence of SEQ ID NO: 299 (DKTHTCPPCP). In some embodiments, an Fc domain comprises the amino acid sequence of SEQ ID NO: 300 (EPKSSDKTHTCPPCP). In some embodiments, the hinge sequence of SEQ ID NO: 209 or SEQ ID NO: 300 may be used in the Fc domain of a “Free Arm for IgE Depletion” (e.g., in a second polypeptide that does not include an antibody variable domain that binds to a constant domain of an IgE antibody). In this context, it is to be understood that any of the exemplary Fc domain sequences provided in Table 3 that include a hinge sequence of SEQ ID NO: 299 (e.g., SEQ ID NOs: 104, 106, 108, 110, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, or 377) can be modified by replacing the hinge sequence of SEQ ID NO: 299 (DKTHTCPPCP) with the hinge sequence of SEQ ID NO: 300 (EPKSSDKTHTCPPCP) or any other suitable hinge sequence including variants of the hinge sequence of SEQ ID NO: 299 or SEQ ID NO: 300 that include 1, 2, 3, 4, 5 or more mutations.
[0191] In some embodiments, an Fc domain comprises the amino acid sequence of SEQ ID NO: 301 (ERKCCVECPPCP). In some embodiments, an Fc domain comprises the amino acid sequence of SEQ ID NO: 302 (ELKTRPLGDTTHTCPPCP). In some embodiments, an Fc domain comprises the amino acid sequence of SEQ ID NO: 303 (ELKTRPLGDTTHTCPRCP(EPKSCDTPPPCPRCP)3). In some embodiments, an Fc domain comprises the amino acid sequence of SEQ ID NO: 304 (ESKYGPPCPPCP). In some embodiments, an Fc domain comprises the amino acid sequence of SEQ ID NO: 305 (EPKSCDKTHTCPPCP). In some embodiments, an Fc domain comprises the amino acid sequence of SEQ ID NO: 306 (EPKSCDKTHTCCVECPPCP). In some embodiments, the hinge sequence of any one of SEQ ID NOs: 301-306 may be used in the Fc domain of a “Binder Arm for IgE Depletion” (e.g, in a first polypeptide that also includes an antibody variable domain that binds to a constant domain of an IgE antibody). In this context, it is to be understood that any of the exemplary Fc domain sequences provided in Table 3 that include a hinge sequence of SEQ ID NO: 305 (e.g., SEQ ID NOs: 103, 105, 107, 109, 111, Page 82 of 203 12904890v1Attorney Docket No.: 2017420-0028 113, 115, 117, 119, 121, 123, 125, 127, 129, 131, 133, 135, 137, 139-164, or 374-376) can be modified by replacing the hinge sequence of SEQ ID NO: 305 (EPKSCDKTHTCPPCP) with the hinge sequence of SEQ ID NO: 301 (ERKCCVECPPCP), SEQ ID NO: 302 (ELKTRPLGDTTHTCPPCP), SEQ ID NO: 303 (ELKTRPLGDTTHTCPRCP(EPKSCDTPPPCPRCP)3), SEQ ID NO: 304 (ESKYGPPCPPCP), or SEQ ID NO: 306 (EPKSCDKTHTCCVECPPCP) or any other suitable hinge sequence including variants of the hinge sequences of SEQ ID NOs: 301-306 that include 1, 2, 3, 4, 5 or more mutations. Mutations to increase binding to internalizing receptors
[0192] In some embodiments, additional mutations are introduced into Fc domains of molecules described herein in order to target cell surface receptors that bind and internalize ligands and target them to the lysosome (i.e., internalizing receptors or endocytic receptors). By modifying Fc domains to increase binding to internalizing receptors, molecules described herein and their bound autoantibodies are targeted for internalization and lysosomal degradation.
[0193] In some embodiments, a molecule comprises a first and / or second Fc domain that comprises one of more mutated amino acid residues that alters its binding to an internalizing receptor on a cell, where the internalizing receptor is capable of shuttling its cargo to the lysosome of the cell leading to degradation. In some embodiments, altered binding to the internalizing receptor comprises increased binding to an internalizing receptor. Without wishing to be bound to any theory, once a molecule bound to an IgE antibody binds to an internalizing receptor on a cell, the internalizing receptor internalizes the molecule and the IgE antibody is shuttled to the lysosome of the cell for degradation.
[0194] Exemplary internalizing receptors include but are not limited to FcγRIIB, FcRn, ASGPR, BCMA, CD38, SLAMF7, GPCR5D, or CD138.
[0195] In some embodiments, a first and / or second Fc domain comprises one or more mutated amino acid residues that increase binding to the human FcγR, specifically FcγRIIB. In some embodiments, such a mutation comprises at least one of the following mutated amino acid residues: S267E and L328F, according to the EU numbering scheme. In some embodiments, a first and / or second Fc domain comprise a combination of the Page 83 of 203 12904890v1Attorney Docket No.: 2017420-0028 following mutated amino acid residues: S267E and L328F, according to the EU numbering scheme. In some embodiments, a first and / or second Fc domain comprises the mutated amino acid residue P238D, according to the EU numbering scheme. In some embodiments, a first and / or second Fc domain comprises at least one of the following mutated amino acid residues: L234A, L235A, and P238D, according to the EU numbering scheme. In some embodiments, a first and / or second Fc domain comprises the following mutated amino acid residues: L234A, L235A, and P238D, according to the EU numbering scheme. In some embodiments, a first and / or second Fc domain comprises at least one of the following mutated amino acid residues: L234A, L235A, P238D and P329G, according to the EU numbering scheme. In some embodiments, a first and / or second Fc domain comprises the following mutated amino acid residues: L234A, L235A, P238D and P329G, according to the EU numbering scheme. In some embodiments, a first and / or second Fc domain comprises at least one of the following mutated amino acid residues: L234A, L235A, and P238D, according to the EU numbering scheme. In some embodiments, a first and / or second Fc domain comprises the following mutated amino acid residues: L234A, L235A, and P238D, according to the EU numbering scheme. In some embodiments, a first and / or second Fc domain comprises at least one of the following mutated amino acid residues: N297A and P238D, according to the EU numbering scheme. In some embodiments, a first and / or second Fc domain comprises the following mutated amino acid residues: N297A and P238D, according to the EU numbering scheme.
[0196] In some embodiments, a first and / or second Fc domain comprises a P238D mutation and at least one of the following mutated amino acid residues: L234A and L235A, according to the EU numbering scheme. In some embodiments, a first and / or second Fc domain comprises the following mutated amino acid residues: L234A, L235A, and P238D, according to the EU numbering scheme. In some embodiments, a first and / or second Fc domain comprises P238D and P329G mutations and at least one of the following mutated amino acid residues: L234A and L235A, according to the EU numbering scheme. In some embodiments, a first and / or second Fc domain comprises the following mutated amino acid residues: L234A, L235A, P238D and P329G, according to the EU numbering scheme.
[0197] In some embodiments, a first and / or second Fc domain comprises P238D and P271G mutations and at least one of the following mutated amino acid residues: L234A and L235A, according to the EU numbering scheme. In some embodiments, a first and / or Page 84 of 203 12904890v1Attorney Docket No.: 2017420-0028 second Fc domain comprises the following mutated amino acid residues: L234A, L235A, P238D, and P271G according to the EU numbering scheme. In some embodiments, a first and / or second Fc domain comprises P238D, P271G, and P329G mutations and at least one of the following mutated amino acid residues: L234A and L235A, according to the EU numbering scheme. In some embodiments, a first and / or second Fc domain comprises the following mutated amino acid residues: L234A, L235A, P238D, P271G, and P329G, according to the EU numbering scheme.
[0198] In some embodiments, a first and / or second Fc domain comprises G237D, P238D, P271G, and A330R mutations and at least one of the following mutated amino acid residues: L234A, and L235A, and P238D, according to the EU numbering scheme. In some embodiments, a first and / or second Fc domain comprises the following mutated amino acid residues: L234A, L235A, and P238DG237D, P238D, P271G, and A330R according to the EU numbering scheme. In some embodiments, a first and / or second Fc domain comprises G237D, P238D, P271G, A330R, and P329G mutations and at least one of the following mutated amino acid residues: L234A and L235A, according to the EU numbering scheme. In some embodiments, a first and / or second Fc domain comprises at least one of the following mutated amino acid residues: N297A andL234A, L235A, G237D, P238D, P271G, A330R, and P329G, according to the EU numbering scheme.
[0199] In some embodiments, a first and / or second Fc domain comprises the following mutated amino acid residues: N297A and P238D, according to the EU numbering scheme. In some embodiments, a first and / or second Fc domain comprises the following mutated amino acid residues: N297A, P238D, and P271G according to the EU numbering scheme. In some embodiments, a first and / or second Fc domain comprises the following mutated amino acid residues: N297A, G237D, P238D, P271G, and A330R, according to the EU numbering scheme.
[0200] In some embodiments, one or more Fc mutations are introduced in order to increase binding to the human neonatal receptor (FcRn). In some embodiments, an Fc domain is an IgG1 Fc domain. Human IgG1 naturally binds FcRn at an acidic pH, which allows it to, upon binding FcRn and internalization into a cell, be recycled back to the surface of the cell and not to be degraded in the lysosome. In some embodiments, Fc mutations comprise mutation that increase binding to FcRn in neutral pH environments (e.g., Page 85 of 203 12904890v1Attorney Docket No.: 2017420-0028 extracellular environment). Without wishing to be bound by any theory, such mutations are included in the molecules described herein in order to increase binding of the Fc domain to FcRn on the surface of a cell in a neutral pH environment, such that there will be increased receptor-mediated internalization into cells and shuttling of the autoantibodies (bound to the molecule) to the lysosome.
[0201] In some embodiments, a first and / or second Fc domain comprises one or more mutated amino acid residues that increase binding to FcRn at a neutral or near-neutral pH (e.g., pH between about 6.8 and 7.5). In some embodiments, a first and / or second Fc domain comprises a human IgG1 isotype and has remains bound to FcRn upon entry into an environment having an acidic pH and / or having low calcium concentration (e.g., into an endosome of a cell). In some embodiments, a first and / or second Fc domain comprises at least one of the following mutated amino acid residues: M252Y, S254T, T256E, H433K, and N434F, according to the EU numbering scheme. In some embodiments, such mutations include a combination that includes the following mutations: M252Y, S254T, T256E, H433K, N434F (i.e., “MST-HN”), according to the EU numbering scheme. In some embodiments, the first and / or second Fc domain comprises a combination of the following mutated amino acid residues: M252Y, S254T, T256E, H433K, and N434F (i.e., “MST-HN”), according to the EU numbering scheme.
[0202] In some embodiments, a first and / or second Fc domain comprises at least one mutated amino acid sequence that decreases binding to one or more Fc-gamma receptors (FcγRs). Such modifications may prevent immune crosslinking (i.e., of a molecule, IgE antibody, FcγRs) that leads to inflammatory responses. Such mutations may focus the primary mechanism of action of the molecules, i.e., to the targeted internalization and subsequent degradation of autoantibodies. In some embodiments, a first and / or second Fc domain comprises at least one of the following mutated amino acid residues: G236R and L328R, according to the EU numbering scheme. In some embodiments, a first and / or second Fc domain comprises the following mutated amino acid residues: G236R and L328R, according to the EU numbering scheme.
[0203] In some embodiments, a molecule described herein may include any combination of the above-described Fc mutations that alter binding to an internalizing receptor or Fc receptor. In some embodiments, a molecule described herein includes an Fc Page 86 of 203 12904890v1Attorney Docket No.: 2017420-0028 domain that comprises an “MST-HN” modification described herein in combination with an “RR” mutation described herein. In some embodiments, a molecule described herein includes an Fc domain that comprises an “MST-HN” modification described herein in combination with the “P238D” mutation described herein. In some embodiments, a molecule described herein includes an Fc domain that comprises an “MST-HN” modification described herein in combination with an “RR” mutation and “P238D” mutation described herein. In some embodiments, a molecule described herein includes an Fc domain that comprises an “MST-HN” modification described herein in combination with P238D and P271G mutations, according to the EU number scheme. In some embodiments, a molecule described herein includes an Fc domain that comprises an “MST-HN” modification described herein in combination with an “RR” mutation and P238D and P271G mutations, according to the EU number scheme. In some embodiments, a molecule described herein includes an Fc domain that comprises an “MST-HN” modification described herein in combination with G237D, P238D, P271G, and A330R mutations, according to the EU number scheme. In some embodiments, a molecule described herein includes an Fc domain that comprises an “MST-HN” modification described herein in combination with an “RR” mutation and G237D, P238D, P271G, and A330R mutations, according to the EU number scheme. Exemplary FcγRIIB Mutations
[0204] In some embodiments, an Fc domain comprises one or more amino acid mutations that increase affinity for FcγRIIB. In some embodiments FcγRIIB is human FcγRIIB. In some embodiments, FcγRIIB is murine FcγRIIB.
[0205] In some embodiments, an Fc domain is utilized in a molecule described herein that comprises one or more mutations that enhances binding kinetics of an immune complex comprising the one or more molecules bound to a target antibody to FcγRIIB. In some embodiments, enhanced binding kinetics comprises at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, or at least 50% or greater binding affinity. In some embodiments, enhanced binding kinetics comprises an increase in avidity, stability, strength, frequency, and / or duration of binding between the immune complex and FcγRIIB. In some embodiments, enhanced binding kinetics comprise an Page 87 of 203 12904890v1Attorney Docket No.: 2017420-0028 increase in the rate of association, a decrease in the rate of disassociation, and / or a change in the equilibrium dissociation constant.
[0206] In some embodiments, molecules described herein having a first and second Fc domain comprise one or more mutations in the first and / or second Fc domain to increase binding to FcγRIIB, wherein upon binding of two molecules to the target antibody, an immune complex is formed that has enhanced binding kinetics with FcγRIIB relative to an immune complex that comprises the target antibody bound to two corresponding molecules with wild-type Fc domains. Without wishing to be bound by any theory, a molecule described herein may have one or more mutations that increase binding affinity for FcγRIIB, but the binding affinity of the molecule alone to FcγRIIB is moderate. In some embodiments, a molecule binds to FcγRIIB with an affinity within the range of about 1 µM to 0.001 µM. In some embodiments, a molecule binds to FcγRIIB with an affinity within the range of about 1 µM to 0.01 µM. In some embodiments, a molecule binds to FcγRIIB with an affinity within the range of about 0.1 µM to 0.01 µM. In some embodiments, such mutations when introduced into an Fc domain of a molecule described herein confer an avidity-mediated binding effect to FcγRIIB when two or more molecules are present in an immune complex with a target antibody. In some embodiments, a molecule described herein has increased binding to FcγRIIB when the immune complex comprises two molecules bound to a target antibody compared to an immune complex with only one molecule bound to the target antibody. Without wishing to be bound by any theory, such avidity-mediated effects allow for selective binding and depletion of immune complexes and weaker binding (and hence depletion) of molecules when they are not part of an immune complex. These characteristics allow for molecules described herein to remain circulating longer in the bloodstream of a subject before being cleared by FcγRIIB-mediated internalization and degradation.
[0207] Additionally, the present disclosure provides Fc domain mutations that achieve the binding affinity to FcγRIIB to confer avidity-mediated effects to take advantage of the benefits and additional selectively described herein. Exemplary Fc domain mutations that may be used to achieve these binding kinetics with FcγRIIB include, e.g., in some embodiments, one or more of the following mutations: E233V, L234D, L235F, G236R, G237D, S239L, S267D, H268P, S298G, T299A, A327L, L328A, A330H, E333I, R292Q, E233P, P238D, H268D, P271G, A330R, L234Y, T250V, V264I, T307P, Q311R, A330K, Page 88 of 203 12904890v1Attorney Docket No.: 2017420-0028 P343R, M428L, N434A, Y436T, Q438R, S440E, G236N, S267E, L235R, D270E, E233D, and G237D, according to the EU numbering scheme.
[0208] In some embodiments, an Fc domain mutation comprises one or more of the following mutations E233V, L234D, L235F, G236R, G237D, S239L, S267D, H268P, S298G, T299A, A327L, L328A, A330H, or E333I. In some embodiments, an Fc domain comprises the following set of mutations: E233V, L234D, L235F, G236R, G237D, S239L, S267D, H268P, S298G, T299A, A327L, L328A, A330H, and E333I, according to the EU numbering scheme (e.g., see SEQ ID NOs: 113, 114, and 139).
[0209] In some embodiments, an Fc domain mutation comprises one or more of the following mutations: E233V, L234D, L235F, G236R, G237D, S239L, S267D, R292Q, H268P, S298G, T299A, A327L, L328A, A330H, or E333I, according to the EU numbering scheme. In some embodiments, an Fc domain comprises the following set of mutations: E233V, L234D, L235F, G236R, G237D, S239L, S267D, R292Q, H268P, S298G, T299A, A327L, L328A, A330H, and E333I, according to the EU numbering scheme (e.g., see SEQ ID NOs: 115, 116, and 140).
[0210] In some embodiments, an Fc domain mutation comprises one or more of the following mutations: E233V, L234D, L235F, G236R, G237D, S239L, H268P, R292Q, S298G, T299A, A327L, L328A, A330H, or E333I, according to the EU numbering scheme. In some embodiments, an Fc domain comprises the following set of mutations: E233V, L234D, L235F, G236R, G237D, S239L, H268P, R292Q, S298G, T299A, A327L, L328A, A330H, and E333I, according to the EU numbering scheme (e.g., see SEQ ID NOs: 117, 118, and 141).
[0211] In some embodiments, an Fc domain mutation comprises one or more of the following mutations: L234Y, P238D, T250V, V264I, T307P, Q311R, A330K, P343R, M428L, N434A, Y436T, Q438R, or S440E, according to the EU numbering scheme. In some embodiments, an Fc domain comprises the following set of mutations: L234Y, P238D, T250V, V264I, T307P, Q311R, A330K, P343R, M428L, N434A, Y436T, Q438R, and S440E, according to the EU numbering scheme (e.g., see SEQ ID NOs: 119, 120, and 142).
[0212] In some embodiments, an Fc domain mutation comprises one or more of the following mutations: L234D, G236N, or S267E, according to the EU numbering scheme. In Page 89 of 203 12904890v1Attorney Docket No.: 2017420-0028 some embodiments, an Fc domain comprises the following set of mutations: L234D, G236N, and S267E, according to the EU numbering scheme (e.g., see SEQ ID NOs: 121, 122, and 143).
[0213] In some embodiments, an Fc domain mutation comprises L235R, according to the EU numbering scheme (e.g., see SEQ ID NOs: 123, 124, and 144).
[0214] In some embodiments, an Fc domain mutation comprises one or both of the following mutations G236N and S267E, according to the EU numbering scheme. In some embodiments, an Fc domain comprises the following set of mutations: G236N and S267E, according to the EU numbering scheme (e.g., see SEQ ID NOs: 125, 126, and 145).
[0215] In some embodiments, an Fc domain mutation comprises one or both of the following mutations P238D and D270E, according to the EU numbering scheme. In some embodiments, an Fc domain comprises the following set of mutations: P238D and D270E, according to the EU numbering scheme (e.g., see SEQ ID NOs: 127, 128, and 146).
[0216] In some embodiments, an Fc domain mutation comprises one or both of the following mutations P238D and P271G, according to the EU numbering scheme. In some embodiments, an Fc domain comprises the following set of mutations: P238D and P271G, according to the EU numbering scheme (e.g., see SEQ ID NOs: 129, 130, 147, 392, 393, 394, 395, 396, 397, 398, and 399).
[0217] In some embodiments, an Fc domain mutation comprises one or more of the following mutations: P238D, D270E, or P271G, according to the EU numbering scheme. In some embodiments, an Fc domain comprises the following set of mutations: P238D, D270E, and P271G, according to the EU numbering scheme (e.g., see SEQ ID NOs: 131, 132, and 148).
[0218] In some embodiments, an Fc domain mutation comprises one or more of the following mutations: G237D, P238D, P271G, or A330R, according to the EU numbering scheme. In some embodiments, an Fc domain comprises the following set of mutations: G237D, P238D, P271G, and A330R, according to the EU numbering scheme (e.g., see SEQ ID NOs: 133, 134, 149, 400, 401, 402, 403, 404, 405, 406, 407, 514, 515, 516, 517, 518, 519, 527, 528, 533, and 534). Page 90 of 203 12904890v1Attorney Docket No.: 2017420-0028
[0219] In some embodiments, an Fc domain mutation comprises one or more of the following mutations: G237D, P238D, D270E, P271G, or A330R, according to the EU numbering scheme. In some embodiments, an Fc domain comprises the following set of mutations: G237D, P238D, D270E, P271G, and A330R, according to the EU numbering scheme (e.g., see SEQ ID NOs: 135, 136, and 163).
[0220] In some embodiments, an Fc domain mutation comprises one or more of the following mutations: E233D, G237D, P238D, H268D, P271G, or A330R, according to the EU numbering scheme. In some embodiments, an Fc domain comprises the following set of mutations: E233D, G237D, P238D, H268D, P271G, and A330R, according to the EU numbering scheme (e.g., see SEQ ID NOs: 137, 138, and 164).
[0221] In some embodiments, an Fc domain mutation comprises P238D, according to the EU numbering scheme (e.g., see SEQ ID NOs: 107 and 108).
[0222] In some embodiments, Fc domains with mutations that increase binding affinity for FcγRIIB also have decreased or undetectable binding to certain activating Fc receptors. In some embodiments, an activating Fc receptor includes one or more of FcγRI, FcγRIIA167H, FcγRIIA167R, FcγRIIIA176F, FcγRIIIA176V, FcγRIIIB, and / or FcRn. Such binding properties lead to additional beneficial properties of molecules described herein including, e.g., a low risk of toxicity as there is less risk of activating the innate immune response (through activating Fc receptors) in response to molecules being introduced.
[0223] In some embodiments, an Fc domain described herein comprises one or more modifications such that a molecule described herein does not activate immune cells (e.g., does not activate immune cells to secrete pro-inflammatory cytokines, e.g., IL-6). Mutations for heterodimerization
[0224] In some embodiments, Fc mutations are introduced to promote heterodimerization of the two polypeptides, where each polypeptide comprises an Fc domain, and the first and second Fc domains heterodimerize in order to generate the full molecule.
[0225] Challenges exist in producing heterodimerized Fc domains of two different polypeptides from a single composition, particularly because the random pairing of different Page 91 of 203 12904890v1Attorney Docket No.: 2017420-0028 polypeptides can yield undesired species. Due to the presence of mispaired byproducts, and significantly reduced production yields, sophisticated purification procedures are required to isolate the desired antibody agent in those situations. In general, the same problem of mispaired byproducts remains if recombinant expression techniques are used. One approach to solve the problem of mispaired byproducts is known as “knob-into-holes technology” (KIH), which aims to force the pairing of two different polypeptides containing Fc domains by introducing mutations into the CH3 regions of the Fc domains to modify the contact interface. On one CH3 region, bulky amino acids are replaced by amino acids with short side chains to create a “hole” and amino acids with large side chains are introduced into the other CH3 region, to create a “knob”. For example, co-expressing two heavy chains of an antibody with such a modification with two light chains, leads to high yields of heterodimer formation versus homodimer was observed (see Ridgway et al., Protein Eng.9:617 (1996); and WO 1996 / 027011, which are herein incorporated by reference). In some embodiments, a molecule described herein utilizes KIH technology as described in, e.g., WO 1998 / 050431, which is herein incorporated by reference in its entirety.
[0226] As described herein, a molecule comprises a first Fc domain and a second Fc domain. In some embodiments a first Fc domain and / or a second Fc domain comprises a CH2 region variant and / or a CH3 region variant, wherein such variants each independently comprise at least one different amino acid substitution such that a heterodimeric domain pair is generated such that heterodimerization of the first and second Fc domains of the inventive molecule is favored over homodimerization.
[0227] As described herein, a first and / or second Fc domain in a molecule described herein may comprise certain mutations that utilize KIH technology that include, but are not limited to, a CH3 modification. In some embodiments, a molecule comprises first and second Fc domains that form a heterodimer using knobs-in-holes (KIH) modifications. In some embodiments, a KIH mutation comprises Y349T and T394F, according to the EU numbering scheme. In some embodiments, the first Fc domain comprises the Y349T mutation and the second Fc domain comprises the T394F mutation. In some embodiments, the first Fc domain comprises the T394F mutation and the second Fc domain comprises the Y349T mutation. In some embodiments, a KIH mutation comprises T366W, S354C, T366S, L368A, Y407V, and Y349C, according to the EU numbering scheme. In some embodiments, the first Fc domain comprises the T366W and S354C mutations and the Page 92 of 203 12904890v1Attorney Docket No.: 2017420-0028 second Fc domain comprises the T366S, L368A, Y407V, and Y349C mutations. In some embodiments, the first Fc domain comprises the T366S, L368A, Y407V, and Y349C mutations and the second Fc domain comprises the T366W and S354C mutations.
[0228] One of skill in the art will understand that other known KIH mutations or other Fc modifications are known in the art to promote heterodimerization and may be used in the molecules described herein, such as charge-to-charge swap design (e.g., “DD-KK” mutation pairs) and isotype strand swap design (e.g., “SEED Fc” ) (see Ha et al., Frontiers in Immunology 7: 394 (2016), which is herein incorporated by reference in its entirety). Mutations for half-life extension
[0229] In some embodiments, a first and / or second Fc domain in a molecule includes one or more mutated amino acid residues that increase half-life. In some embodiments, a first and / or second Fc domain comprises one of the following mutated amino acid residues: M252Y, S254T, and T256E (“MST” or “YTE”), according to the EU numbering scheme to increase half-life. In some embodiments, a first and / or second Fc domain comprises a combination of the following mutated amino acid residues: M252Y, S254T, and T256E, according to the EU numbering scheme to increase half-life. In some embodiments, a first and / or second Fc domain comprises one of the following mutated amino acid residues: M428L and N434S (“LS”), according to the EU numbering scheme. In some embodiments, a first and / or second Fc domain comprises a combination of the following mutated amino acid residues: M428L and N434S, according to the EU numbering scheme.
[0230] In some embodiments, a first and / or second Fc domain in a molecule includes the following mutated amino acid residues: P238D, M428L, and N434S, according to the EU numbering scheme. In some embodiments, a first and / or second Fc domain in a molecule includes the following mutated amino acid residues: P238D, P271G, M428L, and N434S, according to the EU numbering scheme. In some embodiments, a first and / or second Fc domain in a molecule includes the following mutated amino acid residues: G237D, P238D, P271G, A330R, M428L, and N434S, according to the EU numbering scheme. In some embodiments, a first and / or second Fc domain in a molecule includes the following mutated amino acid residues: G237D, P238D, D270E, P271G, A330R, M428L, and N434S, according to the EU numbering scheme. Page 93 of 203 12904890v1Attorney Docket No.: 2017420-0028
[0231] In some embodiments, a first and / or second Fc domain in a molecule includes the following mutated amino acid residues: P238D, M252Y, S254T, and T256E, according to the EU numbering scheme. In some embodiments, a first and / or second Fc domain in a molecule includes the following mutated amino acid residues: P238D, P271G, M252Y, S254T, and T256E, according to the EU numbering scheme. In some embodiments, a first and / or second Fc domain in a molecule includes the following mutated amino acid residues: G237D, P238D, P271G, A330R, M252Y, S254T, and T256E, according to the EU numbering scheme. In some embodiments, a first and / or second Fc domain in a molecule includes the following mutated amino acid residues: G237D, P238D, D270E, P271G, A330R, M252Y, S254T, and T256E, according to the EU numbering scheme.
[0232] In some embodiments, a first and / or second Fc domain comprises one of the following mutated amino acid residues: T250Q and M428L (“QL”), according to the EU numbering scheme to increase half-life. In some embodiments, a first and / or second Fc domain comprises one of the following mutated amino acid residues: H433K and N434F (“KF”), according to the EU numbering scheme to increase half-life. In some embodiments, a first and / or second Fc domain comprises one of the following mutated amino acid residues: T307A, E380A and N434A (“AAA”), according to the EU numbering scheme to increase half-life. In some embodiments, a first and / or second Fc domain comprises the following mutated amino acid residues: V308P, according to the EU numbering scheme to increase half-life. In some embodiments, a first and / or second Fc domain comprises one of the following mutated amino acid residues: M252Y, V308P, and N434Y (“YPY”), according to the EU numbering scheme to increase half-life. In some embodiments, a first and / or second Fc domain comprises one of the following mutated amino acid residues: H285D, T307Q, and A378V (“DQV”), according to the EU numbering scheme to increase half-life. In some embodiments, a first and / or second Fc domain comprises one of the following mutated amino acid residues: L309D, Q311H, N434S (“DHS”), according to the EU numbering scheme to increase half-life. Exemplary Fc mutations are described in e.g., Liu et al., Antibodies 9(4): 64 (2020), which is hereby incorporated by reference in its entirety. Page 94 of 203 12904890v1Attorney Docket No.: 2017420-0028 Mutations to ablate effector function
[0233] In some embodiments, additional Fc mutations are introduced in order to ablate effector function of molecules described herein. By ablating the Fc effector function of the molecule, molecules not bound to an IgE antibody will not be targeted for destruction.
[0234] In some embodiments, a first and / or second Fc domain of a molecule includes a modification that silences effector function. In some embodiments, a modification that silences effector function comprises one or more of the following mutations: L234A,L235A, P329G, P329A, N297A, or N297D, according to the EU numbering scheme. Insome embodiments, a modification that silences effector function comprises the following mutated amino acid residues: L234A and L235A (“LALA”), according to the EU numbering scheme. In some embodiments, mutations used to ablate effector function include the following: L234A, L235A, and P329G (“LALAPG”), according to EU numbering. In some embodiments, a modification that silences effector function comprises the following mutated amino acid residues: L234A, L235A, and P329A (“LALAPA”), according to the EU numbering scheme.
[0235] In some embodiments, a modification that silences effector function further comprises N297A, or N297D. In some embodiments, a modification that silences effector function includes the following Fc mutations: L234A, L235A, P329G and N297A. In some embodiments, a modification that silences effector function includes the following Fc mutations: L234A, L235A, P329G, and N297D. In some embodiments, a modification that silences effector function includes the following Fc mutations: L234A, L235A, and N297A. In some embodiments, a modification that silences effector function includes the following Fc mutations: L234A, L235A, and N297D. In some embodiments, a modification that silences effector function includes the following Fc mutations: L234A, L235A, P329A, and N297A. In some embodiments, a modification that silences effector function includes the following Fc mutations: L234A, L235A, P329A, and N297D.
[0236] In some embodiments, a modification that silences effector function includes the following Fc mutations: G236R and L328R (“GRLR”). In some embodiments, a modification that silences effector function includes the following Fc mutations: L234S, L235T, and G236R (“STR”). In some embodiments, a modification that silences effector Page 95 of 203 12904890v1Attorney Docket No.: 2017420-0028 function includes the following Fc mutations: L234A and L235E (“LALE”). In some embodiments, a modification that silences effector function includes the following Fc mutations: D265A and P329A (“DAPA”). In some embodiments, a modification that silences effector function includes the following Fc mutations: L234A, L235A, and K322A (“LALAKA”). In some embodiments, a modification that silences effector function includes the following Fc mutations: L234F, L235E, and P331S (“FES”). In some embodiments, a modification that silences effector function includes the following Fc mutations: L234F, L235Q, and K322Q (“FQQ”). In some embodiments, a modification that silences effector function includes the following Fc mutations: L234A, L235A, G237A, P238S, H268A, A330S, and P331S (“Sigma”). In some embodiments, a modification that silences effector function includes the following Fc mutations: E233P, L234V, L235A, D236G, A327G, A330S, P331S (“PVA-GSS”). In some embodiments, a modification that silences effector function includes the following Fc mutations: L235G and G236R (“LGGR”). One of ordinary skill in the art will appreciate that other modifications known in the art could be used in order to ablate effector function. Linkers
[0237] Molecules described herein include an Fc domain linked to an antibody variable domain. In some embodiments, an antibody variable domain is connected directly to an Fc domain. In some embodiments, an antibody variable domain is connected to an Fc domain through a linker. Various linkers are contemplated to be used in molecules described herein. While linkers may be between an antibody variable domain and an Fc domain they may also be between other domains of the molecule, e.g., connecting one or more sequences within the antibody variable domain.
[0238] In some embodiments, a linker includes a flexible linker so as to provide flexibility in a molecule (e.g., between an antibody variable domain and an Fc domain). In some embodiments, a flexible linker contains at least 1 flexible amino acid (e.g., Gly).
[0239] Exemplary flexible linkers include glycine polymers (G)n, glycine-serine polymers (including, for example, (GS)n, (GSGGS: SEQ ID NO: 156)n and (GGGS: SEQ ID NO: 151)n, where n is an integer of at least one), glycine-alanine polymers, alanine-serine polymers, and other flexible linkers known in the art. Glycine and glycine-serine polymers Page 96 of 203 12904890v1Attorney Docket No.: 2017420-0028 are relatively unstructured, and therefore may be able to serve as a neutral tether between components. Glycine accesses significantly more phi-psi space than even alanine, and is much less restricted than residues with longer side chains (see Scheraga, Rev. Computational Chem.11:173-142 (1992)). In some embodiments, a linker comprises the amino acid sequence of SEQ ID NO: 150 (GGGGS), SEQ ID NO: 151 (GGGGSGGGGS), SEQ ID NO: 152 (GGGGSGGGGSGGGGS) or SEQ ID NO: 153 (VDGGGGSGGGGSGGGGSG).
[0240] Additional exemplary flexible linkers include, but are not limited to, SEQ ID NO: 157 (GGSG), SEQ ID NO: 158 (GGSGG), SEQ ID NO: 159 (GSGSG), SEQ ID NO: 160 (GSGGG), SEQ ID NO: 161 (GGGSG), SEQ ID NO: 162 (GSSSG), and the like. Additional exemplary linkers also include the following: GGGGSGGGGSGGGGSGGGGS (SEQ ID NO: 154) and GGGGSGGGGSGGGGSGGGGSSGGGGS (SEQ ID NO: 155).
[0241] The ordinarily skilled artisan will recognize that the design of a molecule described herein can include a linker that is all or partially flexible, such that the linker can include a flexible linker as well as one or more portions that confer less flexible structure to provide for a desired molecule structure.
[0242] Suitable linkers can be readily selected and can be of various lengths, such as from 1 amino acid (e.g., Gly) to 20 amino acids or more, from 2 amino acids to 15 amino acids, from 3 amino acids to 12 amino acids, including 4 amino acids to 10 amino acids, 5 amino acids to 9 amino acids, 6 amino acids to 8 amino acids, or 7 amino acids to 8 amino acids (e.g., at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or 19 amino acids).
[0243] In some embodiments a linker may be or comprise a synthetic linker that does not comprise amino acids, e.g., a polyethylene (PEG) linker or other known synthetic linkers that are commonly used for chemical conjugation, e.g., in antibody-drug conjugates. In this context, it is also to be understood that the molecules described herein encompass molecules where the components of the first or second polypeptides (e.g., antibody variable domain and Fc domain) are linked via chemical conjugation, e.g., “click” or other chemistry, optionally with an intervening amino acid or synthetic linker.
[0244] In some embodiments, a molecule described herein is a fusion protein wherein the first and second polypeptides can be encoded by a single nucleic acid sequence. Page 97 of 203 12904890v1Attorney Docket No.: 2017420-0028 In some embodiments, a molecule described herein is a chemically conjugated molecule that includes components conjugated using synthetic chemistry. Exemplary Configurations
[0245] Various configurations of molecules as described herein are contemplated. Such configurations include various elements of molecules as described herein including a first polypeptide comprising an antibody variable domain linked to a first Fc domain, and a second polypeptide comprising a second Fc domain. Exemplary antibody variable domains that bind IgE, Fc domains, and linkers are described. Such components may be assembled in different configurations to generate a molecule as described herein.
[0246] Exemplary combinations of specific antibody variable domains, Fc domain, and linkers are provided in Table 4 below.
[0247] In some embodiments, a combination in Table 4 may be included in a bivalent molecule configuration as shown, e.g., in FIG.2A. In such a configuration, the first polypeptide (HC1 / LC1) includes an antibody variable domain linked to an Fc domain (Fc1) though an optional linker (L1) and the second polypeptide (HC2 / LC2) includes an antibody variable domain linked to an Fc domain (Fc2) though an optional linker (L2). In some embodiments, the first and second polypeptides are identical and the molecule is a homodimer. In some embodiments, the first and second polypeptides are not identical and the molecule is a heterodimer.
[0248] In some embodiments, a combination in Table 4 may be included in a monovalent molecule configuration as shown, e.g., in FIG.2B. In such a configuration, the first polypeptide (HC1 / LC1) includes an antibody variable domain linked to an Fc domain (Fc1) though an optional linker (L1) and the second polypeptide (HC2) includes an Fc domain (Fc2) and does not include an antibody variable domain. In such embodiments, the first and second polypeptides are not identical and the molecule is a heterodimer. Table 4: Exemplary anti-IgE molecules for IgE Antibody Depletion Molecule ID Name HC1 LC1 L1 Fc1 HC2 LC2 L2 Fc212904890v1Attorney Docket No.: 2017420-0028 Molecule ID Name HC1 LC1 L1 Fc1 HC2 LC2 L2 Fc212904890v1Attorney Docket No.: 2017420-0028 Molecule ID Name HC1 LC1 L1 Fc1 HC2 LC2 L2 Fc2Page 100 of 203 12904890v1Attorney Docket No.: 2017420-0028 Molecule ID Name HC1 LC1 L1 Fc1 HC2 LC2 L2 Fc2 or orsequence comprising any of the combinations of sequences shown in Table 4. In some embodiments, a molecule comprises an amino acid sequence comprising any of the Page 101 of 203 12904890v1Attorney Docket No.: 2017420-0028 combinations of sequences shown in Table 4 and includes a linker (L) between the antibody variable binding domain and the Fc domain.
[0250] In some embodiments, a molecule described herein comprises a first polypeptide, wherein the first polypeptide comprises: (i) an amino acid sequence that is at least 90% identical to SEQ ID NO: 1 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 2; (ii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 11 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 12; (iii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 13 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 14; (iv) an amino acid sequence that is at least 90% identical to SEQ ID NO: 23 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 24; (v) an amino acid sequence that is at least 90% identical to SEQ ID NO: 33 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 34; (vi) an amino acid sequence that is at least 90% identical to SEQ ID NO: 43 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 44; (vii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 53 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 54; (viii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 63 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 65; (ix) an amino acid sequence that is at least 90% identical to SEQ ID NO: 66 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 67; (x) an amino acid sequence that is at least 90% identical to SEQ ID NO: 68 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 69; (xi) an amino acid sequence that is at least 90% identical to SEQ ID NO: 70 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 72; (xii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 73 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 75; (xiii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 76 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 78; (xiv) an amino acid sequence that is at least 90% identical to SEQ ID NO: 79 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 80; (xv) an amino acid sequence that is at least 90% identical to SEQ ID NO: 81 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 182; (xvi) an amino acid sequence that is at least 90% identical to SEQ ID NO: 83 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 84; (xvii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 97 and an amino acid Page 102 of 203 12904890v1Attorney Docket No.: 2017420-0028 sequence that is at least 90% identical to SEQ ID NO: 98; (xviii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 99 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 100; (xix) an amino acid sequence that is at least 90% identical to SEQ ID NO: 101 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 102; (xx) an amino acid sequence that is at least 90% identical to SEQ ID NO: 165 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 166; (xxi) an amino acid sequence that is at least 90% identical to SEQ ID NO: 167 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 168; (xxii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 169 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 170; (xxiii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 171 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 172; (xxiv) an amino acid sequence that is at least 90% identical to SEQ ID NO: 173 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 174; (xxv) an amino acid sequence that is at least 90% identical to SEQ ID NO: 175 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 176; (xxvi) an amino acid sequence that is at least 90% identical to SEQ ID NO: 177; an amino acid sequence that is at least 90% identical to SEQ ID NO: 178; (xxvii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 179 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 180; (xxviii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 181 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 172; or (xxix) an amino acid sequence that is at least 90% identical to SEQ ID NO: 182 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 174.
[0251] In some embodiments, a molecule described herein comprises a first polypeptide, wherein the first polypeptide comprises the amino acid sequence of: (i) SEQ ID NO: 1 and SEQ ID NO: 2; (ii) SEQ ID NO: 11 and SEQ ID NO: 12; (iii) SEQ ID NO: 13 and SEQ ID NO: 14; (iv) SEQ ID NO: 23 and SEQ ID NO: 24; (v) SEQ ID NO: 33 and SEQ ID NO: 34; (vi) SEQ ID NO: 43 and SEQ ID NO: 44; (vii) SEQ ID NO: 53 and SEQ ID NO: 54; (viii) SEQ ID NO: 63 and SEQ ID NO: 65; (ix) SEQ ID NO: 66 and SEQ ID NO: 67; (x) SEQ ID NO: 68 and SEQ ID NO: 69; (xi) SEQ ID NO: 70 and SEQ ID NO: 72; (xii) SEQ ID NO: 73 and SEQ ID NO: 75; (xiii) SEQ ID NO: 76 and SEQ ID NO: 78; (xiv) SEQ ID NO: 79 and SEQ ID NO: 80; (xv) SEQ ID NO: 81 and SEQ ID NO: 182; (xvi): SEQ ID NO: 83 and SEQ ID NO: 84; (xvii) SEQ ID NO: 97 and SEQ ID NO: 98; (xviii) Page 103 of 203 12904890v1Attorney Docket No.: 2017420-0028 SEQ ID NO: 99 and SEQ ID NO: 100; (xix) SEQ ID NO: 101 and SEQ ID NO: 102; (xx) SEQ ID NO: 165 and SEQ ID NO: 166; (xxi) SEQ ID NO: 167 and SEQ ID NO: 168; (xxii) SEQ ID NO: 169 and SEQ ID NO: 170; (xxiii) SEQ ID NO: 171 and SEQ ID NO: 172; (xxiv) SEQ ID NO: 173 and SEQ ID NO: 174; (xxv) SEQ ID NO: 175 and SEQ ID NO: 176; (xxvi) SEQ ID NO: 177 and SEQ ID NO: 178; (xxvii) SEQ ID NO: 179 and SEQ ID NO: 180; (xxviii) SEQ ID NO: 181 and SEQ ID NO: 172; or (xxix) SEQ ID NO: 182 and SEQ ID NO: 174.
[0252] In some embodiments, a molecule described herein comprises a second polypeptide, wherein the second polypeptide comprises: (i) an amino acid sequence that is at least 90% identical to SEQ ID NO: 1 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 2; (ii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 11 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 12; (iii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 13 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 14; (iv) an amino acid sequence that is at least 90% identical to SEQ ID NO: 23 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 24; (v) an amino acid sequence that is at least 90% identical to SEQ ID NO: 33 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 34; (vi) an amino acid sequence that is at least 90% identical to SEQ ID NO: 43 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 44; (vii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 53 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 54; (viii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 64; (ix) an amino acid sequence that is at least 90% identical to SEQ ID NO: 66 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 67; (x) an amino acid sequence that is at least 90% identical to SEQ ID NO: 68 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 69; (xi) an amino acid sequence that is at least 90% identical to SEQ ID NO: 71; (xii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 74; (xiii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 77; (xiv) an amino acid sequence that is at least 90% identical to SEQ ID NO: 79 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 80; (xv) an amino acid sequence that is at least 90% identical to SEQ ID NO: 81 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 182; (xvi) an amino acid sequence that is at least 90% identical to SEQ ID NO: 83 and an amino acid sequence that is Page 104 of 203 12904890v1Attorney Docket No.: 2017420-0028 at least 90% identical to SEQ ID NO: 84; (xvii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 97 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 98; (xviii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 99 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 100 (xix) an amino acid sequence that is at least 90% identical to SEQ ID NO: 101 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 102; (xx) an amino acid sequence that is at least 90% identical to SEQ ID NO: 165 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 166; (xxi) an amino acid sequence that is at least 90% identical to SEQ ID NO: 167 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 168; (xxii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 169 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 170; (xxiii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 171 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 172; (xxiv) an amino acid sequence that is at least 90% identical to SEQ ID NO: 173 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 174; (xxv) an amino acid sequence that is at least 90% identical to SEQ ID NO: 175 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 176; (xxvi) an amino acid sequence that is at least 90% identical to SEQ ID NO: 177 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 178; (xxvii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 179 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 180; (xxviii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 181 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 172; or (xxix) an amino acid sequence that is at least 90% identical to SEQ ID NO: 182 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 174.
[0253] In some embodiments, a molecule described herein comprises a second polypeptide, wherein the second polypeptide comprises the amino acid sequence of: (i) SEQ ID NO: 1 and SEQ ID NO: 2; (ii) SEQ ID NO: 11 and SEQ ID NO: 12; (iii) SEQ ID NO: 13 and SEQ ID NO: 14; (iv) SEQ ID NO: 23 and SEQ ID NO: 24; (v) SEQ ID NO: 33 and SEQ ID NO: 34; (vi) SEQ ID NO: 43 and SEQ ID NO: 44; (vii) SEQ ID NO: 53 and SEQ ID NO: 54; (viii) SEQ ID NO: 64; (ix) SEQ ID NO: 66 and SEQ ID NO: 67; (x) SEQ ID NO: 68 and SEQ ID NO: 69; (xi) SEQ ID NO: 71; (xii) SEQ ID NO: 74; (xiii) SEQ ID NO: 77; (xiv) SEQ ID NO: 79 and SEQ ID NO: 80; (xv) SEQ ID NO: 81 and SEQ ID NO: 182; (xvi) SEQ ID NO: 83 and SEQ ID NO: 84; (xvii) SEQ ID NO: 97 and SEQ ID NO: 98; Page 105 of 203 12904890v1Attorney Docket No.: 2017420-0028 (xviii) SEQ ID NO: 99 and SEQ ID NO: 100; (xix) SEQ ID NO: 101 and SEQ ID NO: 102; (xx) SEQ ID NO: 165 and SEQ ID NO: 166; (xxi) SEQ ID NO: 167 and SEQ ID NO: 168; (xxii) SEQ ID NO: 169 and SEQ ID NO: 170; (xxiii) SEQ ID NO: 171 and SEQ ID NO: 172; (xxiv) SEQ ID NO: 173 and SEQ ID NO: 174; (xxv) SEQ ID NO: 175 and SEQ ID NO: 176; (xxvi) SEQ ID NO: 177 and SEQ ID NO: 178; (xxvii) SEQ ID NO: 179 and SEQ ID NO: 180; (xxviii) SEQ ID NO: 181 and SEQ ID NO: 172; or (xxix) SEQ ID NO: 182 and SEQ ID NO: 174.
[0254] In some embodiments, a molecule described herein comprises a first and second polypeptide, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 1 and SEQ ID NO: 2, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 1 and SEQ ID NO: 2.
[0255] In some embodiments, a molecule described herein comprises a first and second polypeptide, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 11 and SEQ ID NO: 12, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 11 and SEQ ID NO: 12.
[0256] In some embodiments, a molecule described herein comprises a first and second polypeptide, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 13 and SEQ ID NO: 14, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 13 and SEQ ID NO: 14.
[0257] In some embodiments, a molecule described herein comprises a first and second polypeptide, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 23 and SEQ ID NO: 24, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 23 and SEQ ID NO: 24.
[0258] In some embodiments, a molecule described herein comprises a first and second polypeptide, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 33 and SEQ ID NO: 34, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 33 and SEQ ID NO: 34.
[0259] In some embodiments, a molecule described herein comprises a first and second polypeptide, wherein the first polypeptide comprises the amino acid sequence of Page 106 of 203 12904890v1Attorney Docket No.: 2017420-0028 SEQ ID NO: 43 and SEQ ID NO: 44, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 43 and SEQ ID NO: 44.
[0260] In some embodiments, a molecule described herein comprises a first and second polypeptide, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 53 and SEQ ID NO: 53, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 53 and SEQ ID NO: 54.
[0261] In some embodiments, a molecule described herein comprises a first and second polypeptide, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 63 and SEQ ID NO: 65, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 64.
[0262] In some embodiments, a molecule described herein comprises a first and second polypeptide, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 66 and SEQ ID NO: 67, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 66 and SEQ ID NO: 67.
[0263] In some embodiments, a molecule described herein comprises a first and second polypeptide, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 68 and SEQ ID NO: 69, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 68 and SEQ ID NO: 69.
[0264] In some embodiments, a molecule described herein comprises a first and second polypeptide, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 70 and SEQ ID NO: 72, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 71.
[0265] In some embodiments, a molecule described herein comprises a first and second polypeptide, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 73 and SEQ ID NO: 75, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 74.
[0266] In some embodiments, a molecule described herein comprises a first and second polypeptide, wherein the first polypeptide comprises the amino acid sequence of Page 107 of 203 12904890v1Attorney Docket No.: 2017420-0028 SEQ ID NO: 76 and SEQ ID NO: 78, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 77.
[0267] In some embodiments, a molecule described herein comprises a first and second polypeptide, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 79 and SEQ ID NO: 80, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 79 and SEQ ID NO: 80.
[0268] In some embodiments, a molecule described herein comprises a first and second polypeptide, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 81 and SEQ ID NO: 82, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 81 and SEQ ID NO: 82.
[0269] In some embodiments, a molecule described herein comprises a first and second polypeptide, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 83 and SEQ ID NO: 84, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 83 and SEQ ID NO: 84.
[0270] In some embodiments, a molecule described herein comprises a first and second polypeptide, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 97 and SEQ ID NO: 98, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 97 and SEQ ID NO: 98.
[0271] In some embodiments, a molecule described herein comprises a first and second polypeptide, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 99 and SEQ ID NO: 100, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 99 and SEQ ID NO: 100.
[0272] In some embodiments, a molecule described herein comprises a first and second polypeptide, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 101 and SEQ ID NO: 102, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 101 and SEQ ID NO: 102.
[0273] In some embodiments, a molecule described herein comprises a first and second polypeptide, wherein the first polypeptide comprises the amino acid sequence of Page 108 of 203 12904890v1Attorney Docket No.: 2017420-0028 SEQ ID NO: 165 and SEQ ID NO: 166, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 165 and SEQ ID NO: 166.
[0274] In some embodiments, a molecule described herein comprises a first and second polypeptide, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 167 and SEQ ID NO: 168, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 167 and SEQ ID NO: 168.
[0275] In some embodiments, a molecule described herein comprises a first and second polypeptide, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 169 and SEQ ID NO: 170, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 169 and SEQ ID NO: 170.
[0276] In some embodiments, a molecule described herein comprises a first and second polypeptide, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 171 and SEQ ID NO: 172, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 171 and SEQ ID NO: 172.
[0277] In some embodiments, a molecule described herein comprises a first and second polypeptide, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 173 and SEQ ID NO: 174, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 173 and SEQ ID NO: 174.
[0278] In some embodiments, a molecule described herein comprises a first and second polypeptide, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 175 and SEQ ID NO: 176, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 175 and SEQ ID NO: 176.
[0279] In some embodiments, a molecule described herein comprises a first and second polypeptide, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 177 and SEQ ID NO: 178, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 177 and SEQ ID NO: 178.
[0280] In some embodiments, a molecule described herein comprises a first and second polypeptide, wherein the first polypeptide comprises the amino acid sequence of Page 109 of 203 12904890v1Attorney Docket No.: 2017420-0028 SEQ ID NO: 179 and SEQ ID NO: 180, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 179 and SEQ ID NO: 180.
[0281] In some embodiments, a molecule described herein comprises a first and second polypeptide, wherein the first polypeptide comprises an amino acid sequence that is at least 90% identical to SEQ ID NO: 181 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 172, and the second polypeptide comprises an amino acid sequence that is at least 90% identical to SEQ ID NO: 181 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 172.
[0282] In some embodiments, a molecule described herein comprises a first and second polypeptide, wherein the first polypeptide comprises an amino acid sequence that is at least 90% identical to SEQ ID NO: 182 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 174, and the second polypeptide comprises an amino acid sequence that is at least 90% identical to SEQ ID NO: 182 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 174.
[0283] In some embodiments, a molecule described herein comprises a first and second polypeptide, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 181 and SEQ ID NO: 172, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 181 and SEQ ID NO: 172.
[0284] In some embodiments, a molecule described herein comprises a first and second polypeptide, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 182 and SEQ ID NO: 174, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 182 and SEQ ID NO: 174.
[0285] In some embodiments, the first and / or second polypeptide may consist essentially of an amino acid sequence that is at least 90% identical to any of the aforementioned sequences. In some embodiments, the first and / or second polypeptide may consist essentially of any of the aforementioned sequences. Characteristics of Exemplary Molecules
[0286] Molecules described herein may be identified, assessed, and / or characterized for one or more of their physical / chemical properties and / or biological activities. Those Page 110 of 203 12904890v1Attorney Docket No.: 2017420-0028 skilled in the art will be aware of a variety of approaches, including particular assays, that may be utilized for such identification, assessment, and / or characterization. Antibody variable domains of molecules described herein may be selected according to various criteria including, but not limited to, binding affinity, or the potency of the response (e.g., neutralization / removal of IgE antibodies). Binding Properties
[0287] Antibody variable domains can be selected based on, among other things, their binding properties for their targets. The binding properties of an antibody variable domain of molecules described herein can be measured by methods known in the art, e.g., one of the following methods: BIACORE analysis, Enzyme Linked Immunosorbent Assay (ELISA), x-ray crystallography, sequence analysis and scanning mutagenesis. The binding interaction of an antibody variable domain and an IgE antibody can be analyzed using surface plasmon resonance (SPR). SPR or Biomolecular Interaction Analysis (BIA) detects bio-specific interactions in real time, without labeling any of the interactants. Changes in the mass at the binding surface (indicative of a binding event) of the BIA chip result in alterations of the refractive index of light near the surface. The changes in the refractivity generate a detectable signal, which are measured as an indication of real-time reactions between biological molecules. Methods for using SPR are described, for example, in U.S. Pat. No.5,641,640; Raether (1988) Surface Plasmons Springer Verlag; Sjolander and Urbaniczky, Anal. Chem.63:2338-2345 (1991); Szabo et al., Curr. Opin. Struct. Biol.5:699- 705 (1995) and on-line resources provided by BIAcore (Cytiva, USA). Additionally, a KinExA (Kinetic Exclusion Assay) assay, available from Sapidyne Instruments (Boise, Idaho), and / or an Octet BLI (Bio-Layer Interferometry) from Sartorius (Goettingen, Germany) can also be used.
[0288] Information from SPR or from similar BIA methods can be used to provide an accurate and quantitative measure of the equilibrium dissociation constant (KD), and kinetic parameters, including Kon and Koff, for the binding of an antibody variable domain to an IgE antibody. Such data can be used to compare different molecules. Information from SPR can also be used to develop structure-activity relationships (SAR). Variant amino acids at given positions can be identified that correlate with particular binding parameters, e.g., high affinity. Page 111 of 203 12904890v1Attorney Docket No.: 2017420-0028
[0289] In some embodiments, an antibody variable domain a described herein exhibits high affinity for binding for an IgE antibody or an internalizing receptor. In various embodiments, KDof an antibody variable domain as described herein for a target IgE antibody is less than about 10-4, 10-5, 10-6, 10-7, 10-8, 10-9, 10-10, 10-11, 10-12, 10-13, 10-14, or 10-15M or any range there between. In certain instances, KDof an antibody variable domain as described herein for an immune cell target is between 0.001 and 1 nM, e.g., 0.001 nM, 0.005 nM, 0.01 nM, 0.05 nM, 0.1 nM, 0.5 nM, or 1 nM or any range there between.
[0290] In some embodiments, an antibody variable domain binds to an IgE antibody with a high binding affinity. In various embodiments, KD of an antibody variable domain as described herein for an IgE antibody is less than about 10-4, 10-5, 10-6, 10-7, 10-8, 10-9, 10-10, 10-11, 10-12, 10-13, 10-14, or 10-15M or any range there between. In some embodiments, an antibody variable domain binds to an IgE antibody with a binding affinity that is comparable or higher than an affinity of a natural IgE receptor to an IgE antibody. In certain instances, KD of an antibody variable domain for an IgE antibody is between 0.001 and 1 nM, e.g., 0.001 nM, 0.005 nM, 0.01 nM, 0.05 nM, 0.1 nM, 0.5 nM, or 1 nM or any range there between.
[0291] In some embodiments, a molecule is characterized in its ability to selectively reduce or deplete circulating IgE antibodies in a sample or patient.
[0292] In some embodiments, levels of IgE antibodies in a subject or in a biological sample from the subject after administration is reduced relative to a level before administration. In some embodiments, a level of IgE antibodies is reduced by at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% relative to a level before the administration of the molecule. In some embodiments, level of IgE antibodies is sustained over time. In some embodiments, a sustained period of time comprises at least 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 10 weeks, 12 weeks, or longer.
[0293] In some embodiments, a molecule described herein has an increased affinity for FcγRIIB. In some embodiments FcγRIIB is human FcγRIIB. In some embodiments, Page 112 of 203 12904890v1Attorney Docket No.: 2017420-0028 FcγRIIB is murine FcγRIIB. In some embodiments, an increased affinity for FcγRIIB is provided by mutating one or both of the molecule’s Fc domains, as described herein.
[0294] In some embodiments, a molecule described herein comprises one or more mutations in one of both of the Fc domains that enhances binding kinetics of an immune complex comprising one or more molecules and a target IgE antibody to FcγRIIB. In some embodiments, enhanced binding kinetics comprises at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, or at least 50% or greater binding affinity. In some embodiments, enhanced binding kinetics comprises an increase in avidity, stability, strength, frequency, and / or duration of binding between the immune complex and FcγRIIB. In some embodiments, enhanced binding kinetics comprise an increase in the rate of association, a decrease in the rate of disassociation, and / or a change in the equilibrium dissociation constant.
[0295] In some embodiments, molecules described herein having a first and second Fc domain comprise one or more mutations in the first and / or second Fc domain to increase binding to FcγRIIB, wherein upon binding of a molecule to an antibody (e.g., and IgE antibody), an immune complex is formed that has enhanced binding kinetics with FcγRIIB relative to an immune complex that comprises the antibody (e.g., and IgE antibody) bound to a corresponding molecule with wild-type Fc domains.
[0296] In some embodiments, molecules described herein having a first and second Fc domain comprise one or more mutations in the first and / or second Fc domain to increase binding to FcγRIIB, wherein upon binding of two molecules to an IgE antibody, an immune complex is formed that has enhanced binding kinetics with FcγRIIB relative to an immune complex that comprises the IgE antibody bound to two corresponding molecules with wild- type Fc domains.
[0297] In some embodiments, a molecule described herein that is not present in an immune complex has a moderate binding affinity to FcγRIIB (e.g., where the Fc domains of the molecule have slightly increased binding affinity to FcγRIIB compared to a molecule comprising wildtype Fc domains). In some embodiments, the molecule binds to FcγRIIB with an affinity within the range of about 1 µM to 0.001 µM. In some embodiments, the molecule binds to FcγRIIB with an affinity within the range of about 1 µM to 0.01 µM. In Page 113 of 203 12904890v1Attorney Docket No.: 2017420-0028 some embodiments, the molecule binds to FcγRIIB with an affinity within the range of about 0.1 µM to 0.01 µM. In some embodiments, a molecule described herein exhibits avidity-mediated binding to FcγRIIB when part of an immune complex comprising two molecules bound to an IgE antibody. In some embodiments, a molecule described herein has increased binding to FcγRIIB when the molecule is present in an immune complex with two molecules bound to an IgE antibody compared to the same immune complex with only one molecule bound to the IgE antibody. In some embodiments, a molecule described herein has increased binding to FcγRIIB when the molecule is present in an immune complex with two molecules bound to an IgE antibody compared to the IgE antibody alone. Without wishing to be bound by any theory, such avidity-mediated effects allow for selective binding and depletion of immune complexes, i.e., two molecules described herein and one IgE antibody and weaker binding to the molecules when they are not part of an immune complex. These characteristics allow for molecules described herein to remain circulating longer in the bloodstream of a subject before being cleared by FcγRIIB-mediated internalization and degradation.
[0298] In some embodiments, a molecule described herein having a first and second Fc domain comprises one or more mutations in the first and / or second Fc domain to increase binding to FcγRIIB, and upon binding of a molecule described herein to an IgE antibody, an immune complex is formed that has no binding affinity, or decreased binding affinity, or slight increased binding affinity (e.g., within a 2-fold increase) to FcγRI, FcγRIIA167H, FcγRIIA167R, FcγRIIIA176F, FcγRIIIA176V, FcγRIIIB, and / or FcRn relative to an immune complex that comprises the IgE antibody and a corresponding molecule with wild-type Fc domains. In some embodiments, a molecule described herein having a first and second Fc domain comprises one or more mutations in the first and / or second Fc domain to increase binding to FcγRIIB, and upon binding of the molecule to an IgE antibody, an immune complex is formed that has no binding affinity, or decreased binding affinity, or slight increased binding affinity (e.g., within a 2-fold increase) to FcγRI, FcγRIIA167H, FcγRIIA167R, FcγRIIIA176F, FcγRIIIA176V, FcγRIIIB, and / or FcRn relative to the IgE antibody alone.
[0299] In some embodiments, molecules described herein having a first Fc domain and a second Fc domain comprise one or more mutations in the first and / or second Fc domain to increase binding to FcγRIIB, and upon binding of two molecules to an IgE Page 114 of 203 12904890v1Attorney Docket No.: 2017420-0028 antibody, an immune complex is formed that has no binding affinity, or decreased binding affinity, or slight increased binding affinity (e.g., within a 2-fold increase) to FcγRI, FcγRIIA167H, FcγRIIA167R, FcγRIIIA176F, FcγRIIIA176V, FcγRIIIB, and / or FcRn relative to an immune complex that comprises the IgE antibody and two corresponding molecules with wild-type Fc domains. In some embodiments, molecules described herein having a first Fc domain and a second Fc domain comprise one or more mutations in the first and / or second Fc domain to increase binding to FcγRIIB, and upon binding of two molecules to an IgE antibody, an immune complex is formed that has no binding affinity, or decreased binding affinity, or slight increased binding affinity (e.g., within a 2-fold increase) to FcγRI, FcγRIIA167H, FcγRIIA167R, FcγRIIIA176F, FcγRIIIA176V, FcγRIIIB, and / or FcRn relative to an immune complex that comprises the IgE antibody bound to only a single molecule. In some embodiments, upon binding of two molecules to an IgE antibody, an immune complex is formed that has no binding affinity, or decreased binding affinity, or slight increased binding affinity (e.g., within a 2-fold increase) to FcγRI, FcγRIIA167H, FcγRIIA167R, FcγRIIIA176F, FcγRIIIA176V, FcγRIIIB, and / or FcRn relative to the IgE antibody alone.
[0300] In some embodiments, the decreased binding affinity comprises at least 10% decrease in binding affinity of the immune complex to FcγRI, FcγRIIA167H, FcγRIIA167R, FcγRIIIA176F, FcγRIIIA176V, FcγRIIIB, and / or FcRn. In some embodiments, the at least 10% decrease binding affinity comprises at least 15% decrease, at least 20% decrease, at least 25% decrease, at least 30% decrease, at least 35% decrease, at least 40% decrease, at least 45% decrease, or at least 50% or greater decrease in binding affinity. In some embodiments, the binding affinity comprises binding affinity to a cell line (e.g., a CHO cell line) endogenously expressing or overexpressing FcγRI, FcγRIIA167H, FcγRIIA167R, FcγRIIIA176F, FcγRIIIA176V, FcγRIIIB, and / or FcRn measured by flow cytometry.
[0301] Additionally, the present disclosure provides molecules comprising Fc domains that that have increased binding affinity for FcγRIIB and also have decreased or undetectable binding to certain activating Fc receptors. In some embodiments, an activating Fc receptor includes one or more of FcγRI, FcγRIIA167H, FcγRIIA167R, FcγRIIIA176F, FcγRIIIA176V, FcγRIIIB, and / or FcRn. In some embodiments, Fc domains of molecules described herein have decreased binding affinity to FcγRI, FcγRIIA167H, FcγRIIA167R, FcγRIIIA176F, FcγRIIIA176V, FcγRIIIB, and / or FcRn relative to the corresponding wild- Page 115 of 203 12904890v1Attorney Docket No.: 2017420-0028 type Fc domain. In some embodiments, Fc domains of molecules described herein have substantially no binding affinity to FcγRI, FcγRIIA167H, FcγRIIA167R, FcγRIIIA176F, FcγRIIIA176V, FcγRIIIB, and / or FcRn relative to the corresponding wild-type Fc domain. Such binding properties are beneficial in molecules described herein and may lessen risk of toxicity as there is less risk of activating the innate immune response (through activating Fc receptors) in response to the molecules being introduced into the body of a subject.
[0302] In some embodiments, a molecule described herein preferentially binds to immune cells expressing FcγRIIB over immune cells expressing FcγRIIA. In some embodiments, a molecule described herein has substantially no binding affinity for cells that do not express FcγRIIB (e.g., T cells, NK cells, neutrophils, and / or eosinophils). Immune cells known to express FcγRIIB include B cells, monocytes and / or basophils.
[0303] In some embodiments, a molecule described herein prevents binding of an IgE antibody to its target Fc receptor. In some embodiments, a molecule described herein blocks engagement of the IgE antibodies with FceR1A and / or FcεRII. In some embodiments, a molecule described herein neutralizes an IgE antibody. In some embodiments, one or more molecules described herein form an immune complex with an IgE antibody and the immune complex is internalized and degraded by an immune cell expressing FcγRIIB. In some embodiments, an immune complex comprises one or more molecules (e.g., two or more molecules) bound to an IgE antibody and is cleared from circulation, e.g., destroyed. FcγRIIB is an internalizing receptor that binds to its target, internalizes the complex and shuttles the target to the lysosome for degradation. Without wishing to be bound by any theory, molecules described herein that have increased FcγRIIB binding may deplete target autoantibodies and / or antigen-specific B cells producing autoantibodies through various mechanisms. In some embodiments, a potential mechanism of action includes clearing autoantibodies by targeting FcγRIIB isoform 2 on liver sinusoidal endothelial cells (LSECs). In this exemplary mechanism of action, the antibody variable domain of the molecule binds to an IgE antibody and the Fc domain binds to FcγRIIB isoform 2 on liver sinusoidal endothelial cells. IgE antibodies are internalized into the liver sinusoidal endothelial cells and targeted to the lysosome for degradation. In another exemplary mechanism, molecules described herein may target pathogenic B cells producing IgE antibodies, by targeting FcγRIIB isoform 1 on a B cell that comprises antigen-specific Page 116 of 203 12904890v1Attorney Docket No.: 2017420-0028 B-cell receptor (BCR) (e.g., an IgE antibody expressed on the surface of the B cell), which leads to B cell apoptosis and inhibition.
[0304] In some embodiments, an Fc domain described herein comprises one or more modifications such that a molecule described herein does not activate immune cells (e.g., does not activate immune cells to secrete pro-inflammatory cytokines, e.g., IL-6).
[0305] In some embodiments, molecules described herein do not bind to certain components of the complement system (e.g., C1q). In some embodiments, molecules described herein do not bind to C1q. In some embodiments, molecules described herein do not activate the complement system. Methods of Generating Exemplary Molecules
[0306] The present disclosure features methods that include generating a molecule described herein.
[0307] Molecules as described herein may be produced using recombinant methods and compositions (see, e.g., U.S. Pat. No.4,816,567). In some embodiments, an isolated nucleic acid encoding a molecule as described herein can be provided. Such nucleic acid may encode an amino acid sequence comprising the first and / or second polypeptide. In a further embodiment, one or more vectors comprising such nucleic acid can be provided. A vector can be a nucleic acid molecule capable of propagating another nucleic acid to which it is linked. The term can include the vector as a self-replicating nucleic acid structure as well as the vector incorporated into the genome of a host cell into which it has been introduced. Certain vectors can be capable of directing the expression of nucleic acids to which they are operatively linked.
[0308] In a further embodiment, a host cell comprising such nucleic acid can be provided. Host cells can be cells into which an exogenous nucleic acid has been introduced, including the progeny of such cells. Host cells can include “transformants” and “transformed cells,” which can include the primary transformed cell and progeny derived therefrom without regard to the number of passages. Progeny may not be completely identical in nucleic acid content to a parent cell, but may contain mutations. Mutant progeny that have the same function or biological activity as screened or selected for in the originally Page 117 of 203 12904890v1Attorney Docket No.: 2017420-0028 transformed cell are included herein. In one such embodiment, a host cell can comprise (e.g., has been transformed with) a vector comprising a nucleic acid that encodes an amino acid sequence comprising a first polypeptide and a second polypeptide of a molecule. In some embodiments, a first vector comprises a nucleic acid that encodes an amino acid sequence comprising a first polypeptide of a molecule and a second vector comprising a nucleic acid that encodes an amino acid sequence comprising the second polypeptide of a molecule. In some embodiments, the host cell can be eukaryotic, e.g., a Chinese Hamster Ovary (CHO) cell, a lymphoid cell (e.g., Y0, NS0, Sp20 cell), or a Human Embryonic Kidney (HEK293) cell. In some embodiments, a method of making molecule and / or an antibody variable domain described herein can be provided, wherein the method can comprise culturing a host cell comprising a nucleic acid encoding the molecule and / or an antibody variable domain, as provided above, under conditions suitable for expression of the molecule and / or an antibody variable domain, and optionally recovering the molecule from the host cell or host cell culture medium.
[0309] For recombinant production of a molecule and / or an antibody variable domain, an isolated nucleic acid encoding a molecule and / or an antibody variable domain, e.g., as described above, can be inserted into one or more vectors for further cloning and / or expression in a host cell. Such nucleic acid may be readily isolated and sequenced using conventional procedures.
[0310] Suitable host cells for cloning or expression of antibody-encoding vectors can include prokaryotic or eukaryotic cells described herein. For example, molecules and / or an antibody variable domains may be produced in bacteria, e.g., when glycosylation and Fc effector function are not needed (see, e.g., U.S. Pat. Nos.5,648,237, 5,789,199, and 5,840,523; Charlton, Methods in Molecular Biology 248:245-254 (2003)). After expression, the molecule and / or an antibody variable domain may be isolated from the bacterial cell paste in a soluble fraction and can be further purified.
[0311] In addition to prokaryotes, eukaryotic microbes such as filamentous fungi or yeast can be suitable cloning or expression hosts for molecule and / or an antibody variable domain-encoding vectors (see, e.g., Gerngross Nat. Biotech.22:1409-1414 (2004) and Li et al. Nat. Biotech.24:210-215(2006)). Suitable host cells for the expression of glycosylated antibody can also be derived from multicellular organisms, including invertebrates and Page 118 of 203 12904890v1Attorney Docket No.: 2017420-0028 vertebrates. Examples of invertebrates can include plant and insect cells (see, e.g., U.S. Pat. Nos.5,959,177, 6,040,498, 6,420,548, 7,125,978, and 6,417,429). Examples of vertebrate cells can include mammalian cell lines, monkey kidney CV1 line transformed by SV40 (COS-7); human embryonic kidney line (293 or 293T cells as described, e.g., in Graham et al., J. Gen Virol.36:59-74 (1977)); baby hamster kidney cells (BHK); mouse sertoli cells (TM4 cells); monkey kidney cells (CV1); African green monkey kidney cells (VERO-76); human cervical carcinoma cells (HELA); canine kidney cells (MDCK; buffalo rat liver cells (BRL 3A); human lung cells (W138); human liver cells (Hep G2); mouse mammary tumor (MMT 060562); TR1 cells; MRC 5 cells; FS4 cells; Chinese hamster ovary (CHO) cells, including DHFR− CHO cells; and myeloma cell lines such as Y0, NS0 and Sp2 / 0. (see, e.g., Yazaki and Wu, Methods in Molecular Biology 248:255-268 (2003)).
[0312] Molecules described herein may be purified by any technique. For example, not wishing to be bound by theory, molecules described herein can be recovered and purified from recombinant cell cultures by well-known methods including, but not limited to, protein A purification, protein G purification, ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, hydroxylapatite chromatography and lectin chromatography. High performance liquid chromatography (“HPLC”) can also be employed for purification. See, e.g., Colligan, Current Protocols in Immunology, or Current Protocols in Protein Science, John Wiley & Sons, NY, N.Y., (1997- 2001), e.g., chapters 1, 4, 6, 8, 9, and 10, each entirely incorporated herein by reference.
[0313] As discussed herein, some or all of the components of a molecule may also be linked using “click” or other chemistry, optionally via an amino acid or synthetic linker. For such molecules some or all of the components of the molecule may be prepared recombinantly and then chemically modified for conjugation. Suitable methods are well known in the art, e.g., as used in the preparation of antibody-drug conjugates.
[0314] Purified molecules and antibody variable domains included in such can be characterized by, for example, ELISA, ELISPOT, flow cytometry, immunocytology, BIACORE analysis, Octet BLI analysis, KINEXA kinetic exclusion assay, SDS-PAGE and Western blot, or by HPLC analysis as well as by a number of other functional assays disclosed herein. The contents of all cited references (including literature references, issued Page 119 of 203 12904890v1Attorney Docket No.: 2017420-0028 patents, published patent applications, and co-pending patent applications) cited throughout this application are hereby expressly incorporated by reference. Applications
[0315] The present disclosure provides technologies for selective depletion of IgE antibodies implicated in allergic disease such as food allergy, allergic asthma, and chronic hives.
[0316] In some embodiments, a molecule can be administered in a pharmaceutical composition can be used in combination with, by administering before, concurrently or after administration of a second therapy.
[0317] In some embodiments, molecules of the present disclosure are used to treat a subject suffering from an allergic disease (an allergic disease caused by IgE antibodies) that would benefit from the selective neutralization and / or depletion of IgE antibodies. Such molecules are generated such that they bind to an internalizing receptor and include an antibody variable domain that binds to IgE antibodies. Molecules may also include a modification to enhance binding to internalizing receptors.
[0318] For use in therapeutic methods, molecules of the present disclosure would be formulated, dosed, and administered in a fashion consistent with good medical practice. Factors for consideration in this context include the particular disease or disorder being treated, the particular subject being treated, the clinical condition of the individual subject, the cause of the disorder, the site of delivery of the agent, the method of administration, the scheduling of administration, and other factors known to medical practitioners.
[0319] In some embodiments, the present disclosure provides a method for treating a disease. In some embodiments, the method comprises administering to an subject having such disease a therapeutically effective amount of a molecule described herein. In some embodiments, a composition is administered to said subject, comprising a molecule described herein in a pharmaceutically acceptable form. In some embodiments, the disease to be treated is an allergic disease. In some embodiments, the allergic disease is caused by IgE antibodies. In some embodiments, the allergic disease is allergic asthma. In some embodiments the method further comprises administering to the subject a therapeutically Page 120 of 203 12904890v1Attorney Docket No.: 2017420-0028 effective amount of at least one additional therapeutic agent. A “subject” may be a mammal, including a human.
[0320] Any of such methods can optionally comprise administering an effective amount of at least one composition or pharmaceutical composition comprising at least one molecule described herein to a subject in need of such modulation, treatment, diagnosis, and / or therapy (e.g., a subject suffering from an allergic disease such as food allergy, allergic asthma, and chronic hives.
[0321] In some embodiments, provided methods include therapeutic methods that comprise administering an effective amount of a composition that comprises and / or delivers a molecule described herein to a subject such that the molecule binds an IgE antibody and an internalizing receptor, such that the complex is internalized and targeted to the lysosome. In some embodiments a target antibody is an IgE antibody and the internalizing receptor is FcγRIIB.
[0322] In some embodiments, provided methods include therapeutic methods that comprise administering an effective amount of a composition that comprises and / or delivers a molecule described herein to a subject such that the molecule binds an antibody variable domain, where the antibody variable domain binds to a receptor on a cell that then internalizes the bound molecule. In some embodiments, an antibody variable domain binds to an internalizing receptor such as ASPGR, FcRn, and / or FcγRIIB). A molecule that targets an internalizing receptor such as FcγRIIB may inhibit B cells on which the IgE antibody is expressed (e.g., as described in Chu, S. Y. et al., Mol Immunol 45, 3926–3933 (2008), which is herein incorporated by reference in its entirety).
[0323] Therapeutic methods described herein can optionally further comprise co- administration or combination therapy for treating such diseases, wherein the administering a composition comprises a molecule described herein, further comprises administering, before concurrently, and / or after, at least one additional therapeutic agent.
[0324] The present disclosure also provides methods of treating a subject suffering from or susceptible to an allergic disease (e.g., food allergy, allergic asthma, and chronic hives, or another allergic disease involving IgE antibodies), for example, by administering to the subject a pharmaceutical composition comprising a molecule described herein, a nucleic Page 121 of 203 12904890v1Attorney Docket No.: 2017420-0028 acid molecule encoding the molecule. In some embodiments, such a treatment decreases or ameliorates one or more signs or symptoms of an allergic disease.
[0325] In some embodiments, treatment with a molecule described herein reduces the levels of IgE antibodies in a subject or in a biological sample relative to a level before administration. In some embodiments, a level of IgE antibodies is reduced by at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% relative to a level before the administration. In some embodiments, treatment with a molecule described herein reduces autoantibodies in a subject for a sustained period of time, e.g., at least 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 10 weeks, 12 weeks, or longer. Pharmaceutical Compositions
[0326] In some embodiments, a molecule described herein may be formulated as a pharmaceutical composition and administered to a subject (e.g., to treat an autoimmune disease). In various embodiments, molecules described herein can be incorporated into pharmaceutical compositions. Such a pharmaceutical composition can be useful, e.g., for the prevention and / or treatment of diseases, e.g., autoimmune diseases. Pharmaceutical compositions can be formulated by methods known to those skilled in the art (such as described in Remington’s Pharmaceutical Sciences, 17thedition, ed. Alfonso R. Gennaro, Mack Publishing Company, Easton, Pa. (1985)).
[0327] In some embodiments, a pharmaceutical composition comprises a nucleic acid molecule comprising a nucleotide sequence encoding a molecule described herein and a pharmaceutically acceptable carrier. In some embodiments, a molecule is expressed in a host cell containing a nucleic acid molecule comprising a nucleotide sequence encoding a molecule described herein. In some embodiments, a molecule described herein is encoded by a vector (e.g., a viral vector such as a retroviral vector, a lentiviral vector, an adeno- associated viral (AAV) vector, or an adenoviral vector).
[0328] In some embodiments, a pharmaceutical composition comprises a first molecule described herein or a nucleic acid molecule encoding the molecule, and also Page 122 of 203 12904890v1Attorney Docket No.: 2017420-0028 comprises a therapeutic agent or a nucleic acid molecule encoding a second therapeutic agent that selectively depletes pathogenic plasma cells that produce the autoantibodies; and a pharmaceutically acceptable carrier.
[0329] In some embodiments, a pharmaceutical composition can be formulated to include a pharmaceutically acceptable carrier or excipient. Examples of pharmaceutically acceptable carriers include, without limitation, any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like that are physiologically compatible. Compositions of the present disclosure can include a pharmaceutically acceptable salt, e.g., an acid addition salt or a base addition salt.
[0330] In some embodiments, a composition including a molecule as described herein, e.g., a sterile formulation for injection, can be formulated in accordance with conventional pharmaceutical practices using distilled water for injection as a vehicle. For example, physiological saline or an isotonic solution containing glucose and other supplements such as D-sorbitol, D-mannose, D-mannitol, and sodium chloride may be used as an aqueous solution for injection, optionally in combination with a suitable solubilizing agent, such as, for example, an alcohol such as ethanol and / or a polyalcohol such as propylene glycol or polyethylene glycol, and / or a nonionic surfactant such as polysorbate 80 or HCO-50.
[0331] As disclosed herein, a pharmaceutical composition may be in any form known in the art. Such forms include, e.g., liquid, semi-solid and solid dosage forms, such as liquid solutions (e.g., injectable and infusible solutions), dispersions or suspensions, tablets, pills, powders, liposomes and suppositories.
[0332] Selection or use of any particular form may depend, in part, on the intended mode of administration and therapeutic application. For example, compositions containing a composition intended for systemic or local delivery can be in the form of injectable or infusible solutions. Accordingly, compositions can be formulated for administration by a parenteral mode (e.g., intravenous, subcutaneous, intraperitoneal, or intramuscular injection). As used herein, parenteral administration refers to modes of administration other than enteral and topical administration, usually by injection, and include, without limitation, intravenous, intranasal, intraocular, pulmonary, intramuscular, intraarterial, intrathecal, Page 123 of 203 12904890v1Attorney Docket No.: 2017420-0028 intracapsular, intraorbital, intracardiac, intradermal, intrapulmonary, intraperitoneal, transtracheal, subcutaneous, subcuticular, intraarticular, subcapsular, subarachnoid, intraspinal, epidural, intracerebral, intracranial, intracarotid and intrasternal injection and infusion.
[0333] Route of administration can be parenteral, for example, administration by injection, transnasal administration, transpulmonary administration, or transcutaneous administration. Administration can be systemic or local by intravenous injection, intramuscular injection, intraperitoneal injection, or subcutaneous injection.
[0334] In some embodiments, a pharmaceutical composition of the present disclosure can be formulated as a solution, microemulsion, dispersion, liposome, or other ordered structure suitable for stable storage at high concentration. Sterile injectable solutions can be prepared by incorporating a composition described herein in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filter sterilization. Generally, dispersions are prepared by incorporating a composition described herein into a sterile vehicle that contains a basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, methods for preparation include vacuum drying and freeze-drying that yield a powder of a composition described herein plus any additional desired ingredient (see below) from a previously sterile- filtered solution thereof. The proper fluidity of a solution can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. Prolonged absorption of injectable compositions can be brought about by including in the composition a reagent that delays absorption, for example, monostearate salts, and gelatin.
[0335] In some embodiments, a composition described herein can be therapeutically delivered to a subject by way of local administration. As used herein, “local administration” or “local delivery,” can refer to delivery that does not rely upon transport of the composition or agent to its intended target tissue or site via the vascular system. For example, the composition may be delivered by injection or implantation of the composition or agent or by injection or implantation of a device containing the composition or agent. In some embodiments, following local administration in the vicinity of a target tissue or site, the Page 124 of 203 12904890v1Attorney Docket No.: 2017420-0028 composition or agent, or one or more components thereof, may diffuse to an intended target tissue or site that is not the site of administration.
[0336] In some embodiments, compositions can be formulated with a carrier that will protect the compound against rapid release, such as a controlled release formulation, including implants and microencapsulated delivery systems. Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Many methods for the preparation of such formulations are known in the art. See, e.g., J. R. Robinson (1978) “Sustained and Controlled Release Drug Delivery Systems,” Marcel Dekker, Inc., New York.
[0337] In some embodiments, administration of a molecule as described herein is achieved by administering to a subject a nucleic acid encoding the molecule. In some embodiments, a nucleic acid is an RNA (e.g., an mRNA). In some embodiments an RNA encoding a molecule described herein is associated with a delivery agent, i.e., a substance or entity that is non-covalently or covalently associated with a molecule or is co-administered with a molecule and serves one or more functions that increase the stability and / or efficacy of the biologically active agent beyond that which would result if the biologically active agent was delivered (e.g., administered to a subject) in the absence of the delivery agent. For example, a delivery agent may protect an RNA from degradation (e.g., in blood), may facilitate entry of an RNA into cells or into a cellular compartment of interest (e.g., the cytoplasm), and / or may enhance associations with particular cells containing the molecular target to be modulated. Those of ordinary skill in the art are aware of numerous delivery agents that may be used to deliver inhibitory RNA, e.g., mRNAs. See Kanasty, R., et al. Nat Mater.12(11):967-77 (2013). In some embodiments, e.g., for administering an RNA systemically, the RNA may be associated with a delivery agent such as a nanoparticle, a dendrimer, a polymer, liposomes, or a cationic delivery system. Without wishing to be bound by any theory, positively charged cationic delivery systems are believed to facilitate binding of a negatively charged RNA and also enhance interactions at the negatively charged cell membrane to permit efficient uptake of an RNA by the cell. Lipids (e.g., cationic lipids, or neutral lipids), dendrimers, or polymers may be bound to an inhibitory RNA or may form a vesicle or micelle that encapsulates an inhibitory RNA. Methods for making and administering complexes comprising a cationic agent and an RNA are known in the art. In some embodiments it is particularly contemplated to use any of the delivery Page 125 of 203 12904890v1Attorney Docket No.: 2017420-0028 agents described in US Pub.2016 / 0298124. In some embodiments an RNA encoding a molecule described herein is administered in association with a lipid or lipid-containing particle. In some embodiments an RNA is administered in association with a cationic polymer (which may be a polypeptide or a non-polypeptide polymer), a lipid, a peptide, PEG, cyclodextrin, or combination thereof, which may be in the form of a nanoparticle or microparticle. The lipid or peptide may be cationic. A nanoparticle may have a targeting moiety and / or cell-penetrating moiety or membrane active moiety covalently or noncovalently attached thereto. Nanoparticles, such as lipid nanoparticles, are described in, e.g., Tatiparti et al., Nanomaterials 7:77 (2017).
[0338] Nucleic acids encoding a molecule described herein can be incorporated into a gene construct to be used as a part of a gene therapy protocol to deliver nucleic acids that can be used to express and produce a molecule within cells. Expression constructs of such components may be administered in any therapeutically effective carrier, e.g., any formulation or composition capable of effectively delivering the component gene to cells in vivo. Approaches include insertion of the subject gene in viral vectors including recombinant retroviruses, adenovirus, adeno-associated virus, lentivirus, and herpes simplex virus-1 (HSV-1), or recombinant bacterial or eukaryotic plasmids. Viral vectors can transfect cells directly; plasmid DNA can be delivered with the help of, for example, cationic liposomes (lipofectin) or derivatized, polylysine conjugates, gramicidin S, artificial viral envelopes or other such intracellular carriers, as well as direct injection of the gene construct or CaPO4precipitation (see, e.g., WO 2004 / 060407). Examples of suitable retroviruses include pLJ, pZIP, pWE and pEM which are known to those skilled in the art (see, e.g., Eglitis et al., Science 230:1395-1398 (1985); Danos and Mulligan Proc. Natl. Acad. Sci. USA 85:6460-6464 (1988); Wilson et al., Proc. Natl. Acad. Sci. USA 85:3014- 3018 (1988); Armentano et al., Proc. Natl. Acad. Sci. USA 87:6141-6145 (1990); Huber et al., Proc. Natl. Acad. Sci. USA 88:8039-8043 (1991); Ferry et al., Proc. Natl. Acad. Sci. USA 88:8377-8381 (1991); Chowdhury et al. Science 254:1802-1805 (1991); van Beusechem et al., Proc. Natl. Acad. Sci. USA 89:7640-7644 (1992); Kay et al., Human Gene Therapy 3:641-647 (1992); Dai et al., Proc. Natl. Acad. Sci. USA 89:10892-10895 (1992); Hwu et al., J Immunol 150:4104-4115 (1993); U.S. Pat. Nos.4,868,116 and 4,980,286; and PCT Publication Nos. WO 1989 / 07136, WO 1989 / 02468, WO 1989 / 05345, and WO 1992 / 07573). Another viral gene delivery system utilizes adenovirus-derived vectors (see, Page 126 of 203 12904890v1Attorney Docket No.: 2017420-0028 e.g., Berkner et al., BioTechniques 6:616 (1988); Rosenfeld et al., Science 252:431-434 (1991); and Rosenfeld et al., Cell 68:143-155 (1992)). Suitable adenoviral vectors derived from the adenovirus strain Ad type 5 dl324 or other strains of adenovirus (e.g., Ad2, Ad3, Ad7, etc.) are known to those skilled in the art. Yet another viral vector system useful for delivery of the subject gene is the adeno-associated virus (AAV). See, e.g., Flotte et al., Am J Respir Cell Mol Biol 7:349-356 (1992); Samulski et al., J Virol 63:3822-3828 (1989); and McLaughlin et al., J Virol 62:1963-1973 (1989).
[0339] A pharmaceutical solution can include a therapeutically effective amount of a composition described herein. Such effective amounts can be readily determined by one of ordinary skill in the art based, in part, on the effect of the administered composition, or the combinatorial effect of the composition and one or more additional agents, if more than one agent is used. A therapeutically effective amount of a composition described herein can also vary according to factors such as the disease state, age, sex, and weight of the individual, and the ability of the composition (and one or more additional agents) to elicit a desired response in the individual, e.g., amelioration of at least one condition parameter, e.g., amelioration of at least one symptom of an autoimmune disease. For example, a therapeutically effective amount of a composition described herein can inhibit (lessen the severity of or eliminate the occurrence of) and / or prevent a particular disorder, and / or any one of the symptoms of the particular disorder known in the art or described herein. A therapeutically effective amount is also one in which any toxic or detrimental effects of the composition are outweighed by the therapeutically beneficial effects.
[0340] Suitable human doses of any of the compositions described herein can further be evaluated in, e.g., Phase I dose escalation studies. See, e.g., van Gurp et al., Am J Transplantation 8(8):1711-1718 (2008); Hanouska et al., Clin Cancer Res 13(2, part 1):523- 531 (2007); and Hetherington et al., Antimicrobial Agents and Chemotherapy 50(10): 3499- 3500 (2006).
[0341] Toxicity and therapeutic efficacy of compositions can be determined by known pharmaceutical procedures in cell cultures or experimental animals (e.g., animal models of any of the cancers described herein). These procedures can be used, e.g., for determining the LD50(the dose lethal to 50% of the population) and the ED50(the dose therapeutically effective in 50% of the population). The dose ratio between toxic and Page 127 of 203 12904890v1Attorney Docket No.: 2017420-0028 therapeutic effects is the therapeutic index and it can be expressed as the ratio LD50 / ED50. A composition described herein that exhibits a high therapeutic index is preferred. While compositions that exhibit toxic side effects may be used, care should be taken to design a delivery system that targets such compounds to the site of affected tissue and to minimize potential damage to normal cells and, thereby, reduce side effects.
[0342] Those of skill in the art will appreciate that data obtained from cell culture assays and animal studies can be used in formulating a range of dosage for use in humans. Appropriate dosages of compositions described herein lie generally within a range of circulating concentrations of the compositions that include the ED50 with little or no toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration utilized. For a composition described herein, the therapeutically effective dose can be estimated initially from cell culture assays. A dose can be formulated in animal models to achieve a circulating plasma concentration range that includes the IC50 (i.e., the concentration of the antibody which achieves a half-maximal inhibition of symptoms) as determined in cell culture. Such information can be used to more accurately determine useful doses in humans. Levels in plasma may be measured, for example, by high performance liquid chromatography. In some embodiments, e.g., where local administration (e.g., to the eye or a joint) is desired, cell culture or animal modeling can be used to determine a dose required to achieve a therapeutically effective concentration within the local site.
[0343] All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting. Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art. Although methods and materials similar or equivalent to those described herein can be used, suitable methods and materials are described herein.
[0344] The disclosure is further illustrated by the following examples. The examples are provided for illustrative purposes only. They are not to be construed as limiting the scope or content of the disclosure in any way. Page 128 of 203 12904890v1Attorney Docket No.: 2017420-0028 Additional Embodiments
[0345] In some embodiments, molecules described herein comprise: a first polypeptide comprising a first Fc domain and a first antibody variable domain that binds to a constant domain of an IgE antibody; and a second polypeptide comprising a second Fc domain; wherein the first Fc domain and the second Fc domain form a homodimer or heterodimer of the first polypeptide and the second polypeptide; and wherein the first and / or second Fc domain comprises one or more mutated amino acid residues that increases binding to FcγRIIB. Molecules described herein comprising increased binding to FcγRIIB target and bind to IgE antibodies that implicate various allergic diseases through the antibody variable domain, and are shuttled to the lysosome of a cell for degradation through FcγRIIB.
[0346] Combining increased binding to the endocytic receptor FcγRIIB and also including a particular antibody variable domain that binds IgE allows for selective depletion of IgE antibodies. One of skill in the art will appreciate that such molecules may be used to treat a variety of allergic diseases that are implicated by IgE antibodies.
[0347] In some embodiments, molecules described herein may be used in the treatment of allergic diseases caused by IgE antibodies. In some embodiments, a molecule described herein used to treat an allergic disease such as food allergy, allergic asthma, and chronic hives comprises an antibody variable domain that targets IgE antibodies and an Fc domain that comprises one or more modifications that increase its binding to FcγRIIB, as described herein.
[0348] Other antibodies that are involved in the development of particular allergic diseases are known in the art, and molecules described herein may include antibody variable domains that bind these antibodies in order to selectively target and deplete these antibodies. EXAMPLES Example 1: Generation and Testing of Exemplary Molecules
[0349] The present Example demonstrates generation and testing of exemplary molecules described herein that target and selectively deplete circulating IgE antibodies. In this Example, exemplary molecules were generated with modifications to enhance their Page 129 of 203 12904890v1Attorney Docket No.: 2017420-0028 ability to deplete circulating IgE antibodies. In the present Example, exemplary molecules are anti-IgE antibodies that have been modified to, among other things, increase FcγRIIB- mediated clearance. Enhanced and selective clearance of circulating IgE antibodies provides a new therapeutic solution to treatment of, e.g., allergic disease such as food allergy, allergic asthma, and chronic hives. Generation of Exemplary Molecules
[0350] Anti-IgE antibodies: Exemplary molecules in this Example were designed to include an antibody variable domain that specifically binds to a region on an IgE antibody (e.g., a conserved region such as the constant region of an IgE antibody). Various IgE antibody variable domains were tested for their ability to selectively target and deplete IgE antibodies. The exemplary antibody variable domains that bind IgE utilized in this Example were selected for their ability to block engagement of the IgE antibody with its high affinity receptors (e.g., FcεRIA on basophils, mast cells, etc.). The exemplary antibody variable domains that bind IgE selected in this Example have differences in their ability to block engagement of the IgE antibody with its low affinity FcεRII receptor (e.g., in B cells, monocytes, dendritic cells, and intestinal epithelial cells). The FcεRIA binding site on the Fc domain of IgE antibodies is located primarily on the Cε3 domain. Additionally, it is known that FcεRII binds to a site on IgE antibodies that includes both the Cε3 and Cε4 domains on the Fc domain of IgE antibodies (see, Jabs et al., Nature Communications 9(1):7 (2018)). Accordingly, the exemplary antibody variable domains that bind IgE utilized in the Examples target regions that include the Cε3 domain or both the Cε3 and Cε4 or Cε3 and Cε2 domains on the Fc domain of IgE antibodies.
[0351] Sequences of antibody variable domains that bind IgE used in the exemplary molecules made and tested in this Example are shown in Table 5 below. Table 5: Exemplary Anti-IgE antibody variable domains Name Targeted Description SEQ Sequenceg 12904890v1Attorney Docket No.: 2017420-0028 NYNPSVKGRITISRDDSKNTFYLQMNSLR AEDTAVYYCARGSHYFGHWHFAVWGQGTLPage 131 of 203 12904890v1Attorney Docket No.: 2017420-0028 AADTAVYYCARGSHYFGHWHFAVWGAGTL VTVSSPage 132 of 203 12904890v1Attorney Docket No.: 2017420-0028 VL 52QSVLTQPPSVSGAPGQRVTISCTGSSSNI GAGYDVHWYQQLPGTAPKLLIYDNFNRPSan Fc domain comprising particular mutations.
[0353] In this Example, Fc domains of the exemplary molecules were modified to increase targeted internalization and subsequent degradation of IgE / molecule complexes by introducing Fc mutations to increase binding of the Fc domains to FcγRIIB. FcγRIIB is an Page 133 of 203 12904890v1Attorney Docket No.: 2017420-0028 internalizing receptor that binds to its target, internalizes the complex and shuttles the target to the lysosome for degradation. Without wishing to be bound by any theory, molecules described herein that have increased FcγRIIB binding may deplete IgE antibodies through various mechanisms. In some embodiments, an exemplary molecule may target and bind to FcγRIIB isoform 2 on liver sinusoidal endothelial cells (LSECs). In this exemplary mechanism of action, the molecule binds to IgE antibodies and the Fc domain binds to FcγRIIB isoform 2 on liver sinusoidal endothelial cells. Autoantibodies are internalized into the liver sinusoidal endothelial cells and targeted to the lysosome for degradation. In another exemplary mechanism, molecules described herein may target FcγRIIB isoform 1 to the B-cell receptor (BCR), which leads to B cell apoptosis and inhibition. In another exemplary mechanism, molecules described herein may target FcγRIIB on T cells and prevent T-cell activation.
[0354] Such mutations include: S267E and L328F and / or P238D, according to EU numbering. Such mutations allow for binding to FcγRIIB at neutral pH. Upon binding, the IgE / molecule complex is internalized into the cell and targeted to the lysosome for degradation. Binding to FcγRIIB is enhanced which targets the IgE / molecule complex for degradation. This exemplary mechanism of action is shown, e.g., in FIG.1.
[0355] Fc domains (i.e., wildtype IgG1 Fc domains) are known to bind to various Fc receptors. Some Fc receptors are considered to be “activating Fc receptors” (e.g., FcγRIIA- H131, FcγRIIA-R131) and some Fc receptors are known to be inhibitors of immune response (e.g., FcγRIIB). The S267E / L328F or “SE / LF” mutation when introduced into the Fc domain of an antibody has been shown to have increased binding affinity for FcγRIIB and also for FcγRIIA activating receptors. The P238D mutation when introduced into the Fc domain of an antibody has been shown to have enhanced affinity for FcγRIIB (although less than Fc domains with the SE / LF mutation), but also little to no binding to activating Fc receptors such as FcγRIIA. Without wishing to be bound by any theory, having selective affinity for the inhibitory FcγRIIB presents certain advantages such as allowing for avidity- induced FcγRIIB-mediated intracellular uptake and degradation. Additionally, molecules described herein with the P238D mutation present a low risk of intracellular toxicity in part due to the relatively small size of the molecule and little to no affinity for activating Fcγ receptors. Page 134 of 203 12904890v1Attorney Docket No.: 2017420-0028
[0356] In this Example, Fc mutations were also introduced in some of the exemplary molecules (monovalent molecules) to promote heterodimerization of the two polypeptides, where each polypeptide comprises an Fc domain, and the first and second Fc domains heterodimerize in order to generate the full molecule. Such mutations are known as knobs- in-holes (KIH) modifications. The specific mutations used in this Example include: T366W, and S354C mutation (on one Fc domain) and T366S, L368A, Y407V, and Y349C (on the other Fc domain). While the exemplary molecules tested herein included the T366W and S354C mutations on the first Fc domain and the T366S, L368A, Y407V, and Y349C mutations on the second Fc domain, one of skill in the art will understand that the present disclosure encompasses molecules where the T366W and S354C mutations are included on the second Fc domain and the T366S, L368A, Y407V, and Y349C mutations are included on the first Fc domain. One of skill in the art will also understand that other known KIH mutations or other Fc modifications are known in the art to promote heterodimerization and may be used in the molecules described in this Example and as described in the disclosure.
[0357] In some molecules, Fc mutations were also introduced to increase the half- life of the exemplary molecule. The specific mutations used in this Example include the following mutations: M428L and N434S (“LS”). One of skill in the art will understand that other known mutations or modifications are known in the art to increase half-life, e.g., M252Y, S254T and T256E (“MST” or “YTE”) and may be used in the molecules described in this Example and as described in the disclosure.
[0358] Exemplary Fc domain sequences used in the molecules made and tested in this Example are shown below in Table 6. Some of these exemplary Fc domain sequences were used in control molecules. Hinge sequences are shown in italics and mutations are in bold. Table 6: Exemplary Fc Domain Sequences SEQ ID Fc Descri tion Se uence V L C K H12904890v1Attorney Docket No.: 2017420-0028 SEQ ID Fc Description Sequence NO: V L C K H V L C K H S E I G L S E I G L S E I G L V S S D S S E I G LPage 136 of 203 12904890v1Attorney Docket No.: 2017420-0028 SEQ ID Fc Description Sequence NO: S E I G L S E I G L V S S D S S E I G L V S S D S S E I G L V S S D SPage 137 of 203 12904890v1Attorney Docket No.: 2017420-0028 SEQ ID Fc Description Sequence NO: S E I G L E R R P E E R R P E E R R P E E R R P E E R R P E E R R P E E R R PPage 138 of 203 12904890v1Attorney Docket No.: 2017420-0028 SEQ ID Fc Description Sequence NO: E E R R P E E R R P E S E I G L S E I G L S E I G L T E I G Lwere used to generate exemplary molecules as described below in Table 7. Page 139 of 203 12904890v1Attorney Docket No.: 2017420-0028
[0360] These sequences were encoded by expression plasmids (e.g., pTT5, pcDNA) then transfected into a suitable host cell (e.g., CHO, HEK293) and expressed transiently using standard transfection techniques. After expression for 5-14 days or if cell viability dropped, cells were harvested. Conditioned media was then purified using standard chromatography techniques such as protein A affinity, ion exchange chromatography, and size exclusion chromatography to generate molecules with greater than 95% purity (as assessed by SEC-HPLC). Molecules were then buffer exchanged to a suitable formulation buffer and stored at 4C or -80C prior to use. Table 7: Exemplary Molecules Molecule Description Component SEQ Sequence ID ID WNSR HF TA QS VD PK EV YK RD YK VL SYSG KV FY LS RG WNSR HF TA QS VD PK EV YK RD YKPage 140 of 203 12904890v1Attorney Docket No.: 2017420-0028 TTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVM HEALHNHYTQKSLSLSPGK SYSG KV FY LS RG EWTA YD GG VL TK PK GV KE PS NN CS WYFT KR EA LT WNSR HF TA QS VD PK EV YK RD YK VL SYSG KL FY LS RG YWTA GY12904890v1Attorney Docket No.: 2017420-0028 P238D / M428 DYWGRGTLVTVSSASTKGPSVFPLAPSSKSTSGGTA L / N434S ALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVD PK EV YK RD YK VL VHTS KL DF AS EC YWTA GY TA QS VD PK EV YK RD YK VL VHTS KL DF AS EC HWTA AY AL SG KK DT HN CK EL TT HEPage 142 of 203 12904890v1Attorney Docket No.: 2017420-0028 Light Chain 54DIQLTQSPSSLSASVGDRVTITCRASQSVDYDGDTYMNWYQQKPGKAPKLLIYAASNLDSGVPSRFSGSGSG TDFTLTISSL PEDFATYYC TNEDPWTFG GTKV FY LS RG WN SR HF TA QS VD PK EV YK RD YK VL RT PR AL VS DS HY SYSG KV FY LS RG WNSR HF TA QS VD PK EV YK RD YK VM SYSG KV FY12904890v1Attorney Docket No.: 2017420-0028 PREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS STLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG EC WNSR HF TA QS VD PK EV YK RD YK VM SYSG KV FY LS RG WN SR HF TA QS VD PK EV YK RD YK VM RT PR AL VS DS HY SYSG KV FY LS RGPage 144 of 203 12904890v1Attorney Docket No.: 2017420-0028 Variant A6 Omalizumab Heavy Chain 173EVQLVESGGGLVQPGGSLRLSCAVSGYSITSGYSWN hIgG1- WIRQAPGKGLEWVASITYDGSTNYNPSVKGRITISR S354C, DDSKNTFYL MNSLRAEDTAVYYCARGSHYFGHWHF TA QS VD PK EV YK RD YK VM RT PR AF VS DS HY SYSG KV FY LS RG WN SR HF TA QS VD PK EV YK RD YK VM RT PR AL VS DS HY SYSG KV FY12904890v1Attorney Docket No.: 2017420-0028 PREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLS STLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG EC EWTA YD GG VL TK PK GV KE PS NN CS WYFT KR EA LT WNSR HF TA QS VD PK EV YK RD YK VM SYSG KL FY LS RG WNSR HF TA QS VD PK EV YKage 6 o 03 12904890v1Attorney Docket No.: 2017420-0028 CKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRD ELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYK TTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVM SYSG KL FY LS RG WNSR HF TA QS VD PK EV YK RD YK VM SYSG KL FY LS RG WNSR HF TA QS VD PK EV YK RD YK VM SYSG KV FY LS RG12904890v1Attorney Docket No.: 2017420-0028 Variant A9 OmalizumabHeavy Chain 101EVQLVESGGGLVQPGGSLRLSCAVSGYSITSGYSWNhIgG1- WIRQAPGKGLEWVASITYDGSTNYNPSVKGRITISR DDSKNTFYL MNSLRAEDTAVYYCARGSHYFGHWHF TA QS VD PK EV YK RD YK VM SYSG KV FY LS RG WNSR HF TA QS VD PK EV YK RD YK VL SYSG KV FY LS RG WNSR HF TA QS VD PK EV YK RD YKPage 148 of 203 12904890v1Attorney Docket No.: 2017420-0028 TTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVM HEALHNHYTQKSLSLSPGK SYSG KV FY LS RG WNSR HF TA QS VD PK EV YK RD YK VM SYSG KV FY LS RG WNSR HF TA QS VD PK EV YK RD YK VL WN SR HF TA QS VD PK EV YKage 9 o 03 12904890v1Attorney Docket No.: 2017420-0028 CKVSNKALPRPIEKTISKAKGQPREPQVYTLPPSRE EMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYK TTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVL SYSG KV FY LS RG WNSR HF TA QS VD PK EV YK RD YK VM WN SR HF TA QS VD PK EV YK RE YK VM SYSG KV FY LS RG WNSR HF TA QS VD PKage 50 o 03 12904890v1Attorney Docket No.: 2017420-0028 DTLMISRTPEVTCVVVDVSHEEGEVKFNWYVDGVEV HNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYK CKVSNKALPRPIEKTISKAKGQPREPQVYTLPPSRD YK VM SYSG KV FY LS RG WNSR HF TA QS VD PK EV YK RD YK VL SYSG KV FY LS RG WNSR HF TA QS VD PK EV YK RD YK VM SYSG KV FY LSage 5 o 03 12904890v1Attorney Docket No.: 2017420-0028 STLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG EC
[0361] Cells expressing FcRn, are seeded in a 96-well plate and incubated for 1 hour, followed by serum starvation and division into two groups – pH 6.0 and pH 7.0. Varying dilutions of exemplary molecule comprising modifications that enhance FcRn binding as described above are added with varying dilutions of IgE antibodies and are co- incubated with the cells for 4 hours. Cells are then washed in HBSS and the pH is adjusted to neutral (pH 7.4) and incubated at 37C for 4 hours or overnight. Cell supernatant is harvested and analyzed in anti-human IgG ELISA to quantify the amount of IgE antibody recycled into the supernatant.
[0362] The IgE antibody is labelled with a fluorescent tag (i.e., PE). A complex is then formed by co-incubating an exemplary molecule comprising modifications that enhance FcγRIIB binding as described above with labelled IgE antibody for 15 minutes at room temperature at either a 1:1 or 4:1 ratio (molecule:IgE antibody). Cells expressing FcγRIIB are seeded in a 96-well plate and stained with Live / Dead Violet Fixable Dye. Next, the pre-complexed molecule and IgE antibody are incubated with the cells at various concentrations at either 4C (to assess binding) or 37C (to assess uptake). After incubation, cells are washed with PBS (binding) or acidic media to remove surface-bound complexes (uptake). Cellular fluorescence is determined by flow cytometry. In vitro SEC-based Assessment of Immune Complexes
[0363] To assess the size of the immune complexes formed upon IgE antibody binding to an exemplary molecule, the exemplary molecule is incubated with patient serum containing IgE antibodies, or with IgE antibodies as positive control. Analysis of the size of the immune complexes formed between the exemplary molecule and IgE antibodies present in patient serum is estimated using SEC-based method similar as described in Boysen et al., Journal of Immunology Research 2:1-9 (2016), which is herein incorporated by reference. Example 2: In vitro Expression of Exemplary Molecules
[0364] The present Example tests the ability to express various exemplary molecules described in Example 1 from a CHO host cell. Molecules were encoded into pcDNA3.1 then Page 152 of 203 12904890v1Attorney Docket No.: 2017420-0028 transfected into CHO cells and expressed transiently using standard transfection techniques. After expression for 5-14 days or if cell viability dropped, cells were harvested. Clarified conditioned media was purified using protein A affinity chromatography following standard protocols. The eluted and neutralized fractions containing the molecules were then assessed for product quality using SEC-HPLC. If needed, molecules were further purified using preparative SEC. The molecules were buffer exchanged to a suitable platform buffer and frozen down for storage.
[0365] FIG.3 shows a representative HPLC-SEC profile of exemplary molecule Variant A3 described herein (bivalent omalizumab hIgG1 with P238D mutation). FIG.4 shows a representative HPLC-SEC profile of exemplary molecule Variant A5 described herein (monovalent omalizumab hIgG1 with P238D mutation). Table 8 below shows that the exemplary molecules were well expressed. Table 8: Expression of Exemplary Molecules Purity Total mg 0Page 153 of 203 12904890v1Attorney Docket No.: 2017420-0028 Purity Total mg Conc SEC- (from 100Example 3: Characterization of Exemplary Molecules Binding Affinity to FcγRIIB
[0366] Exemplary molecules were tested for their ability to bind FcγRIIB. Specifically, the molecule Variant A1, which includes the omalizumab antibody variable domain and an Fc domain that includes P238D and LS mutations, Variant A3, which includes the omalizumab antibody variable domain and an Fc domain that includes the P238D mutation, and Variant A4, which includes the omalizumab antibody variable domain and an Fc domain that includes the SE / LF (S267E / L328F) mutations, were tested. Variant A8, which includes the omalizumab antibody variable domain and a wildtype hIgG1 Fc domain and Variant A2, which includes the omalizumab antibody variable domain and an Fc domain that includes the LALAPG (Fc null) mutations, were used as control molecules.
[0367] In this Example, IgE antibodies and the molecules were pre-complexed at 2:1 ratio of molecule:IgE. FcγRIIB-expressing CHO cells were incubated with immune IgE antibody / molecule complexes. Complexes were then stained with Fluor-labeled anti-IgE Page 154 of 203 12904890v1Attorney Docket No.: 2017420-0028 molecules and cells bound to FcγRIIB-expressing CHO cells were detected via flow cytometry. Cells incubated without IgE or molecule and cells incubated with IgE alone were used as controls.
[0368] The results of this experiment are presented in FIG.5 and show that Variant A1 and Variant A3 have enhanced affinity for FcγRIIB compared to the Variant A8 (wildtype control molecule) and reduced binding compared to Variant A4 (FIG.5).
[0369] In a second experiment, binding affinity of the same molecules were compared to additional molecules including Variant B1 and Variant B2, which include a different antibody variable domain that binds to IgE (Ligelizumab). Variant B1 includes an hIgG1 Fc domain with P238D and LS mutations while Variant B2 includes an hIgG1 Fc domain with P238D mutation. Variant C4, which includes a different antibody variable domain that binds to IgE (XmAb7195) and an Fc domain that includes the SE / LF (S267E / L328F) mutations was also tested. IgE antibodies and the molecules were pre- complexed at 2:1 ratio of molecule:IgE. FcγRIIB-expressing CHO cells were incubated with immune IgE antibody / molecule complexes. Complexes were then stained with Fluor- labeled anti-IgE molecules and cells bound to FcγRIIB-expressing CHO cells were detected via flow cytometry. Cells incubated without IgE or molecule and cells incubated with IgE alone were used as controls.
[0370] The results of this second experiment are presented in FIG.6 and show that Variant A1, Variant A3, Variant B1 and Variant B2 molecules (which all include the P238D mutation) have enhanced affinity for FcγRIIB compared to the Variant A8 (wildtype control molecule) and reduced binding compared to Variant A4 and Variant C4 molecules which both include the SE / LF (S267E / L328F) mutations. Mechanism of action of Exemplary Molecules
[0371] Exemplary molecules are assessed for their ability to internalize IgE containing complexes ex vivo in liver sinusoidal endothelial cells (LSECs).
[0372] Exemplary molecules are assessed for their ability to inhibit production of IgE producing PBMCs. Human PBMCs are cultured with molecules at varying concentrations for 14 days at 37C in RPMI-1640 containing 10% FBS, 5 ng / mL Page 155 of 203 12904890v1Attorney Docket No.: 2017420-0028 recombinant human IL-4 and 250 ng / mL agonistic antihuman CD40 antibody. IgE production in culture medium is assessed by ELISA.
[0373] Exemplary molecules are assessed for their ability to block IgE binding to its high and / or low affinity receptors, FcεRIA and / or FcεRII.
[0374] Exemplary molecules are assessed for their ability to block activation and degranulation of primary basophils. Example 4: In vivo Testing of Exemplary Molecules
[0375] The present Example examines in vivo activity of exemplary molecules described in Example 1. To assess the clearance activity of IgE antibodies by exemplary molecules, mouse models are injected with an IgE antibody followed by injection of exemplary molecules or control and IgE antibody clearance is assessed over time. In vitro pilot study to assess IgE antibody and molecule detection using ELISAs
[0376] To test the sensitivity of an Enzyme Linked Immunosorbent Assay (ELISA) for the purpose of detecting exemplary molecules in mouse serum, an ELISA detecting IgE antibodies or exemplary molecules is performed using known concentrations in vitro.
[0377] A general ELISA protocol is as follows: capture antibody is coated at 4C overnight. Plates are blocked with blocking buffer (PBS with 5% BSA vol / vol) for 2 hours at room temperature. Plates are washed with washing buffer (PBS+0.05% Tween 20 or similar), and samples are added and incubated for 1 hour at room temperature. Plates are washed, and detection antibody solution is added and incubated for 1 hour at room temperature. Plates are washed and incubated with TMB substrate for 15 minutes at room temperature, protected from light. The reaction is stopped with 2M H2SO4 and read on a microplate reader set to 450 nm – 570 nm. In vitro pilot study to assess labeling and detection of IgE antibodies
[0378] For the detection of IgE antibody, varying concentrations are titrated into buffer, buffer containing 1% mouse serum, or 10% mouse serum, and detected using ELISA. The capture antibody used to bind the IgE antibody is a combination of three mouse Page 156 of 203 12904890v1Attorney Docket No.: 2017420-0028 monoclonal antibodies specific for human IgE, and the detection antibody is HRP-labeled goat anti-human kappa or lambda light chain antibodies, depending on the light chain of the IgE antibody.
[0379] In addition to using the ELISA method to detect IgE antibodies, as described above, IgE antibodies can be labeled with biotin for detection. In this in vitro pilot study, IgE antibodies are labeled with biotin per manufacturers protocol in PBS. Next, varying concentrations of labeled IgE antibodies are titrated into buffer, buffer containing 1% mouse serum, or 10% mouse serum, to assess detection sensitivity. The capture antibody used to bind the IgE antibody is goat anti-human Fc, and the detection antibody is Streptavidin Poly- HRP. In vitro pilot study to assess detection of exemplary molecules
[0380] For the detection of exemplary molecules, varying concentrations of exemplary molecules are titrated into buffer, buffer containing 1% mouse serum, or 10% mouse serum, and detected using ELISA. The capture antibody used to bind the exemplary molecules is goat anti-human Fc, and the detection antibodies are mouse anti-human IgE followed by HRP-labeled anti-mouse IgG or HRP-labeled goat anti-human kappa or lambda light chain antibodies depending on the light chain of the exemplary molecule. Pilot study to assess pK of exemplary molecules in vivo
[0381] To assess clearance of an exemplary molecule, Variant A3 (80 µg / mouse) was injected intravenously into hFcgR / hFcRn mice (obtained from genOway) in 20 mM Histidine, 150 mM NaCl, pH 6.0 and serum was collected at 30 minutes, 3, 12, 24, 72 hours and 7, 10, and 14 days after injection. Molecule in mouse serum was detected using methods described before, and serum from mice that had not been injected with the molecule were used as a negative control, whereas spiking that serum ex vivo with the molecule was used as a positive control. The results are presented in FIG.7 and show that Variant A3 exhibits an antibody-like half-life of 224 ± 2.75 hours. Pilot study to assess pK of IgE antibodies in vivo
[0382] To assess clearance of IgE antibody in wild-type mice, 20 µg or 100 µg of IgE antibody in 20 mM Histidine, 150 mM NaCl, pH 6.0 is injected per mouse and serum is Page 157 of 203 12904890v1Attorney Docket No.: 2017420-0028 collected at 10 minutes, 30 minutes, and 1, 3, 6, 12, 24 and 48 hours after injection. IgE antibody in mouse serum is detected using methods described before, and serum from mice that have not been injected with IgE antibody is used as a negative control, whereas spiking that serum ex vivo with IgE antibody is used as a positive control. Assessing clearance of IgE antibodies by exemplary molecules in vivo
[0383] Informed by the exemplary molecule clearance assessed above, mice are injected with a concentration of IgE antibody in 20 mM Histidine, 150 mM NaCl, pH 6.0. One 10 minutes after injection, mice are injected with 4 or 5-fold molar excess of exemplary molecule or with vehicle as control. Clearance of IgE antibodies is assessed using methods described above. Exemplary molecule and IgE complex clearance in humanized FcγR / FcRn Mice
[0384] In this experiment, humanized FcγR / FcRn mice are injected with exemplary molecule / IgE complexes. Serum from the mice is collected and analyzed for concentration of exemplary molecule and IgE at various timepoints (e.g., 10 minutes, 30 minutes, 1 hour, 3 hours, 6 hours, 12 hours, 24 hours, 48 hours, and 7 days) after administration of the exemplary molecule / IgE complexes. Exemplary molecule and IgE sequential clearance in humanized FcγR / FcRn Mice
[0385] In this experiment, humanized FcγR / FcRn mice are injected with an exemplary molecule and 24 hours later the mice are injected with human IgE. Serum from the mice is collected and analyzed for concentration of exemplary molecule and IgE at various timepoints (e.g., 10 minutes, 30 minutes, 1 hour, 3 hours, 6 hours, 12 hours, 24 hours, 48 hours, and 7 days) after administration of the exemplary molecule and / or after administration of the IgE. Suppression of human IgE in human SCID mice
[0386] For huSCID mouse models, immunodeficient SCID mice were treated on day 1 with 100 mL of anti-asialo GM antibody to deplete natural killer cells and on day 0 with an intraperitoneal injection of 3.0. Human PBMCs obtained by leukapheresis under an institutional review board–approved protocol. Mice were dosed intraperitoneally with Page 158 of 203 12904890v1Attorney Docket No.: 2017420-0028 antibodies on day 8 or 9 or as described. Blood was collected by retro-orbital sinus puncture for the determination of total human IgM, IgG, and IgE, free human IgE, and therapeutic antibody levels by using the methods described below. SPR binding to IgE
[0387] Molecules are tested for binding to human IgE using SPR. Briefly, anti- human IgG antibody are immobilized on a sensor surface and used to capture exemplary molecules. Human IgE is then used as analyte, allowing one to measure monovalent binding affinity. Multi-cycle kinetics are then performed at pH 7.4 and at pH 6.0. Example 5: Testing and Characterization of Molecules with Alternative Fc Mutations Identification of Fc mutations that confer specific binding to FcγRIIB
[0388] Additional molecules with alternative Fc mutations were tested for their ability to selectively bind to FcγRIIB through their Fc domains and to have decreased or no binding affinity for other Fc receptors FcγRIIA167H and FcγRIIA167R.
[0389] Binding assays using SPR were performed to determine the binding affinity of molecules comprising an autoantibody-binding domain (derived from an autoantigen domain, not based on an antibody variable domain that binds IgE) and exemplary Fc domain sequences for use in accordance with the present disclosure. The Fc mutations in each molecule are summarized in Table 9 below. Molecules were captured on a CM5 SPR chip. Increasing concentrations of FcγR analyte (FcγRIIA167H, FcγRIIA167R or FcγRIIB) were subsequently injected over the captured molecules and a single dissociation performed using single cycle kinetics. The data was then analyzed using steady state analysis which is suitable for low affinity interactions. In particular, a plot of response at equilibrium against the molecule concentration was generated. The KD value is equal to the concentration that gives 50% of the maximum response. The molecules represented include: a control IgG1 (Trastuzumab antibody), Variant G1, Variant G2, Variant G3, Variant G4, Variant G6, Variant G7, Variant G8, Variant G9, Variant G10, Variant G11, Variant G12, Variant G13, and Variant G14 for various Fc receptors: FcγRIIA167H, FcγRIIA167R and FcγRIIB. Trastuzumab and a molecule with a wild-type Fc domain (WT IgG1 Fc) were used as positive controls. Page 159 of 203 12904890v1Attorney Docket No.: 2017420-0028
[0390] Results from the binding assays are shown in Table 9 below and FIGs.17-22. Specifically, FIG.8 shows binding activity of Trastuzumab (positive control) (A), Variant G1 (B), Variant G2 (C), Variant G3 (D), Variant G6 (E), Variant G7 (F), and Variant G8 (G) to activating receptor FcγRIIA167R, when molecules were captured onto an SPR sensor chip and FcγR used as the analyte. FIG.9 shows binding activity of Variant G9 (A), Variant G10 (B), Variant G11 (C), Variant G12 (D), Variant G13 (E), Variant G14 (F), and Variant G4 (G) to activating receptor FcγRIIA167R when molecules were captured onto an SPR sensor chip and FcγR used as the analyte.
[0391] FIG.10 shows binding activity of Trastuzumab (positive control) (A), Variant G1 (B), Variant G2 (C), Variant G3 (D), Variant G6 (E), Variant G14 (F), and Variant G8 (G) to activating receptor FcγRIIA167H, when molecules were captured onto an SPR sensor chip and FcγR used as the analyte. FIG.11 shows binding activity of Variant G9 (A), Variant G10 (B), Variant G11 (C), Variant G12 (D), Variant G13 (E), Variant G14 (F), and Variant G4 (G) to activating receptor FcγRIIA167H when molecules were captured onto an SPR sensor chip and FcγR used as the analyte.
[0392] FIG.12 shows binding activity of Trastuzumab (positive control) (A), Variant G1 (B), Variant G2 (C), Variant G3 (D), Variant G6 (E), Variant G14 (F), and Variant G8 (G) to inhibitory receptor FcγRIIB, when molecules were captured onto an SPR sensor chip and FcγR used as the analyte. FIG.13 shows binding activity of Variant G9 (A), Variant G10 (B), Variant G11 (C), Variant G12 (D), Variant G13 (E), Variant G14 (F), and Variant G4 (G) to inhibitory receptor FcγRIIB when molecules were captured onto an SPR sensor chip and FcγR used as the analyte.
[0393] Table 9 below shows kinetic parameters for molecules binding to activating receptors FcγRIIA167R and FcγRIIA167H, and inhibitory receptor FcγRIIB; where KD is dissociation constant, NB indicates non-binding, and UTD indicates a KD was unable to be determined. Page 160 of 203 12904890v1Attorney Docket No.: 2017420-0028 Table 9: Molecules captured onto SPR sensor chip and FcγR used as analyte Molecule FcγRIIA167R FcγRIIA167H FcγRIIB Fc mutations Immobilized KD(M) KD(M) KD(M)Page 161 of 203 12904890v1Attorney Docket No.: 2017420-0028 Molecule FcγRIIA167R FcγRIIA167H FcγRIIB Fc mutations Immobilized KD(M) KD(M) KD(M)Testing of Molecules for Avidity-Mediated Effects
[0394] In this experiment, CHO cells expressing FcγRIIB (CHO-FcγRIIB+) were incubated with the molecules and an autoantibody that binds the autoantibody-binding domain of the molecules with and without 2B6 antibody which is an anti-FcγRIIB antibody that blocks binding of FcγRIIB to antibody Fc domains. The molecules tested include Variant D3, Variant B3, Variant G1, Variant G2, Variant G5, Variant G10, Variant G11, Variant G12, Variant G13, and Variant G14. Variant B3 was designed to have enhanced binding to FcγRIIB by introducing the mutations S267E / L328F. Variant D3 includes the mutation P238D in its Fc domain to increase binding to FcγRIIB.
[0395] FIGs.14-15 show that the Fc mutations in Variant G1, Variant G2, Variant G5, and Variant G11 result in comparable lack or very weak binding of free molecule to FcγRIIB compared to Variant D3, which binds weakly to FcγRIIB in free form at only the highest concentration tested (1 μM). In contrast, the Fc mutations in Variant G10, Variant G12, Variant G13, and Variant G14 lead to increased binding to FcγRIIB which is molecule concentration-dependent. Variant G14, specifically, exhibits a similar binding profile to FcγRIIB compared to Variant B3, which binds strongly to FcγRIIB in free form in a concentration-dependent manner. Binding of all molecules tested is shown to be dependent on FcγRIIB as assay signal is diminished upon pre-treatment with anti-FcγRIIB antibody clone 2B6. The Fc mutation D270E confers reduced binding affinity to FcγRIIB as observed in Variant G11 and Variant G13, relative to Variant G10 and Variant G12, Page 162 of 203 12904890v1Attorney Docket No.: 2017420-0028 respectively, which are the same molecules that do not contain said Fc mutation. These observations are consistent with surface plasmon resonance (SPR) results evaluating binding of the same molecules to FcγRIIB.
[0396] FIGs.16-17 show that, similar to Variant D3, the Fc mutations in Variant G1, Variant G2, and Variant G5 result in lack of binding to FcγRIIA167R, while the Fc mutations in Variant G10, Variant G11, and Variant G13 demonstrate binding only at the highest concentration tested (1 μM). In contrast, the Fc mutations in Variant G12 and Variant G14 result in stronger, molecule concentration-dependent binding, which for Variant G14 is already detectable at the lowest concentration tested (10 nM). The binding profile of Variant G14 to FcγRIIA167R is similar to Variant B3, which binds strongly to FcγRIIA167R. Binding of all molecules tested is shown to be dependent on FcγRIIA167R as assay signal is diminished upon pre-treatment with anti-FcγRIIA antibody clone IV.3. The Fc mutation D270E confers reduced binding affinity to FcγRIIA167R in the context of Variant G13, relative to Variant G12 which contains the same mutations in the absence of D270E. These observations are consistent with surface plasmon resonance (SPR) results evaluating binding of the same molecules to FcγRIIA167R. Example 6: In vivo Testing of Exemplary Molecules
[0397] The present Example demonstrates, among other things, the ability of exemplary molecules described in Example 1 to rapidly clear IgE in serum of mice.
[0398] In this Example, anti-IgE molecules Variant A8, Variant A9, Variant A12, and Variant A15 were tested for their ability to clear IgE from serum of mice. Variant A8 includes omalizumab with a wildtype hIgG1 Fc domain. Variant A9 includes the antibody omalizumab with a hIgG1 Fc domain including P238D and P271G mutations. Variant A12 includes the antibody omalizumab with a hIgG1 Fc domain including the following mutations: G237D, P238D, P271G, and A330R. Variant A15 includes the antibody omalizumab with a hIgG1 Fc domain including the following mutations: G237D, P238D, D270E, P271G, and A330R.
[0399] Humanized FcγR / FcRn mice were injected with human IgE (3mg / kg) and 10 minutes later the mice were injected with the exemplary molecules at 5X molar excess (12mg / kg). The anti-IgE antibody XmAb7195 was used as a positive control and mice Page 163 of 203 12904890v1Attorney Docket No.: 2017420-0028 injected with IgE alone were used as a negative control. Serum from the mice was collected at various timepoints (e.g., between 0 and 80 hours) and analyzed for concentration of total IgE by ELISA.
[0400] FIG.18 shows clearance of IgE by the exemplary anti-IgE molecules. IgE concentration dropped rapidly in mice injected with XmAb7195 and Variant A12. Lowered body temperature and low activity, suggestive of a hypersensitivity reaction, was only observed XmAb7195. These results confirm that the exemplary anti-IgE molecules rapidly clear human IgE in a humanized FcγR / FcRn mouse model.
[0401] In another experiment, humanized FcγR / FcRn mice were injected with exemplary anti-IgE molecules (Variant A8, Variant A9, Variant A12, and Variant A15) and XmAb7195 as a positive control at 2.5mg / kg. Serum from the mice was collected and analyzed for concentration of remaining molecule to determine terminal half-life, drug clearance and area under the curve. FIG.19 shows pharmacokinetic profile of the anti-IgE molecules. These results show that the exemplary anti-IgE molecules have favorable PK properties. Example 7: Testing and Characterization of Exemplary Molecules with a Cell Line Overexpressing Human IgE
[0402] The present Example provides for generation of a cell line that overexpresses the short and long isoform of IgE and testing and characterizing exemplary anti-IgE molecules using the same.
[0403] In this Example, Raji B cells were transduced with lentiviral constructs containing the long (“mIgE L”) and short (“mIgE S”) isoforms of membrane-bound IgE against the bet v1 allergen. After purification, cells were labelled with Fluorescently conjugated anti-IgE (MHE18) to determine surface level expression of IgE by flow cytometry.
[0404] FIG.20 shows surface expression of the long and short isoforms of membrane-bound IgE in Raji cells. These results show that both isoforms are highly expressed with the long isoform having lower mean fluorescence intensity (MFI) than the short isoform. Page 164 of 203 12904890v1Attorney Docket No.: 2017420-0028
[0405] In another experiment, the IgE-expressing Raji cells were activated by incubating cells with exemplary anti-IgE molecules containing human Fc domains that contain mutations which increase the Fc affinity to FcγRIIB (Variant A8, Variant A3, Variant A4, Variant A9, Variant A12, and Variant A15), and other control molecules including a wildtype IgG1 Fc with LALAPG mutations (Variant A2), a wildtype IgG1 Fc (Variant A8), Xmab7195 and obexelimab with SE / LF mutations. Raptor was used as a loading control. After 10 minutes, the cells were lysed and expression of phosphorylated FcγRIIB (CD32B) was measured by western blot and compared to the Raptor control.
[0406] FIG.21 shows phosphorylated FcγRIIB (CD32B) levels in Raji B cells that overexpress either the mIgE L or mIgE S isoform of membrane-bound IgE against the bet v1 allergen. These results show differences in FcγRIIB phosphorylation observed in the cells overexpressing the mIgE L isoform compared to the cells overexpressing the mIgE S isoform. Example 8: Evaluating the Binding of Exemplary Anti-IgE Molecules to Human PBMCs
[0407] The present Example evaluates the binding of exemplary anti-IgE molecules to human PBMCs.
[0408] Isolated human PBMCs were incubated with increasing concentrations of exemplary anti-IgE molecules (Variant A9, Variant A12, and Variant A15, and Variant A2) and omalizumab or XmAb7195 as controls. Cells were washed and the anti-IgE molecules were detected using a labelled IgE molecule. PBMCs were stained for cell surface markers to identify cell type and were analyzed via flow cytometry.
[0409] FIGs.22A-E show binding of exemplary anti-IgE molecules to PBMCs. Specifically, binding was measured between exemplary anti-IgE molecules to CD19+ B cells (FIG.22A), CD14+ monocytes (FIG.22B), CD56+ NK cells (FIG.22C), CD123+CD193+ basophils (FIG.22D), and CD3+ T cells (FIG.22E) with increasing concentrations of exemplary anti-IgE molecules. These results show that anti-IgE molecules have cell binding that is specific to FcγRIIB expression. Page 165 of 203 12904890v1Attorney Docket No.: 2017420-0028 Example 9: Evaluating Exemplary anti-IgE Molecules for C1q binding
[0410] In the present Example, exemplary anti-IgE molecules were evaluated for their ability to bind to complement component C1q via ELISA.
[0411] Free exemplary anti-IgE molecules were coated on a Nunc MaxiASorp ELISA plate at 4°C overnight on a rocker according to a 7-point 2.5-fold serial dilution in duplicates. After washing and blocking the plate, 100 µL / well of a 3 µg / mL of purified human C1q protein (QuidelOrtho) was added to the wells and incubated for 1 hour at room temperature on a rocker. After washing the plate, 100 µL / well of a 1:7000 dilution of biotin anti-C1q antibody was added to the wells and incubated for 1 hour at room temperature on a rocker. After washing the plate, 100 µL / well of a 1 µg / mL of HRP-Streptavidin was added to the wells and incubated for 1 hour at room temperature on a rocker. After washing the plate, 100 µL / well of TMB substrate was added to the wells and incubated for 5 minutes at room temperature on a rocker. After incubation, 100 µL / well of ELISA stop solution was added to the wells to quench the TMB reaction.
[0412] The plate was analyzed using a Varioskan plate reader at 450 nm (primary wavelength) and 630 nm (reference wavelength). Data was analyzed by subtracting the reference wavelength (630 nm) values from the primary wavelength (450 nm) values for each well, and the lowest resulting value was subtracted from each well. Replicate average was used for final analysis.
[0413] FIG.23 shows the results from a C1q ELISA experiment. These results demonstrate that the exemplary anti-IgE molecules do not bind C1q.
[0414] In another experiment, anti-IgE molecules were tested for their ability to aggregate...
Claims
Attorney Docket No.: 2017420-0028 CLAIMS 1. A molecule comprising: a first polypeptide comprising a first Fc domain and a first antibody variable domain that binds to a constant domain of an IgE antibody; and a second polypeptide comprising a second Fc domain; wherein the first Fc domain and the second Fc domain form a homodimer or heterodimer of the first polypeptide and the second polypeptide, and, wherein the first and / or second Fc domain comprises one or more mutated amino acid residues that increases binding affinity to FcγRIIB relative to a corresponding wild-type Fc domain.
2. The molecule of claim 1, wherein the second polypeptide further comprises an antibody variable domain that binds to IgE antibodies and the molecule is a homodimer.
3. The molecule of claim 1, wherein the second polypeptide further comprises an antibody variable domain that binds to IgE antibodies and the molecule is a heterodimer.
4. The molecule of claim 1, wherein the second polypeptide does not comprise an antibody variable domain that binds to IgE antibodies and the molecule is a heterodimer.
5. The molecule of claim 1, wherein the first antibody variable domain is covalently linked to the first Fc domain.
6. The molecule of claim 5, wherein the C-terminus of the first antibody variable domain is covalently linked to the N-terminus of the first Fc domain.
7. The molecule of claim 5, wherein the N-terminus of the first antibody variable domain is covalently linked to the C-terminus of the first Fc domain.
8. The molecule of any one of claims 1-7, wherein the first and second Fc domains form a heterodimer as a result of knobs-in-holes (KIH) mutations. Page 175 of 203 12904890v1Attorney Docket No.: 2017420-0028 9. The molecule of claim 8, wherein the KIH mutations comprise Y349T and T394F, according to EU numbering scheme.
10. The molecule of claim 9, wherein the first Fc domain comprises the Y349T mutation and the second Fc domain comprises the T394F mutation.
11. The molecule of claim 8, wherein the KIH mutations comprise T366W, S354C, T366S, L368A, Y407V, and Y349C, according to the EU numbering scheme.
12. The molecule of claim 11, wherein the first Fc domain comprises the T366W and S354C mutations and the second Fc domain comprises the T366S, L368A, Y407V, and Y349C mutations, according to the EU numbering scheme.
13. The molecule of any one of claims 1-12, wherein the first and / or second Fc domains comprise an IgG1 isotype.
14. The molecule of claim 13, wherein the first and / or second Fc domains comprise a human IgG1 isotype.
15. The molecule of any one of claims 1-14, wherein the first and / or second Fc domain comprises one or more mutated amino acid residues that increase half-life.
16. The molecule of claim 15, wherein the first and / or second Fc domain comprises one of the following mutated amino acid residues: M252Y, S254T, and T256E, according to the EU numbering scheme.
17. The molecule of claim 15 or 16, wherein the first and / or second Fc domain comprises a combination of the following mutated amino acid residues: M252Y, S254T, and T256E, according to the EU numbering scheme.
18. The molecule of claim 15, wherein the first and / or second Fc domain comprises one or more of the following mutated amino acid residues: M428L and N434S, according to the EU numbering scheme. Page 176 of 203 12904890v1Attorney Docket No.: 2017420-0028 19. The molecule of claim 15 or 16, wherein the first and / or second Fc domain comprises a combination of the following mutated amino acid residues: M428L and N434S, according to the EU numbering scheme.
20. The molecule of any one of claims 1-19, wherein the first and / or second Fc domain comprising one or more mutated amino acid residues does not have increased binding affinity to FcγRI, FcγRIIA167H, FcγRIIA167R, FcγRIIIA176F, FcγRIIIA176V, FcγRIIIB, and / or FcRn relative to the corresponding wild-type Fc domain.
21. The molecule of claim 20, wherein the first and / or second Fc domain comprising one or more mutated amino acid residues has decreased binding affinity to FcγRI, FcγRIIA167H, FcγRIIA167R, FcγRIIIA176F, FcγRIIIA176V, FcγRIIIB, and / or FcRn relative to the corresponding wild-type Fc domain.
22. The molecule of claim 20-21, wherein the first and / or second Fc domain comprising one or more mutated amino acid residues has substantially no binding affinity to FcγRI, FcγRIIA167H, FcγRIIA167R, FcγRIIIA176F, FcγRIIIA176V, FcγRIIIB, and / or FcRn relative to the corresponding wild-type Fc domain.
23. The molecule of any one of claims 1-22, wherein upon binding of two molecules to an IgE antibody, an immune complex is formed that has enhanced binding kinetics with FcγRIIB relative to an immune complex that comprises the IgE antibody and two corresponding molecules with wild-type Fc domains.
24. The molecule of any one of claims 1-23, wherein upon binding of two molecules to an IgE antibody, an immune complex is formed that has enhanced binding kinetics with FcγRIIB relative to an immune complex that comprises the IgE antibody bound to only a single molecule.
25. The molecule of any one of claims 1-24, wherein upon binding of two molecules to an IgE antibody, an immune complex is formed that has enhanced binding kinetics with FcγRIIB relative to the IgE antibody alone Page 177 of 203 12904890v1Attorney Docket No.: 2017420-0028 26. The molecule of any one of claims 23-25, wherein the enhanced binding kinetics comprise an increase in the rate of association, a decrease in the rate of disassociation, and / or a change in the equilibrium dissociation constant.
27. The molecule of any one of claims 23-26, wherein the enhanced binding kinetics produce an increase in avidity, stability, strength, frequency, and / or duration of binding between the immune complex and FcγRIIB.
28. The molecule of any one of claims 23-27, wherein the enhanced binding kinetics comprises at least 10% greater binding affinity of the immune complex to FcγRIIB.
29. The molecule of claim 28, wherein the at least 10% greater binding affinity comprises at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, or at least 50% or greater binding affinity.
30. The molecule of claim 28, wherein the molecule binds to FcγRIIB with an affinity within the range of about 1 µM to 0.001 µM.
31. The molecule of claim 30, wherein the molecule binds to FcγRIIB with an affinity within the range of about 1 µM to 0.001 µM.
32. The molecule of claim 31, wherein the molecule binds to FcγRIIB with an affinity within the range of about 0.1 µM to 0.01 µM.
33. The molecule of claim 28 or 29, wherein the binding affinity comprises binding affinity to a cell line (e.g., a CHO cell line) overexpressing FcγRIIB as measured by flow cytometry.
34. The molecule of any one of claims 1-33, wherein the molecule does not bind to complement component C1q. Page 178 of 203 12904890v1Attorney Docket No.: 2017420-0028 35. The molecule of any one of claims 1-34, wherein the molecule preferentially binds to immune cells expressing FcγRIIB over immune cells expressing FcγRIIA.
36. The molecule of claim 35, wherein the molecule comprises substantially no binding affinity for cells that do not express FcγRIIB.
37. The molecule of claim 35 or 36, wherein the immune cells expressing FcγRIIB comprise B cells, monocytes and / or basophils.
38. The molecule of claim 36 or 37, wherein the immune cells that do not express FcγRIIB comprise T cells, NK cells, neutrophils, and / or eosinophils.
39. The molecule of any one of claims 1-38, wherein the molecule prevents binding of the IgE antibody to its target Fc receptor.
40. The molecule of any one of claims 1-39, wherein the molecule does not activate immune cells (e.g., does not activate immune cells to secrete pro-inflammatory cytokines, e.g., IL-6).
41. The molecule of any one of claims 1-40, wherein the first and / or second Fc domain comprises one or more of the following amino acid mutations, according to the EU numbering scheme: E233V, L234D, L235F, G236R, G237D, S239L, S267D, H268P, S298G, T299A, A327L, L328A, A330H, E333I, R292Q, E233P, P238D, H268D, P271G, A330R, L234Y, T250V, V264I, T307P, Q311R, A330K, P343R, M428L, N434A, Y436T, Q438R, S440E, G236N, S267E, L235R, D270E, E233D, and G237D.
42. The molecule of claim 41, wherein the first and / or second Fc domain comprises one or more of the following sets of amino acid mutations, according to the EU numbering scheme: (i) E233V, L234D, L235F, G236R, G237D, S239L, S267D, H268P, S298G, T299A, A327L, L328A, A330H, and E333I; (ii) E233V, L234D, L235F, G236R, G237D, S239L, S267D, R292Q, H268P, S298G, T299A, A327L, L328A, A330H, and E333I; Page 179 of 203 12904890v1Attorney Docket No.: 2017420-0028 (iii) E233V, L234D, L235F, G236R, G237D, S239L, H268P, R292Q, S298G, T299A, A327L, L328A, A330H, and E333I; (iv) E233P, G237D, P238D, H268D, P271G, and A330R; (v) L234Y, P238D, T250V, V264I, T307P, Q311R, A330K, P343R, M428L, N434A, Y436T, Q438R, and S440E; (vi) L234D, G236N, and S267E; (vii) L235R; (viii) G236N and S267E; (ix) P238D and D270E; (x) P238D and P271G; (xi) P238D, D270E and P271G; (xii) G237D, P238D, P271G, and A330R; (xiii) G237D, P238D, D270E, P271G, and A330R; (xiv) E233D, G237D, P238D, H268D, P271G, and A330R; and (xv) P238D.
43. The molecule of any one of claims 1-42, wherein the first and / or second Fc domain comprises the mutated amino acid residue P238D, according to the EU numbering scheme.
44. The molecule of any one of claims 1-43, wherein the first and / or second Fc domain comprises the following mutated amino acid residues: P238D and P271G, according to the EU numbering scheme.
45. The molecule of any one of claims 1-44, wherein the first and / or second Fc domain comprises the following mutated amino acid residues: G237D, P238D, P271G, and A330R, according to the EU numbering scheme.
46. The molecule of any one of claims 1-45, wherein the first and / or second Fc domain comprises the following mutated amino acid residues: G237D, P238D, D270E, P271G, and A330R, according to the EU numbering scheme. Page 180 of 203 12904890v1Attorney Docket No.: 2017420-0028 47. The molecule of claim 1-43, wherein the first and / or second Fc domain comprises the following mutated amino acid residues: M428L, N434S, and P238D, according to the EU numbering scheme.
48. The molecule of claim 1-44, wherein the first and / or second Fc domain comprises the following mutated amino acid residues: M428L, N434S, P238D, and P271G, according to the EU numbering scheme.
49. The molecule of claim 1-45, wherein the first and / or second Fc domain comprises the following mutated amino acid residues: M428L, N434S, G237D, P238D, P271G, A330R, according to the EU numbering scheme.
50. The molecule of claim 1-46, wherein the first and / or second Fc domain comprises the following mutated amino acid residues: M428L, N434S, G237D, P238D, D270E, P271G, A330R, according to the EU numbering scheme.
51. The molecule of claim 1-43, wherein the first and / or second Fc domain comprises the following mutated amino acid residues: P238D, M252Y, S254T, and T256E according to the EU numbering scheme.
52. The molecule of claim 1-44, wherein the first and / or second Fc domain comprises the following mutated amino acid residues: P238D, M252Y, S254T, T256E and P271G, according to the EU numbering scheme.
53. The molecule of claim 1-45, wherein the first and / or second Fc domain comprises the following mutated amino acid residues: M252Y, S254T, T256E, G237D, P238D, P271G, A330R, according to the EU numbering scheme.
54. The molecule of claim 1-46, wherein the first and / or second Fc domain comprises the following mutated amino acid residues: M252Y, S254T, T256E, G237D, P238D, D270E, P271G, A330R, according to the EU numbering scheme. Page 181 of 203 12904890v1Attorney Docket No.: 2017420-0028 55. The molecule of any one of claims 1-54, wherein the first Fc domain comprises a sequence selected from SEQ ID NOs: 90, 92, 94, 103, 105, 107, 109, 111-113, 115, 117, 119, 121, 123, 125, 127, 129, 131, 133, 135, 137, 139-149, 163-164, 374-376, 378, 392-407, or 514-534 or a fragment or variant thereof (e.g., a sequence selected from SEQ ID NOs: 107, 109, 113, 115, 119, 131, 139, 140, 142, 148, 374, 378, 533, or 534).
56. The molecule of any one of claims 1-55, wherein the second Fc domain comprises a sequence selected from SEQ ID NOs: 91, 93, 95, 104, 106, 108, 110, 111, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 139-149, 163-164, 374-375, 377, 379, 392-407, or 514-534, or a fragment or variant thereof (e.g., a sequence selected from SEQ ID NOs: 108, 110, 114, 116, 120, 132, 139, 140, 142, 148, 374, 379, 533, or 534).
57. The molecule of any one of claims 1-56, wherein the first and second antibody variable domains are the same.
58. The molecule of any one of claims 1-57, wherein the first and second antibody variable domains are different.
59. The molecule of any one of claims 1-58, wherein the first and second antibody variable domains bind to different epitopes on an IgE antibody.
60. The molecule of any one of claims 1-59, wherein the molecule is capable of selectively depleting IgE antibodies that bind to the antibody variable domain when administered to a subject.
61. The molecule of claim 60, wherein the IgE antibodies that bind to the antibody variable domain are selectively depleted by uptake into cells and shuttling of the IgE antibodies to the lysosome for degradation.
62. The molecule of any one of claims 1-58, wherein the first and / or second antibody variable domain comprises a Fab, Fab’, Fab’2, Fab2, Fab3, F(ab’)2, Fd, Fv, sdAb, scFv, SMIP, diabody, triabody, tetrabody, minibody, nanobody, maxibody, tandab, DVD, BiTe, TandAb, VHH, or any combination thereof. Page 182 of 203 12904890v1Attorney Docket No.: 2017420-0028 63. The molecule of claim 62, wherein the first and / or second antibody variable domain that binds to the IgE antibody comprises a Fab.
64. The molecule of any one of claims 1-63, wherein the first and / or second antibody variable domains block engagement of the IgE antibody with FcεRIA and / or FcεRII.
65. The molecule of any one of claims 1-64, wherein the first and / or second antibody variable domain that binds to the IgE antibody comprises: (i) an HCDR1 comprising an amino acid sequence of SEQ ID NO: 3, an HCDR2 comprising an amino acid sequence of SEQ ID NO: 4, an HCDR3 comprising an amino acid sequence of SEQ ID NO: 5, an LCDR1 comprising an amino acid sequence of SEQ ID NO: 6, an LCDR2 comprising an amino acid sequence of SEQ ID NO: 7, and an LCDR3 comprising an amino acid sequence of SEQ ID NO: 8; (ii) an HCDR1 comprising an amino acid sequence of SEQ ID NO: 15, an HCDR2 comprising an amino acid sequence of SEQ ID NO: 16, an HCDR3 comprising an amino acid sequence of SEQ ID NO: 17, an LCDR1 comprising an amino acid sequence of SEQ ID NO: 18, an LCDR2 comprising an amino acid sequence of SEQ ID NO: 19, and an LCDR3 comprising an amino acid sequence of SEQ ID NO: 20; (iii) an HCDR1 comprising an amino acid sequence of SEQ ID NO: 25, an HCDR2 comprising an amino acid sequence of SEQ ID NO: 26, an HCDR3 comprising an amino acid sequence of SEQ ID NO: 27, an LCDR1 comprising an amino acid sequence of SEQ ID NO: 28, an LCDR2 comprising an amino acid sequence of SEQ ID NO: 29, and an LCDR3 comprising an amino acid sequence of SEQ ID NO: 30; (iv) an HCDR1 comprising an amino acid sequence of SEQ ID NO: 35, an HCDR2 comprising an amino acid sequence of SEQ ID NO: 36, an HCDR3 comprising an amino acid sequence of SEQ ID NO: 37, an LCDR1 comprising an amino acid sequence of SEQ ID NO: 38, an LCDR2 comprising an amino acid sequence of SEQ ID NO: 39, and an LCDR3 comprising an amino acid sequence of SEQ ID NO: 40; (v) an HCDR1 comprising an amino acid sequence of SEQ ID NO: 45, an HCDR2 comprising an amino acid sequence of SEQ ID NO: 46, an HCDR3 comprising an amino acid sequence of SEQ ID NO: 47, an LCDR1 comprising an amino acid sequence of SEQ Page 183 of 203 12904890v1Attorney Docket No.: 2017420-0028 ID NO: 48, an LCDR2 comprising an amino acid sequence of SEQ ID NO: 49, and an LCDR3 comprising an amino acid sequence of SEQ ID NO: 50; or (vi) an HCDR1 comprising an amino acid sequence of SEQ ID NO: 55, an HCDR2 comprising an amino acid sequence of SEQ ID NO: 56, an HCDR3 comprising an amino acid sequence of SEQ ID NO: 57, an LCDR1 comprising an amino acid sequence of SEQ ID NO: 58, an LCDR2 comprising an amino acid sequence of SEQ ID NO: 59, and an LCDR3 comprising an amino acid sequence of SEQ ID NO:
60.
66. The molecule of any one of claims 1-65, wherein the first and / or second antibody variable domain that binds to the IgE antibody comprises a VH comprising an amino acid sequence having at least 90% identity to any one of SEQ ID NOs: 9, 21, 31, 41, 51, and 61.
67. The molecule of any one of claims 1-66, wherein the first and / or second antibody variable domain that binds to the IgE antibody comprises a VH comprising an amino acid sequence of any one of SEQ ID NOs: 9, 21, 31, 41, 51, and 61.
68. The molecule of any one of claims 62-67, wherein the first and / or second antibody variable domain that binds to the IgE antibody comprises a VL comprising an amino acid sequence having at least 90% identity to any one of SEQ ID NOs: 10, 22, 32, 42, 52, and 62.
69. The molecule of any one of claims 62-68, wherein the first and / or second antibody variable domain that binds to the IgE antibody comprises a VL comprising an amino acid sequence of any one of SEQ ID NOs: 10, 22, 32, 42, 52, and 62.
70. The molecule of any one of claims 1-69, wherein the first polypeptide comprises: (i) an amino acid sequence that is at least 90% identical to SEQ ID NO: 1 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 2; (ii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 11 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 12; (iii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 13 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 14; (iv) an amino acid sequence that is at least 90% identical to SEQ ID NO: 23 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 24; Page 184 of 203 12904890v1Attorney Docket No.: 2017420-0028 (v) an amino acid sequence that is at least 90% identical to SEQ ID NO: 33 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 34; (vi) an amino acid sequence that is at least 90% identical to SEQ ID NO: 43 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 44; (vii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 53 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 54; (viii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 63 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 65; (ix) an amino acid sequence that is at least 90% identical to SEQ ID NO: 66 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 67; (x) an amino acid sequence that is at least 90% identical to SEQ ID NO: 68 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 69; (xi) an amino acid sequence that is at least 90% identical to SEQ ID NO: 70 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 72; (xii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 73 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 75; (xiii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 76 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 78; (xiv) an amino acid sequence that is at least 90% identical to SEQ ID NO: 79 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 80; (xv) an amino acid sequence that is at least 90% identical to SEQ ID NO: 81 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 182; (xvi) an amino acid sequence that is at least 90% identical to SEQ ID NO: 83 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 84; (xvii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 97 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 98; (xviii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 99 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 100; (xix) an amino acid sequence that is at least 90% identical to SEQ ID NO: 101 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 102; (xx) an amino acid sequence that is at least 90% identical to SEQ ID NO: 165 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 166; Page 185 of 203 12904890v1Attorney Docket No.: 2017420-0028 (xxi) an amino acid sequence that is at least 90% identical to SEQ ID NO: 167 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 168; (xxii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 169 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 170; (xxiii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 171 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 172; (xxiv) an amino acid sequence that is at least 90% identical to SEQ ID NO: 173 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 174; (xxv) an amino acid sequence that is at least 90% identical to SEQ ID NO: 175 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 176; (xxvi) an amino acid sequence that is at least 90% identical to SEQ ID NO: 177 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 178; (xxvii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 179 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 180; (xxviii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 181 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 172; or (xxix) an amino acid sequence that is at least 90% identical to SEQ ID NO: 182 and an amino acid sequence that is at least 90% identical to SEQ ID NO:
174.
71. The molecule of claim 69 or 70, wherein the first polypeptide comprises: (i) the amino acid sequence of SEQ ID NO: 1 and the amino acid sequence of SEQ ID NO: 2; (ii) the amino acid sequence of SEQ ID NO: 11 and the amino acid sequence of SEQ ID NO: 12; (iii) the amino acid sequence of SEQ ID NO: 13 and the amino acid sequence of SEQ ID NO: 14; (iv) the amino acid sequence of SEQ ID NO: 23 and the amino acid sequence of SEQ ID NO: 24; (v) the amino acid sequence of SEQ ID NO: 33 and the amino acid sequence of SEQ ID NO: 34; (vi) the amino acid sequence of SEQ ID NO: 43 and the amino acid sequence of SEQ ID NO: 44; Page 186 of 203 12904890v1Attorney Docket No.: 2017420-0028 (vii) the amino acid sequence of SEQ ID NO: 53 and the amino acid sequence of SEQ ID NO: 54; (viii) the amino acid sequence of SEQ ID NO: 63 and the amino acid sequence of SEQ ID NO: 65; (ix) the amino acid sequence of SEQ ID NO: 66 and the amino acid sequence of SEQ ID NO: 67; (x) the amino acid sequence of SEQ ID NO: 68 and the amino acid sequence of SEQ ID NO: 69; (xi) the amino acid sequence of SEQ ID NO: 70 and the amino acid sequence of SEQ ID NO: 72; (xii) the amino acid sequence of SEQ ID NO: 73 and the amino acid sequence of SEQ ID NO: 75; (xiii) the amino acid sequence of SEQ ID NO: 76 and the amino acid sequence of SEQ ID NO: 78; (xiv) the amino acid sequence of SEQ ID NO: 79 and the amino acid sequence of SEQ ID NO: 80; (xv) the amino acid sequence of SEQ ID NO: 81 and the amino acid sequence of SEQ ID NO: 182; (xvi): the amino acid sequence of SEQ ID NO: 83 and the amino acid sequence of SEQ ID NO: 84; (xvii) the amino acid sequence of SEQ ID NO: 97 and the amino acid sequence of SEQ ID NO: 98; (xviii) the amino acid sequence of SEQ ID NO: 99 and the amino acid sequence of SEQ ID NO: 100; (xix) the amino acid sequence of SEQ ID NO: 101 and the amino acid sequence of SEQ ID NO: 102; (xx) the amino acid sequence of SEQ ID NO: 165 and the amino acid sequence of SEQ ID NO: 166; (xxi) the amino acid sequence of SEQ ID NO: 167 and the amino acid of SEQ ID NO: 168; (xxii) the amino acid sequence of SEQ ID NO: 169 and the amino acid sequence of SEQ ID NO: 170; Page 187 of 203 12904890v1Attorney Docket No.: 2017420-0028 (xxiii) the amino acid sequence of SEQ ID NO: 171 and the amino acid sequence of SEQ ID NO: 172; (xxiv) the amino acid sequence of SEQ ID NO: 173 and the amino acid sequence of SEQ ID NO: 174; (xxv) the amino acid sequence of SEQ ID NO: 175 and the amino acid sequence of SEQ ID NO: 176; (xxvi) the amino acid sequence of SEQ ID NO: 177 and the amino acid sequence of SEQ ID NO: 178; (xxvii) the amino acid sequence of SEQ ID NO: 179 and the amino acid sequence of SEQ ID NO: 180; (xxviii) the amino acid sequence of SEQ ID NO: 181 and the amino acid sequence of SEQ ID NO: 172; or (xxix) the amino acid sequence of SEQ ID NO: 182 and the amino acid sequence of SEQ ID NO:
174.
72. The molecule of any one of claims 1-71, wherein the second polypeptide comprises: (i) an amino acid sequence that is at least 90% identical to SEQ ID NO: 1 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 2; (ii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 11 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 12; (iii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 13 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 14; (iv) an amino acid sequence that is at least 90% identical to SEQ ID NO: 23 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 24; (v) an amino acid sequence that is at least 90% identical to SEQ ID NO: 33 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 34; (vi) an amino acid sequence that is at least 90% identical to SEQ ID NO: 43 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 44; (vii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 53 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 54; (viii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 64; (ix) an amino acid sequence that is at least 90% identical to SEQ ID NO: 66 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 67; Page 188 of 203 12904890v1Attorney Docket No.: 2017420-0028 (x) an amino acid sequence that is at least 90% identical to SEQ ID NO: 68 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 69; (xi) an amino acid sequence that is at least 90% identical to SEQ ID NO: 71; (xii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 74; (xiii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 77; (xiv) an amino acid sequence that is at least 90% identical to SEQ ID NO: 79 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 80; (xv) an amino acid sequence that is at least 90% identical to SEQ ID NO: 81 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 182; (xvi): an amino acid sequence that is at least 90% identical to SEQ ID NO: 83 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 84; (xvii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 97 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 98; (xviii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 99 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 100; (xix) an amino acid sequence that is at least 90% identical to SEQ ID NO: 101 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 102; (xx) an amino acid sequence that is at least 90% identical to SEQ ID NO: 165 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 166; (xxi) an amino acid sequence that is at least 90% identical to SEQ ID NO: 167 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 168; (xxii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 169 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 170; (xxiii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 171 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 172; (xxiv) an amino acid sequence that is at least 90% identical to SEQ ID NO: 173 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 174; (xxv) an amino acid sequence that is at least 90% identical to SEQ ID NO: 175 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 176; (xxvi) an amino acid sequence that is at least 90% identical to SEQ ID NO: 177 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 178; (xxvii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 179 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 180; Page 189 of 203 12904890v1Attorney Docket No.: 2017420-0028 (xxviii) an amino acid sequence that is at least 90% identical to SEQ ID NO: 181 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 172; or (xxix) an amino acid sequence that is at least 90% identical to SEQ ID NO: 182 and an amino acid sequence that is at least 90% identical to SEQ ID NO:
174.
73. The molecule of claim 72, wherein the second polypeptide comprises: (i) the amino acid sequence of SEQ ID NO: 1 and the amino acid sequence of SEQ ID NO: 2; (ii) the amino acid sequence of SEQ ID NO: 11 and the amino acid sequence of SEQ ID NO: 12; (iii) the amino acid sequence of SEQ ID NO: 13 and the amino acid sequence of SEQ ID NO: 14; (iv) the amino acid sequence of SEQ ID NO: 23 and the amino acid sequence of SEQ ID NO: 24; (v) the amino acid sequence of SEQ ID NO: 33 and the amino acid sequence of SEQ ID NO: 34; (vi) the amino acid sequence of SEQ ID NO: 43 and the amino acid sequence of SEQ ID NO: 44; (vii) the amino acid sequence of SEQ ID NO: 53 and the amino acid sequence of SEQ ID NO: 54; (viii) the amino acid sequence of SEQ ID NO: 64; (ix) the amino acid sequence of SEQ ID NO: 66 and the amino acid sequence of SEQ ID NO: 67; (x) the amino acid sequence of SEQ ID NO: 68 and the amino acid sequence of SEQ ID NO: 69; (xi) the amino acid sequence of SEQ ID NO: 71; (xii) the amino acid sequence of SEQ ID NO: 74; (xiii) the amino acid sequence of SEQ ID NO: 77; (xiv) the amino acid sequence of SEQ ID NO: 79 and the amino acid sequence of SEQ ID NO: 80; (xv) the amino acid sequence of SEQ ID NO: 81 and the amino acid sequence of SEQ ID NO: 182; Page 190 of 203 12904890v1Attorney Docket No.: 2017420-0028 (xvi): the amino acid sequence of SEQ ID NO: 83 and the amino acid sequence of SEQ ID NO: 84; (xvii) the amino acid sequence of SEQ ID NO: 97 and the amino acid sequence of SEQ ID NO: 98; (xviii) the amino acid sequence of SEQ ID NO: 99 and the amino acid sequence of SEQ ID NO: 100; (xix) the amino acid sequence of SEQ ID NO: 101 and the amino acid sequence of SEQ ID NO: 102; (xx) the amino acid sequence of SEQ ID NO: 165 and the amino acid sequence of SEQ ID NO: 166; (xxi) the amino acid sequence of SEQ ID NO: 167 and the amino acid of SEQ ID NO: 168; (xxii) the amino acid sequence of SEQ ID NO: 169 and the amino acid sequence of SEQ ID NO: 170; (xxiii) the amino acid sequence of SEQ ID NO: 171 and the amino acid sequence of SEQ ID NO: 172; (xxiv) the amino acid sequence of SEQ ID NO: 173 and the amino acid sequence of SEQ ID NO: 174; (xxv) the amino acid sequence of SEQ ID NO: 175 and the amino acid sequence of SEQ ID NO: 176; (xxvi) the amino acid sequence of SEQ ID NO: 177 and the amino acid sequence of SEQ ID NO: 178; (xxvii) the amino acid sequence of SEQ ID NO: 179 and the amino acid sequence of SEQ ID NO: 180; (xxviii) the amino acid sequence of SEQ ID NO: 181 and the amino acid sequence that of SEQ ID NO: 172; or (xxix) the amino acid sequence of SEQ ID NO: 182 and the amino acid sequence of SEQ ID NO:
174.
74. The molecule of any one of claims 1-73, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 1 and SEQ ID NO: 2, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 1 and SEQ ID NO:
2. Page 191 of 203 12904890v1Attorney Docket No.: 2017420-0028 75. The molecule of any one of claims 1-73, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 11 and SEQ ID NO: 12, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 11 and SEQ ID NO:
12.
76. The molecule of any one of claims 1-73, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 13 and SEQ ID NO: 14, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 13 and SEQ ID NO:
14.
77. The molecule of any one of claims 1-73, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 23 and SEQ ID NO: 24, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 23 and SEQ ID NO:
24.
78. The molecule of any one of claims 1-73, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 33 and SEQ ID NO: 34, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 33 and SEQ ID NO:
34.
79. The molecule of any one of claims 1-73, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 43 and SEQ ID NO: 44, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 43 and SEQ ID NO:
44.
80. The molecule of any one of claims 1-73, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 53 and SEQ ID NO: 53, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 53 and SEQ ID NO:
54.
81. The molecule of any one of claims 1-73, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 63 and SEQ ID NO: 65, and the second polypeptide comprises the amino acid sequence of SEQ ID NO:
64.
82. The molecule of any one of claims 1-73, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 66 and SEQ ID NO: 67, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 66 and SEQ ID NO:
67. Page 192 of 203 12904890v1Attorney Docket No.: 2017420-0028 83. The molecule of any one of claims 1-73, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 68 and SEQ ID NO: 69, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 68 and SEQ ID NO:
69.
84. The molecule of any one of claims 1-73, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 70 and SEQ ID NO: 72, and the second polypeptide comprises the amino acid sequence of SEQ ID NO:
71.
85. The molecule of any one of claims 1-73, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 73 and SEQ ID NO: 75, and the second polypeptide comprises the amino acid sequence of SEQ ID NO:
74.
86. The molecule of any one of claims 1-73, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 76 and SEQ ID NO: 78, and the second polypeptide comprises the amino acid sequence of SEQ ID NO:
77.
87. The molecule of any one of claims 1-73, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 79 and SEQ ID NO: 80, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 79 and SEQ ID NO:
80.
88. The molecule of any one of claims 1-73, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 81 and SEQ ID NO: 82, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 81 and SEQ ID NO:
82.
89. The molecule of any one of claims 1-73, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 83 and SEQ ID NO: 84, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 83 and SEQ ID NO:
84.
90. The molecule of any one of claims 1-73, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 97 and SEQ ID NO: 98, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 97 and SEQ ID NO:
98. Page 193 of 203 12904890v1Attorney Docket No.: 2017420-0028 91. The molecule of any one of claims 1-73, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 99 and SEQ ID NO: 100, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 99 and SEQ ID NO:
100.
92. The molecule of any one of claims 1-73, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 101 and SEQ ID NO: 102, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 101 and SEQ ID NO:
102.
93. The molecule of any one of claims 1-73, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 165 and SEQ ID NO: 166, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 165 and SEQ ID NO:
166.
94. The molecule of any one of claims 1-73, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 167 and SEQ ID NO: 168, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 167 and SEQ ID NO:
168.
95. The molecule of any one of claims 1-73, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 169 and SEQ ID NO: 170, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 169 and SEQ ID NO:
170.
96. The molecule of any one of claims 1-73, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 171 and SEQ ID NO: 172, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 171 and SEQ ID NO:
172.
97. The molecule of any one of claims 1-73, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 173 and SEQ ID NO: 174, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 173 and SEQ ID NO:
174.
98. The molecule of any one of claims 1-73, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 175 and SEQ ID NO: 176, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 175 and SEQ ID NO:
176. Page 194 of 203 12904890v1Attorney Docket No.: 2017420-0028 99. The molecule of any one of claims 1-73, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 177 and SEQ ID NO: 178, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 177 and SEQ ID NO:
178.
100. The molecule of any one of claims 1-73, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 179 and SEQ ID NO: 180, and the second polypeptide comprise the amino acid sequence of SEQ ID NO: 179 and SEQ ID NO:
180.
101. The molecule of any one of claims 1-70, wherein the first polypeptide comprises an amino acid sequence that is at least 90% identical to SEQ ID NO: 181 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 172, and the second polypeptide comprises an amino acid sequence that is at least 90% identical to SEQ ID NO: 181 and an amino acid sequence that is at least 90% identical to SEQ ID NO:
172.
102. The molecule of any one of claims 1-70, wherein the first polypeptide comprises an amino acid sequence that is at least 90% identical to SEQ ID NO: 182 and an amino acid sequence that is at least 90% identical to SEQ ID NO: 174, and the second polypeptide comprises an amino acid sequence that is at least 90% identical to SEQ ID NO: 182 and an amino acid sequence that is at least 90% identical to SEQ ID NO:
174.
103. The molecule of any one of claims 1-73, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 181 and the amino acid sequence of SEQ ID NO: 172, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 181 and the amino acid sequence of SEQ ID NO:
172.
104. The molecule of any one of claims 1-73, wherein the first polypeptide comprises the amino acid sequence of SEQ ID NO: 182 and the amino acid sequence of SEQ ID NO: 174, and the second polypeptide comprises the amino acid sequence of SEQ ID NO: 182 and the amino acid sequence of SEQ ID NO:
174.
105. The molecule of any one of claims 1-104, wherein the second Fc domain further comprises a second autoantibody-binding domain. Page 195 of 203 12904890v1Attorney Docket No.: 2017420-0028 106. The molecule of claim 105, wherein the N-terminus of the second Fc domain is covalently linked to the C-terminus of the second autoantibody-binding domain.
107. The molecule of claim 105, wherein the C-terminus of the second Fc domain is covalently linked to the N-terminus of the second autoantibody-binding domain.
108. The molecule of any one of claims 105-107, wherein the second autoantibody- binding domain binds to an IgE antibody.
109. The molecule of claim 108, wherein the first and second antibody variable domains are the same.
110. The molecule of claim 108, wherein the first and second antibody variable domains are different.
111. The molecule of any one of claims 1-110, wherein the second polypeptide does not comprise an antibody variable domain that binds to an IgE antibody.
112. A nucleic acid comprising a nucleotide sequence encoding the molecule of any one of claims 1-111.
113. A host cell containing the nucleic acid of claim 112.
114. A vector comprising the nucleic acid of claim 112.
115. The vector of claim 114, wherein the vector comprises a viral vector.
116. The vector of claim 115, wherein the viral vector comprises a retroviral vector, a lentiviral vector, an adeno-associated viral (AAV) vector, or an adenoviral vector.
117. A pharmaceutical composition comprising the molecule of any one of claims 1-111 or a nucleic acid encoding the molecule of any one of claims 1-111 and a pharmaceutically acceptable carrier. Page 196 of 203 12904890v1Attorney Docket No.: 2017420-0028 118. A method of making a molecule, the method comprising expressing the nucleic acid of claim 112 in a host cell and recovering the molecule.
119. A method of treating a subject suffering from or susceptible to an allergic disease, the method comprising: administering to the subject a pharmaceutical composition comprising the molecule of any one of claims 1-111 or a nucleic acid encoding the molecule of any one of claims 1- 111.
120. The method of claim 118 or 119, wherein the allergic disease is associated with an elevated level of IgE antibodies that is targeted by the antibody variable domain of the molecule.
121. The method of claim 118 or 119, wherein the level of circulating IgE antibodies is reduced within less than 12 hours of administering the pharmaceutical composition to the subject.
122. The method of claim 121, wherein the level of IgE antibodies in the subject or in a biological sample from the subject is reduced after administration relative to a level before administration.
123. The method of claim 122, wherein the level of IgE antibodies is reduced by at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% relative to a level before the administration.
124. The method of claim 122 or 123, wherein the reduced level IgE antibodies is sustained over time. Page 197 of 203 12904890v1Attorney Docket No.: 2017420-0028 125. The method of claim 124, wherein a sustained period of time comprises at least 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 10 weeks, 12 weeks, or longer.
126. A method of reducing the level of circulating IgE antibodies in a subject suffering from an allergic disease, the method comprising: administering to the subject the pharmaceutical composition of claim 117 to the subject.
127. The method of claim 126, wherein the level of circulating IgE antibodies is reduced within less than 12 hours of administering the pharmaceutical composition.
128. The method of claim 127, wherein the level of IgE antibodies in the subject or in a biological sample from the subject is reduced after administration relative to a level before administration.
129. The method of any one of claims 126-128, wherein reduction of the IgE antibodies occurs within 30 minutes of administering the pharmaceutical composition to the subject.
130. The method of any one of claims 126-150, wherein the molecule in the pharmaceutical composition blocks engagement of the IgE antibodies with FceR1a and / or FcεRII / CD23.
131. The method of any one of claims 118-130, wherein at least two molecules in the pharmaceutical composition form an immune complex with a circulating IgE antibody when the first and / or second antibody variable domain of the molecules bind to the circulating IgE antibody.
132. The method of claim 131, wherein the circulating IgE antibodies are cleared from the subject through FcγRIIB-mediated cellular uptake of the immune complex by B-cells expressing FcγRIIB. Page 198 of 203 12904890v1Attorney Docket No.: 2017420-0028 133. The method of claim 131 or 132, wherein the circulating IgE antibodies are cleared from the subject through FcγRIIB-mediated cellular uptake of the immune complex by liver sinusoidal endothelial cells expressing FcγRIIB.
134. The method of any one of claims 126-133, wherein when the pharmaceutical composition is administered to the subject, it reduces IgE antibody-stimulating activity in the serum of the subject.
135. The method of any one of claims 119-134, wherein the pharmaceutical composition is administered intravenously, intramuscularly, or subcutaneously to the subject.
136. The method of any one of claims 119-135, wherein the subject is a human.
137. A composition for decreasing the titer of IgE antibody in the blood serum of a subject in need thereof, the composition comprising: a plurality of molecules, each molecule comprising (a) a first polypeptide comprising a first antibody variable domain that binds specifically to an IgE antibody operably linked to a first Fc domain ; and (b) a second polypeptide comprising a second Fc domain, wherein the first Fc domain and the second Fc domain form a homodimer or heterodimer of the first polypeptide and the second polypeptide; wherein the first and / or second Fc domain comprises one or more mutated amino acid residues and has increased binding affinity to FcγRIIB relative to a corresponding wild- type Fc domain, and wherein, upon administration of the plurality of molecules, the molecules bind to IgE antibodies to form immune complexes comprising two molecules bound to an IgE antibody, and wherein the immune complex binds to FcγRIIB expressed on the surface of liver sinusoidal endothelial cells (LSECs) and are endocytosed thereby decreasing the titer of the IgE antibodies in the subject’s blood serum.
138. The composition of claim 137, wherein the immune complex binds with higher avidity to FcγRIIB expressed on the surface of liver sinusoidal endothelial cells (LSECs), and wherein the higher avidity is relative to an immune complex comprising two molecules with wild-type Fc domains. Page 199 of 203 12904890v1Attorney Docket No.: 2017420-0028 139. The composition of claim 137, wherein the molecules are molecules of any one of claims 1-111.
140. An immune complex comprising: (i) an IgE antibody; and (ii) two molecules, wherein each molecule comprises: a first polypeptide comprising a first antibody variable domain that binds to a constant domain of an IgE antibody operably linked to a first Fc domain; and a second polypeptide comprising a second Fc domain; wherein the first Fc domain and the second Fc domain form a homodimer or heterodimer of the first polypeptide and the second polypeptide, wherein the first and / or second Fc domain comprises one or more mutated amino acid residues and has increased binding affinity to FcγRIIB relative to a corresponding wild-type Fc domain.
141. The immune complex of claim 140, wherein the immune complex has enhanced binding kinetics with FcγRIIB relative to an immune complex that comprises the IgE antibody bound to two corresponding molecules with wild-type Fc domains.
142. The immune complex of claim 140, wherein the immune complex has enhanced binding kinetics with FcγRIIB relative to an immune complex that comprises the IgE antibody and only a single molecule.
143. The immune complex of claim 140, wherein the immune complex has enhanced binding kinetics with FcγRIIB relative to the IgE antibody alone.
144. The immune complex of any one of claims 140-143, wherein the binding domain of each of the two molecules is bound to the IgE antibody.
145. The immune complex of any one of claims 140-144, wherein the enhanced binding kinetics comprise an increase in the rate of association, a decrease in the rate of disassociation, and / or a change in the equilibrium dissociation constant. Page 200 of 203 12904890v1Attorney Docket No.: 2017420-0028 146. The immune complex of any one of claims 140-145, wherein the enhanced binding kinetics produce an increase in avidity, stability, strength, frequency, and / or duration of the binding between the immune complex and FcγRIIB.
147. The immune complex of any one of claims 140-146, wherein the first and / or second Fc domain comprising one or more mutated amino acid residues does not have increased binding affinity to FcγRI, FcγRIIA167H, FcγRIIA167R, FcγRIIIA176F, FcγRIIIA176V, FcγRIIIB, and / or FcRn relative to the corresponding wild-type Fc domain.
148. The immune complex of any one of claims 140-147, wherein the first and / or second Fc domain comprising one or more mutated amino acid residues has decreased binding affinity to FcγRI, FcγRIIA167H, FcγRIIA167R, FcγRIIIA176F, FcγRIIIA176V, FcγRIIIB, and / or FcRn relative to the corresponding wild-type Fc domain.
149. The immune complex of any one of claims 140-148, wherein the first and / or second Fc domain comprising one or more mutated amino acid residues has negligible or no binding affinity to FcγRI, FcγRIIA167H, FcγRIIA167R, FcγRIIIA176F, FcγRIIIA176V, FcγRIIIB, and / or FcRn relative to the corresponding wild-type Fc domain.
150. The immune complex of any one of claims 140-149, wherein the enhanced binding kinetics comprises at least 10% greater binding affinity of the immune complex to FcγRIIB.
151. The immune complex of claim 150, wherein the at least 10% greater binding affinity comprises at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, or at least 50% or greater binding affinity.
152. The immune complex of claim 150 or 151, wherein the binding affinity comprises binding affinity to a cell line (e.g., a CHO cell line) overexpressing FcγRIIB measured by flow cytometry. Page 201 of 203 12904890v1Attorney Docket No.: 2017420-0028 153. The immune complex of any one of claims 140-152, wherein the immune complex preferentially binds to immune cells expressing FcγRIIB over immune cells expressing FcγRIIA.
154. The immune complex of any one of claims 140-153, wherein the immune complex cross-links FcγRIIB with a B cell receptor on a B cell.
155. The immune complex of any one of claims 140-154, wherein the molecules are molecules of any one of claims 1-111.
156. The method of claim 119 or 126, wherein the allergic disease is food allergy. Page 202 of 203 12904890v1