RNA compositions targeting HIV
Patent Information
- Authority / Receiving Office
- EP · EP
- Patent Type
- Applications
- Current Assignee / Owner
- BIONTECH SE
- Filing Date
- 2024-08-01
- Publication Date
- 2026-06-10
AI Technical Summary
Current HIV treatments face challenges such as the high cost and complexity of developing individual therapies, regulatory hurdles for combination therapies, painful and time-consuming administration of antibodies, and the short serum half-life of recombinant antibodies.
The use of polyribonucleotides encoding antibody agents, known as RiboMabs, which are administered to subjects and expressed by the body, allowing for the delivery of single or multiple anti-HIV antibody agents with improved manufacturing efficiency, reduced regulatory burdens, and enhanced patient compliance.
This approach enables the safe, reliable, and potent delivery of anti-HIV antibody agents, addressing the challenges of cost, complexity, and administration, while also extending the serum half-life of antibody therapies.
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Figure IB2024057481_06022025_PF_FP_ABST
Abstract
Description
Attorney Docket No: 2013237-1144 (P1577WO01) RNA COMPOSITIONS TARGETING HIV RELATED APPLICATIONS
[0001] This application claims priority to and the benefit of U.S. Provisional Patent Application No. 63 / 517,596, filed on August 3, 2023, the entire contents of which are hereby incorporated by reference in its entirety. SEQUENCE LISTING
[0002] The present specification makes reference to a Sequence Listing (submitted electronically as a .xml file named “2013237-1144_ST26.xml” on August 1, 2024). The .xml file was generated on July 25, 2024, and is 3,328,554 bytes in size. The entire contents of the Sequence Listing are herein incorporated by reference. BACKGROUND
[0003] Human Immunodeficiency Virus (HIV) is an infectious virus associated with Acquired Immune Deficiency Syndrome (AIDS). According to the World Health Organization, over 37 million people worldwide are currently affected with HIV. In 2020, approximately 680,000 people died from HIV-related causes and approximately 1.5 million people acquired HIV. There is currently no cure for HIV. SUMMARY
[0004] The present disclosure recognizes that HIV mutates rapidly. The highly mutable nature of HIV virions allows them to escape pressure from host immunity and / or treatment. To combat viral escape, combination therapies targeting HIV, including anti-HIV antibody agents, have been considered. However, the development of such combination therapies has been hindered by a number of challenges. First, development of individual HIV therapies is time consuming and expensive. For instance, anti-HIV antibody development is challenged by demanding and costly production, including purification and formulation methods associated with protein therapeutics. Second, combination therapies present regulatory challenges. In addition to ensuring that a combination therapy will be safe and efficacious, tight regulation over manufacture of the individual therapies, compounding of the multiple therapies together, and quality control during storage and administration complicate the use of combination therapies. Third, administration of antibodies to a subject can be painful and time consuming. Generally, antibodies are administered intravenously over a longer period of time. Administration of multiple antibodies can add to the complexity of antibody administration, increasing patient discomfort and taking up additional time. Finally, recombinant antibodies can have a short serum half-life.
[0005] The present disclosure provides insights that address these challenges, making it possible to not only deliver single anti-HIV antibody agents to a subject safely, reliably, and with strong potency, but also making it possible to deliver multiple anti-HIV therapeutics, including multiple anti-HIV antibody agents to a subject. For example, the present disclosure describes antibody agents or portions thereof (e.g., immunoglobulin chains) that are delivered to a subject via polyribonucleotides. An antibody agent that is delivered to a subject as one or more polyribonucleotides that encode the antibody agent are referred to herein as “RiboMabs.” After delivery of one or more polyribonucleotides that encode an antibody agent to a subject, the antibody agent, i.e., the RiboMab” is expressed by the subject’s body. Further, the term “RibobNAb” refers to a RiboMab that comprises all or part of a - 1 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) broadly neutralizing antibody (bNAb), e.g., a broadly neutralizing antibody targeting HIV. Utilizing polyribonucleotides as a therapeutic agent (in contrast to administering an antibody agent itself) involves simpler and less expensive manufacturing processes. The less complex production of polyribonucleotides encoding antibody agent(s) (e.g., anti- HIV antibody agent(s)) can streamline manufacture (e.g., by circumventing the need for intensive glycan production and profiling), mitigating regulatory and production challenges associated with developing and using antibody agents themselves. Additionally, polyribonucleotides are effective at producing similar effects to recombinant proteins but tend to require much lower volumes be administered to a subject. This is because polyribonucleotides encoding, e.g., anti-HIV antibody agent(s), can be administered to a subject and the subject’s body produces the anti-HIV antibody agent(s) itself. Using a lower volume can provide a patient with a more pleasant experience and increase patient compliance with a treatment regimen. The present disclosure also provides technologies that address certain limitations of recombinant antibody technologies, including for example, the short serum half-life of recombinant antibodies by utilizing RNA technologies as a modality to express antibody agents directly in the patient’s cells.
[0006] RiboMab technology also allows for two or more antibody agents to be administered to a subject simultaneously. Typically, an antibody produced by, e.g., humans, comprises four polypeptide chains – two “heavy” chains and two “light” chains. Each polypeptide chain (whether heavy or light) includes (1) a “variable” domain, having a sequence that varies among antibodies and a structure that determines the antigen to which an antibody binds, and (2) a “constant” domain(s), having a sequence and a structure that generally remain unchanged across antibodies of a given class, thus imparting little effect on antigen binding. In humans, specialized white blood cells, “B cells,” produce antibodies. Heavy chains and light chains are assembled to form an antibody through two key pairings: (1) the fragment crystallizable (Fc) domains of the two heavy chains pair together, and (2) the two light chains each pair with a heavy chain via disulfide linkages. During normal antibody production in a human, a single antibody is produced by a single B cell. In that situation, the correct pairing of heavy and light chains is ensured because only one species of heavy chain and one species of light chain are present in each B cell. However, the administration of a nucleic acid composition encoding more than one antibody agent to a subject requires the correct assembly of immunoglobulin chains (e.g., heavy chains and light chains) so that unwanted side products (e.g., antibody agents with unintended pairings) do not form.
[0007] Among other things, the present disclosure provides polyribonucleotides encoding an immunoglobulin chain of an antibody agent.
[0008] In one aspect, an immunoglobulin chain comprises a heavy chain variable (VH) domain. In some embodiments, a VH domain comprises a heavy chain complementarity determining region (HCDR)1 comprising an amino acid sequence according to SEQ ID NO: 6, an HCDR2 comprising an amino acid sequence according to SEQ ID NO: 9, and an HCDR3 comprising an amino acid sequence according to SEQ ID NO: 12 or SEQ ID NO: 34.
[0009] In some embodiments, a VH domain comprises or consists of an amino acid sequence according to SEQ ID NO: 24, 39, or 42. In some embodiments, a VH domain comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 24, 39, or 42.
[0010] In some embodiments, a polyribonucleotide comprises a VH domain-encoding sequence. In some embodiments, a VH domain-encoding sequence comprises (a) the HCDR1-encoding sequence that comprises or - 2 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) consists of the ribonucleic acid sequence according to SEQ ID NO: 7, (b) the HCDR2-encoding sequence that comprises or consists of the ribonucleic acid sequence according to SEQ ID NO: 10 or SEQ ID NO: 32, and (c) the HCDR3-encoding sequence that comprises or consists of the ribonucleic acid sequence according to SEQ ID NO: 13, 35, or 37.
[0011] In some embodiments, a VH domain-encoding sequence comprises a ribonucleic acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to a ribonucleic acid sequence according to SEQ ID NO: 25, 40, or 43. In some embodiments, a VH domain-encoding sequence comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 25, 40, or 43.
[0012] In some embodiments, an immunoglobulin chain comprising a VH domain as described herein comprises one or more constant domains. In some embodiments, a VH domain is operably linked to one or more constant domains.
[0013] In some embodiments, an immunoglobulin chain comprising a VH domain as described herein comprises one or more constant domains. In some embodiments, a VH domain is operably linked to one or more constant domains.
[0014] In some embodiments, one or more constant domains comprise a CH2 domain. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH2 domain.
[0015] In some embodiments, one or more constant domains comprise a CH3 domain. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH3 domain.
[0016] In some embodiments, one or more constant domains comprise a hinge domain. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the hinge domain.
[0017] In some embodiments, one or more constant domains comprise a CH1 domain. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes a CH1 domain.
[0018] In some embodiments, one or more constant domains comprise a CL domain. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes a CL domain.
[0019] In some embodiments, an immunoglobulin chain comprising a VH domain as described herein comprises a CH1 domain, a hinge domain, a CH2 domain, and a CH3 domain.
[0020] In some embodiments, an immunoglobulin chain comprising a VH domain as described herein comprises a CL domain, a hinge domain, a CH2 domain, and a CH3 domain.
[0021] The present disclosure further provides a polyribonucleotide encoding an immunoglobulin chain of an antibody agent, where the immunoglobulin chain comprises a light chain variable (VL) domain.
[0022] In some embodiments, a VL domain comprises (a) a light chain complementarity determining region (LCDR)1 comprising an amino acid sequence according to SEQ ID NO: 15, (b) an LCDR2 comprising an amino acid sequence of GKN, and (c) an LCDR3 comprising an amino acid sequence according to SEQ ID NO: 21.
[0023] In some embodiments, a polyribonucleotide comprises a VL domain-encoding sequence. In some embodiments, a VL domain-encoding sequence comprises an LCDR1-encoding sequence that comprises or consists of - 3 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) a ribonucleic acid sequence according to SEQ ID NO: 16, an LCDR2-encoding sequence that comprises or consists of a ribonucleic acid sequence of GGCAAGAAC, and an LCDR3-encoding sequence that comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 22.
[0024] In some embodiments, a VL domain comprises or consists of an amino acid sequence according to SEQ ID NO: 29 or 45. In some embodiments, a VL domain-encoding sequence comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 30 or 46.
[0025] In some embodiments, an immunoglobulin chain comprising a VL domain further comprises a constant domain. In some embodiments, a VL domain is operably linked to a constant domain. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the constant domain.
[0026] In some embodiments, an immunoglobulin chain comprising a VL domain further comprises a CL domain. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CL domain. In some embodiments, a CL domain is a kappa constant domain. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the light chain constant domain.
[0027] In some embodiments, an immunoglobulin chain comprising a VL domain further comprises a CH1 domain. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH1 domain.
[0028] Among other things, the present disclosure provides a polyribonucleotide encoding an immunoglobulin chain of an antibody agent, where the immunoglobulin chain comprises a heavy chain variable (VH) domain and a light chain variable (VL) domain. In some embodiments, VH domain comprises an HCDR1 comprising an amino acid sequence according to SEQ ID NO: 6, an HCDR2 comprising an amino acid sequence according to SEQ ID NO: 9, and an HCDR3 comprising an amino acid sequence according to SEQ ID NO: 12 or SEQ ID NO: 34. In some embodiments, a VL domain comprises an LCDR1 comprising an amino acid sequence according to SEQ ID NO: 15, an LCDR2 comprising an amino acid sequence of GKN, and an LCDR3 comprising an amino acid sequence according to SEQ ID NO: 21.
[0029] In some embodiments, a polyribonucleotide comprises a VH domain-encoding sequence and a VL domain-encoding sequence. In some embodiments, a VH domain-encoding sequence comprises an HCDR1-encoding sequence that comprises or consists of the ribonucleic acid sequence according to SEQ ID NO: 7, the HCDR2- encoding sequence that comprises or consists of the ribonucleic acid sequence according to SEQ ID NO: 10 or SEQ ID NO: 32, and the HCDR3-encoding sequence that comprises or consists of the ribonucleic acid sequence according to SEQ ID NO: 13, 35, or 37. In some embodiments, a VL domain-encoding sequence comprises an LCDR1-encoding sequence that comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 16, an LCDR2-encoding sequence that comprises or consists of a ribonucleic acid sequence of GGCAAGAAC, and an LCDR3-encoding sequence that comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 22.
[0030] In some embodiments, an immunoglobulin chain comprises a single chain fragment variable (scFv). In some embodiments, an scFv comprises a VH domain, a linker, and a VL domain.
[0031] In some embodiments, an scFv comprises, in order, a VH domain, a linker, and a VL domain. In some embodiments, an scFv comprises, in order, a VH domain comprising or consisting of an amino acid sequence - 4 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) according to SEQ ID NO: 24, 39, or 42, a linker, and a VL domain comprising or consisting of an amino acid sequence according to SEQ ID NO: 29 or 45.
[0032] In some embodiments, an scFv comprises, in order, a VL domain, a linker, and a VH domain. In some embodiments, an scFv comprises, in order, a VL domain comprising or consisting of an amino acid sequence according to SEQ ID NO: 29 or 45, a linker, and a VH domain comprising or consisting of an amino acid sequence according to SEQ ID NO: 24, 39, or 42.
[0033] In some embodiments, a linker comprises an amino acid sequence according to SEQ ID NO: 54, 57, 60, 63, 66, 69, or 72. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the linker and comprises or consists of a sequence according to SEQ ID NO: 55, 58, 61, 64, 67, 70, or 73.
[0034] In some embodiments, a linker comprises an amino acid sequence according to SEQ ID NO: 75. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the linker and comprises or consists of a sequence according to SEQ ID NO: 76.
[0035] In some embodiments, an immunoglobulin chain comprising a VH domain and a VL domain as described herein comprises one or more constant domains. In some embodiments, a VH domain and a VL domain are operably linked to one or more constant domains.
[0036] In some embodiments, an immunoglobulin chain comprises one or more constant domains, and a hinge domain is between the scFv and the one or more constant domains.
[0037] In some embodiments, one or more constant domains comprise a CH2 domain. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH2 domain.
[0038] In some embodiments, one or more constant domains comprise a CH3 domain. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH3 domain.
[0039] In some embodiments, one or more constant domains comprise a hinge domain. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the hinge domain.
[0040] In some embodiments, one or more constant domains comprise a CH1 domain. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes a CH1 domain.
[0041] According to the present disclosure, a CH2 domain of any of the embodiments above can comprise an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 104. In some embodiments, a CH2 domain comprises or consists of an amino acid sequence according to SEQ ID NO: 104.
[0042] In some embodiments, a ribonucleic acid sequence that encodes a CH2 domain comprises a ribonucleic acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to a ribonucleic acid sequence according to SEQ ID NO: 105. In some embodiments, a ribonucleic acid sequence that encodes the CH2 domain comprises or consists of a sequence according to SEQ ID NO: 105. - 5 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01)
[0043] In some embodiments, a CH2 domain comprises one or more substitution mutations. In some embodiments, one or more substitution mutations in a CH2 domain comprise or consist of G236A, A330L, I332E, or a combination thereof, and wherein the substitution mutation positions are according to EU numbering. In some embodiments, one or more substitution mutations in a CH2 domain comprise or consist of G236A, and wherein the substitution mutation positions are according to EU numbering. In some embodiments, one or more substitution mutations in a CH2 domain comprise or consist of I332E, and wherein the substitution mutation positions are according to EU numbering. In some embodiments, one or more substitution mutations in a CH2 domain comprise or consist of G236A and I332E, and wherein the substitution mutation positions are according to EU numbering. In some embodiments, one or more substitution mutations in a CH2 domain comprise or consist of G236A, A330L, and I332E, and wherein the substitution mutation positions are according to EU numbering.
[0044] In some embodiments, a CH2 domain comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 107. In some embodiments, a CH2 domain comprises or consists of an amino acid sequence according to SEQ ID NO: 107.
[0045] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes a CH2 domain with a ribonucleic acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to a ribonucleic acid sequence according to SEQ ID NO: 108. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes a CH2 domain and comprises or consists of a sequence according to SEQ ID NO: 108.
[0046] In some embodiments, a CH2 domain comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 110. In some embodiments, a CH2 domain comprises or consists of an amino acid sequence according to SEQ ID NO: 110.
[0047] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes a CH2 domain and has at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to a ribonucleic acid sequence according to SEQ ID NO: 111. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes a CH2 domain and comprises or consists of a sequence according to SEQ ID NO: 111.
[0048] In some embodiments, a CH2 domain comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 113. In some embodiments, a CH2 domain comprises or consists of an amino acid sequence according to SEQ ID NO: 113.
[0049] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes a CH2 domain and has at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to a ribonucleic acid sequence according to SEQ ID NO: 114. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes a CH2 domain and comprises or consists of a sequence according to SEQ ID NO: 114. - 6 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01)
[0050] In some embodiments, a CH2 domain comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 116. In some embodiments, a CH2 domain comprises or consists of an amino acid sequence according to SEQ ID NO: 116.
[0051] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH2 domain and has at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to a ribonucleic acid sequence according to SEQ ID NO: 117. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH2 domain and comprises or consists of a sequence according to SEQ ID NO: 117.
[0052] According to the present disclosure, a CH3 domain of any of the embodiments above can comprise an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 119. In some embodiments, a CH3 domain comprises or consists of an amino acid sequence according to SEQ ID NO: 119.
[0053] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH3 domain and has at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to a ribonucleic acid sequence according to SEQ ID NO: 120. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH3 domain and comprises or consists of a sequence according to SEQ ID NO: 120.
[0054] In some embodiments, a CH3 domain comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 122. In some embodiments, a CH3 domain comprises or consists of an amino acid sequence according to SEQ ID NO: 122.
[0055] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH3 domain and has at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to a ribonucleic acid sequence according to SEQ ID NO: 123. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH3 domain and comprises or consists of a sequence according to SEQ ID NO: 123.
[0056] In some embodiments, a CH3 domain comprises one or more substitution mutations. In some embodiments, one or more substitution mutations in a CH3 domain comprise or consist of M428L, N434S, or a combination thereof, and wherein the substitution mutation positions are according to EU numbering.
[0057] In some embodiments, a CH3 domain comprises or consists of an amino acid sequence according to SEQ ID NO: 74 or 77. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH3 domain and comprises or consists of a sequence according to SEQ ID NO: 75 or 78.
[0058] In some embodiments, a CH3 domain comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 149. In some embodiments, a CH3 domain comprises or consists of an amino acid sequence according to SEQ ID NO: 149. - 7 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01)
[0059] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH3 domain and has at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to a ribonucleic acid sequence according to SEQ ID NO: 150. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH3 domain and comprises or consists of a sequence according to SEQ ID NO: 150.
[0060] In some embodiments, a CH3 domain comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 152. In some embodiments, a CH3 domain comprises or consists of an amino acid sequence according to SEQ ID NO: 152.
[0061] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH3 domain and has at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to a ribonucleic acid sequence according to SEQ ID NO: 153. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH3 domain and comprises or consists of a sequence according to SEQ ID NO: 153.
[0062] In some embodiments, one or more substitution mutations in a CH3 domain comprise or consist of Y349C, T366S, L368A, Y407V, or a combination thereof, and wherein the substitution mutation positions are according to EU numbering. In some embodiments, one or more substitution mutations in a CH3 domain comprise or consist of Y349C, T366S, L368A, Y407V, M428L, N434S, or a combination thereof, and wherein the substitution mutation positions are according to EU numbering. In some embodiments, one or more substitution mutations in a CH3 domain comprise or consist of Y349C, T366S, L368A, Y407V, M428L, and N434S, and wherein the substitution mutation positions are according to EU numbering.
[0063] In some embodiments, a CH3 domain comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 125. In some embodiments, a CH3 domain comprises or consists of an amino acid sequence according to SEQ ID NO: 125.
[0064] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH3 domain and has at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to a ribonucleic acid sequence according to SEQ ID NO: 126. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH3 domain and comprises or consists of a sequence according to SEQ ID NO: 126.
[0065] In some embodiments, a CH3 domain comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 128. In some embodiments, a CH3 domain comprises or consists of an amino acid sequence according to SEQ ID NO: 128.
[0066] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH3 domain and has at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to a ribonucleic acid sequence according to SEQ ID NO: 129. In some embodiments, a - 8 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH3 domain and comprises or consists of a sequence according to SEQ ID NO: 129.
[0067] In some embodiments, a CH3 domain comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 131. In some embodiments, a CH3 domain comprises or consists of an amino acid sequence according to SEQ ID NO: 131.
[0068] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH3 domain and has at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to a ribonucleic acid sequence according to SEQ ID NO: 132. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH3 domain and comprises or consists of a sequence according to SEQ ID NO: 131.
[0069] In some embodiments, a CH3 domain comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 134. In some embodiments, a CH3 domain comprises or consists of an amino acid sequence according to SEQ ID NO: 134.
[0070] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH3 domain and has at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to a ribonucleic acid sequence according to SEQ ID NO: 135. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH3 domain and comprises or consists of a sequence according to SEQ ID NO: 135.
[0071] In some embodiments, one or more substitution mutations in a CH3 domain comprise or consist of S354C, T366W, or a combination thereof, and wherein the substitution mutation positions are according to EU numbering. In some embodiments, one or more substitution mutations in a CH3 domain comprise or consist of S354C, T366W, M428L, N434S, or a combination thereof, and wherein the substitution mutation positions are according to EU numbering. In some embodiments, one or more substitution mutations in a CH3 domain comprise or consist of S354C, T366W, M428L, and N434S, and wherein the substitution mutation positions are according to EU numbering.
[0072] In some embodiments, a CH3 domain comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 137. In some embodiments, a CH3 domain comprises or consists of an amino acid sequence according to SEQ ID NO: 137.
[0073] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH3 domain and has at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to a ribonucleic acid sequence according to SEQ ID NO: 138. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH3 domain and comprises or consists of a sequence according to SEQ ID NO: 138. - 9 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01)
[0074] In some embodiments, a CH3 domain comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 140. In some embodiments, a CH3 domain comprises or consists of an amino acid sequence according to SEQ ID NO: 140.
[0075] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH3 domain and has at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to a ribonucleic acid sequence according to SEQ ID NO: 141. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH3 domain and comprises or consists of a sequence according to SEQ ID NO: 141.
[0076] In some embodiments, a CH3 domain comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 143. In some embodiments, a CH3 domain comprises or consists of an amino acid sequence according to SEQ ID NO: 143.
[0077] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH3 domain and has at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to a ribonucleic acid sequence according to SEQ ID NO: 144. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH3 domain and comprises or consists of a sequence according to SEQ ID NO: 144.
[0078] In some embodiments, a CH3 domain comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 146. In some embodiments, a CH3 domain comprises or consists of an amino acid sequence according to SEQ ID NO: 146.
[0079] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH3 domain and has at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to a ribonucleic acid sequence according to SEQ ID NO: 147. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH3 domain and comprises or consists of a sequence according to SEQ ID NO: 147.
[0080] According to the present disclosure, a hinge domain of any of the embodiments above can comprise an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 170. In some embodiments, a hinge domain comprises or consists of an amino acid sequence according to SEQ ID NO: 170.
[0081] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the hinge domain and has at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to a ribonucleic acid sequence according to SEQ ID NO: 171. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the hinge domain and comprises or consists of a sequence according to SEQ ID NO: 171. - 10 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01)
[0082] In some embodiments, a hinge domain comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 173. In some embodiments, a hinge domain comprises or consists of an amino acid sequence according to SEQ ID NO: 173.
[0083] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the hinge domain and has at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to a ribonucleic acid sequence according to SEQ ID NO: 174. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the hinge domain and comprises or consists of a sequence according to SEQ ID NO: 174.
[0084] In some embodiments, a hinge domain comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 176. In some embodiments, a hinge domain comprises or consists of an amino acid sequence according to SEQ ID NO: 176.
[0085] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the hinge domain and has at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to a ribonucleic acid sequence according to SEQ ID NO: 177. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the hinge domain and comprises or consists of a sequence according to SEQ ID NO: 177.
[0086] According to the present disclosure, a CH1 domain of any of the embodiments above can comprise an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 86. In some embodiments, a CH1 domain comprises or consists of an amino acid sequence according to SEQ ID NO: 86.
[0087] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes a CH1 domain and has at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to a ribonucleic acid sequence according to SEQ ID NO: 87. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes a CH1 domain and comprises or consists of a sequence according to SEQ ID NO: 87.
[0088] In some embodiments, a CH1 domain comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 89. In some embodiments, a CH1 domain comprises or consists of an amino acid sequence according to SEQ ID NO: 89.
[0089] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes a CH1 domain and has at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to a ribonucleic acid sequence according to SEQ ID NO: 90. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes a CH1 domain and comprises or consists of a sequence according to SEQ ID NO: 90. - 11 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01)
[0090] In some embodiments, a CH1 domain comprises one or more substitution mutations. In some embodiments, one or more substitution mutations in a CH1 domain comprise or consist of K147E, K213D, or a combination thereof, and wherein the substitution mutation positions are according to EU numbering.
[0091] In some embodiments, a CH1 domain comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 92. In some embodiments, a CH1 domain comprises or consists of an amino acid sequence according to SEQ ID NO: 92.
[0092] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH1 domain and has at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to a ribonucleic acid sequence according to SEQ ID NO: 93. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH1 domain and comprises or consists of a sequence according to SEQ ID NO: 93.
[0093] In some embodiments, a CH1 domain comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 95. In some embodiments, a CH1 domain comprises or consists of an amino acid sequence according to SEQ ID NO: 95.
[0094] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH1 domain and has at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to a ribonucleic acid sequence according to SEQ ID NO: 96. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH1 domain and comprises or consists of a sequence according to SEQ ID NO: 96.
[0095] In some embodiments, a CH1 domain comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 98. In some embodiments, a CH1 domain comprises or consists of an amino acid sequence according to SEQ ID NO: 98.
[0096] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH1 domain and has at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to a ribonucleic acid sequence according to SEQ ID NO: 99. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH1 domain and comprises or consists of a sequence according to SEQ ID NO: 99.
[0097] In some embodiments, a CH1 domain comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 101. In some embodiments, a CH1 domain comprises or consists of an amino acid sequence according to SEQ ID NO: 101.
[0098] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH1 domain and has at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to a ribonucleic acid sequence according to SEQ ID NO: 102. In some embodiments, a - 12 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) polyribonucleotide comprises a ribonucleic acid sequence that encodes the CH1 domain and comprises or consists of a sequence according to SEQ ID NO: 102.
[0099] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the light chain constant domain CL domain comprises one or more substitution mutations. In some embodiments, one or more substitution mutations in a CL domain comprise or consist of Q124E, and wherein the substitution mutation positions are according to EU numbering. In some embodiments, one or more substitution mutations in a CL domain comprise or consist of R108A, T109S, or a combination thereof, and wherein the substitution mutation positions are according to EU numbering. In some embodiments, one or more substitution mutations in a CL domain comprise or consist of R108A, T109S, Q124E or a combination thereof, and wherein the substitution mutation positions are according to EU numbering.
[0100] In some embodiments, a CL domain comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 155. In some embodiments, a CL domain comprises or consists of an amino acid sequence according to SEQ ID NO: 155.
[0101] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the light chain constant domain and has at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to a ribonucleic acid sequence according to SEQ ID NO: 156. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the light chain constant domain and comprises or consists of a sequence according to SEQ ID NO: 156.
[0102] In some embodiments, a CL domain comprises a lambda light chain domain. According to the present disclosure, a CL domain of any of the embodiments above can comprise an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 158. In some embodiments, a CL domain of any of the embodiments above can comprise or consists of an amino acid sequence according to SEQ ID NO: 158.
[0103] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CL domain and has at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to a ribonucleic acid sequence according to SEQ ID NO: 159. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the CL domain and comprises or consists of a sequence according to SEQ ID NO: 159.
[0104] In some embodiments, a CL domain comprises one or more substitution mutations. In some embodiments, one or more substitution mutations in a CL domain comprise or consist of E123K, Q124R, or a combination thereof, and wherein the substitution mutation positions are according to EU numbering.
[0105] In some embodiments, a CL domain comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 161. In some embodiments, a CL domain comprises or consists of an amino acid sequence according to SEQ ID NO: 161. - 13 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01)
[0106] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the light chain constant domain and has at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to a ribonucleic acid sequence according to SEQ ID NO: 162. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the light chain constant domain and comprises or consists of a sequence according to SEQ ID NO: 162.
[0107] In some embodiments, a one or more substitution mutations in a CL domain comprise or consist of E123R, Q124K, or a combination thereof, and wherein the substitution mutation positions are according to EU numbering.
[0108] In some embodiments, a CL domain comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 164. In some embodiments, a CL domain comprises or consists of an amino acid sequence according to SEQ ID NO: 164.
[0109] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the light chain constant domain and has at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to a ribonucleic acid sequence according to SEQ ID NO: 165. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the light chain constant domain and comprises or consists of a sequence according to SEQ ID NO: 165.
[0110] In some embodiments, a CL domain comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 167. In some embodiments, a CL domain comprises or consists of an amino acid sequence according to SEQ ID NO: 167.
[0111] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the light chain constant domain and has at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to a ribonucleic acid sequence according to SEQ ID NO: 168. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that encodes the light chain constant domain and comprises or consists of a sequence according to SEQ ID NO: 168.
[0112] In some embodiments, a polyribonucleotide as provided herein encodes an immunoglobulin chain, wherein: (i) the polyribonucleotide comprises a ribonucleic acid sequence that encodes a CH2 domain, and the CH2 domain comprises one or more substitution mutations, wherein the one or more substitution mutations comprise or consist of G236A, A330L, I332E, or a combination thereof, (ii) the polyribonucleotide comprises a ribonucleic acid sequence that encodes a CH3 domain, and the CH3 domain comprises one or more substitution mutations, wherein the one or more substitution mutations comprise or consist of Y349C, S354C, T366S, T366W, L368A, Y407V, M428L, N434S, or a combination thereof, (iii) the polyribonucleotide comprises a ribonucleic acid sequence that encodes a CH1 domain, and the CH1 domain comprises one or more substitution mutations, wherein the one or more substitution mutations comprise or consist of K147E, K213D, or a combination thereof, - 14 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) (iv) the polyribonucleotide comprises a ribonucleic acid sequence that encodes a CL domain, and the CL domain comprises one or more substitution mutations, wherein the one or more substitution mutations comprise or consist of R108A, T109S, E123K, E123R, Q124E, Q124K, Q124R, or a combination thereof, or (v) a combination thereof; wherein the substitution mutation positions are according to EU numbering.
[0113] In some embodiments, a polyribonucleotide as provided herein encodes an immunoglobulin chain that comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 252. In some embodiments, a polyribonucleotide as provided herein encodes an immunoglobulin chain that comprises or consists of an amino acid sequence according to SEQ ID NO: 252.
[0114] In some embodiments, a polyribonucleotide as provided herein comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to a ribonucleic acid sequence according to SEQ ID NO: 253. In some embodiments, a polyribonucleotide comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 253.
[0115] In some embodiments, a polyribonucleotide as provided herein encodes an immunoglobulin chain that comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 354. In some embodiments, a polyribonucleotide as provided herein encodes an immunoglobulin chain that comprises or consists of an amino acid sequence according to SEQ ID NO: 354.
[0116] In some embodiments, a polyribonucleotide as provided herein comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to SEQ ID NO: 355. In some embodiments, a polyribonucleotide as provided herein comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 355.
[0117] In some embodiments, a polyribonucleotide as provided herein encodes an immunoglobulin chain that comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 456. In some embodiments, a polyribonucleotide as provided herein encodes an immunoglobulin chain that comprises or consists of an amino acid sequence according to SEQ ID NO: 456.
[0118] In some embodiments, a polyribonucleotide as provided herein comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to SEQ ID NO: 457. In some embodiments, a polyribonucleotide as provided herein comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 457.
[0119] In some embodiments, a polyribonucleotide as provided herein encodes an immunoglobulin chain that comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 560. In some embodiments, a polyribonucleotide as provided herein encodes an immunoglobulin chain that comprises or consists of an amino acid sequence according to SEQ ID NO: 560. - 15 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01)
[0120] In some embodiments, a polyribonucleotide as provided herein comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to SEQ ID NO: 561. In some embodiments, a polyribonucleotide as provided herein comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 561.
[0121] In some embodiments, a polyribonucleotide as provided herein encodes an immunoglobulin chain that comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 700. In some embodiments, a polyribonucleotide as provided herein encodes an immunoglobulin chain that comprises or consists of an amino acid sequence according to SEQ ID NO: 700.
[0122] In some embodiments, a polyribonucleotide as provided herein comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to SEQ ID NO: 701. In some embodiments, a polyribonucleotide as provided herein comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 701.
[0123] In some embodiments, a polyribonucleotide as provided herein encodes an immunoglobulin chain that comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 774. In some embodiments, a polyribonucleotide as provided herein encodes an immunoglobulin chain that comprises or consists of an amino acid sequence according to SEQ ID NO: 774.
[0124] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to SEQ ID NO: 775. In some embodiments, a polyribonucleotide as provided herein comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 775.
[0125] In some embodiments, a polyribonucleotide as provided herein encodes an immunoglobulin chain that comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 780. In some embodiments, a polyribonucleotide as provided herein encodes an immunoglobulin chain that comprises or consists of an amino acid sequence according to SEQ ID NO: 780.
[0126] In some embodiments, a polyribonucleotide as provided herein comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to SEQ ID NO: 781. In some embodiments, a polyribonucleotide as provided herein comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 781.
[0127] In some embodiments, a polyribonucleotide as provided herein encodes an immunoglobulin chain that comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 852. In some embodiments, a polyribonucleotide as provided herein encodes an immunoglobulin chain that comprises or consists of an amino acid sequence according to SEQ ID NO: 852. - 16 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01)
[0128] In some embodiments, a polyribonucleotide as provided herein comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to SEQ ID NO: 853. In some embodiments, a polyribonucleotide as provided herein comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 853.
[0129] In some embodiments, a polyribonucleotide as provided herein encodes an immunoglobulin chain that comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 930. In some embodiments, a polyribonucleotide as provided herein encodes an immunoglobulin chain that comprises or consists of an amino acid sequence according to SEQ ID NO: 930.
[0130] In some embodiments, a polyribonucleotide as provided herein comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to SEQ ID NO: 931. In some embodiments, a polyribonucleotide as provided herein comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 931.
[0131] In some embodiments, a polyribonucleotide as provided herein encodes an immunoglobulin chain that comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 1008. In some embodiments, a polyribonucleotide as provided herein encodes an immunoglobulin chain that comprises or consists of an amino acid sequence according to SEQ ID NO: 1008.
[0132] In some embodiments, a polyribonucleotide as provided herein comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to SEQ ID NO: 1009. In some embodiments, a polyribonucleotide as provided herein comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 1009.
[0133] In some embodiments, a polyribonucleotide as provided herein encodes an immunoglobulin chain that comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 1044. In some embodiments, a polyribonucleotide as provided herein encodes an immunoglobulin chain that comprises or consists of an amino acid sequence according to SEQ ID NO: 1044.
[0134] In some embodiments, a polyribonucleotide as provided herein comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to SEQ ID NO: 1045. In some embodiments, a polyribonucleotide as provided herein comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 1045.
[0135] In some embodiments, a polyribonucleotide as provided herein encodes an immunoglobulin chain that comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 1047. In some embodiments, a polyribonucleotide as provided herein encodes an immunoglobulin chain that comprises or consists of an amino acid sequence according to SEQ ID NO: 1047. - 17 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01)
[0136] In some embodiments, a polyribonucleotide as provided herein comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to SEQ ID NO: 1048. In some embodiments, a polyribonucleotide as provided herein comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 1048.
[0137] In some embodiments, a polyribonucleotide as provided herein encodes an immunoglobulin chain that comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 1053. In some embodiments, a polyribonucleotide as provided herein encodes an immunoglobulin chain that comprises or consists of an amino acid sequence according to SEQ ID NO: 1053.
[0138] In some embodiments, a polyribonucleotide as provided herein comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to SEQ ID NO: 1054. In some embodiments, a polyribonucleotide as provided herein comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 1054.
[0139] In some embodiments, a polyribonucleotide as provided herein encodes an immunoglobulin chain that comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 1077. In some embodiments, a polyribonucleotide as provided herein encodes an immunoglobulin chain that comprises or consists of an amino acid sequence according to SEQ ID NO: 1077.
[0140] In some embodiments, a polyribonucleotide as provided herein comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to SEQ ID NO: 1078. In some embodiments, a polyribonucleotide as provided herein polyribonucleotide comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 1078.
[0141] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence encoding a secretion signal.
[0142] In some embodiments, a secretion signal comprises a ribonucleic acid sequence according to SEQ ID NO: 2, 4, 48, 50, or 52.
[0143] In some embodiments, a polyribonucleotide comprises one or more non-coding sequence elements.
[0144] In some embodiments, one or more non-coding sequence elements enhances RNA stability and / or translation efficiency.
[0145] In some embodiments, one or more non-coding sequence elements comprise a 3' untranslated region (UTR), a 5' UTR, a 5'-cap, a polyadenine (polyA) tail, or combination thereof.
[0146] In some embodiments, a polyA tail is or comprises a modified polyA sequence, preferably an interrupted polyA tail. - 18 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01)
[0147] In some embodiments, a polyA tail comprises or consists of a sequence that is at least 90%, at least 95%, or at least 99% identical to SEQ ID NO: 180.
[0148] In some embodiments, a 3' UTR comprises or consists of a nucleic acid sequence that is at least 90%, at least 95%, or at least 99% identical to SEQ ID NO: 79 or 81.
[0149] In some embodiments, a 5' UTR comprises or consists of a nucleic acid sequence that is at least 90%, at least 95%, or at least 99% identical to SEQ ID NO: 83 or 85.
[0150] In some embodiments, a 5'-cap is (m27,3’-O)Gppp(m2’-O)ApG.
[0151] In some embodiments, a polyribonucleotide comprises one or more modified ribonucleotides. In some embodiments, one or more modified ribonucleotides comprise pseudouridine.
[0152] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to SEQ ID NO: 1087. In some embodiments, a polyribonucleotide comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 1087.
[0153] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to SEQ ID NO: 1135. In some embodiments, a polyribonucleotide comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 1135.
[0154] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to SEQ ID NO: 1183. In some embodiments, a polyribonucleotide comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 1183.
[0155] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to SEQ ID NO: 1231. In some embodiments, a polyribonucleotide comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 1231.
[0156] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to SEQ ID NO: 1295. In some embodiments, a polyribonucleotide comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 1295.
[0157] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to SEQ ID NO: 1343. In some embodiments, a polyribonucleotide comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 1343.
[0158] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic - 19 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) acid sequence according to SEQ ID NO: 1353. In some embodiments, a polyribonucleotide comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 1353.
[0159] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to SEQ ID NO: 1375. In some embodiments, a polyribonucleotide comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 1375.
[0160] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to SEQ ID NO: 1407. In some embodiments, a polyribonucleotide comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 1407.
[0161] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to SEQ ID NO: 1439. In some embodiments, a polyribonucleotide comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 1439.
[0162] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to SEQ ID NO: 1470. In some embodiments, a polyribonucleotide comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 1470.
[0163] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to SEQ ID NO: 1471. In some embodiments, a polyribonucleotide comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 1471.
[0164] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to SEQ ID NO: 1476. In some embodiments, a polyribonucleotide comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 1476.
[0165] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to SEQ ID NO: 1483. In some embodiments, a polyribonucleotide comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 1483.
[0166] In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to any one of SEQ ID NOs: 1086-1483. In some embodiments, a polyribonucleotide comprises or consists of a ribonucleic acid sequence according to any one of SEQ ID NO: 1086-1483.
[0167] In some embodiments, a polyribonucleotide is a non-natural polyribonucleotide.
[0168] In some embodiments, a polyribonucleotide is an engineered polyribonucleotide. - 20 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01)
[0169] In some embodiments, a polyribonucleotide is an isolated polyribonucleotide.
[0170] Among other things, the present disclosure provides composition comprising one or more polyribonucleotides as described herein.
[0171] In some embodiments, a composition comprises or consists of a polyribonucleotide encoding an immunoglobulin chain that comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 252 and a polyribonucleotide encoding an immunoglobulin chain that comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 1044.
[0172] In some embodiments, a composition comprises or consists of a polyribonucleotide that comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to any one of SEQ ID NO: 253 and a polyribonucleotide that comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to any one of SEQ ID NO: 1045.
[0173] In some embodiments, a composition comprises or consists of a polyribonucleotide encoding an immunoglobulin chain that comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 354 and a polyribonucleotide encoding an immunoglobulin chain that comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 1044.
[0174] In some embodiments, a composition comprises or consists of a polyribonucleotide that comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to any one of SEQ ID NO: 355 and a polyribonucleotide that comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to any one of SEQ ID NO: 1045.
[0175] In some embodiments, a composition comprises or consists of a polyribonucleotide encoding an immunoglobulin chain that comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 456 and a polyribonucleotide encoding an immunoglobulin chain that comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 1044.
[0176] In some embodiments, a composition comprises or consists of a polyribonucleotide that comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to any one of SEQ ID NO: 457 and a polyribonucleotide that comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at - 21 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to any one of SEQ ID NO: 1045.
[0177] In some embodiments, a composition comprises or consists of a polyribonucleotide encoding an immunoglobulin chain that comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 252 and a polyribonucleotide encoding an immunoglobulin chain that comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 1047.
[0178] In some embodiments, a composition comprises or consists of a polyribonucleotide that comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to any one of SEQ ID NO: 253 and a polyribonucleotide that comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to any one of SEQ ID NO: 1048.
[0179] In some embodiments, a composition comprises or consists of a polyribonucleotide encoding an immunoglobulin chain that comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 354 and a polyribonucleotide encoding an immunoglobulin chain that comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 1047.
[0180] In some embodiments, a composition comprises or consists of a polyribonucleotide that comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to any one of SEQ ID NO: 355 and a polyribonucleotide that comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to any one of SEQ ID NO: 1048.
[0181] In some embodiments, a composition comprises or consists of a polyribonucleotide encoding an immunoglobulin chain that comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 456 and a polyribonucleotide encoding an immunoglobulin chain that comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 1047.
[0182] In some embodiments, a composition comprises or consists of a polyribonucleotide that comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to any one of SEQ ID NO: 457 and a polyribonucleotide that comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at - 22 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to any one of SEQ ID NO: 1048.
[0183] In some embodiments, a composition comprises or consists of a polyribonucleotide encoding an immunoglobulin chain that comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 560 and a polyribonucleotide encoding an immunoglobulin chain that comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 1053.
[0184] In some embodiments, a composition comprises or consists of a polyribonucleotide that comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to any one of SEQ ID NO: 561 and a polyribonucleotide that comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to any one of SEQ ID NO: 1054.
[0185] In some embodiments, a composition comprises or consists of a polyribonucleotide encoding an immunoglobulin chain that comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 700 and a polyribonucleotide encoding an immunoglobulin chain that comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to an amino acid sequence according to SEQ ID NO: 1077.
[0186] In some embodiments, a composition comprises or consists of a polyribonucleotide that comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to any one of SEQ ID NO: 701 and a polyribonucleotide that comprises a ribonucleic acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a ribonucleic acid sequence according to any one of SEQ ID NO: 1078.
[0187] In some embodiments, a composition further comprises lipid nanoparticles, polyplexes (PLX), lipidated polyplexes (LPLX), or liposomes, where the one or more polyribonucleotides are fully or partially encapsulated within the lipid nanoparticles, polyplexes (PLX), lipidated polyplexes (LPLX), or liposomes.
[0188] In some embodiments, a composition further comprises lipid nanoparticles, where the one or more polyribonucleotides are encapsulated within the lipid nanoparticles.
[0189] In some embodiments, lipid nanoparticles target liver cells.
[0190] In some embodiments, lipid nanoparticles target secondary lymphoid organ cells.
[0191] In some embodiments, lipid nanoparticles target lung cells.
[0192] In some embodiments, lipid nanoparticles are cationic lipid nanoparticles. - 23 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01)
[0193] In some embodiments, lipid nanoparticles each comprise a polymer-conjugated lipid, a cationic lipid, and one or more neutral lipids.
[0194] In some embodiments, a polymer-conjugated lipid comprises a PEG-conjugated lipid.
[0195] In some embodiments, a polymer-conjugated lipid comprises 2-[(polyethylene glycol)-2000]-N,N- ditetradecylacetamide.
[0196] In some embodiments, one or more neutral lipids comprise 1,2-Distearoyl-sn-glycero-3- phosphocholine (DPSC).
[0197] In some embodiments, one or more neutral lipids comprise cholesterol.
[0198] In some embodiments, a cationic lipid comprises ((3-hydroxypropyl)azanediyl)bis(nonane-9,1-diyl) bis(2-butyloctanoate).
[0199] In some embodiments, lipid nanoparticles each comprise 2-[(polyethylene glycol)-2000]-N,N- ditetradecylacetamide, DPSC, cholesterol, and ((3-hydroxypropyl)azanediyl)bis(nonane-9,1-diyl) bis(2- butyloctanoate).
[0200] In some embodiments, lipid nanoparticles comprise the polymer-conjugated lipid at about 1-2.5 mol% of the total lipids, the cationic lipid at 35-65 mol% of the total lipids, and the one or more neutral lipids are present in 35-65 mol% of the total lipids.
[0201] In some embodiments, lipid nanoparticles have an average diameter of about 50-150 nm.
[0202] The present disclosure also provides pharmaceutical compositions. In some embodiments, a pharmaceutical composition comprises a composition provided herein and at least one pharmaceutically acceptable excipient.
[0203] In some embodiments, a pharmaceutical comprises a cryoprotectant. In some embodiments, a pharmaceutical comprises an aqueous buffered solution.
[0204] Among other things, the present disclosure provides methods.
[0205] In some embodiments, a method comprises administering a pharmaceutical composition provided herein to a subject.
[0206] In some embodiments, a pharmaceutical composition provided herein is for use in the treatment of HIV comprising administering the pharmaceutical composition to a subject.
[0207] In some embodiments, a pharmaceutical composition provided herein is for use in the prevention of HIV comprising administering the pharmaceutical composition to a subject.
[0208] In some embodiments, a method or pharmaceutical composition for use provided herein, comprises administering the pharmaceutical composition to the subject, which results in expression in the subject of an immunoglobulin chain of antibody agent, an antibody agent, or both.
[0209] In some embodiments, an immunoglobulin chain of antibody agent, the antibody agent, or both is expressed in the subject at a titer of at least 1 µg / ml in plasma or serum. - 24 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01)
[0210] In some embodiments, an antibody agent exhibits a geometric mean IC50 of five neutralized strains of less than 0.3 μg / ml against the neutralized strains of a global reference panel when tested in the TZM-bl cell pseudovirus neutralization assay at antibody agent concentrations up to 25 μg / ml.
[0211] In some embodiments, an antibody agent is capable of neutralizing one or more HIV strains when tested in the TZM-bl cell pseudovirus neutralization assay at antibody agent concentrations up to 25 μg / ml.
[0212] In some embodiments, an antibody agent is capable of neutralizing one or more HIV strains at a level that is within 3-fold of a level of an equivalent amount of recombinant benchmark antibody.
[0213] In some embodiments, a recombinant benchmark antibody is an unmodified wild-type IgG antibody comprising the same HCDR1, HCDR2, HCDR2, LCDR1, LCDR2, and LCDR3 as the antibody agent.
[0214] In some embodiments, administering the pharmaceutical composition to the subject comprises administering one or more doses of the pharmaceutical composition to the subject. In some embodiments, one or more doses of the pharmaceutical composition are administered to the subject weekly. In some embodiments, one or more doses of the pharmaceutical composition are administered to the subject bi-weekly.
[0215] In some embodiments, a pharmaceutical composition is administered intravenously. In some embodiments, a pharmaceutical composition is administered intramuscularly. In some embodiments, a pharmaceutical composition is administered subcutaneously.
[0216] In some embodiments, a subject has or is at risk of developing an HIV infection.
[0217] In some embodiments, a method is a method of treating an HIV infection.
[0218] In some embodiments, a method is a method of preventing an HIV infection.
[0219] Also provided herein are uses of polyribonucleotides, compositions, and pharmaceutical compositions described herein.
[0220] In some embodiments, provided are uses of a composition or pharmaceutical composition as provided herein for the treatment of HIV in a subject.
[0221] In some embodiments, provided are uses of a composition or pharmaceutical composition as provided herein for the prevention of HIV in a subject.
[0222] In some embodiments, a subject has or is at risk of developing an HIV infection.
[0223] Further, the present disclosure provides methods of producing an antibody agent. In some embodiments, a method comprises administering to cells a composition or pharmaceutical composition as provided herein so that the cells express and secrete the antibody agent.
[0224] In some embodiments, cells are liver cells.
[0225] In some embodiments, cells are in a subject.
[0226] In some embodiments, cells are ex vivo cells. - 25 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01)
[0227] In some embodiments, an antibody agent is produced at a therapeutically relevant plasma concentration or a therapeutically relevant serum concentration. In some embodiments, therapeutically relevant plasma concentration or the therapeutically relevant serum concentration is at least 1µg / ml.
[0228] The present disclosure further provides methods of determining one or more features of an antibody agent expressed from a polyribonucleotide, a composition or a pharmaceutical composition provided herein. In some embodiments, a polyribonucleotide, a composition or a pharmaceutical composition provided herein are introduced into cells. In some embodiments, one or more features comprises: (i) protein expression level of the antibody agent; (ii) binding specificity of the antibody agent to the membrane proximal external region (MPER) binding site of HIV; (iii) efficacy of the antibody agent to mediate target cell death through antibody-dependent cellular cytotoxicity (ADCC); and (iv) efficacy of the antibody agent to mediate target cell death through complement dependent cytotoxicity (CDC).
[0229] The present disclosure further provides methods comprising contacting cells with a polyribonucleotide, a composition or a pharmaceutical composition provided herein. In some embodiments, a method further comprises detecting the antibody agent produced by the cells.
[0230] In some embodiments, cells are liver cells.
[0231] In some embodiments, the step of determining comprises comparing the one or more features of the antibody agent with that of a reference antibody that specifically binds to a MPER binding site of HIV.
[0232] In some embodiments, the step of determining comprises assessing the protein expression level of the antibody agent above a threshold level.
[0233] In some embodiments, a threshold level is a level that is sufficient to induce ADCC.
[0234] In some embodiments, the step of determining comprises assessing binding of the antibody agent to a MPES binding site of HIV.
[0235] In some embodiments, the step of determining comprises assessing the antibody agent in the TZM-bl cell pseudovirus neutralization assay at antibody agent concentrations up to 25 μg / ml.
[0236] In some embodiments, cells are present in a subject.
[0237] In some embodiments, cells are ex vivo cells.
[0238] In some embodiments, one or more features include antibody level in one or more tissues in the subject.
[0239] The present disclosure also provides methods of manufacture. In some embodiments, a method comprises (a) determining one or more features of a polyribonucleotide, a composition or a pharmaceutical composition provided herein, which one or more features comprise or consist of: (i) length and / or sequence of the polyribonucleotide; (ii) integrity of the polyribonucleotide; (iii) presence and / or location of one or more chemical moieties of the polyribonucleotide; (iv) extent of expression of the antibody agent when the polyribonucleotide is introduced into a cell; - 26 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) (v) stability of the polyribonucleotide or composition thereof; (vi) level of antibody agent in a biological sample from an organism into which the polyribonucleotide has been introduced; (vii) binding specificity of the antibody agent expressed from the polyribonucleotide, optionally to a MPER binding site of HIV; (viii) efficacy of the antibody agent to mediate target cell death through ADCC; (ix) efficacy of the antibody agent to mediate target cell death through complement dependent cytotoxicity (CDC); (x) lipid identity and amount / concentration within the composition; (xi) size of lipid nanoparticles within the composition; (xii) polydispersity of lipid nanoparticles within the composition; (xiii) amount / concentration of the polyribonucleotide within the composition; (xiv) extent of encapsulation of the polyribonucleotide within lipid nanoparticles; (xv) a level of double stranded RNA; and (xvi) combinations thereof; (b) comparing the one or more features of the polyribonucleotide with that of an appropriate reference standard; and (c) (i) designating the polyribonucleotide or composition thereof for one or more further steps of manufacturing and / or distribution if the comparison demonstrates that the polyribonucleotide or composition thereof meets or exceeds the reference standard; or (c) (ii) taking an alternative action if the comparison demonstrates that the polyribonucleotide or composition thereof does not meet or exceed the reference standard.
[0240] In some embodiments, a polyribonucleotide is assessed, and the one or more further steps of step (C)(i) are or comprise at least formulation of the polyribonucleotide.
[0241] In some embodiments, a composition or the pharmaceutical composition is assessed, and the one or more further steps of step (C)(i) are or comprise release and distribution of the composition or the pharmaceutical composition.
[0242] The present disclosure thus provides technologies that allow for multiple anti-HIV antibodies to be expressed in a subject, increasing the breadth and potency of the anti-HIV antibodies present in a subject at one time and decreasing the likelihood of viral escape.
[0243] The provided technologies, including exemplary polyribonucleotides, compositions comprising such polyribonucleotides, and methods of making and using such polyribonucleotides, are described in more detail herein. BRIEF DESCRIPTION OF THE DRAWING
[0244] Figs.1A-1B shows a schematic of the HIV genome (Fig.1A) and the structure of a HIV virion particle (Fig.1B). Drawings modified from Musumeci et al., 2015 Molecules, which is incorporated herein by reference in its entirety. - 27 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01)
[0245] Fig.2 shows potential epitope regions on an HIV virion particle to which an antibody agent (e.g., a broadly neutralizing antibody (bNAb) or variant thereof) can bind. Drawing modified from McCoy and Burton, 2017 Immunol Rev., which is incorporated herein by reference in its entirety.
[0246] Fig.3 shows an exemplary therapeutic strategy utilizing RiboMab technology as described herein for delivery and expression of anti-HIV RibobNAbs.
[0247] Figs.4A-E shows exemplary formats of 10E8 RibobNAbs as described herein. Exemplary formats may include IgG (Fig.4A), CrossMabCH1-CLx(Fig.4B), CrossMabCH1-CLcv(Fig.4C), or various orientations / linkers of scFv-Fc RibobNAbs (Figd.4D and 4E). “10E8” as used herein, is meant to refer to 10E8 and variants disclosed herein (e.g., 10E8, 10E8v4, and 10E8v4-5R-100cF). Fig.4 discloses SEQ ID NOs: 54 and 75, respectively, in order of appearance.
[0248] Figs.5A-5D shows exemplary Fc modifications of 10E8 RibobNAbs as described herein. Exemplary RibobNAb formats may include an unmodified Fc domain (Fig.5A), or modifications shown in 5B-D, including GAALIE, / GAIE / GA / IE (Fig.5B), L / S, (Fig.5C), and / or knob-into-holes RibobNAbs (Fig.5D).
[0249] Figs.6A-6B shows schematics of exemplary polyribonucleotides which encode a heavy chain (Fig. 6A) and a light chain (Fig.6B) of an exemplary 10E8 IgG1 antibody agent.
[0250] Fig.7 shows % breadth and potency of various broadly neutralizing antibodies to HIV, including 10E8, as tested against a panel of 109 pseudoviruses.
[0251] Figs.8A-8B shows schematics of exemplary polyribonucleotides which encode scFv-Fc 10E8 antibody agents: 10E8 scFv-Fc VH-LL4 / LL5-VL (Fig.8A) and 10E8 scFv-Fc VL-LL4 / LL5-VH (Fig.8B).
[0252] Fig.9A-9B shows schematics of exemplary polyribonucleotides which encode heavy chain (Fig. 9A) and light chain (Fig.9B) of an exemplary 10E8 CrossMabCH1-CLxantibody agent.
[0253] Fig.10A-10B shows schematics of exemplary polyribonucleotides which encode heavy chain (Fig. 10A) and light chain (Fig.10B) of an exemplary 10E8 CrossMabCH1-CLcvantibody agent.
[0254] Fig.11 shows exemplary concentrations of 10E8, 10E8v4, and 10E8v4-5R-100cF scFv-Fc L / S RibobNAbs (e.g., VH-LL4-VL, VL-LL5-VH, VH-LL5-VL, and VL-LL4-VH) compared to a control RiboMab and a parental IgG as determined by Gyros ELISA from Example 5 and Example 6.
[0255] Fig.12 shows exemplary Western Blot analysis of 10E8, 10E8v4, and 10E8v4-5R-100cF10E8v4 IgG and scFv-Fc L / S RibobNAbs compared to a control RiboMab under nonreducing and reducing conditions from Examples 5-6.
[0256] FIG.13 shows exemplary results from a pseudovirus viral neutralization test (pVNT) where TSM.b1 cells were exposed to 10E8, 10E8v4, and 10E8v4-5R-100cF IgG L / S IgG RibobNAbs and pseudoviruses TRO.11, Du156.12, RHPA4259.7, ZM249M.PL1, Q259.d2.17, 933.v4.c4, and a Murine Leukemia Virus (MuLV) pseudovirus as a negative control. Results are expressed as IC50 and IC80 values or antibody / IgG concentrations resulting in a 50% and 80% reduction in relative luminescence units (RLUs) compared to untreated virus control wells. - 28 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) DEFINITIONS
[0257] Compounds of this disclosure include those described generally above and are further illustrated by the classes, subclasses, and species disclosed herein. As used herein, the following definitions shall apply unless otherwise indicated. For purposes of this disclosure, the chemical elements are identified in accordance with the Periodic Table of Elements, CAS version, Handbook of Chemistry and Physics, 75th Ed. Additionally, general principles of organic chemistry are described in “Organic Chemistry”, Thomas Sorrell, University Science Books, Sausalito: 1999, and “March’s Advanced Organic Chemistry”, 5th Ed., Ed.: Smith, M.B. and March, J., John Wiley & Sons, New York: 2001, the entire contents of which are hereby incorporated by reference.
[0258] Unless otherwise stated, structures depicted herein are meant to include all stereoisomeric (e.g., enantiomeric or diastereomeric) forms of the structure, as well as all geometric or conformational isomeric forms of the structure. For example, the R and S configurations of each stereocenter are contemplated as part of the disclosure. Therefore, single stereochemical isomers, as well as enantiomeric, diastereomeric, and geometric (or conformational) mixtures of provided compounds are within the scope of the disclosure. For example, in some cases, provided compounds show one or more stereoisomers of a compound, and unless otherwise indicated, represents each stereoisomer alone and / or as a mixture. Unless otherwise stated, all tautomeric forms of provided compounds are within the scope of the disclosure.
[0259] Unless otherwise indicated, structures depicted herein are meant to include compounds that differ only in the presence of one or more isotopically enriched atoms. For example, compounds having the present structures including replacement of hydrogen by deuterium or tritium, or replacement of a carbon by 13C- or 14C- enriched carbon are within the scope of this disclosure.
[0260] About: The term “about”, when used herein in reference to a value, refers to a value that is similar, in context to the referenced value. In general, those skilled in the art, familiar with the context, will appreciate the relevant degree of variance encompassed by “about” in that context. For example, in some embodiments, the term “about” may encompass a range of values that within 25%, 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, or less of the referred value.
[0261] Agent: As used herein, the term “agent,” may refer to a physical entity. In some embodiments, an agent may be characterized by a particular feature and / or effect. For example, as used herein, the term “therapeutic agent” refers to a physical entity has a therapeutic effect and / or elicits a desired biological and / or pharmacological effect. In some embodiments, an agent may be a compound, molecule, or entity of any chemical class including, for example, a small molecule, polypeptide, nucleic acid, saccharide, lipid, metal, or a combination or complex thereof.
[0262] Aliphatic: The term “aliphatic” refers to a straight-chain (i.e., unbranched) or branched, substituted or unsubstituted hydrocarbon chain that is completely saturated or that contains one or more units of unsaturation, or a monocyclic hydrocarbon or bicyclic hydrocarbon that is completely saturated or that contains one or more units of unsaturation, but which is not aromatic (also referred to herein as “cycloaliphatic”), that has a single point or more than one points of attachment to the rest of the molecule. Unless otherwise specified, aliphatic groups contain 1-12 aliphatic carbon atoms. In some embodiments, aliphatic groups contain 1-6 aliphatic carbon atoms (e.g., C1-6). In some embodiments, aliphatic groups contain 1-5 aliphatic carbon atoms (e.g., C1-5). In other - 29 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) embodiments, aliphatic groups contain 1-4 aliphatic carbon atoms (e.g., C1-4). In still other embodiments, aliphatic groups contain 1-3 aliphatic carbon atoms (e.g., C1-3), and in yet other embodiments, aliphatic groups contain 1-2 aliphatic carbon atoms (e.g., C1-2). Suitable aliphatic groups include, but are not limited to, linear or branched, substituted or unsubstituted alkyl, alkenyl, or alkynyl groups and hybrids thereof. A preferred aliphatic group is C1-6 alkyl.
[0263] Alkyl: The term “alkyl,” used alone or as part of a larger moiety, refers to a saturated, optionally substituted straight or branched chain hydrocarbon group having (unless otherwise specified) 1-12, 1-10, 1-8, 1-6, 1- 4, 1-3, or 1-2 carbon atoms (e.g., C1-12, C1-10, C1-8, C1-6, C1-4, C1-3, or C1-2). Exemplary alkyl groups include methyl, ethyl, propyl, butyl, pentyl, hexyl, and heptyl.
[0264] Alkylene: The term “alkylene” is refers to a bivalent alkyl group. In some embodiments, “alkylene” is a bivalent straight or branched alkyl group. In some embodiments, an "alkylene chain" is a polymethylene group, i.e., -(CH2)n-, wherein n is a positive integer, e.g., from 1 to 6, from 1 to 4, from 1 to 3, from 1 to 2, or from 2 to 3. An optionally substituted alkylene chain is a polymethylene group in which one or more methylene hydrogen atoms is optionally replaced with a substituent. Suitable substituents include those described below for a substituted aliphatic group and also include those described in the specification herein. It will be appreciated that two substituents of the alkylene group may be taken together to form a ring system. In certain embodiments, two substituents can be taken together to form a 3- to 7-membered ring. The substituents can be on the same or different atoms. The suffix “-ene” or “-enyl” when appended to certain groups herein are intended to refer to a bifunctional moiety of said group. For example, “-ene” or “-enyl”, when appended to “cyclopropyl” becomes “cyclopropylene” or “cyclopropylenyl” and is intended to refer to a bifunctional cyclopropyl group, .
[0265] Alkenyl: The term “alkenyl”, usedpart of a larger moiety, refers to an optionally substituted straight or branched chain or cyclic hydrocarbon group having at least one double bond and having (unless otherwise specified) 2-12, 2-10, 2-8, 2-6, 2-4, or 2-3 carbon atoms (e.g., C2-12, C2-10, C2-8, C2-6, C2-4, or C2-3). Exemplary alkenyl groups include ethenyl, propenyl, butenyl, pentenyl, hexenyl, and heptenyl. The term “cycloalkenyl” refers to an optionally substituted non-aromatic monocyclic or multicyclic ring system containing at least one carbon-carbon double bond and having about 3 to about 10 carbon atoms. Exemplary monocyclic cycloalkenyl rings include cyclopentenyl, cyclohexenyl, and cycloheptenyl.
[0266] Alkynyl: The term “alkynyl”, used alone or as part of a larger moiety, refers to an optionally substituted straight or branched chain hydrocarbon group having at least one triple bond and having (unless otherwise specified) 2-12, 2-10, 2-8, 2-6, 2-4, or 2-3 carbon atoms (e.g., C2-12, C2-10, C2-8, C2-6, C2-4, or C2-3). Exemplary alkynyl groups include ethynyl, propynyl, butynyl, pentynyl, hexynyl, and heptynyl.
[0267] Amino acid: In its broadest sense, as used herein, the term “amino acid” refers to a compound and / or substance that can be, is, or has been incorporated into a polypeptide chain, e.g., through formation of one or more peptide bonds. In some embodiments, an amino acid has the general structure H2N–C(H)(R)–COOH. In some embodiments, an amino acid is a naturally-occurring amino acid. In some embodiments, an amino acid is a non-natural amino acid; in some embodiments, an amino acid is a D-amino acid; in some embodiments, an amino - 30 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) acid is an L-amino acid. “Standard amino acid” refers to any of the twenty standard L-amino acids commonly found in naturally occurring peptides. “Nonstandard amino acid” refers to any amino acid, other than the standard amino acids, regardless of whether it is prepared synthetically or obtained from a natural source. In some embodiments, an amino acid, including a carboxy- and / or amino-terminal amino acid in a polypeptide, can contain a structural modification as compared with the general structure above. For example, in some embodiments, an amino acid may be modified by methylation, amidation, acetylation, pegylation, glycosylation, phosphorylation, and / or substitution (e.g., of the amino group, the carboxylic acid group, one or more protons, and / or the hydroxyl group) as compared with the general structure. In some embodiments, such modification may, for example, alter the circulating half-life of a polypeptide containing the modified amino acid as compared with one containing an otherwise identical unmodified amino acid. In some embodiments, such modification does not significantly alter a relevant activity of a polypeptide containing the modified amino acid, as compared with one containing an otherwise identical unmodified amino acid. As will be clear from context, in some embodiments, the term “amino acid” may be used to refer to a free amino acid; in some embodiments it may be used to refer to an amino acid residue of a polypeptide.
[0268] Antibody agent: As used herein, the term “antibody agent” refers to any polypeptide or polypeptide complex that includes immunoglobulin structural elements sufficient to confer specific binding to a particular antigen. Exemplary antibody agents include, but are not limited to monoclonal antibodies or polyclonal antibodies. In some embodiments, an antibody agent may include one or more constant region sequences that are characteristic of mouse, rabbit, primate, or human antibodies. In some embodiments, an antibody agent may include one or more sequence elements are humanized, primatized, chimeric, etc., as is known in the art. In some embodiments, the term “antibody agent” is used to refer to one or more 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 agent 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 (e.g., Zybodies®, etc.); CrossMabs (e.g., CrossMabCH1-CL; CrossMabCH1-CLcv; bispecific CrossMabCH1-CLwith knob-in-hole); antibody fragments such as Fab fragments, Fab' fragments, F(ab')2 fragments, Fd' fragments, Fd fragments, and isolated complementarity determining regions (CDRs) or sets thereof; single chain Fvs (scFvs); scFv-Fc fusions; polypeptide- Fc fusions; single domain antibodies (e.g., shark single domain antibodies such as IgNAR or fragments thereof); cameloid antibodies; masked antibodies (e.g., Probodies®); Small Modular ImmunoPharmaceuticals (“SMIPsTM”); single chain or Tandem diabodies (TandAb®); VHHs; Anticalins®; Nanobodies® minibodies; BiTE®s; ankyrin repeat proteins or DARPINs®; Avimers®; DARTs; TCR-like antibodies; Adnectins®; Affilins®; Trans-bodies®; Affibodies®; TrimerX®; MicroProteins; Fynomers®, Centyrins®; and KALBITOR®s. In some embodiments, chains and / or fragments of such antibodies and fragments may be used in combination, e.g., an scFv-Fc arm with a conventional antibody arm. In some embodiments, an antibody agent is a broadly neutralizing antibody agent (e.g., a broadly neutralizing antibody (bNAb)). A “broadly neutralizing antibody agent” is an antibody agent that is capable of neutralizing two or more genetic variants (e.g., strains) of a virus (e.g., HIV). 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 payload (e.g., a detectable moiety, a therapeutic moiety, a catalytic moiety, etc.), or other pendant group (e.g., poly-ethylene glycol, etc.)). In many embodiments, an antibody agent is or comprises a polypeptide whose amino acid sequence includes - 31 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) one or more structural elements recognized by those skilled in the art as a complementarity determining region (CDR); in some embodiments an antibody agent is or comprises a polypeptide whose amino acid sequence includes at least one CDR (e.g., at least one heavy chain CDR and / or at least one light chain CDR) that is substantially identical to one found in a reference antibody. In some embodiments an included CDR is substantially identical to a reference CDR in that it is either identical in sequence or contains between 1-5 amino acid substitutions as compared with the reference CDR. In some embodiments an included CDR is substantially identical to a reference CDR in that it shows at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with the reference CDR. In some embodiments, an included CDR is substantially identical to a reference CDR in that it shows at least 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with the reference CDR. In some embodiments an included CDR is substantially identical to a reference CDR in that at least one amino acid within the included CDR is deleted, added, or substituted as compared with the reference CDR but the included CDR has an amino acid sequence that is otherwise identical with that of the reference CDR. In some embodiments an included CDR is substantially identical to a reference CDR in that 1-5 amino acids within the included CDR are deleted, added, or substituted as compared with the reference CDR but the included CDR has an amino acid sequence that is otherwise identical to the reference CDR. In some embodiments, an included CDR is substantially identical to a reference CDR in that at least one amino acid within the included CDR is substituted as compared with the reference CDR but the included CDR has an amino acid sequence that is otherwise identical with that of the reference CDR. In some embodiments, an included CDR is substantially identical to a reference CDR in that 1-5 amino acids within the included CDR are deleted, added, or substituted as compared with the reference CDR but the included CDR has an amino acid sequence that is otherwise identical to the reference CDR. In some embodiments, an antibody agent is or comprises a polypeptide whose amino acid sequence includes structural elements recognized by those skilled in the art as an immunoglobulin variable domain. In some embodiments, an antibody agent is a polypeptide protein having a binding domain which is homologous or largely homologous to an immunoglobulin- binding domain.
[0269] Aryl: The term “aryl” refers to monocyclic and bicyclic ring systems having a total of six to fourteen ring members (e.g., C6-C14), wherein at least one ring in the system is aromatic and wherein each ring in the system contains three to seven ring members. In some embodiments, an “aryl” group contains between six and twelve total ring members (e.g., C6-C12). The term “aryl” may be used interchangeably with the term “aryl ring”. In certain embodiments, “aryl” refers to an aromatic ring system which includes, but not limited to, phenyl, biphenyl, naphthyl, anthracyl and the like, which may bear one or more substituents. Unless otherwise specified, “aryl” groups are hydrocarbons. In some embodiments, an “aryl” ring system is an aromatic ring (e.g., phenyl) that is fused to a non-aromatic ring (e.g., cycloalkyl). Examples of aryl rings include that are fused include , , and .
[0270] 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 - 32 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) 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). In some embodiments, two or more entities are physically “associated” with one another if they interact, directly or indirectly, so that they are and / or remain in physical proximity with one another. In some embodiments, two or more entities that are physically associated with one another are covalently linked to one another; in some embodiments, two or more entities that are physically associated with one another are not covalently linked to one another but are non- covalently associated, for example by means of hydrogen bonds, van der Waals interaction, hydrophobic interactions, magnetism, and combinations thereof.
[0271] Co-administration: As used herein, the term “co-administration” refers to use of a composition (e.g., a pharmaceutical composition) described herein and one or more additional therapeutic agents. In some embodiments, one or more additional therapeutic agents comprises at least one polyribonucleotide encoding another antibody agent (e.g., an anti-HIV antigen antibody agent). The combined use of a composition (e.g., a pharmaceutical composition) described herein and an additional therapeutic agent may be performed concurrently or separately (e.g., sequentially in any order). In some embodiments, a composition (e.g., a pharmaceutical composition) described herein and an additional therapeutic agent may be combined in one pharmaceutically- acceptable excipient, or they may be placed in separate excipient and delivered to a target cell or administered to a subject at different times. Each of these situations is contemplated as falling within the meaning of “co- administration” or “combination,” provided that a composition (e.g., a pharmaceutical composition) described herein and an additional therapeutic agent are delivered or administered sufficiently close in time that there is at least some temporal overlap in biological effect(s) generated by each on a target cell or a subject being treated.
[0272] Combination therapy: As used herein, the term “combination therapy” refers to those situations in which a subject is simultaneously exposed to two or more therapeutic regimens (e.g., two or more therapeutic agents (e.g., two or more antibody agents)). In some embodiments, the two or more regimens may be administered simultaneously; in some embodiments, such regimens may be administered sequentially (e.g., all “doses” of a first regimen are administered prior to administration of any doses of a second regimen); in some embodiments, such agents are administered in overlapping dosing regimens. In some embodiments, administration of combination therapy may involve administration of one or more agent(s) or modality(ies) to a subject receiving the other agent(s) or modality(ies) in the combination. For clarity, combination therapy does not require that individual agents be administered together in a single composition (or even necessarily at the same time), although in some embodiments, two or more agents, or active moieties thereof, may be administered together in a combination composition. In some embodiments, a combination therapy comprises polyribonucleotides encoding two or more antibody agents (e.g., anti-HIV antibody agents).
[0273] Comparable: As used herein, the term “comparable” refers to two or more agents, entities, situations, sets of conditions, etc., that may not be identical to one another but that are sufficiently similar to permit comparison there between so that one skilled in the art will appreciate that conclusions may reasonably be drawn based on differences or similarities observed. In some embodiments, comparable sets of conditions, circumstances, individuals, or populations are characterized by a plurality of substantially identical features and one or a small - 33 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) number of varied features. Those of ordinary skill in the art will understand, in context, what degree of identity is required in any given circumstance for two or more such agents, entities, situations, sets of conditions, etc. to be considered comparable. For example, those of ordinary skill in the art will appreciate that sets of circumstances, individuals, or populations are comparable to one another when characterized by a sufficient number and type of substantially identical features to warrant a reasonable conclusion that differences in results obtained or phenomena observed under or with different sets of circumstances, individuals, or populations are caused by or indicative of the variation in those features that are varied.
[0274] Corresponding to: As used herein, the term “corresponding to” refers to a relationship between two or more entities. For example, the term “corresponding to” may be used to designate the position / identity of a structural element in a compound or composition relative to another compound or composition (e.g., to an appropriate reference compound or composition). For example, in some embodiments, a monomeric residue in a polymer (e.g., an amino acid residue in a polypeptide or a nucleic acid residue in a polynucleotide) may be identified as “corresponding to” a residue in an appropriate reference polymer. For example, those of ordinary skill will appreciate that, for purposes of simplicity, residues in a polypeptide are often designated using a canonical numbering system based on a reference related polypeptide, so that an amino acid “corresponding to” a residue at position 190, for example, need not actually be the 190thamino acid in a particular amino acid chain but rather corresponds to the residue found at 190 in the reference polypeptide; those of ordinary skill in the art readily appreciate how to identify “corresponding” amino acids. For example, those skilled in the art will be aware of various sequence alignment strategies, including software programs such as, for example, BLAST, CS-BLAST, CUSASW++, DIAMOND, FASTA, GGSEARCH / GLSEARCH, Genoogle, HMMER, HHpred / HHsearch, IDF, Infernal, KLAST, USEARCH, parasail, PSI-BLAST, PSI-Search, ScalaBLAST, Sequilab, SAM, SSEARCH, SWAPHI, SWAPHI-LS, SWIMM, or SWIPE that can be utilized, for example, to identify “corresponding” residues in polypeptides and / or nucleic acids in accordance with the present disclosure. Those of skill in the art will also appreciate that, in some instances, the term “corresponding to” may be used to describe an event or entity that shares a relevant similarity with another event or entity (e.g., an appropriate reference event or entity). To give but one example, a gene or protein in one organism may be described as “corresponding to” a gene or protein from another organism in order to indicate, in some embodiments, that it plays an analogous role or performs an analogous function and / or that it shows a particular degree of sequence identity or homology, or shares a particular characteristic sequence element.
[0275] Cycloaliphatic: As used herein, the term “cycloaliphatic” refers to a monocyclic C3-8 hydrocarbon or a bicyclic C6-10hydrocarbon that is completely saturated or that contains one or more units of unsaturation, but which is not aromatic, that has a single point or more than one points of attachment to the rest of the molecule.
[0276] Cycloalkyl: As used herein, the term “cycloalkyl” refers to an optionally substituted saturated ring monocyclic or polycyclic system of about 3 to about 10 ring carbon atoms. Exemplary monocyclic cycloalkyl rings include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, and cycloheptyl.
[0277] Derived: In the context of an amino acid sequence (peptide or polypeptide) “derived from” a designated amino acid sequence (peptide or polypeptide), it refers to a structural analogue of a designated amino acid sequence. In some embodiments, an amino acid sequence which is derived from a particular amino acid sequence has an amino acid sequence that is identical, essentially identical or homologous to that particular - 34 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) sequence or a fragment thereof. Amino acid sequences derived from a particular amino acid sequence may be variants of that particular sequence or a fragment thereof. For example, antibody agents utilized according to the present disclosure may include amino acid sequences (e.g., CDRs, variable domains, constant domains, etc.) derived from other antibodies, e.g., naturally produced antibodies.
[0278] Detecting: The term “detecting” is used broadly herein to include appropriate means of determining the presence or absence of an entity of interest or any form of measurement of an entity of interest in a sample. Thus, “detecting” may include determining, measuring, assessing, or assaying the presence or absence, level, amount, and / or location of an entity of interest. Quantitative and qualitative determinations, measurements or assessments are included, including semi-quantitative. Such determinations, measurements or assessments may be relative, for example when an entity of interest is being detected relative to a control reference, or absolute. As such, the term “quantifying” when used in the context of quantifying an entity of interest can refer to absolute or to relative quantification. Absolute quantification may be accomplished by correlating a detected level of an entity of interest to known control standards (e.g., through generation of a standard curve). Alternatively, relative quantification can be accomplished by comparison of detected levels or amounts between two or more different entities of interest to provide a relative quantification of each of the two or more different entities of interest, i.e., relative to each other.
[0279] Dosing regimen: Those skilled in the art will appreciate that the term “dosing regimen” (or “therapeutic regimen”) may be used to refer to a set of unit doses (typically more than one) that are administered individually to a subject, typically separated by periods of time. In some embodiments, a given therapeutic agent has a recommended dosing regimen, which may involve one or more doses.
[0280] Encode: As used herein, the term “encode” or “encoding” refers to sequence information of a first molecule that guides production of a second molecule having a defined sequence of nucleotides (e.g., a polyribonucleotide) or a defined sequence of amino acids. For example, a DNA molecule can encode an RNA molecule (e.g., by a transcription process that includes a DNA-dependent RNA polymerase enzyme). An RNA molecule can encode a polypeptide (e.g., by a translation process). Thus, a gene, a cDNA, or an RNA molecule encodes a polypeptide if transcription and translation of RNA corresponding to that gene produces the polypeptide in a cell or other biological system. In some embodiments, a coding region of a polyribonucleotide encoding a target antigen refers to a coding strand, the nucleotide sequence of which is identical to the polyribonucleotide sequence of such a target antigen. In some embodiments, a coding region of a polyribonucleotide encoding a target antigen refers to a non-coding strand of such a target antigen, which may be used as a template for transcription of a gene or cDNA.
[0281] Engineered: In general, the term “engineered” refers to the aspect of having been manipulated by the hand of man. For example, a polynucleotide is considered to be “engineered” when two or more sequences that are not linked together in that order in nature are manipulated by the hand of man to be directly linked to one another in the engineered polynucleotide and / or when a particular residue in a polynucleotide is non-naturally occurring and / or is caused through action of the hand of man to be linked with an entity or moiety with which it is not linked in nature. - 35 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01)
[0282] Epitope: As used herein, the term “epitope” refers to a moiety that is specifically recognized by an immunoglobulin (e.g., antibody or receptor) binding component. For example, an epitope may be recognized by a T cell, a B cell, or an antibody. In some embodiments, an epitope 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). Accordingly, in some embodiments, an epitope of an antigen may include a continuous or discontinuous portion of the antigen. In some embodiments, an epitope is or comprises a T cell epitope. In some embodiments, an epitope may have a length of about 5 to about 30 amino acids, or about 10 to about 25 amino acids, or about 5 to about 15 amino acids, or about 5 to 12 amino acids, or about 6 to about 9 amino acids.
[0283] Expression: As used herein, the term “expression” of a nucleic acid sequence refers to the generation of a gene product from the nucleic acid sequence. In some embodiments, a gene product can be a transcript, e.g., a polyribonucleotide as provided herein. 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, etc.); (3) translation of an RNA into a polypeptide or protein; and / or (4) post-translational modification of a polypeptide or protein.
[0284] Heteroaliphatic: The term “heteroaliphatic” or “heteroaliphatic group,” as used herein, denotes an optionally substituted hydrocarbon moiety having, in addition to carbon atoms, from one to five heteroatoms, that may be straight–chain (i.e., unbranched), branched, or cyclic (“heterocyclic”) and may be completely saturated or may contain one or more units of unsaturation, but which is not aromatic. The term “heteroatom” refers to nitrogen, oxygen, or sulfur, and includes any oxidized form of nitrogen or sulfur, and any quaternized form of a basic nitrogen. The term “nitrogen” also includes a substituted nitrogen. Unless otherwise specified, heteroaliphatic groups contain 1–10 carbon atoms wherein 1–3 carbon atoms are optionally and independently replaced with heteroatoms selected from oxygen, nitrogen, and sulfur. In some embodiments, heteroaliphatic groups contain 1–4 carbon atoms, wherein 1–2 carbon atoms are optionally and independently replaced with heteroatoms selected from oxygen, nitrogen, and sulfur. In yet other embodiments, heteroaliphatic groups contain 1–3 carbon atoms, wherein 1 carbon atom is optionally and independently replaced with a heteroatom selected from oxygen, nitrogen, and sulfur. Suitable heteroaliphatic groups include, but are not limited to, linear or branched, heteroalkyl, heteroalkenyl, and heteroalkynyl groups. For example, a 1- to 10 atom heteroaliphatic group includes the following exemplary groups: - O-CH3, -CH2-O-CH3, -O-CH2-CH2-O-CH2-CH2-O-CH3, and the like.
[0285] Heteroaryl: The terms “heteroaryl” and “heteroar–”, used alone or as part of a larger moiety, e.g., “heteroaralkyl”, or “heteroaralkoxy”, refer to monocyclic or bicyclic ring groups having 5 to 10 ring atoms (e.g., 5- to 6-membered monocyclic heteroaryl or 9- to 10-membered bicyclic heteroaryl); having 6, 10, or 14 π-electrons shared in a cyclic array; and having, in addition to carbon atoms, from one to five heteroatoms. Heteroaryl groups include, without limitation, thienyl, furanyl, pyrrolyl, imidazolyl, pyrazolyl, triazolyl, tetrazolyl, oxazolyl, isoxazolyl, - 36 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) oxadiazolyl, thiazolyl, isothiazolyl, thiadiazolyl, pyridyl, pyridazinyl, pyrimidinyl, pyrazinyl, indolizinyl, purinyl, naphthyridinyl, pteridinyl, imidazo[1,2-a]pyrimidinyl, imidazo[1,2-a]pyridyl, imidazo[4,5-b]pyridyl, imidazo[4,5- c]pyridyl, pyrrolopyridyl, pyrrolopyrazinyl, thienopyrimidinyl, triazolopyridyl, and benzoisoxazolyl. The terms “heteroaryl” and “heteroar–”, as used herein, also include groups in which a heteroaromatic ring is fused to one or more aryl, cycloaliphatic, or heterocyclyl rings, where the radical or point of attachment is on the heteroaromatic ring (i.e., a bicyclic heteroaryl ring having 1 to 3 heteroatoms). Nonlimiting examples include indolyl, isoindolyl, benzothienyl, benzofuranyl, dibenzofuranyl, indazolyl, benzimidazolyl, benzotriazolyl, benzothiazolyl, benzothiadiazolyl, benzoxazolyl, quinolyl, isoquinolyl, cinnolinyl, phthalazinyl, quinazolinyl, quinoxalinyl, 4H– quinolizinyl, carbazolyl, acridinyl, phenazinyl, phenothiazinyl, phenoxazinyl, tetrahydroquinolinyl, tetrahydroisoquinolinyl, pyrido[2,3–b]–1,4–oxazin–3(4H)–one, 4H-thieno[3,2-b]pyrrole, and benzoisoxazolyl. The term “heteroaryl” may be used interchangeably with the terms “heteroaryl ring”, “heteroaryl group”, or “heteroaromatic”, any of which terms include rings that are optionally substituted.
[0286] Heteroatom: The term “heteroatom” as used herein refers to nitrogen, oxygen, or sulfur, and includes any oxidized form of nitrogen or sulfur, and any quaternized form of a basic nitrogen.
[0287] Heterocycle: As used herein, the terms “heterocycle”, “heterocyclyl”, “heterocyclic radical”, and “heterocyclic ring” are used interchangeably and refer to a stable 3- to 8-membered monocyclic, a 6- to 10- membered bicyclic, or a 10- to 16-membered polycyclic heterocyclic moiety that is either saturated or partially unsaturated, and having, in addition to carbon atoms, one or more, such as one to four, heteroatoms, as defined above. When used in reference to a ring atom of a heterocycle, the term "nitrogen" includes a substituted nitrogen. As an example, in a saturated or partially unsaturated ring having 0–3 heteroatoms selected from oxygen, sulfur or nitrogen, the nitrogen may be N (as in 3,4-dihydro-2H-pyrrolyl), NH (as in pyrrolidinyl), or NR+(as in N-substituted pyrrolidinyl). A heterocyclic ring can be attached to its pendant group at any heteroatom or carbon atom that results in a stable structure and any of the ring atoms can be optionally substituted. Examples of such saturated or partially unsaturated heterocyclic radicals include, without limitation, azetidinyl, oxetanyl, tetrahydrofuranyl, tetrahydrothienyl, pyrrolidinyl, piperidinyl, decahydroquinolinyl, oxazolidinyl, piperazinyl, dioxanyl, dioxolanyl, diazepinyl, oxazepinyl, thiazepinyl, morpholinyl, and thiamorpholinyl. A heterocyclyl group may be mono-, bi-, tri-, or polycyclic, preferably mono-, bi-, or tricyclic, more preferably mono- or bicyclic. A bicyclic heterocyclic ring also includes groups in which the heterocyclic ring is fused to one or more aryl rings. Exemplary bicyclic heterocyclic groups include indolinyl, isoindolinyl, benzodioxolyl, 1,3-dihydroisobenzofuranyl, 2,3-dihydrobenzofuranyl, and tetrahydroquinolinyl. A bicyclic heterocyclic ring can also be a spirocyclic ring system (e.g., 7- to 11-membered spirocyclic fused heterocyclic ring having, in addition to carbon atoms, one or more heteroatoms as defined above (e.g., one, two, three or four heteroatoms)). A bicyclic heterocyclic ring can also be a bridged ring system (e.g., 7- to 11-membered bridged heterocyclic ring having one, two, or three bridging atoms.
[0288] Homology: As used herein, the term “homology” or “homolog” refers to the overall relatedness between polynucleotide molecules (e.g., DNA molecules and / or RNA molecules) and / or between polypeptide molecules. In some embodiments, polynucleotide molecules (e.g., DNA molecules and / or RNA molecules) and / or polypeptide molecules are considered to be “homologous” to one another if their sequences are at least 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% identical. In some - 37 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) embodiments, polynucleotide molecules (e.g., DNA molecules and / or RNA molecules) and / or polypeptide molecules are considered to be “homologous” 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% similar (e.g., containing residues with related chemical properties at corresponding positions). For example, as is well known by those of ordinary skill in the art, certain amino acids are typically classified as similar to one another as “hydrophobic” or “hydrophilic” amino acids, and / or as having “polar” or “non-polar” side chains. Substitution of one amino acid for another of the same type may often be considered a “homologous” substitution.
[0289] Identity: As used herein, the term “identity” refers to the overall relatedness between polynucleotide molecules (e.g., DNA molecules and / or RNA molecules) and / or between polypeptide molecules. In some embodiments, polynucleotide molecules (e.g., DNA molecules and / or RNA molecules) and / or between polypeptide molecules are considered to be “substantially identical” to one another if their sequences are at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 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 sequence for optimal alignment and non-identical sequences can be disregarded for comparison purposes). In certain 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 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, 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, 1989, 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.
[0290] Increased, Induced, or Reduced: As used herein, these terms 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 a provided composition (e.g., a pharmaceutical composition) may be “increased” relative to that obtained with a comparable reference composition. Alternatively or additionally, in some embodiments, an assessed value achieved in a subject may be “increased” relative to that obtained in the same subject under different conditions (e.g., prior to or after an event; or presence or absence of an event such as administration of a composition (e.g., a pharmaceutical composition) as described herein, or in a different, comparable subject (e.g., in a comparable subject that differs from the subject of interest in prior exposure to a condition, e.g., absence of administration of a composition (e.g., a pharmaceutical composition) as described herein.). In some embodiments, comparative terms refer to statistically relevant differences (e.g., that are of a - 38 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) 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. In some embodiments, the term “reduced” or equivalent terms refers to a reduction in the level of an assessed value by at least 5%, at least 10%, at least 20%, at least 50%, at least 75% or higher, as compared to a comparable reference. In some embodiments, the term “reduced” or equivalent terms refers to a complete or essentially complete inhibition, i.e., a reduction to zero or essentially to zero. In some embodiments, the term “increased” or “induced” refers to an increase in the level of an assessed value by at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 80%, at least 100%, at least 200%, at least 500%, or higher, as compared to a comparable reference.
[0291] In order: As used herein with reference to a polynucleotide or polyribonucleotide, “in order” refers to the order of features from 5' to 3' along the polynucleotide or polyribonucleotide. As used herein with reference to a polypeptide, “in order” refers to the order of features moving from the N-terminal-most of the features to the C- terminal-most of the features along the polypeptide. “In order” does not mean that no additional features can be present among the listed features. For example, if Features A, B, and C of a polynucleotide are described herein as being “in order, Feature A, Feature B, and Feature C,” this description does not exclude, e.g., Feature D being located between Features A and B.
[0292] Ionizable: The term “ionizable” refers to a compound or group or atom that is charged at a certain pH. In the context of an ionizable amino lipid, such a lipid or a function group or atom thereof bears a positive charge at a certain pH. In some embodiments, an ionizable amino lipid is positively charged at an acidic pH. In some embodiments, an ionizable amino lipid is predominately neutral at physiological pH values, e.g., in some embodiments about 7.0-7.4, but becomes positively charged at lower pH values. In some embodiments, an ionizable amino lipid may have a pKa within a range of about 5 to about 7.
[0293] Isolated: The term “isolated” means altered or removed from the natural state. For example, a nucleic acid or a peptide naturally present in a living animal is not “isolated,” but the same nucleic acid or peptide partially or completely separated from the coexisting materials of its natural state is “isolated.” An isolated nucleic acid or protein can exist in substantially purified form, or can exist in a non-native environment such as, for example, a host cell.
[0294] Lipid: As used herein, the terms “lipid” and “lipid-like material” are broadly defined as molecules which comprise one or more hydrophobic moieties or groups and optionally also one or more hydrophilic moieties or groups. Molecules comprising hydrophobic moieties and hydrophilic moieties are also typically denoted as amphiphiles.
[0295] RNA lipid nanoparticle: As used herein, the term “RNA lipid nanoparticle” refers to a nanoparticle comprising at least one lipid and RNA molecule(s), e.g., one or more polyribonucleotides as provided herein. In some embodiments, an RNA lipid nanoparticle comprises at least one cationic amino lipid. In some embodiments, an RNA lipid nanoparticle comprises at least one cationic amino lipid, at least one helper lipid, and at least one polymer-conjugated lipid (e.g., PEG-conjugated lipid). In various embodiments, RNA lipid nanoparticles as described herein can have an average size (e.g., Z-average) of about 100 nm to 1000 nm, or about 200 nm to 900 nm, or about 200 nm to 800 nm, or about 250 nm to about 700 nm. In some embodiments of the present disclosure, - 39 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) RNA lipid nanoparticles can have a particle size (e.g., Z-average) of about 30 nm to about 200 nm, or about 30 nm to about 150 nm, about 40 nm to about 150 nm, about 50 nm to about 150 nm, about 60 nm to about 130 nm, about 70 nm to about 110 nm, about 70 nm to about 100 nm, about 80 nm to about 100 nm, about 90 nm to about 100 nm, about 70 to about 90 nm, about 80 nm to about 90 nm, or about 70 nm to about 80 nm. In some embodiments, an average size of lipid nanoparticles is determined by measuring the average particle diameter. In some embodiments, RNA lipid nanoparticles may be prepared by mixing lipids with RNA molecules described herein.
[0296] Neutralization: As used herein, the term “neutralization” refers to an event in which binding agents such as antibodies bind to a biological active site of a virus such as a receptor binding protein, thereby inhibiting the parasitic infection of cells. In some embodiments, the term “neutralization” refers to an event in which binding agents eliminate or significantly reduce ability of infecting cells.
[0297] Nucleic acid / Polynucleotide: As used herein, the term “nucleic acid” refers to a polymer of at least 10 nucleotides or more. In some embodiments, a nucleic acid is or comprises DNA. In some embodiments, a nucleic acid is or comprises RNA. In some embodiments, a nucleic acid is or comprises peptide nucleic acid (PNA). In some embodiments, a nucleic acid is or comprises a single stranded nucleic acid. In some embodiments, a nucleic acid is or comprises a double-stranded nucleic acid. 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 on 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-deazaguanosine, 8-oxoadenosine, 8- oxoguanosine, 6-O-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, 200, 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, 5500, 6000, 6500, 7000, 7500, 8000, 8500, 9000, 9500, 10,000, 10,500, 11,000, 11,500, 12,000, 12,500, 13,000, 13,500, 14,000, 14,500, 15,000, 15,500, 16,000, 16,500, 17,000, 17,500, 18,000, 18,500, 19,000, 19,500, or 20,000 or more residues or nucleotides long. - 40 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01)
[0298] Pharmaceutically effective amount: The term “pharmaceutically effective amount” or “therapeutically effective amount” refers to the amount which achieves a desired reaction or a desired effect alone or together with further doses. In the case of the treatment of a particular disease (e.g., HIV), a desired reaction in some embodiments relates to inhibition of the course of the disease (e.g., HIV). In some embodiments, such inhibition may comprise slowing down the progress of a disease (e.g., HIV) and / or interrupting or reversing the progress of the disease (e.g., HIV). In some embodiments, a desired reaction in a treatment of a disease (e.g., HIV) may be or comprise delay or prevention of the onset of a disease (e.g., HIV) or a condition (e.g., an HIV associated condition). An effective amount of a composition (e.g., a pharmaceutical composition) described herein will depend, for example, on disease (e.g., HIV) or a condition (e.g., an HIV associated condition) to be treated, the severity of such a disease (e.g., HIV) or a condition (e.g., an HIV associated condition), individual parameters of the patient, including, e.g., age, physiological condition, size and weight, the duration of treatment, the type of an accompanying therapy (if present), the specific route of administration and similar factors. Accordingly, doses of a composition (e.g., a pharmaceutical composition) described herein may depend on various of such parameters. In the case that a reaction in a patient is insufficient with an initial dose, higher doses (or effectively higher doses achieved by a different, more localized route of administration) may be used.
[0299] Polypeptide: As used herein, the term “polypeptide” refers to a polymeric chain of amino acids. In some embodiments, a polypeptide has an amino acid sequence that occurs in nature. In some embodiments, a polypeptide has an amino acid sequence that does not occur in nature. In some embodiments, a polypeptide has an amino acid sequence that is engineered in that it is designed and / or produced through action of the hand of man. In some embodiments, a polypeptide may comprise or consist of natural amino acids, non-natural amino acids, or both. In some embodiments, a polypeptide may comprise or consist of only natural amino acids or only non-natural amino acids. In some embodiments, a polypeptide may comprise D-amino acids, L-amino acids, or both. In some embodiments, a polypeptide may comprise only D-amino acids. In some embodiments, a polypeptide may comprise only L-amino acids. In some embodiments, a polypeptide may include one or more pendant groups or other modifications, e.g., modifying or attached to one or more amino acid side chains, at the polypeptide’s N-terminus, at the polypeptide’s C-terminus, or any combination thereof. In some embodiments, such pendant groups or modifications comprise acetylation, amidation, lipidation, methylation, pegylation, etc., including combinations thereof. In some embodiments, a polypeptide may be cyclic, and / or may comprise a cyclic portion. In some embodiments, a polypeptide is not cyclic and / or does not comprise any cyclic portion. In some embodiments, a polypeptide is linear. In some embodiments, a polypeptide may be or comprise a stapled polypeptide. In some embodiments, the term “polypeptide” may be appended to a name of a reference polypeptide, activity, or structure; in such instances it is used herein to refer to polypeptides that share the relevant activity or structure and thus can be considered to be members of the same class or family of polypeptides. For each such class, the present specification provides and / or those skilled in the art will be aware of exemplary polypeptides within the class whose amino acid sequences and / or functions are known; in some embodiments, such exemplary polypeptides are reference polypeptides for the polypeptide class or family. In some embodiments, a member of a polypeptide class or family shows significant sequence homology or identity with, shares a common sequence motif (e.g., a characteristic sequence element) with, and / or shares a common activity (in some embodiments at a comparable level or within a designated range) with a reference polypeptide of the class; in some embodiments with all polypeptides within the - 41 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) class). For example, in some embodiments, a member polypeptide shows an overall degree of sequence homology or identity with a reference polypeptide that is at least about 30-40%, and is often greater than about 50%, 60%, 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more and / or includes at least one region (e.g., a conserved region that may in some embodiments be or comprise a characteristic sequence element) that shows very high sequence identity, often greater than 90% or even 95%, 96%, 97%, 98%, or 99%. Such a conserved region usually encompasses at least 3-4 and often up to 35 or more amino acids; in some embodiments, a conserved region encompasses at least one stretch of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 or more contiguous amino acids. In some embodiments, a relevant polypeptide may comprise or consist of a fragment of a parent polypeptide.
[0300] Prevent: As used herein, the term “prevent” or “prevention” when used in connection with the occurrence of a disease, disorder, and / or condition, refers to reducing the risk of developing the disease, disorder and / or condition and / or to delaying onset of one or more characteristics or symptoms of the disease, disorder or condition. Prevention may be considered complete when onset of a disease, disorder or condition has been delayed for a predefined period of time.
[0301] Reference: As used herein, the term “reference” describes a standard or control relative to which a comparison is performed. For example, in some embodiments, an agent, animal, individual, population, sample, sequence or value of interest is compared with a reference or control agent, animal, individual, population, sample, sequence or value. In some embodiments, a reference or control is tested and / or determined substantially simultaneously with the testing or determination of interest. In some embodiments, a reference or control is a historical reference or control, optionally embodied in a tangible medium. Typically, as would be understood by those skilled in the art, a reference or control is determined or characterized under comparable conditions or circumstances to those under assessment. Those skilled in the art will appreciate when sufficient similarities are present to justify reliance on and / or comparison to a particular possible reference or control.
[0302] Ribonucleic acid (RNA) or Polyribonucleotide: As used herein, the term “ribonucleic acid,” “RNA,” or “polyribonucleotide” refers to a polymer of ribonucleotides. In some embodiments, an RNA is single stranded. In some embodiments, an RNA is double stranded. In some embodiments, an RNA comprises both single and double stranded portions. In some embodiments, an RNA can comprise a backbone structure as described in the definition of “Nucleic acid / Polynucleotide” above. An RNA can be a regulatory RNA (e.g., siRNA, microRNA, etc.), or a messenger RNA (mRNA). In some embodiments, an RNA is a mRNA. In some embodiments, where an RNA is a mRNA, a RNA typically comprises at its 3' end a poly(A) region. In some embodiments, where an RNA is a mRNA, an RNA typically comprises at its 5' end an art-recognized cap structure, e.g., for recognizing and attachment of a mRNA to a ribosome to initiate translation. In some embodiments, an RNA is a synthetic RNA. Synthetic RNAs include RNAs that are synthesized in vitro (e.g., by enzymatic synthesis methods and / or by chemical synthesis methods).
[0303] Ribonucleotide: As used herein, the term “ribonucleotide” encompasses unmodified ribonucleotides and modified ribonucleotides. For example, unmodified ribonucleotides include the purine bases adenine (A) and guanine (G), and the pyrimidine bases cytosine (C) and uracil (U). Modified ribonucleotides may include one or more modifications including, but not limited to, for example, (a) end modifications, e.g., 5' end modifications (e.g., phosphorylation, dephosphorylation, conjugation, inverted linkages, etc.), 3' end modifications - 42 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) (e.g., conjugation, inverted linkages, etc.), (b) base modifications, e.g. , replacement with modified bases, stabilizing bases, destabilizing bases, or bases that base pair with an expanded repertoire of partners, or conjugated bases, (c) sugar modifications (e.g., at the 2' position or 4' position) or replacement of the sugar, and (d) internucleoside linkage modifications, including modification or replacement of the phosphodiester linkages. The term “ribonucleotide” also encompasses ribonucleotide triphosphates including modified and non-modified ribonucleotide triphosphates.
[0304] Risk: As will be understood from context, “risk” of a disease, disorder, and / or condition refers to a likelihood that a particular individual will develop the disease, disorder, and / or condition. In some embodiments, risk is expressed as a percentage. In some embodiments, risk is expressed as a risk relative to a risk associated with a reference sample or group of reference samples. In some embodiments, a reference sample or group of reference samples have a known risk of a disease, disorder, condition and / or event. In some embodiments, a reference sample or group of reference samples are from individuals comparable to a particular individual. In some embodiments, risk may reflect one or more genetic attributes, e.g., which may predispose an individual toward development (or not) of a particular disease, disorder and / or condition. In some embodiments, risk may reflect one or more epigenetic events or attributes and / or one or more lifestyle or environmental events or attributes.
[0305] Selective or specific: The term “selective” or “specific,” when used herein in reference to an agent having an activity, is understood by those skilled in the art to mean that the agent discriminates between potential target entities, states, or cells. For example, in some embodiments, an agent is said to bind “specifically” to its target if it binds preferentially with that target in the presence of one or more competing alternative targets. In many embodiments, specific interaction is dependent upon the presence of a particular structural feature of the target entity (e.g., an epitope, a cleft, a binding site). It is to be understood that specificity need not be absolute. In some embodiments, specificity may be evaluated relative to that of a target-binding moiety for one or more other potential target entities (e.g., competitors). In some embodiments, specificity is evaluated relative to that of a reference specific binding moiety. In some embodiments, specificity is evaluated relative to that of a reference non- specific binding moiety.
[0306] Substituted or optionally substituted: As described herein, compounds of the invention may contain “optionally substituted” moieties. In general, the term “substituted,” whether preceded by the term “optionally” or not, means that one or more hydrogens of the designated moiety are replaced with a suitable substituent. “Substituted” applies to one or more hydrogens that are either explicit or implicit from the structure- 43 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) given structure may be substituted with more than one substituent selected from a specified group, the substituent may be either the same or different at every position. Combinations of substituents envisioned by this invention are preferably those that result in the formation of stable or chemically feasible compounds. The term “stable,” as used herein, refers to compounds that are not substantially altered when subjected to conditions to allow for their production, detection, and, in certain embodiments, their recovery, purification, and use for one or more of the purposes provided herein. Groups described as being “substituted” preferably have between 1 and 4 substituents, more preferably 1 or 2 substituents. Groups described as being “optionally substituted” may be unsubstituted or be “substituted” as described above.
[0307] Suitable monovalent substituents on a substitutable carbon atom of an “optionally substituted” group are independently halogen; –(CH2)0–4R°; –(CH2)0–4OR°; -O(CH2)0-4Ro, –O–(CH2)0–4C(O)OR°; –(CH2)0–4CH(OR°)2; –(CH2)0–4SR°; –(CH2)0–4Ph, which may be substituted with R°; –(CH2)0–4O(CH2)0–1Ph which may be substituted with R°; –CH=CHPh, which may be substituted with R°; –(CH2)0–4O(CH2)0–1-pyridyl which may be substituted with R°; –NO2; –CN; –N3; -(CH2)0–4N(R°)2; –(CH2)0–4N(R°)C(O)R°; –N(R°)C(S)R°; –(CH2)0–4N(R°)C(O)NR°2; -N(R°)C(S)NR°2; –(CH2)0–4N(R°)C(O)OR°; - N(R°)N(R°)C(O)R°; -N(R°)N(R°)C(O)NR°2; -N(R°)N(R°)C(O)OR°; –(CH2)0–4C(O)R°; C(S)R°; –(CH2)0–4C(O)OR°; – 2;- CH2-(5- to 6-membered heteroaryl ring), or a 3- to 6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or, notwithstanding the definition above, two independent occurrences of R°, taken together with their intervening atom(s), form a 3- to 12-membered saturated, partially unsaturated, or aryl mono– or bicyclic ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, which may be substituted as defined below.
[0308] Suitable monovalent substituents on R° (or the ring formed by taking two independent occurrences of R° together with their intervening atoms), are independently halogen, –(CH2)0–2Rl, –(haloRl), –(CH2)0–2OH, – (CH2)0–2ORl, –(CH2)0–2CH(ORl)2, -O(haloRl), –CN, –N3, –(CH2)0–2C(O)Rl, –(CH2)0–2C(O)OH, –(CH2)0–2C(O)ORl, –(CH2)0–2SRl, –(CH2)0–2SH, –(CH2)0–2NH2, –(CH2)0–2NHRl, –(CH2)0–2NRl2, –NO2, –SiRl3, –OSiRl3, -C(O)SRl,–(C1–4straight or branched alkylene)C(O)ORl, or –SSRlwherein each Rlis unsubstituted or where preceded by “halo” is substituted only with one or more halogens, and is independently selected from C1–4 aliphatic, –CH2Ph, –O(CH2)0–1Ph, or a 3- to 6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. Suitable divalent substituents on a saturated carbon atom of R° include =O and =S.
[0309] Suitable divalent substituents on a saturated carbon atom of an “optionally substituted” group include the following: =O (“oxo”), =S, =NNR*2, =NNHC(O)R*, =NNHC(O)OR*, =NNHS(O)2R*, =NR*, =NOR*, – O(C(R*2))2–3O–, or –S(C(R*2))2–3S–, wherein each independent occurrence of R*is selected from hydrogen, C1–6 aliphatic which may be substituted as defined below, or an unsubstituted 5- to 6-membered saturated, partially - 44 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) unsaturated, or aryl ring having 0–4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. Suitable divalent substituents that are bound to vicinal substitutable carbons of an “optionally substituted” group include: – O(CR*2)2–3O–, wherein each independent occurrence of R*is selected from hydrogen, C1–6aliphatic which may be substituted as defined below, or an unsubstituted 5–6–membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.
[0310] Suitable substituents on the aliphatic group of R*include halogen, –Rl, -(haloRl), -OH, –ORl, – O(haloRl), –CN, –C(O)OH, –C(O)ORl, –NH2, –NHRl, –NRl2, or –NO2, wherein each Rlis unsubstituted or where preceded by “halo” is substituted only with one or more halogens, and is independently C1–4 aliphatic, –CH2Ph, – O(CH2)0–1Ph, or a 3- to 6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.
[0311] Suitable substituents on a substitutable nitrogen of an “optionally substituted” group include –R†, – NR†2, –C(O)R†, –C(O)OR†, –C(O)C(O)R†, –C(O)CH2C(O)R†, -S(O)2R†, -S(O)2NR†2, –C(S)NR†2, –C(NH)NR†2, or – N(R†)S(O)2R†; wherein each R†is independently hydrogen, C1–6aliphatic which may be substituted as defined below, unsubstituted –OPh, or an unsubstituted 3- to 6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or, notwithstanding the definition above, two independent occurrences of R†, taken together with their intervening atom(s) form an unsubstituted 3- to 12- membered saturated, partially unsaturated, or aryl mono- or bicyclic ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.
[0312] Suitable substituents on the aliphatic group of R†are independently halogen, –Rl, -(haloRl), –OH, – ORl, –O(haloRl), –CN, –C(O)OH, –C(O)ORl, –NH2, –NHRl, –NRl2, or -NO2, wherein each Rlis unsubstituted or where preceded by “halo” is substituted only with one or more halogens, and is independently C1–4 aliphatic, –CH2Ph, – O(CH2)0–1Ph, or a 3- to 6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.
[0313] Subject: As used herein, the term “subject” refers to an organism to be administered with a composition described herein, e.g., for experimental, diagnostic, prophylactic, and / or therapeutic purposes. Typical subjects include animals (e.g., mammals such as mice, rats, rabbits, non-human primates, domestic pets, etc.) and humans. In some embodiments, a subject is a human subject. In some embodiments, a subject is suffering from a disease, disorder, or condition (e.g., HIV, an HIV-associated condition, etc.). In some embodiments, a subject is susceptible to a disease, disorder, or condition (e.g., HIV, an HIV-associated condition, etc.). In some embodiments, a subject displays one or more symptoms or characteristics of a disease, disorder, or condition (e.g., HIV, an HIV- associated condition, etc.). In some embodiments, a subject displays one or more non-specific symptoms of a disease, disorder, or condition (e.g., HIV, an HIV-associated condition, etc.). In some embodiments, a subject does not display any symptom or characteristic of a disease, disorder, or condition (e.g., HIV, an HIV-associated condition, etc.). In some embodiments, a subject is someone with one or more features characteristic of susceptibility to or risk of a disease, disorder, or condition (e.g., HIV, an HIV-associated condition, etc.). 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. - 45 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01)
[0314] Suffering from: An individual who is “suffering from” a disease, disorder, and / or condition (e.g., HIV, an HIV-associated condition, etc.) has been diagnosed with and / or displays one or more symptoms of a disease, disorder, and / or condition.
[0315] Susceptible to: An individual who is “susceptible to” a disease, disorder, and / or condition (e.g., HIV, an HIV-associated condition, etc.) is one who has a higher risk of developing the disease, disorder, and / or condition (e.g., HIV, an HIV-associated condition, etc.) than does a member of the general public. In some embodiments, an individual who is susceptible to a disease, disorder and / or condition (e.g., HIV, an HIV-associated condition, etc.) may not have been diagnosed with the disease, disorder, and / or condition (e.g., HIV, an HIV- associated condition, etc.). In some embodiments, an individual who is susceptible to a disease, disorder, and / or condition (e.g., HIV, an HIV-associated condition, etc.) may exhibit symptoms of the disease, disorder, and / or condition (e.g., HIV, an HIV-associated condition, etc.). In some embodiments, an individual who is susceptible to a disease, disorder, and / or condition (e.g., HIV, an HIV-associated condition, etc.) may not exhibit symptoms of the disease, disorder, and / or condition (e.g., HIV, an HIV-associated condition, etc.). In some embodiments, an individual who is susceptible to a disease, disorder, and / or condition (e.g., HIV, an HIV-associated condition, etc.) will develop the disease, disorder, and / or condition (e.g., HIV, an HIV-associated condition, etc.). In some embodiments, an individual who is susceptible to a disease, disorder, and / or condition (e.g., HIV, an HIV-associated condition, etc.) will not develop the disease, disorder, and / or condition (e.g., HIV, an HIV-associated condition, etc.).
[0316] Therapy: The term “therapy” refers to an administration or delivery of an agent or intervention that has a therapeutic effect and / or elicits a desired biological and / or pharmacological effect (e.g., has been demonstrated to be statistically likely to have such effect when administered to a relevant population). In some embodiments, a therapeutic agent or therapy is any substance that can be used to alleviate, ameliorate, relieve, inhibit, prevent, delay onset of, reduce severity of, and / or reduce incidence of one or more symptoms or features of a disease, disorder, and / or condition (e.g., HIV, an HIV-associated condition, etc.). In some embodiments, a therapeutic agent or therapy is a medical intervention (e.g., surgery, radiation, phototherapy) that can be performed to alleviate, relieve, inhibit, present, delay onset of, reduce severity of, and / or reduce incidence of one or more symptoms or features of a disease, disorder, and / or condition.
[0317] Treat: As used herein, the term “treat,” “treatment,” or “treating” refers to any method used to partially or completely alleviate, ameliorate, relieve, inhibit, prevent, delay onset of, reduce severity of, and / or reduce incidence of one or more symptoms or features of a disease, disorder, and / or condition (e.g., HIV, an HIV-associated condition, etc.). Treatment may be administered to a subject who does not exhibit signs of a disease, disorder, and / or condition (e.g., HIV, an HIV-associated condition, etc.). In some embodiments, treatment may be administered to a subject who exhibits only early signs of the disease, disorder, and / or condition (e.g., HIV, an HIV- associated condition, etc.), 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 at a later-stage of disease, disorder, and / or condition (e.g., HIV, an HIV-associated condition, etc.). - 46 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) DETAILED DESCRIPTION OF CERTAIN EMBODIMENTS I. Human Immunodeficiency Virus (HIV)
[0318] Human Immunodeficiency Virus (HIV) is a lentivirus within the family Retroviridae. A mature HIV particle is generally round in shape and approximately 100nm in diameter. It is composed of (from innermost to outermost) a core comprising of two identical single-stranded RNA molecules, a capsid, and an envelope (Fig.1B) (Musumeci et al., Molecules 20.9 (2015): 17511-17532, which is herein incorporated by reference). The envelope is composed of a lipid bilayer and Env proteins. These Env proteins exist as trimers of gp120 surface protein anchored in the envelope membrane through a gp41 transmembrane protein. The viral capsid, surrounded by the envelope, comprises a symmetrical outer capsid membrane, which is made up of matrix protein p17. Within the outer capsid membrane is the conical capsid comprised of inner capsid protein p24. The inner capsid is attached to the outer capsid membrane at its tapered cone. The inner capsid contains the viral RNA (two identical copies) and viral enzymes: reverse transcriptase, integrase, and protease. Also contained with the viral particle are oligopeptides generated by proteolytic processing of Gag and Gag / Pol precursor proteins p55 and p160 that occurs during the maturation of the viral particle (GAC, Transfusion Medicine Hemotherapy, 43:203–222, 2016, which is herein incorporated by reference).
[0319] There are two main types of HIV, HIV-1 and HIV-2. HIV-1 is the most common type of HIV and accounts for 95% of all infections worldwide. HIV-2 is relatively uncommon and less infectious. HIV-2 is mainly concentrated in West Africa and the surrounding countries.
[0320] HIV-1 and HIV-2 have many similarities including their intracellular replication pathways, transmission modes and clinical effects leading to acquired immune deficiency syndrome (AIDS). However, HIV-2 is less likely to progress into AIDS because of its lower transmissibility. Thus, individuals infected by HIV-2 generally do not see disease progression for a long period of time, while patients infected by HIV-1 progress faster and tend to contract AIDS.
[0321] Once progression begins, however, the pathological process for both viruses is largely similar. One difference is that HIV-2 is found to progress at higher CD4 counts. Additionally, HIV-2 infections are characterized by lower viral loads of over 10,000 copies / mL compared to millions of copies / mL of HIV-1. A subject’s immune response tends to be more protective in the case of HIV-2 infection, thus slowing down disease progression.
[0322] HIV-1 and HIV-2 are, in turn, further divided into groups and subtypes. HIV-1 is divided into main or M group, outlier or O group and non-M / O or N group. The most common group is group M, which is mostly responsible for the HIV epidemic worldwide. The other groups are relatively uncommon and are seen in select geographies including Gabon, Cameroon and Equatorial Guinea.
[0323] Group M is still further divided into genetically distinct subtypes: A, B, C, D, F, G, H, J and K. Some of these subtypes combine to form a hybrid virus called “circulating recombinant form.” Globally, subtype B accounts for 12% of HIV infections. Subtype B is the dominant HIV-1 subtype found in the Americas, Australasia, and Western Europe. As a result, most of the clinical research on HIV to date is focused on these populations.
[0324] Although subtype C represents almost 50% of all HIV affected individuals, less research has focused on this subtype. Subtype C is commonly found in countries in Southern Africa, where the incidence of HIV is - 47 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) very high. Cameroon and the Democratic Republic of Congo, the region of origin of HIV-1, have great diversity of HIV-1 subtypes. However, the pattern of subtype distribution across the globe is changing now, due to population mixing and migration.
[0325] There are about eight HIV-2 subtypes identified to date. The two main subtypes of HIV-2 that are considered epidemic are A and B. HIV-2 group A infections are mostly seen in West Africa, though a few cases have been reported in Brazil, Europe, US and India. HIV-2 group B infections have only been seen in West Africa.
[0326] Because HIV subtypes can be geographically diverse, ideal therapeutics are able to target and neutralize more than one subtype, and even more preferably, multiple strains of HIV. As discussed further below, anti-HIV antibodies capable of binding to and at least temporarily neutralizing HIV virions have been developed. Nonetheless, issues persist with such anti-HIV antibodies, including challenges with administration, antibody persistence in vivo, and viral escape. Polyribonucleotides and compositions of the present disclosure address these challenges, as described herein. A. HIV Genome
[0327] HIV contains two identical copies of single-stranded DNA encoding its genome. When the virus integrates into a host cell, reverse transcription of the viral RNA into double stranded DNA occurs, which leads to degradation of the RNA and integration of the double stranded DNA, or proviral DNA, into the host genome. The HIV genome is flanked at both ends by an LTR (long terminal repeat) region, including a 5' LTR encoding a transcriptional promotor. The RNA genome is 9749 nucleotides and comprises a 5' cap, a 3' poly(A) tail, and several open reading frames ORFs (Wain-Hobson et al., Cell 40(1):9-17, 1985, which is herein incorporated by reference).
[0328] The HIV genome includes the following genes: gag, pol, vif, vpr, tat, rev, vpu, env, and nef (see Fig.1A). The proteins encoded by gag, pol, and env are viral structural proteins. The proteins encoded by tat and rev are essential regulatory proteins. The proteins encoded by nef, vpr, vif, and vpu are accessory regulatory proteins. The gag gene encodes a P555Gag precursor protein of proteins of the outer core membrane (p17), the capsid protein (p24), the nucleoprotein (p7), Pr55Gag, and p6 protein. Protein p24 forms the conical capsid and protein p17 forms the inner membrane layer. Protein p6 is involved in viral particle release.
[0329] The pol gene encodes Pr160GagPol precursor protein, protease enzyme p10, reverse transcriptase (p51), and RNase H (p15) or both together as p66 protein, and integrase p32. Pr160GagPol is the precursor of the viral enzymes p10, p51, and p15. Proteolytic cleavage of Gag (Pr55) and Gag-Pol (Pr160GagPol) results in protease p10. Protein p51 reverse transcriptase is responsible for transcription of HIV RNA into proviral DNA. Protein p55 (RNAse H) functions to degrade viral RNA in the viral RNA / DNA complex when proviral DNA is generated. Protein p32 integrase functions in integrating proviral DNA into a host cell genome.
[0330] The env gene encodes precursor protein PrGp160 of two envelope glycoproteins gp120 (surface protein) and gp41 (transmembrane protein). Proteins gp120 and gp41 are generated by protease cleavage of precursor protein PrGp160. Protein gp120 functions in the attachment of the virus to a target host cell. Protein gp41 anchors gp120 into the viral membrane and functions to fuse the viral and target cell membrane.
[0331] The gene tat encodes Tat protein p14 (transactivator protein), which activates transcription of viral genes. The rev gene encodes Rev protein p19 (RNA splicing-regulator), which regulates export of mRNA (both non- - 48 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) spliced and partially spliced). The nef gene encodes Nef protein p27 (negative regulating factor), which functions in HIV replication and enhances the infectivity of the virus in a host cell. Protein p27 also functions to downregulate CD4 and HLA on target cells. The vif gene encodes Vif protein p23 (viral infectivity factor), which functions in the production of the virus in a host cell. The gene vpr encodes Vpr protein p15 (virus protein r). This protein interacts with p6 protein and facilitates infectivity of the virus in a host cell. The gene vpu encodes Vpu protein p16 (virus protein unique), which allows for efficient release of the viral particle and controls CD4 degradation on a target cell. Protein p16 also controls intracellular signaling. The gene vpx encodes Vpx protein p15 (virus protein x), which functions to interact with p6 protein and is important in the early phases of viral replication. The gene tev encodes Tat / Rev protein p26, which is a fusion protein that regulates Tat and Rev proteins (GAC, Transfusion Medicine Hemotherapy, 43:203–222, 2016, which is herein incorporated by reference). B. Lifecycle
[0332] The lifecycle of HIV involves HIV virion entry into a target host cell, reverse transcription of the viral genome, integration into the host genome, and protein maturation. To initiate infection, an HIV particle comes into contact with a target host cell. Surface glycoprotein env gp120 of a mature HIV particle binds to a CD4 receptor on the target host cell, which initiates the additional binding of gp120 to a co-receptor, i.e., chemokine receptor 5 (CCR5) or chemokine receptor 4 (CXCR4 of fusin). Binding of gp120 to CD4 and the co-receptor triggers a conformational change of gp120 so that gp41 is presented on the viral membrane and can fuse with the plasma membrane of the target host cell. The viral capsid then enters the cytoplasm of the host cell. The capsid is taken up by an endosome releases its contents, i.e., the viral RNA. Upon entry and release of the virus into the target host cell, the virus undergoes reverse transcription, where the viral RNA is reverse transcribed into single stranded cDNA. The RNA strand is then degraded by RNase H, and the single stranded cDNA is converted to double stranded DNA by DNA-dependent DNA polymerase activity by the reverse transcriptase enzyme.
[0333] The double-stranded DNA, or proviral DNA, forms a complex with integrase and is transported into the nucleus of the host cell, and inserts itself at random into the host cell genome. Once integrated into the genome, the proviral genome is replicated. The proviral genome can be replicated with the host cell genome as part of cell division or can replicate using its own machinery. For example, the LTR promotor creates an attachment site for cellular DNA-dependent RNA polymerases and transcription factors to initiate transcription. Transcription of proviral DNA is accelerated by the Tat protein.
[0334] The process of entry into a target host cell, reverse transcription, integration and protein maturation can be completed in less than 24 hours, and progeny viral particles have been detected within 12 hours of infection. The first progeny viral particles after infection may be released from the infected cells about 24 hours after infection. Infected T cells are typically eliminated at a rate of 2-4 days by the immune system (e.g., by cytotoxic T cells). As HIV infected T cells are destroyed and production of T cells is limited, there is a decline in T helper cells. The proteins nef and tat also inhibit maturation and replacement of helper T cells. As a result, an HIV infection over time will result in immunodeficiency (GAC, Transfusion Medicine Hemotherapy, 43:203–222, 2016, which is herein incorporated by reference). - 49 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) C. Transmission and Pathology
[0335] HIV enters the body through intact mucous membranes, injured skin or by parenteral inoculation. HIV is most commonly transmitted sexually. Upon infection, HIV can be detected throughout the body by about 10- 14 days, and transmission via blood or transplanted organs is possible after about 5-6 days post infection. Clinical symptoms typically manifest after 3-6 weeks post infection and can include fever, lymph node enlargement, fatigue, rash, gastrointestinal symptoms, acute neuropathy, myalgias and / or malaise. However, during this acute phase some individuals are asymptomatic. These symptoms of the acute or primary infection can persist for 2–6 weeks. This initial symptomatic phase is then typically followed by an asymptomatic phase or one with occasional symptoms, which can last several years.
[0336] Left untreated, HIV infection causes progressive CD4+ T cell loss, which can lead to a suite of immunological abnormalities and an increased risk of infectious and oncological complications. Additionally, HIV infection also implicates cardiovascular disease, bone disease, renal and hepatic dysfunction, and several other common morbidities.
[0337] Although antiviral therapies (ART) have been developed to treat HIV infection, ART can only prevent new cells from becoming infected, i.e., ART cannot eliminate infection if a cell already contains viral DNA integrated into its genome. Additionally, HIV establishes a latent infection in CD4+ T cells that can be maintained indefinitely, some having the capability of self-renewal. HIV may continue to reinitiate replication in a cell once it is integrated into its genome. (Deeks et al. Nature reviews 1.12015 and GAC, Transfusion Medicine Hemotherapy, 43:203–222, 2016, which are herein incorporated by reference). D. Therapeutic Strategies
[0338] Development of therapeutics targeting HIV face many challenges. One challenging factor is the heterogeneity of the virus. HIV can be divided into at least two major types (HIV-1, found worldwide, and HIV-2, found largely in west Africa), while HIV-1 has been further subdivided into three subgroups (M, N, O and P), and M has been still further subdivided into subtypes A-L. Subtypes are also able to recombine upon co-infection, resulting in yet further recombinant subtypes.
[0339] Another challenging factor is that the high mutation rate of HIV in vivo. A recent study quantified the HIV-1 genome-wide rate of spontaneous mutation in DNA sequences from peripheral blood mononuclear cells and revealed an extremely high mutation rate of (4.1 ± 1.7) × 10−3per base per cell, which is the highest rate reported for any biological entity (Cuevas et al, PloS Biol 2015, which is herein incorporated by reference). The ability to identify and develop a therapeutic targeting a conserved epitope across the multiple groups and subtypes of a continuously mutating HIV sequence is therefore extremely challenging, and the virus has a unique ability to evade the immune system.
[0340] Aside from the high mutational frequency, HIV presents other challenges for the immune system that make it uniquely challenging to treat. Therapeutic targets on HIV include the HIV envelop protein (HIV Env), however, the HIV Env is heavily glycosylated and the Env sites are therefore shielded from a therapeutic by the glycans present. Additionally, Env glycans are derived from the host and can be extremely heterogeneous. - 50 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01)
[0341] A recent therapeutic strategy involves use of broadly neutralizing antibodies (bNAbs), which are antibodies that can neutralize a diversity of global HIV isolates. Such antibodies have been identified from individuals infected by HIV considered to be “Elite Neutralizers,” making up <10% of HIV patients (Burton and Hangartner, Ann. Rev. Immunol. 2016, which is herein incorporated by reference). Such antibodies provide insights for potential target epitopes and structures of therapeutics. Other advances to aid the advance of therapeutics include the generation of a stable HIV Env spike trimer (Sanders and Moore, Immunol. Rev. 2017, which is herein incorporated by reference) and characterization of its structure at high resolution (Ward and Wilson, Immunol. Rev. 2017, which is herein incorporated by reference). Examples of Env sites that are potential targets include the apex site, the high-mannose patch of the gp120 region, the gp120-gp41 interface region, the gp41 membrane proximal region (MPER), and the CD4 binding site (see Fig.2, from McCoy and Burton, Immunol Rev. 275.111-202017, which is herein incorporated by reference). These sites each face unique challenges as a therapeutic target for bNAbs. For examples, bNAbs that target the gp41–gp120 interface must be able bind to complex heterogeneous glycans. BNAbs that target the CD4 binding site of the Env protein have been found to show high levels of somatic hypermutation.
[0342] 10E8, as well as 2F5 and 4E10, is in a class of bnAbs that target the MPER (Huang J, Ofek G, Laub L, et al. Broad and potent neutralization of HIV-1 by a gp41-specific human antibody. Nature. 2012; 491: 406– 412; Buchacher A, Predl R, Tauer C, et al. Human monoclonal antibodies against gp41 and gp120 as potential agents for passive immunization. In: F Brown, R Chanock, HS Ginsberg, R Lerner, eds. Vaccines ‘92: Modern Approaches to New Vaccines Including Prevention of AIDS. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory; 1992: 191– 194.; Stiegler G, Kunert R, Purtscher M, et al. A potent cross-clade neutralizing human monoclonal antibody against a novel epitope on gp41 of human immunodeficiency virus type 1. AIDS Res Hum Retroviruses. 2001; 17: 1757– 1765; Zwick MB, Labrijn AF, Wang M, et al. Broadly neutralizing antibodies targeted to the membrane-proximal external region of human immunodeficiency virus type 1 glycoprotein gp41. J Virol. 2001, 75: 10892– 10905.; Muster T, Steindl F, Purtscher M, et al. A conserved neutralizing epitope on gp41 of human immunodeficiency virus type 1. J Virol. 1993; 67: 6642– 6647.) 10E8 is highly potent and does not display any autoreactivity nor does it bind lipids as has been reported for other MPER Abs (Irimia A, Sarkar A, Stanfield RL, Wilson IA. Crystallographic identification of lipid as an integral component of the epitope of HIV broadly neutralizing antibody 4E10. Immunity. 2016; 44: 21– 31.). This may be because 10E8 approaches MPER from an altered angle and uses a different binding mode to, e.g., 4E10 (Huang J, Ofek G, Laub L, et al. Broad and potent neutralization of HIV-1 by a gp41-specific human antibody. Nature. 2012; 491: 406– 412.).
[0343] The present disclosure provides, among other things, polyribonucleotides that encode antibody agents, e.g., bNAbs, that target a broader group of HIV variants, and as such and are able to treat a greater number of HIV patients. Additionally, the present disclosure provides compositions for the delivery of polyribonucleotides that encode antibody agents, e.g., bNAbs, targeting various HIV sequences. 1. Anti-Viral Treatments for HIV
[0344] HIV infection is currently, primarily treated with antiretroviral therapy (ART). ART is a type of drug that can reduce HIV multiplication, increase CD4 cell count, and reduce transmission risk in an infected individual. The World Health Organization (WHO) recommends that ART be initiated in all adults infected with HIV regardless of clinical stage or CD4 cell count (Consolidated guidelines on HIV prevention, testing, treatment, service delivery and - 51 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) monitoring: recommendations for a public health approach. Geneva: World Health Organization; 2021, which is herein incorporated by reference). However, ART is not a curative therapy, and viremia (e.g., viral load) will quickly rebound if an infected individual stops taking ART. The high mutation rate of HIV also constrains patient in having a strict observance with their therapy to avoid the emergence of escape mutants and treatment failure. Thus, ART is intended to be taken every day for the entirety of an infected subject’s life.
[0345] There are several classes of FDA-approved ART to treat HIV that act via different mechanisms. Effective management of HIV infection often involves combinations of at least 3 ARTs to treat the complex pathogenicity of the disease. The most effective combination of ARTs is often different between infected individuals (see, for example, Bhatti et al., Cureus 2016, which is herein incorporated by reference). Cihlar et al., Current opinion in virology, 2016, hereby incorporated by reference in its entirety, reviews the classes of ART drugs for the treatment of HIV. Table 1: Exemplary classes of ART used to treat HIV, mechanisms of action, and exemplary compounds in each class ART Class Mechanism of Action Examples CCR5 Antagonist Inhibits HIV entry into cell by Maraviroc blocking CCR5 and viral interaction Fusion Inhibitors Inhibits HIV envelope from merging Enfuvirtide with host cell membrane Integrase Strand Transfer Inhibitor Inhibits integration of viral DNA into Bictegravir, Dolutegravir, (INSTI) host genome by blocking integrase Elvitegravir, Raltegravir enzyme Non-Nucleoside Reverse Inhibits HIV replication by blocking Delavirdine, Doravirine, Efavirenz, Transcriptase Inhibitors (NNRTI) reverse transcriptase enzyme to Etravirine, Nevirapine, Rilpivirine, suppress conversion of RNA into DNA Nucleoside Reverse Transcriptase Inhibits HIV replication by blocking Abacavir, Emtricitabine, Lamivudine, Inhibitors (NRTI) reverse transcriptase enzyme to Tenofovir, Zidovudine suppress conversion of RNA into DNA Post-Attachment Inhibitor Inhibits HIV entry into cell after Ibalizumab binding has occurred Protease Inhibitors Inhibits HIV particle development Atazanavir, Darunavir, and maturity by blocking protease Fosamprenavir, Lopinavir, enzyme Nelfinavir, Ritonavir, Tipranavir 2. HIV Antibody Agents
[0346] In addition to ART, anti-HIV antibodies have been developed. Using anti-HIV antibodies for treating HIV generally requires antibodies having specific characteristics, including safety, a favorable pharmacokinetic profile, highly potent neutralizing activity, and broad neutralizing activity to effectively target the diversity present in HIV virions. As with other HIV therapeutics (including, e.g., ART), viral escape from anti-HIV antibodies present a significant challenge.
[0347] For example, Barouch, et al. infected rhesus macaques with SHIV-SF162P3 (Barouch, et al., Nature 503: 7475224-228, 2013), which is incorporated herein by reference in its entirety. The rhesus macaques were then treated with 3 monoclonal antibodies (mAbs): N332 glycan-dependent mAb PGT121 and CD4 binding site-specific mAbs 3BNC117 and b12. mAbs were administered as a cocktail on days 0 and 7 at 10 mg / kg each, as a cocktail on - 52 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) day 0 alone at 10 mg / kg each or as a combination of just PGT121 and 3BNC117 at 10 mg / kg each. Transient viral suppression was observed until bNAbs level dropped below 10 µg / mL. mAbs were also singly administered to macaques, and PGT121 alone resulted in rapid virologic control which rebounded after 6-8 weeks in most animals. The macaques that received a combination of PGT121 and 3BNC117 were given a second dose on day 105, after viral levels had rebounded. Viral re-suppression was observed, although the control was less durable than the previous administration.
[0348] Shingai, et al. describes rhesus macaques were infected with SHIVAD8EO(Shingai, et al., Nature 503: 7475277-280, 2013, which is incorporated herein by reference in its entirety). The rhesus macaques were then treated with 10-1074 and 3BNC117 mAbs singly or in combination. When administered singly at 12 weeks post inoculation at 10 mg / kg, both antibodies caused rapid viral suppression, but virus levels quickly rebounded. Administration of both antibodies in combination to chronically infected animals resulted in longer periods of suppression and increased CD4+ T cell levels, although viral levels did rebound later. In other studies, both antibodies were singly pre-treated to macaques and were found to prevent virus acquisition. Single genome analysis of rebounded virus in 10-074 treated macaques revealed mutations that eliminated the gp120 N332 glycan, rendering resistance to the mAb. However, SGA analysis of rebounded virus in macaques treated with both 10-074 and 3BNC117 revealed that not all of the macaques contained virus with changes that imparted mAb resistance.
[0349] Caskey, et al. describe a first-in-human dose escalation phase 1 clinical trial of 3BNC117 (CD4 binding site antibody) (Caskey, et al., Nature 522.7557: 487-491, 2015, which is incorporated herein by reference in its entirety). Uninfected and HIV-1-infected individuals were enrolled in the trial. 1, 3, 10, or 30 mg / kg doses of 3BNC117 were found to be generally safe and well tolerated; no grade 3, 4, or serious adverse events were observed. HIV-1-infected individuals were observed to have a quicker clearance rate of the antibody than uninfected control subjects. The effect of the treatment on viral load was dose-dependent; 10 and 30 mg / kg doses decreased viral load by up to 2.5 log. Viral resistance was observed to develop in some individuals regardless of mAb dose, but not in other individuals. Viruses were cloned and sequenced, G459D was a commonly observed mutation in the 10 mg / kg group, others showed a longer V5 loop (other mutations described). Both mutations can alter sensitivity to anti-CD4bs.
[0350] Caskey, et al. also assessed 10-074, which is a highly potent mAb that targets the V3 loop of the HIV-1 envelope spike (Caskey et al., Nature Medicine 23.2: 185-191, 2017), which is incorporated herein by reference in its entirety. An open label phase 1 first-in-human clinical trial was performed with 14 uninfected and 19 HIV-1-infected individuals. A single intravenous infusion was administered at 3, 10, or 30 mg / kg. The mAb was found to be generally safe and well-tolerated; no grade 3, 4, or serious adverse events were observed. HIV-1-infected individuals were observed to have a quicker clearance rate of the antibody than uninfected controls. Treatment suppressed viral load in individuals with 10-074 sensitive strains, followed by rebound. Single genome sequencing (SGS) of rebounded virus revealed all patients that responded to treatment displayed a PNGS at position N332 and an intact324G(D / N)IR327motif. Four weeks after infusion, 91% of envelope sequences contained amino acid mutations, 97% of which eliminated the PNGS at position 332 by mutating either N332 or S334. 3% of mutated sequences showed changes at D / N325 in the324G(D / N)IR327motif. Majority of mutations at nucleic acid level were transitions, consistent with reverse transcriptase errors. Neutralization assay testing showed that mutated HIV-1 - 53 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) resistant to 10-074 was not resistant to 3BNC117, VRC01, or PGDM1400 (mAbs targeting other regions of HIV-1). SGS performed 1 week after infusion revealed that resistant variants are pre-existing or rapidly generated.
[0351] Bar, et al. performed two open-lab trials, which were conducted on the safety, side-effect profile, pharmacokinetic properties, and antiviral activity of VRC01 (bNAb targeting CD4-binding site of HIV) in patients undergoing interruption of antiretroviral therapy (ART) (Bar et al., New England Journal of Medicine 375.21: 2037- 2050, 2016, which is incorporated herein by reference in its entirety). In one trial, 40 mg / kg was infused 3 times over a 6 week period, and in the other trial, 40 mg / kg was infused 8 times over a 6 month period. Treatment was well tolerated, no grade 3 or higher adverse events were observed. Neither trial produced durable suppression of plasma viremia, although a slight increase in time to rebound was found relative to historical controls. Regardless of time to rebound, resistance to VRC01 increased almost universally in participants in one trial. Viral isolates showed greater resistance to VRC01 neutralization in pre-treated samples versus post-treated. Treatment with VRC01 did not impact the susceptibility to neutralization with other bNAbs.
[0352] Mendoza, et al. performed a phase 1b clinical trial assessing the combination of 3BNC117 and 10- 1074, which were infused at 30 mg / kg dose on weeks 0, 3, and 6 (Mendoza, et al., Nature 561.7724: 479-484, 2018, which is incorporated herein by reference in its entirety). These two bNAbs target independent sites on HIV-1 envelope spike. Infusions were generally found to be safe and well tolerated with no reported serious adverse events. Median time to rebound was significantly extended with combination bNAb treatment. Two earliest rebounder individuals were found to previously harbor strains resistant to one or the other bNAb. Rebounded virus clustered within low diversity lineages consistent with expansion of 1-2 recrudescent viruses (escape). Most rebounded virus was found to contain 10-1074 mutations as compared to 3BNC117 mutations. However, combination bNAb therapy proved more effective at containing viral escape than single bNAb treatment.
[0353] Gautam, et al. assayed rhesus macaques that were infected with SHIVAD8EO and treated with 3BNC117-LS and 10-074-LS mAbs (Gautam, Rajeev, et al., Nature Medicine 24.5: 610-616, 2018, which is incorporated herein by reference in its entirety). M428L and N343S (collectively referred to as LS) are mutations in the fragment domains of the mAbs to increase half-life. The LS mutations had no effect on virus neutralization in in vitro assays. LS mAbs were administered singly at 20 mg / kg, and were well tolerated in all monkeys. 10-1074-LS recipients demonstrated increased protection from virus acquisition than 3BNC117-LS recipients, but LS mutations in both antibodies were more effective than WT. 10-1074-LS decayed at a slower rate than 3BNC117-LS in serum. mAb concentration / neutralization activity were determined to be predictive of the probability of infection. Only experiments in which antibody pre-treatment followed by virus challenge were performed.
[0354] Schommers, et al. characterized an anti-HIV antibody, referred to as “1-18,” in in vitro assays, as well as HIV-1 infected humanized mice. 1-18 was reported to bind to the CD4 binding site of HIV and have strong potency and breadth against HIV strains. Schommers reported that 1-18 had certain characteristics previously found in other anti-HIV antibodies, which seemed to contribute to 1-18’s potency and breadth: (1) 1-18 has an aromatic residue that mimics residue Phe43 of CD4 to target the “Phe43gp120 pocket,” a characteristic previously reported for the anti-HIV antibody, N6; (2) 1-18 contacts with the adjacent gp120 protomer, as previously observed with the anti- HIV antibody, 3BNC117, but with increased buried surface area (via its six-residue insertion in CDRH1); and (3) a larger buried surface area on gp120 than other the anti-HIV antibodies. In addition, 1-18 was reported to contact - 54 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) conserved residues on HIV gp120 that other anti-HIV antibodies did not contact. Schommers hypothesized that these contacts may allow 1-18 to rely less on classical CD4 binding site contacts, which may make viral escape more difficult. Nonetheless, Schommers observed that a small number of HIV strains was found to be 1-18 resistant.
[0355] Together, the above data suggest that administration of antibodies can be effective for treating or preventing HIV. However, the difficulties with targeting such a mutable virus are evident from the studies above, as well as studies showing that (1) when a single broadly neutralizing antibody (bNAb) was used for therapy, HIV resistance to the therapy developed within a few weeks (Bar et al., Effect of HIV Antibody VRC01 on Viral Rebound after Treatment Interruption, N. Engl. J. Med. 375, 2037–2050 (2016); Caskey et al., Viraemia suppressed in HIV-1- infected humans by broadly neutralizing antibody 3BNC117. Nature 522, 487–491 (2015); Caskey et al., Antibody 10- 1074 suppresses viremia in HIV-1-infected individuals. Nat. Med. 23, 185–191 (2017); Klein et al., HIV therapy by a combination of broadly neutralizing antibodies in humanized mice, Nature 492, 118–122 (2012); Lynch et al., Virologic effects of broadly neutralizing antibody VRC01 administration during chronic HIV-1 infection, Sci. Transl. Med. 7, 319ra206 (2015); Scheid et al., HIV-1 antibody 3BNC117 suppresses viral rebound in humans during treatment interruption, Nature 535, 556–560 (2016), each of which is herein incorporated by reference in its entirety), and (2) certain antibody combinations resulted in improved viral control by preventing early development of resistance (Bar-On et al., Safety and antiviral activity of combination HIV-1 broadly neutralizing antibodies in viremic individuals, Nat. Med. 24, 1701–1707 (2018); Klein et al., 2012; Mendoza et al., Combination therapy with anti-HIV-1 antibodies maintains viral suppression, Nature 561, 479–484 (2018), each of which is herein incorporated by reference in its entirety). The viral rebound observed with some of these antibodies suggests that the antibodies may only be effective for a limited time, e.g., prior to HIV escape mutations developing.
[0356] An approach to improve antibody solubility and potency was taken for the gp41 membrane proximal external region (MPER) binding antibody, 10E8 (Huang J, et al., Broad and potent neutralization of HIV-1 by a gp41-specific human antibody. Nature. 2012;491:406–12, which is herein incorporated by reference in its entirety). 10E8 bNAb was identified from an HIV-1 infected individual and is one of the broadest antibodies reported to date, neutralizing > 95% of circulating HIV-1 strains. However, 10E8 is naturally prone to aggregation, which limited its clinical manufacturability potential. By identifying somatic variants of 10E8 with inherently better solubility, and then using structural data to mutate a hydrophobic patch distal from the binding site of this antibody, a significantly more soluble variant of 10E8 was obtained (Kwon YD, et al., Optimization of the solubility of HIV-1-neutralizing antibody 10E8 through somatic variation and structure-based design. J Virol. 2016;90:5899–914, which is herein incorporated by reference in its entirety). Because germline variants often exhibit reduced potency compared to their affinity matured antibody counterparts, residues from 10E8 critical for binding to MPER were then grafted onto this more soluble antibody. The new 10E8 variants retained the improved solubility but now also exhibited potency similar to the originally identified 10E8. The top variants, 10E8v4 and 10E8v5, exhibited improved pharmacokinetic profiles in mice and rhesus macaques as compared to 10E8, and 10E8v5 has been advanced for clinical evaluation (VRC 610: Phase I Safety and Pharmacokinetics Study to Evaluate a Human Monoclonal Antibody (MAB) VRC-HIVMAB095-00-AB (10E8VLS) Administered Alone or Concurrently with MAB VRC- HIVMAB075-00-AB (VRC07-523LS) via Subcutaneous Injection in Healthy Adults (ClinicalTrials.gov. U.S. National Library of Medicine. https: / / clinicaltrials.gov / ct2 / show / NCT03565315. Accessed 03 Aug 2018). An additional 10E8v4 variant, known as 10E8v4-5R-100cF, was recently reported to improve the potency of 10E8v4 by an additional ~ 10-fold using a surface-matrix screening - 55 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) approach (Kwon YD, et al., Surface-matrix screening identifies semi-specific interactions that improve potency of a near pan-reactive HIV-1-neutralizing antibody. Cell Rep. 2018;22:1798–809, which is herein incorporated by reference in its entirety).
[0357] Treatments and prophylactic therapeutics that can avoid viral escape and remain effective for HIV neutralization are still needed. As discussed herein, the present disclosure provides technologies useful for administering polyribonucleotides encoding one or more antibody agents, e.g., anti-HIV antibody agents, to a subject. Use of the technologies and approaches described herein allows for, e.g., simultaneous production of different antibody agents from polyribonucleotides. The formats of antibody agents have been designed to minimize or eliminate the risk of immunoglobulin chain mispairing. Being able to combine multiple antibody agent formulations as described herein (e.g., including a 10E8v4-5R-100cF antibody agent) allows for the development of a composition (e.g., a pharmaceutical composition) that delivers multiple antibody agents together so that they can bind different epitopes of the HIV virus, thereby minimizing viral escape through mutations and increasing overall efficacy. II. Polyribonucleotides for Delivery of Antibody Agents
[0358] The present disclosure, among other things, utilizes RNA technologies as a modality to express antibody agents directly in a subject as a novel class of antibody-based therapeutics. In some embodiments, a polyribonucleotide as described herein encodes an immunoglobulin chain of an antibody agent.
[0359] In some embodiments, an antibody agent targets HIV. In some embodiments, an antibody agent targeting HIV specifically binds to particular epitope of an HIV polypeptide. For example, in some embodiments, an antibody agent specifically binds to an epitope encompassing the CD4 binding site or a portion thereof. See Fig.2, from McCoy and Burton, Immunol Rev. 275.111-20, 2017, which is herein incorporated by reference.
[0360] In some embodiments, an antibody agent may have a binding affinity (e.g., as measured by a dissociation constant) for an HIV epitope (e.g., an epitope of the MPER binding site) of at least about 10-4M, at least about 10-5M, at least about 10-6M, at least about 10-7M, at least about 10-8M, at least about 10-9M, or lower. In some embodiments, an HIV antibody agent selectively binds a target epitope of HIV such that binding between the HIV antibody agent and the target epitope is greater than 2-fold, greater than 5-fold, greater than 10-fold, or greater than 100-fold as compared with binding of the HIV antibody agent to a non-target epitope. In some embodiments, an HIV antibody agent may have binding affinity for an HIV epitope and also variants of said HIV epitope. Those skilled in the art will appreciate that, in some cases, binding affinity (e.g., as measured by a dissociation constant) may be influenced by non-covalent intermolecular interactions such as hydrogen bonding, electrostatic interactions, hydrophobic and Van der Waals forces between the two molecules. Alternatively or additionally, binding affinity between a ligand and its target molecule may be affected by the presence of other molecules. Those skilled in the art will be familiar with a variety of technologies for measuring binding affinity and / or dissociation constants in accordance with the present disclosure, including, e.g., but not limited to ELISAs, gel-shift assays, pull-down assays, equilibrium dialysis, analytical ultracentrifugation, surface plasmon resonance (SPR), bio-layer interferometry, grating-coupled interferometry, and spectroscopic assays.
[0361] In some embodiments, an antibody agent targeting HIV may comprise or be derived from a broadly neutralizing antibody (bNAb). In some embodiments, an antibody agent targeting HIV may be any one of the - 56 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) HIV-targeting antibodies described in Barouch, et al., Nature 503: 7475224-228, 2013, Shingai, et al., Nature 503: 7475277-280, 2013, Caskey, et al., Nature 522.7557: 487-491, 2015, Caskey et al., Nature Medicine 23.2: 185-191, 2017, Bar et al., New England Journal of Medicine 375.21: 2037-2050, 2016, Mendoza, et al., Nature 561.7724: 479- 484, 2018, Gautam, Rajeev, et al., Nature Medicine 24.5: 610-616, 2018, the contents of each of which are incorporated herein by reference in their entirety for the purposes described herein.
[0362] In some embodiments, an antibody agent targeting HIV may be e.g., 10E8v4-5R-100cF, 1-18, PGT121, 3BNC117, b12, 10-1074, 10E8, 10E8v4, VRC01, VRC07-523, VRC07, N6, PG9, 4E10, PGT151, PGT128, 8ANC195, 2F5, IOMA, PGDM1400, fragments thereof, or combinations thereof. Exemplary anti-HIV antibodies that can be used in compositions described herein include, but are not limited to, 10E8v4-5R-100cF, 1-18, PGT121, 3BNC117, b12, 10-1074, 10E8, 10E8v4, VRC01, VRC07-523, VRC07, N6, PG9, 4E10, PGT151, PGT128, 8ANC195, 2F5, IOMA, PGDM1400, fragments thereof, or combinations thereof. For example, in some embodiments, a polyribonucleotide as described herein can comprise one or more heavy chain complementarity determining regions (HCDRs) (e.g., HCDR1, HCDR2, and / or HCDR3) from 10E8v4-5R-100cF, 1-18, PGT121, 3BNC117, b12, 10-1074, 10E8, 10E8v4, VRC01, VRC07-523, VRC07, N6, PG9, 4E10, PGT151, PGT128, 8ANC195, 2F5, IOMA, or PGDM1400. In some embodiments, a polyribonucleotide as described herein can comprise HCDR1, HCDR2, and HCDR3 from 10E8v4-5R-100cF, 1-18, PGT121, 3BNC117, b12, 10-1074, 10E8, 10E8v4, VRC01, VRC07-523, VRC07, N6, PG9, 4E10, PGT151, PGT128, 8ANC195, 2F5, IOMA, or PGDM1400. In some embodiments, a polyribonucleotide as described herein can comprise a heavy chain variable domain from 10E8v4-5R-100cF, 1-18, PGT121, 3BNC117, b12, 10-1074, 10E8, 10E8v4, VRC01, VRC07-523, VRC07, N6, PG9, 4E10, PGT151, PGT128, 8ANC195, 2F5, IOMA, or PGDM1400. In some embodiments, a polyribonucleotide as described herein can comprise one or more light chain complementarity determining regions (LCDRs) (e.g., LCDR1, LCDR2, and / or LCDR3) from 10E8v4-5R-100cF, 1-18, PGT121, 3BNC117, b12, 10-1074, 10E8, 10E8v4, VRC01, VRC07-523, VRC07, N6, PG9, 4E10, PGT151, PGT128, 8ANC195, 2F5, IOMA, or PGDM1400. In some embodiments, a polyribonucleotide as described herein can comprise LCDR1, LCDR2, and LCDR3 from 10E8v4-5R-100cF, 1-18, PGT121, 3BNC117, b12, 10-1074, 10E8, 10E8v4, VRC01, VRC07-523, VRC07, N6, PG9, 4E10, PGT151, PGT128, 8ANC195, 2F5, IOMA, or PGDM1400. In some embodiments, a polyribonucleotide as described herein can comprise a light chain variable domain from 10E8v4-5R-100cF, 1-18, PGT121, 3BNC117, b12, 10-1074, 10E8, 10E8v4, VRC01, VRC07-523, VRC07, N6, PG9, 4E10, PGT151, PGT128, 8ANC195, 2F5, IOMA, or PGDM1400.
[0363] In some embodiments, a plurality of polyribonucleotides that each encode an immunoglobulin chain of an antibody agent can be used to deliver (e.g., by administration to a subject) two or more antibody agents (e.g., 10E8v4-5R-100cF, 1-18, PGT121, 3BNC117, b12, 10-1074, 10E8, 10E8v4, VRC01, VRC07-523, VRC07, N6, PG9, 4E10, PGT151, PGT128, 8ANC195, 2F5, IOMA, or PGDM1400, or fragments or variants thereof). In some embodiments, a plurality of polyribonucleotides that each encode an immunoglobulin chain of an antibody agent can be used to deliver (e.g., by administration to a subject) three or more antibody agents (e.g., 10E8v4-5R-100cF, 1-18, PGT121, 3BNC117, b12, 10-1074, 10E8, 10E8v4, VRC01, VRC07-523, VRC07, N6, PG9, 4E10, PGT151, PGT128, 8ANC195, 2F5, IOMA, or PGDM1400, or fragments or variants thereof). In some embodiments, a plurality of polyribonucleotides that each encode an immunoglobulin chain of an antibody agent can be used to deliver (e.g., by administration to a subject) four or more antibody agents (e.g., 10E8v4-5R-100cF, 1-18, PGT121, 3BNC117, b12, 10- 1074, 10E8, 10E8v4, VRC01, VRC07-523, VRC07, N6, PG9, 4E10, PGT151, PGT128, 8ANC195, 2F5, IOMA, or - 57 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) PGDM1400, or fragments or variants thereof). In some embodiments, a plurality of polyribonucleotides that each encode an immunoglobulin chain of an antibody agent can be used to deliver (e.g., by administration to a subject) two, three, four, five or six antibody agents (e.g., 10E8v4-5R-100cF, 1-18, PGT121, 3BNC117, b12, 10-1074, 10E8, 10E8v4, VRC01, VRC07-523, VRC07, N6, PG9, 4E10, PGT151, PGT128, 8ANC195, 2F5, IOMA, or PGDM1400, or fragments or variants thereof).
[0364] In some embodiments, an antibody agent encoded by one or more polyribonucleotides described herein includes all or part of a 10E8, 10E8v4, or 10E8v4-5R-100cF antibody. In some embodiments, an antibody agent encoded by one or more polyribonucleotides provided herein includes all or part of a 10E8, 10E8v4, or 10E8v4- 5R-100cF antibody. In some embodiments, an antibody agent comprises a heavy chain variable domain comprising: (i) HCDR1 (GFDFDNAW; SEQ ID NO: 6); (ii) HCDR2 (ITGPGEGWSV; SEQ ID NO: 9); (iii) HCDR3 (ARTGKYYDFWFGYPPGEEYFQD; SEQ ID NO: 12 or ARTGKYYDFWSGYPPGEEYFQD; SEQ ID NO: 34); or (iv) a combination thereof. In some embodiments, an antibody agent comprises a heavy chain variable domain comprising: (i) HCDR1 (GFDFDNAW; SEQ ID NO: 6); (ii) HCDR2 (ITGPGEGWSV; SEQ ID NO: 9); and (iii) HCDR3 (ARTGKYYDFWFGYPPGEEYFQD; SEQ ID NO: 12 or ARTGKYYDFWSGYPPGEEYFQD; SEQ ID NO: 34). In some embodiments, an antibody agent comprises a light chain variable domain comprising: (i) LCDR1 (SLRSHY; SEQ ID NO: 15); (ii) LCDR2 (GKN); (iii) LCDR3 (SSRDKSGSRLSV; SEQ ID NO: 21); or (iv) a combination thereof. In some embodiments, an antibody agent comprises a light chain variable domain comprising: (i) LCDR1 (SLRSHY; SEQ ID NO: 15); (ii) LCDR2 (GKN); and (iii) LCDR3 (SSRDKSGSRLSV; SEQ ID NO: 21). In some embodiments, an antibody agent comprises (a) a heavy chain variable domain comprising: (i) HCDR1 (GFDFDNAW; SEQ ID NO: 6); (ii) HCDR2 (ITGPGEGWSV; SEQ ID NO: 9); (iii) HCDR3 (ARTGKYYDFWFGYPPGEEYFQD; SEQ ID NO: 12 or SEQ ID NO: 34; ARTGKYYDFWSGYPPGEEYFQD); or (iv) a combination thereof; and (b) a light chain variable domain comprising: (i) LCDR1 (SLRSHY; SEQ ID NO: 15); (ii) LCDR2 (GKN); (iii) LCDR3 (SSRDKSGSRLSV; SEQ ID NO: 21); or (iv) a combination thereof. In some embodiments, an antibody agent comprises (a) a heavy chain variable domain comprising: (i) HCDR1 (GFDFDNAW; SEQ ID NO: 6); (ii) HCDR2 (ITGPGEGWSV; SEQ ID NO: 9); and (iii) HCDR3 (ARTGKYYDFWFGYPPGEEYFQD; SEQ ID NO: 12 or ARTGKYYDFWSGYPPGEEYFQD; SEQ ID NO: 34); and (b) a light chain variable domain comprising: (i) LCDR1 (SLRSHY; SEQ ID NO: 15); (ii) LCDR2 (GKN); and (iii) LCDR3 (SSRDKSGSRLSV; SEQ ID NO: 21).
[0365] In some embodiments, a polyribonucleotide described herein encodes all or part of a 10E8v4-5R- 100cF antibody. In some embodiments, a polyribonucleotide described herein encodes an immunoglobulin chain comprising a heavy chain variable domain, wherein the heavy chain variable domain comprises: (i) HCDR1 (GFDFDNAW; SEQ ID NO: 6); (ii) HCDR2 (ITGPGEGWSV; SEQ ID NO: 9); (iii) HCDR3 (ARTGKYYDFWFGYPPGEEYFQD; SEQ ID NO: 12 or ARTGKYYDFWSGYPPGEEYFQD; SEQ ID NO: 34); or (iv) a combination thereof. In some embodiments, a polyribonucleotide described herein encodes an immunoglobulin chain comprising a heavy chain variable domain, wherein the heavy chain variable domain comprises: (i) HCDR1 (GFDFDNAW; SEQ ID NO: 6); (ii) HCDR2 (ITGPGEGWSV; SEQ ID NO: 9); and (iii) HCDR3 (ARTGKYYDFWFGYPPGEEYFQD; SEQ ID NO: 12 or ARTGKYYDFWSGYPPGEEYFQD; SEQ ID NO: 34). In some embodiments, a polyribonucleotide described herein encodes an immunoglobulin chain comprising a light chain variable domain, wherein the light chain variable domain comprises: (i) LCDR1 (SLRSHY; SEQ ID NO: 15); (ii) LCDR2 (GKN); (iii) LCDR3 (SSRDKSGSRLSV; SEQ ID NO: 21); or (iv) a combination thereof. In some embodiments, a - 58 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) polyribonucleotide described herein encodes an immunoglobulin chain comprising a light chain variable domain, wherein the light chain variable domain comprises: (i) LCDR1 (SLRSHY; SEQ ID NO: 15); (ii) LCDR2 (GKN); and (iii) LCDR3 (SSRDKSGSRLSV; SEQ ID NO: 21). In some embodiments, a polyribonucleotide described herein encodes an immunoglobulin chain comprising a heavy chain variable domain and a light chain variable domain, wherein the heavy chain variable domain comprises: (i) HCDR1 (GFDFDNAW; SEQ ID NO: 6); (ii) HCDR2 (ITGPGEGWSV; SEQ ID NO: 9); (iii) HCDR3 (ARTGKYYDFWFGYPPGEEYFQD; SEQ ID NO: 12 or ARTGKYYDFWSGYPPGEEYFQD; SEQ ID NO: 34); or (iv) a combination thereof; and the light chain variable domain comprises: (i) LCDR1 (SLRSHY; SEQ ID NO: 15); (ii) LCDR2 (GKN); (iii) LCDR3 (SSRDKSGSRLSV; SEQ ID NO: 21); or (iv) a combination thereof. In some embodiments, a polyribonucleotide described herein encodes an immunoglobulin chain comprising a heavy chain variable domain and a light chain variable domain, wherein the heavy chain variable domain comprises: (i) HCDR1 (GFDFDNAW; SEQ ID NO: 6); (ii) HCDR2 (ITGPGEGWSV; SEQ ID NO: 9); and (iii) HCDR3 (ARTGKYYDFWFGYPPGEEYFQD; SEQ ID NO: 12 or ARTGKYYDFWSGYPPGEEYFQD; SEQ ID NO: 34); and the light chain variable domain comprises: (i) LCDR1 (SLRSHY; SEQ ID NO: 15); (ii) LCDR2 (GKN); and (iii) LCDR3 (SSRDKSGSRLSV; SEQ ID NO: 21). In some embodiments, a polyribonucleotide described herein encodes two immunoglobulin chains: a first immunoglobulin chain comprising a heavy chain variable domain, wherein the heavy chain variable domain comprises: (i) HCDR1 (GFDFDNAW; SEQ ID NO: 6); (ii) HCDR2 (ITGPGEGWSV; SEQ ID NO: 9); (iii) HCDR3 (ARTGKYYDFWFGYPPGEEYFQD; SEQ ID NO: 12 or ARTGKYYDFWSGYPPGEEYFQD; SEQ ID NO: 34); or (iv) a combination thereof; and a second immunoglobulin chain comprising a light chain variable domain, wherein the light chain variable domain comprises: (i) LCDR1 (SLRSHY; SEQ ID NO: 15); (ii) LCDR2 (GKN); (iii) LCDR3 (SSRDKSGSRLSV; SEQ ID NO: 21); or (iv) a combination thereof. In some embodiments, a polyribonucleotide described herein encodes two immunoglobulin chains: a first immunoglobulin chain comprising a heavy chain variable domain, wherein the heavy chain variable domain comprises: (i) HCDR1 (GFDFDNAW; SEQ ID NO: 6); (ii) HCDR2 (ITGPGEGWSV; SEQ ID NO: 9); and (iii) HCDR3 (ARTGKYYDFWFGYPPGEEYFQD; SEQ ID NO: 12 or ARTGKYYDFWSGYPPGEEYFQD; SEQ ID NO: 34); and a second immunoglobulin chain comprising a light chain variable domain, wherein the light chain variable domain comprises: (i) LCDR1 (SLRSHY; SEQ ID NO: 15); (ii) LCDR2 (GKN); and (iii) LCDR3 (SSRDKSGSRLSV; SEQ ID NO: 21).
[0366] In some embodiments, an antibody agent encoded by one or more polyribonucleotides provided herein comprises a heavy chain variable domain having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to an amino acid sequence represented by SEQ ID NO: 24, 39, or 42. In some embodiments, an antibody agent encoded by one or more polyribonucleotides provided herein comprises a light chain variable domain having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to an amino acid sequence represented by SEQ ID NO: 29 or 45. In some embodiments, an antibody agent comprises a heavy chain variable domain represented by SEQ ID NO: 24, 39, or 42. In some embodiments, an antibody agent comprises a light chain variable domain represented by SEQ ID NO: 29 or 45.
[0367] In some embodiments, a polyribonucleotide described herein encodes an immunoglobulin chain comprising a heavy chain variable domain having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to an amino acid sequence represented by SEQ ID NO: 24, 39, or 42. In some embodiments, a polyribonucleotide described herein encodes an immunoglobulin chain comprising a light chain variable domain having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence - 59 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) identity to an amino acid sequence represented by SEQ ID NO: 29 or 45. In some embodiments, a polyribonucleotide described herein encodes an immunoglobulin chain comprising a heavy chain variable domain and a light chain variable domain, wherein the heavy chain variable domain has at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to an amino acid sequence represented by SEQ ID NO: 24, 39, or 42, and wherein the light chain variable domain has at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to an amino acid sequence represented by SEQ ID NO: 29 or 45.
[0368] In some embodiments, a polyribonucleotide as described herein encodes an immunoglobulin chain of an antibody agent, where the immunoglobulin chain comprises a heavy chain variable (VH) domain. In some embodiments, a VH domain comprises a VH domain of a 10E8v4-5R-100cF antibody. In some embodiments, a polyribonucleotide encodes a VH domain of an antibody selected from: 10E8v4-5R-100cF, 1-18, PGT121, 3BNC117, b12, 10-1074, 10-1074, 10E8, VRC01, VRC07-523, VRC07, N6, PG9, 4E10, PGT151, PGT128, 8ANC195, 2F5, IOMA, or PGDM1400 (e.g., as described herein).
[0369] In some embodiments, a polyribonucleotide comprises a VH domain encoding sequence that comprises (a) an HCDR1-encoding sequence that comprises a ribonucleic acid sequence according to SEQ ID NO: 7; (b) an HCDR2-encoding sequence that comprises a ribonucleic acid sequence according to SEQ ID NO: 10; (c) an HCDR3-encoding sequence that comprises a ribonucleic acid sequence according to SEQ ID NO: 13, 35, or 37 , or (d) a combination thereof. In some embodiments, a polyribonucleotide comprises a VH domain encoding sequence that comprises (a) an HCDR1-encoding sequence that comprises a ribonucleic acid sequence according to SEQ ID NO: 7; (b) an HCDR2-encoding sequence that comprises a ribonucleic acid sequence according to SEQ ID NO: 10 or SEQ ID NO: 32; and (c) an HCDR3-encoding sequence that comprises a ribonucleic acid sequence according to SEQ ID NO: 13, 35, or 37. In some embodiments, a polyribonucleotide encodes a VH domain, and comprises a VH-encoding sequence that is at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% to identical to SEQ ID NO: 25, 40, or 43. In some embodiments, a polyribonucleotide encodes a VH domain, and comprises a VH-encoding sequence according to SEQ ID NO: 25, 40, or 43.
[0370] In some embodiments, a polyribonucleotide as described herein comprises an immunoglobulin chain of an antibody agent, where the immunoglobulin chain comprises a light chain variable (VL) domain. In some embodiments, a VL domain comprises the VL domain of a 10E8v410E8v4-5R-100cF antibody. In some embodiments, a polyribonucleotide encodes a VL domain of an antibody selected from: 1-18, 10E8v4-5R-100cF, PGT121, 3BNC117, b12, 10-1074, 10-1074, 10E8, VRC01, VRC07-523, VRC07, N6, PG9, 4E10, PGT151, PGT128, 8ANC195, 2F5, IOMA, or PGDM1400 (e.g., as described herein).
[0371] In some embodiments, a polyribonucleotide comprises one or more coding regions that encode an immunoglobulin chain of an antibody agent, where the immunoglobulin chain comprises a light chain variable (VL) domain. In some embodiments, a polyribonucleotide comprises a VL domain encoding sequence that comprises (a) an LCDR1-encoding sequence that comprises a ribonucleic acid sequence according to SEQ ID NO: 16; (b) an LCDR2-encoding sequence that comprises a ribonucleic acid sequence of GGCAAGAAC; (c) an LCDR3-encoding sequence that comprises a ribonucleic acid sequence according to SEQ ID NO: 22; or (d) a combination thereof. In some embodiments, a polyribonucleotide comprises a VL domain encoding sequence that comprises (a) an LCDR1- encoding sequence that comprises a ribonucleic acid sequence according to SEQ ID NO: 16; (b) an LCDR2-encoding - 60 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) sequence that comprises a ribonucleic acid sequence of GGCAAGAAC; and (c) an LCDR3-encoding sequence that comprises a ribonucleic acid sequence according to SEQ ID NO: 22. In some embodiments, a polyribonucleotide encodes a VL domain, and comprises a VL-encoding sequence that is at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 30 or 46. In some embodiments, a polyribonucleotide encodes a VL domain, and comprises a VL-encoding sequence according to SEQ ID NO: 30 or 46.
[0372] Antibody agents (e.g., 10E8 antibody agents), as described herein, may be characterized by the amino acid sequence of one or more domains within their antibody structure. For example, an antibody agent can comprise at least one heavy (H) chain and at least one light (L) chain interconnected, e.g., by disulfide bonds. Each H chain comprises a heavy chain variable region (abbreviated herein as VH) and a heavy chain constant region. Each light chain comprises a light chain variable region (abbreviated herein as VL) and a light chain constant region. The variable regions of each light / heavy chain (VL / VH) pair form the antigen-binding domain.
[0373] Within each light or heavy chain variable domain, there are three short segments called the complementarity determining regions (“CDRs”). The six CDRs in an antibody variable domain (three in the light chain variable domain and three in the heavy chain variable domain) fold up together in 3-dimensional space to form the actual antibody binding site. The terms “LCDR1,” “LCDR2” and “LCDR3” as provided herein refer to the complementarity determining regions (CDR) 1, 2, and 3 of the variable light (L) chain of an antibody agent. In some embodiments, the light chain variable domain provided herein includes in N-terminal to C-terminal direction a LCDR1, a LCDR2 and a LCDR3. Likewise, the terms “HCDR1,” “HCDR2” and “HCDR3” as provided herein refer to the complementarity determining regions (CDR) 1, 2, and 3 of the variable heavy (H) chain of an antibody agent. In certain embodiments, the heavy chain variable domain provided herein includes in N-terminal to C-terminal direction a HCDR1, a HCDR2 and a HCDR3.
[0374] Also within the variable region, but not contained within the CDRs, are regions called the framework regions (“FR”). Thus, the complementarity determining regions (CDRs) are interspersed with the framework regions. Accordingly, each VH and VL comprises three CDRs and four FRs, arranged from amino-terminus to carboxy-terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3, and FR4. Generally, framework regions are more conserved than variable regions across naturally produced antibodies.
[0375] 10E8 antibodies, including their nucleotide and amino acid sequences, are disclosed in WO 2017 / 079479; Kwon YD, et al., Optimization of the solubility of HIV-1-neutralizing antibody 10E8 through somatic variation and structure-based design. J Virol. 2016; 90:5899–914; and Kwon YD, et al., Surface-matrix screening identifies semi-specific interactions that improve potency of a near pan-reactive HIV-1-neutralizing antibody. Cell Rep. 2018; 22:1798–809, which are herein incorporated by reference in their entirety.
[0376] In some embodiments, a 10E8 antibody agent comprises an HCDR1, an HCDR2, and an HCDR3 of the heavy chain variable domain comprising an amino acid sequence according to SEQ ID NO: 24, 39, or 42. In some embodiments, an 10E8 antibody agent comprises an LCDR1, and LCDR2, and an LCDR3 of the light chain variable domain comprising an amino acid sequence according to SEQ ID NO: 29 or 45.
[0377] The positions of the CDRs and framework regions within the VH and VL domains of an antibody agent described herein (e.g., a 10E8 antibody agent) can be determined using various numbering systems known in - 61 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) the art, e.g., Kabat, Chothia, AbM and IMGT (see, e.g., Johnson et al., Nucleic Acids Res., 29:205-206 (2001); Chothia and Lesk, J. Mol. Biol., 196:901-917 (1987); Chothia et al., Nature, 342:877-883 (1989); Chothia et al., J. Mol. Biol., 227:799-817 (1992); Al-Lazikani et al., J. Mol. Biol., 273:927-748 (1997) ImMunoGenTics (IMGT) numbering; Lefranc, M.-P., The Immunologist, 7, 132-136 (1999); Lefranc, M.P. et al., Dev. Comp. Immunol., 27, 55- 77 (2003), each of which is incorporated herein by reference). Accordingly, CDRs within 10E8 antibody agents within the same VH or VL domain can be determined by different numbering systems.
[0378] In some embodiments, an antibody agent is formed by one, two, three, or four immunoglobulin chains.
[0379] In some embodiments, a polyribonucleotide as described herein encodes a single immunoglobulin chain. In some embodiments, a first polyribonucleotide encodes a first immunoglobulin chain of an antibody agent. In some embodiments, a first polyribonucleotide encodes a first immunoglobulin chain of an antibody agent and a second polyribonucleotide encodes a second immunoglobulin chain of the antibody agent. In some embodiments, a first polyribonucleotide encodes a first immunoglobulin chain of an antibody agent, a second polyribonucleotide encodes a second immunoglobulin chain of the antibody agent, and a third polyribonucleotide encodes a third immunoglobulin chain of the antibody agent. In some embodiments, a first polyribonucleotide encodes a first immunoglobulin chain of an antibody agent, a second polyribonucleotide encodes a second immunoglobulin chain of the antibody agent, a third polyribonucleotide encodes a third immunoglobulin chain of the antibody agent, and a fourth polyribonucleotide encodes a fourth immunoglobulin chain of the antibody agent.
[0380] In some embodiments, a polyribonucleotide as described herein encodes two immunoglobulin chains. In some embodiments, a single polyribonucleotide can include a first coding region that encodes a first immunoglobulin chain of an antibody and a second coding region that encodes a second immunoglobulin chain of the antibody. In some embodiments, the first coding region and the second coding region are separated by an internal ribosome entry sides (IRES), an internal promoter, or a peptide sequence, such as “self-cleaving” 2A or 2A-like sequences (see, e.g., Szymczak et al. Nat Biotechnol 22:589, May 2004; ePub April 42004, which is herein incorporated by reference) to yield the first immunoglobulin chain and the second immunoglobulin chain from the single polyribonucleotide.
[0381] Antibody agents encoded by one or more polyribonucleotides described herein may be in various formats described herein. Exemplary types of antibody agents include, but are not limited to monoclonal antibodies or polyclonal antibodies. In some embodiments, an antibody agent may include one or more sequence elements that are humanized, chimeric, etc., as is known in the art. An antibody agent utilized in accordance with the present disclosure, in some embodiments, is in a format selected from, but not limited to, intact IgG, IgA, IgG, IgE or IgM antibodies; bi- or multi- specific antibodies (e.g., Zybodies®, etc.); CrossMabs (e.g., CrossMabCH1-CLx; CrossMabCH1-CLcv; bispecific CrossMabCH1-CLxwith knob-in-holes); antibody fragments such as Fab fragments, Fab' fragments, F(ab')2 fragments, Fd' fragments, Fd fragments, and isolated complementarity determining regions (CDRs) or sets thereof; single chain Fvs (scFvs); scFv-Fc fusions; polypeptide-Fc fusions; single domain antibodies (e.g., shark single domain antibodies such as IgNAR or fragments thereof); cameloid antibodies; masked antibodies (e.g., Probodies®); Small Modular ImmunoPharmaceuticals (“SMIPsTM”); single chain or Tandem diabodies (TandAb®); VHHs; Anticalins®; Nanobodies® minibodies; BiTE®s; ankyrin repeat proteins or DARPINs®; Avimers®; DARTs; TCR-like - 62 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) antibodies; Adnectins®; Affilins®; Trans-bodies®; Affibodies®; TrimerX®; MicroProteins; Fynomers®, Centyrins®; and KALBITOR®s. In some embodiments, immunoglobulin chains and / or fragments of such antibodies may be used in combination, e.g., an scFv-Fc arm with a conventional antibody arm.
[0382] Exemplary formats that may be used in accordance with the present disclosure are described further below. A. Conventional Antibody
[0383] In some embodiments, polyribonucleotides described herein can be used to express a conventional antibody. For clarity, the term “conventional antibody” is not intended to imply that an antibody described herein is routine and conventional (e.g., to make or use). Rather, as used herein, a “conventional antibody” refers to an antibody agent that includes two heavy chains and two light chains (see e.g., Fig.5A and Fig.4A). Each heavy chain includes a heavy chain variable domain operably linked to one or more heavy chain constant domains. In some embodiments, one or more heavy chain constant domains comprise a CH1 domain, a hinge domain, a CH2 domain, a CH3 domain, or a combination thereof. In some instances, one or more heavy chain constant domains comprise a CH1 domain, a hinge domain, a CH2 domain, a CH3 domain, a CH4 domain, or a combination thereof. Each light chain includes a light chain variable domain operably linked to a light chain constant domain.
[0384] Typically, a heavy chain variable domain and a light chain variable domain can be further subdivided into regions of variability, termed complementarity determining regions (CDRs), interspersed with regions that are more conserved, termed framework regions (FR). Such heavy chain variable domains and light chain variable domains can each include, e.g., three CDRs and four framework regions, arranged from amino-terminus to carboxyl-terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3, FR4, one or more of which can be engineered as described herein. The CDRs in a heavy chain are designated “HCDR1”, “HCDR2”, and “HCDR3”, respectively, and the CDRs in a light chain are designated “LCDR1”, “LCDR2”, and “LCDR3”.
[0385] A conventional antibody as described herein 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 or IgA antibody. In some embodiments, a conventional antibody described herein comprises a particular isotype selected from the group of IgA and IgG isotypes: IgG1, IgG2, IgG3, IgG4, IgA1, and IgA2. Additionally, in some embodiments, a conventional antibody 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., 9:129-134 (2003); Pluckthun, The Pharmacology of Monoclonal Antibodies, vol. 113, pp. 269-315 (1994); Hollinger et al., Proc. Natl. Acad. Sci. USA, 90: 6444-6448 (1993); WO93 / 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). In addition to the various isotypes, allelic variation is present among the IgG subclasses, giving rise to allotypic variants or allotypes. An IgG antibody agent as described herein may comprises a particular allotype, including but not limited to G1m3, Glm17, G1m17,1 or G1m17,1,2 or G1m3,1 (see Vidarsson et al., Front. Immunol, 5(520): 1-17, 2014, which is incorporated herein by reference in its entirety). - 63 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01)
[0386] The Fc region of conventional antibodies binds 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 glycosylation or other modification. In some embodiments, conventional antibodies produced and / or utilized in accordance with the present invention include glycosylated Fc domains, including Fc domains with modified or engineered such glycosylation. In some embodiments, conventional antibodies are 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, a conventional antibody is polyclonal; in some embodiments, a conventional antibody is monoclonal. In some embodiments, a conventional antibody has constant region sequences that are characteristic of mouse, rabbit, primate, or human antibodies. In some embodiments, a conventional antibody sequence elements are humanized, primatized, chimeric, etc., as is known in the art.
[0387] A conventional antibody as described herein is an antibody having a structure substantially similar to a native antibody structure or having heavy chains that contain an Fc region as defined herein.
[0388] In some embodiments, a conventional antibody encoded by one or more polyribonucleotides provided herein includes all or part of a 10E8v4-5R-100cF antibody. In some embodiments, a conventional antibody comprises a heavy chain variable domain comprising: (i) HCDR1 (GFDFDNAW; SEQ ID NO: 6); (ii) HCDR2 (ITGPGEGWSV; SEQ ID NO: 9); (iii) HCDR3 (ARTGKYYDFWFGYPPGEEYFQD; SEQ ID NO: 12 or ARTGKYYDFWSGYPPGEEYFQD; SEQ ID NO: 34); or (iv) a combination thereof. In some embodiments, a conventional antibody comprises a heavy chain variable domain comprising: (i) HCDR1 (GFDFDNAW; SEQ ID NO: 6); (ii) HCDR2 (ITGPGEGWSV; SEQ ID NO: 9); and (iii) HCDR3 (ARTGKYYDFWFGYPPGEEYFQD; SEQ ID NO: 12 or ARTGKYYDFWSGYPPGEEYFQD; SEQ ID NO: 34). In some embodiments, a conventional antibody comprises a light chain variable domain comprising: (i) LCDR1 (SLRSHY; SEQ ID NO: 15); (ii) LCDR2 (GKN); (iii) LCDR3 (SSRDKSGSRLSV; SEQ ID NO: 21); or (iv) a combination thereof. In some embodiments, a conventional antibody comprises a light chain variable domain comprising: (i) LCDR1 (SLRSHY; SEQ ID NO: 15); (ii) LCDR2 (GKN); and (iii) LCDR3 (SSRDKSGSRLSV; SEQ ID NO: 21). In some embodiments, a conventional antibody comprises (a) a heavy chain variable domain comprising: (i) HCDR1 (GFDFDNAW; SEQ ID NO: 6); (ii) HCDR2 (ITGPGEGWSV; SEQ ID NO: 9); (iii) HCDR3 (ARTGKYYDFWFGYPPGEEYFQD; SEQ ID NO: 12 or ARTGKYYDFWSGYPPGEEYFQD; SEQ ID NO: 34); or (iv) a combination thereof; and (b) a light chain variable domain comprising: (i) LCDR1 (SLRSHY; SEQ ID NO: 15); (ii) LCDR2 (GKN); (iii) LCDR3 (SSRDKSGSRLSV; SEQ ID NO: 21); or (iv) a combination thereof. In some embodiments, a conventional antibody comprises (a) a heavy chain variable domain comprising: (i) HCDR1 (GFDFDNAW; SEQ ID NO: 6); (ii) HCDR2 (ITGPGEGWSV; SEQ ID NO: 9); and (iii) HCDR3 (ARTGKYYDFWFGYPPGEEYFQD; SEQ ID NO: 12 or ARTGKYYDFWSGYPPGEEYFQD; SEQ ID NO: 34); and (b) a light chain variable domain comprising: (i) LCDR1 (SLRSHY; SEQ ID NO: 15); (ii) LCDR2 (GKN); and (iii) LCDR3 (SSRDKSGSRLSV; SEQ ID NO: 21).
[0389] In some embodiments, a polyribonucleotide described herein encodes an immunoglobulin chain of a conventional antibody, wherein the immunoglobulin chain comprises a heavy chain variable domain, and wherein the heavy chain variable domain comprises: (i) HCDR1 (GFDFDNAW; SEQ ID NO: 6); (ii) HCDR2 (ITGPGEGWSV; SEQ ID NO: 9); (iii) HCDR3 (ARTGKYYDFWFGYPPGEEYFQD; SEQ ID NO: 12 or ARTGKYYDFWSGYPPGEEYFQD; SEQ ID - 64 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) NO: 34); or (iv) a combination thereof. In some embodiments, a polyribonucleotide described herein encodes an immunoglobulin chain of a conventional antibody, wherein the immunoglobulin chain comprises a heavy chain variable domain, and wherein the heavy chain variable domain comprises: (i) HCDR1 (GFDFDNAW; SEQ ID NO: 6); (ii) HCDR2 (ITGPGEGWSV; SEQ ID NO: 9); and (iii) HCDR3 (ARTGKYYDFWFGYPPGEEYFQD; SEQ ID NO: 12 or ARTGKYYDFWSGYPPGEEYFQD; SEQ ID NO: 34). In some embodiments, a polyribonucleotide described herein encodes an immunoglobulin chain of a conventional antibody, wherein the immunoglobulin chain comprises a light chain variable domain, and wherein the light chain variable domain comprises: (i) LCDR1 (SLRSHY; SEQ ID NO: 15); (ii) LCDR2 (GKN); (iii) LCDR3 (SSRDKSGSRLSV; SEQ ID NO: 21); or (iv) a combination thereof. In some embodiments, a polyribonucleotide described herein encodes an immunoglobulin chain of a conventional antibody, wherein the immunoglobulin chain comprises a light chain variable domain, and wherein the light chain variable domain comprises: (i) LCDR1 (SLRSHY; SEQ ID NO: 15); (ii) LCDR2 (GKN); and (iii) LCDR3 (SSRDKSGSRLSV; SEQ ID NO: 21). In some embodiments, a polyribonucleotide described herein encodes two immunoglobulin chains of a conventional antibody: a first immunoglobulin chain comprising a heavy chain variable domain, wherein the heavy chain variable domain comprises: (i) HCDR1 (GFDFDNAW; SEQ ID NO: 6); (ii) HCDR2 (ITGPGEGWSV; SEQ ID NO: 9); (iii) HCDR3 (ARTGKYYDFWFGYPPGEEYFQD; SEQ ID NO: 12 or ARTGKYYDFWSGYPPGEEYFQD; SEQ ID NO: 34); or (iv) a combination thereof; and a second immunoglobulin chain comprising a light chain variable domain, wherein the light chain variable domain comprises: (i) LCDR1 (SLRSHY; SEQ ID NO: 15); (ii) LCDR2 (GKN); (iii) LCDR3 (SSRDKSGSRLSV; SEQ ID NO: 21); or (iv) a combination thereof. In some embodiments, a polyribonucleotide described herein encodes two immunoglobulin chains of a conventional antibody: a first immunoglobulin chain comprising a heavy chain variable domain, wherein the heavy chain variable domain comprises: (i) HCDR1 (GFDFDNAW; SEQ ID NO: 6); (ii) HCDR2 (ITGPGEGWSV; SEQ ID NO: 9); and (iii) HCDR3 (ARTGKYYDFWFGYPPGEEYFQD; SEQ ID NO: 12 or ARTGKYYDFWSGYPPGEEYFQD; SEQ ID NO: 34); and a second immunoglobulin chain comprising a light chain variable domain, wherein the light chain variable domain comprises: (i) LCDR1 (SLRSHY; SEQ ID NO: 15); (ii) LCDR2 (GKN); and (iii) LCDR3 (SSRDKSGSRLSV; SEQ ID NO: 21).
[0390] In some embodiments, a conventional antibody encoded by one or more polyribonucleotides provided herein comprises a heavy chain variable domain having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to an amino acid sequence represented by SEQ ID NO: 24, 39, or 42. In some embodiments, a conventional antibody encoded by one or more polyribonucleotides provided herein comprises a light chain variable domain having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to an amino acid sequence represented by SEQ ID NO: 29 or 45. In some embodiments, a conventional antibody comprises a heavy chain variable domain represented by SEQ ID NO: 24, 39, or 42. In some embodiments, conventional antibody comprises a light chain variable domain represented by SEQ ID NO: 29 or 45.
[0391] In some embodiments, a polyribonucleotide described herein encodes an immunoglobulin chain of a conventional antibody, wherein the immunoglobulin chain comprises a heavy chain variable domain having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to an amino acid sequence represented by SEQ ID NO: 24, 39, or 42. In some embodiments, a polyribonucleotide described herein encodes an immunoglobulin chain of a conventional antibody, wherein the immunoglobulin chain comprises a light chain variable domain having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to an amino acid sequence represented by SEQ ID NO: 29 or 45. - 65 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01)
[0392] Conventional antibodies encoded by one or more polyribonucleotides as described herein may comprise one or more heavy chain constant domains. In some embodiments, one or more heavy chain constant domains comprise a CH3 domain. In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises a CH3 domain that comprises a G1m3, G1m17, or a Glm17,1 allotype. In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises a CH3 domain having an amino acid sequence at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to a sequence represented in any one of SEQ ID NOs: 119, 122, 125, 128, 131, 134, 137, 140, 143, 146, 149, or 152. In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises a CH3 domain having an amino acid sequence represented in any one of SEQ ID NOs: 119, 122, 125, 128, 131, 134, 137, 140, 143, 146, 149, or 152.
[0393] Conventional antibodies encoded by one or more polyribonucleotides as described herein may comprise one or more heavy chain constant domains comprising an amino acid modification (e.g., a substitution or deletion) at one or more amino acid positions. For example, a conventional antibody encoded by one or more polyribonucleotides as described herein may include an L / S mutation within a CH3 region (for enhanced FcRn binding) (see Zalevsky J et al. Nat Biotechnol. 2010, which is herein incorporated by reference). Such mutations are noted as M428L and N434S according to EU numbering and referred to herein as “LS” or “L / S” (see e.g., Fig.5C). In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises an E294 deletion (for Fc hypersialylation) (see Bas M et al. J Immunol 2019, which is herein incorporated by reference.
[0394] The present disclosure also provides technologies that can be used to express an antibody agent, e.g., as illustrated in Fig.3 or described in Stadler et al. (2016) Oncoimmunology 5(3): e1091555; and / or in Stadler et al. (2017) Nature Medicine 23(7): 815-817. Challenges exist in producing multiple antibody agents from a single composition (e.g., a composition comprising polyribonucleotides sufficient to encode multiple antibody agents), particularly because the random pairing of different antibody heavy and light chains can yield undesired antibody 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 (see, e.g., Morrison, S.L., Nature Biotech. 25, 1233-1234, 2007, which is herein incorporated by reference). 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 antibody heavy chains by introducing mutations into the CH3 domains to modify the contact interface. On one chain bulky amino acids were replaced by amino acids with short side chains to create a “hole” and amino acids with large side chains were introduced into the other CH3 domain, to create a “knob”. By co-expressing these two heavy chains with two light chains, high yields of heterodimer formation versus homodimer was observed (see Ridgway, J.B., et al, Protein Eng. 9, 617-621, 1996; and WO 96 / 027011, which are herein incorporated by reference). In some embodiments, antibody agents described herein utilize KIH technology as described in, e.g., WO 1998 / 050431, which is herein incorporated by reference in its entirety. As described herein, an antibody agent may comprise certain mutations that utilize KIH technology that include, but are not limited to, a CH3 modification. In some embodiments, an antibody agent comprises a CH3 domain comprising one or more of the following mutations: Y349C, T366S, L368A, and Y407V (according to EU numbering). In some embodiments, an antibody agent comprises - 66 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) a CH3 domain, wherein the CH3 domain comprises each of the following mutations: Y349C, T366S, L368A, and Y407V (according to EU numbering). Such a combination of mutations is referred to herein as “cah”. In some embodiments, an antibody agent comprises a CH3 domain comprising one or more mutations selected from: S354C and T366W (according to EU numbering). In some embodiments, an antibody agent comprises a CH3 domain comprising each of the following mutations: S354C and T366W (according to EU numbering). Such a combination of CH3 mutations is referred to herein as “cak”.
[0395] Accordingly, in some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises a CH3 domain comprising one or more of the following mutations: Y349C, T366S, L368A, and Y407V (according to EU numbering). In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises a CH3 domain comprising one or more mutations selected from: S354C and T366W (according to EU numbering).
[0396] In some embodiments, a polyribonucleotide encodes a CH3 domain that comprises one of the following substitution mutations: M428, N434S, or a combination thereof (e.g., an “L / S” mutation). In some embodiments, a polyribonucleotide comprises a CH3 ribonucleic acid sequence that comprises any one of SEQ ID NOs: 132, 135, 144, 147, 150, or 153.
[0397] In some embodiments, a polyribonucleotide encodes a CH3 domain that comprises one or more of the following substitution mutations: Y349C, T366S, L368A, and Y407V (according to EU numbering). In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence according to SEQ ID NO: 126, 129, 132, or 135.
[0398] In some embodiments, a polyribonucleotide encodes a CH3 domain that comprises one or both of the following substitution mutations: S354C and T366W (according to EU numbering). In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence according to SEQ ID NO: 138, 141, 144, or 147.
[0399] In some embodiments, a polyribonucleotide encodes an immunoglobulin chain that VH domain operably linked to one or more constant domains, where the one or more constant domains comprise a CH3 domain. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence according to SEQ ID NO: 123. In some embodiments, polyribonucleotide comprises a CH3 ribonucleic acid sequence that encodes the CH3 domain that comprises a G1m3, G1m17, or a Glm17,1 allotype. In some embodiments, a polyribonucleotide comprises a CH3 ribonucleic acid sequence that comprises any one of SEQ ID NOs: 120 or 123.
[0400] In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises a CH1 domain. In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises a CH1 domain that comprises a G1m3 allotype. In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises a CH1 domain that comprises a G1m17 allotype. In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises a CH1 domain that comprises an amino acid represented in SEQ ID NO: 86 or 89.
[0401] In some embodiments, a polyribonucleotide encodes an immunoglobulin chain that comprises a VH domain operably linked to one or more constant domains, where the one or more constant domains comprise a CH1 - 67 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) domain. In some embodiments, a polyribonucleotide comprises a CH1 ribonucleic acid sequence according to SEQ ID NO: 90. In some embodiments, a polyribonucleotide encodes a CH1 domain that comprises a G1m3 allotype. In some embodiments, a polyribonucleotide encodes a CH1 domain that comprises a G1m17 allotype. In some embodiments, a polyribonucleotide encodes a CH1 ribonucleic acid sequence according to SEQ ID NO: 87 or 90.
[0402] In some embodiments, a polyribonucleotide encodes a CH1 domain that comprises one or more mutations. In some embodiments, a polyribonucleotide encodes a CH1 domain that comprises the addition of one or more serine residues. In some embodiments, a polyribonucleotide encodes a CH1 domain that comprises addition of two additional serine residues (referred to herein as “SS”). In some embodiments, a polyribonucleotide encodes a CH1 ribonucleic acid sequence that is at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 99 or 102. In some embodiments, a polyribonucleotide encodes a CH1 ribonucleic acid sequence represented in SEQ ID NO: 99 or 102. In some embodiments, a polyribonucleotide encodes a CH1 domain that comprises one or more charge variant mutations. In some embodiments, a polyribonucleotide encodes a CH1 domain comprising one or more substitution mutations selected from: K147E, K213D, or a combination thereof. In some embodiments, a polyribonucleotide encodes a CH1 ribonucleic acid sequence that has at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 93 or 96. In some embodiments, a polyribonucleotide encodes a CH1 ribonucleic acid sequence according to SEQ ID NO: 93 or 96.
[0403] In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises a hinge domain. In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises a hinge domain that comprises an amino acid sequence represented in SEQ ID NO: 170 (herein referred to as “hinge” in Tables 2 and 4).
[0404] In some embodiments, a polyribonucleotide encodes a hinge domain. In some embodiments, a polyribonucleotide encodes a hinge ribonucleic acid sequence that represented in SEQ ID NO: 171. In some embodiments, a polyribonucleotide encodes a hinge domain that comprises an amino acid modification that comprises a deletion of one or more amino acid residues.
[0405] In some embodiments, a polyribonucleotide encodes a hinge domain an amino acid modification that comprises a deletion of amino acid residues EPKSC (SEQ ID NO: 1508) in a conventional Ig hinge domain (represented in SEQ ID NO: 176). Such a modification is referred to herein as “Hinge (del216-220)” or “ΔEPKSC”. In some embodiments, a polyribonucleotide encodes a hinge ribonucleic acid sequence represented in SEQ ID NO: 177.
[0406] In some embodiments, a polyribonucleotide encodes a hinge domain that comprises an amino acid modification that comprises a C220S mutation (according to EU numbering). Such a mutated hinge domain is referred to herein as “Hinge (C220S)” or “C / S”. In some embodiments, a polyribonucleotide encodes a hinge ribonucleic acid sequence represented in SEQ ID NO: 174.
[0407] In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises a CH2 domain. In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises a CH2 domain having an amino acid sequence at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to an amino acid sequence represented in SEQ ID NO: - 68 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) 104. In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises a CH2 domain having an amino acid sequence represented in SEQ ID NO: 104.
[0408] In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises a CH2 domain having one or more mutations (e.g., with respect to SEQ ID NO: 104). For example, in some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises one or more of the following mutations: G236A, A330L, and I332E (according to EU numbering). In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises the following mutations: G236A, A330L, and I332E (according to EU numbering), referred to herein as “GAALIE”. Such mutations in the CH2 domain have been associated with increased affinity to Fc receptors FcgRIIA and FcgRIII for enhanced antibody effector function. In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises a CH2 domain having an amino acid sequence that is at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 110. In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises a CH2 domain having an amino acid sequence represented in SEQ ID NO: 110.
[0409] In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises one or more mutations selected from: G236A and I332E (according to EU numbering). In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises the mutations selected from: G236A and I332E (according to EU numbering), referred to herein as “GAIE”. In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises a CH2 domain having an amino acid sequence at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 113. In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises a CH2 domain having an amino acid sequence represented in SEQ ID NO: 113.
[0410] In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises a mutation: G236A (according to EU numbering), referred to herein as “GA”. In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises a CH2 domain having an amino acid sequence at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 107. In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises a CH2 domain having an amino acid sequence represented in SEQ ID NO: 107.
[0411] In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises a mutation: I332E (according to EU numbering), referred to herein as “IE”. In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises a CH2 domain having an amino acid sequence at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 116. In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises a CH2 domain having an amino acid sequence represented in SEQ ID NO: 116. - 69 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01)
[0412] In some embodiments, a polyribonucleotide encodes an immunoglobulin chain that comprises a VH domain operably linked to one or more constant domains, wherein the one or more constant domains comprise a CH2 domain. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that according to SEQ ID NO: 105. In some embodiments, a CH2 ribonucleic acid encodes a CH2 domain with one or more amino acid substitution mutations. For example, in some embodiments, a CH2 ribonucleic acid sequence encodes one or more of the following mutations: G236A, A330L, and I332E (according to EU numbering), referred to herein as “GAALIE”. Such mutations in the CH2 domain have been associated with increased affinity to Fc receptors FcgRIIA and FcgRIII for enhanced antibody effector function. In some embodiments, a CH2 ribonucleic sequence comprises or consists of a sequence according to SEQ ID NO: 111. In some embodiments, a CH2 ribonucleic acid sequence encodes one or more of the following mutations: G236A and I332E (according to EU numbering), referred to herein as “GAIE”. In some embodiments, a CH2 ribonucleic sequence comprises of a sequence according to SEQ ID NO: 114. In some embodiments, a CH2 ribonucleic acid sequence encodes the mutation G236A (according to EU numbering), referred to herein as “GA”. In some embodiments, a CH2 ribonucleic sequence comprises of a sequence according to SEQ ID NO: 108. In some embodiments, a CH2 ribonucleic acid sequence encodes the mutation: I332E (according to EU numbering), referred to herein as “IE”. In some embodiments, a CH2 ribonucleic sequence comprises of a sequence according to SEQ ID NO: 117. In some embodiments, a CH2 ribonucleic acid sequence encodes a CH2 domain that comprises an E294 deletion (according to EU numbering).
[0413] In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises a signal peptide comprising a human signal peptide. In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises a signal peptide comprising SEQ ID NO: 1.
[0414] In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises a light chain constant domain, where the light chain constant domain comprises a kappa light chain constant domain. In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises a light chain constant domain, where the light chain constant domain comprises a lambda light chain constant domain. In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises a kappa light chain constant domain having an amino acid sequence at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 158. In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises a kappa light chain constant domain having an amino acid sequence represented in SEQ ID NO: 158. In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises a lambda chain variable domain.
[0415] In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises an immunoglobulin chain (e.g., an immunoglobulin heavy chain) encoded by a nucleic acid sequence that has at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to a sequence represented by SEQ ID NO: 182, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, 205, 207, 209, 211, 213, 216, 219, 221, 223, 225, 227, 229, 231, 233, 235, 237, 239, 241, 243, 245, 247, 250, 255, 257, 259, 261, 263, 265, 267, 269, 271, 273, 275, 277, 279, 281, 284, 287, 289, 291, 293, 295, 297, 299, 301, 303, 305, 307, - 70 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) 309, 311, 313, 315, 318, 321, 323, 325, 327, 329, 331, 333, 335, 337, 339, 341, 343, 345, 347, 349, 352, 357, 359, 361, 363, 365, 367, 369, 371, 373, 375, 377, 379, 381, 383, 386, 389, 391, 393, 395, 397, 399, 401, 403, 405, 407, 409, 411, 413, 415, 417, 420, 423, 425, 427, 429, 431, 433, 435, 437, 439, 441, 443, 445, 447, 449, 451, 454, 459, 461, 463, 465, 467, 469, 471, 473, 475, 477, 479, 481, 483, or 485. In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises an immunoglobulin chain (e.g., an immunoglobulin heavy chain) encoded by a nucleic acid sequence represented by any one of SEQ ID NOs: 182, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, 205, 207, 209, 211, 213, 216, 219, 221, 223, 225, 227, 229, 231, 233, 235, 237, 239, 241, 243, 245, 247, 250, 255, 257, 259, 261, 263, 265, 267, 269, 271, 273, 275, 277, 279, 281, 284, 287, 289, 291, 293, 295, 297, 299, 301, 303, 305, 307, 309, 311, 313, 315, 318, 321, 323, 325, 327, 329, 331, 333, 335, 337, 339, 341, 343, 345, 347, 349, 352, 357, 359, 361, 363, 365, 367, 369, 371, 373, 375, 377, 379, 381, 383, 386, 389, 391, 393, 395, 397, 399, 401, 403, 405, 407, 409, 411, 413, 415, 417, 420, 423, 425, 427, 429, 431, 433, 435, 437, 439, 441, 443, 445, 447, 449, 451, 454, 459, 461, 463, 465, 467, 469, 471, 473, 475, 477, 479, 481, 483, or 485. In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises an immunoglobulin chain (e.g., an immunoglobulin light chain) encoded by a nucleic acid sequence that has at least at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 1045 or 1048. In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises an immunoglobulin chain (e.g., an immunoglobulin light chain) encoded by a nucleic acid sequence represented by SEQ ID NO: 1045 or 1048.
[0416] In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises an immunoglobulin chain (e.g., an immunoglobulin heavy chain) encoded by a nucleic acid sequence that has at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to a sequence represented by any one of SEQ ID NO: 253, 355, or 457. In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises an immunoglobulin chain (e.g., an immunoglobulin light chain) encoded by a nucleic acid sequence that has at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to a sequence represented by SEQ ID NO: 1045 or 1048. In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises an immunoglobulin chain (e.g., an immunoglobulin heavy chain) encoded by a nucleic acid sequence represented by any one of SEQ ID NOs: 253, 355, or 457. In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises an immunoglobulin chain (e.g., an immunoglobulin light chain) encoded by a nucleic acid sequence represented by SEQ ID NO: 1045 or 1048.
[0417] In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises an immunoglobulin chain (e.g., an immunoglobulin heavy chain) that comprises an amino acid sequence that has at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to a sequence represented by any one of SEQ ID NOs: 254, 356, or 458. In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises an immunoglobulin chain (e.g., an immunoglobulin heavy chain) that comprises an amino acid sequence represented by any one of SEQ ID NOs: 254, 356, or 458. In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises an immunoglobulin chain (e.g., an immunoglobulin light chain) that comprises an amino acid sequence that has at least at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, - 71 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 1046 or 1049. In some embodiments, a conventional antibody encoded by one or more polyribonucleotides as described herein comprises an immunoglobulin chain (e.g., an immunoglobulin light chain) that comprises an amino acid sequence represented by SEQ ID NO: 1046 or 1049.
[0418] Exemplary immunoglobulin chain (e.g., immunoglobulin heavy chain or light chain) configurations of a conventional antibody, as described herein, are shown in Table 2 below. Table 2: Exemplary Immunoglobulin Chain Configurations Name VH Hinge CH2 CH3 CH3 Allotype 10E8 VH G1m3 Hinge VH Hinge G1m3 10E8 VH G1m3 Hinge LS VH Hinge LS G1m3 10E8 VH G1m3 Hinge cah LS VH Hinge LS cah G1m3 10E8 VH G1m3 Hinge cak LS VH Hinge LS cak G1m3 10E8 VH G1m3 Hinge GAALIE LS VH Hinge GAALIE LS G1m3 10E8 VH G1m3 Hinge GAIE LS VH Hinge GAIE LS G1m3 10E8 VH G1m3 Hinge GA LS VH Hinge GA LS G1m3 10E8 VH G1m3 Hinge IE LS VH Hinge IE LS G1m3 10E8 VH G1m3 Hinge GAALIE cah LS VH Hinge GAALIE LS cah G1m3 10E8 VH G1m3 Hinge GAIE cah LS VH Hinge GAIE LS cah G1m3 10E8 VH G1m3 Hinge GA cah LS VH Hinge GA LS cah G1m3 10E8 VH G1m3 Hinge IE cah LS VH Hinge IE LS cah G1m3 10E8 VH G1m3 Hinge GAALIE cak LS VH Hinge GAALIE LS cak G1m3 10E8 VH G1m3 Hinge GAIE cak LS VH Hinge GAIE LS cak G1m3 10E8 VH G1m3 Hinge GA cak LS VH Hinge GA LS cak G1m3 10E8 VH G1m3 Hinge IE cak LS VH Hinge IE LS cak G1m3 10E8 VH G1m17 Hinge VH Hinge G1m17 10E8 VH G1m17 Hinge LS VH Hinge LS G1m17 10E8 VH G1m17 Hinge cah LS VH Hinge LS cah G1m17 10E8 VH G1m17 Hinge cak LS VH Hinge LS cak G1m17 10E8 VH G1m17 Hinge GAALIE LS VH Hinge GAALIE LS G1m17 10E8 VH G1m17 Hinge GAIE LS VH Hinge GAIE LS G1m17 10E8 VH G1m17 Hinge GA LS VH Hinge GA LS G1m17 10E8 VH G1m17 Hinge IE LS VH Hinge IE LS G1m17 10E8 VH G1m17 Hinge GAALIE cah LS VH Hinge GAALIE LS cah G1m17 10E8 VH G1m17 Hinge GAIE cah LS VH Hinge GAIE LS cah G1m17 10E8 VH G1m17 Hinge GA cah LS VH Hinge GA LS cah G1m17 10E8 VH G1m17 Hinge IE cah LS VH Hinge IE LS cah G1m17 10E8 VH G1m17 Hinge GAALIE cak LS VH Hinge GAALIE LS cak G1m17 10E8 VH G1m17 Hinge GAIE cak LS VH Hinge GAIE LS cak G1m17 10E8 VH G1m17 Hinge GA cak LS VH Hinge GA LS cak G1m17 - 72 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) Name VH Hinge CH2 CH3 CH3 Allotype 10E8 VH G1m17 Hinge IE cak LS VH Hinge IE LS cak G1m17 10E8 VH G1m17,1 Hinge VH Hinge G1m17,1 10E8 VH G1m17,1 Hinge LS VH Hinge LS G1m17,1 10E8 VH G1m17,1 Hinge cah LS VH Hinge LS cah G1m17,1 10E8 VH G1m17,1 Hinge cak LS VH Hinge LS cak G1m17,1 10E8 VH G1m17,1 Hinge GAALIE LS VH Hinge GAALIE LS G1m17,1 10E8 VH G1m17,1 Hinge GAIE LS VH Hinge GAIE LS G1m17,1 10E8 VH G1m17,1 Hinge GA LS VH Hinge GA LS G1m17,1 10E8 VH G1m17,1 Hinge IE LS VH Hinge IE LS G1m17,1 10E8 VH G1m17,1 Hinge GAALIE cah LS VH Hinge GAALIE LS cah G1m17,1 10E8 VH G1m17,1 Hinge GAIE cah LS VH Hinge GAIE LS cah G1m17,1 10E8 VH G1m17,1 Hinge GA cah LS VH Hinge GA LS cah G1m17,1 10E8 VH G1m17,1 Hinge IE cah LS VH Hinge IE LS cah G1m17,1 10E8 VH G1m17,1 Hinge GAALIE cak LS VH Hinge GAALIE LS cak G1m17,1 10E8 VH G1m17,1 Hinge GAIE cak LS VH Hinge GAIE LS cak G1m17,1 10E8 VH G1m17,1 Hinge GA cak LS VH Hinge GA LS cak G1m17,1 10E8 VH G1m17,1 Hinge IE cak LS VH Hinge IE LS cak G1m17,1 10E8v4 VH G1m3 Hinge VH Hinge G1m3 10E8v4 VH G1m3 Hinge LS VH Hinge LS G1m3 10E8v4 VH G1m3 Hinge cah LS VH Hinge LS cah G1m3 10E8v4 VH G1m3 Hinge cak LS VH Hinge LS cak G1m3 10E8v4 VH G1m3 Hinge GAALIE LS VH Hinge GAALIE LS G1m3 10E8v4 VH G1m3 Hinge GAIE LS VH Hinge GAIE LS G1m3 10E8v4 VH G1m3 Hinge GA LS VH Hinge GA LS G1m3 10E8v4 VH G1m3 Hinge IE LS VH Hinge IE LS G1m3 10E8v4 VH G1m3 Hinge GAALIE cah LS VH Hinge GAALIE LS cah G1m3 10E8v4 VH G1m3 Hinge GAIE cah LS VH Hinge GAIE LS cah G1m3 10E8v4 VH G1m3 Hinge GA cah LS VH Hinge GA LS cah G1m3 10E8v4 VH G1m3 Hinge IE cah LS VH Hinge IE LS cah G1m3 10E8v4 VH G1m3 Hinge GAALIE cak LS VH Hinge GAALIE LS cak G1m3 10E8v4 VH G1m3 Hinge GAIE cak LS VH Hinge GAIE LS cak G1m3 10E8v4 VH G1m3 Hinge GA cak LS VH Hinge GA LS cak G1m3 10E8v4 VH G1m3 Hinge IE cak LS VH Hinge IE LS cak G1m3 10E8v4 VH G1m17 VH Hinge G1m17 10E8v4 VH G1m17 Hinge LS VH Hinge LS G1m17 10E8v4 VH G1m17 Hinge cah LS VH Hinge LS cah G1m17 10E8v4 VH G1m17 Hinge cak LS VH Hinge LS cak G1m17 - 73 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) Name VH Hinge CH2 CH3 CH3 Allotype 10E8v4 VH G1m17 Hinge GAALIE LS VH Hinge GAALIE LS G1m17 10E8v4 VH G1m17 Hinge GAIE LS VH Hinge GAIE LS G1m17 10E8v4 VH G1m17 Hinge GA LS VH Hinge GA LS G1m17 10E8v4 VH G1m17 Hinge IE LS VH Hinge IE LS G1m17 10E8v4 VH G1m17 Hinge GAALIE cah LS VH Hinge GAALIE LS cah G1m17 10E8v4 VH G1m17 Hinge GAIE cah LS VH Hinge GAIE LS cah G1m17 10E8v4 VH G1m17 Hinge GA cah LS VH Hinge GA LS cah G1m17 10E8v4 VH G1m17 Hinge IE cah LS VH Hinge IE LS cah G1m17 10E8v4 VH G1m17 Hinge GAALIE cak LS VH Hinge GAALIE LS cak G1m17 10E8v4 VH G1m17 Hinge GAIE cak LS VH Hinge GAIE LS cak G1m17 10E8v4 VH G1m17 Hinge GA cak LS VH Hinge GA LS cak G1m17 10E8v4 VH G1m17 Hinge IE cak LS VH Hinge IE LS cak G1m17 10E8v4 VH G1m17,1 Hinge VH Hinge G1m17,1 10E8v4 VH G1m17,1 Hinge LS VH Hinge LS G1m17,1 10E8v4 VH G1m17,1 Hinge cah LS VH Hinge LS cah G1m17,1 10E8v4 VH G1m17,1 Hinge cak LS VH Hinge LS cak G1m17,1 10E8v4 VH G1m17,1 Hinge GAALIE LS VH Hinge GAALIE LS G1m17,1 10E8v4 VH G1m17,1 Hinge GAIE LS VH Hinge GAIE LS G1m17,1 10E8v4 VH G1m17,1 Hinge GA LS VH Hinge GA LS G1m17,1 10E8v4 VH G1m17,1 Hinge IE LS VH Hinge IE LS G1m17,1 10E8v4 VH G1m17,1 Hinge GAALIE cah LS VH Hinge GAALIE LS cah G1m17,1 10E8v4 VH G1m17,1 Hinge GAIE cah LS VH Hinge GAIE LS cah G1m17,1 10E8v4 VH G1m17,1 Hinge GA cah LS VH Hinge GA LS cah G1m17,1 10E8v4 VH G1m17,1 Hinge IE cah LS VH Hinge IE LS cah G1m17,1 10E8v4 VH G1m17,1 Hinge GAALIE cak LS VH Hinge GAALIE LS cak G1m17,1 10E8v4 VH G1m17,1 Hinge GAIE cak LS VH Hinge GAIE LS cak G1m17,1 10E8v4 VH G1m17,1 Hinge GA cak LS VH Hinge GA LS cak G1m17,1 10E8v4 VH G1m17,1 Hinge IE cak LS VH Hinge IE LS cak G1m17,1 10E8v4-5R-100cF VH G1m3 Hinge VH Hinge G1m3 10E8v4-5R-100cF VH G1m3 Hinge LS VH Hinge LS G1m3 10E8v4-5R-100cF VH G1m3 Hinge cah LS VH Hinge LS cah G1m3 10E8v4-5R-100cF VH G1m3 Hinge cak LS VH Hinge LS cak G1m3 10E8v4-5R-100cF VH G1m3 Hinge GAALIE LS VH Hinge GAALIE LS G1m3 10E8v4-5R-100cF VH G1m3 Hinge GAIE LS VH Hinge GAIE LS G1m3 10E8v4-5R-100cF VH G1m3 Hinge GA LS VH Hinge GA LS G1m3 10E8v4-5R-100cF VH G1m3 Hinge IE LS VH Hinge IE LS G1m3 10E8v4-5R-100cF VH G1m3 Hinge GAALIE cah LS VH Hinge GAALIE LS cah G1m3 - 74 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) Name VH Hinge CH2 CH3 CH3 Allotype 10E8v4-5R-100cF VH G1m3 Hinge GAIE cah LS VH Hinge GAIE LS cah G1m3 10E8v4-5R-100cF VH G1m3 Hinge GA cah LS VH Hinge GA LS cah G1m3 10E8v4-5R-100cF VH G1m3 Hinge IE cah LS VH Hinge IE LS cah G1m3 10E8v4-5R-100cF VH G1m3 Hinge GAALIE cak LS VH Hinge GAALIE LS cak G1m3 10E8v4-5R-100cF VH G1m3 Hinge GAIE cak LS VH Hinge GAIE LS cak G1m3 10E8v4-5R-100cF VH G1m3 Hinge GA cak LS VH Hinge GA LS cak G1m3 10E8v4-5R-100cF VH G1m3 Hinge IE cak LS VH Hinge IE LS cak G1m3 10E8v4-5R-100cF VH G1m17 Hinge VH Hinge G1m17 10E8v4-5R-100cF VH G1m17 Hinge LS VH Hinge LS G1m17 10E8v4-5R-100cF VH G1m17 Hinge cah LS VH Hinge LS cah G1m17 10E8v4-5R-100cF VH G1m17 Hinge cak LS VH Hinge LS cak G1m17 10E8v4-5R-100cF VH G1m17 Hinge GAALIE LS VH Hinge GAALIE LS G1m17 10E8v4-5R-100cF VH G1m17 Hinge GAIE LS VH Hinge GAIE LS G1m17 10E8v4-5R-100cF VH G1m17 Hinge GA LS VH Hinge GA LS G1m17 10E8v4-5R-100cF VH G1m17 Hinge IE LS VH Hinge IE LS G1m17 10E8v4-5R-100cF VH G1m17 Hinge GAALIE cah LS VH Hinge GAALIE LS cah G1m17 10E8v4-5R-100cF VH G1m17 Hinge GAIE cah LS VH Hinge GAIE LS cah G1m17 10E8v4-5R-100cF VH G1m17 Hinge GA cah LS VH Hinge GA LS cah G1m17 10E8v4-5R-100cF VH G1m17 Hinge IE cah LS VH Hinge IE LS cah G1m17 10E8v4-5R-100cF VH G1m17 Hinge GAALIE cak LS VH Hinge GAALIE LS cak G1m17 10E8v4-5R-100cF VH G1m17 Hinge GAIE cak LS VH Hinge GAIE LS cak G1m17 10E8v4-5R-100cF VH G1m17 Hinge GA cak LS VH Hinge GA LS cak G1m17 10E8v4-5R-100cF VH G1m17 Hinge IE cak LS VH Hinge IE LS cak G1m17 10E8v4-5R-100cF VH G1m17,1 Hinge VH Hinge G1m17,1 10E8v4-5R-100cF VH G1m17,1 Hinge LS VH Hinge LS G1m17,1 10E8v4-5R-100cF VH G1m17,1 Hinge cah LS VH Hinge LS cah G1m17,1 10E8v4-5R-100cF VH G1m17,1 Hinge cak LS VH Hinge LS cak G1m17,1 10E8v4-5R-100cF VH G1m17,1 Hinge GAALIE LS VH Hinge GAALIE LS G1m17,1 10E8v4-5R-100cF VH G1m17,1 Hinge GAIE LS VH Hinge GAIE LS G1m17,1 10E8v4-5R-100cF VH G1m17,1 Hinge GA LS VH Hinge GA LS G1m17,1 10E8v4-5R-100cF VH G1m17,1 Hinge IE LS VH Hinge IE LS G1m17,1 10E8v4-5R-100cF VH G1m17,1 Hinge GAALIE cah LS VH Hinge GAALIE LS cah G1m17,1 10E8v4-5R-100cF VH G1m17,1 Hinge GAIE cah LS VH Hinge GAIE LS cah G1m17,1 10E8v4-5R-100cF VH G1m17,1 Hinge GA cah LS VH Hinge GA LS cah G1m17,1 10E8v4-5R-100cF VH G1m17,1 Hinge IE cah LS VH Hinge IE LS cah G1m17,1 - 75 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) Name VH Hinge CH2 CH3 CH3 Allotype 10E8v4-5R-100cF VH G1m17,1 Hinge GAALIE cak LS VH Hinge GAALIE LS cak G1m17,1 10E8v4-5R-100cF VH G1m17,1 Hinge GAIE cak LS VH Hinge GAIE LS cak G1m17,1 10E8v4-5R-100cF VH G1m17,1 Hinge GA cak LS VH Hinge GA LS cak G1m17,1 10E8v4-5R-100cF VH G1m17,1 Hinge IE cak LS VH Hinge IE LS cak G1m17,1 B. CrossMabCH1-CLx
[0419] The present disclosure also provides technologies that can be used to deliver and express an antibody agent as described herein in “CrossMab” format (see e.g., WO2015 / 101588 Al, WO 2009 / 080253A1, and Schaefer, W. et al, PNAS, 108, 11187-1191, 2011, which are herein incorporated by reference in their entirety). In some embodiments, antibody agents in CrossMab format contain a CL-CH1 crossover in one or both binding arms (referred to herein as “CrossMabCH1-CLx” or “CH1-CLx”). Such a modification reduces the byproduct formation caused by a mismatch of a light chain of a first antibody that specifically binds to a first antigen with the wrong heavy chain of a second antibody that specifically binds to a second antigen (when compared to approaches without such domain exchanges).
[0420] In some embodiments, an antibody agent encoded by one or more polyribonucleotides provided herein comprises a first immunoglobulin chain and a second immunoglobulin chain. In some embodiments, a polyribonucleotide may encode a first immunoglobulin chain and a second immunoglobulin chain of a CrossMabCH1-CLxantibody agent as described herein. In some embodiments, a polyribonucleotide encoding a first immunoglobulin chain comprises a ribonucleic acid sequence encoding a VH domain, a CL domain, a hinge domain, a CH2 domain, and a CH3 domain. In some embodiments, a polyribonucleotide encoding a second immunoglobulin chain comprises a ribonucleic acid sequence encoding a light chain variable (VL) domain and a CH1 domain (see e.g., Fig.4B). In some embodiments, a polyribonucleotide encoding a CrossMabCH1-CLxantibody agent comprises a ribonucleic acid sequence that encodes any one of the immunoglobulin chain configurations in Table 3, corresponding to SEQ ID NOs: 488, 491, 493, 496, 498, 500, 502, 504, 506, 508, 510, 512, 514, 516, 518, 520, 523, 526, 528, 531, 533, 535, 537, 539, 541, 543, 545, 547, 549, 551, 553, 555, 558, 563, 566, 568, 570, 572, 574, 576, 578, 580, 582, 584, 586, 588, 590, 593, 596, 598, 601, 603, 605, 607, 609, 611, 613, 615, 617, 619, 621, 623, or 625. In some embodiments, a polyribonucleotide encoding a CrossMabCH1-CLxagent antibody comprises a ribonucleic acid sequence that encodes any one of the immunoglobulin chain configurations in Table 3, corresponding to SEQ ID NOs: 1051, 1057, 1060, 1063, 1066, 1069, or 1072.
[0421] In some embodiments, a CrossMabCH1-CLxantibody agent may be encoded by two separate polyribonucleotide: a first polyribonucleotide comprising a coding region that encodes (in 5’ to 3’ order): a heavy chain variable domain (VH), a light chain constant region (CL), a hinge region, a CH2 domain, and a CH3 domain (see e.g., Fig.9A); and a second polyribonucleotide comprising a coding region that encodes (in 5’ to 3’ order): a light chain variable domain (VL) and a CH1 domain (see e.g., Fig.9B).
[0422] In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides provided herein includes all or part of a 10E8v4-5R-100cF antibody. In some embodiments, a - 76 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) CrossMabCH1-CLxantibody agent comprises a heavy chain variable domain comprising: (i) HCDR1 (GFDFDNAW; SEQ ID NO: 6); (ii) HCDR2 (ITGPGEGWSV; SEQ ID NO: 9); (iii) HCDR3 (ARTGKYYDFWFGYPPGEEYFQD; SEQ ID NO: 12 or ARTGKYYDFWSGYPPGEEYFQD; SEQ ID NO: 34); or (iv) a combination thereof. In some embodiments, a CrossMabCH1-CLxantibody agent comprises a heavy chain variable domain comprising: (i) HCDR1 (GFDFDNAW; SEQ ID NO: 6); (ii) HCDR2 (ITGPGEGWSV; SEQ ID NO: 9); and (iii) HCDR3 (ARTGKYYDFWFGYPPGEEYFQD; SEQ ID NO: 12 or ARTGKYYDFWSGYPPGEEYFQD; SEQ ID NO: 34). In some embodiments, a CrossMabCH1-CLxantibody agent comprises a light chain variable domain comprising: (i) LCDR1 (SLRSHY; SEQ ID NO: 15); (ii) LCDR2 (GKN); (iii) LCDR3 (SSRDKSGSRLSV; SEQ ID NO: 21); or (iv) a combination thereof. In some embodiments, a CrossMabCH1-CLxantibody agent comprises a light chain variable domain comprising: (i) LCDR1 (SLRSHY; SEQ ID NO: 15); (ii) LCDR2 (GKN); and (iii) LCDR3 (SSRDKSGSRLSV; SEQ ID NO: 21). In some embodiments, a CrossMabCH1-CLxantibody agent comprises (a) a heavy chain variable domain comprising: (i) HCDR1 (GFDFDNAW; SEQ ID NO: 6); (ii) HCDR2 (ITGPGEGWSV; SEQ ID NO: 9); (iii) HCDR3 (ARTGKYYDFWFGYPPGEEYFQD; SEQ ID NO: 12 or ARTGKYYDFWSGYPPGEEYFQD; SEQ ID NO: 34); or (iv) a combination thereof; and (b) a light chain variable domain comprising: (i) LCDR1 (SLRSHY; SEQ ID NO: 15); (ii) LCDR2 (GKN); (iii) LCDR3 (SSRDKSGSRLSV; SEQ ID NO: 21); or (iv) a combination thereof. In some embodiments, a CrossMabCH1-CLxantibody agent comprises (a) a heavy chain variable domain comprising: (i) HCDR1 (GFDFDNAW; SEQ ID NO: 6); (ii) HCDR2 (ITGPGEGWSV; SEQ ID NO: 9); and (iii) HCDR3 (ARTGKYYDFWFGYPPGEEYFQD; SEQ ID NO: 12 or ARTGKYYDFWSGYPPGEEYFQD; SEQ ID NO: 34); and (b) a light chain variable domain comprising: (i) LCDR1 (SLRSHY; SEQ ID NO: 15); (ii) LCDR2 (GKN); and (iii) LCDR3 (SSRDKSGSRLSV; SEQ ID NO: 21).
[0423] In some embodiments, a polyribonucleotide described herein encodes an immunoglobulin chain of a CrossMabCH1-CLxantibody agent, wherein the immunoglobulin chain comprises a heavy chain variable domain, and wherein the heavy chain variable domain comprises: (i) HCDR1 (GFDFDNAW; SEQ ID NO: 6); (ii) HCDR2 (ITGPGEGWSV; SEQ ID NO: 9); (iii) HCDR3 (ARTGKYYDFWFGYPPGEEYFQD; SEQ ID NO: 12 or ARTGKYYDFWSGYPPGEEYFQD; SEQ ID NO: 34); or (iv) a combination thereof. In some embodiments, a polyribonucleotide described herein encodes an immunoglobulin chain of a CrossMabCH1-CLxantibody agent, wherein the immunoglobulin chain comprises a heavy chain variable domain, and wherein the heavy chain variable domain comprises: (i) HCDR1 (GFDFDNAW; SEQ ID NO: 6); (ii) HCDR2 (ITGPGEGWSV; SEQ ID NO: 9); and (iii) HCDR3 (ARTGKYYDFWFGYPPGEEYFQD; SEQ ID NO: 12 or ARTGKYYDFWSGYPPGEEYFQD; SEQ ID NO: 34). In some embodiments, a polyribonucleotide described herein encodes an immunoglobulin chain of a CrossMabCH1-CLxantibody agent, wherein the immunoglobulin chain comprises a light chain variable domain, and wherein the light chain variable domain comprises: (i) LCDR1 (SLRSHY; SEQ ID NO: 15); (ii) LCDR2 (GKN); (iii) LCDR3 (SSRDKSGSRLSV; SEQ ID NO: 21); or (iv) a combination thereof. In some embodiments, a polyribonucleotide described herein encodes an immunoglobulin chain of a CrossMabCH1-CLxantibody agent, wherein the immunoglobulin chain comprises a light chain variable domain, and wherein the light chain variable domain comprises: (i) LCDR1 (SLRSHY; SEQ ID NO: 15); (ii) LCDR2 (GKN); and (iii) LCDR3 (SSRDKSGSRLSV; SEQ ID NO: 21). In some embodiments, a polyribonucleotide described herein encodes two immunoglobulin chains of a CrossMabCH1-CLxantibody agent: a first immunoglobulin chain comprising a heavy chain variable domain, wherein the heavy chain variable domain comprises: (i) HCDR1 (GFDFDNAW; SEQ ID NO: 6); (ii) HCDR2 (ITGPGEGWSV; SEQ ID NO: 9); (iii) HCDR3 (ARTGKYYDFWFGYPPGEEYFQD; SEQ ID NO: 12 or ARTGKYYDFWSGYPPGEEYFQD; SEQ ID NO: 34); or (iv) a - 77 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) combination thereof; and a second immunoglobulin chain comprising a light chain variable domain, wherein the light chain variable domain comprises: (i) LCDR1 (SLRSHY; SEQ ID NO: 15); (ii) LCDR2 (GKN); (iii) LCDR3 (SSRDKSGSRLSV; SEQ ID NO: 21); or (iv) a combination thereof. In some embodiments, a polyribonucleotide described herein encodes two immunoglobulin chains of a CrossMabCH1-CLxantibody agent: a first immunoglobulin chain comprising a heavy chain variable domain, wherein the heavy chain variable domain comprises: (i) HCDR1 (GFDFDNAW; SEQ ID NO: 6); (ii) HCDR2 (ITGPGEGWSV; SEQ ID NO: 9); and (iii) HCDR3 (ARTGKYYDFWFGYPPGEEYFQD; SEQ ID NO: 12 or ARTGKYYDFWSGYPPGEEYFQD; SEQ ID NO: 34); and a second immunoglobulin chain comprising a light chain variable domain, wherein the light chain variable domain comprises: (i) LCDR1 (SLRSHY; SEQ ID NO: 15); (ii) LCDR2 (GKN); and (iii) LCDR3 (SSRDKSGSRLSV; SEQ ID NO: 21).
[0424] In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides provided herein comprises a heavy chain variable domain having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to an amino acid sequence represented by SEQ ID NO: 24, 39, or 42. In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides provided herein comprises a light chain variable domain having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to an amino acid sequence represented by SEQ ID NO: 29 or 45. In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides provided herein comprises a heavy chain variable domain represented by SEQ ID NO: 24, 39, or 42. In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides provided herein comprises a light chain variable domain represented by SEQ ID NO: 29 or 45.
[0425] In some embodiments, a polyribonucleotide described herein encodes an immunoglobulin chain of a CrossMabCH1-CLxantibody agent, wherein the immunoglobulin chain comprises a heavy chain variable domain having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to an amino acid sequence represented by SEQ ID NO: 24, 39, or 42. In some embodiments, a polyribonucleotide described herein encodes an immunoglobulin chain of a CrossMabCH1-CLxantibody agent, wherein the immunoglobulin chain comprises a light chain variable domain having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to an amino acid sequence represented by SEQ ID NO: 29 or 45. In some embodiments, a polyribonucleotide described herein encodes an immunoglobulin chain of a CrossMabCH1-CLxantibody agent, wherein the immunoglobulin chain comprises a heavy chain variable domain represented by SEQ ID NO: 24, 39, or 42. In some embodiments, a polyribonucleotide described herein encodes an immunoglobulin chain of a CrossMabCH1-CLxantibody agent, wherein the immunoglobulin chain comprises a light chain variable domain represented by SEQ ID NO: 29 or 45.
[0426] As described above, CrossMabCH1-CLxantibody agents encoded by one or more polyribonucleotides as described herein may comprise one or more heavy chain constant domains. In some embodiments, one or more heavy chain constant domains comprise a CH3 domain. In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides as described herein comprises a CH3 domain that comprises a G1m3, G1m17, or a Glm17,1 allotype. In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides as described herein comprises a CH3 domain having an amino acid sequence at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to a sequence represented in any one of SEQ ID NOs: - 78 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) 119, 122, 125, 128, 131, 134, 137, 140143, 146, 149, or 152. In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides as described herein comprises a CH3 domain having an amino acid sequence represented in any one of SEQ ID NOs: 119, 122, 125, 128, 131, 134, 137, 140143, 146, 149, or 152.
[0427] CrossMabCH1-CLxantibody agents encoded by one or more polyribonucleotides as described herein may comprise one or more heavy chain constant domains comprising an amino acid modification (e.g., a substitution or deletion) at one or more amino acid positions. For example, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides as described herein may include an L / S mutation within a CH3 region (for enhanced FcRn binding) (see Zalevsky J et al. Nat Biotechnol. 2010, which is herein incorporated by reference). Such mutations are noted as M428L and N434S according to EU numbering and referred to herein as “LS” or “L / S” (see e.g., Fig.5C). In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides as described herein comprise an E294 deletion (for Fc hypersialylation) (see Bas M et al. J Immunol 2019, which is herein incorporated by reference).
[0428] In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides as described herein comprises a CH3 domain comprising one or more of the following mutations: Y349C, T366S, L368A, and Y407V (according to EU numbering). This combination of mutations is referred to herein as “cah”. In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides as described herein comprises a CH3 domain comprising one or more mutations selected from: S354C and T366W (according to EU numbering). This combination of CH3 mutations is referred to herein as “cak”.
[0429] In some embodiments, a polyribonucleotide encodes a CH3 domain that comprises one of the following substitution mutations: M428, N434S, or a combination thereof (e.g., an “L / S” mutation). In some embodiments, a polyribonucleotide comprises a CH3 ribonucleic acid sequence that comprises any one of SEQ ID NOs: 132, 135, 144, 147, 150, or 153. In some embodiments, a polyribonucleotide encodes a CH3 domain that comprises one of the following substitution mutations: Y349C, T366S, L368A, and Y407V (according to EU numbering). In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence according to SEQ ID NO: 126, 129, 132, or 135. In some embodiments, a polyribonucleotide encodes a CH3 domain that comprises one of the following substitution mutations: S354C and T366W (according to EU numbering). In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence according to SEQ ID NO: 138, 141, 144, or 147.
[0430] In some embodiments, a polyribonucleotide encodes an immunoglobulin chain that VH domain operably linked to one or more constant domains, where the one or more constant domains comprise a CH3 domain. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence according to SEQ ID NO: 123. In some embodiments, polyribonucleotide comprises a CH3 ribonucleic acid sequence that encodes the CH3 domain that comprises a G1m3, G1m17, or a Glm17,1 allotype. In some embodiments, a polyribonucleotide comprises a CH3 ribonucleic acid sequence that comprises any one of SEQ ID NOs: 120 or 123.
[0431] In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides as described herein comprises a light chain constant domain. In some embodiments, a light chain constant domain comprises a kappa light chain constant domain. In some embodiments, a light chain constant domain comprises a lambda light chain constant domain. In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides as described herein comprises a kappa light chain constant domain - 79 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) having an amino acid sequence at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 161 or 164. In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides as described herein comprises a kappa light chain constant domain having an amino acid sequence represented in SEQ ID NO: 161 or 164. In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides as described herein comprises a lambda chain variable domain.
[0432] In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides as described herein comprises a hinge domain. In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides as described herein comprises a hinge domain that comprises an amino acid sequence represented in SEQ ID NO: 170 (herein referred to as “hinge” in Tables 2 and 4).
[0433] In some embodiments, a polyribonucleotide encodes a hinge domain. In some embodiments, a polyribonucleotide encodes a hinge ribonucleic acid sequence that represented in SEQ ID NO: 171. In some embodiments, a polyribonucleotide encodes a hinge domain that comprises an amino acid modification that comprises a deletion of one or more amino acid residues. In some embodiments, a polyribonucleotide encodes a hinge domain an amino acid modification that comprises a deletion of amino acid residues EPKSC (SEQ ID NO: 1508) in a conventional Ig hinge domain (represented in SEQ ID NO: 176). Such a modification is referred to herein as “Hinge (del216-220)” or “ΔEPKSC”. In some embodiments, a polyribonucleotide encodes a hinge ribonucleic acid sequence represented in SEQ ID NO: 177. In some embodiments, a polyribonucleotide encodes a hinge domain that comprises an amino acid modification that comprises a C220S mutation (according to EU numbering). Such a mutated hinge domain is referred to herein as “Hinge (C220S)” or “C / S”. In some embodiments, a polyribonucleotide encodes a hinge ribonucleic acid sequence represented in SEQ ID NO: 174.
[0434] In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides as described herein comprises a CH2 domain. In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides as described herein comprises a CH2 domain having an amino acid sequence at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to represented in SEQ ID NO: 104. In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides as described herein comprises a CH2 domain having an amino acid sequence represented in SEQ ID NO: 104.
[0435] In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides as described herein comprises a CH2 domain having one or more mutations (e.g., with respect to SEQ ID NO: 104). For example, in some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides as described herein comprises one or more of the following mutations: G236A, A330L, and I332E (according to EU numbering). Such a combination of mutations is referred to herein as “GAALIE”. Such mutations in the CH2 domain have been associated with increased affinity to Fc receptors FcgRIIA and FcgRIII for enhanced antibody effector function.
[0436] In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides as described herein comprises a CH2 domain having an amino acid sequence that is at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 110. In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides as described herein comprises a CH2 domain having an amino acid sequence represented in SEQ ID NO: 110. - 80 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01)
[0437] In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides as described herein comprises one or more mutations selected from: G236A and I332E (according to EU numbering). Such a combination of CH2 mutations is referred to herein as “GAIE”. In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides as described herein comprises a CH2 domain having an amino acid sequence at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 113. In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides as described herein comprises a CH2 domain having an amino acid sequence represented in SEQ ID NO: 113.
[0438] In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides as described herein comprises a mutation: G236A (according to EU numbering), referred to herein as “GA”. In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides as described herein comprises a CH2 domain having an amino acid sequence at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 107. In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides as described herein comprises a CH2 domain having an amino acid sequence represented in SEQ ID NO: 107.
[0439] In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides as described herein comprises a mutation: I332E (according to EU numbering), referred to herein as “IE”. In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides as described herein comprises a CH2 domain having an amino acid sequence at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 116. In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides as described herein comprises a CH2 domain having an amino acid sequence represented in SEQ ID NO: 116.
[0440] In some embodiments, a polyribonucleotide encodes an immunoglobulin chain that comprises a VH domain operably linked to one or more constant domains, wherein the one or more constant domains comprise a CH2 domain. In some embodiments, a polyribonucleotide comprises a ribonucleic acid sequence that according to SEQ ID NO: 105. In some embodiments, a CH2 ribonucleic acid encodes a CH2 domain with one or more amino acid substitution mutations. For example, in some embodiments, a CH2 ribonucleic acid sequence encodes one or more of the following mutations: G236A, A330L, and I332E (according to EU numbering), referred to herein as “GAALIE”. Such mutations in the CH2 domain have been associated with increased affinity to Fc receptors FcgRIIA and FcgRIII for enhanced antibody effector function. In some embodiments, a CH2 ribonucleic sequence comprises or consists of a sequence according to SEQ ID NO: 111. In some embodiments, a CH2 ribonucleic acid sequence encodes one or more of the following mutations: G236A and I332E (according to EU numbering), referred to herein as “GAIE”. In some embodiments, a CH2 ribonucleic sequence comprises of a sequence according to SEQ ID NO: 114. In some embodiments, a CH2 ribonucleic acid sequence encodes the mutation G236A (according to EU numbering), referred to herein as “GA”. In some embodiments, a CH2 ribonucleic sequence comprises of a sequence according to SEQ ID NO: 108. In some embodiments, a CH2 ribonucleic acid sequence encodes the mutation: I332E (according to EU numbering), referred to herein as “IE”. In some embodiments, a CH2 ribonucleic sequence comprises of a sequence - 81 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) according to SEQ ID NO: 117. In some embodiments, a CH2 ribonucleic acid sequence encodes a CH2 domain that comprises a E294 deletion (according to EU numbering), referred to herein as “E294del”.
[0441] In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides as described herein comprises a CH1 domain. In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides as described herein comprises a CH1 domain that comprises a G1m3 allotype. In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides as described herein comprises a CH1 domain that comprises a G1m17 allotype. In some embodiments, a CrossMabCH1-CLxantibody agent encoded by one or more polyribonucleotides as described herein comprises a CH1 domain that comprises an amino acid represented in SEQ ID NO: 86 or 89.
[0442] In some embodiments, a polyribonucleotide encodes an immunoglobulin chain that comprises a VH domain operably linked to one or more constant domains, where the one or more constant domains comprise a CH1 domain. In some embodiments, a polyribonucleotide comprises a CH1 ribonucleic acid sequence according to SEQ ID NO: 90. In some embodiments, a polyribonucleotide encodes a CH1 domain that comprises a G1m3 allotype. In some embodiments, a polyribonucleotide encodes a CH1 domain that comprises a G1m17 allotype. In some embodiments, a polyribonucleotide encodes a CH1 ribonucleic acid sequence according to SEQ ID NO: 87 or 90.
[0443] In some embodiments, a polyribonucleotide encodes a CH1 domain that comprises one or more mutations. In some embodiments, a polyribonucleotide encodes a CH1 domain that comprises the addition of one or more serine residues. In some embodiments, a polyribonucleotide encodes a CH1 domain that comprises addition of two additional serine residues (referred to herein as “SS”). In some embodiments, a polyribonucleotide encodes a CH1 ribonucleic acid sequence that is at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to SEQ ID NO: 99 or 102 In some embodiments, a polyribonucleotide encodes a CH1 ribonucleic acid sequence represented in SEQ ID NO: 99 or 102. In some embodime...
Claims
Attorney Docket No: 2013237-1144 (P1577WO01) CLAIMS 1. A polyribonucleotide encoding an immunoglobulin chain of an antibody agent, wherein the immunoglobulin chain comprises a heavy chain variable (VH) domain, and the VH domain comprises: (a) a heavy chain complementarity determining region (HCDR)1 comprising an amino acid sequence according to SEQ ID NO: 6; (b) an HCDR2 comprising an amino acid sequence according to SEQ ID NO: 9; and (c) an HCDR3 comprising an amino acid sequence according to SEQ ID NO: 12 or SEQ ID NO:
34.
2. The polyribonucleotide of claim 1, wherein the immunoglobulin chain further comprises one or more constant domains, and wherein the VH domain is operably linked to the one or more constant domains.
3. The polyribonucleotide of claim 2, wherein the one or more constant domains comprise a CH2 domain.
4. The polyribonucleotide of claim 2 or 3, wherein the one or more constant domains comprise a CH3 domain.
5. The polyribonucleotide of any one of claims 2-4, wherein the one or more constant domains comprise a hinge domain.
6. The polyribonucleotide of any one of claims 2-5, wherein the one or more constant domains comprise a CH1 domain.
7. The polyribonucleotide of claim 6, wherein one or more constant domains comprise, in order, the CH1 domain, the hinge domain, the CH2 domain, and the CH3 domain.
8. The polyribonucleotide of claim 6 or 7, wherein the immunoglobulin chain comprises or consists of an amino acid sequence according to SEQ ID NO:
252.
9. The polyribonucleotide of any one of claims 6-8, wherein the polyribonucleotide comprises or consists of a ribonucleic acid sequence according to SEQ ID NO:
253.
10. The polyribonucleotide of claim 6 or 7, wherein the first immunoglobulin chain comprises or consists of an amino acid sequence according to SEQ ID NO:
354.
11. The polyribonucleotide of any one of claims 6, 7, and 10, wherein the polyribonucleotide comprises or consists of a ribonucleic acid sequence according to SEQ ID NO:
355.
12. The polyribonucleotide of claim 6 or 7, wherein the first immunoglobulin chain comprises or consists of an amino acid sequence according to SEQ ID NO:
456. - 257 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) 13. The polyribonucleotide of any one of claims 6, 7, and 12, wherein the polyribonucleotide comprises or consists of a ribonucleic acid sequence according to SEQ ID NO:
457.
14. The polyribonucleotide of claim 6 or 7, wherein the first immunoglobulin chain comprises or consists of an amino acid sequence according to SEQ ID NO:
700.
15. The polyribonucleotide of any one of claims 6, 7, and 14, wherein the polyribonucleotide comprises or consists of a ribonucleic acid sequence according to SEQ ID NO:
701.
16. The polyribonucleotide of any one of claims 2-5, wherein the one or more constant domains comprise a light chain constant (CL) domain.
17. The polyribonucleotide of claim 16, wherein one or more constant domains comprise, in order, the CL domain, the hinge domain, the CH2 domain, and the CH3 domain.
18. The polyribonucleotide of claim 16 or 17, wherein the immunoglobulin chain comprises or consists of an amino acid sequence according to SEQ ID NO:
560.
19. The polyribonucleotide of any one of claims 16-18, wherein the polyribonucleotide comprises or consists of a ribonucleic acid sequence according to SEQ ID NO:
561.
20. A polyribonucleotide encoding an immunoglobulin chain of an antibody agent, wherein the immunoglobulin chain comprises a light chain variable (VL) domain, and the VL domain comprises: (a) a light chain complementarity determining region (LCDR)1 comprising an amino acid sequence according to SEQ ID NO: 15; (b) an LCDR2 comprising an amino acid sequence according to SEQ ID NO: 18; and (c) an LCDR3 comprising an amino acid sequence according to SEQ ID NO:
21.
21. The polyribonucleotide of claim 20, wherein the immunoglobulin chain further comprises a CL domain, and wherein the VL domain is operably linked to the CL domain.
22. The polyribonucleotide of claim 21, wherein the CL domain is a kappa or lambda light chain constant domain.
23. The polyribonucleotide of claim 21 or 22, wherein the immunoglobulin chain comprises or consists of an amino acid sequence according to SEQ ID NO: 1044.
24. The polyribonucleotide of any one of claims 21-23, wherein the polyribonucleotide comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 1045. - 258 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) 25. The polyribonucleotide of claim 21 or 22, wherein the immunoglobulin chain comprises or consists of an amino acid sequence according to SEQ ID NO: 1047.
26. The polyribonucleotide of any one of claims 21, 22, and 25, wherein the polyribonucleotide comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 1048.
27. The polyribonucleotide of claim 21 or 22, wherein the immunoglobulin chain comprises or consists of an amino acid sequence according to SEQ ID NO: 1077.
28. The polyribonucleotide of any one of claims 21, 22, and 27, wherein the polyribonucleotide comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 1078.
29. The polyribonucleotide of claim 20, wherein the immunoglobulin chain further comprises a CH1 domain, and wherein the VL domain is operably linked to the CH1 domain.
30. The polyribonucleotide of claim 29, wherein the CH1 domain comprises or consists of an amino acid sequence according to SEQ ID NO:
101.
31. The polyribonucleotide of claim 29, wherein the immunoglobulin chain comprises or consists of an amino acid sequence according to SEQ ID NO: 1053.
32. The polyribonucleotide of claim 29 or 30, wherein the polyribonucleotide comprises or consists of a ribonucleic acid sequence according to SEQ ID NO: 1054.
33. A polyribonucleotide encoding an immunoglobulin chain of an antibody agent, wherein the immunoglobulin chain comprises a heavy chain variable (VH) domain and a light chain variable (VL) domain, wherein the VH domain comprises: (a) an HCDR1 comprising an amino acid sequence according to SEQ ID NO: 6; (b) an HCDR2 comprising an amino acid sequence according to SEQ ID NO: 9; and (c) an HCDR3 comprising an amino acid sequence according to SEQ ID NO: 12 or 34; and wherein the VL domain comprises: (d) an LCDR1 comprising an amino acid sequence according to SEQ ID NO: 15; (e) an LCDR2 comprising an amino acid sequence according to SEQ ID NO: 18; and (f) an LCDR3 comprising an amino acid sequence according to SEQ ID NO:
21.
34. A polyribonucleotide comprising or consisting of a ribonucleic acid sequence according to any one of SEQ ID NO: 1086-1483.
35. A plurality of polyribonucleotides comprising three or more different polyribonucleotides, - 259 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) wherein each polyribonucleotide of the three or more different polyribonucleotides encodes an immunoglobulin chain, wherein each of the three or more different polyribonucleotides encode a different immunoglobulin chain, wherein at least one of the polyribonucleotides of the plurality is a polyribonucleotide of any one of claims 1- 34, and wherein, when immunoglobulin chains are expressed from the three or more different polyribonucleotides in a cell, the immunoglobulin chains form: (a) at least two different antibody agents; and (b) at most (2x+n+1) / 2 different antibody agents, wherein x is equal to the number of polyribonucleotides in the three or more polyribonucleotides that encode an immunoglobulin chain comprising an scFV, and n is equal to the number of polyribonucleotides in the three or more polyribonucleotides minus x.
36. A composition comprising one or more polyribonucleotides of any one of claims 1-34.
37. The composition of claim 36, wherein the one or more polyribonucleotides comprise or consist of: (a) the polyribonucleotide of claim 8 or 9; and (b) the polyribonucleotide of claim 23 or 24.
38. The composition of claim 36, wherein the one or more polyribonucleotides comprise or consist of: (a) the polyribonucleotide of claim 10 or 11; and (b) the polyribonucleotide of claim 23 or 24.
39. The composition of claim 36, wherein the one or more polyribonucleotides comprise or consist of: (a) the polyribonucleotide of claim 12 or 13; and (b) the polyribonucleotide of claim 23 or 24.
40. The composition of claim 36, wherein the one or more polyribonucleotides comprise or consist of: (a) the polyribonucleotide of claim 8 or 9; and (b) the polyribonucleotide of claim 25 or 26.
41. The composition of claim 36, wherein the one or more polyribonucleotides comprise or consist of: (a) the polyribonucleotide of claim 10 or 11; and (b) the polyribonucleotide of claim 25 or 26.
42. The composition of claim 36, wherein the one or more polyribonucleotides comprise or consist of: (a) the polyribonucleotide of claim 12 or 13; and (b) the polyribonucleotide of claim 25 or 26.
43. The composition of claim 36, wherein the one or more polyribonucleotides comprise or consist of: (a) the polyribonucleotide of claim 18 or 19; and - 260 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) (b) the polyribonucleotide of claim 31 or 32.
44. The composition of claim 36, wherein the one or more polyribonucleotides comprise or consist of: (a) the polyribonucleotide of claim 14 or 15; and (b) the polyribonucleotide of claim 27 or 28.
45. The composition of any one of claims 36-44, wherein the composition further comprises lipid nanoparticles, polyplexes (PLX), lipidated polyplexes (LPLX), or liposomes, wherein the one or more polyribonucleotides are fully or partially encapsulated within the lipid nanoparticles, polyplexes (PLX), lipidated polyplexes (LPLX), or liposomes.
46. A pharmaceutical composition comprising the composition of any one of claims 36-45 and at least one pharmaceutically acceptable excipient.
47. A method comprising administering the pharmaceutical composition of claim 46 to a subject.
48. Use of the composition of any one of claims 36-45 or the pharmaceutical composition of claim 46 for the treatment or prevention of HIV in a subject.
49. A method of producing an antibody agent comprising administering to cells the composition of any one of claims 36-45 or the pharmaceutical composition of claim 46 so that the cells express and secrete the antibody agent.
50. A method comprising a step of: determining one or more features of an antibody agent expressed from the polyribonucleotide of any one of claims 1-34, the composition of any one of claims 36-45, or the pharmaceutical composition of claim 46 introduced into cells, wherein the one or more features comprises: (i) protein expression level of the antibody agent; (ii) binding specificity of the antibody agent to the CD4 binding site of HIV; (iii) efficacy of the antibody agent to mediate target cell death through antibody-dependent cellular cytotoxicity (ADCC); and (iv) efficacy of the antibody agent to mediate target cell death through complement dependent cytotoxicity (CDC).
51. A method comprising the steps of: contacting cells with the polyribonucleotide of any one of claims 1-34, the composition of any one of claims 36-45, or the pharmaceutical composition of claim 46 introduced into cells; and detecting the antibody agent produced by the cells.
52. A method of manufacture, the method comprising steps of: (a) determining one or more features of a polyribonucleotide of any one of claims 1-34, the composition of any one of claims 36-45, or the pharmaceutical composition of claim 46, which one or more features comprise or consist of: (i) length and / or sequence of the polyribonucleotide; (ii) integrity of the polyribonucleotide; - 261 of 263 - 12197150v1Attorney Docket No: 2013237-1144 (P1577WO01) (iii) presence and / or location of one or more chemical moieties of the polyribonucleotide; (iv) extent of expression of the antibody agent when the polyribonucleotide is introduced into a cell; (v) stability of the polyribonucleotide or composition thereof; (vi) level of antibody agent in a biological sample from an organism into which the polyribonucleotide has been introduced; (vii) binding specificity of the antibody agent expressed from the polyribonucleotide, optionally to a CD4 binding site of HIV; (viii) efficacy of the antibody agent to mediate target cell death through ADCC; (ix) efficacy of the antibody agent to mediate target cell death through complement dependent cytotoxicity (CDC); (x) lipid identity and amount / concentration within the composition; (xi) size of lipid nanoparticles within the composition; (xii) polydispersity of lipid nanoparticles within the composition; (xiii) amount / concentration of the polyribonucleotide within the composition; (xiv) extent of encapsulation of the polyribonucleotide within lipid nanoparticles; (xv) a level of double stranded RNA; and (xvi) combinations thereof; (b) comparing the one or more features of the polyribonucleotide with that of an appropriate reference standard; and (c) (i) designating the polyribonucleotide or composition thereof for one or more further steps of manufacturing and / or distribution if the comparison demonstrates that the polyribonucleotide or composition thereof meets or exceeds the reference standard; or (ii) taking an alternative action if the comparison demonstrates that the polyribonucleotide or composition thereof does not meet or exceed the reference standard. - 262 of 263 - 12197150v1