Methods of identifying HIV patients susceptible to therapy with antibodies directed against the gp120 v3 glycan

Abstract

The present invention provides methods for identifying a patient population infected with HIV that is targetable by an antibody that binds to the HIV gl20 V3 glycan region.

Description

[0001] Cross-reference to related applications

[0002] This patent application claims the benefit of U.S. Provisional Application 62 / 850,994, filed May 21, 2019, pursuant to Section 119(e) of Title 35 of the United States Code, which is incorporated herein by reference in its entirety for all purposes.

[0003] SEQUENCE LISTING

[0004] This patent application includes a sequence list submitted electronically in ASCII format, the entire contents of which are incorporated herein by reference. The ASCII copy was created on April 27, 2020, named 1289PF_SL.txt, and is 199,543 bytes in size. Background Technology

[0005] Human immunodeficiency virus (HIV) infection and related diseases are a major public health problem worldwide. Most currently approved HIV treatments target viral reverse transcriptase, protease, and integrase; however, HIV resistance to these existing drugs, long-term toxicity, and lack of patient adherence to daily dosing regimens have proven to be problems associated with these treatments. Therefore, the discovery and development of new HIV drugs is of paramount importance.

[0006] WO 2009 / 066702, WO 2012 / 030904, WO 2014 / 063059, WO 2016 / 149698, WO 2017 / 106346; WO 2018 / 075564 and WO 2018 / 125813, McCoy, Retrovirology, 2018, Vol. 15, p. 70; Sok and Burton, Nat Immunol., 2018, Vol. 19, No. 11, pp. 1179-1188; Possas et al., Expert Opinion Ther Pat., July 2018, Vol. 28, No. 7, pp. 551-560; and Stephenson and Barouch, Curr HIV / AIDS Rep., 2016, Vol. 13, pp. 31-37, describes a human anti-HIV antibody derived from memory B cells of an HIV-infected donor. This human anti-HIV antibody targets the V3 glycan region of gp120 and is able to inhibit infection from multiple HIV-1 strains from various clades. The therapeutic use of the antibody may be limited because it requires identification of patients infected with HIV-1 strains that can be targeted by antibodies targeting the V3 glycan region of HIV gp120. Summary of the Invention

[0007] The present invention provides methods of identifying patients most likely to benefit from therapy with antibodies that target the V3 glycan region of HIV gp120.

[0008] Accordingly, in one aspect, the present application provides a method of treating or preventing HIV in a human subject in need thereof, the method comprising: a) identifying a human subject infected with an HIV or a population of HIVs that express a gpl20 comprising a glycosylated asparagine at a position corresponding to amino acid residue position 332 (N332 glycan), an aspartic acid at a position corresponding to amino acid residue position 325 (D325), and one or more amino acid residues selected from the group consisting of: a threonine at a position corresponding to amino acid residue position 63 (T63), a leucine at a position corresponding to amino acid residue position 179 (L179), a threonine at a position corresponding to amino acid residue position 320 (T320), and a histidine at a position corresponding to amino acid residue position 330 (H330), wherein the amino acid positions are with reference to SEQ ID NO: 4; and b) administering to the subject an effective amount of an antibody or antigen-binding fragment thereof that competes with or comprises VH and VL regions that bind to an epitope of gpl20 within the third variable loop (V3) and / or the high mannose patch comprising the N332 oligomannose glycan. In some embodiments, the method requires identifying a subject infected with an HIV or a population of HIVs that express a gpl20 comprising: i. the N332 glycan, D325, and T63; ii. the N332 glycan, D325, and L179; iii. the N332 glycan, D325, and T320; iv. the N332 glycan, D325, and H330; v. the N332 glycan, D325, T63, and L179; vi. the N332 glycan, D325, T63, and T320; vii. the N332 glycan, D325, T63, and H330; viii. the N332 glycan, D325, L179, and T320; ix. the N332 glycan, D325, L179, and H330; x. the N332 glycan, D325, T320, and H330; xi. the N332 glycan, D325, T63, T320, and H330; xii. the N332 glycan, D325, T63, L179, and T320; xiii. the N332 glycan, D325, T63, L179, and H330; xiv. the N332 glycan, D325, L179, T320, and H330; or xv. the N332 glycan, D325, T63, L179, T320, and H330, wherein the amino acid positions are with reference to SEQ ID NO: 4.In some embodiments, the method entails identifying a subject infected with an HIV or a population of HIVs expressing a gpl20 comprising: i. N332 glycan, D325, and T63; ii. N332 glycan, D325, and L179; iii. N332 glycan, D325, and T320; or iv. N332 glycan, D325, and H330, wherein the amino acid positions are with reference to SEQ ID NO: 4. In some embodiments, the method entails identifying a subject infected with an HIV or a population of HIVs expressing a gpl20 comprising: i. N332 glycan, D325, T63, and L179; ii. N332 glycan, D325, T63, and T320; iii. N332 glycan, D325, T63, and H330; iv. N332 glycan, D325, L179, and T320; v. N332 glycan, D325, L179, and H330; or vi. N332 glycan, D325, T320, and H330, wherein the amino acid positions are with reference to SEQ ID NO: 4. In some embodiments, the method entails identifying a subject infected with an HIV or a population of HIVs expressing a gpl20 comprising: i. N332 glycan, D325, L179, T320, and H330; ii. N332 glycan, D325, T63, T320, and H330; iii. N332 glycan, D325, T63, L179, and T320; or iv. N332 glycan, D325, T63, L179, and H330, wherein the amino acid positions are with reference to SEQ ID NO: 4. In some embodiments, the method entails identifying a subject infected with an HIV or a population of HIVs expressing a gpl20 comprising: i. N332 glycan, D325, T63, and H330; ii. N332 glycan, D325, T320, and H330; iii. N332 glycan, D325, L179, T320, and H330; or iv. N332 glycan, D325, T63, L179, T320, and H330, wherein the amino acid positions are with reference to SEQ ID NO: 4.In some embodiments, the subject is infected with an HIV or a population of HIVs expressing a gpl20 that further comprises one or more of the following amino acid residues: a glycan at amino acid residue 301 (glycan301); a lysine at amino acid residue 677 (K677); an amino acid residue other than tryptophan at position 17 (e.g., A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y) (not_W17); an amino acid residue other than arginine at position 747 (e.g., A, C, D, E, F, G, H, I, K, L, M, N, P, Q, S, T, V, W, or Y) (not_R747); insertion_321.01 (e.g., an insertion of any amino acid between positions G321 and K322 (e.g., A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y)); a glutamic acid at position 429 (E429); a glutamine at position 442 (Q442); an arginine at position 335 (R335); an isoleucine at position 165 (1165); a serine at position 393 (S393); an isoleucine at position 307 (I307); a glycan at position 295 (295_glycan); and / or an asparagine at position 300 (N300), wherein the amino acid positions are with reference to SEQ ID NO: 4. In some embodiments, at least 90%, e.g., at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100%, of the HIV species in the population comprise the amino acid residue. In some embodiments, the administered antibody or antigen-binding fragment thereof competes with or comprises the VH and VL regions from an antibody selected from the group consisting of GS-9722 (ebricitide), GS-9721, PGT-121, PGT-121.66, PGT-121.414, PGT-122, PGT-123, PGT-124, PGT-125, PGT-126, PGT-128, PGT-130, PGT-133, PGT-134, PGT-135, PGT-136, PGT-137, PGT-138, PGT-139, 10-1074, 10-1074-J, VRC24, 2G12, BG18, 354BG8, 354BG18, 354BG42, 354BG33, 354BG129, 354BG188, 354BG411, 354BG426, DH270.1, DH270.6, PGDM12, VRC41.01, PGDM21, PCDN-33A, BF520.1, and VRC29.03.In some embodiments, the antibody or antigen-binding fragment thereof competes with or comprises VH and VL regions from an antibody selected from the group consisting of GS-9722, GS-9721, PGT-121, PGT-121.66, PGT-121.414, PGT-124, PGT-134, GS-2872, 10-1074, 10-1074-J, PGT-122, and PGT-123. In some embodiments, the methods comprise administering an antibody comprising an Fc region comprising one or more amino acid substitutions that prolong serum half-life. In some embodiments, the methods comprise administering an antibody comprising an Fc region comprising the following amino acids at the indicated positions (EU index numbering): i. tyrosine at position 252, threonine at position 254, and glutamic acid at position 256 (YTE); or ii. leucine at position 428 and serine at position 434 (LS). In some embodiments, the methods comprise administering an antibody comprising an Fc region comprising the following amino acids at the indicated positions (EU index numbering): i. aspartic acid at position 239 and glutamic acid at position 332 (DE); ii. aspartic acid at position 239, glutamic acid at position 332, and leucine at position 330 (DEL); iii. aspartic acid at position 239, glutamic acid at position 332, alanine at position 236 (DEA); or iv. aspartic acid at position 239, glutamic acid at position 332, alanine at position 236, and leucine at position 330 (DEAL). In some embodiments, the methods comprise administering an antigen-binding fragment. In some embodiments, the antigen-binding fragment is selected from the group consisting of scFv, Fab, Fab2, Fab’, F(ab’)2, Fv, and diabody. In some embodiments, the antibody is one or more arms of a multispecific antibody (e.g., a bispecific antibody). In some embodiments, the human subject is acutely infected with HIV. In some embodiments, the antibody is administered to a human subject with HIV infection at Fiebig stage IV or earlier, e.g., Fiebig stage III, Fiebig stage II, or Fiebig stage I. In some embodiments, the antibody is administered to a human subject who has not undergone seroconversion. In some embodiments, the human subject has recently been infected with HIV, e.g., within 1 week, 2 weeks, 3 weeks, or 4 weeks, or prior to detection, seroconversion, or manifestation of symptoms. In some embodiments, the antibody is administered to a human subject with HIV infection at Fiebig stage V or Fiebig stage VI. In some embodiments, the human subject is chronically infected with HIV. In some embodiments, the human subject is infected with an HIV clade B virus.In some embodiments, the human subject is infected with an HIV clade B virus, and the methods entail identifying a subject infected with an HIV or population of HIVs expressing a gpl20 comprising: i. an N332 glycan, D325, T63, and H330; ii. an N332 glycan, D325, LI 79, T320, and H330; or iii. an N332 glycan, D325, T63, LI 79, T320, and H330. In some embodiments, the human subject is infected with an HIV clade A virus. In some embodiments, the human subject is infected with an HIV clade C virus. In some embodiments, the methods further comprise administering to the subject one or more additional therapeutic agents for treating HIV infection. In some embodiments, the subject is not receiving antiretroviral therapy (ART), or ART is discontinued prior to administration of the antibody. In some embodiments, ART is discontinued after one or more administrations of the antibody or antigen-binding fragment thereof. In some embodiments, the methods further comprise administering to the subject one or more antiretroviral therapy (ART) agents. In some embodiments, the methods further comprise administering to the subject a second antibody or antigen-binding fragment thereof that binds to an epitope or region of gpl20 selected from: the second variable loop (V2) and / or Env trimer apex; the CD4 binding site (CD4bs); the gpl20 / gp41 interface; or the gpl20 silent face. In some embodiments, the second antibody or antigen-binding fragment thereof binds to an epitope or region of gpl20 in the second variable loop (V2) and / or Env trimer apex, and competes with or comprises VH and VL regions from an antibody selected from: PG9, PG16, PGC14, PGG14, PGT-142, PGT-143, PGT-144, PGT-145, CH01, CH59, PGDM1400, CAP256, CAP256-VRC26.08, CAP256-VRC26.09, CAP256-VRC26.25, PCT64-24E, and VRC38.01.In some embodiments, the second antibody or antigen-binding fragment thereof binds to an epitope or region of gpl20 in the CD4 binding site (CD4bs) and competes with or comprises the VH and VL regions from an antibody selected from the group consisting of b12, F105, VRC01, VRC07, VRC07-523, VRC03, VRC06, VRC06b01 VRC08, VRC0801, NIH45-46, GS-9723, GS-5423, 3BNC117, 3BNC60, VRC-PG04, PGV04; CH103, 44-VRC13.01, 1NC9, 12A12, N6, N6LS (VRC-HIVMAB091-00-AB), N49-P7, NC-Cowl, IOMA, CH235 and CH235.12, N49P6, N49P7, N49Pll, N49P9 and N60P25. In some embodiments, the second antibody or antigen-binding fragment thereof binds to an epitope or region of gpl20 in the gpl20 / gp41 interface and competes with or comprises the VH and VL regions from an antibody selected from the group consisting of PGT-151, CAP248-2B, 35022, 8ANC195, ACS202, VRC34 and VRC34.01. In some embodiments, the second antibody or antigen-binding fragment thereof binds to an epitope or region of gpl20 in the gpl20 silent face and competes with or comprises the VH and VL regions from the antibody VRC-PG05. In some embodiments, the second antibody or antigen-binding fragment thereof binds to an epitope or region of gp41 in the membrane proximal region (MPER) and competes with or comprises the VH and VL regions from an antibody selected from the group consisting of 10E8, 10E8v4, 10E8-5R-100cF, 4E10, DH511.11P, 2F5, 7b2 and LN01. In some embodiments, the second antibody or antigen-binding fragment thereof binds to an epitope or region of gp41 fusion peptide and competes with or comprises the VH and VL regions from an antibody selected from the group consisting of VRC34 and ACS202. In some embodiments, the methods further comprise administering a TLR agonist to the subject. In some embodiments, the TLR agonist is a TLR2 agonist, a TLR3 agonist, a TLR7 agonist, a TLR8 agonist, or a TLR9 agonist. In some embodiments, the TLR7 agonist is selected from the group consisting of vesatolimod, imiquimod, and resiquimod. In some embodiments, the methods comprise administering the antibody or antigen-binding fragment thereof multiple times at predetermined intervals, optionally with the TLR agonist.In some embodiments, after one or more administrations of the antibody or antigen binding fragment thereof, in the absence of antiretroviral therapy (ART), the subject does not exhibit symptoms of HIV or AIDS for at least 6 months, at least 1 year, at least 2 years, at least 3 years, at least 4 years, at least 5 years, or more. In some embodiments, after one or more administrations of the antibody, in the absence of antiretroviral therapy (ART), the subject has a viral load of HIV of less than 500, e.g., less than 400, less than 300, less than 200, less than 100, less than 50 copies per ml of blood for at least 6 months, at least 1 year, at least 2 years, at least 3 years, or more.

[0009] In another aspect, the application provides methods of identifying a human subject infected with an HIV or a population of HIV that is susceptible to an antibody or antigen-binding fragment thereof that competes with or comprises VH and VL regions that bind to an epitope of gpl20 within the third variable loop (V3) and / or a high mannose patch comprising N332 oligomannose glycans. In some embodiments, the methods comprise identifying in a biological sample from the human subject gpl20 comprising a glycosylated asparagine at a position corresponding to amino acid residue position 332 (N332 glycan), an aspartic acid at a position corresponding to amino acid residue position 325 (D325), and one or more amino acid residues selected from the group consisting of: a threonine at a position corresponding to amino acid residue position 63 (T63), a leucine at a position corresponding to amino acid residue position 179 (L179), a threonine at a position corresponding to amino acid residue position 320 (T320), and a histidine at a position corresponding to amino acid residue position 330 (H330), wherein the amino acid positions are with reference to SEQ ID NO: 4. In some embodiments, the methods entail identifying a subject infected with an HIV or a population of HIV that expresses gpl20 comprising: i. the N332 glycan, D325, and T63; ii. the N332 glycan, D325, and L179; iii. the N332 glycan, D325, and T320; iv. the N332 glycan, D325, and H330; v. the N332 glycan, D325, T63, and L179; vi. the N332 glycan, D325, T63, and T320; vii. the N332 glycan, D325, T63, and H330; viii. the N332 glycan, D325, L179, and T320; ix. the N332 glycan, D325, L179, and H330; x. the N332 glycan, D325, T320, and H330; xi. the N332 glycan, D325, T63, T320, and H330; xii. the N332 glycan, D325, T63, L179, and T320; xiii. the N332 glycan, D325, T63, L179, and H330; xiv. the N332 glycan, D325, L179, T320, and H330; or xv. the N332 glycan, D325, T63, L179, T320, and H330, wherein the amino acid positions are with reference to SEQ ID NO: 4.In some embodiments, the method entails identifying a subject infected with an HIV or a population of HIVs expressing a gpl20 comprising: i. N332 glycan, D325, and T63; ii. N332 glycan, D325, and L179; iii. N332 glycan, D325, and T320; or iv. N332 glycan, D325, and H330, wherein the amino acid positions are with reference to SEQ ID NO: 4. In some embodiments, the method entails identifying a subject infected with an HIV or a population of HIVs expressing a gpl20 comprising: i. N332 glycan, D325, T63, and L179; ii. N332 glycan, D325, T63, and T320; iii. N332 glycan, D325, T63, and H330; iv. N332 glycan, D325, L179, and T320; v. N332 glycan, D325, L179, and H330; or vi. N332 glycan, D325, T320, and H330, wherein the amino acid positions are with reference to SEQ ID NO: 4. In some embodiments, the method entails identifying a subject infected with an HIV or a population of HIVs expressing a gpl20 comprising: i. N332 glycan, D325, L179, T320, and H330; ii. N332 glycan, D325, T63, T320, and H330; iii. N332 glycan, D325, T63, L179, and T320; or iv. N332 glycan, D325, T63, L179, and H330, wherein the amino acid positions are with reference to SEQ ID NO: 4. In some embodiments, the method entails identifying a subject infected with an HIV or a population of HIVs expressing a gpl20 comprising: i. N332 glycan, D325, T63, and H330; ii. N332 glycan, D325, T320, and H330; iii. N332 glycan, D325, L179, T320, and H330; or iv. N332 glycan, D325, T63, L179, T320, and H330, wherein the amino acid positions are with reference to SEQ ID NO: 4.In some embodiments, the subject is infected with an HIV or a population of HIVs expressing a gpl20 that further comprises one or more of the following amino acid residues: a glycan at amino acid residue 301 (glycan301); a lysine at amino acid residue 677 (K677); an amino acid residue other than tryptophan at position 17 (e.g., A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, or Y) (not_W17); an amino acid residue other than arginine at position 747 (e.g., A, C, D, E, F, G, H, I, K, L, M, N, P, Q, S, T, V, W, or Y) (not_R747); insertion_321.01 (e.g., an insertion of any amino acid between positions G321 and K322 (e.g., A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y)); a glutamic acid at position 429 (E429); a glutamine at position 442 (Q442); an arginine at position 335 (R335); an isoleucine at position 165 (1165); a serine at position 393 (S393); an isoleucine at position 307 (1107); a glycan at position 295 (295_glycan); and / or an asparagine at position 300 (N300), wherein the amino acid positions are with reference to SEQ ID NO: 4. In some embodiments, the antibody or antigen-binding fragment thereof competes with or comprises a VH region and a VL region from an antibody selected from the group consisting of GS-9722, GS-9721, PGT-121, PGT-121.66, PGT-121.414, PGT-122, PGT-123, PGT-124, PGT-125, PGT-126, PGT-128, PGT-130, PGT-133, PGT-134, PGT-135, PGT-136, PGT-137, PGT-138, PGT-139, 10-1074, 10-1074-J, VRC24, 2G12, BG18, 354BG8, 354BG18, 354BG42, 354BG33, 354BG129, 354BG188, 354BG411, 354BG426, DH270.1, DH270.6, PGDM12, VRC41.01, PGDM21, PCDN-33A, BF520.1, and VRC29.03.In some embodiments, the antibody or antigen-binding fragment thereof competes with or comprises a VH region and a VL region from an antibody selected from the group consisting of GS-9722, GS-9721, PGT-121, PGT-121.66, PGT-121.414, PGT-124, PGT-134, GS-2872, 10-1074, 10-1074-J, PGT-122, and PGT-123. In some embodiments, the human subject is acutely infected with HIV. In some embodiments, the antibody is administered to a human subject having an HIV infection of Fiebig stage IV or earlier. In some embodiments, the antibody is administered to a human subject who has not seroconverted. In some embodiments, the human subject has recently been infected with HIV. In some embodiments, the antibody is administered to a human subject having an HIV infection of Fiebig stage V or Fiebig stage VI. In some embodiments, the human subject is chronically infected with HIV. In some embodiments, the human subject is infected with an HIV clade B virus. In some embodiments, the human subject is infected with an HIV clade B virus, and the methods require identifying a subject infected with an HIV or population of HIVs expressing a gpl20 comprising: i. an N332 glycan, D325, T63, and H330; ii. an N332 glycan, D325, L179, T320, and H330; or iii. an N332 glycan, D325, T63, L179, T320, and H330. In some embodiments, the human subject is infected with an HIV clade A virus. In some embodiments, the human subject is infected with an HIV clade C virus.

[0010] With respect to additional embodiments of the methods described herein, in some embodiments, the gpl20 amino acid is identified in one or more gpl20 polypeptide sequences expressed in an HIV or HIV population isolated from a subject. In some embodiments, the gpl20 amino acid is identified in one or more gpl20 polynucleotide sequences encoding a gpl20 polypeptide from an HIV or HIV population isolated from a subject. In various embodiments, these methods entail next generation sequencing (NGS) of gpl20-encoding polynucleotide sequences from an HIV population. In some embodiments, the gpl20 variant is detected at a frequency level of about 1% (e.g., at a frequency level of about 0.5%) of the viral population. In some embodiments, the gpl20 amino acid is identified in one or more biological samples from a subject, wherein the one or more biological samples are obtained from blood, peripheral blood mononuclear cells (PBMCs), serum, plasma, semen, or lymph nodes. In some embodiments, these methods entail identifying an HIV RNA population in a serum or plasma sample. In some embodiments, these methods further comprise the step of obtaining one or more biological samples from a subject. In some embodiments, two or more biological samples are obtained from a subject. In some embodiments, two or more biological samples are obtained from the same tissue or fluid at two or more different time points. In some embodiments, two or more biological samples are obtained from different tissues or fluids or from different anatomical locations.

[0011] Definitions

[0012] The words “a” and “an” mean one or more, unless otherwise indicated.

[0013] By “about” is meant an amount, level, value, number, frequency, percentage, dimension, size, quantity, weight, or length that is up to 30%, 25%, 20%, 15%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or 1% different from a reference amount, level, value, number, frequency, percentage, dimension, size, quantity, weight, or length. In any embodiment discussed in the context of a numerical value used in conjunction with the term “about,” it is specifically contemplated that the term “about” can be omitted.

[0014] Unless the context requires otherwise, throughout the present specification and claims, the word “comprise,” and variations such as “comprises” and “comprising,” will be understood to mean the same as the word “include,” and variations such as “includes” and “including.” Where the term “comprise,” or variations such as “comprises” or “comprising,” is used in the context of a process, method, composition, or apparatus, the term “comprise” is taken to mean that the process, method, composition, or apparatus includes the recited elements, but not excluding others.

[0015] By "comprises" or "comprising" it is meant that the phrase "comprises" or "comprising" when used in a clause of the form "A comprises B" or "comprising B", that B is included in A or vice versa. Thus, the phrase "comprises" or "comprising" indicates that the inclusion of B is a necessary or mandatory feature of A, and that other features can or can not be present.

[0016] By "consisting essentially of" it is meant that the phrase "consists essentially of" when used in a clause of the form "consists essentially of A" or "consisting essentially of A" that A is included in the composition, mixture, method or process of the present disclosure and that the composition, mixture, method or process is limited to other elements not affecting the activity or action of the listed elements. Thus, the phrase "consists essentially of" indicates that the listed elements are necessary or mandatory, but that other elements are optional and can or can not be present depending on whether they affect the activity or action of the listed elements.

[0017] Reference throughout this specification to "one embodiment" or "an embodiment" means that a particular feature, structure or characteristic described in connection with the embodiment is included in at least one embodiment described herein. Thus, the appearances of the phrase "in one embodiment" or "in an embodiment" in various places throughout this specification are not necessarily all referring to the same embodiment. Furthermore, the particular features, structures, or characteristics can be combined in any suitable manner in one or more embodiments.

[0018] An "increased" or "enhanced" amount is typically a "statistically significant" amount and can include an increase of 1.1 fold, 1.2 fold, 1.3 fold, 1.4 fold, 1.5 fold, 1.6 fold, 1.7 fold, 1.8 fold, 1.9 fold, 2 fold, 2.5 fold, 3 fold, 3.5 fold, 4 fold, 4.5 fold, 5 fold, 6 fold, 7 fold, 8 fold, 9 fold, 10 fold, 15 fold, 20 fold, 30 fold, 40 fold, or 50 fold or more (e.g., 100 fold, 500 fold, 1000 fold) of an amount or level described herein (including all integer and decimal points in between 1 and greater than 1, e.g., 2.1, 2.2, 2.3, 2.4, etc.). It can also include an increase of at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, at least 150%, at least 200%, at least 500%, or at least 1000% of an amount or level described herein.

[0019] A "reduced" or "decreased" or "less" amount is typically a "statistically significant" amount and can include a reduction of about 1.1 fold, 1.2 fold, 1.3 fold, 1.4 fold, 1.5 fold, 1.6 fold, 1.7 fold, 1.8 fold, 1.9 fold, 2 fold, 2.5 fold, 3 fold, 3.5 fold, 4 fold, 4.5 fold, 5 fold, 6 fold, 7 fold, 8 fold, 9 fold, 10 fold, 15 fold, 20 fold, 30 fold, 40 fold, or 50 fold or more (e.g., 100 fold, 500 fold, 1000 fold) of the amount or level described herein (including all whole and fractional points between 1 and greater than 1, e.g., 1.5, 1.6, 1.7, 1.8, etc.). It can also include a reduction of at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, or at least 90%, at least 100%, at least 150%, at least 200%, at least 500%, or at least 1000% of the amount or level described herein.

[0020] A "composition" can include an active agent, such as a contrast agent, and an inert or active carrier, such as a pharmaceutically acceptable carrier, diluent, or excipient. The composition can be a pharmaceutical composition. In particular embodiments, the composition is sterile, substantially endotoxin-free, or non-toxic to the recipient at the dose or concentration employed.

[0021] A "pharmaceutically acceptable carrier, diluent, or excipient" includes, but is not limited to, any auxiliary agent, carrier, excipient, glidant, sweetening agent, diluent, preservative, dye / colorant, flavor enhancer, surfactant, wetting agent, dispersing agent, suspending agent, stabilizer, isotonic agent, solvent, or emulsor that has been approved by the U.S. Food and Drug Administration as acceptable for use in humans or domestic animals.

[0022] A "biological sample" or "sample" refers to any fluid, cell, or solid tissue sample from a subject having or suspected of having detectable HIV.

[0023] A "subject," "individual," or "patient" refers to any mammal, including humans and non-human primates. In particular embodiments, the mammal is a human.

[0024] As used herein, the term "buffer" means a pharmaceutically acceptable excipient that stabilizes the pH of a pharmaceutical formulation. Suitable buffers are well known in the art. Suitable pharmaceutically acceptable buffers include, but are not limited to, acetate buffers, histidine buffers, citrate buffers, succinate buffers, tris buffers, and phosphate buffers. In certain embodiments, the concentration of the buffer is about 0.01 mM to about 1000 mM, about 0.1 mM to about 1000 mM, about 0.1 mM to about 500 mM, about 0.1 mM to about 200 mM, about 0.1 mM to about 100 mM, about 1 mM to about 1000 mM, about 1 mM to about 500 mM, about 1 mM to about 200 mM, about 1 mM to about 100 mM, about 1 mM to about 50 mM, about 2 mM to about 60 mM, about 4 mM to about 60 mM, or about 4 mM to about 40 mM, about 5 mM to about 20 mM, or about 5 mM to about 25 mM.

[0025] "Optional" or "optionally" means that the subsequently described event or circumstance can or can not occur, and that the description includes instances where the event or circumstance occurs and instances where it does not.

[0026] "Pharmaceutical composition" refers to a preparation of a compound and a medium generally accepted in the art for the delivery of biologically active compounds to mammals (e.g., humans). Such medium can include any pharmaceutically acceptable carrier, diluent, or excipient.

[0027] "Effective amount" or "therapeutically effective amount" refers to the amount of an antibody or antigen-binding fragment thereof that, when administered to a cell, tissue, or subject, either alone or in combination with another therapeutic agent, is sufficient to effect a treatment or beneficial result in the subject. The amount constituting an "effective amount" will vary depending on the antibody or antigen-binding fragment thereof and its particular use, as well as the potential disorder and its severity, the mode of administration, and the age of the subject to be treated, but can be routinely determined by one of ordinary skill in the art in view of his own knowledge and this disclosure. A therapeutically effective dose is also one in which toxic or detrimental effects of the antibody or antigen-binding fragment thereof are outweighed by the therapeutically beneficial effects. When applicable to individual antibodies or antigen-binding fragments thereof administered alone, a therapeutically effective dose refers to the active ingredient alone. When applicable to combinations, a therapeutically effective dose refers to the combined amounts of the active ingredients that give the therapeutic result, whether administered in combination, serially, or simultaneously.

[0028] As used herein, “treat” or “treating” or “treatment” covers the treatment of a subject (e.g., a mammal, such as a human) having a disease or disorder of interest, e.g., an HIV-1 infection, and includes: (i) inhibiting the disease, injury or condition, i.e., arresting its development; (ii) relieving or reducing the disease, injury or condition, i.e., causing regression of the disease or condition; or (iii) relieving the symptoms resulting from the disease, injury or condition. As used herein, the terms “disease,” “disorder,” and “condition” are used interchangeably. As used herein, “inhibit,” “treatment” and “amelioration” are used interchangeably and refer to, e.g., stasis of symptoms, lengthened survival, partial or complete amelioration of symptoms, and partial or complete eradication of the condition, disease or disorder.

[0029] As used herein, “prevent” or “prevention” includes (i) preventing or inhibiting the occurrence of a disease, injury or condition in a subject, particularly when such subject is predisposed to the condition but has not yet been diagnosed as having it; or (ii) reducing the likelihood of a subject developing a disease, injury or condition.

[0030] As used herein, the term “antibody” means an isolated or recombinant binding agent comprising the necessary variable region sequences that specifically bind to an epitope of an antigen. Thus, an antibody is any form of an antibody or fragment thereof that exhibits a desired biological activity (e.g., binding to a specific target antigen). Thus, it is used in the broadest sense and specifically encompasses monoclonal antibodies (including full length monoclonal antibodies), polyclonal antibodies, human antibodies, humanized antibodies, chimeric antibodies, nanobodies, diabodies, multispecific antibodies (e.g., bispecific antibodies), and antibody fragments, including, but not limited to, scFv, Fab, and Fab2, so long as they exhibit the desired biological activity.

[0031] The term “human antibody” refers to an antibody comprising sequences of human origin except for possible non-human CDR regions, and does not imply the presence of the complete structure of an Ig molecule, only that the antibody has minimal immunogenic effect in humans.

[0032] An“antibody fragment” comprises a portion of an intact antibody, e.g., the antigen binding or variable region of the intact antibody. Examples of antibody fragments include Fab, Fab’, F(ab’)2, and Fv fragments; diabodies; linear antibodies (e.g., Zapata et al., Protein Eng., vol. 8, no. 10, pp. 1057-1062, 1995); single-chain antibody molecules (e.g., scFv); and multispecific antibodies formed from antibody fragments. Papain digestion of antibodies produces two identical antigen binding fragments, called“Fab” fragments, each with a single antigen binding site, and a residual“Fc” fragment, which designation reflects the ability to crystallize readily. Treatment with pepsin yields F(ab’)2 fragments that have two antigen binding sites and are still capable of cross-linking antigen.

[0033] “Fv” is the minimum antibody fragment that contains a complete antigen recognition and binding site. This region consists of a dimer of one heavy chain variable domain and one light chain variable domain connected by a linker. In this configuration, the three CDRs of each variable domain interact to define an antigen binding site on the surface of the VH-VL dimer. In general, the six CDRs in combination confer antibody antigen binding specificity to the antibody, but examples exist where antigen binding specificity is maintained when one or more of the six CDRs is missing or modified, e.g., by altering the amino acid sequence of the one or more CDRs, e.g., by amino acid insertion, deletion or substitution. In addition, even a single variable domain (or half of an Fv comprising only three CDRs specific for an antigen) has the ability to recognize and bind antigen, although at a lower affinity than the entire binding site. Residues other than those in the CDRs can also contribute to or play a role in antigen binding and / or specificity, as shown for PGT121 and closely related somatic variants that use residues in the light chain framework 3 to interact with the gpl20 antigen (Julien et al., Science, vol. 342, pp. 1477-1483, 2013; Julien et al., PLOS Pathog., vol. 9, p. e1003342, (2013)). These residues are in part derived from an unusual three amino acid insertion that extends a normally short surface loop in PGT121 and related somatic variants (e.g., PGT122, PGT123, PGT124, PGT133, PGT134, 10-1074) that contacts both the N332-linked glycan and protein residues on HIV Env, effectively creating an additional (e.g., fourth) complementarity determining region (CDR) loop in the PGT121 light chain between LCCDR 2 and LC CDR 3.

[0034] The term "hypervariable region" refers to amino acid residues of an antibody that are typically responsible for antigen binding. The hypervariable region typically comprises amino acid residues from a "complementarity determining region" or "CDR" (e.g., around about residues 24-34 (L1), 50-56 (L2), and 89-97 (L3) in the VL and around about residues 31-35 (H1), 50-65 (H2), and 95-102 (H3) in the VH when numbered in accordance with the Kabat numbering system; Kabat et al., Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, Md., 1991); and / or those residues from a "hypervariable loop" (e.g., around about residues 24-34 (L1), 50-56 (L2), and 89-97 (L3) in the VL and around about residues 26-32 (H1), 52-56 (H2), and 95-101 (H3) in the VH when numbered in accordance with the Chothia numbering system; Chothia and Lesk, J. Mol. Biol., 196:901-917, 1987); and / or those residues from a "hypervariable loop" VCDR (e.g., around about residues 27-38 (L1), 56-65 (L2), and 105-120 (L3) in the VL and around about residues 27-38 (H1), 56-65 (H2), and 105-120 (H3) in the VH when numbered in accordance with the IMGT numbering system; Lefranc, M.P. et al., Nucl. Acids Res., 27:209-212, 1999; Ruiz, M. et al., Nucl. Acids Res., 28:219-221, 2000). Optionally, the antibody has one or more symmetric insertions at the following positions in the VL: 28, 36 (L1), 63, 74-75 (L2), and 123 (L3) and in the VH: 28, 36 (H1), 63, 74-75 (H2), and 123 (H3) when numbered in accordance with AHo numbering; Honneger, A. and Plunkthun, A., J. Mol. Biol., 309:657-670, 2001).

[0035] A "Fab" fragment is the region of an antibody that binds to an antigen. It is composed of one constant and one variable domain of each of the heavy and light chains. These domains shape the paratope (antigen binding site) at the amino-terminal end of the monomer. The two variable domains bind to an epitope on its specific antigen. Fab fragments differ from Fab' fragments by the addition of a few residues at the carboxy terminus of the heavy chain CH1 domain, including one or more cysteines from the antibody hinge region. Fab'-SH is the designation herein for Fab' in which the cysteine residue(s) of the constant domains carry free thiol groups. F(ab')2 antibody fragments originally were produced as pairs of Fab' fragments which have hinge cysteines between them. Other chemical couplings of antibody fragments are known.

[0036] The "light chains" of antibodies (immunoglobulins) from any vertebrate species can be assigned to one of two clearly distinct types, called kappa and lambda, based on the amino acid sequences of their variable and constant domains. Depending on the amino acid sequences of the constant domains of their heavy chains, immunoglobulins can be assigned to different classes. There are five major classes of immunoglobulins: IgA, IgD, IgE, IgG, and IgM, and several of these can be further divided into subclasses (isotypes) e.g., IgG1, IgG2, IgG3, IgG4, IgA, and IgA2.

[0037] "Single-chain Fv" or "scFv" or "sFv" antibody fragments comprise the VH and VL domains of antibody, wherein these domains are present in a single polypeptide chain. In some embodiments, the Fv polypeptide further comprises a polypeptide linker between the VH and VL domains, which enables the sFv to form the desired structure for antigen binding.

[0038] The term "diabodies" refers to small antibody fragments with two antigen-binding sites, which fragments comprise a heavy chain variable domain (VH) connected to a light chain variable domain (VL) in the same polypeptide chain (VH-VL). By using a linker that is too short to allow pairing between the two domains on the same chain, the domains are forced to pair with the complementary domains of another chain and create two antigen- binding sites. Diabodies are described more fully in, for example, EP 404,097; WO 93 / 11161; and Hollinger et al., Proc. Natl. Acad. Sci. USA, vol. 90, pp. 6444-6448, 1993.

[0039] An "isolated" antibody or antigen-binding fragment thereof is one which has been identified and separated and / or recovered from a component of its natural environment. Contaminant components of its natural environment are materials which would interfere with diagnostic or therapeutic uses for the antibody, and can include enzymes, hormones, and other proteinaceous or nonproteinaceous solutes. In some embodiments, the antibody will be purified (1) to greater than 95% by weight of antibody, such as 99% by weight, of the antibody as determined by the Lowry method, (2) to a degree sufficient to obtain at least 15 residues of N-terminal or internal amino acid sequence by use of a spinning cup sequenator, or (3) to homogeneity at the resolution of a SDS-PAGE under reducing or nonreducing conditions using Coomassie blue or silver stain. Isolated antibody includes an antibody in situ within recombinant cells, because at least one component of the antibody's natural environment will not be present. Ordinarily, however, isolated antibody will be prepared by at least one purification step.

[0040] An antibody or antigen-binding fragment thereof that "specifically binds to" or is "specific for" a particular polypeptide or an epitope on a particular polypeptide is one which binds to that particular polypeptide or epitope on a particular polypeptide and does not substantially bind to any other polypeptide or polypeptide epitope. In some embodiments, an antibody of the present disclosure specifically binds to an antigen, e.g., an HIV-1 gpl20 polypeptide, in the form of a monoclonal antibody, scFv, Fab, or other form of antibody measured at a temperature of about 4°C, 25°C, 37°C, or 42°C, e.g., with a dissociation constant, Kd, equal to or lower than 100 nM, optionally lower than 10 nM, optionally lower than 1 nM, optionally lower than 0.5 nM, optionally lower than 0.1 nM, optionally lower than 0.01 nM, or optionally lower than 0.005 nM. The affinity of an antibody can be readily determined using conventional techniques, e.g., those described by Scatchard et al. (Ann. N. Y. Acad. Sci. USA, Vol. 51, p. 660, 1949), ELISA assays, Bio-Layer Interferometry (BLI) assays, and Surface Plasmon Resonance (SPR) assays. The binding properties of an antibody to an antigen, cell, or tissue thereof can generally be determined and assessed using immunoassay methods, including, e.g., immuno-fluorescence-based assays such as immunohistochemistry (IHC) and / or fluorescence-activated cell sorting (FACS).

[0041] As used herein, an "internalized" antibody is one that is taken up (i.e., enters) a cell upon binding to an antigen on the surface of the mammalian cell (e.g., a cell surface polypeptide or receptor). Internalized antibodies will, of course, include antibody fragments, human or chimeric antibodies, and antibody conjugates. For certain therapeutic applications, in vivo internalization is contemplated. The number of internalized antibody molecules will be sufficient or adequate to kill or inhibit the growth of a cell, particularly an infected cell. Depending on the potency of the antibody or antibody conjugate, in some cases, uptake of a single antibody molecule into a cell will be sufficient to kill the target cell to which the antibody binds. For example, certain toxins are highly potent in killing, such that internalization of one molecule of toxin conjugated to an antibody will be sufficient to kill the infected cell.

[0042] The term "antagonist" antibody is used in the broadest sense, and includes an antibody that partially or completely blocks, suppresses or neutralizes a biological activity of an epitope, polypeptide or cell to which it specifically binds. Methods for identifying antagonist antibodies can include contacting a polypeptide or cell specifically bound by a candidate antagonist antibody with the candidate antagonist antibody, and measuring a detectable change in one or more biological activities normally associated with the polypeptide or cell.

[0043] An "antibody that inhibits the growth of an infected cell" or "growth-inhibitory" antibody is one that binds to an infected cell expressing or capable of expressing an HIV1 epitope bound by the antibody and results in a measurable inhibition of growth of the infected cell. Preferred growth-inhibitory antibodies inhibit the growth of an infected cell by greater than 20%, preferably from about 20% to about 50%, and even more preferably greater than 50% (e.g., from about 50% to about 100%) growth inhibition as compared to a suitable control (which is usually infected cells that have not been treated with the antibody being tested). Growth inhibition can be measured in cell culture at antibody concentrations of from about 0.1 μg / ml to about 30 μg / ml or from about 0.5 nM to about 200 nM, where growth inhibition is determined from 1 day to 10 days after exposure of the infected cells to the antibody. Inhibition of growth of infected cells in vivo can be determined in various ways known in the art. An antibody is growth-inhibitory in vivo if administration of the antibody at from about 1 μg / kg to about 100 mg / kg body weight results in a decrease in the percentage of infected cells or the total number of infected cells from about 5 days to 3 months, preferably from about 5 days to 30 days, after the first administration of the antibody.

[0044] An antibody that "induces apoptosis" is one that induces programmed cell death as determined by annexin V binding, DNA fragmentation, cell shrinkage, dilation of endoplasmic reticulum, cell fragmentation, and / or formation of membrane vesicles called apoptotic bodies. Preferably, the cell is an infected cell. There are a variety of methods available to assess cellular events associated with apoptosis. For example, phosphatidylserine (PS) translocation can be measured by annexin binding; DNA fragmentation can be assessed by DNA laddering; and nuclear / chromatin condensation along with DNA fragmentation can be assessed by any increase in hypodiploid cells. Preferably, an antibody that induces apoptosis is one that results in about 2-fold to 50-fold, preferably about 5-fold to 50-fold, and most preferably about 10-fold to 50-fold annexin binding relative to untreated cells in an annexin binding assay.

[0045] Antibody "effector functions" refer to those biological activities attributable to a Fc region of an antibody (a native sequence Fc region or an amino acid sequence variant Fc region), and vary with the antibody isotype. Examples of antibody effector functions include: Clq binding and complement dependent cytotoxicity; Fc receptor binding; antibody-dependent cell-mediated cytotoxicity (ADCC); phagocytosis (e.g., antibody-dependent cell-mediated phagocytosis (ADCP)); down regulation of cell surface receptors (e.g., B cell receptor); and B cell activation.

[0046] "Antibody-dependent cell-mediated cytotoxicity" or "ADCC" refers to a form of cytotoxicity in which secreted or exogenously applied Ig binds to Fc receptors (FcRs) on certain cytotoxic cells (e.g., natural killer (NK) cells, neutrophils, and macrophages), enabling these cytotoxic effector cells to specifically bind to target cells carrying antigens and subsequently kill the target cells with cytotoxins. Antibodies "arm" cytotoxic cells and are required for this type of killing. Primary NK cells used to mediate ACC express only FcγRIII, while monocytes express FcγRI, FcγRII, and FcγRIII. Table 4, Ravetch and Kinet, Annu. Rev. Immunol, Vol. 9, pp. 457–492, 1991, p. 464, summarizes the expression of FcR on hematopoietic cells. To assess the ADCC activity of the molecule of interest, an in vitro ADCC assay can be performed, such as those described in U.S. Patent 5,500,362 or U.S. Patent 5,821,337. Effector cells that can be used for such assays include peripheral blood mononuclear cells (PBMCs) and natural killer (NK) cells. Alternatively or additionally, the ADCC activity of an antibody or its antigen-binding fragment can be assessed in vivo, for example, in animal models, such as those disclosed in Clynes et al., Proc. Natl. Acad. Sci. (USA), Vol. 95, pp. 652-656, 1998.

[0047] “Fc receptor” or“FcR” describes a receptor which binds to the Fc region of an antibody. In certain embodiments, the FcR is a native sequence human FcR. Moreover, a preferred FcR is one which specifically binds the Fc region of an IgG antibody (a gamma receptor) and includes receptors of the FcyRI, FcyRII, and FcyRIII subclasses, including allelic variants and alternatively spliced forms of these receptors. FcyRII receptors include FcyRIIA (“activating receptors”) and FcyRIIB (“inhibiting receptors”), which have similar amino acid sequences that differ primarily in the cytoplasmic domains of the receptors, as well as FcyRIIC, which includes the FcyRIIB extracellular domain fused to an activating cytoplasmic region. The activating receptor FcyRIIA contains immunoreceptor tyrosine-based activation motifs (ITAM) in its cytoplasmic domain. The inhibiting receptor FcyRIIB contains immunoreceptor tyrosine-based inhibition motifs (ITIM) in its cytoplasmic domain (see review M. in Daeron, Annu. Rev. Immunol., vol. 15, pp. 203-234, 1997). FcRs are reviewed in Ravet and Kinet, Annu. Rev. Immunol, vol. 9, pp. 457-492, 1991; Capel et al., Immunol Methods, vol. 4, pp. 25-34, 1994; and de Haas et al., J. Lab. Clin. Med., vol. 126, pp. 330-341, 1995. The term“FcR” herein also encompasses other FcRs including those to be identified in the future. The term also includes the neonatal receptor FcRn, which is responsible for the transfer of maternal IgG to the fetus (Guyer et al., J. Immunol., vol. 117, p. 587, 1976; and Kim et al., J. Immunol., vol. 24, p. 249, 1994) and plays a role in the recycling of IgG from lysosomal degradation by FcRn-dependent recycling after endocytosis. FcRn binding after pinocytosis by endothelial cells has been shown to be important for maintaining the prolonged pharmacokinetic half-life of antibodies. Assessment of pH-dependent human FcRn binding of antibodies in vitro can be performed to provide a prediction of the potential for favorable clinical pharmacokinetics (Datta-Mannan and Wroblewski, Drug Metab. Dispos., vol. 42, pp. 1867-1872, 2014).

[0048] A "human effector cell" is a leukocyte that expresses one or more FcRs and performs effector functions. Preferably, the cell expresses at least FcyRIII and performs ADCC effector functions. Examples of human leukocytes that mediate ADCC include PBMC, NK cells, monocytes, cytotoxic T cells, and neutrophils; with PBMC and NK cells being preferred. The effector cells can be isolated from a natural source, e.g., from blood.

[0049] "Complement dependent cytotoxicity" or "CDC" refers to the lysis of a target cell in the presence of complement. Activation of the classical complement pathway is initiated by the binding of the first component of the complement system (Clq) to antibody of the appropriate subclass bound to its cognate antigen. To assess complement activation, a CDC assay, e.g., as described in Gazzano-Santoro et al., J. Immunol. Methods, Vol. 202, p. 163, 1996, can be performed.

[0050] A "neutralizing antibody" is an antibody that can neutralize the ability of the pathogen to initiate and / or sustain infection in a host and / or target cell in vitro. Described herein are neutralizing monoclonal human antibodies and antigen-binding fragments thereof, wherein the antibody recognizes an antigen from HIV, e.g., a gpl20 polypeptide. In certain embodiments, a "neutralizing antibody" can inhibit entry of an HIV-1 virus, e.g., where the neutralization index is >1.5 or >2.0 for SF162 and / or JR-CSF (Kostrikis LG et al., J. Virol., Vol. 70, No. 1, pp. 445-458, 1996). By "broadly neutralizing antibody" is meant an antibody that neutralizes more than one HIV-1 virus species (from different clades and different strains within clades) in a neutralization assay. A broadly neutralizing antibody can neutralize at least 2, 3, 4, 5, 6, 7, 8, 9, or more different strains of HIV-1 that belong to the same or different clades. In particular embodiments, a broadly neutralizing antibody can neutralize multiple HIV-1 species that belong to at least 2, 3, 4, 5, or 6 different clades. In certain embodiments, the inhibitory concentration of a monoclonal antibody can be less than about 0.0001 μg / ml, less than about 0.001 μg / ml, less than about 0.01 μg / ml, less than about 0.1 μg / ml, less than about 0.5 μg / ml, less than about 1.0 μg / ml, less than about 5 μg / ml, less than about 10 μg / ml, less than about 25 μg / ml, less than about 50 μg / ml, or less than about 100 μg / ml to neutralize about 50% of the input virus in a neutralization assay.

[0051] The HIV virus is classified into specific groups M, N, O, and P, with M being the “major” group and responsible for the majority of HIV / AIDS globally. Group M is further subdivided into subtypes (also called clades) with prevalence in different geographic locations based on their genetic sequence.

[0052] M group “subtypes” or “clades” are subtypes of HIV-1 group M defined by genetic sequence data. Examples of group M subtypes include subtypes A-K. Some of the subtypes are known to be more virulent or resistant to different drugs. There are also “circulating recombinant forms” or CRFs that are derived from recombination between viruses of different subtypes, each with a number. For example, CRF12 BF is a recombination between subtypes B and F. Subtype A is common in West Africa. Subtype B is the predominant form in Europe, the Americas, Japan, Thailand, and Australia. Subtype C is the predominant form in southern Africa, East Africa, India, Nepal, and parts of China. Subtype D is usually found only in East and Central Africa. Subtype E has never been identified as a non-recombinant, only recombining with subtype A as CRF01 AE. Subtype F has been found in Central Africa, South America, and Eastern Europe. Subtype G (and CRF02 AG) has been found in Africa and Central Europe. Subtype H is limited to Central Africa. Subtype I was originally used to describe a strain now believed to be CRF04 cpx, with cpx used for “complex” recombination of several subtypes. Subtype J is primarily found in North, Central, and West Africa, while Caribbean subtype K is limited to the Democratic Republic of the Congo and Cameroon. These subtypes are sometimes further divided into sub-subtypes, such as Al and A2 or Fl and F2. In 2015, strain CRF19 was found to be a recombinant of subtype A, subtype D, and subtype G, with its subtype D protease being closely associated with rapid progression of AIDS in Cuba.

[0053] “HIV tropism” refers to the specificity of the HIV virus for a particular host cell, which is determined in part by the interaction of viral surface structures with receptors present on the surface of the host cell. HIV tropism can be measured, for example, by sequencing analysis or by the Monogram BioRNA® assay (monogrambio.com). (See, e.g., Lee et al., AIDS Res Hum Retroviruses., 2013, vol. 29, no. 6, pp. 979-984).

[0054] ​HIV can infect a variety of cells, such as CD4+ helper T cells and macrophages, which express CD4 molecules on their surface. HIV-1 entry into macrophages and T helper cells is mediated not only by the interaction of the viral envelope glycoprotein (e.g., gpl20) with CD4 molecules on the target cell, but also with its chemokine co-receptors. HIV-1 macrophage (M-tropic) strains or non-syncytium-inducing strains (NSI) use the beta-chemokine receptor CCR5 for entry and are thus able to replicate in macrophages and CD4+ T cells. These strains are referred to as R5 viruses. This CCR5 co-receptor is used by almost all primary HIV-1 isolates, regardless of viral genetic subtype. T cell-tropic isolates or syncytium-inducing (SI) strains replicate in primary CD4+ T cells as well as macrophages and use the alpha-chemokine receptor CXC R4 for entry. These strains are referred to as X4 viruses. Viruses that use only the CCR5 receptor are referred to as R5, those that use only CXCR4 are referred to as X4, and those that use both are referred to as X4R5 or dual / mixed tropic. However, the use of co-receptors alone does not explain viral tropism, as not all R5 viruses are able to use CCR5 for productive infection on macrophages.

[0055] Also described herein are "non-neutralizing antibodies," which in certain embodiments are antibodies that bind to one or more viral strains but do not neutralize the virus. However, the non-neutralizing antibodies can still eliminate cells expressing viral antigens that bind the antibodies but are not neutralized by the antibodies with respect to Fc-mediated killing. Thus, in certain embodiments, the antibodies can bind to viral antigens and eliminate cells infected with the virus without neutralizing the virus.

[0056] The term "nucleic acid molecule" refers to a polymeric form of nucleotides and includes both sense and antisense strands of RNA, cDNA, genomic DNA, and synthetic forms and mixed polymers thereof. In particular embodiments, nucleotides refer to ribonucleotides, deoxyribonucleotides, or modified forms of either type of nucleotide, as well as combinations thereof. The term also includes, but is not limited to, DNA in either single- or double-stranded form. Additionally, a polynucleotide, such as a cDNA or mRNA, can include one or both of naturally occurring and modified nucleotides linked together by naturally occurring and / or non-naturally occurring nucleotide linkages. As will be readily understood by one of skill in the art, nucleic acid molecules can be chemically or biochemically modified, or can contain non-natural or derivatized nucleotide bases. Such modifications include, for example, labeling, methylation, substitution of one or more of the naturally occurring nucleotides with an analog thereof, internucleotide modifications such as uncharged linkages (e.g., methyl phosphonates, phosphotriesters, amino phosphonates, amino -methvl phosphonates, phosphoramidates, etc.), charged linkages (e.g., phosphonates, phosphodiester, phosphorothioates, phosphorodithioates, etc.), pendent moieties (e.g., peptides), intercalators (e.g., acridine, psoralen, etc.), chelators, alkylators, and modified linkages (e.g., alpha anomeric nucleic acids, etc.). The above list of modifications is not all inclusive and is meant to exemplify conventional modifications rather than limit the scope of the application. The above terms are also intended to include any topological conformation. Unless otherwise indicated, a reference to a nucleic acid sequence is to be taken as including its complementary sequence. Thus, a reference to a nucleic acid molecule having a particular sequence is to be understood as encompassing the complementary strand having its complementary sequence, as well as its complementary sequence. The term also includes codon-optimized nucleic acids.

[0057] The term "operably linked" refers to two or more nucleic acid sequence elements that are generally physically linked and in a functional relationship to one another. For example, a promoter is operably linked to a coding sequence if the promoter is capable of initiating or modulating transcription or expression of the coding sequence, in which case the coding sequence is understood to be "under the control" of the promoter.

[0058] As used herein, "substitution" means that one or more amino acids or nucleotides are replaced by a different amino acid or nucleotide, respectively.

[0059] An "isolated" nucleic acid refers to a nucleic acid molecule that has been separated from a component of its natural environment. An isolated nucleic acid includes a nucleic acid molecule contained in cells that are typically also contained in the natural environment of the nucleic acid molecule, but the nucleic acid molecule is present extrachromosomally or at a chromosomal location that is different from its natural chromosomal location.

[0060] An "isolated nucleic acid encoding an antibody or fragment thereof" refers to one or more nucleic acid molecules encoding the heavy and light chains of an antibody (or fragment thereof), including such nucleic acid molecules in a single vector, or separate vectors, and such nucleic acid molecules present at one or more locations within a host cell.

[0061] As used herein, the term "vector" refers to a nucleic acid molecule capable of propagating another nucleic acid to which it is linked. The term includes the vector as a self-replicating nucleic acid structure as well as the vector incorporated into the genome of a host cell into which the vector has been introduced. Certain vectors are capable of directing the expression of nucleic acids to which they are operatively linked. Such vectors are referred to herein as "expression vectors."

[0062] As used herein, the term polynucleotide "variant" is a polynucleotide that generally differs from a specifically disclosed polynucleotide herein in one or more substitutions, deletions, additions and / or insertions. Such variants can be naturally occurring or can be synthetically generated, for example, by modifying one or more of the polynucleotide sequences described herein and evaluating one or more biological activities of the encoded polypeptides as described herein and / or using any of a number of techniques well known in the art.

[0063] As used herein, the term polypeptide "variant" is a polypeptide that generally differs from a specifically disclosed polypeptide herein in one or more substitutions, deletions, additions and / or insertions. Such variants can be naturally occurring or can be synthetically generated, for example, by modifying one or more of the polynucleotide sequences described herein and evaluating one or more biological activities of the encoded polypeptides as described herein and / or using any of a number of techniques well known in the art.

[0064] The term "variant" can also refer to any naturally occurring or engineered molecule comprising one or more nucleotide or amino acid mutations. In one embodiment, the molecule is an antibody. For example, a somatic variant can encompass all related naturally occurring antibodies that are part of or derived from the same B cell lineage. An engineered variant can encompass all single or combined mutations made to an antibody.

[0065] Modifications can be made in the structure of the polynucleotides and polypeptides of the application and still obtain a functional molecule encoding a variant or derivative polypeptide having the desired properties. When it is desirable to alter the amino acid sequence of a polypeptide to produce an equivalent or even improved variant or portion of a polypeptide of the application, one will typically alter one or more of the codons of the encoding DNA sequence.

[0066] For example, certain amino acids can be substituted for other amino acids in a protein structure without appreciable loss of its binding activity or cell binding activity. Since it is the binding activity and nature of a protein that defines that protein's biological function, certain amino acid substitutions can be made in a protein sequence, and, of course, certain amino acid substitutions can be made in the underlying DNA encoding sequences, and still obtain a protein of similar properties. It is thus contemplated that various changes can be made in the polypeptide sequences of the disclosed antibodies and antigen-binding fragments thereof, or in the corresponding DNA sequences encoding such polypeptides, without appreciable loss of their biological utility or activity.

[0067] In many cases, polypeptide variants will comprise one or more conservative substitutions. A "conservative substitution" is one in which the amino acid is replaced with another amino acid having similar properties, such that the secondary structure and the hydrophilicity of the polypeptide are expected to be substantially unchanged by the substitution.

[0068] When comparing polynucleotide and polypeptide sequences, two sequences are "identical" if the sequences of nucleotides or amino acids in the two sequences are the same when aligned for maximum correspondence, as described below. Comparisons between two sequences are typically performed by comparing the sequences over a comparison window to identify and compare local regions of sequence similarity. As used herein, a "comparison window" refers to a segment of at least about 20 contiguous positions, usually 30 to about 75, 40 to about 50, in which a sequence can be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned. The optimal alignment of two sequences for the purpose of comparison can be determined using various methods known in the art.

[0069] Sequence alignments for comparison purposes were performed using the Megalign program in the Lasergene suite of bioinformatics programs (DNASTAR, Inc., Madison, WI) using default parameters. This program embodies several alignment schemes described in the following references: Dayhoff, M.O., 1978, A model of evolutionary change in proteins - Matrices for detecting distant relationships, Dayhoff, M.O. (ed.), Atlas of Protein Sequence and Structure, National Biomedical Research Foundation, Washington DC, vol. 5, suppl. 3, pp. 345-358; Hein J., 1990, Unified Approach to Alignment and Phylogenes, pp. 626-645, Methods in Enzymology, vol. 183, Academic Press, Inc., San Diego, CA; Higgins, D.G. and Sharp, P.M., 1989, CABIOS, vol. 5, pp. 151-153; Myers, E.W. and Muller W., 1988, CABIOS, vol. 4, pp. 11-17; Robinson, E.D., 1971, Comb. Theor, vol. 77, pp. 105; Santou, N. Nes, M., 1987, Mol. Biol. Evol., vol. 4, pp. 406-425; Sneath, P.H.A. and Sokal, R.R., 1973, Numerical Taxonomy - the Principles and Practice of Numerical Taxonomy, Freeman Press, San Francisco, CA; Wilbur, W.J. and Lipman, D.J., 1983, Proc. Natl. Acad., Sci. USA, vol. 80, pp. 726-730.

[0070] Alternatively, sequence comparisons for the purpose of identifying a polynucleotide of the present application can be performed by computerized implementations of various comparison algorithms (GAP, BESTFIT, BLAST, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, WI), or by inspection.

[0071] One example of an algorithm that is suitable for determining percent sequence identity and sequence similarity, is the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al., 1977, Nucl. Acids Res., vol. 25, pp. 3389-3402; and Altschul et al., 1990, J. Mol. Biol., vol. 215, pp. 403-410, respectively. BLAST and BLAST 2.0 can be used, e.g., with the parameters described herein, to determine percent sequence identity for the polynucleotides and polypeptides described herein. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information.

[0072] In one illustrative example, for nucleotide sequences, the parameters W, T, and X can be set as follows: to achieve an alignment score of 50, the words W can be set to 11, the percent of query length T can be set to 10, and the number of residues X can be set to 40. BLASTN program (for nucleotide sequences) uses as defaults a word length of 11, an expectation value of 10, and a BLOSUM62 scoring matrix (see Henikoff and Henikoff, 1989, Proc. Natl. Acad. Sci. USA, vol. 89, pp. 10915) alignments where the (B) is 50, expect (E) is 10, M=5, N=-4, and a comparison of both strands.

[0073] For amino acid sequences, the scoring matrix can be used to calculate cumulative scores. Extension of the word hits in each direction is terminated when: the cumulative alignment score falls off by a quantity X from its maximum attained value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the comparison.

[0074] In one approach, the "percent sequence identity" is determined by comparing two optimally aligned sequences over a comparison window of at least 20 positions, wherein the portion of the polynucleotide or polypeptide sequence in the comparison window can comprise additions or deletions (i.e., gaps) of 20% or less, usually 5 to 15%, or 10 to 12%, as compared to the reference sequence (i.e., the sequence used for the alignment) used for the comparison. The percent sequence identity is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the reference sequence (i.e., the window size), and multiplying the result by 100 to yield the percent sequence identity.

[0075] "Homology" refers to the percentage of residues in a polynucleotide or polypeptide sequence variant that are identical with the non-variant sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent homology.

[0076] "Binding affinity" can refer to a binding dissociation constant (Kd) or apparent affinity (e.g., EC50) value. BRIEF DESCRIPTION OF DRAWINGS

[0077] Figure 1 The number of screening subjects from the Zurich Prospective HIV Infection Cohort Study whose genotype predicted sensitivity to GS-9722 (elpivirumab) is shown. Plasma samples from 92 individuals prior to ART were analyzed in the GenoSure HIV Envelope RNA assay. "None" indicates that none of the specific amino acids in the HIV envelope gene were selected for the individuals screened. The amino acid positions indicated for each category.

[0078] Figure 2 The number of screening clade B subjects from the Zurich Prospective HIV Infection Cohort Study whose genotype predicted sensitivity to GS-9722 is shown. Plasma samples from 59 clade B infected individuals prior to ART were analyzed in the GenoSure HIV Envelope RNA assay. "None" indicates that none of the specific amino acids in the HIV envelope gene were selected for the individuals screened. The amino acid positions indicated for each category.

[0079] Figure 3Sensitivity of bulk virus derived from pre-ART plasma samples from the Zurich Prospective HIV Infection Cohort Study to GS-9722 is shown. In Virus from 29 samples with a positive predictive value of 80.7% or greater were analyzed in the HIV entry assay (Monogram Biosciences). The amino acid positions indicated for each category.

[0080] Figure 4 Sensitivity of subcloned viruses from bulk virus derived from pre-ART plasma samples from the Zurich Prospective HIV Infection Cohort Study to GS-9722 is shown. In Twenty individual viruses from four pre-ART plasma samples in which the bulk virus was predicted to be sensitive by genotypic and tested to be sensitive by phenotypic typing were analyzed in the HIV entry assay (Monogram Biosciences). The solid line indicates the IC50 of the bulk virus. DETAILED DESCRIPTION

[0081] 1. INTRODUCTION

[0082] The methods of the present application are based, in part, on the unexpected discovery of a population of HIV-infected patients who respond to administration of an anti-HIV gp120 V3 glycan-directed antibody or antigen-binding fragment thereof, in the absence of co-administration of an additional anti-HIV antibody directed to other HIV antigens (e.g., gp41) or non-overlapping epitopes of the same HIV antigen (e.g., to gp 120 in the CD4 binding site region or the V2 apex region). Such patients are infected with a species of HIV having a gp120 protein that is bound by the V3 glycan-directed antibody or antigen-binding fragment thereof.

[0083] Typically, the methods entail identifying a human subject infected with an HIV or HIV population expressing a gp120 comprising a glycosylated asparagine at a position corresponding to amino acid residue position 332 (N332 glycan), an aspartic acid at a position corresponding to amino acid residue position 325 (D325), and one or more amino acid residues selected from the group consisting of a threonine at a position corresponding to amino acid residue position 63 (T63), a leucine at a position corresponding to amino acid residue position 179 (L179), a threonine at a position corresponding to amino acid residue position 320 (T320), and a histidine at a position corresponding to amino acid residue position 330 (H330), wherein the amino acid positions are with reference to SEQ ID NO: 4 (i.e., residues 1-511 of NCBI Reference Sequence No. NP_057856.1). In various embodiments, the glycan is an oligomannose.

[0084] 2. Identifying subjects responsive to treatment with an antibody or antigen binding fragment thereof directed against the HIV gp120 V3 glycan .

[0085] In some embodiments, the patient is identified by receiving a report of the HIV species that infected the patient that identifies the HIV gp120 amino acid residues present at the specified amino acid positions of interest, e.g., positions 332 and 325, and one or more amino acid positions selected from the group consisting of: 63, 179, 320, and 330, wherein the amino acid positions are with reference to SEQ ID NO: 4. In some embodiments, the patient is identified by performing one or more assays (e.g., polynucleotide or polypeptide sequencing) to determine the amino acid sequence of gp120 or the amino acid residues present at the specified amino acid positions of interest of the gp120 protein of the HIV species that infected the patient. The identification of the full-length or partial sequence of the gp120 protein obtained from the subject can be determined at the polynucleotide or polypeptide level. In some embodiments, the amino acids present at the gp120 residue positions of interest are determined at the polypeptide level.

[0086] In various embodiments, the methods require identifying a subject infected with an HIV or HIV population that expresses a gp120 comprising the following amino acid residues: N332 glycan, D325, and T63, wherein the amino acid positions are with reference to SEQ ID NO: 4.

[0087] In various embodiments, the methods require identifying a subject infected with an HIV or HIV population that expresses a gp120 comprising the following amino acid residues: N332 glycan, D325, and L179, wherein the amino acid positions are with reference to SEQ ID NO: 4.

[0088] In various embodiments, the methods require identifying a subject infected with an HIV or HIV population that expresses a gp120 comprising the following amino acid residues: N332 glycan, D325, and T320, wherein the amino acid positions are with reference to SEQ ID NO: 4.

[0089] In various embodiments, the methods require identifying a subject infected with an HIV or HIV population that expresses a gp120 comprising the following amino acid residues: N332 glycan, D325, and H330, wherein the amino acid positions are with reference to SEQ ID NO: 4.

[0090] In various embodiments, the methods require identifying a subject infected with an HIV or HIV population that expresses a gp120 comprising the following amino acid residues: N332 glycan, D325, T63, and L179, wherein the amino acid positions are with reference to SEQ ID NO: 4.

[0091] In various embodiments, the methods require identifying a subject infected with an HIV or a population of HIVs expressing a gpl20 comprising the following amino acid residues: N332 glycan, D325, T63, and T320, where the amino acid positions are with reference to SEQ ID NO: 4.

[0092] In some embodiments, the subject is infected with an HIV clade B virus. In various embodiments, the methods require identifying a subject infected with an HIV or a population of HIVs expressing a gpl20 comprising the following amino acid residues: N332 glycan, D325, T63, and H330, where the amino acid positions are with reference to SEQ ID NO: 4. In various embodiments, the methods require identifying a subject infected with an HIV or a population of HIVs expressing a gpl20 comprising the following amino acid residues: N332 glycan, D325, T63, L179, T320, and H330, where the amino acid positions are with reference to SEQ ID NO: 4.

[0093] In various embodiments, the methods require identifying a subject infected with an HIV or a population of HIVs expressing a gpl20 comprising the following amino acid residues: N332 glycan, D325, T320, and H330, where the amino acid positions are with reference to SEQ ID NO: 4.

[0094] In various embodiments, the methods require identifying a subject infected with an HIV or a population of HIVs expressing a gpl20 comprising the following amino acid residues: N332 glycan, D325, L179, T320, and H330, where the amino acid positions are with reference to SEQ ID NO: 4. In some embodiments, the subject is infected with an HIV clade A and / or HIV clade C virus. In some embodiments, the subject is infected with an HIV clade A, clade B, and / or HIV clade C virus.

[0095] In various embodiments, the methods require identifying a subject infected with an HIV or a population of HIVs expressing a gpl20 comprising the following amino acid residues: N332 glycan, D325, T63, L179, and T320, where the amino acid positions are with reference to SEQ ID NO: 4.

[0096] In various embodiments, the methods require identifying a subject infected with an HIV or a population of HIVs expressing a gpl20 comprising the following amino acid residues: N332 glycan, D325, T63, L179, and H330, where the amino acid positions are with reference to SEQ ID NO: 4.

[0097] In some embodiments, the subject is infected with an HIV or a population of HIVs that express a gpl20 that further comprises one or more of the following amino acid residues: a glycan at amino acid residue 301 (glycan301); a lysine at amino acid residue 677 (K677); an amino acid residue other than tryptophan (Trp, W) (e.g., alanine (Ala, A); cysteine (Cys, C); aspartic acid or aspartate (Asp, D); glutamic acid or glutamate (Glu, E); phenylalanine (Phe, F); glycine (Gly, g); histidine (His, H); isoleucine (lie, I); lysine (Lys, K); leucine (Leu, L); methionine (Met, M); asparagine (Asn, N); proline (Pro, P); glutamine (Gln, Q); arginine (Arg, R); serine (Ser, S); threonine (Thr, T); valine (Val, V) or tyrosine (Tyr, Y) at position 17 (not_W17); an amino acid residue other than arginine at position 747 (e.g., A, C, D, E, F, G, H, I, K, L, M, N, P, Q, S, T, V, W, or Y) (not_R747); insertion_321.01 (e.g., an insertion of any amino acid between positions G321 and K322 (e.g., A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, or Y)); a glutamic acid at position 429 (E429); a glutamine at position 442 (Q442); an arginine at position 335 (R335); an isoleucine at position 165 (1165); a serine at position 393 (S393); an isoleucine at position 307 (I307); a glycan at position 295 (295_glycan); and / or an asparagine at position 300 (N300), wherein the amino acid positions are with reference to SEQ ID NO: 4.

[0098] gp120

[0099] The envelope glycoprotein gpl20 (or gpl20) is a 120 kDa glycoprotein that is part of the outer layer of HIV. It exists on its own as a viral membrane spike, consisting of three gpl20 molecules linked together, and is anchored to the membrane by the gp41 protein. Gpl20 is essential for viral infection, as it facilitates HIV entry into host cells through its interaction with cell surface receptors. These receptors include DC-SIGN, heparan sulfate proteoglycans, and the CD4 receptor. Binding to CD4 on helper T cells induces the initiation of a cascade of conformational changes in gpl20 and gp41, which leads to fusion of the virus with the host cell membrane.

[0100] Gp120 is encoded by the HIV env gene. The env gene encodes a gene product of approximately 850 amino acids. The major env product is the protein gp160, which is cleaved in the endoplasmic reticulum by the cellular protease furin into gp120 (about 480 amino acids) and gp41 (about 345 amino acids).

[0101] The V3 glycan site on gpl20 is formed in part by a portion of the CCR5 co-receptor site and in part by surrounding decoy glycans (so-called "high mannose patches") (Sok et al., Immunity, 2016, vol. 45, pp. 31-45). Broadly neutralizing antibodies (bnAbs) to the V3 glycan site are the most common of all antibodies found in HIV infection (Walker et al., PLoS Pathog., 2010, vol. 6, p. e1001028, 2010; Landais et al., PLoS Pathog., 2016, vol. 12, p. e1005369; Georgiev et al., Science, 2013, vol. 340, pp. 751-756). The consensus sequence for the V3 region of gpl20 (Milich et al., J Virol., vol. 67 no. 9, pp. 5623-5634, 1993) is provided below:

[0102] CTRPNNNTRKSIHIGPGRAFYTTGEIIGDIRQAHC (SEQ ID NO: 1).

[0103] The amino acid sequence of an exemplary gpl60 polypeptide of HIV clone WITO is provided below (V3 hypervariable loop is bolded, and N332 potential N-linked glycosylation site is bolded and underlined):

[0104]

[0105]

[0106] The amino acid sequence of an exemplary gpl60 polypeptide of HIV clone identified in NCBI Reference Sequence No. NP_057856.1 is provided below (V3 hypervariable loop is bolded, and N332 potential N-linked glycosylation site is bolded and underlined):

[0107]

[0108]

[0109] The amino acid sequence of an exemplary gp 120 polypeptide of HIV-1 isolate HXB2B subtype B is provided below (GenBank Accession No. K0345; corresponding to residues 1-511 of NCBI Reference Sequence No. NP_057856.1):

[0110]

[0111] The amino acid sequence of an exemplary gp 120 polypeptide is provided below:

[0112]

[0113] The amino acid sequence of another exemplary gp 120 polypeptide (see, bioafrica.net / proteomics / ENV-GP120prot.html) is provided below:

[0114] TEKLWVTVYY GVPVWKEATT TLFCASDAKA YDTEVHNVWA THACVPTDPN PQEVVLVNVTENFNMWKNDM VEQMHEDIIS LWDQSLKPCV KLTPLCVSLK CTDLKNDTNT NSSSGRMIME KGEIKNCSFNISTSIRGKVQ KEYAFFYKLD IIPIDNDTTS YKLTSCNTSV ITQACPKVSF EPIPIHYCAP AGFAILKCNNKTFNGTGPCT NVSTVQCTHG IRPVVSTQLL LNGSLAEEEV VIRSVNFTDN AKTIIVQLNT SVEINCTRPNNNTRKRIRIQ RGPGRAFVTI GKIGNMRQAH CNISRAKWNN TLKQIASKLR EQFGNNKTII FKQSSGGDPEIVTHSFNCGG EFFYCNSTQL FNSTWFNSTW STEGSNNTEG SDTITLPCRI KQIINMWQKV GKAMYAPPISGQIRCSSNIT GLLLTRDGGN SNNESEIFRP GGGDMRDNWR SELYKYKVVK IEPLGVAPTK AKRRVVQREKR (SEQ ID NO: 6)

[0115] Genomic diversity among independent human immunodeficiency virus type 1 (HIV-1) isolates, between sequential isolates from the same patient, and even within a single patient isolate, is a well-known feature of HIV-1. Although this sequence heterogeneity is distributed throughout the genome, most of the heterogeneity is in the env gene. Comparison of predicted amino acid sequences from several different isolates has shown that sequence heterogeneity is concentrated in the five variable regions of the surface glycoprotein gpl20, designated V1 through V5. The V3 region, although only 35 amino acids long, exhibits considerable sequence variability. Interestingly, despite this variability, the V3 region includes a determinant that mediates interaction with CD4 + cells. Increased variability in gpl20 results in higher levels of viral replication, suggesting increased viral fitness of individuals infected with different HIV-1 variants. Variability in potential N-linked glycosylation sites (PNGS) also results in increased viral fitness. PNGS allow long chain carbohydrates to be attached to the hypervariable regions of gpl20. Thus, the number of PNGS in env can influence the fitness of a virus by providing more or less sensitivity to neutralizing antibodies.

[0116] Biological sample

[0117] The HIV gp120 amino acid residues of interest are determined from HIV present or suspected to be present in a biological sample from a subject. The biological sample can be from a solid tissue or biological fluid of a subject known or suspected to contain HIV. In various embodiments, the biological sample comprises or is from blood, peripheral blood mononuclear cells (PBMCs), serum, plasma, semen, or lymph nodes. In some embodiments, the biological sample comprises or is from bile, blood, plasma, serum, breast milk, feces, pus, saliva, sebum, semen, sweat, tears, urine, or vomit. In patients with suppressed viral levels, for example, by anti-retroviral (ART) therapy, the biological sample comprises a solid tissue or biological fluid of a subject known or suspected to contain HIV reservoirs, for example, solid tissues and / or biological fluids comprising potentially HIV-infected CD4+ T cells (including memory and non-memory effector CD4+ T cells), hematopoietic progenitor cells of CD4+ T cells, gd T cells (including memory and non-memory effector gd T cells), natural killer (NK) cells, myeloid cells (including monocytes and macrophages), hematopoietic progenitor cells of myeloid cells, and follicular dendritic cells. Anatomical reservoirs that can harbor potentially HIV-infected cells include lymphoid tissues, brain and central nervous system, gastrointestinal tract and gut-associated lymphoid tissue (GALT), genital tract, lung, and skin. Tissues and cells found to harbor potentially HIV-infected cells and HIV reservoirs are described in, for example, Kuo et al., Curr Opin HIV AIDS., 2018, vol. 13, no. 2, pp. 137-142; Mzingwane et al., Rev Med Virol., March 2017, vol. 27, no. 2, doi: 10.1002 / rmv, 1924, (PMID 28128885); Churchill et al., Nat Rev Microbiol., 2016, vol. 14, no. 1, pp. 55-60; Barton et al., Trends Microbiol., 2016, vol. 24, no. 5, pp. 345-355, which are hereby incorporated by reference in their entireties for all purposes.

[0118] In some embodiments, multiple biological samples from a single patient are evaluated. For example, in some embodiments, two or more biological samples from two or more different tissues or two or more different anatomical reservoirs of a single patient are evaluated.

[0119] Infection stage

[0120] In various embodiments, the human individual is an adult, an adolescent, or an infant. The subject can be symptomatic (e.g., viremic) or asymptomatic (e.g., acutely infected or ART-suppressed). In some embodiments, the human subject is acutely infected or recently infected with HIV. In certain embodiments, the subject has not seroconverted. In some embodiments, the human subject is chronically infected with HIV. The subject can or can not be receiving a regimen of antiretroviral therapy (ART).

[0121] Patients can be classified into Fiebig stages I through VI, which is based on successive gains in positive HIV-1 clinical diagnostic assays (viral RNA measured by PCR, p24 and p31 viral antigens measured by enzyme-linked immunosorbent assay (ELISA)). The p24 antigen is a viral core protein that transiently appears in the blood during the ascending phase once HIV-1 RNA levels rise above 10,000 copies / mL and before detectable HIV antibody production. In Fiebig stage I, only HIV-1 RNA is detectable in the blood during the ascending viremia. Fiebig stage II begins about 7 days later when tests that detect the p24 antigen turn positive. In Fiebig stage III, IgM anti-HIV-1 antibodies can be detected with a sufficiently sensitive enzyme immunoassay (EIA) (e.g., a third-generation EIA) within about 5 days after the p24 antigen test turns positive. Stage III typically occurs 1 to 2 weeks after the onset of acute retroviral symptoms. Fiebig stage IV represents the development of indeterminate Western blot tests and occurs about 3 days after the EIA test shows a positive result. Conversion to a clearly positive Western blot test, i.e., Fiebig stage V, typically occurs 7 more days or about 1 month after the initial infection. Fiebig stages of HIV infection are described, e.g., in Fiebig et al., AIDS, 2003, vol. 17, no. 13, pp. 1871-1879; Cohen et al., J Infect Dis., 2010, vol. 202, Suppl 2, pp. S270-277; and McMichael et al., Nature Reviews Immunology, 2010, vol. 10, pp. 11-23, which are hereby incorporated by reference in their entireties for all purposes. In some embodiments, the biological sample being evaluated is from a human subject with HIV infection at Fiebig stage IV or earlier, e.g., Fiebig stage I, Fiebig stage II, Fiebig stage III, or Fiebig stage IV. In some embodiments, the biological sample being evaluated is from a human subject with HIV infection at Fiebig stage V or Fiebig stage VI.

[0122] In some embodiments, the methods further comprise the step of obtaining a biological sample from the subject. In some embodiments, the methods entail receiving a report of the presence of HIV gp120 amino acid residues at specified positions of interest, e.g., 332 and 325, and one or more amino acid positions selected from 63, 179, 320, and 330, wherein the amino acid positions are with reference to SEQ ID NO: 4.

[0123] Determining gp120 amino acids of interest

[0124] The HIV gp120 sequence of a subject can be determined at the polynucleotide or polypeptide level for the amino acid residues at specified positions of interest, e.g., 332 and 325, and one or more amino acid positions selected from 63, 179, 320, and 330, wherein the amino acid positions are with reference to SEQ ID NO: 4. At the polynucleotide level, HIV RNA or proviral DNA isolated from one or more biological samples can be sequenced using methods known in the art. In some embodiments, HIV RNA or proviral DNA isolated from two or more biological samples of a subject are sequenced. In some embodiments, the two or more biological samples are obtained from different tissue sources, e.g., blood, peripheral blood mononuclear cells, lymph nodes, and / or semen. In some embodiments, the two or more biological samples are obtained at different time points, e.g., 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, or 8 weeks apart, 3 months, 4 months, 5 months, 6 months, 7 months, 8 months, 9 months, 10 months, 11 months, or 12 months apart.

[0125] As appropriate, primers that anneal to and amplify HIV env-encoding sequences, particularly the V3 variable region of gpl20, can be used. In some embodiments, nested primer sets can be used. In various embodiments, RNA is sequenced directly or reverse transcriptase polymerase chain reaction (RT-PCR) can be performed. In some embodiments, Sanger sequencing can be performed, for example, when sequencing to determine amino acid residues in the V3 region, or when sequencing samples from patients in early stages of disease (e.g., prior to Fiebig stage III, such as Fiebig stage I or II). In various embodiments, single genome amplification (SGA) and sequencing is performed. Methods for single genome amplification (SGA) and sequencing of plasma HIV virion RNA are described, for example, in Salazar-Gonzalez et al., 2008, J Virol, vol. 82, pp. 3952-3970; and Keele et al., Proc Natl Acad Sci U S A., 2008, vol. 105 no. 21, pp. 7552-7557. SGA for determining amino acid sequence changes in HIV gpl20 sequences and use in the methods described herein are described, for example, in Bar et al., N Engl J Med., 2016, vol. 375 no. 21, pp. 2037-2050; and Mendoza et al., Nature, 2018, vol. 561 no. 7724, pp. 479-484. In various embodiments, high-throughput next generation sequencing (NGS), massively parallel or deep sequencing technologies are employed to sequence gpl20 (including at least the V3 variable region) of the population of HIV species in one or more biological samples from a single patient or subject. In such cases, multiple nucleic acid sequences encoding at least the V3 variable region of gpl20 are sequenced and aligned. In some embodiments, the full length of gpl20 is sequenced. Exemplary platforms for NGS sequencing that can be used to determine gpl20 sequences of HIV species in one or more biological samples from a patient include Illumina (Solexa) (illumina.com), Ion torrent: Proton / PGM sequencing (thermofisher.com), SOLiD (thermofisher.com), and Single Molecule, Real-Time (SMRT) sequencing (Pacific Biosciences, pacb.com).Methods for isolating and sequencing HIV gp120, including at least the V3 glycan region, from a patient and applicable to the methods of the application are described, for example, in Shioda et al., J Virol., 1997, vol. 71 no. 7, pp. 4871-4881; Colon et al., J Virol Antivir Res., 2015, vol. 4 no. 3, pii: p. 143 (PMID: 27358904); Kafando et al., PLoS One., 2017, vol. 12 no. 12, p. e0189999; Hebberecht et al., PLoS One., 2018, vol. 13 no. 4, p. e0195679; Andrews et al., Sci Rep., 2018, vol. 8 no. 1, p. 5743; and Landais et al., Immunity., 2017, vol. 47 no. 5, pp. 990-1003. As appropriate, shorter sequence reads of nucleic acid sequences (“contigs”) can be assembled into longer sequences, including at least the V3 variable region of gp120. Contig assembly methods for HIV genome sequences applicable in the methods of the application are described, for example, in Huang et al., Bioinformation, 2018, vol. 14 no. 8, pp. 449-454; Hiener et al., J Vis Exp., 2018 Oct 16, vol. 140, doi: 10.3791 / 58016; and Wymant et al., Virus Evol., 2018 May 18, vol. 4 no. 1, vey007, doi: 10.1093 / ve / vey007.

[0126] In some embodiments, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% of the sequenced V3 variable region of gpl20 in the HIV population obtained from one or more biological samples of a single patient comprises an amino acid sequence comprising one or more of: a glycosylated asparagine at a position corresponding to amino acid residue position 332 (N332 glycan), an aspartic acid at a position corresponding to amino acid residue position 325 (D325), and a threonine at a position corresponding to amino acid residue position 63 (T63), a leucine at a position corresponding to amino acid residue position 179 (L179), a threonine at a position corresponding to amino acid residue position 320 (T320), and a histidine at a position corresponding to amino acid residue position 330 (H330), wherein the amino acid positions are with reference to SEQ ID NO: 4. As used herein, when the position of any given polymer component (e.g., amino acid, nucleotide, also referred to generally as “residue”) is specified by reference to the same or equivalent position in a selected amino acid or nucleic acid polymer (e.g., based on optimal alignment or consensus sequence), rather than by the actual numerical position of the component in a given polymer, the numbering of the given amino acid polymer or nucleic acid polymer “corresponds to,” “is relative to,” or “is with reference to” the numbering of the selected or reference amino acid polymer or nucleic acid polymer. In some embodiments, the HIV gpl20 variant is detected at a frequency level of about 1% of the viral population (e.g., 1% mutation or variant frequency). In some embodiments, the HIV gpl20 variant is detected at a frequency level of about 0.5% of the viral population. Empirically, reliable detection of a variant at 1% frequency would require an HIV RNA level of at least 1000 copies / mL. See, e.g., Casadellà et al., Virus Research, Vol. 239, 2017, pp. 69-81; Noguera-Julian et al., J Infect Dis., 2017, Vol. 216 Suppl 9, pp. S829-S833; and Lee et al., Sci Rep., 2020, Vol. 10, Issue 1, p. 1634.

[0127] 3. Administration of an antibody or antigen binding fragment thereof directed against the HIV gp120 V3 glycan

[0128] In certain embodiments, the methods require administration of an anti-HIV antibody or antigen-binding fragment thereof or antigen-binding molecule that targets the V3 glycan binding region of gpl20.

[0129] HIV-1 is the predominant family of HIV and accounts for 95% of all infections worldwide. HIV-2 is primarily found in a few West African countries.

[0130] HIV viruses are classified into specific groups, M, N, O, and P, with M being the "major" group and responsible for the majority of HIV / AIDS globally. The M group is further subdivided into subtypes (also called clades) based on their genetic sequences that have prevalence in different geographic locations.

[0131] M group "subtypes" or "clades" are subtypes of HIV-1 group M defined by genetic sequence data. Examples of group M subtypes include subtypes A-K. Some of the subtypes are known to be more virulent or resistant to different drugs. There are also "circulating recombinant forms" or CRFs that are derived from recombination between viruses of different subtypes, each with a number. For example, CRF12 BF is a recombination between subtypes B and F. Subtype A is common in West Africa. Subtype B is the predominant form in Europe, the Americas, Japan, Thailand, and Australia. Subtype C is the predominant form in southern Africa, East Africa, India, Nepal, and parts of China. Subtype D is usually found only in East and Central Africa. Subtype E has never been identified as a non-recombinant, only recombining with subtype A as CRF01 AE. Subtype F has been found in Central Africa, South America, and Eastern Europe. Subtype G (and CRF02 AG) has been found in Africa and Central Europe. Subtype H is limited to Central Africa. Subtype I was originally used to describe a strain now believed to be CRF04 cpx, where cpx is used for "complex" recombination of several subtypes. Subtype J is primarily found in North, Central, and West Africa, while Caribbean subtype K is limited to the Democratic Republic of the Congo and Cameroon. These subtypes are sometimes further divided into sub-subtypes, such as Al and A2 or Fl and F2. In 2015, strain CRF19 was discovered to be a recombinant of subtype A, subtype D, and subtype G, with its subtype D protease being closely associated with rapid progression of AIDS in Cuba.

[0132] The present disclosure provides, among other things, methods that require administration of human anti-HIV neutralizing antibodies (e.g., broadly neutralizing Abs) that target the V3 glycan region of the gpl20 polypeptide on the surface of HIV infected cells. Neutralizing antibodies against the viral envelope protein provide adaptive immune defense against HIV-1 exposure by blocking infection of susceptible cells. Broadly neutralizing indicates that the antibody can neutralize HIV-1 isolates from different clades. Thus, the anti-HIV gpl20 V3 glycan directed antibodies or antigen binding fragments described herein have cross-clade binding activity.

[0133] Antibodies and antigen binding fragments thereof directed against the V3 glycan region of HIV gp120

[0134] In certain embodiments of the methods described herein, an antibody or antigen-binding fragment thereof, or antigen-binding molecule that binds to the HIV gp120 protein within the V3 glycan region, e.g., an epitope or region of the gp120 third variable loop (V3) and / or a high mannose patch comprising N332 oligomannose glycans, is administered to the subject. In certain embodiments, the administered antibody or antigen-binding fragment thereof or antigen-binding molecule binds to an HIV-1 antigen expressed on the surface of a cell and eliminates or kills the infected cell.

[0135] In certain embodiments, the administered antibody or antigen-binding fragment thereof or antigen-binding molecule is or is derived from a human neutralizing antibody (e.g., a monoclonal antibody) that targets HIV-1. A "neutralizing antibody" is an antibody that can neutralize the ability of HIV to initiate and / or sustain infection in a host and / or target cell in vitro. The present disclosure provides neutralizing monoclonal human antibodies, wherein the antibody recognizes an antigen from HIV, e.g., a gpl20 polypeptide. In certain embodiments, a "neutralizing antibody" can inhibit entry of an HIV-1 virus, e.g., SF162 and / or JR-CSF, with a neutralization index > 1.5 or > 2.0 (Kostrikis LG et al., J. Virol., Vol. 70, No. 1, pp. 445-458, 1996).

[0136] In some embodiments, the administered antibody or antigen-binding fragment thereof or antigen-binding molecule is or is derived from a human broadly neutralizing antibody (e.g., a monoclonal antibody) that targets HIV-1. By "broadly neutralizing antibody" is meant an antibody that neutralizes more than one HIV-1 viral species (from different clades and different strains within clades) in a neutralization assay. A broadly neutralizing antibody can neutralize at least 2, 3, 4, 5, 6, 7, 8, 9, or more different strains of HIV-1 that belong to the same or different clades. In particular embodiments, a broadly neutralizing antibody can neutralize multiple HIV-1 species that belong to at least 2, 3, 4, 5, or 6 different clades. In certain embodiments, an anti-HIV gpl20 V3 glycan-directed antibody or antigen-binding fragment can have an inhibitory concentration of less than about 0.0001 μg / ml, less than about 0.001 μg / ml, less than about 0.01 μg / ml, less than about 0.1 μg / ml, less than about 0.5 μg / ml, less than about 1.0 μg / ml, less than about 5 μg / ml, less than about 10 μg / ml, less than about 25 μg / ml, less than about 50 μg / ml, or less than about 100 μg / ml to neutralize about 50% of the input virus in a neutralization assay.

[0137] Exemplary broadly neutralizing antibodies that bind to gpl20 in the third variable loop (V3) and / or high mannose patch containing N332 oligomannose glycans and that can be used in the methods described herein include, but are not limited to, GS-9722 (ebricitide), GS-9721, PGT-121, PGT-121.66, PGT-121.414, PGT-122, PGT-123, PGT-124, PGT-125, PGT-126, PGT-128, PGT-130, PGT-133, PGT-134, PGT-135, PGT-136, PGT-137, PGT-138, PGT-139, 10-1074, 10-1074-J, VRC24, 2G12, BG18, 354BG8, 354BG18, 354BG42, 354BG33, 354BG129, 354BG188, 354BG411, 354BG426, DH270.1, DH270.6, PGDM12, VRC41.01, PGDM21, PCDN-33A, BF520.1, and VRC29.03. Additional broadly neutralizing antibodies that bind to gpl20 in the third variable loop (V3) and / or high mannose patch containing N332 oligomannose glycans and that can be used in the methods described herein are described, for example, in WO 2012 / 030904; WO 2014 / 063059; WO 2016 / 149698; WO 2017 / 106346; WO 2018 / 075564, WO 2018 / 125813; WO 2018 / 237148, WO 2019 / 226829, WO 2020 / 023827, WO 2020 / 056145, and Kerwin et al., J Pharm Sci. 2020 Jan;109(l):233-246, all of which are hereby incorporated by reference in their entireties for all purposes.

[0138] Exemplary sequences of complementarity determining regions (CDRs) of antibodies or antigen-binding fragments that target the HIV gpl20 V3 glycan region are provided in Tables A1-A4. Exemplary sequences of VH and VL of antibodies or antigen-binding fragments that target the HIV gpl20 V3 glycan region are provided in Table B.

[0139]

[0140]

[0141]

[0142]

[0143]

[0144]

[0145]

[0146]

[0147]

[0148]

[0149]

[0150]

[0151]

[0152]

[0153]

[0154]

[0155]

[0156]

[0157]

[0158]

[0159] In some embodiments, the anti-HIV gp120 V3 glycan-directed antibody or antigen binding fragment thereof comprises a VH comprising a VH-CDR1, a VH-CDR2, and a VH-CDR3; and a VL comprising a VL-CDR1, a VL-CDR2, and a second VH-CDR3; wherein the VH-CDR1, VH-CDR2, VH-CDR3, VL-CDR1, VL-CDR2, and VH-CDR3 comprise the sequences set forth as: SEQ ID NOs: 7, 8, 9, 10, 11, and 12; SEQ ID NOs: 7, 13, 9, 10, 11, and 12; SEQ ID NOs: 14, 15, 16, 17, 11, and 18; SEQ ID NOs: 14, 19, 20, 17, 11, and 18; SEQ ID NOs: 21, 22, 23, 24, 25, and 26; SEQ ID NOs: 21, 22, 27, 24, 25, and 26; SEQ ID NOs: 28, 29, 30, 31, 32, and 33; SEQ ID NOs: 34, 35, 36, 37, 25, and 38; SEQ ID NOs: 39, 40, 41, 42, 43, and 44; SEQ ID NOs: 45, 46, 47, 48, 49, and 50; SEQ ID NOs: 45, 51, 52, 53, 49, and 54; SEQ ID NOs: 55, 56, 57, 58, 59, and 44; SEQ ID NOs: 61, 46, 63, 58, 49, and 44; SEQ ID NOs: 64, 65, 66, 67, 68, and 69; SEQ ID NOs: 70, 71, 72, 73, 74, and 75; SEQ ID NOs: 76, 77, 78, 79, 80, and 75; SEQ ID NOs: 81, 82, 83, 84, 85, and 75; SEQ ID NOs: 85, 86, 87, 88, 89, and 90; SEQ ID NOs: 85, 91, 92, 93, 94, and 90; SEQ ID NOs: 85, 96, 92, 93, 94, and 90; SEQ ID NOs: 85, 86, 87, 97, 98, and 90; SEQ ID NOs: 85, 99, 100, 101, 102, and 95; SEQ ID NOs: 85, 99, 100, 101, 102, and 103; SEQ ID NOs: 85, 99, 100, 104, 102, and 90; SEQ ID NOs: 85, 105, 92, 93, 94, and 90; SEQ ID NOs: 85, 99, 100, 101, 102, and 107; SEQ ID NOs: 108, 109, 110, 111, 112, and 113; SEQ ID NOs: 108, 114, 115, 111, 116, and 117;or SEQ ID NO: 108, 118, 119, 111, 120, and 121 (CDRs according to Kabat).

[0160] In some embodiments, the anti-HIV gp120 V3 glycan-directed antibody or antigen binding fragment thereof comprises a VH comprising a VH-CDR1, a VH-CDR2, and a VH- CDR3; and a VL comprising a VL-CDR1, a VL-CDR2, and a second VH-CDR3; wherein the VH- CDR1, VH-CDR2, VH-CDR3, VL-CDR1, VL-CDR2, and VH-CDR3 comprise the sequences set forth as: SEQ ID NOs: 123, 124, 9, 10, 11, and 12; SEQ ID NOs: 125, 126, 16, 17, 11, and 18; SEQ ID NOs: 127, 128, 20, 17, 11, and 18; SEQ ID NOs: 129, 130, 23, 24, 25, and 26; SEQ ID NOs: 129, 130, 27, 24, 25, and 26; SEQ ID NOs: 131, 132, 30, 31, 32, and 33; SEQ ID NOs: 133, 134, 36, 37, 25, and 38; SEQ ID NOs: 135, 136, 41, 42, 43, and 44; SEQ ID NOs: 137, 138, 47, 48, 49, and 50; SEQ ID NOs: 137, 138, 52, 53, 49, and 54; SEQ ID NOs: 139, 56, 57, 58, 59, and 44; SEQ ID NOs: 141, 138, 63, 58, 49, and 44; SEQ ID NOs: 142, 143, 66, 67, 68, and 69; SEQ ID NOs: 144, 145, 72, 73, 74, and 75; SEQ ID NOs: 146, 147, 78, 79, 80, and 75; SEQ ID NOs: 146, 147, 83, 84, 85, and 75; SEQ ID NOs: 149, 150, 87, 88, 89, and 90; SEQ ID NOs: 151, 150, 87, 88, 89, and 90; SEQ ID NOs: 152, 153, 92, 93, 94, and 90; SEQ ID NOs: 151, 150, 87, 97, 98, and 90; SEQ ID NOs: 152, 153, 100, 101, 102, and 95; SEQ ID NOs: 152, 153, 100, 101, 102, and 103; SEQ ID NOs: 152, 153, 100, 104, 102, and 90; SEQ ID NOs: 152, 153, 100, 101, 102, and 107; SEQ ID NOs: 154, 155, 110, 111, 116, and 117; SEQ ID NOs: 156, 157, 115, 111, 116, and 117;or SEQ ID NOs: 158, 159, 119, 111, 120, and 121 (CDRs according to Chothia).

[0161] In some embodiments, the anti-HIV gp120 V3 glycan-directed antibody or antigen binding fragment thereof comprises a VH comprising a VH-CDR1, a VH-CDR2, and a VH-CDR3; and a VL comprising a VL-CDR1, a VL-CDR2, and a second VH-CDR3; wherein the VH-CDR1, VH-CDR2, VH-CDR3, VL-CDR1, VL-CDR2, and VH-CDR3 comprise the sequences set forth as: SEQ ID NOs: 160, 161, 162, 163, 164, and 12; SEQ ID NOs: 165, 166, 167, 168, 164, and 18; SEQ ID NOs: 165, 166, 461, 168, 164, and 18; SEQ ID NOs: 169, 170, 171, 168, 164, and 18; SEQ ID NOs: 172, 173, 174, 175, 164, and 26; SEQ ID NOs: 172, 173, 176, 175, 164, and 26; SEQ ID NOs: 177, 178, 179, 180, 164, and 38; SEQ ID NOs: 181, 182, 183, 184, 185, and 33; SEQ ID NOs: 186, 187, 188, 189, 190, and 44; SEQ ID NOs: 191, 192, 193, 194, 195, and 50; SEQ ID NOs: 191, 196, 197, 198, 195, and 54; SEQ ID NOs: 199, 200, 201, 202, 399, and 44; SEQ ID NOs: 203, 204, 205, 202, 195, and 44; SEQ ID NOs: 206, 207, 208, 209, 210, and 69; 211, 212, 213, 214, 215, and 75; SEQ ID NOs: 216, 217, 218, 219, 220, and 75; SEQ ID NOs: 221, 217, 83, 223, 224, and 75; SEQ ID NOs: 225, 226, 87, 227, 228, and 90; SEQ ID NOs: 229, 226, 87, 227, 228, and 90; SEQ ID NOs: 230, 231, 92, 232, 233, and 90; SEQ ID NOs: 230, 234, 92, 232, 233, and 90; SEQ ID NOs: 229, 226, 87, 235, 398, and 90; SEQ ID NOs: 230, 236, 100, 232, 233, and 95; SEQ ID NOs: 230, 236, 100, 232, 233, and 103; SEQ ID NOs: 230, 236, 100, 237, 233, and 90; SEQ ID NOs: 230, 238, 92, 232, 233, and 107;SEQ ID NO: 239, 240, 110, 241, 242, and 113; SEQ ID NO: 243, 244, 115, 241, 245, and 117; or SEQ ID NO: 243, 246, 119, 241, 247, and 121 (CDRs according to IMGT).

[0162] In some embodiments, the anti-HIV gp120 V3 glycan-directed antibody or antigen binding fragment thereof comprises a VH comprising a VH-CDR1, a VH-CDR2, and a VH-CDR3; and a VL comprising a VL-CDR1, a VL-CDR2, and a second VH-CDR3; wherein the VH-CDR1, the VH-CDR2, the VH-CDR3, the VL-CDR1, the VL-CDR2, and the VH-CDR3 comprise the sequences set forth as: SEQ ID NOs: 248, 249, 250, 251, 252, and 253; SEQ ID NOs: 248, 254, 250, 251, 252, and 253; SEQ ID NOs: 255, 256, 257, 258, 252, and 259; SEQ ID NOs: 260, 261, 262, 258, 252, and 259; SEQ ID NOs: 263, 264, 265, 266, 267, and 268; SEQ ID NOs: 263, 264, 397, 266, 267, and 268; SEQ ID NOs: 269, 270, 271, 272, 273, and 274; SEQ ID NOs: 275, 276, 277, 278, 279, and 280; SEQ ID NOs: 281, 282, 283, 284, 285, and 286; SEQ ID NOs: 287, 288, 289, 290, 291, and 286; SEQ ID NOs: 287, 292, 293, 294, 295, and 296; SEQ ID NOs: 297, 298, 299, 300, 301, and 286; SEQ ID NOs: 302, 288, 303, 300, 295, and 286; SEQ ID NOs: 304, 305, 306, 307, 308, and 309; SEQ ID NOs: 310, 311, 312, 313, 314, and 315; SEQ ID NOs: 316, 316, 318, 319, 320, and 315; SEQ ID NOs: 321, 322, 323, 324, 325, and 315; 326, 327, 328, 329, 330, and 331; SEQ ID NOs: 332, 327, 328, 329, 330, and 331; SEQ ID NOs: 333, 334, 335, 336, 337, and 338; SEQ ID NOs: 333, 339, 335, 336, 337, and 338; SEQ ID NOs: 332, 327, 328, 340, 341, and 338; SEQ ID NOs: 342, 343, 344, 336, 345, and 346; SEQ ID NOs: 342, 343, 344, 336, 347, and 348; SEQ ID NOs: 342, 343, 344, 349, 350, and 338;SEQ ID NO: 333, 351, 335, 336, 337, and 338; SEQ ID NO: 342, 343, 344, 336, 347, and 352; SEQ ID NO: 353, 354, 355, 356, 357, and 358; SEQ ID NO: 359, 360, 361, 356, 362, and 363; or SEQ ID NO: 359, 364, 365, 356, 366, and 358. (According to CDRs of Honegger).

[0163] Exemplary embodiments of CDR sequences of anti-HIV gpl20 V3 glycan directed antibodies or antigen-binding fragments thereof useful in the methods described herein are provided in Tables A1-A4.

[0164] In some embodiments, the anti-HIV gp120 V3 glycan-directed antibody or antigen-binding fragment thereof comprises a VH and a VL comprising an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to the indicated amino acid sequence selected from the group consisting of: SEQ ID NOs: 400 and 401; SEQ ID NOs: 402 and 403; SEQ ID NOs: 402 and 404; SEQ ID NOs: 462 and 463; SEQ ID NOs: 464 and 465; SEQ ID NOs: 405 and 406; SEQ ID NOs: 466 and 467; SEQ ID NOs: 407 and 408; SEQ ID NOs: 409 and 410; SEQ ID NOs: 411 and 412; SEQ ID NOs: 413 and 414; SEQ ID NOs: 415 and 416; SEQ ID NOs: 417 and 418; SEQ ID NOs: 419 and 420; SEQ ID NOs: 421 and 422; SEQ ID NOs: 423 and 424; SEQ ID NOs: 425 and 426; SEQ ID NOs: 427 and 428; SEQ ID NOs: 429 and 430; SEQ ID NOs: 431 and 432; SEQ ID NOs: 433 and 434; SEQ ID NOs: 435 and 436; SEQ ID NOs: 437 and 438; SEQ ID NOs: 439 and 440; SEQ ID NOs: 441 and 442; SEQ ID NOs: 443 and 444; SEQ ID NOs: 445 and 446; SEQ ID NOs: 447 and 448; SEQ ID NOs: 449 and 450; SEQ ID NOs: 451 and 452; SEQ ID NOs: 453 and 454; SEQ ID NOs: 455 and 456; SEQ ID NOs: 457 and 458; or SEQ ID NOs: 459 and 460. Exemplary embodiments of variable domain VH and VL sequences of anti-HIV gp120 V3 glycan-directed antibodies or antigen-binding fragments thereof useful in the methods described herein are provided in Table B.

[0165] In some embodiments, the anti-HIV gp120 V3 glycan-directed antibody comprises VH and VL amino acid sequences that are at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the amino acid sequences set forth below, respectively, and comprises one or more of the following amino acids at the indicated positions (numbering of positions according to Kabat): SEQ ID NO: 400 or 402, which comprises one or more of the following amino acids: Ser-Ser-Val (SSV) or Thr-Gly-Val (TGV) at positions 82a-82c, any of Gln (Q) at position 39, Asn (N) at position 60, His (H) at position 68, Lys (K), His (H), or Thr (T) at position 105, Leu (L) at position 2, Ala (A) at position 32, and / or Ala (A) at position 95; and SEQ ID NO: 401, 403, or 404, which comprises one or more of the following amino acids: Gly (G) at position 67, Tyr (Y), Phe (F), or Thr (T) at position 67a, Arg (R) at position 67b, Pro (P) at position 67c, and / or Lys (K) at position 103. In some embodiments, the anti-HIV gp120 V3 glycan-directed antibody comprises VH and VL amino acid sequences that are at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the amino acid sequences set forth below, respectively, and comprises one or more of the following amino acids at the indicated positions (numbering of positions according to Kabat): SEQ ID NO: 400 or 402, which comprises Thr-Gly-Val (TGV) at positions 82a-82c, any of Asn (N) at position 60, His (H) at position 68, Lys (K), His (H), and / or Thr (T) at position 105; and SEQ ID NO: 401, 403, or 404, which comprises one or more of the following amino acids: Gly (G) at position 67, Tyr (Y), Phe (F), or Thr (T) at position 67a, Arg (R) at position 67b, Pro (P) at position 67c.

[0166] Fc mutations that increase serum half-life

[0167] In some embodiments, the Fc region or Fc domain of the anti-HIV gpl20 V3 glycan directed antibody comprises amino acid modifications that promote an increase in serum half-life of the anti-binding molecule. Mutations that increase the half-life of an antibody have been described. In one embodiment, the Fc region or Fc domain of one or both of the CD3-targeting heavy chain and the HIV antigen-targeting heavy chain comprises a substitution of methionine to tyrosine at position 252 (EU numbering), a substitution of serine to threonine at position 254 (EU numbering), and a substitution of threonine to glutamic acid at position 256 (EU numbering). See, e.g., U.S. Patent 7,658,921. Mutants of this type, designated “YTE mutants,” exhibit a four-fold increase in half-life relative to the wild-type version of the same antibody (Dall’Acqua et al., J Biol Chem, vol. 281, pp. 23514-23524, 2006; Robbie et al., Antimicrob Agents Chemotherap., vol. 57 no. 12, pp. 6147-6153, 2013. In certain embodiments, the Fc region or Fc domain of one or both of the CD3-targeting heavy chain and the HIV antigen-targeting heavy chain comprises an IgG constant domain comprising one, two, three or more amino acid substitutions of amino acid residues at positions 251-257, 285-290, 308-314, 385-389, and 428-436 (EU numbering). Alternatively, M428L and N434S (“LS”) substitutions can increase the pharmacokinetic half-life of the multispecific antigen binding molecule. In other embodiments, the Fc region or Fc domain of one or both of the CD3-targeting heavy chain and the HIV antigen-targeting heavy chain comprises M428L and N434S substitutions (EU numbering). In other embodiments, the Fc region or Fc domain of one or both of the CD3-targeting heavy chain and the HIV antigen-targeting heavy chain comprises T250Q and M428L (EU numbering) mutants. In other embodiments, the Fc region or Fc domain of one or both of the CD3-targeting heavy chain and the HIV antigen-targeting heavy chain comprises H433K and N434F (EU numbering) mutants.

[0168] Fc mutants that enhance effector activity

[0169] In some embodiments, the Fc region or Fc domain of the anti-HIV gp120 V3 glycan-directed antibody comprises post-translational and / or amino acid modifications that increase effector activity, e.g., with improved Fcyllla binding and increased antibody-dependent cellular cytotoxicity (ADCC). In some embodiments, the Fc region or Fc domain of the anti-HIV gp120 V3 glycan-directed antibody comprises DE modifications in the Fc region (i.e., S239D and I332E, EU numbering). In some embodiments, the Fc region or Fc domain of the anti-HIV gp120 V3 glycan-directed antibody comprises DEL modifications in the Fc region (i.e., S239D, I332E, and A330L, EU numbering). In some embodiments, the Fc region or Fc domain of the anti-HIV gp120 V3 glycan-directed antibody comprises DEA modifications in the Fc region (i.e., S239D, I332E, and G236A, EU numbering). In some embodiments, the Fc region or Fc domain of the anti-HIV gp120 V3 glycan-directed antibody comprises DEAL modifications in the Fc region (i.e., S239D, I332E, G236A, and A330L, EU numbering). See, e.g., U.S. Patents 7,317,091; 7,662,925; 8,039,592; 8,093,357; 8,093,359; 8,383,109; 8,388,955; 8,735,545; 8,858,937; 8,937,158; 9,040,041; 9,353,187; 10,184,000; and 10,584,176. Additional amino acid modifications that increase effector activity, e.g., with improved Fcyllla binding and increased antibody-dependent cellular cytotoxicity (ADCC), include, but are not limited to, (EU numbering) F243L / R292P / Y300L / V305I / P396L; S298A / E333A / K334A; or L234Y / L235Q / G236W / S239M / H268D / D270E / S298A on a first Fc domain and D270E / K326D / A330M / K334E on a second Fc domain. Amino acid mutations that increase Clq binding and complement-dependent cytotoxicity (CDC) include, but are not limited to, (EU numbering) S267E / H268F / S324T or K326W / E333S. Fc region mutations that enhance effector activity are reviewed, e.g., in Wang et al., Protein Cell, 2018, Vol. 9, No. 1, pp. 63-73; and Saunders, Front Immunol., 2019, Vol. 10, p. 1296.

[0170] In other embodiments, the anti-HIV gp120 V3 glycan-directed antibody or antigen-binding fragment thereof has modified glycosylation, which can be introduced, for example, post-translationally or by genetic engineering. In some embodiments, the anti-HIV gp120 V3 glycan-directed antibody or antigen-binding fragment thereof is non-fucosylated, for example, at the glycosylation site present in the antibody or antigen-binding fragment thereof. Most approved monoclonal antibodies have an IgGl isotype, in which two N-linked biantennary complex-type oligosaccharides are associated with the Fc region. The Fc region exerts effector functions of ADCC through its interaction with leukocyte receptors of the FcyR family. Non-fucosylated monoclonal antibodies are monoclonal antibodies engineered so that the oligosaccharides in the Fc region of the antibody do not have any fucose units.

[0171] In some embodiments, the Fc region or Fc domain of the anti-HIV gp120 V3 glycan-directed antibody can comprise post-translational and / or amino acid modifications, as appropriate, for increasing serum half-life and enhancing effector activity.

[0172] 4. Combination therapy with two or more anti-HIV antibodies

[0173] In certain embodiments, the present disclosure provides a method for treating or preventing an HIV infection in a human subject having or at risk of an HIV infection. The method comprises administering to the human subject a therapeutically effective amount of an anti-HIV 120 V3 glycan-directed antibody or antigen-binding fragment as disclosed herein, or a pharmaceutical composition thereof, and a therapeutically effective amount of one or more (e.g., one, two, three, one or two, or one to three) additional therapeutic agents. In one embodiment, a method for treating an HIV infection in a human subject having or at risk of an infection is provided, the method comprising administering to the human subject a therapeutically effective amount of one or more antibodies disclosed herein, or a pharmaceutically acceptable salt thereof, and a therapeutically effective amount of one or more (e.g., one, two, three, one or two, or one to three) additional therapeutic agents.

[0174] Antibody combination therapy

[0175] In some embodiments, the anti-V3 glycan antibody or antigen-binding fragment thereof is co-administered with a second anti-HIV antibody. In some embodiments, the anti-V3 glycan antibody or antigen-binding fragment thereof is co-administered with a second anti-HIV antibody that binds to an epitope or region of gpl20 selected from: (i) the second variable loop (V2) and / or Env trimer apex; (ii) the CD4 binding site (CD4bs); (iii) the gpl20 / gp41 interface; or (v) the gpl20 silent face. The foregoing epitopes or regions of gpl20 bound by broadly neutralizing antibodies are described, e.g., in McCoy, Retrovirology, 2018, vol. 15, p. 70; Sok and Burton, Nat Immunol., 2018, vol. 19, no. 11, pp. 1179-1188; Possas et al., Expert Opin Ther Pat., 2018 Jul, vol. 28, no. 7, pp. 551-560; and Stephenson and Barouch, Curr HIV / AIDS Rep, 2016, vol. 13, pp. 31-37, all of which are hereby incorporated by reference in their entireties herein for all purposes.

[0176] In some embodiments, the combination therapy entails co-administration of an anti-V3 glycan antibody or antigen-binding fragment thereof and another anti-HIV broadly neutralizing antibody or bNAb (i.e., a neutralizing antibody that neutralizes multiple HIV-1 viral strains). Various bNAbs are known in the art and can be used as a combination therapeutic. Exemplary bNAbs for use include antibodies comprising VH and VL that bind to or compete with an epitope or region of gpl20 selected from: (i) the second variable loop (V2) and / or Env trimer apex; (ii) the CD4 binding site (CD4bs); (iii) the gpl20 / gp41 interface; or (v) the gpl20 silent face. Exemplary bNAbs for anti-HIV antibody combination therapy include antibodies comprising VH and VL that bind to or compete with: 2F5, 4E10, M66.6, CAP206-CH12, 10E8, 10E8v4, 10E8-5R-100cF, DH511.11P, 7b2, and LN01 (all of which bind to the MPER of gp41); PG9, PG16, CH01-04 (all of which bind to V1V2-glycan), 2G12 (which binds to an outer domain glycan); b12, F105, VRC01, VRC07, VRC07-523, VRC03, VRC06, VRC06b01 VRC08, VRC0801, NIH45-46, GS-9723, GS-5423, 3BNC117, 3BNC60, VRC-PG04, PGV04; CH103, 44-VRC13.01, 1NC9, 12A12, N6, N6LS (VRC-HIVMAB091-00-AB), N49-P7, NC-Cowl, IOMA, CH235 and CH235.12, N49P6, N49P7, N49P11, N49P9, and N60P25 (all of which bind to the CD4 binding site).

[0177] In some embodiments, the combination therapy includes an antibody that binds to an epitope or region of gpl20 in the second variable loop (V2) and / or Env trimer apex and competes with or comprises CDRs and / or VH and VL regions from an antibody selected from: PG9, PG16, PGC14, PGG14, PGT-142, PGT-143, PGT-144, PGT-145, CH01, CH59, PGDM1400, CAP256, CAP256-VRC26.08, CAP256-VRC26.09, CAP256-VRC26.25, PCT64-24E, and VRC38.01.

[0178] In some embodiments, the combination therapy includes an antibody that binds to an epitope or region of gpl20 in the CD4 binding site (CD4bs) and competes with or comprises CDRs and / or VH and VL regions from an antibody selected from the group consisting of b12, F105, VRCOl, VRC07, VRC07-523, VRC03, VRC06, VRC06b01 VRC08, VRC0801, NIH45-46, GS-9723, GS-5423, 3BNC117, 3BNC60, VRC-PG04, PGV04; CH103, 44-VRC13.01, 1NC9, 12A12, N6, N6LS (VRC-HIVMAB091-00-AB), N49-P7, NC-Cowl, IOMA, CH235 and CH235.12, N49P6, N49P7, N49Pl l, N49P9, and N60P25.

[0179] In some embodiments, the combination therapy includes an antibody that binds to an epitope or region of gpl20 in the gpl20 / gp41 interface and competes with or comprises CDRs and / or VH and VL regions from an antibody selected from the group consisting of PGT-151, CAP248-2B, 35022, 8ANC195, ACS202, VRC34, and VRC34.01.

[0180] In some embodiments, the combination therapy includes an antibody that binds to an epitope or region of gpl20 in the gpl20 / gp41 interface and competes with or comprises CDRs and / or VH and VL regions from an antibody selected from the group consisting of PGT-151, CAP248-2B, 35022, 8ANC195, ACS202, VRC34, and VRC34.01.

[0181] In some embodiments, the combination therapy includes an antibody that binds to an epitope or region of gpl20 in the gpl20 / gp41 interface and competes with or comprises CDRs and / or VH and VL regions from an antibody selected from the group consisting of PGT-151, CAP248-2B, 35022, 8ANC195, ACS202, VRC34, and VRC34.01.

[0182] In some embodiments, the combination therapy includes an antibody that binds to an epitope or region of the gp41 fusion peptide and competes with or comprises a second VH and VL region from an antibody selected from VRC34 and ACS202.

[0183] In some embodiments, the combination therapy includes a multispecific antibody, such as a bispecific or trispecific antibody that binds to an HIV antigen. Examples of HIV bispecific and trispecific antibodies include: MGD014, B12BiTe, BiIA-SG, TMB-bispecific, SAR-441236, VRC-01 / PGDM-1400 / 10E8v4, 10E8.4 / iMab, and 10E8v4 / PGT121-VRC01.

[0184] Prior to administration, bNAbs can be improved to have enhanced drug-like properties, reduced immunogenicity, enhanced ADCC, and suitable pharmacokinetic properties. Such antibodies display binding to HIV envelope glycoproteins expressed on the surface of virions or infected cells and mediate potent NK, monocyte, and PBMC killing of these cells as well as direct neutralization of the virus. This property allows the antibodies to treat HIV infection by neutralizing the virus and also killing and eliminating potential HIV infected cells in the infected individual, potentially leading to sterilizing treatment of HIV.

[0185] In various embodiments, all antibodies administered in a combination anti-HIV antibody therapy can have Fc and / or post-translational modifications that increase serum half-life and / or enhance effector activity, as described above.

[0186] In various embodiments, the anti-HIV gp120 V3 glycan-directed antibody or antigen binding fragment, and optionally the combination bNAb, can be delivered in vivo, for example expressed in vivo by an administered mRNA or engineered B cell. Examples of bNAbs delivered in vivo include AAV8-VRC07; mRNA encoding anti-HIV antibody VRC01; and engineered B cells encoding 3BNC117 (Hartweger et al., J. Exp. Med., 2019, p. 1301).

[0187] 5. Combination therapy with other anti-HIV therapeutic agents

[0188] In certain embodiments, methods are provided for treating or preventing an HIV infection in a human having or at risk of having an infection, the method comprising administering to the human a therapeutically effective amount of an anti-HIV gp120 V3 glycan-directed antibody or antigen-binding fragment, as disclosed herein, and a therapeutically effective amount of one or more (e.g., one, two, three, one or two, or one to three) additional therapeutic agents. In some embodiments, methods are provided for treating an HIV infection in a human having or at risk of having an infection, the method comprising administering to the human a therapeutically effective amount of an anti-HIV gp120 V3 glycan-directed antibody or antigen-binding fragment, as disclosed herein, and a therapeutically effective amount of one or more (e.g., one, two, three, one or two, or one to three) additional therapeutic agents.

[0189] In one embodiment, pharmaceutical compositions are provided comprising an anti-HIV gp120 V3 glycan-directed antibody or antigen-binding fragment, as disclosed herein, and one or more (e.g., one, two, three, one or two, or one to three) additional therapeutic agents, and a pharmaceutically acceptable carrier, diluent, or excipient.

[0190] In certain embodiments, methods are provided for treating an HIV infection, the methods comprising administering to a patient in need thereof a therapeutically effective amount of an anti-HIV gp120 V3 glycan-directed antibody or antigen-binding fragment thereof, as described herein, and a therapeutically effective amount of one or more additional therapeutic agents suitable for treating an HIV infection.

[0191] In certain embodiments, the anti-HIV gp120 V3 glycan-directed antibody or antigen-binding fragment thereof is combined with one, two, three, four or more additional therapeutic agents. In certain embodiments, the anti-HIV gp120 V3 glycan-directed antibody or antigen-binding fragment thereof is combined with two additional therapeutic agents. In other embodiments, the anti-HIV gp120 V3 glycan-directed antibody or antigen-binding fragment thereof is combined with three additional therapeutic agents. In further embodiments, the anti-HIV gp120 V3 glycan-directed antibody or antigen-binding fragment thereof is combined with four additional therapeutic agents. The one, two, three, four or more additional therapeutic agents can be different therapeutic agents selected from the same class of therapeutic agents (e.g., one or more anti-HIV broadly neutralizing antibodies), and / or they can be selected from different classes of therapeutic agents.

[0192] Administration of HIV combination therapy

[0193] In certain embodiments, an anti-HIV gpl20 V3 glycan-directed antibody or antigen-binding fragment thereof, as described herein, is co-administered with one or more additional therapeutic agents. Co-administration of an anti-HIV gpl20 V3 glycan-directed antibody or antigen-binding fragment disclosed herein with one or more additional therapeutic agents generally refers to the simultaneous or sequential administration of an anti-HIV gpl20 V3 glycan-directed antibody or antigen-binding fragment disclosed herein with one or more additional therapeutic agents, such that a therapeutically effective amount of both the anti-HIV gpl20 V3 glycan-directed antibody or antigen-binding fragment disclosed herein and the one or more additional therapeutic agents are present in the patient's body. When administered sequentially, the combination can be administered in two or more administrations.

[0194] Co-administration includes simultaneous administration and administration of unit doses of an anti-HIV gpl20 V3 glycan-directed antibody or antigen-binding fragment thereof, as described herein, prior to or following administration of unit doses of one or more additional therapeutic agents. For example, an anti-HIV 120 V3 glycan-directed antibody or antigen-binding fragment thereof, as described herein, can be administered within seconds, minutes, hours, or days of administration of the one or more additional therapeutic agents. In some embodiments, a unit dose of an anti-HIV gpl20 V3 glycan-directed antibody or antigen-binding fragment disclosed herein is administered first, followed within seconds, minutes, hours, or days by administration of a unit dose of one or more additional therapeutic agents. Alternatively, a unit dose of one or more additional therapeutic agents is administered first, followed within seconds, minutes, hours, or days by administration of a unit dose of an anti-HIV gpl20 V3 glycan-directed antibody or antigen-binding fragment disclosed herein. In other embodiments, a unit dose of an anti-HIV gpl20 V3 glycan-directed antibody or antigen-binding fragment disclosed herein is administered first, followed after a period of hours (e.g., 1-12 hours, 1-24 hours, 1-36 hours, 1-48 hours, 1-60 hours, 1-72 hours) by administration of a unit dose of one or more additional therapeutic agents. In other embodiments, a unit dose of one or more additional therapeutic agents is administered first, followed after a period of hours (e.g., 1-12 hours, 1-24 hours, 1-36 hours, 1-48 hours, 1-60 hours, 1-72 hours) by administration of a unit dose of an anti-HIV gpl20 V3 glycan-directed antibody or antigen-binding fragment disclosed herein.

[0195] In certain embodiments, an anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment disclosed herein is combined with one or more additional therapeutic agents in a single dosage form for simultaneous administration to a patient, e.g., as a solid, liquid or suspension dosage form for oral, intravenous, intramuscular or subcutaneous administration.

[0196] In certain embodiments, an anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment is formulated as a liquid solution or suspension, which can optionally comprise one or more other compounds useful in the treatment of HIV. In certain embodiments, the liquid solution or suspension can comprise another active ingredient for the treatment of HIV, such as an HIV protease inhibitor, an HIV reverse transcriptase non-nucleoside or non-nucleotide inhibitor, an HIV reverse transcriptase nucleoside or nucleotide inhibitor, an HIV integrase inhibitor, an HIV non-catalytic site (or allosteric) integrase inhibitor, a pharmacokinetic enhancer, and combinations thereof.

[0197] In certain embodiments, such liquid solutions or suspensions are suitable for once daily, once weekly (i.e., QW), once every two weeks (i.e., every other week, or biweekly, or Q2W), once monthly (i.e., QM), or once every two months (i.e., every other month, or bimonthly, or Q2M) dosing or dosing intervals. In some embodiments, an anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment is administered once daily, once weekly (i.e., QW), once every two weeks (i.e., every other week, or biweekly, or Q2W), once monthly (i.e., QM), once every two months (i.e., every other month, or bimonthly, or Q2M), once every three months (i.e., Q3M), once every four months (i.e., Q4M).

[0198] HIV combination therapy

[0199] In the above embodiments, the additional therapeutic agent can be an anti-HIV agent. HIV protease inhibitors, HIV reverse transcriptase non-nucleoside or non-nucleotide inhibitors, HIV reverse transcriptase nucleoside or nucleotide inhibitors, HIV integrase inhibitors, HIV non-catalytic site (or allosteric) integrase inhibitors, HIV entry inhibitors, HIV maturation inhibitors, HIV capsid inhibitors, HIV Tat or Rev inhibitors, immunomodulators (e.g., immune stimulants), immunotherapeutics, immunomodulators, immunotherapeutics, antibody-drug conjugates, gene modulators, gene editors (such as CRISPR / Cas9, zinc finger nucleases, homing nucleases, synthetic nucleases, TALENs), cellular therapies (such as chimeric antigen receptor T-cells, CAR-T and engineered T-cell receptors, TCR-T, autologous T-cell therapies), latency reversing agents, compounds targeting the HIV capsid, immune-based therapies, phosphatidylinositol 3-kinase (PI3K) inhibitors, HIV antibodies, bispecific antibodies and “antibody-like” therapeutic proteins, HIV p17 matrix protein inhibitors, IL-13 antagonists, peptide based prolyl cis-trans isomerase A modulators, protein disulfide isomerase inhibitors, complement C5a receptor antagonists, DNA methyltransferase inhibitors, fatty acid synthase inhibitors, HIV vif gene modulators, Vif dimerization antagonists, HIV-1 viral infectivity factor inhibitors, TAT protein inhibitors, HIV-1 Nef modulators (e.g., Nef inhibitors), Hck tyrosine kinase modulators, mixed lineage kinase-3 (MLK-3) inhibitors, HIV-1 splicing inhibitors, Rev protein inhibitors, integrin antagonists, nucleoprotein inhibitors, splicing factor modulators, COMM domain containing protein 1 modulators, HIV ribonuclease H inhibitors, defensin modulators, CDK-4 inhibitors, CDK-6 inhibitors, CDK-9 inhibitors, dendritic ICAM-3 grabbing nonintegrin 1 inhibitors, HIV GAG protein inhibitors, HIV POL protein inhibitors, complement factor H modulators, ubiquitin ligase inhibitors, deoxycytidine kinase inhibitors, cyclin-dependent kinase inhibitors, proprotein convertase PC9 stimulators, ATP-dependent RNA helicase DDX3X inhibitors, reverse transcriptase initiation complex inhibitors, G6PD and NADH oxidase inhibitors, mTOR complex 1 inhibitors, mTOR complex 2 inhibitors, P-glycoprotein modulators, TAT protein inhibitors, prolyl endopeptidase inhibitors, phospholipase A2 inhibitors, pharmacokinetic enhancers, HIV gene therapies, TNF alpha ligand inhibitors, IFN antagonists, HIV vaccines, and combinations thereof.

[0200] In some embodiments, the additional therapeutic agent is selected from the group consisting of combination drugs for HIV, other drugs for the treatment of HIV, HIV protease inhibitors, HIV reverse transcriptase inhibitors, HIV integrase inhibitors, HIV non-catalytic site (or allosteric) integrase inhibitors, HIV entry (fusion) inhibitors, HIV maturation inhibitors, delay of reverse agent, HIV capsid inhibitors, HIV Tat or Rev inhibitors, immunomodulators (e.g., immune stimulants), immunotherapeutics, immune-based therapies, PI3K inhibitors, HIV antibodies, and bispecific antibodies and “antibody-like” therapeutic proteins, and combinations thereof.

[0201] HIV combination drugs

[0202] In certain embodiments, the anti-HIV gp120 V3 glycan-directed antibodies or antigen binding fragments described herein are combined with one, two, three, four or more additional anti-HIV therapeutic agents. Exemplary anti-HIV therapeutic agents that can be combined include, but are not limited to (Atripla® (efavirenz, tenofovir disoproxil fumarate, and emtricitabine)); (Atripla® (efavirenz, tenofovir disoproxil fumarate, and emtricitabine)); (Atripla® (efavirenz, tenofovir disoproxil fumarate, and emtricitabine)); (Atripla® (efavirenz, tenofovir disoproxil fumarate, and emtricitabine)); (Atripla® (efavirenz, tenofovir disoproxil fumarate, and emtricitabine)); (Atripla® (efavirenz, tenofovir disoproxil fumarate, and emtricitabine)); (Atripla® (efavirenz, tenofovir disoproxil fumarate, and emtricitabine)); (Atripla® (efavirenz, tenofovir disoproxil fumarate, and emtricitabine)); (Atripla® (efavirenz, tenofovir disoproxil fumarate, and emtricitabine)); (Atripla® (efavirenz, tenofovir disoproxil fumarate, and emtricitabine)); (Atripla® (efavirenz, tenofovir disoproxil fumarate, and emtricitabine)); (Atripla® (efavirenz, tenofovir disoproxil fumarate, and emtricitabine)); (Atripla® (efavirenz, tenofovir disoproxil fumarate, and emtricitabine)); (Atripla® (efavirenz, tenofovir disoproxil fumarate, and emtricitabine)); Abacavir sulfate, zidovudine, and lamivudine; ABC+AZT+3TC); atazanavir and cobicistat; atazanavir sulfate and cobicistat; atazanavir sulfate and ritonavir; darunavir; darunavir and cobicistat; dolutegravir and rilpivirine; dolutegravir and rilpivirine hydrochloride; dolutegravir, abacavir sulfate, and lamivudine; lamivudine, nevirapine, and zidovudine; raltegravir and lamivudine; doravirine, lamivudine, and tenofovir disoproxil fumarate; doravirine, lamivudine, and tenofovir disoproxil fumarate; dolutegravir + lamivudine, lamivudine + abacavir + zidovudine, lamivudine + abacavir, lamivudine + tenofovir disoproxil fumarate, lamivudine + zidovudine + nevirapine, lopinavir + ritonavir, lopinavir + ritonavir + abacavir + lamivudine, lopinavir + ritonavir + zidovudine + lamivudine, tenofovir + lamivudine, and tenofovir disoproxil fumarate + emtricitabine + rilpivirine hydrochloride, lopinavir, ritonavir, zidovudine, and lamivudine; cabotegravir + rilpivirine; elsulfavirine (VM-1500; VM-1500A); rilpivirine; rilpivirine hydrochloride; atazanavir sulfate and cobicistat; atazanavir and cobicistat; darunavir and cobicistat; atazanavir; atazanavir sulfate; dolutegravir; elvitegravir; ritonavir; atazanavir sulfate and ritonavir; darunavir; lamivudine; alpha 1 -proteinase inhibitor; fosamprenavir; fosamprenavir calcium efavirenz; efavirenz, lamivudine, and emtricitabine; inciveir; nelfinavir; nelfinavir mesylate; interferon; didanosine; stavudine; indinavir; indinavir sulfate; tenofovir and lamivudine; zidovudine; nevirapine; saquinavir; saquinavir mesylate; aldesleukin; zalcitabine; tipranavir; amprenavir; delavirdine; delavirdine mesylate; Radha-108 (receptol); lamivudine and tenofovir disoproxil fumarate; efavirenz, lamivudine, and tenofovir disoproxil fumarate; phosphazide; lamivudine, nevirapine, and zidovudine; abacavir; and abacavir sulfate.

[0203] Other HIV drugs

[0204]

[04] Examples of other drugs for treating HIV that can be combined with the agents of the present disclosure include aspernigrin C, acetyldinaline, ala- boceprevir, BanLec, deferiprone, Gamimune, metenkavir, naltrexone, alpha 1 - protease inhibitor, REP 9, RPI-MN, VSSP, H1 viral, SB-728-T, 1,5- dicaffeoylquinic acid, rHIV7-shl-TAR-CCR5RZ, AAV-eCD4-Ig gene therapy, MazF gene therapy, BlockAide, bevirimat derivative, ABX-464, AG-1105, APH-0812, bryostatin analog, BIT-225, CYT-107, CS-TATI-1, fluoro-beta-D-arabinonucleic acid (FANA)-modified antisense oligonucleotide, FX-101, griffithsin, HGTV-43, HPH-116, HS-10234, hydroxylated chloroquine, IMB-10035, IMO-3100, IND-02, JL-18008, LADAVRU, MK-1376, MK-2048, MK-4250, MK-8507, MK-8558, MK-8591 (elisavanir), NOV-205, OB-002H, ODE-Bn-TFV, M1-TFV, PA-1050040 (PA-040), PC-707, PGN-007, QF-036, S-648414, SCY-635, SB-9200, SCB-719, TR-452, TEV-90110, TEV-90112, TEV-90111, TEV-90113, RN-18, DIACC-1010, Fasnall, Immuglo, 2-CLIPS peptide, HRF-4467, thrombospondin analog, TBL-1004HI, VG-1177, xl-081, rfhSP-D, 18 F]-MC-225, URMC-099-C, RES-529, and VIR-576.

[0205] HIV protease inhibitors

[0206] In certain embodiments, an anti-HIV gp120 V3 glycan-directed antibody or antigen- binding fragment described herein is combined with an HIV protease inhibitor. Examples of HIV protease inhibitors include amprenavir, atazanavir, brecanavir, darunavir, fosamprenavir, fosamprenavir calcium, indinavir, indinavir sulfate, lopinavir, nelfinavir, nelfinavir mesylate, ritonavir, saquinavir, saquinavir mesylate, tipranavir, AEBL-2, DG-17, GS-1156, TMB-657 (PPL-100), T-169, BL-008, MK-8122, TMB-607, GRL-02031, and TMC-310911.

[0207] HIV ribonuclease H inhibitors

[0208] In certain embodiments, an anti-HIV gp120 V3 glycan-directed antibody or antigen- binding fragment described herein is combined with an HIV ribonuclease H inhibitor. An example of an HIV ribonuclease H inhibitor that can be combined includes NSC-727447.

[0209] HIV Nef inhibitors

[0210] In certain embodiments, an anti-HIV gp120 V3 glycan-directed antibody or antigen- binding fragment described herein is combined with an HIV Nef inhibitor. An example of an HIV Nef inhibitor that can be combined includes FP-1.

[0211] HIV reverse transcriptase inhibitors

[0212] In certain embodiments, an anti-HIV gp120 V3 glycan-directed antibody or antigen- binding fragment described herein is combined with a non-nucleoside or non-nucleotide inhibitor. Examples of non-nucleoside or non-nucleotide inhibitors of HIV reverse transcriptase include dapivirine, delavirdine, delavirdine mesylate, doravirine, efavirenz, etravirine, lentinan, nevirapine, rilpivirine, ACC-007, ACC-008, AIC-292, F-18, KM-023, PC-1005, VM-1500 A-LAI, PF-3450074, elsulfavirine (sustained release oral, HIV infection), elsulfavirine (long-acting injectable nanosuspension, HIV infection), and elsulfavirine (VM-1500).

[0213] In certain embodiments, the anti-HIV gp120 V3 glycan-directed antibodies or antigen binding fragments described herein are combined with an HIV nucleoside or nucleotide inhibitor. Examples of HIV reverse transcriptase nucleoside or nucleotide inhibitors include: adefovir, adefovir dipivoxil, azvudine, emtricitabine, tenofovir, tenofovir alafenamide, tenofovir alafenamide fumarate, tenofovir alafenamide hemifumarate, tenofovir disoproxil, tenofovir disoproxil fumarate, tenofovir octadecyl oxyl ethyl ester (AGX-1009), tenofovir disoproxil hemifumarate, and VIDEX (didanosine, ddl), abacavir, abacavir sulfate, alovudine, alitretinoin, censavudine, didanosine, elvucitabine, festinavir, fosalvudine tidoxil, CMX-157, dapivirine, doravirine, edoxudine, OCR-5753, tenofovir disoproxil fumarate, fozivudine tidoxil, lamivudine, phosphazide, stavudine, zalcitabine, zidovudine, rovafovir etalafenamide (GS-9131), GS-9148, MK-8504, MK-8591, MK-858, VM-2500, and KP-1461.

[0214] HIV integrase inhibitors

[0215] In certain embodiments, the anti-HIV gp120 V3 glycan-directed antibodies or antigen binding fragments described herein are combined with an HIV integrase inhibitor. Examples of HIV integrase inhibitors include elvucitabine, elvucitabine (extended release microcapsules), curcumin, curcumin derivatives, chicoric acid, chicoric acid derivatives, 3,5-dicaffeoylquinic acid, 3,5-dicaffeoylquinic acid derivatives, aurantrione, aurantrione derivatives, caffeic acid phenethyl ester, caffeic acid phenethyl ester derivatives, tyrosine phosphorylation inhibitors, tyrosine phosphorylation inhibitor derivatives, quercetin, quercetin derivatives, raltegravir, pegylated raltegravir, dolutegravir, JTK-351, bictegravir, AVX-15567, cabotegravir (long-acting injectable), benzochinon-4-1 derivatives, integrase-LEDGF inhibitors, ledgins, M-522, M-532, MK-0536, NSC-310217, NSC-371056, NSC-48240, NSC-642710, NSC-699171, NSC-699172, NSC-699173, NSC-699174, stilbenedisulfonic acid, T-169, STP-0404, VM-3500, and cabotegravir.

[0216] In certain embodiments, the anti-HIV gp120 V3 glycan-directed antibodies or antigen binding fragments described herein are combined with HIV non-catalytic site or allosteric integrase inhibitors (NCINI). Examples of HIV non-catalytic site or allosteric integrase inhibitors (NCINI) include CX-05045, CX-05168, and CX-14442.

[0217] HIV entry inhibitors

[0218] In certain embodiments, the anti-HIV gp120 V3 glycan-directed antibodies or antigen binding fragments described herein are combined with HIV entry inhibitors. Examples of HIV entry (fusion) inhibitors include AAR-501, LBT-5001, Cenicriviroc, CCR5 inhibitors, gp41 inhibitors, CD4 attachment inhibitors, gp120 inhibitors, gp160 inhibitors, and CXCR4 inhibitors.

[0219] In certain embodiments, the anti-HIV gp120 V3 glycan-directed antibodies or antigen binding fragments described herein are combined with CCR5 inhibitors. Examples of CCR5 inhibitors include Apelisib, Vicriviroc, Maraviroc, Maraviroc (long-acting injectable nanoemulsion), Cenicriviroc, Leronlimab (PRO-140), adaptavir (RAP-101), Nelfibrio (TD-0232), anti-GP120 / CD4 or CCR5 bispecific antibodies, B-07, MB-66, polypeptide C25P, TD-0680, Selatrevir, and vMIP (Haimipu).

[0220] In certain embodiments, the anti-HIV gp120 V3 glycan-directed antibodies or antigen binding fragments described herein are combined with CXCR4 inhibitors. Examples of CXCR4 inhibitors include Plegridy, ALT-1188, N15 peptide, and vMIP (Haimipu).

[0221] In certain embodiments, the anti-HIV gp120 V3 glycan-directed antibodies or antigen binding fragments described herein are combined with gp41 inhibitors. Examples of gp41 inhibitors include Albuvirtide, Enfuvirtide, Grifinol (gp41 / gp120 / gp160 inhibitor), BMS-986197, Enfuvirtide modified biosimilar, Enfuvirtide biosimilar, HIV-1 fusion inhibitors, (P26-Bapc), ITV-1, ITV-2, ITV-3, ITV-4, CPT-31, Cl3hmAb, PIE-12 trimer, and Selumate.

[0222] In certain embodiments, an anti-HIV gp120 V3 glycan-directed antibody or antigen binding fragment described herein is combined with a CD4 attachment inhibitor. Examples of CD4 attachment inhibitors include ibalizumab and CADA analogs

[0223] In certain embodiments, an anti-HIV gp120 V3 glycan-directed antibody or antigen binding fragment described herein is combined with a gp120 inhibitor. Examples of gp120 inhibitors include anti-HIV microbicides, Radha-108 (receptol) 3B3-PE38, BanLec, bentonite-based nanomedicine, fostemsavir tromethamine, IQP-0831, WTX-004, and BMS-663068.

[0224] In certain embodiments, an anti-HIV gp120 V3 glycan-directed antibody or antigen binding fragment described herein is combined with a gp160 inhibitor. Examples of gp160 inhibitors that can be combined include fangchinoline.

[0225] HIV maturation inhibitors

[0226] In certain embodiments, an anti-HIV gp120 V3 glycan-directed antibody or antigen binding fragment described herein is combined with an HIV maturation inhibitor. Examples of HIV maturation inhibitors include BMS-955176, GSK-3640254, and GSK-2838232.

[0227] Latency reversing agents

[0228] In certain embodiments, the anti-HIV gp120 V3 glycan-directed antibodies or antigen binding fragments described herein are combined with an HIV latency reversing agent. Examples of latency reversing agents that can be combined with the one or more multi-specific antigen binding molecules described herein include IL-15 receptor agonists (e.g., ALT-803; interleukin-15 / Fc fusion proteins (e.g., XmAb24306); recombinant interleukin-15 (e.g., AM0015, NIZ-985); pegylated IL-15 (e.g., NKTR-255)); toll-like receptor (TLR) agonists (including TLR7 agonists, such as GS-9620, and TLR8 agonists, such as GS-9688), histone deacetylase (HDAC) inhibitors, proteasome inhibitors such as bortezomib, protein kinase C (PKC) activators, Smyd2 inhibitors, BET-bromodomain 4 (BRD4) inhibitors, ionomycin, IAP antagonists (inhibitors of apoptosis proteins, such as APG-1387, LBW-242), SMAC mimetics (including TL32711, LCL161, GDC-0917, HGS1029, AT-406), Debio-1143, PMA, SAHA (vorinostat or suberoylanilide hydroxamic acid), NIZ-985, IL-15 modulating antibodies (including IL-15, IL-15 fusion proteins, and IL-15 receptor agonists, such as ALT-803), JQ1, disulfiram, amphotericin B, and ubiquitin inhibitors such as lagerstatin, APH-0812, and GSK-343. Examples of HDAC inhibitors include romidepsin, vorinostat, and panobinostat. Examples of PKC activators include indolactam, prostratin, largazole, and DAG-lactones.

[0229] Toll-like receptor (TLR) agonists

[0230] In certain embodiments, an anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment described herein is combined with a toll-like receptor (TLR) agonist, e.g., a TLR1 agonist (NCBI Gene ID: 7096), a TLR2 agonist (NCBI Gene ID: 7097), a TLR3 agonist (NCBI Gene ID: 7098), a TLR4 agonist (NCBI Gene ID: 7099), a TLR5 agonist (NCBI Gene ID: 7100), a TLR6 agonist (NCBI Gene ID: 10333), a TLR7 agonist (NCBI Gene ID: 51284), a TLR8 agonist (NCBI Gene ID: 51311), a TLR9 agonist (NCBI Gene ID: 54106), and / or a TLR10 agonist (NCBI Gene ID: 81793).Exemplary TLR7 agonists that can be co-administered or combined with the one or more multispecific antigen-binding molecules described herein include, but are not limited to, AL-034, DSP-0509, GS-9620 (vesatolimod), a vesatolimod analog, LHC-165, TMX-101 (imiquimod), GSK-2245035, resiquimod, DSR-6434, DSP-3025, IMO-4200, MCT-465, MEDI-9197, 3M-051, SB-9922, 3M-052, Limtop, TMX-30X, TMX-202, RG-7863, RG-7854, RG-7795, and the compounds disclosed in US20100143301 (Gilead Sciences), US20110098248 (Gilead Sciences), and US20090047249 (Gilead Sciences), US20140045849 (Janssen), US20140073642 (Janssen), WO2014 / 056953 (Janssen), WO2014 / 076221 (Janssen), WO2014 / 128189 (Janssen), US20140350031 (Janssen), WO2014 / 023813 (Janssen), US20080234251 (Array Biopharma), US20080306050 (Array Biopharma), US20100029585 (Ventirx Pharma), US20110092485 (Ventirx Pharma), US20110118235 (Ventirx Pharma), US20120082658 (Ventirx Pharma), US20120219615 (Ventirx Pharma), US20140066432 (Ventirx Pharma), US20140088085 (Ventirx Pharma), US20140275167 (Novira Therapeutics), and US20130251673 (Novira Therapeutics). TLR7 / TLR8 agonists that can be co-administered are NKTR-262, telratolimod, and BDB-001.Exemplary TLR8 agonists that can be co-administered or combined with the one or more multispecific antigen-binding molecules described herein include, but are not limited to, E-6887, IMO-4200, IMO-8400, IMO-9200, MCT-465, MEDI-9197, motolimod, resiquimod, GS-9688, VTX-1463, VTX-763, 3M-051, 3M-052, and the compounds disclosed in US20140045849 (Janssen), US20140073642 (Janssen), WO2014 / 056953 (Janssen), WO2014 / 076221 (Janssen), WO2014 / 128189 (Janssen), US20140350031 (Janssen), WO2014 / 023813 (Janssen), US20080234251 (Array Biopharma), US20080306050 (Array Biopharma), US20100029585 (Ventirx Pharma), US20110092485 (Ventirx Pharma), US20110118235 (Ventirx Pharma), US20120082658 (Ventirx Pharma), US20120219615 (Ventirx Pharma), US20140066432 (Ventirx Pharma), US20140088085 (Ventirx Pharma), US20140275167 (Novira Therapeutics), and US20130251673 (Novira Therapeutics). Exemplary TLR9 agonists that can be co-administered include, but are not limited to, AST-008, custorimod, CMP-001, IMO-2055, IMO-2125, linomotide, MGN-1601, BB-001, BB-006, IMO-3100, IMO-8400, IR-103, IMO-9200, atorimidod, DIMS-9054, DV-1079, DV-1179, AZD-1419, letolimod (MGN-1703), CYT-003, CYT-003-QbG10, tilsotolimod, and PUL-042. Examples of TLR3 agonists include: linomotide, poly ICLC, Apoxxim, IPH-33, MCT-465, MCT-475, and ND-1.1. Examples of TLR4 agonists include: G-100 and GSK-1795091.

[0231] Histone deacetylase (HDAC) inhibitors

[0232] In certain embodiments, an anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment described herein is combined with an inhibitor of histone deacetylase, e.g., histone deacetylase 1, histone deacetylase 9 (HDAC9, HD7, HD7b, HD9, HDAC, HDAC7, HDAC7B, HDAC9B, HDAC9FL, HDRP, MITR; Gene ID: 9734). Examples of HDAC inhibitors include, but are not limited to, abexinostat, ACY-241, AR-42, BEBT-908, belinostat, CKD-581, CS-055 (HBI-8000), CT-101, CUDC-907 (non-metinostat), entinostat, givinostat, mocetinostat, parpimycin, pracinostat, quinoxyryl, (JNJ-26481585), resminostat, ricolinostat, romidepsin, SHP-141, TMB-ADC, valproic acid (VAL-001), vorinostat, tinostamustine, resminostat, and entinostat.

[0233] Cyclin-dependent kinase (CDK) inhibitors or antagonists

[0234] In certain embodiments, an anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment described herein is combined with a cyclin-dependent kinase (CDK) inhibitor or antagonist, e.g., cyclin-dependent kinase 4 (CDK4; NCBI Gene ID: 1019), cyclin-dependent kinase 6 (CDK6; NCBI Gene ID: 1021), cyclin-dependent kinase 9 (CDK9; NCBI Gene ID: 1025). In some embodiments, the CDK4 / CDK6 / CDK9 inhibitor or antagonist is selected from VS2-370.

[0235] Stimulator of interferon genes (STING) agonists

[0236] In some embodiments, the anti-HIV gpl20 V3 glycan-directed antibodies or antigen binding fragments described herein are combined with an interferon-stimulating substance (STING). In some embodiments, the STING receptor agonist or activator is selected from ADU-S100 (MIW-815), SB-11285, MK-1454, SR-8291, AdVCA0848, GSK-532, SYN-STING, MSA--1, SR-8291, 5,6-dimethylxanthone-4-acetic acid (DMXAA), cyclic GAMP (cGAMP), and cyclic di-AMP.

[0237] RIG-I agonists

[0238] In certain embodiments, the anti-HIV gpl20 V3 glycan-directed antibodies or antigen binding fragments described herein are combined with DExD / H-box helicase 58 (DDX58; also known as, RIG-I, RIG1, RIGI, RL R-1, SGMRT2; NCBI Gene ID: 23586). In some embodiments, the agents described herein are combined with a RIG-I modulator such as RGT-100 or a NOD2 modulator such as SB-9200 (also known as, GS 9992; inarigivir) and IR-103. An exemplary RIG-I agonist is KIN1148, described in Hemann et al., J Immunol, 2016 May 1, vol. 196 Suppl 1) 76.1. Additional RIG-I agonists are described in, e.g., Elion et al., Cancer Res., 2018, vol. 78 no. 21, pp. 6183-6195; and Liu et al., J Virol., 2016, vol. 90 no. 20, pp. 9406-9419. RIG-I agonists are commercially available, e.g., from Invivogen (invivogen.com).

[0239] LAG-3 and TIM-3 inhibitors

[0240] In certain embodiments, the anti-HIV gpl20 V3 glycan-directed antibodies or antigen binding fragments described herein are combined with an anti-TIM-3 (also known as Hepatitis A Virus Cellular Receptor 2 antibody (HAVCR2; NCBI Gene ID: 84868) such as TSR-022, LY-3321367, MBG-453, INCAGN-2390. In some embodiments, the anti-HIV gpl20 V3 glycan-directed antibodies or antigen binding fragments described herein are combined with an anti-LAG-3 (lymphocyte activation) (NCBI Gene ID: 3902) antibody such as relatlimab (ONO-4482), LAG-525, MK-4280, REGN-3767, INCAGN2385.

[0241] Capsid inhibitors

[0242] In certain embodiments, the anti-HIV gpl20 V3 glycan-directed antibodies or antigen binding fragments described herein are combined with a capsid inhibitor. Examples of capsid inhibitors that can be combined with the agents of the present disclosure include capsid polymerization inhibitors or capsid interfering compounds, HIV nuclear capsid P7 (NCp7) inhibitors such as azodicarbonamide, HIV p24 capsid protein inhibitors, GS-6207, GS-CA1, AVI-621, AVI-101, AVI-201, AVI-301, and the AVI-CAN1-15 series, PF-3450074, and the compounds described in International Patent Publication WO2019 / 087016.

[0243] Immune-based therapies

[0244] In certain embodiments, the anti-HIV gp120 V3 glycan-directed antibodies or antigen binding fragments described herein are combined with an immune-based therapy. Examples of immune-based therapies include toll-like receptor (TLR) modulators such as TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, TLR9, TLR10, TLR11, TLR12, and TLR13; programmed cell death protein 1 (PD-1) modulators; programmed death ligand 1 (PD-L1) inhibitors; IL-15 inhibitors (e.g., IL-15 receptor agonists (e.g., ALT-803; interleukin-15 / Fc fusion proteins (e.g., XmAb24306); recombinant interleukin-15 (e.g., AM0015, NIZ-985); pegylated IL-15 (e.g., NKTR-255)); DermaVir; interleukin-7; hydroxychloroquine (Plaquenil); interleukin (aldesleukin, IL-2); interferon alpha; interferon alpha-2b; interferon alpha-n3; pegylated interferon alpha; interferon gamma; hydroxyurea; mycophenolic acid morpholide (MPA) and its ester derivative mycophenolate mofetil (MMF); ribavirin; the polymer polyethyleneimine (PEI); gepon; IL-12; WF-10; VGV-1; MOR-22; BMS-936559; CYT-107, Nomvax, peginterferon alfa-2a, peginterferon alfa-2b, RPI-MN, STING modulators, RIG-I modulators, NOD2 modulators, SB-9200, and IR-103.

[0245] In certain embodiments, the anti-HIV gp120 V3 glycan-directed antibodies or antigen binding fragments described herein are combined with a TLR agonist. Examples of TLR agonists include, but are not limited to, vesatolimod (GS-9620), letolimod, tilsotolimod, resiquimod, DSP-0509, AL-034, G-100, custolimod, AST-008, motolimod, GSK-1795091, GSK-2245035, VTX-1463, GS-9688, LHC-165, BDB-001, RG-7854, telratolimod.

[0246] Modulators of immune checkpoint receptor proteins

[0247] In various embodiments, the anti-HIV gpl20 V3 glycan-directed antibodies or antigen binding fragments described herein are combined with one or more blockers or inhibitors of inhibitory immune checkpoint proteins or receptors and / or with one or more stimulators, activators or agonists of one or more stimulatory immune checkpoint proteins or receptors. Blockade or inhibition of inhibitory immune checkpoints can positively modulate T cell or NK cell activation and prevent immune escape of infected cells. Activation or stimulation of stimulatory immune checkpoints can enhance the effect of immune checkpoint inhibitors in infectious treatment. In various embodiments, the immune checkpoint proteins or receptors modulate T cell responses (e.g., reviewed in Xu et al., J Exp Clin Cancer Res., 2018, vol. 37, p. 110). In various embodiments, the immune checkpoint proteins or receptors modulate NK cell responses (e.g., reviewed in Davis et al., Semin Immunol., 2017, vol. 31, p. 64-75, and Chiossone et al., Nat Rev Immunol., 2018, vol. 18, no. 11, p. 671-688).

[0248] Examples of immune checkpoint proteins or receptors that can be combined with the anti-HIV gp120 V3 glycan-directed antibodies or antigen-binding fragments described herein include, but are not limited to, CD27, CD70; CD40, CD40LG; CD47, CD48 (SLAMF2), transmembrane and immunoglobulin domain 2 (TMIGD2, CD28H), CD84 (LY9B, SLAMF5), CD96, CD160, MS4A1 (CD20), CD244 (SLAMF4); CD276 (B7H3); V-set domain-containing T- cell activation inhibitor 1 (VTCN1, B7H4); V-set immunoregulatory receptor (VSIR, B7H5, VISTA); immunoglobulin superfamily member 11 (IGSF11, VSIG3); natural killer cell cytotoxicity receptor 3 ligand 1 (NCR3LG1, B7H6); HERV-H LTR- associated 2 (HHLA2, B7H7); inducible T-cell costimulator (ICOS, CD278); inducible T-cell costimulator ligand (ICOSLG, B7H2); TNF receptor superfamily member 4 (TNFRSF4, OX40); TNF superfamily member 4 (TNFSF4, OX40L); TNFRSF8 (CD30), TNFSF8 (CD30L); TNFRSF10A (CD261, DR4, TRAILR1), TNFRSF9 (CD137), TNFSF9 (CD137L); TNFRSF10B (CD262, DR5, TRAILR2), TNFRSF10 (TRAIL); TNFRSF14 (HVEM, CD270), TNFSF14 (HVEML); CD272 (B and T lymphocyte-associated (BTLA)); TNFRSF17 (BCMA, CD269), TNFSF13B (BAFF); TNFRSF18 (GITR), TNFSF18 (GITRL); MHC class I polypeptide-related sequence A (MICA); MHC class I polypeptide-related sequence B (MICB); CD274 (CD274, PDL1, PD-L1); programmed cell death protein 1 (PDCD1, PD1, PD-1); cytotoxic T-lymphocyte-associated protein 4 (CTLA4, CD152); CD80 (B7-1), CD28; fibronectin cell adhesion molecule 2 (NECTIN2, CD112); CD226 (DNAM-1); poliovirus receptor (PVR) cell adhesion molecule (PVR, CD155); PVR-related immunoglobulin domain-containing (PVRIG, CD112R); T-cell immunoreceptor with Ig and ITIM domains (TIGIT); T-cell immunoglobulin and mucin domain-containing 4 (TIMD4; TIM4);Hepatitis A Virus Cellular Receptor 2 (HAVCR2, TIMD3, TIM3); Galectin 9 (LGALS9); Lymphocyte Activation 3 (LAG3, CD223); Signaling Lymphocyte Activation Molecule Family Member 1 (SLAMF1, SLAM, CD150); Lymphocyte Antigen 9 (LY9, CD229, SLAMF3); SLAM Family Member 6 (SLAMF6, CD352); SLAM Family Member 7 (SLAMF7, CD319); UL16 Binding Protein 1 (ULBP1); UL16 Binding Protein 2 (ULBP2); UL16 Binding Protein 3 (ULBP3); Retinoic Acid Early Transcript 1E (RAET1E; ULBP4); Retinoic Acid Early Transcript 1G (RAET1G; ULBP5); Retinoic Acid Early Transcript 1L (RAET1L; ULBP6); Lymphocyte Activation 3 (CD223); Killer Cell Immunoglobulin Like Receptor, Three Ig Domains and Long Cytoplasmic Tail 1 (KIR, CD158E1); Killer Cell Lectin Like Receptor C1 (KLRC1, NKG2A, CD159A); Killer Cell Lectin Like Receptor K1 (KLRK1, NKG2D, CD314); Killer Cell Lectin Like Receptor C2 (KLRC2, CD159c, NKG2C); Killer Cell Lectin Like Receptor C3 (KLRC3, NKG2E); Killer Cell Lectin Like Receptor C4 (KLRC4, NKG2F); Killer Cell Immunoglobulin Like Receptor, Two Ig Domains and Long Cytoplasmic Tail 1 (KIR2DL1); Killer Cell Immunoglobulin Like Receptor, Two Ig Domains and Long Cytoplasmic Tail 2 (KIR2DL2); Killer Cell Immunoglobulin Like Receptor, Two Ig Domains and Long Cytoplasmic Tail 3 (KIR2DL3); Killer Cell Immunoglobulin Like Receptor, Three Ig Domains and Long Cytoplasmic Tail 1 (KIR3DL1); Killer Cell Lectin Like Receptor D1 (KLRD1); and SLAM Family Member 7 (SLAMF7).

[0249] In various embodiments, an anti-HIV gpl20 V3 glycan-directed antibody or antigen-binding fragment described herein is combined with one or more blockers or inhibitors of one or more T-cell inhibitory immune checkpoint proteins or receptors. Exemplary T-cell inhibitory immune checkpoint proteins or receptors include, but are not limited to, CD274 (CD274, PDL1, PD-L1); programmed cell death 1 ligand 2 (PDCD1LG2, PD-L2, CD273); programmed cell death 1 (PDCD1, PD1, PD-1); cytotoxic T-lymphocyte-associated protein 4 (CTLA4, CD152); CD276 (B7H3); V-set domain-containing T- cell activation inhibitor 1 (VTCN1, B7H4); V-set immunoregulatory receptor (VSIR, B7H5, VISTA); immunoglobulin superfamily member 11 (IGSF11, VSIG3); TNFRSF14 (HVEM, CD270), TNFSF14 (HVEML); CD272 (B- and T-lymphocyte-associated (BTLA)); PVR-related immunoglobulin domain- containing (PVRIG, CD112R); T-cell immunoreceptor with Ig and ITIM domains (TIGIT); lymphocyte-activation gene 3 (LAG3, CD223); hepatitis A virus cellular receptor 2 (HAVCR2, TIMD3, TIM3); galectin 9 (LGALS9); killer-cell immunoglobulin-like receptor, three Ig domains and long cytoplasmic tail 1 (KIR, CD158E1); killer-cell immunoglobulin-like receptor, two Ig domains and long cytoplasmic tail 1 (KIR2DL1); killer-cell immunoglobulin-like receptor, two Ig domains and long cytoplasmic tail 2 (KIR2DL2); killer-cell immunoglobulin-like receptor, two Ig domains and long cytoplasmic tail 3 (KIR2DL3); and killer-cell immunoglobulin-like receptor, three Ig domains and long cytoplasmic tail 1 (KIR3DL1). In various embodiments, an anti-HIV gpl20 V3 glycan-directed antibody or antigen-binding fragment described herein is combined with one or more agonists or activators of one or more T-cell stimulatory immune checkpoint proteins or receptors.Exemplary T cell stimulatory immune checkpoint proteins or receptors include, but are not limited to, CD27, CD70; CD40, CD40LG; inducible T cell costimulator (ICOS, CD278); inducible T cell costimulator ligand (ICOSLG, B7H2); TNF receptor superfamily member 4 (TNFRSF4, OX40); TNF superfamily member 4 (TNFSF4, OX40L); TNFRSF9 (CD137), TNFSF9 (CD137L); TNFRSF18 (GITR), TNFSF18 (GITRL); CD80 (B7-1), CD28; fibronectin cell adhesion molecule 2 (NECTIN2, CD112); CD226 (DNAM-1); CD244 (2B4, SLAMF4), Poliovirus receptor (PVR) cell adhesion molecule (PVR, CD155). See, e.g., Xu et al., J Exp Clin Cancer Res., 2018, vol. 37, p. 110.

[0250] In various embodiments, the anti-HIV gpl20 V3 glycan-directed antibodies or antigen binding fragments described herein are combined with one or more blockers or inhibitors of one or more NK cell inhibitory immune checkpoint proteins or receptors. Exemplary NK cell inhibitory immune checkpoint proteins or receptors include, but are not limited to, killer cell immunoglobulin-like receptor, three Ig domains and long cytoplasmic tail 1 (KIR, CD158E1); killer cell immunoglobulin-like receptor, two Ig domains and long cytoplasmic tail 1 (KIR2DL1); killer cell immunoglobulin-like receptor, two Ig domains and long cytoplasmic tail 2 (KIR2DL2); killer cell immunoglobulin-like receptor, two Ig domains and long cytoplasmic tail 3 (KIR2DL3); killer cell immunoglobulin-like receptor, three Ig domains and long cytoplasmic tail 1 (KIR3DL1); killer cell lectin-like receptor Cl (KLRC1, NKG2A, CD159A); and killer cell lectin-like receptor Dl (KLRD1, CD94). In various embodiments, the anti-HIV gpl20 V3 glycan-directed antibodies or antigen binding fragments described herein are combined with one or more agonists or activators of one or more NK cell stimulatory immune checkpoint proteins or receptors. Exemplary NK cell stimulatory immune checkpoint proteins or receptors include, but are not limited to, CD16, CD226 (DNAM-1); CD244 (2B4, SLAMF4); killer cell lectin-like receptor Kl (KLRK1, NKG2D, CD314); SLAM family member 7 (SLAMF7). See, e.g., Davis et al., Semin Immunol., 2017, 31:64-75; Fang et al., Semin Immunol., 2017, 31:37-54; and Chiossone et al., Nat Rev Immunol., 2018, 18(11):671-688.

[0251] In some embodiments, the one or more immune checkpoint inhibitors include a proteinaceous (e.g., an antibody or fragment thereof, or an antibody mimetic) inhibitor of PD-L1 (CD274), PD-1 (PDCD1), or CTLA4. In some embodiments, the one or more immune checkpoint inhibitors include a small organic molecule inhibitor of PD-L1 (CD274), PD-1 (PDCD1), or CTLA4.

[0252] Examples of inhibitors of CTLA4 that can be co-administered include, but are not limited to, ipilimumab, tremelimumab, BMS-986218, AGEN1181, AGEN1884, BMS-986249, MK-1308, REGN-4659, ADU-1604, CS-1002, BCD-145, APL-509, JS-007, BA-3071, ONC-392, AGEN-2041, JHL-1155, KN-044, CG-0161, ATOR-1144, PBI-5D3H5, BPI-002, and the multispecific inhibitors FPT-155 (CTLA4 / PD-L1 / CD28), PF-06936308 (PD-1 / CTLA4), MGD-019 (PD-1 / CTLA4), KN-046 (PD-1 / CTLA4), MEDI-5752 (CTLA4 / PD-1), XmAb-20717 (PD-1 / CTLA4), and AK-104 (CTLA4 / PD-1).

[0253] Examples of co-administrable inhibitors of PD-L1 (CD274) or PD-1 (PDCD1) include, but are not limited to, pembrolizumab, nivolumab, cemiplimab, pidilizumab, AMP-224, MEDI0680 (AMP-514), spartalizumab, atezolizumab, avelumab, durvalumab, BMS-936559, CK-301, PF-06801591, BGB-A317 (tislelizumab), GLS-010 (WBP-3055), AK-103 (HX-008), AK-105, CS-1003, HLX-10, MGA-012, BI-754091, AGEN-2034, JS-001 (toripalimab), JNJ-63723283, genolimzumab (CBT-501), LZM-009, BCD-100, LY-3300054, SHR-1201, SHR-1210 (camrelizumab), Sym-021, ABBV-181 (bulevirtide), PD1-PIK, BAT-1306, (MSB0010718C), CX-072, CBT-502, TSR-042 (domvanalimab), MSB-2311, JTX-4014, BGB-A333, SHR-1316, CS-1001 (WBP-3155), KN-035, IBI-308 (sintilimab), HLX-20, KL-A167, STI-A1014, STI-A1015 (IMC-001), BCD-135, FAZ-053, TQB-2450, MDX1105-01, GS-4224, GS-4416, INCB086550, MAX10181, and the multispecific inhibitors FPT-155 (CTLA4 / PD-L1 / CD28), PF-06936308 (PD-1 / CTLA4), MGD-013 (PD-1 / LAG-3), FS-118 (LAG-3 / PD-L1) MGD-019 (PD-1 / CTLA4), KN-046 (PD-1 / CTLA4), MEDI-5752 (CTLA4 / PD-1), RO-7121661 (PD-1 / TIM-3), XmAb-20717 (PD-1 / CTLA4), AK-104 (CTLA4 / PD-1), M7824 (PD-L1 / TGFβ-EC domain), CA-170 (PD-L1 / VISTA), CDX-527 (CD27 / PD-L1), LY-3415244 (TIM3 / PDL1), and INBRX-105 (4-1BB / PDL1).

[0254] In some embodiments, the small molecule inhibitor of CD274 or PDCD1 is selected from GS-4224, GS-4416, INCB086550, and MAX10181. In some embodiments, the small molecule inhibitor of CTLA4 comprises BPI-002.

[0255] In various embodiments, the antibody or antigen binding fragment as described herein is combined with an anti-TIGIT antibody, such as BMS-986207, RG-6058, AGEN-1307.

[0256] Agonists or activators of members of the TNF receptor superfamily (TNFRSF)

[0257] In various embodiments, an anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment described herein is combined with an agonist of one or more TNF receptor superfamily (TNFRSF) members, e.g., TNFRSF1A (NCBI Gene ID: 7132), TNFRSF1B (NCBI Gene ID: 7133), TNFRSF4 (OX40, CD134; NCBI Gene ID: 7293), TNFRSF5 (CD40; NCBI Gene ID: 958), TNFRSF6 (FAS, NCBI Gene ID: 355), TNFRSF7 (CD27, NCBI Gene ID: 939), TNFRSF8 (CD30, NCBI Gene ID: 943), TNFRSF9 (4-1BB, CD137, NCBI Gene ID: 3604), TNFRSF10A (CD261, DR4, TRAILR1, NCBI Gene ID: 8797), TNFRSF10B (CD262, DR5, TRAILR2, NCBI Gene ID: 8795), TNFRSF10C (CD263, TRAILR3, NCBI Gene ID: 8794), TNFRSF10D (CD264, TRAILR4, NCBI Gene ID: 8793), TNFRSF11A (CD265, RANK, NCBI Gene ID: 8792), TNFRSF11B (NCBI Gene ID: 4982), TNFRSF12A (CD266, NCB Gene ID: 51330), TNFRSF13B (CD267, NCBI Gene ID: 23495), TNFRSF13C (CD268, NCBI Gene ID: 115650), TNFRSF16 (NGFR, CD271, NCBI Gene ID: 4804), TNFRSF17 (BCMA, CD269, NCBI Gene ID: 608), TNFRSF18 (GITR, CD357, NCBI Gene ID: 8784), TNFRSF19 (NCBI Gene ID: 55504), TNFRSF21 (CD358, DR6, NCBI Gene ID: 27242), and TNFRSF25 (DR3, NCBI Gene ID: 8718).

[0258] Exemplary anti-TNFRSF4 (OX40) antibodies that can be co-administered include, but are not limited to, MEDI6469, MEDI6383, MEDI0562 (tebotulinumab), MOXR0916, PF-04518600, RG-7888, GSK-3174998, INCAGN1949, BMS-986178, GBR-8383, ABBV-368, and antibodies described in WO2016179517, WO2017096179, WO2017096182, WO2017096281, and WO2018089628.

[0259] Exemplary anti-TNFRSF5 (CD40) antibodies that can be co-administered include, but are not limited to, RG7876, SEA-CD40, APX-005M, and ABBV-428.

[0260] In some embodiments, the anti-TNFRSF7 (CD27) antibody that is co-administered is varlilumab (CDX-1127).

[0261] Exemplary anti-TNFRSF9 (4-1BB, CD137) antibodies that can be co-administered include, but are not limited to, urelumab, utomilumab (PF-05082566), AGEN2373, and ADG-106.

[0262] Exemplary anti-TNFRSF18 (GITR) antibodies that can be co-administered include, but are not limited to, MEDI1873, FPA-154, INCAGN-1876, TRX-518, BMS-986156, MK-1248, GWN-323, and antibodies described in WO2017096179, WO2017096276, WO2017096189, and WO2018089628. In some embodiments, an antibody or fragment thereof that co-targets TNFRSF4 (OX40) and TNFRSF18 (GITR) is co-administered. Such antibodies are described, e.g., in WO2017096179 and WO2018089628.

[0263] Agonists of interleukin receptors

[0264] In certain embodiments, the anti-HIV gpl20 V3 glycan-directed antibodies or antigen binding fragments described herein are combined with interleukin receptor agonists, such as IL-2 antagonists, IL-7 antagonists, IL-15 antagonists, IL-10 antagonists, IL-12 antagonists; examples of IL-2 receptor antagonists such as interleukin (aldesleukin, IL-2); pegylated IL-2 (e.g., NKTR-214); modified variants of IL-2 (e.g., THOR-707), bempegaldesleukin, AIC-284, ALKS-4230, CUI-101, Neo-2 / 15; IL-15 receptor antagonists such as ALT-803, NKTR-255, and hetIL-15, interleukin 15 / Fc fusion protein, AM-0015, NIZ-985, SO-C101, IL-15 Synthorin (pegylated IL-15), P-22339, and IL-15-PD-1 fusion protein N-809; examples of IL-7 include CYT-107.

[0265] Additional interleukin receptor agonists that can be combined with the anti-HIV gpl20 V3 glycan-directed antibodies or antigen binding fragments described herein include interferon alpha; interferon alpha-2b; interferon alpha-n3; pegylated interferon alpha; interferon gamma; Flt3 agonists such as CDX-301; gepon; nomifensine, peginterferon alfa-2a, peginterferon alfa-2b, RPI-MN.

[0266] Bispecific and trispecific natural killer (NK) cell engagers

[0267] In various embodiments, the anti-HIV gpl20 V3 glycan-directed antibodies or antigen binding fragments described herein are combined with bispecific NK cell engagers (BiKEs) or trispecific NK cell engagers (TriKEs) (e.g., without Fc) or bispecific antibodies (e.g., with Fc) directed against NK cell activating receptors such as CD16A, C-type lectin receptors (CD94 / NKG2C, NKG2D, NKG2E / H, and NKG2F), natural cytotoxicity receptors (NKp30, NKp44, and NKp46), killer cell C-type lectin-like receptors (NKp65, NKp80), Fc receptors FcyR (which mediate antibody-dependent cellular cytotoxicity), SLAM family receptors (e.g., 2B4, SLAM6, and SLAM7), killer cell immunoglobulin-like receptors (KIR) (KIR-2DS and KIR-3DS), DNAM-1, and CD137 (4-1BB). Exemplary anti-CD16 bispecific antibodies, BiKEs, or TriKEs that can be co-administered include AFM26 (BCMA / CD16A) and AFM-13 (CD16 / CD30). Optionally, the anti-CD16 binding bispecific molecules can or can not have an Fc. BiKEs and TriKEs are described, e.g., in Felices et al., Methods Mol Biol. 2016; 1441:333-346; Fang et al., Semin Immunol. 2017; 31:37-54. Examples of trispecific NK cell engagers (TRiKEs) include OXS-3550 and CD16-IL-15-B7H3 TriKe.

[0268] Phosphatidylinositol 3-kinase (PI3K) inhibitors

[0269] In certain embodiments, an anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment described herein is combined with a PI3K inhibitor. Examples of PI3K inhibitors include idelalisib, alpelisib, buparlisib, CAI orotic acid, copanlisib, duvelisib, gedatolisib, neratinib, panulisib, perifosine, pictilisib, pilaralisib, plinabulin mesylate, rigosiltib, rigosiltib sodium, sonolisib, taselisib, AMG-319, AZD-8186, BAY-1082439, CLR-1401, CLR-457, CUDC-907, DS-7423, EN-3342, GSK-2126458, GSK-2269577, GSK-2636771, INCB-040093, LY-3023414, MLN-1117, PQR-309, RG-7666, RP-6530, RV-1729, SAR-245409, SAR-260301, SF-1126, TGR-1202, UCB-5857, VS-5584, XL-765, and ZSTK-474.

[0270] Alpha-4 / beta-7 antagonists

[0271] In certain embodiments, an anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment described herein is combined with an alpha-4 / beta-7 antagonist. Examples of integrin alpha-4 / beta-7 antagonists include PTG-100, TRK-170, atorulimab, etrolizumab, metelimumab, and vedolizumab.

[0272] Pharmacokinetic enhancers

[0273] In certain embodiments, an anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment described herein is combined with a pharmacokinetic enhancer. Examples of pharmacokinetic enhancers include cobicistat and ritonavir.

[0274] Additional therapeutic agents

[0275] Examples of additional therapeutic agents include the compounds disclosed in WO 2004 / 096286 (Gilead Sciences); WO 2006 / 015261 (Gilead Sciences); WO 2006 / 110157 (Gilead Sciences); WO 2012 / 003497 (Gilead Sciences); WO 2012 / 003498 (Gilead Sciences); WO 2012 / 145728 (Gilead Sciences); WO 2013 / 006738 (Gilead Sciences); WO 2013 / 159064 (Gilead Sciences); WO 2014 / 100323 (Gilead Sciences), US 2013 / 0165489 (University of Pennsylvania), US 2014 / 0221378 (Japan Tobacco), US 2014 / 0221380 (Japan Tobacco); WO 2009 / 062285 (Boehringer Ingelheim); WO 2010 / 130034 (Boehringer Ingelheim); WO 2013 / 006792 (Pharma Resources), US 20140221356 (Gilead Sciences), US 20100143301 (Gilead Sciences and WO 2013 / 091096 (Boehringer Ingelheim).

[0276] HIV combination therapy

[0277] In one embodiment, the anti-HIV 120 V3 glycan-directed antibody or antigen binding fragment described herein is combined with one, two, three, four or more additional therapeutic agents selected from (Atripla® (efavirenz, tenofovir disoproxil fumarate and emtricitabine); (Atripla® (efavirenz, tenofovir disoproxil fumarate and emtricitabine); (Atripla® (efavirenz, tenofovir disoproxil fumarate and emtricitabine); (Atripla® (efavirenz, tenofovir disoproxil fumarate and emtricitabine); (Atripla® (efavirenz, tenofovir disoproxil fumarate and emtricitabine); (Atripla® (efavirenz, tenofovir disoproxil fumarate and emtricitabine); (Atripla® (efavirenz, tenofovir disoproxil fumarate and emtricitabine); (Tenofovir alafenamide, emtricitabine, cobistatin and ertiravir); Adefovir; Adefovir dipyridamole; Cobistatin; Emtricitabine; Tenofovir; Tenofovir disoproxil fumarate; Tenofovir disoproxil fumarate; Tenofovir alafenamide hemifumarate; (Durutexvir, Abacavir and Lamivudine); Durutvir, Abacavir Sulfate and Lamivudine; Rettagvir; Rettagvir and Lamivudine; Maraviro; Enfuvirtide; ( Lopinavir and ritonavir); (Zidovudine and Lamivudine; AZT+3TC); ( Abacavir sulfate and lamivudine; ABC+3TC); (Abacavir sulfate, zidovudine, and lamivudine; ABC+AZT+3TC); Rilpivirine; Rilpivirine hydrochloride; Atazanavir sulfate and cobistat; Atazanavir and cobistat; Duriravir and cobistat; Atazanavir; Atazanavir sulfate; Dulutevir; Ertirapvir; Ritonavir; Atazanavir sulfate and Ritonavir; Duriravir; Lamivudine; α1-protease inhibitor; Fosanavir; Fosanavir calcium efavirenz; Etravirine; Nefernavir mesylate; Interferon; Didanoxin Stavudine; Indinavir; Indinavir sulfate; Tenofovir and Lamivudine; Zidovudine; Nevirapine; Saquinavir; Saquinavir mesylate; Aldehyde interleukin; Zacitabine; Telanavir; Ampravir; Delavudine; Delavudine mesylate; Radha-108 (receptol); Lamivudine and Tenofovir disoproxil fumarate; Efavirex, Lamivudine and Tenofovir disoproxil fumarate; Aziphosphonate; Lamivudine, Nevirapine and Zidovudine; Abacavir; and Abacavir sulfate.

[0278] Those skilled in the art will understand that the additional therapeutic agents listed above may include more than one of the categories listed above. Specific categories are not intended to limit the function of the compounds listed in those categories.

[0279] In one embodiment, an anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment described herein is combined with a nucleoside or nucleotide inhibitor of HIV reverse transcriptase and a non-nucleoside inhibitor of HIV reverse transcriptase. In another embodiment, an anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment described herein is combined with a nucleoside or nucleotide inhibitor of HIV reverse transcriptase and an HIV protease inhibiting compound. In a further embodiment, an anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment described herein is combined with a nucleoside or nucleotide inhibitor of HIV reverse transcriptase, a non-nucleoside inhibitor of HIV reverse transcriptase, and a pharmacokinetic enhancer. In certain embodiments, an anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment described herein is combined with at least one nucleoside inhibitor of HIV reverse transcriptase, an integrase inhibitor, and a pharmacokinetic enhancer. In another embodiment, an anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment described herein is combined with two nucleoside or nucleotide inhibitors of HIV reverse transcriptase.

[0280] In one embodiment, an anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment described herein is combined with abacavir sulfate, tenofovir, tenofovir disoproxil, tenofovir disoproxil fumarate, tenofovir disoproxil hemifumarate, tenofovir alafenamide, or tenofovir alafenamide hemifumarate.

[0281] In one embodiment, an anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment described herein is combined with tenofovir, tenofovir disoproxil, tenofovir disoproxil fumarate, tenofovir alafenamide, or tenofovir alafenamide hemifumarate.

[0282] In one embodiment, an anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment described herein is combined with a first additional therapeutic agent selected from the group consisting of: abacavir sulfate, tenofovir, tenofovir disoproxil, tenofovir disoproxil fumarate, tenofovir alafenamide, and tenofovir alafenamide hemifumarate, and a second additional therapeutic agent selected from the group consisting of: emtricitabine and lamivudine.

[0283] In one embodiment, an anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment described herein is combined with a first additional therapeutic agent selected from the group consisting of tenofovir, tenofovir disoproxil, tenofovir disoproxil fumarate, tenofovir alafenamide, and tenofovir alafenamide hemifumarate, and a second additional therapeutic agent, wherein the second additional therapeutic agent is emtricitabine.

[0284] In certain embodiments, an anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment described herein is combined with one or more additional therapeutic agents in a therapeutically effective dose, for example, in the range of 1 mg to 50 mg, 75 mg, 100 mg, 150 mg, 200 mg, 250 mg, 300 mg, 400 mg, 500 mg, 1000 mg, or 1500 mg of the anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment. In certain embodiments, an anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment described herein is combined with one or more additional therapeutic agents in a therapeutically effective dose, for example, in the range of about 0.1 mg / kg to about 0.5 mg / kg, 1 mg / kg, 2 mg / kg, 3 mg / kg, 4 mg / kg, 5 mg / kg, 8 mg / kg, 10 mg / kg, 15 mg / kg, 20 mg / kg, 25 mg / kg, 30 mg / kg, 35 mg / kg, 40 mg / kg, 45 mg / kg, or 50 mg / kg of the anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment. In certain embodiments, an anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment described herein is combined with one or more additional therapeutic agents in a therapeutically effective dose, for example, in the range of about 5 mg to about 10 mg, 20 mg, 25 mg, 50 mg, 100 mg, 125 mg, 150 mg, 250 mg, 300 mg, 500 mg, 1000 mg, or 1500 mg of the anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment.

[0285] In certain embodiments, an anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment described herein is combined with 5 mg-30 mg of tenofovir alafenamide fumarate, tenofovir alafenamide hemifumarate, or tenofovir alafenamide, and 200 mg of emtricitabine. In certain embodiments, an anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment described herein is combined with 5 mg-10 mg, 5 mg-15 mg, 5 mg-20 mg, 5 mg-25 mg, 25 mg-30 mg, 20 mg-30 mg, 15 mg-30 mg, or 10 mg-30 mg of tenofovir alafenamide fumarate, tenofovir alafenamide hemifumarate, or tenofovir alafenamide, and 200 mg of emtricitabine. In certain embodiments, an anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment described herein is combined with 10 mg of tenofovir alafenamide fumarate, tenofovir alafenamide hemifumarate, or tenofovir alafenamide, and 200 mg of emtricitabine. In certain embodiments, an anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment described herein is combined with 25 mg of tenofovir alafenamide fumarate, tenofovir alafenamide hemifumarate, or tenofovir alafenamide, and 200 mg of emtricitabine. In some embodiments, an anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment described herein is combined with any of the agents provided herein at any dosage of the anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment (e.g., 1 mg to 500 mg of the anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment, as described herein) as if each and every combination of dosage were individually and specifically listed.

[0286] In certain embodiments, an anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment described herein is combined with 200 mg - 400 mg of tenofovir disoproxil fumarate, tenofovir disoproxil hemifumarate, or tenofovir disoproxil, and 200 mg of emtricitabine. In certain embodiments, an anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment described herein is combined with 200 mg - 250 mg, 200 mg - 300 mg, 200 mg - 350 mg, 250 mg - 350 mg, 250 mg - 400 mg, 350 mg - 400 mg, 300 mg - 400 mg, or 250 mg - 400 mg of tenofovir disoproxil fumarate, tenofovir disoproxil hemifumarate, or tenofovir disoproxil, and 200 mg of emtricitabine. In certain embodiments, an anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment described herein is combined with 300 mg of tenofovir disoproxil fumarate, tenofovir disoproxil hemifumarate, or tenofovir disoproxil, and 200 mg of emtricitabine. The anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment can be combined with the agents provided herein at any dose (e.g., 1 mg to 500 mg of the anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment), as if each combination of dose were specifically and individually listed.

[0287] Long-acting HIV inhibitors

[0288] In some embodiments, an anti-HIV gpl20 V3 glycan-directed antibody or antigen binding fragment described herein can be co-administered with a long-acting HIV inhibitor. Examples of drugs being developed as long-acting HIV inhibitors include, but are not limited to, cabotegravir LA, rilpivirine LA, any integrase LA, VM-1500 LAI, maraviroc (LAI), tenofovir implant, MK-8591 implant, long-acting dolutegravir.

[0289] In one embodiment, the kit comprises an anti-HIV 120 V3 glycan-directed antibody or antigen binding fragment described herein, and one or more (e.g., one, two, three, one or two, or one to three) additional therapeutic agents.

[0290] HIV vaccines

[0291] In certain embodiments, the anti-HIV gp120 V3 glycan-directed antibodies or antigen-binding fragments described herein are combined with an HIV vaccine. Examples of HIV vaccines include peptide vaccines, recombinant subunit protein vaccines, live vector vaccines, DNA vaccines, HIV MAG DNA vaccines, CD4-derived peptide vaccines, vaccine combinations, adenoviral vector vaccines (e.g., Ad5, Ad26, or Ad35), simian adenoviruses (chimpanzee, gorilla, rhesus macaque, i.e., rhAd), adeno-associated viral vector vaccines, chimpanzee adenovirus vaccines (e.g., ChAdOX1, ChAd68, ChAd3, ChAd63, ChAd83, ChAd155, ChAd157, Pan5, Pan6, Pan7, Pan9), coxsackievirus-based vaccines, enterovirus-based vaccines, gorilla adenovirus vaccines, lentiviral vector-based vaccines, two- or three-part arenavirus-based vaccines (e.g., LCMV, Pichinde virus), trimer-based HIV-1 vaccines, measles virus-based vaccines, flavivirus vector-based vaccines, tobacco mosaic virus vector-based vaccines, varicella zoster virus-based vaccines, human parainfluenza virus 3 (PIV3)-based vaccines, poxvirus-based vaccines (modified vaccinia Ankara (MVA), NYVAC derived from orthopoxvirus, and ALVAC (Avianpox virus) strain of canarypox virus); fowlpox virus-based vaccines, rhabdovirus-based vaccines such as vesicular stomatitis virus (VSV) and Maraba virus; recombinant human CMV (rhCMV)-based vaccines, alpha-virus-based vaccines such as Semliki forest virus, Venezuelan equine encephalitis virus, and Sindbis virus (see, e.g., Lauer et al., Clin Vaccine Immunol., 2017, Vol. 24, No. 1, pp. e00298-16). LNP-formulated mRNA-based therapeutic vaccines; and LNP-formulated self-replicating / self-amplifying RNA vaccines.

[0292] Examples of HIV vaccines include, but are not limited to, Anti-CD40.Env-gp140 vaccine, Ad4-EnvC150, BG505 SOSIP.664 gp140 adjuvanted vaccine, BG505 SOSIP.GT1.1 gp140 adjuvanted vaccine, Chimigen HIV vaccine, ConMSOSIP.v7 gp140, rgp120 (AIDSVAX), ALVAC HIV (vCP1521) / AIDSVAX B / E (gp120) (RV144), monomeric gp120 HIV-1 subtype C vaccine, MPER-656 liposomal subunit vaccine, Remune, ITV-1, Contre Vir, Ad5-ENVA-48, DCVax-001 (CDX-2401), Vacc-4x, Vacc-C5, VAC-3S, polyvalent DNA recombinant adenovirus-5 (rAd5), rAd5 gag-pol env A / B / C vaccine, Pennvax-G, Pennvax-GP, Pennvax-G / MVA-CMDR, HIV-TriMix-mRNA vaccine, HIV-LAMP-vax, Ad35, Ad35-GRIN, NAcGM3 / VSSP ISA-51, poly ICLC adjuvanted vaccine, TatImmune, GTU-multiHIV (FIT-06), ChAdV63.HIVconsv, gp140[delta]V2.TV1 + MF-59, rVSVIN HIV-1 gag vaccine, SeV-EnvF, SeV-Gag vaccine, AT-20, DNK-4, ad35-Grin / ENV, TBC-M4, HIVAX, HIVAX-2, N123-VRC-34.01 epitope-based HIV vaccine inducing, NYVAC-HIV-PT1, NYVAC-HIV-PT4, DNA-HIV-PT123, rAAV1-PG9DP, GOVX-B11, GOVX-B21, GOVX-C55, TVI-HIV-1, Ad-4 (Ad4-env clade C + Ad4-mGag), Paxvax, EN41-UGR7C, EN41-FPA2, ENOB-HV-11, PreVaxTat, AE-H, MYM-V101, CombiHIVvac, ADVAX, MYM-V201, MVA-CMDR, MagaVax, DNA-Ad5 gag / pol / nef / nev (HVTN505), MVATG-17401, ETV-01, CDX-1401, DNA and Sev vector vaccines expressing SCaVII, rcAD26.MOS1.HIV-Env, Ad26.Mod.HIV vaccine, Ad26.Mod. HIV + MVA mosaic vaccine + gp140, AGS-004, AVX-101, AVX-201, PEP-6409, SAV-001, ThV-01, TL-01, TUTI-16, VGX-3300, VIR-1111, IHV-001, and virus-like particle vaccines such as Pseudovirus particle vaccine, CombiVICHvac, LFn-p24 B / C fusion vaccine, GTU-based DNA vaccine, HIV gag / pol / nef / env DNA vaccine, Anti-TAT HIV vaccine, Binding polypeptide vaccine, Dendritic cell vaccine, gag-based DNA vaccine, GI-2010, gp41 HIV-1 vaccine, HIV vaccine (PIKA adjuvant), Ii-key / MHC class II epitope hybrid peptide vaccine, ITV-2, ITV-3, ITV-4, LIPO-5, Poly- clade Env vaccine, MVA vaccine, Pennvax-GP, pp71-deficient HCMV vector HIV gag vaccine, Recombinant peptide vaccine (HIV infection), NCI, rgp160 HIV vaccine, RNActive HIV vaccine, SCB-703, Tat Oyi vaccine, TBC-M4, Therapeutic HIV vaccine, UBI HIV gp120, Vacc-4x + romidepsin, Variant gp120 polypeptide vaccine, rAd5 gag-pol env A / B / C vaccine; DNA.HTI and MVA.HTI, VRC-HIVDNA016-00-VP + VRC-HIVADV014-00-VP, INO-6145, JNJ-9220, gp145C.6980; eOD-GT8 60mer-based vaccine, PD-201401, ENV (A, B, C, A / E) / gag (C) DNA vaccine, gp120 (A, B, C, A / E) protein vaccine, PDPHV-201401, Ad4-EnvCN54, EnvSeq-1 Env HIV-1 vaccine (GLA-SE adjuvant), HIV p24 gag primer boost plasmid DNA vaccine, HIV-1 iglb12 neutralizing VRC-01 antibody stimulating anti-CD4 vaccine, MVA-BN HIV-1 vaccine regimen, UBI HIV gp120, mRNA-based prophylactic vaccine, VPI-211, and TBL-1203HI.

[0293] Birth control (contraceptives) combination therapy

[0294] In certain embodiments, the anti-HIV gpl20 V3 glycan-directed antibodies or antigen binding fragments described herein are combined with a birth control or contraceptive regimen. Therapeutic agents for controlling birth (contraceptives) include cyproterone acetate, desogestrel, dienogest, drospirenone, estradiol valerate, ethinyl estradiol, norethindrone, etonogestrel, levomefesine, levonorgestrel, lynestrenol, medroxyprogesterone acetate, mestranol, mifepristone, misoprostol, nomegestrol acetate, norethisterone, norgestimate, ormeloxifene, segestersone acetate, ulipristal acetate, and any combination thereof.

[0295] Gene therapy and cell therapy

[0296] In certain embodiments, the anti-HIV gpl20 V3 glycan-directed antibodies or antigen binding fragments described herein are combined with a gene or cell therapy regimen. Gene therapy and cell therapy include, but are not limited to, gene modification to silence genes; gene methods to directly kill infected cells; infusion of immune cells designed to replace a large portion of a patient’s own immune system to enhance the immune response to infected cells, or to activate a patient’s own immune system to kill infected cells, or to find and kill infected cells; gene methods to modify the activity of cells to further alter the endogenous immune response to infection. Examples of cell therapy include LB-1903, ENOB-HV-01, GOVX-B01, and SupTl cell-based therapies. Examples of dendritic cell therapy include AGS-004. CCR5 gene editing agents include SB-728T. CCR5 gene inhibitors include Cal-1. In some embodiments, C34-CCR5 / C34-CXCR4 expressing CD4 positive T cells are co-administered with the anti-HIV gpl20 V3 glycan-directed antibodies or antigen binding fragments. In some embodiments, the anti-HIV gpl20 V3 glycan-directed antibodies or antigen binding fragments are co-administered with AGT-103-transduced autologous T cell therapy or AAV-eCD4-Ig gene therapy.

[0297] Gene editors

[0298] In certain embodiments, the anti-HIV gpl20 V3 glycan-directed antibodies or antigen binding fragments described herein are combined with a gene editor, such as an HIV-targeting gene editor. In various embodiments, the genome editing system can be selected from the group consisting of: a CRISPR / Cas9 complex, a zinc finger nuclease complex, a TALEN complex, a homing endonuclease complex, and a meganuclease complex. Exemplary HIV-targeting CRISPR / Cas9 systems include, but are not limited to, EBT-101.

[0299] CAR-T cell therapy

[0300] In some embodiments, the anti-HIV gpl20 V3 glycan-directed antibodies or antigen binding fragments described herein can be co-administered with a population of immune effector cells engineered to express a chimeric antigen receptor (CAR), wherein the CAR comprises an HIV antigen binding domain. The HIV antigen includes HIV envelope protein or a portion thereof, gpl20 or a portion thereof, CD4 binding site on gpl20, CD4 induced binding site on gpl20, N-glycan on gpl20, V2 of gpl20, membrane proximal region on gp41. The immune effector cell is a T cell or a NK cell. In some embodiments, the T cell is a CD4+ T cell, a CD8+ T cell, or a combination thereof. The cell can be autologous or allogeneic. Examples of HIV CAR-T include switchable CAR-T, VC-CAR-T, anti-CD4 CART cell therapy, autologous hematopoietic stem cells genetically engineered to express a CD4 CAR, and C46 peptide.

[0301] TCR-T cell therapy

[0302] In certain embodiments, the anti-HIV gpl20 V3 glycan-directed antibodies or antigen binding fragments described herein are combined with a population of TCR-T cells. The TCR-T cells are engineered to target an HIV-derived peptide present on the surface of a virally infected cell.

[0303] 6. Kits

[0304] Also provided are kits for performing the diagnostic and therapeutic methods as described herein. In some embodiments, the kit includes primers for amplifying and sequencing at least the gp120 V3 glycan region of an HIV species in a biological sample. In some embodiments, the kit includes one or a set of nested primers for amplifying and sequencing at least the gp120 V3 glycan region of an HIV species in a biological sample. In some embodiments, the kit includes a pair of primers or a set of nested primers for amplifying and sequencing full-length gp120. In some embodiments, the kit includes sample preparation, nucleic acid quantification, amplification, and / or sequencing reagents, such as nucleic acid isolation reagents to isolate RNA and / or DNA, protein denaturation solvents, buffers, dNTPs, reverse transcriptase, polymerase, and / or detection tags. In some embodiments, the kit includes library preparation reagents, such as barcoding reagents and / or target-specific primers. In some embodiments, the kit includes analysis guidelines and / or software, such as to facilitate the practice of the diagnostic methods described herein. In some embodiments, the kit includes instructions for sequencing at least the gp120 V3 glycan region of an HIV species in a biological sample and detecting or identifying an HIV species expressing a gp120 comprising a glycosylated asparagine at a position corresponding to amino acid residue position 332 (N332 glycan), an aspartic acid at a position corresponding to amino acid residue position 325 (D325), and one or more amino acid residues selected from the group consisting of: a threonine at a position corresponding to amino acid residue position 63 (T63), a leucine at a position corresponding to amino acid residue position 179 (L179), a threonine at a position corresponding to amino acid residue position 320 (T320), and a histidine at a position corresponding to amino acid residue position 330 (H330), wherein the amino acid positions are with reference to SEQ ID NO: 4 (i.e., residues 1-511 of NCBI Reference Sequence No. NP_057856.1), as described herein.

[0305] In one embodiment, the kit comprises one or more pharmaceutical pack(s) comprising one or more containers (e.g., vials, ampules, pre-loaded syringes) containing one or more components of a pharmaceutical composition described herein, such as an antibody or antigen-binding fragment thereof directed against an HIV gpl20 V3 glycan region, or one or more polynucleotides encoding such an antibody or antigen-binding fragment, as provided herein. In some cases, the kit comprises a pharmaceutical composition described herein. In some embodiments, the kit comprises one or more containers comprising an antibody or antigen-binding fragment thereof directed against an HIV gpl20 V3 glycan region, or one or more polynucleotides encoding such an antibody or antigen-binding fragment, in aqueous solution or lyophilized form. Optionally associated with such container(s) can be a notice in the form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals or biological products, reflecting approval by the agency of the manufacture, use or sale of the

[0306] Examples

[0307] The following examples are provided to illustrate, but not limit, the application protected by the claims.

[0308] Example 1

[0309] Identification of HIV infected patients responsive to therapy with an antibody or antigen binding fragment thereof directed against the HIV gp120 V3 glycan Table 1

[0310] This example demonstrates the identification of Env genotypes associated with susceptibility of viruses to neutralization by PGT121 and its derivative GS-9722 (ebrubercept) for pre-screening of HIV-infected subjects for PGT121 / GS-9722 susceptibility.

[0311] High levels of sequence diversity in the HIV envelope gene make pre-screening of subjects for clinical trials of broadly neutralizing antibodies (bNAbs) attractive to increase the likelihood of high response rates. To identify Env genotypes that predict susceptibility of viruses to PGT121 and GS-9722, we examined 206 clade B Envs for PGT121 and GS-9722 neutralization data and corresponding Env sequences.

[0312] GS-9722 is an engineered variant of PGT121 that maintains the same neutralization activity as PGT121, as evidenced by the highly statistically significant correlation of neutralization IC50s of PGT121 and GS-9722 in 397 HIV strains tested with PGT121 and GS-9722 (r 2= 0.9698, P < 0.0001). Thus, we combined the GS-9722 neutralization data obtained for 140 clade B Env isolates from viremic subjects enrolled in Gilead-sponsored clinical trials with published PGT121 neutralization data (n = 66) obtained from the Los Alamos HIV sequence database to increase statistical power.

[0313] Full-length Env amino acid sequences were aligned using ClustalW and manually adjusted upon visual inspection. To identify genotypes associated with susceptibility to PGT121 / GS-9722 neutralization, we compared the frequency of amino acids and potential N-linked glycosylation sites (PNGS) at each residue in PGT121 / GS-9722 sensitive viruses to the frequency in PGT121 / GS-9722 resistant viruses by Fisher's exact test. The N-linked glycosylation motif is N-X-S / T, where X is any residue except proline. Susceptibility to neutralization by PGT121 / GS-9722 was defined as IC50< 1 pg / mL. For residues statistically significantly associated with susceptibility to PGT121 / GS-9722, the positive predictive value (PPV; i.e., the probability that Env is susceptible to PGT121 / GS-9722 when the genotype is present) and the sensitivity (i.e., the probability that the genotype is present when Env is susceptible to PGT121 / GS-9722) were calculated as follows:

[0314] 2x2 table for calculating PPV, NPV, sensitivity, and specificity of PGT121 / GS-9722 susceptibility genotype determinants

[0315] Table 2 Individual genotypes associated with susceptibility to PGT121 / GS-9722 neutralization in clade B Env

[0316]

[0317]

[0318]

[0319] Mann-Whitney tests were also applied to identify determinants of susceptibility independent of the 1 pg / mL cutoff defining Env as "susceptible" versus "resistant".

[0320] Table 2 lists residues statistically associated with PGT121 / GS-9722 susceptibility and / or previously reported to be associated with PGT121 susceptibility, ranked by decreasing PPV. Among the previously reported residues conferring PGT121 susceptibility, 307I, 295PNGS, and 300PNGS were not statistically associated with PGT121 / GS-9722 susceptibility in this clade B dataset. We identified a number of previously unreported residues that were significantly associated with PGT121 / GS-9722 susceptibility.

[0321] Figure 1

[0322] Table 3

[0323]

[0324] 1 Viral genotype, indicating the presence of specific amino acid residues translated from the HIV envelope gene

[0325] Residues reported in the literature to confer PGT121 neutralization susceptibility (Julg et al., Sci Transl Med., 2017, vol. 9, p. 408).

[0326] Since epitopes are composed of more than one residue, combinations of genotypic determinants statistically associated with PGT121 / GS-9722 susceptibility were evaluated to see if combining individual genotypic determinants would improve PPV by preferentially enriching true positives over false positives. Sensitivity was also considered, since genotypes with low sensitivity would require screening a larger number of subjects in order to enroll a sufficient number of subjects in a clinical trial.

[0327] Combinatorial genotypes providing the highest PPV and sensitivity are listed in Table 3 and shown in Figure Individual genotypes and combined genotypes associated with susceptibility to PGT121 / GS-9722 neutralization in clade B Env Several combinatorial genotypes incorporating previously unreported genotypes associated with PGT121 / GS-9722 neutralization susceptibility provided a higher PPV than was obtainable using only previously described genotypes. The highest PPV obtained was 98.4% for viruses containing amino acids N332 glycan / D325 / H330 / T63 / T320 / L179, which is a 57% increase over the positive predictive value of 62.6% without genotype selection.

[0328] Table 4

[0329] Individual genotypes and combined genotypes associated with susceptibility to PGT121 neutralization in clade A Env Table 5

[0330]

[0331] 1 Viral genotype indicating the presence of specific amino acid residues translated from the HIV envelope gene

[0332] 3 None, indicating that the 66 clade A viruses did not select for specific amino acids in the HIV envelope gene

[0333] *Indicates a genotype composed of residues previously reported in the literature to be associated with susceptibility to PGT121 See, e.g., Julg et al., Sci Transl Med., 2017, vol. 9, p. 408.

[0334] Using neutralization data and corresponding Env sequences for 66 clade A Env and 258 clade C Env, the combined genotype of PGT121 / GS-9722 for clade B in Table 3 was used to determine PPV, sensitivity, and prevalence for clade A (Table 4) and clade C (Table 5). The clade A and clade C datasets are publicly available data obtained from the Los Alamos HIV Sequence Database. The highest PPV obtained for clade A was 93.8% (for viruses containing amino acids N332 glycan / D325 / H330 / T320 / L179), which is an 88% increase from the positive predictive value of 50% without genotype selection. The highest PPV obtained for clade C was 89.3% (for viruses containing amino acids N332 glycan / D325 / H330 / T320 / L179), which is a 53% increase from the positive predictive value of 58.5% without genotype selection.

[0335] Individual genotypes and combined genotypes associated with susceptibility to PGT121 neutralization in clade C Env

[0336] Table 6

[0337]

[0338] 1 Viral genotype indicating the presence of specific amino acid residues translated from the HIV envelope gene

[0339] 2 None, indicating that the 66 clade A viruses did not select for specific amino acids in the HIV envelope gene

[0340] Prevalence of individual amino acids in clade A, clade B, and clade C viruses

[0341] Table 7

[0342]

[0343] 1Viral genotype, indicating the presence of specific amino acid residues translated from the HIV envelope gene

[0344] 2 No, indicating that 258 clade C viruses did not select for specific amino acids in the HIV envelope gene

[0345] The prevalence of individual amino acids (T63, L179, T320, D325, H330, N332, NotP333, and S / T334) used in the PGT121 / GS-9722 combination genotype was determined for clade A, clade B, and clade C viral sequences (Table 6). The prevalence of all amino acids was higher than 60% in clade B, clade A except L179 (51.5%) and in clade C except T63 (10.1%).

[0346] Individual genotypes and combined genotypes associated with susceptibility to 10-1074 neutralization in clade B Env

[0347] Figure 1

[0348]

[0349] 1 Based on analysis of 66 clade A, 206 clade B, and 258 clade C viruses from the PGT121 / GS-9722 dataset

[0350] 10-1074 is a broadly neutralizing antibody that targets the V3 glycan region of HIV gp120 and is related to PGT121 / GS-9722. See, e.g., Mouquet et al., Proc Natl Acad Sci U S A. 2012 Nov 20; 109(47): 3268-3277, and Walker et al., Nature. 2011 Sep 22; 477(7365): 466-470. Using neutralization data and corresponding Env sequences of 315 clade B Envs (Table 7), the combination genotype of PGT121 / GS-9722 in Table 3 was used to determine the PPV, sensitivity, and prevalence of 10-1074. This 315 clade B dataset included 143 clade B Envs isolated from viremic subjects enrolled in Gilead-sponsored clinical trials, and 172 clade B Envs from publicly available data obtained from the Los Alamos HIV sequence database. The highest PPV obtained was 100% (for viruses containing amino acids N332 glycan / D325 / H330 / T63 / T320 / L179), which was a 61% increase from the positive predictive value of 62.2% without genotypic selection.

[0351] Figure 2

[0352] Table 8 100% conservation of individual amino acids in ZPHI subjects

[0353]

[0354] 1 Viral genotype, indicating the presence of specific amino acid residues translated from the HIV envelope gene

[0355] 2 None, indicating that the 315 clade B viruses did not select for specific amino acids in the HIV envelope gene

[0356] Subsequently, the highest scoring genotype algorithm (Table 3) was applied to analyze pre-ART plasma samples from HIV-infected individuals from the Zurich Prospective HIV Cohort Study (ZPHI) to predict whether they would be susceptible to GS-9722 treatment. A total of 92 individual plasma samples were analyzed in NGS assays of the HIV envelope gene (GenoSure HIV Envelope RNA Assay, Monogram Biosciences, South San Francisco, CA). If the derived viral sequence contained the amino acid specified by the algorithm without sequence variability (zero sequence variability at the specified position), the subject was characterized as positive for the given genotype. According to these criteria, 47 / 92, 37 / 92, 32 / 92, 27 / 92, 22 / 92, and 16 / 92 subjects were predicted to be susceptible to GS-9722 (Table 3), with corresponding positive predictive values of 80.7%, 83.5%, 86.1%, 91.6%, 93.7%, and 98.4%, respectively. Figure 2 For subjects infected with clade B (59 of 92 subjects), 35 / 59, 27 / 59, 22 / 59, 23 / 59, 18 / 59, and 12 / 59 were predicted to be susceptible to GS-9722 (Table 3), with corresponding positive predictive values of 80.7%, 83.5%, 86.1%, 91.6%, 93.7%, and 98.4%, respectively. Figure 4 For pre-ART plasma samples of all subjects (n = 92) and the subset of subjects infected with clade B (n = 59), 100% conservation (zero sequence variability at the specified position) of each amino acid in the combined genotype for GS-9722 susceptibility prediction (T63, L179, T320, D325, H330, N332, NotP333, and S / T334) was determined (Table 8).

[0357]

[0358] ​ ​

[0359] ​

[0360]

[0361] 1 Analysis of 92 (all subjects) and 59 (clade B subjects) pre-ART plasma samples from ZPHI individuals

[0362] To confirm genotype prediction of sensitivity to GS-9722, viral populations from pre-ART plasma samples from ZPHI were cloned and evaluated in a GS-9722 neutralization assay (PhenoSense HIV Entry Assay, Monogram Biosciences, South San Francisco, CA). Viruses were derived from 29 clade B samples with a positive predictive value of 80.7% or greater. Derived viruses were characterized as GS-9722 sensitive when the IC50 was 1 pg / ml or less. According to these criteria, 25 / 29, 20 / 22, 16 / 18, 18 / 20, 14 / 16, and 10 / 11 viruses were confirmed to be sensitive to GS-9722 ​ ), with corresponding positive predictive values of 80.7%, 83.5%, 86.1%, 91.6%, 93.7%, and 98.4%, respectively (Table 3).

[0363] To further confirm genotype prediction and phenotypic sensitivity to GS-9722, 20 individual viruses from 4 viral populations from pre-ART plasma samples from ZPHI were subcloned and evaluated in a GS-9722 neutralization assay (PhenoSense HIV Entry Assay, Monogram Biosciences, South San Francisco, CA). All individual viruses were sensitive to GS-9722 with IC50s comparable to the population viruses ​ ).

[0364] It is to be understood that the embodiments and implementations described herein are only for illustrative purposes and that various modifications or changes in light thereof will be suggested to persons skilled in the art and they are to be included within the spirit and purview of this patent application and scope of the appended claims. All publications, patents, and patent applications cited herein are hereby incorporated by reference in their entirety for all purposes.

Claims

1. Use of reagents and antibodies or antigen-binding fragments thereof in the preparation of a kit for performing a method of treating a human subject in need of HIV-1 clade B, wherein the reagents identify HIV-1 clade B species having the following viral genotypes: gp120 N332 polysaccharide, D325, and H330, wherein the amino acid positions are referenced to SEQ ID NO:

4. The method includes: a) Using the reagent, identify in plasma samples from the human subjects infected with HIV-1 clade B or HIV-1 clade B population with the gp120 viral genotype; and b) Administering an effective amount of the antibody or its antigen-binding fragment, comprising the amino acid sequences of the VH and VL regions as shown below, to the human subject: i. SEQ ID NO: 400 and 401; ii. SEQ ID NO: 402 and 404; or iii. SEQ ID NO: 405 and 406.

2. The use according to claim 1, wherein the reagent identifies HIV-1 clade B species with the following viral genotypes: gp120: N332 polysaccharide, D325, H330, and T63; or N332 polysaccharide, D325, H330 and T320.

3. The use according to claim 1, wherein the reagent identifies HIV-1 clade B species with the following viral genotypes: gp120: N332 polysaccharide, D325, H330, T63, and T320; or N332 polysaccharide, D325, H330, T320 and L179.

4. The use according to claim 1, wherein 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% of the HIV-1 clade B population contains the viral genotype.

5. The use according to any one of claims 1 to 4, wherein the antibody comprises an Fc region, the Fc region comprising the following amino acids at a specified position according to the EU index number: i. Tyrosine at position 252, threonine at position 254, and glutamic acid at position 256; or ii. Leucine at position 428 and serine at position 434.

6. The use according to any one of claims 1 to 4, wherein the antibody comprises an Fc region containing the following amino acids at designated positions according to EU index numbers: aspartic acid at position 239 and glutamic acid at position 332.

7. The use according to any one of claims 1 to 4, wherein the antibody comprises an Fc region containing the following amino acids at designated positions according to EU index numbers: aspartic acid at position 239, glutamic acid at position 332, and leucine at position 330.

8. The use according to any one of claims 1 to 4, wherein the antibody comprises an Fc region containing the following amino acids at designated positions according to EU index numbers: aspartic acid at position 239, glutamic acid at position 332, and alanine at position 236.

9. The use according to any one of claims 1 to 4, wherein the antibody comprises an Fc region containing the following amino acids at designated positions according to EU index numbers: aspartic acid at position 239, glutamic acid at position 332, alanine at position 236, and leucine at position 330.

10. The use according to any one of claims 1 to 4, wherein the method comprises administering an antigen-binding fragment.

11. The use according to claim 10, wherein the antigen-binding fragment is selected from: scFv, Fab, Fab', F(ab')2 and Fv.

12. The use according to claim 10, wherein the antigen-binding fragment is a bivalent antibody.

13. The use according to any one of claims 1 to 4, wherein the antibody is a multispecific antibody.

14. The use according to any one of claims 1 to 4, wherein the human subject is acutely infected with HIV-1 clade B.

15. The use according to claim 14, wherein the antibody is administered to a human subject with Fiebig stage IV or earlier HIV-1 clade B infection.

16. The use according to claim 14, wherein the antibody is administered to a human subject who has not undergone seroconversion.

17. The use according to any one of claims 1 to 4, wherein the antibody is administered to a human subject infected with HIV-1 clade B in Fiebig stage V or Fiebig stage VI.

18. The use according to any one of claims 1 to 4, wherein the human subject is chronically infected with HIV-1 clade B.

19. The use according to any one of claims 1 to 4, wherein the method further comprises administering to the human subject one or more additional therapeutic agents for treating HIV infection.

20. The use according to any one of claims 1 to 4, wherein the human subject has not received antiretroviral therapy or has discontinued antiretroviral therapy prior to administration of the antibody.

21. The use according to any one of claims 1 to 4, wherein antiretroviral therapy is discontinued after one or more administrations of the antibody or its antigen-binding fragment.

22. The use according to any one of claims 1 to 4, wherein the method further comprises administering one or more antiretroviral therapeutic agents to the human subject.

23. The use according to any one of claims 1 to 4, wherein the method further comprises administering a TLR agonist to the human subject.

24. The use according to claim 23, wherein the TLR agonist is a TLR2 agonist, a TLR3 agonist, a TLR7 agonist, a TLR8 agonist, or a TLR9 agonist.

25. The use according to claim 24, wherein the TLR7 agonist is selected from: vesamidine, imiquimod, and requimod.

26. The use according to any one of claims 1 to 4, wherein the method comprises administering the antibody or an antigen-binding fragment thereof multiple times at predetermined intervals.

27. The use according to claim 26, wherein the antibody or its antigen-binding fragment is administered together with a TLR agonist.

28. The use according to any one of claims 1 to 4, wherein the viral genotype of said gp120 is identified in one or more gp120 polypeptide sequences expressed in HIV-1 clade B or HIV-1 clade B population isolated from said human subject.

29. The use according to any one of claims 1 to 4, wherein the viral genotype of said gp120 is identified in one or more gp120 polynucleotide sequences in HIV-1 clade B or HIV-1 clade B population isolated from said human subject.

30. The use according to claim 29, wherein the method comprises next-generation sequencing of a polynucleotide sequence encoding gp120 from HIV-1 clade B population.

31. Use of the reagent in the preparation of a kit for performing a method for identifying a human subject infected with HIV-1 clade B or an HIV-1 clade B population sensitive to antibodies or antigen-binding fragments thereof, wherein the reagent identifies HIV-1 clade B species having the following viral genotypes: gp120 N332 polysaccharide, D325, and H330, wherein the amino acid positions are referenced to SEQ ID NO:

4. The method includes using the reagent to identify HIV-1 clade B or HIV-1 clade B population with the viral genotype gp120 in a plasma sample from the human subject, wherein the antibody or its antigen-binding fragment comprises the amino acid sequences of the VH and VL regions as shown below, respectively: i. SEQ ID NO: 400 and 401; ii. SEQ ID NO: 402 and 404; or iii. SEQ ID NO: 405 and 406.

32. The use according to claim 31, wherein the reagent identifies HIV-1 clade B species with the following viral genotypes: gp120: N332 polysaccharide, D325, H330, and T63; or N332 polysaccharide, D325, H330 and T320.

33. The use according to claim 31, wherein the reagent identifies HIV-1 clade B species having the following viral genotypes: gp120 N332 polysaccharide, D325, H330, T63, and T320; or N332 polysaccharide, D325, H330, T320 and L179.

34. The use according to claim 31, wherein 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% of the HIV-1 clade B population contains the viral genotype.

35. The use according to any one of claims 31 to 34, wherein the human subject is acutely infected with HIV-1 clade B.

36. The use according to claim 35, wherein the antibody is administered to a human subject with Fiebig stage IV or earlier HIV-1 clade B infection.

37. The use according to claim 36, wherein the antibody is administered to a human subject who has not undergone seroconversion.

38. The use according to any one of claims 31 to 34, wherein the antibody is administered to a human subject infected with HIV-1 clade B in Fiebig stage V or Fiebig stage VI.

39. The use according to any one of claims 31 to 34, wherein the human subject is chronically infected with HIV-1 clade B.

40. The use according to any one of claims 31 to 34, wherein the viral genotype of said gp120 is identified in one or more gp120 polypeptide sequences expressed in HIV-1 clade B or HIV-1 clade B population isolated from said human subject.

41. The use according to any one of claims 31 to 34, wherein the viral genotype of said gp120 is identified in one or more gp120 polynucleotide sequences in HIV-1 clade B or HIV-1 clade B population isolated from said human subject.

42. The use according to claim 41, wherein the method comprises next-generation sequencing of a polynucleotide sequence encoding gp120 from HIV-1 clade B population.

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