WO2014043386A1 - Clonal lineage antibodies - Google Patents

Clonal lineage antibodies Download PDF

Info

Publication number
WO2014043386A1
WO2014043386A1 PCT/US2013/059515 US2013059515W WO2014043386A1 WO 2014043386 A1 WO2014043386 A1 WO 2014043386A1 US 2013059515 W US2013059515 W US 2013059515W WO 2014043386 A1 WO2014043386 A1 WO 2014043386A1
Authority
WO
WIPO (PCT)
Prior art keywords
antibody
chi
hiv
antibodies
lineage
Prior art date
Application number
PCT/US2013/059515
Other languages
French (fr)
Inventor
Barton F. Haynes
John Mascola
Thomas B. Kepler
Hua-Xin Liao
Scott Boyd
Rebecca M. LYNCH
Tongqing Zhou
Peter Kwong
Original Assignee
Duke University
The Government Of The United States Of America As Represented By The Secretary Of The Department Of Health & Human Services
The Board Of Trustees Of The Leland Stanford Junior University
Trustees Of Boston University
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Duke University, The Government Of The United States Of America As Represented By The Secretary Of The Department Of Health & Human Services, The Board Of Trustees Of The Leland Stanford Junior University, Trustees Of Boston University filed Critical Duke University
Publication of WO2014043386A1 publication Critical patent/WO2014043386A1/en

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/08—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses
    • C07K16/10—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses from RNA viruses
    • C07K16/1036—Retroviridae, e.g. leukemia viruses
    • C07K16/1045—Lentiviridae, e.g. HIV, FIV, SIV
    • C07K16/1063—Lentiviridae, e.g. HIV, FIV, SIV env, e.g. gp41, gp110/120, gp160, V3, PND, CD4 binding site
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/12—Antivirals
    • A61P31/14—Antivirals for RNA viruses
    • A61P31/18—Antivirals for RNA viruses for HIV
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/20—Immunoglobulins specific features characterized by taxonomic origin
    • C07K2317/21—Immunoglobulins specific features characterized by taxonomic origin from primates, e.g. man
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
    • C07K2317/76—Antagonist effect on antigen, e.g. neutralization or inhibition of binding

Definitions

  • the present invention relates, in general, to HIV- 1 and, in particular, to broadly neutralizing anti-HIV-1 antibodies (and fragments thereof) and to methods of using same to inhibit HIV-1 infection in a subject (e.g., a human).
  • the invention further relates to compositions comprising such antibodies (or fragments).
  • the invention also relates to methods of using the antibodies (and fragments thereof) as templates for vaccine design.
  • BnAbs broadly neutralizing antibodies
  • Many BnAbs have excessive levels of somatic mutations and undergo complex antibody maturation pathways with large insertional or deletion mutation events that would be difficult to reproduce with a vaccine.
  • many BnAbs are polyreactive and/or have long HCDR3 antibody regions (Haynes et al, Nature Biotech. 30:423-33 (2012)).
  • the present invention results, at least in part, from studies that involved the isolation of a CD4 binding site BnAb clonal lineage (CHI 03 lineage) from an HIV-1 infected patient followed from time of infection to development of BnAbs. These studies were undertaken, in part, to define the earliest stages of BnAb development, and to isolate members of BnAb clonal lineages to a) define the maturation pathway of BnAb development and b) then use the antibodies of the clonal lineage as templates for Env antigen design for optimal immunogens that can be administered to a mammal (e.g., a human) to drive the maturation of such a B cell BnAb lineage.
  • a mammal e.g., a human
  • This clonal lineage contains CD4 binding site BnAbs, contains no unusual insertional mutations, and is only one-half as somatically mutated as VRCOl and VRCCl -like (e.g., CH30-CH34) CD4 binding site BnAbs.
  • the present invention relates to HIV- 1. More specifically, the invention relates to broadly neutralizing anti-HIV- 1 antibodies (and fragments thereof (e.g., antigen-binding fragments)) and to compositions comprising same. The invention also relates to nucleic acids comprising nucleotide sequences encoding such anti HIV-1 antibodies and fragments thereof. The invention further relates to methods of using such antibodies (and fragments thereof) to inhibit HIV-1 infection in a subject (e.g., a human).
  • a subject e.g., a human
  • Figure 7 Clonal lineage tree of Clone CHI 03 from CH0505 - VH mutations.
  • Figure 8 Clonal lineage tree of Clone CHI 03 from CH0505 - binding to 1086.CD7 gpl 20 (EC50 mg/ml).
  • Figure 9 Clonal lineage tree of Clone CHI 03 from CH0505 - binding to 63521.
  • B gpl20 (EC50 Mg/ml).
  • Figure 10 Clonal lineage tree of Clone CHI 03 from CH0505 - binding to 63521.
  • B gpl20 Kd in nM by SPR.
  • FIG. 1 Clonal lineage tree of Clone CH I 03 from CH0505 - neutralization of Tier 1 SF162.B.
  • Figure 12. Clonal lineage tree of Clone CH103 from CH0505 - neutralization of Tier 2 BG1 168.B (EC50, ⁇ g/ml).
  • Figures 21A-21 C Development of CH103-clonal family with time of appearance, VH mutations, affinity for HIV-1 Env, and HIV-1 neutralization.
  • Fig. 21 A Phylogenetic tree rooted from the unmutated common ancestor with time of appearance after transmission and VH mutation percentage indicated.
  • Fig. 2 IB Affinity for HIV-1 gpl20 Env mapped on the phylogenetic tree.
  • Fig. 21 C Neutralization of HIV-1 mapped on the phylogenetic tree.
  • FIGS 22A-22D Structure of antibody CHI 03 in complex with the outer domain of HIV-1 gpl 20 (OD), Fig. 22 A. Overall structure of complex with gpl 20 polypeptide depicted in ribbon representation and CHI 03 shown as a molecular surface. The gpl20 OD is shown in red, with recognizing antibody CH103 shown in green (heavy chain) and blue (light chain). Fig. 22B.
  • Fig. 22C CHI 03 epitope (green) on OD (red) with the initial CD4-binding site superposed (yellow boundaries) in surface representation.
  • Fig. 22D Sequence alignment of HIV- 1 gpl20 outer domains. Secondary structure elements are labeled above the alignment, and residues that contact CHI 03 are highlighted. The sequence of the crystallized gpl 20 is shown on the first line, followed by sequences of diverse gpl20s recognized by CHI 03 (see Fig. 21 B for binding of CHI 03 to these gpl 20s.
  • FIG. 23A CH103 paratope, critical residues, and required immune precursors.
  • Fig. 23A Overall structure of complex with variable domains of CHI 03 depicted in ribbon representation and gpl 20 shown as a molecular surface. The color scheme is the same as Fig. 22A.
  • Fig. 23B CHI 03 paratope surface displayed on top of an underlying polypeptide ribbon. The surface is colored and labeled by contributing antibody components.
  • Fig. 23C CHI 03 paratope surface colored by maturation states of the underlying residues. Unmutated residues are colored magenta while affinity matured residues are colored green and light blue for heavy and light chains respectively.
  • Fig.23D CH103 paratope, critical residues, and required immune precursors.
  • Fig. 23A Overall structure of complex with variable domains of CHI 03 depicted in ribbon representation and gpl 20 shown as a molecular surface. The color scheme is the same as Fig. 22A.
  • Fig. 23B CHI 03 para
  • FIG. 24 Sequences of CHI 03 clonal lineage antibodies: CHI 86, CH I 87, CHI 88, CH200, CH243, CH244, CH245, CH246, CH247 and CH248.
  • HIV-1 BnAbs Induction of HIV-1 BnAbs is a key goal of HIV-1 vaccine development.
  • One main target of HI V vaccine development is the gpl 20 binding site of the HIV-1 receptor, CD4.
  • the VRCOl -class of CD4 binding site antibodies represents one of the most potent BnAbs that bind at this site but share unusual antibody traits that include remarkably high levels of somatic mutations, including mutations that create frequent insertions and deletions.
  • the present invention results, at least in part, from studies that involved the isolation of a CD4 binding site BnAb clonal lineage (CHI 03 lineage) from an HIV-1 infected patient followed from time of infection to development of BnAbs.
  • This clonal lineage contains RSC3+, RSC3Delta371 - CD4 binding site BnAbs, contains no unusual insertional mutations, and is only one-half as somatically mutated as the most CD4 binding site BnAbs.
  • the present invention relates to these BnAbs, and fragments thereof (e.g., antigen-binding fragments), and to methods of using same to inhibit HIV-1 infection in a subject (e.g., a human).
  • the invention also relates to nucleic acids comprising nucleotide sequences encoding such BnAbs and fragments thereof.
  • the invention further relates to a method designed to induce the production of such BnAbs in a subject (e.g., a human), and to immunogens designed using the clonal lineage antibody members suitable for use in such a method. (See also Fig. 20.)
  • B cell lineage immunogen design (Haynes et al. Nature Biotech. 30: 423-433 (2012)).
  • This method is based on the use of clonal lineage antibody members as templates for design of HIV envelope proteins that bind well to lineage members.
  • This method is based on the use of clonal lineage antibody members as templates for design of HIV envelope proteins that bind well to lineage members.
  • This method is based on the principle that those antigens that bind best to na ' ive BnAb B cell receptors (the unmutated ancestors of mature BnAbs) will be the best
  • immunogens for driving such a clonal lineage are isolated, their intermediate ancestor and unmutated ancestor precursors inferred, and the clonal lineage tree reconstructed by Baysian probability statistics and maximum likelihood analysis, and then the tree antibodies are made by recombinant techniques (Haynes et al, Nature Biotech. 30:423-433 (2012)). Then, by screening Envs, or by solving antibody and Env structures and then rational design of Envs that optimally bind to clonal tree members, immunogens are designed and produced for vaccination studies (Haynes et al, Nature Biotech. 30:423-433 (2012)).
  • Envs can be identified that bind optimally to each stage of this clonal lineage and used as a prime and boosts as outlined in Haynes et al (Nature Biotech. 30: 423-433 (2012)).
  • Preferred Envs (63521B delta 1 1 and 1086C delta 7) are described in the Example that follows.
  • An additional optimal strategy is to prime with the transmitted Founder Envelope and then boost with one or more of the sequential envelopes isolated during the course of infection of CH0505 patient.
  • These envs can be administered sequentially or all together in a "swarm' of envs to recreate the high level of mutations that are driving BnAb development, (see U.S. Provisional Application Nos. 61 /700,252, filed September 12, 2012, 61/708,466, filed October 1 , 2012 and 61/764,421 , filed February 13, 2013, the entire contents of each of which are incorporated herein by reference).
  • Preferred antibodies of the invention for therapeutic use include those comprising variable heavy (VH) and light (VL) chain amino acid sequences selected from those shown in Figs. 4, 5 and 24.
  • VH variable heavy
  • VL light chain amino acid sequences selected from those shown in Figs. 4, 5 and 24.
  • either the intact antibody or a fragment thereof can be used.
  • Either single chain Fv, bispecific antibody for T cell engagement, and chimeric antigen receptors can be used (Chow et al, Adv. Exp. Biol. Med. 746: 121 -41 (2012)). That is, for example, intact antibody, a Fab fragment, a diabody, or a bispecific whole antibody can be used to inhibit HIV-1 infection in a subject (e.g., a human).
  • a bispecific F(ab) 2 can also be used with one arm a targeting molecule like CD3 to deliver it to T cells and the other arm the arm of the native antibody (Chow et al, Adv. Exp. Biol. Med. 746: 121-41 (2012)).
  • Toxins that can be bound to the antibodies or antibody fragments described herein include unbound antibody, radioisotopes, biological toxins, boronated dendrimers, and immunoliposomes (Chow et al, Adv. Exp. Biol. Med. 746: 121 -41 , 2012)).
  • Toxins can be conjugated to the antibody or antibody fragment using methods well known in the art (Chow et al, Adv. Exp. Biol. Med.
  • the invention also includes variants of the antibodies (and fragments) disclosed herein, including variants that retain the ability to bind to recombinant Env protein, and methods of using same to, for example, reduce HIV-1 infection risk. Combinations of the antibodies, or fragments thereof, disclosed herein can also be used in the methods of the invention.
  • compositions can comprise the BnAb (or antibody fragment) dissolved or dispersed in a pharmaceutically acceptable carrier (e.g., an aqueous medium).
  • a pharmaceutically acceptable carrier e.g., an aqueous medium.
  • the compositions can be sterile and can be in an injectable form (e.g., a form suitable for intravenous injection).
  • the antibodies (and fragments thereof) can also be formulated as a composition appropriate for topical administration to the skin or mucosa. Such compositions can take the form of liquids, ointments, creams, gels and pastes.
  • the antibodies (and fragments thereof) can also be formulated as a composition appropriate for intranasal administration.
  • the antibodies (and fragments thereof) can be formulated so as to be administered as a post-coital douche or with a condom. Standard formulation techniques can be used in preparing suitable compositions.
  • the BnAbs (and fragments thereof) described herein have utility, for example, in settings including the following:
  • the antibodies described herein (or fragments thereof) in the setting of anticipated known exposure to HIV-1 infection, the antibodies described herein (or fragments thereof) and be administered prophylactically (e.g., IV, topically or intranasally) as a microbiocide,
  • the antibodies described herein in the setting of known or suspected exposure, such as occurs in the setting of rape victims, or commercial sex workers, or in any homosexual or heterosexual transmission without condom protection, can be administered as post-exposure prophylaxis, e.g., IV or topically, and
  • the antibodies described herein in the setting of Acute HIV infection (AHI), can be administered as a treatment for AHI to control the initial viral load or for the elimination of virus-infected CD4 T cells.
  • Suitable dose ranges can depend on the antibody (or fragment) and on the nature of the formulation and route of administration. Optimum doses can be determined by one skilled in the art without undue experimentation. Doses of antibodies in the range of 1 -50 mg/kg can be used.
  • the BnAbs (or antibody fragments) described herein can be administered prior to contact of the subject or the subject's immune system/cells with HIV-1 or within about 48 hours of such contact. Administration within this time frame can maximize inhibition of infection of vulnerable cells of the subject with HIV-1.
  • Antibodies of the invention and fragments thereof can be produced recombmantly using nucleic acids comprising nucleotide sequences encoding VH and VL sequences selected from those shown in Figs 4, 5 and 24.
  • the antibody profile of the CH505 patient sera shows that they bind with resurfaced stabilized core 3 (RSC3+) and not with RSC3delta 371 protein.
  • This pattern is that of serum reactivity pattern of CD4 binding site BnAbs and is associated in this patent with a breadth of neutralization, as manifested by neutralization of all 6 isolates in the lower right box, are shown in Fig. 1.
  • Fig. 2 shows broad neutralization breadth of tier 2 HIV-1 strains with inhibitory concentration 50% (IC50) values shown in the boxes.
  • CH505 new mabs CHI 03, CH I 04, and CHI 06 mAbs have breadth for tier 2 HIV strains and, as well, have selective binding to the RSC3 protein but not to RSC3delta 371 , as seen in the CH0505 patient sera in Fig. 1 (mAb binding data not shown).
  • the clonal lineage members of clonal lineage 103 from patient CH0505 are shown in Fig. 3. Three of the VHs (1ASCETI5VH, 1AH92UVH, 1 A102R16VH) are from 454 deep sequencing of CH0505 B cell mRNA. The pairing of VH and VL chains for all members of the clonal lineage are shown.
  • Fig. 4 shows alignment of the antibody heavy variable chain (VH) sequences of clonal lineage 103. There are no insertions or deletions in the VHs, Fig. 5 shows alignment of the antibody light variable chain (VL) sequences of clonal lineage 103. There are no insertion or deletions in the VLs except for one 3 nucleotide deletion in the LC of CHI 03.
  • VH antibody heavy variable chain
  • VL antibody light variable chain
  • Fig. 6 Shown in Fig. 6 is the clonal lineage tree of Clone CHI 03 from patient CH0505 with time after transmission of mAb isolation noted (137 weeks after enrollment in the CHAVIOOI acute HIV infection protocol), with three sequences obtained from 454 VH sequencing at 62 and 140 weeks after enrollment. 11 -18 show inferred intermediate antibodies.
  • UCA is the unmutated common ancestor antibody.
  • Fig. 8 shows binding of clonal lineage members to the 1086Cdelta 7 gpl 20 Env (see PCT/US2012/045530). That 1 086.C delta 7 gpl20 Env binds to all of the key members of the CHI 03 clonal lineage that lead to BnAbs suggests that 1086C is a candidate Env for B cell lineage immunogen design and iterative improvement in its binding of clonal lineage members.
  • Fig. 9 shows binding of clonal lineage members to the 6352 IB delta 1 1 gpl20 Env (see PCT/US2012/045530). That 63521B delta 1 1 gpl20 Env binds to all of the key members of the CHI 03 clonal lineage that lead to BnAbs suggests that 16352 I B is a candidate Env for B cell lineage immunogen design and iterative improvement in its binding of clonal lineage members. Thus, for this lineage, 6352 I B and 1086C envs can be used as prime and or boosts for inducing such lineage antibodies in mammals. Alternatively, screens of other HIV envs can yield additional Envs with more optimized binding to clonal template members.
  • An additional optimal strategy is to prime with the transmitted Founder Envelope and then boost with one or more of the sequential envelopes isolated during the course of infection of CH0505 patient.
  • These envs could be administered sequentially or all together in a "swarm' of envs to recreate the high level of mutations that are driving BnAb development, (see U.S. Provisional Application entitled “Antibody Evolution Immunogens", filed concurrently herewith (Attorney Docket No. 1579-1832).
  • the affinity of the transmitted founder Env gpl40 of CH0505 for the unmutated ancestor antibody of the CHI 03 lineage has been measured and it was found to be ⁇ 5 nM with an EC50 of 0.7 ⁇ g/ml in ELISA.
  • this env can be a potent immunogen for this lineage.
  • Fig. 1 1 shows the neutralization of tier 1 HIV strain SF162 by clonal lineage members as maturation progresses from left to right with neutralization first seen in the 13 ab.
  • Fig. 12 shows the neutralization of tier 2 HIV strain BGl 168 by clonal lineage members as maturation progresses from left to right with neutralization first seen in the 12 ab.
  • Fig. 14 shows that the CHI 03 clonal lineage IA1 member polyreactivity was determined by the more mature light chain of IA1 and did not occur with the less mature LC of IA2.
  • the CHI 03 clonal lineage early UCA and 1A members are not polyreactive, as determined by reactivity with a panel of autoantigens in the Athena luminex assay (see Fig. 15). In this assay, only mature abs CHI 03, CHI 04 and CHI 06 and the immediately preceding IA1 and IA2 are
  • Figs. 17, 18 and 19 show the SPR histograms that gave rise to the data in Fig. 15.
  • Fig. 16 shows the on rates and off rates of all antibodies in the CHI 03 clonal lineage in binding to the transmitted/founder Env 6352 I B,
  • Fig. 21 Shown in Fig. 21 is the development of the CH103-clonal family with time of appearance, VH mutations, affinity for HIV-1 Env, and HIV-1 neutralization.
  • the VH mutations and the timing of antibodies developed in the CHI 03 clonal lineage after transmission are shown in Fig. 21 A. Shown in Fig.
  • 21 B is the binding by mAbs in the CHI 03 clonal lineage to CH505 autologous T/F Env gpl40 (EC50 mg/ml), the binding to B.63521 gpl20 (EC50 ⁇ g/ml) by mAbs in the CHI 03 clonal lineage, and the binding to C.1086 gpl20 (EC50 ⁇ g/ml) by mAbs in the CHI 03 clonal lineage.
  • Autologous neutralization of tier 2 virus CH505 (IC50, ⁇ g/ml) by mAbs in CH103 clonal lineage is depicted in Fig. 21 C.
  • Fig. 21 C Neutralization of tier 2 virus A.Q842 (IC50, ⁇ g/ml) by mAbs in the CHI 03 clonal lineage is also shown in Fig. 21 C, as is neutralization of tier 2 virus B.BG1 168 (IC50, ⁇ g/ml) by mAbs in CHI 03 clonal lineage
  • Fig. 22 The structure of antibody CHI 03 in complex with the outer domain of HIV-1 gpl 20 (OD) is shown in Fig. 22.
  • Fig. 23 shows the CHI 03 paratope, critical residues, and required immune precursors.
  • Table TZlc shows hydrogen bonds and salt bridges between CH103 and ZM176.66 gpl20.
  • Table TZld lists the CH103 heavy chain residues that interact with ZMl 76.66 gpl20.
  • Table TZle lists the CHI 03 light chain residues that interact with ZM176.66 gpl20.
  • Table TZl f lists the ZMl 76.66 gpl20 residues that interact with CHI 03 heavy chain.
  • Table TZl g lists the ZM176.66 gpl20 residues that interact with CH103 light chain.
  • Table TZld List of CH103 heavy chain residues that interact with Z 176.66 gpl20.
  • Table TZl e List of CH 103 light chain residues that interact with ZM 176.66 gp!20.
  • Table TZlf. List of Z 176.66 gpl20 residues that interact with CH103 heavy chain.

Abstract

The present invention relates, in general, to HIV-1 and, in particular, to broadly neutralizing anti-HIV-1 antibodies (and fragments thereof) and to methods of using same to inhibit HIV-1 infection in a subject (e.g., a human). The invention also relates to compositions comprising such antibodies (or fragments).

Description

CLONAL LINEAGE ANTIBODIES
This application claims priority from U.S. Provisional Application No. 61/700,234, filed September 12, 2012 and U.S. Provisional Application No. 61/708,413, filed October 1 , 2012, the entire contents of each of which are incorporated herein by reference.
This invention was made with government support under Grant No. Uml - AI 100645 awarded by the National Institutes of Health. The government has certain rights in the invention.
TECHNICAL FIELD
The present invention relates, in general, to HIV- 1 and, in particular, to broadly neutralizing anti-HIV-1 antibodies (and fragments thereof) and to methods of using same to inhibit HIV-1 infection in a subject (e.g., a human). The invention further relates to compositions comprising such antibodies (or fragments). The invention also relates to methods of using the antibodies (and fragments thereof) as templates for vaccine design.
BACKGROUND
Induction of high levels of plasma broadly neutralizing antibodies (BnAbs) to the HIV-1 envelope only occurs after years in -10% of chronically HIV-1 infected subjects. Many BnAbs have excessive levels of somatic mutations and undergo complex antibody maturation pathways with large insertional or deletion mutation events that would be difficult to reproduce with a vaccine. In addition, many BnAbs are polyreactive and/or have long HCDR3 antibody regions (Haynes et al, Nature Biotech. 30:423-33 (2012)).
The present invention results, at least in part, from studies that involved the isolation of a CD4 binding site BnAb clonal lineage (CHI 03 lineage) from an HIV-1 infected patient followed from time of infection to development of BnAbs. These studies were undertaken, in part, to define the earliest stages of BnAb development, and to isolate members of BnAb clonal lineages to a) define the maturation pathway of BnAb development and b) then use the antibodies of the clonal lineage as templates for Env antigen design for optimal immunogens that can be administered to a mammal (e.g., a human) to drive the maturation of such a B cell BnAb lineage. This clonal lineage contains CD4 binding site BnAbs, contains no unusual insertional mutations, and is only one-half as somatically mutated as VRCOl and VRCCl -like (e.g., CH30-CH34) CD4 binding site BnAbs.
SUMMARY OF THE INVENTION
In general, the present invention relates to HIV- 1. More specifically, the invention relates to broadly neutralizing anti-HIV- 1 antibodies (and fragments thereof (e.g., antigen-binding fragments)) and to compositions comprising same. The invention also relates to nucleic acids comprising nucleotide sequences encoding such anti HIV-1 antibodies and fragments thereof. The invention further relates to methods of using such antibodies (and fragments thereof) to inhibit HIV-1 infection in a subject (e.g., a human).
Objects and advantages of the present invention will be clear from the description that follows.
BRIEF DESCRIPTION OF THE DRAWINGS
Figure 1. ELIZA profile of CHAVI 505 sera and IC50s of CHAVI 505 sera at week 137.
Figure 2. Neutralization analysis of 3 CH505 HlV-specific mAbs. Figure 3 VH and VL gene family analysis of antibody members in Clonal
103.
Figure 4 Alignment of VH sequences of antibody members in Clonal
103.
Figure 5 Alignment of VL sequences of antibody members in Clonal
103.
Figure 6. Clonal lineage tree of Clone CHI 03 from patient CH0505 with time after transmission of mAb noted and 454 analysis.
Figure 7. Clonal lineage tree of Clone CHI 03 from CH0505 - VH mutations.
Figure 8. Clonal lineage tree of Clone CHI 03 from CH0505 - binding to 1086.CD7 gpl 20 (EC50 mg/ml).
Figure 9. Clonal lineage tree of Clone CHI 03 from CH0505 - binding to 63521. B gpl20 (EC50 Mg/ml).
Figure 10. Clonal lineage tree of Clone CHI 03 from CH0505 - binding to 63521. B gpl20 (Kd in nM by SPR).
Figure 1 1. Clonal lineage tree of Clone CH I 03 from CH0505 - neutralization of Tier 1 SF162.B. Figure 12. Clonal lineage tree of Clone CH103 from CH0505 - neutralization of Tier 2 BG1 168.B (EC50, μg/ml).
Figure 13. Polyreactivity within clonal lineage tree of Clone CHI 03 from CH0505.
Figure 14. Acquisition of HEp-2 cell reactivity of CH505 BnAbs during affinity maturation.
Figure 15. Polyreactivity within clonal lineage tree of Clone CH I 03 from CH0505.
Figure 16. CH103 clonal lineage antibodies binding to 63521 Dl 1 gpl20. Figures 17, 18 and 19. SPR histograms supportive of data in Figure 15.
Figure 20. Path to induction of HIV-1 broad neutralizing antibodies.
Figures 21A-21 C. Development of CH103-clonal family with time of appearance, VH mutations, affinity for HIV-1 Env, and HIV-1 neutralization. Fig. 21 A. Phylogenetic tree rooted from the unmutated common ancestor with time of appearance after transmission and VH mutation percentage indicated. Fig. 2 IB. Affinity for HIV-1 gpl20 Env mapped on the phylogenetic tree.
Fig. 21 C. Neutralization of HIV-1 mapped on the phylogenetic tree.
Figures 22A-22D. Structure of antibody CHI 03 in complex with the outer domain of HIV-1 gpl 20 (OD), Fig. 22 A. Overall structure of complex with gpl 20 polypeptide depicted in ribbon representation and CHI 03 shown as a molecular surface. The gpl20 OD is shown in red, with recognizing antibody CH103 shown in green (heavy chain) and blue (light chain). Fig. 22B.
Superposition of OD (red) and core gpl20 (gray) with polypeptide shown in ribbon representation. Fig. 22C. CHI 03 epitope (green) on OD (red) with the initial CD4-binding site superposed (yellow boundaries) in surface representation. Fig. 22D. Sequence alignment of HIV- 1 gpl20 outer domains. Secondary structure elements are labeled above the alignment, and residues that contact CHI 03 are highlighted. The sequence of the crystallized gpl 20 is shown on the first line, followed by sequences of diverse gpl20s recognized by CHI 03 (see Fig. 21 B for binding of CHI 03 to these gpl 20s.
Figures 23A-23D. CH103 paratope, critical residues, and required immune precursors. Fig. 23A. Overall structure of complex with variable domains of CHI 03 depicted in ribbon representation and gpl 20 shown as a molecular surface. The color scheme is the same as Fig. 22A. Fig. 23B. CHI 03 paratope surface displayed on top of an underlying polypeptide ribbon. The surface is colored and labeled by contributing antibody components. Fig. 23C. CHI 03 paratope surface colored by maturation states of the underlying residues. Unmutated residues are colored magenta while affinity matured residues are colored green and light blue for heavy and light chains respectively. Fig.23D. Sequence alignment of mature CFI103 heavy and light chains from week 137 with germline precursors and maturation intermediates numbered by week of first identification. Framework and CDR residues are labeled, as are residues that interact with the gpl20 (open circle, main chain interaction; open circle with rays, side chain interactions; solid circle, both main chain and side chain interactions). The unmutated paratope residues are hightlighted white with magenta
background. Figure 24. Sequences of CHI 03 clonal lineage antibodies: CHI 86, CH I 87, CHI 88, CH200, CH243, CH244, CH245, CH246, CH247 and CH248.
DETAILED DESCRIPTION OF THE INVENTION
Induction of HIV-1 BnAbs is a key goal of HIV-1 vaccine development. One main target of HI V vaccine development is the gpl 20 binding site of the HIV-1 receptor, CD4. The VRCOl -class of CD4 binding site antibodies represents one of the most potent BnAbs that bind at this site but share unusual antibody traits that include remarkably high levels of somatic mutations, including mutations that create frequent insertions and deletions.
The present invention results, at least in part, from studies that involved the isolation of a CD4 binding site BnAb clonal lineage (CHI 03 lineage) from an HIV-1 infected patient followed from time of infection to development of BnAbs. This clonal lineage contains RSC3+, RSC3Delta371 - CD4 binding site BnAbs, contains no unusual insertional mutations, and is only one-half as somatically mutated as the most CD4 binding site BnAbs. The present invention relates to these BnAbs, and fragments thereof (e.g., antigen-binding fragments), and to methods of using same to inhibit HIV-1 infection in a subject (e.g., a human). The invention also relates to nucleic acids comprising nucleotide sequences encoding such BnAbs and fragments thereof. The invention further relates to a method designed to induce the production of such BnAbs in a subject (e.g., a human), and to immunogens designed using the clonal lineage antibody members suitable for use in such a method. (See also Fig. 20.)
Recently, a method of making HIV vaccine immunogens based on their ability to bind to early members of a BnAb clonal lineage was proposed (US Prov. Appln. 61/542,469, filed October 3, 201 1 ). This method is termed B cell lineage immunogen design (Haynes et al. Nature Biotech. 30: 423-433 (2012)). This method is based on the use of clonal lineage antibody members as templates for design of HIV envelope proteins that bind well to lineage members. This method is based on the use of clonal lineage antibody members as templates for design of HIV envelope proteins that bind well to lineage members. This method is based on the principle that those antigens that bind best to na'ive BnAb B cell receptors (the unmutated ancestors of mature BnAbs) will be the best
immunogens for driving such a clonal lineage. Thus, mature antibodies are isolated, their intermediate ancestor and unmutated ancestor precursors inferred, and the clonal lineage tree reconstructed by Baysian probability statistics and maximum likelihood analysis, and then the tree antibodies are made by recombinant techniques (Haynes et al, Nature Biotech. 30:423-433 (2012)). Then, by screening Envs, or by solving antibody and Env structures and then rational design of Envs that optimally bind to clonal tree members, immunogens are designed and produced for vaccination studies (Haynes et al, Nature Biotech. 30:423-433 (2012)).
The CHI 03 clonal lineage of broad neutralizing antibodies described herein does not have any of the traits that would predict that this type of lineage would be limited by the immune system tolerance mechanisms. Thus, in accordance with the present vaccine design strategy, Envs can be identified that bind optimally to each stage of this clonal lineage and used as a prime and boosts as outlined in Haynes et al (Nature Biotech. 30: 423-433 (2012)). Preferred Envs (63521B delta 1 1 and 1086C delta 7) are described in the Example that follows.
An additional optimal strategy is to prime with the transmitted Founder Envelope and then boost with one or more of the sequential envelopes isolated during the course of infection of CH0505 patient. These envs can be administered sequentially or all together in a "swarm' of envs to recreate the high level of mutations that are driving BnAb development, (see U.S. Provisional Application Nos. 61 /700,252, filed September 12, 2012, 61/708,466, filed October 1 , 2012 and 61/764,421 , filed February 13, 2013, the entire contents of each of which are incorporated herein by reference).
Preferred antibodies of the invention for therapeutic use include those comprising variable heavy (VH) and light (VL) chain amino acid sequences selected from those shown in Figs. 4, 5 and 24. In accordance with the methods of the present invention, either the intact antibody or a fragment thereof can be used. Either single chain Fv, bispecific antibody for T cell engagement, and chimeric antigen receptors can be used (Chow et al, Adv. Exp. Biol. Med. 746: 121 -41 (2012)). That is, for example, intact antibody, a Fab fragment, a diabody, or a bispecific whole antibody can be used to inhibit HIV-1 infection in a subject (e.g., a human). A bispecific F(ab)2 can also be used with one arm a targeting molecule like CD3 to deliver it to T cells and the other arm the arm of the native antibody (Chow et al, Adv. Exp. Biol. Med. 746: 121-41 (2012)). Toxins that can be bound to the antibodies or antibody fragments described herein include unbound antibody, radioisotopes, biological toxins, boronated dendrimers, and immunoliposomes (Chow et al, Adv. Exp. Biol. Med. 746: 121 -41 , 2012)). Toxins can be conjugated to the antibody or antibody fragment using methods well known in the art (Chow et al, Adv. Exp. Biol. Med. 746: 121 -41 (2012)). The invention also includes variants of the antibodies (and fragments) disclosed herein, including variants that retain the ability to bind to recombinant Env protein, and methods of using same to, for example, reduce HIV-1 infection risk. Combinations of the antibodies, or fragments thereof, disclosed herein can also be used in the methods of the invention.
The antibodies, and fragments thereof, described above can be formulated as a composition (e.g., a pharmaceutical composition). Suitable compositions can comprise the BnAb (or antibody fragment) dissolved or dispersed in a pharmaceutically acceptable carrier (e.g., an aqueous medium). The compositions can be sterile and can be in an injectable form (e.g., a form suitable for intravenous injection). The antibodies (and fragments thereof) can also be formulated as a composition appropriate for topical administration to the skin or mucosa. Such compositions can take the form of liquids, ointments, creams, gels and pastes. The antibodies (and fragments thereof) can also be formulated as a composition appropriate for intranasal administration. The antibodies (and fragments thereof) can be formulated so as to be administered as a post-coital douche or with a condom. Standard formulation techniques can be used in preparing suitable compositions.
The BnAbs (and fragments thereof) described herein have utility, for example, in settings including the following:
i) in the setting of anticipated known exposure to HIV-1 infection, the antibodies described herein (or fragments thereof) and be administered prophylactically (e.g., IV, topically or intranasally) as a microbiocide,
ii) in the setting of known or suspected exposure, such as occurs in the setting of rape victims, or commercial sex workers, or in any homosexual or heterosexual transmission without condom protection, the antibodies described herein (or fragments thereof) can be administered as post-exposure prophylaxis, e.g., IV or topically, and
iii) in the setting of Acute HIV infection (AHI), the antibodies described herein (or fragments thereof) can be administered as a treatment for AHI to control the initial viral load or for the elimination of virus-infected CD4 T cells.
Suitable dose ranges can depend on the antibody (or fragment) and on the nature of the formulation and route of administration. Optimum doses can be determined by one skilled in the art without undue experimentation. Doses of antibodies in the range of 1 -50 mg/kg can be used.
In accordance with the invention, the BnAbs (or antibody fragments) described herein can be administered prior to contact of the subject or the subject's immune system/cells with HIV-1 or within about 48 hours of such contact. Administration within this time frame can maximize inhibition of infection of vulnerable cells of the subject with HIV-1.
Antibodies of the invention and fragments thereof can be produced recombmantly using nucleic acids comprising nucleotide sequences encoding VH and VL sequences selected from those shown in Figs 4, 5 and 24.
Certain aspects of the invention can be described in greater detail in the non-limiting Examples that follows. (See also Provisional Appln. 61/613,222, filed March 20, 2012, Provisional Application No. 61/700,234, filed
September 12, 2012 and Provisional Application No. 61/700,252, filed
September 12, 2012, as well as Provisional Application Nos. 61/700,252, filed September 12, 2012, 61/708,466, filed October 1 , 2012 and 61/764,421 , filed February 13, 2013, the entire contents of each of which are incorporated herein by reference).
EXAMPLE 1
The antibody profile of the CH505 patient sera shows that they bind with resurfaced stabilized core 3 (RSC3+) and not with RSC3delta 371 protein. This pattern is that of serum reactivity pattern of CD4 binding site BnAbs and is associated in this patent with a breadth of neutralization, as manifested by neutralization of all 6 isolates in the lower right box, are shown in Fig. 1. Fig. 2 shows broad neutralization breadth of tier 2 HIV-1 strains with inhibitory concentration 50% (IC50) values shown in the boxes. CH505 new mabs CHI 03, CH I 04, and CHI 06 mAbs have breadth for tier 2 HIV strains and, as well, have selective binding to the RSC3 protein but not to RSC3delta 371 , as seen in the CH0505 patient sera in Fig. 1 (mAb binding data not shown).
The clonal lineage members of clonal lineage 103 from patient CH0505 are shown in Fig. 3. Three of the VHs (1ASCETI5VH, 1AH92UVH, 1 A102R16VH) are from 454 deep sequencing of CH0505 B cell mRNA. The pairing of VH and VL chains for all members of the clonal lineage are shown.
Fig. 4 shows alignment of the antibody heavy variable chain (VH) sequences of clonal lineage 103. There are no insertions or deletions in the VHs, Fig. 5 shows alignment of the antibody light variable chain (VL) sequences of clonal lineage 103. There are no insertion or deletions in the VLs except for one 3 nucleotide deletion in the LC of CHI 03.
Shown in Fig. 6 is the clonal lineage tree of Clone CHI 03 from patient CH0505 with time after transmission of mAb isolation noted (137 weeks after enrollment in the CHAVIOOI acute HIV infection protocol), with three sequences obtained from 454 VH sequencing at 62 and 140 weeks after enrollment. 11 -18 show inferred intermediate antibodies. UCA is the unmutated common ancestor antibody.
The clonal lineage VH mutations are shown in Fig. 7.
Fig. 8 shows binding of clonal lineage members to the 1086Cdelta 7 gpl 20 Env (see PCT/US2012/045530). That 1 086.C delta 7 gpl20 Env binds to all of the key members of the CHI 03 clonal lineage that lead to BnAbs suggests that 1086C is a candidate Env for B cell lineage immunogen design and iterative improvement in its binding of clonal lineage members.
Fig. 9 shows binding of clonal lineage members to the 6352 IB delta 1 1 gpl20 Env (see PCT/US2012/045530). That 63521B delta 1 1 gpl20 Env binds to all of the key members of the CHI 03 clonal lineage that lead to BnAbs suggests that 16352 I B is a candidate Env for B cell lineage immunogen design and iterative improvement in its binding of clonal lineage members. Thus, for this lineage, 6352 I B and 1086C envs can be used as prime and or boosts for inducing such lineage antibodies in mammals. Alternatively, screens of other HIV envs can yield additional Envs with more optimized binding to clonal template members. Such a strategy is referenced in US Prov. Appln. 61/542,469. The binding of clonal lineage members to the 63521 B delta 1 1 gpl20 Env as measured by surface plasmon reasonance and Kd determination is shown in Fig. 10. The affinity of binding increases 4 logs across the lineage from left to right.
An additional optimal strategy is to prime with the transmitted Founder Envelope and then boost with one or more of the sequential envelopes isolated during the course of infection of CH0505 patient. These envs could be administered sequentially or all together in a "swarm' of envs to recreate the high level of mutations that are driving BnAb development, (see U.S. Provisional Application entitled "Antibody Evolution Immunogens", filed concurrently herewith (Attorney Docket No. 1579-1832). The affinity of the transmitted founder Env gpl40 of CH0505 for the unmutated ancestor antibody of the CHI 03 lineage has been measured and it was found to be ~5 nM with an EC50 of 0.7 μg/ml in ELISA. Thus this env can be a potent immunogen for this lineage.
Fig. 1 1 shows the neutralization of tier 1 HIV strain SF162 by clonal lineage members as maturation progresses from left to right with neutralization first seen in the 13 ab. Fig. 12 shows the neutralization of tier 2 HIV strain BGl 168 by clonal lineage members as maturation progresses from left to right with neutralization first seen in the 12 ab.
The CHI 03 clonal lineage early UCA and IA members are not
polyreactive as determined by reactivity with the HEp-2 cell line in indirect immunofluorescence (see Fig. 13). Black boxes show no reactivity. In this assay, only mature abs CHI 06 and the immediately preceeding IA1 are
polyreactive/autoreactive. This indicates that this antibody will not be removed by early tolerance mechanisms in the bone marrow, and that polyreactivity was acquired in the germinal center— a normal event. Fig. 14 shows that the CHI 03 clonal lineage IA1 member polyreactivity was determined by the more mature light chain of IA1 and did not occur with the less mature LC of IA2.
The CHI 03 clonal lineage early UCA and 1A members are not polyreactive, as determined by reactivity with a panel of autoantigens in the Athena luminex assay (see Fig. 15). In this assay, only mature abs CHI 03, CHI 04 and CHI 06 and the immediately preceding IA1 and IA2 are
polyreactive/autoreactive. This indicates that this antibody will not be removed by early tolerance mechanisms in the bone marrow, and that polyreactivity was acquired in the germinal center— a normal event. Figs. 17, 18 and 19 show the SPR histograms that gave rise to the data in Fig. 15.
Fig. 16 shows the on rates and off rates of all antibodies in the CHI 03 clonal lineage in binding to the transmitted/founder Env 6352 I B,
EXAMPLE 2
Shown in Fig. 21 is the development of the CH103-clonal family with time of appearance, VH mutations, affinity for HIV-1 Env, and HIV-1 neutralization. The VH mutations and the timing of antibodies developed in the CHI 03 clonal lineage after transmission are shown in Fig. 21 A. Shown in Fig. 21 B is the binding by mAbs in the CHI 03 clonal lineage to CH505 autologous T/F Env gpl40 (EC50 mg/ml), the binding to B.63521 gpl20 (EC50 μg/ml) by mAbs in the CHI 03 clonal lineage, and the binding to C.1086 gpl20 (EC50 μg/ml) by mAbs in the CHI 03 clonal lineage. Autologous neutralization of tier 2 virus CH505 (IC50, μg/ml) by mAbs in CH103 clonal lineage is depicted in Fig. 21 C. Neutralization of tier 2 virus A.Q842 (IC50, μg/ml) by mAbs in the CHI 03 clonal lineage is also shown in Fig. 21 C, as is neutralization of tier 2 virus B.BG1 168 (IC50, μg/ml) by mAbs in CHI 03 clonal lineage The structure of antibody CHI 03 in complex with the outer domain of HIV-1 gpl 20 (OD) is shown in Fig. 22. Fig. 23 shows the CHI 03 paratope, critical residues, and required immune precursors.
The methods of crystallization used were those previously described (Zhou et al, Science 329:81 1 -7 (2010)).
The crystal structure of Fig. 22 and Tables TZl a and l b below show that 84 % of the heavy chain contacts and 44 % of the light chain contacts of the antibody for the envelope in the crystal structure of CHI 03 and the ZMl 76.66 outer domain of gpl 20 are present in the unmutated common ancestor antibody VH and VL, i.e., are unmutated. This finding explains the good binding of the CH0505 (CH505) transmitted founder virus Env gpl40C to the unmutated common ancestor (UA or UCA). These data show that the CH0505 Env and CH0505 Envs that evolved after transmission provide a set of sequential immunogens for inducing these types of CD4 binding site broad neutralizing antibodies.
Table TZlc below shows hydrogen bonds and salt bridges between CH103 and ZM176.66 gpl20. Table TZld below lists the CH103 heavy chain residues that interact with ZMl 76.66 gpl20. Table TZle below lists the CHI 03 light chain residues that interact with ZM176.66 gpl20. Table TZl f below lists the ZMl 76.66 gpl20 residues that interact with CHI 03 heavy chain. Table TZl g below lists the ZM176.66 gpl20 residues that interact with CH103 light chain.
By mapping on to the Env structure crystallized with the CHI 03 monoclonal broadly neutralizing antibody, one can see the mutations of the Env that have occurred at the touchpoints of the CFI103 ab with Env. Thus, it will be possible to construct an immunogen precisely comprised of sequential Envs designed to induce those somatic mutations in the antibodies needed to recognize the CHI 03 touchpoints on HIV Env gpl20. Tables TZla-Tlg. Analysis of interactions between ZM 176.66 gpl20 and C III 03 ble TZla. Contact areas at the interface of ZM176.66 gp l 20 and CH103.
interface on CH103 (A2) Interface on gpl20 (A2)
Heavy chain 493 429
Light chain 377 i 378
Total 870 807
TZl b. Contribution of unmutated residues to the paratope of CH103.
Total paratope (A2) Unmutated contact residues (A2) %
Heavy chain 493 414 84 Light chain 377 164 44
Total 870 578 66
Table TZlc. Hydrogen bonds and salt bridges between CH103 and ZM176.66 gpl20.
CH103 hydrogen bonds with gp!20
Chain:Residue Dist. (A) gpl20 Residue
H-.TYR 33[OH] 2.17 G:ASP 368[ OD1]
H:TYR 50[OH ] 3.68 G:GLY 367[0 ]
H:ARG 97[NH1] 3.81 G:SER256[ OG ]
H:ARG 97[NH2] 2.59 G:GLU 370[OE1]
H:GLN 99[NE21 3.10 G:SER 365[OG]
H:LEU 100[N ] 2.41 G:SER 365[0 ]
H:LEU 100[N ] 3.22 G:SER 365[OG]
H:VAL lOOAf N ] 3.18 G:SER 365[OG]
L:ASN 32[ND2] 2.97 G:GLY458[0 ]
L:ASN 51[ND2] 2.92 G:ASP461[0D1]
L:LYS 53[NZ] 3.19 G'.ASN 280[ OD1]
L:LYS 66[NZ] 3.16 G:ASP 461[OD2]
L:GLU 50[OE2] 3.07 G:ASN 280[ ND2]
CHI 03 Salt bridges with gpl20
Chain:Residue Dist. (A) gpl20 Residue
H:ARG 97[NE] 3.93 G:ASP 368[ODl]
H-.ARG 97[NE1 2.58 G'.ASP 368[ OD2]
H:ARG 97[NH2] 2.59 G:GLU 370[OE1]
H:ARG 97[NH2] 2.73 G:ASP368[OD2]
L:LYS 66[NZ] 3.65 G:ASP461[ OD1]
L:LYS 66[NZ] 3.16 G:ASP 461 [ OD2]
Table TZld. List of CH103 heavy chain residues that interact with Z 176.66 gpl20.
Chain:Residue Bond* ASA* BSA* AiG*
H:TYR 33 H 32.31 32.31 minim -0.04
H:TYR 50 H 31.31 21.67 jl!IHI -0.05
H:PHE 52 15,69 12.Π mum 0.19
H:THR 54 96.73 7.68 j 0.12
H:GLU 56 H 122.06 59.46 D -0.41
H;ASN 58 66.83 2.011 0.03
H:ARG 97 HS 157.07 82.19 H H -1.22
H:GLY 98 44.20 23.45 Hill 0.11
H:GLN 99 H 151.92 120.00|||!|||| -0,57
H:LEU 100 H 77,09 27.19 HI 0.29
H:VAL 100A H 120.39 55.44 Hill 0.82
H:ASN 100B 128.47 50.10 |||[ -0.59
* Bond type: H: Hydrogen, D: Disulphide bond, S: Salt bridge, C Covalent link
ASA: Accessible Surface Area, A2
BSA: Buried Surface Area, A2
jG: Solvation energy effect, kcal/mol
||||: Buried area percentage, one bar per 10%
Detailed gpl20:CH103 interface data was calculated on the EBI Γ server
(http://www.ebi.ac.uk/msdsrv/prot_int/cgi-bin/piserver)
Table TZl e. List of CH 103 light chain residues that interact with ZM 176.66 gp!20.
Chain:Residue Bond* ASA* BSA* AiG*
L:SER 27 106. 16 3.68 1 -0,04
L.THR 3 1 56.39 14.17 111 0.23
L;ASN 32 H 94.17 52.10 mm -0,64
L:GLU 50 H 85.70 38.67 11111 -0.20
L:ASN 5 1 H 28.62 27.91 -0.21
L:TYR 52 133.51 32.84 HI 0.51
L:LYS 53 H 71 .67 22.45 i -0.61
L:SER 65 64,57 9.04 II 0.14
L: LYS 66 HS 49.44 43.83 inin -0.70
L:SER 67 89.35 25.47 HI 0.41
L:GLY 68 57.78 36. 10 mini 0.28
L:TRP 91 139.62 70.62 mm 0.89
* Bond type: H: Hydrogen, D: Disulphide bond, S: Salt bridge, C Covalent link
ASA: Accessible Surface Area, A2
BSA: Buried Surface Area, A2
\,G : Solvation energy effect, kcal/mol
||]|: Buried area percentage, one bar per 10%
Detailed gpl20:CH 103 interface data was calculated on the EBI server
(http://www.ebi.ac.uk/msdsrv/prot_int/cgi-bin/piserver)
Table TZlf. List of Z 176.66 gpl20 residues that interact with CH103 heavy chain.
Chain:Residue Bond* ASA* BSA* AiG*
G:SER256 H 54.93 11.72111 0.02
G:ASN 280 53.47 12.38 1 -0,14
G:HIS 364 43.22 13.21 mi 0.15
G:SER 365 H 85.82 53.96||||jj| -0.27
G:GLY 366 37.35 17.71 Km 0.12
G:GLY 367 H 79.03 68.46111111 0.19
G:ASP368 HS 68.81 65.44 llll!l! 0.56
G:LEU 369 H 85.35 18.72 HI 0.09
G:GLU370 HS 98.66 28.69111 -0.22
G:ILE371 48.02 38.90 11 0.62
G:THR455 32.88 18.59111 0.30
G:ASP457 56.94 35.32 mini 0.05
G:GLY458 33.99 9.87 HI -0.05
G:ARG 469 58.28 23.84 inn -0.21
G:GLY 471 10.21 5.35 H 0.09
G:GLY 472 69.17 5.851 0.00
* Bond type: H: Hydrogen, D: Disulphide bond, S: Salt bridge, C: Covalent link
ASA: Accessible Surface Area, A2
BSA: Buried Surface Area, A2
AjG: Solvation energy effect, kcal/niol
||||: Buried area percentage, one bar per 10%
Detailed gpl20:CH103 interface data was calculated on the EBI PISA server
(http://www.ebi.ac.uk/msdsrv/prot_int/cgi-bin/piserver)
Table TZl g. List of ZM 176.66 gpl20 resides that interact with CH103 light chain.
Chain:Residue Bond* ASA* BSA* AiG*
G:ASP 279 54.47 3.56 1 -0.10
G:ASN 280 H 53.47 39.83 HI II ! -0.56
G:HIS 364 43.22 3.56 1 -0.04
G:SER 365 85.82 3 1 .86 mi 0.43
G:GLY 366 37.35 3.61 1 -0.04
G:ASP 457 56.94 13.05 HI 0.2 1
G:GLY 458 H 33.99 24.12 ilium -0.09
G:GLY 459 72.21 50.36 lllilll 0.48
G:ASN 460 137.07 50.77 1111 -0.03
G:ASP 46 I HS 121.21 69.50 mill -0.50
G:ASP 462 129.01 36.60 (11 0. 16
G:ASN 463 129.15 15.46 1! -0.08
G:ARG 469 58.28 34.44 Him -1 .12
* Bond type: H: Hydrogen, D: Disulphide bond, S: Salt bridge, C Covalent link
ASA: Accessible Surface Area, A2
BSA: Buried Surface Area, A2
A|G: Solvation energy effect, kcal/mol
||||: Buried area percentage, one bar per 10%
Detailed gpl20:CH 103 interface data was calculated on the EBI server
(http://www.ebi.ac.uk/msdsrv/prot_int/cgi-bin/piserver)
* * *
All documents and other information sources cited herein are hereby incorporated in their entirety by reference.

Claims

WHAT IS CLAIMED IS:
1. An isolated broadly neutralizing CHI 03 clonal lineage anti-HIV- 1 antibody, or antigen binding fragment thereof.
2. The antibody according to claim 1 wherein said antibody comprises a heavy or light chain amino acid sequence set forth in Figure 4, 5 or 24.
3. The antibody according to claim 1 wherein said antibody has the binding specificity of monoclonal antibody CHI 86, CH I 87, CHI 88, CH200, CH243, CH244, CH245, CH246, CH247 and CH248 or an antibody of Figure 4 or 5.
4. An isolated nucleic acid comprising a nucleotide sequence encoding the antibody according to claim 1 , or binding fragment thereof.
5. The nucleic acid according to claim 4 wherein said nucleic acid is present in a vector.
6. A method of preventing or treating HIV-1 comprising
administering to a subject in need thereof an antibody, or fragment thereof, according to claim 1 in an amount sufficient to effect said prevention or treatment.
7. The method according to claim 6 wherein said subject is a human.
8. A method of preventing or treating HIV-1 comprising
administering to a subject in need thereof said nucleic acid according to claim 4 under conditions such that said nucleotide sequence is expressed and said antibody, or fragment thereof, is produced in an amount sufficient to effect said prevention or treatment.
9. A composition comprising the antibody, or fragment thereof, according to claim 1 , or the nucleic acid according to claim 4, and a carrier,
13. The composition according to claim 12 wherein said composition is in a form suitable for injection.
14. The composition according to claim 12 wherein said composition is in the form of a cream or ointment.
PCT/US2013/059515 2012-09-12 2013-09-12 Clonal lineage antibodies WO2014043386A1 (en)

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US201261700234P 2012-09-12 2012-09-12
US61/700,234 2012-09-12
US201261708413P 2012-10-01 2012-10-01
US61/708,413 2012-10-01

Publications (1)

Publication Number Publication Date
WO2014043386A1 true WO2014043386A1 (en) 2014-03-20

Family

ID=50278682

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2013/059515 WO2014043386A1 (en) 2012-09-12 2013-09-12 Clonal lineage antibodies

Country Status (1)

Country Link
WO (1) WO2014043386A1 (en)

Cited By (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9695230B2 (en) 2011-12-08 2017-07-04 The United States Of America, As Represented By The Secretary, Department Of Health And Human Services Broadly neutralizing HIV-1 VRC07 antibodies that bind to the CD4-binding site of the envelope protein
WO2018067580A1 (en) * 2016-10-03 2018-04-12 Duke University Methods to identify immunogens by targeting improbable mutations
US10562960B2 (en) 2015-03-20 2020-02-18 The United States Of America, As Represented By The Secretary, Department Of Health And Human Services Neutralizing antibodies to gp120 and their use
EP3589315A4 (en) * 2017-03-03 2021-06-23 Duke University Compositions and methods for inducing hiv-1 antibodies
US11246920B2 (en) 2016-03-03 2022-02-15 Duke University Compositions and methods for inducing HIV-1 antibodies
US11318197B2 (en) 2016-03-03 2022-05-03 Duke University Compositions and methods for inducing HIV-1 antibodies

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2011038290A2 (en) * 2009-09-25 2011-03-31 The U. S. A., As Represented By The Secretary, Department Of Health And Human Services Neutralizing antibodies to hiv-1 and their use
WO2011046623A2 (en) * 2009-10-16 2011-04-21 Duke University Hiv-1 antibodies

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2011038290A2 (en) * 2009-09-25 2011-03-31 The U. S. A., As Represented By The Secretary, Department Of Health And Human Services Neutralizing antibodies to hiv-1 and their use
WO2011046623A2 (en) * 2009-10-16 2011-04-21 Duke University Hiv-1 antibodies

Non-Patent Citations (4)

* Cited by examiner, † Cited by third party
Title
BONSIGNORI, MATTIA ET AL.: "Analysis of a clonal lineage of HIV-1 envelope V2/V3 conformational epitope-specific broadly neutralizing antibodies and their inferred unmutated common ancestors", JOURNAL OF VIROLOGY, vol. 85, no. 19, 27 July 2011 (2011-07-27), pages 9998 - 10009 *
BONSIGNORI, MATTIA ET AL.: "Two distinct broadly neutralizing antibody specificities of different clonal lineages in a single HIV-1-infected donor: implications for vaccine design", JOURNAL OF VIROLOGY, vol. 86, no. 8, 1 February 2012 (2012-02-01), pages 4688 - 4692 *
HAYNES, BARTON F. ET AL.: "B-cell-lineage immunogen design in vaccine development with HIV-1 as a case study", NATURE BIOTECHNOLOGY, vol. 30, no. 5, 7 May 2012 (2012-05-07), pages 423 - 433 *
LIAO, HUA-XIN ET AL.: "Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus", NATURE, vol. 496, no. 7746, 3 April 2013 (2013-04-03), pages 469 - 476 *

Cited By (11)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9695230B2 (en) 2011-12-08 2017-07-04 The United States Of America, As Represented By The Secretary, Department Of Health And Human Services Broadly neutralizing HIV-1 VRC07 antibodies that bind to the CD4-binding site of the envelope protein
US10035844B2 (en) 2011-12-08 2018-07-31 The United States Of America, As Represented By The Secretary, Department Of Health And Human Services Broadly neutralizing HIV-1 VRC07 antibodies that bind to the CD4-binding site of the envelope protein
US10815295B2 (en) 2011-12-08 2020-10-27 The United States Of America, As Represented By The Secretary, Department Of Health And Human Services Broadly neutralizing HIV-1 antibodies that bind to the CD4-binding site of the envelope protein
US10562960B2 (en) 2015-03-20 2020-02-18 The United States Of America, As Represented By The Secretary, Department Of Health And Human Services Neutralizing antibodies to gp120 and their use
US11246920B2 (en) 2016-03-03 2022-02-15 Duke University Compositions and methods for inducing HIV-1 antibodies
US11318197B2 (en) 2016-03-03 2022-05-03 Duke University Compositions and methods for inducing HIV-1 antibodies
WO2018067580A1 (en) * 2016-10-03 2018-04-12 Duke University Methods to identify immunogens by targeting improbable mutations
EP3519428A4 (en) * 2016-10-03 2020-07-08 Duke University Methods to identify immunogens by targeting improbable mutations
US11161895B2 (en) 2016-10-03 2021-11-02 Duke University Methods to identify immunogens by targeting improbable mutations
US11746143B2 (en) 2016-10-03 2023-09-05 Duke University Methods to identify immunogens by targeting improbable mutations
EP3589315A4 (en) * 2017-03-03 2021-06-23 Duke University Compositions and methods for inducing hiv-1 antibodies

Similar Documents

Publication Publication Date Title
US11396557B2 (en) Bispecific antibody or antibody mixture with common light chains
CA2858347C (en) V1v2 immunogens
US10849970B2 (en) Antibody evolution immunogens
US11248027B2 (en) Engineered outer domain (eOD) of HIV GP120, mutants and use thereof
WO2014043386A1 (en) Clonal lineage antibodies
US10450368B2 (en) HIV-1 neutralizing antibodies and uses thereof (CD4bs antibodies)
US8147840B2 (en) Human immunodeficiency virus (HIV) immunization strategies employing conformationally-stabilized, surface-occluded peptides comprising a gp41 2F5 epitope in association with lipid
WO2020098599A1 (en) Anti-cd73 antibody, antigen-binding fragment thereof and application thereof
US20230002480A1 (en) Broadly neutralizing antibodies against hiv
WO2022033435A1 (en) Anti-coronavirus antibody and use thereof
US10519222B2 (en) Broadly neutralizing monoclonal antibodies against HIV-1 V1V2 Env region
CN106565840B (en) Antibody against hepatitis B surface antigen and use thereof
Chan et al. Structural comparison of human anti-HIV-1 gp120 V3 monoclonal antibodies of the same gene usage induced by vaccination and chronic infection
WO2018053328A1 (en) Bispecific molecules comprising an hiv-1 envelope targeting arm
EP4214237A1 (en) Antibodies that target hla-e-host peptide complexes and uses thereof
KR20230024904A (en) Potent neutralizing antibodies against SARS-COV-2, their generation and uses
CN115715297A (en) anti-FLT 3 antibodies and compositions
US20210363195A1 (en) Recombinant hiv env polypeptides and their use
US20230265170A1 (en) Antibodies
CN114751987A (en) Multispecific antibody for neutralizing coronavirus
CN114751988A (en) Multispecific antibodies for neutralizing coronaviruses
CA3229447A1 (en) Antibodies that target hla-e-host peptide complexes and uses thereof
WO2023122211A2 (en) Coronavirus antibodies and uses thereof
CN114751986A (en) Multispecific antibodies for neutralizing novel coronaviruses
CN116041492A (en) anti-RBD antibody and application thereof

Legal Events

Date Code Title Description
121 Ep: the epo has been informed by wipo that ep was designated in this application

Ref document number: 13837353

Country of ref document: EP

Kind code of ref document: A1

NENP Non-entry into the national phase

Ref country code: DE

122 Ep: pct application non-entry in european phase

Ref document number: 13837353

Country of ref document: EP

Kind code of ref document: A1