Focused evolution of HIV-1 neutralizing antibodies revealed by crystal structures and deep sequencing
Inventors
Mascola, John R. • Nabel, Gary • Haynes, Barton F. • Wu, Xueling • Kepler, Thomas B. • Kwong, Peter
Assignees
Duke University • US Department of Health and Human Services • Office of Technology Transfer
Publication Number
US-10273291-B2
Publication Date
2019-04-30
Expiration Date
2032-03-23
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Abstract
Antibody VRC01 represents a human immunoglobulin that neutralizes—˜90% of diverse HIV-1 isolates. To understand how such broadly neutralizing HIV-1 antibodies develop and recognize the viral envelope, we used X-ray crystallography and 454 pyrosequencing to characterize additional antibodies from HIV-1-infected individuals. Crystal structures revealed a convergent mode of binding of different antibodies to the same CD4-binding-site epitope. Antibody recognition was achieved through the evolution of complementary contact domains that were generated in diverse ways. Phylogenetic analysis of expressed heavy and light chains determined by deep sequencing revealed a common pathway of antibody heavy chain maturation confined to IGHV1-2*02 lineage that could pair with different light chains. The maturation pathway inferred by antibodyomics reveals that diverse antibodies evolve to a highly affinity-matured state to recognize an invariant viral structure, providing insight into the development and evolution of broadly neutralizing HIV-1 immunity.
Core Innovation
The invention relates to broadly neutralizing human immunoglobulin antibodies, particularly those that neutralize approximately 90% of diverse HIV-1 isolates by targeting the CD4-binding site of the HIV-1 envelope glycoprotein gp120. Using X-ray crystallography and deep sequencing (454 pyrosequencing), the inventors characterized additional antibodies from HIV-1-infected individuals to understand how such antibodies develop and recognize the viral envelope. Crystal structures revealed a convergent mode of binding of different antibodies to the same CD4-binding-site epitope, achieved through the evolution of complementary contact domains generated in diverse ways. Phylogenetic analysis revealed a common heavy chain maturation pathway confined to the IGHV1-2*02 lineage that could pair with different light chains.
The problem addressed is the extraordinary genetic diversity of HIV-1 and its multiple mechanisms to evade the humoral immune response, which complicates vaccine development and antibody-mediated neutralization. Broadly neutralizing antibodies isolated thus far accumulate unusually high levels of somatic mutation, and it was unclear whether the mode of recognition, genetic origin, and maturation pathways of these antibodies represented generalizable features of the B-cell response to HIV-1. The invention seeks to elucidate these features by isolating and analyzing broadly neutralizing antibodies from multiple donors, identifying maturation pathways and structural features that underlie broad HIV-1 neutralization.
The invention further provides methods of analyzing human antibody repertoires (antibodyomes) via deep sequencing combined with bioinformatics to identify sequences with high likelihood of broad neutralization, enabling functional assessment by expression of chimeric antibodies. The structural convergence among different antibodies from different individuals shows that despite divergent amino acid sequences, the antibodies achieve convergent recognition of a conserved viral epitope. This focused antibody evolution to a site of HIV-1 vulnerability provides insight into antibody development and suggests novel immunogen designs can be developed based on inferred maturation intermediates to elicit such antibodies.
Claims Coverage
The independent claims disclose isolated recombinant antibodies or antigen binding fragments thereof against the HIV-1 envelope CD4 binding site, along with compositions and methods of use. The main inventive features cover the amino acid sequences of specific variable heavy and light chains from antibodies CH30, CH31, CH32, and inferred intermediates; functional variants with defined mutations; antibody isotypes; engineered constant domains; and methods of administering the antibodies for inhibition of HIV-1 infection.
Isolated recombinant antibodies with defined heavy and light chain variable regions
Antibodies or antigen binding fragments comprising variable heavy (VH) chain amino acid sequences of antibodies CH30, CH31, CH32, or inferred intermediates I1, I2, I3, I4, paired with variable light (VL) chain amino acid sequences of antibodies CH30, CH31, CH32, or I2, directed against the CD4 binding site of HIV-1 envelope.
Functional variants with specific amino acid substitutions
Recombinant antibodies comprising VH and VL sequences primarily based on CH31 with amino acid substitutions at defined positions (e.g., position 42 TYR in VH, positions 40 ALA/PRO in VL), maintaining binding to the CD4 binding site of HIV-1 envelope.
Antibody isotypes and engineered constant domains
The antibodies can be of IgG or IgA isotype and may comprise engineered constant domains to modify properties or functions.
Compositions comprising the recombinant antibodies or fragments with carriers
Pharmaceutical compositions including the recombinant antibodies or antigen binding fragments combined with a carrier suitable for administration.
Methods of inhibiting HIV-1 infection by administering antibody compositions
Therapeutic or prophylactic methods involving administration of compositions containing the recombinant antibodies or antigen binding fragments to patients in amounts effective to inhibit or prevent HIV-1 infection, via parenteral or mucosal routes.
The independent claims cover isolated recombinant antibodies targeting the HIV-1 envelope CD4 binding site defined by particular VH and VL sequences from CH30-CH32 and intermediates, specified functional variants, their compositions, and methods of administration to inhibit HIV-1 infection.
Stated Advantages
Broad and potent neutralization of approximately 90% of diverse HIV-1 isolates by targeting a conserved viral epitope.
Insight into antibody maturation pathways enabling rational vaccine design to elicit broadly neutralizing antibodies.
Ability to identify and produce functional antibodies from deep sequencing data allowing broad neutralizing activity assessment.
Documented Applications
Prophylactic use of the antibodies to prevent HIV-1 infection, including pre-exposure and post-exposure prophylaxis.
Therapeutic use of the antibodies to treat HIV-1 infected individuals, including during pregnancy and perinatal infection in infants.
Use of antibodies in passive immunotherapy strategies, potentially as adjuncts with other anti-HIV therapies.
Formulation of antibodies as sterile injectable compositions or topical microbicides for mucosal application to prevent HIV-1 infection.
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