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Structures of HIV-1 Env V1V2 with broadly neutralizing antibodies reveal commonalities that enable vaccine design

Nature Structural & Molecular Biology volume 23, pages 81–90 (2016)Cite this article

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Abstract

Broadly neutralizing antibodies (bNAbs) against HIV-1 Env V1V2 arise in multiple donors. However, atomic-level interactions had previously been determined only with antibodies from a single donor, thus making commonalities in recognition uncertain. Here we report the cocrystal structure of V1V2 with antibody CH03 from a second donor and model Env interactions of antibody CAP256-VRC26 from a third donor. These V1V2-directed bNAbs used strand-strand interactions between a protruding antibody loop and a V1V2 strand but differed in their N-glycan recognition. Ontogeny analysis indicated that protruding loops develop early, and glycan interactions mature over time. Altogether, the multidonor information suggested that V1V2-directed bNAbs form an 'extended class', for which we engineered ontogeny-specific antigens: Env trimers with chimeric V1V2s that interacted with inferred ancestor and intermediate antibodies. The ontogeny-based design of vaccine antigens described here may provide a general means for eliciting antibodies of a desired class.

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Figure 1: Design of scaffolded V1V2s and cocrystal structure with bNAb CH03 from donor CH0219.
Figure 2: CH03 V1V2 interactions.
Figure 3: CH03 epitope in PDB 1VH8-scaffold and trimeric Env contexts.
Figure 4: Modeling of bNAb CAP256-VRC26 bound to Env suggests a common mode of recognition.
Figure 5: Properties of UCA or the earliest known ancestor of V1V2-directed bNAb lineages.
Figure 6: Inferred ancestor and intermediates of V1V2-directed bNAbs neutralize a common set of HIV-1 isolates.
Figure 7: Ontogeny-based vaccine design.

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NCBI Reference Sequence

Protein Data Bank

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Acknowledgements

We thank members of the Structural Biology Section and Structural Bioinformatics Core, Vaccine Research Center, NIH, for discussions and comments on the manuscript, and Weill Cornell Medical College, The Scripps Research Institute, Academic Medical Center and the HIV Vaccine Research and Design team comprising investigators from these three institutions for their contributions to the design and validation of near-native mimicry for soluble BG505 SOSIP.664 trimers. We thank J. Baalwa, D. Ellenberger, F. Gao, B. Hahn, K. Hong, J. Kim, F. McCutchan, D. Montefiori, L. Morris, J. Overbaugh, E. Sanders-Buell, G. Shaw, R. Swanstrom, M. Thomson, S. Tovanabutra, C. Williamson and L. Zhang for contributions to HIV-1-Env plasmids used in neutralization assessments. We thank R. Sanders for providing the PGDM1400–1412 sequences and the International AIDS Vaccine Initiative (IAVI) for PG9, PG16 and PGT141–145. Support for this work was provided by the Intramural Research Program of the Vaccine Research Center, US National Institute of Allergy and Infectious Diseases (NIAID) (to A.B.M., J.R. Mascola and P.D.K.); the Division of AIDS, NIAID, NIH (1U01-AI116086-01 to P.L.M., L.M., J.R. Mascola and P.D.K.; R21-AI112389 to K.K.L.); the Bill and Melinda Gates Foundation Collaboration for AIDS Vaccine Discovery (OPP1033102 to K.K.L.); IAVI; and the Center for HIV/AIDS Vaccine Immunology-Immunogen Discovery grant (CHAVI-ID; UM1 AI100645 to M.B. and B.F.H.). This project was funded in part with Federal funds to U.B. from the Frederick National Laboratory for Cancer Research, NIH, under contract HHSN261200800001E. Use of sector 22 (Southeast Region Collaborative Access team) at the Advanced Photon Source was supported by the US Department of Energy, Basic Energy Sciences, Office of Science, under contract number W-31-109-Eng-38. Modeling and molecular dynamics were carried out through the NIH's Biowulf computing cluster.

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Authors and Affiliations

  1. Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, Maryland, USA

    Jason Gorman, Cinque Soto, Max M Yang, Robert T Bailer, Michael Chambers, Gwo-Yu Chuang, Brandon J DeKosky, Nicole A Doria-Rose, Aliaksandr Druz, Michael J Ernandes, Ivelin S Georgiev, Marissa C Jarosinski, M Gordon Joyce, Sherman Leung, Mark K Louder, Sandeep Narpala, Marie Pancera, Jonathan Stuckey, Xueling Wu, Yongping Yang, Baoshan Zhang, Tongqing Zhou, Adrian B McDermott, Lawrence Shapiro, John R Mascola & Peter D Kwong

  2. Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA

    Thaddeus M Davenport, Miklos Guttman & Kelly K Lee

  3. Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA

    Brandon J DeKosky, Jonathan R McDaniel & George Georgiou

  4. Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA

    Thomas M Lemmin

  5. NIH Intramural Sequencing Center (NISC), National Human Genome Research Institute, NIH, Bethesda, Maryland, USA

    NISC Comparative Sequencing Program & James C Mullikin

  6. Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA

    Ulrich Baxa

  7. Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA

    Mattia Bonsignori & Barton F Haynes

  8. Center for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa

    Penny L Moore & Lynn Morris

  9. Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa

    Penny L Moore & Lynn Morris

  10. Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Congella, South Africa

    Penny L Moore & Lynn Morris

  11. Department of Biochemistry & Molecular Biophysics, Columbia University, New York, New York, USA

    Lawrence Shapiro

  12. Department of Systems Biology, Columbia University, New York, New York, USA

    Lawrence Shapiro

Authors
  1. Jason Gorman
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  2. Cinque Soto
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  3. Max M Yang
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  4. Thaddeus M Davenport
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  5. Miklos Guttman
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  6. Robert T Bailer
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  7. Michael Chambers
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  8. Gwo-Yu Chuang
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  9. Brandon J DeKosky
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  10. Nicole A Doria-Rose
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  13. Ivelin S Georgiev
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  14. Marissa C Jarosinski
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  15. M Gordon Joyce
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  16. Thomas M Lemmin
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  17. Sherman Leung
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  18. Mark K Louder
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  19. Jonathan R McDaniel
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  20. Sandeep Narpala
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  21. Marie Pancera
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  22. Jonathan Stuckey
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  23. Xueling Wu
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  24. Yongping Yang
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  25. Baoshan Zhang
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  26. Tongqing Zhou
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  27. NISC Comparative Sequencing Program
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  28. James C Mullikin
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  30. George Georgiou
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  34. Penny L Moore
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  35. Lynn Morris
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  36. Kelly K Lee
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  37. Lawrence Shapiro
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  38. John R Mascola
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  39. Peter D Kwong
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Contributions

J.G. headed the determination of the V1V2-bound CH03 and CH04 crystal structures, revertant neutralization strategy and chimeric SOSIP design and assessment, and assisted with VRC26 model development; C.S. headed the next-generation-sequencing lineage analysis and VRC26 modeling; M.M.Y. assisted with crystallization. T.M.D., M.G. and K.K.L. performed HDX experiments and analyzed the data; R.T.B. and M.K.L. and J.R. Mascola assessed neutralization breadth; S.N., M.C. and A.B.M. performed antigenic analyses; G.-Y.C. performed frequentist probability analysis; B.J.D., J.R. McDaniel, G.G., X.W., J.C.M. and J.R. Mascola and NISC contributed next-generation sequencing data; J.G., C.S., M.P., N.A.D.-R., M.J.E., M.C.J. and B.Z. contributed to paratope mapping; A.D. expressed V1V2 scaffold and antibodies; J.G., I.S.G., Y.Y. and S.L. contributed to V1V2 scaffold design and assessment; C.S., T.M.L. and J.G. contributed to MDFF analysis; M.P. assisted with chimeric SOSIP design; J.S. assisted with figure conception and design; U.B. performed EM; T.Z. and M.G.J. contributed to reverted VRC01 experiments; M.B. and B.F.H. contributed CH0219 materials; P.L.M. and L.M. contributed CAP256 materials; J.G., C.S., L.S. and P.D.K. assembled and wrote the paper, on which all principal investigators commented.

Corresponding author

Correspondence to Peter D Kwong.

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Competing interests

The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Design and crystallization of trimeric scaffolded V1V2 with V1V2-directed broadly neutralizing antibodies.

(a) Using the trimeric orientation of V1V2 on the viral spike we used structure-based design to stabilize the domains on trimeric scaffolds. (b) Constructs were expressed in GnTI- cells by transient transfection in 96 well plates and screening was carried out using the trimer-specific antibodies PGT145 and VRC26. PGT145 binding was observed for 4 wells consisting of 2 different scaffolds, PDB IDs 1VH8 (yellow) and 4F2K (green). (c) Design examples of scaffolds which were bound by PGT145, 4F2K with various linker lengths at the c-terminal and 1VH8 which incorporated the V1V2 domain internally on the molecule. (d) These two and several others which showed good binding to PG9 were expressed at the 1 liter level and tested for binding by ELISA or SPR (fit in red). (e) The promising 1VH8 scaffold was optimized further by screening through 12 different HIV-1 strains and crystals were obtained for CH03 and CH04 bound to 1VH8CAP256SU and 1VH8A244 respectively.

Supplementary Figure 2 CH04 structure with PDB1VH8–scaffolded V1V2 from HIV-1 strain A244.

(a) The asymmetric unit of the crystal contains two fabs and two scaffolds. The structure was solved to 4.2 Å in space group P63, although significant twinning was observed. (b) The symmetry mates of one the molecule are shown as represented in figure 1 showing 3 fabs bound to the trimer in the biological assembly.

Supplementary Figure 3 Modeling the CAP256-VRC26 structure with V1V2.

(a) A model of VRC26.09 obtained through a combination of molecular dynamics (MD) and molecular dynamics flexible-fitting (MDFF) is shown with a negative stain 3D reconstruction of the fab complexed with BG505 SOSIP (EMD #5856). (b) HDX-MS is shown for BG505 SOSIP unliganded or in complex with VRC26.03. The difference between the bound and unbound data are plotted on one lobe of the trimer with regions of increased (blue) and decreased protection (red) mapped onto the structure (right panel) highlighting the region that VRC26.03 binds is similar to that seen in PG9, PG16, CH03 and CH04 complex crystal structures. (c) Paratope mapping of CAP256-VRC26 by arginine scanning. The left panel highlights the entire region scanned in green. Below, centroids of the introduced arginines are shown as red spheres. (right) Arginine variants were screened for neutralization across a panel of nine strains from multiple clades. The difference in neutralization compared to the WT antibody are shown in the table with differences greater than 20 fold indicated in red. Variants that significantly knocked down or knocked out neutralization were primarily localized to the CDR H3.

Supplementary Figure 4 Sequence features and structural role of the CDR H3 DDY motif.

(a) Sequence features of V1V2 bNAbs. Remarkably, although they use different germ-line genes, the amino acid sequence of the V-gene from donors CAP256 and IAVI24 are virtually identical. (b) Alignment of the CDR H3s from PG9 and CAP256-VRC26.09. The YYD motif is highlighted in red. (c) Structures of PG9 and VRC26.09 are aligned in the upper panel. The sulfated tyrosines of PG9 make electrostatic contacts with positively charged residues on the C-strand of the protomer with which the antibody is making main chain contacts. VRC26.09, however makes contacts with the positively charged side chains of each of the neighboring protomers at residue 169. Note that VRC26.09 also contains electrostatic interactions with the positively charged residues on the C strand it makes main chain contacts with (including residue 169), however it does not employ the YYD motif for this (Figure 5). We note that the VRC26.09 structure is a model and therefore the exact contacts may differ, for instance residue Arg166 of the neighboring V1V2 protomer is within range to make contacts with the sulfated tyrosine by selecting an alternative rotamer.

Supplementary Figure 5 NGS trees for donors IAVI 84 and CH0219.

(a) Sequence identity to neutralizing antibody PGT145 versus germline divergence to the germline gene IgHV1-8 for the Intra-donor positive data set. Sequence identity and germline divergence are expressed as a percentage. (b) Maximum likelihood tree for donor IAVI84 is shown colored according to the PGDM1400 series (blue) or the PGT141 series (green). (c-d) NGS tree for lineage CH01-CH04 from donor CH0219. (c) Sequence identity to neutralizing antibody CH04 versus germline divergence to the germline gene IgHV3-20 for the Illumina NGS data set. Sequence identity and germline divergence are expressed as a percentage. The corresponding sequence identity and germline divergence for the CH04 antibody is shown on the figure (note: there are no sequences in the NGS data sets with 100% identity to CH04). (d) Histogram distribution of CDR H3 lengths by V-germline (upper panel) and by V and J-germlines (lower panel). (e) Maximum likelihood tree for donor CH0219 is shown colored according to the method used to obtain the sequences with 454 in green and Illumina in blue.

Supplementary Figure 6 Somatic hypermutation and glycan recognition of V1V2-directed antibodies in donors CH0219 and IAVI24.

(a) V1V2 glycan interactions with PG16 and CH03 are shown. All residues on the antibodies which interact through hydrogen binding or have greater than 10% of their surface area buried by a glycan are shown as surface representation. Residues which are mutated from germline are colored red. Note that the atomic interactions with the glycan of the neighboring protomer for PG16 are not known. (b) Germline and mature sequences are shown for donors IAVI24 and CH0219. Residues that interact with glycan in the mature antibody structures (displayed as surface representation in (a)) are highlighted in grey. Somatically matured residues which interact with glycans are shown in red. 12 out of 21 residues that interact with glycans were not present in the earliest calculated intermediate for PG16 (2 positions are unknown and counted in the 12). 7 out of 24 residues that interact with glycans were not present in the earliest calculated intermediate for CH03.

Supplementary Figure 7 Antigenic characterization of BG505 DS-SOSIP.664 chimeras with V1V2 regions from diverse HIV-1 strains.

(a) Strains of HIV-1 colored according to the representative dots in Figure 6. Sequences of the V1V2 domain (residue 126-196) from each strain are shown on the right with secondary structure derived from the BG505 structure shown below (b) MSD-ECLIA shows that the V1V2 chimeric BG505.SOSIPs behave antigenically similar to the native strain. Very low V3-directed antibody binding is seen following negative selection, comparable to levels of the BG505.SOSIP control. The constructs used here contain a D368R mutation to knock out CD4 binding which also knocks out VRC01 binding in this assay. Notably the trimers display variable levels of binding to PGT145 and VRC26, anticipated from their neutralization profiles of each strain. (c) ELISA experiments run in triplicate show specific strains bind reverted V1V2-directed antibodies better than others, even when mature binding is similar. With few exceptions, the binding correlates with the neutralization potency of each antibody. Strains are colored as in Fig. 6.

Supplementary Figure 8 Neutralization by germline-reverted VRC01-class antibodies identifies strains capable of interacting with early-lineage members.

(a) Strains neutralized by multiple germline-reverted VRC01-class antibodies were highlighted with colors. (b) Neutralization titers, loop D and loop V5 sequences and their potential glycosylation sites for strains neutralized by VRC01 germline antibodies were listed. (c) Location of loop D, V5 and CD4-binding loop on the HIV-1 Env.

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Gorman, J., Soto, C., Yang, M. et al. Structures of HIV-1 Env V1V2 with broadly neutralizing antibodies reveal commonalities that enable vaccine design. Nat Struct Mol Biol 23, 81–90 (2016). https://doi.org/10.1038/nsmb.3144

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