Mapping essential somatic hypermutations in a CD4-binding site bNAb informs HIV-1 vaccine design

Creators: Dam, Kim-Marie A.¹; Gristick, Harry B.¹; Li, Yancheng E.¹; Yang, Zhi¹; Gnanapragasam, Priyanthi N. P.¹; West, Anthony P.¹; Seaman, Michael S.^{2, 3}; Bjorkman, Pamela J.¹

1. California Institute of Technology
2. Beth Israel Deaconess Medical Center
3. Harvard University

Abstract

HIV-1 broadly neutralizing antibodies (bNAbs) targeting the CD4-binding site (CD4bs) contain rare features that pose challenges to elicit these bNAbs through vaccination. The IOMA class of CD4bs bNAbs includes fewer rare features and somatic hypermutations (SHMs) to achieve broad neutralization, thus presenting a potentially accessible pathway for vaccine-induced bNAb development. Here, we created a library of IOMA variants in which each SHM was individually reverted to the inferred germline counterpart to investigate the roles of SHMs in conferring IOMA's neutralization potency and breadth. Impacts on neutralization for each variant were evaluated, and this information was used to design minimally mutated IOMA-class variants (IOMAmin) that incorporated the fewest SHMs required for achieving IOMA's neutralization breadth. A cryoelectron microscopy (cryo-EM) structure of an IOMAmin variant bound to Env was used to further interpret characteristics of IOMA variants to elucidate how IOMA's structural features correlate with its neutralization mechanism, informing the design of IOMA-targeting immunogens.

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Acknowledgement

We thank J. Vielmetter, A. Rorick, K. Storm, A. Lam, and the Protein Expression Center in the Beckman Institute at Caltech for assistance with expression and Z. Wu and J. Keeffe for help with polyreactivity assays. Electron microscopy was performed in the Caltech Cryo-EM Center with assistance from S. Chen. This work was supported by the National Institute of Allergy and Infectious Diseases Grant HIVRAD P01 AI100148 (P.J.B.) and NIH 1U54AI170856 (P.J.B.). The contents of this publication are solely the responsibility of the authors and do not necessarily represent the official views of NIAID or NIH. This work was also supported in part by the Bill & Melinda Gates Foundation grants INV-002143 (P.J.B.) and INV-036842 (M.S.S.). Under the grant conditions of the Foundation, a Creative Commons Attribution 4.0 Generic License has already been assigned to the Author Accepted Manuscript version that might arise from this submission.

Funding

This work was supported by the National Institute of Allergy and Infectious Diseases Grant HIVRAD P01 AI100148 (P.J.B.) and NIH 1U54AI170856 (P.J.B.). The contents of this publication are solely the responsibility of the authors and do not necessarily represent the official views of NIAID or NIH. This work was also supported in part by the Bill & Melinda Gates Foundation grants INV-002143 (P.J.B.) and INV-036842 (M.S.S.). Under the grant conditions of the Foundation, a Creative Commons Attribution 4.0 Generic License has already been assigned to the Author Accepted Manuscript version that might arise from this submission.

Contributions

Conceptualization, K.A.D., H.B.G., and P.J.B.; methodology, K.A.D., Y.E.L., Z.Y., P.N.P.G., and M.S.S.; formal analysis, K.A.D. and A.P.W., Jr.; investigation, K.A.D., Y.E.L., Z.Y., P.N.P.G., and M.S.S.; resources, M.S.S. and P.J.B.; data curation, K.A.D. and Z.Y.; writing – original draft, K.A.D. and P.J.B.; writing – review and editing, K.A.D., H.B.G., A.P.W., Jr., M.S.S., and P.J.B.; visualization, K.A.D.; supervision, K.A.D., H.B.G., and P.J.B.; project administration, K.A.D. and P.J.B.; funding acquisition, M.S.S. and P.J.B.

Data Availability

Cryo-EM maps and atomic structures were deposited in the Protein DataBank (PDB) and Electron Microscopy DataBank under accession codes 9EHL and EMD-48059 for the structure of IOMAmin5–BG505–10-1074 class I and under accession codes 9EHM and EMD-48060 for the structure of IOMAmin5–BG505–10-1074 class II.

Conflict of Interest

The authors declare no competing interests.

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