Vaccine-elicited primate antibodies use a distinct approach to the HIV-1 primary receptor binding site informing vaccine redesign

Karen Tran,Christopher Sundling,Robyn L Stanfield,Richard Wilson,Javier Guenaga,Ian A Wilson,Yuxing Li,Natalia De Val,Christian Poulsen,Andrew B Ward,Richard T Wyatt,Gunilla B Karlsson Hedestam

doi:10.1073/pnas.1319512111

Abstract

HIV-1 neutralization requires Ab accessibility to the functional envelope glycoprotein (Env) spike. We recently reported the isolation of previously unidentified vaccine-elicited, CD4 binding site (CD4bs)-directed mAbs from rhesus macaques immunized with soluble Env trimers, indicating that this region is immunogenic in the context of subunit vaccination. To elucidate the interaction of the trimer-elicited mAbs with gp120 and their insufficient interaction with the HIV-1 primary isolate spike, we crystallized the Fab fragments of two mAbs, GE136 and GE148. Alanine scanning of their complementarity-determining regions, coupled with epitope scanning of their epitopes on gp120, revealed putative contact residues at the Ab/gp120 interface. Docking of the GE136 and GE148 Fabs to gp120, coupled with EM reconstructions of these nonbroadly neutralizing mAbs (non-bNAbs) binding to gp120 monomers and EM modeling to well-ordered trimers, suggested Ab approach to the CD4bs by a vertical angle of access relative to the more lateral mode of interaction used by the CD4bs-directed bNAbs VRC01 and PGV04. Fitting the structures into the available cryo-EM native spike density indicated clashes between these two vaccine-elicited mAbs and the topside variable region spike cap, whereas the bNAbs duck under this quaternary shield to access the CD4bs effectively on primary HIV isolates. These results provide a structural basis for the limited neutralizing breadth observed by current vaccine-induced, CD4bs-directed Abs and highlight the need for better ordered trimer immunogens. The analysis presented here therefore provides valuable information to guide HIV-1 vaccine immunogen redesign.

Highlights

We recently reported the isolation of previously unidentified vaccine-elicited, CD4 binding site (CD4bs)directed mAbs from rhesus macaques immunized with soluble envelope glycoprotein (Env) trimers, indicating that this region is immunogenic in the context of subunit vaccination
To define the properties of CD4bs-directed Abs elicited by YU2 gp140-F trimers in nonhuman primates (NHPs), we analyzed the interactions of GE136 and GE148 with several forms of Env
The overall structures of the GE136 [Protein Data Bank (PDB) ID code 4KTD] and GE148 (PDB ID code 4KTE) Fabs reveal that the six CDRs of both Fabs form a discontinuous surface that comprises their binding sites (Fig. 1B, Top)

Summary

Results

These mAbs bind with high affinity to monomeric gp120, their neutralization breadth is largely restricted to neutralization-sensitive tier 1 viruses, with limited activity against tier 2 viruses in the TZM-bl neutralization assay [19]. Analysis with University of California, San Francisco Chimera software revealed the hydrophobic character of the molecular surface of each mAb, demonstrating that the Ab HCDR3 loops were highly hydrophobic at their surface-exposed “tips” (Fig. 1B, Bottom), IMMUNOLOGY

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Discussion

Materials and Methods