Structure-based design of native-like HIV-1 envelope trimers to silence non-neutralizing epitopes and eliminate CD4 binding

Abstract

Elicitation of broadly neutralizing antibodies (bnAbs) is a primary HIV vaccine goal. Native-like trimers mimicking virion-associated spikes present nearly all bnAb epitopes and are therefore promising vaccine antigens. However, first generation native-like trimers expose epitopes for non-neutralizing antibodies (non-nAbs), which may hinder bnAb induction. We here employ computational and structure-guided design to develop improved native-like trimers that reduce exposure of non-nAb epitopes in the V3-loop and trimer base, minimize both CD4 reactivity and CD4-induced non-nAb epitope exposure, and increase thermal stability while maintaining bnAb antigenicity. In rabbit immunizations with native-like trimers of the 327c isolate, improved trimers suppress elicitation of V3-directed and tier-1 neutralizing antibodies and induce robust autologous tier-2 neutralization, unlike a first-generation trimer. The improved native-like trimers from diverse HIV isolates, and the design methods, have promise to assist in the development of a HIV vaccine.

Structure-based immunogen design — leading the way to the new age of precision vaccines

“…The introduction of two glycans on V3 was shown to dampen the immune response against this site upon rabbit immunization [15]. Similarly, glycosylation of the Env base showed reduced reactivity with sera of animals immunized with non-masked Env, indicating that glycan masking can render non-neutralizing epitopes inaccessible [16 ].…”

“…To reduce the V3 conformational dynamics, structure-based design was employed to strengthen hydrophobic packing, preventing V3 loop to adopt the open conformation [29,30]. Similarly, Kulp et al employed computational design to replace a network of buried hydrophilic residues by hydrophobic amino acids, thereby limiting V3 exposure [16 ]. Both stabilization strategies reduced reactivity to V3 directed antibodies, and immunogenicity studies in rabbits confirmed dampened antibody responses against the V3 loop.…”

“…To prevent the CD4-induced conformational change while maintaining an epitope targeted by bnAbs, de Taeye et al introduced two mutations that occur in HIV-1 strains unable to undergo CD4-induced conformational changes [30]. Using a computational multi-state design protocol, Kulp et al rationally designed mutations that abrogate CD4 binding to Env, while maintaining binding to bnAbs targeting the CD4 receptor binding site (CD4bs) [16 ]. While these engineered Envs showed reduced binding to antibodies targeting CD4-induced epitopes, neither study could prove a direct impact of such modifications on antibody specificity or neutralization in vivo.…”

Strategies for a multi-stage neutralizing antibody-based HIV vaccine

“…In this approach, immunizations consisting of a cocktail of multi-clade Env-derived trimers would be administered repeatedly until bnAbs develop. These native trimer immunogen design approaches incorporate stabilizing mutations to increase thermostablity, prevent CD4-induced trimer opening, and improve immunogenicity by masking non-essential immunodominant epitopes [15,17,25,26]. …”

B-cell restriction – an alternative piece to the puzzle

“…Strategically placing glyco-moieties to shield surfaces of the spike protein has been proposed so to leave only the neutralizing surfaces exposed and subject to B-cell scrutiny. 44,45 In essence, the use of trimeric spike proteins, as in the case of SOSIP trimers for HIV-1, ensures that the inner surfaces of gp120 "chaff decoys" are avoided. [46][47][48]…”