Virus-like Particles Identify an HIV V1V2 Apex-Binding Neutralizing Antibody that Lacks a Protruding Loop

Abstract

SUMMARY Most HIV-1-specific neutralizing antibodies isolated to date exhibit unusual characteristics that complicate their elicitation. Neutralizing antibodies that target the V1V2 apex of the HIV-1 envelope (Env) trimer feature unusually long protruding loops, which enable them to penetrate the HIV-1 glycan shield. As antibodies with loops of requisite length are created through uncommon recombination events, an alternative mode of apex binding has been sought. Here, we isolated a lineage of Env apex-directed neutralizing antibodies, N90-VRC38.01-11, by using virus-like particles and conformationally stabilized Env trimers as B cell probes. A crystal structure of N90-VRC38.01 with a scaffolded V1V2 revealed a binding mode involving side-chain to side-chain interactions that reduced the distance the antibody loop must traverse the glycan shield, thereby facilitating V1V2 binding via a non-protruding loop. The N90-VRC38 lineage thus identifies a solution for V1V2-apex binding that provides a more conventional B cell pathway for vaccine design.

Structural survey of HIV-1-neutralizing antibodies targeting Env trimer delineates epitope categories and suggests vaccine templates

“…In some cases, multiple runs were averaged. The values used here differed slightly, generally within 2 fold of previous median IC 50 , from previously reported values in references (5,7,11,22,(24)(25)(26)(27)(28)(29)(30)(31)(32)(33)(34)(35)(36)(37)(38)(39)(40).…”

“…For the PGT121 class, we chose 8 antibody 10-1074 (14); for the VRC01 class, we chose antibody N6 (24); and for the 8ANC131 class we chose antibody CH235.12 (25). Notably, the newly measured median neutralization IC50 generally differed by less than 2 fold from prior reported values (5,7,11,22,(24)(25)(26)(27)(28)(29)(30)(31)(32)(33)(34)(35)(36)(37)(38)(39)(40), with the breadth for all 20 classes averaging 56.7%, with an average geometric mean IC 50 of 0.27 μ g/ml.…”

“…Data are expressed as the antibody concentration required to achieve 50% neutralization (IC50) and calculated using a dose-response curve fit with a 5-parameter nonlinear function. We used a previously described panel (5,34,60) of 208 geographically and genetically diverse Env pseudoviruses representing the major subtypes and circulating recombinant forms.…”

An HIV-1 broadly neutralizing antibody from a clade C infected pediatric elite neutralizer potently neutralizes the contemporaneous and autologous evolving viruses

“…By nested PCR based amplification of antibody variable heavy and light chain genes using specific primers (41), we obtained seven pairs of heavy and light chain genes amplified from single B cell and sequenced. By applying the criteria of having SHM >5% (42) in the amplified antibody genes, we identified a singular pediatric HIV-1 bNAb AIIMS-P01. Therefore, for further experiments, only AIIMS-P01 was characterized.…”

The Neutralizing Antibody Response to the HIV-1 Env Protein

“…This was followed by B cell culture and micro-neutralization (functional) screens, and by the use of flow cytometry-based isolation of single B cells using peptide and protein “baits”. Most recently, the design of soluble, recombinant Env trimers and virus-like particles comparable to native Env trimers has provided alternative antigen-specific B cell selection strategies [43–45]. These strategies have enabled the isolation of many dozens of antibodies from elite neutralizers, and some of these have exceptional breadth (approaching 99% of circulating viruses) and potency in the picomolar range [44, 46–48].…”