Distinct conformations of the HIV-1 V3 loop crown are targetable for broad neutralization

Nikolas Friedrich ,Huldrych F Günthard ,Claus Kadelka ,Thomas Lemmin ,Mustafa Eroğlu ,Umut Karakus ,Roger D Kouyos ,Yufan Wu ,Patrick Erñst ,Branislav Ivan ,John A Robinson ,Emanuel Stiegeler ,Stephan Ursprung ,Caio Foulkes ,Axel Mann ,Liridona Maliqi ,Simon Hansen ,Thomas Liechti ,Andreas Plückthun ,Peter Rusert ,Thomas Reinberg ,Matthias Glögl ,Mylène Morin ,Jonas V Schaefer ,Alexandra Trkola

doi:10.1038/s41467-021-27075-0

Abstract

The V3 loop of the HIV-1 envelope (Env) protein elicits a vigorous, but largely non-neutralizing antibody response directed to the V3-crown, whereas rare broadly neutralizing antibodies (bnAbs) target the V3-base. Challenging this view, we present V3-crown directed broadly neutralizing Designed Ankyrin Repeat Proteins (bnDs) matching the breadth of V3-base bnAbs. While most bnAbs target prefusion Env, V3-crown bnDs bind open Env conformations triggered by CD4 engagement. BnDs achieve breadth by focusing on highly conserved residues that are accessible in two distinct V3 conformations, one of which resembles CCR5-bound V3. We further show that these V3-crown conformations can, in principle, be attacked by antibodies. Supporting this conclusion, analysis of antibody binding activity in the Swiss 4.5 K HIV-1 cohort (n = 4,281) revealed a co-evolution of V3-crown reactivities and neutralization breadth. Our results indicate a role of V3-crown responses and its conformational preferences in bnAb development to be considered in preventive and therapeutic approaches.

Highlights

The variable loop 3 (V3) loop of the HIV-1 envelope (Env) protein elicits a vigorous, but largely nonneutralizing antibody response directed to the V3-crown, whereas rare broadly neutralizing antibodies target the V3-base
A vigorous V3 antibody response is elicited in almost all HIV-1 infected individuals, but bears little to no neutralization activity as it is mostly constituted of V3crown Abs[9,13,14]
Using the Designed Ankyrin Repeat Proteins (DARPin) technology[26], we previously developed the V3-crown specific DARPin 5m3_D12 that shares features with cross-neutralizing V3-crown Abs and has activity against difficult to neutralize (Tier-2) strains of HIV-1 subtype B27

Summary

Introduction

The V3 loop of the HIV-1 envelope (Env) protein elicits a vigorous, but largely nonneutralizing antibody response directed to the V3-crown, whereas rare broadly neutralizing antibodies (bnAbs) target the V3-base. Challenging this view, we present V3-crown directed broadly neutralizing Designed Ankyrin Repeat Proteins (bnDs) matching the breadth of V3base bnAbs. While most bnAbs target prefusion Env, V3-crown bnDs bind open Env conformations triggered by CD4 engagement. Rare broadly neutralizing antibodies (bnAbs) targeting V3 overcome the access restriction on the trimer by binding to the conserved V3-base, involving the GDIR motif and surrounding glycans[15,16]. Building on the discovery of 5m3_D12, we here exploit the DARPin technology in order to define conformational states of the V3-crown that are targetable for broad neutralization

Methods

Results

Conclusion