Towards conformational fidelity of a quaternary HIV-1 epitope: computational design and directed evolution of a minimal V1V2 antigen.

Jennifer I Lai,Margaret E Ackerman,Deeptak Verma,Chris Bailey-Kellogg

doi:10.1093/protein/gzy010

Jennifer I Lai, Margaret E Ackerman + Show 2 more

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https://doi.org/10.1093/protein/gzy010

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Abstract

Structure-based approaches to antigen design utilize insights from antibody (Ab):antigen interactions and a refined understanding of protective Ab responses to engineer novel antigens presenting epitopes with conformations relevant to eliciting or discovering protective humoral responses. For human immunodeficiency virus-1 (HIV-1), one model of protection is provided by broadly neutralizing Abs (bnAbs) against epitopes present in the closed prefusion trimeric conformation of HIV-1 envelope glycoprotein, such as the variable loops 1–2 (V1V2) apex. Here, computational design and directed evolution yielded a novel V1V2 sequence variant with potential utility for inclusion in an immunogen for eliciting bnAbs, or as an epitope probe for their detection. The computational design goal was to engineer a minimal single-chain antigen with three copies of the V1V2 loops to support maintenance of closed prefusion V1V2 trimeric conformation and presentation of bnAb epitopes. Via directed evolution of this computationally designed single-chain antigen, we isolated a V1V2 sequence variant that in monomeric form exhibited preferential recognition by quaternary-preferring and conformation-dependent mAbs. Structural context and transferability of this phenotype to V1V2 sequences from all strains of HIV-1 tested suggest a conformation-stabilizing effect. This example demonstrates the potential utility of computational design and directed evolution-based protein engineering strategies to develop minimal, conformation-stabilized epitope-specific antigens.

Highlights

Structure-based design approaches for next-generation immunogens and probes utilize structural information of antibody (Ab):antigen recognition to present epitopes against which potent or broadly neutralizing Ab responses develop (Kulp and Schief, 2013; McLellan et al, 2013; Correia et al, 2014; Impagliazzo et al, 2015; Rappuoli et al, 2016)
We demonstrate the use of computational structurebased protein design, and directed evolution towards development of an human immunodeficiency virus-1 (HIV-1) V1V2 antigen that faithfully presents conformational epitopes recognized by broadly neutralizing Abs (bnAbs)
Application of the K-M substitution in V1V2 immunogens or probes may enable elicitation or dissection of conformation-dependent humoral responses directed at the V1V2 loops in settings of vaccination and infection

Summary

Introduction

Structure-based design approaches for next-generation immunogens and probes utilize structural information of antibody (Ab):antigen recognition to present epitopes against which potent or broadly neutralizing Ab (bnAb) responses develop (Kulp and Schief, 2013; McLellan et al, 2013; Correia et al, 2014; Impagliazzo et al, 2015; Rappuoli et al, 2016). As the conformational state of an epitope may relate to its cognate Ab’s neutralization potency (Sanders et al, 2013), novel immunogens and probes require (i) understanding the structural determinants of epitopes recognized by protective Abs, and (ii) selective presentation of the epitope(s) of interest in conformations relevant to recognition by bnAbs. Successful design solutions to this protein engineering problem will result in novel antigens that may serve as promising vaccine immunogens to elicit desired immune responses and/or as epitope probes to characterize. The human immunodeficiency virus-1 (HIV-1) variable loops 1–2 (V1V2 loops) on the envelope glycoprotein (gp120) comprise a promising antigenic site for vaccine targeting and humoral profiling; the V1V2 loops, despite high sequence variability, are structurally and functionally conserved (Zolla-Pazner and Cardozo, 2010), and are targeted by an extended class of highly potent V1V2-targeting bnAbs, of which PG9 and PG16 are prototypical examples (Walker et al, 2009; McLellan et al, 2011). That there exist distinct classes of anti-V1V2 loop mAbs recognizing quaternary, conformational or linear epitopes overlapping in sequence suggests that the V1V2 loops may exist dynamically depending on their molecular context within a monomer or trimer (Alter and Ackerman, 2013)

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