Assessing bnAb potency in the context of HIV-1 Envelope conformational plasticity

Abstract

The ability of broadly neutralizing antibodies (bnAbs) to interact with the closed, pre-fusion HIV-1 envelope (Env) trimer distinguishes them from weakly neutralizing antibodies (weak-nAbs) that depend on trimer opening to bind. Comparative analysis of neutralization data from the CATNAP database revealed a nuanced relationship between bnAb activity and Env conformational plasticity, with substantial epitope-specific variation of bnAb potency ranging from increased to decreased activity against open, neutralization-sensitive Env. To systematically investigate the impact of Env conformational dynamics on bnAb potency we screened 126 JR-CSF point mutants for generalized neutralization sensitivity to weak-nAbs and plasma from people with chronic HIV-1 infection. 23 mutations at highly conserved sites resulted in neutralization phenotype with high Tier 1 sensitivity, which was associated with destabilization of the closed, prefusion conformation. Including 19 of these mutants into a Sensitivity Env mutant panel (SENSE-19), we classified bnAbs according to potency variations in response to trimer opening. To verify that these sensitivity patterns are independent of the in vitro assay system, replication-competent SENSE-19 mutant viruses were tested on primary CD4 T cells. While loss of potency on SENSE-19 was registered for bnAbs recognizing quaternary epitopes on pre-triggered Env, structural destabilization benefitted MPER bnAbs and other inhibitors known to have post-CD4 attachment neutralization activity. Importantly, for certain bnAbs targeting CD4bs, V3-glycan and interface epitopes, particularly low potency variation was noted, suggesting that Env conformational tolerance can be achieved but is not the rule. In summary, SENSE-19 screens revealed distinct Env flexibility tolerance levels between bnAb types that provide mechanistic insights in their function and broaden current neutralization breadth assessments. Author summaryConsistently high potency and neutralizing breadth against genetically divergent strains circulating worldwide are central to the applicability of HIV-1 broadly neutralizing antibodies (bnAbs) for prevention and therapy. The trimeric Envelope protein complex on these viruses is the target for nAbs and because of its inherent flexibility can be presented in different shapes. However, the activity of nAbs depends to different degree on the presentation of certain shapes, limiting their potency and breadth. Here we assemble a virus panel that can be used to estimate this dependence, enabling the identification of bnAbs tolerating the presentation of different shapes.