Clade-specific influences of glycans on the interactions between HIV-1 envelope and broadly neutralizing antibodies

Abstract N-linked glycans are important in the elicitation and the activity of many broadly neutralizing antibodies (bNAbs) against HIV-1. The high conformational flexibility of glycans hindered detailed atomistic investigations of glycan-bNAb interactions, including glycan shielding of bN-Abs. Importantly, how these interactions vary across different HIV-1 clades remains unclear. The variability in the number and location of potential N-linked glycosylation sites (PNGS) on the HIV-1 envelope (Env) protein across clades can lead to differences in glycan dynamics and topology, potentially affecting Env-bNAb interactions and the clade-specific efficacy of bNAb-based therapies. Here, we combined comprehensive glycan conformational sampling, using the software glycoSHIELD, and molecular dynamics (MD) simulations to model fully glycosylated trimeric Env for six HIV-1 strains, one from each of the major clades A, B, C, G, CRF01 AE (01 AE) and CRF07 BC (07 BC). We assessed the interactions of 50 different bNAbs, drawn from all the major bNAb classes, with each of these strains, quantifying glycan shielding, glycan-bNAb interactions, and their clade-specific variations for each bNAb in microscopic detail. Our findings reveal that while glycans cover most of the exposed surface area in all clades, the amount of accessible surface varies, with clade B having the minimum and clade 07 BC the maximum antibody accessible surface area. The number of glycan conformers per glycosylation site also varies with clades, even for conserved sites. Overall, we observed that bNAbs interact with more glycans than previously reported in experimental and computational studies. Important variations emerge in Env-bNAb interactions with clade and bNAb-class. These atomic-level insights will be valuable for improving bNAb-based therapies and vaccine design strategies against HIV-1. Competing Interest Statement The authors have declared no competing interest. Footnotes ↵* E-mail: maiti{at}iisc.ac.in Figures 7, 8, 11, and 12 have been updated for clarity. Their corresponding explanation in the results section has also been revised to explain the changes and revised results in the manuscript. In the Introduction section, we have included more relevant references.