A Strain-Specific Inhibitor of Receptor-Bound HIV-1 Targets a Pocket near the Fusion Peptide

Gabriel Ozorowski,Jonathan L Torres,Diogo Santos-Martins,Stefano Forli,Andrew B Ward

doi:10.1016/j.celrep.2020.108428

Gabriel Ozorowski, Jonathan L Torres + Show 3 more

Open Access

https://doi.org/10.1016/j.celrep.2020.108428

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Abstract

SummaryDisruption of viral fusion represents a viable, albeit under-explored, target for HIV therapeutics. Here, while studying the receptor-bound envelope glycoprotein conformation by cryoelectron microscopy (cryo-EM), we identify a pocket near the base of the trimer containing a bound detergent molecule and perform in silico drug screening by using a library of drug-like and commercially available molecules. After down-selection, we solve cryo-EM structures that validate the binding of two small molecule hits in very similar manners to the predicted binding poses, including interactions with aromatic residues within the fusion peptide. One of the molecules demonstrates low micromolar inhibition of the autologous virus by using a very rare phenylalanine in the fusion peptide and stabilizing the surrounding region. This work demonstrates that small molecules can target the fusion process, providing an additional target for anti-HIV therapeutics, and highlights the need to explore how fusion peptide sequence variations affect receptor-mediated conformational states across diverse HIV strains.

Highlights

IntroductionDespite advances in the characterization of HIV and treatment of infected individuals, both a functional cure and prophylactic vaccine are lacking(1, 2)
Both of the new maps contain additional resolved density for a long and narrow small molecule proximal to the fusion peptide (FP) in all protomers, in the asymmetric reconstruction this is less prominent in the protomer with a lessresolved FP
Because cryo-EM freezing techniques often include sub-critical micellar concentration (CMC) amounts of detergent to increase the number and tumbling of protein particles trapped over holes in vitreous ice, we hypothesized that the unassigned density could be the DDM (n-dodecyl-β-D-maltoside) used in our experiment

Summary

Introduction

Despite advances in the characterization of HIV and treatment of infected individuals, both a functional cure and prophylactic vaccine are lacking(1, 2). Current ART methods utilize small molecule drugs, recently a new class of potential HIV therapeutics, broadly neutralizing antibodies, has been shown to suppress viremia in infected individuals(4). The elicitation of such antibodies is the ultimate goal of HIV vaccine efforts, and the utility of recombinantly expressed versions of these antibodies for prophylaxis and ART continues to be heavily investigated. Approved ART drugs target either HIV-specific enzymes (reverse transcriptase, protease, integrase), HIV fusion, or HIV receptors/co-receptors (CD4, CCR5)

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