A new class of capsid-targeting inhibitors that specifically block HIV-1 nuclear import

• Published in: EMBO molecular medicine 2024-10, Vol.16 (11), p.2918-2945
• Main Authors: Boulay, Aude, Quevarec, Emmanuel, Malet, Isabelle, Nicastro, Giuseppe, Chamontin, Célia, Perrin, Suzon, Henriquet, Corinne, Pugnière, Martine, Courgnaud, Valérie, Blaise, Mickaël, Marcelin, Anne-Geneviève, Taylor, Ian A, Chaloin, Laurent, Arhel, Nathalie J
• Format: Article
• Language: English
• Subjects: Active Transport, Cell Nucleus - drug effects; Animals; Anti-HIV Agents - chemistry; Anti-HIV Agents - pharmacology; Antiretroviral Therapy; Biomedical and Life Sciences; Biomedicine; Capsid; Capsid - drug effects; Capsid - metabolism; Capsid Proteins - antagonists & inhibitors; Capsid Proteins - genetics; Capsid Proteins - metabolism; Drug Discovery; Drug Evaluation, Preclinical; EMBO08; EMBO23; HIV Infections - drug therapy; HIV Infections - metabolism; HIV Infections - virology; HIV-1; HIV-1 - drug effects; Humans; Life Sciences; Microbiology and Parasitology; Models, Molecular; Molecular Medicine; Nuclear Import; Virology
• ISSN: 1757-4684; 1757-4676; 1757-4684
• DOI: 10.1038/s44321-024-00143-w

HIV-1 capsids cross nuclear pore complexes (NPCs) by engaging with the nuclear import machinery. To identify compounds that inhibit HIV-1 nuclear import, we screened drugs in silico on a three-dimensional model of a CA hexamer bound by Transportin-1 (TRN-1). Among hits, compound H27 inhibited HIV-1 with a low micromolar IC 50 . Unlike other CA-targeting compounds, H27 did not alter CA assembly or disassembly, inhibited nuclear import specifically, and retained antiviral activity against PF74- and Lenacapavir-resistant mutants. The differential sensitivity of divergent primate lentiviral capsids, capsid stability and H27 escape mutants, together with structural analyses, suggest that H27 makes multiple low affinity contacts with assembled capsid. Interaction experiments indicate that H27 may act by preventing CA from engaging with components of the NPC machinery such as TRN-1. H27 exhibited good metabolic stability in vivo and was efficient against different subtypes and circulating recombinant forms from treatment-naïve patients as well as strains resistant to the four main classes of antiretroviral drugs. This work identifies compounds that demonstrate a novel mechanism of action by specifically blocking HIV-1 nuclear import. Synopsis A major unresolved challenge to curing HIV-1 is its presence in the nucleus of infected cells. This study reports on new compounds that specifically block HIV-1 nuclear import by targeting the viral capsid. Graphical abstract by Sophie Desgraupes. The virtual screening of the HIV-1 CA hexamer - Transportin-1/TNPO1/TRN-1 interface identified a single antiviral hit, H27. H27 makes multiple low affinity contacts with assembled capsid. H27 inhibits HIV-1 nuclear import without disrupting reverse transcription, CA assembly or disassembly and has negligible toxicity in vivo. Divergent primate lentiviruses are differentially sensitive to H27. Structural analogues of H27 improved the IC50 to ~0.5 µM. A major unresolved challenge to curing HIV-1 is its presence in the nucleus of infected cells. This study reports on new compounds that specifically block HIV-1 nuclear import by targeting the viral capsid.