Covalent anti-HIV compound that induces HIV-1 capsid multimerization and degradation decomposes the viral core

Abstract Drugs that covalently bind to their target molecules form strong and irreversible interactions with each other. Covalent inhibitors have recently attracted attention because of their enhanced structural selectivity within the target cavity, which results in prolonged interactions, even at low doses. Here, we report that ACAi-001 is a human immunodeficiency virus (HIV)-1 capsid (CA)-targeting compound with covalent binding to CA, estimating long-lasting effects for HIV inhibition. Using a library of millions of compounds, ACAi-001 was identified through in silico screening. This compound is designed to target the hydrophobic cavity in the N-terminal domain of CA and, in a cell-based assay, was found to inhibit HIV-1 replication. ACAi-001 covalently bound to CA and induced aberrant CA multimerization and degradation, as assessed by western blotting, size-exclusion chromatography, thermal stability assay, enzyme-linked immunosorbent assay, and liquid chromatography-mass spectrometry. ACAi-001, which has two putative covalent interactions in its chemical structure, binds directly to serine 16 in the N-terminal domain-targeting cavity and to cysteine 198 or 218 in the C-terminal domain of CA. This unique binding profile of ACAi-001 to CA induces multiple CA dysfunctions such as CA multimerization and degradation, resulting in disruption of the HIV core, thereby inhibiting HIV-1 infection and replication. ACAi-001, which covalently binds to and degrades CA in an unique manner, may reveal new aspects of HIV core assembly and disassembly and is a promising candidate as a next-generation anti-HIV-1 CA inhibitor. Significance Statement Lenacapavir (LEN) is a first-in-class CA inhibitor used clinically to inhibit HIV-1 replication. LEN is a long-acting capsid inhibitor with a convenient dosing regimen and is effective for both treating multidrug-resistant HIV and as pre-exposure prophylaxis. ACAi-001 targets specific CA cavities and covalently binds to CA in a distinct manner from LEN. ACAi-001 forms two covalent interactions with CA, leading to CA multimerization and degradation to cause multiple CA dysfunctions. Therefore, more potent derivatives of ACAi-001 with covalent interactions may serve as long-acting capsid inhibitors. ACAi-001 shows potential as a next-generation HIV-1 capsid inhibitor against HIV-1 infection and can be used to reveal details on HIV core assembly and disassembly in the HIV-1 life cycle.