Journal article
Structural and mechanistic bases for resistance of the M66I capsid variant to lenacapavir
mBio, Vol.16(5), p.e0361324
05/14/2025
DOI: 10.1128/mbio.03613-24
PMCID: PMC12077090
PMID: 40231850
Abstract
Lenacapavir (LEN) is the first-in-class viral capsid protein (CA) targeting antiretroviral for treating multi-drug-resistant HIV-1 infection. Clinical trials and cell culture experiments have identified resistance-associated mutations (RAMs) in the vicinity of the hydrophobic CA pocket targeted by LEN. The M66I substitution conferred by far the highest level of resistance to the inhibitor compared to other RAMs. Here we investigated structural and mechanistic bases for how the M66I change affects LEN binding to CA and viral replication. The high-resolution X-ray structure of the CA(M66I) hexamer revealed that the β-branched side chain of Ile66 induces steric hindrance specifically to LEN, thereby markedly reducing the inhibitor binding affinity. By contrast, the M66I substitution did not affect the binding of Phe-Gly (FG)-motif-containing cellular cofactors CPSF6, NUP153, or SEC24C, which engage the same hydrophobic pocket of CA. In cell culture, the M66I variant did not acquire compensatory mutations. Analysis of viral replication intermediates revealed that HIV-1
predominantly formed correctly matured viral cores, which were more stable than their wild-type counterparts. The mutant cores stably bound to the nuclear envelope but failed to penetrate inside the nucleus. Furthermore, the M66I substitution markedly altered HIV-1 integration targeting. Taken together, our findings elucidate mechanistic insights into how the M66I change confers remarkable resistance to LEN and affects HIV-1 replication. Moreover, our structural findings provide a powerful means for future medicinal chemistry efforts to rationally develop second-generation inhibitors with a higher barrier to resistance.IMPORTANCELenacapavir (LEN) is a highly potent and long-acting antiretroviral that works by a unique mechanism of targeting the viral capsid protein. The inhibitor is used in combination with other antiretrovirals to treat multi-drug-resistant HIV-1 infection in heavily treatment-experienced adults. Furthermore, LEN is in clinical trials for preexposure prophylaxis (PrEP) with interim results indicating 100% efficacy to prevent HIV-1 infections. However, one notable shortcoming is a relatively low barrier of viral resistance to LEN. Clinical trials and cell culture experiments identified emergent resistance mutations near the inhibitor binding site on capsid. The M66I variant was the most prevalent capsid substitution identified in patients receiving LEN to treat multi-drug-resistant HIV-1 infections. The studies described here elucidate the underlying mechanism by which the M66I substitution confers a marked resistance to the inhibitor. Furthermore, our structural findings will aid future efforts to develop the next generation of capsid inhibitors with enhanced barriers to resistance.
Details
- Title: Subtitle
- Structural and mechanistic bases for resistance of the M66I capsid variant to lenacapavir
- Creators
- Lorenzo Briganti - University of Colorado Anschutz Medical CampusArun S Annamalai - University of Colorado Anschutz Medical CampusStephanie M Bester - University of Colorado Anschutz Medical CampusGuochao Wei - University of Colorado Anschutz Medical CampusJonathan R Andino-Moncada - Florida State UniversitySatya P Singh - Florida State UniversityAlex B Kleinpeter - Center for Cancer ResearchMeghna Tripathi - Center for Cancer ResearchBinh Nguyen - Center for Cancer ResearchRajalingam Radhakrishnan - Dana-Farber Cancer InstituteParmit K Singh - Dana-Farber Cancer InstituteJuliet Greenwood - Dana-Farber Cancer InstituteLauren I Schope - University of Colorado Anschutz Medical CampusReed Haney - University of Colorado Anschutz Medical CampusSzu-Wei Huang - University of Colorado Anschutz Medical CampusEric O Freed - Center for Cancer ResearchAlan N Engelman - Dana-Farber Cancer InstituteAshwanth C Francis - Florida State UniversityMamuka Kvaratskhelia - University of Colorado Anschutz Medical Campus
- Resource Type
- Journal article
- Publication Details
- mBio, Vol.16(5), p.e0361324
- DOI
- 10.1128/mbio.03613-24
- PMID
- 40231850
- PMCID
- PMC12077090
- NLM abbreviation
- mBio
- ISSN
- 2161-2129
- eISSN
- 2150-7511
- Grant note
- R01 AI052014 / NIAID NIH HHS K99 AI174891 / NIAID NIH HHS U54 AI170791 / NIAID NIH HHS R01 AI157802 / NIAID NIH HHS U54 AI170855 / NIAID NIH HHS R01 AI181627 / NIAID NIH HHS R21 AI174879 / NIAID NIH HHS T32 AI150547 / NIAID NIH HHS R01 AI162665 / NIAID NIH HHS
- Language
- English
- Date published
- 05/14/2025
- Academic Unit
- Microbiology and Immunology
- Record Identifier
- 9984826360702771
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