Derek Hansen

Lenacapavir (LEN) is a first-in-class capsid (CA) inhibitor for the treatment and prevention of HIV-1 infection. While LEN has shown potent antiviral activity across all major HIV-1 subtypes, the impact of existing HIV-1 CA sequence diversity on the activity of LEN remains to be determined. Here, we identified natural polymorphisms within the LEN-binding site and assessed each for their impact on viral infectivity and susceptibility to LEN. Using a co-crystal structure of LEN in complex with a CA hexamer, we identified 29 binding site residues within five angstroms of LEN and analyzed each for naturally occurring polymorphisms across a multiclade collection of >10,000 unique HIV-1 gag sequences. Eleven of these CA residues, including five (M66, Q67, K70, N74, and A105) previously associated with LEN resistance when mutated, were invariant across these sequences. The remaining 18 residues showed one or more substitutions with a ≥0.5% prevalence for a total of 54 CA polymorphisms. When introduced as site-directed mutants (SDMs) in an NL4.3-based reporter virus and evaluated for infectivity and drug susceptibility in MT-4 cells, 74% (40/54) showed impaired infectivity (0.01%–77% of wild type), with 96% (46/48) exhibiting minimal change (less than threefold) in susceptibility to LEN. While CA substitutions L56V and N57H conferred high-level resistance to LEN (72- and 4,890-fold, respectively), both variants showed diminished replication capacity in primary T-cells relative to the wild-type virus. Collectively, these results indicate that existing CA natural HIV-1 sequence diversity within the LEN-binding site is rare and should minimally impact LEN efficacy in treatment-naïve individuals. IMPORTANCE: HIV-1 capsid protein mediates multiple essential functions throughout the viral replication cycle, making it an attractive target for therapeutic intervention. Lenacapavir (LEN), a first-in-class HIV-1 capsid inhibitor, is being evaluated as a long-acting option in multiple ongoing clinical studies for HIV treatment and prevention. Twice-yearly lenacapavir is approved in multiple countries for the treatment of adults with multi-drug-resistant HIV-1 in combination with other antiretrovirals, and its investigational use for pre-exposure prophylaxis has shown 99.9%–100% efficacy in preventing HIV infection among a broad and geographically diverse range of study participants. In this report, we investigated how HIV-1 sequence diversity within the LEN binding site may impact virus replication capacity and sensitivity to LEN. Our data demonstrate high capsid sequence conservation across a large and diverse collection of HIV-1 variants, with the majority of naturally occurring capsid polymorphisms having a detrimental effect on viral infectivity and minimal impact on susceptibility to LEN.

Long-acting antiretroviral agents for preexposure prophylaxis (PrEP) represent a promising new alternative to daily oral regimens for HIV prevention. Lenacapavir (LEN) is a first-in-class long-acting capsid inhibitor approved for the treatment of HIV-1 infection. Here, we assessed the efficacy of LEN for PrEP using a single high-dose simian-human immunodeficiency virus (SHIV) rectal challenge macaque model. In vitro, LEN showed potent antiviral activity against SHIV, as it did for HIV-1. In macaques, a single subcutaneous administration of LEN demonstrated dose proportional increases in and durability of drug plasma levels. A high-dose SHIV inoculum for the PrEP efficacy evaluation was identified via virus titration in untreated macaques. LEN-treated macaques were challenged with high-dose SHIV 7 weeks after drug administration, and the majority remained protected from infection, as confirmed by plasma PCR, cell-associated proviral DNA, and serology testing. Complete protection and superiority to the untreated group was observed among animals whose LEN plasma exposure exceeded its model-adjusted clinical efficacy target at the time of challenge. All infected animals had subprotective LEN concentrations and showed no emergent resistance. These data demonstrate effective SHIV prophylaxis in a stringent macaque model at clinically relevant LEN exposures and support the clinical evaluation of LEN for HIV PrEP in humans.