Design, synthesis and profiling of highly potent antivirals targeting emerging drug-resistant HIV-1 variants

Lenacapavir (LEN), the first-in-class HIV capsid inhibitor (CAI), is approved by FDA as a long acting injectable (LAI) for both treatment and pre-exposure prophylaxis (PrEP). Despite its exceptional potency and long pharmacokinetics (PK), a few major resistant mutations have been selected in LEN-treated patients, underscoring the need to develop second-generation LEN analogs to mitigate resistance. Particularly, the M66I mutation confers an extraordinarily high-level LEN resistance, essentially abrogating LEN potency. In this work, we have designed and synthesized LEN analogs featuring a cycloalkyl R² in subunit B drastically different from known analogs. Against wild-type HIV-1, the potency of our analog 3 (EC₅₀ = 0.073 nM) was 2.6-fold higher than LEN (EC₅₀ = 0.19 nM). More importantly, against the M66I mutant, 3 (EC₅₀ = 5.8 nM) was decisively more potent than LEN (EC₅₀ > 15 μM) or any known analogs. We have also shown that the size of the R² cycloalkyl ring is a major pharmacophore factor as a smaller (cyclopropyl, analog 1) or bigger (cyclohexyl, analog 4) ring confers weaker antiviral potency against both WT HIV-1 and M66I. The vastly improved profile of our lead 3 against M66I was confirmed in the target binding thermal shift assay. These results strongly validate our design and may represent a breakthrough in LEN-based HIV therapy and prophylaxis.