Rational Design of Broad-Spectrum Non-Nucleoside Reverse Transcriptase Inhibitors via Pharmacophore-Oriented Generative Artificial Intelligence

Guided by the pharmacophore-oriented molecular generation platform PhoreGen, we employed rilpivirine (RPV) as a lead compound to generate 300 structurally diverse analogs that preserve key pharmacophoric features. Subsequent drug-likeness evaluation, molecular docking score, and synthetic feasibility led to the identification of compound No.102 (A19), which displayed potent inhibition activity against WT HIV-1 (EC50 = 3.15 nM) and low cytotoxicity (CC50 > 335 μM). Subsequent structure–activity relationship optimization identified A24, which demonstrated robust activity against clinically relevant drug-resistant HIV-1 mutants (EC50 = 2.07–28.8 nM). Notably, compared to RPV, A24 exhibited significantly reduced cytotoxicity (CC50 = 82.3 μM vs. 3.98 μM) and enhanced potency against the Y188L (EC50 = 28.8 nM vs. 79.4 nM) and F227L + V106A (EC50 = 19.0 nM vs. 81.6 nM) mutants. Pharmacokinetic evaluations revealed that A24 exhibited attenuated CYP enzyme inhibition (IC50 ≥ 1.88 μM), reduced hERG-related toxicity (IC50 = 2.633 μM), and improved metabolic stability (human t1/2 = 39.1 min). Collectively, these favorable properties position A24 as a promising NNRTI for further development.