1. Academic Validation
  2. Rational Design of Broad-Spectrum Non-Nucleoside Reverse Transcriptase Inhibitors via Pharmacophore-Oriented Generative Artificial Intelligence

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

  • J Med Chem. 2026 Apr 9;69(7):8503-8520. doi: 10.1021/acs.jmedchem.6c00048.
Kun Zhang 1 2 Yuhan Lin 3 Ling Dong 1 2 Yuting Niu 1 2 Jian Peng 4 Christophe Pannecouque 5 Erik De Clercq 5 Phuong-Thao Tran 6 Guobo Li 4 Tiancong Zhao 7 Xudong Li 3 Shuo Su 8 Shuai Wang 1 Fen-Er Chen 1 2
Affiliations

Affiliations

  • 1 Department of Chemistry, Engineering Center of Catalysis and Synthesis for Chiral Molecules, Shanghai Engineering Research Center of Industrial Asymmetric Catalysis of Chiral Drugs, State Key Laboratory of Green Chemical Synthesis and Conversion, Fudan University, Shanghai 200433, China.
  • 2 Institute of Pharmaceutical Research and School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China.
  • 3 School of Data Science, Shanghai, Fudan University, Shanghai 200433, China.
  • 4 Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China.
  • 5 Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium.
  • 6 Department of Pharmaceutical Chemistry, Hanoi University of Pharmacy, 13-15 Le Thanh Tong,Cua Nam, Hanoi 10000, Viet Nam.
  • 7 College of Smart Materials and Future Energy, Fudan University, Shanghai 200433, China.
  • 8 Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai 200032, China.
Abstract

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.

Figures
Products