Structure- and Privileged Fragment-Based Iterative Optimization: Discovery of 2,4-Disubstituted-6-aminopyrimidines as Novel HIV‑1 NNRTIs with Potent Activity against Drug-Resistant Strains and Favorable Safety Profiles

There is an urgent need to develop next-generation non-nucleoside reverse transcriptase inhibitors (NNRTIs) to combat the rapid emergence of drug-resistant HIV-1 variants. Guided by cocrystal structures of ETR and K-5a2 bound to HIV-1 reverse transcriptase (RT), a privileged-fragment hybridization strategy was employed to enhance antiviral activity and resistance profiles. Through three rounds of optimization, compound 18d exhibited potent activity against wild-type (WT) and seven clinically relevant mutant HIV-1 strains, with EC50 values of 1.5–31 nM, surpassing ETR (2.6–41 nM). Molecular dynamics simulations revealed that the aminopyrimidine and pyridine fragments of 18d formed extensive hydrogen bonds with surrounding residues, contributing to its strong resistance barrier. Moreover, 18d displayed favorable metabolic stability in vivo (T1/2 = 1.42 h) and an excellent safety profile. Collectively, these findings highlight 18d as a promising next-generation NNRTI candidate for further development.