Exploring the HIV-1 Reverse Transcriptase p51/p66 Interface: Structure-Based Design and Optimization of Novel 2,4,6-Trisubstituted Pyrimidines as Potent NNRTIs with Improved Resistance Profiles

The emerging challenge of HIV-1 drug resistance urgently demands the development of next-generation HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs). Herein, we designed and synthesized two series of novel 2,4,6-trisubstituted pyrimidines that target a previously insufficiently explored binding site at the interface between the p66 and p51 subunits of HIV-1 reverse transcriptase (RT). After iterative structural optimization, <b>15k</b> turned out to exhibit potent antiviral activity to wild-type and mutant HIV-1 strains, with EC₅₀ values ranging from 0.0046 to 0.033 μM and relatively low cytotoxicity (CC₅₀ = 26.64 μM). Molecular modeling revealed that <b>15k</b> adopts a unique "Y-shaped" conformation within the NNRTI-binding pocket (NNIBP), forming novel hydrogen bonds with E138 and K101 at the p51-p66 interface─a key factor contributing to its potent resistance profile. Moreover, <b>15k</b> exhibits favorable <i>in vivo</i> metabolic (<i>T</i>_1/2 = 2.12 h) and safety profiles. In summary, newly discovered <b>15k</b> represents a promising anti-HIV-1 drug candidate for further development.