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, 15k 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 15k 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, 15k exhibits favorable in vivo metabolic (T_1/2 = 2.12 h) and safety profiles. In summary, newly discovered 15k represents a promising anti-HIV-1 drug candidate for further development.