Systematic Structure–Activity Relationship Investigation on Novel 5-Alkyl-6-benzyl-2-{[(methylthio/phenylthio)alkyl]thio}-pyrimidin-4(3H)-ones Endowed with Potent Anti-HIV-1 Activity

Four series of 5-alkyl-6-benzyl-2-[(methylthio/phenylthio)alkyl]thiopyrimidin-4(3H)-ones were systematically diversified at C2, C5, and C6 and evaluated as anti-HIV-1 agents. In MT-4 cells, these compounds displayed low-to-moderate cytotoxicity and subnanomolar-to-submicromolar inhibition of WT HIV-1, with potency governed by a balanced SAR. Ortho-dihalogenated C6-benzyl groups, particularly 2,6-F2 and 2,6-Cl2, were generally favored. In the 2,6-dihalobenzyl series, optimal activity required C5 methyl combined with para-substituted phenylthiomethyl groups at C2, whereas 3,5-Me2-benzyl analogues benefited from C5 isopropyl paired with methylthioethyl (24l) or unsubstituted phenylthiomethyl (24m) C2 side chains. The p-methoxyphenylthiomethyl thiothymine derivatives 21e (2,6-F2) and 23e (2,6-Cl2) emerged as lead inhibitors, showing high selectivity, potent activity against WT and clinically relevant HIV-1 variants, superior efficacy compared with nevirapine and efavirenz, dapivirine-like potency, and improved resistance tolerance relative to phenethyl-S-DABO bioisosteres. Together, biological and QSAR and docking data contribute to defining optimization strategies aimed at achieving durable anti-HIV-1 activity within the investigated chemotype and support further development of next-generation NNRTIs with improved efficacy against clinically relevant HIV-1 strains.