Discovery, synthesis, and optimization of an N-alkoxy indolylacetamide against HIV-1 carrying NNRTI-resistant mutations from the Isatis indigotica root

From an aqueous decoction of the traditional Chinese medicine "ban lan gen" (the Isatis indigotica root), an Antiviral natural product CI - 39 was isolated as an NNRTI (non-nucleoside Reverse Transcriptase Inhibitor) (EC₅₀ = 3.40 μM). Its novel structure was determined as methyl (1-methoxy-1H-indol-3-yl)acetamidobenzoate by spectroscopic data and confirmed by single crystal X-ray diffraction. Through synthesis and structure-activity relationship (SAR) investigation of CI - 39 and 57 new derivatives (24 with EC₅₀ values of 0.06-8.55 μM), two optimized derivatives 10f and 10i (EC₅₀: 0.06 μM and 0.06 μM) having activity comparable to that of NVP (EC₅₀ = 0.03 μM) were obtained. Further evaluation verified that 10f and 10i were RT DNA polymerase inhibitors and exhibited better activities and drug resistance folds compared to NVP against seven NNRTI-resistant strains carrying different mutations. Especially, 10i (EC₅₀ = 0.43 μM) was more active to the L100I/K103N double-mutant strain as compared to both NVP (EC₅₀ = 0.76 μM) and EFV (EC₅₀ = 1.08 μM). The molecular docking demonstrated a possible binding pattern between 10i and RT and revealed activity mechanism of 10i against the NNRTI-resistant strains.