Synthesis, characterization, proteolytic activity inhibition, ADMET prediction, and molecular docking studies of novel indole derivatives as potential SARS-CoV-2 protease inhibitors

Both the main protease (M^pro) and papain protease (PL^pro) are fundamental enzymes in SARS-CoV-2 life cycle. In this study, we have targeted these two enzymes using novel indole derivatives as antiviral agents. The synthesized compounds were thoroughly characterized by Fourier-transform infrared spectroscopy (FT-IR), UV–vis, ¹H, ¹³C, and 2D nuclear magnetic resonance (NMR), high-resolution mass spectrometry (HRMS), and melting point (m.p.). The optimized structure, reactivity, and stability of the synthesized compounds were calculated using Density Functional Theory (DFT) at the B3LYP/6–31G(d,p) level. Using in silico ADMET prediction along with molecular docking, we found that the synthesized compounds presented good docking scores and very low predicted inhibition constants (Pki) from low micromolar to nanomolar ranges. In particular, compounds 10 and 11 with respective Pki values of 1.68 μM and 387.71 nM for M^pro and 402.50 nM and 27.10 nM for PL^pro. These two compounds are engaged in vast range of interactions with the active sites of both enzymes. Further in vitro investigations using fluorescence resonance energy transfer (FRET) assays demonstrated that compounds 10 and 11 inhibited M^pro proteolytic activity with approximate IC₅₀ values of 20 µM and 10 µM, respectively. These findings suggest that these new indole derivatives could serve as promising candidates for the development of drugs against SARS-CoV-2 and potentially other future coronaviruses.