Anastasia A Pronina, Dmitriy N Shcherbakov, Artem P Sanchez-Pimentel, Eugeniya V Nikitina, Fedor I Zubkov, Yulia V Meshkova, Mariya K Marenina, Nikolay V Maltsev, Svetlana V Belenkaya, Vadim O Trufanov, Ekaterina A Volosnikova, Anna V Zaykovskay, Sophia S Borisevich, Edward M Khamitov, Dmitriy S Baev, Egor A Mustaev, Alexey Yu Fedorov, Sergey G Arkhipov, Anna V Vlaskina, Anastasia R Nemchinova, Valeriya R Samygina, Oleg V Pyankov, Olga Yarovaya, Wei Xu, Nariman F Salakhutdinov, Mikhail V Khvostov
This study presents the design, synthesis, and evaluation of a novel series of covalent broad-spectrum inhibitors targeting the coronavirus main protease (3CLpro). The designed compounds feature a tetrahydroquinoline (THQ) scaffold functionalized with a chloroacetamide warhead. The most potent of this series in the primary screening assay, 4bf and 5bf, exhibited low micromolar IC₅₀ values against 3CLpro of SARS-CoV-2, SARS-CoV, and MERS-CoV, thereby demonstrating significant cross-reactivity. Structural analysis via X-ray crystallography confirmed covalent binding to the catalytic Cys145 residue. Complementary molecular dynamics simulations revealed stable binding modes and key interactions, highlighting differences in flexibility and residue contacts between the top inhibitors. While in vitro cytotoxicity was observed in Vero E6 cells, acute toxicity studies in mice revealed an LD₅₀ exceeding 1000 mg/kg for the lead compounds, indicating a promising in vivo safety profile. These findings establish substituted tetrahydroquinolines as a viable scaffold for the development of broad-spectrum anticoronaviral agents.