Structure-based drug design and structural biology study of novel nonpeptide inhibitors of severe acute respiratory syndrome coronavirus main protease

Severe acute respiratory syndrome coronavirus (SARS-CoV) main protease (M^pro), a protein required for the maturation of SARS-CoV, is vital for its life cycle, making it an attractive target for structure-based drug design of anti-SARS drugs. The structure-based virtual screening of a chemical database containing 58 855 compounds followed by the testing of potential compounds for SARS-CoV M^pro inhibition leads to two hit compounds. The core structures of these two hits, defined by the docking study, are used for further analogue search. Twenty-one analogues derived from these two hits exhibited IC₅₀ values below 50 μM with the most potent one showing 0.3 μM. Furthermore, the complex structures of two potent inhibitors with SARS-CoV M^pro were solved by X-ray crystallography. They bind to the protein in a distinct manner compared to all published SARS-CoV M^pro complex structures. They inhibit SARS-CoV M^pro activity via intensive H-bond network and hydrophobic interactions, without the formation of a covalent bond. Interestingly, the most potent inhibitor induces protein conformational changes, and the inhibition mechanisms, particularly the disruption of catalytic dyad (His41 and Cys145), are elaborated.