Molecular modeling and chemical modification for finding peptide inhibitor against severe acute respiratory syndrome coronavirus main proteinase

Abstract

Severe acute respiratory syndrome (SARS) is a respiratory disease caused by a newly found virus, called SARS coronavirus. In this study, the cleavage mechanism of the SARS coronavirus main proteinase (M ^pro or 3CL ^pro) on the octapeptide NH ₂-AVLQ ↓ SGFR-COOH was investigated using molecular mechanics and quantum mechanics simulations based on the experimental structure of the proteinase. It has been observed that the catalytic dyad (His-41/Cys-145) site between domains I and II attracts the π electron density from the peptide bond Gln–Ser, increasing the positive charge on C(CO) of Gln and the negative charge on N(NH) of Ser, so as to weaken the Gln–Ser peptide bond. The catalytic functional group is the imidazole group of His-41 and the S in Cys-145. N _δ1 on the imidazole ring plays the acid–base catalytic role. Based on the “distorted key theory” [K.C. Chou, Anal. Biochem. 233 (1996) 1–14], the possibility to convert the octapeptide to a competent inhibitor has been studied. It has been found that the chemical bond between Gln and Ser will become much stronger and no longer cleavable by the SARS enzyme after either changing the carbonyl group CO of Gln to CH ₂ or CF ₂ or changing the NH of Ser to CH ₂ or CF ₂. The octapeptide thus modified might become an effective inhibitor or a potential drug candidate against SARS.