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 (Mpro or 3CLpro) on the octapeptide NH2-AVLQ downward arrowSGFR-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 pi 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. Ndelta1 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 CH2 or CF2 or changing the NH of Ser to CH2 or CF2. The octapeptide thus modified might become an effective inhibitor or a potential drug candidate against SARS.

Fig. 1

Schematic illustration to show (A) a cleavable octapeptide is chemically effectively bound to the active site of SARS enzyme and (B) although still bound to the active site, the peptide has lost its cleavability after its scissile bond was modified from a hybrid peptide bond to a strong bond. Adapted from Chou with permission.

Fig. 2

(A) Crystal structure of SARS CoV M^pro consists of two protomers A and B. Each protomer has three domains and the two protomers form a right angle at the domain III. The N finger of protomer B plugs into the domain II of protomer A. The green signs “<” represent the solvation water molecules. (B) The complex structure obtained by docking the octapeptide to SARS CoV M^pro and a follow-up energy minimization. The catalytic dyad of His-41 and Cys-145 is marked by an arrow and the peptide bond to be cleaved of the octapeptide is shown in green.

Fig. 3

(A) Catalytic active region of SARS CoV M^pro and the location of octapeptide (white). The catalytic dyad of His-41 and Cys-145 is shown in ball and stick form, the peptide bond Gln–Ser is in green, and the N finger is in pink. (B) Bridge water molecule (W) between SARS CoV M^pro and octapeptide. The distance O(W)–C(CO) is 4.70 Å, H₁(W)–N_δ1(His-41) is 2.39 Å, H₂(W)–N(NH) is 4.20 Å, and H(NH)–S(Cys-145) is 4.12 Å.

Fig. 4

(A) Hydrophilic and hydrophobic surfaces of octapeptide NH-AVLQ ↓ SGFR-COOH. The green parts are hydrophobic surfaces and the blue parts are hydrophilic surfaces. The four hydrophobic amino acid residues are R4(Ala), R3(Val), R3′(Phe), and R4′(Arg). (B) Hydrophilic and hydrophobic surfaces of SARS CoV M^pro. The hydrophobic residues R4(Ala) and R3(Val) are exposed in solvent, while R3′(Phe) and R4′(Arg) are covered by hydrophobic surfaces of the proteinase.

Fig. 5

(A) Electron density contour map of the peptide bond Gln–Ser in the π plane containing the carbonyl C and O atoms of Gln and N(NH) of Ser, as calculated in the gaseous phase. (B) Contour map of the differential electron density of peptide bond Gln–Ser in octapeptide AVLQSGFR, obtained by subtracting the electron density in the gaseous phase from the electron density in the proteinase background and solvent water.