QM/QM studies for Michael reaction in coronavirus main protease (3CL Pro)

Abstract

Severe acute respiratory syndrome (SARS) is an illness caused by a novel corona virus wherein the main proteinase called 3CL(Pro) has been established as a target for drug design. The mechanism of action involves nucleophilic attack by Cys145 present in the active site on the carbonyl carbon of the scissile amide bond of the substrate and the intermediate product is stabilized by hydrogen bonds with the residues of the oxyanion hole. Based on the X-ray structure of 3CL(Pro) co-crystallized with a trans-alpha,beta-unsaturated ethyl ester (Michael acceptor), a set of QM/QM and QM/MM calculations were performed, yielding three models with increasingly higher the number of atoms. A previous validation step was performed using classical theoretical calculation and PROCHECK software. The Michael reaction studies show an exothermic process with -4.5 kcal/mol. During the reaction pathway, an intermediate is formed by hydrogen and water molecule migration from a histidine residue and solvent, respectively. In addition, similar with experimental results, the complex between N3 and 3CL(Pro) is 578 kcal/mol more stable than N1-3CL(Pro) using Own N-layer Integrated molecular Orbital molecular Mechanics (ONIOM) approach. We suggest 3CL(Pro) inhibitors need small polar groups to decrease the energy barrier for alkylation reaction. These results can be useful for the development of new compounds against SARS.

Fig. 1

(A) N1: In red the selected atoms with higher layer and in black atoms with lower layer, (B) N3 and (C) AG7088.

Fig. 2

Model of N1 complexed with oxyanion and catalytic system. The colors red, black, and * symbol were used to assign atoms with higher layer, lower layer, and frozen respectively.

Fig. 3

Selected MO plots for N1 (A–D) and AG7088 (E and F) in vacuum system. All hydrogens were hidden for a best visualization. (A) N1: HOMO–PM3MM; (B) N1: LUMO–PM3MM ; (C) N1: HOMO–B3LYP/6-31G(d); (D) N1: LUMO–B3LYP/6-31G(d); (E) N3: HOMO–B3LYP/6-31G(d); (F) N3: LUMO–B3LYP/6-31G(d); (G) AG7088 HOMO–B3LYP/6-31G(d); (H) AG7088 LUMO–B3LYP/6-31G(d).

Fig. 4

Minimum energy reaction path. The x-axis defines the nucleophilic attack coordinate (interatomic distance between C₁ and S(Cys145), and the y-axis defines relative energy. The distances are in angstroms. The colors red and black define atoms with higher and lower layer respectively.

Fig. 5

Oxyprod: The distances are in angstroms. The colors red and black define atoms with higher and lower layer respectively.

Fig. 6

Ramachandran plot for: (A) X-ray structure, (B) AMBER, (C) UFF, (D) PM3MM:UFF and (E) AM1:UFF. Amino acids found in disallowed region are in red.

Fig. 7

(A) Interaction between active site and N1; (B) select hydrogen bonds between ligand and N1 and N3 by PM3MM:UFF.