An insight into the interaction between α-ketoamide- based inhibitor and coronavirus main protease: A detailed in silico study

Abstract

The search for therapeutic drugs that can neutralize the effects of COVID-2019 (SARS-CoV-2) infection is the main focus of current research. The coronavirus main protease (M pro ) is an attractive target for anti-coronavirus drug design. Further, α-ketoamide is proved to be very effective as a reversible covalent-inhibitor against cysteine proteases. Herein, we report on the non-covalent to the covalent adduct formation mechanism of α-ketoamide-based inhibitor with the enzyme active site amino acids by QM/SQM model (QM = quantum mechanical, SQM = semi-empirical QM). To uncover the mechanism, we focused on two approaches: a concerted and a stepwise fashion. The concerted pathway proceeds via deprotonation of the thiol of cysteine (here, Cys 145 SγH) and simultaneous reversible nucleophilic attack of sulfur onto the α-ketoamide warhead. In this work, we propose three plausible concerted pathways. On the contrary, in a traditional two-stage pathway, the first step is proton transfer from Cys 145 SγH to His 41 Nδ forming an ion pair, and consecutively, in the second step, the thiolate ion attacks the α-keto group to form a thiohemiketal. In this reaction, we find that the stability of the tetrahedral intermediate oxyanion/hydroxyl group plays an important role. Moreover, as the α-keto group has two faces Si or Re for the nucleophilic attack, we considered both possibilities of attack leading to S- and R-thiohemiketal. We computed the structural, electronic, and energetic parameters of all stationary points including transition states via ONIOM and pure DFT method. Additionally, to characterize covalent, weak noncovalent interaction (NCI) and hydrogen-bonds, we applied NCI-reduced density gradient (NCI-RDG) methods along with Bader's Quantum Theory of Atoms-in-Molecules (QTAIM) and natural bonding orbital (NBO) analysis

Targeting SARS-CoV-2 Non-Structural Proteins

“…Another inhibitor is calpain inhibitor I ( 10 ), a synthetic tripeptide aldehyde that inhibits the main protease by forming a reversible tetrahedral complex with the cysteine residue of the enzyme [ 46 , 73 ].…”

Targeting SARS-CoV-2 Main Protease for Treatment of COVID-19: Covalent Inhibitors Structure–Activity Relationship Insights and Evolution Perspectives

“…The hydroxy group of the hemithioacetal gives a hydrogen bond to His 41 , while the oxygen of the carboxamide moiety accepts hydrogen bonds from the main-chain amides of Gly 143 , Cys 145 , and Ser 144 (Figure ). ,, …”

“…The hydroxy group of the hemithioacetal gives a hydrogen bond to His 41 , while the oxygen of the carboxamide moiety accepts hydrogen bonds from the main-chain amides of Gly 143 , Cys 145 , and Ser 144 (Figure 14). 14,56,57 In accordance with the potential covalent inhibitory effect, the α-ketoamide warhead has been extensively used to develop new SARS-CoV-2 M PRO inhibitors.…”

The role of quantum chemistry in covalent inhibitor design

“…Inhibition of cysteine proteases by α-ketoamide compounds was investigated [115] by reaction mechanism calculations on model systems using ONIOM-B3LYP/6-31G(d):PM6 geometry optimizations and single point ωB97X-D/6-31G(d,p):PM6 energy evaluations. It was found that the deprotonation of the cysteine thiol and the nucleophilic attack of sulfur onto the α-ketoamide warhead can proceed both with stepwise and concerted mechanisms.…”