Inhibition Mechanism of SARS‐CoV‐2 Main Protease with Ketone‐Based Inhibitors Unveiled by Multiscale Simulations. Insights for Improved Designs

<p>We present the results of combined classical and QM/MM simulations for the inhibition of SARS-CoV-2 3CL protease by a recently proposed ketone-based covalent inhibitor, PF-00835231, that is under clinical trial. In the noncovalent complex formed after binding into the active site the carbonyl group of this inhibitor is accommodated into the oxyanion hole formed by the NH main chain groups of residues 143 to 145. The P1-P3 groups of the inhibitor establish similar interaction with the enzyme to those of equivalent groups in the natural peptide substrate, while the hydroxymethyl moiety of the inhibitor partly mimics the interactions established by the P1’ group of the peptide in the active site. Regarding the formation of the covalent complex, the reaction is initiated after the proton transfer from Cys145 to His41. Formation of the covalent hemithioacetal complex takes place by means of the nucleophilic attack of the Sg atom of Cys145 on the electron deficient carbonyl carbon atom and a proton transfer from the catalytic His41 to the carbonyl oxygen atom mediated by the hydroxyl group. Our findings can be used as a guide to propose modifications of the inhibitor in order to increase its affinity by the 3CL protease.</p>

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Insights into the Binding and Covalent Inhibition Mechanism of PF-07321332 to SARS-CoV-2 Mpro

10.33774/chemrxiv-2021-fq3mg ◽

2021 ◽

Author(s):

Son Tung Ngo ◽

Trung Hai Nguyen ◽

Nguyen Thanh Tung ◽

Binh Khanh Mai

Keyword(s):

Ligand Binding ◽

Bound State ◽

Catalytic Triad ◽

Inhibition Mechanism ◽

Binding Process ◽

Covalent Inhibition ◽

Main Protease ◽

Dynamics Simulations ◽

Covalent Inhibitor

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been causing the COVID-19 pandemic resulting in several million death were reported. Numerous investigations have been carried out to discover a compound that can inhibit the biological activity of SARS-CoV-2 main protease, which is an enzyme related to the viral replication. Among these, PF-07321332 is currently under clinical trial for COVID-19 therapy. Therefore, in this work, atomistic and electronic simulations were performed to unravel the binding and covalent inhibition mechanism of the compound to Mpro. Initially, 5 µs of steered-molecular dynamics simulations were carried out to evaluate the ligand-binding process to SARS-CoV-2 Mpro. Successfully generated bound state between two molecules showed the important role of the PF-07321332 pyrrolidinyl group and the residues Glu166 and Gln189 in the ligand-binding process. Moreover, from the MD-refined structure, quantum mechanics/molecular mechanics (QM/MM) calculations were carried out to unravel the reaction mechanism for the formation of thioimidate product from SARS-CoV-2 Mpro and PF07321332 inhibitor. We found that the catalytic triad Cys145–His41–Asp187 of SARS-CoV-2 Mpro plays important role in the activation of PF-07321332 covalent inhibitor, which renders the deprotonation of Cys145 and, thus, facilitates further reaction. Our results are definitely beneficial for better understanding on the inhibition mechanism and designing new effective inhibitors for SARS-CoV-2 Mpro.

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Novel inhibition mechanism of SARS-CoV-2 main protease by ebselen and its derivatives

10.1101/2021.03.11.434764 ◽

2021 ◽

Author(s):

Kangsa Amporndanai ◽

Xiaoli Meng ◽

Weijuan Shang ◽

Zhenmig Jin ◽

Yao Zhao ◽

...

Keyword(s):

Mass Spectrometry ◽

Chemical Reactivity ◽

Inhibition Mechanism ◽

Selenium Atom ◽

Binding Modes ◽

Selenium Compounds ◽

Main Protease ◽

Therapeutic Development ◽

Infected Cells ◽

Molecular Mode

AbstractThe global emergence of SARS-CoV-2 has triggered numerous efforts to develop therapeutic options for COVID-19 pandemic. The main protease of SARS-CoV-2 (Mpro), which is a critical enzyme for transcription and replication of SARS-CoV-2, is a key target for therapeutic development against COVID-19. An organoselenium drug called ebselen has recently been demonstrated to have strong inhibition against Mpro and antiviral activity but its molecular mode of action is unknown preventing further development. We have examined the binding modes of ebselen and its derivative in Mpro via high resolution co-crystallography and investigated their chemical reactivity via mass spectrometry. Stronger Mpro inhibition than ebselen and potent ability to rescue infected cells were observed for a number of ebselen derivatives. A free selenium atom bound with cysteine 145 of Mpro catalytic dyad has been revealed by crystallographic studies of Mpro with ebselen and MR6-31-2 suggesting hydrolysis of the enzyme bound organoselenium covalent adduct, formation of a phenolic by-product is confirmed by mass spectrometry. The target engagement of these compounds with an unprecedented mechanism of SARS-CoV-2 Mpro inhibition suggests wider therapeutic applications of organo-selenium compounds in SARS-CoV-2 and other zoonotic beta-corona viruses.

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Initial study on SARS-CoV-2 main protease inhibition mechanism of some potential drugs using molecular docking simulation

Vietnam Journal of Science and Technology ◽

10.15625/2525-2518/58/5/14914 ◽

2020 ◽

Vol 58 (6) ◽

pp. 665

Author(s):

Quan Minh PHAM ◽

Thuy Huong Thi LE ◽

Toan Quoc TRAN ◽

Tung Son NGO ◽

Dan Trong NGUYEN ◽

...

Keyword(s):

Antiviral Treatment ◽

Docking Simulation ◽

Data Bank ◽

Initial Study ◽

Atomic Level ◽

Inhibition Mechanism ◽

Protease Inhibition ◽

Molecular Docking Simulation ◽

Main Protease ◽

Docking Protocol

The infection by the new coronavirus SARS-CoV-2 (called as COVID-19 disease) is a worldwide emergency, however, there is no antiviral treatment or vaccine until now. The crystal structure of SARS-CoV-2 main protease has been made publicity in the Protein Data Bank recently. Many efforts have been conducted by scientists including the use of several commercial medicines, however, understanding at atomic level how these compounds prevent SARS-CoV-2 protease is still lacking. In this context docking protocol was employed to rapidly estimate the binding affinity and binding pose of six drugs on the main protease.

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The Se–S Bond Formation in the Covalent Inhibition Mechanism of SARS-CoV-2 Main Protease by Ebselen-like Inhibitors: A Computational Study

International Journal of Molecular Sciences ◽

10.3390/ijms22189792 ◽

2021 ◽

Vol 22 (18) ◽

pp. 9792

Author(s):

Angela Parise ◽

Isabella Romeo ◽

Nino Russo ◽

Tiziana Marino

Keyword(s):

Potential Energy Surfaces ◽

Density Functional ◽

Computational Study ◽

Noncovalent Complex ◽

Covalent Bond ◽

Hydroxyl Group ◽

Inhibition Mechanism ◽

Hybrid Functional ◽

Main Protease ◽

Donor And Acceptor

The inhibition mechanism of the main protease (Mpro) of SARS-CoV-2 by ebselen (EBS) and its analog with a hydroxyl group at position 2 of the benzisoselenazol-3(2H)-one ring (EBS-OH) was studied by using a density functional level of theory. Preliminary molecular dynamics simulations on the apo form of Mpro were performed taking into account both the hydrogen donor and acceptor natures of the Nδ and Nε of His41, a member of the catalytic dyad. The potential energy surfaces for the formation of the Se–S covalent bond mediated by EBS and EBS-OH on Mpro are discussed in detail. The EBS-OH shows a distinctive behavior with respect to EBS in the formation of the noncovalent complex. Due to the presence of canonical H-bonds and noncanonical ones involving less electronegative atoms, such as sulfur and selenium, the influence on the energy barriers and reaction energy of the Minnesota hybrid meta-GGA functionals M06, M06-2X and M08HX, and the more recent range-separated hybrid functional wB97X were also considered. The knowledge of the inhibition mechanism of Mpro by the small protease inhibitors EBS or EBS-OH can enlarge the possibilities for designing more potent and selective inhibitor-based drugs to be used in combination with other antiviral therapies.

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Crystal Structure of Feline Infectious Peritonitis Virus Main Protease in Complex with Synergetic Dual Inhibitors

Journal of Virology ◽

10.1128/jvi.02685-15 ◽

2015 ◽

Vol 90 (4) ◽

pp. 1910-1917 ◽

Cited By ~ 15

Author(s):

Fenghua Wang ◽

Cheng Chen ◽

Xuemeng Liu ◽

Kailin Yang ◽

Xiaoling Xu ◽

...

Keyword(s):

Crystal Structure ◽

Zinc Ion ◽

Inhibition Mechanism ◽

Granulomatous Disease ◽

Feline Infectious Peritonitis Virus ◽

Feline Infectious Peritonitis ◽

Main Protease ◽

Michael Acceptor ◽

Dual Inhibitors ◽

Dual Inhibition

ABSTRACTCoronaviruses (CoVs) can cause highly prevalent diseases in humans and animals. Feline infectious peritonitis virus (FIPV) belongs to the genusAlphacoronavirus, resulting in a lethal systemic granulomatous disease called feline infectious peritonitis (FIP), which is one of the most important fatal infectious diseases of cats worldwide. No specific vaccines or drugs have been approved to treat FIP. CoV main proteases (Mpros) play a pivotal role in viral transcription and replication, making them an ideal target for drug development. Here, we report the crystal structure of FIPV Mproin complex with dual inhibitors, a zinc ion and a Michael acceptor. The complex structure elaborates a unique mechanism of two distinct inhibitors synergizing to inactivate the protease, providing a structural basis to design novel antivirals and suggesting the potential to take advantage of zinc as an adjunct therapy against CoV-associated diseases.IMPORTANCECoronaviruses (CoVs) have the largest genome size among all RNA viruses. CoV infection causes various diseases in humans and animals, including severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS). No approved specific drugs or vaccinations are available to treat their infections. Here, we report a novel dual inhibition mechanism targeting CoV main protease (Mpro) from feline infectious peritonitis virus (FIPV), which leads to lethal systemic granulomatous disease in cats. Mpro, conserved across all CoV genomes, is essential for viral replication and transcription. We demonstrated that zinc ion and a Michael acceptor-based peptidomimetic inhibitor synergistically inactivate FIPV Mpro. We also solved the structure of FIPV Mprocomplexed with two inhibitors, delineating the structural view of a dual inhibition mechanism. Our study provides new insight into the pharmaceutical strategy against CoV Mprothrough using zinc as an adjuvant therapy to enhance the efficacy of an irreversible peptidomimetic inhibitor.

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