Mechanism of inhibition of SARS-CoV-2 Mpro by N3 peptidyl Michael acceptor explained by QM/MM simulations and design of new derivatives with tunable chemical reactivity

The SARS-CoV-2 main protease (Mpro) is essential for replication of the virus responsible for the COVID-19 pandemic, and one of the main targets for drug design. Here, we simulate the inhibition process of SARS-CoV-2 Mpro with a known Michael acceptor (peptidyl) inhibitor, N3. The free energy landscape for the mechanism of the formation of the covalent enzyme-inhibitor product is computed with QM/MM molecular dynamics methods. The simulations show a two-step mechanism, and give structures and calculated barriers in good agreement with experiment. Using these results and information from our previous investigation on the proteolysis reaction of SARS-CoV-2 Mpro, we design two new, synthetically accessible N3-analogues as potential inhibitors, in which the recognition and warhead motifs are modified. QM/MM modelling of the mechanism of inhibition of Mpro by these novel compounds indicates that both may be promising candidates as drug leads against COVID-19, one as an irreversible inhibitor and one as a potential reversible inhibitor.

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Mechanism of Inhibition of SARS-CoV-2 Mpro by N3 Peptidyl Michael Acceptor Explained by QM/MM Simulations and Design of New Derivatives with Tunable Chemical Reactivity

10.26434/chemrxiv.12941819 ◽

2020 ◽

Author(s):

Kemel Arafet ◽

Natalia Serrano-Aparicio ◽

Alessio Lodola ◽

Adrian Mulholland ◽

Florenci V. González ◽

...

Keyword(s):

Enzyme Inhibitor ◽

Chemical Reactivity ◽

Reversible Inhibitor ◽

Irreversible Inhibitor ◽

Mechanism Of Inhibition ◽

Main Protease ◽

Michael Acceptor ◽

Molecular Dynamics Methods ◽

Potential Inhibitors ◽

Drug Leads

The SARS-CoV-2 main protease (Mpro) is essential for replication of the virus responsible for the COVID-19 pandemic, and one of the main targets for drug design. Here, we simulate the inhibition process of SARS-CoV-2 Mpro with a known Michael acceptor (peptidyl) inhibitor, N3. The free energy landscape for the mechanism of the formation of the covalent enzyme-inhibitor product is computed with QM/MM molecular dynamics methods. The simulations show a two-step mechanism, and give structures and calculated barriers in good agreement with experiment. Using these results and information from our previous investigation on the proteolysis reaction of SARS-CoV-2 Mpro, we design two new, synthetically accessible N3-analogues as potential inhibitors, in which the recognition and warhead motifs are modified. QM/MM modelling of the mechanism of inhibition of Mpro by these novel compounds indicates that both may be promising candidates as drug leads against COVID-19, one as an irreversible inhibitor and one as a potential reversible inhibitor.

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

Nature Communications ◽

10.1038/s41467-021-23313-7 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Kangsa Amporndanai ◽

Xiaoli Meng ◽

Weijuan Shang ◽

Zhenmig Jin ◽

Michael Rogers ◽

...

Keyword(s):

Mass Spectrometry ◽

Chemical Reactivity ◽

Inhibition Mechanism ◽

Selenium Atom ◽

Binding Modes ◽

Mechanism Of Inhibition ◽

Main Protease ◽

Therapeutic Development ◽

Infected Cells ◽

Corona Viruses

AbstractThe SARS-CoV-2 pandemic has triggered global efforts to develop therapeutics. The main protease of SARS-CoV-2 (Mpro), critical for viral replication, is a key target for therapeutic development. An organoselenium drug called ebselen has been demonstrated to have potent Mpro inhibition and antiviral activity. 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 derivatives. A free selenium atom bound with cysteine of catalytic dyad has been revealed in crystallographic structures of Mpro with ebselen and MR6-31-2 suggesting hydrolysis of the enzyme bound organoselenium covalent adduct and formation of a phenolic by-product, confirmed by mass spectrometry. The target engagement with selenation mechanism of inhibition suggests wider therapeutic applications of these compounds against SARS-CoV-2 and other zoonotic beta-corona viruses.

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Investigation of Some Antiviral N-Heterocycles as COVID 19 Drug: Molecular Docking and DFT Calculations

International Journal of Molecular Sciences ◽

10.3390/ijms21113922 ◽

2020 ◽

Vol 21 (11) ◽

pp. 3922 ◽

Cited By ~ 19

Author(s):

Mohamed Hagar ◽

Hoda A. Ahmed ◽

Ghadah Aljohani ◽

Omaima A. Alhaddad

Keyword(s):

Dipole Moment ◽

Molecular Docking ◽

Dft Calculations ◽

Binding Affinity ◽

Electrostatic Potential ◽

Density Functional ◽

Molecular Electrostatic Potential ◽

Hydrophobic Interactions ◽

Chemical Reactivity ◽

Main Protease

The novel coronavirus, COVID-19, caused by SARS-CoV-2, is a global health pandemic that started in December 2019. The effective drug target among coronaviruses is the main protease Mpro, because of its essential role in processing the polyproteins that are translated from the viral RNA. In this study, the bioactivity of some selected heterocyclic drugs named Favipiravir (1), Amodiaquine (2), 2′-Fluoro-2′-deoxycytidine (3), and Ribavirin (4) was evaluated as inhibitors and nucleotide analogues for COVID-19 using computational modeling strategies. The density functional theory (DFT) calculations were performed to estimate the thermal parameters, dipole moment, polarizability, and molecular electrostatic potential of the present drugs; additionally, Mulliken atomic charges of the drugs as well as the chemical reactivity descriptors were investigated. The nominated drugs were docked on SARS-CoV-2 main protease (PDB: 6LU7) to evaluate the binding affinity of these drugs. Besides, the computations data of DFT the docking simulation studies was predicted that the Amodiaquine (2) has the least binding energy (−7.77 Kcal/mol) and might serve as a good inhibitor to SARS-CoV-2 comparable with the approved medicines, hydroxychloroquine, and remdesivir which have binding affinity −6.06 and −4.96 Kcal/mol, respectively. The high binding affinity of 2 was attributed to the presence of three hydrogen bonds along with different hydrophobic interactions between the drug and the critical amino acids residues of the receptor. Finally, the estimated molecular electrostatic potential results by DFT were used to illustrate the molecular docking findings. The DFT calculations showed that drug 2 has the highest of lying HOMO, electrophilicity index, basicity, and dipole moment. All these parameters could share with different extent to significantly affect the binding affinity of these drugs with the active protein sites.

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Molecular Docking Study on Several Benzoic Acid Derivatives against SARS-CoV-2

Molecules ◽

10.3390/molecules25245828 ◽

2020 ◽

Vol 25 (24) ◽

pp. 5828

Author(s):

Amalia Stefaniu ◽

Lucia Pirvu ◽

Bujor Albu ◽

Lucia Pintilie

Keyword(s):

Molecular Docking ◽

Benzoic Acid ◽

Density Functional ◽

Chemical Reactivity ◽

Principal Component ◽

Docking Study ◽

Docking Studies ◽

Molecular Docking Study ◽

Alkyl Gallates ◽

Main Protease

Several derivatives of benzoic acid and semisynthetic alkyl gallates were investigated by an in silico approach to evaluate their potential antiviral activity against SARS-CoV-2 main protease. Molecular docking studies were used to predict their binding affinity and interactions with amino acids residues from the active binding site of SARS-CoV-2 main protease, compared to boceprevir. Deep structural insights and quantum chemical reactivity analysis according to Koopmans’ theorem, as a result of density functional theory (DFT) computations, are reported. Additionally, drug-likeness assessment in terms of Lipinski’s and Weber’s rules for pharmaceutical candidates, is provided. The outcomes of docking and key molecular descriptors and properties were forward analyzed by the statistical approach of principal component analysis (PCA) to identify the degree of their correlation. The obtained results suggest two promising candidates for future drug development to fight against the coronavirus infection.

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Explaining SARS-CoV-2 3CL Mpro binding to peptidyl Michael acceptor and a ketone-based inhibitors using Molecular fractionation with conjugate caps method

10.21826/viiiseedmol2020185 ◽

2020 ◽

Author(s):

C Solis-Calero ◽

PA Morais ◽

FF Maia Jr ◽

VN Freire ◽

HF Carvalho

Keyword(s):

Amino Acid ◽

Density Functional ◽

Radial Distance ◽

Amino Acid Residues ◽

Functional Theory ◽

Main Protease ◽

The Density Functional Theory ◽

Michael Acceptor ◽

Total Interaction ◽

Molecular Fractionation

The main protease SARS-CoV-2 3CL Mpro (3CL-Mpro) is an attractive target for developing antiviral inhibitors due to its essential role in processing the polyproteins translated from viral coronavirus RNA. In this work, it was obtained non-covalent complexes of this protease with two distinct ligands, a peptidyl Michael acceptor (N3) and a ketone-based compound (V2M). The complexes were modeled from processed crystallographic data (PDB id: 6LU7 and 6XHM respectively) using combined quantum mechanics/molecular mechanics (QM/MM) calculations. The QM region was treated at the PBE-def2-SV(P) level, while the Amber-ff19SB force field was used to describe the MM region. The obtained models were used to perform calculations for describing the protease/ligand binding, based in the framework of the Density Functional Theory (DFT) and within the Molecular Fractionation with Conjugated Caps (MFCC) scheme. Our results have shown values for the total interaction energies of -111.84 and -111.64 kcal mol-1 having as ligands a N3 and V2M, respectively. Most importantly, it was possible to assess the relative individual amino acid energy contribution for the binding of both ligands considering residues around them up to 10 Å of radial distance. Residues Gln189, Met165, Glu166, His164, and Asn142 were identified as main interacting amino acid residues for both complexes, being their negative interaction energy contributions higher than -5.0 kcal mol-1. In the case of 3CL-Mpro/ V2M complex, we should add His41, Ser144, and Cys145 as main contributing residues. Our data also have shown that interactions of type π-amide, π-alkyl and alkyl-alkyl and carbon hydrogen bonds should be also considered in order to explain the binding of 3CL-Mpro with the selected inhibitors. Our results also determined that the carbonyl-L-leucinamide scaffold of both inhibitors is its main determinant of binding with a contribution to the energy of interaction of 54.51 and 50.69 kcal mol-1 for N3 and V2M, respectively.

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Potential Exploration of Recent FDA-Approved Anticancer Drugs Against Models of SARS-CoV-2’s Main Protease and Spike Glycoprotein: A Computational Study

Biointerface Research in Applied Chemistry ◽

10.33263/briac113.1005910073 ◽

2020 ◽

Vol 11 (3) ◽

pp. 10059-10073

Keyword(s):

Anticancer Drugs ◽

Computational Study ◽

Chemical Reactivity ◽

Dipole Moments ◽

Amino Acid Residues ◽

Spike Glycoprotein ◽

Binding Ability ◽

Reactivity Descriptors ◽

Main Protease ◽

Chemical Reactivity Descriptors

COVID-19 has become a worldwide risk to the healthcare system of practically every nation of the world, which originated from Wuhan, China. To date, no specific drugs are available to treat this disease. The exact source of the SARS-CoV-2 is yet unknown, although the early cases are associated with the Seafood market in Huanan, South China. This manuscript reports the in silico molecular modeling of recent FDA-approved anticancer drugs (Capmatinib, Pemigatinib, Selpercatinib, and Tucatinib) for their inhibitory action against COVID-19 targets. The selected anticancer drugs are docked on SARS-CoV-2 main protease (PDB ID: 6LU7) and SARS-CoV-2 spike glycoprotein (PDB ID: 6M0J) to ascertain the binding ability of these drugs. ADMET parameters of the drugs are assessed, and in addition, DFT calculations are done to investigate the pharmacokinetics, thermal parameters, dipole moments, and chemical reactivity descriptors. The docking energies (ΔG) and the interacting amino acid residues are discussed. Promising molecular docking conclusions have been accomplished, which demonstrated the potential of selected anticancer drugs for plausible drug development to fight COVID-19. Further optimizations with the drug may support the much-needed rapid response to mitigate the pandemic.

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Supercomputer simulation of the covalent inhibition of the main protease of SARS-CoV-2

Russian Chemical Bulletin ◽

10.1007/s11172-021-3319-8 ◽

2021 ◽

Vol 70 (11) ◽

pp. 2084-2089

Author(s):

A. V. Nemukhin ◽

B. L. Grigorenko ◽

S. V. Lushchekina ◽

S. D. Varfolomeev

Keyword(s):

Covalent Inhibition ◽

Main Protease

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Structural basis of main proteases of coronavirus bound to drug candidate PF-07321332

10.1101/2021.11.05.467529 ◽

2021 ◽

Author(s):

Jian Li ◽

Cheng Lin ◽

Xuelan Zhou ◽

Fanglin Zhong ◽

Pei Zeng ◽

...

Keyword(s):

Binding Site ◽

Binding Sites ◽

Binding Mode ◽

Structural Basis ◽

Drug Candidate ◽

Structural Determinants ◽

Inhibitor Binding ◽

Mechanism Of Inhibition ◽

Main Protease ◽

Multiple Variants

The high mutation rate of COVID-19 and the prevalence of multiple variants strongly support the need for pharmacological options to complement vaccine strategies. One region that appears highly conserved among different genus of coronaviruses is the substrate binding site of the main protease (Mpro or 3CLpro), making it an attractive target for the development of broad-spectrum drugs for multiple coronaviruses. PF-07321332 developed by Pfizer is the first orally administered inhibitor targeting the main protease of SARS-CoV-2, which also has shown potency against other coronaviruses. Here we report three crystal structures of main protease of SARS-CoV-2, SARS-CoV and MERS-CoV bound to the inhibitor PF-07321332. The structures reveal a ligand-binding site that is conserved among SARS-CoV-2, SARS-CoV and MERS-CoV, providing insights into the mechanism of inhibition of viral replication. The long and narrow cavity in the cleft between domains I and II of main protease harbors multiple inhibitor binding sites, where PF-07321332 occupies subsites S1, S2 and S4 and appears more restricted compared with other inhibitors. A detailed analysis of these structures illuminated key structural determinants essential for inhibition and elucidated the binding mode of action of main proteases from different coronaviruses. Given the importance of main protease for the treatment of SARS-CoV-2 infection, insights derived from this study should accelerate the design of safer and more effective antivirals.

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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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