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Tam D, Lorenzo-Leal AC, Hernández LR, Bach H. Targeting SARS-CoV-2 Non-Structural Proteins. Int J Mol Sci 2023; 24:13002. [PMID: 37629182 PMCID: PMC10455537 DOI: 10.3390/ijms241613002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an enveloped respiratory β coronavirus that causes coronavirus disease (COVID-19), leading to a deadly pandemic that has claimed millions of lives worldwide. Like other coronaviruses, the SARS-CoV-2 genome also codes for non-structural proteins (NSPs). These NSPs are found within open reading frame 1a (ORF1a) and open reading frame 1ab (ORF1ab) of the SARS-CoV-2 genome and encode NSP1 to NSP11 and NSP12 to NSP16, respectively. This study aimed to collect the available literature regarding NSP inhibitors. In addition, we searched the natural product database looking for similar structures. The results showed that similar structures could be tested as potential inhibitors of the NSPs.
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Affiliation(s)
- Donald Tam
- Division of Infectious Disease, Department of Medicine, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada; (D.T.); (A.C.L.-L.)
| | - Ana C. Lorenzo-Leal
- Division of Infectious Disease, Department of Medicine, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada; (D.T.); (A.C.L.-L.)
| | - Luis Ricardo Hernández
- Laboratorio de Investigación Fitoquímica, Departamento de Ciencias Químico Biológicas, Universidad de las Américas Puebla, Ex Hacienda Sta. Catarina Mártir S/N, San Andrés Cholula 72810, Mexico;
| | - Horacio Bach
- Division of Infectious Disease, Department of Medicine, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada; (D.T.); (A.C.L.-L.)
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La Monica G, Bono A, Lauria A, Martorana A. Targeting SARS-CoV-2 Main Protease for Treatment of COVID-19: Covalent Inhibitors Structure-Activity Relationship Insights and Evolution Perspectives. J Med Chem 2022; 65:12500-12534. [PMID: 36169610 PMCID: PMC9528073 DOI: 10.1021/acs.jmedchem.2c01005] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Indexed: 02/07/2023]
Abstract
The viral main protease is one of the most attractive targets among all key enzymes involved in the SARS-CoV-2 life cycle. Covalent inhibition of the cysteine145 of SARS-CoV-2 MPRO with selective antiviral drugs will arrest the replication process of the virus without affecting human catalytic pathways. In this Perspective, we analyzed the in silico, in vitro, and in vivo data of the most representative examples of covalent SARS-CoV-2 MPRO inhibitors reported in the literature to date. In particular, the studied molecules were classified into eight different categories according to their reactive electrophilic warheads, highlighting the differences between their reversible/irreversible mechanism of inhibition. Furthermore, the analyses of the most recurrent pharmacophoric moieties and stereochemistry of chiral carbons were reported. The analyses of noncovalent and covalent in silico protocols, provided in this Perspective, would be useful for the scientific community to discover new and more efficient covalent SARS-CoV-2 MPRO inhibitors.
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Affiliation(s)
| | | | - Antonino Lauria
- Dipartimento di Scienze e
Tecnologie Biologiche Chimiche e Farmaceutiche, University of Palermo, Viale delle Scienze, Ed. 17, I-90128 Palermo, Italy
| | - Annamaria Martorana
- Dipartimento di Scienze e
Tecnologie Biologiche Chimiche e Farmaceutiche, University of Palermo, Viale delle Scienze, Ed. 17, I-90128 Palermo, Italy
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4
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Boonamnaj P, Pandey R, Sompornpisut P. Effect of pH on stability of dimer structure of the main protease of coronavirus-2. Biophys Chem 2022; 287:106829. [PMID: 35635893 PMCID: PMC9119281 DOI: 10.1016/j.bpc.2022.106829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/04/2022] [Accepted: 05/14/2022] [Indexed: 02/09/2023]
Abstract
The viral main protease (Mpro) from a novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a key enzyme essential for viral replication and has become an attractive target for antiviral drug development. The Mpro forms a functional dimer and exhibits a pH-dependent enzyme activity and dimerization. Here, we report a molecular dynamics (MD) investigation to gain insights into the structural stability of the enzyme dimer at neutral and acidic pH. Our data shows larger changes in structure of the protein with the acidic pH than that with the neutral pH. Structural analysis of MD trajectories reveals a substantial increase in intersubunit separation, the loss of domain contacts, binding free energy and interaction energy of the dimer which implies the protein instability and tendency of dimer dissociation at acidic pH. The loss in the interaction energy is mainly driven by electrostatic interactions. We have identified the intersubunit hydrogen-bonding residues involved in the decreased dimer stability. These findings may be helpful for rational drug design and target evaluation against COVID-19.
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Affiliation(s)
- Panisak Boonamnaj
- The Center of Excellence in Computational Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - R.B. Pandey
- School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Pornthep Sompornpisut
- The Center of Excellence in Computational Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand,Corresponding author
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Andi B, Kumaran D, Kreitler DF, Soares AS, Keereetaweep J, Jakoncic J, Lazo EO, Shi W, Fuchs MR, Sweet RM, Shanklin J, Adams PD, Schmidt JG, Head MS, McSweeney S. Hepatitis C virus NS3/4A inhibitors and other drug-like compounds as covalent binders of SARS-CoV-2 main protease. Sci Rep 2022; 12:12197. [PMID: 35842458 PMCID: PMC9287821 DOI: 10.1038/s41598-022-15930-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 07/01/2022] [Indexed: 12/15/2022] Open
Abstract
Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), threatens global public health. The world needs rapid development of new antivirals and vaccines to control the current pandemic and to control the spread of the variants. Among the proteins synthesized by the SARS-CoV-2 genome, main protease (Mpro also known as 3CLpro) is a primary drug target, due to its essential role in maturation of the viral polyproteins. In this study, we provide crystallographic evidence, along with some binding assay data, that three clinically approved anti hepatitis C virus drugs and two other drug-like compounds covalently bind to the Mpro Cys145 catalytic residue in the active site. Also, molecular docking studies can provide additional insight for the design of new antiviral inhibitors for SARS-CoV-2 using these drugs as lead compounds. One might consider derivatives of these lead compounds with higher affinity to the Mpro as potential COVID-19 therapeutics for further testing and possibly clinical trials.
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Affiliation(s)
- Babak Andi
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA. .,National Virtual Biotechnology Laboratory (NVBL), US Department of Energy, Washington, DC, USA.
| | - Desigan Kumaran
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA. .,National Virtual Biotechnology Laboratory (NVBL), US Department of Energy, Washington, DC, USA.
| | - Dale F Kreitler
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Alexei S Soares
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | | | - Jean Jakoncic
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Edwin O Lazo
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Wuxian Shi
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Martin R Fuchs
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Robert M Sweet
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - John Shanklin
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Paul D Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Bioengineering, University of California, Berkeley, CA, 94720, USA.,National Virtual Biotechnology Laboratory (NVBL), US Department of Energy, Washington, DC, USA
| | - Jurgen G Schmidt
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.,National Virtual Biotechnology Laboratory (NVBL), US Department of Energy, Washington, DC, USA
| | - Martha S Head
- Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,National Virtual Biotechnology Laboratory (NVBL), US Department of Energy, Washington, DC, USA
| | - Sean McSweeney
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA. .,Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA. .,National Virtual Biotechnology Laboratory (NVBL), US Department of Energy, Washington, DC, USA.
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Nocentini A, Capasso C, Supuran CT. Perspectives on the design and discovery of α-ketoamide inhibitors for the treatment of novel coronavirus: where do we stand and where do we go? Expert Opin Drug Discov 2022; 17:547-557. [DOI: 10.1080/17460441.2022.2052847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Alessio Nocentini
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Firenze, Italy
| | - Clemente Capasso
- Department of Biology, Agriculture and Food Sciences, Institute of Biosciences and Bioresources, Napoli, Italy
| | - Claudiu T. Supuran
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Firenze, Italy
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Awoonor-Williams E, Abu-Saleh AAAA. Covalent and non-covalent binding free energy calculations for peptidomimetic inhibitors of SARS-CoV-2 main protease. Phys Chem Chem Phys 2021; 23:6746-6757. [PMID: 33711090 DOI: 10.1039/d1cp00266j] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
COVID-19, the disease caused by the newly discovered coronavirus-SARS-CoV-2, has created a global health, social, and economic crisis. As of mid-January 2021, there are over 90 million confirmed cases and more than 2 million reported deaths due to COVID-19. Currently, there are very limited therapeutics for the treatment or prevention of COVID-19. For this reason, it is important to find drug targets that will lead to the development of safe and effective therapeutics against the disease. The main protease (Mpro) of the virus is an attractive target for the development of effective antiviral therapeutics because it is required for proteolytic cleavage of viral polyproteins. Furthermore, the Mpro has no human homologues, so drugs designed to bind to this target directly have less risk for off-target effects. Recently, several high-resolution crystallographic structures of the Mpro in complex with inhibitors have been determined-to guide drug development and to spur efforts in structure-based drug design. One of the primary objectives of modern structure-based drug design is the accurate prediction of receptor-ligand binding affinities for rational drug design and discovery. Here, we perform rigorous alchemical absolute binding free energy calculations and QM/MM calculations to give insight into the total binding energy of two recently crystallized inhibitors of SARS-CoV-2 Mpro, namely, N3 and α-ketoamide 13b. The total binding energy consists of both covalent and non-covalent binding components since both compounds are covalent inhibitors of the Mpro. Our results indicate that the covalent and non-covalent binding free energy contributions of both inhibitors to the Mpro target differ significantly. The N3 inhibitor has more favourable non-covalent interactions, particularly hydrogen bonding, in the binding site of the Mpro than the α-ketoamide inhibitor. Also, the Gibbs energy of reaction for the Mpro-N3 covalent adduct is greater than the Gibbs reaction energy for the Mpro-α-ketoamide covalent adduct. These differences in the covalent and non-covalent binding free energy contributions for both inhibitors could be a plausible explanation for their in vitro differences in antiviral activity. Our findings are consistent with the reversible and irreversible character of both inhibitors as reported by experiment and highlight the importance of both covalent and non-covalent binding free energy contributions to the absolute binding affinity of a covalent inhibitor towards its target. This information could prove useful in the rational design, discovery, and evaluation of potent SARS-CoV-2 Mpro inhibitors for targeted antiviral therapy.
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Affiliation(s)
- Ernest Awoonor-Williams
- Department of Chemistry, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada.
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