1
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Stubbing LA, Hubert JG, Bell-Tyrer J, Hermant YO, Yang SH, McSweeney AM, McKenzie-Goldsmith GM, Ward VK, Furkert DP, Brimble MA. P 1 Glutamine isosteres in the design of inhibitors of 3C/3CL protease of human viruses of the Pisoniviricetes class. RSC Chem Biol 2023; 4:533-547. [PMID: 37547456 PMCID: PMC10398354 DOI: 10.1039/d3cb00075c] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 06/19/2023] [Indexed: 08/08/2023] Open
Abstract
Viral infections are one of the leading causes of acute morbidity in humans and much endeavour has been made by the synthetic community for the development of drugs to treat associated diseases. Peptide-based enzyme inhibitors, usually short sequences of three or four residues, are one of the classes of compounds currently under development for enhancement of their activity and pharmaceutical properties. This review reports the advances made in the design of inhibitors targeting the family of highly conserved viral proteases 3C/3CLpro, which play a key role in viral replication and present minimal homology with mammalian proteases. Particular focus is put on the reported development of P1 glutamine isosteres to generate potent inhibitors mimicking the natural substrate sequence at the site of recognition.'
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Affiliation(s)
- Louise A Stubbing
- School of Chemical Sciences, The University of Auckland 23 Symonds Street and 3b Symonds Street Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 3b Symonds Street Auckland 1142 New Zealand
| | - Jonathan G Hubert
- School of Chemical Sciences, The University of Auckland 23 Symonds Street and 3b Symonds Street Auckland 1142 New Zealand
| | - Joseph Bell-Tyrer
- School of Chemical Sciences, The University of Auckland 23 Symonds Street and 3b Symonds Street Auckland 1142 New Zealand
| | - Yann O Hermant
- School of Chemical Sciences, The University of Auckland 23 Symonds Street and 3b Symonds Street Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 3b Symonds Street Auckland 1142 New Zealand
| | - Sung Hyun Yang
- School of Chemical Sciences, The University of Auckland 23 Symonds Street and 3b Symonds Street Auckland 1142 New Zealand
| | - Alice M McSweeney
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 3b Symonds Street Auckland 1142 New Zealand
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago PO Box 56, 720 Cumberland Street Dunedin 9054 New Zealand
| | - Geena M McKenzie-Goldsmith
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 3b Symonds Street Auckland 1142 New Zealand
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago PO Box 56, 720 Cumberland Street Dunedin 9054 New Zealand
| | - Vernon K Ward
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 3b Symonds Street Auckland 1142 New Zealand
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago PO Box 56, 720 Cumberland Street Dunedin 9054 New Zealand
| | - Daniel P Furkert
- School of Chemical Sciences, The University of Auckland 23 Symonds Street and 3b Symonds Street Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 3b Symonds Street Auckland 1142 New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences, The University of Auckland 23 Symonds Street and 3b Symonds Street Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 3b Symonds Street Auckland 1142 New Zealand
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2
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Sahoo P, Lenka DR, Batabyal M, Pain PK, Kumar S, Manna D, Kumar A. Detailed Insights into the Inhibitory Mechanism of New Ebselen Derivatives against Main Protease (M pro) of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). ACS Pharmacol Transl Sci 2022; 6:171-180. [PMID: 36650888 PMCID: PMC9797022 DOI: 10.1021/acsptsci.2c00203] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Indexed: 12/24/2022]
Abstract
SARS-CoV-2 main protease (Mpro/3CLpro) is a crucial target for therapeutics, which is responsible for viral polyprotein cleavage and plays a vital role in virus replication and survival. Recent studies suggest that 2-phenylbenzisoselenazol-3(2H)-one (ebselen) is a potent covalent inhibitor of Mpro, which affects its enzymatic activity and virus survival. Herein, we synthesized various ebselen derivatives to understand the mechanism of Mpro inhibition by ebselen. Using ebselen derivatives, we characterized the detailed interaction mechanism with Mpro. We discovered that modification of the parent ebselen inhibitor with an electron-withdrawing group (NO2) increases the inhibition efficacy by 2-fold. We also solved the structure of an Mpro complex with an ebselen derivative showing the mechanism of inhibition by blocking the catalytic Cys145 of Mpro. Using a combination of crystal structures and LC-MS data, we showed that Mpro hydrolyzes the new ebselen derivative and leaves behind selenium (Se) bound with Cys145 of the catalytic dyad of Mpro. We also described the binding profile of ebselen-based inhibitors using molecular modeling predictions supported by binding and inhibition assays. Furthermore, we have also solved the crystal structure of catalytically inactive mutant H41N-Mpro, which represents the inactive state of the protein where the substrate binding pocket is blocked. The inhibited structure of H41N-Mpro shows gatekeeper residues in the substrate binding pocket responsible for blocking the substrate binding; mutation of these gatekeeper residues leads to hyperactive Mpro.
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Affiliation(s)
- Pritiranjan Sahoo
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Bhopal, Bhopal, Madhya Pradesh 462066, India
| | - Dipti Ranjan Lenka
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Bhopal, Bhopal, Madhya Pradesh 462066, India
| | - Monojit Batabyal
- Department
of Chemistry, Indian Institute of Science
Education and Research (IISER) Bhopal, Bhopal, Madhya Pradesh 462066, India
| | - Pritam Kumar Pain
- Department
of Chemistry, Indian Institute of Science
Education and Research (IISER) Bhopal, Bhopal, Madhya Pradesh 462066, India
| | - Sangit Kumar
- Department
of Chemistry, Indian Institute of Science
Education and Research (IISER) Bhopal, Bhopal, Madhya Pradesh 462066, India
| | - Debasish Manna
- Department
of Chemistry, Indian Institute of Science
Education and Research (IISER) Bhopal, Bhopal, Madhya Pradesh 462066, India
| | - Atul Kumar
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Bhopal, Bhopal, Madhya Pradesh 462066, India,
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3
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Sajid Jamal QM, Alharbi AH, Ahmad V. Identification of doxorubicin as a potential therapeutic against SARS-CoV-2 (COVID-19) protease: a molecular docking and dynamics simulation studies. J Biomol Struct Dyn 2022; 40:7960-7974. [PMID: 33826483 PMCID: PMC8043163 DOI: 10.1080/07391102.2021.1905551] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 03/15/2021] [Indexed: 02/08/2023]
Abstract
After one year, the COVID-19 pandemic caused by SARS-CoV-2 is still the largest concern for the scientific community. Of the many recognized drug targets of SARS-CoV-2, the main protease is one of the most important target due to its function in viral replication. We conducted an in silico study with repurposing drugs of antibiotics class against virus protease and peptidase using AutoDock tool. The following significant binding energy interaction was observed with protease (PDB: 6LU7) like piperacillin -7.25; tobramycin -9.20 and doxorubicin (Doxo) -10.04 kcal/mol and with peptidase (PDB: 2GTB) piperacillin -7.08; tobramycin -8.54 and Doxo -9.89 kcal/mol. Furthermore, the interaction and stability behavior of the Doxo-protease and Doxo-peptidase complexes were analyzed for a 100-nanosecond (ns) time. Calculated RMSD values observed using molecular dynamics simulation (MDS) were found to be 0.15-0.25 nm, RMSF calculation per residues showed a value near 0.2 nm and Rg values remained approximately 2.25 nm. MM-PBSA analysis of total binding energy calculation of Doxo-protease and Doxo-peptidase complexes are found to be -148.692 and -105.367 kJ/mol, respectively. Moreover, amino acid residue ASP-197 showed the lowest contribution binding energy i.e. -18.1185 kJ/mol, and amino acid residue ASP-187 showed -17.0267 kJ/mol contribution energy. Thus, significant docking interaction and stable dynamicity of Doxo-protease complex with time was suggested that Doxo could be a choice to inhibit potentially the viral proteases that could prevent the entry inside the host cell to control the COVID-19 disease. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Qazi Mohammad Sajid Jamal
- Department of Health Informatics, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah, Saudi Arabia
| | - Ali H. Alharbi
- Department of Health Informatics, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah, Saudi Arabia
| | - Varish Ahmad
- Health Information Technology Department, Faculty of Applied Studies, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
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4
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Shamsi TN, Yin J, James ME, James MN. Porcine Epidemic Diarrhea: Causative Agent, Epidemiology, Clinical
Characteristics, and Treatment Strategy Targeting Main Protease. Protein Pept Lett 2022; 29:392-407. [DOI: 10.2174/0929866529666220316145149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 11/22/2021] [Accepted: 11/28/2021] [Indexed: 11/22/2022]
Abstract
Aims:
This aimed to study the causative agent, epidemiology, clinical characteristics, and
treatment strategy targeting the main protease in porcine epidemic diarrhea.
Background:
Porcine epidemic diarrhea (PED) is a contagious intestinal viral infection causing
severe diarrhea, vomiting, and dehydration in pigs. High rates of mortalities and severe morbidities,
approaching 100%, are reported in piglets infected with PEDV. In recent years, PED has been
observed to influence the swine-farming nations in Europe, Asia, the USA, South Korea, and
Canada. The PED virus (PEDV) transmission takes place through a faecal-oral route.
Objective:
The objective is to review the characteristics of PEDV and its role in the disease. In
addition, we aim to outline some possible methods to combat PED infection, including targeting the
main protease of coronavirus and their future perspectives.
Method:
This study is a review of literature on the PED virus.
Results:
Apart from symptomatic treatment and supportive care, there is no available specific
treatment for PEDV. Appropriate disinfectants and cleaning are pivotal for the control of PEDV. To
date, apart from anti-PEDV inhibitors, there are no specific drugs available commercially to treat
the disease. Therefore, 3C-like protease (3CLpro) in PEDV that has highly conserved structure and
catalytic mechanism serves as an alluring drug as it plays a vital role during viral polyprotein
processing at the time of infection.
Conclusion:
A well synchronized and collective effort of scientists, swine veterinarians, pork
industry experts, and associated authorities is essential for the accomplishment of proper execution
of these required measures.
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Affiliation(s)
- Tooba N. Shamsi
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2H7,
Canada
| | - Jiang Yin
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2H7,
Canada
| | - Michelle E. James
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2H7,
Canada
| | - Michael N.G. James
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2H7,
Canada
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5
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In silico studies on structural inhibition of SARS-CoV-2 main protease Mpro by major secondary metabolites of Andrographis paniculata and Cinchona officinalis. Biologia (Bratisl) 2022; 77:1373-1389. [PMID: 35250036 PMCID: PMC8883239 DOI: 10.1007/s11756-022-01012-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/10/2022] [Indexed: 12/15/2022]
Abstract
The COVID-19 infection by Novel Corona Virus (SARS-CoV-2) has become one of the largest pandemic diseases, with cumulative confirmed infections of 275,233,892 and 5,364,996 deaths to date according to World Health Organization. Due to the absence of any approved antiviral drug to treat COVID-19, its lethality is getting severe with time. The main protease of SARS-CoV-2, Mpro is considered one of the potential drug targets because of its role in processing proteins translated from viral RNA. In the present study, four of the plant metabolites, 14-deoxy-11,12-didehydroandrographolide, andrograpanin, quinine, cinchonine from two eminent medicinal plants Andrographis paniculata and Cinchona officinalis, have been evaluated against the main protease of SARS-CoV-2 through in-silico molecular docking and molecular dynamics simulation study. From the result interpretations, it is found that andrograpanin has strong binding affinities with the target protein in its active site with potential negative energies. Molecular Dynamic simulation and MMGBSA studies suggest that earlier reported N3 inhibitor and andrograpanin exhibit effective binding interactions involving identical amino acid residues with the same binding pockets of the main protease of SARS-CoV-2. Therefore, the theoretical experiment suggests that andrograpanin, could be considered the promising inhibitor against SARS-CoV-2 Mpro.
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6
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Han SH, Goins CM, Arya T, Shin WJ, Maw J, Hooper A, Sonawane DP, Porter MR, Bannister BE, Crouch RD, Lindsey AA, Lakatos G, Martinez SR, Alvarado J, Akers WS, Wang NS, Jung JU, Macdonald JD, Stauffer SR. Structure-Based Optimization of ML300-Derived, Noncovalent Inhibitors Targeting the Severe Acute Respiratory Syndrome Coronavirus 3CL Protease (SARS-CoV-2 3CL pro). J Med Chem 2022; 65:2880-2904. [PMID: 34347470 PMCID: PMC8353992 DOI: 10.1021/acs.jmedchem.1c00598] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Indexed: 12/18/2022]
Abstract
Starting from the MLPCN probe compound ML300, a structure-based optimization campaign was initiated against the recent severe acute respiratory syndrome coronavirus (SARS-CoV-2) main protease (3CLpro). X-ray structures of SARS-CoV-1 and SARS-CoV-2 3CLpro enzymes in complex with multiple ML300-based inhibitors, including the original probe ML300, were obtained and proved instrumental in guiding chemistry toward probe compound 41 (CCF0058981). The disclosed inhibitors utilize a noncovalent mode of action and complex in a noncanonical binding mode not observed by peptidic 3CLpro inhibitors. In vitro DMPK profiling highlights key areas where further optimization in the series is required to obtain useful in vivo probes. Antiviral activity was established using a SARS-CoV-2-infected Vero E6 cell viability assay and a plaque formation assay. Compound 41 demonstrates nanomolar activity in these respective assays, comparable in potency to remdesivir. These findings have implications for antiviral development to combat current and future SARS-like zoonotic coronavirus outbreaks.
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Affiliation(s)
- Sang Hoon Han
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Christopher M. Goins
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Tarun Arya
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Woo-Jin Shin
- Cleveland Clinic Florida Research & Innovation Center, Port St. Lucie, FL, 34987, USA
| | - Joshua Maw
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Alice Hooper
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Dhiraj P. Sonawane
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Matthew R. Porter
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Breyanne E. Bannister
- Department of Pharmaceutical Science, Lipscomb University College of Pharmacy, Nashville, TN, 37204, USA
| | - Rachel D. Crouch
- Department of Pharmaceutical Science, Lipscomb University College of Pharmacy, Nashville, TN, 37204, USA
| | - A. Abigail Lindsey
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Gabriella Lakatos
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Steven R. Martinez
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Joseph Alvarado
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Wendell S. Akers
- Department of Pharmaceutical Science, Lipscomb University College of Pharmacy, Nashville, TN, 37204, USA
| | - Nancy S. Wang
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Jae U. Jung
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Center for Global and Emerging Pathogens Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Jonathan D. Macdonald
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Shaun R. Stauffer
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
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7
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Kidera A, Moritsugu K, Ekimoto T, Ikeguchi M. Allosteric Regulation of 3CL Protease of SARS-CoV-2 and SARS-CoV Observed in the Crystal Structure Ensemble. J Mol Biol 2021; 433:167324. [PMID: 34717972 PMCID: PMC8550881 DOI: 10.1016/j.jmb.2021.167324] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/16/2021] [Accepted: 10/18/2021] [Indexed: 01/08/2023]
Abstract
The 3C-like protease (3CLpro) of SARS-CoV-2 is a potential therapeutic target for COVID-19. Importantly, it has an abundance of structural information solved as a complex with various drug candidate compounds. Collecting these crystal structures (83 Protein Data Bank (PDB) entries) together with those of the highly homologous 3CLpro of SARS-CoV (101 PDB entries), we constructed the crystal structure ensemble of 3CLpro to analyze the dynamic regulation of its catalytic function. The structural dynamics of the 3CLpro dimer observed in the ensemble were characterized by the motions of four separate loops (the C-loop, E-loop, H-loop, and Linker) and the C-terminal domain III on the rigid core of the chymotrypsin fold. Among the four moving loops, the C-loop (also known as the oxyanion binding loop) causes the order (active)-disorder (collapsed) transition, which is regulated cooperatively by five hydrogen bonds made with the surrounding residues. The C-loop, E-loop, and Linker constitute the major ligand binding sites, which consist of a limited variety of binding residues including the substrate binding subsites. Ligand binding causes a ligand size dependent conformational change to the E-loop and Linker, which further stabilize the C-loop via the hydrogen bond between the C-loop and E-loop. The T285A mutation from SARS-CoV 3CLpro to SARS-CoV-2 3CLpro significantly closes the interface of the domain III dimer and allosterically stabilizes the active conformation of the C-loop via hydrogen bonds with Ser1 and Gly2; thus, SARS-CoV-2 3CLpro seems to have increased activity relative to that of SARS-CoV 3CLpro.
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Affiliation(s)
- Akinori Kidera
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.
| | - Kei Moritsugu
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Toru Ekimoto
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Mitsunori Ikeguchi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
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8
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Üstün E, Düşünceli SD, Coşkun F, Özdemir İ. Molybdenum Carbonyl Complexes with Benzimidazole Derivatives Against SARS-CoV-2 by Molecular Docking and DFT/TDDFT Methods. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2021. [DOI: 10.1142/s2737416521500502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Benzimidazole derivative molecules attract attention of scientists due to their bioactivities. The dramatic changes in recorded activities according to the type and position of the substituents motivate synthesis and analysis of new molecules. Commercial benzimidazole-based molecules have been used in therapeutic procedures. It is known that the activities of metal complexes with benzimidazole derivative ligands have different activities when compared to the benzimidazole main structure. Nowadays, one of the most important health problems is COVID-19, which caused the pandemic that we are still experiencing. Although vaccine studies are important to overcome acute problems, regarding the possible post-vaccination adverse effects, the need for new drugs against the virus is obvious. Considering the urgency and the limited facilities during the pandemic, preliminary in silico studies of candidate molecules are essential. In this study, {[bis-(N-benzylbenzimidazole)] tetracarbonylmolybdenum}, {[bis-(N-4-chlorobenzylbenzimidazole)] tetracarbonylmolybdenum} and {[bis-(N-4-methoxybenzylbenzimidazole)] tetracarbonylmolybdenum} were synthesized and characterized. The optimization and the structural analysis of these molecules were performed by DFT/TDDFT methods. The molecules were docked into SARS coronavirus main peptidase (PDB ID: 2gtb), COVID-19 main protease in complex with Z219104216 (PDB ID: 5r82), COVID-19 main protease in complex with an inhibitor N3 (PDB ID: 6lu7) and Papain-like protease of SARS-CoV-2 (PDB ID: 6w9c) crystal structures for evaluation of their anti-viral activity.
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Affiliation(s)
- Elvan Üstün
- Department of Chemistry, Faculty of Art and Science, Ordu University, 52200 Ordu, Turkey
| | - Serpil Demir Düşünceli
- Department of Chemistry Faculty of Art and Science, İnönü University, 44280 Malatya, Turkey
- Catalysis Research and Application Center, İnönü University, 44280 Malatya, Turkey
| | - Feyzullah Coşkun
- Department of Chemistry Faculty of Art and Science, İnönü University, 44280 Malatya, Turkey
- Catalysis Research and Application Center, İnönü University, 44280 Malatya, Turkey
| | - İsmail Özdemir
- Department of Chemistry Faculty of Art and Science, İnönü University, 44280 Malatya, Turkey
- Catalysis Research and Application Center, İnönü University, 44280 Malatya, Turkey
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9
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Ullrich S, Sasi VM, Mahawaththa MC, Ekanayake KB, Morewood R, George J, Shuttleworth L, Zhang X, Whitefield C, Otting G, Jackson C, Nitsche C. Challenges of short substrate analogues as SARS-CoV-2 main protease inhibitors. Bioorg Med Chem Lett 2021; 50:128333. [PMID: 34418570 PMCID: PMC8378659 DOI: 10.1016/j.bmcl.2021.128333] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/09/2021] [Accepted: 08/16/2021] [Indexed: 12/22/2022]
Abstract
Specific anti-coronaviral drugs complementing available vaccines are urgently needed to fight the COVID-19 pandemic. Given its high conservation across the betacoronavirus genus and dissimilarity to human proteases, the SARS-CoV-2 main protease (Mpro) is an attractive drug target. SARS-CoV-2 Mpro inhibitors have been developed at unprecedented speed, most of them being substrate-derived peptidomimetics with cysteine-modifying warheads. In this study, Mpro has proven resistant towards the identification of high-affinity short substrate-derived peptides and peptidomimetics without warheads. 20 cyclic and linear substrate analogues bearing natural and unnatural residues, which were predicted by computational modelling to bind with high affinity and designed to establish structure-activity relationships, displayed no inhibitory activity at concentrations as high as 100 μM. Only a long linear peptide covering residues P6 to P5' displayed moderate inhibition (Ki = 57 µM). Our detailed findings will inform current and future drug discovery campaigns targeting Mpro.
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Affiliation(s)
- Sven Ullrich
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Vishnu M Sasi
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Mithun C Mahawaththa
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Kasuni B Ekanayake
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Richard Morewood
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Josemon George
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Laura Shuttleworth
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Xiaobai Zhang
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Cassidy Whitefield
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Colin Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
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10
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Costa AN, de Sá ÉRA, Bezerra RDS, Souza JL, Lima FDCA. Constituents of buriti oil ( Mauritia flexuosa L.) like inhibitors of the SARS-Coronavirus main peptidase: an investigation by docking and molecular dynamics. J Biomol Struct Dyn 2021; 39:4610-4617. [PMID: 32567501 PMCID: PMC7332871 DOI: 10.1080/07391102.2020.1778538] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 06/01/2020] [Indexed: 12/23/2022]
Abstract
Statistics show alarming numbers of infected and killed in the world, caused by the Covid-19 pandemic, which still doesn't have a specific treatment and effective in combating all efforts to seek treatments and medications against this disease. Natural products are of relevant interest in the search for new drugs. Thus, Buriti oil (Mauritia flexuosa L.) is a natural product extracted from the fruit of the palm and is quite common in the legal Amazon region, Brazil. In the present work, the anti-Covid-19 biological activity of some constituents of Buriti oil was investigated using in silico methods of Molecular Docking and Molecular Dynamics Simulations. The main results of Molecular Docking revealed favorable interaction energies in the formation of the 2GTB peptidase complex (main peptidase of SARS-CoV) with the 13-cis-β-carotene ligands (ΔGbind = -10.23Kcal mol-1), 9-cis -β-carotene (ΔGbind = -9.82Kcal mol-1), and α-carotene (ΔGbind = -8.34Kcal mol-1). Molecular Dynamics simulations demonstrated considerable interaction for these ligands with emphasis on α-carotene. Such theoretical results encourage and enable a direction for experimental studies in vitro and in vivo, essential in the development of new drugs with enzymatic inhibitory action for Covid-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Allan N. Costa
- Pará/Conceição do Araguaia Campus, Federal Institute of Education, Science and Technology, Conceição do Araguaia, Brazil
| | - Ézio R. A. de Sá
- Piauí/Picos Campus, Federal Institute of Education, Science and Technology, Picos, Brazil
| | - Roosevelt D. S. Bezerra
- Piauí/Teresina-Central Campus, Federal Institute of Education, Science and Technology, Teresina, Brazil
| | - Janilson L. Souza
- Maranhão/Bacabal Campus, Federal Institute of Education, Science and Technology, Bacabal, Brazil
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11
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Gossen J, Albani S, Hanke A, Joseph BP, Bergh C, Kuzikov M, Costanzi E, Manelfi C, Storici P, Gribbon P, Beccari AR, Talarico C, Spyrakis F, Lindahl E, Zaliani A, Carloni P, Wade RC, Musiani F, Kokh DB, Rossetti G. A Blueprint for High Affinity SARS-CoV-2 Mpro Inhibitors from Activity-Based Compound Library Screening Guided by Analysis of Protein Dynamics. ACS Pharmacol Transl Sci 2021; 4:1079-1095. [PMID: 34136757 PMCID: PMC8009102 DOI: 10.1021/acsptsci.0c00215] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Indexed: 12/27/2022]
Abstract
The SARS-CoV-2 coronavirus outbreak continues to spread at a rapid rate worldwide. The main protease (Mpro) is an attractive target for anti-COVID-19 agents. Unexpected difficulties have been encountered in the design of specific inhibitors. Here, by analyzing an ensemble of ∼30 000 SARS-CoV-2 Mpro conformations from crystallographic studies and molecular simulations, we show that small structural variations in the binding site dramatically impact ligand binding properties. Hence, traditional druggability indices fail to adequately discriminate between highly and poorly druggable conformations of the binding site. By performing ∼200 virtual screenings of compound libraries on selected protein structures, we redefine the protein's druggability as the consensus chemical space arising from the multiple conformations of the binding site formed upon ligand binding. This procedure revealed a unique SARS-CoV-2 Mpro blueprint that led to a definition of a specific structure-based pharmacophore. The latter explains the poor transferability of potent SARS-CoV Mpro inhibitors to SARS-CoV-2 Mpro, despite the identical sequences of the active sites. Importantly, application of the pharmacophore predicted novel high affinity inhibitors of SARS-CoV-2 Mpro, that were validated by in vitro assays performed here and by a newly solved X-ray crystal structure. These results provide a strong basis for effective rational drug design campaigns against SARS-CoV-2 Mpro and a new computational approach to screen protein targets with malleable binding sites.
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Affiliation(s)
- Jonas Gossen
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich, 52425, Germany
- Institute
for Advanced Simulations (IAS-5) “Computational biomedicine”, Forschungszentrum Jülich, Jülich, 52425, Germany
- Faculty of
Mathematics, Computer Science and Natural Sciences, RWTH Aachen, Aachen, 52062, Germany
| | - Simone Albani
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich, 52425, Germany
- Institute
for Advanced Simulations (IAS-5) “Computational biomedicine”, Forschungszentrum Jülich, Jülich, 52425, Germany
- Faculty of
Mathematics, Computer Science and Natural Sciences, RWTH Aachen, Aachen, 52062, Germany
| | - Anton Hanke
- Molecular
and Cellular Modeling Group, Heidelberg
Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, Heidelberg, 69118, Germany
- Institute
of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Im Neuenheimer Feld 364, Heidelberg, 69120, Germany
| | - Benjamin P. Joseph
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich, 52425, Germany
- Institute
for Advanced Simulations (IAS-5) “Computational biomedicine”, Forschungszentrum Jülich, Jülich, 52425, Germany
- Faculty of
Mathematics, Computer Science and Natural Sciences, RWTH Aachen, Aachen, 52062, Germany
| | - Cathrine Bergh
- Science for
Life Laboratory & Swedish e-Science Research Center, Department
of Applied Physics, KTH Royal Institute
of Technology, Stockholm, 11428, Sweden
| | - Maria Kuzikov
- Department
of Screening Port, Fraunhofer Institute
for Translational Medicine and Pharmacology ITMP, Schnackenburgallee 114, Hamburg, 22525, Germany
| | - Elisa Costanzi
- Elettra-Sincrotrone
Trieste S.C.p.A., SS 14-km 163,5 in AREA Science Park, Basovizza,
Trieste, 34149, Italy
| | - Candida Manelfi
- Dompé
Farmaceutici SpA, Via Campo di Pile, L’Aquila, 67100, Italy
| | - Paola Storici
- Elettra-Sincrotrone
Trieste S.C.p.A., SS 14-km 163,5 in AREA Science Park, Basovizza,
Trieste, 34149, Italy
| | - Philip Gribbon
- Department
of Screening Port, Fraunhofer Institute
for Translational Medicine and Pharmacology ITMP, Schnackenburgallee 114, Hamburg, 22525, Germany
| | | | - Carmine Talarico
- Dompé
Farmaceutici SpA, Via Campo di Pile, L’Aquila, 67100, Italy
| | - Francesca Spyrakis
- Department
of Drug Science and Technology, University
of Turin, via Giuria
9, Turin, 10125, Italy
| | - Erik Lindahl
- Science for
Life Laboratory & Swedish e-Science Research Center, Department
of Applied Physics, KTH Royal Institute
of Technology, Stockholm, 11428, Sweden
- Science
for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, SE-106 91, Sweden
| | - Andrea Zaliani
- Department
of Screening Port, Fraunhofer Institute
for Translational Medicine and Pharmacology ITMP, Schnackenburgallee 114, Hamburg, 22525, Germany
| | - Paolo Carloni
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich, 52425, Germany
- Institute
for Molecular Neuroscience and Neuroimaging (INM-11), Forschungszentrum Jülich, Jülich, 52425, Germany
- Institute
for Advanced Simulations (IAS-5) “Computational biomedicine”, Forschungszentrum Jülich, Jülich, 52425, Germany
- Faculty of
Mathematics, Computer Science and Natural Sciences, RWTH Aachen, Aachen, 52062, Germany
| | - Rebecca C. Wade
- Molecular
and Cellular Modeling Group, Heidelberg
Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, Heidelberg, 69118, Germany
- Zentrum
für Molekulare Biologie der University Heidelberg, DKFZ-ZMBH
Alliance, INF 282, Heidelberg, 69120, Germany
- Interdisciplinary
Center for Scientific Computing (IWR), Heidelberg
University, INF 368, Heidelberg, 69120, Germany
| | - Francesco Musiani
- Laboratory
of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Daria B. Kokh
- Molecular
and Cellular Modeling Group, Heidelberg
Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, Heidelberg, 69118, Germany
| | - Giulia Rossetti
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich, 52425, Germany
- Institute
for Advanced Simulations (IAS-5) “Computational biomedicine”, Forschungszentrum Jülich, Jülich, 52425, Germany
- Jülich
Supercomputing Center (JSC), Forschungszentrum
Jülich, Jülich, 52425, Germany
- Department
of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, RWTH Aachen University, Aachen, 44517, Germany
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12
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Saakre M, Mathew D, Ravisankar V. Perspectives on plant flavonoid quercetin-based drugs for novel SARS-CoV-2. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2021; 10:21. [PMID: 33782651 PMCID: PMC7989718 DOI: 10.1186/s43088-021-00107-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 03/02/2021] [Indexed: 12/15/2022] Open
Abstract
Background The world pandemic COVID-19 caused by SARS-CoV-2 is currently claiming thousands of lives. Flavonoids abundantly present in the fruits and vegetables, especially quercetin, are shown to have antiviral activities. Main text This paper reviews the capability of the plant flavonoid quercetin to fight the novel coronavirus and the possibility for drug development based on this. The mode of action explaining the known pathways through which this molecule succeeds in the antiviral activity, action of quercetin on SARS-CoV-2 main protease 3CLpro, antiviral activities of its derivatives on human viruses, effect of combination of zinc co-factor along with quercetin in the COVID-19 treatment, and the regulation of miRNA genes involved in the viral pathogenesis are discussed. Proof for this concept is provided following the virtual screening using ten key enzymes of SARS-CoV-2 and assessing their interactions. Active residues in the 3D structures have been predicted using CASTp and were docked against quercetin. Key proteins 3CLpro, spike glycoprotein/ human ACE2-BOAT1 complex, RNA-dependent RNA polymerase, main peptidase, spike glycoprotein, RNA replicase, RNA binding protein, papain-like protease, SARS papain-like protease/ deubiquitinase, and complex of main peptidase with an additional Ala at the N-terminus of each protomer, have shown the binding energies ranging between − 6.71 and − 3.37 kcal/ Mol, showing that quercetin is a potential drug candidate inhibiting multiple SARS-CoV-2 enzymes. Conclusion The antiviral properties of flavonoid and the molecular mechanisms involved are reviewed. Further, proof for this concept is given by docking of key proteins from SARS-CoV-2 with quercetin. Graphical abstract ![]()
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Affiliation(s)
- Manjesh Saakre
- National Institute for Plant Biotechnology, Indian Agricultural Research Institute, Pusa, New Delhi, 110 012 India
| | - Deepu Mathew
- Bioinformatics Centre, Kerala Agricultural University, Thrissur, 680 656 India
| | - V Ravisankar
- Bioinformatics Centre, Kerala Agricultural University, Thrissur, 680 656 India
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13
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Besednova NN, Andryukov BG, Zaporozhets TS, Kryzhanovsky SP, Fedyanina LN, Kuznetsova TA, Zvyagintseva TN, Shchelkanov MY. Antiviral Effects of Polyphenols from Marine Algae. Biomedicines 2021; 9:200. [PMID: 33671278 PMCID: PMC7921925 DOI: 10.3390/biomedicines9020200] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/12/2021] [Accepted: 02/14/2021] [Indexed: 02/07/2023] Open
Abstract
The disease-preventive and medicinal properties of plant polyphenolic compounds have long been known. As active ingredients, they are used to prevent and treat many noncommunicable diseases. In recent decades, marine macroalgae have attracted the attention of biotechnologists and pharmacologists as a promising and almost inexhaustible source of polyphenols. This heterogeneous group of compounds contains many biopolymers with unique structure and biological properties that exhibit high anti-infective activity. In the present review, the authors focus on the antiviral potential of polyphenolic compounds (phlorotannins) from marine algae and consider the mechanisms of their action as well as other biological properties of these compounds that have effects on the progress and outcome of viral infections. Effective nutraceuticals, to be potentially developed on the basis of algal polyphenols, can also be used in the complex therapy of viral diseases. It is necessary to extend in vivo studies on laboratory animals, which subsequently will allow proceeding to clinical tests. Polyphenolic compounds have a great potential as active ingredients to be used for the creation of new antiviral pharmaceutical substances.
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Affiliation(s)
- Natalya N. Besednova
- G.P. Somov Institute of Epidemiology and Microbiology, Russian Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 690087 Vladivostok, Russia; (B.G.A.); (T.S.Z.); (T.A.K.); (M.Y.S.)
| | - Boris G. Andryukov
- G.P. Somov Institute of Epidemiology and Microbiology, Russian Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 690087 Vladivostok, Russia; (B.G.A.); (T.S.Z.); (T.A.K.); (M.Y.S.)
- School of Biomedicine, Far Eastern Federal University (FEFU), 690091 Vladivostok, Russia;
| | - Tatyana S. Zaporozhets
- G.P. Somov Institute of Epidemiology and Microbiology, Russian Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 690087 Vladivostok, Russia; (B.G.A.); (T.S.Z.); (T.A.K.); (M.Y.S.)
| | - Sergey P. Kryzhanovsky
- Medical Association of the Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia;
| | - Ludmila N. Fedyanina
- School of Biomedicine, Far Eastern Federal University (FEFU), 690091 Vladivostok, Russia;
| | - Tatyana A. Kuznetsova
- G.P. Somov Institute of Epidemiology and Microbiology, Russian Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 690087 Vladivostok, Russia; (B.G.A.); (T.S.Z.); (T.A.K.); (M.Y.S.)
| | | | - Mikhail Yu. Shchelkanov
- G.P. Somov Institute of Epidemiology and Microbiology, Russian Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 690087 Vladivostok, Russia; (B.G.A.); (T.S.Z.); (T.A.K.); (M.Y.S.)
- School of Biomedicine, Far Eastern Federal University (FEFU), 690091 Vladivostok, Russia;
- Federal Scientific Center of the Eastern Asia Terrestrial Biodiversity, Far Eastern Branch of Russian Academy of Sciences, 690091 Vladivostok, Russia
- National Scientific Center of Marine Biology, Far Eastern Branch of Russian Academy of Sciences, 690091 Vladivostok, Russia
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14
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Behnam MAM. Protein structural heterogeneity: A hypothesis for the basis of proteolytic recognition by the main protease of SARS-CoV and SARS-CoV-2. Biochimie 2021; 182:177-184. [PMID: 33484784 PMCID: PMC7817518 DOI: 10.1016/j.biochi.2021.01.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 01/15/2021] [Accepted: 01/15/2021] [Indexed: 02/06/2023]
Abstract
The main protease (Mpro) of SARS-CoV and SARS-CoV-2 is a key enzyme in viral replication and a promising target for the development of antiviral therapeutics. The understanding of this protein is based on a number of observations derived from earlier x-ray structures, which mostly consider substrates or ligands as the main reason behind modulation of the active site. This lead to the concept of substrate-induced subsite cooperativity as an initial attempt to explain the dual binding specificity of this enzyme in recognizing the cleavage sequences at its N- and C-termini, which are important processing steps in obtaining the mature protease. The presented hypothesis proposes that structural heterogeneity is a property of the enzyme, independent of the presence of a substrate or ligand. Indeed, the analysis of Mpro structures of SARS-CoV and SARS-CoV-2 reveals a conformational diversity for the catalytically competent state in ligand-free structures. Variation in the binding site appears to result from flexibility at residues lining the S1 subpocket and segments incorporating methionine 49 and glutamine 189. The structural evidence introduces “structure-based recognition” as a new paradigm in substrate proteolysis by Mpro. In this concept, the binding space in subpockets of the enzyme varies in a non-cooperative manner, causing distinct conformations, which recognize and process different cleavage sites, as the N- and C-termini. Insights into the recognition basis of the protease provide explanation to the ordered processing of cleavage sites. The hypothesis expands the conformational space of the enzyme and consequently opportunities for drug development and repurposing efforts.
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Affiliation(s)
- Mira A M Behnam
- Institute of Pharmacy and Molecular Biotechnology, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany.
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15
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Ng CS, Stobart CC, Luo H. Innate immune evasion mediated by picornaviral 3C protease: Possible lessons for coronaviral 3C-like protease? Rev Med Virol 2021; 31:1-22. [PMID: 33624382 PMCID: PMC7883238 DOI: 10.1002/rmv.2206] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 01/10/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 is the etiological agent of the ongoing pandemic of coronavirus disease-2019, a multi-organ disease that has triggered an unprecedented global health and economic crisis. The virally encoded 3C-like protease (3CLpro ), which is named after picornaviral 3C protease (3Cpro ) due to their similarities in substrate recognition and enzymatic activity, is essential for viral replication and has been considered as the primary drug target. However, information regarding the cellular substrates of 3CLpro and its interaction with the host remains scarce, though recent work has begun to shape our understanding more clearly. Here we summarized and compared the mechanisms by which picornaviruses and coronaviruses have evolved to evade innate immune surveillance, with a focus on the established role of 3Cpro in this process. Through this comparison, we hope to highlight the potential action and mechanisms that are conserved and shared between 3Cpro and 3CLpro . In this review, we also briefly discussed current advances in the development of broad-spectrum antivirals targeting both 3Cpro and 3CLpro .
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Affiliation(s)
- Chen Seng Ng
- Centre for Heart Lung Innovation, St Paul's Hospital, University of British Columbia, Vancouver, Canada.,Department of Pathology and Laboratory of Medicine, University of British Columbia, Vancouver, Canada
| | | | - Honglin Luo
- Centre for Heart Lung Innovation, St Paul's Hospital, University of British Columbia, Vancouver, Canada.,Department of Pathology and Laboratory of Medicine, University of British Columbia, Vancouver, Canada
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16
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Umadevi P, Manivannan S, Fayad AM, Shelvy S. In silico analysis of phytochemicals as potential inhibitors of proteases involved in SARS-CoV-2 infection. J Biomol Struct Dyn 2020; 40:5053-5059. [PMID: 33372574 PMCID: PMC7876729 DOI: 10.1080/07391102.2020.1866669] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In silico analysis of six phytochemicals, flabelliferin, marmelosin, piperine, ocimin, curcumin and leucoanthocyanin, along with three drug compounds, nelfinavir, remdesivir and hydroxychloroquine, as positive control against drug targets of one SARS-CoV-2 viral protease, COVID-19 main protease (SARS CoV-2 3CLpro/Mpro), two coronavirus proteases, SARS-CoV main peptidase (SARS CoV Mpro), SARS-CoV main proteinase (SARS CoV 3CLpro), and one human cellular transmembrane serine proteinase (TMPRSS2), was carried out. Except leucoanthocyanin all other phytochemicals proved better than all three positive control drugs against SARS-CoV main peptidase, whereas, flabelliferin was found to be the potential inhibitor for SARS-CoV main proteinase out performing all the positive control drugs and phytochemicals. Amongst the compounds studied, the best inhibitor for COVID-19 main protease was nelfinavir followed by flabelliferin and ocimin. Flabelliferin was found to the best promising inhibitor of human cellular transmembrane serine proteinase, followed by nelfinavir, curcumin, piperine and marmelosin. The result on the inhibition of human cellular transmembrane serine proteinase against COVID-19 has a stable therapeutic advantage as mutation may quickly occur on viral drug targets. Hence, all the phytochemicals tested in the present study are the potential inhibitors of the all the four drug targets and can form a part of therapeutics against COVID-19 with further clinical studies. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Palaniyandi Umadevi
- Division of Crop Improvement & Biotechnology, ICAR- Indian Institute of Spices Research, Kozhikode, India.,Rice Breeding & Genetics Research Centre, ICAR-Indian Agricultural Research Institute, Aduthurai, India
| | | | - Abdulkabeer Muhammed Fayad
- Division of Crop Improvement & Biotechnology, ICAR- Indian Institute of Spices Research, Kozhikode, India
| | - Sreekumar Shelvy
- Division of Crop Improvement & Biotechnology, ICAR- Indian Institute of Spices Research, Kozhikode, India
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17
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Shitrit A, Zaidman D, Kalid O, Bloch I, Doron D, Yarnizky T, Buch I, Segev I, Ben-Zeev E, Segev E, Kobiler O. Conserved interactions required for inhibition of the main protease of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Sci Rep 2020; 10:20808. [PMID: 33257760 PMCID: PMC7704658 DOI: 10.1038/s41598-020-77794-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 11/17/2020] [Indexed: 12/13/2022] Open
Abstract
The COVID-19 pandemic caused by the SARS-CoV-2 requires a fast development of antiviral drugs. SARS-CoV-2 viral main protease (Mpro, also called 3C-like protease, 3CLpro) is a potential target for drug design. Crystal and co-crystal structures of the SARS-CoV-2 Mpro have been solved, enabling the rational design of inhibitory compounds. In this study we analyzed the available SARS-CoV-2 and the highly similar SARS-CoV-1 crystal structures. We identified within the active site of the Mpro, in addition to the inhibitory ligands' interaction with the catalytic C145, two key H-bond interactions with the conserved H163 and E166 residues. Both H-bond interactions are present in almost all co-crystals and are likely to occur also during the viral polypeptide cleavage process as suggested from docking of the Mpro cleavage recognition sequence. We screened in silico a library of 6900 FDA-approved drugs (ChEMBL) and filtered using these key interactions and selected 29 non-covalent compounds predicted to bind to the protease. Additional screen, using DOCKovalent was carried out on DrugBank library (11,414 experimental and approved drugs) and resulted in 6 covalent compounds. The selected compounds from both screens were tested in vitro by a protease activity inhibition assay. Two compounds showed activity at the 50 µM concentration range. Our analysis and findings can facilitate and focus the development of highly potent inhibitors against SARS-CoV-2 infection.
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Affiliation(s)
- Alina Shitrit
- The Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel-Aviv University, 69978, Tel Aviv, Israel
| | - Daniel Zaidman
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | | | - Itai Bloch
- Biotechnology Department, Migal - Galilee Research Institute, Kiryat-Shmona, Israel
| | - Dvir Doron
- Chemical & Computational Toxicology, Non-Clinical Development, Global R&D, Teva Pharmaceutical Industries Ltd., Netanya, Israel
| | - Tali Yarnizky
- Tali Yarnizky Scientific Consulting, Maccabim-Reut, Israel
| | - Idit Buch
- Emendo Biotherapeutics Ltd., Ness Ziona, Israel
| | | | - Efrat Ben-Zeev
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Elad Segev
- Department of Applied Mathematics, Faculty of Science, Holon Institute of Technology, Holon, Israel
| | - Oren Kobiler
- The Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel-Aviv University, 69978, Tel Aviv, Israel.
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18
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Pillaiyar T, Wendt LL, Manickam M, Easwaran M. The recent outbreaks of human coronaviruses: A medicinal chemistry perspective. Med Res Rev 2020; 41:72-135. [PMID: 32852058 PMCID: PMC7461420 DOI: 10.1002/med.21724] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/22/2020] [Accepted: 08/08/2020] [Indexed: 01/18/2023]
Abstract
Coronaviruses (CoVs) infect both humans and animals. In humans, CoVs can cause respiratory, kidney, heart, brain, and intestinal infections that can range from mild to lethal. Since the start of the 21st century, three β‐coronaviruses have crossed the species barrier to infect humans: severe‐acute respiratory syndrome (SARS)‐CoV‐1, Middle East respiratory syndrome (MERS)‐CoV, and SARS‐CoV‐2 (2019‐nCoV). These viruses are dangerous and can easily be transmitted from human to human. Therefore, the development of anticoronaviral therapies is urgently needed. However, to date, no approved vaccines or drugs against CoV infections are available. In this review, we focus on the medicinal chemistry efforts toward the development of antiviral agents against SARS‐CoV‐1, MERS‐CoV, SARS‐CoV‐2, targeting biochemical events important for viral replication and its life cycle. These targets include the spike glycoprotein and its host‐receptors for viral entry, proteases that are essential for cleaving polyproteins to produce functional proteins, and RNA‐dependent RNA polymerase for viral RNA replication.
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Affiliation(s)
- Thanigaimalai Pillaiyar
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn, Germany
| | - Lukas L Wendt
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn, Germany
| | - Manoj Manickam
- Department of Chemistry, PSG Institute of Technology and Applied Research, Coimbatore, Tamil Nadu, India
| | - Maheswaran Easwaran
- Department of Biomedical Engineering, Sethu Institute of Technology, Virudhunagar, Tamilnadu, India
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19
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Hijikata A, Shionyu-Mitsuyama C, Nakae S, Shionyu M, Ota M, Kanaya S, Shirai T. Knowledge-based structural models of SARS-CoV-2 proteins and their complexes with potential drugs. FEBS Lett 2020; 594:1960-1973. [PMID: 32379896 PMCID: PMC7267562 DOI: 10.1002/1873-3468.13806] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/27/2020] [Accepted: 04/29/2020] [Indexed: 12/28/2022]
Abstract
The World Health Organization (WHO) has declared the coronavirus disease 2019 (COVID‐19) caused by the novel coronavirus SARS‐CoV‐2 a pandemic. There is, however, no confirmed anti‐COVID‐19 therapeutic currently. In order to assist structure‐based discovery efforts for repurposing drugs against this disease, we constructed knowledge‐based models of SARS‐CoV‐2 proteins and compared the ligand molecules in the template structures with approved/experimental drugs and components of natural medicines. Our theoretical models suggest several drugs, such as carfilzomib, sinefungin, tecadenoson, and trabodenoson, that could be further investigated for their potential for treating COVID‐19.
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Affiliation(s)
- Atsushi Hijikata
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Japan
| | | | - Setsu Nakae
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Japan
| | - Masafumi Shionyu
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Japan
| | - Motonori Ota
- Department of Complex Systems Science, Graduate School of Informatics, Nagoya University, Japan
| | - Shigehiko Kanaya
- Computational Biology Laboratory, Division of Information Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), Ikoma, Japan
| | - Tsuyoshi Shirai
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Japan
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20
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Huang J, Song W, Huang H, Sun Q. Pharmacological Therapeutics Targeting RNA-Dependent RNA Polymerase, Proteinase and Spike Protein: From Mechanistic Studies to Clinical Trials for COVID-19. J Clin Med 2020; 9:E1131. [PMID: 32326602 PMCID: PMC7231166 DOI: 10.3390/jcm9041131] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 04/10/2020] [Accepted: 04/13/2020] [Indexed: 01/08/2023] Open
Abstract
An outbreak of novel coronavirus-related pneumonia COVID-19, that was identified in December 2019, has expanded rapidly, with cases now confirmed in more than 211 countries or areas. This constant transmission of a novel coronavirus and its ability to spread from human to human have prompted scientists to develop new approaches for treatment of COVID-19. A recent study has shown that remdesivir and chloroquine effectively inhibit the replication and infection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2, 2019-nCov) in vitro. In the United States, one case of COVID-19 was successfully treated with compassionate use of remdesivir in January of 2020. In addition, a clinically proven protease inhibitor, camostat mesylate, has been demonstrated to inhibit Calu-3 infection with SARS-CoV-2 and prevent SARS-2-spike protein (S protein)-mediated entry into primary human lung cells. Here, we systemically discuss the pharmacological therapeutics targeting RNA-dependent RNA polymerase (RdRp), proteinase and S protein for treatment of SARS-CoV-2 infection. This review should shed light on the fundamental rationale behind inhibition of SARS-CoV-2 enzymes RdRp as new therapeutic approaches for management of patients with COVID-19. In addition, we will discuss the viability and challenges in targeting RdRp and proteinase, and application of natural product quinoline and its analog chloroquine for treatment of coronavirus infection. Finally, determining the structural-functional relationships of the S protein of SARS-CoV-2 will provide new insights into inhibition of interactions between S protein and angiotensin-converting enzyme 2 (ACE2) and enable us to develop novel therapeutic approaches for novel coronavirus SARS-CoV-2.
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Affiliation(s)
- Jiansheng Huang
- Department of Medicine, Vanderbilt University Medical Center, 318 Preston Research Building, 2200 Pierce Avenue, Nashville, TN 37232, USA
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Wenliang Song
- Department of Medicine, Vanderbilt University Medical Center, 318 Preston Research Building, 2200 Pierce Avenue, Nashville, TN 37232, USA
| | - Hui Huang
- Center of Structural Biology, Vanderbilt University, 2200 Pierce Avenue, Nashville, TN 37232, USA
| | - Quancai Sun
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China
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21
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Pillaiyar T, Manickam M, Namasivayam V, Hayashi Y, Jung SH. An Overview of Severe Acute Respiratory Syndrome-Coronavirus (SARS-CoV) 3CL Protease Inhibitors: Peptidomimetics and Small Molecule Chemotherapy. J Med Chem 2016; 59:6595-628. [PMID: 26878082 PMCID: PMC7075650 DOI: 10.1021/acs.jmedchem.5b01461] [Citation(s) in RCA: 504] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Indexed: 01/17/2023]
Abstract
Severe acute respiratory syndrome (SARS) is caused by a newly emerged coronavirus that infected more than 8000 individuals and resulted in more than 800 (10-15%) fatalities in 2003. The causative agent of SARS has been identified as a novel human coronavirus (SARS-CoV), and its viral protease, SARS-CoV 3CL(pro), has been shown to be essential for replication and has hence been recognized as a potent drug target for SARS infection. Currently, there is no effective treatment for this epidemic despite the intensive research that has been undertaken since 2003 (over 3500 publications). This perspective focuses on the status of various efficacious anti-SARS-CoV 3CL(pro) chemotherapies discovered during the last 12 years (2003-2015) from all sources, including laboratory synthetic methods, natural products, and virtual screening. We describe here mainly peptidomimetic and small molecule inhibitors of SARS-CoV 3CL(pro). Attempts have been made to provide a complete description of the structural features and binding modes of these inhibitors under many conditions.
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Affiliation(s)
- Thanigaimalai Pillaiyar
- Pharmaceutical
Institute, Pharmaceutical Chemistry I, University
of Bonn, An der Immenburg
4, D-53121 Bonn, Germany
| | - Manoj Manickam
- College
of Pharmacy and Institute of Drug Research and Development, Chungnam National University, Daejeon 34134, South Korea
| | - Vigneshwaran Namasivayam
- Pharmaceutical
Institute, Pharmaceutical Chemistry I, University
of Bonn, An der Immenburg
4, D-53121 Bonn, Germany
| | - Yoshio Hayashi
- Department
of Medicinal Chemistry, Tokyo University
of Pharmacy and Life Sciences, Tokyo 192-0392, Japan
| | - Sang-Hun Jung
- College
of Pharmacy and Institute of Drug Research and Development, Chungnam National University, Daejeon 34134, South Korea
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22
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Berry M, Fielding BC, Gamieldien J. Potential Broad Spectrum Inhibitors of the Coronavirus 3CLpro: A Virtual Screening and Structure-Based Drug Design Study. Viruses 2015; 7:6642-60. [PMID: 26694449 PMCID: PMC4690886 DOI: 10.3390/v7122963] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 11/16/2015] [Accepted: 11/30/2015] [Indexed: 01/29/2023] Open
Abstract
Human coronaviruses represent a significant disease burden; however, there is currently no antiviral strategy to combat infection. The outbreak of severe acute respiratory syndrome (SARS) in 2003 and Middle East respiratory syndrome (MERS) less than 10 years later demonstrates the potential of coronaviruses to cross species boundaries and further highlights the importance of identifying novel lead compounds with broad spectrum activity. The coronavirus 3CL(pro) provides a highly validated drug target and as there is a high degree of sequence homology and conservation in main chain architecture the design of broad spectrum inhibitors is viable. The ZINC drugs-now library was screened in a consensus high-throughput pharmacophore modeling and molecular docking approach by Vina, Glide, GOLD and MM-GBSA. Molecular dynamics further confirmed results obtained from structure-based techniques. A highly defined hit-list of 19 compounds was identified by the structure-based drug design methodologies. As these compounds were extensively validated by a consensus approach and by molecular dynamics, the likelihood that at least one of these compounds is bioactive is excellent. Additionally, the compounds segregate into 15 significantly dissimilar (p < 0.05) clusters based on shape and features, which represent valuable scaffolds that can be used as a basis for future anti-coronaviral inhibitor discovery experiments. Importantly though, the enriched subset of 19 compounds identified from the larger library has to be validated experimentally.
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Affiliation(s)
- Michael Berry
- South African Medical Research Council Bioinformatics Capacity Development Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa.
- Molecular Biology and Virology Laboratory, Department of Medical BioSciences, Faculty of Natural Sciences, University of the Western Cape, Western Cape, Bellville 7535, South Africa.
| | - Burtram C Fielding
- Molecular Biology and Virology Laboratory, Department of Medical BioSciences, Faculty of Natural Sciences, University of the Western Cape, Western Cape, Bellville 7535, South Africa.
| | - Junaid Gamieldien
- South African Medical Research Council Bioinformatics Capacity Development Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa.
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23
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Needle D, Lountos GT, Waugh DS. Structures of the Middle East respiratory syndrome coronavirus 3C-like protease reveal insights into substrate specificity. ACTA ACUST UNITED AC 2015; 71:1102-11. [PMID: 25945576 PMCID: PMC4427198 DOI: 10.1107/s1399004715003521] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 02/19/2015] [Indexed: 11/21/2022]
Abstract
Middle East respiratory syndrome coronavirus (MERS‐CoV) is a highly pathogenic virus that causes severe respiratory illness accompanied by multi‐organ dysfunction, resulting in a case fatality rate of approximately 40%. As found in other coronaviruses, the majority of the positive‐stranded RNA MERS‐CoV genome is translated into two polyproteins, one created by a ribosomal frameshift, that are cleaved at three sites by a papain‐like protease and at 11 sites by a 3C‐like protease (3CLpro). Since 3CLpro is essential for viral replication, it is a leading candidate for therapeutic intervention. To accelerate the development of 3CLpro inhibitors, three crystal structures of a catalytically inactive variant (C148A) of the MERS‐CoV 3CLpro enzyme were determined. The aim was to co‐crystallize the inactive enzyme with a peptide substrate. Fortuitously, however, in two of the structures the C‐terminus of one protomer is bound in the active site of a neighboring molecule, providing a snapshot of an enzyme–product complex. In the third structure, two of the three protomers in the asymmetric unit form a homodimer similar to that of SARS‐CoV 3CLpro; however, the third protomer adopts a radically different conformation that is likely to correspond to a crystallographic monomer, indicative of substantial structural plasticity in the enzyme. The results presented here provide a foundation for the structure‐based design of small‐molecule inhibitors of the MERS‐CoV 3CLpro enzyme.
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Affiliation(s)
- Danielle Needle
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, USA
| | - George T Lountos
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, USA
| | - David S Waugh
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, USA
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24
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Paasche A, Zipper A, Schäfer S, Ziebuhr J, Schirmeister T, Engels B. Evidence for substrate binding-induced zwitterion formation in the catalytic Cys-His dyad of the SARS-CoV main protease. Biochemistry 2014; 53:5930-46. [PMID: 25196915 DOI: 10.1021/bi400604t] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The coronavirus main protease (M(pro)) represents an attractive drug target for antiviral therapy of coronavirus (CoV) infections, including severe acute respiratory syndrome (SARS). The SARS-CoV M(pro) and related CoV proteases have several distinct features, such as an uncharged Cys-His catalytic dyad embedded in a chymotrypsin-like protease fold, that clearly separate these enzymes from archetypical cysteine proteases. To further characterize the catalytic system of CoV main proteases and to obtain information about improved inhibitors, we performed comprehensive simulations of the proton-transfer reactions in the SARS-CoV M(pro) active site that lead to the Cys(-)/His(+) zwitterionic state required for efficient proteolytic activity. Our simulations, comprising the free enzyme as well as substrate-enzyme and inhibitor-enzyme complexes, lead us to predict that zwitterion formation is fostered by substrate binding but not inhibitor binding. This indicates that M(pro) employs a substrate-induced catalytic mechanism that further enhances its substrate specificity. Our computational data are in line with available experimental results, such as X-ray geometries, measured pKa values, mutagenesis experiments, and the measured differences between the kinetic parameters of substrates and inhibitors. The data also provide an atomistic picture of the formerly postulated electrostatic trigger involved in SARS-CoV M(pro) activity. Finally, they provide information on how a specific microenvironment may finely tune the activity of M(pro) toward specific viral protein substrates, which is known to be required for efficient viral replication. Our simulations also indicate that the low inhibition potencies of known covalently interacting inhibitors may, at least in part, be attributed to insufficient fostering of the proton-transfer reaction. These findings suggest ways to achieve improved inhibitors.
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Affiliation(s)
- Alexander Paasche
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg , Emil-Fischer-Straße 42, 97074 Würzburg, Germany
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25
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Hilgenfeld R. From SARS to MERS: crystallographic studies on coronaviral proteases enable antiviral drug design. FEBS J 2014; 281:4085-96. [PMID: 25039866 PMCID: PMC7163996 DOI: 10.1111/febs.12936] [Citation(s) in RCA: 435] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 07/07/2014] [Accepted: 07/15/2014] [Indexed: 01/08/2023]
Abstract
This review focuses on the important contributions that macromolecular crystallography has made over the past 12 years to elucidating structures and mechanisms of the essential proteases of coronaviruses, the main protease (M(pro) ) and the papain-like protease (PL(pro) ). The role of X-ray crystallography in structure-assisted drug discovery against these targets is discussed. Aspects dealt with in this review include the emergence of the SARS coronavirus in 2002-2003 and of the MERS coronavirus 10 years later and the origins of these viruses. The crystal structure of the free SARS coronavirus M(pro) and its dependence on pH is discussed, as are efforts to design inhibitors on the basis of these structures. The mechanism of maturation of the enzyme from the viral polyprotein is still a matter of debate. The crystal structure of the SARS coronavirus PL(pro) and its complex with ubiquitin is also discussed, as is its orthologue from MERS coronavirus. Efforts at predictive structure-based inhibitor development for bat coronavirus M(pro) s to increase the preparedness against zoonotic transmission to man are described as well. The paper closes with a brief discussion of structure-based discovery of antivirals in an academic setting.
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Affiliation(s)
- Rolf Hilgenfeld
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, and German Center for Infection Research, University of Lübeck, Germany
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26
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Lim L, Shi J, Mu Y, Song J. Dynamically-driven enhancement of the catalytic machinery of the SARS 3C-like protease by the S284-T285-I286/A mutations on the extra domain. PLoS One 2014; 9:e101941. [PMID: 25036652 PMCID: PMC4103764 DOI: 10.1371/journal.pone.0101941] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 06/13/2014] [Indexed: 11/18/2022] Open
Abstract
Previously we revealed that the extra domain of SARS 3CLpro mediated the catalysis via different mechanisms. While the R298A mutation completely abolished the dimerization, thus resulting in the inactive catalytic machinery, N214A inactivated the enzyme by altering its dynamics without significantly perturbing its structure. Here we studied another mutant with S284-T285-I286 replaced by Ala (STI/A) with a 3.6-fold activity increase and slightly enhanced dimerization. We determined its crystal structure, which still adopts the dimeric structure almost identical to that of the wild-type (WT), except for slightly tighter packing between two extra-domains. We then conducted 100-ns molecular dynamics (MD) simulations for both STI/A and WT, the longest reported so far for 3CLpro. In the simulations, two STI/A extra domains become further tightly packed, leading to a significant volume reduction of the nano-channel formed by residues from both catalytic and extra domains. The enhanced packing appears to slightly increase the dynamic stability of the N-finger and the first helix residues, which subsequently triggers the redistribution of dynamics over residues directly contacting them. This ultimately enhances the dynamical stability of the residues constituting the catalytic dyad and substrate-binding pockets. Further correlation analysis reveals that a global network of the correlated motions exists in the protease, whose components include all residues identified so far to be critical for the dimerization and catalysis. Most strikingly, the N214A mutation globally decouples this network while the STI/A mutation alters the correlation pattern. Together with previous results, the present study establishes that besides the classic structural allostery, the dynamic allostery also operates in the SARS 3CLpro, which is surprisingly able to relay the perturbations on the extra domain onto the catalytic machinery to manifest opposite catalytic effects. Our results thus imply a promising avenue to design specific inhibitors for 3CL proteases by disrupting their dynamic correlation network.
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Affiliation(s)
- Liangzhong Lim
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Republic of Singapore
| | - Jiahai Shi
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Republic of Singapore
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
| | - Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Republic of Singapore
- * E-mail:
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27
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Turlington M, Chun A, Tomar S, Eggler A, Grum-Tokars V, Jacobs J, Daniels JS, Dawson E, Saldanha A, Chase P, Baez-Santos YM, Lindsley CW, Hodder P, Mesecar AD, Stauffer SR. Discovery of N-(benzo[1,2,3]triazol-1-yl)-N-(benzyl)acetamido)phenyl) carboxamides as severe acute respiratory syndrome coronavirus (SARS-CoV) 3CLpro inhibitors: identification of ML300 and noncovalent nanomolar inhibitors with an induced-fit binding. Bioorg Med Chem Lett 2013; 23:6172-7. [PMID: 24080461 PMCID: PMC3878165 DOI: 10.1016/j.bmcl.2013.08.112] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 08/26/2013] [Accepted: 08/29/2013] [Indexed: 12/22/2022]
Abstract
Herein we report the discovery and SAR of a novel series of SARS-CoV 3CLpro inhibitors identified through the NIH Molecular Libraries Probe Production Centers Network (MLPCN). In addition to ML188, ML300 represents the second probe declared for 3CLpro from this collaborative effort. The X-ray structure of SARS-CoV 3CLpro bound with a ML300 analog highlights a unique induced-fit reorganization of the S2-S4 binding pockets leading to the first sub-micromolar noncovalent 3CLpro inhibitors retaining a single amide bond.
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Affiliation(s)
- Mark Turlington
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Center for Neuroscience Drug Discovery, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Specialized Chemistry Center for Probe Development (MLPCN), Nashville, TN 37232, USA
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28
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Paasche A, Schirmeister T, Engels B. Benchmark Study for the Cysteine-Histidine Proton Transfer Reaction in a Protein Environment: Gas Phase, COSMO, QM/MM Approaches. J Chem Theory Comput 2013; 9:1765-77. [PMID: 26587634 DOI: 10.1021/ct301082y] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Proton transfer reactions are of crucial interest for the investigation of proteins. We have investigated the accuracy of commonly used quantum chemical methods for the description of proton transfer reactions in different environments (gas phase, COSMO, QM/MM) using the proton transfer between the catalytic dyad residues cysteine 145 and histidine 41 of SARS coronavirus main protease as a case study. The test includes thermodynamic, kinetic, and structural properties. The study comprises computationally demanding ab initio approaches (HF, CC2, MP2, SCS-CC2, SCS-MP2, CCSD(T)), popular density functional theories (BLYP, B3LYP, M06-2X), and semiempirical methods (MNDO/d, AM1, RM1, PM3, PM6). The approximated coupled cluster approach LCCSD(T) is taken as a reference method. We find that the robustness of the tested methods with respect to the environment correlates well with the level of theory. As an example HF, CC2, MP2, and their SCS variants show similar errors for gas phase, COSMO, or QM/MM computations. In contrast for semiempirical methods, the errors strongly diversify if one goes from gas phase to COSMO or QM/MM. Particular problems are observed for the recent semiempirical methods PM6 and RM1, which show the best performance for gas phase calculations but possess larger errors in conjunction with COSMO. Finally, a combination of SCS-MP2 and B3LYP or M06-2X allows reliable estimates about remaining errors.
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Affiliation(s)
- Alexander Paasche
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Emil-Fischer-Str. 42, 97074 Würzburg, Germany
| | - Tanja Schirmeister
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz, Staudinger Weg 5, 55128 Mainz, Germany
| | - Bernd Engels
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Emil-Fischer-Str. 42, 97074 Würzburg, Germany
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29
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Schomburg D, Schomburg I. SARS coronavirus main proteinase 3.4.22.69. CLASS 3.4–6 HYDROLASES, LYASES, ISOMERASES, LIGASES 2013. [PMCID: PMC7123336 DOI: 10.1007/978-3-642-36260-6_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
EC number 3.4.22.69 Recommended name SARS coronavirus main proteinase Synonyms 3C-like protease <2,3> [9,16,38,49,51] 3CL protease <2> [14,48] 3cLpro <1,2,3> [7,11,13,16,19,28,38,49,51] C30.004 (Merops-ID) Mpro SARS 3C-like protease <2> [17] SARS 3C-like proteinase <2> [15,18,27] SARS 3CL protease <2> [31] SARS 3CLpro <2> [49] SARS CoV main proteinase <2> [1,2,4,5] SARS CoVMpro <2> [33] SARS Mpro <2> [25] SARS coronavirus 3C-like protease <2> [48] SARS coronavirus 3C-like proteinase <2> [50] SARS coronavirus 3CL protease <2> [20] SARS coronavirus main peptidase <2> [23] SARS coronavirus main protease <2> [25] SARS coronavirus main proteinase <2> [5,33] SARS main protease <2> [12,25] SARS-3CL protease <2> [48] SARS-3CLpro <2> [29,50] SARS-CoV 3C-like peptidaseSARS-CoV 3C-like peptidase<2> [24] SARS-CoV 3C-like protease<1> [19] SARS-CoV 3CL protease <2> [22,30,44,46] SARS-CoV 3CLpro <2> [32,36,38,44,45] SARS-CoV 3CLpro enzyme <2> [11] SARS-CoV Mpro <2> [21,40] SARS-CoV main protease <2> [21,26,43] SARS-coronavirus 3CL protease <2> [8] SARS-coronavirus main protease <2> [47] TGEV Mpro coronavirus 3C-like protease <1> [19] porcine transmissible gastroenteritis virus Mpro severe acute respiratory syndrome coronavirus 3C-like protease <2> [41,42] severe acute respiratory syndrome coronavirus main protease <2> [21] severe acute respiratory syndrome coronavirus main proteinase <2> [33] CAS registry number 218925-73-6 37353-41-6
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Affiliation(s)
- Dietmar Schomburg
- Bioinformatics & Systems Biology, Technical University Braunschweig, Langer Kamp 19b, 38106 Braunschweig, Germany
| | - Ida Schomburg
- Bioinformatics & Systems Biology, Technical University Braunschweig, Langer Kamp 19b, 38106 Braunschweig, Germany
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30
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31
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Someya Y. From head to toe of the norovirus 3C-like protease. Biomol Concepts 2012; 3:41-56. [DOI: 10.1515/bmc.2011.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 11/02/2011] [Indexed: 01/25/2023] Open
Abstract
AbstractNoroviruses are major causative agents of viral gastroenteritis in humans. Currently, there are no therapeutic medications to treat noroviral infections, nor are there effective vaccines against these pathogens. The viral 3C-like protease is solely responsible for the maturation of viral protein components. The crystal structures of the proteases were resolved at high atomic resolution. The protease was also explored by means of mutagenesis. These studies revealed the active-site amino acid residues and factors determining and affecting substrate specificity as well as the principle of architecting the protease molecule. The possible mechanism of proteolysis was also suggested. Consideration of the data accumulated thus far will be useful for development of therapeutic drugs targeting the viral protease.
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Affiliation(s)
- Yuichi Someya
- 1Department of Virology II, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashi-Murayama, Tokyo 208-0011, Japan
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32
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Mukherjee P, Shah F, Desai P, Avery M. Inhibitors of SARS-3CLpro: virtual screening, biological evaluation, and molecular dynamics simulation studies. J Chem Inf Model 2011; 51:1376-92. [PMID: 21604711 PMCID: PMC3929308 DOI: 10.1021/ci1004916] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
SARS-CoV from the coronaviridae family has been identified as the etiological agent of Severe Acute Respiratory Syndrome (SARS), a highly contagious upper respiratory disease that reached epidemic status in 2002. SARS-3CL(pro), a cysteine protease indispensible to the viral life cycle, has been identified as one of the key therapeutic targets against SARS. A combined ligand and structure-based virtual screening was carried out against the Asinex Platinum collection. Multiple low micromolar inhibitors of the enzyme were identified through this search, one of which also showed activity against SARS-CoV in a whole cell CPE assay. Furthermore, multinanosecond explicit solvent simulations were carried out using the docking poses of the identified hits to study the overall stability of the binding site interactions as well as identify important changes in the interaction profile that were not apparent from the docking study. Cumulative analysis of the evaluated compounds and the simulation studies led to the identification of certain protein-ligand interaction patterns which would be useful in further structure based design efforts.
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Affiliation(s)
| | - Falgun Shah
- Department of Medicinal Chemistry, School of Pharmacy, University of Mississippi, University, MS 38677
| | | | - Mitchell Avery
- Department of Medicinal Chemistry, School of Pharmacy, University of Mississippi, University, MS 38677
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33
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Shi J, Han N, Lim L, Lua S, Sivaraman J, Wang L, Mu Y, Song J. Dynamically-driven inactivation of the catalytic machinery of the SARS 3C-like protease by the N214A mutation on the extra domain. PLoS Comput Biol 2011; 7:e1001084. [PMID: 21390281 PMCID: PMC3044768 DOI: 10.1371/journal.pcbi.1001084] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Accepted: 01/18/2011] [Indexed: 11/18/2022] Open
Abstract
Despite utilizing the same chymotrypsin fold to host the catalytic machinery, coronavirus 3C-like proteases (3CLpro) noticeably differ from picornavirus 3C proteases in acquiring an extra helical domain in evolution. Previously, the extra domain was demonstrated to regulate the catalysis of the SARS-CoV 3CLpro by controlling its dimerization. Here, we studied N214A, another mutant with only a doubled dissociation constant but significantly abolished activity. Unexpectedly, N214A still adopts the dimeric structure almost identical to that of the wild-type (WT) enzyme. Thus, we conducted 30-ns molecular dynamics (MD) simulations for N214A, WT, and R298A which we previously characterized to be a monomer with the collapsed catalytic machinery. Remarkably, three proteases display distinctive dynamical behaviors. While in WT, the catalytic machinery stably retains in the activated state; in R298A it remains largely collapsed in the inactivated state, thus implying that two states are not only structurally very distinguishable but also dynamically well separated. Surprisingly, in N214A the catalytic dyad becomes dynamically unstable and many residues constituting the catalytic machinery jump to sample the conformations highly resembling those of R298A. Therefore, the N214A mutation appears to trigger the dramatic change of the enzyme dynamics in the context of the dimeric form which ultimately inactivates the catalytic machinery. The present MD simulations represent the longest reported so far for the SARS-CoV 3CLpro, unveiling that its catalysis is critically dependent on the dynamics, which can be amazingly modulated by the extra domain. Consequently, mediating the dynamics may offer a potential avenue to inhibit the SARS-CoV 3CLpro. Severe acute respiratory syndrome (SARS) is the first emerging infectious disease of the 21st century which has not only caused rapid infection and death, but also triggered a dramatic social crisis. Its 3C-like protease is crucial for reproducing virus and thus represents a top target for drug design. Interestingly, unlike 3C protease such as from picorovirus, the SARS protease evolutionarily acquired a C-terminal extra domain with previously-unknown function. Immediately after SARS outbreak, we revealed that the extra domain was able to regulate the catalysis by controlling the dimerization essential for activity. Here, we studied one mutant with only slightly-weakened dimerization but almost completely abolished activity. We determined its three-dimensional structure but very unexpectedly it is almost identical to that of the wild-type enzyme. Therefore, we initiated 30-ns molecular dynamic simulations for five forms of the enzyme and the results demonstrate that the dynamical changes in this mutant are responsible for its inactivation. Therefore, the extra domain can also control the catalysis by modulating the enzyme dynamics. This is not only of fundamental significance to understanding how enzymes evolve, but also implies a novel avenue for design of anti-SARS molecules.
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Affiliation(s)
- Jiahai Shi
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
| | - Nanyu Han
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Liangzhong Lim
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
| | - Shixiong Lua
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
| | - J. Sivaraman
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore
- * E-mail: (JS); (YM)
| | - Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine and National University of Singapore, Singapore
- * E-mail: (JS); (YM)
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34
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Verschueren KHG, Pumpor K, Anemüller S, Chen S, Mesters JR, Hilgenfeld R. A structural view of the inactivation of the SARS coronavirus main proteinase by benzotriazole esters. ACTA ACUST UNITED AC 2008; 15:597-606. [PMID: 18559270 PMCID: PMC7110992 DOI: 10.1016/j.chembiol.2008.04.011] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2007] [Revised: 04/16/2008] [Accepted: 04/17/2008] [Indexed: 01/04/2023]
Abstract
The main proteinase (Mpro) of the severe acute respiratory syndrome (SARS) coronavirus is a principal target for the design of anticoronaviral compounds. Benzotriazole esters have been reported as potent nonpeptidic inhibitors of the enzyme, but their exact mechanism of action remains unclear. Here we present crystal structures of SARS-CoV Mpro, the active-site cysteine of which has been acylated by benzotriazole esters that act as suicide inhibitors. In one of the structures, the thioester product has been hydrolyzed and benzoic acid is observed to bind to the hydrophobic S2 pocket. This structure also features the enzyme with a shortened N-terminal segment (“amputated N finger”). The results further the understanding of the important role of the N finger for catalysis as well as the design of benzotriazole inhibitors with improved specificity.
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Affiliation(s)
- Koen H G Verschueren
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Lübeck, Germany
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35
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Shi J, Sivaraman J, Song J. Mechanism for controlling the dimer-monomer switch and coupling dimerization to catalysis of the severe acute respiratory syndrome coronavirus 3C-like protease. J Virol 2008; 82:4620-9. [PMID: 18305031 PMCID: PMC2293028 DOI: 10.1128/jvi.02680-07] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Accepted: 02/20/2008] [Indexed: 01/07/2023] Open
Abstract
Unlike 3C protease, the severe acute respiratory syndrome coronavirus (SARS-CoV) 3C-like protease (3CLpro) is only enzymatically active as a homodimer and its catalysis is under extensive regulation by the unique extra domain. Despite intense studies, two puzzles still remain: (i) how the dimer-monomer switch is controlled and (ii) why dimerization is absolutely required for catalysis. Here we report the monomeric crystal structure of the SARS-CoV 3CLpro mutant R298A at a resolution of 1.75 A. Detailed analysis reveals that Arg298 serves as a key component for maintaining dimerization, and consequently, its mutation will trigger a cooperative switch from a dimer to a monomer. The monomeric enzyme is irreversibly inactivated because its catalytic machinery is frozen in the collapsed state, characteristic of the formation of a short 3(10)-helix from an active-site loop. Remarkably, dimerization appears to be coupled to catalysis in 3CLpro through the use of overlapped residues for two networks, one for dimerization and another for the catalysis.
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Affiliation(s)
- Jiahai Shi
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Republic of Singapore.
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36
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Mukherjee P, Desai P, Ross L, White EL, Avery MA. Structure-based virtual screening against SARS-3CL(pro) to identify novel non-peptidic hits. Bioorg Med Chem 2008; 16:4138-49. [PMID: 18343121 PMCID: PMC7127700 DOI: 10.1016/j.bmc.2008.01.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2007] [Revised: 01/04/2008] [Accepted: 01/07/2008] [Indexed: 01/01/2023]
Abstract
Severe acute respiratory syndrome is a highly infectious upper respiratory tract disease caused by SARS-CoV, a previously unidentified human coronavirus. SARS-3CL(pro) is a viral cysteine protease critical to the pathogen's life cycle and hence a therapeutic target of importance. The recently elucidated crystal structures of this enzyme provide an opportunity for the discovery of inhibitors through rational drug design. In the current study, Gold docking program was utilized to conduct extensive docking studies against the target crystal structure to develop a robust and predictive docking protocol. The validated docking protocol was used to conduct a structure-based virtual screening of the Asinex Platinum collection. Biological evaluation of a screened selection of compounds was carried out to identify novel inhibitors of the viral protease.
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Affiliation(s)
- Prasenjit Mukherjee
- Department of Medicinal Chemistry, School of Pharmacy, University of Mississippi, Faser 417, University, MS 38677, USA
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