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Lohachova KO, Kyrychenko A, Kalugin ON. Critical assessment of popular biomolecular force fields for molecular dynamics simulations of folding and enzymatic activity of main protease of coronavirus SARS-CoV-2. Biophys Chem 2024; 311:107258. [PMID: 38776839 DOI: 10.1016/j.bpc.2024.107258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/09/2024] [Accepted: 05/11/2024] [Indexed: 05/25/2024]
Abstract
The main cysteine protease (Mpro) of coronavirus SARS-CoV-2 has become a promising target for computational development in anti-COVID-19 treatments. Here, we benchmarked the performance of six biomolecular molecular dynamics (MD) force fields (OPLS-AA, CHARMM27, CHARMM36, AMBER03, AMBER14SB and GROMOS G54A7) and three water models (TIP3P, TIP4P and SPC) for reproducing the native fold and the enzymatic activity of Mpro as monomeric and dimeric units. The MD sampling up to 1 μs suggested that the proper choice of the force fields and water models plays an essential role in reproducing the tertiary structure and the inter-residue distance between the catalytic dyad His41-Cys145. We found that while most benchmarked all-atom force fields reproduce well the native fold of Mpro, the CHARMM27/TIP3P and OPLS-AA/TIP4P setups revealed a good performance in reproducing the structure of the catalytic domain. In addition, these FF setups were also well-adopted for MD sampling of Mpro at the physiologic conditions by mimicking the presence of 100 mM NaCl and the elevated temperature of 310 K. Finally, both FFs were also performed well in reproducing the native fold of Mpro in a dimeric form. Therefore, comparing the preservation of the native fold of Mpro and the stability of its catalytic site architecture, our MD benchmarking suggests that the OPLS-AA/TIP4P and CHARMM27/TIP3P MD setups at the physiologic conditions may be well-suited for rapid in silico screening and developing broad-spectrum anti-coronaviral therapeutic agents.
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Affiliation(s)
- Kateryna O Lohachova
- School of Chemistry, V.N. Karazin Kharkiv National University, 4 Svobody sq., 61022 Kharkiv, Ukraine
| | - Alexander Kyrychenko
- School of Chemistry, V.N. Karazin Kharkiv National University, 4 Svobody sq., 61022 Kharkiv, Ukraine.
| | - Oleg N Kalugin
- School of Chemistry, V.N. Karazin Kharkiv National University, 4 Svobody sq., 61022 Kharkiv, Ukraine
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2
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Yang W, Wang Y, Han D, Tang W, Sun L. Recent advances in application of computer-aided drug design in anti-COVID-19 Virials Drug Discovery. Biomed Pharmacother 2024; 173:116423. [PMID: 38493593 DOI: 10.1016/j.biopha.2024.116423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 03/19/2024] Open
Abstract
Corona Virus Disease 2019 (COVID-19) is a global pandemic epidemic caused by severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), which poses a serious threat to human health worldwide and results in significant economic losses. With the continuous emergence of new virus strains, small molecule drugs remain the most effective treatment for COVID-19. The traditional drug development process usually requires several years; however, the development of computer-aided drug design (CADD) offers the opportunity to develop innovative drugs quickly and efficiently. The literature review describes the general process of CADD, the viral proteins that play essential roles in the life cycle of SARS-CoV-2 and can serve as therapeutic targets, and examples of drug screening of viral target proteins by applying CADD methods. Finally, the potential of CADD in COVID-19 therapy, the deficiency, and the possible future development direction are discussed.
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Affiliation(s)
- Weiying Yang
- Department of Emergency Medicine, First Hospital of Jilin University, Changchun 130021, China
| | - Ye Wang
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Dongfeng Han
- Department of Emergency Medicine, First Hospital of Jilin University, Changchun 130021, China
| | - Wenjing Tang
- Department of Emergency Medicine, First Hospital of Jilin University, Changchun 130021, China
| | - Lichao Sun
- Department of Emergency Medicine, First Hospital of Jilin University, Changchun 130021, China.
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3
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Sayaf AM, Ullah Khalid S, Hameed JA, Alshammari A, Khan A, Mohammad A, Alghamdi S, Wei DQ, Yeoh K. Exploring the natural products chemical space through a molecular search to discover potential inhibitors that target the hypoxia-inducible factor (HIF) prolyl hydroxylase domain (PHD). Front Pharmacol 2023; 14:1202128. [PMID: 37670941 PMCID: PMC10475833 DOI: 10.3389/fphar.2023.1202128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 06/30/2023] [Indexed: 09/07/2023] Open
Abstract
Introduction: Hypoxia-inducible factor (HIF) prolyl hydroxylase domain (PHD) enzymes are major therapeutic targets of anemia and ischemic/hypoxia diseases. To overcome safety issues, liver failure, and problems associated with on-/off-targets, natural products due to their novel and unique structures offer promising alternatives as drug targets. Methods: In the current study, the Marine Natural Products, North African, South African, East African, and North-East African chemical space was explored for HIF-PHD inhibitors discovery through molecular search, and the final hits were validated using molecular simulation and free energy calculation approaches. Results: Our results revealed that CMNPD13808 with a docking score of -8.690 kcal/mol, CID15081178 with a docking score of -8.027 kcal/mol, CID71496944 with a docking score of -8.48 kcal/mol and CID11821407 with a docking score of -7.78 kcal/mol possess stronger activity than the control N-[(4-hydroxy-8-iodoisoquinolin-3-yl)carbonyl]glycine, 4HG (-6.87 kcal/mol). Interaction analysis revealed that the target compounds interact with Gln239, Tyr310, Tyr329, Arg383 and Trp389 residues, and chelate the active site iron in a bidentate manner in PHD2. Molecular simulation revealed that these target hits robustly block the PHD2 active site by demonstrating stable dynamics. Furthermore, the half-life of the Arg383 hydrogen bond with the target ligands, which is an important factor for PHD2 inhibition, remained almost constant in all the complexes during the simulation. Finally, the total binding free energy of each complex was calculated as CMNPD13808-PHD2 -72.91 kcal/mol, CID15081178-PHD2 -65.55 kcal/mol, CID71496944-PHD2 -68.47 kcal/mol, and CID11821407-PHD2 -62.06 kcal/mol, respectively. Conclusion: The results show the compounds possess good activity in contrast to the control drug (4HG) and need further in vitro and in vivo validation for possible usage as potential drugs against HIF-PHD2-associated diseases.
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Affiliation(s)
- Abrar Mohammad Sayaf
- School of Chemical Sciences, Universiti Sains Malaysia, Gelugor, Penang, Malaysia
| | | | | | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Nayang, Henan, China
| | - Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman, Kuwait
| | - Saeed Alghamdi
- Department of Pharmacy, Riyadh Security Forces Hospital, Ministry of Interior, Riyadh, Saudi Arabia
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Nayang, Henan, China
- State Key Laboratory of Microbial Metabolism, Joint Laboratory of International Laboratory of Metabolic and Developmental Sciences, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Peng Cheng Laboratory, Shenzhen, Guangdong, China
| | - KarKheng Yeoh
- School of Chemical Sciences, Universiti Sains Malaysia, Gelugor, Penang, Malaysia
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4
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Pieroni M, Madeddu F, Di Martino J, Arcieri M, Parisi V, Bottoni P, Castrignanò T. MD-Ligand-Receptor: A High-Performance Computing Tool for Characterizing Ligand-Receptor Binding Interactions in Molecular Dynamics Trajectories. Int J Mol Sci 2023; 24:11671. [PMID: 37511429 PMCID: PMC10380688 DOI: 10.3390/ijms241411671] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/15/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Molecular dynamics simulation is a widely employed computational technique for studying the dynamic behavior of molecular systems over time. By simulating macromolecular biological systems consisting of a drug, a receptor and a solvated environment with thousands of water molecules, MD allows for realistic ligand-receptor binding interactions (lrbi) to be studied. In this study, we present MD-ligand-receptor (MDLR), a state-of-the-art software designed to explore the intricate interactions between ligands and receptors over time using molecular dynamics trajectories. Unlike traditional static analysis tools, MDLR goes beyond simply taking a snapshot of ligand-receptor binding interactions (lrbi), uncovering long-lasting molecular interactions and predicting the time-dependent inhibitory activity of specific drugs. With MDLR, researchers can gain insights into the dynamic behavior of complex ligand-receptor systems. Our pipeline is optimized for high-performance computing, capable of efficiently processing vast molecular dynamics trajectories on multicore Linux servers or even multinode HPC clusters. In the latter case, MDLR allows the user to analyze large trajectories in a very short time. To facilitate the exploration and visualization of lrbi, we provide an intuitive Python notebook (Jupyter), which allows users to examine and interpret the results through various graphical representations.
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Affiliation(s)
- Michele Pieroni
- Department of Computer Science, "Sapienza" University of Rome, V. le Regina Elena 295, 00161 Rome, Italy
| | - Francesco Madeddu
- Department of Computer Science, "Sapienza" University of Rome, V. le Regina Elena 295, 00161 Rome, Italy
| | - Jessica Di Martino
- Department of Ecological and Biological Sciences, Tuscia University, Viale dell'Università s.n.c., 01100 Viterbo, Italy
| | - Manuel Arcieri
- Department of Health Technology, Technical University of Denmark, Anker Engelunds Vej 101, 2800 Kongens Lyngby, Denmark
| | - Valerio Parisi
- Department of Physics, "Sapienza" University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy
| | - Paolo Bottoni
- Department of Computer Science, "Sapienza" University of Rome, V. le Regina Elena 295, 00161 Rome, Italy
| | - Tiziana Castrignanò
- Department of Ecological and Biological Sciences, Tuscia University, Viale dell'Università s.n.c., 01100 Viterbo, Italy
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5
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Rescifina A. Progress of the "Molecular Informatics" Section in 2022. Int J Mol Sci 2023; 24:ijms24119442. [PMID: 37298393 DOI: 10.3390/ijms24119442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
This is the first Editorial of the "Molecular Informatics" Section (MIS) of the International Journal of Molecular Sciences (IJMS), which was created towards the end of 2018 (the first article was submitted on 27 September 2018) and has experienced significant growth from 2018 to now [...].
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Affiliation(s)
- Antonio Rescifina
- Department of Drug and Health Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
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6
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Rungruangmaitree R, Phoochaijaroen S, Chimprasit A, Saparpakorn P, Pootanakit K, Tanramluk D. Structural analysis of the coronavirus main protease for the design of pan-variant inhibitors. Sci Rep 2023; 13:7055. [PMID: 37120654 PMCID: PMC10148699 DOI: 10.1038/s41598-023-34305-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 04/27/2023] [Indexed: 05/01/2023] Open
Abstract
With the rapid rate of SARS-CoV-2 Main protease (Mpro) structures deposition, a computational method that can combine all the useful structural features becomes crucial. This research focuses on the frequently occurring atoms and residues to find a generalized strategy for inhibitor design given a large amount of protein complexes from SARS-CoV in contrast to SARS-CoV-2 Mpro. By superposing large numbers of the ligands onto the protein template and grid box, we can analyse which part of the structure is conserved from position-specific interaction for both data sets for the development of pan-Mpro antiviral design. The difference in conserved recognition sites from the crystal structures can be used to determine specificity determining residues for designing selective drugs. We can display pictures of the imaginary shape of the ligand by unionising all atoms from the ligand. We also pinpoint the most probable atom adjustments to imitate the frequently found densities from the ligand atoms statistics. With molecular docking, Molecular Dynamics simulation, and MM-PBSA methods, a carbonyl replacement at the nitrile warhead (N5) of Paxlovid's Nirmatrelvir (PF-07321332) was suggested. By gaining insights into the selectivity and promiscuity regions for proteins and ligands, crucial residues are highlighted, and the antiviral design strategies are proposed.
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Affiliation(s)
| | - Sakao Phoochaijaroen
- Integrative Computational BioScience (ICBS) Center, Mahidol University, Salaya, Nakhon Pathom, 73170, Thailand
| | - Aunlika Chimprasit
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Patchreenart Saparpakorn
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Kusol Pootanakit
- Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, 73170, Thailand
| | - Duangrudee Tanramluk
- Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, 73170, Thailand.
- Integrative Computational BioScience (ICBS) Center, Mahidol University, Salaya, Nakhon Pathom, 73170, Thailand.
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7
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Noske GD, Song Y, Fernandes RS, Chalk R, Elmassoudi H, Koekemoer L, Owen CD, El-Baba TJ, Robinson CV, Oliva G, Godoy AS. An in-solution snapshot of SARS-COV-2 main protease maturation process and inhibition. Nat Commun 2023; 14:1545. [PMID: 36941262 PMCID: PMC10027274 DOI: 10.1038/s41467-023-37035-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 02/28/2023] [Indexed: 03/23/2023] Open
Abstract
The main protease from SARS-CoV-2 (Mpro) is responsible for cleavage of the viral polyprotein. Mpro self-processing is called maturation, and it is crucial for enzyme dimerization and activity. Here we use C145S Mpro to study the structure and dynamics of N-terminal cleavage in solution. Native mass spectroscopy analysis shows that mixed oligomeric states are composed of cleaved and uncleaved particles, indicating that N-terminal processing is not critical for dimerization. A 3.5 Å cryo-EM structure provides details of Mpro N-terminal cleavage outside the constrains of crystal environment. We show that different classes of inhibitors shift the balance between oligomeric states. While non-covalent inhibitor MAT-POS-e194df51-1 prevents dimerization, the covalent inhibitor nirmatrelvir induces the conversion of monomers into dimers, even with intact N-termini. Our data indicates that the Mpro dimerization is triggered by induced fit due to covalent linkage during substrate processing rather than the N-terminal processing.
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Affiliation(s)
- Gabriela Dias Noske
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil
| | - Yun Song
- Electron Bio-imaging Centre, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
| | - Rafaela Sachetto Fernandes
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil
| | - Rod Chalk
- Centre for Medicines Discovery, Oxford University, OX1 3QU, Oxford, UK
| | - Haitem Elmassoudi
- Centre for Medicines Discovery, Oxford University, OX1 3QU, Oxford, UK
| | - Lizbé Koekemoer
- Centre for Medicines Discovery, Oxford University, OX1 3QU, Oxford, UK
| | - C David Owen
- Electron Bio-imaging Centre, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
| | - Tarick J El-Baba
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, OX1 3TA, Oxford, UK
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, South Parks Road, OX1 3QU, Oxford, UK
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, OX1 3TA, Oxford, UK
- The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, South Parks Road, OX1 3QU, Oxford, UK
| | - Glaucius Oliva
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil
| | - Andre Schutzer Godoy
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil.
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8
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Garg A, Goel N, Abhinav N, Varma T, Achari A, Bhattacharjee P, Kamal IM, Chakrabarti S, Ravichandiran V, Reddy AM, Gupta S, Jaisankar P. Virtual screening of natural products inspired in-house library to discover potential lead molecules against the SARS-CoV-2 main protease. J Biomol Struct Dyn 2023; 41:2033-2045. [PMID: 35043750 DOI: 10.1080/07391102.2022.2027271] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
SARS-CoV-2, a new coronavirus emerged in 2019, causing a global healthcare epidemic. Although a variety of drug targets have been identified as potential antiviral therapies, and effective candidate against SARS-CoV-2 remains elusive. One of the most promising targets for combating COVID-19 is SARS-CoV-2 Main protease (Mpro, a protein responsible for viral replication. In this work, an in-house curated library was thoroughly evaluated for druggability against Mpro. We identified four ligands (FG, Q5, P5, and PJ4) as potential inhibitors based on docking scores, predicted binding energies (MMGBSA), in silico ADME, and RMSD trajectory analysis. Among the selected ligands, FG, a natural product from Andrographis nallamalayana, exhibited the highest binding energy of -10.31 kcal/mol close to the docking score of clinical candidates Boceprevir and GC376. Other ligands (P5, natural product from cardiospermum halicacabum and two synthetic molecules Q5 and PJ4) have shown comparable docking scores ranging -7.65 kcal/mol to -7.18 kcal/mol. Interestingly, we found all four top ligands had Pi bond interaction with the main amino acid residues HIS41 and CYS145 (catalytic dyad), H-bonding interactions with GLU166, ARG188, and GLN189, and hydrophobic interactions with MET49 and MET165 in the binding site of Mpro. According to the ADME analysis, Q5 and P5 are within the acceptable range of drug likeliness, compared to FG and PJ4. The interaction stability of the lead molecules with viral protease was verified using replicated MD simulations. Thus, the present study opens up the opportunity of developing drug candidates targeting SARS-CoV-2 main protease (Mpro) to mitigate the disease.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aakriti Garg
- National Institute of Pharmaceutical Education and Research (NIPER), Kolkata, Chunilal Bhawan, Kolkata, India.,Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Narender Goel
- National Institute of Pharmaceutical Education and Research (NIPER), Kolkata, Chunilal Bhawan, Kolkata, India.,Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Nipun Abhinav
- National Institute of Pharmaceutical Education and Research (NIPER), Kolkata, Chunilal Bhawan, Kolkata, India.,Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Tanmay Varma
- National Institute of Pharmaceutical Education and Research (NIPER), Kolkata, Chunilal Bhawan, Kolkata, India
| | - Anushree Achari
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Pinaki Bhattacharjee
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Izaz Monir Kamal
- Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Saikat Chakrabarti
- Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Velayutham Ravichandiran
- National Institute of Pharmaceutical Education and Research (NIPER), Kolkata, Chunilal Bhawan, Kolkata, India
| | | | - Sreya Gupta
- National Institute of Pharmaceutical Education and Research (NIPER), Kolkata, Chunilal Bhawan, Kolkata, India
| | - Parasuraman Jaisankar
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, Kolkata, India
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9
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Application Potential of Luteolin in the Treatment of Viral Pneumonia. J Food Biochem 2023. [DOI: 10.1155/2023/1810503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Aim of the Review. This study aims to summarize the therapeutic effect of luteolin on the pathogenesis of viral pneumonia, explore its absorption and metabolism in the human body, evaluate the possibility of luteolin as a drug to treat viral pneumonia, and provide a reference for future research. Materials and Methods. We searched MEDLINE/PubMed, Web of Science, China National Knowledge Infrastructure, and Google Scholar and collected research on luteolin in the treatment of viral pneumonia and related diseases since 2003. Then, we summarized the efficacy and potential of luteolin in directly inhibiting viral activity, limiting inflammatory storms, reducing pulmonary inflammation, and treating pneumonia complications. Results and Conclusion. Luteolin has the potential to treat viral pneumonia in multiple ways. Luteolin has a direct inhibitory effect on coronavirus, influenza virus, and respiratory syncytial virus. Luteolin can alleviate the inflammatory factor storm induced by multiple factors by inhibiting the function of macrophages or mast cells. Luteolin can reduce pulmonary inflammation, pulmonary edema, or pulmonary fibrosis induced by multiple factors. In addition, viral pneumonia may cause multisystem complications, while luteolin has extensive protective effects on the gastrointestinal system, cardiovascular system, and nervous system. However, due to the first-pass metabolism mediated by phase II enzymes, the bioavailability of oral luteolin is low. The bioavailability of luteolin can be improved, and its potential value can be further developed by changing the dosage form or route of administration.
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Arumugam GS, Sen A, Dash SS, Mitra K, Doble M, Rajaraman G, Gummadi SN. Arjunetin as a promising drug candidate against SARS-CoV-2: molecular dynamics simulation studies. J Biomol Struct Dyn 2022; 40:12358-12379. [PMID: 34533107 PMCID: PMC8459932 DOI: 10.1080/07391102.2021.1970627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Stem and bark of the tree Terminalia arjuna Wight & Arn. (Combretaceae) has been documented to exhibit therapeutic properties like cardiotonic, anticancer, antiviral, antibacterial, antifungal, hypercholesterolemia, hypolipidemic, and anti-coagulant. Our previous studies have shown that, ethanolic extract of T. arjuna bark exhibits radical scavenging anti-oxidant activity and also effectively inhibited catalase activity. In this study, oleanane triterpenoids type compounds viz., oleanolic acid, arjunolic acid, arjunolitin, arjunetin were isolated from ethanolic bark extract as bio-active compound and their structures were elucidated using 1H, 13C NMR, HR-ESIMS, IR. Of the various compounds, Arjunetin showed significant inhibition of catalase activity as compared to the other compounds. Based on the structural similarity between arjunetin and current antiviral drugs, we propose that arjunetin might exhibit antiviral activity. Molecular docking and molecular dynamics studies showed that arjunetin binds to the binds to key targets of SARS-CoV-2 namely, 3CLpro, PLpro, and RdRp) with a higher binding energy values (3CLpro, -8.4 kcal/mol; PLpro, -7.6 kcal/mol and RdRp, -8.1 kcal/mol) as compared with FDA approved protease inhibitor drugs to Lopinavir (3CLpro, -7.2 kcal/mole and PLpro -7.7 kcal/mole) and Remdesivir (RdRp -7.6 kcal/mole). To further investigate this, we performed 200-500 ns molecular dynamics simulation studies. The results transpired that the binding affinity of Arjunetin is higher than Remdesivir in the RNA binding cavity of RdRp. Based on structural similarity between arjunetin and Saikosaponin (a known antiviral agents) and based on our molecular docking and molecular dynamic simulation studies, we propose that arjunetin can be a promising drug candidate against Covid-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gandarvakottai Senthilkumar Arumugam
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Applied and Industrial Microbiology Laboratory, Indian Institute of Technology Madras, Chennai, India
| | - Asmita Sen
- Department of Chemistry, Molecular Modelling Group (MMG), Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Swati S. Dash
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Applied and Industrial Microbiology Laboratory, Indian Institute of Technology Madras, Chennai, India
| | - Kartik Mitra
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Drug Design Laboratory, Indian Institute of Technology Madras, Chennai, India
| | - Mukesh Doble
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Drug Design Laboratory, Indian Institute of Technology Madras, Chennai, India
| | - Gopalan Rajaraman
- Department of Chemistry, Molecular Modelling Group (MMG), Indian Institute of Technology Bombay, Powai, Mumbai, India,Rajaraman Gopalan Department of Chemistry, Molecular Modelling Group (MMG), Indian Institute of Technology Bombay, Powai, Mumbai400076, India
| | - Sathyanarayana N. Gummadi
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Applied and Industrial Microbiology Laboratory, Indian Institute of Technology Madras, Chennai, India,CONTACT Sathyanarayana N. Gummadi Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Applied and Industrial Microbiology Laboratory, Indian Institute of Technology Madras, Chennai, 600 036, India;
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11
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de Souza AS, de Souza RF, Guzzo CR. Quantitative structure-activity relationships, molecular docking and molecular dynamics simulations reveal drug repurposing candidates as potent SARS-CoV-2 main protease inhibitors. J Biomol Struct Dyn 2022; 40:11339-11356. [PMID: 34370631 DOI: 10.1080/07391102.2021.1958700] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The current outbreak of COVID-19 is leading an unprecedented scientific effort focusing on targeting SARS-CoV-2 proteins critical for its viral replication. Herein, we performed high-throughput virtual screening of more than eleven thousand FDA-approved drugs using backpropagation-based artificial neural networks (q2LOO = 0.60, r2 = 0.80 and r2pred = 0.91), partial-least-square (PLS) regression (q2LOO = 0.83, r2 = 0.62 and r2pred = 0.70) and sequential minimal optimization (SMO) regression (q2LOO = 0.70, r2 = 0.80 and r2pred = 0.89). We simulated the stability of Acarbose-derived hexasaccharide, Naratriptan, Peramivir, Dihydrostreptomycin, Enviomycin, Rolitetracycline, Viomycin, Angiotensin II, Angiotensin 1-7, Angiotensinamide, Fenoterol, Zanamivir, Laninamivir and Laninamivir octanoate with 3CLpro by 100 ns and calculated binding free energy using molecular mechanics combined with Poisson-Boltzmann surface area (MM-PBSA). Our QSAR models and molecular dynamics data suggest that seven repurposed-drug candidates such as Acarbose-derived Hexasaccharide, Angiotensinamide, Dihydrostreptomycin, Enviomycin, Fenoterol, Naratriptan and Viomycin are potential SARS-CoV-2 main protease inhibitors. In addition, our QSAR models and molecular dynamics simulations revealed that His41, Asn142, Cys145, Glu166 and Gln189 are potential pharmacophoric centers for 3CLpro inhibitors. Glu166 is a potential pharmacophore for drug design and inhibitors that interact with this residue may be critical to avoid dimerization of 3CLpro. Our results will contribute to future investigations of novel chemical scaffolds and the discovery of novel hits in high-throughput screening as potential anti-SARS-CoV-2 properties.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anacleto Silva de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Robson Francisco de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Cristiane Rodrigues Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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12
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Beccari AR, Vistoli G. Exscalate4CoV: Innovative High Performing Computing (HPC) Strategies to Tackle Pandemic Crisis. Int J Mol Sci 2022; 23:ijms231911576. [PMID: 36232873 PMCID: PMC9569893 DOI: 10.3390/ijms231911576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 09/28/2022] [Indexed: 11/07/2022] Open
Affiliation(s)
- Andrea R. Beccari
- EXSCALATE, Dompé Farmaceutici S.p.A., Via Tommaso De Amicis 95, I-80131 Napoli, Italy
| | - Giulio Vistoli
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli 25, I-20133 Milano, Italy
- Correspondence:
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13
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Kashyap P, Thakur M, Singh N, Shikha D, Kumar S, Baniwal P, Yadav YS, Sharma M, Sridhar K, Inbaraj BS. In Silico Evaluation of Natural Flavonoids as a Potential Inhibitor of Coronavirus Disease. Molecules 2022; 27:molecules27196374. [PMID: 36234910 PMCID: PMC9572657 DOI: 10.3390/molecules27196374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 01/08/2023] Open
Abstract
The recent coronavirus disease (COVID-19) outbreak in Wuhan, China, has led to millions of infections and the death of approximately one million people. No targeted therapeutics are currently available, and only a few efficient treatment options are accessible. Many researchers are investigating active compounds from natural plant sources that may inhibit COVID-19 proliferation. Flavonoids are generally present in our diet, as well as traditional medicines and are effective against various diseases. Thus, here, we reviewed the potential of flavonoids against crucial proteins involved in the coronavirus infectious cycle. The fundamentals of coronaviruses, the structures of SARS-CoV-2, and the mechanism of its entry into the host’s body have also been discussed. In silico studies have been successfully employed to study the interaction of flavonoids against COVID-19 Mpro, spike protein PLpro, and other interactive sites for its possible inhibition. Recent studies showed that many flavonoids such as hesperidin, amentoflavone, rutin, diosmin, apiin, and many other flavonoids have a higher affinity with Mpro and lower binding energy than currently used drugs such as hydroxylchloroquine, nelfinavir, ritonavir, and lopinavir. Thus, these compounds can be developed as specific therapeutic agents against COVID-19, but need further in vitro and in vivo studies to validate these compounds and pave the way for drug discovery.
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Affiliation(s)
- Piyush Kashyap
- Department of Food Technology and Nutrition, School of Agriculture, Lovely Professional University, Phagwara 144401, India
| | - Mamta Thakur
- Department of Food Technology, School of Sciences, ITM University, Gwalior 474001, India
| | - Nidhi Singh
- Centre of Bioinformatics, University of Allahabad, Prayraj 211002, India
| | - Deep Shikha
- Department of Food Technology, Bhai Gurdas Institute of Engineering and Technology, Sangrur 148001, India
| | - Shiv Kumar
- MMICT & BM (HM), Maharishi Markandeshwar Deemed to be University, Mullana, Ambala 133207, India
- Correspondence: (S.K.); or (K.S.); or (B.S.I.)
| | - Poonam Baniwal
- Department of Quality Control, Food Corporation of India, New Delhi 110001, India
| | - Yogender Singh Yadav
- Department of Dairy Engineering, College of Dairy Science and Technology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar 125004, India
| | - Minaxi Sharma
- Laboratoire de Chimieverte et Produits Biobasés, Département AgroBioscience et Chimie, Haute Ecole Provinciale du Hainaut-Condorcet, 11, 7800 ATH Rue de la Sucrerie, Belgium
| | - Kandi Sridhar
- UMR1253, Science et Technologie du Lait et de l’œuf, INRAE, L’InstitutAgro, Rennes-Angers, 65 Rue de Saint Brieuc, F-35042 Rennes, France
- Correspondence: (S.K.); or (K.S.); or (B.S.I.)
| | - Baskaran Stephen Inbaraj
- Department of Food Science, Fu Jen Catholic University, New Taipei City 242 05, Taiwan
- Correspondence: (S.K.); or (K.S.); or (B.S.I.)
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14
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Alzyoud L, Ghattas MA, Atatreh N. Allosteric Binding Sites of the SARS-CoV-2 Main Protease: Potential Targets for Broad-Spectrum Anti-Coronavirus Agents. Drug Des Devel Ther 2022; 16:2463-2478. [PMID: 35941927 PMCID: PMC9356625 DOI: 10.2147/dddt.s370574] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/23/2022] [Indexed: 12/23/2022] Open
Abstract
The current pandemic caused by the COVID-19 disease has reached everywhere in the world and has affected every aspect of our lives. As of the current data, the World Health Organization (WHO) has reported more than 300 million confirmed COVID-19 cases worldwide and more than 5 million deaths. Mpro is an enzyme that plays a key role in the life cycle of the SARS-CoV-2 virus, and it is vital for the disease progression. The Mpro enzyme seems to have several allosteric sites that can hinder the enzyme catalytic activity. Furthermore, some of these allosteric sites are located at or nearby the dimerization interface which is essential for the overall Mpro activity. In this review paper, we investigate the potential of the Mpro allosteric site to act as a drug target, especially since they interestingly appear to be resistant to mutation. The work is illustrated through three subsequent sections: First, the two main categories of Mpro allosteric sites have been explained and discussed. Second, a total of six pockets have been studied and evaluated for their druggability and cavity characteristics. Third, the experimental and computational attempts for the discovery of new allosteric inhibitors have been illustrated and discussed. To sum up, this review paper gives a detailed insight into the feasibility of developing new Mpro inhibitors to act as a potential treatment for the COVID-19 disease.
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Affiliation(s)
- Lara Alzyoud
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
| | - Mohammad A Ghattas
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi, United Arab Emirates
- Correspondence: Mohammad A Ghattas; Noor Atatreh, Email ;
| | - Noor Atatreh
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi, United Arab Emirates
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15
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Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022; 122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.
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Affiliation(s)
- Kaifu Gao
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Limei Cheng
- Clinical
Pharmacology and Pharmacometrics, Bristol
Myers Squibb, Princeton, New Jersey 08536, United States
| | - Jaclyn Frishcosy
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Huzumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuchi Qiu
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tom Schluckbier
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaoqi Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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16
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Zaliani A, Vangeel L, Reinshagen J, Iaconis D, Kuzikov M, Keminer O, Wolf M, Ellinger B, Esposito F, Corona A, Tramontano E, Manelfi C, Herzog K, Jochmans D, De Jonghe S, Chiu W, Francken T, Schepers J, Collard C, Abbasi K, Claussen C, Summa V, Beccari AR, Neyts J, Gribbon P, Leyssen P. Cytopathic SARS-CoV-2 screening on VERO-E6 cells in a large-scale repurposing effort. Sci Data 2022; 9:405. [PMID: 35831315 PMCID: PMC9279437 DOI: 10.1038/s41597-022-01532-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 06/29/2022] [Indexed: 01/13/2023] Open
Abstract
Worldwide, there are intensive efforts to identify repurposed drugs as potential therapies against SARS-CoV-2 infection and the associated COVID-19 disease. To date, the anti-inflammatory drug dexamethasone and (to a lesser extent) the RNA-polymerase inhibitor remdesivir have been shown to be effective in reducing mortality and patient time to recovery, respectively, in patients. Here, we report the results of a phenotypic screening campaign within an EU-funded project (H2020-EXSCALATE4COV) aimed at extending the repertoire of anti-COVID therapeutics through repurposing of available compounds and highlighting compounds with new mechanisms of action against viral infection. We screened 8702 molecules from different repurposing libraries, to reveal 110 compounds with an anti-cytopathic IC50 < 20 µM. From this group, 18 with a safety index greater than 2 are also marketed drugs, making them suitable for further study as potential therapies against COVID-19. Our result supports the idea that a systematic approach to repurposing is a valid strategy to accelerate the necessary drug discovery process. Measurement(s) | Cytopathic Effect | Technology Type(s) | confocal fluorescence microscopy | Factor Type(s) | Cellular toxicity | Sample Characteristic - Organism | Chlorocebus sabaeus | Sample Characteristic - Environment | continuant | Sample Characteristic - Location | Belgium |
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Affiliation(s)
- Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, Schnackenburgallee 114, 22525, Hamburg, Germany. .,Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany.
| | - Laura Vangeel
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49 - box 1043, 3000, Leuven, Belgium
| | - Jeanette Reinshagen
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, Schnackenburgallee 114, 22525, Hamburg, Germany.,Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Daniela Iaconis
- Dompé Farmaceutici SpA, via Campo di Pile, 67100, L'Aquila, Italy
| | - Maria Kuzikov
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, Schnackenburgallee 114, 22525, Hamburg, Germany.,Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Oliver Keminer
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, Schnackenburgallee 114, 22525, Hamburg, Germany.,Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Markus Wolf
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, Schnackenburgallee 114, 22525, Hamburg, Germany.,Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Bernhard Ellinger
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, Schnackenburgallee 114, 22525, Hamburg, Germany.,Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Francesca Esposito
- Dipartimento di Scienze della vita e dell'ambiente, Cittadella Universitaria di Monserrato, SS554, 09042, Monserrato, Cagliari, Italy
| | - Angela Corona
- Dipartimento di Scienze della vita e dell'ambiente, Cittadella Universitaria di Monserrato, SS554, 09042, Monserrato, Cagliari, Italy
| | - Enzo Tramontano
- Dipartimento di Scienze della vita e dell'ambiente, Cittadella Universitaria di Monserrato, SS554, 09042, Monserrato, Cagliari, Italy
| | - Candida Manelfi
- Dompé Farmaceutici SpA, via Campo di Pile, 67100, L'Aquila, Italy
| | - Katja Herzog
- EU-OPENSCREEN ERIC, Campus Berlin Buch, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Dirk Jochmans
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49 - box 1043, 3000, Leuven, Belgium
| | - Steven De Jonghe
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49 - box 1043, 3000, Leuven, Belgium
| | - Winston Chiu
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49 - box 1043, 3000, Leuven, Belgium
| | - Thibault Francken
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49 - box 1043, 3000, Leuven, Belgium
| | - Joost Schepers
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49 - box 1043, 3000, Leuven, Belgium
| | - Caroline Collard
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49 - box 1043, 3000, Leuven, Belgium
| | - Kayvan Abbasi
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49 - box 1043, 3000, Leuven, Belgium
| | - Carsten Claussen
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, Schnackenburgallee 114, 22525, Hamburg, Germany.,Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Vincenzo Summa
- Department of Excellence of Pharmacy, University of Naples Federico II, Via D. Montesano, 49, 80131, Naples, Italy
| | - Andrea R Beccari
- Dompé Farmaceutici SpA, via Campo di Pile, 67100, L'Aquila, Italy
| | - Johan Neyts
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49 - box 1043, 3000, Leuven, Belgium
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, Schnackenburgallee 114, 22525, Hamburg, Germany.,Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Pieter Leyssen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49 - box 1043, 3000, Leuven, Belgium
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17
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Glab-ampai K, Kaewchim K, Saenlom T, Thepsawat W, Mahasongkram K, Sookrung N, Chaicumpa W, Chulanetra M. Human Superantibodies to 3CL pro Inhibit Replication of SARS-CoV-2 across Variants. Int J Mol Sci 2022; 23:ijms23126587. [PMID: 35743031 PMCID: PMC9223907 DOI: 10.3390/ijms23126587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/08/2022] [Accepted: 06/11/2022] [Indexed: 11/16/2022] Open
Abstract
Broadly effective and safe anti-coronavirus agent is existentially needed. Major protease (3CLpro) is a highly conserved enzyme of betacoronaviruses. The enzyme plays pivotal role in the virus replication cycle. Thus, it is a good target of a broadly effective anti-Betacoronavirus agent. In this study, human single-chain antibodies (HuscFvs) of the SARS-CoV-2 3CLpro were generated using phage display technology. The 3CLpro-bound phages were used to infect Escherichia coli host for the production the 3CLpro-bound HuscFvs. Computerized simulation was used to guide the selection of the phage infected-E. coli clones that produced HuscFvs with the 3CLpro inhibitory potential. HuscFvs of three phage infected-E. coli clones were predicted to form contact interface with residues for 3CLpro catalytic activity, substrate binding, and homodimerization. These HuscFvs were linked to a cell-penetrating peptide to make them cell-penetrable, i.e., became superantibodies. The superantibodies blocked the 3CLpro activity in vitro, were not toxic to human cells, traversed across membrane of 3CLpro-expressing cells to co-localize with the intracellular 3CLpro and most of all, they inhibited replication of authentic SARS-CoV-2 Wuhan wild type and α, β, δ, and Omicron variants that were tested. The superantibodies should be investigated further towards clinical application as a safe and broadly effective anti-Betacoronavirus agent.
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Affiliation(s)
- Kittirat Glab-ampai
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (K.G.-a.); (K.K.); (T.S.); (W.T.); (K.M.); (N.S.); (W.C.)
| | - Kanasap Kaewchim
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (K.G.-a.); (K.K.); (T.S.); (W.T.); (K.M.); (N.S.); (W.C.)
- Graduate Program in Immunology, Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Thanatsaran Saenlom
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (K.G.-a.); (K.K.); (T.S.); (W.T.); (K.M.); (N.S.); (W.C.)
| | - Watayagorn Thepsawat
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (K.G.-a.); (K.K.); (T.S.); (W.T.); (K.M.); (N.S.); (W.C.)
| | - Kodchakorn Mahasongkram
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (K.G.-a.); (K.K.); (T.S.); (W.T.); (K.M.); (N.S.); (W.C.)
| | - Nitat Sookrung
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (K.G.-a.); (K.K.); (T.S.); (W.T.); (K.M.); (N.S.); (W.C.)
- Biomedical Research Incubator Unit, Department of Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Wanpen Chaicumpa
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (K.G.-a.); (K.K.); (T.S.); (W.T.); (K.M.); (N.S.); (W.C.)
| | - Monrat Chulanetra
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (K.G.-a.); (K.K.); (T.S.); (W.T.); (K.M.); (N.S.); (W.C.)
- Correspondence: ; Tel.: +662-419-2934
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18
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Wieczór M, Genna V, Aranda J, Badia RM, Gelpí JL, Gapsys V, de Groot BL, Lindahl E, Municoy M, Hospital A, Orozco M. Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2022; 13:e1622. [PMID: 35935573 PMCID: PMC9347456 DOI: 10.1002/wcms.1622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/25/2022] [Accepted: 04/28/2022] [Indexed: 06/15/2023]
Abstract
Exascale computing has been a dream for ages and is close to becoming a reality that will impact how molecular simulations are being performed, as well as the quantity and quality of the information derived for them. We review how the biomolecular simulations field is anticipating these new architectures, making emphasis on recent work from groups in the BioExcel Center of Excellence for High Performance Computing. We exemplified the power of these simulation strategies with the work done by the HPC simulation community to fight Covid-19 pandemics. This article is categorized under:Data Science > Computer Algorithms and ProgrammingData Science > Databases and Expert SystemsMolecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods.
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Affiliation(s)
- Miłosz Wieczór
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Department of Physical ChemistryGdansk University of TechnologyGdańskPoland
| | - Vito Genna
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Juan Aranda
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | | | - Josep Lluís Gelpí
- Barcelona Supercomputing CenterBarcelonaSpain
- Department of Biochemistry and BiomedicineUniversity of BarcelonaBarcelonaSpain
| | - Vytautas Gapsys
- Max Planck Institute for Multidisciplinary SciencesComputational Biomolecular Dynamics GroupGoettingenGermany
| | - Bert L. de Groot
- Max Planck Institute for Multidisciplinary SciencesComputational Biomolecular Dynamics GroupGoettingenGermany
| | - Erik Lindahl
- Department of Applied PhysicsSwedish e‐Science Research Center, KTH Royal Institute of TechnologyStockholmSweden
- Department of Biochemistry and Biophysics, Science for Life LaboratoryStockholm UniversityStockholmSweden
| | | | - Adam Hospital
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Department of Biochemistry and BiomedicineUniversity of BarcelonaBarcelonaSpain
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19
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Farouq MAH, Acevedo R, Ferro VA, Mulheran PA, Al Qaraghuli MM. The Role of Antibodies in the Treatment of SARS-CoV-2 Virus Infection, and Evaluating Their Contribution to Antibody-Dependent Enhancement of Infection. Int J Mol Sci 2022; 23:ijms23116078. [PMID: 35682757 PMCID: PMC9181534 DOI: 10.3390/ijms23116078] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/26/2022] [Accepted: 05/26/2022] [Indexed: 02/06/2023] Open
Abstract
Antibodies play a crucial role in the immune response, in fighting off pathogens as well as helping create strong immunological memory. Antibody-dependent enhancement (ADE) occurs when non-neutralising antibodies recognise and bind to a pathogen, but are unable to prevent infection, and is widely known and is reported as occurring in infection caused by several viruses. This narrative review explores the ADE phenomenon, its occurrence in viral infections and evaluates its role in infection by SARS-CoV-2 virus, which causes coronavirus disease 2019 (COVID-19). As of yet, there is no clear evidence of ADE in SARS-CoV-2, though this area is still subject to further study.
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Affiliation(s)
- Mohammed A. H. Farouq
- Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow G1 1XJ, UK; (P.A.M.); (M.M.A.Q.)
- Correspondence: ; Tel.: +44-(0)1415524400
| | - Reinaldo Acevedo
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK;
| | - Valerie A. Ferro
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK;
| | - Paul A. Mulheran
- Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow G1 1XJ, UK; (P.A.M.); (M.M.A.Q.)
| | - Mohammed M. Al Qaraghuli
- Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow G1 1XJ, UK; (P.A.M.); (M.M.A.Q.)
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK;
- EPSRC Future Manufacturing Research Hub for Continuous Manufacturing and Advanced Crystallisation (CMAC), University of Strathclyde, 99 George Street, Glasgow G1 1RD, UK
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20
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Iaconis D, Bordi L, Matusali G, Talarico C, Manelfi C, Cesta MC, Zippoli M, Caccuri F, Bugatti A, Zani A, Filippini F, Scorzolini L, Gobbi M, Beeg M, Piotti A, Montopoli M, Cocetta V, Bressan S, Bucci EM, Caruso A, Nicastri E, Allegretti M, Beccari AR. Characterization of raloxifene as a potential pharmacological agent against SARS-CoV-2 and its variants. Cell Death Dis 2022; 13:498. [PMID: 35614039 PMCID: PMC9130985 DOI: 10.1038/s41419-022-04961-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 05/12/2022] [Accepted: 05/17/2022] [Indexed: 12/14/2022]
Abstract
The new coronavirus SARS-CoV-2 is the causative agent of the COVID-19 pandemic, which so far has caused over 6 million deaths in 2 years, despite new vaccines and antiviral medications. Drug repurposing, an approach for the potential application of existing pharmaceutical products to new therapeutic indications, could be an effective strategy to obtain quick answers to medical emergencies. Following a virtual screening campaign on the most relevant viral proteins, we identified the drug raloxifene, a known Selective Estrogen Receptor Modulator (SERM), as a new potential agent to treat mild-to-moderate COVID-19 patients. In this paper we report a comprehensive pharmacological characterization of raloxifene in relevant in vitro models of COVID-19, specifically in Vero E6 and Calu-3 cell lines infected with SARS-CoV-2. A large panel of the most common SARS-CoV-2 variants isolated in Europe, United Kingdom, Brazil, South Africa and India was tested to demonstrate the drug's ability in contrasting the viral cytopathic effect (CPE). Literature data support a beneficial effect by raloxifene against the viral infection due to its ability to interact with viral proteins and activate protective estrogen receptor-mediated mechanisms in the host cells. Mechanistic studies here reported confirm the significant affinity of raloxifene for the Spike protein, as predicted by in silico studies, and show that the drug treatment does not directly affect Spike/ACE2 interaction or viral internalization in infected cell lines. Interestingly, raloxifene can counteract Spike-mediated ADAM17 activation in human pulmonary cells, thus providing new insights on its mechanism of action. A clinical study in mild to moderate COVID-19 patients (NCT05172050) has been recently completed. Our contribution to evaluate raloxifene results on SARS-CoV-2 variants, and the interpretation of the mechanisms of action will be key elements to better understand the trial results, and to design new clinical studies aiming to evaluate the potential development of raloxifene in this indication.
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Affiliation(s)
| | - Licia Bordi
- grid.419423.90000 0004 1760 4142National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS, Rome, Italy
| | - Giulia Matusali
- grid.419423.90000 0004 1760 4142National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS, Rome, Italy
| | | | | | | | | | - Francesca Caccuri
- grid.7637.50000000417571846Department of Molecular and Translational Medicine, Section of Microbiology and Virology, University of Brescia Medical School, Brescia, Italy
| | - Antonella Bugatti
- grid.7637.50000000417571846Department of Molecular and Translational Medicine, Section of Microbiology and Virology, University of Brescia Medical School, Brescia, Italy
| | - Alberto Zani
- grid.7637.50000000417571846Department of Molecular and Translational Medicine, Section of Microbiology and Virology, University of Brescia Medical School, Brescia, Italy
| | - Federica Filippini
- grid.7637.50000000417571846Department of Molecular and Translational Medicine, Section of Microbiology and Virology, University of Brescia Medical School, Brescia, Italy
| | - Laura Scorzolini
- grid.419423.90000 0004 1760 4142National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS, Rome, Italy
| | - Marco Gobbi
- grid.4527.40000000106678902Department of Biochemistry and Molecular Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Marten Beeg
- grid.4527.40000000106678902Department of Biochemistry and Molecular Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Arianna Piotti
- grid.4527.40000000106678902Department of Biochemistry and Molecular Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Monica Montopoli
- grid.5608.b0000 0004 1757 3470Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, VIMM Veneto Institute Molecular Medicine, Padua, Italy
| | - Veronica Cocetta
- grid.5608.b0000 0004 1757 3470Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, VIMM Veneto Institute Molecular Medicine, Padua, Italy
| | - Silvia Bressan
- grid.5608.b0000 0004 1757 3470Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, VIMM Veneto Institute Molecular Medicine, Padua, Italy
| | - Enrico M. Bucci
- grid.264727.20000 0001 2248 3398Sbarro Health Research Organization, Biology Department CFT, Temple University, Philadelphia, PA USA
| | - Arnaldo Caruso
- grid.7637.50000000417571846Department of Molecular and Translational Medicine, Section of Microbiology and Virology, University of Brescia Medical School, Brescia, Italy
| | - Emanuele Nicastri
- grid.419423.90000 0004 1760 4142National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS, Rome, Italy
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21
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Liu SY, Wang W, Ke JP, Zhang P, Chu GX, Bao GH. Discovery of Camellia sinensis catechins as SARS-CoV-2 3CL protease inhibitors through molecular docking, intra and extra cellular assays. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 96:153853. [PMID: 34799184 PMCID: PMC8575542 DOI: 10.1016/j.phymed.2021.153853] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 10/26/2021] [Accepted: 11/06/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND AND PURPOSE Previous studies suggest that major Camellia sinensis (tea) catechins can inhibit 3-chymotrypsin-like cysteine protease (3CLpro), inspiring us to study 3CLpro inhibition of the recently discovered catechins from tea by our group. METHODS Autodock was used to dock 3CLpro and 16 tea catechins. Further, a 3CLpro activity detection system was used to test their intra and extra cellular 3CLpro inhibitory activity. Surface plasmon resonance (SPR) was used to analyze the dissociation constant (KD) between the catechins and 3CLpro. RESULTS Docking data suggested that 3CLpro interacted with the selected 16 catechins with low binding energy through the key amino acid residues Thr24, Thr26, Asn142, Gly143, His163, and Gln189. The selected catechins other than zijuanin D (3) and (-)-8-(5''R)-N-ethyl-2-pyrrolidinone-3-O-cinnamoylepicatechin (11) can inhibit 3CLpro intracellularly. The extracellular 3CLpro IC50 values of (-)-epicatechin 3-O-caffeoate (EC-C, 1), zijuanin C (2), etc-pyrrolidinone C and D (6), etc-pyrrolidinone A (9), (+)-gallocatechin gallate (GCG), and (-)-epicatechin gallate (ECG) are 1.58 ± 0.21, 41.2 ± 3.56, 0.90 ± 0.03, 46.71 ± 10.50, 3.38 ± 0.48, and 71.78 ± 8.36 µM, respectively. The KD values of 1, 6, and GCG are 4.29, 3.46, and 3.36 µM, respectively. CONCLUSION Together, EC-C (1), etc-pyrrolidinone C and D (6), and GCG are strong 3CLpro inhibitors. Our results suggest that structural modification of catechins could be conducted by esterificating the 3-OH as well as changing the configuration of C-3, C-3''' or C-5''' to discover strong SARS-CoV-2 inhibitors.
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Affiliation(s)
- Shi-Yu Liu
- Natural Products Laboratory, State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, People's Republic of China
| | - Wei Wang
- Natural Products Laboratory, State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, People's Republic of China; Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, 237000, China
| | - Jia-Ping Ke
- Natural Products Laboratory, State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, People's Republic of China
| | - Peng Zhang
- Natural Products Laboratory, State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, People's Republic of China
| | - Gang-Xiu Chu
- School of information and computer, Anhui Agricultural University, Hefei, People's Republic of China.
| | - Guan-Hu Bao
- Natural Products Laboratory, State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, People's Republic of China.
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22
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Yu PC, Huang CH, Kuo CJ, Liang PH, Wang LHC, Pan MYC, Chang SY, Chao TL, Ieong SM, Fang JT, Huang HC, Juan HF. Drug Repurposing for the Identification of Compounds with Anti-SARS-CoV-2 Capability via Multiple Targets. Pharmaceutics 2022; 14:176. [PMID: 35057070 PMCID: PMC8779140 DOI: 10.3390/pharmaceutics14010176] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/27/2021] [Accepted: 01/07/2022] [Indexed: 02/07/2023] Open
Abstract
Since 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been rapidly spreading worldwide, causing hundreds of millions of infections. Despite the development of vaccines, insufficient protection remains a concern. Therefore, the screening of drugs for the treatment of coronavirus disease 2019 (COVID-19) is reasonable and necessary. This study utilized bioinformatics for the selection of compounds approved by the U.S. Food and Drug Administration with therapeutic potential in this setting. In addition, the inhibitory effect of these compounds on the enzyme activity of transmembrane protease serine 2 (TMPRSS2), papain-like protease (PLpro), and 3C-like protease (3CLpro) was evaluated. Furthermore, the capability of compounds to attach to the spike-receptor-binding domain (RBD) was considered an important factor in the present assessment. Finally, the antiviral potency of compounds was validated using a plaque reduction assay. Our funnel strategy revealed that tamoxifen possesses an anti-SARS-CoV-2 property owing to its inhibitory performance in multiple assays. The proposed time-saving and feasible strategy may accelerate drug screening for COVID-19 and other diseases.
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Affiliation(s)
- Pei-Chen Yu
- Department of Life Science and Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan;
| | - Chen-Hao Huang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan;
| | - Chih-Jung Kuo
- Department of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan;
| | - Po-Huang Liang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan;
- Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Lily Hui-Ching Wang
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 30004, Taiwan; (L.H.-C.W.); (M.Y.-C.P.)
| | - Max Yu-Chen Pan
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 30004, Taiwan; (L.H.-C.W.); (M.Y.-C.P.)
| | - Sui-Yuan Chang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei 10048, Taiwan; (S.-Y.C.); (T.-L.C.); (S.-M.I.); (J.-T.F.)
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei 10002, Taiwan
| | - Tai-Ling Chao
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei 10048, Taiwan; (S.-Y.C.); (T.-L.C.); (S.-M.I.); (J.-T.F.)
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Si-Man Ieong
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei 10048, Taiwan; (S.-Y.C.); (T.-L.C.); (S.-M.I.); (J.-T.F.)
| | - Jun-Tung Fang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei 10048, Taiwan; (S.-Y.C.); (T.-L.C.); (S.-M.I.); (J.-T.F.)
| | - Hsuan-Cheng Huang
- Institute of Biomedical Informatics, National Yang Ming Chaio Tung University, Taipei 11230, Taiwan
| | - Hsueh-Fen Juan
- Department of Life Science and Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan;
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan;
- Center for Computational and Systems Biology, National Taiwan University, Taipei 10617, Taiwan
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23
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A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. BIOLOGY 2021; 10:biology10121276. [PMID: 34943191 PMCID: PMC8698902 DOI: 10.3390/biology10121276] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 11/26/2021] [Accepted: 12/03/2021] [Indexed: 01/02/2023]
Abstract
Simple Summary The pathogenicity and transmissibility of the COVID-19 pandemic causative agent, the SARS-CoV-2 virus, is related to the functions of the proteins synthesized intracellularly, as guided by viral RNA. It is vitally important to accurately pinpoint novel variants of concern of the SARS-CoV-2 virus, in order to understand the molecular features of novel mutations and manage the on-going battle against the COVID-19 pandemic. We focused on A105V mutation in the ORF7a accessory protein. Sequencing and clinical data showed that this mutation is associated with increased severity and lethality in a group of Romanian patients, despite a lower viral copy number and a lower number of associated comorbidities. This effect is primarily due to increased protein stability through allosteric effects as shown by molecular dynamics analyses. This behavior manifests especially among residues 39–56, and the ones adjacent to 26–30 loop, placed in direct contact with potential interaction partners. Together, the results provide novel insights into the role of ORF7a in the pathogenicity of SARS-CoV-2. Abstract The ongoing COVID-19 pandemic follows an unpredictable evolution, driven by both host-related factors such as mobility, vaccination status, and comorbidities and by pathogen-related ones. The pathogenicity of its causative agent, SARS-CoV-2 virus, relates to the functions of the proteins synthesized intracellularly, as guided by viral RNA. These functions are constantly altered through mutations resulting in increased virulence, infectivity, and antibody-evasion abilities. Well-characterized mutations in the spike protein, such as D614G, N439K, Δ69–70, E484K, or N501Y, are currently defining specific variants; however, some less studied mutations outside the spike region, such as p. 3691 in NSP6, p. 9659 in ORF-10, 8782C > T in ORF-1ab, or 28144T > C in ORF-8, have been proposed for altering SARS-CoV-2 virulence and pathogenicity. Therefore, in this study, we focused on A105V mutation of SARS-CoV-2 ORF7a accessory protein, which has been associated with severe COVID-19 clinical manifestation. Molecular dynamics and computational structural analyses revealed that this mutation differentially alters ORF7a dynamics, suggesting a gain-of-function role that may explain its role in the severe form of COVID-19 disease.
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24
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Luo D, Tong JB, Xiao XC, Bian S, Zhang X, Wang J, Xu HY. Theoretically exploring selective-binding mechanisms of BRD4 through integrative computational approaches. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:985-1011. [PMID: 34845959 DOI: 10.1080/1062936x.2021.1999317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
The origin of cancer is related to the dysregulation of multiple signal pathways and of physiological processes. Bromodomain-containing protein 4 (BRD4) has become an attractive target for the development of anticancer and anti-inflammatory agents since it can epigenetically regulate the transcription of growth-promoting genes. The synthesized BRD4 inhibitors with new chemical structures can reduce the drug resistance, but their binding modes and the inhibitory mechanism remain unclear. Here, we initially constructed robust QSAR models based on 68 reported tetrahydropteridin analogues using topomer CoMFA and HQSAR. On the basis of QSAR results, we designed 16 novel tetrahydropteridin analogues with modified structures and carried out docking studies. Instead of significant hydrogen bondings with amino acid residue Asn140 as reported in previous research, the molecular docking modelling suggested a novel docking pose that involves the amino acid residues (Trp81, Pro82, Val87, Leu92, Leu94, Cys136, Asp144, and Ile146) at the active site of BRD4. The MD simulations, free energy calculations, and residual energy contributions all indicate that hydrophobic interactions are decisive factors affecting bindings between inhibitors and BRD4. The current study provides new insights that can aid the discovery of BRD4 inhibitors with enhanced anti-cancer ability.
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Affiliation(s)
- D Luo
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, China
- Shaanxi Key Laboratory of Chemical Additives for Industry, Shaanxi University of Science and Technology, Xi'an China
| | - J B Tong
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, China
- Shaanxi Key Laboratory of Chemical Additives for Industry, Shaanxi University of Science and Technology, Xi'an China
| | - X C Xiao
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, China
- Shaanxi Key Laboratory of Chemical Additives for Industry, Shaanxi University of Science and Technology, Xi'an China
| | - S Bian
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, China
- Shaanxi Key Laboratory of Chemical Additives for Industry, Shaanxi University of Science and Technology, Xi'an China
| | - X Zhang
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, China
- Shaanxi Key Laboratory of Chemical Additives for Industry, Shaanxi University of Science and Technology, Xi'an China
| | - J Wang
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, China
- Shaanxi Key Laboratory of Chemical Additives for Industry, Shaanxi University of Science and Technology, Xi'an China
| | - H Y Xu
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, China
- Shaanxi Key Laboratory of Chemical Additives for Industry, Shaanxi University of Science and Technology, Xi'an China
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25
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Vishvakarma VK, Pal S, Singh P, Bahadur I. Interactions between main protease of SARS-CoV-2 and testosterone or progesterone using computational approach. J Mol Struct 2021; 1251:131965. [PMID: 34840349 PMCID: PMC8604630 DOI: 10.1016/j.molstruc.2021.131965] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/13/2021] [Accepted: 11/17/2021] [Indexed: 12/17/2022]
Abstract
SARS-CoV-2 is drastically spread across the globe in a short period of time and affects the lives of billions. There is a need to find the promising drugs like candidates against the inhibition of novel corona virus or SARS-CoV-2. Herein, the interaction on sex hormones (testosterone and progesterone) with Mpro of SARS-CoV-2 was investigated with the help of molecular docking. The binding energy for the formation complex between the progesterone and testosterone with main protease of SARS-CoV-2 are -86.05 and -91.84 kcal/mol, respectively. From this, it can be understood that testosterone showed better binding affinity with Mpro of nCoV and thus, more inhibition of the main protease. Then, the binding was further studied using molecular dynamics simulations at different temperatures (300, 310 and 325) K. It has been observed that the formations of complex between the Mpro of nCoV with testosterone/ progesterone is better at 300 K than 310 and 325 K. Further, it is found that the more effective binding of testosterone with Mpro of nCoV is observed than the progesterone based on the RMSD, RMSF and H-bond trajectories. Results indicate the promising nature of testosterone towards the inhibition of Mpro of nCoV.
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Affiliation(s)
- Vijay Kumar Vishvakarma
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India
| | - Shweta Pal
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India
| | - Prashant Singh
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India
| | - Indra Bahadur
- Chemistry Department, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho 2735, South Africa
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26
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Kuroda D, Tsumoto K. Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. Biophys Physicobiol 2021; 18:215-222. [PMID: 34631338 PMCID: PMC8470906 DOI: 10.2142/biophysico.bppb-v18.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 08/19/2021] [Indexed: 12/03/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes the coronavirus disease 2019 (COVID-19), spread rapidly around the globe. The main protease encoded by SARS-CoV-2 is essential for processing of the polyproteins translated from the viral RNA genome, making this protein a potential drug target. A recently reported mutation in the protease, P108S, may be responsible for milder symptoms observed in COVID-19 patients in Tokyo. Starting from a crystal structure of the SARS-CoV-2 main protease in the dimeric form, we performed triplicate 5.0-μs molecular dynamics simulations of the wild-type and P108S mutant. Our computational results suggest a link between the mutation P108S and dynamics of the catalytic sites in the main protease: The catalytic dyad become considerably inaccessible to substrates in the P108S mutant. Our results also demonstrate the potential of molecular dynamics simulations to complement experimental techniques and other computational methods, such as protein design calculations, which predict effects of mutations based on static crystal structures. Further studies are certainly necessary to quantitively understand the relationships between the P108S mutation and physical properties of the main protease, but the results of our study will immediately inform development of new protease inhibitors.
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Affiliation(s)
- Daisuke Kuroda
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo 108-8639, Japan
- Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo 108-8639, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo 108-8639, Japan
- Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo 108-8639, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
- Laboratory of Medical Proteomics, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
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27
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Farouq MA, Al Qaraghuli MM, Kubiak-Ossowska K, Ferro VA, Mulheran PA. Biomolecular interactions with nanoparticles: applications for coronavirus disease 2019. Curr Opin Colloid Interface Sci 2021; 54:101461. [PMID: 33907504 PMCID: PMC8062422 DOI: 10.1016/j.cocis.2021.101461] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nanoparticles are small particles sized 1-100 nm, which have a large surface-to-volume ratio, allowing efficient adsorption of drugs, proteins, and other chemical compounds. Consequently, functionalized nanoparticles have potential diagnostic and therapeutic applications. A variety of nanoparticles have been studied, including those constructed from inorganic materials, biopolymers, and lipids. In this review, we focus on recent work targeting the severe acute respiratory syndrome coronavirus 2 virus that causes coronavirus disease (COVID-19). Understanding the interactions between coronavirus-specific proteins (such as the spike protein and its host cell receptor angiotensin-converting enzyme 2) with different nanoparticles paves the way to the development of new therapeutics and diagnostics that are urgently needed for the fight against COVID-19, and indeed for related future viral threats that may emerge.
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Affiliation(s)
- Mohammed A.H. Farouq
- Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow, G1 1XJ, UK,Corresponding author: Farouq, M.A.H
| | - Mohammed M. Al Qaraghuli
- Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow, G1 1XJ, UK
| | - Karina Kubiak-Ossowska
- Department of Physics/Archie-West HPC, University of Strathclyde, 107 Rottenrow East, Glasgow, G4 0NG, UK
| | - Valerie A. Ferro
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - Paul A. Mulheran
- Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow, G1 1XJ, UK
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28
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Jiménez-Avalos G, Vargas-Ruiz AP, Delgado-Pease NE, Olivos-Ramirez GE, Sheen P, Fernández-Díaz M, Quiliano M, Zimic M. Comprehensive virtual screening of 4.8 k flavonoids reveals novel insights into allosteric inhibition of SARS-CoV-2 M PRO. Sci Rep 2021; 11:15452. [PMID: 34326429 PMCID: PMC8322093 DOI: 10.1038/s41598-021-94951-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 06/29/2021] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2 main protease is a common target for inhibition assays due to its high conservation among coronaviruses. Since flavonoids show antiviral activity, several in silico works have proposed them as potential SARS-CoV-2 main protease inhibitors. Nonetheless, there is reason to doubt certain results given the lack of consideration for flavonoid promiscuity or main protease plasticity, usage of short library sizes, absence of control molecules and/or the limitation of the methodology to a single target site. Here, we report a virtual screening study where dorsilurin E, euchrenone a11, sanggenol O and CHEMBL2171598 are proposed to inhibit main protease through different pathways. Remarkably, novel structural mechanisms were observed after sanggenol O and CHEMBL2171598 bound to experimentally proven allosteric sites. The former drastically affected the active site, while the latter triggered a hinge movement which has been previously reported for an inactive SARS-CoV main protease mutant. The use of a curated database of 4.8 k flavonoids, combining two well-known docking software (AutoDock Vina and AutoDock4.2), molecular dynamics and MMPBSA, guaranteed an adequate analysis and robust interpretation. These criteria can be considered for future screening campaigns against SARS-CoV-2 main protease.
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Affiliation(s)
- Gabriel Jiménez-Avalos
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Departamento de Ciencias Celulares y Moleculares, Universidad Peruana Cayetano Heredia (UPCH), 15102, Lima, Peru.
| | - A Paula Vargas-Ruiz
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Departamento de Ciencias Celulares y Moleculares, Universidad Peruana Cayetano Heredia (UPCH), 15102, Lima, Peru
| | - Nicolás E Delgado-Pease
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Departamento de Ciencias Celulares y Moleculares, Universidad Peruana Cayetano Heredia (UPCH), 15102, Lima, Peru
| | - Gustavo E Olivos-Ramirez
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Departamento de Ciencias Celulares y Moleculares, Universidad Peruana Cayetano Heredia (UPCH), 15102, Lima, Peru
| | - Patricia Sheen
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Departamento de Ciencias Celulares y Moleculares, Universidad Peruana Cayetano Heredia (UPCH), 15102, Lima, Peru
| | | | - Miguel Quiliano
- Faculty of Health Sciences, Centre for Research and Innovation, Universidad Peruana de Ciencias Aplicadas (UPC), 15023, Lima, Peru
| | - Mirko Zimic
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Departamento de Ciencias Celulares y Moleculares, Universidad Peruana Cayetano Heredia (UPCH), 15102, Lima, Peru.
- Farmacológicos Veterinarios - FARVET S.A.C. Chincha, Lima, Peru.
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29
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Sun LY, Chen C, Su J, Li JQ, Jiang Z, Gao H, Chigan JZ, Ding HH, Zhai L, Yang KW. Ebsulfur and Ebselen as highly potent scaffolds for the development of potential SARS-CoV-2 antivirals. Bioorg Chem 2021; 112:104889. [PMID: 33915460 PMCID: PMC8026246 DOI: 10.1016/j.bioorg.2021.104889] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 01/25/2023]
Abstract
The emerging COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has raised a global catastrophe. To date, there is no specific antiviral drug available to combat this virus, except the vaccine. In this study, the main protease (Mpro) required for SARS-CoV-2 viral replication was expressed and purified. Thirty-six compounds were tested as inhibitors of SARS-CoV-2 Mpro by fluorescence resonance energy transfer (FRET) technique. The half-maximal inhibitory concentration (IC50) values of Ebselen and Ebsulfur analogs were obtained to be in the range of 0.074-0.91 μM. Notably, the molecules containing furane substituent displayed higher inhibition against Mpro, followed by Ebselen 1i (IC50 = 0.074 μM) and Ebsulfur 2k (IC50 = 0.11 μM). The action mechanism of 1i and 2k were characterized by enzyme kinetics, pre-incubation and jump dilution assays, as well as fluorescent labeling experiments, which suggested that both compounds covalently and irreversibly bind to Mpro, while molecular docking suggested that 2k formed an SS bond with the Cys145 at the enzymatic active site. This study provides two very potent scaffolds Ebsulfur and Ebselen for the development of covalent inhibitors of Mpro to combat COVID-19.
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Affiliation(s)
- Le-Yun Sun
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Cheng Chen
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Jianpeng Su
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Jia-Qi Li
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Zhihui Jiang
- Department of Pharmacy, General Hospital of Southern Theatre Command of PLA, Guangzhou 510010, PR China
| | - Han Gao
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Jia-Zhu Chigan
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Huan-Huan Ding
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Le Zhai
- Shaanxi Key Laboratory of Phytochemistry, College of Chemistry and Chemical Engineering, Baoji University of Arts and Sciences, Baoji 72101, Shaanxi Province, PR China
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China.
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30
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Cho E, Rosa M, Anjum R, Mehmood S, Soban M, Mujtaba M, Bux K, Moin ST, Tanweer M, Dantu S, Pandini A, Yin J, Ma H, Ramanathan A, Islam B, Mey ASJ, Bhowmik D, Haider S. Dynamic Profiling of β-Coronavirus 3CL M pro Protease Ligand-Binding Sites. J Chem Inf Model 2021; 61:3058-3073. [PMID: 34124899 PMCID: PMC8230960 DOI: 10.1021/acs.jcim.1c00449] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Indexed: 01/11/2023]
Abstract
β-coronavirus (CoVs) alone has been responsible for three major global outbreaks in the 21st century. The current crisis has led to an urgent requirement to develop therapeutics. Even though a number of vaccines are available, alternative strategies targeting essential viral components are required as a backup against the emergence of lethal viral variants. One such target is the main protease (Mpro) that plays an indispensable role in viral replication. The availability of over 270 Mpro X-ray structures in complex with inhibitors provides unique insights into ligand-protein interactions. Herein, we provide a comprehensive comparison of all nonredundant ligand-binding sites available for SARS-CoV2, SARS-CoV, and MERS-CoV Mpro. Extensive adaptive sampling has been used to investigate structural conservation of ligand-binding sites using Markov state models (MSMs) and compare conformational dynamics employing convolutional variational auto-encoder-based deep learning. Our results indicate that not all ligand-binding sites are dynamically conserved despite high sequence and structural conservation across β-CoV homologs. This highlights the complexity in targeting all three Mpro enzymes with a single pan inhibitor.
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Affiliation(s)
- Eunice Cho
- UCL
School of Pharmacy, London WC1N 1AX, U.K.
| | | | - Ruhi Anjum
- Department
of Biochemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India
| | - Saman Mehmood
- Department
of Zoology, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India
| | - Mariya Soban
- Department
of Biochemistry, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India
| | - Moniza Mujtaba
- Herricks
High School, New Hyde
Park, New York 11040 United States
| | - Khair Bux
- Third
World Center for Science and Technology, H.E.J. Research Institute
of Chemistry, International Centre of Chemical and Biological Sciences, University of Karachi, Karachi 75270 Pakistan
| | - Syed T. Moin
- Third
World Center for Science and Technology, H.E.J. Research Institute
of Chemistry, International Centre of Chemical and Biological Sciences, University of Karachi, Karachi 75270 Pakistan
| | | | - Sarath Dantu
- Department
of Computer Science, Brunel University, Uxbridge UB8 3PH, U.K.
| | - Alessandro Pandini
- Department
of Computer Science, Brunel University, Uxbridge UB8 3PH, U.K.
| | - Junqi Yin
- Center
for Computational Sciences, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Heng Ma
- Data
Science and Learning Division, Argonne National
Laboratory, Lemont, Illinois 60439, United States
| | - Arvind Ramanathan
- Data
Science and Learning Division, Argonne National
Laboratory, Lemont, Illinois 60439, United States
- Consortium
for Advanced Science and Engineering, University
of Chicago, Chicago, Illinois 60637, United
States
| | - Barira Islam
- Department
of Bioscience, University of Huddersfield, Huddersfield HD1 3DH, U.K.
| | - Antonia S. J.
S. Mey
- EaStCHEM
School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, U.K.
| | - Debsindhu Bhowmik
- Computer
Sciences and Engineering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37830, United States
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31
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Yuce M, Cicek E, Inan T, Dag AB, Kurkcuoglu O, Sungur FA. Repurposing of FDA-approved drugs against active site and potential allosteric drug-binding sites of COVID-19 main protease. Proteins 2021; 89:1425-1441. [PMID: 34169568 PMCID: PMC8441840 DOI: 10.1002/prot.26164] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/02/2021] [Accepted: 06/06/2021] [Indexed: 02/06/2023]
Abstract
The novel coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) still has serious negative effects on health, social life, and economics. Recently, vaccines from various companies have been urgently approved to control SARS-CoV-2 infections. However, any specific antiviral drug has not been confirmed so far for regular treatment. An important target is the main protease (Mpro ), which plays a major role in replication of the virus. In this study, Gaussian and residue network models are employed to reveal two distinct potential allosteric sites on Mpro that can be evaluated as drug targets besides the active site. Then, Food and Drug Administration (FDA)-approved drugs are docked to three distinct sites with flexible docking using AutoDock Vina to identify potential drug candidates. Fourteen best molecule hits for the active site of Mpro are determined. Six of these also exhibit high docking scores for the potential allosteric regions. Full-atom molecular dynamics simulations with MM-GBSA method indicate that compounds docked to active and potential allosteric sites form stable interactions with high binding free energy (∆Gbind ) values. ∆Gbind values reach -52.06 kcal/mol for the active site, -51.08 kcal/mol for the potential allosteric site 1, and - 42.93 kcal/mol for the potential allosteric site 2. Energy decomposition calculations per residue elucidate key binding residues stabilizing the ligands that can further serve to design pharmacophores. This systematic and efficient computational analysis successfully determines ivermectine, diosmin, and selinexor currently subjected to clinical trials, and further proposes bromocriptine, elbasvir as Mpro inhibitor candidates to be evaluated against SARS-CoV-2 infections.
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Affiliation(s)
- Merve Yuce
- Department of Chemical Engineering, Istanbul Technical University, Istanbul, Turkey
| | - Erdem Cicek
- Computational Science and Engineering Division, Informatics Institute, Istanbul Technical University, Istanbul, Turkey
| | - Tugce Inan
- Department of Chemical Engineering, Istanbul Technical University, Istanbul, Turkey
| | - Aslihan Basak Dag
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey
| | - Ozge Kurkcuoglu
- Department of Chemical Engineering, Istanbul Technical University, Istanbul, Turkey
| | - Fethiye Aylin Sungur
- Computational Science and Engineering Division, Informatics Institute, Istanbul Technical University, Istanbul, Turkey
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32
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Kuzikov M, Costanzi E, Reinshagen J, Esposito F, Vangeel L, Wolf M, Ellinger B, Claussen C, Geisslinger G, Corona A, Iaconis D, Talarico C, Manelfi C, Cannalire R, Rossetti G, Gossen J, Albani S, Musiani F, Herzog K, Ye Y, Giabbai B, Demitri N, Jochmans D, Jonghe SD, Rymenants J, Summa V, Tramontano E, Beccari AR, Leyssen P, Storici P, Neyts J, Gribbon P, Zaliani A. Identification of Inhibitors of SARS-CoV-2 3CL-Pro Enzymatic Activity Using a Small Molecule in Vitro Repurposing Screen. ACS Pharmacol Transl Sci 2021; 4:1096-1110. [PMID: 35287429 PMCID: PMC7986981 DOI: 10.1021/acsptsci.0c00216] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Indexed: 02/08/2023]
Abstract
Compound repurposing is an important strategy for the identification of effective treatment options against SARS-CoV-2 infection and COVID-19 disease. In this regard, SARS-CoV-2 main protease (3CL-Pro), also termed M-Pro, is an attractive drug target as it plays a central role in viral replication by processing the viral polyproteins pp1a and pp1ab at multiple distinct cleavage sites. We here report the results of a repurposing program involving 8.7 K compounds containing marketed drugs, clinical and preclinical candidates, and small molecules regarded as safe in humans. We confirmed previously reported inhibitors of 3CL-Pro and have identified 62 additional compounds with IC50 values below 1 μM and profiled their selectivity toward chymotrypsin and 3CL-Pro from the Middle East respiratory syndrome virus. A subset of eight inhibitors showed anticytopathic effect in a Vero-E6 cell line, and the compounds thioguanosine and MG-132 were analyzed for their predicted binding characteristics to SARS-CoV-2 3CL-Pro. The X-ray crystal structure of the complex of myricetin and SARS-Cov-2 3CL-Pro was solved at a resolution of 1.77 Å, showing that myricetin is covalently bound to the catalytic Cys145 and therefore inhibiting its enzymatic activity.
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Affiliation(s)
- Maria Kuzikov
- Fraunhofer
Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Elisa Costanzi
- Elettra-Sincrotrone
Trieste S.C.p.A., SS 14 - km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Jeanette Reinshagen
- Fraunhofer
Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Francesca Esposito
- Dipartimento
di Scienze della vita e dell’ambiente, Cittadella Universitaria di Monserrato, SS-554 Monserrato, Cagliari, Italy
| | - Laura Vangeel
- Department
of Microbiology, Immunology and Transplantation, Rega Institute for
Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, Box 1043, 3000 Leuven, Belgium
| | - Markus Wolf
- Fraunhofer
Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Bernhard Ellinger
- Fraunhofer
Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Carsten Claussen
- Fraunhofer
Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Gerd Geisslinger
- Fraunhofer Institute for Translational Medicine and
Pharmacology
ITMP, Theodor Stern Kai
7, 60596 Frankfurt
am Main, Germany
- Institute
of Clinical Pharmacology, Goethe-University, Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Angela Corona
- Dipartimento
di Scienze della vita e dell’ambiente, Cittadella Universitaria di Monserrato, SS-554 Monserrato, Cagliari, Italy
| | - Daniela Iaconis
- Dompé
Farmaceutici SpA, via Campo di Pile, 67100 L’Aquila, Italy
| | - Carmine Talarico
- Dompé
Farmaceutici SpA, via Campo di Pile, 67100 L’Aquila, Italy
| | - Candida Manelfi
- Dompé
Farmaceutici SpA, via Campo di Pile, 67100 L’Aquila, Italy
| | - Rolando Cannalire
- Department
of Pharmacy, University of Naples Federico
II, Via D. Montesano,
49, 80131 Naples, Italy
| | - Giulia Rossetti
- Institute
of Neuroscience and Medicine (INM-9)/Institute for Advanced Simulation
(IAS-5) and Jülich Supercomputing Centre (JSC) Forschungszentrum
Jülich, D-52425 Jülich, Germany
- Faculty
of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Jonas Gossen
- Institute
of Neuroscience and Medicine (INM-9)/Institute for Advanced Simulation
(IAS-5) and Jülich Supercomputing Centre (JSC) Forschungszentrum
Jülich, D-52425 Jülich, Germany
| | - Simone Albani
- Institute
of Neuroscience and Medicine (INM-9)/Institute for Advanced Simulation
(IAS-5) and Jülich Supercomputing Centre (JSC) Forschungszentrum
Jülich, D-52425 Jülich, Germany
| | - Francesco Musiani
- Laboratory
of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, 40216 Bologna, Italy
| | - Katja Herzog
- EU-OPENSCREEN
ERIC, Robert-Rössle-Straße
10, 13125 Berlin, Germany
| | - Yang Ye
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Barbara Giabbai
- Elettra-Sincrotrone
Trieste S.C.p.A., SS 14 - km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Nicola Demitri
- Elettra-Sincrotrone
Trieste S.C.p.A., SS 14 - km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Dirk Jochmans
- Department
of Microbiology, Immunology and Transplantation, Rega Institute for
Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, Box 1043, 3000 Leuven, Belgium
| | - Steven De Jonghe
- Department
of Microbiology, Immunology and Transplantation, Rega Institute for
Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, Box 1043, 3000 Leuven, Belgium
| | - Jasper Rymenants
- Department
of Microbiology, Immunology and Transplantation, Rega Institute for
Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, Box 1043, 3000 Leuven, Belgium
| | - Vincenzo Summa
- Department
of Pharmacy, University of Naples Federico
II, Via D. Montesano,
49, 80131 Naples, Italy
| | - Enzo Tramontano
- Dipartimento
di Scienze della vita e dell’ambiente, Cittadella Universitaria di Monserrato, SS-554 Monserrato, Cagliari, Italy
| | | | - Pieter Leyssen
- Department
of Microbiology, Immunology and Transplantation, Rega Institute for
Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, Box 1043, 3000 Leuven, Belgium
| | - Paola Storici
- Elettra-Sincrotrone
Trieste S.C.p.A., SS 14 - km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Johan Neyts
- Department
of Microbiology, Immunology and Transplantation, Rega Institute for
Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, Box 1043, 3000 Leuven, Belgium
| | - Philip Gribbon
- Fraunhofer
Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Andrea Zaliani
- Fraunhofer
Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
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33
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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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34
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Kuzikov M, Costanzi E, Reinshagen J, Esposito F, Vangeel L, Wolf M, Ellinger B, Claussen C, Geisslinger G, Corona A, Iaconis D, Talarico C, Manelfi C, Cannalire R, Rossetti G, Gossen J, Albani S, Musiani F, Herzog K, Ye Y, Giabbai B, Demitri N, Jochmans D, Jonghe SD, Rymenants J, Summa V, Tramontano E, Beccari AR, Leyssen P, Storici P, Neyts J, Gribbon P, Zaliani A. Identification of Inhibitors of SARS-CoV-2 3CL-Pro Enzymatic Activity Using a Small Molecule in Vitro Repurposing Screen. ACS Pharmacol Transl Sci 2021; 4:1096-1110. [PMID: 35287429 DOI: 10.1101/2020.12.16.422677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Indexed: 05/18/2023]
Abstract
Compound repurposing is an important strategy for the identification of effective treatment options against SARS-CoV-2 infection and COVID-19 disease. In this regard, SARS-CoV-2 main protease (3CL-Pro), also termed M-Pro, is an attractive drug target as it plays a central role in viral replication by processing the viral polyproteins pp1a and pp1ab at multiple distinct cleavage sites. We here report the results of a repurposing program involving 8.7 K compounds containing marketed drugs, clinical and preclinical candidates, and small molecules regarded as safe in humans. We confirmed previously reported inhibitors of 3CL-Pro and have identified 62 additional compounds with IC50 values below 1 μM and profiled their selectivity toward chymotrypsin and 3CL-Pro from the Middle East respiratory syndrome virus. A subset of eight inhibitors showed anticytopathic effect in a Vero-E6 cell line, and the compounds thioguanosine and MG-132 were analyzed for their predicted binding characteristics to SARS-CoV-2 3CL-Pro. The X-ray crystal structure of the complex of myricetin and SARS-Cov-2 3CL-Pro was solved at a resolution of 1.77 Å, showing that myricetin is covalently bound to the catalytic Cys145 and therefore inhibiting its enzymatic activity.
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Affiliation(s)
- Maria Kuzikov
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Elisa Costanzi
- Elettra-Sincrotrone Trieste S.C.p.A., SS 14 - km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Jeanette Reinshagen
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Francesca Esposito
- Dipartimento di Scienze della vita e dell'ambiente, Cittadella Universitaria di Monserrato, SS-554 Monserrato, Cagliari, Italy
| | - Laura Vangeel
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, Box 1043, 3000 Leuven, Belgium
| | - Markus Wolf
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Bernhard Ellinger
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Carsten Claussen
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Gerd Geisslinger
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor Stern Kai 7, 60596 Frankfurt am Main, Germany
- Institute of Clinical Pharmacology, Goethe-University, Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Angela Corona
- Dipartimento di Scienze della vita e dell'ambiente, Cittadella Universitaria di Monserrato, SS-554 Monserrato, Cagliari, Italy
| | - Daniela Iaconis
- Dompé Farmaceutici SpA, via Campo di Pile, 67100 L'Aquila, Italy
| | - Carmine Talarico
- Dompé Farmaceutici SpA, via Campo di Pile, 67100 L'Aquila, Italy
| | - Candida Manelfi
- Dompé Farmaceutici SpA, via Campo di Pile, 67100 L'Aquila, Italy
| | - Rolando Cannalire
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano, 49, 80131 Naples, Italy
| | - Giulia Rossetti
- Institute of Neuroscience and Medicine (INM-9)/Institute for Advanced Simulation (IAS-5) and Jülich Supercomputing Centre (JSC) Forschungszentrum Jülich, D-52425 Jülich, Germany
- Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Jonas Gossen
- Institute of Neuroscience and Medicine (INM-9)/Institute for Advanced Simulation (IAS-5) and Jülich Supercomputing Centre (JSC) Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Simone Albani
- Institute of Neuroscience and Medicine (INM-9)/Institute for Advanced Simulation (IAS-5) and Jülich Supercomputing Centre (JSC) Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, 40216 Bologna, Italy
| | - Katja Herzog
- EU-OPENSCREEN ERIC, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Yang Ye
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Barbara Giabbai
- Elettra-Sincrotrone Trieste S.C.p.A., SS 14 - km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Nicola Demitri
- Elettra-Sincrotrone Trieste S.C.p.A., SS 14 - km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Dirk Jochmans
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, Box 1043, 3000 Leuven, Belgium
| | - Steven De Jonghe
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, Box 1043, 3000 Leuven, Belgium
| | - Jasper Rymenants
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, Box 1043, 3000 Leuven, Belgium
| | - Vincenzo Summa
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano, 49, 80131 Naples, Italy
| | - Enzo Tramontano
- Dipartimento di Scienze della vita e dell'ambiente, Cittadella Universitaria di Monserrato, SS-554 Monserrato, Cagliari, Italy
| | - Andrea R Beccari
- Dompé Farmaceutici SpA, via Campo di Pile, 67100 L'Aquila, Italy
| | - Pieter Leyssen
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, Box 1043, 3000 Leuven, Belgium
| | - Paola Storici
- Elettra-Sincrotrone Trieste S.C.p.A., SS 14 - km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Johan Neyts
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, Box 1043, 3000 Leuven, Belgium
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
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35
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Borocci S, Cerchia C, Grottesi A, Sanna N, Prandi IG, Abid N, Beccari AR, Chillemi G, Talarico C. Altered Local Interactions and Long-Range Communications in UK Variant (B.1.1.7) Spike Glycoprotein. Int J Mol Sci 2021; 22:5464. [PMID: 34067272 PMCID: PMC8196891 DOI: 10.3390/ijms22115464] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 12/24/2022] Open
Abstract
The COVID-19 pandemic is caused by SARS-CoV-2. Currently, most of the research efforts towards the development of vaccines and antibodies against SARS-CoV-2 were mainly focused on the spike (S) protein, which mediates virus entry into the host cell by binding to ACE2. As the virus SARS-CoV-2 continues to spread globally, variants have emerged, characterized by multiple mutations of the S glycoprotein. Herein, we employed microsecond-long molecular dynamics simulations to study the impact of the mutations of the S glycoprotein in SARS-CoV-2 Variant of Concern 202012/01 (B.1.1.7), termed the "UK variant", in comparison with the wild type, with the aim to decipher the structural basis of the reported increased infectivity and virulence. The simulations provided insights on the different dynamics of UK and wild-type S glycoprotein, regarding in particular the Receptor Binding Domain (RBD). In addition, we investigated the role of glycans in modulating the conformational transitions of the RBD. The overall results showed that the UK mutant experiences higher flexibility in the RBD with respect to wild type; this behavior might be correlated with the increased transmission reported for this variant. Our work also adds useful structural information on antigenic "hotspots" and epitopes targeted by neutralizing antibodies.
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Affiliation(s)
- Stefano Borocci
- Department for Innovation in Biological, Agro-Food and Forest Systems, DIBAF, University of Tuscia, Via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy; (S.B.); (N.S.)
- Institute for Biological Systems, ISB, CNR, Via Salaria, Km 29.500, Monterotondo, 00015 Rome, Italy
| | - Carmen Cerchia
- Department of Pharmacy, University of Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy;
| | | | - Nico Sanna
- Department for Innovation in Biological, Agro-Food and Forest Systems, DIBAF, University of Tuscia, Via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy; (S.B.); (N.S.)
| | - Ingrid Guarnetti Prandi
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via Giuseppe Moruzzi 3, 56124 Pisa, Italy;
| | - Nabil Abid
- Laboratory of Transmissible Diseases and Biological Active Substances LR99ES27, Faculty of Pharmacy, University of Monastir, Rue Ibn Sina, Monastir 5000, Tunisia;
- High Institute of Biotechnology of Sidi Thabet, Department of Biotechnology, University of Manouba, BP-66, Ariana-Tunis 2020, Tunisia
| | | | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-Food and Forest Systems, DIBAF, University of Tuscia, Via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy; (S.B.); (N.S.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, IBIOM, CNR, Via Giovanni Amendola, 122/O, 70126 Bari, Italy
| | - Carmine Talarico
- Dompé Farmaceutici SpA, Via Campo di Pile, 67100 L’Aquila, Italy;
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36
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Miroshnychenko KV, Shestopalova AV. Combined use of the hepatitis C drugs and amentoflavone could interfere with binding of the spike glycoprotein of SARS-CoV-2 to ACE2: the results of a molecular simulation study. J Biomol Struct Dyn 2021; 40:8672-8686. [PMID: 33896392 PMCID: PMC8074653 DOI: 10.1080/07391102.2021.1914168] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 04/05/2021] [Indexed: 12/14/2022]
Abstract
The worldwide rapid spread of the COVID-19 disease necessitates the search for fast and effective treatments. The repurposing of existing drugs seems to be the best solution in this situation. In this study, the molecular docking method was used to test 248 drugs against the receptor-binding domain (RBD) of spike glycoprotein of SARS-CoV-2, which is responsible for viral entry into the host cell. Among the top-ranked ligands are drugs that are used for hepatitis C virus (HCV) treatments (paritaprevir, ledipasvir, simeprevir) and a natural biflavonoid amentoflavone. The binding sites of the HCV drugs and amentoflavone are different. Therefore, the ternary complexes of the HCV drug, amentoflavone, and RBD can be created. For the 5 top-ranked ligands, the validating molecular dynamics simulations of binary and ternary complexes with RBD were performed. According to the MMPBSA-binding free energies, the HCV drugs ledipasvir and paritaprevir (in a neutral form) are the most efficient binders of the RBD when used in combination with amentoflavone.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Anna V. Shestopalova
- O. Ya. Usikov Institute for Radiophysics and Electronics of NAS of Ukraine, Kharkiv, Ukraine
- V. N. Karazin Kharkiv National University, Kharkiv, Ukraine
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37
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Mengist HM, Dilnessa T, Jin T. Structural Basis of Potential Inhibitors Targeting SARS-CoV-2 Main Protease. Front Chem 2021; 9:622898. [PMID: 33889562 PMCID: PMC8056153 DOI: 10.3389/fchem.2021.622898] [Citation(s) in RCA: 173] [Impact Index Per Article: 57.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/04/2021] [Indexed: 12/23/2022] Open
Abstract
The Coronavirus disease-19 (COVID-19) pandemic is still devastating the world causing significant social, economic, and political chaos. Corresponding to the absence of globally approved antiviral drugs for treatment and vaccines for controlling the pandemic, the number of cases and/or mortalities are still rising. Current patient management relies on supportive treatment and the use of repurposed drugs as an indispensable option. Of a crucial role in the viral life cycle, ongoing studies are looking for potential inhibitors to the main protease (Mpro) of severe acute respiratory syndrome Coronavirus -2 (SARS-CoV-2) to tackle the pandemic. Although promising results have been achieved in searching for drugs inhibiting the Mpro, work remains to be done on designing structure-based improved drugs. This review discusses the structural basis of potential inhibitors targeting SARS-CoV-2 Mpro, identifies gaps, and provides future directions. Further, compounds with potential Mpro based antiviral activity are highlighted.
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Affiliation(s)
- Hylemariam Mihiretie Mengist
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of innate immunity and chronic disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Department of Medical Laboratory Science, College of Health Science, Debre Markos University, Debre Markos, Ethiopia
| | - Tebelay Dilnessa
- Department of Medical Laboratory Science, College of Health Science, Debre Markos University, Debre Markos, Ethiopia
| | - Tengchuan Jin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of innate immunity and chronic disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Science, Shanghai, China
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38
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Denesyuk AI, Permyakov SE, Johnson MS, Permyakov EA, Uversky VN, Denessiouk K. Structural leitmotif and functional variations of the structural catalytic core in (chymo)trypsin-like serine/cysteine fold proteinases. Int J Biol Macromol 2021; 179:601-609. [PMID: 33713772 DOI: 10.1016/j.ijbiomac.2021.03.042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/03/2021] [Accepted: 03/09/2021] [Indexed: 11/29/2022]
Abstract
Proteinases with the (chymo)trypsin-like serine/cysteine fold comprise a large superfamily performing their function through the Acid - Base - Nucleophile catalytic triad. In our previous work (Denesyuk AI, Johnson MS, Salo-Ahen OMH, Uversky VN, Denessiouk K. Int J Biol Macromol. 2020;153:399-411), we described a universal three-dimensional (3D) structural motif, NBCZone, that contains eleven amino acids: dipeptide 42 T-43 T, pentapeptide 54 T-55 T-56 T-57 T(base)-58 T, tripeptide 195 T(nucleophile)-196 T-197 T and residue 213 T (T - numeration of amino acids in trypsin). The comparison of the NBCZones among the members of the (chymo)trypsin-like protease family suggested the existence of 15 distinct groups. Within each group, the NBCZones incorporate an identical set of conserved interactions and bonds. In the present work, the structural environment of the catalytic acid at the position 102 T and the fourth member of the "catalytic tetrad" at the position 214 T was analyzed in 169 3D structures of proteinases with the (chymo)trypsin-like serine/cysteine fold. We have identified a complete Structural Catalytic Core (SCC) consisting of two classes and four groups. The proteinases belonging to different classes and groups differ from each other by the nature of the interaction between their N- and C-terminal β-barrels. Comparative analysis of the 3CLpro(s) from SARS-CoV-2 and SARS-CoV, used as an example, showed that the amino acids at positions 103 T and 179 T affect the nature of the interaction of the "catalytic acid" core (102 T-Core, N-terminal β-barrel) with the "supplementary" core (S-Core, C-terminal β-barrel), which ultimately results in the modulation of the enzymatic activity. The reported analysis represents an important standalone contribution to the analysis and systematization of the 3D structures of (chymo)trypsin-like serine/cysteine fold proteinases. The use of the developed approach for the comparison of 3D structures will allow, in the event of the appearance of new representatives of a given fold in the PDB, to quickly determine their structural homologues with the identification of possible differences.
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Affiliation(s)
- Alexander I Denesyuk
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow region 142290, Russia; Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku 20520, Finland.
| | - Sergei E Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow region 142290, Russia
| | - Mark S Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku 20520, Finland
| | - Eugene A Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow region 142290, Russia
| | - Vladimir N Uversky
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow region 142290, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
| | - Konstantin Denessiouk
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku 20520, Finland
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39
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Carli M, Sormani G, Rodriguez A, Laio A. Candidate Binding Sites for Allosteric Inhibition of the SARS-CoV-2 Main Protease from the Analysis of Large-Scale Molecular Dynamics Simulations. J Phys Chem Lett 2021; 12:65-72. [PMID: 33306377 PMCID: PMC7755075 DOI: 10.1021/acs.jpclett.0c03182] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/08/2020] [Indexed: 05/20/2023]
Abstract
We analyzed a 100 μs MD trajectory of the SARS-CoV-2 main protease by a non-parametric data analysis approach which allows characterizing a free energy landscape as a simultaneous function of hundreds of variables. We identified several conformations that, when visited by the dynamics, are stable for several hundred nanoseconds. We explicitly characterize and describe these metastable states. In some of these configurations, the catalytic dyad is less accessible. Stabilizing them by a suitable binder could lead to an inhibition of the enzymatic activity. In our analysis we keep track of relevant contacts between residues which are selectively broken or formed in the states. Some of these contacts are formed by residues which are far from the catalytic dyad and are accessible to the solvent. Based on this analysis we propose some relevant contact patterns and three possible binding sites which could be targeted to achieve allosteric inhibition.
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Affiliation(s)
- Matteo Carli
- Scuola
Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy
| | - Giulia Sormani
- Scuola
Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy
| | - Alex Rodriguez
- The
Abdus Salam International Centre for Theoretical Physics (ICTP), Str. Costiera, 11, 34151 Trieste, Italy
| | - Alessandro Laio
- Scuola
Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy
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40
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Menichetti R, Giulini M, Potestio R. A journey through mapping space: characterising the statistical and metric properties of reduced representations of macromolecules. THE EUROPEAN PHYSICAL JOURNAL. B 2021; 94:204. [PMID: 34720709 PMCID: PMC8550479 DOI: 10.1140/epjb/s10051-021-00205-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/13/2021] [Indexed: 05/04/2023]
Abstract
ABSTRACT A mapping of a macromolecule is a prescription to construct a simplified representation of the system in which only a subset of its constituent atoms is retained. As the specific choice of the mapping affects the analysis of all-atom simulations as well as the construction of coarse-grained models, the characterisation of the mapping space has recently attracted increasing attention. We here introduce a notion of scalar product and distance between reduced representations, which allows the study of the metric and topological properties of their space in a quantitative manner. Making use of a Wang-Landau enhanced sampling algorithm, we exhaustively explore such space, and examine the qualitative features of mappings in terms of their squared norm. A one-to-one correspondence with an interacting lattice gas on a finite volume leads to the emergence of discontinuous phase transitions in mapping space, which mark the boundaries between qualitatively different reduced representations of the same molecule.
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Affiliation(s)
- Roberto Menichetti
- Physics Department, University of Trento, via Sommarive, 14, 38123 Trento, Italy
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, via Sommarive, 14, 38123 Trento, Italy
| | - Marco Giulini
- Physics Department, University of Trento, via Sommarive, 14, 38123 Trento, Italy
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, via Sommarive, 14, 38123 Trento, Italy
| | - Raffaello Potestio
- Physics Department, University of Trento, via Sommarive, 14, 38123 Trento, Italy
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, via Sommarive, 14, 38123 Trento, Italy
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41
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Deeks HM, Walters RK, Barnoud J, Glowacki DR, Mulholland AJ. Interactive Molecular Dynamics in Virtual Reality Is an Effective Tool for Flexible Substrate and Inhibitor Docking to the SARS-CoV-2 Main Protease. J Chem Inf Model 2020; 60:5803-5814. [PMID: 33174415 PMCID: PMC7671099 DOI: 10.1021/acs.jcim.0c01030] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Indexed: 01/19/2023]
Abstract
The main protease (Mpro) of the SARS-CoV-2 virus is one focus of drug development efforts for COVID-19. Here, we show that interactive molecular dynamics in virtual reality (iMD-VR) is a useful and effective tool for creating Mpro complexes. We make these tools and models freely available. iMD-VR provides an immersive environment in which users can interact with MD simulations and so build protein complexes in a physically rigorous and flexible way. Recently, we have demonstrated that iMD-VR is an effective method for interactive, flexible docking of small molecule drugs into their protein targets (Deeks et al. PLoS One 2020, 15, e0228461). Here, we apply this approach to both an Mpro inhibitor and an oligopeptide substrate, using experimentally determined crystal structures. For the oligopeptide, we test against a crystallographic structure of the original SARS Mpro. Docking with iMD-VR gives models in agreement with experimentally observed (crystal) structures. The docked structures are also tested in MD simulations and found to be stable. Different protocols for iMD-VR docking are explored, e.g., with and without restraints on protein backbone, and we provide recommendations for its use. We find that it is important for the user to focus on forming binding interactions, such as hydrogen bonds, and not to rely on using simple metrics (such as RMSD), in order to create realistic, stable complexes. We also test the use of apo (uncomplexed) crystal structures for docking and find that they can give good results. This is because of the flexibility and dynamic response allowed by the physically rigorous, atomically detailed simulation approach of iMD-VR. We make our models (and interactive simulations) freely available. The software framework that we use, Narupa, is open source, and uses commodity VR hardware, so these tools are readily accessible to the wider research community working on Mpro (and other COVID-19 targets). These should be widely useful in drug development, in education applications, e.g., on viral enzyme structure and function, and in scientific communication more generally.
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Affiliation(s)
- Helen M. Deeks
- Intangible Realities Laboratory,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
- Centre for Computational Chemistry,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
- Department of Computer Science, Merchant
Venturers Building, University of Bristol,
Woodland Road, Bristol BS8 1UB, United
Kingdom
| | - Rebecca K. Walters
- Intangible Realities Laboratory,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
- Centre for Computational Chemistry,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
- Department of Computer Science, Merchant
Venturers Building, University of Bristol,
Woodland Road, Bristol BS8 1UB, United
Kingdom
| | - Jonathan Barnoud
- Intangible Realities Laboratory,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
- Centre for Computational Chemistry,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
| | - David R. Glowacki
- Intangible Realities Laboratory,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
- Centre for Computational Chemistry,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
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- Department of Computer Science, Merchant
Venturers Building, University of Bristol,
Woodland Road, Bristol BS8 1UB, United
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| | - Adrian J. Mulholland
- Centre for Computational Chemistry,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
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Tagliamonte MS, Abid N, Borocci S, Sangiovanni E, Ostrov DA, Kosakovsky Pond SL, Salemi M, Chillemi G, Mavian C. Multiple Recombination Events and Strong Purifying Selection at the Origin of SARS-CoV-2 Spike Glycoprotein Increased Correlated Dynamic Movements. Int J Mol Sci 2020; 22:E80. [PMID: 33374797 PMCID: PMC7794730 DOI: 10.3390/ijms22010080] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 01/12/2023] Open
Abstract
Our evolutionary and structural analyses revealed that the severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2) spike gene is a complex mosaic resulting from several recombination events. Additionally, the fixation of variants has mainly been driven by purifying selection, suggesting the presence of conserved structural features. Our dynamic simulations identified two main long-range covariant dynamic movements of the novel glycoprotein, and showed that, as a result of the evolutionary duality, they are preserved. The first movement involves the receptor binding domain with the N-terminal domain and the C-terminal domain 2 and is maintained across human, bat and pangolin coronaviruses. The second is a complex network of long-range dynamics specific to SARS-CoV-2 involving the novel PRRA and the conserved KR*SF cleavage sites, as well as conserved segments in C-terminal domain 3. These movements, essential for host cell binding, are maintained by hinges conserved across human, bat, and pangolin coronaviruses glycoproteins. The hinges, located around Threonine 333 and Proline 527 within the N-terminal domain and C-terminal domain 2, represent candidate targets for the future development of novel pan-coronavirus inhibitors. In summary, we show that while recombination created a new configuration that increased the covariant dynamic movements of the SARS-CoV-2 glycoprotein, negative selection preserved its inter-domain structure throughout evolution in different hosts and inter-species transmissions.
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Affiliation(s)
- Massimiliano S. Tagliamonte
- Emerging Pathogen Institute, University of Florida, Gainesville, FL 32608, USA;
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA;
| | - Nabil Abid
- Laboratory of Transmissible Diseases and Biological Active Substances LR99ES27, Faculty of Pharmacy, University of Monastir, Rue Ibn Sina, 5000 Monastir, Tunisia;
- Department of Biotechnology, High Institute of Biotechnology of Sidi Thabet, University of Manouba, BP-66, 2020 Ariana-Tunis, Tunisia
| | - Stefano Borocci
- Department for Innovation in Biological, Agro-food and Forest Systems (DIBAF), University of Tuscia, via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy; (S.B.); (E.S.)
- Institute for Biological Systems, National Research Council, Via Salaria, Km 29.500, 00015 Monterotondo, Rome, Italy
| | - Elisa Sangiovanni
- Department for Innovation in Biological, Agro-food and Forest Systems (DIBAF), University of Tuscia, via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy; (S.B.); (E.S.)
| | - David A. Ostrov
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA;
| | | | - Marco Salemi
- Emerging Pathogen Institute, University of Florida, Gainesville, FL 32608, USA;
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA;
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-food and Forest Systems (DIBAF), University of Tuscia, via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy; (S.B.); (E.S.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Via Giovanni Amendola, 122/O, 70126 Bari, Italy
| | - Carla Mavian
- Emerging Pathogen Institute, University of Florida, Gainesville, FL 32608, USA;
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA;
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43
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Ensemble Docking Coupled to Linear Interaction Energy Calculations for Identification of Coronavirus Main Protease (3CL pro) Non-Covalent Small-Molecule Inhibitors. Molecules 2020; 25:molecules25245808. [PMID: 33316996 PMCID: PMC7763084 DOI: 10.3390/molecules25245808] [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: 11/05/2020] [Revised: 12/03/2020] [Accepted: 12/06/2020] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2, or severe acute respiratory syndrome coronavirus 2, represents a new strain of Coronaviridae. In the closing 2019 to early 2020 months, the virus caused a global pandemic of COVID-19 disease. We performed a virtual screening study in order to identify potential inhibitors of the SARS-CoV-2 main viral protease (3CLpro or Mpro). For this purpose, we developed a novel approach using ensemble docking high-throughput virtual screening directly coupled with subsequent Linear Interaction Energy (LIE) calculations to maximize the conformational space sampling and to assess the binding affinity of identified inhibitors. A large database of small commercial compounds was prepared, and top-scoring hits were identified with two compounds singled out, namely 1-[(R)-2-(1,3-benzimidazol-2-yl)-1-pyrrolidinyl]-2-(4-methyl-1,4-diazepan-1-yl)-1-ethanone and [({(S)-1-[(1H-indol-2-yl)methyl]-3-pyrrolidinyl}methyl)amino](5-methyl-2H-pyrazol-3-yl)formaldehyde. Moreover, we obtained a favorable binding free energy of the identified compounds, and using contact analysis we confirmed their stable binding modes in the 3CLpro active site. These compounds will facilitate further 3CLpro inhibitor design.
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