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Liu X, Zheng M, Zhang H, Feng B, Li J, Zhang Y, Zhang J, Zhao N, Li C, Song N, Song B, Yang D, Chen J, Qi A, Zhao L, Luo C, Zang Y, Liu H, Li J, Zhang B, Zhou Y, Zheng J. Characterization and noncovalent inhibition of the K63-deubiquitinase activity of SARS-cov-2 PLpro. Antiviral Res 2024; 228:105944. [PMID: 38914283 DOI: 10.1016/j.antiviral.2024.105944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 06/21/2024] [Accepted: 06/22/2024] [Indexed: 06/26/2024]
Abstract
SARS-CoV-2 papain-like protease (PLpro) could facilitate viral replication and host immune evasion by respectively hydrolyzing viral polyprotein and host ubiquitin conjugates, thereby rendering itself as an important antiviral target. Yet few noncovalent PLpro inhibitors of SARS-CoV-2 have been reported with improved directed towards pathogenic deubiquitinating activities inhibition. Herein, we report that coronavirus PLpro proteases have distinctive substrate bias and are conserved to deubiquitylate K63-linked polyubiquitination, thereby attenuating host type I interferon response. We identify a noncovalent compound specifically optimized towards halting the K63-deubiquitinase activity of SARS-CoV-2 PLpro, but not other coronavirus (CoV) counterparts or host deubiquitinase. Contrasting with GRL-0617, a SARS-CoV-1 PLpro inhibitor, SIMM-036 is 50-fold and 7-fold (half maximal inhibitory concentration (IC50)) more potent to inhibit viral replication during SARS-CoV-2 infection and restore the host interferon-β (IFN-β) response in human angiotensin-converting enzyme 2 (hACE2)-HeLa cells, respectively. Structure-activity relationship (SAR) analysis further reveals the importance of BL2 groove of PLpro, which could determine the selectivity of K63-deubiquitinase activity of the enzyme.
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Affiliation(s)
- Xin Liu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Miao Zheng
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Hongqing Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Bo Feng
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Jiaqi Li
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Yanan Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Ji Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Na Zhao
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Chaoqiang Li
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Ning Song
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Bin Song
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Dongyuan Yang
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Jin Chen
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ao Qi
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, 310024, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Linxiang Zhao
- Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Cheng Luo
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yi Zang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Hong Liu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Jia Li
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; Shenyang Pharmaceutical University, Shenyang, 110016, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, 310024, China
| | - Bo Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Yu Zhou
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; Shenyang Pharmaceutical University, Shenyang, 110016, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, 310024, China
| | - Jie Zheng
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, 310024, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Shanghai Institute of Virology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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2
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Alsrhani A, Farhana A, Khan YS, Ashraf GM, Shahwan M, Shamsi A. Phytoconstituents as potential therapeutic agents against COVID-19: a computational study on inhibition of SARS-CoV-2 main protease. J Biomol Struct Dyn 2023:1-12. [PMID: 37713337 DOI: 10.1080/07391102.2023.2257328] [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: 07/19/2023] [Accepted: 09/04/2023] [Indexed: 09/17/2023]
Abstract
The Coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) has become a global health crisis, and the urgent need for effective treatments is evident. One potential target for COVID-19 therapeutics is the main protease (Mpro) of SARS‑CoV‑2, an essential enzyme for viral replication. Natural compounds have been explored as a source of potential inhibitors for Mpro due to their safety and availability. In this study, we employed a computational approach to screen a library of phytoconstituents and identified potential Mpro inhibitors based on their binding affinities and molecular interactions. The top-ranking compounds were further validated through molecular dynamics simulations (MDS) and free energy calculations. As a result of the above procedures, we identified two phytoconstituents, Khelmarin B and Neogitogenin, with appreciable binding affinity and specificity towards the Mpro binding pocket. Our results suggest that Khelmarin B and Neogitogenin could potentially serve as Mpro inhibitors and have the potential to be developed as COVID-19 therapeutics. Further experimental studies are required to confirm the efficacy and safety of these compounds.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abdullah Alsrhani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, Saudi Arabia
| | - Aisha Farhana
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, Saudi Arabia
| | - Yusuf Saleem Khan
- Department of Anatomy, College of Medicine, Jouf University, Sakaka, Saudi Arabia
| | - Ghulam Md Ashraf
- Department of Medical Laboratory Sciences, College of Health Sciences, and Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Moyad Shahwan
- Center of Medical and Bio-Allied Health Sciences Research (CMBHSR), Ajman University, Ajman, United Arab Emirates
| | - Anas Shamsi
- Center of Medical and Bio-Allied Health Sciences Research (CMBHSR), Ajman University, Ajman, United Arab Emirates
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3
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Brian Chia CS, Pheng Lim S. A Patent Review on SARS Coronavirus Papain-Like Protease (PL pro ) Inhibitors. ChemMedChem 2023; 18:e202300216. [PMID: 37248169 DOI: 10.1002/cmdc.202300216] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/29/2023] [Accepted: 05/29/2023] [Indexed: 05/31/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is an unprecedented global health emergency causing more than 6.6 million fatalities by 31 December 2022. So far, only three antiviral drugs have been granted emergency use authorisation or approved by the FDA. The SARS-CoV-2 papain-like protease (PLpro ) is deemed an attractive drug target as it plays an essential role in viral polyprotein processing and pathogenesis although no inhibitors have yet been approved. This patent review discusses coronavirus PLpro inhibitors reported in patents published between 1 January 2003 to 2 March 2023, giving an overview on the inhibitors that have generated commercial interest, especially amongst drug companies.
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Affiliation(s)
- C S Brian Chia
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, Chromos #08-01, Singapore, 138670, Singapore
| | - Siew Pheng Lim
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, Chromos #08-01, Singapore, 138670, Singapore
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4
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Akinyele OF, Fakola EG, Adeboye OO, Chinuomah SC. Investigation of Methyl-5-(pentan-3-yloxy)-7-oxabicyclo[4.1.0]hept-3-ene-3-carboxyhydrazide Derivatives as Potential Inhibitors of COVID-19 Main Protease: DFT and Molecular Docking Study. Bioinform Biol Insights 2023; 17:11779322231182050. [PMID: 37377795 PMCID: PMC10291222 DOI: 10.1177/11779322231182050] [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: 01/31/2023] [Accepted: 05/27/2023] [Indexed: 06/29/2023] Open
Abstract
The search for effective therapeutics to combat COVID-19 has led to the exploration of the biological activity of numerous compounds. In this study, hydrazones derived from oseltamivir intermediate, methyl 5-(pentan-3-yloxy)-7-oxabicyclo[4.1.0]hept-3-ene-3-carboxylate have been investigated for their potential as drug candidates against the COVID-19 virus using computational methods, including density functional theory (DFT) studies, molecular docking, and absorption, distribution, metabolism, excretion and toxicity (ADMET) analysis. The DFT studies provide information on the electronic properties of the compounds while the molecular docking results using AutoDock reported the binding energies between the main protease of COVID-19 and the compounds. The DFT results revealed that the energy gap of the compounds ranged from 4.32 to 5.82 eV while compound HC had the highest energy gap (5.82 eV) and chemical potential (2.90 eV). The electrophilicity index values of the 11 compounds ranged from 2.49 to 3.86, thus they were classified as strong electrophiles. The molecular electrostatic potential (MESP) revealed electron-rich and electron-deficient regions of the compounds. The docking results reveal that all the compounds had better docking scores than remdesivir and chloroquine, frontline drugs employed in combating COVID-19, with HC having the best docking score of -6.5. The results were visualized using Discovery studio, which revealed hydrogen bonding, pi-alkyl interaction, alkyl interaction, salt bridge interaction, halogen interaction as being responsible for the docking scores. The drug-likeness results showed that the compounds qualify as oral drug candidates as none of them violated Vebers and Lipinski's rule. Thus, they could serve as potential inhibitors of COVID-19.
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5
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Preparation and characterization of nanobodies targeting SARS-CoV-2 papain-like protease. Protein Expr Purif 2023; 207:106267. [PMID: 37030644 PMCID: PMC10076250 DOI: 10.1016/j.pep.2023.106267] [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: 01/23/2023] [Revised: 03/21/2023] [Accepted: 03/26/2023] [Indexed: 04/09/2023]
Abstract
Coronavirus Papain-like protease (PLpro) mediates the cleavage of viral polyproteins and assists the virus escaping from innate immune response. Thus, PLpro is an attractive target for the development of broad-spectrum drugs as it has a conserved structure across different coronaviruses. In this study, we purified SARS-CoV-2 PLpro as an immune antigen, constructed a nanobody phage display library, and identified a set of nanobodies with high affinity for SARS-CoV-2. In addition, enzyme activity experiments demonstrated that two nanobodies had a significant inhibitory effect on the PLpro. These nanobodies should therefore be investigated as candidates for the treatment of coronaviruses.
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6
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Tian S, Zhang J, Yuan S, Wang Q, Lv C, Wang J, Fang J, Fu L, Yang J, Zu X, Zhao J, Zhang W. Exploring pharmacological active ingredients of traditional Chinese medicine by pharmacotranscriptomic map in ITCM. Brief Bioinform 2023; 24:7017365. [PMID: 36719094 DOI: 10.1093/bib/bbad027] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/18/2022] [Accepted: 01/10/2023] [Indexed: 02/01/2023] Open
Abstract
With the emergence of high-throughput technologies, computational screening based on gene expression profiles has become one of the most effective methods for drug discovery. More importantly, profile-based approaches remarkably enhance novel drug-disease pair discovery without relying on drug- or disease-specific prior knowledge, which has been widely used in modern medicine. However, profile-based systematic screening of active ingredients of traditional Chinese medicine (TCM) has been scarcely performed due to inadequate pharmacotranscriptomic data. Here, we develop the largest-to-date online TCM active ingredients-based pharmacotranscriptomic platform integrated traditional Chinese medicine (ITCM) for the effective screening of active ingredients. First, we performed unified high-throughput experiments and constructed the largest data repository of 496 representative active ingredients, which was five times larger than the previous one built by our team. The transcriptome-based multi-scale analysis was also performed to elucidate their mechanism. Then, we developed six state-of-art signature search methods to screen active ingredients and determine the optimal signature size for all methods. Moreover, we integrated them into a screening strategy, TCM-Query, to identify the potential active ingredients for the special disease. In addition, we also comprehensively collected the TCM-related resource by literature mining. Finally, we applied ITCM to an active ingredient bavachinin, and two diseases, including prostate cancer and COVID-19, to demonstrate the power of drug discovery. ITCM was aimed to comprehensively explore the active ingredients of TCM and boost studies of pharmacological action and drug discovery. ITCM is available at http://itcm.biotcm.net.
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Affiliation(s)
- Saisai Tian
- School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Jinbo Zhang
- School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
- Department of Pharmacy, Tianjin Rehabilitation Center of Joint Logistics Support Force, Tianjin, 300110, China
| | - Shunling Yuan
- School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Qun Wang
- The Research Center for Traditional Chinese Medicine, Shanghai Institute of Infectious Diseases and Biosafety, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Chao Lv
- The Research Center for Traditional Chinese Medicine, Shanghai Institute of Infectious Diseases and Biosafety, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jinxing Wang
- School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Jiansong Fang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lu Fu
- School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Jian Yang
- School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Xianpeng Zu
- School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Jing Zhao
- The Research Center for Traditional Chinese Medicine, Shanghai Institute of Infectious Diseases and Biosafety, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Weidong Zhang
- School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
- The Research Center for Traditional Chinese Medicine, Shanghai Institute of Infectious Diseases and Biosafety, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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7
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Chavda VP, Patel AB, Vora LK, Singla RK, Shah P, Uversky VN, Apostolopoulos V. Nitric Oxide and its Derivatives Containing Nasal Spray and Inhalation Therapy for the Treatment of COVID-19. Curr Pharm Des 2022; 28:3658-3670. [PMID: 36284382 DOI: 10.2174/1381612829666221024124848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 09/11/2022] [Accepted: 09/26/2022] [Indexed: 01/28/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a major health concern worldwide and has evolved into different variants. SARS-CoV-2 possesses a spike glycoprotein on its envelope that binds to the angiotensin-converting enzyme 2 (ACE-2) receptor of the host cell via the receptor-binding domain (RBD) in the upper respiratory tract. Since the SARS-CoV-2 virus variants change the severity of the diesease and treatment scenarios, repurposing current medicines may provide a quick and appealing method with established safety features. The efficacy and safety of antiviral medicines against the coronavirus disease 2019 (COVID-19) have been investigated, and several of them are now undergoing clinical studies. Recently, it has been found that nitric oxide (NO) shows antiviral properties against SARS-CoV-2 and prevents the virus from binding to a host cell. In addition, NO is a well-known vasodilator and acts as an important coagulation mediator. With the fast-track development of COVID-19 treatments and vaccines, one avenue of research aimed at improving therapeutics is exploring different forms of drug delivery, including intranasal sprays and inhalation therapy. The nasal mucosa is more prone to be the site of infection as it is in more direct contact with the physical environment via air during inhalation and exhalation. Thus, the use of exogenous nasal NO therapy via the intranasal route displays a distinct advantage. Therefore, the objective of this review is to summarize the relevant actions of NO via the intranasal spray and inhalation delivery, its mechanism of action, and its use in the treatment of COVID-19.
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Affiliation(s)
- Vivek P Chavda
- Department of Pharmaceutics and Pharmaceutical Technology, LM College of Pharmacy, Ahmedabad - 380009, India
| | - Aayushi B Patel
- Department of Pharmaceutics and Pharmaceutical Technology, LM College of Pharmacy, Ahmedabad - 380009, India
| | - Lalitkumar K Vora
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, BT9 7BL, U.K
| | - Rajeev K Singla
- Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Xinchuan Road 2222, Chengdu, Sichuan, China.,School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab-144411, India
| | - Priyal Shah
- Department of Pharmaceutics and Pharmaceutical Technology, LM College of Pharmacy, Ahmedabad - 380009, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Vasso Apostolopoulos
- Institute for Health and Sport, Victoria University, Melbourne VIC 3030, Australia
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8
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Maghsoudi S, Taghavi Shahraki B, Rameh F, Nazarabi M, Fatahi Y, Akhavan O, Rabiee M, Mostafavi E, Lima EC, Saeb MR, Rabiee N. A review on computer-aided chemogenomics and drug repositioning for rational COVID-19 drug discovery. Chem Biol Drug Des 2022; 100:699-721. [PMID: 36002440 PMCID: PMC9539342 DOI: 10.1111/cbdd.14136] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/07/2022] [Accepted: 08/21/2022] [Indexed: 11/29/2022]
Abstract
Application of materials capable of energy harvesting to increase the efficiency and environmental adaptability is sometimes reflected in the ability of discovery of some traces in an environment-either experimentally or computationally-to enlarge practical application window. The emergence of computational methods, particularly computer-aided drug discovery (CADD), provides ample opportunities for the rapid discovery and development of unprecedented drugs. The expensive and time-consuming process of traditional drug discovery is no longer feasible, for nowadays the identification of potential drug candidates is much easier for therapeutic targets through elaborate in silico approaches, allowing the prediction of the toxicity of drugs, such as drug repositioning (DR) and chemical genomics (chemogenomics). Coronaviruses (CoVs) are cross-species viruses that are able to spread expeditiously from the into new host species, which in turn cause epidemic diseases. In this sense, this review furnishes an outline of computational strategies and their applications in drug discovery. A special focus is placed on chemogenomics and DR as unique and emerging system-based disciplines on CoV drug and target discovery to model protein networks against a library of compounds. Furthermore, to demonstrate the special advantages of CADD methods in rapidly finding a drug for this deadly virus, numerous examples of the recent achievements grounded on molecular docking, chemogenomics, and DR are reported, analyzed, and interpreted in detail. It is believed that the outcome of this review assists developers of energy harvesting materials and systems for detection of future unexpected kinds of CoVs or other variants.
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Affiliation(s)
- Saeid Maghsoudi
- Faculty of Medicine, Department of Physiology and PathophysiologyUniversity of ManitobaWinnipegManitobaCanada
- Biology of Breathing Group, Children's Hospital Research Institute of Manitoba (CHRIM), University of ManitobaWinnipegManitobaCanada
| | | | | | - Masoomeh Nazarabi
- Faculty of Organic Chemistry, Department of ChemistryUniversity of KashanKashanIran
| | - Yousef Fatahi
- Department of Pharmaceutical Nanotechnology, Faculty of PharmacyTehran University of Medical SciencesTehranIran
- Nanotechnology Research Center, Faculty of PharmacyTehran University of Medical SciencesTehranIran
| | - Omid Akhavan
- Department of PhysicsSharif University of TechnologyTehranIran
| | - Mohammad Rabiee
- Biomaterials Group, Department of Biomedical EngineeringAmirkabir University of TechnologyTehranIran
| | - Ebrahim Mostafavi
- Stanford Cardiovascular Institute, Stanford University School of MedicineStanfordCaliforniaUSA
- Department of MedicineStanford University School of MedicineStanfordCaliforniaUSA
| | - Eder C. Lima
- Institute of Chemistry, Federal University of Rio Grande Do Sul (UFRGS)Porto AlegreBrazil
| | - Mohammad Reza Saeb
- Department of Polymer Technology, Faculty of ChemistryGdańsk University of TechnologyGdańskPoland
| | - Navid Rabiee
- Department of PhysicsSharif University of TechnologyTehranIran
- School of EngineeringMacquarie UniversitySydneyNew South WalesAustralia
- Department of Materials Science and EngineeringPohang University of Science and Technology (POSTECH)PohangSouth Korea
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9
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Karges J. Rhenium complexes as antiviral agents for COVID-19. J COORD CHEM 2022. [DOI: 10.1080/00958972.2022.2084395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Johannes Karges
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, United States
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10
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Zhou H, Ni WJ, Huang W, Wang Z, Cai M, Sun YC. Advances in Pathogenesis, Progression, Potential Targets and Targeted Therapeutic Strategies in SARS-CoV-2-Induced COVID-19. Front Immunol 2022; 13:834942. [PMID: 35450063 PMCID: PMC9016159 DOI: 10.3389/fimmu.2022.834942] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/07/2022] [Indexed: 01/18/2023] Open
Abstract
As the new year of 2020 approaches, an acute respiratory disease quietly caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), also known as coronavirus disease 2019 (COVID-19) was reported in Wuhan, China. Subsequently, COVID-19 broke out on a global scale and formed a global public health emergency. To date, the destruction that has lasted for more than two years has not stopped and has caused the virus to continuously evolve new mutant strains. SARS-CoV-2 infection has been shown to cause multiple complications and lead to severe disability and death, which has dealt a heavy blow to global development, not only in the medical field but also in social security, economic development, global cooperation and communication. To date, studies on the epidemiology, pathogenic mechanism and pathological characteristics of SARS-CoV-2-induced COVID-19, as well as target confirmation, drug screening, and clinical intervention have achieved remarkable effects. With the continuous efforts of the WHO, governments of various countries, and scientific research and medical personnel, the public’s awareness of COVID-19 is gradually deepening, a variety of prevention methods and detection methods have been implemented, and multiple vaccines and drugs have been developed and urgently marketed. However, these do not appear to have completely stopped the pandemic and ravages of this virus. Meanwhile, research on SARS-CoV-2-induced COVID-19 has also seen some twists and controversies, such as potential drugs and the role of vaccines. In view of the fact that research on SARS-CoV-2 and COVID-19 has been extensive and in depth, this review will systematically update the current understanding of the epidemiology, transmission mechanism, pathological features, potential targets, promising drugs and ongoing clinical trials, which will provide important references and new directions for SARS-CoV-2 and COVID-19 research.
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Affiliation(s)
- Hong Zhou
- Department of Pharmacy, Anhui Provincial Cancer Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Wei-Jian Ni
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China.,Anhui Provincial Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Wei Huang
- The Third People's Hospital of Hefei, The Third Clinical College of Anhui Medical University, Hefei, China
| | - Zhen Wang
- Anhui Provincial Children's Hospital, Children's Hospital of Fudan University-Anhui Campus, Hefei, China
| | - Ming Cai
- Department of Pharmacy, The Second Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China.,School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Yan-Cai Sun
- Department of Pharmacy, Anhui Provincial Cancer Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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11
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Novel Inhibitors of 2′-O-Methyltransferase of the SARS-CoV-2 Coronavirus. Molecules 2022; 27:molecules27092721. [PMID: 35566072 PMCID: PMC9100384 DOI: 10.3390/molecules27092721] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/17/2022] [Accepted: 04/20/2022] [Indexed: 12/24/2022] Open
Abstract
The COVID-19 pandemic is still affecting many people worldwide and causing a heavy burden to global health. To eliminate the disease, SARS-CoV-2, the virus responsible for the pandemic, can be targeted in several ways. One of them is to inhibit the 2′-O-methyltransferase (nsp16) enzyme that is crucial for effective translation of viral RNA and virus replication. For methylation of substrates, nsp16 utilizes S-adenosyl methionine (SAM). Binding of a small molecule in the protein site where SAM binds can disrupt the synthesis of viral proteins and, as a result, the replication of the virus. Here, we performed high-throughput docking into the SAM-binding site of nsp16 for almost 40 thousand structures, prepared for compounds from three libraries: Enamine Coronavirus Library, Enamine Nucleoside Mimetics Library, and Chemdiv Nucleoside Analogue Library. For the top scoring ligands, semi-empirical quantum-chemical calculations were performed, to better estimate protein–ligand binding enthalpy. Relying upon the calculated binding energies and predicted docking poses, we selected 21 compounds for experimental testing.
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12
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Montaño LM, Sommer B, Gomez-Verjan JC, Morales-Paoli GS, Ramírez-Salinas GL, Solís-Chagoyán H, Sanchez-Florentino ZA, Calixto E, Pérez-Figueroa GE, Carter R, Jaimez-Melgoza R, Romero-Martínez BS, Flores-Soto E. Theophylline: Old Drug in a New Light, Application in COVID-19 through Computational Studies. Int J Mol Sci 2022; 23:ijms23084167. [PMID: 35456985 PMCID: PMC9030606 DOI: 10.3390/ijms23084167] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/04/2022] [Accepted: 04/04/2022] [Indexed: 02/04/2023] Open
Abstract
Theophylline (3-methyxanthine) is a historically prominent drug used to treat respiratory diseases, alone or in combination with other drugs. The rapid onset of the COVID-19 pandemic urged the development of effective pharmacological treatments to directly attack the development of new variants of the SARS-CoV-2 virus and possess a therapeutical battery of compounds that could improve the current management of the disease worldwide. In this context, theophylline, through bronchodilatory, immunomodulatory, and potentially antiviral mechanisms, is an interesting proposal as an adjuvant in the treatment of COVID-19 patients. Nevertheless, it is essential to understand how this compound could behave against such a disease, not only at a pharmacodynamic but also at a pharmacokinetic level. In this sense, the quickest approach in drug discovery is through different computational methods, either from network pharmacology or from quantitative systems pharmacology approaches. In the present review, we explore the possibility of using theophylline in the treatment of COVID-19 patients since it seems to be a relevant candidate by aiming at several immunological targets involved in the pathophysiology of the disease. Theophylline down-regulates the inflammatory processes activated by SARS-CoV-2 through various mechanisms, and herein, they are discussed by reviewing computational simulation studies and their different applications and effects.
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Affiliation(s)
- Luis M. Montaño
- Departamento de Farmacología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México 04510, CP, Mexico; (L.M.M.); (R.J.-M.); (B.S.R.-M.)
| | - Bettina Sommer
- Laboratorio de Hiperreactividad Bronquial, Instituto Nacional de Enfermedades Respiratorias “Ismael Cosío Villegas”, Ciudad de México 14080, CP, Mexico;
| | - Juan C. Gomez-Verjan
- Dirección de Investigación, Instituto Nacional de Geriatría, Ciudad de México 10200, CP, Mexico; (J.C.G.-V.); (G.S.M.-P.)
| | - Genaro S. Morales-Paoli
- Dirección de Investigación, Instituto Nacional de Geriatría, Ciudad de México 10200, CP, Mexico; (J.C.G.-V.); (G.S.M.-P.)
| | - Gema Lizbeth Ramírez-Salinas
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón S/N, Col. Santo Tomas, Ciudad de México 11340, CP, Mexico;
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito Escolar s/n, Ciudad de México 14510, CP, Mexico
| | - Héctor Solís-Chagoyán
- Laboratorio de Neurofarmacología, Instituto Nacional de Psiquiatría “Ramón de la Fuente Muñiz”, Ciudad de México 14370, CP, Mexico; (H.S.-C.); (Z.A.S.-F.)
| | - Zuly A. Sanchez-Florentino
- Laboratorio de Neurofarmacología, Instituto Nacional de Psiquiatría “Ramón de la Fuente Muñiz”, Ciudad de México 14370, CP, Mexico; (H.S.-C.); (Z.A.S.-F.)
| | - Eduardo Calixto
- Departamento de Neurobiología, Dirección de Investigación en Neurociencias, Instituto Nacional de Psiquiatría “Ramón de la Fuente Muñiz”, Ciudad de México 14370, CP, Mexico;
| | - Gloria E. Pérez-Figueroa
- Instituto Nacional de Neurología y Neurocirugía, Unidad Periférica en el Estudio de la Neuroinflamación en Patologías Neurológicas, Ciudad de México 06720, CP, Mexico;
- Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México Federico Gómez, Ciudad de México 06720, CP, Mexico
| | - Rohan Carter
- FRACGP/MBBS, Murchison Outreach Service Mount Magnet Western Australia, Mount Magnet, WA 6530, Australia;
| | - Ruth Jaimez-Melgoza
- Departamento de Farmacología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México 04510, CP, Mexico; (L.M.M.); (R.J.-M.); (B.S.R.-M.)
| | - Bianca S. Romero-Martínez
- Departamento de Farmacología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México 04510, CP, Mexico; (L.M.M.); (R.J.-M.); (B.S.R.-M.)
| | - Edgar Flores-Soto
- Departamento de Farmacología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México 04510, CP, Mexico; (L.M.M.); (R.J.-M.); (B.S.R.-M.)
- Correspondence: ; Tel.: +52-555-6232279
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Chavda VP, Kapadia C, Soni S, Prajapati R, Chauhan SC, Yallapu MM, Apostolopoulos V. A global picture: therapeutic perspectives for COVID-19. Immunotherapy 2022; 14:351-371. [PMID: 35187954 PMCID: PMC8884157 DOI: 10.2217/imt-2021-0168] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 01/19/2022] [Indexed: 02/06/2023] Open
Abstract
The COVID-19 pandemic is a lethal virus outbreak by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which has severely affected human lives and the global economy. The most vital part of the research and development of therapeutic agents is to design drug products to manage COVID-19 efficiently. Numerous attempts have been in place to determine the optimal drug dose and combination of drugs to treat the disease on a global scale. This article documents the information available on SARS-CoV-2 and its life cycle, which will aid in the development of the potential treatment options. A consolidated summary of several natural and repurposed drugs to manage COVID-19 is depicted with summary of current vaccine development. People with high age, comorbity and concomitant illnesses such as overweight, metabolic disorders, pulmonary disease, coronary heart disease, renal failure, fatty liver and neoplastic disorders are more prone to create serious COVID-19 and its consequences. This article also presents an overview of post-COVID-19 complications in patients.
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Affiliation(s)
- Vivek P Chavda
- Department of Pharmaceutics & Pharmaceutical Technology, L.M. College of Pharmacy, Ahmedabad, Gujarat, 380009, India
- Department of Pharmaceutics, K B Institute of Pharmaceutical Education & Research, Kadi Sarva Vishwavidhyalaya, Gandhinagar, Gujarat, 382023, India
| | - Carron Kapadia
- Department of Pharmaceutics & Pharmaceutical Technology, L.M. College of Pharmacy, Ahmedabad, Gujarat, 380009, India
| | - Shailvi Soni
- Department of Pharmaceutics & Pharmaceutical Technology, L.M. College of Pharmacy, Ahmedabad, Gujarat, 380009, India
| | - Riddhi Prajapati
- Department of Pharmaceutics & Pharmaceutical Technology, L.M. College of Pharmacy, Ahmedabad, Gujarat, 380009, India
| | - Subhash C Chauhan
- Department of Immunology & Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78503, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78503, USA
| | - Murali M Yallapu
- Department of Immunology & Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78503, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78503, USA
| | - Vasso Apostolopoulos
- Institute for Health & Sport, Victoria University, Melbourne, VIC, 3030, Australia
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Khiali S, Khani E, B Rouy S, Entezari-Maleki T. Comprehensive review on molnupiravir in COVID-19: a novel promising antiviral to combat the pandemic. Future Microbiol 2022; 17:377-391. [PMID: 35199608 PMCID: PMC8961474 DOI: 10.2217/fmb-2021-0252] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Despite the progress in the management of COVID-19, effective oral antiviral agents are still lacking. In the present review, the potential beneficial effects of molnupiravir in the management of COVID-19 are discussed. A literature search in Google Scholar, Scopus, PubMed and clinicaltrials.gov for the relevant articles regarding the pharmacokinetics, pharmacodynamics and clinical trials of molnupiravir in the management of COVID-19 is conducted. Most of the preclinical studies and available clinical trials showed a favorable short-term safety profile of molnupiravir; however, given its possible genotoxic effects, further trials are required to confirm the long-term efficacy and safety of molnupiravir in patients with COVID-19.
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Affiliation(s)
- Sajad Khiali
- Department of clinical pharmacy, Faculty of pharmacy, Tabriz University of Medical Sciences, Tabriz, 5166414766, Iran
| | - Elnaz Khani
- Department of clinical pharmacy, Faculty of pharmacy, Tabriz University of Medical Sciences, Tabriz, 5166414766, Iran
| | - Samineh B Rouy
- Department of clinical pharmacy, Faculty of pharmacy, Tabriz University of Medical Sciences, Tabriz, 5166414766, Iran
| | - Taher Entezari-Maleki
- Department of clinical pharmacy, Faculty of pharmacy, Tabriz University of Medical Sciences, Tabriz, 5166414766, Iran
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15
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Wang Z, Yang L, Zhao XE. Co-crystallization and structure determination: An effective direction for anti-SARS-CoV-2 drug discovery. Comput Struct Biotechnol J 2021; 19:4684-4701. [PMID: 34426762 PMCID: PMC8373586 DOI: 10.1016/j.csbj.2021.08.029] [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: 03/28/2021] [Revised: 07/29/2021] [Accepted: 08/17/2021] [Indexed: 01/18/2023] Open
Abstract
Safer and more-effective drugs are urgently needed to counter infections with the highly pathogenic SARS-CoV-2, cause of the COVID-19 pandemic. Identification of efficient inhibitors to treat and prevent SARS-CoV-2 infection is a predominant focus. Encouragingly, using X-ray crystal structures of therapeutically relevant drug targets (PLpro, Mpro, RdRp, and S glycoprotein) offers a valuable direction for anti-SARS-CoV-2 drug discovery and lead optimization through direct visualization of interactions. Computational analyses based primarily on MMPBSA calculations have also been proposed for assessing the binding stability of biomolecular structures involving the ligand and receptor. In this study, we focused on state-of-the-art X-ray co-crystal structures of the abovementioned targets complexed with newly identified small-molecule inhibitors (natural products, FDA-approved drugs, candidate drugs, and their analogues) with the assistance of computational analyses to support the precision design and screening of anti-SARS-CoV-2 drugs.
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Key Words
- 3CLpro, 3C-Like protease
- ACE2, angiotensin-converting enzyme 2
- COVID-19, coronavirus disease 2019
- Candidate drugs
- Co-crystal structures
- DyKAT, dynamic kinetic asymmetric transformation
- EBOV, Ebola virus
- EC50, half maximal effective concentration
- EMD, Electron Microscopy Data
- FDA, U.S. Food and Drug Administration
- FDA-approved drugs
- HCoV-229E, human coronavirus 229E
- HPLC, high-performance liquid chromatography
- IC50, half maximal inhibitory concentration
- MD, molecular dynamics
- MERS-CoV, Middle East respiratory syndrome coronavirus
- MMPBSA, molecular mechanics Poisson-Boltzmann surface area
- MTase, methyltransferase
- Mpro, main protease
- Natural products
- Nsp, nonstructural protein
- PDB, Protein Data Bank
- PLpro, papain-like protease
- RTP, ribonucleoside triphosphate
- RdRp, RNA-dependent RNA polymerase
- SAM, S-adenosylmethionine
- SARS-CoV, severe acute respiratory syndrome coronavirus
- SARS-CoV-2
- SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
- SI, selectivity index
- Ugi-4CR, Ugi four-component reaction
- cryo-EM, cryo-electron microscopy
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Affiliation(s)
- Zhonglei Wang
- Key Laboratory of Green Natural Products and Pharmaceutical Intermediates in Colleges and Universities of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, PR China
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, PR China
| | - Liyan Yang
- School of Physics and Physical Engineering, Qufu Normal University, Qufu 273165, PR China
| | - Xian-En Zhao
- Key Laboratory of Green Natural Products and Pharmaceutical Intermediates in Colleges and Universities of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, PR China
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16
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Otava T, Šála M, Li F, Fanfrlík J, Devkota K, Perveen S, Chau I, Pakarian P, Hobza P, Vedadi M, Boura E, Nencka R. The Structure-Based Design of SARS-CoV-2 nsp14 Methyltransferase Ligands Yields Nanomolar Inhibitors. ACS Infect Dis 2021; 7:2214-2220. [PMID: 34152728 PMCID: PMC8265718 DOI: 10.1021/acsinfecdis.1c00131] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Indexed: 12/23/2022]
Abstract
In this study, we have focused on the structure-based design of the inhibitors of one of the two SARS-CoV-2 methyltransferases (MTases), nsp14. This MTase catalyzes the transfer of the methyl group from S-adenosyl-l-methionine (SAM) to cap the guanosine triphosphate moiety of the newly synthesized viral RNA, yielding the methylated capped RNA and S-adenosyl-l-homocysteine (SAH). As the crystal structure of SARS-CoV-2 nsp14 is unknown, we have taken advantage of its high homology to SARS-CoV nsp14 and prepared its homology model, which has allowed us to identify novel SAH derivatives modified at the adenine nucleobase as inhibitors of this important viral target. We have synthesized and tested the designed compounds in vitro and shown that these derivatives exert unprecedented inhibitory activity against this crucial enzyme. The docking studies nicely explain the contribution of an aromatic part attached by a linker to the position 7 of the 7-deaza analogues of SAH.
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Affiliation(s)
- Tomáš Otava
- Institute of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, v.v.i., Gilead Sciences Research Centre at the IOCB
Prague, Flemingovo nam. 2., 166 10 Prague 6, Czech
Republic
- Faculty of Food and Biochemical Technology,
University of Chemistry and Technology, 166 28, Prague 6,
Czech Republic
| | - Michal Šála
- Institute of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, v.v.i., Gilead Sciences Research Centre at the IOCB
Prague, Flemingovo nam. 2., 166 10 Prague 6, Czech
Republic
| | - Fengling Li
- Structural Genomics Consortium, and
Department of Pharmacology and Toxicology, University of
Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, v.v.i., Gilead Sciences Research Centre at the IOCB
Prague, Flemingovo nam. 2., 166 10 Prague 6, Czech
Republic
| | - Kanchan Devkota
- Structural Genomics Consortium, and
Department of Pharmacology and Toxicology, University of
Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Sumera Perveen
- Structural Genomics Consortium, and
Department of Pharmacology and Toxicology, University of
Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Irene Chau
- Structural Genomics Consortium, and
Department of Pharmacology and Toxicology, University of
Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Paknoosh Pakarian
- Structural Genomics Consortium, and
Department of Pharmacology and Toxicology, University of
Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, v.v.i., Gilead Sciences Research Centre at the IOCB
Prague, Flemingovo nam. 2., 166 10 Prague 6, Czech
Republic
| | - Masoud Vedadi
- Structural Genomics Consortium, and
Department of Pharmacology and Toxicology, University of
Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, v.v.i., Gilead Sciences Research Centre at the IOCB
Prague, Flemingovo nam. 2., 166 10 Prague 6, Czech
Republic
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, v.v.i., Gilead Sciences Research Centre at the IOCB
Prague, Flemingovo nam. 2., 166 10 Prague 6, Czech
Republic
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17
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Sulimov AV, Shikhaliev KS, Pyankov OV, Shcherbakov DN, Chirkova VY, Ilin IS, Kutov DC, Tashchilova AS, Krysin MY, Krylskiy DV, Stolpovskaya NV, Volosnikova EA, Belenkaya SV, Sulimov VB. [Development of antiviral drugs based on inhibitors of the SARS-COV-2 main protease]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2021; 67:259-267. [PMID: 34142533 DOI: 10.18097/pbmc20216703259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Docking and quantum-chemical methods have been used for screening of drug-like compounds from the own database of the Voronezh State University to find inhibitors the SARS-CoV-2 main protease, an important enzyme of the coronavirus responsible for the COVID-19 pandemic. Using the SOL program more than 42000 3D molecular structures were docked into the active site of the main protease, and more than 1000 ligands with most negative values of the SOL score were selected for further processing. For all these top ligands, the protein-ligand binding enthalpy has been calculated using the PM7 semiempirical quantum-chemical method with the COSMO implicit solvent model. 20 ligands with the most negative SOL scores and the most negative binding enthalpies have been selected for further experimental testing. The latter has been made by measurements of the inhibitory activity against the main protease and suppression of SARS-CoV-2 replication in a cell culture. The inhibitory activity \of the compounds was determined using a synthetic fluorescently labeled peptide substrate including the proteolysis site of the main protease. The antiviral activity was tested against SARS-CoV-2 virus in the Vero cell culture. Eight compounds showed inhibitory activity against the main protease of SARS-CoV-2 in the submicromolar and micromolar ranges of the IC50 values. Three compounds suppressed coronavirus replication in the cell culture at the micromolar range of EC50 values and had low cytotoxicity. The found chemically diverse inhibitors can be used for optimization in order to obtain a leader compound, the basis of new direct-acting antiviral drugs against the SARS-CoV-2 coronavirus.
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Affiliation(s)
- A V Sulimov
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russia; Dimonta Ltd., Moscow, Russia
| | | | - O V Pyankov
- State Research Centre of Virology and Biotechnology "Vector", Koltsovo, Russia
| | - D N Shcherbakov
- State Research Centre of Virology and Biotechnology "Vector", Koltsovo, Russia; Altai State University, Barnaul, Russia
| | | | - I S Ilin
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russia; Dimonta Ltd., Moscow, Russia
| | - D C Kutov
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russia; Dimonta Ltd., Moscow, Russia
| | - A S Tashchilova
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russia; Dimonta Ltd., Moscow, Russia
| | | | | | | | - E A Volosnikova
- State Research Centre of Virology and Biotechnology "Vector", Koltsovo, Russia
| | - S V Belenkaya
- State Research Centre of Virology and Biotechnology "Vector", Koltsovo, Russia; Novosibirsk State University, Novosibirsk, Russia
| | - V B Sulimov
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russia; Dimonta Ltd., Moscow, Russia
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18
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Singh N, Villoutreix BO. Resources and computational strategies to advance small molecule SARS-CoV-2 discovery: Lessons from the pandemic and preparing for future health crises. Comput Struct Biotechnol J 2021; 19:2537-2548. [PMID: 33936562 PMCID: PMC8074526 DOI: 10.1016/j.csbj.2021.04.059] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/22/2021] [Accepted: 04/24/2021] [Indexed: 12/11/2022] Open
Abstract
There is an urgent need to identify new therapies that prevent SARS-CoV-2 infection and improve the outcome of COVID-19 patients. This pandemic has thus spurred intensive research in most scientific areas and in a short period of time, several vaccines have been developed. But, while the race to find vaccines for COVID-19 has dominated the headlines, other types of therapeutic agents are being developed. In this mini-review, we report several databases and online tools that could assist the discovery of anti-SARS-CoV-2 small chemical compounds and peptides. We then give examples of studies that combined in silico and in vitro screening, either for drug repositioning purposes or to search for novel bioactive compounds. Finally, we question the overall lack of discussion and plan observed in academic research in many countries during this crisis and suggest that there is room for improvement.
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Affiliation(s)
- Natesh Singh
- Université de Paris, Inserm UMR 1141 NeuroDiderot, Robert-Debré Hospital, 75019 Paris, France
| | - Bruno O. Villoutreix
- Université de Paris, Inserm UMR 1141 NeuroDiderot, Robert-Debré Hospital, 75019 Paris, France
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Sulimov AV, Ilin IS, Kutov DC, Stolpovskaya NV, Shikhaliev KS, Sulimov VB. Supercomputing, Docking and Quantum Mechanics in Quest for Inhibitors of Papain-like Protease of SARS-CoV-2. LOBACHEVSKII JOURNAL OF MATHEMATICS 2021; 42. [PMCID: PMC8351772 DOI: 10.1134/s1995080221070222] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Lomonosov-2 supercomputer is used to search for new organic compounds that can suppress the replication of the SARS-CoV-2 coronavirus. The latter is responsible for the COVID-19 pandemic. Docking and a quantum-chemical semiempirical atomistic modeling method are used to find inhibitors of the SARS-CoV-2 papain-like protease, which is one of the key coronavirus enzymes responsible for its replication. The atomistic model of the papain-like protease of this coronavirus is based on the high-resolution structure deposited in the Protein Data Bank. The SOL docking program has been used for virtual screening of more than \documentclass[12pt]{minimal}
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\begin{document}$$40000$$\end{document} low molecular weight molecules (ligands). Ligands with the highest protein-ligand binding energy, selected using the docking results, were subjected to quantum-chemical calculations. The latters are performed by the PM7 semiempirical method with the COSMO implicit solvent model using the MOPAC program. The enthalpy of protein-ligand binding is calculated for the best position of the ligand in the protein. \documentclass[12pt]{minimal}
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\begin{document}$$19$$\end{document} ligands were selected for experimental in vitro testing as candidates for papain-like protease inhibitors base on docking and quantum-chemical results. In case of experimental confirmation, these compounds may become the basis for direct-acting antiviral drugs for the SARS-CoV-2 coronavirus.
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Affiliation(s)
- A. V. Sulimov
- Research Computing Center of Lomonosov Moscow State University, 119234 Moscow, Russia
- Moscow Center of Fundamental and Applied Mathematics, 119234 Moscow, Russia
| | - I. S. Ilin
- Research Computing Center of Lomonosov Moscow State University, 119234 Moscow, Russia
- Moscow Center of Fundamental and Applied Mathematics, 119234 Moscow, Russia
| | - D. C. Kutov
- Research Computing Center of Lomonosov Moscow State University, 119234 Moscow, Russia
- Moscow Center of Fundamental and Applied Mathematics, 119234 Moscow, Russia
| | - N. V. Stolpovskaya
- Department of Organic Chemistry, Faculty of Chemistry, Voronezh State University, 394006 Voronezh, Russia
| | - Kh. S. Shikhaliev
- Department of Organic Chemistry, Faculty of Chemistry, Voronezh State University, 394006 Voronezh, Russia
| | - V. B. Sulimov
- Research Computing Center of Lomonosov Moscow State University, 119234 Moscow, Russia
- Moscow Center of Fundamental and Applied Mathematics, 119234 Moscow, Russia
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