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Chen CY, Wang WJ, Wu CS, Wang SC, Chang WC, Hung MC. Tannic acids and proanthocyanidins in tea inhibit SARS-CoV-2 variants infection. Am J Cancer Res 2024; 14:2555-2569. [PMID: 38859869 PMCID: PMC11162682 DOI: 10.62347/qjbg3026] [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: 04/17/2024] [Accepted: 05/15/2024] [Indexed: 06/12/2024] Open
Abstract
The COVID-19 pandemic has caused hundreds million cases and millions death as well as continues to infect human life in the world since late of 2019. The breakthrough infection caused from mutation of SARS-CoV-2 is rising even the vaccinated population has been increasing. Currently, the severe threat posed by SARS-CoV-2 has been alleviated worldwide, and the situation has transitioned to coexisting with the virus. The dietary food with antiviral activities may improve to prevent virus infection for living with COVID-19 pandemic. Teas containing enriched phenolic ingredients such as tannins have been reported to be antitumor agents as well as be good inhibitors for coronavirus. This study developed a highly sensitive and selective ultra-high performance liquid chromatography-high resolution mass spectrometric method for quantification of tannic acids, a hydrolysable tannin, and proanthocyanidins, a condense tannin, in teas with different levels of fermentation. The in vitro pseudoviral particles (Vpp) infection assay was used to evaluate the inhibition activities of various teas. The results of current research demonstrate that the tannins in teas are effective inhibitors against infection of SARS-CoV-2 and its variants.
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Affiliation(s)
- Chung-Yu Chen
- Research Center for Cancer Biology, China Medical UniversityTaichung 406040, Taiwan
| | - Wei-Jan Wang
- Research Center for Cancer Biology, China Medical UniversityTaichung 406040, Taiwan
- Department of Biological Science and Technology, China Medical UniversityTaichung 406040, Taiwan
| | - Chen-Shiou Wu
- Research Center for Cancer Biology, China Medical UniversityTaichung 406040, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical UniversityTaichung 406040, Taiwan
| | - Shao-Chun Wang
- Research Center for Cancer Biology, China Medical UniversityTaichung 406040, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical UniversityTaichung 406040, Taiwan
- Center for Molecular Medicine, China Medical University Hospital, China Medical UniversityTaichung 406040, Taiwan
- Cancer Biology and Precision Therapeutics Center, China Medical University Hospital, China Medical UniversityTaichung 406040, Taiwan
- Department of Biotechnology, Asia UniversityTaichung 413305, Taiwan
| | - Wei-Chao Chang
- Center for Molecular Medicine, China Medical University Hospital, China Medical UniversityTaichung 406040, Taiwan
| | - Mien-Chie Hung
- Research Center for Cancer Biology, China Medical UniversityTaichung 406040, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical UniversityTaichung 406040, Taiwan
- Center for Molecular Medicine, China Medical University Hospital, China Medical UniversityTaichung 406040, Taiwan
- Cancer Biology and Precision Therapeutics Center, China Medical University Hospital, China Medical UniversityTaichung 406040, Taiwan
- Institute of Biochemistry and Molecular Biology, China Medical University Hospital, China Medical UniversityTaichung 406040, Taiwan
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Hu C. Marine natural products and human immunity: novel biomedical resources for anti-infection of SARS-CoV-2 and related cardiovascular disease. NATURAL PRODUCTS AND BIOPROSPECTING 2024; 14:12. [PMID: 38282092 PMCID: PMC10822835 DOI: 10.1007/s13659-024-00432-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 01/17/2024] [Indexed: 01/30/2024]
Abstract
Marine natural products (MNPs) and marine organisms include sea urchin, sea squirts or ascidians, sea cucumbers, sea snake, sponge, soft coral, marine algae, and microalgae. As vital biomedical resources for the discovery of marine drugs, bioactive molecules, and agents, these MNPs have bioactive potentials of antioxidant, anti-infection, anti-inflammatory, anticoagulant, anti-diabetic effects, cancer treatment, and improvement of human immunity. This article reviews the role of MNPs on anti-infection of coronavirus, SARS-CoV-2 and its major variants (such as Delta and Omicron) as well as tuberculosis, H. Pylori, and HIV infection, and as promising biomedical resources for infection related cardiovascular disease (irCVD), diabetes, and cancer. The anti-inflammatory mechanisms of current MNPs against SARS-CoV-2 infection are also discussed. Since the use of other chemical agents for COVID-19 treatment are associated with some adverse effects in cardiovascular system, MNPs have more therapeutic advantages. Herein, it's time to protect this ecosystem for better sustainable development in the new era of ocean economy. As huge, novel and promising biomedical resources for anti-infection of SARS-CoV-2 and irCVD, the novel potential mechanisms of MNPs may be through multiple targets and pathways regulating human immunity and inhibiting inflammation. In conclusion, MNPs are worthy of translational research for further clinical application.
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Affiliation(s)
- Chunsong Hu
- Department of Cardiovascular Medicine, Jiangxi Academy of Medical Science, Nanchang University, Hospital of Nanchang University, No. 461 Bayi Ave, Nanchang, 330006, Jiangxi, China.
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Mandal SK, Rehman MDMU, Katyal A, Rajvanshi K, Kannan M, Garg M, Murugesan S, Deepa P. In silico anti-viral assessment of phytoconstituents in a traditional (Siddha Medicine) polyherbal formulation - Targeting Mpro and pan-coronavirus post-fusion Spike protein. J Tradit Complement Med 2024; 14:55-69. [PMID: 38223813 PMCID: PMC10785248 DOI: 10.1016/j.jtcme.2023.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 06/16/2023] [Accepted: 07/06/2023] [Indexed: 01/16/2024] Open
Abstract
Background and aim Novel nature of the viral pathogen SARS-CoV-2 and the absence of standard drugs for treatment, have been a major challenge to combat this deadly infection. Natural products offer safe and effective remedy, for which traditional ethnic medicine can provide leads. An indigenous poly-herbal formulation, Kabasura Kudineer from Siddha system of medicine was evaluated here using a combination of computational approaches, to identify potential inhibitors against two anti-SARS-CoV-2 targets - post-fusion Spike protein (structural protein) and main protease (Mpro, non-structural protein). Experimental procedure We docked 32 phytochemicals from the poly-herbal formulation against viral post-fusion Spike glycoprotein and Mpro followed by molecular dynamics using Schrodinger software. Drug-likeness analysis was performed using machine learning (ML) approach and pkCSM. Results The binding affinity of the phytochemicals in Kabasura Kudineer revealed the following top-five bioactives: Quercetin > Luteolin > Chrysoeriol > 5-Hydroxy-7,8-Dimethoxyflavone > Scutellarein against Mpro target, and Gallic acid > Piperlonguminine > Chrysoeriol > Elemol > Piperine against post-fusion Spike protein target. Quercetin and Gallic acid exhibited binding stability in complexation with their respective viral-targets and favourable free energy change as revealed by the molecular dynamics simulations and MM-PBSA analysis. In silico predicted pharmacokinetic profiling of these ligands revealed appropriate drug-likeness properties. Conclusion These outcomes provide: (a) potential mechanism for the anti-viral efficacy of the indigenous Siddha formulation, targeting Mpro and post-fusion Spike protein (b) top bioactive lead-molecules that may be developed as natural product-based anti-viral pharmacotherapy and their pleiotropic protective effects may be leveraged to manage co-morbidities associated with COVID-19.
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Affiliation(s)
- Sumit Kumar Mandal
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS Pilani), Pilani Campus, Pilani, 333031, Rajasthan, India
| | - MD Muzaffar-Ur Rehman
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani, 333031, Rajasthan, India
| | - Ashish Katyal
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS Pilani), Pilani Campus, Pilani, 333031, Rajasthan, India
| | - Kanishk Rajvanshi
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS Pilani), Pilani Campus, Pilani, 333031, Rajasthan, India
| | - Manoj Kannan
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS Pilani), Pilani Campus, Pilani, 333031, Rajasthan, India
- Plaksha University, SAS Nagar, Mohali, 140306, Punjab, India
| | - Mohit Garg
- Department of Chemical Engineering, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani, 333031, Rajasthan, India
| | - Sankaranarayanan Murugesan
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani, 333031, Rajasthan, India
| | - P.R. Deepa
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS Pilani), Pilani Campus, Pilani, 333031, Rajasthan, India
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Singh R, Purohit R. Multi-target approach against SARS-CoV-2 by stone apple molecules: A master key to drug design. Phytother Res 2024; 38:7-10. [PMID: 36786431 DOI: 10.1002/ptr.7772] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/21/2022] [Accepted: 01/23/2023] [Indexed: 02/15/2023]
Affiliation(s)
- Rahul Singh
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, India
- Biotechnology Division, CSIR-IHBT, Palampur, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, India
| | - Rituraj Purohit
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, India
- Biotechnology Division, CSIR-IHBT, Palampur, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, India
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Mushebenge AGA, Ugbaja SC, Mbatha NA, B. Khan R, Kumalo HM. Assessing the Potential Contribution of In Silico Studies in Discovering Drug Candidates That Interact with Various SARS-CoV-2 Receptors. Int J Mol Sci 2023; 24:15518. [PMID: 37958503 PMCID: PMC10647470 DOI: 10.3390/ijms242115518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
The COVID-19 pandemic has spurred intense research efforts to identify effective treatments for SARS-CoV-2. In silico studies have emerged as a powerful tool in the drug discovery process, particularly in the search for drug candidates that interact with various SARS-CoV-2 receptors. These studies involve the use of computer simulations and computational algorithms to predict the potential interaction of drug candidates with target receptors. The primary receptors targeted by drug candidates include the RNA polymerase, main protease, spike protein, ACE2 receptor, and transmembrane protease serine 2 (TMPRSS2). In silico studies have identified several promising drug candidates, including Remdesivir, Favipiravir, Ribavirin, Ivermectin, Lopinavir/Ritonavir, and Camostat Mesylate, among others. The use of in silico studies offers several advantages, including the ability to screen a large number of drug candidates in a relatively short amount of time, thereby reducing the time and cost involved in traditional drug discovery methods. Additionally, in silico studies allow for the prediction of the binding affinity of the drug candidates to target receptors, providing insight into their potential efficacy. This study is aimed at assessing the useful contributions of the application of computational instruments in the discovery of receptors targeted in SARS-CoV-2. It further highlights some identified advantages and limitations of these studies, thereby revealing some complementary experimental validation to ensure the efficacy and safety of identified drug candidates.
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Affiliation(s)
- Aganze Gloire-Aimé Mushebenge
- Discipline of Pharmaceutical Sciences, University of KwaZulu-Natal, Westville, Durban 4000, South Africa;
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa
- Faculty of Pharmaceutical Sciences, University of Lubumbashi, Lubumbashi 1825, Democratic Republic of the Congo
| | - Samuel Chima Ugbaja
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa
- Africa Health Research Institute, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Nonkululeko Avril Mbatha
- KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Rene B. Khan
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Hezekiel M. Kumalo
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa
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Azimi S, Merza MS, Ghasemi F, Dhahi HA, Baradarbarjastehbaf F, Moosavi M, Kargar PG, Len C. Green and rapid and instrumental one-pot method for the synthesis of imidazolines having potential anti-SARS-CoV-2 main protease activity. SUSTAINABLE CHEMISTRY AND PHARMACY 2023; 34:101136. [PMID: 37333050 PMCID: PMC10239909 DOI: 10.1016/j.scp.2023.101136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/02/2023] [Accepted: 05/25/2023] [Indexed: 06/20/2023]
Abstract
The Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) is responsible for ongoing epidemics in humans and some other mammals and has been declared a public health emergency of international concern. In this project, several small non-peptide molecules were synthesized to inhibit the major proteinase (Mpro) of SARS-CoV-2 using rational strategies of drug design and medicinal chemistry. Mpro is a key enzyme of coronaviruses and plays an essential role in mediating viral replication and transcription in human lung epithelial and stem cells, making it an attractive drug target for SARS-CoV. The antiviral potential of imidazoline derivatives as inhibitors of (SARS-CoV-2) Mpro was evaluated using in-silico techniques such as molecular docking simulation, molecular dynamics (MD), and ADMET prediction. The docking scores of these imidazoline derivatives were compared to that of the N3 crystal inhibitor and showed that most of these compounds, particularly compound E07, interacted satisfactorily in the active site of the coronavirus and strongly interacted with the residues (Met 165, Gln 166, Met 165, His 41, and Gln 189). Furthermore, the results were confirmed by MD simulations after exposure to long-term MD simulations and ADMET predictions.
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Affiliation(s)
- Sabikeh Azimi
- Department of Chemistry, Faculty of Sciences, University of Birjand, Birjand, 97175-615, Iran
| | - Muna S Merza
- Prosthetic Dental Techniques Department, Al-Mustaqbal University College, Babylon, 51001, Iraq
| | - Fatemeh Ghasemi
- MSC in Software Engineering, Kowsar, The Institute of Higher Education, Ministry of Science, Research and Technology, Computer Engineering Department, Qazvin, Iran
| | - Hasan Ali Dhahi
- National University of Science and Technology, Dhi Qar, Iraq
| | - Farid Baradarbarjastehbaf
- Faculty of Pharmacy, Department of Pharmaceutical Technology and Biopharmacy, University of Pécs, Pécs, Hungary
| | - Mehdi Moosavi
- Department of Chemistry, Faculty of Chemistry, Mazandaran University, Babolsar, Iran
| | - Pouya Ghamari Kargar
- Department of Chemistry, Faculty of Sciences, University of Birjand, Birjand, 97175-615, Iran
| | - Christophe Len
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, 11 Rue Pierre et Marie Curie, F-75005, Paris, France
- Sorbonne Universités, Universite de Technologie de Compiegne, F- 60200, Compiegne, France
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Rajan M, Prabhakaran S, Prusty JS, Chauhan N, Gupta P, Kumar A. Phytochemicals of Cocculus hirsutus deciphered SARS-CoV-2 inhibition by targeting main proteases in molecular docking, simulation, and pharmacological analyses. J Biomol Struct Dyn 2023; 41:7406-7420. [PMID: 36099182 DOI: 10.1080/07391102.2022.2121758] [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: 04/27/2022] [Accepted: 08/31/2022] [Indexed: 10/14/2022]
Abstract
The COVID-19 pandemic is spreading rapidly due to the outbreak of novel coronavirus SARS-CoV-2 across the globe. Anti-COVID-19 drugs are urgently required in this situation. In this regard, the discovery of promising new anti-COVID-19 moieties is expected from traditional medicine. The study is aimed to discover phytochemicals of Cocculus hirsutus having anti-COVID-19 activity via inhibiting main proteases of SARS-CoV-2. Main proteases (Mpro) of SARS-CoV-2 serve as a protuberant target for anti-COVID-19 drug discovery because it is a key enzyme of coronaviruses and has a pivotal role in mediating viral replication and transcription that makes it an attractive drug target. Recent studies indicated the utility of C. hirsutus in the treatment of viral disorders like Dengue. Phytochemicals from C. hirsutus were docked against SARS-CoV-2 main proteases (6LU7, 5R7Y, 5R7Z, 5R80, 5R81, 5R82) using the PyRx virtual screen tool and discovery studio visualizer. Further, molecular dynamics simulations were performed (for 100 ns) to see conformational stability for all complexes. Pharmacokinetic properties and drug-likeness prediction of selected C. hirsutus phytoconstituents were also performed. Betulin, coclaurine, and quinic acid of C. hirsutus were found promising with significant binding affinity to SARS-CoV-2 Mpro in comparison to control. They have shown stable interactions with the amino acid residues present on the active site of most of the SARS-CoV-2 Mpro and were found as promising anti-COVID-19 candidates. These compounds could be potential leads for the development of target-specific anti-COVID-19 therapeutics while ethnomedicinal uses of this herb could further needed for its detailed antiviral therapeutic exploration.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mariappan Rajan
- Department of Natural Product Chemistry, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - Selvakani Prabhakaran
- Department of Natural Product Chemistry, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - Jyoti Sankar Prusty
- Department of Biotechnology, National Institute of Technology, Raipur, Chhattisgarh, India
| | - Nagendra Chauhan
- Drugs testing LaboratoryAvam Anusandhan Kendra, NPA Government Ayurved College, Raipur, Chhattisgarh, India
| | - Prashant Gupta
- Ayurinformatics Lab, Department of Kaumarbhritya, All India Institute of Ayurveda, New Delhi, India
| | - Awanish Kumar
- Department of Biotechnology, National Institute of Technology, Raipur, Chhattisgarh, India
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Guo X, Lin Y, He F, Jin Y, Chen S, Li T, Wu C, Zhang L, Chen X. Identification of active compounds of traditional chinese medicine derived from maxing shigan decoction for COVID-19 treatment: a meta-analysis and in silico study. Expert Rev Anti Infect Ther 2023; 21:871-889. [PMID: 37481738 DOI: 10.1080/14787210.2023.2238899] [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: 03/01/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023]
Abstract
BACKGROUND Coronavirus 2019 (COVID-19) poses a serious threat to human health. In China, traditional Chinese medicine (TCM), mainly based on the Maxing Shigan decoction (MXSGD), is used in conjunction with western medicine to treat COVID-19. RESEARCH DESIGN AND METHODS We conducted a network meta-analysis to investigate whether MXSGD-related TCM combined with western medicine is more effective in treating COVID-19 compared to western medicine alone. Additionally, using network pharmacology, cross-docking, and molecular dynamics (MD) simulation to explore the potential active compounds and possible targets underlying the therapeutic effects of MXSGD-related TCM. RESULTS MXSGD-related TCM combined with western medicine was better for treating COVID-19 compared to western medicine alone. Network pharmacological analysis identified 43 shared ingredients in the MXSGD-related TCM prescriptions and 599 common target genes. Cross-docking of the 43 compounds with 154 proteins that matched these genes led to the identification of 60 proteins. Pathway profiling revealed that the active ingredients participated in multiple signaling pathways that contribute to their efficacy. Molecular docking and MD simulation demonstrated that MOL007214, the most promising molecule, could stably bind to the active site of SARS-CoV-2 3CLpro. CONCLUSION This study demonstrates the important role of MXSGD-related TCM in the treatment of COVID-19.
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Affiliation(s)
- Xiaodan Guo
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Yihua Lin
- Department of Respiratory and Critical Care Medicine, School of Medicine, Xiamen University, Xiamen, China
| | - Fengming He
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Ying Jin
- Department of Cardiology, Xiamen Key Laboratory of Cardiac Electrophysiology, Xiamen Institute of Cardiovascular Diseases, School of Medicine, Xiamen University, Xiamen, China
| | - Simian Chen
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Ting Li
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Caisheng Wu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Lin Zhang
- School of Population Medicine and Public Health, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xueqin Chen
- Department of Traditional Chinese Medicine, School of Medicine, Xiamen University, Xiamen, China
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Molecular modeling and simulations of some antiviral drugs, benzylisoquinoline alkaloid, and coumarin molecules to investigate the effects on Mpro main viral protease inhibition. Biochem Biophys Rep 2023; 34:101459. [PMID: 36987522 PMCID: PMC10037929 DOI: 10.1016/j.bbrep.2023.101459] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/26/2023] Open
Abstract
Background SARS-CoV-2 is a deadly viral disease and uncounted deaths occurs since its first appearance in the year 2019. The antiviral drugs, benzylisoquinoline alkaloids, and coumarin molecules were searched using different online engines for drug repurposing with SARS-CoV-2 and to investigate the effects on main viral protease (Mpro) upon their bindings. Methods A database composed of antiviral drugs, benzylisoquinoline alkaloids, and Coumarin molecules was screened through a molecular docking strategy to uncover the interactions of collected molecules with SARS-CoV-2 Mpro. Further, molecular dynamics simulations (MDS) were implemented for 100 ns to calculate the stability of the best complexed molecular scaffold with Mpro. The conformations of the simulated complexes were investigated by using principal component analysis (PCA) and Gibbs energy landscape (FEL) and DSSP together. Next, free binding energy (ΔGbind) was calculated using the mmpbsa method. Results Molecular docking simulations demonstrate 17 molecules exhibited better binding affinity out of 99 molecules present in the database with the viral protease Mpro, followed ADMET properties and were documented. The Coumarin-EM04 molecular scaffold exhibited interactions with catalytical dyad HIS41, CYS145, and neighboring amino acids SER165 and GLN189 in the catalytical site. The crucial factor RMSD was calculated to determine the orientations of Coumarin-EM04. The Coumarin-EM04 complexed with Mpro was found stable in the binding site during MDS. Furthermore, the free energy binding ΔGbind of Coumarin-EM04 was found to be −187.471 ± 2.230 kJ/mol, and for Remdesivir ΔGbind was −171.926 ± 2.237 kJ/mol with SARS-CoV-2 Mpro. Conclusion In this study, we identify potent molecules that exhibit interactions with catalytical dyad HIS41 and CYS145 amino acids and unravel Coumarin-EM04 exhibited ΔGbind higher than Remdesivir against Mpro and thus may serve better antiviral agent against SARS-CoV-2.
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Rampogu S, Jung TS, Ha MW, Lee KW. Repurposing and computational design of PARP inhibitors as SARS-CoV-2 inhibitors. Sci Rep 2023; 13:10583. [PMID: 37386052 PMCID: PMC10310815 DOI: 10.1038/s41598-023-36342-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 06/01/2023] [Indexed: 07/01/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a recent pandemic that caused serious global emergency. To identify new and effective therapeutics, we employed a drug repurposing approach. The poly (ADP ribose) polymerase inhibitors were used for this purpose and were repurposed against the main protease (Mpro) target of severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2). The results from these studies were used to design compounds using the 'Grow Scaffold' modules available on Discovery Studio v2018. The three designed compounds, olaparib 1826 and olaparib 1885, and rucaparib 184 demonstrated better CDOCKER docking scores for Mpro than their parent compounds. Moreover, the compounds adhered to Lipinski's rule of five and demonstrated a synthetic accessibility score of 3.55, 3.63, and 4.30 for olaparib 1826, olaparib 1885, and rucaparib 184, respectively. The short-range Coulombic and Lennard-Jones potentials also support the potential binding of the modified compounds to Mpro. Therefore, we propose these three compounds as novel SARS-CoV-2 inhibitors.
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Affiliation(s)
- Shailima Rampogu
- Department of Bio and Medical Big Data (BK4 Program), Division of Life Sciences, Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), Jinju, Republic of Korea.
| | - Tae Sung Jung
- Laboratory of Aquatic Animal Diseases, College of Veterinary Medicine, Research Institute of Natural Science, Gyeongsang National University, Jinju, 52828, Republic of Korea.
| | - Min Woo Ha
- Interdisciplinary Graduate Program in Advanced Convergence Technology and Science, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, Republic of Korea.
| | - Keun Woo Lee
- Department of Bio and Medical Big Data (BK4 Program), Division of Life Sciences, Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), Jinju, Republic of Korea.
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Bhat S, Pradeep S, Patil SS, Flores-Holguín N, Glossman-Mitnik D, Frau J, Sommano SR, Ali N, Mohany M, Shivamallu C, Prasad SK, Kollur SP. Preliminary Evaluation of Lablab purpureus Phytochemicals for Anti-BoHV-1 Activity Using In Vitro and In Silico Approaches. ACS OMEGA 2023; 8:22684-22697. [PMID: 37396248 PMCID: PMC10308559 DOI: 10.1021/acsomega.3c01478] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 05/31/2023] [Indexed: 07/04/2023]
Abstract
Lablab purpureus from the Fabaceae family has been reported to have antiviral properties and used in traditional medical systems like ayurveda and Chinese medicine and has been employed to treat a variety of illnesses including cholera, food poisoning, diarrhea, and phlegmatic diseases. The bovine alphaherpesvirus-1 (BoHV-1) is notorious for causing significant harm to the veterinary and agriculture industries. The removal of the contagious BoHV-1 from host organs, particularly in those reservoir creatures, has required the use of antiviral drugs that target infected cells. This study developed LP-CuO NPs from methanolic crude extracts, and FTIR, SEM, and EDX analyses were used to confirm their formation. SEM analysis revealed that the LP-CuO NPs had a spherical shape with particle sizes between 22 and 30 nm. Energy-dispersive X-ray pattern analysis revealed the presence of only copper and oxide ions. By preventing viral cytopathic effects in the Madin-Darby bovine kidney cell line, the methanolic extract of Lablab purpureus and LP-CuO NPs demonstrated a remarkable dose-dependent anti-BoHV-1 action in vitro. Furthermore, molecular docking and molecular dynamics simulation studies of bio-actives from Lablab purpureus against the BoHV-1 viral envelope glycoprotein disclosed effective interactions between all phytochemicals and the protein, although kievitone was found to have the highest binding affinity, with the greatest number of interactions, which was also validated with molecular dynamics simulation studies. Understanding the chemical reactivity qualities of the four ligands was taken into consideration facilitated by the global and local descriptors, which aimed to predict the chemical reactivity descriptors of the studied molecules through the conceptual DFT methodology, which, along with ADMET finding, support the in vitro and in silico results.
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Affiliation(s)
- Smitha
S. Bhat
- Department
of Biotechnology and Bioinformatics, JSS
Academy of Higher Education and Research, Mysuru 570 015, India
| | - Sushma Pradeep
- Department
of Biotechnology and Bioinformatics, JSS
Academy of Higher Education and Research, Mysuru 570 015, India
| | - Sharanagouda S. Patil
- ICAR-National
Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru 560 064, India
| | - Norma Flores-Holguín
- Laboratorio
Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua, Chihuahua 31136, Mexico
| | - Daniel Glossman-Mitnik
- Laboratorio
Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua, Chihuahua 31136, Mexico
| | - Juan Frau
- Departament
de Química, Facultat de Ciences, Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain
| | - Sarana Rose Sommano
- Plant
Bioactive Compound Laboratory, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Nemat Ali
- Department
of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohamed Mohany
- Department
of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Chandan Shivamallu
- Department
of Biotechnology and Bioinformatics, JSS
Academy of Higher Education and Research, Mysuru 570 015, India
| | - Shashanka K. Prasad
- Department
of Biotechnology and Bioinformatics, JSS
Academy of Higher Education and Research, Mysuru 570 015, India
- Plant
Bioactive Compound Laboratory, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Shiva Prasad Kollur
- School
of Physical Sciences, Amrita Vishwa Vidyapeetham,
Mysuru Campus, Mysuru, Karnataka 570 026, India
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12
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Choudhary P, Singh T, Amod A, Singh S. Evaluation of phytoconstituents of Tinospora cordifolia against K417N and N501Y mutant spike glycoprotein and main protease of SARS-CoV-2- an in silico study. J Biomol Struct Dyn 2023; 41:4106-4123. [PMID: 35467486 DOI: 10.1080/07391102.2022.2062787] [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: 12/02/2021] [Accepted: 04/02/2022] [Indexed: 10/18/2022]
Abstract
Coronavirus disease 2019 (COVID-19) caused appalling conditions over the globe, which is currently faced by the entire human population. One of the primary reasons behind the uncontrollable situation is the lack of specific therapeutics. In such conditions, drug repurposing of available drugs (viz. Chloroquine, Lopinavir, etc.) has been proposed, but various clinical and preclinical investigations indicated the toxicity and adverse side effects of these drugs. This study explores the inhibition potency of phytochemicals from Tinospora cordifolia (Giloy) against SARS CoV-2 drugable targets (spike glycoprotein and Mpro proteins) using molecular docking and MD simulation studies. ADMET, virtual screening, MD simulation, postsimulation analysis (RMSD, RMSF, Rg, SASA, PCA, FES) and MM-PBSA calculations were carried out to predict the inhibition efficacy of the phytochemicals against SARS CoV-2 targets. Tinospora compounds showed better binding affinity than the corresponding reference. Their binding affinity ranges from -9.63 to -5.68 kcal/mole with spike protein and -10.27 to -7.25 kcal/mole with main protease. Further 100 ns exhaustive simulation studies and MM-PBSA calculations supported favorable and stable binding of them. This work identifies Nine Tinospora compounds as potential inhibitors. Among those, 7-desacetoxy-6,7-dehydrogedunin was found to inhibit both spike (7NEG) and Mpro (7MGS and 6LU7) proteins, and Columbin was found to inhibit selected spike targets (7NEG and 7NX7). In all the analyses, these compounds performed well and confirms the stable binding. Hence the identified compounds, advocated as potential inhibitors can be taken for further in vitro and in vivo experimental validation to determine their anti-SARS-CoV-2 potential.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Princy Choudhary
- Applied Science Department, Indian Institute of Information Technology, Allahabad, Uttar Pradesh, India
| | - Tanu Singh
- Applied Science Department, Indian Institute of Information Technology, Allahabad, Uttar Pradesh, India
| | - Ayush Amod
- Applied Science Department, Indian Institute of Information Technology, Allahabad, Uttar Pradesh, India
| | - Sangeeta Singh
- Applied Science Department, Indian Institute of Information Technology, Allahabad, Uttar Pradesh, India
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13
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Valipour M, Di Giacomo S, Di Sotto A, Irannejad H. Discovery of Chalcone-Based Hybrid Structures as High Affinity and Site-Specific Inhibitors against SARS-CoV-2: A Comprehensive Structural Analysis Based on Various Host-Based and Viral Targets. Int J Mol Sci 2023; 24:ijms24108789. [PMID: 37240149 DOI: 10.3390/ijms24108789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 05/01/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
Previous studies indicated that natural-based chalcones have significant inhibitory effects on the coronavirus enzymes 3CLpro and PLpro as well as modulation of some host-based antiviral targets (HBATs). In this study, a comprehensive computational and structural study was performed to investigate the affinity of our compound library consisting of 757 chalcone-based structures (CHA-1 to CHA-757) for inhibiting the 3CLpro and PLpro enzymes and against twelve selected host-based targets. Our results indicated that CHA-12 (VUF 4819) is the most potent and multi-target inhibitor in our chemical library over all viral and host-based targets. Correspondingly, CHA-384 and its congeners containing ureide moieties were found to be potent and selective 3CLpro inhibitors, and benzotriazole moiety in CHA-37 was found to be a main fragment for inhibiting the 3CLpro and PLpro. Surprisingly, our results indicate that the ureide and sulfonamide moieties are integral fragments for the optimum 3CLpro inhibition while occupying the S1 and S3 subsites, which is fully consistent with recent reports on the site-specific 3CLpro inhibitors. Finding the multi-target inhibitor CHA-12, previously reported as an LTD4 antagonist for the treatment of inflammatory pulmonary diseases, prompted us to suggest it as a concomitant agent for relieving respiratory symptoms and suppressing COVID-19 infection.
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Affiliation(s)
- Mehdi Valipour
- Razi Drug Research Center, Iran University of Medical Sciences, Tehran 1545913487, Iran
| | - Silvia Di Giacomo
- Department of Physiology and Pharmacology "V. Erspamer", Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Antonella Di Sotto
- Department of Physiology and Pharmacology "V. Erspamer", Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Hamid Irannejad
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari 4847116547, Iran
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14
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Investigation of the effects of N-Acetylglucosamine on the stability of the spike protein in SARS-CoV-2 by molecular dynamics simulations. COMPUT THEOR CHEM 2023; 1222:114049. [PMID: 36743995 PMCID: PMC9890939 DOI: 10.1016/j.comptc.2023.114049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/22/2023] [Accepted: 01/25/2023] [Indexed: 02/04/2023]
Abstract
A lot of effort has been made in developing vaccine and therapeutic agents against the SARS-CoV-2, concentrating on the Spike protein that binds angiotensin-converting enzyme 2 on human cells. Nowadays, some researches study the role of the N-linked glycans as potential targets for vaccines and new agents. Due to the flexibility and diversity of the N-linked glycans, in this work, we focus on the N-Acetylglucosamine moiety, which is the precursor of nearly all eukaryotic glycans. We performed molecular dynamics simulations to study the effects of the N-Acetylglucosamine on the stability of the spike glycoprotein in SARS-CoV-2. After a 100 ns of simulation on the spike proteins without and with the N-Acetylglucosamine molecules, we found that the presence of N-Acetylglucosamine increases the local stability in their vicinity; even though their effect on the full structure is negligible. Thus; it can be inferred that the N-Acetylglucosamine moieties can potentially affect the interaction of the S protein with the ACE2 receptor. We also found that the S1 domain is more flexible than the S2 domain. We propose which of the experimentally observed glycans found on the spike may be more functional than the others. Detailed understanding of glycans is key for the development of new therapeutic strategies.
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15
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Identification of RdRp inhibitors against SARS-CoV-2 through E-pharmacophore-based virtual screening, molecular docking and MD simulations approaches. Int J Biol Macromol 2023; 237:124169. [PMID: 36990409 PMCID: PMC10043960 DOI: 10.1016/j.ijbiomac.2023.124169] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 03/10/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023]
Abstract
The outbreak of novel Coronavirus, an enduring pandemic declared by WHO, has consequences to an alarming ongoing public health menace which has already claimed several million human lives. In addition to numerous vaccinations and medications for mild to moderate COVID-19 infection, lack of promising medication or therapeutic pharmaceuticals remains a serious concern to counter the ongoing coronavirus infections and to hinder its dreadful spread. Global health emergencies have called for urgency for potential drug discovery and time is the biggest constraint apart from the financial and human resources required for the high throughput drug screening. However, computational screening or in-silico approaches appeared to be an effective and faster approach to discover potential molecules without sacrificing the model animals. Accumulated shreds of evidence on computational studies against viral diseases have revealed significance of in-silico drug discovery approaches especially in the time of urgency. The central role of RdRp in SARS-CoV-2 replication makes it promising drug target to curtain on going infection and its spread. The present study aimed to employ E-pharmacophore-based virtual screening to reveal potent inhibitors of RdRp as potential leads to block the viral replication. An energy-optimised pharmacophore model was generated to screen the Enamine REAL DataBase (RDB). Then, ADME/T profiles were determined to validate the pharmacokinetics and pharmacodynamics properties of the hit compounds. Moreover, High Throughput Virtual Screening (HTVS) and molecular docking (SP & XP) were employed to screen the top hits from pharmacophore-based virtual screening and ADME/T screen. The binding free energies of the top hits were calculated by conducting MM-GBSA analysis followed by MD simulations to determine the stability of molecular interactions between top hits and RdRp protein. These virtual investigations revealed six compounds having binding free energies of −57.498, −45.776, −46.248, −35.67, −25.15 and −24.90 kcal/mol respectively as calculated by the MM-GBSA method. The MD simulation studies confirmed the stability of protein ligand complexes, hence, indicating as potent RdRp inhibitors and are promising candidate drugs to be further validated and translated into clinics in future.
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16
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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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17
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Yang T, Wang SC, Ye L, Maimaitiyiming Y, Naranmandura H. Targeting viral proteins for restraining SARS-CoV-2: focusing lens on viral proteins beyond spike for discovering new drug targets. Expert Opin Drug Discov 2023; 18:247-268. [PMID: 36723288 DOI: 10.1080/17460441.2023.2175812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
INTRODUCTION Emergence of highly infectious SARS-CoV-2 variants are reducing protection provided by current vaccines, requiring constant updates in antiviral approaches. The virus encodes four structural and sixteen nonstructural proteins which play important roles in viral genome replication and transcription, virion assembly, release , entry into cells, and compromising host cellular defenses. As alien proteins to host cells, many viral proteins represent potential targets for combating the SARS-CoV-2. AREAS COVERED Based on literature from PubMed and Web of Science databases, the authors summarize the typical characteristics of SARS-CoV-2 from the whole viral particle to the individual viral proteins and their corresponding functions in virus life cycle. The authors also discuss the potential and emerging targeted interventions to curb virus replication and spread in detail to provide unique insights into SARS-CoV-2 infection and countermeasures against it. EXPERT OPINION Our comprehensive analysis highlights the rationale to focus on non-spike viral proteins that are less mutated but have important functions. Examples of this include: structural proteins (e.g. nucleocapsid protein, envelope protein) and extensively-concerned nonstructural proteins (e.g. NSP3, NSP5, NSP12) along with the ones with relatively less attention (e.g. NSP1, NSP10, NSP14 and NSP16), for developing novel drugs to overcome resistance of SARS-CoV-2 variants to preexisting vaccines and antibody-based treatments.
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Affiliation(s)
- Tao Yang
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Si Chun Wang
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Linyan Ye
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yasen Maimaitiyiming
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Zhejiang Province Key Laboratory of Haematology Oncology Diagnosis and Treatment, Hangzhou, Zhejiang, China.,Department of Neurobiology, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Brain Science and Brain Medicine, and MOE Frontier Science Center for Brain Science and Brain-machine Integration, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Hua Naranmandura
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Zhejiang Province Key Laboratory of Haematology Oncology Diagnosis and Treatment, Hangzhou, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
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18
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Xiang Y, Zhai G, Li Y, Wang M, Chen X, Wang R, Xie H, Zhang W, Ge G, Zhang Q, Xu Y, Caflisch A, Xu J, Chen H, Chen L. Ginkgolic acids inhibit SARS-CoV-2 and its variants by blocking the spike protein/ACE2 interplay. Int J Biol Macromol 2023; 226:780-792. [PMID: 36521705 PMCID: PMC9743696 DOI: 10.1016/j.ijbiomac.2022.12.057] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/03/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022]
Abstract
Targeting the interaction between the spike protein receptor binding domain (S-RBD) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and angiotensin-converting enzyme 2 (ACE2) is a potential therapeutic strategy for treating coronavirus disease 2019 (COVID-19). However, we still lack small-molecule drug candidates for this target due to the missing knowledge in the hot spots for the protein-protein interaction. Here, we used NanoBiT technology to identify three Ginkgolic acids from an in-house traditional Chinese medicine (TCM) library, and they interfere with the S-RBD/ACE2 interplay. Our pseudovirus assay showed that one of the compounds, Ginkgolic acid C17:1 (GA171), significantly inhibits the entry of original SARS-CoV-2 and its variants into the ACE2-overexpressed HEK293T cells. We investigated and proposed the binding sites of GA171 on S-RBD by combining molecular docking and molecular dynamics simulations. Site-directed mutagenesis and surface plasmon resonance revealed that GA171 specifically binds to the pocket near R403 and Y505, critical residues of S-RBD for S-RBD interacting with ACE2. Thus, we provide structural insights into developing new small-molecule inhibitors and vaccines against the proposed S-RBD binding site.
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Affiliation(s)
- Yusen Xiang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Guanglei Zhai
- Shanghai HighsLab Therapeutics. Inc., Shanghai 201203, China
| | - Yaozong Li
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland,Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
| | - Mengge Wang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xixiang Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China,Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Ruyu Wang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Hang Xie
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Weidong Zhang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China,Shanghai Institute of Infectious Diseases and Biosafety, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Guangbo Ge
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Qian Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Yechun Xu
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Jianrong Xu
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China,Shanghai Universities Collaborative Innovation Center for Translational Medicine, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China,Corresponding authors
| | - Hongzhuan Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China,Corresponding authors
| | - Lili Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China,Corresponding authors
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19
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Shokry S, Hegazy A, Abbas AM, Mostafa I, Eissa IH, Metwaly AM, Yahya G, El-Shazly AM, Aboshanab KM, Mostafa A. Phytoestrogen β-Sitosterol Exhibits Potent In Vitro Antiviral Activity against Influenza A Viruses. Vaccines (Basel) 2023; 11:228. [PMID: 36851106 PMCID: PMC9964242 DOI: 10.3390/vaccines11020228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/14/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023] Open
Abstract
Influenza is a contagious infection in humans that is caused frequently by low pathogenic seasonal influenza viruses and occasionally by pathogenic avian influenza viruses (AIV) of H5, H7, and H9 subtypes. Recently, the clinical sector in poultry and humans has been confronted with many challenges, including the limited number of antiviral drugs and the rapid evolution of drug-resistant variants. Herein, the anti-influenza activities of various plant-derived phytochemicals were investigated against highly pathogenic avian influenza A/H5N1 virus (HPAIV H5N1) and seasonal low pathogenic human influenza A/H1N1 virus (LPHIV H1N1). Out of the 22 tested phytochemicals, the steroid compounds β-sitosterol and β-sitosterol-O-glucoside have very potent activity against the predefined influenza A viruses (IAV). Both steroids could induce such activity by affecting multiple stages during IAV replication cycles, including viral adsorption and replication with a major and significant impact on the virus directly in a cell-free status "viricidal effect". On a molecular level, several molecular docking studies suggested that β-sitosterol and β-sitosterol-O-glucoside exhibited viricidal effects through blocking active binding sites of the hemagglutinin surface protein, as well as showing inhibitory effects against replication through the binding with influenza neuraminidase activity and blocking the active sites of the M2 proton channel activity. The phytoestrogen β-sitosterol has structural similarity with the active form of the female sex hormone estradiol, and this similarity is likely one of the molecular determinants that enables the phytoestrogen β-sitosterol and its derivative to control IAV infection in vitro. This promising anti-influenza activity of β-sitosterol and its O-glycoside derivative, according to both in vitro and cheminformatics studies, recommend both phytochemicals for further studies going through preclinical and clinical phases as efficient anti-influenza drug candidates.
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Affiliation(s)
- Sara Shokry
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Abbassia, Cairo 11566, Egypt
| | - Akram Hegazy
- Department of Agricultural Microbiology, Faculty of Agriculture, Cairo University, Giza District, Giza 12613, Egypt
| | - Ahmad M. Abbas
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Abbassia, Cairo 11566, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, King Salman International University (KSIU), Sinai 46612, Egypt
| | - Islam Mostafa
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Ibrahim H. Eissa
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
| | - Ahmed M. Metwaly
- Pharmacognosy and Medicinal Plants Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
- Biopharmaceutical Products Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City), Alexandria 21934, Egypt
| | - Galal Yahya
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Assem M. El-Shazly
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
- Faculty of Pharmacy, El Saleheya El Gadida University, El Saleheya El Gadida 44813, Sharkia, Egypt
| | - Khaled M. Aboshanab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Abbassia, Cairo 11566, Egypt
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt
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20
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Ge J, Song T, Li M, Chen W, Li J, Gong S, Zhao Y, Ma L, Yu H, Li X, Fu K. The medicinal value of tea drinking in the management of COVID-19. Heliyon 2023; 9:e12968. [PMID: 36647394 PMCID: PMC9833859 DOI: 10.1016/j.heliyon.2023.e12968] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 01/06/2023] [Accepted: 01/10/2023] [Indexed: 01/13/2023] Open
Abstract
Corona Virus Disease 2019 (COVID-19) is presently the largest international public health event, individuals infected by the virus not only have symptoms such as fever, dry cough, and lung infection at the time of onset, but also possibly have sequelae in the cardiovascular system, respiratory system, nervous system, mental health and other aspects. However, numerous studies have depicted that the active ingredients in tea show good antiviral effects and can treat various diseases by regulating multiple pathways, and the therapeutic effects are associated with the categories of chemical components in tea. In this review, the differences in the content of key active ingredients in different types of tea are summarized. In addition, we also highlighted their effects on COVID-19 and connected sequelae, further demonstrating the possibility of developing a formulation for the prevention and treatment of COVID-19 and its sequelae through tea extracts. We have a tendency to suggest forestalling and treating COVID-19 and its sequelae through scientific tea drinking.
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Affiliation(s)
- Jiaming Ge
- Tianjin University of Traditional Chinese Medicine, 301617, Tianjin, China
| | - Tianbao Song
- Tianjin University of Traditional Chinese Medicine, 301617, Tianjin, China
| | - Mengyuan Li
- Tianjin University of Traditional Chinese Medicine, 301617, Tianjin, China
| | - Weisan Chen
- Tianjin University of Traditional Chinese Medicine, 301617, Tianjin, China
| | - Jiarong Li
- Tianjin University of Traditional Chinese Medicine, 301617, Tianjin, China
| | - Sihan Gong
- Tianjin University of Traditional Chinese Medicine, 301617, Tianjin, China
| | - Ying Zhao
- Tianjin University of Traditional Chinese Medicine, 301617, Tianjin, China
| | - Lin Ma
- Tianjin University of Traditional Chinese Medicine, 301617, Tianjin, China
| | - Hongjian Yu
- Wuxi Century Bioengineering Co., Ltd., Wuxi 214000, China
| | - Xiankuan Li
- Tianjin University of Traditional Chinese Medicine, 301617, Tianjin, China,Corresponding author10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, China.
| | - Kun Fu
- Second Teaching Hospital of Tianjin University of Traditional Chinese Medicine, 300120, Tianjin, China,Corresponding author. 69 Increasen Road, Hebei District, Tianjin, China.
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21
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Boonserm P, Khunrae P, Sutthibutpong T. A computational study on the molecular mechanisms of panduratin A as a potential inhibitor on SARS-CoV-2 protein targets. Heliyon 2023; 9:e12780. [PMID: 36628324 PMCID: PMC9816080 DOI: 10.1016/j.heliyon.2022.e12780] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/24/2022] [Accepted: 12/30/2022] [Indexed: 01/08/2023] Open
Abstract
Panduratin A from Boesebergia rotunda was recently reported as a potent anti-SARS-CoV-2 compound. However, the molecular mechanisms underlying the inhibition by Panduratin A and its target remained unclear. Molecular docking calculations were performed between panduratin A and five important proteins, i.e., main protease (Mpro), papain-like protease (PLpro), receptor binding domain (RBD) of spike proteins, RNA-dependent-RNA-polymerase (RdRp), and 2'-O-methyltransferase (MTase). The estimated binding free energy and the interaction networks extracted from the best docking mode for each complex suggested that MTase was the most probable target for panduratin A inhibition. To further validate the ability of panduratin A to inhibit MTase, molecular dynamics (MD) simulations and binding free energy calculations were performed for panduratin A-MTase complex, in comparison with another MTase complex with sinefungin as a positive control. Chemical features of panduratin A and sinefungin were compared for their contribution in MTase binding. It was found that both molecules could bind to the S-Adenosyl methionine (SAM) binding pocket and prevent the SAM entrance co-substrate, which could eventually halt the function of MTase. Despite a slightly weaker binding free energy, the equilibrated positional binding of panduratin A was found at a closer distance to the active sites. Therefore, this study proposed MTase as a possible target of panduratin A, along with the mechanisms of inhibition, prompting another future in vitro study as a verification.
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Affiliation(s)
- Patamalai Boonserm
- Department of Microbiology, Faculty of Science, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Pongsak Khunrae
- Department of Microbiology, Faculty of Science, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Thana Sutthibutpong
- Department of Physics, Faculty of Science, King Mongkut's University of Technology Thonburi, Bangkok, Thailand,Center of Excellence in Theoretical and Computational Science (TACS-CoE), Faculty of Science, King Mongkut's University of Technology Thonburi, Bangkok, Thailand,Corresponding author. Theoretical and Computational Science Center (TaCS), Science Laboratory Building, Faculty of Science, King Mongkut's University of Technology Thonburi (KMUTT), 126 Pracha-Uthit Road, Bang Mod, Thrung Khru, Bangkok, Thailand.,
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22
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Baranova A, Song Y, Cao H, Yue W, Zhang F. Causal associations of tea intake with COVID-19 infection and severity. Front Nutr 2023; 9:1005466. [PMID: 36687732 PMCID: PMC9848307 DOI: 10.3389/fnut.2022.1005466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/18/2022] [Indexed: 01/05/2023] Open
Abstract
Tea ingredients can effectively inhibit SARS-CoV-2 infection at adequate concentrations. It is not known whether tea intake could impact the susceptibility to COVID-19 or its severity. We aimed to evaluate the causal effects of tea intake on COVID-19 outcomes. We performed Mendelian randomization (MR) analyses to assess the causal associations between tea intake (N = 441,279) and three COVID-19 outcomes, including SARS-CoV-2 infection (122,616 cases and 2,475,240 controls), hospitalized COVID-19 (32,519 cases and 2,062,805 controls), and critical COVID-19 (13,769 cases and 1,072,442 controls). The MR analyses indicated that genetic propensity for tea consumption conferred a negative causal effect on the risk of SARS-CoV-2 infection (OR: 0.87, 95% confidence interval (CI): 0.78-0.97, P = 0.015). No causal effects on hospitalized COVID-19 (0.84, 0.64-1.10, P = 0.201) or critical COVID-19 (0.73, 0.51-1.03, P = 0.074) were detected. Our study revealed that tea intake could decrease the risk of SARS-CoV-2 infection, highlighting the potential preventive effect of tea consumption on COVID-19 transmission.
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Affiliation(s)
- Ancha Baranova
- School of Systems Biology, George Mason University, Manassas, VA, United States,Research Centre for Medical Genetics, Moscow, Russia
| | - Yuqing Song
- Peking University Sixth Hospital/Institute of Mental Health, Beijing, China,NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Hongbao Cao
- School of Systems Biology, George Mason University, Manassas, VA, United States
| | - Weihua Yue
- Peking University Sixth Hospital/Institute of Mental Health, Beijing, China,NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China,PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, China,Chinese Institute for Brain Research, Beijing, China
| | - Fuquan Zhang
- Institute of Neuropsychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China,Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China,*Correspondence: Fuquan Zhang ✉
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23
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Isolation of a Novel Anti-Diabetic α-Glucosidase Oligo-Peptide Inhibitor from Fermented Rice Bran. Foods 2023; 12:foods12010183. [PMID: 36613397 PMCID: PMC9818066 DOI: 10.3390/foods12010183] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/03/2023] Open
Abstract
At present, the incidence rate of diabetes is increasing gradually, and inhibiting α-glucosidase is one of the effective methods used to control blood sugar. This study identified new peptides from rice bran fermentation broth and evaluated their inhibitory activity and mechanism against α-glucosidase. Rice bran was fermented with Bacillus subtilis MK15 and the polypeptides of <3 kDa were isolated by ultrafiltration and chromatographic column, and were then subjected to LC-MS/MS mass spectrometry analysis. The results revealed that the oligopeptide GLLGY showed the greatest inhibitory activity in vitro. Docking studies with GLLGY on human α-glucosidase (PDB ID 5NN8) suggested a binding energy of −7.1 kcal/mol. GLLGY acts as a non-competitive inhibitor and forms five hydrogen bonds with Asp282, Ser523, Asp616, and His674 of α-glucosidase. Moreover, it retained its inhibitory activity even in a simulated digestion environment in vitro. The oligopeptide GLLGY could be developed into a potential anti-diabetic agent.
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24
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Srivastava S, He F, Huang Y, Niu M, Adholeya A, Peng WK. A Brief Review on Medicinal Plants-At-Arms against COVID-19. Interdiscip Perspect Infect Dis 2023; 2023:7598307. [PMID: 37139479 PMCID: PMC10151152 DOI: 10.1155/2023/7598307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 03/09/2023] [Accepted: 03/22/2023] [Indexed: 05/05/2023] Open
Abstract
COVID-19 pandemic caused by the novel SARS-CoV-2 has impacted human livelihood globally. Strenuous efforts have been employed for its control and prevention; however, with recent reports on mutated strains with much higher infectivity, transmissibility, and ability to evade immunity developed from previous SARS-CoV-2 infections, prevention alternatives must be prepared beforehand in case. We have perused over 128 recent works (found on Google Scholar, PubMed, and ScienceDirect as of February 2023) on medicinal plants and their compounds for anti-SARS-CoV-2 activity and eventually reviewed 102 of them. The clinical application and the curative effect were reported high in China and in India. Accordingly, this review highlights the unprecedented opportunities offered by medicinal plants and their compounds, candidates as the therapeutic agent, against COVID-19 by acting as viral protein inhibitors and immunomodulator in (32 clinical trials and hundreds of in silico experiments) conjecture with modern science. Moreover, the associated foreseeable challenges for their viral outbreak management were discussed in comparison to synthetic drugs.
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Affiliation(s)
- Shivani Srivastava
- Centre for Mycorrhizal Research, Sustainable Agriculture Division, The Energy and Resources Institute (TERI), TERI Gram, Gwal Pahari, Gurugram 122001, India
| | - Fangzhou He
- Songshan Lake Materials Laboratory, University Innovation Park, Dongguan 523-808, China
| | - Yuanding Huang
- Songshan Lake Materials Laboratory, University Innovation Park, Dongguan 523-808, China
| | - Meng Niu
- China Medical University, Shenyang, China
| | - Alok Adholeya
- Centre for Mycorrhizal Research, Sustainable Agriculture Division, The Energy and Resources Institute (TERI), TERI Gram, Gwal Pahari, Gurugram 122001, India
| | - Weng Kung Peng
- Songshan Lake Materials Laboratory, University Innovation Park, Dongguan 523-808, China
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25
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Chugh A, Sehgal I, Khurana N, Verma K, Rolta R, Vats P, Salaria D, Fadare OA, Awofisayo O, Verma A, Phartyal R, Verma M. Comparative docking studies of drugs and phytocompounds for emerging variants of SARS-CoV-2. 3 Biotech 2023; 13:36. [PMID: 36619821 PMCID: PMC9815891 DOI: 10.1007/s13205-022-03450-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 12/20/2022] [Indexed: 01/07/2023] Open
Abstract
In the last three years, COVID-19 has impacted the world with back-to-back waves leading to devastating consequences. SARS-CoV-2, the causative agent of COVID-19, was first detected in 2019 and since then has spread to 228 countries. Even though the primary focus of research groups was diverted to fight against COVID-19, yet no dedicated drug has been developed to combat the emergent life-threatening medical conditions. In this study, 35 phytocompounds and 43 drugs were investigated for comparative docking analysis. Molecular docking and virtual screening were performed against SARS-CoV-2 spike glycoprotein of 13 variants using AutoDock Vina tool 1.5.6 and Discovery Studio, respectively, to identify the most efficient drugs. Selection of the most suitable compounds with the best binding affinity was done after screening for toxicity, ADME (absorption, distribution, metabolism and excretion) properties and drug-likeliness. The potential candidates were discovered to be Liquiritin (binding affinities ranging between -7.0 and -8.1 kcal/mol for the 13 variants) and Apigenin (binding affinities ranging between -6.8 and -7.3 kcal/mol for the 13 variants) based on their toxicity and consistent binding affinity with the Spike protein of all variants. The stability of the protein-ligand complex was determined using Molecular dynamics (MD) simulation of Apigenin with the Delta plus variant of SARS-CoV-2. Furthermore, Liquiritin and Apigenin were also found to be less toxic than the presently used drugs and showed promising results based on in silico studies, though, confirmation using in vitro studies is required. This in-depth comparative investigation suggests potential drug candidates to fight against SARS-CoV-2 variants. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03450-6.
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Affiliation(s)
- Ananya Chugh
- Sri Venkateswara College, University of Delhi, New Delhi, 110021 India
| | - Ishita Sehgal
- Sri Venkateswara College, University of Delhi, New Delhi, 110021 India
| | - Nimisha Khurana
- Sri Venkateswara College, University of Delhi, New Delhi, 110021 India
| | - Kangna Verma
- Sri Venkateswara College, University of Delhi, New Delhi, 110021 India
| | - Rajan Rolta
- Department of Pharmacology, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012 India
| | - Pranjal Vats
- School of Biological Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PL UK
| | - Deeksha Salaria
- Department of Pharmacology, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012 India
| | - Olatomide A. Fadare
- Organic Chemistry Research Lab, Department of Chemistry, Obafemi Awolowo University, Ile-Ife, Osun 220282 Nigeria
| | - Oladoja Awofisayo
- Department of Pharmaceutical and Medical Chemistry, University of Uyo, Uyo, 520003 Nigeria
| | - Anita Verma
- Sri Venkateswara College, University of Delhi, New Delhi, 110021 India
| | - Rajendra Phartyal
- Sri Venkateswara College, University of Delhi, New Delhi, 110021 India
| | - Mansi Verma
- Department of Zoology, Hansraj College, University of Delhi, Delhi, 110007 India
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26
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Chaube U, Patel BD, Bhatt HG. A hypothesis on designing strategy of effective RdRp inhibitors for the treatment of SARS-CoV-2. 3 Biotech 2023; 13:12. [PMID: 36532857 PMCID: PMC9755803 DOI: 10.1007/s13205-022-03430-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
Vaccines are used as one of the major weapons for the eradication of pandemic. However, the rise of different variants of the SARS-CoV-2 virus is creating doubts regarding the end of the pandemic. Hence, there is an urgent need to develop more drug candidates which can be useful for the treatment of COVID-19. In the present research for the scientific hypothesis, emphasis was given on the direct antiviral therapy available for the treatment of COVID-19. In lieu of this, the available molecular targets which include Severe Acute Respiratory Syndrome Chymotrypsin-like Protease (SARS-3CLpro), Papain-Like Cysteine Protease (PLpro), and RNA-Dependent RNA Polymerase (RdRp) were explored. As per the current scientific reports and literature, among all the available molecular targets, RNA-Dependent RNA Polymerase (RdRp) was found to be a crucial molecular target for the treatment of COVID-19. Most of the inhibitors which are reported against this target consisted of the free amine group and carbonyl group which might be playing an important role in the binding interaction with the RdRp protein. Among all the reported RdRp inhibitors, remdesivir, favipiravir, and molnupiravir were found to be the most promising drugs against COVID-19. Overall, the structural features of this RNA-Dependent RNA Polymerase (RdRp) inhibitors proved the importance of pyrrolo-triazine and pyrimidine scaffolds. Previous computational models of these drug molecules indicated that substitution with the polar functional group, hydrogen bond donor, and electronegative atoms on these scaffolds may increase the activity against the RdRp protein. Hence, in line with the proposed hypothesis, in the present research work for the evaluation of the hypothesis, new molecules were designed from the pyrrolo-triazine and pyrimidine scaffolds. Further, molecular docking and MD simulation studies were performed with these designed molecules. All these designed molecules (DM-1, DM-2, and DM-3) showed the results as per the proposed hypothesis. Among all the designed molecules, DM-1 showed promising results against the RdRp protein of SARS-CoV-2. In the future, these structural features can be used for the development of new RdRp inhibitors with improved activity. Also, in the future lead compound DM-1 can be explored against the RdRp protein for the treatment of COVID-19.
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Affiliation(s)
- Udit Chaube
- grid.412204.10000 0004 1792 2351Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat 382481 India
| | - Bhumika D. Patel
- grid.412204.10000 0004 1792 2351Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat 382481 India
| | - Hardik G. Bhatt
- grid.412204.10000 0004 1792 2351Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat 382481 India
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27
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Lopes SM, de Medeiros HIR, Scotti MT, Scotti L. Natural Products Against COVID-19 Inflammation: A Mini-Review. Comb Chem High Throughput Screen 2022; 25:2358-2369. [PMID: 35088662 DOI: 10.2174/1386207325666220128114547] [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: 09/02/2021] [Revised: 11/03/2021] [Accepted: 11/18/2021] [Indexed: 01/27/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) is a virus whose genetic material is positive single-stranded RNA, being responsible for coronavirus disease 2019 (COVID- 19), an infection that compromises the lungs and consequently the respiratory capacity of the infected individual, according to the WHO in November 2021, 249,743,428 cases were confirmed, of which 5,047,652 individuals died due to complications resulting from the infection caused by SARSCOV- 2. As the infection progresses, the individual may experience loss of smell and taste, as well as breathing difficulties, severe respiratory failure, multiple organ failure, and death. Due to this new epidemiological agent in March 2020 it was announced by the director general of the World Health Organization (WHO) a pandemic status, and with that, many research groups are looking for new therapeutic alternatives through synthetic and natural bioactives. This research is a literature review of some in silico studies involving natural products against COVID-19 inflammation published in 2020 and 2021. Work like this presents relevant information to the scientific community, boosting future research and encouraging the use of natural products for the search for new antivirals against COVID-19.
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Affiliation(s)
- Simone Mendes Lopes
- Postgraduate Program in Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraíba, João Pessoa Pb, Brazil
| | - Herbert Igor Rodrigues de Medeiros
- Postgraduate Program in Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraíba, João Pessoa Pb, Brazil
| | - Marcus Tullius Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraíba, João Pessoa Pb, Brazil
| | - Luciana Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraíba, João Pessoa Pb, Brazil.,Lauro Wanderley University Hospital (HULW), Health Sciences Center, Federal University of Paraíba, João Pessoa Pb, Brazil
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28
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Singh R, Bhardwaj VK, Purohit R. Inhibition of nonstructural protein 15 of SARS-CoV-2 by golden spice: A computational insight. Cell Biochem Funct 2022; 40:926-934. [PMID: 36203381 PMCID: PMC9874790 DOI: 10.1002/cbf.3753] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/16/2022] [Accepted: 09/15/2022] [Indexed: 01/27/2023]
Abstract
The quick widespread of the coronavirus and speedy upsurge in the tally of cases demand the fast development of effective drugs. The uridine-directed endoribonuclease activity of nonstructural protein 15 (Nsp15) of the coronavirus is responsible for the invasion of the host immune system. Therefore, developing potential inhibitors against Nsp15 is a promising strategy. In this concern, the in silico approach can play a significant role, as it is fast and cost-effective in comparison to the trial and error approaches of experimental investigations. In this study, six turmeric derivatives (curcuminoids) were chosen for in silico analysis. The molecular interactions, pharmacokinetics, and drug-likeness of all the curcuminoids were measured. Further, the stability of Nsp15-curcuminoids complexes was appraised by employing molecular dynamics (MD) simulations and MM-PBSA approaches. All the molecules were affirmed to have strong interactions and pharmacokinetic profile. The MD simulations data stated that the Nsp15-curcuminoids complexes were stable during simulations. All the curcuminoids showed stable and high binding affinity, and these curcuminoids could be admitted as potential modulators for Nsp15 inhibition.
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Affiliation(s)
- Rahul Singh
- Structural Bioinformatics Lab, CSIR‐Institute of Himalayan Bioresource Technology (CSIR‐IHBT)The Himalayan Centre for High‐throughput Computational Biology (HiCHiCoB, A BIC Supported by DBT)PalampurIndia,Biotechnology divisionCSIR‐IHBTPalampurIndia,Academy of Scientific & Innovative Research (AcSIR)GhaziabadIndia
| | - Vijay K. Bhardwaj
- Structural Bioinformatics Lab, CSIR‐Institute of Himalayan Bioresource Technology (CSIR‐IHBT)The Himalayan Centre for High‐throughput Computational Biology (HiCHiCoB, A BIC Supported by DBT)PalampurIndia,Biotechnology divisionCSIR‐IHBTPalampurIndia,Academy of Scientific & Innovative Research (AcSIR)GhaziabadIndia
| | - Rituraj Purohit
- Structural Bioinformatics Lab, CSIR‐Institute of Himalayan Bioresource Technology (CSIR‐IHBT)The Himalayan Centre for High‐throughput Computational Biology (HiCHiCoB, A BIC Supported by DBT)PalampurIndia,Biotechnology divisionCSIR‐IHBTPalampurIndia,Academy of Scientific & Innovative Research (AcSIR)GhaziabadIndia
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29
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Aleissa MS, AL-Zharani M, Hasnain MS, Alkahtani S. Screening, molecular simulation & in silico kinetics of virtually designed covid-19 main protease inhibitors. JOURNAL OF KING SAUD UNIVERSITY - SCIENCE 2022; 34:102283. [PMID: 36062199 PMCID: PMC9428119 DOI: 10.1016/j.jksus.2022.102283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/27/2022] [Accepted: 08/13/2022] [Indexed: 11/07/2022]
Abstract
Coronavirus (covid-19) infection is considered to be deadliest ever pandemic experienced by the human being. It has very badly affected the socio-economic health of human and stuck the scientific community to think and rethink about its complete eradication. But due to no effective treatment or unavailability of vaccine the health professional could not show any significant improvement to control the pandemic. The situation needs newer molecule, vaccine or effective treatment to control covid-19 infection. Different target in viruses has been explored and proteases enzymes were found to be therapeutically effective target for the design of potential anti-covid-19 molecule as it plays the vital role in viral replication and assembly. Structure-based drug design was employed to discover the small molecule of anti-covid-19. Here we considered the small library of naturally occurring polyphenolic compounds and molecular docking, Molecular dynamics (MD) simulations, free binding energy calculation and in-silico ADME calculations to identify the newer HITs. Based upon their score the two molecules were identified as promising candidate. The docking scores were found to be −7.643 and −7.065 for the HIT1 and HIT-2 respectively. In MD simulations study the RMSD values were found to be 4.3 Å & 4.9 Å respectively. To validate these results MM-GBSA was performed and their binding free energies were computationally determined. The prime energy values of identified HITs (−13412.45 & −13441.8 kJ/mole) were found to be very close proximity to reference molecule (−13493.05 kJ/mole). Then in-silico ADME calculations were performed to calculate the drug likeliness identified HITs. BY considering all the values comparative to reference molecule and obtained in-silico pharmacokinetic properties of identified HITs we can suggest that HIT-1 and HIT-2 would be the most promising molecules that can inhibit the main protease enzyme of covid-19. These two molecules would become the potential drug candidate for the treatment of covid-19 infections.
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30
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Agrawal S, Pathak E, Mishra R, Mishra V, Parveen A, Mishra SK, Byadgi PS, Dubey SK, Chaudhary AK, Singh V, Chaurasia RN, Atri N. Computational exploration of the dual role of the phytochemical fortunellin: Antiviral activities against SARS-CoV-2 and immunomodulatory abilities against the host. Comput Biol Med 2022; 149:106049. [PMID: 36103744 PMCID: PMC9452420 DOI: 10.1016/j.compbiomed.2022.106049] [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: 01/11/2022] [Revised: 08/16/2022] [Accepted: 08/20/2022] [Indexed: 01/18/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections generate approximately one million virions per day, and the majority of available antivirals are ineffective against it due to the virus's inherent genetic mutability. This necessitates the investigation of concurrent inhibition of multiple SARS-CoV-2 targets. We show that fortunellin (acacetin 7-O-neohesperidoside), a phytochemical, is a promising candidate for preventing and treating coronavirus disease (COVID-19) by targeting multiple key viral target proteins. Fortunellin supports protective immunity while inhibiting pro-inflammatory cytokines and apoptosis pathways and protecting against tissue damage. Fortunellin is a phytochemical found in Gojihwadi kwath, an Indian traditional Ayurvedic formulation with an antiviral activity that is effective in COVID-19 patients. The mechanistic action of its antiviral activity, however, is unknown. The current study comprehensively evaluates the potential therapeutic mechanisms of fortunellin in preventing and treating COVID-19. We have used molecular docking, molecular dynamics simulations, free-energy calculations, host target mining of fortunellin, gene ontology enrichment, pathway analyses, and protein-protein interaction analysis. We discovered that fortunellin reliably binds to key targets that are necessary for viral replication, growth, invasion, and infectivity including Nucleocapsid (N-CTD) (-54.62 kcal/mol), Replicase-monomer at NSP-8 binding site (-34.48 kcal/mol), Replicase-dimer interface (-31.29 kcal/mol), Helicase (-30.02 kcal/mol), Papain-like-protease (-28.12 kcal/mol), 2'-O-methyltransferase (-23.17 kcal/mol), Main-protease (-21.63 kcal/mol), Replicase-monomer at dimer interface (-22.04 kcal/mol), RNA-dependent-RNA-polymerase (-19.98 kcal/mol), Nucleocapsid-NTD (-16.92 kcal/mol), and Endoribonuclease (-16.81 kcal/mol). Furthermore, we identify and evaluate the potential human targets of fortunellin and its effect on the SARS-CoV-2 infected tissues, including normal-human-bronchial-epithelium (NHBE) and lung cells and organoids such as pancreatic, colon, liver, and cornea using a network pharmacology approach. Thus, our findings indicate that fortunellin has a dual role; multi-target antiviral activities against SARS-CoV-2 and immunomodulatory capabilities against the host.
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Affiliation(s)
- Shivangi Agrawal
- Bioinformatics, MMV, Institute of Science, Banaras Hindu University, India
| | - Ekta Pathak
- Institute of Diabetes and Obesity, Helmholtz Zentrum München, Neuherberg, Germany.
| | - Rajeev Mishra
- Bioinformatics, MMV, Institute of Science, Banaras Hindu University, India.
| | - Vibha Mishra
- Bioinformatics, MMV, Institute of Science, Banaras Hindu University, India
| | - Afifa Parveen
- Bioinformatics, MMV, Institute of Science, Banaras Hindu University, India
| | | | | | - Sushil Kumar Dubey
- Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, India
| | | | | | | | - Neelam Atri
- Department of Botany, MMV, Banaras Hindu University, India
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Gentile D, Coco A, Patamia V, Zagni C, Floresta G, Rescifina A. Targeting the SARS-CoV-2 HR1 with Small Molecules as Inhibitors of the Fusion Process. Int J Mol Sci 2022; 23:ijms231710067. [PMID: 36077465 PMCID: PMC9456533 DOI: 10.3390/ijms231710067] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
The rapid and global propagation of the novel human coronavirus that causes severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has produced an immediate urgency to discover promising targets for the treatment of this virus. In this paper, we studied the spike protein S2 domain of SARS-CoV-2 as it is the most conserved component and controls the crucial fusion process of SARS-CoV-2 as a target for different databases of small organic compounds. Our in silico methodology, based on pharmacophore modeling, docking simulation and molecular dynamics simulations, was first validated with ADS-J1, a potent small-molecule HIV fusion inhibitor that has already proved effective in binding the HR1 domain and inhibiting the fusion core of SARS-CoV-1. It then focused on finding novel small molecules and new peptides as fusion inhibitors. Our methodology identified several small molecules and peptides as potential inhibitors of the fusion process. Among these, NF 023 hydrate (MolPort-006-822-583) is one of the best-scored compounds. Other compounds of interest are ZINC00097961973, Salvianolic acid, Thalassiolin A and marine_160925_88_2. Two interesting active peptides were also identified: AP00094 (Temporin A) and AVP1227 (GBVA5). The inhibition of the spike protein of SARS-CoV-2 is a valid target to inhibit the virus entry in human cells. The discussed compounds reported in this paper led to encouraging results for future in vitro tests against SARS-CoV-2.
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Wu J, Zhang J, Zhang HX. Computational Design of Miniprotein Inhibitors Targeting SARS-CoV-2 Spike Protein. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:10690-10703. [PMID: 35984970 PMCID: PMC9437664 DOI: 10.1021/acs.langmuir.2c01699] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/31/2022] [Indexed: 05/16/2023]
Abstract
The ongoing pandemic of COVID-19 caused by SARS-CoV-2 has become a global health problem. There is an urgent need to develop therapeutic drugs, effective therapies, and vaccines to prevent the spread of the virus. The virus first enters the host cell through the interaction between the receptor binding domain (RBD) of spike protein and the peptidase domain (PD) of the angiotensin-converting enzyme 2 (ACE2). Therefore, blocking the binding of RBD and ACE2 is a promising strategy to inhibit the invasion and infection of the virus in the host cell. In the study, we designed several miniprotein inhibitors against SARS-CoV-2 by single/double/triple-point mutant, based on the initial inhibitor LCB3. Molecular dynamics (MD) simulations and trajectory analysis were performed for an in-depth analysis of the structural stability, essential protein motions, and per-residue energy decomposition involved in the interaction of inhibitors with the RBD. The results showed that the inhibitors have adapted the protein RBD in the binding interface, thereby forming stable complexes. These inhibitors display low binding free energy in the MM/PBSA calculations, substantiating their strong interaction with RBD. Moreover, the binding affinity of the best miniprotein inhibitor, H6Y-M7L-L17F mutant, to RBD was ∼45 980 times (ΔG = RT ln Ki) higher than that of the initial inhibitor LCB3. Following H6Y-M7L-L17F mutant, the inhibitors with strong binding activity are successively H6Y-L17F, L17F, H6Y, and F30Y mutants. Our research proves that the miniprotein inhibitors can maintain their secondary structure and have a highly stable blocking (binding) effect on SARS-CoV-2. This study proposes novel miniprotein mutant inhibitors with enhanced binding to spike protein and provides potential guidance for the rational design of new SARS-CoV-2 spike protein inhibitors.
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Affiliation(s)
- Jianhua Wu
- Institute
of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, Jilin, People’s Republic of China
| | - Jilong Zhang
- Institute
of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, Jilin, People’s Republic of China
| | - Hong-Xing Zhang
- Institute
of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, Jilin, People’s Republic of China
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Considering epitopes conservity in targeting SARS-CoV-2 mutations in variants: a novel immunoinformatics approach to vaccine design. Sci Rep 2022; 12:14017. [PMID: 35982065 PMCID: PMC9386201 DOI: 10.1038/s41598-022-18152-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 08/05/2022] [Indexed: 11/08/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has gained mutations at an alarming rate in the past years. Developing mutations can increase the virus's pathogenicity and virulence; reduce the efficacy of vaccines, antibodies neutralization, and even challenge adaptive immunity. So, it is essential to identify conserved epitopes (with fewer mutations) in different variants with appropriate antigenicity to target the variants by an appropriate vaccine design. Yet as, 3369 SARS-CoV-2 genomes were collected from global initiative on sharing avian flu data. Then, mutations in the immunodominant regions (IDRs), immune epitope database (IEDB) epitopes, and also predicted epitopes were calculated. In the following, epitopes conservity score against the total number of events (mutations) and the number of mutated sites in each epitope was weighted by Shannon entropy and then calculated by the Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS). Based on the TOPSIS conservity score and antigenicity score, the epitopes were plotted. The result demonstrates that almost all epitopes and IDRs with various lengths have gained different numbers of mutations in dissimilar sites. Herein, our two-step calculation for conservity recommends only 8 IDRs, 14 IEDB epitopes, and 10 predicted epitopes among all epitopes. The selected ones have higher conservity and higher immunogenicity. This method is an open-source multi-criteria decision-making platform, which provides a scientific approach to selecting epitopes with appropriate conservity and immunogenicity; against ever-changing viruses.
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Tripathi MK, Singh P, Kumar M, Sharma K, Singh TP, Ethayathulla AS, Kaur P. Identification of a promising inhibitor from Illicium verum (star anise) against the main protease of SARS-CoV-2: insights from the computational study. J Biomol Struct Dyn 2022:1-17. [PMID: 35980746 DOI: 10.1080/07391102.2022.2112621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
SARS-CoV-2, the causing agent of coronavirus disease (COVID-19), first broke out in Wuhan and rapidly spread worldwide, resulting in a global health emergency. The lack of specific drugs against the coronavirus has made its spread challenging to control. The main protease (Mpro) is a key enzyme of SARS-CoV-2 used as a key target in drug discovery against the coronavirus. Medicines derived from plant phytoconstituents have been widely exploited to treat various diseases. The present study has evaluated the potential of Illicium verum (star anise) phytoconstituents against Mpro by implementing a computational approach. We performed molecular docking and molecular dynamics simulation study with a set of 60 compounds to identify their potential to inhibit the main protease (Mpro) of SARS-CoV-2. DFT study and post dynamics free energy calculations were also performed to strengthen the findings. The identified four compounds by docking study exhibited the highest potential compared to other selected phytoconstituents. Further, density functional theory (DFT) calculation, molecular dynamics simulation and post dynamics MM-GBSA energy calculation predicted Verimol-G as a potential compound, which formed stable interactions through the catalytic dyad residues. The HOMO orbital energy (-0.250038) from DFT and the post dynamics binding free energy calculation (-73.33 Kcal/mol) correlate, suggesting Verimol-G is the best inhibitor compared to the other phytoconstituents. This compound also complies with the ADME properties of drug likeliness. Thus, based on a computational study, we suggest that Verimol G may be developed as a potential inhibitor against the main protease to combat COVID-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Pushpendra Singh
- State Virus Research and Diagnostic Laboratory, Department of Microbiology, All India Institute of Medical Sciences, Raipur, India
| | - Mukesh Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Kuldeep Sharma
- State Virus Research and Diagnostic Laboratory, Department of Microbiology, All India Institute of Medical Sciences, Raipur, India
| | - T P Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - A S Ethayathulla
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
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More-Adate P, Lokhande KB, Swamy KV, Nagar S, Baheti A. GC-MS profiling of Bauhinia variegata major phytoconstituents with computational identification of potential lead inhibitors of SARS-CoV-2 Mpro. Comput Biol Med 2022; 147:105679. [PMID: 35667152 PMCID: PMC9158327 DOI: 10.1016/j.compbiomed.2022.105679] [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: 03/11/2022] [Revised: 05/26/2022] [Accepted: 05/30/2022] [Indexed: 01/18/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 was originally identified in Wuhan city of China in December 2019 and it spread rapidly throughout the globe, causing a threat to human life. Since targeted therapies are deficient, scientists all over the world have an opportunity to develop novel drug therapies to combat COVID-19. After the declaration of a global medical emergency, it was established that the Food and Drug Administration (FDA) could permit the use of emergency testing, treatments, and vaccines to decrease suffering, and loss of life, and restore the nation's health and security. The FDA has approved the use of remdesivir and its analogs as an antiviral medication, to treat COVID-19. The primary protease of SARS-CoV-2, which has the potential to regulate coronavirus proliferation, has been a viable target for the discovery of medicines against SARS-CoV-2. The present research deals with the in silico technique to screen phytocompounds from a traditional medicinal plant, Bauhinia variegata for potential inhibitors of the SARS-CoV-2 main protease. Dried leaves of the plant B. variegata were used to prepare aqueous and methanol extract and the constituents were analyzed using the GC-MS technique. A total of 57 compounds were retrieved from the aqueous and methanol extract analysis. Among these, three lead compounds (2,5 dimethyl 1-H Pyrrole, 2,3 diphenyl cyclopropyl methyl phenyl sulphoxide, and Benzonitrile m phenethyl) were shown to have the highest binding affinity (−5.719 to −5.580 kcal/mol) towards SARS-CoV-2 Mpro. The post MD simulation results also revealed the favorable confirmation and stability of the selected lead compounds with Mpro as per trajectory analysis. The Prime MM/GBSA binding free energy supports this finding, the top lead compound 2,3 diphenyl cyclopropyl methyl phenyl sulphoxide showed high binding free energy (−64.377 ± 5.24 kcal/mol) towards Mpro which reflects the binding stability of the molecule with Mpro. The binding free energy of the complexes was strongly influenced by His, Gln, and Glu residues. All of the molecules chosen are found to have strong pharmacokinetic characteristics and show drug-likeness properties. The lead compounds present acute toxicity (LD50) values ranging from 670 mg/kg to 2500 mg/kg; with toxicity classifications of 4 and 5 classes. Thus, these compounds could behave as probable lead candidates for treatment against SARS-CoV-2. However further in vitro and in vivo studies are required for the development of medication against SARS-CoV-2.
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36
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In-silico screening and in-vitro assay show the antiviral effect of Indomethacin against SARS-CoV-2. Comput Biol Med 2022; 147:105788. [PMID: 35809412 PMCID: PMC9245396 DOI: 10.1016/j.compbiomed.2022.105788] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/30/2022] [Accepted: 06/26/2022] [Indexed: 11/28/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the worldwide spread of coronavirus disease 19 (COVID-19), and till now, it has caused death to more than 6.2 million people. Although various vaccines and drug candidates are being tested globally with limited to moderate success, a comprehensive therapeutic cure is yet to be achieved. In this study, we applied computational drug repurposing methods complemented with the analyses of the already existing gene expression data to find better therapeutics in treatment and recovery. Primarily, we identified the most crucial proteins of SARS-CoV-2 and host human cells responsible for viral infection and host response. An in-silico screening of the existing drugs was performed against the crucial proteins for SARS-CoV-2 infection, and a few existing drugs were shortlisted. Further, we analyzed the gene expression data of SARS-CoV-2 in human lung epithelial cells and investigated the molecules that can reverse the cellular mRNA expression profiles in the diseased state. LINCS L1000 and Comparative Toxicogenomics Database (CTD) were utilized to obtain two sets of compounds that can be used to counter SARS-CoV-2 infection from the gene expression perspective. Indomethacin, a nonsteroidal anti-inflammatory drug (NSAID), and Vitamin-A were found in two sets of compounds, and in the in-silico screening of existing drugs to treat SARS-CoV-2. Our in-silico findings on Indomethacin were further successfully validated by in-vitro testing in Vero CCL-81 cells with an IC50 of 12 μM. Along with these findings, we briefly discuss the possible roles of Indomethacin and Vitamin-A to counter the SARS-CoV-2 infection in humans.
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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: 31] [Impact Index Per Article: 15.5] [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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38
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Ebrahimi M, Karami L, Alijanianzadeh M. Computational repurposing approach for targeting the critical spike mutations in B.1.617.2 (delta), AY.1 (delta plus) and C.37 (lambda) SARS-CoV-2 variants using exhaustive structure-based virtual screening, molecular dynamic simulations and MM-PBSA methods. Comput Biol Med 2022; 147:105709. [PMID: 35728285 PMCID: PMC9170597 DOI: 10.1016/j.compbiomed.2022.105709] [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: 03/02/2022] [Revised: 05/03/2022] [Accepted: 06/04/2022] [Indexed: 11/26/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the contagious coronavirus disease 2019 (COVID-19) which was first identified in Wuhan, China, in December 2019. Around the world, many researchers focused their research on identifying inhibitors against the druggable SARS-CoV-2 targets. The reported genomic mutations have a direct effect on the receptor-binding domain (RBD), which interacts with host angiotensin-converting enzyme 2 (ACE-2) for viral cell entry. These mutations, some of which are variants of concern (VOC), lead to increased morbidity and mortality rates. The newest variants including B.1.617.2 (Delta), AY.1 (Delta plus), and C.37 (Lambda) were considered in this study. Thus, an exhaustive structure-based virtual screening of a ligand library (in which FDA approved drugs are also present) using the drug-likeness screening, molecular docking, ADMET profiling was performed followed by molecular dynamics (MD) simulation, and Molecular Mechanics-Poisson Boltzmann Surface Area (MM-PBSA) calculation to identify compounds or drugs can be repurposed for inhibiting the wild type, Delta, Delta plus and Lambda variants of RBD of the spike protein. Based on the virtual screening steps, two FDA approved drugs, Atovaquone (atv) and Praziquantel (prz), were selected and repurposed as the best candidates of SARS-CoV-2 RBD inhibitors. Molecular docking results display that both atv and prz contribute in different interaction with binding site residues (Gln493, Asn501 and Gly502 in the hydrogen bond formation, Phe490 and Tyr505 in the π- π stacking and Tyr449, Ser494, and Phe497 in the vdW interactions) in the wild type, Delta, Delta plus and Lambda variants of RBD of the spike protein. MD simulations revealed that among the eight studied complexes, the wild type-atv and Delta-prz complexes have the most structural stability over the simulation time. Furthermore, MM-PBSA calculation showed that in the atv containing complexes, highest binding affinity is related to the wild type-atv complex and in the prz containing complexes, it is related to the Delta-prz complex. The validation of docking results was done by comparing with experimental data (heparin in complex with wild type and Delta variants). Also, comparison of the obtained results with the result of simulation of the k22 with the studied proteins showed that atv and prz are suitable inhibitors for these proteins, especially wild type t and Delta variant, respectively. Thus, we found that atv and prz are the best candidate for inhibition of wild type and Delta variant of the spike protein. Also, atv can be an appropriate inhibitor for the Lambda variant. Obtained in silico results may help the development of new anti-COVID-19 drugs.
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Affiliation(s)
- Maryam Ebrahimi
- Department of Plant Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Leila Karami
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran.
| | - Mahdi Alijanianzadeh
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran.
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Mind the feline coronavirus: Comparison with SARS-CoV-2. Gene 2022; 825:146443. [PMID: 35337854 PMCID: PMC8938304 DOI: 10.1016/j.gene.2022.146443] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/25/2022] [Accepted: 03/18/2022] [Indexed: 12/13/2022]
Abstract
Both feline coronavirus (FCoV) and SARS-CoV-2 are coronaviruses that infect cats and humans, respectively. However, cats have been shown to be susceptible to SARS-CoV-2, and FCoV also had been shown to infect human. To elucidate the relationship between FCoV and SARS-CoV-2, we highlight the main characteristics of the genome, the receptor usage, and the correlation of the receptor-binding domain (RBD) of spike proteins in FCoV and SARS-CoV-2. It is demonstrated that FCoV and SARS-CoV-2 are closely related to the main characteristics of the genome, receptor usage, and RBD of spike proteins with similar furin cleavage sites. In particular, the affinity of the conserved feline angiotensin-converting enzyme 2 (fACE2) receptor to the RBD of SARS-CoV-2 suggests that cats are susceptible to SARS-CoV-2. In addition, cross-species of coronaviruses between cats and humans or other domesticated animals are also discussed. This review sheds light on cats as potential intermediate hosts for SARS-CoV-2 transmission, and cross-species transmission or zoonotic infection of FCoV and SARS-CoV-2 between cats and humans was identified.
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40
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Fischer TR, Meidner L, Schwickert M, Weber M, Zimmermann RA, Kersten C, Schirmeister T, Helm M. Chemical biology and medicinal chemistry of RNA methyltransferases. Nucleic Acids Res 2022; 50:4216-4245. [PMID: 35412633 PMCID: PMC9071492 DOI: 10.1093/nar/gkac224] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/17/2022] [Accepted: 04/08/2022] [Indexed: 12/24/2022] Open
Abstract
RNA methyltransferases (MTases) are ubiquitous enzymes whose hitherto low profile in medicinal chemistry, contrasts with the surging interest in RNA methylation, the arguably most important aspect of the new field of epitranscriptomics. As MTases become validated as drug targets in all major fields of biomedicine, the development of small molecule compounds as tools and inhibitors is picking up considerable momentum, in academia as well as in biotech. Here we discuss the development of small molecules for two related aspects of chemical biology. Firstly, derivates of the ubiquitous cofactor S-adenosyl-l-methionine (SAM) are being developed as bioconjugation tools for targeted transfer of functional groups and labels to increasingly visible targets. Secondly, SAM-derived compounds are being investigated for their ability to act as inhibitors of RNA MTases. Drug development is moving from derivatives of cosubstrates towards higher generation compounds that may address allosteric sites in addition to the catalytic centre. Progress in assay development and screening techniques from medicinal chemistry have led to recent breakthroughs, e.g. in addressing human enzymes targeted for their role in cancer. Spurred by the current pandemic, new inhibitors against coronaviral MTases have emerged at a spectacular rate, including a repurposed drug which is now in clinical trial.
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Affiliation(s)
- Tim R Fischer
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Laurenz Meidner
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Marvin Schwickert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Marlies Weber
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Robert A Zimmermann
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
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41
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Khattab AR, Teleb M. In silico discovery of non-psychoactive scaffolds in Cannabis halting SARS-CoV-2 host entry and replication machinery. Future Virol 2022; 0. [PMID: 35399958 PMCID: PMC8982993 DOI: 10.2217/fvl-2021-0309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/17/2022] [Indexed: 11/21/2022]
Abstract
Aim: Coronavirus disease still poses a global health threat which advocates continuous research efforts to develop effective therapeutics. Materials & methods: We screened out an array of 29 cannabis phytoligands for their viral spike-ACE2 complex and main protease (Mpro) inhibitory actions by in silico modeling to explore their possible dual viral entry and replication machinery inhibition. Physicochemical and pharmacokinetic parameters (ADMET) formulating drug-likeness were computed. Results: Among the studied phytoligands, cannabigerolic acid (2), cannabigerol (8), and its acid methyl ether (3) possessed the highest binding affinities to SARS-CoV-hACE2 complex essential for viral entry. Canniprene (24), cannabigerolic methyl ether (3) and cannabichromene (9) were the most promising Mpro inhibitors. Conclusion: These non-psychoactive cannabinoids could represent plausible therapeutics with added-prophylactic value as they halt both viral entry and replication machinery.
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Affiliation(s)
- Amira R Khattab
- Pharmacognosy Department, College of Pharmacy, Arab Academy for Science, Technology & Maritime Transport, Alexandria, 1029, Egypt
| | - Mohamed Teleb
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt
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Rudrapal M, Celik I, Khan J, Ansari MA, Alomary MN, Yadav R, Sharma T, Tallei TE, Pasala PK, Sahoo RK, Khairnar SJ, Bendale AR, Zothantluanga JH, Chetia D, Walode SG. Identification of bioactive molecules from Triphala (Ayurvedic herbal formulation) as potential inhibitors of SARS-CoV-2 main protease (Mpro) through computational investigations. JOURNAL OF KING SAUD UNIVERSITY. SCIENCE 2022; 34:101826. [PMID: 35035181 PMCID: PMC8744360 DOI: 10.1016/j.jksus.2022.101826] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/20/2021] [Accepted: 01/05/2022] [Indexed: 05/28/2023]
Abstract
Severe acute respiratory syndrome coronavirus disease (SARS-CoV-2) induced coronavirus disease 2019 (COVID-19) pandemic is the present worldwide health emergency. The global scientific community faces a significant challenge in developing targeted therapies to combat the SARS-CoV-2 infection. Computational approaches have been critical for identifying potential SARS-CoV-2 inhibitors in the face of limited resources and in this time of crisis. Main protease (Mpro) is an intriguing drug target because it processes the polyproteins required for SARS-CoV-2 replication. The application of Ayurvedic knowledge from traditional Indian systems of medicine may be a promising strategy to develop potential inhibitor for different target proteins of SARS-CoV-2. With this endeavor, we docked bioactive molecules from Triphala, an Ayurvedic formulation, against Mpro followed by molecular dynamics (MD) simulation (100 ns) to investigate their inhibitory potential against SARS-CoV-2. The top four best docked molecules (terflavin A, chebulagic acid, chebulinic acid, and corilagin) were selected for MD simulation study and the results obtained were compared to native ligand X77. From docking and MD simulation studies, the selected molecules showed promising binding affinity with the formation of stable complexes at the active binding pocket of Mpro and exhibited negative binding energy during MM-PBSA calculations, indication their strong binding affinity with the target protein. The identified bioactive molecules were further analyzed for drug-likeness by Lipinski's filter, ADMET and toxicity studies. Computational (in silico) investigations identified terflavin A, chebulagic acid, chebulinic acid, and corilagin from Triphala formulation as promising inhibitors of SARS-CoV-2 Mpro, suggesting experimental (in vitro/in vivo) studies to further explore their inhibitory mechanisms.
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Affiliation(s)
- Mithun Rudrapal
- Department of Pharmaceutical Chemistry, Rasiklal M. Dhariwal Institute of Pharmaceutical Education & Research, Pune 411019, Maharashtra, India
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri 38039, Turkey
| | - Johra Khan
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia
- Health and Basic Sciences Research Center, Majmaah University, Al Majmaah 11952, Saudi Arabia
| | - Mohammad Azam Ansari
- Department of Epidemic Disease Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabaia
| | - Mohammad N Alomary
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia
- Health and Basic Sciences Research Center, Majmaah University, Al Majmaah 11952, Saudi Arabia
- National Centre for Biotechnology, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - Rohitash Yadav
- Department of Pharmacology, All India Institute of Medical Sciences, Rishikesh 249203, India
| | - Tripti Sharma
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Siksha O Anusandhan Deemed to be University, Bhubaneswar 751003, Odisha, India
| | - Trina Ekawati Tallei
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, North Sulawesi, Indonesia
- The University Center of Excellence for Biotechnology and Conservation of Wallacea, Sam Ratulangi University, Manado, North Sulawesi 95115, Indonesia
| | | | - Ranjan Kumar Sahoo
- School of Pharmacy and Life Sciences, Centurion University of Technology and Management, Bhubaneswar 752050, Odisha, India
| | | | - Atul R Bendale
- Sandip Institute of Pharmaceutical Sciences, Nashik 422213, India
| | - James H Zothantluanga
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh 786004, Assam, India
| | - Dipak Chetia
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh 786004, Assam, India
| | - Sanjay G Walode
- Department of Pharmaceutical Chemistry, Rasiklal M. Dhariwal Institute of Pharmaceutical Education & Research, Pune 411019, Maharashtra, India
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43
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Chan WKB, Olson KM, Wotring JW, Sexton JZ, Carlson HA, Traynor JR. In silico analysis of SARS-CoV-2 proteins as targets for clinically available drugs. Sci Rep 2022; 12:5320. [PMID: 35351926 PMCID: PMC8963407 DOI: 10.1038/s41598-022-08320-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 03/02/2022] [Indexed: 12/20/2022] Open
Abstract
The ongoing pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires treatments with rapid clinical translatability. Here we develop a multi-target and multi-ligand virtual screening method to identify FDA-approved drugs with potential activity against SARS-CoV-2 at traditional and understudied viral targets. 1,268 FDA-approved small molecule drugs were docked to 47 putative binding sites across 23 SARS-CoV-2 proteins. We compared drugs between binding sites and filtered out compounds that had no reported activity in an in vitro screen against SARS-CoV-2 infection of human liver (Huh-7) cells. This identified 17 "high-confidence", and 97 "medium-confidence" drug-site pairs. The "high-confidence" group was subjected to molecular dynamics simulations to yield six compounds with stable binding poses at their optimal target proteins. Three drugs-amprenavir, levomefolic acid, and calcipotriol-were predicted to bind to 3 different sites on the spike protein, domperidone to the Mac1 domain of the non-structural protein (Nsp) 3, avanafil to Nsp15, and nintedanib to the nucleocapsid protein involved in packaging the viral RNA. Our "two-way" virtual docking screen also provides a framework to prioritize drugs for testing in future emergencies requiring rapidly available clinical drugs and/or treating diseases where a moderate number of targets are known.
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Affiliation(s)
- Wallace K B Chan
- Department of Pharmacology, University of Michigan, 2301 MSRBIII, 1150 W Medical Center Dr, Ann Arbor, MI, 48190-5606, USA
- Edward F Domino Research Center, University of Michigan, Ann Arbor, MI, 48190, USA
| | - Keith M Olson
- Department of Pharmacology, University of Michigan, 2301 MSRBIII, 1150 W Medical Center Dr, Ann Arbor, MI, 48190-5606, USA
- Edward F Domino Research Center, University of Michigan, Ann Arbor, MI, 48190, USA
| | - Jesse W Wotring
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, 48190, USA
| | - Jonathan Z Sexton
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, 48190, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48190, USA
| | - Heather A Carlson
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, 48190, USA
| | - John R Traynor
- Department of Pharmacology, University of Michigan, 2301 MSRBIII, 1150 W Medical Center Dr, Ann Arbor, MI, 48190-5606, USA.
- Edward F Domino Research Center, University of Michigan, Ann Arbor, MI, 48190, USA.
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, 48190, USA.
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Ghaznavi H, Shirvaliloo M, Sargazi S, Mohammadghasemipour Z, Shams Z, Hesari Z, Shahraki O, Nazarlou Z, Sheervalilou R, Shirvalilou S. SARS-CoV-2 and Influenza Viruses: Strategies to Cope with Co-infection and Bioinformatics Perspective. Cell Biol Int 2022; 46:1009-1020. [PMID: 35322909 PMCID: PMC9083817 DOI: 10.1002/cbin.11800] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/18/2022] [Accepted: 03/20/2022] [Indexed: 12/15/2022]
Abstract
Almost a century after the devastating pandemic of the Spanish flu, humankind is facing the relatively comparable global outbreak of COVID‐19. COVID‐19 is an infectious disease caused by SARS‐CoV‐2 with an unprecedented transmission pattern. In the face of the recent repercussions of COVID‐19, many have argued that the clinical experience with influenza through the last century may have tremendous implications in the containment of this newly emerged viral disease. During the last 2 years, from the emergence of COVID‐19, tremendous advances have been made in diagnosing and treating coinfections. Several approved vaccines are available now for the primary prevention of COVID‐19 and specific treatments exist to alleviate symptoms. The present review article aims to discuss the pathophysiology, diagnosis, and treatment of SARS‐CoV‐2 and influenza A virus coinfection while delivering a bioinformatics‐based insight into this subject matter.
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Affiliation(s)
- Habib Ghaznavi
- Pharmacology Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Milad Shirvaliloo
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Saman Sargazi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Zahra Mohammadghasemipour
- Department of Infectious Disease, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Zinat Shams
- Department of Biological Science, Kharazmi University, Tehran, Iran
| | - Zahra Hesari
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Omolbanin Shahraki
- Pharmacology Research Center, Zahedan University of Medical Sciences, Zahedan, Iran.,Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Ziba Nazarlou
- Material Engineering Department, College of Science Koç University, Istanbul, 34450, Turkey
| | - Roghayeh Sheervalilou
- Pharmacology Research Center, Zahedan University of Medical Sciences, Zahedan, Iran.,Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Sakine Shirvalilou
- Finetech in Medicine Research Center, Iran University of Medical Sciences, Tehran, Iran
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Zia SR. Identification of Potential Ligands of the Main Protease of Coronavirus SARS-CoV-2 (2019-nCoV) Using Multimodal Generative Neural-Networks. FRENCH-UKRAINIAN JOURNAL OF CHEMISTRY 2022. [DOI: 10.17721/fujcv10i1p30-47] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The recent outbreak of coronavirus disease 2019 (COVID-19) is posing a global threat to human population. The pandemic caused by novel coronavirus (2019-nCoV), also called as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2); first emerged in Wuhan city, Hubei province of China in December 2019. The rapid human to human transmission has caused the contagion to spread world-wide affecting 244,385,444 (244.4 million) people globally causing 4,961,489 (5 million) fatalities dated by 27 October 2021. At present, 6,697,607,393 (6.7 billion) vaccine doses have been administered dated by 27 October 2021, for the prevention of COVID-19 infections. Even so, this critical and threatening situation of pandemic and due to various variants’ emergence, the pandemic control has become challenging; this calls for gigantic efforts to find new potent drug candidates and effective therapeutic approaches against the virulent respiratory disease of COVID-19. In the respiratory morbidities of COVID-19, the functionally crucial drug target for the antiviral treatment could be the main protease/3-chymotrypsin protease (Mpro/3CLpro) enzyme that is primarily involved in viral maturation and replication. In view of this, in the current study I have designed a library of small molecules against the main protease (Mpro) of coronavirus SARS-CoV-2 (2019-nCoV) by using multimodal generative neural-networks. The scaffold-based molecular docking of the series of compounds at the active site of the protein was performed; binding poses of the molecules were evaluated and protein-ligand interaction studies followed by the binding affinity calculations validated the findings. I have identified a number of small promising lead compounds that could serve as potential inhibitors of the main protease (Mpro) enzyme of coronavirus SARS-CoV-2 (2019-nCoV). This study would serve as a step forward in the development of effective antiviral therapeutic agents against the COVID-19.
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46
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Azeem M, Mustafa G, Mahrosh HS. Virtual screening of phytochemicals by targeting multiple proteins of severe acute respiratory syndrome coronavirus 2: Molecular docking and molecular dynamics simulation studies. Int J Immunopathol Pharmacol 2022; 36:3946320221142793. [PMID: 36442514 PMCID: PMC9716588 DOI: 10.1177/03946320221142793] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 11/14/2022] [Indexed: 07/30/2023] Open
Abstract
OBJECTIVE Medicinal herbs are being investigated for medicationhg development against SARS-CoV-2 as a rich source of bioactive chemicals. One of the finest approaches for finding therapeutically effective drug molecules in real time is virtual screening scheme such as molecular docking in conjunction with molecular dynamics (MD) simulation. These virtual techniques provide an ample opportunity for the screening of plausible inhibitors of SARS-CoV-2 different target proteins from a comprehensive and extensive phytochemical library. The study was designed to identify potential phytochemicals by virtual screening against different receptor proteins. METHODS In the current study, a library of plant secondary metabolites was created by manually curating 120 phytochemicals known to have antimicrobial as well as antiviral properties. In the current study, different potential phytochemicals were identified by virtual screening against various selected receptor proteins (i.e., viral main proteases, RNA-dependent RNA polymerase (RdRp), ADP ribose phosphatase, nonstructural proteins NSP7, NSP8, and NSP9) which are key proteins responsible for transcription, replication and maturation of SARS-CoV-2 in the host. Top three phytochemicals were selected against each viral receptor protein based on their best S-scores, RMSD values, molecular interactions, binding patterns and drug-likeness properties. RESULTS The results of molecular docking study revealed that phytochemicals (i.e., baicalin, betaxanthin, epigallocatechin, fomecin A, gallic acid, hortensin, ichangin, kaempferol, limonoic acid, myricetin hexaacetat, pedalitin, quercetin, quercitrin, and silvestrol) have strong antiviral potential against SARS-CoV-2. Additionally, the reported preeminent reliable phytochemicals also revealed toxicity by no means during the evaluation through ADMET profiling. Moreover, the MD simulation study also exhibited thermal stability and stable binding affinity of the pedalitin with SARS-CoV-2 RdRp and SARS-CoV-2 main protease which suggests appreciable efficacy of the lead optimization. CONCLUSION The biological activity and pharmacologically distinguishing characteristics of these lead compounds also satisfied as repurposing antiviral drug contenders and are worth substantial evaluation in the biological laboratory for the recommendation of being plausible antiviral drug candidates against SARS-CoV-2.
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Affiliation(s)
- Muhammad Azeem
- Department of Biochemistry, Government College University Faisalabad, Faisalabad, Pakistan
| | - Ghulam Mustafa
- Department of Biochemistry, Government College University Faisalabad, Faisalabad, Pakistan
| | - Hafiza S Mahrosh
- Department of Biochemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
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Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. Comput Biol Med 2021; 141:105170. [PMID: 34968862 PMCID: PMC8709794 DOI: 10.1016/j.compbiomed.2021.105170] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 01/08/2023]
Abstract
SARS-CoV-2, an RNA virus, has been prone to high mutations since its first emergence in Wuhan, China, and throughout its spread. Its genome has been sequenced continuously by many countries, including Pakistan, but the results vary. Understanding its genomic patterns and connecting them with phenotypic features will help in devising therapeutic strategies. Thus, in this study, we explored the mutation landscape of 250 Pakistani isolates of SARS-CoV-2 genomes to check the genome diversity and examine the impact of these mutations on protein stability and viral pathogenesis in comparison with a reference sequence (Wuhan NC 045512.2). Our results revealed that structural proteins mainly exhibit more mutations than others in the Pakistani isolates; in particular, the nucleocapsid protein is highly mutated. In comparison, the spike protein is the most mutated protein globally. Furthermore, nsp12 was found to be the most mutated NSP in the Pakistani isolates and worldwide. Regarding accessory proteins, ORF3A is the most mutated in the Pakistani isolates, whereas ORF8 is highly mutated in world isolates. These mutations decrease the structural stability of their proteins and alter different biological pathways. Molecular docking, the dissociation constant (KD), and MM/GBSA analysis showed that mutations in the S protein alter its binding with ACE2. The spike protein mutations D614G-S943T-V622F (−75.17 kcal/mol), D614G-Q677H (−75.78 kcal/mol), and N74K-D614G (−73.84 kcal/mol) exhibit stronger binding energy than the wild type (−66.34 kcal/mol), thus increasing infectivity. Furthermore, the simulation results strongly corroborated the predicted protein servers. Our analysis findings also showed that E, M, ORF6, ORF7A, ORF7B, and ORF10 are the most stable coding genes; they may be suitable targets for vaccine and drug development.
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48
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Rodal Canales FJ, Pérez-Campos Mayoral L, Hernández-Huerta MT, Sánchez Navarro LM, Matias-Cervantes CA, Martínez Cruz M, Cruz Parada E, Zenteno E, Ramos-Martínez EG, Pérez-Campos Mayoral E, Romero Díaz C, Pérez-Campos E. Interaction of Spike protein and lipid membrane of SARS-CoV-2 with Ursodeoxycholic acid, an in-silico analysis. Sci Rep 2021; 11:22288. [PMID: 34782703 PMCID: PMC8593036 DOI: 10.1038/s41598-021-01705-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 11/01/2021] [Indexed: 12/18/2022] Open
Abstract
Numerous repositioned drugs have been sought to decrease the severity of SARS-CoV-2 infection. It is known that among its physicochemical properties, Ursodeoxycholic Acid (UDCA) has a reduction in surface tension and cholesterol solubilization, it has also been used to treat cholesterol gallstones and viral hepatitis. In this study, molecular docking was performed with the SARS-CoV-2 Spike protein and UDCA. In order to confirm this interaction, we used Molecular Dynamics (MD) in “SARS-CoV-2 Spike protein-UDCA”. Using another system, we also simulated MD with six UDCA residues around the Spike protein at random, naming this “SARS-CoV-2 Spike protein-6UDCA”. Finally, we evaluated the possible interaction between UDCA and different types of membranes, considering the possible membrane conformation of SARS-CoV-2, this was named “SARS-CoV-2 membrane-UDCA”. In the “SARS-CoV-2 Spike protein-UDCA”, we found that UDCA exhibits affinity towards the central region of the Spike protein structure of − 386.35 kcal/mol, in a region with 3 alpha helices, which comprises residues from K986 to C1032 of each monomer. MD confirmed that UDCA remains attached and occasionally forms hydrogen bonds with residues R995 and T998. In the presence of UDCA, we observed that the distances between residues atoms OG1 and CG2 of T998 in the monomers A, B, and C in the prefusion state do not change and remain at 5.93 ± 0.62 and 7.78 ± 0.51 Å, respectively, compared to the post-fusion state. Next, in “SARS-CoV-2 Spike protein-6UDCA”, the three UDCA showed affinity towards different regions of the Spike protein, but only one of them remained bound to the region between the region's heptad repeat 1 and heptad repeat 2 (HR1 and HR2) for 375 ps of the trajectory. The RMSD of monomer C was the smallest of the three monomers with a value of 2.89 ± 0.32, likewise, the smallest RMSF was also of the monomer C (2.25 ± 056). In addition, in the simulation of “SARS-CoV-2 membrane-UDCA”, UDCA had a higher affinity toward the virion-like membrane; where three of the four residues remained attached once they were close (5 Å, to the centre of mass) to the membrane by 30 ns. However, only one of them remained attached to the plasma-like membrane and this was in a cluster of cholesterol molecules. We have shown that UDCA interacts in two distinct regions of Spike protein sequences. In addition, UDCA tends to stay bound to the membrane, which could potentially reduce the internalization of SARS-CoV-2 in the host cell.
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Affiliation(s)
- Francisco Javier Rodal Canales
- Research Centre Faculty of Medicine UNAM-UABJO, Faculty of Medicine and Surgery, Autonomous University "Benito Juárez" of Oaxaca, 68020, Oaxaca, Mexico
| | - Laura Pérez-Campos Mayoral
- Research Centre Faculty of Medicine UNAM-UABJO, Faculty of Medicine and Surgery, Autonomous University "Benito Juárez" of Oaxaca, 68020, Oaxaca, Mexico
| | | | - Luis Manuel Sánchez Navarro
- Research Centre Faculty of Medicine UNAM-UABJO, Faculty of Medicine and Surgery, Autonomous University "Benito Juárez" of Oaxaca, 68020, Oaxaca, Mexico
| | | | | | - Eli Cruz Parada
- National Technology of Mexico/IT Oaxaca, 68030, Oaxaca, Mexico
| | - Edgar Zenteno
- Faculty of Medicine, National Autonomous University of Mexico, 04360, Mexico City, Mexico
| | | | - Eduardo Pérez-Campos Mayoral
- Research Centre Faculty of Medicine UNAM-UABJO, Faculty of Medicine and Surgery, Autonomous University "Benito Juárez" of Oaxaca, 68020, Oaxaca, Mexico
| | - Carlos Romero Díaz
- Research Centre Faculty of Medicine UNAM-UABJO, Faculty of Medicine and Surgery, Autonomous University "Benito Juárez" of Oaxaca, 68020, Oaxaca, Mexico.
| | - Eduardo Pérez-Campos
- National Technology of Mexico/IT Oaxaca, 68030, Oaxaca, Mexico. .,Clinical Pathology Laboratory, "Eduardo Pérez Ortega", 68000, Oaxaca, Mexico.
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Choudhury M, Dhanabalan AK, Goswami N. Understanding the binding mechanism for potential inhibition of SARS-CoV-2 Mpro and exploring the modes of ACE2 inhibition by hydroxychloroquine. J Cell Biochem 2021; 123:347-358. [PMID: 34741481 PMCID: PMC8657325 DOI: 10.1002/jcb.30174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 10/23/2021] [Accepted: 10/27/2021] [Indexed: 12/27/2022]
Abstract
As per the World Health Organization report, around 226 844 344 confirmed positive cases and 4 666 334 deaths are reported till September 17, 2021 due to the recent viral outbreak. A novel coronavirus (severe acute respiratory syndrome coronavirus 2 [SARS‐CoV‐2]) is responsible for the associated coronavirus disease (COVID‐19), which causes serious or even fatal respiratory tract infection and yet no approved therapeutics or effective treatment is currently available to combat the outbreak. Due to the emergency, the drug repurposing approach is being explored for COVID‐19. In this study, we attempt to understand the potential mechanism and also the effect of the approved antiviral drugs against the SARS‐CoV‐2 main protease (Mpro). To understand the mechanism of inhibition of the malaria drug hydroxychloroquine (HCQ) against SARS‐CoV‐2, we performed molecular interaction studies. The studies revealed that HCQ docked at the active site of the Human ACE2 receptor as a possible way of inhibition. Our in silico analysis revealed that the three drugs Lopinavir, Ritonavir, and Remdesivir showed interaction with the active site residues of Mpro. During molecular dynamics simulation, based on the binding free energy contributions, Lopinavir showed better results than Ritonavir and Remdesivir.
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Affiliation(s)
- Manisha Choudhury
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, Maharashtra, India
| | - Anantha K Dhanabalan
- CAS in Crystallography and Biophysics, University of Madras, Chennai, Tamil Nadu, India
| | - Nabajyoti Goswami
- Bioinformatics Infrastructure Facility, College of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati, Assam, India
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50
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Potential of turmeric-derived compounds against RNA-dependent RNA polymerase of SARS-CoV-2: An in-silico approach. Comput Biol Med 2021; 139:104965. [PMID: 34717229 PMCID: PMC8532373 DOI: 10.1016/j.compbiomed.2021.104965] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/18/2021] [Accepted: 10/18/2021] [Indexed: 01/18/2023]
Abstract
The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic. Currently, there are no particular antivirals available to battle with COVID-19. The RNA-dependent RNA polymerase (RdRp) has emerged as a novel drug target due to its essential role in virus replication. In this study, turmeric-derived compounds were chosen and subjected to in-silico analysis to evaluate their binding affinity against the RdRp-RNA complex of SARS-CoV-2. Our in-silico approach included the analysis of protein-ligand interactions by molecular docking and molecular dynamics simulations, followed by free energy calculations by molecular mechanics Poisson-Boltzmann surface area analysis. Curcumin and diacetylcurcumin showed stability and good binding affinity at the active site of the SARS-CoV-2 RdRp-RNA complex. Furthermore, to validate the potency of selected compounds, we compared them with Favipiravir and Remdesivir antiviral drugs from our previous analysis on targeting tea bioactive molecules to inhibit RdRp-RNA complex. The comparative analysis revealed that the selected compounds showed higher potential to be developed as RdRp-RNA inhibitors than antiviral medicines Remdesivir and Favipiravir. However, these compounds need to be further validated by in-vitro and in-vivo investigations.
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