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Arundina I, Frimayanti N, Surboyo MDC, Budhy TI, Iskandar B. 6-Octadecenoic and Oleic Acid in Liquid Smoke Rice Husk Showed COVID-19 Inhibitor Properties. Adv Pharmacol Pharm Sci 2024; 2024:8105595. [PMID: 38699656 PMCID: PMC11065493 DOI: 10.1155/2024/8105595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 04/04/2024] [Accepted: 04/15/2024] [Indexed: 05/05/2024] Open
Abstract
In recent years, liquid smoke rice husk (LSRH) has shown its therapeutic potency to diabetes, wound healing, stomatitis, and periodontitis. The phenol, 6-octadecenoic acid, oleic acid, and 9-octadecanoic acid were responsible for their therapeutic effect. The LSRH also demonstrated their potential for infectious diseases such as coronavirus disease (COVID-19). Therefore, the molecular dynamics (MDs) simulation and pharmacophore analysis was performed to analyse the binding stability of 6-octadecenoic and oleic acid. Based on MD simulation, 6-octadecenoic and oleic acids seemed to retain their interactions with Ser144 and Thr24, respectively, with hydrogen bond distance less than 2.9 Å. This interaction was stable during the simulation and has hydrophobic and hydrogen bonds/acceptors. The 6-octadecenoic acid and oleic acid were confirmed to have great potency as inhibitors for COVID-19. These compounds also showed that the existence of hydrophobic and hydrogen bonds/acceptors could increase biological activity.
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Affiliation(s)
- Ira Arundina
- Department of Oral Biology, Faculty of Dental Medicine, Universitas Airlangga, Surabaya 60132, Indonesia
| | - Neni Frimayanti
- Sekolah Tinggi Ilmu Farmasi (STIFAR), Pekanbaru, Riau, Indonesia
| | | | - Theresia Indah Budhy
- Department of Oral Pathology and Maxillofacial, Faculty of Dental Medicine, Universitas Airlangga, Surabaya 60132, Indonesia
| | - Benni Iskandar
- Sekolah Tinggi Ilmu Farmasi (STIFAR), Pekanbaru, Riau, Indonesia
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
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2
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Dakpa G, Kumar KJS, Nelen J, Pérez-Sánchez H, Wang SY. Antcin-B, a phytosterol-like compound from Taiwanofungus camphoratus inhibits SARS-CoV-2 3-chymotrypsin-like protease (3CL Pro) activity in silico and in vitro. Sci Rep 2023; 13:17106. [PMID: 37816832 PMCID: PMC10564890 DOI: 10.1038/s41598-023-44476-x] [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: 06/30/2023] [Accepted: 10/09/2023] [Indexed: 10/12/2023] Open
Abstract
Despite the remarkable development of highly effective vaccines, including mRNA-based vaccines, within a limited timeframe, coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is not been entirely eradicated. Thus, it is crucial to identify new effective anti-3CLPro compounds, pivotal for the replication of SARS-CoV-2. Here, we identified an antcin-B phytosterol-like compound from Taiwanofungus camphoratus that targets 3CLPro activity. MTT assay and ADMET prediction are employed for assessing potential cytotoxicity. Computational molecular modeling was used to screen various antcins and non-antcins for binding affinity and interaction type with 3CLPro. Further, these compounds were subjected to study their inhibitory effects on 3CLPro activity in vitro. Our results indicate that antcin-B has the best binding affinity by contacting residues like Leu141, Asn142, Glu166, and His163 via hydrogen bond and salt bridge and significantly inhibits 3CLPro activity, surpassing the positive control compound (GC376). The 100 ns molecular dynamics simulation studies showed that antcin-B formed consistent, long-lasting water bridges with Glu166 for their inhibitory activity. In summary, antcin-B could be useful to develop therapeutically viable drugs to inhibit SARS-CoV-2 replication alone or in combination with medications specific to other SARS-CoV-2 viral targets.
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Affiliation(s)
- Gyaltsen Dakpa
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 108, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 402, Taiwan
| | - K J Senthil Kumar
- Bachelor Program of Biotechnology, National Chung Hsing University, Taichung, 402, Taiwan
| | - Jochem Nelen
- Structural Bioinformatics and High-Performance Computing Research Group (BIO-HPC), HiTech Innovation Hub, Universidad Católica de Murcia (UCAM), 30107, Murcia, Spain
| | - Horacio Pérez-Sánchez
- Structural Bioinformatics and High-Performance Computing Research Group (BIO-HPC), HiTech Innovation Hub, Universidad Católica de Murcia (UCAM), 30107, Murcia, Spain
| | - Sheng-Yang Wang
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 108, Taiwan.
- Department of Forestry, National Chung Hsing University, Taichung, 402, Taiwan.
- Special Crop and Metabolome Discipline Cluster, Academy of Circle Economy, National Chung Hsing University, Taichung, 402, Taiwan.
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 108, Taiwan.
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3
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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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4
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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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5
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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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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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7
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de Oliveira OV, Cristina Andreazza Costa M, Marques da Costa R, Giordano Viegas R, Paluch AS, Miguel Castro Ferreira M. Traditional herbal compounds as candidates to inhibit the SARS-CoV-2 main protease: an in silico study. J Biomol Struct Dyn 2023; 41:1603-1616. [PMID: 36719113 DOI: 10.1080/07391102.2021.2023646] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
COVID-19, a disease caused by the SARS-CoV-2 virus, is responsible for a pandemic since March 2020 and it has no cure. Therefore, herein, different theoretical methods were used to obtain potential candidates from herbal compounds to inhibit the SARS-CoV-2 main protease (Mpro). Initially, the 16 best-scored compounds were selected from a library containing 4066 ligands using virtual screening by molecular docking. Among them, six molecules (physalin B 5,6-epoxide (PHY), methyl amentoflavone (MAM), withaphysalin C (WPC), daphnoline or trilobamine (TRI), cepharanoline (CEP) and tetrandrine (TET)) were selected based on Lipinski's rule and ADMET analysis as criteria. These compounds complexed with the Mpro were submitted to triplicate 100 ns molecular dynamics simulations. RMSD, RMSF, and radius of gyration results show that the overall protein structure is preserved along the simulation time. The average ΔGbinding values, calculated by the MM/PBSA method, were -41.7, -55.8, -45.2, -38.7, -49.3, and -57.9 kcal/mol for the PHY-Mpro, MAM-Mpro, WPC-Mpro, CEP-Mpro, TRI-Mpro, and TET-Mpro complexes, respectively. Pairwise decomposition analyses revealed that the binding pocket is formed by His41-Val42, Met165-Glu166-Leu167, Asp187, and Gln189. The PLS regression model generated by QSPR analysis indicated that non-polar and polar groups with the presence of hydrogen bond acceptors play an important role in the herbal compounds-Mpro interactions. Overall, we found six potential candidates to inhibit the SARS-CoV-2 Mpro and highlighted key residues from the binding pocket that can be used for future drug design. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | | | | | - Andrew S Paluch
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, OH, USA
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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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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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10
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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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11
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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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12
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Naidu SAG, Mustafa G, Clemens RA, Naidu AS. Plant-Derived Natural Non-Nucleoside Analog Inhibitors (NNAIs) against RNA-Dependent RNA Polymerase Complex (nsp7/nsp8/nsp12) of SARS-CoV-2. J Diet Suppl 2023; 20:254-283. [PMID: 34850656 DOI: 10.1080/19390211.2021.2006387] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The emergence of fast-spreading SARS-CoV-2 mutants has sparked a new phase of COVID-19 pandemic. There is a dire necessity for antivirals targeting highly conserved genomic domains on SARS-CoV-2 that are less prone to mutation. The nsp12, also known as the RNA-dependent RNA-polymerase (RdRp), the core component of 'SARS-CoV-2 replication-transcription complex', is a potential well-conserved druggable antiviral target. Several FDA-approved RdRp 'nucleotide analog inhibitors (NAIs)' such as remdesivir, have been repurposed to treat COVID-19 infections. The NAIs target RdRp protein translation and competitively block the nucleotide insertion into the RNA chain, resulting in the inhibition of viral replication. However, the replication proofreading function of nsp14-ExoN could provide resistance to SARS-CoV-2 against many NAIs. Conversely, the 'non-nucleoside analog inhibitors (NNAIs)' bind to allosteric sites on viral polymerase surface, change the redox state; thereby, exert antiviral activity by altering interactions between the enzyme substrate and active core catalytic site of the RdRp. NNAIs neither require metabolic activation (unlike NAIs) nor compete with intracellular pool of nucleotide triphosphates (NTPs) for anti-RdRp activity. The NNAIs from phytonutrient origin are potential antiviral candidates compared to their synthetic counterparts. Several in-silico studies reported the antiviral spectrum of natural phytonutrient-NNAIs such as Suramin, Silibinin (flavonolignan), Theaflavin (tea polyphenol), Baicalein (5,6,7-trihydroxyflavone), Corilagin (gallotannin), Hesperidin (citrus bioflavonoid), Lycorine (pyrrolidine alkaloid), with superior redox characteristics (free binding energy, hydrogen-bonds, etc.) than antiviral drugs (i.e. remdesivir, favipiravir). These phytonutrient-NNAIs also exert anti-inflammatory, antioxidant, immunomodulatory and cardioprotective functions, with multifunctional therapeutic benefits in the clinical management of COVID-19.
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Affiliation(s)
| | - Ghulam Mustafa
- Department of Biochemistry, Government College University, Faisalabad, Pakistan
| | - Roger A Clemens
- Department of International Regulatory Science, University of Southern California School of Pharmacy, Los Angeles, CA, USA
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13
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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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14
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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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15
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Sharma S, Sharma A, Bhattacharyya D, Chauhan RS. Computational identification of potential inhibitory compounds in Indian medicinal and aromatic plant species against major pathogenicity determinants of SARS-CoV-2. J Biomol Struct Dyn 2022; 40:14096-14114. [PMID: 34766880 DOI: 10.1080/07391102.2021.2000500] [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] [Indexed: 12/29/2022]
Abstract
SARS-CoV-2 (COVID-19) viral pandemic has been reported across 223 countries and territories. Globalized vaccination programs alongside administration of repurposed drugs will assumingly confer a stronger and longer individual specific immune protection. However, considering possible recurrence of the disease via new variants, a conveniently deliverable phytopharmaceutical drug might be the best option for COVID-19 treatment. In the current study, the efforts have been made to identify potential leads for inhalation therapy as nasal swabs have been reported to transfer viral load prominently. In that direction, 2363 Essential oil (EOs) compounds from Indian medicinal and aromatic plants were screened through docking analysis and potential candidates were shortlisted that can interfere with viral pathogenicity. The main protease (Mpro) of SARS-CoV-2 interacted closely with jatamansin (JM), 6,7-dehydroferruginol (FG) and beta-sitosterol (BS), while Papain-like Protease (PLpro) with friedelane-3-one (F3O) and lantadene D (LD) independently. Reduced Lantadene A (LAR) exhibited preferable interaction with RNA-dependent-RNA-polymerase (RdRp) whereas Lantadene A (LA) with RdRp and spike-glycoprotein (SG-pro) both target proteins. When compared against highest binding affinity conformations of well-known inhibitors of targets, these prioritized compounds conferred superior or comparable SARS-CoV-2 protein inhibition. Additionally, promising results were noted from pharmacokinetics prediction for all shortlisted compounds. Besides, molecular dynamics simulation for 100 ns in two replicates and binding free energy analysis revealed the stability of complexes with optimum compactness. To the best of our knowledge, the current investigation is a unique initial attempt whereby EO compounds have been computationally screened, irrespective of their known medicinal properties to fight COVID-19 infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shilpa Sharma
- Department of Biotechnology, School of Engineering & Applied Sciences, Bennett University, Uttar Pradesh, India
| | - Ashish Sharma
- Department of Biotechnology, School of Engineering & Applied Sciences, Bennett University, Uttar Pradesh, India
| | - Dipto Bhattacharyya
- Department of Biotechnology, School of Engineering & Applied Sciences, Bennett University, Uttar Pradesh, India
| | - Rajinder S Chauhan
- Department of Biotechnology, School of Engineering & Applied Sciences, Bennett University, Uttar Pradesh, India
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16
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Chandel S, Singh R, Gautam A, Ravichandiran V. Screening of Azadirachta indica phytoconstituents as GSK-3β inhibitor and its implication in neuroblastoma: molecular docking, molecular dynamics, MM-PBSA binding energy, and in-vitro study. J Biomol Struct Dyn 2022; 40:12827-12840. [PMID: 34569452 DOI: 10.1080/07391102.2021.1977705] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Glycogen synthase kinase-3 (GSK-3), a constitutively active serine/threonine kinase, primary regulator of various cellular activities varying from glycogen metabolism to cell proliferation and regulation. GSK-3β is associated with the pathogenesis of numerous human diseases, including cancer, metabolic disorder, and Alzheimer's disease. In this study, Azadirachta indica compounds were selected and further screened on the BOILED-Egg model. The compounds showing good GIT absorption were docked with the crystal structure of GSK-3β. The compounds with high docking score were submitted for the molecular dynamic simulation (MDS) and Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA). Based upon the MDS and MM-PBSA study, gedunin showed the highest binding energy throughout the MDS process. Gedunin was isolated from the Azadirachta indica, and its efficacy on GSK-3β inhibition was studied in the human neuroblastoma (SH-SY5Y) cells. Gedunin induced apoptosis and anti-proliferative activity by arresting G2/M phase, as evident by cell-cycle analysis. From immunoblot study, gedunin significantly enhanced the expression of an inhibitory form of GSK-3β (p-GSK-3β Ser9) in concentration-dependent manner. Our findings demonstrate that gedunin may act as an effective GSK-3β inhibitor suggesting that this compound may be used for the management of neuroblastoma. Further preclinical and clinical investigation is desirable.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shivani Chandel
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Rajveer Singh
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Anupam Gautam
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany.,International Max Planck Research School "From Molecules to Organisms", Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Velayutham Ravichandiran
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
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17
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Pisoschi AM, Iordache F, Stanca L, Gajaila I, Ghimpeteanu OM, Geicu OI, Bilteanu L, Serban AI. Antioxidant, Anti-inflammatory, and Immunomodulatory Roles of Nonvitamin Antioxidants in Anti-SARS-CoV-2 Therapy. J Med Chem 2022; 65:12562-12593. [PMID: 36136726 PMCID: PMC9514372 DOI: 10.1021/acs.jmedchem.2c01134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Indexed: 11/28/2022]
Abstract
Viral pathologies encompass activation of pro-oxidative pathways and inflammatory burst. Alleviating overproduction of reactive oxygen species and cytokine storm in COVID-19 is essential to counteract the immunogenic damage in endothelium and alveolar membranes. Antioxidants alleviate oxidative stress, cytokine storm, hyperinflammation, and diminish the risk of organ failure. Direct antiviral roles imply: impact on viral spike protein, interference with the ACE2 receptor, inhibition of dipeptidyl peptidase 4, transmembrane protease serine 2 or furin, and impact on of helicase, papain-like protease, 3-chyomotrypsin like protease, and RNA-dependent RNA polymerase. Prooxidative environment favors conformational changes in the receptor binding domain, promoting the affinity of the spike protein for the host receptor. Viral pathologies imply a vicious cycle, oxidative stress promoting inflammatory responses, and vice versa. The same was noticed with respect to the relationship antioxidant impairment-viral replication. Timing, dosage, pro-oxidative activities, mutual influences, and interference with other antioxidants should be carefully regarded. Deficiency is linked to illness severity.
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Affiliation(s)
- Aurelia Magdalena Pisoschi
- Faculty of Veterinary Medicine, Department Preclinical
Sciences, University of Agronomic Sciences and Veterinary Medicine of
Bucharest, 105 Splaiul Independentei, 050097Bucharest,
Romania
| | - Florin Iordache
- Faculty of Veterinary Medicine, Department Preclinical
Sciences, University of Agronomic Sciences and Veterinary Medicine of
Bucharest, 105 Splaiul Independentei, 050097Bucharest,
Romania
| | - Loredana Stanca
- Faculty of Veterinary Medicine, Department Preclinical
Sciences, University of Agronomic Sciences and Veterinary Medicine of
Bucharest, 105 Splaiul Independentei, 050097Bucharest,
Romania
| | - Iuliana Gajaila
- Faculty of Veterinary Medicine, Department Preclinical
Sciences, University of Agronomic Sciences and Veterinary Medicine of
Bucharest, 105 Splaiul Independentei, 050097Bucharest,
Romania
| | - Oana Margarita Ghimpeteanu
- Faculty of Veterinary Medicine, Department Preclinical
Sciences, University of Agronomic Sciences and Veterinary Medicine of
Bucharest, 105 Splaiul Independentei, 050097Bucharest,
Romania
| | - Ovidiu Ionut Geicu
- Faculty of Veterinary Medicine, Department Preclinical
Sciences, University of Agronomic Sciences and Veterinary Medicine of
Bucharest, 105 Splaiul Independentei, 050097Bucharest,
Romania
- Faculty of Biology, Department Biochemistry and
Molecular Biology, University of Bucharest, 91-95 Splaiul
Independentei, 050095Bucharest, Romania
| | - Liviu Bilteanu
- Faculty of Veterinary Medicine, Department Preclinical
Sciences, University of Agronomic Sciences and Veterinary Medicine of
Bucharest, 105 Splaiul Independentei, 050097Bucharest,
Romania
- Molecular Nanotechnology Laboratory,
National Institute for Research and Development in
Microtechnologies, 126A Erou Iancu Nicolae Street, 077190Bucharest,
Romania
| | - Andreea Iren Serban
- Faculty of Veterinary Medicine, Department Preclinical
Sciences, University of Agronomic Sciences and Veterinary Medicine of
Bucharest, 105 Splaiul Independentei, 050097Bucharest,
Romania
- Faculty of Biology, Department Biochemistry and
Molecular Biology, University of Bucharest, 91-95 Splaiul
Independentei, 050095Bucharest, Romania
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18
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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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19
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Mangrio GR, Maneengam A, Khalid Z, Jafar TH, Chanihoon GQ, Nassani R, Unar A. RP-HPLC Method Development, Validation, and Drug Repurposing of Sofosbuvir Pharmaceutical Dosage Form: A Multidimensional Study. ENVIRONMENTAL RESEARCH 2022; 212:113282. [PMID: 35487258 DOI: 10.1016/j.envres.2022.113282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 04/05/2022] [Accepted: 04/08/2022] [Indexed: 06/14/2023]
Abstract
A smooth, exceptionally sensitive, correct, and extra reproducible RP-HPLC technique was developed and demonstrated to estimate Sofosbuvir (SOF) in pharmaceutical dosage formulations. This process was carried out by Agilent High-Pressure Liquid Chromatograph 1260 with GI311C Quat. Pump, Phenomenex Luna C-18 (150 mm × 4.6 mm × 5 μm) (USA), and Photodiode Array Detector (PDA) G1315D. The cell section, including acetonitrile and methanol with 80:20 v/v and solution (B) 0.1% phosphoric acid (40:60), was used for the study. However, 10 μL of the sample was injected with a drift flow of 1 mL/min. The separation occurred at a column temperature of 30 °C, and the eluents used PDA set at 260 nm. The retention time of SOF was 5 min. The calibration curve was modified linearly within the range of 0.05-0.15 mg/mL with a correlation coefficient of 0.99 and genuine linear dating among top vicinity and consciousness in the calibration curve. The detection and quantification restrictions were 0.001 and 0.003 mg/mL, respectively. SOF recovery from pharmaceutical components ranged from 98% to 99%. The percentage assay of SOF was 99%. Analytical validation parameters, such as specificity, linearity, precision, accuracy, and selectivity, were studied, and the percentage relative standard deviation (%RSD) was less than 2%. All other key parameters were observed within the desired thresholds. Hence, the proposed RP-HPLC technique was proven effective for developing SOF in bulk and pharmaceutical pill dosage forms. SOF was found to interact with SARS-COV-2 nsp12, and molecular docking results revealed its high affinity and firm binding within the active site groove of nsp12. The key interacting residues include; LYS-72, GLN-75, MET-80 ALA-99, ASN-99, TRP-100, TYR-101 with ASN-99 and TRP-100 forming hydrogen bonds. Molecular Dynamics simulation of SOF and nsp12 complex elucidated that the system was stable throughout 20ns. Therefore, this drug repurposing strategy for SOF can be used for treating COVID-19 infections by performing animal experiments and accurate clinical trials in the future.
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Affiliation(s)
| | - Apichit Maneengam
- Department of Mechanical Engineering Technology, College of Industrial Technology, King Mongkut's University of Technology North Bangkok, Wongsawang, Bangsue, Bangkok, 10800, Thailand
| | - Zunera Khalid
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, PR China
| | | | - Ghulam Qadir Chanihoon
- National Center of Excellence in Analytical Chemistry, University of Sindh, Jamshoro, 76090, Pakistan
| | - Rayan Nassani
- Center for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Ahsanullah Unar
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, PR China.
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20
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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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21
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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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22
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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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23
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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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24
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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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25
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Chauhan M, Bhardwaj VK, Kumar A, Kumar V, Kumar P, Enayathullah MG, Thomas J, George J, Kumar BK, Purohit R, Kumar A, Kumar S. Theaflavin 3-gallate inhibits the main protease (M pro) of SARS-CoV-2 and reduces its count in vitro. Sci Rep 2022; 12:13146. [PMID: 35908093 PMCID: PMC9338964 DOI: 10.1038/s41598-022-17558-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 07/27/2022] [Indexed: 12/26/2022] Open
Abstract
The main protease (Mpro) of SARS-CoV-2 has been recognized as an attractive drug target because of its central role in viral replication. Our previous preliminary molecular docking studies showed that theaflavin 3-gallate (a natural bioactive molecule derived from theaflavin and found in high abundance in black tea) exhibited better docking scores than repurposed drugs (Atazanavir, Darunavir, Lopinavir). In this study, conventional and steered MD-simulations analyses revealed stronger interactions of theaflavin 3-gallate with the active site residues of Mpro than theaflavin and a standard molecule GC373 (a known inhibitor of Mpro and novel broad-spectrum anti-viral agent). Theaflavin 3-gallate inhibited Mpro protein of SARS-CoV-2 with an IC50 value of 18.48 ± 1.29 μM. Treatment of SARS-CoV-2 (Indian/a3i clade/2020 isolate) with 200 μM of theaflavin 3-gallate in vitro using Vero cells and quantifying viral transcripts demonstrated reduction of viral count by 75% (viral particles reduced from Log106.7 to Log106.1). Overall, our findings suggest that theaflavin 3-gallate effectively targets the Mpro thus limiting the replication of the SARS-CoV-2 virus in vitro.
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Affiliation(s)
- Mahima Chauhan
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India.,Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
| | - Vijay Kumar Bhardwaj
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India.,Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India.,Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Asheesh Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India.,Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
| | - Vinod Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Pawan Kumar
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India.,Chemical Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - M Ghalib Enayathullah
- CSIR-Center for Cellular and Molecular Biology, Annexe-II, Medical Biotechnology Complex, Uppal Road, Hyderabad, Telangana, 500007, India
| | - Jessie Thomas
- CSIR-Center for Cellular and Molecular Biology, Annexe-II, Medical Biotechnology Complex, Uppal Road, Hyderabad, Telangana, 500007, India
| | - Joel George
- CSIR-Center for Cellular and Molecular Biology, Annexe-II, Medical Biotechnology Complex, Uppal Road, Hyderabad, Telangana, 500007, India
| | - Bokara Kiran Kumar
- CSIR-Center for Cellular and Molecular Biology, Annexe-II, Medical Biotechnology Complex, Uppal Road, Hyderabad, Telangana, 500007, India.
| | - Rituraj Purohit
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India. .,Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India. .,Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India.
| | - Arun Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India. .,Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India.
| | - Sanjay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
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26
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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: 30] [Impact Index Per Article: 15.0] [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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27
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Singh R, Bhardwaj VK, Das P, Bhattacherjee D, Zyryanov GV, Purohit R. Benchmarking the ability of novel compounds to inhibit SARS-CoV-2 main protease using steered molecular dynamics simulations. Comput Biol Med 2022; 146:105572. [PMID: 35551011 PMCID: PMC9052739 DOI: 10.1016/j.compbiomed.2022.105572] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 01/31/2023]
Abstract
BACKGROUND The SARS-CoV-2 main protease (Mpro) is an attractive target in the COVID-19 drug development process. It catalyzes the polyprotein's translation from viral RNA and specifies a particular cleavage site. Due to the absence of identical cleavage specificity in human cell proteases, targeting Mpro with chemical compounds can obstruct the replication of the virus. METHODS To explore the potential binding mechanisms of 1,2,3-triazole scaffolds in comparison to co-crystallized inhibitors 11a and 11b towards Mpro, we herein utilized molecular dynamics and enhanced sampling simulation studies. RESULTS AND CONCLUSION All the 1,2,3-triazole scaffolds interacted with catalytic residues (Cys145 and His41) and binding pocket residues of Mpro involving Met165, Glu166, Ser144, Gln189, His163, and Met49. Furthermore, the adequate binding free energy and potential mean force of the topmost compound 3h was comparable to the experimental inhibitors 11a and 11b of Mpro. Overall, the current analysis could be beneficial in developing the SARS-CoV-2 Mpro potential inhibitors.
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Affiliation(s)
- Rahul Singh
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India,Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vijay Kumar Bhardwaj
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India,Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Pralay Das
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India,Natural Product Chemistry and Process Development, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Dhananjay Bhattacherjee
- Ural Federal University Named After the First President of Russia B. N. Yeltsin, 19 ul. Mira, 620002, Ekaterinburg, Russian Federation
| | - Grigory V. Zyryanov
- Ural Federal University Named After the First President of Russia B. N. Yeltsin, 19 ul. Mira, 620002, Ekaterinburg, Russian Federation,I. Ya. Postovsky Institute of Organic Synthesis, Ural Branch of the Russian Academy of Sciences, 22 ul. S. Kovalevskoi, 620219, Ekaterinburg, Russian Federation
| | - Rituraj Purohit
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India,Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India,Corresponding author. Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India
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28
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Wang K, Wang L, Li M, Xie B, He L, Wang M, Zhang R, Hou N, Zhang Y, Jia F. Real-Word Effectiveness of Global COVID-19 Vaccines Against SARS-CoV-2 Variants: A Systematic Review and Meta-Analysis. Front Med (Lausanne) 2022; 9:820544. [PMID: 35665358 PMCID: PMC9160927 DOI: 10.3389/fmed.2022.820544] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 04/05/2022] [Indexed: 12/14/2022] Open
Abstract
Background Currently, promoted vaccinations against SARS-CoV-2 are being given out globally. However, the occurrence of numerous COVID-19 variants has hindered the goal of rapid mitigation of the COVID-19 pandemic by effective mass vaccinations. The real-word effectiveness of the current vaccines against COVID-19 variants has not been assessed by published reviews. Therefore, our study evaluated the overall effectiveness of current vaccines and the differences between the various vaccines and variants. Methods PubMed, Embase, Cochrane Library, medRxiv, bioRxiv, and arXiv were searched to screen the eligible studies. The Newcastle-Ottawa scale and the Egger test were applied to estimate the quality of the literature and any publication bias, respectively. The pooled incident rates of different variants after vaccination were estimated by single-arm analysis. Meanwhile, the pooled efficacies of various vaccines against variants were evaluated by two-arm analysis using odds ratios (ORs) and vaccine effectiveness (VE). Results A total of 6,118 studies were identified initially and 44 articles were included. We found that the overall incidence of variants post first/second vaccine were 0.07 and 0.03, respectively. The VE of the incidence of variants post first vaccine between the vaccine and the placebo or unvaccinated population was 40% and post second vaccine was 96%, respectively. The sub-single-arm analysis showed a low prevalence rate of COVID-19 variants after specific vaccination with the pooled incidence below 0.10 in most subgroups. Meanwhile, the sub-two-arm analysis indicated that most current vaccines had a good or moderate preventive effect on certain variants considering that the VE in these subgroups was between 66 and 95%, which was broadly in line with the results of the sub-single-arm analysis. Conclusion Our meta-analysis shows that the current vaccines that are used globally could prevent COVID-19 infection and restrict the spread of variants to a great extent. We would also support maximizing vaccine uptake with two doses, as the effectiveness of which was more marked compared with one dose. Although the mRNA vaccine was the most effective against variants according to our study, specific vaccines should be taken into account based on the local dominant prevalence of variants.
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Affiliation(s)
- Kai Wang
- Department of Critical Care Medicine, Zibo Central Hospital, Shandong First Medical University and Shandong Academy of Medical Sciences, Zibo, China
| | - Lin Wang
- Department of Critical Care Medicine, Zibo Central Hospital, Shandong First Medical University and Shandong Academy of Medical Sciences, Zibo, China
| | - Mingzhe Li
- Independent Researcher, Leeds, United Kingdom
| | - Bing Xie
- Department of Hand and Foot Surgery, Zibo Central Hospital, Shandong First Medical University and Shandong Academy of Medical Sciences, Zibo, China
| | - Lu He
- Hubei University of Medicine, Shiyan, China
| | - Meiyu Wang
- Department of Cardiology, The People's Hospital of Zhangdian District, Zibo, China
| | - Rumin Zhang
- Department of Critical Care Medicine, Zibo Central Hospital, Shandong First Medical University and Shandong Academy of Medical Sciences, Zibo, China
| | - Nianzong Hou
- Department of Hand and Foot Surgery, Zibo Central Hospital, Shandong First Medical University and Shandong Academy of Medical Sciences, Zibo, China
| | - Yi Zhang
- Department of Hand and Foot Surgery, Zibo Central Hospital, Shandong First Medical University and Shandong Academy of Medical Sciences, Zibo, China
| | - Fusen Jia
- Department of Hand and Foot Surgery, Zibo Central Hospital, Shandong First Medical University and Shandong Academy of Medical Sciences, Zibo, China
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29
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Rokni M, Sarhadi M, Heidari Nia M, Mohamed Khosroshahi L, Asghari S, Sargazi S, Mirinejad S, Saravani R. Single nucleotide polymorphisms located in TNFA, IL1RN, IL6R, and IL6 genes are associated with COVID-19 risk and severity in an Iranian population. Cell Biol Int 2022; 46:1109-1127. [PMID: 35521908 PMCID: PMC9347541 DOI: 10.1002/cbin.11807] [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: 11/12/2021] [Revised: 01/29/2022] [Accepted: 03/07/2022] [Indexed: 12/12/2022]
Abstract
Cytokines play pivotal functions in coronavirus disease 2019 (COVID-19) pathogenesis. However, little is known about the rationale and importance of genetic variations associated with immune system responses, so-called "immunogenetic profiling." We studied whether polymorphisms of IL6, IL6R, TNFA, and IL1RN affect the disorder severity and outcome in patients infected with COVID19. We recruited 317 hospitalized patients with laboratory-confirmed COVID-19 from Bu-Ali hospital and 317 high-risk participants who had high exposure to COVID-19 patients but with a negative real-time-polymerase chain reaction (PCR) test. Multiple regression analyses were applied. We indicated that participants carrying the A allele in TNFA-rs361525, G>A (p < .004), the C allele in IL1RN-rs419598 T>C (p < .004), the A allele in IL6R-rs2228145, A>C (p = .047) are more susceptible to develop COVID-19. In contrast, those who carry the G allele of IL6-rs2069827, G>T (p = .01), are more protected from COVID-19. Also, we compared the various genotypes regarding the disorder severity and poor prognosis; we found that the AA genotype in TNFA is related to more aggressive illness and bad prognostic in contrast to the other inflammatory cytokines' genotypes. In addition, a high level of inflammatory indications, such as neutrophil-to-lymphocyte ratio and systemic immune-inflammation index, was observed in deceased patients compared with the survived subjects (p < .0001). We advised considering inflammatory cytokines polymorphisms as the main item to realize the therapeutic response against the acute respiratory distress syndrome induced by the SARS-CoV-2 virus.
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Affiliation(s)
- Mohsen Rokni
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Department of Immunology, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mohammad Sarhadi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Milad Heidari Nia
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | | | - Somaye Asghari
- Department of Immunology, Buali Hospital of Laboratory, Zahedan University of Medical Sciences, Zahedan, 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
| | - Shekoufeh Mirinejad
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Ramin Saravani
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran.,Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
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30
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Kicker E, Tittel G, Schaller T, Pferschy-Wenzig EM, Zatloukal K, Bauer R. SARS-CoV-2 neutralizing activity of polyphenols in a special green tea extract preparation. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 98:153970. [PMID: 35144138 PMCID: PMC8801126 DOI: 10.1016/j.phymed.2022.153970] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 01/20/2022] [Accepted: 01/27/2022] [Indexed: 05/05/2023]
Abstract
BACKGROUND The COVID-19 pandemic will continue to threaten our health care systems in the next years. In addition to vaccination there is a need for effective tools for prevention and treatment. Products from natural sources, like standardized plant extracts offer a wide range of antiviral effects and possible applications. PURPOSE The aim of this study was to investigate, whether a sorbitol/lecithin-based throat spray containing concentrated green tea extract (sGTE) interacts with SARS-CoV-2 viral particles and additionally is capable to block the virus replication. STUDY DESIGN AND METHODS The antiviral effect was studied in a VeroE6 cell culture model, including concentration/effect correlations and the biological mechanism of virus blockade, using the Wuhan type of SARS CoV-2 as well as its beta- and delta-mutations. In addition, the qualitative and quantitative tannin profile present on the oral mucosa after spray application has been investigated by LC-MS/MS and HPLC-DAD analyses of (-)-epigallocatechin-3-O-gallate (EGCG) and related catechin derivatives. RESULTS The findings of this study demonstrate, that sGTE has strong neutralizing activity on SARS-CoV-2 resulting in an up to 6,3E+04-fold reduction of infectivity independent from the strain. The type of interaction of sGTE with surface proteins seems to be direct and non-specific concerning the viral surface protein structures and resembles the general non-specific activity of polyphenols. By HPLC-DAD analysis, eight catechins were identified in sGTE, with EGCG and (-)-epicatechin-3-O-gallate as the most abundant ones. The total content of catechin derivatives, calculated as catechin, was 76 g/100 g. LC-MS/MS and HPLC-DAD analyses of throat swabs after application of a sGTE spray have shown that the concentrations of green tea tannins in the pharyngeal mucosa are higher than the effective dose found in the in vitro studies with SARS-CoV-2, even 1 h after the last application. CONCLUSION The findings of this study suggest that sGTE has strong neutralizing activity on SARS-CoV-2 independent from the strain (Wuhan strain, beta- or delta-variants). sGTE might be relevant for reduction of corresponding viral infections when periodically applied to mouth and throat.
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Affiliation(s)
- Eva Kicker
- Diagnostic and Research Center for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; BioTechMed, Mozartgasse 12/II, 8010 Graz, Austria
| | - Gerolf Tittel
- Phytovisions GmbH & Co. KG, Karwendelstrasse 29, 82467 Garmisch-Partenkirchen, Germany
| | - Tanja Schaller
- Dronania pharmaceuticals GmbH, Karl- Benz- Strasse 3, 86825 Bad Woerishofen, Germany
| | - Eva-Maria Pferschy-Wenzig
- Institute of Pharmaceutical Sciences, University of Graz, Beethovenstraße 8, 8010 Graz, Austria; BioTechMed, Mozartgasse 12/II, 8010 Graz, Austria
| | - Kurt Zatloukal
- Diagnostic and Research Center for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; BioTechMed, Mozartgasse 12/II, 8010 Graz, Austria
| | - Rudolf Bauer
- Institute of Pharmaceutical Sciences, University of Graz, Beethovenstraße 8, 8010 Graz, Austria; BioTechMed, Mozartgasse 12/II, 8010 Graz, Austria.
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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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32
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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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Liu SY, Wang W, Ke JP, Zhang P, Chu GX, Bao GH. Discovery of Camellia sinensis catechins as SARS-CoV-2 3CL protease inhibitors through molecular docking, intra and extra cellular assays. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 96:153853. [PMID: 34799184 PMCID: PMC8575542 DOI: 10.1016/j.phymed.2021.153853] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 10/26/2021] [Accepted: 11/06/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND AND PURPOSE Previous studies suggest that major Camellia sinensis (tea) catechins can inhibit 3-chymotrypsin-like cysteine protease (3CLpro), inspiring us to study 3CLpro inhibition of the recently discovered catechins from tea by our group. METHODS Autodock was used to dock 3CLpro and 16 tea catechins. Further, a 3CLpro activity detection system was used to test their intra and extra cellular 3CLpro inhibitory activity. Surface plasmon resonance (SPR) was used to analyze the dissociation constant (KD) between the catechins and 3CLpro. RESULTS Docking data suggested that 3CLpro interacted with the selected 16 catechins with low binding energy through the key amino acid residues Thr24, Thr26, Asn142, Gly143, His163, and Gln189. The selected catechins other than zijuanin D (3) and (-)-8-(5''R)-N-ethyl-2-pyrrolidinone-3-O-cinnamoylepicatechin (11) can inhibit 3CLpro intracellularly. The extracellular 3CLpro IC50 values of (-)-epicatechin 3-O-caffeoate (EC-C, 1), zijuanin C (2), etc-pyrrolidinone C and D (6), etc-pyrrolidinone A (9), (+)-gallocatechin gallate (GCG), and (-)-epicatechin gallate (ECG) are 1.58 ± 0.21, 41.2 ± 3.56, 0.90 ± 0.03, 46.71 ± 10.50, 3.38 ± 0.48, and 71.78 ± 8.36 µM, respectively. The KD values of 1, 6, and GCG are 4.29, 3.46, and 3.36 µM, respectively. CONCLUSION Together, EC-C (1), etc-pyrrolidinone C and D (6), and GCG are strong 3CLpro inhibitors. Our results suggest that structural modification of catechins could be conducted by esterificating the 3-OH as well as changing the configuration of C-3, C-3''' or C-5''' to discover strong SARS-CoV-2 inhibitors.
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Affiliation(s)
- Shi-Yu Liu
- Natural Products Laboratory, State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, People's Republic of China
| | - Wei Wang
- Natural Products Laboratory, State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, People's Republic of China; Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu'an, 237000, China
| | - Jia-Ping Ke
- Natural Products Laboratory, State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, People's Republic of China
| | - Peng Zhang
- Natural Products Laboratory, State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, People's Republic of China
| | - Gang-Xiu Chu
- School of information and computer, Anhui Agricultural University, Hefei, People's Republic of China.
| | - Guan-Hu Bao
- Natural Products Laboratory, State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, People's Republic of China.
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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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Rahbar MR, Jahangiri A, Khalili S, Zarei M, Mehrabani-Zeinabad K, Khalesi B, Pourzardosht N, Hessami A, Nezafat N, Sadraei S, Negahdaripour M. Hotspots for mutations in the SARS-CoV-2 spike glycoprotein: a correspondence analysis. Sci Rep 2021; 11:23622. [PMID: 34880279 PMCID: PMC8654821 DOI: 10.1038/s41598-021-01655-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 11/01/2021] [Indexed: 12/19/2022] Open
Abstract
Spike glycoprotein (Sgp) is liable for binding of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to the host receptors. Since Sgp is the main target for vaccine and drug designing, elucidating its mutation pattern could help in this regard. This study is aimed at investigating the correspondence of specific residues to the SgpSARS-CoV-2 functionality by explorative interpretation of sequence alignments. Centrality analysis of the Sgp dissects the importance of these residues in the interaction network of the RBD-ACE2 (receptor-binding domain) complex and furin cleavage site. Correspondence of RBD to threonine500 and asparagine501 and furin cleavage site to glutamine675, glutamine677, threonine678, and alanine684 was observed; all residues are exactly located at the interaction interfaces. The harmonious location of residues dictates the RBD binding property and the flexibility, hydrophobicity, and accessibility of the furin cleavage site. These species-specific residues can be assumed as real targets of evolution, while other substitutions tend to support them. Moreover, all these residues are parts of experimentally identified epitopes. Therefore, their substitution may affect vaccine efficacy. Higher rate of RBD maintenance than furin cleavage site was predicted. The accumulation of substitutions reinforces the probability of the multi-host circulation of the virus and emphasizes the enduring evolutionary events.
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Affiliation(s)
- Mohammad Reza Rahbar
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abolfazl Jahangiri
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Saeed Khalili
- Department of Biology Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran
| | - Mahboubeh Zarei
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Kamran Mehrabani-Zeinabad
- Department of Biostatistics, Faculty of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Bahman Khalesi
- Department of Research and Production of Poultry Viral Vaccine, Razi Vaccine, and Serum Research Institute, Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Navid Pourzardosht
- Cellular and Molecular Research Center, Faculty of Medicine, Guilan University of Medical Sciences, Rasht, Iran
- Biochemistry Department, Guilan University of Medical Sciences, Rasht, Iran
| | - Anahita Hessami
- School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Navid Nezafat
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Saman Sadraei
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Manica Negahdaripour
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, P.O. Box 71345-1583, Shiraz, Iran.
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36
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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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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: 46] [Impact Index Per Article: 15.3] [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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Characterization of the non-covalent interaction between the PF-07321332 inhibitor and the SARS-CoV-2 main protease. J Mol Graph Model 2021; 110:108042. [PMID: 34653812 PMCID: PMC8491126 DOI: 10.1016/j.jmgm.2021.108042] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/22/2021] [Accepted: 09/27/2021] [Indexed: 12/12/2022]
Abstract
We have studied the non-covalent interaction between PF-07321332 and SARS-CoV-2 main protease at the atomic level using a computational approach based on extensive molecular dynamics simulations with explicit solvent. PF-07321332, whose chemical structure has been recently disclosed, is a promising oral antiviral clinical candidate with well-established anti-SARS-CoV-2 activity in vitro. The drug, currently in phase III clinical trials in combination with ritonavir, relies on the electrophilic attack of a nitrile warhead to the catalytic cysteine of the protease. Nonbonded interaction between the inhibitor and the residues of the binding pocket, as well as with water molecules on the protein surface, have been characterized using two different force fields and the two possible protonation states of the main protease catalytic dyad HIS41-CYS145. When the catalytic dyad is in the neutral state, the non-covalent binding is likely to be stronger. Molecular dynamics simulations seems to lend support for an inhibitory mechanism in two steps: a first non-covalent addition with the dyad in neutral form and then the formation of the thiolate-imidazolium ion pair and the ligand relocation for finalising the electrophilic attack.
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Zhu J, Shen D, Wu W, Jin B, Wu S. Hydration inhibition mechanism of gypsum on tricalcium aluminate from ReaxFF molecular dynamics simulation and quantum chemical calculation. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1984463] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Jie Zhu
- College of Civil and Transportation Engineering, Hohai University, Nanjing, People’s Republic of China
| | - Dejian Shen
- College of Civil and Transportation Engineering, Hohai University, Nanjing, People’s Republic of China
| | - Wei Wu
- School of Energy and Environment, Southeast University, Nanjing, People’s Republic of China
| | - Baosheng Jin
- School of Energy and Environment, Southeast University, Nanjing, People’s Republic of China
| | - Shengxing Wu
- College of Civil and Transportation Engineering, Hohai University, Nanjing, People’s Republic of China
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Shahabadi N, Zendehcheshm S, Mahdavi M, Khademi F. Inhibitory activity of FDA-approved drugs cetilistat, abiraterone, diiodohydroxyquinoline, bexarotene, remdesivir, and hydroxychloroquine on COVID-19 main protease and human ACE2 receptor: A comparative in silico approach. INFORMATICS IN MEDICINE UNLOCKED 2021; 26:100745. [PMID: 34568544 PMCID: PMC8455240 DOI: 10.1016/j.imu.2021.100745] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/20/2021] [Accepted: 09/20/2021] [Indexed: 12/23/2022] Open
Abstract
By September 1, 2021, SARS-CoV-2, a respiratory virus that prompted Coronavirus Disease in 2019, had infected approximately 218,567,442 patients and claimed 4,534,151 lives. There are currently no specific treatments available for this lethal virus, although several drugs, including remdesivir and hydroxychloroquine, have been tested. The purpose of this study is to assess the activity of FDA-approved drugs cetilistat, abiraterone, diiodohydroxyquinoline, bexarotene, remdesivir, and hydroxychloroquine as potential SARS-CoV-2 main protease inhibitors. Additionally, this study aims to provide insight into the development of potential inhibitors that may inhibit ACE2, thereby preventing SARS-CoV-2 entry into the host cell and infection. To this end, remdesivir and hydroxychloroquine were used as comparator drugs. The calculations revealed that cetilistat, abiraterone, diiodohydroxyquinoline, and bexarotene inhibit main protease and ACE2 receptors more effectively than the well-known drug hydroxychloroquine when used against COVID-19. Meanwhile, bexarotene and cetilistat bind more tightly to the SARS-CoV-2 main protease and the ACE2 receptor, respectively, than remdesivir, a potential treatment for COVID-19 that is the first FDA-approved drug against this virus. As a result, the molecular dynamic simulations of these two drugs in the presence of proteins were investigated. The MD simulation results demonstrated that these drugs interact to stabilize the systems, allowing them to be used as effective inhibitors of these proteins. Meanwhile, bexarotene, abiraterone, cetilistat, and diiodohydroxyquinoline's systemic effects should be further investigated in suitable ex vivo human organ culture or organoids, animal models, or clinical trials.
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Affiliation(s)
- Nahid Shahabadi
- Inorganic Chemistry Department, Faculty of Chemistry, Razi University, Kermanshah, Iran
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Saba Zendehcheshm
- Inorganic Chemistry Department, Faculty of Chemistry, Razi University, Kermanshah, Iran
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mohammad Mahdavi
- Inorganic Chemistry Department, Faculty of Chemistry, Razi University, Kermanshah, Iran
| | - Fatemeh Khademi
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
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Singh R, Bhardwaj VK, Sharma J, Kumar D, Purohit R. Identification of potential plant bioactive as SARS-CoV-2 Spike protein and human ACE2 fusion inhibitors. Comput Biol Med 2021; 136:104631. [PMID: 34273770 PMCID: PMC8264305 DOI: 10.1016/j.compbiomed.2021.104631] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 06/29/2021] [Accepted: 07/02/2021] [Indexed: 01/14/2023]
Abstract
The Spike receptor binding domain (S-RBD) from SARS-CoV-2, a crucial protein for the entrance of the virus into target cells is known to cause infection by binding to a cell surface protein. Hence, reckoning therapeutics for the S-RBD of SARS-CoV-2 may address a significant way to target viral entry into the host cells. Herein, through in-silico approaches (Molecular docking, molecular dynamics (MD) simulations, and end-state thermodynamics), we aimed to screen natural molecules from different plants for their ability to inhibit S-RBD of SARS-CoV-2. We prioritized the best interacting molecules (Diacetylcurcumin and Dicaffeoylquinic acid) by analysis of protein-ligand interactions and subjected them for long-term MD simulations. We found that Dicaffeoylquinic acid interacted prominently with essential residues (Lys417, Gln493, Tyr489, Phe456, Tyr473, and Glu484) of S-RBD. These residues are involved in interactions between S-RBD and ACE2 and could inhibit the viral entry into the host cells. The in-silico analyses indicated that Dicaffeoylquinic acid and Diacetylcurcumin might have the potential to act as inhibitors of SARS-CoV-2 S-RBD. The present study warrants further in-vitro and in-vivo studies of Dicaffeoylquinic acid and Diacetylcurcumin for validation and acceptance of their inhibitory potential against S-RBD of SARS-CoV-2.
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Affiliation(s)
- Rahul Singh
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India
| | - Vijay Kumar Bhardwaj
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Jatin Sharma
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India
| | - Dinesh Kumar
- Chemical Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Post Box No. 6, Palampur, 176061, Himachal Pradesh, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rituraj Purohit
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Singh R, Bhardwaj VK, Das P, Purohit R. A computational approach for rational discovery of inhibitors for non-structural protein 1 of SARS-CoV-2. Comput Biol Med 2021; 135:104555. [PMID: 34144270 PMCID: PMC8184359 DOI: 10.1016/j.compbiomed.2021.104555] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 06/03/2021] [Accepted: 06/03/2021] [Indexed: 12/21/2022]
Abstract
Background Non-structural protein 1 (Nsp1), a virulence agent of SARS-CoV-2, has emerged as an important target for drug discovery. Nsp1 shuts down the host gene function by associating with the 40S ribosomal subunit. Methods Molecular interactions, drug-likeness, physiochemical property predictions, and robust molecular dynamics (MD) simulations were employed to discover novel Nsp1 inhibitors. In this study, we evaluated a series of molecules based on the plant (Cedrus deodara) derived α,β,γ-Himachalenes scaffolds. Results The results obtained from estimated affinity and ligand efficiency suggested that BCH10, BCH15, BCH16, and BCH17 could act as potential inhibitors of Nsp1. Moreover, MD simulations comprising various MD driven time-dependent analyses and thermodynamic free energy calculations also suggested stable protein-ligand complexes and strong interactions with the binding site. Furthermore, the selected molecules passed drug likeliness parameters and the physiochemical property analysis showed acceptable bioactivity scores. Conclusion The structural parameters of dynamic simulations revealed that the reported molecules could act as lead compounds against SARS-CoV-2 Nsp1 protein.
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Affiliation(s)
- Rahul Singh
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India
| | - Vijay Kumar Bhardwaj
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Pralay Das
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India; Natural Product Chemistry and Process Development, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palam-pur, India
| | - Rituraj Purohit
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India.
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In-silico evaluation of bioactive compounds from tea as potential SARS-CoV-2 nonstructural protein 16 inhibitors. J Tradit Complement Med 2021; 12:35-43. [PMID: 34099976 PMCID: PMC8172245 DOI: 10.1016/j.jtcme.2021.05.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/29/2021] [Accepted: 05/29/2021] [Indexed: 01/03/2023] Open
Abstract
Background and aim A novel coronavirus, called the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been found to cause COVID-19 in humans and some other mammals. The nonstructural protein 16 (NSP16) of SARS-CoV-2 plays a significant part in the replication of viruses and suppresses the ability of innate immune system to detect the virus. Therefore, inhibiting NSP16 can be a secure path towards identifying a potent medication against SARS-CoV-2. Tea (Camellia sinensis) polyphenols have been reported to exhibit potential treatment options against various viral diseases. Methods We conducted molecular docking and structural dynamics studies with a set of 65 Tea bioactive compounds to illustrate their ability to inhibit NSP16 of SARS-CoV-2. Moreover, post-simulations end state thermodynamic free energy calculations were estimated to strengthen our results. Results and conclusion Six bioactive tea molecules showed better docking scores than the standard molecule sinefungin. These results were further validated by MD simulations, where Theaflavin compound demonstrated lower binding free energy in comparison to the standard molecule sinefungin. The compound theaflavin could be considered as a novel lead compound for further evaluation by in-vitro and in-vivo studies.
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