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Mohan S, Dharani J, Natarajan R, Nagarajan A. Molecular docking and identification of G-protein-coupled receptor 120 (GPR120) agonists as SARS COVID-19 MPro inhibitors. J Genet Eng Biotechnol 2022; 20:108. [PMID: 35849279 PMCID: PMC9289937 DOI: 10.1186/s43141-022-00375-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 06/02/2022] [Indexed: 11/13/2022]
Abstract
COVID-19 has become a pandemic, and any new drug for treating the disease could save millions of lives. Several drugs already in use for other diseases and medical conditions are repurposed for treating COVID-19 in an attempt to find treatment for the disease without spending research time on ADME TOX and other studies on side effects. In this exercise, the drugs repurposed are from antiviral, antibiotics, antiviral for HIV and HCV, anti-cancer, natural medicines, etc. Possible repurposing anti-diabetic GPR-120 agonists used as for SAR-CoV-2 is attempted in the study by carrying out docking of 68 GPR-120 agonists. Ten of these compounds were found to have docking scores −8.3 to −8.0, and the best docking score was observed for an arylsulfonamide and a biarylpropanoic acid belonging to GPR120 agonists previously evaluated for the treatment of type II diabetes. These GPR120 agonists could serve as start point for novel inhibitors for the discovery of drugs to treat COVID-19.
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Affiliation(s)
- Sellappan Mohan
- Karpagam College of Pharmacy, Coimbatore, Tamil Nadu, 641032, India.
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Pillaiyar T, Flury P, Krüger N, Su H, Schäkel L, Barbosa Da Silva E, Eppler O, Kronenberger T, Nie T, Luedtke S, Rocha C, Sylvester K, Petry MR, McKerrow JH, Poso A, Pöhlmann S, Gütschow M, O’Donoghue AJ, Xu Y, Müller CE, Laufer SA. Small-Molecule Thioesters as SARS-CoV-2 Main Protease Inhibitors: Enzyme Inhibition, Structure-Activity Relationships, Antiviral Activity, and X-ray Structure Determination. J Med Chem 2022; 65:9376-9395. [PMID: 35709506 PMCID: PMC9216242 DOI: 10.1021/acs.jmedchem.2c00636] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Indexed: 02/08/2023]
Abstract
The main protease (Mpro, 3CLpro) of SARS-CoV-2 is an attractive target in coronaviruses because of its crucial involvement in viral replication and transcription. Here, we report on the design, synthesis, and structure-activity relationships of novel small-molecule thioesters as SARS-CoV-2 Mpro inhibitors. Compounds 3w and 3x exhibited excellent SARS-CoV-2 Mpro inhibition with kinac/Ki of 58,700 M-1 s-1 (Ki = 0.0141 μM) and 27,200 M-1 s-1 (Ki = 0.0332 μM), respectively. In Calu-3 and Vero76 cells, compounds 3h, 3i, 3l, 3r, 3v, 3w, and 3x displayed antiviral activity in the nanomolar range without host cell toxicity. Co-crystallization of 3w and 3af with SARS-CoV-2 Mpro was accomplished, and the X-ray structures showed covalent binding with the catalytic Cys145 residue of the protease. The potent SARS-CoV-2 Mpro inhibitors also inhibited the Mpro of other beta-coronaviruses, including SARS-CoV-1 and MERS-CoV, indicating that they might be useful to treat a broader range of coronaviral infections.
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Affiliation(s)
- Thanigaimalai Pillaiyar
- Institute of Pharmacy, Pharmaceutical/Medicinal
Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls
University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
Cluster of Excellence iFIT (EXC 2180) “Image-Guided & Functionally Instructed
Tumor Therapies”, University of Tübingen,
Tübingen 72076, Germany
| | - Philipp Flury
- Institute of Pharmacy, Pharmaceutical/Medicinal
Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls
University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
Cluster of Excellence iFIT (EXC 2180) “Image-Guided & Functionally Instructed
Tumor Therapies”, University of Tübingen,
Tübingen 72076, Germany
| | - Nadine Krüger
- Infection Biology Unit, German Primate
Center, Leibniz Institute for Primate Research Göttingen,
Kellnerweg 4, Göttingen 37077, Germany
| | - Haixia Su
- CAS Key Laboratory of Receptor Research, and Stake Key
Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese
Academy of Sciences, Shanghai 201203, China
| | - Laura Schäkel
- PharmaCenter Bonn, Pharmaceutical Institute,
Pharmaceutical & Medicinal Chemistry, University of Bonn,
An der Immenburg 4, Bonn D-53121, Germany
| | - Elany Barbosa Da Silva
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, La Jolla, California
92093, United States
| | - Olga Eppler
- Institute of Pharmacy, Pharmaceutical/Medicinal
Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls
University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
Cluster of Excellence iFIT (EXC 2180) “Image-Guided & Functionally Instructed
Tumor Therapies”, University of Tübingen,
Tübingen 72076, Germany
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal
Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls
University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
Cluster of Excellence iFIT (EXC 2180) “Image-Guided & Functionally Instructed
Tumor Therapies”, University of Tübingen,
Tübingen 72076, Germany
| | - Tianqing Nie
- CAS Key Laboratory of Receptor Research, and Stake Key
Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese
Academy of Sciences, Shanghai 201203, China
| | - Stephanie Luedtke
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, La Jolla, California
92093, United States
| | - Cheila Rocha
- Infection Biology Unit, German Primate
Center, Leibniz Institute for Primate Research Göttingen,
Kellnerweg 4, Göttingen 37077, Germany
| | - Katharina Sylvester
- PharmaCenter Bonn, Pharmaceutical Institute,
Pharmaceutical & Medicinal Chemistry, University of Bonn,
An der Immenburg 4, Bonn D-53121, Germany
| | - Marvin R.I. Petry
- PharmaCenter Bonn, Pharmaceutical Institute,
Pharmaceutical & Medicinal Chemistry, University of Bonn,
An der Immenburg 4, Bonn D-53121, Germany
| | - James H. McKerrow
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, La Jolla, California
92093, United States
| | - Antti Poso
- Institute of Pharmacy, Pharmaceutical/Medicinal
Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls
University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
Cluster of Excellence iFIT (EXC 2180) “Image-Guided & Functionally Instructed
Tumor Therapies”, University of Tübingen,
Tübingen 72076, Germany
- School of Pharmacy, Faculty of Health Sciences,
University of Eastern Finland, Kuopio 70211,
Finland
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate
Center, Leibniz Institute for Primate Research Göttingen,
Kellnerweg 4, Göttingen 37077, Germany
- Faculty of Biology and Psychology,
University Göttingen,Göttingen 37073,
Germany
| | - Michael Gütschow
- PharmaCenter Bonn, Pharmaceutical Institute,
Pharmaceutical & Medicinal Chemistry, University of Bonn,
An der Immenburg 4, Bonn D-53121, Germany
| | - Anthony J. O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, La Jolla, California
92093, United States
| | - Yechun Xu
- CAS Key Laboratory of Receptor Research, and Stake Key
Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese
Academy of Sciences, Shanghai 201203, China
| | - Christa E. Müller
- PharmaCenter Bonn, Pharmaceutical Institute,
Pharmaceutical & Medicinal Chemistry, University of Bonn,
An der Immenburg 4, Bonn D-53121, Germany
| | - Stefan A. Laufer
- Institute of Pharmacy, Pharmaceutical/Medicinal
Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls
University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
Cluster of Excellence iFIT (EXC 2180) “Image-Guided & Functionally Instructed
Tumor Therapies”, University of Tübingen,
Tübingen 72076, Germany
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53
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Lokhande K, Nawani N, K. Venkateswara S, Pawar S. Biflavonoids from Rhus succedanea as probable natural inhibitors against SARS-CoV-2: a molecular docking and molecular dynamics approach. J Biomol Struct Dyn 2022; 40:4376-4388. [PMID: 33300454 PMCID: PMC7738212 DOI: 10.1080/07391102.2020.1858165] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 11/22/2020] [Indexed: 02/07/2023]
Abstract
The recent outbreak of SARS-CoV-2 has quickly become a worldwide pandemic and generated panic threats for both the human population and the global economy. The unavailability of effective vaccines or drugs has enforced researchers to hunt for a potential drug to combat this virus. Plant-derived phytocompounds are of applicable interest in the search for novel drugs. Bioflavonoids from Rhus succedanea are already reported to exert antiviral activity against RNA viruses. SARS-CoV-2 Mpro protease plays a vital role in viral replication and therefore can be considered as a promising target for drug development. A computational approach has been employed to search for promising potent bioflavonoids from Rhus succedanea against SARS-CoV-2 Mpro protease. Binding affinities and binding modes between the biflavonoids and Mpro enzyme suggest that all six biflavonoids exhibit possible interaction with the Mpro catalytic site (-19.47 to -27.04 kcal/mol). However, Amentoflavone (-27.04 kcal/mol) and Agathisflavone (-25.87 kcal/mol) interact strongly with the catalytic residues. Molecular dynamic simulations (100 ns) further revealed that these two biflavonoids complexes with the Mpro enzyme are highly stable and are of less conformational fluctuations. Also, the hydrophobic and hydrophilic surface mapping on the Mpro structure as well as biflavonoids were utilized for the further lead optimization process. Altogether, our findings showed that these natural biflavonoids can be utilized as promising SARS-CoV-2 Mpro inhibitors and thus, the computational approach provides an initial footstep towards experimental studies in in vitro and in vivo, which is necessary for the therapeutic development of novel and safe drugs to control SARS-CoV-2. Communicated by Ramaswamy H. SarmaResearch highlightsRhus succedanea biflavonoids have antiviral activity.The molecular interactions and molecular dynamics displayed that all six biflavonoids bound with a good affinity to the same catalytic site of Mpro.The compound Amentoflavone has a strong binding affinity (-27.0441 kcal/mol) towards Mpro.The binding site properties of SARS-CoV-2-Mpro can be utilized in a novel discovery and lead optimization of the SARS-CoV-2-Mpro inhibitor.
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Affiliation(s)
- Kiran Lokhande
- Dr. D. Y. Patil Vidyapeeth, Bioinformatics Research Laboratory, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Pune, India
| | - Neelu Nawani
- Dr. D. Y. Patil Vidyapeeth, Microbial Diversity Research Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Pune, India
| | - Swamy K. Venkateswara
- Bioinformatics Research Group, MIT School of Bioengineering Sciences & Research, MIT-ADT University, Pune, Maharashtra, India
| | - Sarika Pawar
- Dr. D. Y. Patil Vidyapeeth, Microbial Diversity Research Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Pune, India
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Production of a functionally active recombinant SARS-CoV-2 (COVID-19) 3C-Like protease and a soluble inactive 3C-like protease-RBD chimeric in a prokaryotic expression system. Epidemiol Infect 2022; 150:e128. [PMID: 35723031 PMCID: PMC9300977 DOI: 10.1017/s0950268822001078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
During the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) intracellular life-cycle, two large polyproteins, pp1a and pp1ab, are produced. Processing of these by viral cysteine proteases, the papain-like protease (PLpro) and the chymotrypsin-like 3C-like protease (3CL-pro) release non-structural proteins necessary for the establishment of the viral replication and transcription complex (RTC), crucial for viral replication. Hence, these proteases are considered prime targets against which anti-coronavirus disease 2019 (COVID-19) drugs could be developed. Here, we describe the expression of a highly soluble and functionally active recombinant 3CL-pro using Escherichia coli BL21 cells. We show that the enzyme functions in a dimeric form and exhibits an unexpected inhibitory profile because its activity is potently blocked by serine rather than cysteine protease inhibitors. In addition, we assessed the ability of our 3CL-pro to function as a carrier for the receptor binding domain (RBD) of the Spike protein. The co-expressed chimeric protein, 3CLpro-RBD, did not exhibit 3CL-pro activity, but its enhanced solubility made purification easier and improved RBD antigenicity when tested against serum from vaccinated individuals in ELISAs. Chimeric proteins containing the 3CL-pro could represent an innovative approach to developing new COVID-19 vaccines.
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55
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Chen CC, Zhuang ZJ, Wu CW, Tan YL, Huang CH, Hsu CY, Tsai EM, Hsieh TH. Venetoclax Decreases the Expression of the Spike Protein through Amino Acids Q493 and S494 in SARS-CoV-2. Cells 2022; 11:cells11121924. [PMID: 35741053 PMCID: PMC9221610 DOI: 10.3390/cells11121924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/31/2022] [Accepted: 06/07/2022] [Indexed: 11/16/2022] Open
Abstract
The new coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus (SARS-CoV-2) has been reported and spread globally. There is an urgent need to take urgent measures to treat and prevent further infection of this virus. Here, we use virtual drug screening to establish pharmacophore groups and analyze the ACE2 binding site of the spike protein with the ZINC drug database and DrugBank database by molecular docking and molecular dynamics simulations. Screening results showed that Venetoclax, a treatment drug for chronic lymphocytic leukemia, has a potential ability to bind to the spike protein of SARS-CoV-2. In addition, our in vitro study found that Venetoclax degraded the expression of the spike protein of SARS-CoV-2 through amino acids Q493 and S494 and blocked the interaction with the ACE2 receptor. Our results suggest that Venetoclax is a candidate for clinical prevention and treatment and deserves further research.
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Affiliation(s)
- Chih-Chieh Chen
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 804201, Taiwan; (C.-C.C.); (Z.-J.Z.); (Y.-L.T.)
- Rapid Screening Research Center for Toxicology and Biomedicine, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
| | - Zhi-Jie Zhuang
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 804201, Taiwan; (C.-C.C.); (Z.-J.Z.); (Y.-L.T.)
| | - Chia-Wei Wu
- Department of Medical Research, E-Da Hospital/E-Da Cancer Hospital, I-Shou University, Kaohsiung 82445, Taiwan; (C.-W.W.); (C.-H.H.)
| | - Yi-Ling Tan
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 804201, Taiwan; (C.-C.C.); (Z.-J.Z.); (Y.-L.T.)
| | - Chen-Hsiu Huang
- Department of Medical Research, E-Da Hospital/E-Da Cancer Hospital, I-Shou University, Kaohsiung 82445, Taiwan; (C.-W.W.); (C.-H.H.)
| | - Chia-Yi Hsu
- Department of Obstetrics and Gynecology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan; (C.-Y.H.); (E.-M.T.)
| | - Eing-Mei Tsai
- Department of Obstetrics and Gynecology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80756, Taiwan; (C.-Y.H.); (E.-M.T.)
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
| | - Tsung-Hua Hsieh
- Department of Medical Research, E-Da Hospital/E-Da Cancer Hospital, I-Shou University, Kaohsiung 82445, Taiwan; (C.-W.W.); (C.-H.H.)
- Correspondence: ; Tel.: +886-7615-1100 (ext. 5072)
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56
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Komissarov A, Karaseva M, Roschina M, Kostrov S, Demidyuk I. The SARS-CoV-2 main protease doesn't induce cell death in human cells in vitro. PLoS One 2022; 17:e0266015. [PMID: 35609027 PMCID: PMC9129031 DOI: 10.1371/journal.pone.0266015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 03/11/2022] [Indexed: 11/19/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of coronavirus disease 2019 (COVID-19) which has extremely rapidly spread worldwide. In order to develop the effective antiviral therapies, it is required to understand the molecular mechanisms of the SARS-CoV-2 pathogenesis. The main protease, or 3C-like protease (3CLpro), plays the essential role in the coronavirus replication that makes the enzyme a promising therapeutic target. Viral enzymes are known to be multifunctional. Particularly, 3CLpro of SARS-CoV was shown to induce apoptosis in addition to its main function. In the present study we analyzed the cytotoxicity of active SARS-CoV-2 3CLpro and its inactivated form upon their individual expression in four human cell lines. For this purpose, we constructed a protein biosensor which allows to detect the proteolytic activity of SARS-CoV-2 3CLpro and confirmed the expression of the active protease in all cell lines used. We studied viability and morphology of the cells and found that both active and inactivated enzyme variants induce no cell death in contrast to the homologous 3CL protease of SARS-CoV. These results indicate that SARS-CoV-2 3CLpro is unlikely contribute to the cytopathic effect observed during viral infection directly.
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Affiliation(s)
- Alexey Komissarov
- Institute of Molecular Genetics of National Research Centre Kurchatov Institute, Moscow, Russian Federation
| | - Maria Karaseva
- Institute of Molecular Genetics of National Research Centre Kurchatov Institute, Moscow, Russian Federation
| | - Marina Roschina
- Institute of Molecular Genetics of National Research Centre Kurchatov Institute, Moscow, Russian Federation
| | - Sergey Kostrov
- Institute of Molecular Genetics of National Research Centre Kurchatov Institute, Moscow, Russian Federation
| | - Ilya Demidyuk
- Institute of Molecular Genetics of National Research Centre Kurchatov Institute, Moscow, Russian Federation
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Eskandari V. Repurposing the natural compounds as potential therapeutic agents for COVID-19 based on the molecular docking study of the main protease and the receptor-binding domain of spike protein. J Mol Model 2022; 28:153. [PMID: 35578055 PMCID: PMC9110024 DOI: 10.1007/s00894-022-05138-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/26/2022] [Indexed: 12/03/2022]
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV-2) enters the cell by interacting with the human angiotensin-converting enzyme 2 (ACE2) receptor through the receptor-binding domain (RBD) of spike (S) protein. In the cell, the viral 3-chymotrypsin-like cysteine protease (3CLpro) enzyme is essential for its life cycle and controls coronavirus replication. Therefore, the S-RBD and 3CLpro are hot targets for drug discovery against SARS-CoV-2. This study was to identify repurposing drugs using in silico screening, docking, and molecular dynamics simulation. The study identified bentiamine, folic acid, benfotiamine, and vitamin B12 against the RBD of S protein and bentiamine, folic acid, fursultiamine, and riboflavin to 3CLpro. The strong and stable binding of these safe and cheap vitamins at the important residues (R403, K417, Y449, Y453, N501, and Y505) in the S-protein–ACE2 interface and 3CLpro binding site residues especially active site residues (His 41 and Cys 145), indicating that they could be valuable repurpose drugs for inhibiting SARS-CoV-2 entry into the host and replication.
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Affiliation(s)
- Vajiheh Eskandari
- Department of Biology, Faculty of Science, University of Zanjan, Zanjan, Iran.
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Rational Discovery of Antiviral Whey Protein-Derived Small Peptides Targeting the SARS-CoV-2 Main Protease. Biomedicines 2022; 10:biomedicines10051067. [PMID: 35625804 PMCID: PMC9139167 DOI: 10.3390/biomedicines10051067] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 04/30/2022] [Accepted: 04/30/2022] [Indexed: 11/17/2022] Open
Abstract
In the present work, and for the first time, three whey protein-derived peptides (IAEK, IPAVF, MHI), endowed with ACE inhibitory activity, were examined for their antiviral activity against the SARS-CoV-2 3C-like protease (3CLpro) and Human Rhinovirus 3C protease (3Cpro) by employing molecular docking. Computational studies showed reliable binding poses within 3CLpro for the three investigated small peptides, considering docking scores as well as the binding free energy values. Validation by in vitro experiments confirmed these results. In particular, IPAVF exhibited the highest inhibitory activity by returning an IC50 equal to 1.21 μM; it was followed by IAEK, which registered an IC50 of 154.40 μM, whereas MHI was less active with an IC50 equal to 2700.62 μM. On the other hand, none of the assayed peptides registered inhibitory activity against 3Cpro. Based on these results, the herein presented small peptides are introduced as promising molecules to be exploited in the development of “target-specific antiviral” agents against SARS-CoV-2.
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59
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Fang S, Zheng R, Lei C, Wang J, Zhou R, Li M. In Silico Prediction of New Mutations That Can Improve the Binding Abilities Between 2019-nCoV Coronavirus and Human ACE2. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:1694-1702. [PMID: 33560990 PMCID: PMC9328728 DOI: 10.1109/tcbb.2021.3058265] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 01/27/2021] [Accepted: 02/06/2021] [Indexed: 06/12/2023]
Abstract
The Coronavirus Disease 2019 (COVID-19) has become an international public health emergency, posing a serious threat to human health and safety around the world. The 2019-nCoV coronavirus spike protein was confirmed to be highly susceptible to various mutations, which can trigger apparent changes of virus transmission capacity and the pathogenic mechanism. In this article, the binding interface was obtained by analyzing the interaction modes between 2019-nCoV coronavirus and the human ACE2. Based on the "SIFT server" and the "bubble" identification mechanism, 9 amino acid sites were selected as potential mutation-sites from the 2019-nCoV-S1-ACE2 binding interface. Subsequently, a total number of 171 mutant systems for 9 mutation-sites were optimized for binding-pattern comparsion analysis, and 14 mutations that may improve the binding capacity of 2019-nCoV-S1 to ACE2 were selected. The Molecular Dynamic Simulations were conducted to calculate the binding free energies of all the 14 mutant systems. Finally, we found that most of the 14 mutations on the 2019-nCoV-S1 protein could enhance the binding ability between 2019-nCoV coronavirus and human ACE2. Among which, the binding capacities for G446R, Y449R and F486Y mutations could be increased by 20 percent, and that for S494R mutant increased even by 38.98 percent. We hope this research could provide significant help for the future epidemic detection, drug and vaccine development.
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Affiliation(s)
- Senbiao Fang
- Hunan Provincial Key Lab on BioinformaticsSchool of Computer Science and EngineeringCentral South UniversityChangsha410083China
| | - Ruoqian Zheng
- Hunan Provincial Key Lab on BioinformaticsSchool of Computer Science and EngineeringCentral South UniversityChangsha410083China
| | - Chuqi Lei
- Hunan Provincial Key Lab on BioinformaticsSchool of Computer Science and EngineeringCentral South UniversityChangsha410083China
| | - Jianxin Wang
- Hunan Provincial Key Lab on BioinformaticsSchool of Computer Science and EngineeringCentral South UniversityChangsha410083China
| | - Renyi Zhou
- Hunan Provincial Key Lab on BioinformaticsSchool of Computer Science and EngineeringCentral South UniversityChangsha410083China
| | - Min Li
- Hunan Provincial Key Lab on BioinformaticsSchool of Computer Science and EngineeringCentral South UniversityChangsha410083China
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Khurana P, Varshney R, Gupta A. A Network-Biology led Computational Drug repurposing Strategy to prioritize therapeutic options for COVID-19. Heliyon 2022; 8:e09387. [PMID: 35578630 PMCID: PMC9093055 DOI: 10.1016/j.heliyon.2022.e09387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 11/17/2021] [Accepted: 05/03/2022] [Indexed: 12/15/2022] Open
Abstract
The alarming pandemic situation of novel Severe Acute Respiratory Syndrome Coronavirus 2 (nSARS-CoV-2) infection, high drug development cost and slow process of drug discovery have made repositioning of existing drugs for therapeutics a popular alternative. It involves the repurposing of existing safe compounds which results in low overall development costs and shorter development timeline. In the present study, a computational network-biology approach has been used for comparing three candidate drugs i.e. quercetin, N-acetyl cysteine (NAC), and 2-deoxy-glucose (2-DG) to be effectively repurposed against COVID-19. For this, the associations between these drugs and genes of Severe Acute Respiratory Syndrome (SARS) and the Middle East Respiratory Syndrome (MERS) diseases were retrieved and a directed drug-gene-gene-disease interaction network was constructed. Further, to quantify the associations between a target gene and a disease gene, the shortest paths from the target gene to the disease genes were identified. A vector DV was calculated to represent the extent to which a disease gene was influenced by these drugs. Quercetin was quantified as the best among the three drugs, suited for repurposing with DV of -70.19, followed by NAC with DV of -39.99 and 2-DG with DV of -13.71. The drugs were also assessed for their safety and efficacy balance (in terms of therapeutic index) using network properties. It was found that quercetin was a forerunner than other two drugs.
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61
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Hua Y, Dai X, Xu Y, Xing G, Liu H, Lu T, Chen Y, Zhang Y. Drug repositioning: Progress and challenges in drug discovery for various diseases. Eur J Med Chem 2022; 234:114239. [PMID: 35290843 PMCID: PMC8883737 DOI: 10.1016/j.ejmech.2022.114239] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 02/20/2022] [Accepted: 02/24/2022] [Indexed: 12/17/2022]
Abstract
Compared with traditional de novo drug discovery, drug repurposing has become an attractive drug discovery strategy due to its low-cost and high efficiency. Through a comprehensive analysis of the candidates that have been identified with drug repositioning potentials, it is found that although some drugs do not show obvious advantages in the original indications, they may exert more obvious effects in other diseases. In addition, some drugs have a synergistic effect to exert better clinical efficacy if used in combination. Particularly, it has been confirmed that drug repositioning has benefits and values on the current public health emergency such as the COVID-19 pandemic, which proved the great potential of drug repositioning. In this review, we systematically reviewed a series of representative drugs that have been repositioned for different diseases and illustrated successful cases in each disease. Especially, the mechanism of action for the representative drugs in new indications were explicitly explored for each disease, we hope this review can provide important insights for follow-up research.
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Affiliation(s)
- Yi Hua
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Xiaowen Dai
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Yuan Xu
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Guomeng Xing
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Haichun Liu
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Tao Lu
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, China
| | - Yadong Chen
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China.
| | - Yanmin Zhang
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China.
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62
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Repurposing of Four Drugs as Anti-SARS-CoV-2 Agents and Their Interactions with Protein Targets. Sci Pharm 2022. [DOI: 10.3390/scipharm90020024] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Although there are existing vaccines against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), new COVID-19 cases are increasing due to low immunization coverage and the emergence of new variants. For this reason, new drugs to treat and prevent severe COVID-19 are needed. Here, we provide four different FDA-approved drugs against SARS-CoV-2 proteins involved in the entry and replication process, aiming to identify potential drugs to treat COVID-19. We use the main protease (Mpro), the spike glycoprotein (S protein), and RNA-dependent RNA polymerase (RdRp) as protein targets for anti- SARS-CoV-2 drugs. In our constructed database, we selected different drugs against each target (Mpro, S protein, and RdRp) based on their common interactions with relevant residues involved in viral entry at the host cell and replication. Furthermore, their stability inside the binding pocket, as well as their predicted binding-free energy, allow us to provide new insight into the possible drug repurposing of viomycin (interacting with Mpro) due to its interactions with key residues, such as Asn 143, Glu 166, and Gln 189 at the same time as hesperidin (interacting with the S protein) is interacting with residues Tyr 449, Ser 494, and Thr 500, keeping inside the predicted binding pocket, as well as interacting with residues in different variants of concern. Finally, we also suggest nystatin and elvitegravir (interacting with RdRp) as possible drugs due to their stability within the predicted pocket along the simulation and their interaction with key residues, such as Asp 760, Asp 761, and Asp 618. Altogether our results provide new knowledge about the possible mechanism of the inhibition of viomycin, hesperidin, elvitegravir, and nystatin to inhibit the viral life cycle of SARS-CoV-2 and some of its variants of concern (VOC). Additionally, some iodide-based contrast agents were also found to bind the S protein strongly, i.e., iohexol (−58.99 Kcal/mol), iotrolan (−76.19 Kcal/mol), and ioxilan (−62.37 Kcal/mol). Despite the information we report here as the possible strong interaction between these contrast agents and the SARS-CoV-2′s S protein, Mpro, and RdRp, we believe that further investigation, including chemical modifications in their structures, are needed for COVID-19 treatment.
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Ghosh R, Badavath VN, Chowdhuri S, Sen A. Identification of Alkaloids from Terminalia chebula as Potent SARS- CoV-2 Main Protease Inhibitors: An In Silico Perspective. ChemistrySelect 2022; 7:e202200055. [PMID: 35600910 PMCID: PMC9111116 DOI: 10.1002/slct.202200055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/28/2022] [Indexed: 11/12/2022]
Abstract
Natural compounds in medicinal plants are best remedies for different diseases and are important to develop new drugs. This work was dedicated to understand the role of different natural compounds of Terminalia Chebula, a well-known herbal plant, in the treating of Covid 19. In this article, we have investigated interactions of such natural compounds from Terminalia Chebula with the main protease (Mpro) of the SARS-CoV-2, which is a key component for cleavage of viral polyprotein, and an important target for the development of drugs towards COVID-19. We have performed molecular docking study on 22 different molecules of Terminalia Chebula and proposed that 7 of the natural compounds (triterpenoids and sterols) interacts with a comparable or stronger interactions than the inhibitor N3. Molecular dynamics simulations (100 ns) revealed that 7 Mpro-Terminalia Chebula complexes are stable, conformationally less fluctuated, slightly less compact, and marginally expanded than ligand-free conformation of Mpro. The intermolecular H-bonding and detailed MM/PBSA and MM-GBSA analysis showed Daucosterol interaction to be the most strong, whereas comparable interactions were observed for Arjunetin, Maslinic acid, and Bellericoside. Our study suggested that these natural compounds can act as potent Mpro inhibitors for SARS-CoV-2, and may evolve as promising anti-COVID-19 drugs in the near future.
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Affiliation(s)
- Rajesh Ghosh
- School of Basic SciencesIndian Institute of Technology BhubaneswarBhubaneswarIndia
| | | | - Snehasis Chowdhuri
- School of Basic SciencesIndian Institute of Technology BhubaneswarBhubaneswarIndia
| | - Anik Sen
- Department of ChemistryInstitute of ScienceGITAM (Deemed to be University)Visakhapatnam530045Andhra PradeshIndia
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64
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Purohit P, Dash JJ, Muya JT, Meher BR. Molecular insights to the binding interactions of APNS containing HIV-protease inhibitors against SARS-CoV-2 M pro: an in silico approach towards drug repurposing. J Biomol Struct Dyn 2022; 41:3900-3913. [PMID: 35388744 DOI: 10.1080/07391102.2022.2059008] [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: 10/18/2022]
Abstract
SARS-CoV-2 Mpro is one of the most vital enzymes of the new coronavirus-2 (SARS-CoV-2) and is a crucial target for drug discovery. Unfortunately, there is not any potential drugs available to combat the action of SARS-CoV-2 Mpro. Based on the reports HIV-protease inhibitors can be applied against the SARS by targeting the SARS-CoV-1 Mpro, we have chosen few clinically trialed experimental and allophenylnorstatine (APNS) containing HIV-protease inhibitors (JE-2147, JE-533, KNI-227, KNI-272 & KNI-1931), to examine their binding affinities with SARS-CoV-2 Mpro and to assess their potential to check for a possible drug candidate against the protease. Here, we have chosen a methodology to understand the binding mechanism of these five inhibitors to SARS-CoV-2 Mpro by merging molecular docking, molecular dynamics (MD) simulation and MM-PBSA based free energy calculations. Our estimations disclose that JE-2147 is highly effective (ΔGBind = -28.31 kcal/mol) due to an increased favorable van der Waals (ΔEvdw) interactions and decreased solvation (ΔGsolv) energies between the inhibitor and viral protease. JE-2147 shows a higher level of interactions as compared to JE-533 (-6.85 kcal/mol), KNI-227 (-18.36 kcal/mol), KNI-272 (-15.69 kcal/mol) and KNI-1931 (-21.59 kcal/mol) against SARS-CoV-2 Mpro. Binding contributions of important residues (His41, Met49, Cys145, His164, Met165, Glu166, Pro168, Gln189, etc.) from the active site or near the active site regions with ≥1.0 kcal/mol suggest a potent binding of the inhibitors. It is anticipated that the current study of binding interactions of these APNS containing inhibitors can pitch some valuable insights to design the significantly effective anti-SARS-CoV-2 Mpro drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Priyanka Purohit
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, India
| | - Jiban Jyoti Dash
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, India
| | - Jules Tshishimbi Muya
- Department of Chemistry, Hanyang University, Seoul, South Korea.,Faculté of Science, Research Centre for Theoretical Chemistry and Physics in Central Africa, University of Kinshasa, Kinshasa, Congo
| | - Biswa Ranjan Meher
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, India
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Messina V, Nevola R, Izzi A, De Lucia Sposito P, Marrone A, Rega R, Fusco R, Lumino P, Rinaldi L, Gaglione P, Simeone F, Sasso FC, Maggi P, Adinolfi LE. Efficacy and safety of the sofosbuvir/velpatasvir combination for the treatment of patients with early mild to moderate COVID-19. Sci Rep 2022; 12:5771. [PMID: 35388092 PMCID: PMC8985058 DOI: 10.1038/s41598-022-09741-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 03/25/2022] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2 is still a health problem worldwide despite the availability of vaccines. Therefore, there is a need for effective and safe antiviral. SARS-CoV-2 and HCV necessitate RNA-dependent RNA polymerase (RdRp) for replication; therefore, it has been hypothesized that RdRp inhibitors used to treat HCV may be effective treating SARS-CoV-2. Accordingly, we evaluated the effect of the sofosbuvir/velpatasvir (SOF/VEL) combination in early SARS-CoV-2 infection. A multicenter case-control study was conducted, enrolling 120 patients with mild or moderate COVID-19, of whom 30, HCV coinfected or not, received SOF/VEL tablets (400/100 mg) once daily for 9 days within a median of 6 days from the beginning of infection and 90 controls were treated with standard care. The primary endpoint was the effect on viral clearance, and the secondary endpoint was the improvement of clinical outcomes. Nasal swabs for SARS-CoV-2 by PCR were performed every 5-7 days. Between 5-14 days after starting SOF/VEL treatment, SAS-CoV-2 clearance was observed in 83% of patients, while spontaneous clearance in the control was 13% (p < 0.001). An earlier SARS-CoV-2 clearance was observed in the SOF/VEL group than in the control group (median 14 vs 22 days, respectively, p < 0.001) also when the first positivity was considered. None of the patients in the SOF/VEL group showed disease progression, while in the control group, 24% required more intensive treatment (high flow oxygen or noninvasive/invasive ventilation), and one patient died (p < 0.01). No significant side effects were observed in the SOF/VEL group. Early SOF/VEL treatment in mild/moderate COVID-19 seems to be safe and effective for faster elimination of SARS-CoV-2 and to prevent disease progression.
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Affiliation(s)
- Vincenzo Messina
- Infectious Disease Unit, Azienda Ospedaliera Di Caserta S. Anna e S. Sebastiano, Caserta, Italy
| | - Riccardo Nevola
- Department of Advanced Medical and Surgery Science, Internal Medicine Covid Center, University of Campania Luigi Vanvitelli, 80100, Naples, Italy.
| | - Antonio Izzi
- Infectious Diseases, 3Rd Covid Center Ospedale Cotugno, Naples, Italy
| | | | - Aldo Marrone
- Department of Advanced Medical and Surgery Science, Internal Medicine Covid Center, University of Campania Luigi Vanvitelli, 80100, Naples, Italy
| | - Roberto Rega
- Infectious Diseases, 3Rd Covid Center Ospedale Cotugno, Naples, Italy
| | | | - Paolina Lumino
- Infectious Diseases, 3Rd Covid Center Ospedale Cotugno, Naples, Italy
| | - Luca Rinaldi
- Department of Advanced Medical and Surgery Science, Internal Medicine Covid Center, University of Campania Luigi Vanvitelli, 80100, Naples, Italy
| | | | - Filomena Simeone
- Infectious Disease Unit, Azienda Ospedaliera Di Caserta S. Anna e S. Sebastiano, Caserta, Italy
| | - Ferdinando Carlo Sasso
- Department of Advanced Medical and Surgery Science, Internal Medicine Covid Center, University of Campania Luigi Vanvitelli, 80100, Naples, Italy
| | - Paolo Maggi
- Infectious Disease Unit, Azienda Ospedaliera Di Caserta S. Anna e S. Sebastiano, Caserta, Italy
| | - Luigi Elio Adinolfi
- Department of Advanced Medical and Surgery Science, Internal Medicine Covid Center, University of Campania Luigi Vanvitelli, 80100, Naples, Italy
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66
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Badavath VN, Kumar A, Samanta PK, Maji S, Das A, Blum G, Jha A, Sen A. Determination of potential inhibitors based on isatin derivatives against SARS-CoV-2 main protease (m pro): a molecular docking, molecular dynamics and structure-activity relationship studies. J Biomol Struct Dyn 2022; 40:3110-3128. [PMID: 33200681 PMCID: PMC7682386 DOI: 10.1080/07391102.2020.1845800] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 10/29/2020] [Indexed: 12/27/2022]
Abstract
SARS-COV-2, the novel coronavirus and root of global pandemic COVID-19 caused a severe health threat throughout the world. Lack of specific treatments raised an effort to find potential inhibitors for the viral proteins. The recently invented crystal structure of SARS-CoV-2 main protease (Mpro) and its key role in viral replication; non-resemblance to any human protease makes it a perfect target for inhibitor research. This article reports a computer-aided drug design (CADD) approach for the screening of 118 compounds with 16 distinct heterocyclic moieties in comparison with 5 natural products and 7 repurposed drugs. Molecular docking analysis against Mpro protein were performed finding isatin linked with a oxidiazoles (A2 and A4) derivatives to have the best docking scores of -11.22 kcal/mol and -11.15 kcal/mol respectively. Structure-activity relationship studies showed a good comparison with a known active Mpro inhibitor and repurposed drug ebselen with an IC50 value of -0.67 μM. Molecular Dynamics (MD) simulations for 50 ns were performed for A2 and A4 supporting the stability of the two compounds within the binding pocket, largely at the S1, S2 and S4 domains with high binding energy suggesting their suitability as potential inhibitors of Mpro for SARS-CoV-2.
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Affiliation(s)
| | - Akhil Kumar
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Pralok K. Samanta
- School of Chemical and Bioprocess Engineering, University College Dublin, Dublin, Ireland
| | - Siddhartha Maji
- Department of Pharmaceutical Sciences and Technology, Birla Institute of Technology, Mesra, Ranchi, India
| | - Anik Das
- Department of Chemistry, Institute of Science, GITAM (Deemed to be University), Visakhapatnam, India
| | - Galia Blum
- Institute for Drug Research, The Hebrew University, Jerusalem, Israel
| | - Anjali Jha
- Department of Chemistry, Institute of Science, GITAM (Deemed to be University), Visakhapatnam, India
| | - Anik Sen
- Department of Chemistry, Institute of Science, GITAM (Deemed to be University), Visakhapatnam, India
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67
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Ullah S, Munir B, Al-Sehemi AG, Muhammad S, Haq IU, Aziz A, Ahmed B, Ghaffar A. Identification of phytochemical inhibitors of SARS-CoV-2 protease 3CL pro from selected medicinal plants as per molecular docking, bond energies and amino acid binding energies. Saudi J Biol Sci 2022; 29:103274. [PMID: 35345871 PMCID: PMC8944115 DOI: 10.1016/j.sjbs.2022.03.024] [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: 12/29/2021] [Revised: 01/22/2022] [Accepted: 03/17/2022] [Indexed: 11/26/2022] Open
Abstract
Recent worldwide outbreak of SARS-COV-2 pandemic has increased the thirst to discover and introduce antiviral drugs to combat it. The bioactive compounds from plant sources, especially terpenoid have protease inhibition activities so these may be much effective for the control of viral epidemics and may reduce the burden on health care system worldwide. Present study aims the use of terpenoid from selected plant source through bioinformatics tools for the inhibition of SARS-COV-2. This study is based on descriptive analysis. The Protein Data Bank and PubChem database were used for the analysis of SARS-COV-2 protease and plant source terpenoids. Molecular docking by using molegro virtual docker (MVD) software was carried out. The findings of study are based on the inhibitory actions of different plant sourced terpenoid against SARS-COV-2. As per the available resources and complementary analysis these phytochemicals have capacity to inhibit 3CLpro protease. The study reports that (3,3-dimethylally) isoflavone (Glycine max), licoleafol (Glycyrrhiza uralensis), myricitrin (Myrica cerifera), thymoquinone (Nigella sativa), bilobalide, ginkgolide A (Ginkgo biloba), Salvinorin A (Salvia divinorum), citral (Backhousia citriodora) and prephenazine (drug) showed high activity against SARS-COV-2 protease 3CLpro. The drug like and ADMET properties revealed that these compounds can safely be used as drugs. Cross structural analysis by using bioinformatics study concludes that these plant source terpenoid compounds can be effectively used as antiprotease drugs for SARS-COV-2 in future.
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Affiliation(s)
- Sami Ullah
- Department of Chemistry, College Science, King Khalid University, Abha 61413, PO Box, 9004, Saudi Arabia
| | - Bushra Munir
- Institute of Chemistry, University of Sargodha, Sargodha, Pakistan
| | - Abdullah G Al-Sehemi
- Department of Chemistry, College Science, King Khalid University, Abha 61413, PO Box, 9004, Saudi Arabia
| | - Shabbir Muhammad
- Department of Physics, College Science, King Khalid University, Abha 61413, PO Box, 9004, Saudi Arabia
| | - Ikram-Ul Haq
- Institute of Biotechnology and Genetic Engineering, IBGE, University of Sindh, Jamshoro 76080, Pakistan
| | - Abida Aziz
- Department of Botany, The Women University, Multan, Pakistan
| | - Bilal Ahmed
- Department of Biochemistry, Government College University Faisalabad, Pakistan
| | - Abdul Ghaffar
- Department of Biochemistry, Government College University Faisalabad, Pakistan
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68
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Campitelli P, Lu J, Ozkan SB. Dynamic Allostery Highlights the Evolutionary Differences between the CoV-1 and CoV-2 Main Proteases. Biophys J 2022; 121:1483-1492. [PMID: 35300968 PMCID: PMC8920573 DOI: 10.1016/j.bpj.2022.03.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/28/2021] [Accepted: 03/08/2022] [Indexed: 11/02/2022] Open
Abstract
The SARS-CoV-2 coronavirus has become one of the most immediate and widely-studied systems since its identification and subsequent global outbreak from 2019-2021. In an effort to understand the biophysical changes as a result of mutations, the mechanistic details of multiple different proteins within the SARS-CoV-2 virus have been studied and compared with SARS-CoV-1. Focusing on the main protease (mPro), we first explored the long-range dynamics using the Dynamic Coupling Index (DCI) to investigate the dynamic coupling between the catalytic site residues and the rest of the protein, both inter and intra chain, for the CoV-1 and CoV-2 mPro. We found that there is significant cross-chain coupling between these active sites and specific distal residues in the CoV-2 mPro not present in CoV-1. The enhanced long distance interactions, particularly between the two chains, suggest subsequently enhanced cooperativity for CoV-2. A further comparative analysis of the dynamic flexibility using the Dynamic Flexibility Index (DFI) between the CoV-1 and CoV-2 mPros shows that the inhibitor binding near active sites induces change in flexibility to a distal region of the protein, opposite in behavior between the two systems; this region becomes more flexible upon inhibitor binding in CoV-1 while it becomes less flexible in the CoV-2 mPro. Upon inspection, we show that, on average, the dynamic flexibility of the sites substituted from CoV-1 to CoV-2 changes significantly less than the average calculated across all residues within the structure, indicating that the differences in behaviors between the two systems is likely the result of allosteric influence, where the new substitutions in CoV-2 induce flexibility and dynamical changes elsewhere in the structure.
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Elgohary MAS, Hasan EM, Ibrahim AA, Abdelsalam MFA, Abdel-Rahman RZ, Zaki AI, Elaatar MB, Elnagar MT, Emam ME, Hamada MM, Abdel-Hamid TM, Abdel-Hafez AS, Seadawy MG, Fatoh AR, Elsaied MA, Sakr MAR, Elkady AO, Shehata MM, Nawar OM, Selem MAE, Abd-aal MS, Lotfy HH, Elnagdy TR, Helmy S, Mubark MA. Efficacy of Sofosbuvir plus Ledipasvir in Egyptian patients with COVID-19 compared to standard treatment: a randomized controlled trial. J Med Life 2022; 15:350-358. [PMID: 35449996 PMCID: PMC9015168 DOI: 10.25122/jml-2021-0175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 11/18/2021] [Indexed: 11/05/2022] Open
Abstract
COVID-19 is a pandemic disease caused by SARS-CoV-2, which is an RNA virus similar to the hepatitis C virus (HCV) in the replication process. Sofosbuvir/ledipasvir is an approved drug to treat HCV infection. This study investigates the efficacy of Sofosbuvir/ledipasvir as a treatment for patients with moderate COVID-19 infection. This is a single-blinded parallel-randomized controlled trial. The participants were randomized equally into the intervention group that received Sofosbuvir/ledipasvir (S.L. group), and the control group received Oseltamivir, Hydroxychloroquine, and Azithromycin (OCH group). The primary outcomes were the cure rate over time and the incidence of serious adverse events. The secondary outcomes included the laboratory findings. 250 patients were divided equally into each group. Both groups were similar regarding gender, but age was higher in the S.L. group (p=0.001). In the S.L. group, 89 (71.2%) patients were cured, while only 51 (40.8%) patients were cured in the OCH group. The cure rate was significantly higher in the S.L. group (RR=1.75, p<0.001). Kaplan-Meir plot showed a considerably higher cure over time in the S.L. group (Log-rank test, p=0.032). There were no deaths in the S.L. group, but there were six deaths (4.8%) in the OCH group (RR=0.08, p=0.013). Seven patients (5.6%) in the S.L. group and six patients (4.8%) in the OCH group were admitted to the intensive care unit (ICU) (RR=1.17, P=0.776). There were no significant differences between treatment groups regarding total leukocyte and neutrophils count, lymph, and urea. Sofosbuvir/ledipasvir is suggestive of being effective in treating patients with moderate COVID-19 infection. Further studies are needed to compare Sofosbuvir/ledipasvir with new treatment protocols.
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Affiliation(s)
| | - Eman Medhat Hasan
- Tropical Medicine Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Amany Ahmad Ibrahim
- Tropical Medicine Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | | | | | | | | | | | | | | | | | | | - Mohamed Gomaa Seadawy
- Biological Prevention Department, Egyptian Army, Cairo, Egypt,Corresponding Author: Mohamed Gomaa Seadawy, Biological Prevention Department, Egyptian Army, Cairo, Egypt. E-mail:
| | | | | | | | | | | | | | | | | | | | | | - Sherine Helmy
- Research & Development, PHARCO Pharmaceuticals, Alexandria, Egypt
| | - Magdy Amin Mubark
- Egyptian Military Medical Services Department, Egyptian Army, Cairo, Egypt
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Srivastava A, Siddiqui S, Ahmad R, Mehrotra S, Ahmad B, Srivastava AN. Exploring nature's bounty: identification of Withania somnifera as a promising source of therapeutic agents against COVID-19 by virtual screening and in silico evaluation. J Biomol Struct Dyn 2022; 40:1858-1908. [PMID: 33246398 PMCID: PMC7755033 DOI: 10.1080/07391102.2020.1835725] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 10/02/2020] [Indexed: 10/25/2022]
Abstract
Coronaviruses are etiological agents of extreme human and animal infection resulting in abnormalities primarily in the respiratory tract. Presently, there is no defined COVID-19 intervention and clinical trials of prospective therapeutic agents are still in the nascent stage. Withania somnifera (L.) Dunal (WS), is an important medicinal plant in Ayurveda. The present study aimed to evaluate the antiviral potential of selected WS phytoconstituents against the novel SARS-CoV-2 target proteins and human ACE2 receptor using in silico methods. Most of the phytoconstituents displayed good absorption and transport kinetics and were also found to display no associated mutagenic or adverse effect(s). Molecular docking analyses revealed that most of the WS phytoconstituents exhibited potent binding to human ACE2 receptor, SAR-CoV and SARS-CoV-2 spike glycoproteins as well as the two main SARS-CoV-2 proteases. Most of the phytoconstituents were predicted to undergo Phase-I metabolism prior to excretion. All phytoconstituents had favorable bioactivity scores with respect to various receptor proteins and target enzymes. SAR analysis revealed that the number of oxygen atoms in the withanolide backbone and structural rearrangements were crucial for effective binding. Molecular simulation analyses of SARS-CoV-2 spike protein and papain-like protease with Withanolides A and B, respectively, displayed a stability profile at 300 K and constant RMSDs of protein side chains and Cα atoms throughout the simulation run time. In a nutshell, WS phytoconstituents warrant further investigations in vitro and in vivo to unravel their molecular mechanism(s) and modes of action for their future development as novel antiviral agents against COVID-19.
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Affiliation(s)
- Aditi Srivastava
- Department of Biochemistry, Era’s Lucknow Medical College and Hospital, Era University, Lucknow, UP, India
| | - Sahabjada Siddiqui
- Department of Biotechnology, Era’s Lucknow Medical College and Hospital, Era University, Lucknow, UP, India
| | - Rumana Ahmad
- Department of Biochemistry, Era’s Lucknow Medical College and Hospital, Era University, Lucknow, UP, India
| | - Sudhir Mehrotra
- Department of Biochemistry, University of Lucknow, Lucknow, UP, India
| | - Bilal Ahmad
- Research Cell, Era’s Lucknow Medical College and Hospital, Era University, Lucknow, UP, India
| | - A. N. Srivastava
- Department of Pathology, Era’s Lucknow Medical College and Hospital, Era University, Lucknow, UP, India
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In silico studies on structural inhibition of SARS-CoV-2 main protease Mpro by major secondary metabolites of Andrographis paniculata and Cinchona officinalis. Biologia (Bratisl) 2022; 77:1373-1389. [PMID: 35250036 PMCID: PMC8883239 DOI: 10.1007/s11756-022-01012-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/10/2022] [Indexed: 12/15/2022]
Abstract
The COVID-19 infection by Novel Corona Virus (SARS-CoV-2) has become one of the largest pandemic diseases, with cumulative confirmed infections of 275,233,892 and 5,364,996 deaths to date according to World Health Organization. Due to the absence of any approved antiviral drug to treat COVID-19, its lethality is getting severe with time. The main protease of SARS-CoV-2, Mpro is considered one of the potential drug targets because of its role in processing proteins translated from viral RNA. In the present study, four of the plant metabolites, 14-deoxy-11,12-didehydroandrographolide, andrograpanin, quinine, cinchonine from two eminent medicinal plants Andrographis paniculata and Cinchona officinalis, have been evaluated against the main protease of SARS-CoV-2 through in-silico molecular docking and molecular dynamics simulation study. From the result interpretations, it is found that andrograpanin has strong binding affinities with the target protein in its active site with potential negative energies. Molecular Dynamic simulation and MMGBSA studies suggest that earlier reported N3 inhibitor and andrograpanin exhibit effective binding interactions involving identical amino acid residues with the same binding pockets of the main protease of SARS-CoV-2. Therefore, the theoretical experiment suggests that andrograpanin, could be considered the promising inhibitor against SARS-CoV-2 Mpro.
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72
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De P, Bhayye S, Kumar V, Roy K. In silico modeling for quick prediction of inhibitory activity against 3CL pro enzyme in SARS CoV diseases. J Biomol Struct Dyn 2022; 40:1010-1036. [PMID: 32954984 PMCID: PMC7544940 DOI: 10.1080/07391102.2020.1821779] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 09/06/2020] [Indexed: 12/24/2022]
Abstract
As of 2 September 2020, the 2019 novel coronavirus or SARS CoV-2 has been responsible for more than 2,56,02,665 infections and 8,52,768 deaths worldwide. There has been an urgent need of newer drug discovery to tackle the situation. Severe acute respiratory syndrome-associated coronavirus 3C-like protease (or 3CLpro) is a potential target as anti-SARS agents as it plays a vital role in the viral life cycle. This study aims at developing a quantitative structure-activity relationship (QSAR) model against a group of 3CLpro inhibitors to study their structural requirements for their inhibitory activity. Further, molecular docking studies were carried out which helped in the justification of the QSAR findings. Moreover, molecular dynamics simulation study was performed for selected compounds to check the stability of interactions as suggested by the docking analysis. The current QSAR model was further used in the prediction and screening of large databases within a short time.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Priyanka De
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Sagar Bhayye
- Center for Informatics, Shiv Nadar University, Dadri, Uttar Pradesh, India
| | - Vinay Kumar
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Kunal Roy
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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73
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Cui Q, Garcia G, Zhang M, Wang C, Li H, Zhou T, Sun G, Arumugaswami V, Shi Y. Compound screen identifies the small molecule Q34 as an inhibitor of SARS-CoV-2 infection. iScience 2022; 25:103684. [PMID: 34977495 PMCID: PMC8704726 DOI: 10.1016/j.isci.2021.103684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 12/18/2021] [Accepted: 12/20/2021] [Indexed: 12/04/2022] Open
Abstract
The COVID-19 outbreak poses a serious threat to global public health. Effective countermeasures and approved therapeutics are desperately needed. In this study, we screened a small molecule library containing the NCI-DTP compounds to identify molecules that can prevent SARS-CoV-2 cellular entry. By applying a luciferase assay-based screening using a pseudotyped SARS-CoV-2-mediated cell entry assay, we identified a small molecule compound Q34 that can efficiently block cellular entry of the pseudotyped SARS-CoV-2 into human ACE2-expressing HEK293T cells, and inhibit the infection of the authentic SARS-CoV-2 in human ACE2-expressing HEK293T cells, human iPSC-derived neurons and astrocytes, and human lung Calu-3 cells. Importantly, the safety profile of the compound is favorable. There is no obvious toxicity observed in uninfected cells treated with the compound. Thus, this compound holds great potential as both prophylactics and therapeutics for COVID-19 and future pandemics by blocking the entry of SARS-CoV-2 and related viruses into human cells. A compound library was screened to identify inhibitors of SARS-CoV-2 cellular entry Small molecule Q34 is a potent inhibitor of cellular entry of pseudotyped SARS-CoV-2 Compound Q34 inhibits authentic SARS-CoV-2 infection of human cells Compound Q34 is non-toxic to human cells without SARS-CoV-2 infection
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Affiliation(s)
- Qi Cui
- Division of Stem Cell Biology Research, Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Gustavo Garcia
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Mingzi Zhang
- Division of Stem Cell Biology Research, Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Cheng Wang
- Division of Stem Cell Biology Research, Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Hongzhi Li
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Tao Zhou
- Division of Stem Cell Biology Research, Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Guihua Sun
- Diabetes and Metabolism Research Institute at City of Hope, Duarte, CA 91010, USA
| | - Vaithilingaraja Arumugaswami
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yanhong Shi
- Division of Stem Cell Biology Research, Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA.,Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
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Moradi M, Golmohammadi R, Najafi A, Moosazadeh Moghaddam M, Fasihi-Ramandi M, Mirnejad R. A contemporary review on the important role of in silico approaches for managing different aspects of COVID-19 crisis. INFORMATICS IN MEDICINE UNLOCKED 2022; 28:100862. [PMID: 35079621 PMCID: PMC8776350 DOI: 10.1016/j.imu.2022.100862] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 01/05/2023] Open
Abstract
In the last century, the emergence of in silico tools has improved the quality of healthcare studies by providing high quality predictions. In the case of COVID-19, these tools have been advantageous for bioinformatics analysis of SARS-CoV-2 structures, studying potential drugs and introducing drug targets, investigating the efficacy of potential natural product components at suppressing COVID-19 infection, designing peptide-mimetic and optimizing their structure to provide a better clinical outcome, and repurposing of the previously known therapeutics. These methods have also helped medical biotechnologists to design various vaccines; such as multi-epitope vaccines using reverse vaccinology and immunoinformatics methods, among which some of them have showed promising results through in vitro, in vivo and clinical trial studies. Moreover, emergence of artificial intelligence and machine learning algorithms have helped to classify the previously known data and use them to provide precise predictions and make plan for future of the pandemic condition. At this contemporary review, by collecting related information from the collected literature on valuable data sources; such as PubMed, Scopus, and Web of Science, we tried to provide a brief outlook regarding the importance of in silico tools in managing different aspects of COVID-19 pandemic infection and how these methods have been helpful to biomedical researchers.
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Affiliation(s)
- Mohammad Moradi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Reza Golmohammadi
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases (BRCGL), Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Najafi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | | | - Mahdi Fasihi-Ramandi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Reza Mirnejad
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
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75
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Cho C, Li SG, Lalonde TJ, Yang KS, Yu G, Qiao Y, Xu S, Ray Liu W. Drug Repurposing for the SARS-CoV-2 Papain-Like Protease. ChemMedChem 2022; 17:e202100455. [PMID: 34423563 PMCID: PMC8653067 DOI: 10.1002/cmdc.202100455] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/17/2021] [Indexed: 12/22/2022]
Abstract
As the pathogen of COVID-19, SARS-CoV-2 encodes two essential cysteine proteases that process the pathogen's two large polypeptide products pp1a and pp1ab in the human cell host to form 15 functionally important, mature nonstructural proteins. One of the two enzymes is papain-like protease or PLPro . It possesses deubiquitination and deISGylation activities that suppress host innate immune responses toward SARS-CoV-2 infection. To repurpose drugs for PLPro , we experimentally screened libraries of 33 deubiquitinase and 37 cysteine protease inhibitors on their inhibition of PLPro . Our results showed that 15 deubiquitinase and 1 cysteine protease inhibitors exhibit strong inhibition of PLPro at 200 μM. More comprehensive characterizations revealed seven inhibitors GRL0617, SJB2-043, TCID, DUB-IN-1, DUB-IN-3, PR-619, and S130 with an IC50 value below 40 μM and four inhibitors GRL0617, SJB2-043, TCID, and PR-619 with an IC50 value below 10 μM. Among four inhibitors with an IC50 value below 10 μM, SJB2-043 is the most unique in that it does not fully inhibit PLPro but has a noteworthy IC50 value of 0.56 μM. SJB2-043 likely binds to an allosteric site of PLPro to convene its inhibition effect, which needs to be further investigated. As a pilot study, the current work indicates that COVID-19 drug repurposing by targeting PLPro holds promise, but in-depth analysis of repurposed drugs is necessary to avoid omitting critical allosteric inhibitors.
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Affiliation(s)
- Chia‐Chuan Cho
- The Texas A&M Drug Discovery Laboratory Department of ChemistryTexas A&M UniversityCollege StationTX 77843USA
| | - Shuhua G. Li
- The Texas A&M Drug Discovery Laboratory Department of ChemistryTexas A&M UniversityCollege StationTX 77843USA
| | - Tyler J. Lalonde
- The Texas A&M Drug Discovery Laboratory Department of ChemistryTexas A&M UniversityCollege StationTX 77843USA
| | - Kai S. Yang
- The Texas A&M Drug Discovery Laboratory Department of ChemistryTexas A&M UniversityCollege StationTX 77843USA
| | - Ge Yu
- The Texas A&M Drug Discovery Laboratory Department of ChemistryTexas A&M UniversityCollege StationTX 77843USA
| | - Yuchen Qiao
- The Texas A&M Drug Discovery Laboratory Department of ChemistryTexas A&M UniversityCollege StationTX 77843USA
| | - Shiqing Xu
- The Texas A&M Drug Discovery Laboratory Department of ChemistryTexas A&M UniversityCollege StationTX 77843USA
| | - Wenshe Ray Liu
- The Texas A&M Drug Discovery Laboratory Department of ChemistryTexas A&M UniversityCollege StationTX 77843USA
- Institute of Biosciences and Technology and Department of Translational Medical Sciences College of MedicineTexas A&M UniversityHoustonTX 77030USA
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTX 77843USA
- Department of Molecular and Cellular Medicine College of MedicineTexas A&M UniversityCollege StationTX 77843USA
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76
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Tam NM, Nguyen TH, Ngan VT, Tung NT, Ngo ST. Unbinding ligands from SARS-CoV-2 Mpro via umbrella sampling simulations. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211480. [PMID: 35116157 PMCID: PMC8790385 DOI: 10.1098/rsos.211480] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 12/20/2021] [Indexed: 05/03/2023]
Abstract
The umbrella sampling (US) simulation is demonstrated to be an efficient approach for determining the unbinding pathway and binding affinity to the SARS-CoV-2 Mpro of small molecule inhibitors. The accuracy of US is in the same range as the linear interaction energy (LIE) and fast pulling of ligand (FPL) methods. In detail, the correlation coefficient between US and experiments does not differ from FPL and is slightly smaller than LIE. The root mean square error of US simulations is smaller than that of LIE. Moreover, US is better than FPL and poorer than LIE in classifying SARS-CoV-2 Mpro inhibitors owing to the reciever operating characteristic-area under the curve analysis. Furthermore, the US simulations also provide detailed insights on unbinding pathways of ligands from the binding cleft of SARS-CoV-2 Mpro. The residues Cys44, Thr45, Ser46, Leu141, Asn142, Gly143, Glu166, Leu167, Pro168, Ala191, Gln192 and Ala193 probably play an important role in the ligand dissociation. Therefore, substitutions at these points may change the mechanism of binding of inhibitors to SARS-CoV-2 Mpro.
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Affiliation(s)
- Nguyen Minh Tam
- Computational Chemistry Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Trung Hai Nguyen
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Vu Thi Ngan
- Laboratory of Computational Chemistry and Modelling, Department of Chemistry, Quy Nhon University, Quy Nhon, Vietnam
| | - Nguyen Thanh Tung
- Institute of Materials Science, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Son Tung Ngo
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City, Vietnam
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Montenegro-Landívar MF, Tapia-Quirós P, Vecino X, Reig M, Valderrama C, Granados M, Cortina JL, Saurina J. Polyphenols and their potential role to fight viral diseases: An overview. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 801:149719. [PMID: 34438146 PMCID: PMC8373592 DOI: 10.1016/j.scitotenv.2021.149719] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 05/23/2023]
Abstract
Fruits, vegetables, spices, and herbs are a potential source of phenolic acids and polyphenols. These compounds are known as natural by-products or secondary metabolites of plants, which are present in the daily diet and provide important benefits to the human body such as antioxidant, anti-inflammatory, anticancer, anti-allergic, antihypertensive and antiviral properties, among others. Plentiful evidence has been provided on the great potential of polyphenols against different viruses that cause widespread health problems. As a result, this review focuses on the potential antiviral properties of some polyphenols and their action mechanism against various types of viruses such as coronaviruses, influenza, herpes simplex, dengue fever, and rotavirus, among others. Also, it is important to highlight the relationship between antiviral and antioxidant activities that can contribute to the protection of cells and tissues of the human body. The wide variety of action mechanisms of antiviral agents, such as polyphenols, against viral infections could be applied as a treatment or prevention strategy; but at the same time, antiviral polyphenols could be used to produce natural antiviral drugs. A recent example of an antiviral polyphenol application deals with the use of hesperidin extracted from Citrus sinensis. The action mechanism of hesperidin relies on its binding to the key entry or spike protein of SARS-CoV-2. Finally, the extraction, purification and recovery of polyphenols with potential antiviral activity, which are essential for virus replication and infection without side-effects, have been critically reviewed.
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Affiliation(s)
- María Fernanda Montenegro-Landívar
- Chemical Engineering Department, Escola d'Enginyeria de Barcelona Est (EEBE), Universitat Politècnica de Catalunya (UPC)-BarcelonaTECH, C/Eduard Maristany 10-14, Campus Diagonal-Besòs, 08930 Barcelona, Spain; Barcelona Research Center for Multiscale Science and Engineering, Campus Diagonal-Besòs, 08930 Barcelona, Spain
| | - Paulina Tapia-Quirós
- Chemical Engineering Department, Escola d'Enginyeria de Barcelona Est (EEBE), Universitat Politècnica de Catalunya (UPC)-BarcelonaTECH, C/Eduard Maristany 10-14, Campus Diagonal-Besòs, 08930 Barcelona, Spain; Barcelona Research Center for Multiscale Science and Engineering, Campus Diagonal-Besòs, 08930 Barcelona, Spain
| | - Xanel Vecino
- Chemical Engineering Department, Escola d'Enginyeria de Barcelona Est (EEBE), Universitat Politècnica de Catalunya (UPC)-BarcelonaTECH, C/Eduard Maristany 10-14, Campus Diagonal-Besòs, 08930 Barcelona, Spain; Barcelona Research Center for Multiscale Science and Engineering, Campus Diagonal-Besòs, 08930 Barcelona, Spain; Chemical Engineering Department, School of Industrial Engineering-CINTECX, University of Vigo, Campus As Lagoas-Marcosende, 36310 Vigo, Spain
| | - Mònica Reig
- Chemical Engineering Department, Escola d'Enginyeria de Barcelona Est (EEBE), Universitat Politècnica de Catalunya (UPC)-BarcelonaTECH, C/Eduard Maristany 10-14, Campus Diagonal-Besòs, 08930 Barcelona, Spain; Barcelona Research Center for Multiscale Science and Engineering, Campus Diagonal-Besòs, 08930 Barcelona, Spain
| | - César Valderrama
- Chemical Engineering Department, Escola d'Enginyeria de Barcelona Est (EEBE), Universitat Politècnica de Catalunya (UPC)-BarcelonaTECH, C/Eduard Maristany 10-14, Campus Diagonal-Besòs, 08930 Barcelona, Spain; Barcelona Research Center for Multiscale Science and Engineering, Campus Diagonal-Besòs, 08930 Barcelona, Spain
| | - Mercè Granados
- Department of Chemical Engineering and Analytical Chemistry, Universitat de Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - José Luis Cortina
- Chemical Engineering Department, Escola d'Enginyeria de Barcelona Est (EEBE), Universitat Politècnica de Catalunya (UPC)-BarcelonaTECH, C/Eduard Maristany 10-14, Campus Diagonal-Besòs, 08930 Barcelona, Spain; Barcelona Research Center for Multiscale Science and Engineering, Campus Diagonal-Besòs, 08930 Barcelona, Spain; CETAQUA, Carretera d'Esplugues, 75, 08940 Cornellà de Llobregat, Spain.
| | - Javier Saurina
- Department of Chemical Engineering and Analytical Chemistry, Universitat de Barcelona, Diagonal 645, 08028 Barcelona, Spain
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78
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Kumar B, Misra A, Singh SP, Dhar YV, Rawat P, Chattopadhyay D, Barik SK, Srivastava S. In-silico efficacy of potential phytomolecules from Ayurvedic herbs as an adjuvant therapy in management of COVID-19. J Food Drug Anal 2021; 29:559-580. [PMID: 35649148 PMCID: PMC9931022 DOI: 10.38212/2224-6614.3380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 05/17/2021] [Accepted: 08/26/2021] [Indexed: 11/18/2022] Open
Abstract
The recent COVID-19 outbreak caused by SARS-CoV-2 virus has sparked a new spectrum of investigations, research and studies in multifarious directions. Efforts are being made around the world for discovery of effective vaccines/drugs against COVID-19. In this context, Ayurveda, an alternative traditional system of medicine in India may work as an adjuvant therapy in compromised patients. We selected 40 herbal leads on the basis of their traditional applications. The phytomolecules from these leads were further screened through in-silico molecular docking against two main targets of SARS-CoV-2 i.e. the spike protein (S; structural protein) and the main protease (MPRO; non-structural protein). Out of the selected 40, 12 phytomolecules were able to block or stabilize the major functional sites of the main protease and spike protein. Among these, Ginsenoside, Glycyrrhizic acid, Hespiridin and Tribulosin exhibited high binding energy with both main protease and spike protein. Etoposide showed good binding energy only with Spike protein and Teniposide had high binding energy only with main protease. The above phytocompounds showed promising binding efficiency with target proteins indicating their possible applications against SARS-CoV-2. However, these findings need to be validated through in vitro and in vivo experiments with above mentioned potential molecules as candidate drugs for the management of COVID-19. In addition, there is an opportunity for the development of formulations through different permutations and combinations of these phytomolecules to harness their synergistic potential.
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Affiliation(s)
- Bhanu Kumar
- Pharmacognosy Division, CSIR-National Botanical Research Institute, Lucknow, U.P. 226001,
India
| | - Ankita Misra
- Pharmacognosy Division, CSIR-National Botanical Research Institute, Lucknow, U.P. 226001,
India
| | - Satyendra Pratap Singh
- Pharmacognosy Division, CSIR-National Botanical Research Institute, Lucknow, U.P. 226001,
India
| | - Yogeshwar Vikram Dhar
- Bioinformatics Division, CSIR-National Botanical Research Institute, Lucknow, U.P. 226001,
India
| | - Poonam Rawat
- Pharmacognosy Division, CSIR-National Botanical Research Institute, Lucknow, U.P. 226001,
India
| | | | - Saroj Kanta Barik
- Pharmacognosy Division, CSIR-National Botanical Research Institute, Lucknow, U.P. 226001,
India
| | - Sharad Srivastava
- Pharmacognosy Division, CSIR-National Botanical Research Institute, Lucknow, U.P. 226001,
India
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Lochab A, Thareja R, Gadre SD, Saxena R. Potential Protein and Enzyme Targets for In‐silico Development and Repurposing of Drug Against Coronaviruses. ChemistrySelect 2021. [DOI: 10.1002/slct.202103350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Amit Lochab
- Department of Chemistry Kirori Mal College University of Delhi Delhi India
| | - Rakhi Thareja
- Department of Chemistry St. Stephens College University of Delhi Delhi India
| | - Sangeeta D. Gadre
- Department of Physics Kirori Mal College University of Delhi Delhi India
| | - Reena Saxena
- Department of Chemistry Kirori Mal College University of Delhi Delhi India
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Yapasert R, Khaw-on P, Banjerdpongchai R. Coronavirus Infection-Associated Cell Death Signaling and Potential Therapeutic Targets. Molecules 2021; 26:7459. [PMID: 34946543 PMCID: PMC8706825 DOI: 10.3390/molecules26247459] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/29/2021] [Accepted: 12/06/2021] [Indexed: 12/12/2022] Open
Abstract
COVID-19 is the name of the disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection that occurred in 2019. The virus-host-specific interactions, molecular targets on host cell deaths, and the involved signaling are crucial issues, which become potential targets for treatment. Spike protein, angiotensin-converting enzyme 2 (ACE2), cathepsin L-cysteine peptidase, transmembrane protease serine 2 (TMPRSS2), nonstructural protein 1 (Nsp1), open reading frame 7a (ORF7a), viral main protease (3C-like protease (3CLpro) or Mpro), RNA dependent RNA polymerase (RdRp) (Nsp12), non-structural protein 13 (Nsp13) helicase, and papain-like proteinase (PLpro) are molecules associated with SARS-CoV infection and propagation. SARS-CoV-2 can induce host cell death via five kinds of regulated cell death, i.e., apoptosis, necroptosis, pyroptosis, autophagy, and PANoptosis. The mechanisms of these cell deaths are well established and can be disrupted by synthetic small molecules or natural products. There are a variety of compounds proven to play roles in the cell death inhibition, such as pan-caspase inhibitor (z-VAD-fmk) for apoptosis, necrostatin-1 for necroptosis, MCC950, a potent and specific inhibitor of the NLRP3 inflammasome in pyroptosis, and chloroquine/hydroxychloroquine, which can mitigate the corresponding cell death pathways. However, NF-κB signaling is another critical anti-apoptotic or survival route mediated by SARS-CoV-2. Such signaling promotes viral survival, proliferation, and inflammation by inducing the expression of apoptosis inhibitors such as Bcl-2 and XIAP, as well as cytokines, e.g., TNF. As a result, tiny natural compounds functioning as proteasome inhibitors such as celastrol and curcumin can be used to modify NF-κB signaling, providing a responsible method for treating SARS-CoV-2-infected patients. The natural constituents that aid in inhibiting viral infection, progression, and amplification of coronaviruses are also emphasized, which are in the groups of alkaloids, flavonoids, terpenoids, diarylheptanoids, and anthraquinones. Natural constituents derived from medicinal herbs have anti-inflammatory and antiviral properties, as well as inhibitory effects, on the viral life cycle, including viral entry, replication, assembly, and release of COVID-19 virions. The phytochemicals contain a high potential for COVID-19 treatment. As a result, SARS-CoV-2-infected cell death processes and signaling might be of high efficacy for therapeutic targeting effects and yielding encouraging outcomes.
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Affiliation(s)
- Rittibet Yapasert
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Patompong Khaw-on
- Faculty of Nursing, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Ratana Banjerdpongchai
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand;
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81
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Smith PO, Jin P, Rahman KM. Strategies for drug repurposing against coronavirus targets. CURRENT RESEARCH IN PHARMACOLOGY AND DRUG DISCOVERY 2021; 3:100072. [PMID: 34901833 PMCID: PMC8642829 DOI: 10.1016/j.crphar.2021.100072] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/29/2021] [Accepted: 12/02/2021] [Indexed: 02/07/2023] Open
Abstract
Repurposing regulatory agency approved drugs and investigational compounds with known safety profiles can significantly fast track the drug development timeline over de novo drug discovery, with lower investment requirements and improved attrition rate. These advantages are vital in any epidemic or pandemic situation, where hospital beds are occupied by patients for whom there is no known treatment. Here we examine drug repurposing in the context of human coronaviruses, SARS-CoV, MERS-CoV, and, in particular, SARS-CoV-2, the virus currently causing a continued widespread pandemic with substantial impacts on public health and economy. The key druggable targets explored were those involved in viral entry, viral replication, and viral-induced ARDS, as well as viral proteases, with a focus on the strategy by which the drugs were repurposed.
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Affiliation(s)
- Poppy O. Smith
- School of Cancer and Pharmaceutical Sciences, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
| | - Peiqin Jin
- School of Cancer and Pharmaceutical Sciences, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
| | - Khondaker Miraz Rahman
- School of Cancer and Pharmaceutical Sciences, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
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Aronskyy I, Masoudi-Sobhanzadeh Y, Cappuccio A, Zaslavsky E. Advances in the computational landscape for repurposed drugs against COVID-19. Drug Discov Today 2021; 26:2800-2815. [PMID: 34339864 PMCID: PMC8323501 DOI: 10.1016/j.drudis.2021.07.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/30/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023]
Abstract
The COVID-19 pandemic has caused millions of deaths and massive societal distress worldwide. Therapeutic solutions are urgently needed, but de novo drug development remains a lengthy process. One promising alternative is computational drug repurposing, which enables the prioritization of existing compounds through fast in silico analyses. Recent efforts based on molecular docking, machine learning, and network analysis have produced actionable predictions. Some predicted drugs, targeting viral proteins and pathological host pathways are undergoing clinical trials. Here, we review this work, highlight drugs with high predicted efficacy and classify their mechanisms of action. We discuss the strengths and limitations of the published methodologies and outline possible future directions. Finally, we curate a list of COVID-19 data portals and other repositories that could be used to accelerate future research.
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Affiliation(s)
- Illya Aronskyy
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yosef Masoudi-Sobhanzadeh
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Antonio Cappuccio
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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83
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Adhikari N, Banerjee S, Baidya SK, Ghosh B, Jha T. Ligand-based quantitative structural assessments of SARS-CoV-2 3CL pro inhibitors: An analysis in light of structure-based multi-molecular modeling evidences. J Mol Struct 2021; 1251:132041. [PMID: 34866654 PMCID: PMC8627846 DOI: 10.1016/j.molstruc.2021.132041] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 11/10/2021] [Accepted: 11/26/2021] [Indexed: 12/11/2022]
Abstract
Due to COVID-19, the whole world is undergoing a devastating situation, but treatment with no such drug candidates still has been established exclusively. In that context, 69 diverse chemicals with potential SARS-CoV-2 3CLpro inhibitory property were taken into consideration for building different internally and externally validated linear (SW-MLR and GA-MLR), non-linear (ANN and SVM) QSAR, and HQSAR models to identify important structural and physicochemical characters required for SARS-CoV-2 3CLpro inhibition. Importantly, 2-oxopyrrolidinyl methyl and benzylester functions, and methylene (hydroxy) sulphonic acid warhead group, were crucial for retaining higher SARS-CoV-2 3CLpro inhibition. These GA-MLR and HQSAR models were also applied to predict some already repurposed drugs. As per the GA-MLR model, curcumin, ribavirin, saquinavir, sepimostat, and remdesivir were found to be the potent ones, whereas according to the HQSAR model, lurasidone, saquinavir, lopinavir, elbasvir, and paritaprevir were the highly effective SARS-CoV-2 3CLpro inhibitors. The binding modes of those repurposed drugs were also justified by the molecular docking, molecular dynamics (MD) simulation, and binding energy calculations conducted by several groups of researchers. This current work, therefore, may be able to find out important structural parameters to accelerate the COVID-19 drug discovery processes in the future.
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Affiliation(s)
- Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Suvankar Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Sandip Kumar Baidya
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Balaram Ghosh
- Epigenetic Research Laboratory, Birla Institute of Technology and Science-Pilani Hyderabad Campus, Shamirpet, Hyderabad, India, 500078
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
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84
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Kow CS, Javed A, Ramachandram D, Hasan SS. Clinical outcomes of sofosbuvir-based antivirals in patients with COVID-19: a systematic review and meta-analysis of randomized trials. Expert Rev Anti Infect Ther 2021; 20:567-575. [PMID: 34719324 DOI: 10.1080/14787210.2022.2000861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND Several randomized trials have evaluated the effects of sofosbuvir-based direct-acting antivirals on the clinical outcomes in patients with COVID-19. METHODS A systematic literature search with no language restrictions was performed on electronic databases and preprint repositories to identify eligible randomized trials published up to 8 July 2021. A random-effects model was used to estimate the pooled odds ratio (OR) for outcomes of interest with the use of sofosbuvir combined with direct-acting antiviral agents relative to the nonuse of sofosbuvir-based direct-acting antiviral agents at 95% confidence intervals (CI). RESULTS The meta-analysis of 11 trials (n = 2,161) revealed statistically significant reduction in the odds of mortality (pooled odds ratio = 0.59; 95% confidence interval 0.36 to 0.99) but no statistically significant difference in the odds of development of composite endpoint of severe illness (pooled odds ratio = 0.79; 95% confidence interval 0.43 to 1.44) with the administration of sofosbuvir-based direct-acting antiviral agents among patients with COVID-19, relative to non-administration of sofosbuvir-based direct-acting antiviral agents.Subgroup analysis with seven trials involving sofosbuvir-daclatasvir revealed no significant mortality benefit (pooled odds ratio = 0.77; 95% confidence interval 0.48 to 1.22). CONCLUSION Sofosbuvir-based direct-acting antiviral agents have no protective effects against the development of severe illness in patients with COVID-19 with the current dosing regimen. Whether sofosbuvir-based direct-acting antiviral agents could offer mortality benefits would require further investigations.
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Affiliation(s)
- Chia Siang Kow
- School of Pharmacy, Monash University Malaysia, Petaling Jaya, Malaysia
| | - Amaan Javed
- University College of Medical Sciences, University of Delhi, Delhi, India
| | | | - Syed Shahzad Hasan
- School of Pharmacy, School of Applied Sciences, University of Huddersfield, Huddersfield, UK.,School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia
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85
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Anwaar MU, Adnan F, Abro A, Khan RA, Rehman AU, Osama M, Rainville C, Kumar S, Sterner DE, Javed S, Jamal SB, Baig A, Shabbir MR, Ahsan W, Butt TR, Assir MZ. Combined deep learning and molecular docking simulations approach identifies potentially effective FDA approved drugs for repurposing against SARS-CoV-2. Comput Biol Med 2021; 141:105049. [PMID: 34823857 PMCID: PMC8604796 DOI: 10.1016/j.compbiomed.2021.105049] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 11/11/2021] [Accepted: 11/15/2021] [Indexed: 01/10/2023]
Abstract
The ongoing pandemic of Coronavirus Disease 2019 (COVID-19) has posed a serious threat to global public health. Drug repurposing is a time-efficient approach to finding effective drugs against SARS-CoV-2 in this emergency. Here, we present a robust experimental design combining deep learning with molecular docking experiments to identify the most promising candidates from the list of FDA-approved drugs that can be repurposed to treat COVID-19. We have employed a deep learning-based Drug Target Interaction (DTI) model, called DeepDTA, with few improvements to predict drug-protein binding affinities, represented as KIBA scores, for 2440 FDA-approved and 8168 investigational drugs against 24 SARS-CoV-2 viral proteins. FDA-approved drugs with the highest KIBA scores were selected for molecular docking simulations. We ran around 50,000 docking simulations for 168 selected drugs against 285 total predicted and/or experimentally proven active sites of all 24 SARS-CoV-2 viral proteins. A list of 49 most promising FDA-approved drugs with the best consensus KIBA scores and binding affinity values against selected SARS-CoV-2 viral proteins was generated. Most importantly, 16 drugs including anidulafungin, velpatasvir, glecaprevir, rifapentine, flavin adenine dinucleotide (FAD), terlipressin, and selinexor demonstrated the highest predicted inhibitory potential against key SARS-CoV-2 viral proteins. We further measured the inhibitory activity of 5 compounds (rifapentine, velpatasvir, glecaprevir, anidulafungin, and FAD disodium) on SARS-CoV-2 PLpro using Ubiquitin-Rhodamine 110 Gly fluorescent intensity assay. The highest inhibition of PLpro activity was seen with rifapentine (IC50: 15.18 μM) and FAD disodium (IC50: 12.39 μM), the drugs with high predicted KIBA scores and binding affinities.
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Affiliation(s)
- Muhammad U Anwaar
- Department of Electrical and Computer Engineering, Technical University Munich, Arcisstraße 21, 80333, München, Germany
| | - Farjad Adnan
- Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Asma Abro
- Department of Biotechnology, Faculty of Life Sciences and Informatics, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, 1800, Pakistan
| | - Rayyan A Khan
- Department of Electrical and Computer Engineering, Technical University Munich, Arcisstraße 21, 80333, München, Germany
| | - Asad U Rehman
- Department of Medicine, Allama Iqbal Medical College, University of Health Sciences, Lahore, 54550, Pakistan; Center for Undiagnosed, Rare and Emerging Diseases, Lahore, 54550, Pakistan
| | - Muhammad Osama
- Department of Medicine, Allama Iqbal Medical College, University of Health Sciences, Lahore, 54550, Pakistan; Center for Undiagnosed, Rare and Emerging Diseases, Lahore, 54550, Pakistan
| | | | - Suresh Kumar
- Progenra Inc, 271A Great Valley Parkway, Malvern, PA, 19355, USA
| | - David E Sterner
- Progenra Inc, 271A Great Valley Parkway, Malvern, PA, 19355, USA
| | - Saad Javed
- Department of Medicine, Allama Iqbal Medical College, University of Health Sciences, Lahore, 54550, Pakistan; Center for Undiagnosed, Rare and Emerging Diseases, Lahore, 54550, Pakistan
| | - Syed B Jamal
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Ahmadullah Baig
- Department of Medicine, Allama Iqbal Medical College, University of Health Sciences, Lahore, 54550, Pakistan
| | - Muhammad R Shabbir
- Department of Medicine, Allama Iqbal Medical College, University of Health Sciences, Lahore, 54550, Pakistan; Center for Undiagnosed, Rare and Emerging Diseases, Lahore, 54550, Pakistan
| | - Waseh Ahsan
- Department of Medicine, Allama Iqbal Medical College, University of Health Sciences, Lahore, 54550, Pakistan
| | - Tauseef R Butt
- Progenra Inc, 271A Great Valley Parkway, Malvern, PA, 19355, USA
| | - Muhammad Z Assir
- Department of Medicine, Allama Iqbal Medical College, University of Health Sciences, Lahore, 54550, Pakistan; Center for Undiagnosed, Rare and Emerging Diseases, Lahore, 54550, Pakistan; Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, 44000, Pakistan.
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86
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Chakraborty C, Sharma AR, Bhattacharya M, Agoramoorthy G, Lee SS. The Drug Repurposing for COVID-19 Clinical Trials Provide Very Effective Therapeutic Combinations: Lessons Learned From Major Clinical Studies. Front Pharmacol 2021; 12:704205. [PMID: 34867318 PMCID: PMC8636940 DOI: 10.3389/fphar.2021.704205] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 10/07/2021] [Indexed: 12/15/2022] Open
Abstract
SARS-CoV-2 has spread across the globe in no time. In the beginning, people suffered due to the absence of efficacious drugs required to treat severely ill patients. Nevertheless, still, there are no established therapeutic molecules against the SARS-CoV-2. Therefore, repurposing of the drugs started against SARS-CoV-2, due to which several drugs were approved for the treatment of COVID-19 patients. This paper reviewed the treatment regime for COVID-19 through drug repurposing from December 8, 2019 (the day when WHO recognized COVID-19 as a pandemic) until today. We have reviewed all the clinical trials from RECOVERY trials, ACTT-1 and ACTT-2 study group, and other major clinical trial platforms published in highly reputed journals such as NEJM, Lancet, etc. In addition to single-molecule therapy, several combination therapies were also evaluated to understand the treatment of COVID-19 from these significant clinical trials. To date, several lessons have been learned on the therapeutic outcomes for COVID-19. The paper also outlines the experiences gained during the repurposing of therapeutic molecules (hydroxychloroquine, ritonavir/ lopinavir, favipiravir, remdesivir, ivermectin, dexamethasone, camostatmesylate, and heparin), immunotherapeutic molecules (tocilizumab, mavrilimumab, baricitinib, and interferons), combination therapy, and convalescent plasma therapy to treat COVID-19 patients. We summarized that anti-viral therapeutic (remdesivir) and immunotherapeutic (tocilizumab, dexamethasone, and baricitinib) therapy showed some beneficial outcomes. Until March 2021, 4952 clinical trials have been registered in ClinicalTrials.gov toward the drug and vaccine development for COVID-19. More than 100 countries have participated in contributing to these clinical trials. Other than the registered clinical trials (medium to large-size), several small-size clinical trials have also been conducted from time to time to evaluate the treatment of COVID-19. Four molecules showed beneficial therapeutic to treat COVID-19 patients. The short-term repurposing of the existing drug may provide a successful outcome for COVID-19 patients. Therefore, more clinical trials can be initiated using potential anti-viral molecules by evaluating in different phases of clinical trials.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, India
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging and Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, South Korea
| | | | | | - Sang-Soo Lee
- Institute for Skeletal Aging and Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, South Korea
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87
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Structural and functional significance of the amino acid differences Val 35Thr, Ser 46Ala, Asn 65Ser, and Ala 94Ser in 3C-like proteinases from SARS-CoV-2 and SARS-CoV. Int J Biol Macromol 2021; 193:2113-2120. [PMID: 34774600 PMCID: PMC8580570 DOI: 10.1016/j.ijbiomac.2021.11.043] [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: 09/04/2021] [Revised: 10/07/2021] [Accepted: 11/05/2021] [Indexed: 11/28/2022]
Abstract
Three dimensional structures of (chymo)trypsin-like proteinase (3CLpro) from SARS-CoV-2 and SARS-CoV differ at 8 positions. We previously found that the Val86Leu, Lys88Arg, Phe134His, and Asn180Lys mutations in these enzymes can change the orientation of the N- and C-terminal domains of 3CLpro relative to each other, which leads to a change in catalytic activity. This conclusion was derived from the comparison of the structural catalytic core in 169 (chymo)trypsin-like proteinases with the serine/cysteine fold. Val35Thr, Ser46Ala, Asn65Ser, Ala94Ser mutations were not included in that analysis, since they are located far from the catalytic tetrad. In the present work, the structural and functional roles of these variable amino acids at positions 35, 46, 65, and 94 in the 3CLpro sequences of SARS-CoV-2 and SARS-CoV have been established using a comparison of the same set of proteinases leading to the identification of new conservative elements. Comparative analysis showed that, in addition to interdomain mobility, which could modulate catalytic activity, the 3CLpro(s) can use for functional regulation an autolytic loop and the unique Asp33-Asn95 region (the Asp33-Asn95 Zone) in the N-terminal domain. Therefore, all 4 analyzed mutation sites are associated with the unique structure-functional features of the 3CLpro from SARS-CoV-2 and SARS-CoV. Strictly speaking, the presented structural results are hypothetical, since at present there is not a single experimental work on the identification and characterization of autolysis sites in these proteases.
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88
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Mozafari Z, Chamjangali MA, Arashi M, Goudarzi N. Suggestion of active 3-chymotrypsin like protease (3CL Pro) inhibitors as potential anti-SARS-CoV-2 agents using predictive QSAR model based on the combination of ALASSO with an ANN model. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:863-888. [PMID: 34634208 DOI: 10.1080/1062936x.2021.1975167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 08/28/2021] [Indexed: 06/13/2023]
Abstract
The novel severe acute respiratory syndrome coronavirus (SARS CoV-2) was introduced as an epidemic in 2019 and had millions of deaths worldwide. Given the importance of this disease, the recommendation and design of new active compounds are crucial. 3-chymotrypsin-like protease (3 CLpro) inhibitors have been identified as potent compounds for treating SARS-CoV-2 disease. So, the design of new 3 CLpro inhibitors was proposed using a quantitative structure-activity relationship (QSAR) study. In this context, a powerful adaptive least absolute shrinkage and selection operator (ALASSO) penalized variable selection method with inherent advantages coupled with a nonlinear artificial neural network (ANN) modelling method were used to provide a QSAR model with high interpretability and predictability. After evaluating the accuracy and validity of the developed ALASSO-ANN model, new compounds were proposed using effective descriptors, and the biological activity of the new compounds was predicted. Ligand-receptor (LR) interactions were also performed to confirm the interaction strength of the compounds using molecular docking (MD) study. The pharmacokinetics properties and calculated Lipinski's rule of five were applied to all proposed compounds. Due to the ease of synthesis of these suggested new compounds, it is expected that they have acceptable pharmacological properties.
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Affiliation(s)
- Z Mozafari
- Department of Chemistry, Shahrood University of Technology, Shahrood, Iran
| | - M Arab Chamjangali
- Department of Chemistry, Shahrood University of Technology, Shahrood, Iran
| | - M Arashi
- Department of Statistics, Faculty of Mathematical Sciences, Ferdowsi University of Mashhad, Mashhad, Iran
| | - N Goudarzi
- Department of Chemistry, Shahrood University of Technology, Shahrood, Iran
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89
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Yuan F, Wang L, Fang Y, Wang L. Global SNP analysis of 11,183 SARS-CoV-2 strains reveals high genetic diversity. Transbound Emerg Dis 2021; 68:3288-3304. [PMID: 33207070 PMCID: PMC7753349 DOI: 10.1111/tbed.13931] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/19/2020] [Accepted: 11/13/2020] [Indexed: 02/05/2023]
Abstract
Since first identified in December of 2019, COVID-19 has been quickly spreading to the world in few months and COVID-19 cases are still undergoing rapid surge in most countries worldwide. The causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), adapts and evolves rapidly in nature. With the availability of 16,092 SARS-CoV-2 full genomes in GISAID as of 13 May, we removed the poor-quality genomes and performed mutational profiling analysis for the remaining 11,183 viral genomes. Global analysis of all sequences identified all single nucleotide polymorphisms (SNPs) across the whole genome and critical SNPs with high mutation frequency that contributes to five-clade classification of global strains. A total of 119 SNPs were found with 74 non-synonymous mutations, 43 synonymous mutations and two mutations in intergenic regions. Analysis of geographic pattern of mutational profiling for the whole genome reveals differences between each continent. A transition mutation from C to T represents the most mutation types across the genome, suggesting rapid evolution and adaptation of the virus in host. Amino acid (AA) deletions and insertions found across the genome results in changes in viral protein length and potential function alteration. Mutational profiling for each gene was analysed, and results show that nucleocapsid gene demonstrates the highest mutational frequency, followed by Nsp2, Nsp3 and Spike gene. We further focused on non-synonymous mutational distributions on four key viral proteins, spike with 75 mutations, RNA-dependent-RNA-polymerase with 41 mutations, 3C-like protease with 22 mutations and Papain-like protease with 10 mutations. Results show that non-synonymous mutations on critical sites of these four proteins pose great challenge for development of anti-viral drugs and other countering measures. Overall, this study provides more understanding of genetic diversity/variability of SARS-CoV-2 and insights for development of anti-viral therapeutics.
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Affiliation(s)
- Fangfeng Yuan
- Department of PathobiologyCollege of Veterinary MedicineUniversity of Illinois at Urbana ChampaignUrbanaIllinoisUSA
| | - Liping Wang
- Department of Diagnostic Medicine and PathobiologyCollege of Veterinary MedicineKansas State UniversityManhattanKansasUSA
| | - Ying Fang
- Department of PathobiologyCollege of Veterinary MedicineUniversity of Illinois at Urbana ChampaignUrbanaIllinoisUSA
| | - Leyi Wang
- Veterinary Diagnostic Laboratory and Department of Veterinary Clinical MedicineCollege of Veterinary MedicineUniversity of IllinoisUrbanaIllinoisUSA
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90
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Rath S, Perikala V, Jena AB, Dandapat J. Factors regulating dynamics of angiotensin-converting enzyme-2 (ACE2), the gateway of SARS-CoV-2: Epigenetic modifications and therapeutic interventions by epidrugs. Biomed Pharmacother 2021; 143:112095. [PMID: 34479017 PMCID: PMC8403698 DOI: 10.1016/j.biopha.2021.112095] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 08/20/2021] [Indexed: 12/15/2022] Open
Abstract
Angiotensin-converting enzyme-2 (ACE2) is one of the major components of the renin-angiotensin system (RAS) and participates in the physiological functions of the cardiovascular system and lungs. Recent studies identified ACE2 as the receptor for the S-protein of the novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and thus acts as the gateway for viral entry into the human body. Virus infection causes an imbalance in the RAS axis and induces acute lungs injury and fibrosis. Various factors regulate ACE2 expression patterns as well as control its epigenetic status at both transcription and translational levels. This review is mainly focused on the impact of environmental toxicants, drugs, endocrine disruptors, and hypoxia as controlling parameters for ACE2 expression and its possible modulation by epigenetic changes which are marked by DNA methylation, histone modifications, and micro-RNAs (miRNAs) profile. Furthermore, we have emphasized on interventions of various phytochemicals and bioactive compounds as epidrugs that regulate ACE2-S-protein interaction and thereby curb viral infection. Since ACE2 is an important component of the RAAS axis and a crucial entry point of SARS-CoV-2, the dynamics of ACE2 expression in response to various extrinsic and intrinsic factors are of contemporary relevance. We have collated updated information on ACE2 expression modulated by epidrugs, and urge to take over further studies on these important physiological regulators to unravel many more systemic linkages related to both metabolic and infectious diseases, in general and SARS-CoV-2 in particular for further development of targeted interventions.
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Affiliation(s)
- Suvasmita Rath
- Centre of Environment, Climate Change and Public Health, Utkal University, Vani Vihar, Bhubaneswar 751004, Odisha, India
| | - Venkateswarlu Perikala
- Centre of Environment, Climate Change and Public Health, Utkal University, Vani Vihar, Bhubaneswar 751004, Odisha, India
| | - Atala Bihari Jena
- Centre of Excellence in Integrated Omics and Computational Biology, Utkal University, Bhubaneswar 751004, Odisha, India
| | - Jagneshwar Dandapat
- Centre of Excellence in Integrated Omics and Computational Biology, Utkal University, Bhubaneswar 751004, Odisha, India; Post-Graduate Department of Biotechnology, Utkal University, Bhubaneswar 751004, Odisha, India.
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91
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Hamed MIA, Darwish KM, Soltane R, Chrouda A, Mostafa A, Abo Shama NM, Elhady SS, Abulkhair HS, Khodir AE, Elmaaty AA, Al-Karmalawy AA. β-Blockers bearing hydroxyethylamine and hydroxyethylene as potential SARS-CoV-2 Mpro inhibitors: rational based design, in silico, in vitro, and SAR studies for lead optimization. RSC Adv 2021; 11:35536-35558. [PMID: 35493159 PMCID: PMC9043270 DOI: 10.1039/d1ra04820a] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 10/26/2021] [Indexed: 02/05/2023] Open
Abstract
The global COVID-19 pandemic became more threatening especially after the introduction of the second and third waves with the current large expectations for a fourth one as well. This urged scientists to rapidly develop a new effective therapy to combat SARS-CoV-2. Based on the structures of β-adrenergic blockers having the same hydroxyethylamine and hydroxyethylene moieties present in the HIV-1 protease inhibitors which were found previously to inhibit the replication of SARS-CoV, we suggested that they may decrease the SARS-CoV-2 entry into the host cell through their ability to decrease the activity of RAAS and ACE2 as well. Herein, molecular docking of twenty FDA-approved β-blockers was performed targeting SARS-CoV-2 Mpro. Results showed promising inhibitory activities especially for Carvedilol (CAR) and Nebivolol (NEB) members. Moreover, these two drugs together with Bisoprolol (BIS) as an example from the lower active ones were subjected to molecular dynamics simulations at 100 ns. Great stability across the whole 100 ns timeframe was observed for the top docked ligands, CAR and NEB, over BIS. Conformational analysis of the examined drugs and hydrogen bond investigation with the pocket's crucial residues confirm the great affinity and confinement of CAR and NEB within the Mpro binding site. Moreover, the binding-free energy analysis and residue-wise contribution analysis highlight the nature of ligand-protein interaction and provide guidance for lead development and optimization. Furthermore, the examined three drugs were tested for their in vitro inhibitory activities towards SARS-CoV-2. It is worth mentioning that NEB achieved the most potential anti-SARS-CoV-2 activity with an IC50 value of 0.030 μg ml-1. Besides, CAR was found to have a promising inhibitory activity with an IC50 of 0.350 μg ml-1. Also, the IC50 value of BIS was found to be as low as 15.917 μg ml-1. Finally, the SARS-CoV-2 Mpro assay was performed to evaluate and confirm the inhibitory effects of the tested compounds (BIS, CAR, and NEB) towards the SARS-CoV-2 Mpro enzyme. The obtained results showed very promising SARS-CoV-2 Mpro inhibitory activities of BIS, CAR, and NEB (IC50 = 118.50, 204.60, and 60.20 μg ml-1, respectively) compared to lopinavir (IC50 = 73.68 μg ml-1) as a reference standard.
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Affiliation(s)
- Mohammed I A Hamed
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, Fayoum University Fayoum 63514 Egypt
| | - Khaled M Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University Ismailia 41522 Egypt
| | - Raya Soltane
- Department of Basic Sciences, Adham University College, Umm Al-Qura University Saudi Arabia
- Faculty of Sciences, Tunis El Manar University Tunisia
| | - Amani Chrouda
- Department of Chemistry, College of Science Al-Zulfi, Majmaah University Al-Majmaah 11952 Saudi Arabia
- Laboratory of Interfaces and Advanced Materials, Faculty of Sciences, Monastir University Monastir 5000 Tunisia
- Institute of Analytical Sciences, UMR CNRS-UCBL-ENS 5280 5 Rue la Doua 69100 Villeurbanne CEDEX France
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, National Research Centre Dokki Cairo 12622 Egypt
| | - Noura M Abo Shama
- Center of Scientific Excellence for Influenza Viruses, National Research Centre Dokki Cairo 12622 Egypt
| | - Sameh S Elhady
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University Jeddah 21589 Saudi Arabia
| | - Hamada S Abulkhair
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy (Boys), Al-Azhar University Nasr City 11884 Cairo Egypt
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Horus University-Egypt New Damietta 34518 Egypt
| | - Ahmed E Khodir
- Department of Pharmacology, Faculty of Pharmacy, Horus University-Egypt New Damietta 34518 Egypt
| | - Ayman Abo Elmaaty
- Department of Medicinal Chemistry, Faculty of Pharmacy, Port Said University Port Said 42526 Egypt
| | - Ahmed A Al-Karmalawy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Horus University-Egypt New Damietta 34518 Egypt
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92
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Agrawal PK, Agrawal C, Blunden G. Pharmacological Significance of Hesperidin and Hesperetin, Two Citrus Flavonoids, as Promising Antiviral Compounds for Prophylaxis Against and Combating COVID-19. Nat Prod Commun 2021. [DOI: 10.1177/1934578x211042540] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Hesperidin and hesperetin are flavonoids that are abundantly present as constituents of citrus fruits. These compounds have attracted attention as several computational methods, mostly docking studies, have shown that hesperidin may bind to multiple regions of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (spike protein, angiotensin-converting enzyme 2, and proteases). Hesperidin has a low binding energy, both with the SARS-CoV-2 “spike” protein responsible for internalization, and also with the “PLpro” and “Mpro” responsible for transforming the early proteins of the virus into the complex responsible for viral replication. This suggests that these flavonoids could act as prophylactic agents by blocking several mechanisms of viral infection and replication, and thus helping the host cell to resist viral attack.
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Affiliation(s)
| | | | - Gerald Blunden
- School of Pharmacy & Biomedical Sciences, University of Portsmouth, Portsmouth, UK
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93
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Alturaiki W, Mubarak A, Al Jurayyan A, Hemida MG. The pivotal roles of the host immune response in the fine-tuning the infection and the development of the vaccines for SARS-CoV-2. Hum Vaccin Immunother 2021; 17:3297-3309. [PMID: 34114940 PMCID: PMC8204314 DOI: 10.1080/21645515.2021.1935172] [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: 03/31/2021] [Revised: 05/03/2021] [Accepted: 05/24/2021] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV2 infection induces various degrees of infections ranging from asymptomatic to severe cases and death. Virus/host interplay contributes substantially to these outcomes. This highlights the potential roles of the host immune system in fighting virus infections. SARS-CoV-2. We highlighted the potential roles of host immune response in the modulation of the outcomes of SARS-CoV infections. The newly emerged SARS-CoV-2 mutants complicated the control and mitigation strategies measures. We are highlighting the current progress of some already deployed vaccines worldwide as well as those still in the pipelines. Recent studies from the large ongoing global vaccination campaign are showing promising results in reducing the hospitality rates as well as the number of severe SARS-CoV-2 infected patients. Careful monitoring of the genetic changes of the virus should be practiced. This is to prepare some highly sensitive diagnostic assays as well as to prepare some homologous vaccines matching the circulating strains in the future.
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Affiliation(s)
- Wael Alturaiki
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah, Saudi Arabia
| | - Ayman Mubarak
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Abduallah Al Jurayyan
- Immunology and HLA Department, Pathology and Laboratory Medicine, King Fahad Medical City, Riyadh, Al-Ahsa, Saudi Arabia
| | - Maged Gomaa Hemida
- Department of Microbiology, College of Veterinary Medicine, King Faisal University, Saudi Arabia
- Department of Virology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr Ash Shaykh, Egypt
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94
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Das P, Majumder R, Mandal M, Basak P. In-Silico approach for identification of effective and stable inhibitors for COVID-19 main protease (M pro) from flavonoid based phytochemical constituents of Calendula officinalis. J Biomol Struct Dyn 2021; 39:6265-6280. [PMID: 32705952 PMCID: PMC7441784 DOI: 10.1080/07391102.2020.1796799] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/10/2020] [Indexed: 12/23/2022]
Abstract
The recent outbreak of the coronavirus disease COVID-19 is putting the world towards a great threat. A recent study revealed COVID-19 main protease (Mpro) is responsible for the proteolytic mutation of this virus and is essential for its life cycle. Thus inhibition of this protease will eventually lead to the destruction of this virus. In-Silico Molecular docking was performed with the Native ligand and the 15 flavonoid based phytochemicals of Calendula officinals to check their binding affinity towards the COVID-19 main protease. Finally, the top 3 compounds with the highest affinity have been chosen for molecular dynamics simulation to analyses their dynamic properties and conformational flexibility or stability. In-Silico Docking showed that major phytochemicals of Calendula officinals i.e. rutin, isorhamnetin-3-O-β-D, calendoflaside, narcissin, calendulaglycoside B, calenduloside, calendoflavoside have better binding energy than the native ligand (inhibitor N3). MD simulation of 100 ns revealed that all the protease-ligand docked complexes are overall stable as compare to Mpro-native ligand (inhibitor N3) complex. Overall, rutin and caledoflaside showed better stability, compactness, and flexibility. Our in silico (Virtual molecular docking and Molecular dynamics simulation) studies pointed out that flavonoid based phytochemicals of calendula (rutin, isorhamnetin-3-O-β-D, calendoflaside) may be highly effective for inhibiting Mpro which is the main protease for SARS-CoV-2 causing the deadly disease COVID-19. Rutin is already used as a drug and the other two compounds can be made available for future use. Thus the study points a way to combat COVID-19 by the use of major flavonoid based phytochemicals of Calendula officinals. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pratik Das
- School of Bioscience and Engineering, Jadavpur University, Kolkata, India
| | - Ranabir Majumder
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur, India
| | - Mahitosh Mandal
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur, India
| | - Piyali Basak
- School of Bioscience and Engineering, Jadavpur University, Kolkata, India
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95
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Tripathy S, Verma DK, Thakur M, Patel AR, Srivastav PP, Singh S, Gupta AK, Chávez-González ML, Aguilar CN, Chakravorty N, Verma HK, Utama GL. Curcumin Extraction, Isolation, Quantification and Its Application in Functional Foods: A Review With a Focus on Immune Enhancement Activities and COVID-19. Front Nutr 2021; 8:747956. [PMID: 34621776 PMCID: PMC8490651 DOI: 10.3389/fnut.2021.747956] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 08/23/2021] [Indexed: 12/13/2022] Open
Abstract
An entirely unknown species of coronavirus (COVID-19) outbreak occurred in December 2019. COVID-19 has already affected more than 180 million people causing ~3.91 million deaths globally till the end of June 2021. During this emergency, the food nutraceuticals can be a potential therapeutic candidate. Curcumin is the natural and safe bioactive compound of the turmeric (Curcuma longa L.) plant and is known to possess potent anti-microbial and immuno-modulatory properties. This review paper covers the various extraction and quantification techniques of curcumin and its usage to produce functional food. The potential of curcumin in boosting the immune system has also been explored. The review will help develop insight and new knowledge about curcumin's role as an immune-booster and therapeutic agent against COVID-19. The manuscript will also encourage and assist the scientists and researchers who have an association with drug development, pharmacology, functional foods, and nutraceuticals to develop curcumin-based formulations.
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Affiliation(s)
- Soubhagya Tripathy
- Agricultural and Food Engineering Department, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Deepak Kumar Verma
- Agricultural and Food Engineering Department, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Mamta Thakur
- Department of Food Technology, School of Sciences, ITM University, Gwalior, Madhya Pradesh, India
| | - Ami R. Patel
- Division of Dairy Microbiology, Mansinhbhai Institute of Dairy & Food Technology-MIDFT, Gujarat, India
| | - Prem Prakash Srivastav
- Agricultural and Food Engineering Department, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Smita Singh
- Department of Life Sciences (Food Technology), Graphic Era (Deemed to Be) University, Dehradun, India
- Department of Nutrition and Dietetics, University Institute of Applied Health Sciences, Chandigarh University, Chandigarh, India
| | - Alok Kumar Gupta
- Division of Post-Harvest Management, ICAR-Central Institute for Subtropical Horticulture (Ministry of Agriculture and Farmers Welfare, Government of India), Lucknow, India
| | - Mónica L. Chávez-González
- Bioprocesses Research Group, Food Research Department, School of Chemistry, Universidad Autonoma de Coahuila, Saltillo, Mexico
| | - Cristobal Noe Aguilar
- Bioprocesses Research Group, Food Research Department, School of Chemistry, Universidad Autonoma de Coahuila, Saltillo, Mexico
| | - Nishant Chakravorty
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, West Bengal, India
| | - Henu Kumar Verma
- Department of Immunopathology, Comprehensive Pneumology Center, Institute of Lungs Biology and Disease, Munich, Germany
| | - Gemilang Lara Utama
- Faculty of Agro-Industrial Technology, Universitas Padjadjaran, Sumedang, Indonesia
- Center for Environment and Sustainability Science, Universitas Padjadjaran, Bandung, Indonesia
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96
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El-Demerdash A, Al-Karmalawy AA, Abdel-Aziz TM, Elhady SS, Darwish KM, Hassan AHE. Investigating the structure-activity relationship of marine natural polyketides as promising SARS-CoV-2 main protease inhibitors. RSC Adv 2021; 11:31339-31363. [PMID: 35496831 PMCID: PMC9041294 DOI: 10.1039/d1ra05817g] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/16/2021] [Indexed: 02/05/2023] Open
Abstract
Since its first report in December 2019, the novel coronavirus virus, SARS-CoV-2, has caused an unprecedented global health crisis and economic loss imposing a tremendous burden on the worldwide finance, healthcare system, and even daily life. Even with the introduction of different preventive vaccines, there is still a dire need for effective antiviral therapeutics. Nature has been considered as the historical trove of drug discovery and development, particularly in cases of worldwide crises. Herein, a comprehensive in silico investigation of a highly focused chemical library of 34 pederin-structurally related marine compounds, belonging to four polyketides families, was initiated against the SARS-CoV-2 main protease, Mpro, being the key replicating element of the virus and main target in many drugs development programs. Two of the most potent SARS-CoV-2 Mpro co-crystallized inhibitors, O6K and N3, were added to the tested database as reference standards. Through molecular docking simulation, promising compounds including Pederin (1), Dihydro-onnamide A (11), Onnamide C (14), Pseudo-onnamide A (17), and Theopederin G (29) have been identified from different families based on their superior ligand-protein energies and relevant binding profiles with the key Mpro pocket residues. Thermodynamic behaviors of the identified compounds were investigated through 200 ns all-atom molecular dynamics simulation illustrating their significant stability and pocket accommodation. Furthermore, structural activity preferentiality was identified for the pederin-based marine compounds highlighting the importance of the terminal guanidine and cyclic hemiacetal linker, and the length of the sidechain. Our findings highlight the challenges of targeting SARS-CoV-2 Mpro as well as recommending further in vitro and in vivo studies regarding the examined marine products either alone or in combination paving the way for promising lead molecules.
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Affiliation(s)
- Amr El-Demerdash
- Chemistry Department, Organic Chemistry Division, Faculty of Science, Mansoura University Mansoura 35516 Egypt
- Metabolic Biology & Biological Chemistry Department, John Innes Centre Norwich Research Park Norwich NR4 7UH UK
| | - Ahmed A Al-Karmalawy
- Department of Pharmaceutical Medicinal Chemistry, Faculty of Pharmacy, Horus University-Egypt New Damietta 34518 Egypt
| | - Tarek Mohamed Abdel-Aziz
- Department of Cellular and Integrative Physiology, University of Texas Health Science Centre at San Antonio San Antonio Texas 78229-3900 USA
- Zoology Department, Faculty of Science, Minia University El-Minia 61519 Egypt
| | - Sameh S Elhady
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University Jeddah Saudi Arabia
| | - Khaled M Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University Ismailia Egypt
| | - Ahmed H E Hassan
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University Mansoura 35516 Egypt
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97
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Chen J, Ali F, Khan I, Zhu YZ. Recent progress in the development of potential drugs against SARS-CoV-2. CURRENT RESEARCH IN PHARMACOLOGY AND DRUG DISCOVERY 2021; 2:100057. [PMID: 34870155 PMCID: PMC8437701 DOI: 10.1016/j.crphar.2021.100057] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 08/30/2021] [Accepted: 09/09/2021] [Indexed: 01/18/2023] Open
Abstract
SARS-CoV-2, a newly emerged and highly pathogenic coronavirus, is identified as the causal agent of Coronavirus Disease (2019) (COVID-19) in the late December 2019, in China. The virus has rapidly spread nationwide and spilled over to the other countries around the globe, resulting in more than 120 million infections and 2.6 million deaths until the time of this review. Unfortunately, there are still no specific drugs available against this disease, and it is very necessary to call upon more scientists to work together to stop a further spread. Hence, the recent progress in the development of drugs may help scientific community quickly understand current research status and further develop new effective drugs. Herein, we summarize the cellular entry and replication process of this virus and discuss the recent development of potential viral based drugs that target bio-macromolecules in different stages of the viral life cycle, especially S protein, 3CLPro, PLPro, RdRp and helicase.
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Affiliation(s)
- Jianmin Chen
- School of Pharmacy and State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science & Technology Avenida Wai Long, Taipa, 999078, Macau
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science & Technology Avenida Wai Long, Taipa, 999078, Macau
- School of Pharmacy and Medical Technology, Putian University, No. 1133 Xueyuan Zhong Jie, 351100, Fujian, China
- Key Laboratory of Pharmaceutical Analysis and Laboratory Medicine (Putian University), No. 1133 Xueyuan Zhong Jie, 351100, Fujian Province University, Fujian, China
| | - Fayaz Ali
- School of Pharmacy and State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science & Technology Avenida Wai Long, Taipa, 999078, Macau
| | - Imran Khan
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science & Technology Avenida Wai Long, Taipa, 999078, Macau
| | - Yi Zhun Zhu
- School of Pharmacy and State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science & Technology Avenida Wai Long, Taipa, 999078, Macau
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98
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Hurmach VV, Platonov MO, Prylutska SV, Scharff P, Prylutskyy YI, Ritter U. C 60 fullerene against SARS-CoV-2 coronavirus: an in silico insight. Sci Rep 2021; 11:17748. [PMID: 34493768 PMCID: PMC8423725 DOI: 10.1038/s41598-021-97268-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 08/24/2021] [Indexed: 01/18/2023] Open
Abstract
Based on WHO reports the new SARS-CoV-2 coronavirus is currently widespread all over the world. So far > 162 million cases have been confirmed, including > 3 million deaths. Because of the pandemic still spreading across the globe the accomplishment of computational methods to find new potential mechanisms of virus inhibitions is necessary. According to the fact that C60 fullerene (a sphere-shaped molecule consisting of carbon) has shown inhibitory activity against various protein targets, here the analysis of the potential binding mechanism between SARS-CoV-2 proteins 3CLpro and RdRp with C60 fullerene was done; it has resulted in one and two possible binding mechanisms, respectively. In the case of 3CLpro, C60 fullerene interacts in the catalytic binding pocket. And for RdRp in the first model C60 fullerene blocks RNA synthesis pore and in the second one it prevents binding with Nsp8 co-factor (without this complex formation, RdRp can't perform its initial functions). Then the molecular dynamics simulation confirmed the stability of created complexes. The obtained results might be a basis for other computational studies of 3CLPro and RdRp potential inhibition ways as well as the potential usage of C60 fullerene in the fight against COVID-19 disease.
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Affiliation(s)
- Vasyl V Hurmach
- Taras Shevchenko National University of Kyiv, Kyiv, 01601, Ukraine
| | - Maksim O Platonov
- Institute of Molecular Biology and Genetics of NASU, Kyiv, 03143, Ukraine
| | - Svitlana V Prylutska
- Taras Shevchenko National University of Kyiv, Kyiv, 01601, Ukraine
- National University of Life and Environmental Science of Ukraine, Kyiv, 03041, Ukraine
| | - Peter Scharff
- Institute of Chemistry and Biotechnology, Technical University of Ilmenau, 98693, Ilmenau, Germany
| | | | - Uwe Ritter
- Institute of Chemistry and Biotechnology, Technical University of Ilmenau, 98693, Ilmenau, Germany.
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99
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Mani I, Alexopoulou A. Recent challenges facing patients with preexisting chronic liver disease in the era of the COVID-19 pandemic. Ann Gastroenterol 2021; 34:625-633. [PMID: 34475732 PMCID: PMC8375661 DOI: 10.20524/aog.2021.0628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 02/25/2021] [Indexed: 02/06/2023] Open
Abstract
COVID-19 pandemic has resulted in a growing number of beds in common hospital wards and intensive care units being occupied by COVID-19 patients and the majority of medical and nursing staff being dedicated to their care. The present review summarizes the impact of COVID-19 on patients with underlying chronic liver diseases (CLD). Deferrals of all non-urgent activities in healthcare facilities, including a decrease in liver-clinic visits for patients with CLD, inadequate hepatocellular carcinoma (HCC) surveillance, and postponement of liver transplant activities are the most important consequences. Delays in viral hepatitis elimination programs were also reported, leading to future development of advanced CLD and HCC. Patients with chronic hepatitis B (CHB) and C without cirrhosis are not at risk for a more severe COVID-19 infection course. However, CHB status must be known in patients who are going to receive immunosuppression for preventing disease flare. In addition, checking for drug-drug interactions and potential hepatotoxicity reactions from agents administered to treat both SARS-CoV-2 and CLD are required. Patients with nonalcoholic fatty liver disease appeared to be at a high risk for severe COVID-19, even after adjustment for comorbidities. Patients with cirrhosis may develop decompensation, acute-on-chronic liver failure, or severe COVID-19. The mortality rate is worse in patients with high model for end-stage liver disease score, regardless of the etiology of cirrhosis.
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Affiliation(s)
- Iliana Mani
- 2 Department of Medicine, Medical School, National and Kapodistrian University of Athens, Hippokration General Hospital, Athens, Greece (Iliana Mani, Alexandra Alexopoulou)
| | - Alexandra Alexopoulou
- 2 Department of Medicine, Medical School, National and Kapodistrian University of Athens, Hippokration General Hospital, Athens, Greece (Iliana Mani, Alexandra Alexopoulou)
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100
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Luo L, Qiu Q, Huang F, Liu K, Lan Y, Li X, Huang Y, Cui L, Luo H. Drug repurposing against coronavirus disease 2019 (COVID-19): A review. J Pharm Anal 2021; 11:683-690. [PMID: 34513115 PMCID: PMC8416689 DOI: 10.1016/j.jpha.2021.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 08/16/2021] [Accepted: 09/03/2021] [Indexed: 02/07/2023] Open
Abstract
Since December 2019, severe acute respiratory syndrome coronavirus 2 has been found to be the culprit in the coronavirus disease 2019 (COVID-19), causing a global pandemic. Despite the existence of many vaccine programs, the number of confirmed cases and fatalities due to COVID-19 is still increasing. Furthermore, a number of variants have been reported. Because of the absence of approved anti-coronavirus drugs, the treatment and management of COVID-19 has become a global challenge. Under these circumstances, drug repurposing is an effective method to identify candidate drugs with a shorter cycle of clinical trials. Here, we summarize the current status of the application of drug repurposing in COVID-19, including drug repurposing based on virtual computer screening, network pharmacology, and bioactivity, which may be a beneficial COVID-19 treatment. Mechanism of SARS-CoV-2 infection and drug targets were reviewed. Drug repurposing against COVID-19 based on computer virtual screening, network pharmacology, bioactivity were summarized. The use of drug repurposing in COVID-19 was addressed.
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Affiliation(s)
- Lianxiang Luo
- The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China.,Marine Medical Research Institute of Zhanjiang, Zhanjiang, 524023, Guangdong, China
| | - Qin Qiu
- Graduate School, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Fangfang Huang
- Graduate School, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Kaifeng Liu
- The First Clinical College, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Yongqi Lan
- The First Clinical College, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Xiaoling Li
- Animal Experiment Center, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Yuge Huang
- Department of Pediatrics, the Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Liao Cui
- Guangdong Key Laboratory for Research and Development of Natural Drugs, Guangdong Medical University, Zhanjiang, Guangdong, 524023, China
| | - Hui Luo
- The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
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