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Raghav PK, Mann Z, Ahluwalia SK, Rajalingam R. Potential treatments of COVID-19: Drug repurposing and therapeutic interventions. J Pharmacol Sci 2023; 152:1-21. [PMID: 37059487 PMCID: PMC9930377 DOI: 10.1016/j.jphs.2023.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 01/31/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The infection is caused when Spike-protein (S-protein) present on the surface of SARS-CoV-2 interacts with human cell surface receptor, Angiotensin-converting enzyme 2 (ACE2). This binding facilitates SARS-CoV-2 genome entry into the human cells, which in turn causes infection. Since the beginning of the pandemic, many different therapies have been developed to combat COVID-19, including treatment and prevention. This review is focused on the currently adapted and certain other potential therapies for COVID-19 treatment, which include drug repurposing, vaccines and drug-free therapies. The efficacy of various treatment options is constantly being tested through clinical trials and in vivo studies before they are made medically available to the public.
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Affiliation(s)
- Pawan Kumar Raghav
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA.
| | | | - Simran Kaur Ahluwalia
- Amity Institute of Biotechnology, Amity University, Sector-125, Noida, Uttar Pradesh, India
| | - Raja Rajalingam
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
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Identification of RdRp inhibitors against SARS-CoV-2 through E-pharmacophore-based virtual screening, molecular docking and MD simulations approaches. Int J Biol Macromol 2023; 237:124169. [PMID: 36990409 PMCID: PMC10043960 DOI: 10.1016/j.ijbiomac.2023.124169] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 03/10/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023]
Abstract
The outbreak of novel Coronavirus, an enduring pandemic declared by WHO, has consequences to an alarming ongoing public health menace which has already claimed several million human lives. In addition to numerous vaccinations and medications for mild to moderate COVID-19 infection, lack of promising medication or therapeutic pharmaceuticals remains a serious concern to counter the ongoing coronavirus infections and to hinder its dreadful spread. Global health emergencies have called for urgency for potential drug discovery and time is the biggest constraint apart from the financial and human resources required for the high throughput drug screening. However, computational screening or in-silico approaches appeared to be an effective and faster approach to discover potential molecules without sacrificing the model animals. Accumulated shreds of evidence on computational studies against viral diseases have revealed significance of in-silico drug discovery approaches especially in the time of urgency. The central role of RdRp in SARS-CoV-2 replication makes it promising drug target to curtain on going infection and its spread. The present study aimed to employ E-pharmacophore-based virtual screening to reveal potent inhibitors of RdRp as potential leads to block the viral replication. An energy-optimised pharmacophore model was generated to screen the Enamine REAL DataBase (RDB). Then, ADME/T profiles were determined to validate the pharmacokinetics and pharmacodynamics properties of the hit compounds. Moreover, High Throughput Virtual Screening (HTVS) and molecular docking (SP & XP) were employed to screen the top hits from pharmacophore-based virtual screening and ADME/T screen. The binding free energies of the top hits were calculated by conducting MM-GBSA analysis followed by MD simulations to determine the stability of molecular interactions between top hits and RdRp protein. These virtual investigations revealed six compounds having binding free energies of −57.498, −45.776, −46.248, −35.67, −25.15 and −24.90 kcal/mol respectively as calculated by the MM-GBSA method. The MD simulation studies confirmed the stability of protein ligand complexes, hence, indicating as potent RdRp inhibitors and are promising candidate drugs to be further validated and translated into clinics in future.
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Epigenetic Targets and Pathways Linked to SARS-CoV-2 Infection and Pathology. Microorganisms 2023; 11:microorganisms11020341. [PMID: 36838306 PMCID: PMC9967649 DOI: 10.3390/microorganisms11020341] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/19/2023] [Accepted: 01/19/2023] [Indexed: 02/03/2023] Open
Abstract
The scale at which the SARS-CoV-2/COVID-19 pandemic has spread remains enormous. Provided the genetic makeup of the virus and humans is readily available, the quest for knowing the mechanism and epidemiology continues to prevail across the entire scientific community. Several aspects, including immunology, molecular biology, and host-pathogen interaction, are continuously being dug into for preparing the human race for future pandemics. The exact reasons for vast differences in symptoms, pathophysiological implications of COVID-infections, and mortality differences remain elusive. Hence, researchers are also looking beyond traditional genomics, proteomics, and transcriptomics approach, especially entrusting the environmental regulation of the genetic landscape of COVID-human interactions. In line with these questions lies a critical process called epigenetics. The epigenetic perturbations in both host and parasites are a matter of great interest to unravel the disparities in COVID-19 mortalities and pathology. This review provides a deeper insight into current research on the epigenetic landscape of SARS-CoV-2 infection in humans and potential targets for augmenting the ongoing investigation. It also explores the potential targets, pathways, and networks associated with the epigenetic regulation of processes involved in SARS-CoV-2 pathology.
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Bae JH, Choe HJ, Holick MF, Lim S. Association of vitamin D status with COVID-19 and its severity : Vitamin D and COVID-19: a narrative review. Rev Endocr Metab Disord 2022; 23:579-599. [PMID: 34982377 PMCID: PMC8724612 DOI: 10.1007/s11154-021-09705-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/14/2021] [Indexed: 01/08/2023]
Abstract
Vitamin D is associated with biological activities of the innate and adaptive immune systems, as well as inflammation. In observational studies, an inverse relationship has been found between serum 25-hydroxyvitamin D (25(OH)D) concentrations and the risk or severity of coronavirus disease 2019 (COVID-19). Several mechanisms have been proposed for the role of vitamin D in COVID-19, including modulation of immune and inflammatory responses, regulation of the renin-angiotensin-aldosterone system, and involvement in glucose metabolism and cardiovascular system. Low 25(OH)D concentrations might predispose patients with COVID-19 to severe outcomes not only via the associated hyperinflammatory syndrome but also by worsening preexisting impaired glucose metabolism and cardiovascular diseases. Some randomized controlled trials have shown that vitamin D supplementation is beneficial for reducing severe acute respiratory syndrome coronavirus 2 RNA positivity but not for reducing intensive care unit admission or all-cause mortality in patients with moderate-to-severe COVID-19. Current evidence suggests that taking a vitamin D supplement to maintain a serum concentration of 25(OH)D of at least 30 ng/mL (preferred range 40-60 ng/mL), can help reduce the risk of COVID-19 and its severe outcomes, including mortality. Although further well designed studies are warranted, it is prudent to recommend vitamin D supplements to people with vitamin D deficiency/insufficiency during the COVID-19 pandemic according to international guidelines.
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Affiliation(s)
- Jae Hyun Bae
- grid.411134.20000 0004 0474 0479Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, South Korea
| | - Hun Jee Choe
- grid.412484.f0000 0001 0302 820XDepartment of Internal Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Michael F. Holick
- grid.189504.10000 0004 1936 7558Section of Endocrinology, Diabetes, Nutrition and Weight Management, Department of Medicine, Boston University Medical Campus, 715 Albany St #437, Boston, MA 02118 USA
| | - Soo Lim
- grid.412480.b0000 0004 0647 3378Department of Internal Medicine, Seoul National University College of Medicine, Seoul National University Bundang Hospital, 82, Gumi-ro, 173 Beon-gil, Bundang-gu, Seongnam, 13620 South Korea
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Karthika C, Appu AP, Akter R, Rahman MH, Tagde P, Ashraf GM, Abdel-Daim MM, Hassan SSU, Abid A, Bungau S. Potential innovation against Alzheimer's disorder: a tricomponent combination of natural antioxidants (vitamin E, quercetin, and basil oil) and the development of its intranasal delivery. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:10950-10965. [PMID: 35000160 DOI: 10.1007/s11356-021-17830-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/24/2021] [Indexed: 06/14/2023]
Abstract
Alzheimer's disorder (AD) is very difficult to manage and treat. The complexity of the brain, the blood-brain barrier influencing a multitude of parameters/biomarkers, as well as numerous other factors involved often contribute to the decline in the chances of treatment success. Development of the new drug moiety also takes time, being necessary to consider both its toxicity and related issues. As a strategic plan, a combined strategy is being developed and considered to address AD pathology using several approaches. A combination of vitamin E, quercetin, and basil oil in a nano-based formulation is designed to be administered nasally. The antioxidant present in these natural-based products helps to treat and alleviate AD if a synergistic approach is considered. The three active substances mentioned above are well known for the treatment of neurodegenerative disorders. The nanoformulation helps the co-delivery of the drug moiety to the brain through the intranasal route. In this review, a correlation and use of vitamin E, quercetin, and basil oil in a nano-based formulation is described as an effective way to treat AD. The intranasal administration of drugs is a promising approach for the treatment of neurodegenerative and mental disorders, as this route is non-invasive, enhances the bioavailability, allows a drug dose reduction, bypasses the blood-brain barrier, and reduces the systemic undesired effect. The use of natural products is generally considered to be just as safe; therefore, by using this combined approach, the level of toxicity can be minimized.
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Affiliation(s)
- Chenmala Karthika
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Nilgiris, Ooty, 643001, Tamil Nadu, India
| | | | - Rokeya Akter
- Department of Pharmacy, Jagannath University, Sadarghat, Dhaka, 1100, Bangladesh
- Department of Global Medical Science, Yonsei University Wonju College of Medicine, Yonsei University, Gangwon-do, Wonju, 26426, South Korea
| | - Md Habibur Rahman
- Department of Global Medical Science, Yonsei University Wonju College of Medicine, Yonsei University, Gangwon-do, Wonju, 26426, South Korea.
- Department of Pharmacy, Southeast University, Banani, Dhaka, 1213, Bangladesh.
| | - Priti Tagde
- Bhabha Pharmacy Research Institute, Bhabha University, Bhopal, Madhya Pradesh, 462026, India
| | - Ghulam Md Ashraf
- Pre-Clinical Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohamed M Abdel-Daim
- Department of Pharmaceutical Sciences, Batterjee Medical College, Jeddah, 21442, Saudi Arabia
- Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, 41522, Egypt
| | - Syed Shams Ul Hassan
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China
- Department of Natural Product Chemistry, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Areha Abid
- Department of Food Science, Faculty of Agricultural and Food Sciences, University of Debrecen, 4032, Debrecen, Hungary
| | - Simona Bungau
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, 410028, Oradea, Romania
- Doctoral School of Biological and Biomedical Sciences, University of Oradea, 410087, Oradea, Romania
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Udaya kumar V, Pavan G, Murti K, Kumar R, Dhingra S, Haque M, Ravichandiran V. Rays of immunity: Role of sunshine vitamin in management of COVID-19 infection and associated comorbidities. Clin Nutr ESPEN 2021; 46:21-32. [PMID: 34857198 PMCID: PMC8474796 DOI: 10.1016/j.clnesp.2021.09.727] [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: 03/28/2021] [Revised: 09/10/2021] [Accepted: 09/20/2021] [Indexed: 02/06/2023]
Abstract
The catastrophic pandemic engendered due to the Novel coronavirus (COVID-19) outbreak which causes severe clinical afflictions on the respiratory system has severely high morbidity and mortality rates. The requirement of novel compounds is at utmost importance due to lack of targeted drug molecule to treat the afflictions and restrict the viral infection and for the usage of prophylactic treatment to avoid the spread of the infection is of utmost importance. Vitamin D is one such naturally available multifunctional molecule, which plays an eminent role in the immune system and instigation of numerous cellular pathways further promoting health benefits and enhancing the human quality of life. This article reviews the current standpoint scenario and future prevalence of vitamin D supplementation in the management of covid-19 patients. Novel findings of Vitamin D suggest that along with regulation of cell growth, neuroprotective and mood-stabilizing effects, it regulates the immune response also modulate cytokine Interleukin-6 (IL-6) by inducing progesterone-induced blocking factor (PIBF), given the IL-6 levels are considerably high in COVID-19 patients which increases the further complications. Vitamin D also have its effect on angiotensin converting enzyme (ACEII) inhibitor through which the COVID-19 virus makes cell entry. Numerous research data elucidate the play of Vitamin D, in complications of COVID-19 including the most common comorbid conditions, neurological manifestations and immunological aspects makes it an ideal molecule for adjuvant therapy. Including Vitamin D as add-on therapy in the management of COVID-19 might aid the arrest of infection and helps fight this arduous epidemic.
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Affiliation(s)
- V. Udaya kumar
- Department of Pharmacy Practice, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur, Bihar, India
| | - Garapati Pavan
- Department of Pharmacy Practice, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur, Bihar, India
| | - Krishna Murti
- Department of Pharmacy Practice, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur, Bihar, India,Corresponding author. Department of Pharmacy Practice, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur, 844102, Bihar, India
| | - Rahul Kumar
- Department of Pharmacy Practice, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur, Bihar, India
| | - Sameer Dhingra
- Department of Pharmacy Practice, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur, Bihar, India
| | - Mainul Haque
- The Unit of Pharmacology, Faculty of Medicine and Defence Health Universiti Pertahanan, Nasional Malaysia (National Defence University of Malaysia), Kuala Lumpur, Kem Perdana Sungai Besi, Malaysia
| | - V. Ravichandiran
- Department of Pharmacy Practice, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur, Bihar, India
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Tolah AM, Altayeb LM, Alandijany TA, Dwivedi VD, El-Kafrawy SA, Azhar EI. Computational and In Vitro Experimental Investigations Reveal Anti-Viral Activity of Licorice and Glycyrrhizin against Severe Acute Respiratory Syndrome Coronavirus 2. Pharmaceuticals (Basel) 2021; 14:1216. [PMID: 34959616 PMCID: PMC8703534 DOI: 10.3390/ph14121216] [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: 10/19/2021] [Revised: 11/15/2021] [Accepted: 11/17/2021] [Indexed: 11/17/2022] Open
Abstract
Without effective antivirals, the COVID-19 pandemic will likely continue to substantially affect public health. Medicinal plants and phytochemicals are attractive therapeutic options, particularly those targeting viral proteins essential for replication cycle. Herein, a total 179 phytochemicals of licorice (Glycyrrhiza glabra) were screened and scrutinized against the SARS-CoV-2 main protease (Mpro) with considerable binding affinities in the range of -9.831 to -2.710 kcal/mol. The top 10 compounds with the best docking scores, licuraside, glucoliquiritin apioside, 7,3'-Dihydroxy-5'-methoxyisoflavone, licuroside, kanzonol R, neoisoliquiritin, licochalcone-A, formononetin, isomucronulatol, and licoricone, were redocked using AutoDock Vina, yielding -8.7 to -7.3 kcal/mol binding energy against Glycyrrhizin (-8.0 kcal/mol) as a reference ligand. Four compounds, licuraside, glucoliquiritin apioside, 7,3'-Dihydroxy-5'-methoxyisoflavone, and licuroside, with glycyrrhizin (reference ligand) were considered for the 100 ns MD simulation and post-simulation analysis which support the stability of docked bioactive compounds with viral protein. In vitro studies demonstrated robust anti-SARS-CoV-2 activity of licorice and glycyrrhizin under different treatment protocols (simulations treatment with viral infection, post-infection treatment, and pre-treatment), suggesting multiple mechanisms for action. Although both compounds inhibited SARS-CoV-2 replication, the half-maximal inhibitory concentration (IC50) of glycyrrhizin was substantially lower than licorice. This study supports proceeding with in vivo experimentation and clinical trials and highlights licorice and glycyrrhizin as potential therapeutics for COVID-19.
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Affiliation(s)
- Ahmed M. Tolah
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 128442, Jeddah 21362, Saudi Arabia; (L.M.A.); (T.A.A.); (S.A.E.-K.)
- Department of Medical Laboratory Technology, Faculty of Applied Medical Science, King Abdulaziz University, P.O. Box 21911, Rabigh 344, Saudi Arabia
| | - Lamya M. Altayeb
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 128442, Jeddah 21362, Saudi Arabia; (L.M.A.); (T.A.A.); (S.A.E.-K.)
| | - Thamir A. Alandijany
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 128442, Jeddah 21362, Saudi Arabia; (L.M.A.); (T.A.A.); (S.A.E.-K.)
- Department of Medical Laboratory Technology, Faculty of Applied Medical Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Vivek Dhar Dwivedi
- Center for Bioinformatics, Computational and System Biology, Pathfinder Research and Training Foundation, Greater Noida 201308, India;
| | - Sherif A. El-Kafrawy
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 128442, Jeddah 21362, Saudi Arabia; (L.M.A.); (T.A.A.); (S.A.E.-K.)
- Department of Medical Laboratory Technology, Faculty of Applied Medical Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Esam I. Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 128442, Jeddah 21362, Saudi Arabia; (L.M.A.); (T.A.A.); (S.A.E.-K.)
- Department of Medical Laboratory Technology, Faculty of Applied Medical Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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Koulgi S, Jani V, Uppuladinne M, Sonavane U, Nath AK, Darbari H, Joshi R. Drug repurposing studies targeting SARS-CoV-2: an ensemble docking approach on drug target 3C-like protease (3CL pro). J Biomol Struct Dyn 2021; 39:5735-5755. [PMID: 32679006 PMCID: PMC7441806 DOI: 10.1080/07391102.2020.1792344] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 06/25/2020] [Indexed: 12/13/2022]
Abstract
The COVID-19 pandemic has been responsible for several deaths worldwide. The causative agent behind this disease is the Severe Acute Respiratory Syndrome - novel Coronavirus 2 (SARS-CoV-2). SARS-CoV-2 belongs to the category of RNA viruses. The main protease, responsible for the cleavage of the viral polyprotein is considered as one of the hot targets for treating COVID-19. Earlier reports suggest the use of HIV anti-viral drugs for targeting the main protease of SARS-CoV, which caused SARS in the year 2002-2003. Hence, drug repurposing approach may prove to be useful in targeting the main protease of SARS-CoV-2. The high-resolution crystal structure of the main protease of SARS-CoV-2 (PDB ID: 6LU7) was used as the target. The Food and Drug Administration approved and SWEETLEAD database of drug molecules were screened. The apo form of the main protease was simulated for a cumulative of 150 ns and 10 μs open-source simulation data was used, to obtain conformations for ensemble docking. The representative structures for docking were selected using RMSD-based clustering and Markov State Modeling analysis. This ensemble docking approach for the main protease helped in exploring the conformational variation in the drug-binding site of the main protease leading to the efficient binding of more relevant drug molecules. The drugs obtained as top hits from the ensemble docking possessed anti-bacterial and anti-viral properties. This in silico ensemble docking approach would support the identification of potential candidates for repurposing against COVID-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shruti Koulgi
- High-Performance Computing-Medical and Bioinformatics
Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchavati,
Pashan, Pune, India
| | - Vinod Jani
- High-Performance Computing-Medical and Bioinformatics
Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchavati,
Pashan, Pune, India
| | - Mallikarjunachari Uppuladinne
- High-Performance Computing-Medical and Bioinformatics
Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchavati,
Pashan, Pune, India
| | - Uddhavesh Sonavane
- High-Performance Computing-Medical and Bioinformatics
Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchavati,
Pashan, Pune, India
| | - Asheet Kumar Nath
- High-Performance Computing-Medical and Bioinformatics
Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchavati,
Pashan, Pune, India
| | - Hemant Darbari
- High-Performance Computing-Medical and Bioinformatics
Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchavati,
Pashan, Pune, India
| | - Rajendra Joshi
- High-Performance Computing-Medical and Bioinformatics
Applications Group, Centre for Development of Advanced Computing (C-DAC), Panchavati,
Pashan, Pune, India
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Arun KG, Sharanya CS, Abhithaj J, Francis D, Sadasivan C. Drug repurposing against SARS-CoV-2 using E-pharmacophore based virtual screening, molecular docking and molecular dynamics with main protease as the target. J Biomol Struct Dyn 2021; 39:4647-4658. [PMID: 32571168 PMCID: PMC7335810 DOI: 10.1080/07391102.2020.1779819] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 06/02/2020] [Indexed: 12/23/2022]
Abstract
Since its first report in December 2019 from China, the COVID-19 pandemic caused by the beta-coronavirus SARS-CoV-2 has spread at an alarming pace infecting about 5.59 million, and claiming the lives of more than 0.35 million individuals across the globe. The lack of a clinically approved vaccine or drug remains the biggest bottleneck in combating the pandemic. Drug repurposing can expedite the process of drug development by identifying known drugs which are effective against SARS-CoV-2. The SARS-CoV-2 main protease is a promising drug target due to its indispensable role in viral multiplication inside the host. In the present study an E-pharmacophore hypothesis was generated using a crystal structure of the viral protease in complex with an imidazole carbaximide inhibitor. Drugs available in the superDRUG2 database were used to identify candidate drugs for repurposing. The hits obtained from the pharmacophore based screening were further screened using a structure based approach involving molecular docking at different precisions. The binding energies of the most promising compounds were estimated using MM-GBSA. The stability of the interactions between the selected drugs and the target were further explored using molecular dynamics simulation at 100 ns. The results showed that the drugs Binifibrate and Bamifylline bind strongly to the enzyme active site and hence they can be repurposed against SARS-CoV-2. However, U.S Food and Drug Administration have withdrawn Binifibrate from the market as it was having some adverse health effects on patients.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- K. G. Arun
- Department of Biotechnology & Microbiology, Kannur University, Kannur, Kerala, India
| | - C. S Sharanya
- Department of Biotechnology & Microbiology, Kannur University, Kannur, Kerala, India
| | - J. Abhithaj
- Department of Biotechnology & Microbiology, Kannur University, Kannur, Kerala, India
| | - Dileep Francis
- Department of Life sciences, Kristu Jayanti College, Bengaluru, Karnataka, India
| | - C. Sadasivan
- Department of Biotechnology & Microbiology, Kannur University, Kannur, Kerala, India
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Zhang J, Garrett S, Sun J. Gastrointestinal symptoms, pathophysiology, and treatment in COVID-19. Genes Dis 2021; 8:385-400. [PMID: 33521210 PMCID: PMC7836435 DOI: 10.1016/j.gendis.2020.08.013] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/18/2020] [Accepted: 08/28/2020] [Indexed: 01/08/2023] Open
Abstract
The novel coronavirus Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has emerged and is responsible for the Coronavirus Disease 2019 global pandemic. Coronaviruses, including SARS-CoV-2, are strongly associated with respiratory symptoms during infection, but gastrointestinal symptoms, such as diarrhea, vomiting, nausea, and abdominal pain, have been identified in subsets of COVID-19 patients. This article focuses on gastrointestinal symptoms and pathophysiology in COVID-19 disease. Evidence suggests that the gastrointestinal tract could be a viral target for SARS-CoV-2 infection. Not only is the SARS-CoV-2 receptor ACE2 highly expressed in the GI tract and is associated with digestive symptoms, but bleeding and inflammation are observed in the intestine of COVID-19 patients. We further systemically summarize the correlation between COVID-19 disease, gastrointestinal symptoms and intestinal microbiota. The potential oral-fecal transmission of COVID-19 was supported by viral RNA and live virus detection in the feces of COVID-19 patients. Additionally, the viral balance in the GI tract could be disordered during SARS-CoV-2 infection which could further impact the homeostasis of the gut microbial flora. Finally, we discuss the clinical and ongoing trials of treatments/therapies, including antiviral drugs, plasma transfusion and immunoglobulins, and diet supplementations for COVID-19. By reviewing the pathogenesis of SARS-CoV-2 virus, and understanding the correlation among COVID-19, inflammation, intestinal microbiota, and lung microbiota, we provide perspective in prevention and control, as well as diagnosis and treatment of the COVID-19 disease.
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Affiliation(s)
- Jilei Zhang
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Shari Garrett
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Jun Sun
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
- UIC Cancer Center, University of Illinois at Chicago, Chicago, IL 60612, USA
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Ağagündüz D, Çelik MN, Çıtar Dazıroğlu ME, Capasso R. Emergent Drug and Nutrition Interactions in COVID-19: A Comprehensive Narrative Review. Nutrients 2021; 13:nu13051550. [PMID: 34064534 PMCID: PMC8147951 DOI: 10.3390/nu13051550] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 01/08/2023] Open
Abstract
Coronaviruses are a large family of viruses that are known to cause respiratory tract infections ranging from colds to more severe diseases, such as Middle East Respiratory Syndrome (MERS) and the Severe Acute Respiratory Syndrome (SARS). New Coronavirus Disease 2019 (COVID-19), which led to deaths as well as social and economic disruptions, is an ongoing worldwide pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Currently, there is no approved treatment for COVID-19. Hence, only supportive care has been approved by the World Health Organization (WHO) for now. Pharmacological agents used for the adjunctive treatment of COVID-19 following the current literature and clinical experiences include antiviral, anti-inflammatory, and anti-malaria drugs, and other traditional or untraditional treatments. However, it has been reported that the use of these drugs may have some negative effects and comorbidities. Moreover, the current data have indicated that the risk of drug-drug interactions may also be high in polypharmacy cases, especially in elderly people, some comorbidity situations, and intensive care unit (ICU) patients. It is highly possible that these situations can not only increase the risk of drug-drug interactions but also increase the risk of food/nutrition-drug interactions and affect the nutritional status. However, this issue has not yet been entirely discussed in the literature. In this review, current information on the possible mechanisms as well as pharmacokinetic and pharmacodynamic effects of some pharmacological agents used in the treatment of COVID-19 and/or their secondary interactions with nutrition were evaluated and some future directions were given.
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Affiliation(s)
- Duygu Ağagündüz
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Gazi University, Emek, Ankara 06490, Turkey; (M.N.Ç.); (M.E.Ç.D.)
- Correspondence: (D.A.); (R.C.)
| | - Menşure Nur Çelik
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Gazi University, Emek, Ankara 06490, Turkey; (M.N.Ç.); (M.E.Ç.D.)
| | - Merve Esra Çıtar Dazıroğlu
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Gazi University, Emek, Ankara 06490, Turkey; (M.N.Ç.); (M.E.Ç.D.)
| | - Raffaele Capasso
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Naples, Italy
- Correspondence: (D.A.); (R.C.)
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12
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Abstract
Vitamin D (VitD) deficiency is considered a global problem and might be associated with increased susceptibility to COVID-19 illness. In the light of COVID-19 pandemic, VitD might be a promising agent for fighting the SARS-CoV-2, since VitD is involved in various pathophysiological mechanisms that occur during COVID-19 infection. High-dose VitD supplementation, particularly for risk groups, could be recommended to achieve and maintain optimal (range 40-60 ng/mL) serum 25-hydroxy vitamin D levels (marker of VitD status) both for COVID-19 prevention and treatment.
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Affiliation(s)
- Andrius Bleizgys
- Clinic of Internal Diseases, Family Medicine and OncologyVilnius University Faculty of MedicineVilniusLithuania
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13
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Bharadwaj S, El-Kafrawy SA, Alandijany TA, Bajrai LH, Shah AA, Dubey A, Sahoo AK, Yadava U, Kamal MA, Azhar EI, Kang SG, Dwivedi VD. Structure-Based Identification of Natural Products as SARS-CoV-2 M pro Antagonist from Echinacea angustifolia Using Computational Approaches. Viruses 2021; 13:305. [PMID: 33672054 PMCID: PMC7919488 DOI: 10.3390/v13020305] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/05/2021] [Accepted: 02/10/2021] [Indexed: 12/14/2022] Open
Abstract
Coronavirus disease-19 (COVID-19) pandemic, caused by the novel SARS-CoV-2 virus, continues to be a global threat. The number of cases and deaths will remain escalating due to the lack of effective therapeutic agents. Several studies have established the importance of the viral main protease (Mpro) in the replication of SARS-CoV-2 which makes it an attractive target for antiviral drug development, including pharmaceutical repurposing and other medicinal chemistry approaches. Identification of natural products with considerable inhibitory potential against SARS-CoV-2 could be beneficial as a rapid and potent alternative with drug-likeness by comparison to de novo antiviral drug discovery approaches. Thereof, we carried out the structure-based screening of natural products from Echinacea-angustifolia, commonly used to prevent cold and other microbial respiratory infections, targeting SARS-CoV-2 Mpro. Four natural products namely, Echinacoside, Quercetagetin 7-glucoside, Levan N, Inulin from chicory, and 1,3-Dicaffeoylquinic acid, revealed significant docking energy (>-10 kcal/mol) in the SARS-CoV-2 Mpro catalytic pocket via substantial intermolecular contacts formation against co-crystallized ligand (<-4 kcal/mol). Furthermore, the docked poses of SARS-CoV-2 Mpro with selected natural products showed conformational stability through molecular dynamics. Exploring the end-point net binding energy exhibited substantial contribution of Coulomb and van der Waals interactions to the stability of respective docked conformations. These results advocated the natural products from Echinacea angustifolia for further experimental studies with an elevated probability to discover the potent SARS-CoV-2 Mpro antagonist with higher affinity and drug-likeness.
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Affiliation(s)
- Shiv Bharadwaj
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, Korea;
| | - Sherif Aly El-Kafrawy
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, 21589 Jeddah, Saudi Arabia; (S.A.E.-K.); (T.A.A.); (L.H.B.); (M.A.K.)
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Thamir A. Alandijany
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, 21589 Jeddah, Saudi Arabia; (S.A.E.-K.); (T.A.A.); (L.H.B.); (M.A.K.)
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Leena Hussein Bajrai
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, 21589 Jeddah, Saudi Arabia; (S.A.E.-K.); (T.A.A.); (L.H.B.); (M.A.K.)
- Biochemistry Department, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Altaf Ahmad Shah
- Department of Biosciences, Integral University, Lucknow 226026, India;
| | - Amit Dubey
- Computational Chemistry and Drug Discovery Division, Quanta Calculus Pvt. Ltd., Kushinagar 274203, India;
| | - Amaresh Kumar Sahoo
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad 211015, Uttar Pradesh, India;
| | - Umesh Yadava
- Department of Physics, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur 273009, India;
| | - Mohammad Amjad Kamal
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, 21589 Jeddah, Saudi Arabia; (S.A.E.-K.); (T.A.A.); (L.H.B.); (M.A.K.)
- Enzymoics, 7 Peterlee Place, Novel Global Community Educational Foundation, Hebersham, NSW 2770, Australia
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, 21589 Jeddah, Saudi Arabia; (S.A.E.-K.); (T.A.A.); (L.H.B.); (M.A.K.)
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Sang Gu Kang
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, Korea;
| | - Vivek Dhar Dwivedi
- Centre for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida 201308, India
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14
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Quiles JL, Rivas-García L, Varela-López A, Llopis J, Battino M, Sánchez-González C. Do nutrients and other bioactive molecules from foods have anything to say in the treatment against COVID-19? ENVIRONMENTAL RESEARCH 2020; 191:110053. [PMID: 32835682 PMCID: PMC7442575 DOI: 10.1016/j.envres.2020.110053] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/16/2020] [Accepted: 08/05/2020] [Indexed: 05/03/2023]
Abstract
The repositioning of therapeutic agents already approved by the regulatory agencies for the use of drugs is very interesting due to the immediacy of their use; similarly, the possibility of using molecules derived from foods, whether nutrients or not, is of great importance, also because of their immediate therapeutic applicability. Candidates for these natural therapies against COVID-19 should show certain effects, such as restoring mitochondrial function and cellular redox balance. This would allow reducing the susceptibility of risk groups and the cascade of events after SARS-CoV-2 infection, responsible for the clinical picture, triggered by the imbalance towards oxidation, inflammation, and cytokine storm. Possible strategies to follow through the use of substances of food origin would include: a) the promotion of mitophagy to remove dysfunctional mitochondria originating from free radicals, proton imbalance and virus evasion of the immune system; b) the administration of transition metals whose redox activity would lead to their own oxidation and the consequent generation of a reduced environment, which would normalize the oxidative state and the intracellular pH; c) the administration of molecules with demonstrated antioxidant capacity; d) the administration of compounds with anti-inflammatory and vasodilatory activity; e) the administration of immunomodulatory compounds.
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Affiliation(s)
- José L Quiles
- Biomedical Research Centre, Institute of Nutrition and Food Technology "José Mataix Verdú", Department of Physiology, Faculty of Pharmacy, University of Granada, Avda. Del Conocimiento S/n, 18100, Armilla, Granada, Spain; College of Food Science and Technology, Northwest University, Xi'an, 710069, China.
| | - Lorenzo Rivas-García
- Biomedical Research Centre, Institute of Nutrition and Food Technology "José Mataix Verdú", Department of Physiology, Faculty of Pharmacy, University of Granada, Avda. Del Conocimiento S/n, 18100, Armilla, Granada, Spain; Sport and Health Research Centre. University of Granada, C/. Menéndez Pelayo 32, 18016, Armilla, Granada, Spain
| | - Alfonso Varela-López
- Biomedical Research Centre, Institute of Nutrition and Food Technology "José Mataix Verdú", Department of Physiology, Faculty of Pharmacy, University of Granada, Avda. Del Conocimiento S/n, 18100, Armilla, Granada, Spain
| | - Juan Llopis
- Biomedical Research Centre, Institute of Nutrition and Food Technology "José Mataix Verdú", Department of Physiology, Faculty of Pharmacy, University of Granada, Avda. Del Conocimiento S/n, 18100, Armilla, Granada, Spain; Sport and Health Research Centre. University of Granada, C/. Menéndez Pelayo 32, 18016, Armilla, Granada, Spain
| | - Maurizio Battino
- Department of Clinical Sicences, Università Politecnica Delle Marche, 60131, Ancona, Italy; Nutrition and Food Science Group, Department of Analytical and Food Chemistry, CITACA, CACTI University of Vigo, 36310, Vigo, Spain; International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang, 212013, China
| | - Cristina Sánchez-González
- Biomedical Research Centre, Institute of Nutrition and Food Technology "José Mataix Verdú", Department of Physiology, Faculty of Pharmacy, University of Granada, Avda. Del Conocimiento S/n, 18100, Armilla, Granada, Spain; Sport and Health Research Centre. University of Granada, C/. Menéndez Pelayo 32, 18016, Armilla, Granada, Spain
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15
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Benskin LL. A Basic Review of the Preliminary Evidence That COVID-19 Risk and Severity Is Increased in Vitamin D Deficiency. Front Public Health 2020; 8:513. [PMID: 33014983 PMCID: PMC7513835 DOI: 10.3389/fpubh.2020.00513] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 08/07/2020] [Indexed: 12/15/2022] Open
Abstract
As the world's attention has been riveted upon the growing COVID-19 pandemic, many researchers have written brief reports supporting the hypothesis that vitamin D deficiency is related to the incidence and severity of COVID-19. The clear common thread among the top risk groups-vitamin D deficiency-may be being overlooked because of previous overstated claims of vitamin D benefits. However, the need to decrease COVID-19 fatalities among high-risk populations is urgent. Early researchers reported three striking patterns. Firstly, the innate immune system is impaired by vitamin D deficiency, which would predispose sufferers to viral infections such as COVID-19. Vitamin D deficiency also increases the activity of the X-chromosome-linked "Renin-Angiotensin" System, making vitamin D deficient individuals (especially men) more susceptible to COVID-19's deadly "cytokine storm" (dramatic immune system overreaction). Secondly, the groups who are at highest risk for severe COVID-19 match those who are at highest risk for severe vitamin D deficiency. This includes the elderly, men, ethnic groups whose skin is naturally rich in melanin (if living outside the tropics), those who avoid sun exposure for cultural and health reasons, those who live in institutions, the obese, and/or those who suffer with hypertension, cardiovascular disease, or diabetes. And thirdly, the pattern of geographical spread of COVID-19 reflects higher population vitamin D deficiency. Both within the USA and throughout the world, COVID-19 fatality rates parallel vitamin D deficiency rates. A literature search was performed on PubMed, Google Scholar, and RSMLDS, with targeted Google searches providing additional sources. Although randomized controlled trial results may be available eventually, the correlational and causal study evidence supporting a link between vitamin D deficiency and COVID-19 risks is already so strong that it supports action. The 141 author groups writing primarily about biological plausibility detailed how vitamin D deficiency can explain every risk factor and every complication of COVID-19, but agreed that other factors are undoubtedly at work. COVID-19 was compared with dengue fever, for which oral vitamin D supplements of 4,000 IU for 10 days were significantly more effective than 1,000 IU in reducing virus replication and controlling the "cytokine storm" (dramatic immune system over-reaction) responsible for fatalities. Among the 47 original research studies summarized here, chart reviews found that serum vitamin D levels predicted COVID-19 mortality rates (16 studies) and linearly predicted COVID-19 illness severity (8 studies). Two causal modeling studies and several analyses of variance strongly supported the hypothesis that vitamin D deficiency is a causal, rather than a bystander, factor in COVID-19 outcomes. Three of the four studies whose findings opposed the hypothesis relied upon disproven assumptions. The literature review also found that prophylactically correcting possible vitamin D deficiency during the COVID-19 pandemic is extremely safe. Widely recommending 2,000 IU of vitamin D daily for all populations with limited ability to manufacture vitamin D from the sun has virtually no potential for harm and is reasonably likely to save many lives.
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Affiliation(s)
- Linda L. Benskin
- Independent Researcher for Improving Health in Rural Areas of Tropical Developing Countries, Austin, TX, United States
- Ferris Mfg. Corp., Makers of PolyMem® Multifunctional Dressings, Ft. Worth, TX, United States
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16
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Mukherjee S, Dasgupta S, Adhikary T, Adhikari U, Panja SS. Structural insight to hydroxychloroquine-3C-like proteinase complexation from SARS-CoV-2: inhibitor modelling study through molecular docking and MD-simulation study. J Biomol Struct Dyn 2020; 39:7322-7334. [PMID: 32772895 PMCID: PMC7484585 DOI: 10.1080/07391102.2020.1804458] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The spread of novel coronavirus strain, Severe Acute Respiratory Syndrome 2 (SARS-CoV-2) causes Coronavirus disease (COVID-19) has now spread worldwide and effecting the entire human race. The viral genetic material is transcripted and replicated by 3 C-like protease, as a result, it is an important drug target for COVID-19. Hydroxychloroquine (HCQ) report promising results against this drug target so, we perform molecular docking followed by MD-simulation studies of HCQ and modelled some ligand (Mod-I and Mod-II) molecules with SARS-CoV-2-main protease which reveals the structural organization of the active site residues and presence of a conserve water-mediated catalytic triad that helps in the recognition of Mod-I/II ligand molecules. The study may be helpful to gain a detailed structural insight on the presence of water-mediated catalytic triad which could be useful for inhibitor modelling. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Soumita Mukherjee
- Department of Chemistry, National Institute of Technology-Durgapur, Durgapur, West Bengal, India
| | - Subrata Dasgupta
- Department of Chemistry, National Institute of Technology-Durgapur, Durgapur, West Bengal, India
| | - Tapasendra Adhikary
- Department of Metallurgical & Materials Engineering, Indian Institute of Technology, Kharagpur, West Bengal, India
| | - Utpal Adhikari
- Department of Chemistry, National Institute of Technology-Durgapur, Durgapur, West Bengal, India
| | - Sujit Sankar Panja
- Department of Chemistry, National Institute of Technology-Durgapur, Durgapur, West Bengal, India
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17
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Amin SA, Ghosh K, Gayen S, Jha T. Chemical-informatics approach to COVID-19 drug discovery: Monte Carlo based QSAR, virtual screening and molecular docking study of some in-house molecules as papain-like protease (PLpro) inhibitors. J Biomol Struct Dyn 2020; 39:4764-4773. [PMID: 32568618 PMCID: PMC7332872 DOI: 10.1080/07391102.2020.1780946] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
World Health Organization characterized novel coronavirus disease (COVID-19), caused by severe acute respiratory syndrome (SARS) coronavirus-2 (SARS-CoV-2) as world pandemic. This infection has been spreading alarmingly by causing huge social and economic disruption. In order to response quickly, the inhibitors already designed against different targets of previous human coronavirus infections will be a great starting point for anti-SARS-CoV-2 inhibitors. In this study, our approach integrates different ligand based drug design strategies of some in-house chemicals. The study design was composed of some major aspects: (a) classification QSAR based data mining of diverse SARS-CoV papain-like protease (PLpro) inhibitors, (b) QSAR based virtual screening (VS) to identify in-house molecules that could be effective against putative target SARS-CoV PLpro and (c) finally validation of hits through receptor-ligand interaction analysis. This approach could be used to aid in the process of COVID-19 drug discovery. It will introduce key concepts, set the stage for QSAR based screening of active molecules against putative SARS-CoV-2 PLpro enzyme. Moreover, the QSAR models reported here would be of further use to screen large database. This study will assume that the reader is approaching the field of QSAR and molecular docking based drug discovery against SARS-CoV-2 PLpro with little prior knowledge. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Sk Abdul Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Kalyan Ghosh
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University, Sagar, India
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University, Sagar, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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18
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Chikhale RV, Gurav SS, Patil RB, Sinha SK, Prasad SK, Shakya A, Shrivastava SK, Gurav NS, Prasad RS. Sars-cov-2 host entry and replication inhibitors from Indian ginseng: an in-silico approach. J Biomol Struct Dyn 2020; 39:4510-4521. [PMID: 32568012 PMCID: PMC7332873 DOI: 10.1080/07391102.2020.1778539] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
COVID-19 has ravaged the world and is the greatest of pandemics in modern human history, in the absence of treatment or vaccine, the mortality and morbidity rates are very high. The present investigation identifies potential leads from the plant Withania somnifera (Indian ginseng), a well-known antiviral, immunomodulatory, anti-inflammatory and a potent antioxidant plant, using molecular docking and dynamics studies. Two different protein targets of SARS-CoV-2 namely NSP15 endoribonuclease and receptor binding domain of prefusion spike protein from SARS-CoV-2 were targeted. Molecular docking studies suggested Withanoside X and Quercetin glucoside from W. somnifera have favorable interactions at the binding site of selected proteins, that is, 6W01 and 6M0J. The top-ranked phytochemicals from docking studies, subjected to 100 ns molecular dynamics (MD) suggested Withanoside X with the highest binding free energy (ΔGbind = -89.42 kcal/mol) as the most promising inhibitor. During MD studies, the molecule optimizes its conformation for better fitting with the receptor active site justifying the high binding affinity. Based on proven therapeutic, that is, immunomodulatory, antioxidant and anti-inflammatory roles and plausible potential against n-CoV-2 proteins, Indian ginseng could be one of the alternatives as an antiviral agent in the treatment of COVID 19. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rupesh V Chikhale
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Shailendra S Gurav
- Department of Pharmacognosy, Goa College of Pharmacy, Goa University, Panaji, Goa, India
| | - Rajesh B Patil
- Sinhgad Technical Education Society's, Smt. Kashibai Navale College of Pharmacy, Pune, Maharashtra, India
| | - Saurabh K Sinha
- Department of Pharmaceutical Sciences, Mohanlal Shukhadia University, Udaipur, Rajasthan, India
| | - Satyendra K Prasad
- Department of Pharmaceutical Sciences, R.T.M. University, Nagpur, Maharastra, India
| | - Anshul Shakya
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, Assam, India
| | - Sushant K Shrivastava
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Nilambari S Gurav
- PES's Rajaram and Tarabai Bandekar College of Pharmacy, Goa University, Ponda, Goa, India
| | - Rupali S Prasad
- Department of Pharmaceutical Sciences, R.T.M. University, Nagpur, Maharastra, India
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