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Ganapathy Vilasam Sreekala A, Gupta KK, Nathan VK. Identification of coastal pesticide pollutants as potent inhibitors of Bacillus pasteurii urease mediated calcium carbonate precipitation: a computational approach. J Biomol Struct Dyn 2023:1-11. [PMID: 37691444 DOI: 10.1080/07391102.2023.2252089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 08/21/2023] [Indexed: 09/12/2023]
Abstract
Microbially induced calcite precipitation (MICP) through urease enzyme has attained a lot of recognition in various fields of civil engineering and geotechnology for stabilizing the strength of soil and various concrete materials. The activity of urease has been found to be affected by various factors like temperature, substrate concentrations, pH of the medium, presence of inhibitors, etc. Through this study, the outcome of the interaction of pesticides (commonly found in Indian coastal regions) on Bacillus pasteurii urease, a major organism reported for MICP studies has been investigated in silico. The results from the study revealed that the enzyme has higher interactions of -4.1, -3.2, and -3.4 kJ/mol with common pesticides like dichloro diphenyl dichloro ethane(DDD), dichloro diphenyl trichloroe thane (DDT), and methyl parathion of organochlorides and organophosphates class. From the molecular dynamics simulation analysis, complex 1 (DDD -receptor) has been found to have the highest and more compact structure followed by methyl parathion -receptor. Prime MM-GBSA analysis also revealed the highest binding energy of -27.8 kcal/mol with the protein and DDD. Thus, it can be inferred from the current study that pesticides, particularly, DDD, DDT, and methyl parathion present in the coastal areas may have an impact on urease. This interaction can result in the inhibition of the urease activity of B. pasteurii, thus preventing the biomineralization process. This study would be the first report on the computational approach to understanding the interaction of prominent pesticides on the coastal region and B. pasteurii urease.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Krishna Kant Gupta
- School of Chemical and Biotechnology, SASTRA Deemed to be University, Thirumalasamudram, India
| | - Vinod Kumar Nathan
- School of Chemical and Biotechnology, SASTRA Deemed to be University, Thirumalasamudram, India
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A Critical Review on Role of Available Synthetic Drugs and Phytochemicals in Insulin Resistance Treatment by Targeting PTP1B. Appl Biochem Biotechnol 2022; 194:4683-4701. [PMID: 35819691 DOI: 10.1007/s12010-022-04028-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2022] [Indexed: 11/02/2022]
Abstract
Insulin resistance (IR) is a condition of impaired response of cells towards insulin. It is marked by excessive blood glucose, dysregulated insulin signalling, altered pathways, damaged pancreatic β-cells, metabolic disorders, etc. Chronic hyperglycemic conditions leads to type 2 diabetes mellitus (T2DM) which causes excess generation of highly reactive free radicals, causing oxidative stress, further leading to development and progression of complications like vascular dysfunction, damaged cellular proteins, and DNA. One of the causes for IR is dysregulation of protein tyrosine phosphatase 1B (PTP1B). Advancements in drug therapeutics have helped people manage IR by regulating PTP1B, however have been reported to cause side effects. Therefore, there is a growing interest on usage of phytochemical constituents having IR therapeutic properties and aiding to minimize these complications. Medicinal plants have not been utilized to their full potential as a therapeutic drug due to lack of knowledge of their active and effective chemical constituents, mode of action, regulation of IR parameters, and dosage of administration. This review highlights phytochemical constituents present in medicinal plants or spices, their potential effectiveness on proteins (PTP1B) regulating IR, and reported possible mechanism of action studied on in vitro models. The study gives current knowledge and future recommendations on the above aspects and is expected to be beneficial in developing herbal drug using these phytochemical constituents, either alone or in combination, for medication of IR and diabetes.
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3
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Amani B, Zareei S, Amani B, Zareei M, Zareei N, Shabestan R, Akbarzadeh A. Artesunate, imatinib, and infliximab in COVID‐19: A rapid review and meta‐analysis of current evidence. Immun Inflamm Dis 2022; 10:e628. [PMID: 35634954 PMCID: PMC9092000 DOI: 10.1002/iid3.628] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/26/2022] [Accepted: 03/29/2022] [Indexed: 11/26/2022] Open
Abstract
Background and Objective Despite the pervasive vaccination program against coronavirus disease 2019 (COVID‐19), people who got fully vaccinated are still contaminated by severe acute respiratory syndrome coronavirus 2, making an effective and safe therapeutic intervention a crucial need for the patients' survival. The purpose of the present study is to seek available evidence for the efficacy and safety of three promising medications artesunate, imatinib, and infliximab against COVID‐19. Methods A literature search was conducted in PubMed, Cochrane Library, medRxive, and Google Scholar, and the relevant articles published up to January 2022 were found. Furthermore, the clinical trial databases were screened for finding more citations. Data analysis was carried out applying The Cochrane Collaboration tool and Newcastle–Ottawa scale to assess the included studies. Meta‐analysis was performed using RevMan 5.4.1. Results Five published studies were identified as eligible. Meta‐analysis showed that there was no significant difference between the infliximab and control groups in terms of mortality rate (risk ratio [RR]: 0.65; confidence interval [CI] 95%: 0.40–1.07; p = .09). However, a significant difference was observed between the two groups for the hospital discharge (RR: 1.37; CI 95%: 1.04–1.80; p = .03). No remarkable clinical benefit was observed for using imatinib in COVID‐19 patients. Artesunate showed significant improvement in patients with COVID‐19. Conclusion In the present, limited evidence exists for the efficacy and safety of artesunate, imatinib, and infliximab in patients with COVID‐19. The findings of WHO's Solidarity international trial will provide further information regarding these therapeutic interventions.
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Affiliation(s)
- Bahman Amani
- Department of Health Management and Economics, School of Public Health Tehran University of Medical Sciences Tehran Iran
| | - Sara Zareei
- Department of Cell & Molecular Biology, Faculty of Biological Sciences Kharazmi University Tehran Iran
| | - Behnam Amani
- Department of Health Management and Economics, School of Public Health Tehran University of Medical Sciences Tehran Iran
| | - Mahsa Zareei
- Department of Health Services Management, School of Health Management and Information Sciences Iran University of Medical Sciences Tehran Iran
| | - Neda Zareei
- Shiraz Transplant Research Center Shiraz University of Medical Sciences Shiraz Iran
| | - Rouhollah Shabestan
- Department of Biostatistics and Epidemiology, School of Public Health Tehran University of Medical Sciences Tehran Iran
| | - Arash Akbarzadeh
- Department of Biostatistics and Epidemiology, School of Public Health Tehran University of Medical Sciences Tehran Iran
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In Silico Identification of Potential Inhibitors of the SARS-CoV-2 Nucleocapsid Through Molecular Docking-Based Drug Repurposing. DR. SULAIMAN AL HABIB MEDICAL JOURNAL 2022. [PMCID: PMC9153216 DOI: 10.1007/s44229-022-00004-z] [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: 10/24/2022] Open
Abstract
AbstractSARS-CoV-2 is the virus responsible for the COVID-19 pandemic, and its effects on people worldwide continue to grow. Protein-targeted therapeutics are currently unavailable for this virus. As with other coronaviruses, the nucleocapsid (N) protein is the most conserved RNA-binding structural protein of SARS-CoV-2. The N protein is an appealing target because of its functional role in viral transcription and replication. Therefore, molecular docking method for structure-based drug design was used to investigate the binding energy and binding modes of various anti-N inhibitors in depth. The inhibitors selected were originally developed to target stress granules and other molecules involved in RNA biology, and were either FDA-approved or in the process of clinical trials for COVID-19. We aimed at targeting the N-terminal RNA binding domain (NTD) for molecular docking-based screening, on the basis of the first resolved crystal structure of SARS-CoV-2 N protein (PDB ID: 6M3M) and C-terminal domain (CTD) dimerization of the nucleocapsid phosphoprotein of SARS-COV-2 (PDB ID: 6WJI). Silmitasertib, nintedanib, ternatin, luteolin, and fedratinib were found to interact with RNA binding sites and to form a predicted protein interface with high binding energy. Similarly, silmitasertib, sirolimus-rapamycin, dovitinib, nintedanib, and fedratinib were found to interact with the SARS-CoV-2 N protein at its CTD dimerization sites, according to previous studies. In addition, we investigated an information gap regarding the relationships among the energetic landscape and stability and drug binding of the SARS-CoV-2 N NTD and CTD. Our in silico results clearly indicated that several tested drugs as potent putative inhibitors for COVID-19 therapeutics, thus indicating that they should be further validated as treatments to slow the spread of SARS-CoV-2.
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Identification of phytocompounds as newer antiviral drugs against COVID-19 through molecular docking and simulation based study. J Mol Graph Model 2022; 114:108192. [PMID: 35468453 PMCID: PMC9007924 DOI: 10.1016/j.jmgm.2022.108192] [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: 11/19/2021] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 11/30/2022]
Abstract
COVID-19 pandemic has emerged as a global threat with its highly contagious and mutating nature. Several existing antiviral drugs has been worked on, without proper results and meanwhile the virus is mutating rapidly to create more infectious variant. In order to find some alternatives, phytocompounds can be opted as good one. In this study, three hundred phytocompounds were screened virtually against two viral proteins namely main protease and spike protein. Molecular docking and dynamic simulation study was used to find binding affinity, structural stability and flexibility of the complex. Pharmacokinetic properties were studied through ADMET analysis. To understand energy variation of the complex structure free energy landscape analysis was performed. Among three hundred phytocompounds virtual screening, three phytocompounds were selected for detailed molecular interaction analysis. Oleanderolide, Proceragenin A and Balsaminone A, showed strong binding affinity against both the target proteins and reflected conformational stability throughout the MD run. Oleanderolide, proceragenin A and balsaminone A has docking score −9.4 kcal/mol, −8.6 kcal/mol, and −8.1 kcal/mol respectively against main protease and same −8.3 kcal/mol docking score against spike protein. These three phytocompounds has high gastrointestinal absorption capacity. They were unexplored till now for their antiviral activity. Their promising in silico results suggests that they can be promoted in the long run for development of new antiviral drugs.
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Uma Reddy B, Routhu NK, Kumar A. Multifaceted role of plant derived small molecule inhibitors on replication cycle of sars-cov-2. Microb Pathog 2022; 168:105512. [PMID: 35381324 PMCID: PMC8976571 DOI: 10.1016/j.micpath.2022.105512] [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: 01/18/2022] [Revised: 03/27/2022] [Accepted: 03/30/2022] [Indexed: 11/15/2022]
Abstract
Introduction Coronavirus disease 2019 (COVID-19) is an illness caused by the new coronavirus severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2). It has affected public health and the economy globally. Currently approved vaccines and other drug candidates could be associated with several drawbacks which urges developing alternative therapeutic approaches. Aim To provide a comprehensive review of anti-SARS-CoV-2 activities of plants and their bioactive compounds. Methods Information was gathered from diverse bibliographic platforms such as PubMed, Google Scholar, and ClinicalTrials.gov registry. Results The present review highlights the potential roles of crude extracts of plants as well as plant-derived small molecules in inhibiting SARS-CoV-2 infection by targeting viral or host factors essential for viral entry, polyprotein processing, replication, assembly and release. Their anti-inflammatory and antioxidant properties as well as plant-based therapies that are under development in the clinical trial phases-1 to 3 are also covered. Conclusion This knowledge could further help understanding SARS-CoV-2 infection and anti-viral mechanisms of plant-based therapeutics.
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Affiliation(s)
- B Uma Reddy
- Department of Studies in Botany, Vijayanagara Sri Krishnadevaraya University, Ballari, 583105, India.
| | - Nanda Kishore Routhu
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.
| | - Anuj Kumar
- Cancer Research Center of Lyon (CRCL), INSERM 1052, CNRS UMR 5286, Lyon, 69008, France.
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7
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Kumar P, Bhardwaj T, Kumar A, Gehi BR, Kapuganti SK, Garg N, Nath G, Giri R. Reprofiling of approved drugs against SARS-CoV-2 main protease: an in-silico study. J Biomol Struct Dyn 2022; 40:3170-3184. [PMID: 33179586 PMCID: PMC7678354 DOI: 10.1080/07391102.2020.1845976] [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: 05/15/2020] [Accepted: 10/30/2020] [Indexed: 12/18/2022]
Abstract
Given the COVID-19 pandemic, currently, there are many drugs in clinical trials against this virus. Among the excellent drug targets of SARS-CoV-2 are its proteases (Nsp3 and Nsp5) that plays vital role in polyprotein processing giving rise to functional nonstructural proteins, essential for viral replication and survival. Nsp5 (also known as Mpro) hydrolyzes replicase polyprotein (1ab) at eleven different sites. For targeting Mpro, we have employed drug repurposing approach to identify potential inhibitors of SARS-CoV-2 in a shorter time span. Screening of approved drugs through docking reveals Hyaluronic acid and Acarbose among the top hits which are showing strong interactions with catalytic site residues of Mpro. We have also performed docking of drugs Lopinavir, Ribavirin, and Azithromycin on SARS-CoV-2 Mpro. Further, binding of these compounds (Hyaluronic acid, Acarbose, and Lopinavir) is validated by extensive molecular dynamics simulation of 500 ns where these drugs show stable binding with Mpro. We believe that the high-affinity binding of these compounds will help in designing novel strategies for structure-based drug discovery against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Prateek Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, India
| | - Taniya Bhardwaj
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, India
| | - Ankur Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, India
| | - Bhuvaneshwari R. Gehi
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, India
| | - Shivani K. Kapuganti
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, India
| | - Neha Garg
- Department of Medicinal Chemistry, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Gopal Nath
- Department of Microbiology, Faculty of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, India
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8
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Qu J, Liu Q, You G, Ye L, Jin Y, Kong L, Guo W, Xu Q, Sun Y. Advances in ameliorating inflammatory diseases and cancers by andrographolide: Pharmacokinetics, pharmacodynamics, and perspective. Med Res Rev 2021; 42:1147-1178. [PMID: 34877672 DOI: 10.1002/med.21873] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/07/2021] [Accepted: 11/10/2021] [Indexed: 12/26/2022]
Abstract
Andrographolide, a well-known natural lactone having a range of pharmacological actions in traditional Chinese medicine. It has long been used to cure a variety of ailments. In this review, we cover the pharmacokinetics and pharmacological activity of andrographolide which supports its further clinical application in cancers and inflammatory diseases. Growing evidence shows a good therapeutic effect in inflammatory diseases, including liver diseases, joint diseases, respiratory system diseases, nervous system diseases, heart diseases, inflammatory bowel diseases, and inflammatory skin diseases. As a result, the effects of andrographolide on immune cells and the processes that underpin them are discussed. The preclinical use of andrographolide to different organs in response to malignancies such as colorectal, liver, gastric, breast, prostate, lung, and oral cancers has also been reviewed. In addition, several clinical trials of andrographolide in inflammatory diseases and cancers have been summarized. This review highlights recent advances in ameliorating inflammatory diseases as well as cancers by andrographolide and its analogs, providing a new perspective for subsequent research of this traditional natural product.
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Affiliation(s)
- Jiao Qu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biotechnology and Pharmaceutical Sciences, School of Life Science, Nanjing University, Nanjing, China
| | - Qianqian Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biotechnology and Pharmaceutical Sciences, School of Life Science, Nanjing University, Nanjing, China
| | - Guoquan You
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biotechnology and Pharmaceutical Sciences, School of Life Science, Nanjing University, Nanjing, China
| | - Ling Ye
- Biopharmaceutics, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Yiguang Jin
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing, China
| | - Lingdong Kong
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biotechnology and Pharmaceutical Sciences, School of Life Science, Nanjing University, Nanjing, China
| | - Wenjie Guo
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biotechnology and Pharmaceutical Sciences, School of Life Science, Nanjing University, Nanjing, China
| | - Qiang Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biotechnology and Pharmaceutical Sciences, School of Life Science, Nanjing University, Nanjing, China.,Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yang Sun
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biotechnology and Pharmaceutical Sciences, School of Life Science, Nanjing University, Nanjing, China.,Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
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ARL15 modulates magnesium homeostasis through N-glycosylation of CNNMs. Cell Mol Life Sci 2021; 78:5427-5445. [PMID: 34089346 PMCID: PMC8257531 DOI: 10.1007/s00018-021-03832-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 03/23/2021] [Accepted: 03/30/2021] [Indexed: 02/06/2023]
Abstract
Cyclin M (CNNM1-4) proteins maintain cellular and body magnesium (Mg2+) homeostasis. Using various biochemical approaches, we have identified members of the CNNM family as direct interacting partners of ADP-ribosylation factor-like GTPase 15 (ARL15), a small GTP-binding protein. ARL15 interacts with CNNMs at their carboxyl-terminal conserved cystathionine-β-synthase (CBS) domains. In silico modeling of the interaction between CNNM2 and ARL15 supports that the small GTPase specifically binds the CBS1 and CNBH domains. Immunocytochemical experiments demonstrate that CNNM2 and ARL15 co-localize in the kidney, with both proteins showing subcellular localization in the endoplasmic reticulum, Golgi apparatus and the plasma membrane. Most importantly, we found that ARL15 is required for forming complex N-glycosylation of CNNMs. Overexpression of ARL15 promotes complex N-glycosylation of CNNM3. Mg2+ uptake experiments with a stable isotope demonstrate that there is a significant increase of 25Mg2+ uptake upon knockdown of ARL15 in multiple kidney cancer cell lines. Altogether, our results establish ARL15 as a novel negative regulator of Mg2+ transport by promoting the complex N-glycosylation of CNNMs.
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Jade D, Ayyamperumal S, Tallapaneni V, Joghee Nanjan CM, Barge S, Mohan S, Nanjan MJ. Virtual high throughput screening: Potential inhibitors for SARS-CoV-2 PL PRO and 3CL PRO proteases. Eur J Pharmacol 2021; 901:174082. [PMID: 33823185 PMCID: PMC8018918 DOI: 10.1016/j.ejphar.2021.174082] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/18/2021] [Accepted: 03/30/2021] [Indexed: 01/23/2023]
Abstract
The pandemic, COVID-19, has spread worldwide and affected millions of people. There is an urgent need, therefore, to find a proper treatment for the novel coronavirus, Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), the causative agent. This paper focuses on identifying inhibitors that target SARS-CoV-2 proteases, PLPRO and 3CLPRO, which control the duplication and manages the life cycle of SARS-CoV-2. We have carried out detailed in silico Virtual high-throughput screening using Food and Drug Administration (FDA) approved drugs from the Zinc database, COVID-19 clinical trial compounds from Pubchem database, Natural compounds from Natural Product Activity and Species Source (NPASS) database and Maybridge database against PLPRO and 3CLPRO proteases. After thoroughly analyzing the screening results, we found five compounds, Bemcentinib, Pacritinib, Ergotamine, MFCD00832476, and MFCD02180753 inhibit PLPRO and six compounds, Bemcentinib, Clofazimine, Abivertinib, Dasabuvir, MFCD00832476, Leuconicine F inhibit the 3CLPRO. These compounds are stable within the protease proteins’ active sites at 20ns MD simulation. The stability is revealed by hydrogen bond formations, hydrophobic interactions, and salt bridge interactions. Our study results also reveal that the selected five compounds against PLPRO and the six compounds against 3CLPRO bind to their active sites with good binding free energy. These compounds that inhibit the activity of PLPRO and 3CLPRO may, therefore, be used for treating COVID-19 infection.
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Affiliation(s)
- Dhananjay Jade
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty, 643001, Tamilnadu, India
| | - Selvaraj Ayyamperumal
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty, 643001, Tamilnadu, India
| | - Vyshnavi Tallapaneni
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty, 643001, Tamilnadu, India
| | - Chandrasekar Moola Joghee Nanjan
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty, 643001, Tamilnadu, India.
| | - Sagar Barge
- Biochemistry and Drug Discovery Lab, Institute of Advanced Study in Science and Technology, Paschim Boragaon, Guwahati, 35, Assam, India
| | - Surender Mohan
- School of Biotechnology, Laboratory of Molecular Biology and Genetic Engineering, JNU, New Delhi, 110067 India
| | - Moola Joghee Nanjan
- JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty, 643001, Tamilnadu, India.
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Pande M, Kundu D, Srivastava R. Vitamin C and Vitamin D3 show strong binding with the amyloidogenic region of G555F mutant of Fibrinogen A alpha-chain associated with renal amyloidosis: proposed possible therapeutic intervention. Mol Divers 2021; 26:939-949. [PMID: 33710477 DOI: 10.1007/s11030-021-10205-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 02/22/2021] [Indexed: 12/14/2022]
Abstract
G555F mutant of Fibrinogen A alpha-chain (FGA) is reported to be associated with kidney amyloidosis. In the current study, we have modelled the G555F mutant and examined the mutation's effect on the structural and functional level. We have also docked Vitamin C and D3 on the mutant's amyloidogenic region to identify if these vitamins can bind amyloidogenic regions. Further, we analyzed if they could prevent or modulate amyloid formation by stopping critical interactions in amyloidogenic regions in FGA. We used the wild type FGA model protein as a control. Our docking and molecular dynamics simulation results indicate stronger Vitamin D3 binding than Vitamin C to the amyloidogenic region of the mutant protein. The RMSD, radius of gyration, and RMSF values were higher for the G555F mutant than the FGA wild type protein. Overall, the results support these vitamins' potential as a therapeutic and anti-amyloidogenic agent for FGA renal amyloidosis.
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Affiliation(s)
- Monu Pande
- Department of Biochemistry, Institute of Medical Science, Banaras Hindu University, Varanasi, 221005, India
| | - Debanjan Kundu
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, 221005, India
| | - Ragini Srivastava
- Department of Biochemistry, Institute of Medical Science, Banaras Hindu University, Varanasi, 221005, India.
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12
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Rai H, Barik A, Singh YP, Suresh A, Singh L, Singh G, Nayak UY, Dubey VK, Modi G. Molecular docking, binding mode analysis, molecular dynamics, and prediction of ADMET/toxicity properties of selective potential antiviral agents against SARS-CoV-2 main protease: an effort toward drug repurposing to combat COVID-19. Mol Divers 2021; 25:1905-1927. [PMID: 33582935 PMCID: PMC7882058 DOI: 10.1007/s11030-021-10188-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/19/2021] [Indexed: 12/16/2022]
Abstract
The importance of the main protease (Mpro) enzyme of SARS-CoV-2 in the digestion of viral polyproteins introduces Mpro as an attractive drug target for antiviral drug design. This study aims to carry out the molecular docking, molecular dynamics studies, and prediction of ADMET properties of selected potential antiviral molecules. The study provides an insight into biomolecular interactions to understand the inhibitory mechanism and the spatial orientation of the tested ligands and further, identification of key amino acid residues within the substrate-binding pocket that can be applied for structure-based drug design. In this regard, we carried out molecular docking studies of chloroquine (CQ), hydroxychloroquine (HCQ), remdesivir (RDV), GS441524, arbidol (ARB), and natural product glycyrrhizin (GA) using AutoDock 4.2 tool. To study the drug-receptor complex's stability, selected docking possesses were further subjected to molecular dynamics studies with Schrodinger software. The prediction of ADMET/toxicity properties was carried out on ADMET Prediction™. The docking studies suggested a potential role played by CYS145, HIS163, and GLU166 in the interaction of molecules within the active site of COVID-19 Mpro. In the docking studies, RDV and GA exhibited superiority in binding with the crystal structure of Mpro over the other selected molecules in this study. Spatial orientations of the molecules at the active site of Mpro exposed the significance of S1–S4 subsites and surrounding amino acid residues. Among GA and RDV, RDV showed better and stable interactions with the protein, which is the reason for the lesser RMSD values for RDV. Overall, the present in silico study indicated the direction to combat COVID-19 using FDA-approved drugs as promising agents, which do not need much toxicity studies and could also serve as starting points for lead optimization in drug discovery.
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Affiliation(s)
- Himanshu Rai
- Room # 23, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, Uttar Pradesh, 221005, India
| | - Atanu Barik
- Room # 23, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, Uttar Pradesh, 221005, India
| | - Yash Pal Singh
- Room # 23, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, Uttar Pradesh, 221005, India
| | - Akhil Suresh
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences (MCOPS), Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Lovejit Singh
- Room # 23, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, Uttar Pradesh, 221005, India
| | - Gourav Singh
- Room # 23, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, Uttar Pradesh, 221005, India
| | - Usha Yogendra Nayak
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences (MCOPS), Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.,Manipal McGill Centre for Infectious Diseases, Prasanna School of Public Health, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Vikash Kumar Dubey
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, Uttar Pradesh, 221005, India
| | - Gyan Modi
- Room # 23, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, Uttar Pradesh, 221005, India.
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Kumar S, Mittal A, Babu D, Mittal A. Herbal Medicines for Diabetes Management and its Secondary Complications. Curr Diabetes Rev 2021; 17:437-456. [PMID: 33143632 DOI: 10.2174/1573399816666201103143225] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/26/2020] [Accepted: 10/08/2020] [Indexed: 11/22/2022]
Abstract
Diabetic Mellitus (DM) is a metabolic disorder that is concerning for people all over the world. DM is caused due to lack of insulin or ineffective production of insulin in the pancreas. A total of 463 million people were reported to have diabetes mellitus in 2019 and this number is predicted to rise up to 578 million by the year 2030 and 700 million by 2045. High blood sugar gives rise to many complications like diabetic retinopathy, diabetic nephropathy, atherosclerosis, hypercoagulability, cardiovascular disease, coronary heart disease, abdominal obesity, hypertension, hyperlipidemia, cerebrovascular disease, coronary artery disease, foot damage, skin complications, Alzheimer's disease, hearing impairment, and depression. These life-threatening complications make diabetes more severe than other diseases. Many synthetic drugs have been developed, but still, a complete cure is not provided by any of the molecules. Continuous use of some synthetic agents causes severe side effects, and thus the demand for non-toxic, affordable drugs still persists. Traditional treatments have been an extremely valued source of medicine all over human history. These are extensively used throughout the world, indicating that herbs are a growing part of modern and high-tech medicines. The World Health Organization (WHO) has listed a total of 21,000 plants, which are used for medicinal purposes around the world. Among them, more than 400 plants are available for the treatment of diabetes. Despite the fact that there are many herbal drugs available for treating diabetes, only a small number of these plants have undergone scientific and medical evaluation to assess their efficacy. Trigonella foenum-graecum, Allium sativum, Caesalpinia bonduc, Ferula assafoetida,etc., are some of the medicinal plants used for antidiabetic therapy. The presence of phenolic compounds, flavonoids, terpenoids, and coumarins is responsible for the antidiabetic nature of the medicinal plants. These constituents have shown a reduction in blood glucose levels. Pycnogenol, acarbose, miglitol, and voglibose are some of the examples of marketed drugs, which are obtained from natural origin and used as antidiabetic drugs. The active principles derived from the plants work through many antidiabetic mechanisms, which include inhibition of α-glucosidase, α-amylase, and protein tyrosine phosphatase 1B activities. One of the major advantages of herbal drugs is the low level of side effects attributed to these medicines, and this attracted various researchers to develop new molecules for the treatment of diabetes. In this review, recent advances in the field of herbal drugs to treat diabetes, prevent secondary complications from arising due to diabetes, and various herbal molecules in different stages of clinical trials will be emphasized upon.
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Affiliation(s)
- Shubham Kumar
- Faculty of Pharmaceutical Sciences, PCTE Group of Institutes, Campus-2, Near Baddowal Cantt. Ferozepur Road, Ludhiana-142021, India
| | - Anu Mittal
- Department of Chemistry, Guru Nanak Dev University College, Patti, Distt. Tarn Taran, India
| | - Dinesh Babu
- Faculty of Pharmacy & Pharmaceutical Sciences, Katz Group-Rexall Centre for Pharmacy and Health Research, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Amit Mittal
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road (NH-1), Phagwara (Punjab) 144411, India
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Khandar AA, Mirzaei-Kalar Z, Shahabadi N, Hadidi S, Abolhasani H, Hosseini-Yazdi SA, Jouyban A. Antimicrobial, cytotoxicity, molecular modeling and DNA cleavage/binding studies of zinc-naproxen complex: switching DNA binding mode of naproxen by coordination to zinc ion. J Biomol Struct Dyn 2020; 40:4224-4236. [PMID: 33272098 DOI: 10.1080/07391102.2020.1854858] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The intercalation DNA binding mode of the naproxen, a non-steroidal anti-inflammatory drug, has been reported previously. In this study, calf thymus deoxyribonucleic acid (CT-DNA) binding of zinc-naproxen complex, [Zn(naproxen)2(MeOH)2], at physiological pH has been investigated by multi-spectroscopic techniques and molecular docking. Zinc-naproxen complex displays significant binding property to the CT-DNA (Kb = 0.2 × 105 L.mol-1). All of the experimental results; relative increasing in viscosity of CT-DNA and fluorimetric studies using ethidium bromide (EB) and Hoechst 33258 probes, are indicative of groove binding mode of zinc-naproxen complex to CT-DNA. These results show that the coordination of naproxen to zinc metal switches the mode of binding from intercalation to groove. The molecular modeling also shows that the complex binds to the AT-rich region of minor groove of DNA. Structural and topography changes of DNA in interaction with the complex by atomic force microscopy (AFM) indicated that CT-DNA becomes swollen after interaction. The pUC18 plasmid DNA cleavage ability of zinc-naproxen complex by gel electrophoresis experiments revealed that zinc-naproxen complex cleaved supercoiled pUC18 plasmid DNA to nicked DNA. The cytotoxicity of the zinc complex performed by MTT method on HT29 and MCF7 cancer cell lines and on HEK 293 normal cell lines indicates that zinc complex has no cytotoxic effect on both HT29 and MCF7 cell lines but has better cytotoxicity effect on HEK 293 cell lines compared to cisplatin standard drug. The antimicrobial activity of the complex against Staphylococcus aureus and Escherichia coli bacteria revealed the high antimicrobial activity of the complex.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ali Akbar Khandar
- Department of Inorganic Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz, Iran
| | - Zeinab Mirzaei-Kalar
- Department of Inorganic Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz, Iran
| | - Nahid Shahabadi
- Department of Chemistry, Faculty of Science, Razi University, Kermanshah, Iran.,Medical Biology Research Center (MBRC), Kermanshah University of medical Sciences, Kermanshah, Iran
| | - Saba Hadidi
- Department of Chemistry, Faculty of Science, Razi University, Kermanshah, Iran
| | - Hoda Abolhasani
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, Iran
| | | | - Abolghasem Jouyban
- Phamaceutical Analysis Research Center and Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.,Kimia Idea Pardaz Azarbayjan (KIPA) Science Based Company, Tabriz University of Medical Sciences, Tabriz, Iran
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