Computational identification of selected bioactive compounds from Cedrus deodara as inhibitors against SARS-CoV-2 main protease: a pharmacoinformatics study

{ 'indexed': {'date-parts': [[2024, 3, 21]], 'date-time': '2024-03-21T01:28:16Z', 'timestamp': 1710984496790}, 'reference-count': 35, 'publisher': "Indian Drug Manufacturers' Association (IDMA)", 'issue': '02', 'content-domain': {'domain': [], 'crossmark-restriction': False}, 'published-print': {'date-parts': [[2024, 2, 28]]}, 'abstract': '<jats:p>Amid the ongoing Covid-19 pandemic, the quest for potent antiviral treatments ' 'intensifies. This study focuses on the potential of bioactive compounds from the Himalayan ' 'cedar Cedrus deodara against the SARS-CoV-2 virus. Specifically targeting the main protease ' '(MPro) and spike protein, the study employs docking trials and molecular dynamics ' 'simulations. Compounds such as quercetin, dihydrodehydrodiconiferyl alcohol, and cedeodarin ' 'exhibit notable binding affinity, surpassing the reference drug favipiravir. Molecular ' 'dynamics simulations affirm the stability of these complexes throughout the simulation ' 'period. While these findings underscore promising interactions, it is crucial to emphasize ' 'the need for further research and experimental validation to fully explore the therapeutic ' 'capabilities of C. deodara in combatting Covid-19.</jats:p>', 'DOI': '10.53879/id.61.02.13859', 'type': 'journal-article', 'created': {'date-parts': [[2024, 3, 18]], 'date-time': '2024-03-18T13:23:54Z', 'timestamp': 1710768234000}, 'page': '78-91', 'source': 'Crossref', 'is-referenced-by-count': 0, 'title': 'COMPUTATIONAL IDENTIFICATION OF SELECTED BIOACTIVE COMPOUNDS FROM CEDRUS DEODARA AS INHIBITORS ' 'AGAINST SARS-COV-2 MAIN PROTEASE: A PHARMACOINFORMATICS STUDY', 'prefix': '10.53879', 'volume': '61', 'author': [ {'given': 'Aminabee', 'family': 'Shaik', 'sequence': 'first', 'affiliation': []}, { 'name': 'Department of Pharmacology, V. V. Institute of Pharmaceutical Sciences, ' 'Gudlavalleru-521 356, Andhra Pradesh, India', 'sequence': 'first', 'affiliation': []}, {'given': 'Lakshmana Rao', 'family': 'Atmakuri', 'sequence': 'additional', 'affiliation': []}], 'member': '31700', 'published-online': {'date-parts': [[2024, 3, 14]]}, 'reference': [ { 'key': 'ref0', 'unstructured': '1. World Health Organization. Coronavirus disease 2019 (COVID19): ' 'Situation report. 2020, 70.'}, { 'key': 'ref1', 'doi-asserted-by': 'publisher', 'unstructured': '2. Shaik A., and Atmakuri L.R.: Clinical trials status and approaches of ' 'COVID-19 vaccines developed globally: The Recent Updates. Pharma Times, ' '2022, 54(3), 7-14.', 'DOI': '10.13005/bpj/2214'}, { 'key': 'ref2', 'doi-asserted-by': 'publisher', 'unstructured': '3. Rouchka E.C., Chariker J.H. and Chung D.: Phylogenetic and variant ' 'analysis of 1,040 SARS-CoV-2 Genomes. 2020', 'DOI': '10.20944/preprints202005.0396.v1'}, { 'key': 'ref3', 'unstructured': '4. Lu R., Zhao X. and Li J.: Genomic characterization and epidemiology ' 'of 2019 novel coronavirus: implications for virus origins and receptor ' 'binding. Lancet, 2020, 395, 565-574.'}, { 'key': 'ref4', 'unstructured': '5. Jin Z., Du X. and Xu Y.: Structure of Mpro from COVID-19 virus and ' 'discovery of its inhibitors. bioRxiv. Preprint. 2020'}, { 'key': 'ref5', 'doi-asserted-by': 'publisher', 'unstructured': '6. Hui D.S., Azhar E.I. and Madani T.A.: The continuing 2019-nCoV ' 'epidemic threat of novel coronaviruses to global health - The latest ' '2019 novel coronavirus outbreak in Wuhan, China. Int. J. Infect. Dis., ' '2020, 91, 264-266.', 'DOI': '10.1016/j.ijid.2020.01.009'}, { 'key': 'ref6', 'doi-asserted-by': 'publisher', 'unstructured': '7. Moses T. and Goossens A.: Plants for human health: greening ' 'biotechnology and synthetic biology. J. Exp. Bot., 2017, 68, 4009-4011.', 'DOI': '10.1093/jxb/erx268'}, { 'key': 'ref7', 'doi-asserted-by': 'publisher', 'unstructured': '8. Schaal B.: Plants and people: our shared history and future. Plants ' 'People Planet, 2019, 1, 14-19.', 'DOI': '10.1002/ppp3.12'}, { 'key': 'ref8', 'doi-asserted-by': 'publisher', 'unstructured': '9. Jassim S.A.A. and Naji M. A.: Novel antiviral agents: a medicinal ' 'plant perspective. J. Appl. Microbiol., 2003, 95, 412-427.', 'DOI': '10.1046/j.1365-2672.2003.02026.x'}, { 'key': 'ref9', 'doi-asserted-by': 'publisher', 'unstructured': '10. Hussain W., Haleem K.S. and Khan I.: Medicinal plants: a repository ' 'of antiviral metabolites. Future Virol., 2017, 12, 299-308.', 'DOI': '10.2217/fvl-2016-0110'}, { 'key': 'ref10', 'doi-asserted-by': 'publisher', 'unstructured': '11. Shaik A., Atmakuri L.R. and Maram C.E.: In vivo antioxidant activity ' 'of different fractions of Indigofera barberi against paracetamol induced ' 'toxicity in rats. Turk. J. Pharm. Sci., 2020, 17(2), 136-140.', 'DOI': '10.4274/tjps.galenos.2018.30306'}, { 'key': 'ref11', 'doi-asserted-by': 'publisher', 'unstructured': '12. Chaudhuri S., Symons J.A. and Deval J.: Innovation and trends in the ' 'development and approval of antiviral medicines: 1987-2017 and beyond. ' 'Antivir. Res., 2018, 155, 76-88.', 'DOI': '10.1016/j.antiviral.2018.05.005'}, { 'key': 'ref12', 'doi-asserted-by': 'publisher', 'unstructured': '13. Sander T., Freyss J. and Von Korff M.: Datawarrior: an open-source ' 'program for chemistry aware data visualization and analysis. J. Chem. ' 'Inf. Model, 2015, 55, 460-473.', 'DOI': '10.1021/ci500588j'}, { 'key': 'ref13', 'doi-asserted-by': 'publisher', 'unstructured': '14. Sussman J.L., Lin D. and Jiang J.: Protein Data Bank (PDB): database ' 'of three-dimensional structural information of biological ' 'macromolecules. Acta Crystallogr. D Biol. Crystallogr., 1998, 54, ' '1078-1084.', 'DOI': '10.1107/S0907444998009378'}, { 'key': 'ref14', 'unstructured': '15. Aminabee S.K., Raveesha P., Adithya V., Mohansai M., Shaherbanu, ' 'Harshitha K., Himaja Kasthuri K., Lakshmi Priya M., Chandini Naga ' 'Mallika G. and Lakshmana Rao A.: In vivo antinociceptive activity and In ' 'silico molecular docking of selected phytoconstituents of methanolic ' 'extract of Hypericum japonicum. J. Drug Alcohol Res., 2022, 11(5), ' '01-08.'}, { 'key': 'ref15', 'doi-asserted-by': 'publisher', 'unstructured': '16. Kar P., Sharma N.R. and Singh B.: Natural compounds from ' 'Clerodendrum spp. as possible therapeutic candidates against SARS-CoV-2: ' 'An in silico investigation. J Biomol. Struct. Dyn., 2020, 1-12.', 'DOI': '10.1080/07391102.2020.1780947'}, { 'key': 'ref16', 'doi-asserted-by': 'publisher', 'unstructured': '17. Morris G.M., Huey R. and Lindstrom W.: Autodock4 and AutoDockTools4: ' 'Automated docking with selective receptor flexibility. J. Comput. Chem., ' '2009, 30, 2785-2791.', 'DOI': '10.1002/jcc.21256'}, { 'key': 'ref17', 'doi-asserted-by': 'publisher', 'unstructured': "18. O'Boyle N.M., Banck M. and James C.A. Open Babel: an open chemical " 'toolbox. J Cheminform., 2011, 3, 33.', 'DOI': '10.1186/1758-2946-3-33'}, { 'key': 'ref18', 'doi-asserted-by': 'publisher', 'unstructured': '19. Pangastuti A., Amin I. F. and Amin A.Z.: Natural bioactive compound ' 'from Moringa oleifera against cancer based on in silico screening. J. ' 'Teknol., 2016, 78, 315-318.', 'DOI': '10.11113/jt.v78.8328'}, { 'key': 'ref19', 'unstructured': '20. Prasanth D.S.N.B.K., Aminabee S.K., Lakshmana Rao A., Guntupalli ' 'Ch., Rajasekhar Reddy A., Umasankar K., Koteswara Rao S.N., Rajeshwari ' "P.: Inhibitory effects of Manosa alliacea in Freund's adjuvant arthritis " 'on inflammatory markers and its confirmation by In silico strategy. Thai ' 'J. Pharm. Sci., 2021, 45(6), 532-544.'}, { 'key': 'ref20', 'doi-asserted-by': 'publisher', 'unstructured': '21. Seeliger D. and De Groot B.L.: Ligand docking and binding site ' 'analysis with PyMOL and Autodock/Vina. J. Comput. Aided Mol. Des., 2010, ' '24, 417-422.', 'DOI': '10.1007/s10822-010-9352-6'}, { 'key': 'ref21', 'doi-asserted-by': 'publisher', 'unstructured': '22. Yang H., Lou C. and Sun L.: AdmetSAR 2.0: Web-service for prediction ' 'and optimization of chemical ADMET properties. Bioinformatics., 2019, ' '35, 1067-1069.', 'DOI': '10.1093/bioinformatics/bty707'}, { 'key': 'ref22', 'doi-asserted-by': 'publisher', 'unstructured': '23. Cheng F., Li W. and Zhou Y.: AdmetSAR: A comprehensive source and ' 'free tool for assessment of chemical ADMET properties. J. Chem. Inf. ' 'Model., 2012, 52, 3099-3105.', 'DOI': '10.1021/ci300367a'}, { 'key': 'ref23', 'doi-asserted-by': 'publisher', 'unstructured': '24. Khurana N., Ishar M.P.S. and Gajbhiye A.: PASS assisted prediction ' 'and pharmacological evaluation of novel nicotinic analogs for nootropic ' 'activity in mice. Eur. J. Pharmacol., 2011, 662, 22-30.', 'DOI': '10.1016/j.ejphar.2011.04.048'}, { 'key': 'ref24', 'doi-asserted-by': 'publisher', 'unstructured': '25. Mittal M., Goel R.K. and Bhargava G.: PASS-assisted exploration of ' 'antidepressant activity of 1,3,4-trisubstituted-β-lactam derivatives. ' 'Bioorg. Med. Chem. Lett., 2008, 18, 5347-5349.', 'DOI': '10.1016/j.bmcl.2008.09.064'}, { 'key': 'ref25', 'doi-asserted-by': 'publisher', 'unstructured': '26. Goel R.K., Singh D. and Lagunin A.: PASS-assisted exploration of new ' 'therapeutic potential of natural products. Med. Chem. Res., 2011, 20, ' '1509-1514.', 'DOI': '10.1007/s00044-010-9398-y'}, { 'key': 'ref26', 'doi-asserted-by': 'publisher', 'unstructured': '27. Van Der Spoel D., Lindahl E. and Hess B.: GROMACS: fast, flexible, ' 'and free. J. Comput. Chem., 2005, 26, 1701-1718.', 'DOI': '10.1002/jcc.20291'}, { 'key': 'ref27', 'doi-asserted-by': 'publisher', 'unstructured': '28. Gangadharappa B.S., Sharath R. and Revanasiddappa P.D.: Structural ' 'insights of metallo-beta-lactamase revealed an effective way of ' 'inhibition of enzyme by natural inhibitors. J. Biomol. Struct. Dyn., ' '2020, 38, 3757-3771.', 'DOI': '10.1080/07391102.2019.1667265'}, { 'key': 'ref28', 'doi-asserted-by': 'publisher', 'unstructured': '29. Chandramohan V., Kaphle A. and Chekuri M.: Evaluating ' 'andrographolide as a potent inhibitor of NS3-4A protease and its drug ' 'resistant mutants using in silico approaches. Adv. Virol., 2015, 15, ' '20-67.', 'DOI': '10.1155/2015/972067'}, { 'key': 'ref29', 'unstructured': '30. Prasanth D.S.N.B.K., Aminabee S.K., Lakshmana Rao A., Teja N., ' 'Bhargavi K., Monika Ch., Pujitha B., Sandhya T., Lalitha A. and Siva ' 'Prasad P.: Antihelmintic activity of Mansoa alliacea against Pheretima ' 'posthuma: In vitro and In silico approach. Thai J. Pharm. Sci., 2020, ' '44(3), 86-196.'}, { 'key': 'ref30', 'unstructured': '31. To K.K., Hung I.F. and Chan J.F.: From SARS coronavirus to novel ' 'animal and human coronaviruses. J. Thorac. Dis., 2013, 5(2), S103-S108.'}, { 'key': 'ref31', 'doi-asserted-by': 'publisher', 'unstructured': '32. Zhu N., Zhang D. and Wang W.: A novel coronavirus from patients with ' 'pneumonia in China, 2019. N. Engl. J. Med., 2020, 82, 727-733.', 'DOI': '10.1056/NEJMoa2001017'}, { 'key': 'ref32', 'doi-asserted-by': 'publisher', 'unstructured': '33. Zhou Y., Hou Y. and Shen J.: Network-based drug repurposing for ' 'novel coronavirus 2019-nCoV/SARS-CoV-2. Cell Discov., 2020, 6, 14.', 'DOI': '10.1038/s41421-020-0153-3'}, { 'key': 'ref33', 'doi-asserted-by': 'publisher', 'unstructured': '34. Lin L.T., Hsu W.C. and Lin C.C.: Antiviral natural products and ' 'herbal medicines. J. Tradit. Complement. Med., 2014, 4, 24-35.', 'DOI': '10.4103/2225-4110.124335'}, { 'key': 'ref34', 'doi-asserted-by': 'publisher', 'unstructured': '35. Martinez J.P., Sasse F. and Bronstrup M.: Antiviral drug discovery: ' 'broad-spectrum drugs from nature. Nat. Prod. Rep., 2015, 32, 29-48.', 'DOI': '10.1039/C4NP00085D'}], 'container-title': 'INDIAN DRUGS', 'original-title': [], 'link': [ { 'URL': 'https://www.indiandrugsonline.org//download/February_2024_61_2_78-91.pdf', 'content-type': 'unspecified', 'content-version': 'vor', 'intended-application': 'similarity-checking'}], 'deposited': { 'date-parts': [[2024, 3, 20]], 'date-time': '2024-03-20T10:59:47Z', 'timestamp': 1710932387000}, 'score': 1, 'resource': {'primary': {'URL': 'https://www.indiandrugsonline.org/issuesarticle-details?id=MTU0Nw=='}}, 'subtitle': [], 'short-title': [], 'issued': {'date-parts': [[2024, 2, 28]]}, 'references-count': 35, 'journal-issue': { 'issue': '02', 'published-online': {'date-parts': [[2024, 3, 14]]}, 'published-print': {'date-parts': [[2024, 2, 28]]}}, 'URL': 'http://dx.doi.org/10.53879/id.61.02.13859', 'relation': {}, 'ISSN': ['0019-462X'], 'subject': ['Drug Discovery', 'Pharmaceutical Science', 'Pharmacology'], 'container-title-short': 'IND. 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