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A Molecular Docking Approach to Evaluate the Pharmacological Properties of 1-(4-amino-1,2,5-oxadiazol-3-yl)-N'-(1-(3-hydroxyphenyl)vinyl)-5-(thiophen-2-yl)1H-1,2,3-triazole-4-carbohydrazide Treatment Candidate for Use against COVID-19

Year 2022, , 27 - 31, 30.12.2022
https://doi.org/10.51539/biotech.1110858

Abstract

In recent years, the new coronavirus known as COVID-19 has recently caused a pandemic that has caused serious health problems. Currently, the virus is spreading rapidly all over the world , and finding potential antiviral drugs that can inhibit virus proteins is crucial. Recently, CoVID-19 crystal structure elucidated such as major protease Mpro (PDB: 6LU7), SARS-CoV- main peptidase (2GTB), human ACE2 (PDB: 1O86), human coronavirus papain-like proteases (PDB: 4OW0) SARS-Coronavirus NSP12 protein (PDB: 6NUR), COVID-19 main protease (PDB:6lu7) . These proteins are important for replication of virus , so they are potential targets for CoVID-19 drugs.
In this study, we used the molecular docking models to study the binding interactions between anodyne called 1-(4-amino-1,2,5-oxadiazol-3-yl)-N'-(1-(3-hydroxyphenyl)vinyl)-5-(thiophen-2-yl)-1H-1,2,3-triazole-4-carbohydrazide(Zinc ID 000002613203) using MOE 2015.10.
It has been observed Obtained results by molecular docking showed that a stronger bond and high affinity with 4OW0 -8.1949, 6lu7 -7.7925, 1O86-7.5757, -6.7832 -7.4101, 2GTB -7.2510 kcal/mol)
Based on the binding energy score, these compound are suitable for testing against Coronavirus and could be considered potential inhibitors COVID-19 infection.)

References

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  • Gautret P, Lagier J, Honoré S, Hoang V, Colson P, Raoult D(2021) Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an open label non-randomized clinical trial revisited. Int J Antimicrob Agents 57(1), p.106243.
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  • Gioia D, Bertazzo M, Recanatini M, Masetti M, Cavalli A (2017) Dynamic Docking: A Paradigm Shift in Computational Drug Discovery. Molecules 22(11), p.2029.
  • Holshue M, DeBolt C, Lindquist S, Lofy K, Wiesman J, Bruce H, Spitters C, Ericson K, Wilkerson S, Tural A, DiazG, Cohn A, Fox L, Patel A, Gerber S, Kim L, Tong S, Lu X, Lindstrom S, Pallansch M, Weldon W, Biggs H, Uyeki T, Pillai S ( 2020) First Case of 2019 Novel Coronavirus in the United States. N Eng J Med 382(10), pp.929-936.
  • Jorgensen W (2004) The Many Roles of Computation in Drug Discovery. Science 303(5665), pp.1813-1818.
  • Khan W, Ashfaq UA, Aslam S, Saif S, Aslam T, Tusleem K, Maryam A, Tahir Ul (2017) Anticancer screening of medicinal plant phytochemicals against Cyclin-Dependent Kinase-2 (CDK2): An in-silico approach. ALS www.als-journal.com (Vol. 4). www.als-journal.com
  • Kitchen D, Decornez H, Furr J, Bajorath J (2004) Docking and scoring in virtual screening for drug discovery: methods and applications. Nat Rev Drug Discov 3(11), pp.935-949
  • Kumar S, Sharma PP, Shankar U, Kumar D, Joshi SK, Pena L, Durvasula R, Kumar A, Kempaiah P, Poonam, Rathi B (2020) Discovery of New Hydroxyethylamine Analogs against 3CLproProtein Target of SARS-CoV-2: Molecular Docking, Molecular Dynamics Simulation, and Structure-Activity Relationship Studies. J Chem Inf Model 60(12), 5754–5770. doi:10.1021/ACS.JCIM.0C00326
  • Kuntz I, Blaney J, Oatley S, Langridge R,Ferrin T (1982)A geometric approach to macromolecule-ligand interactions. J Mol Biol 161(2), pp.269-288.
  • Lengauer T, Rarey M (1996) Computational methods for biomolecular docking. Curr Opin Struct Biol 6(3), pp.402-406.
  • Pires DE, Blundell TL, Ascher DB (2015) pkCSM: Predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. J Med Chem 58(9), 4066–4072. doi:10.1021/acs.jmedchem.5b00104
  • Serafim M, Gertrudes J, Costa D, Oliveira P, MaltarolloV, Honorio K ( 2021) Knowing and combating the enemy: a brief review on SARS-CoV-2 and computational approaches applied to the discovery of drug candidates. Biosci Rep 41(3)
  • Song C, Lim S, Tong J ( 2009) Recent advances in computer-aided drug design. Brief Bioinform 10(5), pp.579-591
  • Yao X, Ye F, Zhang M, Cui C, Huang B, Niu P, Liu X, Zhao L, Dong E, Song, C, Zhan S, Lu R, Li H, Tan W, Liu D (2020) In Vitro Antiviral Activity and Projection of Optimized Dosing Design of Hydroxychloroquine for the Treatment of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Clin Infect Dis 71(15), pp.732-739
  • Zhong F, Xing J, Li X, Liu X, Fu Z, Xiong Z, Lu D, Wu X, Zhao J, Tan X, Li F, Luo X, Li Z, Chen K, Zheng M. , Jiang H (2018) Artificial intelligence in drug design. Sci China Life Sci 61(10), pp.1191-1204
Year 2022, , 27 - 31, 30.12.2022
https://doi.org/10.51539/biotech.1110858

Abstract

References

  • References Adebambo K (2020) Computational Investigation of the Interaction of Anti-Influenza Drugs with CoVID-19 Protein. CMB 10(02), pp.45-60.
  • Amin M, Abbas G (2020) Docking study of chloroquine and hydroxychloroquine interaction with RNA binding domain of nucleocapsid phospho-protein–an in silico insight into the comparative efficacy of repurposing antiviral drugs. J Biomol Struct Dyn 1–13. doi:10.1080/07391102.2020.1775703
  • Covid19.who.int. (2022) WHO Coronavirus (COVID-19) Dashboard. [online] Available at. https://covid19.who.int .Accessed 21 March 2022
  • Cao B, WangY, Wen D, Liu W, Wang J, Fan G, Ruan L, Song B, Cai Y, Wei M, Li X, Xia J, Chen N, Xiang J, Yu T, Bai T, Xie X, Zhang L, Li C, Yuan Y, Chen H, Li H, Huang H, Tu S, Gong F, Liu Y, Wei Y, Dong C, Zhou F (2020) A Trial of Lopinavir–Ritonavir in Adults Hospitalized with Severe Covid-19. N Engl J Med 382(19), pp.1787-1799
  • Daina A, Michielin O,Zoete V( 2017) SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep7(1).
  • DiMasi J, Grabowski H, Hansen R (2016) Innovation in the pharmaceutical industry: New estimates of R&D costs. J Health Econ, 47, pp.20-33.
  • Gautret P, Lagier J, Honoré S, Hoang V, Colson P, Raoult D(2021) Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an open label non-randomized clinical trial revisited. Int J Antimicrob Agents 57(1), p.106243.
  • Gurung A, Ali M, Lee J, Farah M , Al-Anazi K ( 2021) An Updated Review of Computer-Aided Drug Design and Its Application to COVID-19. BioMed Res Int 2021, pp.1-18.
  • Gioia D, Bertazzo M, Recanatini M, Masetti M, Cavalli A (2017) Dynamic Docking: A Paradigm Shift in Computational Drug Discovery. Molecules 22(11), p.2029.
  • Holshue M, DeBolt C, Lindquist S, Lofy K, Wiesman J, Bruce H, Spitters C, Ericson K, Wilkerson S, Tural A, DiazG, Cohn A, Fox L, Patel A, Gerber S, Kim L, Tong S, Lu X, Lindstrom S, Pallansch M, Weldon W, Biggs H, Uyeki T, Pillai S ( 2020) First Case of 2019 Novel Coronavirus in the United States. N Eng J Med 382(10), pp.929-936.
  • Jorgensen W (2004) The Many Roles of Computation in Drug Discovery. Science 303(5665), pp.1813-1818.
  • Khan W, Ashfaq UA, Aslam S, Saif S, Aslam T, Tusleem K, Maryam A, Tahir Ul (2017) Anticancer screening of medicinal plant phytochemicals against Cyclin-Dependent Kinase-2 (CDK2): An in-silico approach. ALS www.als-journal.com (Vol. 4). www.als-journal.com
  • Kitchen D, Decornez H, Furr J, Bajorath J (2004) Docking and scoring in virtual screening for drug discovery: methods and applications. Nat Rev Drug Discov 3(11), pp.935-949
  • Kumar S, Sharma PP, Shankar U, Kumar D, Joshi SK, Pena L, Durvasula R, Kumar A, Kempaiah P, Poonam, Rathi B (2020) Discovery of New Hydroxyethylamine Analogs against 3CLproProtein Target of SARS-CoV-2: Molecular Docking, Molecular Dynamics Simulation, and Structure-Activity Relationship Studies. J Chem Inf Model 60(12), 5754–5770. doi:10.1021/ACS.JCIM.0C00326
  • Kuntz I, Blaney J, Oatley S, Langridge R,Ferrin T (1982)A geometric approach to macromolecule-ligand interactions. J Mol Biol 161(2), pp.269-288.
  • Lengauer T, Rarey M (1996) Computational methods for biomolecular docking. Curr Opin Struct Biol 6(3), pp.402-406.
  • Pires DE, Blundell TL, Ascher DB (2015) pkCSM: Predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. J Med Chem 58(9), 4066–4072. doi:10.1021/acs.jmedchem.5b00104
  • Serafim M, Gertrudes J, Costa D, Oliveira P, MaltarolloV, Honorio K ( 2021) Knowing and combating the enemy: a brief review on SARS-CoV-2 and computational approaches applied to the discovery of drug candidates. Biosci Rep 41(3)
  • Song C, Lim S, Tong J ( 2009) Recent advances in computer-aided drug design. Brief Bioinform 10(5), pp.579-591
  • Yao X, Ye F, Zhang M, Cui C, Huang B, Niu P, Liu X, Zhao L, Dong E, Song, C, Zhan S, Lu R, Li H, Tan W, Liu D (2020) In Vitro Antiviral Activity and Projection of Optimized Dosing Design of Hydroxychloroquine for the Treatment of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Clin Infect Dis 71(15), pp.732-739
  • Zhong F, Xing J, Li X, Liu X, Fu Z, Xiong Z, Lu D, Wu X, Zhao J, Tan X, Li F, Luo X, Li Z, Chen K, Zheng M. , Jiang H (2018) Artificial intelligence in drug design. Sci China Life Sci 61(10), pp.1191-1204
There are 21 citations in total.

Details

Primary Language English
Subjects Pharmacology and Pharmaceutical Sciences
Journal Section Research Articles
Authors

Mohamed Alamin Mohammed Ahmed

Publication Date December 30, 2022
Acceptance Date December 21, 2022
Published in Issue Year 2022

Cite

APA Alamin Mohammed Ahmed, M. (2022). A Molecular Docking Approach to Evaluate the Pharmacological Properties of 1-(4-amino-1,2,5-oxadiazol-3-yl)-N’-(1-(3-hydroxyphenyl)vinyl)-5-(thiophen-2-yl)1H-1,2,3-triazole-4-carbohydrazide Treatment Candidate for Use against COVID-19. Bulletin of Biotechnology, 3(2), 27-31. https://doi.org/10.51539/biotech.1110858
AMA Alamin Mohammed Ahmed M. A Molecular Docking Approach to Evaluate the Pharmacological Properties of 1-(4-amino-1,2,5-oxadiazol-3-yl)-N’-(1-(3-hydroxyphenyl)vinyl)-5-(thiophen-2-yl)1H-1,2,3-triazole-4-carbohydrazide Treatment Candidate for Use against COVID-19. Bull. Biotechnol. December 2022;3(2):27-31. doi:10.51539/biotech.1110858
Chicago Alamin Mohammed Ahmed, Mohamed. “A Molecular Docking Approach to Evaluate the Pharmacological Properties of 1-(4-Amino-1,2,5-Oxadiazol-3-Yl)-N’-(1-(3-hydroxyphenyl)vinyl)-5-(thiophen-2-yl)1H-1,2,3-Triazole-4-Carbohydrazide Treatment Candidate for Use Against COVID-19”. Bulletin of Biotechnology 3, no. 2 (December 2022): 27-31. https://doi.org/10.51539/biotech.1110858.
EndNote Alamin Mohammed Ahmed M (December 1, 2022) A Molecular Docking Approach to Evaluate the Pharmacological Properties of 1-(4-amino-1,2,5-oxadiazol-3-yl)-N’-(1-(3-hydroxyphenyl)vinyl)-5-(thiophen-2-yl)1H-1,2,3-triazole-4-carbohydrazide Treatment Candidate for Use against COVID-19. Bulletin of Biotechnology 3 2 27–31.
IEEE M. Alamin Mohammed Ahmed, “A Molecular Docking Approach to Evaluate the Pharmacological Properties of 1-(4-amino-1,2,5-oxadiazol-3-yl)-N’-(1-(3-hydroxyphenyl)vinyl)-5-(thiophen-2-yl)1H-1,2,3-triazole-4-carbohydrazide Treatment Candidate for Use against COVID-19”, Bull. Biotechnol., vol. 3, no. 2, pp. 27–31, 2022, doi: 10.51539/biotech.1110858.
ISNAD Alamin Mohammed Ahmed, Mohamed. “A Molecular Docking Approach to Evaluate the Pharmacological Properties of 1-(4-Amino-1,2,5-Oxadiazol-3-Yl)-N’-(1-(3-hydroxyphenyl)vinyl)-5-(thiophen-2-yl)1H-1,2,3-Triazole-4-Carbohydrazide Treatment Candidate for Use Against COVID-19”. Bulletin of Biotechnology 3/2 (December 2022), 27-31. https://doi.org/10.51539/biotech.1110858.
JAMA Alamin Mohammed Ahmed M. A Molecular Docking Approach to Evaluate the Pharmacological Properties of 1-(4-amino-1,2,5-oxadiazol-3-yl)-N’-(1-(3-hydroxyphenyl)vinyl)-5-(thiophen-2-yl)1H-1,2,3-triazole-4-carbohydrazide Treatment Candidate for Use against COVID-19. Bull. Biotechnol. 2022;3:27–31.
MLA Alamin Mohammed Ahmed, Mohamed. “A Molecular Docking Approach to Evaluate the Pharmacological Properties of 1-(4-Amino-1,2,5-Oxadiazol-3-Yl)-N’-(1-(3-hydroxyphenyl)vinyl)-5-(thiophen-2-yl)1H-1,2,3-Triazole-4-Carbohydrazide Treatment Candidate for Use Against COVID-19”. Bulletin of Biotechnology, vol. 3, no. 2, 2022, pp. 27-31, doi:10.51539/biotech.1110858.
Vancouver Alamin Mohammed Ahmed M. A Molecular Docking Approach to Evaluate the Pharmacological Properties of 1-(4-amino-1,2,5-oxadiazol-3-yl)-N’-(1-(3-hydroxyphenyl)vinyl)-5-(thiophen-2-yl)1H-1,2,3-triazole-4-carbohydrazide Treatment Candidate for Use against COVID-19. Bull. Biotechnol. 2022;3(2):27-31.