اخبار و اعلانات

 آمار

تعداد نشریات24
تعداد شماره‌ها924
تعداد مقالات8,295
تعداد مشاهده مقاله16,558,733
تعداد دریافت فایل اصل مقاله13,968,705
Singh, Pushpendra, Tripathi, Manish, Yasir, Mohammad, Khare, Ruchi, Shrivastava, Rahul. (1400). In silico identification of promising inhibitor against RNA-dependent RNA polymerase target of SARS-CoV-2. , 10(3), 131-140. doi: 10.22099/mbrc.2021.40367.1621
Pushpendra Singh; Manish Kumar Tripathi; Mohammad Yasir; Ruchi Khare; Rahul Shrivastava. "In silico identification of promising inhibitor against RNA-dependent RNA polymerase target of SARS-CoV-2". , 10, 3, 1400, 131-140. doi: 10.22099/mbrc.2021.40367.1621
Singh, Pushpendra, Tripathi, Manish, Yasir, Mohammad, Khare, Ruchi, Shrivastava, Rahul. (1400). 'In silico identification of promising inhibitor against RNA-dependent RNA polymerase target of SARS-CoV-2', , 10(3), pp. 131-140. doi: 10.22099/mbrc.2021.40367.1621
Singh, Pushpendra, Tripathi, Manish, Yasir, Mohammad, Khare, Ruchi, Shrivastava, Rahul. In silico identification of promising inhibitor against RNA-dependent RNA polymerase target of SARS-CoV-2. , 1400; 10(3): 131-140. doi: 10.22099/mbrc.2021.40367.1621

In silico identification of promising inhibitor against RNA-dependent RNA polymerase target of SARS-CoV-2

Molecular Biology Research Communications
دوره 10، شماره 3، 2021، صفحه 131-140    اصل مقاله (695.36 K)
نوع مقاله: Original article
شناسه دیجیتال (DOI): 10.22099/mbrc.2021.40367.1621
نویسندگان
Pushpendra Singh1؛ Manish Kumar Tripathi2؛ Mohammad Yasir3؛ Ruchi Khare4؛ Rahul Shrivastava* 4
1State Virus Research and Diagnostic Laboratory, Department of Microbiology, All India Institute of Medical Sciences, Raipur, Chhattisgarh-492099 India
2Department of Biophysics, All India Institute of Medical Sciences, New Delhi-110029, India
3Department of Nephrology, All India Institute of Medical Science Bhopal, Madhya Pradesh-462020 India
4Department of Biological Science and Engineering, Maulana Azad National Institute of Technology, Bhopal, Madhya Pradesh-462003 India
چکیده
The severe acute respiratory syndrome is a viral respiratory disease recognised as COVID-19, caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Formerly, no precise remedies are available, and many studies regarding COVID-19 prevention and treatment are under development. Several targets for the design of drugs are identified, and studies are in headway to explore the potential target. RNA-dependent RNA polymerase (RdRp) protein identified as a promising target against SARS-CoV-2 infection for the drug design due to its significant role in viral replication. The present study focuses on identifying the binding effect of previously known RdRp inhibitors with RdRp of SARS-CoV-2 using molecular docking and molecular dynamics simulation approaches. Molecular docking and binding free energy calculations against RdRp enzyme identified suramin as a potential compound that showed the highest docking score of -7.83 Kcal/mole and binding energy of -80.83 Kcal/mole as a comparison to other compounds. Further, molecular dynamics simulation studies were moreover showed the stable binding behaviour of suramin docked complex in the protein active site. Thus, the study concludes that suramin might be helpful as a potential inhibitor against RNA-dependent RNA polymerase of SRAS-CoV-2. However, further investigation is needed to assess the possible effect of inhibitors on RdRp through in vitro and in vivo experiments.
کلیدواژه‌ها
SARS-CoV-2؛ COVID-19؛ RNA-dependent RNA polymerase (RdRp)؛ In silico؛ Molecular Docking
سایر فایل های مرتبط با مقاله
مراجع
  1. WHO. Novel Coronavirus (2019-nCoV) Sitution Report 22. http://www.who.int/docs/default-source/coronaviruse/situation-reports/20200211-sitrep-22ncov.pdf?sfvrsn=fb6d49b12.2020. (accessed on: Jan 4,2021).
  2. Lai CC, Shih TP, Ko WC, Tang HJ, Hsueh PR. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): The epidemic and the challenges. Int J Antimicrob Agents 2020;55:105924.
  3. Hui DSC, Chan MCH, Wu AK, Ng PC. Severe acute respiratory syndrome (SARS): epidemiology and clinical features. Postgrad Med J 2004;80:373-381.
  4. Wu C, Liu Y, Yang Y, Zhang P, Zhong W, Wang Y, Wang Q, Xu Y, Li M, Li  X, Zheng  M, Chen L, Li H. Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods. Acta Pharm Sin B  2020;10:766-788
  5. WHO. Weekly epidemiological update on COVID-19-6 April 2021. https://www.who.int/publications/m/item/weekly-epidemiological-update-on-covid-19---6- april-2021. (accessed on: April 10, 2021).
  6. Chan JFW, Yuan S, Kok KH, To KKW, Chu H, Yang J, Xiang F, Liu J, Yip C, Shan-Poon RW, Tsoi HW, Kam-Fai Lo S, Chan KH, Poon VKM, Chan WM, Daniel J, Cai JP, Chung-Cheng VC, Chen H, Ming-Hui CK, Yuen, KY. A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster. Lancet 2020;395:514-523.
  7. WHO. Coronavirus disease 2019 (COVID-19) Situation Report–73. https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200402-sitrep- 73-covid-19.pdf?sfvrsn=5ae25bc7_2. 2020. (accessed on: March 14, 2021)
  8. Kimball A, Hatfield K, Arons M, James A, Taylor J, Spicer K, Bardossy AC, Oakley LP, Tanwar S, Chisty Z, Bell JM, Methner M, Harney J, Jacobs JR, Carlson CM, Mclaughlin HP, Stone N, Clark S, Smith CB, Page LC, Kay M, Lewis J, Russell D, Hiatt B, Gant J, Duchin JS, Clark TA, Honein MA, Reddy SC, Jernigan JA, Baer A, Barnard L, Benoliel E, Fagalde MS, Ferro J, Smith HG, Gonzales E, Hatley N, Hatt G, Hope M, Frazier MH, Kawakami V, Lenahan JL, Lukoff MD, Mier EB, Mckeiranan S, Montgomery P, Morgan JL. Mummert LA, Pogosjanse S, Riedo F, Schwarcz L, Smith D, Stearns S, Sykes KJ, Whitney H, Ali H, Banks M, Balajee A, Chow E, Cooper B, Currie D, Dyal J, Healy J, Hughes M, Mcmichael T, Nolen L, Olson C, Rao A, Schmit K, Schwartz N, Tobolowsky F, Zacks R, Zane SB. Asymptomatic and presymptomatic SARS-CoV-2 infections in residents of a long-term care skilled nursing facility- King County, Washington, March 2020. MMWR Morb Mortal Wkly Rep 2020;69.
  9. Rothe C, Schunk M, Sothmann P, Bretzel G, Froeschl G, Wallrauch C, Zimmer T, Thiel V, Janke C, Guggemos W, Seilmaier M, Drosten C, Vollmar P, Zwirglmaier K, Zange S, Wolfel R, Hoelscher M. Transmission of 2019-nCoV infection from an asymptomatic contact in Germany. N Engl J Med 2020;382:970-971.
  10. Fehr AR, Perlman S. Coronaviruses: an overview of their replication and pathogenesis. Methods Mol Biol 2015;1282:1-23.
  11. Zumla A, Chan JFW, Azhar EI, Hui DSC, Yuen KY. Coronaviruses - drug discovery and therapeutic options. Nat Rev Drug Discov 2016;15:327-347.
  12. Bárcena M, Oostergetel GT, Bartelink W, Faas FGA, Verkleij A, Rottier PJM, Koster AJ, Bosch BJ. Cryo-electron tomography of mouse hepatitis virus: Insights into the structure of the coronavirion. Proc Natl Acad Sci U S A 2009;106:582-587.
  13. Clarke IN, Lambden PR. Organization and expression of calicivirus genes. J Infect Dis. 2000;181 Suppl:S309-316.
  14. Singh P, Tripathi MK, Yasir M, Khare R, Tripathi MK, Shrivastava R. Potential inhibitors for SARS-CoV-2 and functional food components as nutritional supplement for COVID-19: A review. Plant Foods Hum Nutr 2020;75:458-466.
  15. de Groot RJ, Luytjes W, Horzinek MC, van der Zeijst BAM, Spaan WJM, Lenstra JA. Evidence for a coiled-coil structure in the spike proteins of coronaviruses. J Mol Biol 1987; 196:963-966.
  16. Bosch BJ, Zee RVD, Haan CAM, Rottier PJM. The coronavirus spike protein is a class I virus fusion protein: structural and functional characterization of the fusion core complex. J Virol 2003;77:8801-8811.
  17. Tripathi MK, Singh P, Sharma S, Singh TP, Ethayathulla AS, Kaur P. Identification of bioactive molecule from Withania somnifera (Ashwagandha) as SARS-CoV-2 main protease inhibitor. J Biomol Struct Dyn 2020;1-14.
  18. Singh P, Tripathi KM, Shrivastava R. In silico identification of linear B-cell epitope in Coronavirus 2019 (SARS-CoV-2) surface glycoprotein: a prospective towards peptide vaccine. Minerva Biotechnol Biomol Res 2021;33:29-65.
  19. Neuman BW, Kiss G, Kunding AH, Bhella D, Baksh MF, Connelly S, Droese B, Klaus JP, Makino S, Sawicki SG, Siddell SG, Stamou DG, Wilson IA, Kuhn P, Buchmeier MJ. A structural analysis of M protein in coronavirus assembly and morphology. J Struct Biol 2011;174:11-22.
  20. Nieto-Torres JL, DeDiego ML, Verdiá-Báguena C, Jimenez-Guardeño JM, Regla-Nava JA, Fernandez-Delgado R, Castano-Rodriguez C, Alcaraz A, Torres J, Aguilella VM, Enjuanes L. Severe acute respiratory syndrome coronavirus envelope protein ion channel activity promotes virus fitness and pathogenesis. PLoS Pathog 2014;10:e1004077.
  21. Chang C, Sue SC, Yu T, Hsieh CM, Tsai CK, Chiang YC, Lee SJ, Hsiao HH, Wu WJ, Chang WL, Lin CH, Huang TH. Modular organization of SARS coronavirus nucleocapsid protein. J Biomed Sci 2006;13:59-72.
  22. Deval J, Jin Z, Chuang YC, Kao CC. Structure(s), function(s), and inhibition of the RNA-dependent RNA polymerase of noroviruses. Virus Res 2017;234:21-33.
  23. Subissi L, Posthuma CC, Collet A, Zevenhoven-Dobbe JC, Gorbalenya AE, Decroly E, Snijder EJ, Canard B, Imbert I. One severe acute respiratory syndrome coronavirus protein complex integrates processive RNA polymerase and exonuclease activities. Proc Natl Acad Sci USA 2014;111:E3900-3909.
  24. Ju J, Li X, Kumar S, Jockusch S, Chien M, Tao C, Morozova I, Kalachikov S, Kirchdoerfer RN, Russo JJ. Nucleotide analogues as inhibitors of SARS-CoV polymerase. Pharmacol Res Perspect 2020;8:e00674
  25. Xue X, Yu H, Yang H, Xue F, Wu Z, Shen W, Li J, Zhou Z, Ding Y, Zhao Q, Zhang XC, Liao M, Bartlam M, Rao Z. Structures of two coronavirus main proteases: implications for substrate binding and antiviral drug design. J Virol 2008;82:2515-2527.
  26. Wang M, Cao R, Zhang L, Yang X, Liu J, Xu M, Shi Z, Hu Z, Zhong W, Xiao G. Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Res 2020;30:269-271.
  27. Wu YS, Lin WH, Hsu JTA, Hsieh HP. Antiviral drug discovery against SARS-CoV. Curr Med Chem 2006;13:2003-2020.
  28. Schrödinger. Release 2018-2: LigPrep, Schrödinger, LLC, New York, NY, USA. 2018.
  29. Gao Y, Yan L, Huang Y, Liu F, Zhao Y, Cao L, Wang T, Sun Q, Ming Z, Zhasng L, Ge J, Zheng L, Zhang Y, Wang H, Zhu Y, Zhu C, Hu T, Hua T, Zhang B, Yang X, Li J, Yang H, Liu Z, Xu W, Guddat LW, Wang Q, Lou Z, Rao Z. Structure of the RNA-dependent RNA polymerase from COVID-19 virus. Science 2020;15:779-782.
  30. Jorgensen WL, Maxwell DS, Tirado-Rives J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 1996;118:11225-11236.
  31. Schrödinger. Release 2018-2: Sitemap, Schrödinger, LLC, New York, NY, USA. 2018.
  32. Jacobson MP, Pincus DL, Rapp CS, Day TJF, Honig B, Shaw DE, Friesner RA. A hierarchical approach to all-atom protein loop prediction. Proteins 2004;55:351-367.
  33. Bowers KJ, Chow DE, Xu H, Dror RO, Eastwood MP, Gregersen BA, Klepeis JL, Kolossvary I, Moraes MA, Sacerdoti FD, Salmon JK, Shan Y, Shaw DE. Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters. SC’06 Proc 2006 ACM/IEEE Conf Supercomput 2006.p.43.
  34. Kaczor AA, Targowska-Duda KM, Patel JZ, Laitinen T, Parkkari T, Adams Y, Nevalainen TJ, Poso A. Comparative molecular field analysis and molecular dynamics studies of α/β hydrolase domain containing 6 (ABHD6) inhibitors. J Mol Model 2015;21:250.
  35. Li H, Liu SM, Yu XH, Tang SL, Tang CK. Coronavirus disease 2019 (COVID-19): current status and future perspectives. Int J Antimicrob Agents 2020;105951.
  36. Saini S, Saini A, Thakur CJ, Kumar V, Gupta RD, Sharma JK. Genome-wide computational prediction of miRNAs in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) revealed target genes involved in pulmonary vasculature and antiviral innate immunity. Mol Biol Res Commun 2020;9:83–91.
  37. Halpin DMG, Faner R, Sibila O, Badia JR, Agusti A. Do chronic respiratory diseases or their treatment affect the risk of SARS-CoV-2 infection? Lancet Respir Med 2020;8:436-438.
  38. Elfiky AA. Anti-HCV, nucleotide inhibitors, repurposing against COVID-19. Life Sci 2020; 248:117477.
  39. Tripathi MK, Yasir M, Singh P, Shrivastava R. A comparative study to explore the effect of different compounds in immune proteins of human beings against tuberculosis: Insight from docking and molecular dynamics studies. Curr Bioinform 2020;15:155-164.
  40. Shrivastava R, Yasir M, Tripathi M, Singh P. In silico interaction of methyl isocyanate with immune protein responsible for Mycobacterium tuberculosis infection using molecular docking. Toxicol Ind Health 2016;32:162-167.
  41. Halgren TA. Identifying and characterizing binding sites and assessing druggability. J Chem Inf Model 2009;49:377-389.
  42. Tripathi MK, Sharma S, Singh T, Ethayathulla AS, Kaur P. Computational intelligence in drug repurposing for COVID-19. Comput intell methods COVID-19 surveillance. Prev Predict Diagnosis Stud Comput Intell 2021;273-294.
  43. Davies M, Osborne V, Lane S, Roy D, Dhanda S, Evans A, Shakir S. Remdesivir in treatment of COVID-19: A systematic benefit-risk assessment. Drug Saf 2020;43:645-56.
آمار
تعداد مشاهده مقاله: 2,692
تعداد دریافت فایل اصل مقاله: 1,771


سامانه مدیریت نشریات علمی. قدرت گرفته از سیناوب