Docking Based Identification of Bioactive Diosmin as Potential Multi-Targeted Anti SARS-Cov-2 Agent

Indentification of Diosmin as Potential Anti COVID-19 Agent

Authors

  • Debadash Panigrahi College of Pharmaceutical Sciences
  • Basant Kumar Behera College of Pharmaceutical Sciences
  • Susanta Kumar Sahu Utkal University

DOI:

https://doi.org/10.29356/jmcs.v66i3.1683

Keywords:

Diosmin, flavonoid, molecular docking, ADMET, SARS- CoV-2

Abstract

Abstract. The pandemic COVID-19, caused by the organism severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) belongs to the family Coronoviridae has become a serious global healthcare crisis.   The biggest demand of the present time is to develop efficacious medication for the treatment of SARS-CoV-2. In the present study, we performed the interaction of 50 flavonoids selected from the Pubchem database, with five efficacious protein targets for SARS-CoV-2: main protease (Mpro), spike glycoprotein-receptor binding domain (SGp-RBD), RNA-dependent RNA polymerase (RdRp), angiotensin converting enzyme-2 (ACE-2) and non-structural protein15 (NSP15, an endonuclease). All the work involve in the present study was accomplished by using Maestro 12.4 (Schrodinger Suite) to obtain the docking scores and ADME-T study result of selected ligands with the five effective target proteins of SARS-CoV-2. Molecular docking-based results indicated that diosmin has the most favorable docking scores -10.16, -11.52, -9.75, -11.25 and -10.25 kcal/mol for the Mpro, SGp-RBD, ACE-2, RdRp and NSP-15 protein targets and had acceptable drug suitability as a therapeutic agent against COVID-19. The structure of this compound can be further useful to medicinal chemists, pharmacologists, and clinicians for efficiently discovering or developing effective drugs to cure COVID-19.

Author Biographies

Debadash Panigrahi, College of Pharmaceutical Sciences

Drug Research Laboratory, Nodal Research Centre

Basant Kumar Behera, College of Pharmaceutical Sciences

Drug Research Laboratory, Nodal Research Centre

Susanta Kumar Sahu, Utkal University

Dept. of Pharmacy

References

Amawi, H.; Abu Deiab, G.a.I.; AAljabali, A. A.; Dua, K.; Tambuwala. M. M. Ther. Delivery. 2020, 11, 245-268. DOI: 10.4155/tde-2020-0035.

Azhar, E. I.; Hui, D. S. C.; Memish, Z. A.; Drosten, C.; Zumla, A. Infect. Dis. Clin. North Am. 2019, 33, 891-905. DOI: 10.1016/j.idc.2019.08.001.

Li, H.; Liu S. M.; Yu, X.H.; Tang S. L.; Tang, C. K. Int. J. Antimicrob Agents. 2020, 55, 105951-105951. DOI: 10.1016/j.ijantimicag.2020.105951.

Lu, R.; Zhao, X.; Li J.; Niu, P.; Yang, B.; Wu, H.; Wang, W.; Song, H.; Huang, B.; Zhu, N. The Lancet. 2020, 395, 565-574. DOI: 10.1016/S0140-6736(20)30251-8.

Wu, F.; Zhao, S.; Yu, B.; Chen, Y. M.; Wang, W.; Song, Z. G.; Hu, Y.; Tao, Z. W.; Tian, J. H.; Pei, Y. Y. Nature. 2020, 579, 265-269. DOI: doi.org/10.1038/s41586-020-2008-3.

Pan, C.; Chen, L.; Lu, C.; Zhang, W.; Xia, J. A.; Sklar, M.C.; Du, B.; Brochard, L.; Qiu, H. Am. J. Respir. Crit. Care Med. 2020, 20, 1294-1297. DOI: 10.1164/rccm.202003-0527LE.

Acter, T.; Uddin, N.; Das, J.; Akhter, A.; Choudhury, T. R.; Kim, S. Sci. Total Environ. 2020, 730, 138996. DOI: 10.1016/j.scitotenv.2020.138996.

Merrill, J. T.; Erkan, D.; Winakur, J.; James, J. A. Nat. Rev. Rheumatol. 2020, 16, 581-589. DOI: doi.org/10.1038/s41584-020-0474-5.

Dariya, B.; Nagaraju, G.P. Cytokine Growth Factor Rev. 2020, 53, 43-52. DOI: 10.1016/j.cytogfr.2020.05.001.

Pearce, L.; Davidson, S. M.; Yellon, D.M. Expert. Opin. Ther. Targets. 2020, 24, 723-730. DOI: 10.1080/14728222.2020.1783243.

Pandey, P.; Rane, J. S.; Chatterjee, A.; Kumar, A.; Khan, R.; Prakash, A.; Ray, S. J. Biomol. Struct. Dyn. 2020, 39, 6306-6316. DOI: 10.1080/07391102.2020.1796811.

Xue, X.; Yu, H.; Yang, H.; Xue, F.; Wu, Z.; Shen, W.; Li, J.; Zhou, Z.; Ding, Y.; Zhao, Q. J. Virol. 2008, 82, 2515-2527. DOI: 10.1128/JVI.02114-07.

Tariq, A.; Mateen, R.; Afzal, S. S.; Saleem, M. Int. J. Infect. Dis. 2020, 98,166-175. DOI: 10.1016/j.ijid.2020.06.063.

Chan, K. K.; Dorosky, D.; Sharma, P.; Abbasi, S. A.; Dye, J. M.; Kranz, D. M.; Herbert, A. S.; Procko, E. Science. 2020, 369, 1261-1265. DOI: 10.1126/science.abc0870.

Elfiky, A. A. Life Sci. 2020, 253,117592. DOI: 10.1016/j.lfs.2020.117592.

Deng, X.; Hackbart, M.; Mettelman, R. C.; O’Brien, A.; Mielech, A. M.; Yi, G.; Kao, C. C.; Baker, S. C. PNAS. 2017, 114, E4251-E4260. DOI: doi.org/10.1073/pnas.1618310114.

Mohammad, T.; Shamsi, A.; Anwar, S.; Umair, M.; Hussain, A.; Rehman, M. T.; Al Ajmi, M.F.; Islam, A.; Hassan, M. I. Virus Res. 2020, 288, 198102-198102. DOI: 10.1016/j.virusres.2020.198102.

Dai, W.; Zhang, B.; Jiang, X. M.; Su, H.; Li, J.; Zhao, Y.; Xie, X.; Jin, Z.; Peng, J.; Liu, F.; Li, C.; Li, Y.; Bai, F.; Wang, H.; Cheng, X.; Cen, X.; Hu, S.; Yang, X.; Wang, J.; Liu, X.; Xiao, G.; Jiang, H.; Rao, Z.; Zhang, L. K.; Xu, Y.; Yang, H.; Liu, H. Science. 2020, 368, 1331-1335. DOI: 10.1126/science.abb4489.

Yang, H.; Xie, W.; Xue, X.; Yang, K.; Ma, J.; Liang, W.; Zhao, Q.; Zhou, Z.; Pei, D.; Ziebuhr, J. PLoS Biol.2005, 3, e324. DOI: doi.org/10.1371/journal.pbio.0030324.

Das, P.; Majumder, R.; Mandal, M.; Basak, P. J. Biomol. Struct. Dyn. 2021, 39, 6265-6280. DOI: 10.1080/07391102.2020.1796799.

Hall Jr, D.C.; Ji, H. F. Travel Med. Infect. Dis. 2020, 35, 101646. DOI: 10.1016/j.tmaid.2020.101646.

Vankadari, N. Int J Antimicrob Agents. 2020, 56, 105998. DOI: 10.1016/j.ijantimicag.2020.105998

Shang, J.; Wan, Y.; Liu, C.; Yount, B.; Gully, K.; Yang, Y.; Auerbach, A.; Peng, G.; Baric, R.; Li, F. PLoS pathogens. 2020, 16, e1008392. DOI: 10.1371/journal.ppat.1008392.

Li, W.; Moore, M. J.; Vasilieva, N.; Sui, J.; Wong, S. K.; Berne, M. A.; Somasundaran, M.; Sullivan, J. L.; Luzuriaga, K.; Greenough, T. C. Nature. 2003, 426, 450-454. DOI: 10.1038/nature02145.

Hussain, M.; Jabeen, N.; Raza, F.; Shabbir, S.; Baig, A.A.; Amanullah, A.; Aziz, B. J. Med. Virol. 2020, 921, 1580-1586. DOI: 10.1002/jmv.25832.

Li, F.; Li, W.; Farzan, M.; Harrison, S.C. Science. 2005, 309, 1864-1868. DOI: 10.1126/science.1116480.

Lan, J.; Ge, J.; Yu, J.; Shan, S.; Zhou, H.; Fan, S.; Zhang, Q.; Shi, X.; Wang, Q.; Zhang, L. Nature. 2020, 581, 215-220. DOI: doi.org/10.1038/s41586-020-2180-5.

Elfiky, A. A. J. Biomol. Struct. Dyn. 2021, 39, 3204-3212. DOI: 10.1080/07391102.2020.1761882.

Choudhury, S.; Moulick, D.; Saikia, P.; Mazumder, M.K. Med. J. Armed Forces India. 2021, 77, S373- S378. DOI: 10.1016/j.mjafi.2020.05.005.

Furuta, Y.; Komeno, T.; Nakamura, T. Proc. Jpn. Acad. Ser. B Phys. Biol. Sci. 2017, 93, 449-463. DOI: 10.2183/pjab.93.027.

Konkolova, E.; Dejmek, M.; Hřebabecký, H.; Šála, M.; Böserle, J.; Nencka, R.; Boura, E. Antivir. Res. 2020, 182,104899-104899. DOI: 10.1016/j.antiviral.2020.104899.

Hackbart, M.; Deng, X.; Baker, S.C. PNAS. 2020, 117, 8094-8103. DOI: doi.org/10.1073/pnas.1921485117.

Bhardwaj, K.; Guarino, L.; Kao, C.C. J. Virol, 2004, 78,12218-12224. DOI: doi.org/10.1128/JVI.78.22.12218-12224.2004.

Johari, J.; Kianmehr, A.; Mustafa, M.R.; Abubakar, S.; Zandi, K. Int. J. Mol. Sci. 2012, 13,16785-16795. DOI: 10.3390/ijms131216785.

Zandi, K.; Teoh, B.T.; Sam, S.S.; Wong, P.F.; Mustafa, M.R.; Abu Bakar, S. Virol. J. 2011, 8, 560. DOI: doi.org/10.1186/1743-422X-8-560.

Amoros, M.; Simõs, C.; Girre, L.; Sauvager, F.; Cormier, M. J. Nat. Prod. 1992, 55, 1732-1740. DOI: 10.1021/np50090a003.

Qiu, X.; Kroeker, A.; He, S.; Kozak, R.; Audet, J.; Mbikay, M.; Chrétien, M. Antimicrob. Agents Chemother. 2016, 60, 5182-5188. DOI: 10.1128/AAC.00307-16.

Amawi, H.; Ashby, C.R.; Tiwari, A.K. Chin. J. Cancer. 2017, 36, 1-13. DOI: doi.org/10.1186/s40880-017-0217-4

da Silva Hage-Melim, L. I.; Federico, L. B.; de Oliveira, N. K. S.; Francisco, V. C. C. Correa, L. C.; de Lima, H. B.; Gomes, S. Q.; Barcelos, M. P.; Francischini, I. A. G. Life Sci. 2020, 256, 117963. DOI: 10.1016/j.lfs.2020.117963.

Zhang, J.; Shan, Y.; Pan, X.; Wang, C.; Xu, W.; He, L. Chem. Biol Drug. Des. 2011, 78, 709-717. DOI: 10.1111/j.1747-0285.2011.01179.x.

Kant, K.; Lal, U.R.; Kumar, A.; Ghosh, M. Comput. Biol. Chem. 2019, 78, 217-226. DOI: 10.1016/j.compbiolchem.2018.12.005.

Zhang, X.; Wong, S. E.; Lightstone, F. C. J. Chem. Inf. Model. 2014, 54, 324–337. DOI: doi.org/10.1021/ci4005145.

Giardina, S. F.; Werner, D. S.; Pingle, M.; Feinberg, P. B.; Foreman, K. W.; Bergstrom, D. E.; Arnold, L. D.; Barany, F. J. Med. Chem. 2020, 63, 3004-3027. DOI: doi.org/10.1021/acs.jmedchem.9b01689.

Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz, D. T.; Repasky, M.P.; Knoll, E. H.; Shelley, M.; Perry, J. K. J. Med. Chem. 2004, 47, 1739-1749. DOI: doi.org/10.1021/jm030643.

leicher, K.H.; Böhm, H.J.; Müller, K.; Alanine, A.I. Nat. Rev. Drug Discov. 2003, 2, 369-378. DOI: doi.org/10.1038/nrd1086.

Mori, M.; Schult-Dietrich, P.; Szafarowicz, B.; Humbert, N.; Debaene, F.; Sanglier-Cianferani S.; Dietrich, U.; Mély, Y.; Botta, M. Virus Res. 2012, 169, 377-387. DOI: 10.1016/j.virusres.2012.05.011.

Genheden, S.; Ryde, U. Expert Opin. Drug. Discov. 2015, 10, 449-461. DOI: 10.1517/17460441.2015.1032936.

Hou, T.; Wang, J.; Li, Y.; Wang, W. J. Comput. Chem. 2011, 32, 866-877. DOI: 10.1002/jcc.21666.

Alam, S.; Khan, F. Sci. Rep. 2019, 9, 5414. DOI: doi.org/10.1038/s41598-019-41984-7

Kumar, A.; Rathi, E.; Kini, S. G. J. Mol. Struct. 2019, 1189, 299-306. DOI: doi.org/10.1016/j.molstruc.2019.04.023.

Sankar, V.; Engels, S. M. Future J. Pharm. Sci. 2018, 4, 276-283. DOI: doi.org/10.1016/j.fjps.2018.10.004.

Yadav, D. K.; Kumar, S.; Saloni, H. S.; Kim, M.; Sharma, P.; Misra, S.; Khan, F. Drug. Des. Devel Ther. 2017, 11, 1859-1870. DOI: 10.2147/DDDT.S130601.

Benet, L. Z.; Hosey, C. M.; Ursu, O.; Oprea, T. I. Adv. Drug Deliv. Rev. 2016, 101, 89-98. DOI: 10.1016/j.addr.2016.05.007.

Vijayakumar, B. G.; Ramesh, D.; Joji, A.; Kannan, T. Eur. J. Pharmacol. 2020, 886, 173448. DOI: 10.1016/j.ejphar.2020.173448.

Utomo, R.Y.; Putri, D. D. P.; Salsabila, I. A.; Meiyanto, E. Indones. J. Cancer Chemoprevention. 2020, 11, 154-167. DOI: http://dx.doi.org/10.14499/indonesianjcanchemoprev11iss3pp154-167.

Huang, F.; Li, Y.; Leung, E. L. H.; Liu, X.; Liu, K.; Wang, Q.; Lan, Y.; Li, X.; Yu, H.; Cu, L. Pharmacol. Res. 2020, 158, 104929. DOI: 10.1016/j.phrs.2020.104929.

da Silva, F. M. A.; da Silva, K. P. A.; de Oliveira, L. P. M.; Costa, E. V.; Koolen, H. H.; Pinheiro, M. L. B.; de Souza, A. Q. L.; de Souza, A. D. L. Mem. Inst. Oswaldo Cruz. 2020, 115, e200207. DOI: 10.1590/0074-02760200207.

Jin, Z.; Du, X.; Xu, Y.; Deng, Y.; Liu, M.; Zhao, Y.; Zhang, B.; Li, X.; Zhang, L.; Peng, C.; Duan, Y.; Yu, J.; Wang, L.; Yang, K.; Liu, F.; Jiang, R.; Yang, X.; You, T.; Liu, X.; Yang, X.; Bai, F.; Liu, H.; Liu, X.; Guddat, L.W.; Xu, W.; Xiao, G.; Qin, C.; Shi, Z.; Jiang, H.; Rao, Z.; Yang, H. Nature. 2020, 582, 289–293. DOI: doi.org/10.1038/s41586-020-2223-y.

Bahbah, E. I.; Negida, A.; Nabet, M. S. Medical Hypotheses. 2020, 140, 109782. DOI: 10.1016/j.mehy.2020.109782

Han, D. P.; Nicholson A. P.; Cho, M. W. Virology. 2006, 350, 15-25. DOI: 10.1016/j.virol.2006.01.029.

Romano, M.; Ruggiero, A.; Squeglia, F.; Maga, G.; Berisio, R. Cells. 2020, 9, 1267. DOI: 10.3390/cells9051267.

Downloads

Additional Files

Published

2022-07-28

Issue

Section

Regular Articles