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Anti-Infective Agents

Editor-in-Chief

ISSN (Print): 2211-3525
ISSN (Online): 2211-3533

Research Article

Natural Compounds as Potential Anti-COVID Agents

Author(s): Nidhi Rani*, Randhir Singh, Praveen Kumar, Prerna Sharma and Vikas Sharma

Volume 21, Issue 1, 2023

Published on: 09 September, 2022

Article ID: e040422203043 Pages: 11

DOI: 10.2174/2211352520666220404093338

Price: $65

Abstract

Background: Since December 2019, COVID-19 has become a new health crisis in the world and has been declared a public health emergency of international concern by WHO. In search of anti-COVID treatment regimen, we applied molecular docking approach in order to identify the natural compounds that may have potential for anti-COVID treatment with specific target and selective inhibitory mechanism. Our goal is to identify the potential anti-COVID compounds based on virtual screening of the protein of spike glycoprotein as virtual inhibition target.

Methods: Molecular docking was carried out by using Molergo Virtual Docker. 35 compounds from different plant sources were selected and docked in the enzyme pocket.

Results: The docking result revealed that some of the compounds exhibited good potency against the virus and can be used further for developing new drug regimen.

Conclusion: The compounds of natural origin could be a good target and can be used as lead compounds for the treatment of this dreadful disease.

Keywords: Coronavirus, COVID19, natural plants, spike glycoprotein, WHO, MERS.

[1]
Hafeez, A.; Ahmad, S.; Siddqui, S.A.; Ahmad, M.; Mishra, S. A review of COVID-19 (Coronavirus Disease-2019) diagnosis, treatments and prevention. Eur-Asian J. Med. Oncol., 2020, 4(2), 116-125.
[2]
Kitchen, D.B.; Decornez, H.; Furr, J.R.; Bajorath, J. Docking and scoring in virtual screening for drug discovery: Methods and applications. Nat. Rev. Drug Discov., 2004, 3(11), 935-949.
[http://dx.doi.org/10.1038/nrd1549] [PMID: 15520816]
[3]
Thomsen, R.; Christensen, M.H. MolDock: A new technique for high-accuracy molecular docking. J. Med. Chem., 2006, 49(11), 3315-3321.
[http://dx.doi.org/10.1021/jm051197e] [PMID: 16722650]
[4]
Zubair, M.S.; Anam, S.; Khumaidi, A.; Susanto, Y.; Hidayat, M.; Ridhay, A. Molecular docking approach to identify potential anticancer compounds from Begonia (Begonia sp).AIP Conf. Proc., 2016, 1755, p. 080005.
[http://dx.doi.org/10.1063/1.4958513]
[5]
Saeed, M.; Saeed, A.; Alam, M.J.; Alreshidi, M. Receptor-based pharmacophore modeling in the search for natural products for COVID-19 Mpro. Molecules, 2021, 26(6), 1549.
[http://dx.doi.org/10.3390/molecules26061549] [PMID: 33799871]
[6]
Vijayakumar, B.G.; Ramesh, D.; Joji, A.; Jayachandra Prakasan, J.; Kannan, T. In silico pharmacokinetic and molecular docking studies of natural flavonoids and synthetic indole chalcones against essential proteins of SARS-CoV-2. Eur. J. Pharmacol., 2020, 886, 173448.
[http://dx.doi.org/10.1016/j.ejphar.2020.173448] [PMID: 32768503]
[7]
Gogoi, B.; Chowdhury, P.; Goswami, N.; Gogoi, N.; Naiya, T.; Chetia, P.; Mahanta, S.; Chetia, D.; Tanti, B.; Borah, P.; Handique, P.J. Identification of potential plant-based inhibitor against viral proteases of SARS-CoV-2 through molecular docking, MM-PBSA binding energy calculations and molecular dynamics simulation. Mol. Divers., 2021, 25(3), 1963-1977.
[http://dx.doi.org/10.1007/s11030-021-10211-9] [PMID: 33856591]
[8]
Rathinavel, T.; Thangaswamy, S.; Ammasi, S.; Kumarasamy, S. Virtual screening of COVID-19 drug from three Indian traditional medicinal plants through in silico approach. Res. J. Biotechnol., 2020, 15(10), 124-140.
[9]
Mani, J.S.; Johnson, J.B.; Steel, J.C.; Broszczak, D.A.; Neilsen, P.M.; Walsh, K.B.; Naiker, M. Natural product-derived phytochemicals as potential agents against coronaviruses: A review. Virus Res., 2020, 284, 197989.
[http://dx.doi.org/10.1016/j.virusres.2020.197989] [PMID: 32360300]
[10]
Cowan, M.M. Plant products as antimicrobial agents. Clin. Microbiol. Rev., 1999, 12(4), 564-582.
[http://dx.doi.org/10.1128/CMR.12.4.564] [PMID: 10515903]
[11]
Wang, Q.; Zhang, Y.; Wu, L.; Niu, S.; Song, C.; Zhang, Z.; Lu, G.; Qiao, C.; Hu, Y.; Yuen, K.Y.; Wang, Q.; Zhou, H.; Yan, J.; Qi, J. Structural and functional basis of SARS-CoV-2 entry by using human ACE2. Cell, 2020, 181(4), 894-904.e9.
[http://dx.doi.org/10.1016/j.cell.2020.03.045] [PMID: 32275855]
[12]
Pradhan, S. In silico analysis: Blocking SARS-CoV 2 main protease enzyme of COVID 19 by taking Allium sativum. IJONS, 10(60), 20322-20327.
[13]
Kandeel, M.; Kitade, Y.; Almubarak, A. Repurposing FDA-approved phytomedicines, natural products, antivirals and cell protectives against SARS-CoV-2 (COVID-19) RNA-dependent RNA polymerase. PeerJ, 2020, 8, e10480.
[http://dx.doi.org/10.7717/peerj.10480] [PMID: 33335812]
[14]
Wang, Z.Z.; Li, K.; Maskey, A.R.; Huang, W.; Toutov, A.A.; Yang, N.; Srivastava, K.; Geliebter, J.; Tiwari, R.; Miao, M.; Li, X.M. A small molecule compound berberine as an orally active therapeutic candidate against COVID-19 and SARS: A computational and mechanistic study. FASEB J., 2021, 35(4), e21360.
[http://dx.doi.org/10.1096/fj.202001792R] [PMID: 33749932]
[15]
Varghese, S.; Wounderbergh, E.; Overhuel, G.J.; Eleveld, M.J.; Kurver, L.; Heerbeek, N.; Laarhoven, A.; Miesen, P.; Hartog, G.; Jonge, M.I.; Rij, R.P. Berberine and obatoclax inhibit SARS-CoV-2 replication in primary human nasal epithelial cells in vitro. Viruses, 2021, 13(2), 282.
[http://dx.doi.org/10.1101/2020.12.23.424189]
[16]
Zhang, B.Y.; Chen, M.; Chen, X.C.; Cao, K.; You, Y.; Qian, Y.J.; Yu, W.K. Berberine reduces circulating inflammatory mediators in patients with severe COVID-19. Br. J. Surg., 2021, 108(1), e9-e11.
[http://dx.doi.org/10.1093/bjs/znaa021] [PMID: 33640910]
[17]
Katare, A.K.; Singh, B.; Shukla, P.; Gupta, S.; Singh, B.; Yalamanchili, K.; Kulshrestha, N.; Bhanwaria, R.; Sharma, A.K.; Sharma, S.; Sneha; Mindala, D.P.; Roy, S.; Kalgotra, R. Rapid determination and optimisation of berberine from Himalayan Berberis lycium by soxhlet apparatus using CCD-RSM and its quality control as a potential candidate for COVID-19. Nat. Prod. Res., 2022, 36(3), 868-873.
[http://dx.doi.org/10.1080/14786419.2020.1806274] [PMID: 32787584]
[18]
Adem, Ş.; Eyupoglu, V.; Sarfraz, I.; Rasul, A.; Zahoor, A.F.; Ali, M.; Abdalla, M.; Ibrahim, I.M.; Elfiky, A.A. Caffeic acid derivatives (CAFDs) as inhibitors of SARS-CoV-2: CAFDs-based functional foods as a potential alternative approach to combat COVID-19. Phytomedicine, 2021, 85, 153310.
[http://dx.doi.org/10.1016/j.phymed.2020.153310] [PMID: 32948420]
[19]
Kumar, V.; Dhanjal, J.K.; Kaul, S.C.; Wadhwa, R.; Sundar, D. Withanone and caffeic acid phenethyl ester are predicted to interact with main protease (Mpro) of SARS-CoV-2 and inhibit its activity. J. Biomol. Struct. Dyn., 2021, 39(11), 3842-3854.
[http://dx.doi.org/10.1080/07391102.2020.1772108] [PMID: 32431217]
[20]
Javed, H.; Meeran, M.F.N.; Jha, N.K.; Ojha, S. Carvacrol, a plant metabolite targeting viral protease (m pro) and ace2 in host cells can be a possible candidate for COVID-19. Front. Plant Sci., 2021, 11, 601335.
[http://dx.doi.org/10.3389/fpls.2020.601335] [PMID: 33664752]
[21]
Seadawy, M.G.; Gad, A.F.; Elhoseny, M.F.; ELharty, B. E.; Shame, M.D.; Elfiky, A.A.; Ahmed, A.; Zekri, A.R.N. In vitro: Natural compounds (thymol, carvacrol, hesperidine, and thymoquinone) against SARS-COV2 strain isolated from Egyptian patients. bioRxiv, 2020, 2020, 367649.
[http://dx.doi.org/10.1101/2020.11.07.367649]
[22]
Suravajhala, R.; Parashar, A.; Malik, B.; Nagaraj, A.V.; Padmanaban, G.; Kavi Kishor, P.; Polavarapu, R.; Suravajhala, P. Comparative docking studies on curcumin with COVID-19 proteins. Preprints, 2020, 2020, 050439.
[http://dx.doi.org/10.20944/journals202005.0439.v1]
[23]
Gonzalez, L.A.; Lossada, C.A.; Moncayo, L.S.; Romero, F.; Paz, J.L.; Vera-Villalobos, J.; Perez, A.E.; San-Blas, E.; Saias, Y. Theoretical molecular docking study of the structural disruption of the viral 3-CL protease of COVID 19 induced by binding of capsaicin, piperine and curcumin. Part 1: A comparative study with chloroquine and hydrochloroquine two antimalarial drugs. Preprint, 2022. [Epub ahead of print].
[24]
Zahedipour, F.; Hosseini, S.A.; Sathyapalan, T.; Majeed, M.; Jamialahmadi, T.; Al-Rasadi, K.; Banach, M.; Sahebkar, A. Potential effects of curcumin in the treatment of COVID-19 infection. Phytother. Res., 2020, 34(11), 2911-2920.
[http://dx.doi.org/10.1002/ptr.6738] [PMID: 32430996]
[25]
Schlesinger, N.; Firestein, B.L.; Brunetti, L. Colchicine in COVID-19: An old drug, new use. Curr. Pharmacol. Rep., 2020, 6(4), 1-9.
[http://dx.doi.org/10.1007/s40495-020-00225-6] [PMID: 32837853]
[26]
Cumhur Cure, M.; Kucuk, A.; Cure, E. Colchicine may not be effective in COVID-19 infection; it may even be harmful? Clin. Rheumatol., 2020, 39(7), 2101-2102.
[http://dx.doi.org/10.1007/s10067-020-05144-x] [PMID: 32394215]
[27]
Umar, H.I.; Siraj, B.; Ajayi, A.; Jimoh, T.O.; Chukwuemeka, P.O. Molecular docking studies of some selected gallic acid derivatives against five non-structural proteins of novel coronavirus. J. Genet. Eng. Biotechnol., 2021, 19(1), 16.
[http://dx.doi.org/10.1186/s43141-021-00120-7] [PMID: 33492492]
[28]
Saeedi-Boroujeni, A.; Mahmoudian-Sani, M.R. Anti-inflammatory potential of Quercetin in COVID-19 treatment. J. Inflamm. (Lond.), 2021, 18(1), 3.
[http://dx.doi.org/10.1186/s12950-021-00268-6] [PMID: 33509217]
[29]
Zhang, M.; Cen, H.; Wu, Y.; Lu, Z.; Lu, F.; Liu, X.; Lan, H. Quercetin as a potential treatment for COVID-19-induced acute kidney injury: Based on network pharmacology and molecular docking study. Plos One, 2021, 16(1), e0245209.
[http://dx.doi.org/10.1371/journal.pone.0245209]
[30]
Colunga Biancatelli, R.M.L.; Berrill, M.; Catravas, J.D.; Marik, P.E. Quercetin and Vitamin C: An experimental, synergistic therapy for the prevention and treatment of SARS-CoV-2 related disease (COVID-19). Front. Immunol., 2020, 11, 1451.
[http://dx.doi.org/10.3389/fimmu.2020.01451] [PMID: 32636851]
[31]
Agrawal, P.K.; Agrawal, C.; Blunden, G. Quercetin: Antiviral significance and possible COVID-19 integrative considerations. Nat. Prod. Commun., 2020, 15(12), 1-10.
[http://dx.doi.org/10.1177/1934578X20976293]
[32]
Derosa, G.; Maffioli, P.; D’Angelo, A.; Di Pierro, F. A role for quercetin in coronavirus disease 2019 (COVID-19). Phytother. Res., 2021, 35(3), 1230-1236.
[http://dx.doi.org/10.1002/ptr.6887] [PMID: 33034398]
[33]
Kashyap, V.K.; Dhasmana, A.; Yallapu, M.M.; Chauhan, S.C.; Jaggi, M. Withania somnifera as a potential future drug molecule for COVID-19. Future Drug Discov., 2020, 2(4), FDD50.
[http://dx.doi.org/10.4155/fdd-2020-0024] [PMID: 33269342]
[34]
Bitencourt-Ferreira, G.; de Azevedo, W.F., Jr. Molegro virtual docker for docking. Methods Mol. Biol., 2019, 2053, 149-167.
[http://dx.doi.org/10.1007/978-1-4939-9752-7_10] [PMID: 31452104]
[35]
Rani, N.; Singh, D. Design, synthesis, antimicrobial evaluation and molecular modeling study of new 2-mercaptoimidazoles (Series-III). Lett. Drug Des. Discov., 2019, 16(5), 512-521.
[http://dx.doi.org/10.2174/1570180815666181015144431]
[36]
Wiersinga, W.J.; Rhodes, A.; Cheng, A.C.; Peacock, S.J.; Prescott, H.C. Pathophysiology, transmission, diagnosis, and treatment of coronavirus disease 2019 (COVID-19): A review. JAMA, 2020, 324(8), 782-793.
[http://dx.doi.org/10.1001/jama.2020.12839] [PMID: 32648899]
[37]
Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein alexandra C. Walls,1,5 Young-Jun Park,1,5 M. Alejandra Tortorici,1,2 Abigail Wall,3 Andrew T. McGuire,3,4 and David Veesler. Cell, 2020, 180, 281-292.
[http://dx.doi.org/10.1016/j.cell.2020.02.058]
[38]
Dong, Y.; Shamsuddin, A.; Campbell, H.; Theodoratou, E. On behalf of UNCOVER. Current COVID-19 treatments: Rapid review of the literature. J. Glob. Health, 2021, 11, 10003.
[http://dx.doi.org/10.7189/jogh.11.10003]

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