Generic placeholder image

Infectious Disorders - Drug Targets

Editor-in-Chief

ISSN (Print): 1871-5265
ISSN (Online): 2212-3989

Research Article

Can Antimalarial Phytochemicals be a Possible Cure for COVID-19? Molecular Docking Studies of Some Phytochemicals to SARS-CoV-2 3C-like Protease

Author(s): Anamul Hasan, Khoshnur Jannat, Tohmina Afroze Bondhon, Rownak Jahan, Md Shahadat Hossan, Maria de Lourdes Pereira, Veeranoot Nissapatorn*, Christophe Wiart and Mohammed Rahmatullah*

Volume 22, Issue 1, 2022

Published on: 29 July, 2021

Article ID: e290721195143 Pages: 11

DOI: 10.2174/1871526521666210729164054

Abstract

Objective: To evaluate the efficacy of reported anti-malarial phytochemicals as lead compounds for possible drug development against COVID-19.

Methods: An in silico approach was used in this study to determine through molecular docking the binding affinities and site of binding of these phytochemicals to the 3C-like protease of COVID-19 which is considered as the main protease of the virus.

Results: A number of anti-malarial phytochemicals like apigenin-7-O-glucoside, decurvisine, luteolin- 7-O-glucoside, sargabolide J, and shizukaols A, B, F, and G showed predicted high binding energies with ΔG values of -8.0 kcal/mol or higher. Shizukaols F and B demonstrated the best binding energies of -9.5 and -9.8, respectively. The acridone alkaloid 5-hydroxynoracronycine also gave a predicted high binding energy of -7.9 kcal/mol.

Conclusion: This is for the first time that decursivine and several shizukaols were reported as potential anti-viral agents. These compounds merit further studies to determine whether they can be effective drug candidates against COVID-19.

Keywords: COVID-19, anti-malaria, phytochemicals, drug development, shizukaols, SARS-CoV-2 3C-like protease.

Graphical Abstract
[1]
Vijayanand P, Wilkins E, Woodhead M. Severe acute respiratory syndrome (SARS): A review. Clin Med (Lond) 2004; 4(2): 152-60.
[http://dx.doi.org/10.7861/clinmedicine.4-2-152] [http://dx.doi.org/10.7861/clinmedicine.4-2-152] [PMID: 15139736]
[2]
Nassar MS, Bakhrebah MA, Meo SA, Alsuabeyl MS, Zaher WA. Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infection: epidemiology, pathogenesis and clinical characteristics. Eur Rev Med Pharmacol Sci 2018; 22(15): 4956-61.
[http://dx.doi.org/10.26355/eurrev_201808_15635] [PMID: 30070331]
[3]
Lovato A, de Filippis C. Clinical presentation of COVID-19: A systematic review focusing on upper airway symptoms. Ear Nose Throat J 2020; 99(9): 569-76.
[http://dx.doi.org/10.1177/0145561320920762] [http://dx.doi.org/10.1177/0145561320920762] [PMID: 32283980]
[4]
D’Amico F, Baumgart DC, Danese S, Peyrin-Biroulet L. Diarrhea during COVID-19 infection: Pathogenesis, epidemiology, prevention, and management. Clin Gastroenterol Hepatol 2020; 18(8): 1663-72.
[http://dx.doi.org/10.1016/j.cgh.2020.04.001] [http://dx.doi.org/10.1016/j.cgh.2020.04.001] [PMID: 32278065]
[5]
Rabaan AA, Al-Ahmed SH, Haque S, et al. SARS-CoV-2, SARS-CoV, and MERS-COV: A comparative overview. Infez Med 2020; 28(2): 174-84.
[PMID: 32275259]
[6]
Chen YW, Yiu CB, Wong K-Y. Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CL pro) structure: Virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates. F1000 Res 2020; 9: 129.
[http://dx.doi.org/10.12688/f1000research.22457.1] [http://dx.doi.org/10.12688/f1000research.22457.2] [PMID: 32194944]
[7]
Huang C, Wei P, Fan K, Liu Y, Lai L. 3C-like proteinase from SARS coronavirus catalyzes substrate hydrolysis by a general base mechanism. Biochemistry 2004; 43(15): 4568-74.
[http://dx.doi.org/10.1021/bi036022q] [http://dx.doi.org/10.1021/bi036022q] [PMID: 15078103]
[8]
Hsu M-F, Kuo C-J, Chang K-T, et al. Mechanism of the maturation process of SARS-CoV 3CL protease. J Biol Chem 2005; 280(35): 31257-66.
[http://dx.doi.org/10.1074/jbc.M502577200] [http://dx.doi.org/10.1074/jbc.M502577200] [PMID: 15788388]
[9]
Muramatsu T, Takemoto C, Kim Y-T, et al. SARS-CoV 3CL protease cleaves its C-terminal autoprocessing site by novel subsite cooperativity. Proc Natl Acad Sci USA 2016; 113(46): 12997-3002.
[http://dx.doi.org/10.1073/pnas.1601327113] [http://dx.doi.org/10.1073/pnas.1601327113] [PMID: 27799534]
[10]
Tahir ul Qamar M, Alqahtani SM, Alamri MA, Chen L-L. Structural basis of SARS-CoV-2 3CLpro and anti-COVID-19 drug discovery from medicinal plants. J Pharm Anal in press.
[http://dx.doi.org/10.1016/j.jpha.2020.03.009]
[11]
World Health Organization (WHO)Draft landscape of COVID-19 candidate vaccines 2020.Available from:. https://www.who.int/publications/m/item/draft-landscape-of-covid-19-candidate-vaccines
[12]
Jackson JK, Weiss MA, Schwarzenberg AB, Nelson RM. Global economic effects of COVID-19. Congressional Research Service, R46270 2020. Available from:. https://crsreports.congress.govR46270
[13]
Asai A, Konno M, Ozaki M, et al. COVID-19 drug discovery using intensive approaches. Int J Mol Sci 2020; 21(8): 2839.
[http://dx.doi.org/10.3390/ijms21082839] [http://dx.doi.org/10.3390/ijms21082839] [PMID: 32325767]
[14]
Alamgeer YW, Younis W, Asif H, et al. Traditional medicinal plants used for respiratory disorders in Pakistan: A review of the ethno-medicinal and pharmacological evidence. Chin Med 2018; 13(1): 48.
[http://dx.doi.org/10.1186/s-13020-018-0204-y] [http://dx.doi.org/10.1186/s13020-018-0204-y] [PMID: 30250499]
[15]
Keyaerts E, Vijgen L, Pannecouque C, et al. Plant lectins are potent inhibitors of coronaviruses by interfering with two targets in the viral replication cycle. Antiviral Res 2007; 75(3): 179-87.
[http://dx.doi.org/10.1016/j.antiviral.2007.03.003] [http://dx.doi.org/10.1016/j.antiviral.2007.03.003] [PMID: 17428553]
[16]
Priya R, Nirmala M, Shankar T, Malarvizhi A. Chapter 2, Phytochemical compounds of Leucas aspera L. Pharmacological benefits of natural products. 1st. 2018; pp. 19-35..
[17]
Sungula JK, Taba K, Ntumba K, Tshiongo MTC, Theodore KK. In vitro anti-malarial activity of 20 quinones isolated from four plants used by traditional healers in the Democratic Republic of Congo. J Med Plants Res 2010; 4(11): 991-4.
[18]
Liu X, Zhang B, Jin Z, Yang H, Rao Z. The crystal structure of COVID-19 main protease in complex with an inhibitor N3 Available from: https://www.rcsb.org/structure/6LU7[Accessed May 25, 2020]
[19]
Zhavoronkov A, Aladinskiy V, Zhebrak A, et al. Potential COVID-19 3C-like protease inhibitors designed using generative deep learning approaches. 2020.
[20]
Pan W-H, Xu X-Y, Shi N, Tsang SW, Zhang H-J. Antimalarial activity of plant metabolites. Int J Mol Sci 2018; 19(5): 1382.
[http://dx.doi.org/10.3390/ijms19051382] [http://dx.doi.org/10.3390/ijms19051382] [PMID: 29734792]
[21]
Ihlenfeldt WD. Applied ChemoinformaticsPubChem. 2018; pp. 245-58.
[22]
Trott O, Olson AJ. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 2010; 31(2): 455-61.
[http://dx.doi.org/10.1002/jcc.21334.AutoDock] [PMID: 19499576]
[23]
Studio D. Dassault Systemes BIOVIA, Discovery Studio Modelling Environment, Release 45. Accelrys Software Inc. 2015; pp. 98-104.
[24]
Meng X-Y, Zhang H-X, Mezei M, Cui M. Molecular docking: A powerful approach for structure-based drug discovery. Curr Comput Aided Drug Des 2011; 7(2): 146-57.
[http://dx.doi.org/10.2174/157340911795677602] [http://dx.doi.org/10.2174/157340911795677602] [PMID: 21534921]
[25]
Wu J-L, Lu Y-S, Tang B, Peng X-S. Total syntheses of shizukaols A and E. Nat Commun 2018; 9(1): 4040.
[http://dx.doi.org/10.1038/s41467-018-06245-7] [http://dx.doi.org/10.1038/s41467-018-06245-7] [PMID: 30279446]
[26]
Yan X, Qi M, Li P, Zhan Y, Shao H. Apigenin in cancer therapy: anti-cancer effects and mechanisms of action. Cell Biosci 2017; 7: 50.
[http://dx.doi.org/10.1186/s13578-017-0179-x] [http://dx.doi.org/10.1186/s13578-017-0179-x] [PMID: 29034071]
[27]
Lin Y, Shi R, Wang X, Shen H-M. Luteolin, a flavonoid with potential for cancer prevention and therapy. Curr Cancer Drug Targets 2008; 8(7): 634-46.
[http://dx.doi.org/10.2174/156800908786241050] [http://dx.doi.org/10.2174/156800908786241050] [PMID: 18991571]
[28]
Dai W, Bi J, Li F, et al. Antiviral efficacy of flavonoids against Enterovirus 71 infection in vitro and in newborn mice. Viruses 2019; 11(7): 625.
[http://dx.doi.org/10.3390/v11070625] [http://dx.doi.org/10.3390/v11070625] [PMID: 31284698]
[29]
Murali KS, Sivasubramanian S, Vincent S, et al. Anti-chikungunya activity of luteolin and apigenin rich fraction from Cynodon dactylon. Asian Pac J Trop Med 2015; 8(5): 352-8.
[http://dx.doi.org/10.1016/S-1995-7645(14)60343-6] [http://dx.doi.org/10.1016/S1995-7645(14)60343-6] [PMID: 26003593]
[30]
Fan W, Qian S, Qian P, Li X. Antiviral activity of luteolin against Japanese encephalitis virus. Virus Res 2016; 220: 112-6.
[http://dx.doi.org/10.1016/j.virusres.2016.04.021] [http://dx.doi.org/10.1016/j.virusres.2016.04.021] [PMID: 27126774]
[31]
Funakoshi-Tago M, Nakamura K, Tago K, Mashino T, Kasahara T. Anti-inflammatory activity of structurally related flavonoids, Apigenin, Luteolin and Fisetin. Int Immunopharmacol 2011; 11(9): 1150-9.
[http://dx.doi.org/10.1016/j.intimp.2011.03.012] [http://dx.doi.org/10.1016/j.intimp.2011.03.012] [PMID: 21443976]
[32]
Perez RM. Antiviral activity of compounds isolated from plants. Pharm Biol 2003; 41(2): 107-57.
[http://dx.doi.org/10.1076/phbi.41.2.107.14240] [http://dx.doi.org/10.1076/phbi.41.2.107.14240]
[33]
Thawabteh A, Juma S, Bader M, et al. The biological activity of natural alkaloids against herbivores, cancerous cells and pathogens. Toxins (Basel) 2019; 11(11): 656.
[http://dx.doi.org/10.3390/toxins11110656] [http://dx.doi.org/10.3390/toxins11110656] [PMID: 31717922]
[34]
Saiz LC. Chloroquine and hydroxychloroquine as potential therapies against COVID-19 2020.Report (version 6), pre-print. Servicio Navarro de Salud, bitn Available from:. https://www.researchgate.net/publication/340248491_COVID-19_Chloroquine_and_hydroxychloroquine_as_potential_therapies_against_COVID-19
[35]
D’Alessandro S, Scaccabarozzi D, Signorini L, et al. The use of antimalarial drugs against viral infection. Microorganisms 2020; 8(1): 85.
[http://dx.doi.org/10.3390/microorganisms8010085] [http://dx.doi.org/10.3390/microorganisms8010085] [PMID: 31936284]
[36]
Efferth T, Romero MR, Wolf DG, Stamminger T, Marin JJ, Marschall M. The antiviral activities of artemisinin and artesunate. Clin Infect Dis 2008; 47(6): 804-11.
[http://dx.doi.org/10.1086/591195] [http://dx.doi.org/10.1086/591195] [PMID: 18699744]
[37]
Obeid S, Alen J, Nguyen VH, et al. Artemisinin analogues as potent inhibitors of in vitro hepatitis C virus replication. PLoS One 2013; 8(12)e81783
[http://dx.doi.org/10.1371/journal.pone.0081783] [http://dx.doi.org/10.1371/journal.pone.0081783] [PMID: 24349127]
[38]
Mondal A, Chatterji U. Artemisinin represses telomerase subunits and induces apoptosis in HPV-39 infected human cervical cancer cells. J Cell Biochem 2015; 116(9): 1968-81.
[http://dx.doi.org/10.1002/jcb.25152] [http://dx.doi.org/10.1002/jcb.25152] [PMID: 25755006]
[39]
Malakar S, Sreelatha L, Dechtawewat T, et al. Drug repurposing of quinine as antiviral against dengue virus infection. Virus Res 2018; 255: 171-8.
[http://dx.doi.org/10.1016/j.virus.res.2018.07.018] [http://dx.doi.org/10.1016/j.virusres.2018.07.018] [PMID: 30055216]
[40]
Khan M, Santhosh SR, Tiwari M, Lakshmana Rao PV, Parida M. Assessment of in vitro prophylactic and therapeutic efficacy of chloroquine against Chikungunya virus in vero cells. J Med Virol 2010; 82(5): 817-24.
[http://dx.doi.org/10.1002/jmv.21663] [http://dx.doi.org/10.1002/jmv.21663] [PMID: 20336760]
[41]
Han Y, Mesplède T, Xu H, Quan Y, Wainberg MA. The antimalarial drug amodiaquine possesses anti-ZIKA virus activities. J Med Virol 2018; 90(5): 796-802.
[http://dx.doi.org/10.1002/jmv.25031] [http://dx.doi.org/10.1002/jmv.25031] [PMID: 29315671]
[42]
Lin HY, Yang YT, Yu SL, et al. Caveolar endocytosis is required for human PSGL-1-mediated enterovirus 71 infection. J Virol 2013; 87(16): 9064-76.
[http://dx.doi.org/10.1128/JVI.00573-13] [http://dx.doi.org/10.1128/JVI.00573-13] [PMID: 23760234]
[43]
Boonyasuppayakorn S, Reichert ED, Manzano M, Nagarajan K, Padmanabhan R. Amodiaquine, an antimalarial drug, inhibits dengue virus type 2 replication and infectivity. Antiviral Res 2014; 106: 125-34.
[http://dx.doi.org/10.1016/j.antiviral.2014.03.014] [http://dx.doi.org/10.1016/j.antiviral.2014.03.014] [PMID: 24680954]
[44]
Gignoux E, Azman AS, de Smet M, et al. Effect of artesunate-amodiaquine on mortality related to Ebola virus disease. N Engl J Med 2016; 374(1): 23-32.
[http://dx.doi.org/10.1056/NEJMoa1504605] [http://dx.doi.org/10.1056/NEJMoa1504605] [PMID: 26735991]
[45]
Burdick JR, Durand DP. Primaquine diphosphate: inhibition of Newcastle disease virus replication. Antimicrob Agents Chemother 1974; 6(4): 460-4.
[http://dx.doi.org/10.1128/aac.6.4.460] [http://dx.doi.org/10.1128/AAC.6.4.460] [PMID: 4157345]
[46]
Briolant S, Wurtz N, Zettor A, Rogier C, Pradines B. Susceptibility of Plasmodium falciparum isolates to doxycycline is associated with pftetQ sequence polymorphisms and pftetQ and pfmdt copy numbers. J Infect Dis 2010; 201(1): 153-9.
[http://dx.doi.org/10.1086/648594] [http://dx.doi.org/10.1086/648594] [PMID: 19929377]
[47]
Zhao Y, Wang X, Li L, Li C. Doxycycline inhibits proliferation and induces apoptosis of both human papillomavirus positive and negative cervical cancer cell lines. Can J Physiol Pharmacol 2016; 94(5): 526-33.
[http://dx.doi.org/10.1139/cjpp-2015-0481] [http://dx.doi.org/10.1139/cjpp-2015-0481] [PMID: 26913972]
[48]
Yang JM, Chen YF, Tu YY, Yen KR, Yang YL. Combinatorial computational approaches to identify tetracycline derivatives as flavivirus inhibitors. PLoS One 2007; 2(5): e428.
[http://dx.doi.org/10.1371/journal.pone.0000428] [http://dx.doi.org/10.1371/journal.pone.0000428] [PMID: 17502914]
[49]
Dias LRS, Freitas ACC, Nanayakkara D, McChesney JD, Walker L. New chloroquine analogues as antiviral agents. Lat Am J Pharm 2006; 25(3): 351-5. [www.latamjpharm.org ˃ trabajos
[50]
Batista R, Silva Ade J Jr, de Oliveira AB. Plant-derived antimalarial agents: new leads and efficient phytomedicines. Part II. Non-alkaloidal natural products. Molecules 2009; 14(8): 3037-72.
[http://dx.doi.org/10.3390/molecules14083037] [http://dx.doi.org/10.3390/molecules14083037] [PMID: 19701144]
[51]
van Zyl RL, Viljoen AM. In vitro activity of Aloe extracts against Plasmodium falciparum. S Afr J Bot 2002; 68: 106-10.
[http://dx.doi.org/10.1016/S0254-6299(15)30451-8]
[52]
Pandit M, Latha N. In silico studies reveal potential antiviral activity of phytochemicals from medicinal plants for the treatment of COVID-19 infection. Research Square.
[http://dx.doi.org/10.21203/rs.3.rs-22687/v1]

© 2024 Bentham Science Publishers | Privacy Policy