Vol. 2 No. 2 (2021): September
Open Access
Peer Reviewed

In silico analysis of Trisindoline 1 compound against Mpro SARS-CoV-2 as novel potential drugs candidate

Authors

DOI:

10.29303/sjp.v2i2.87

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Received: Jan 31, 2021
Accepted: Sep 12, 2021
Published: Sep 30, 2021

Abstract

The novel coronavirus 2019 (SARS-CoV-2) is one of the viruses that can infect humans and cause high mortality worldwide. The protease (Mpro) is key SARS-CoV-2 an enzyme mediates the viral replication and the transcription. Mpro is currently used as the candidate for the SARS-CoV-2 vaccine because Mpro is one of the key enzymes in the viral life cycle that essential for interactions between the virus and host cell receptor during viral entry. The Mpro can be a target protein to design the novel drug of SARS-CoV-2. The drug design from natural products that are considered to have low toxicity is needed against the virus. The study aims to determines the potential pharmacology of Trisindoline 1 compound from the sponge Hyrtios altum against SARS-CoV-2 and to find the amino acid residues between interaction ligand-protein receptors. The methods of this study use the virtual screening of Auto Dock Vina and visualization the amino acid residue using Bio via Discovery Studio. The result of this study was the selected marine compound from Trisindoline 1 may have potential to developed as inhibitor of SARS-CoV-2.

Keywords: In Silico, Mpro, Sars Cov 2, Trisindoline 1, Sponges

Keywords:

In Silico, Mpro, Sars Cov 2, Trisindoline 1, Sponges

References

Adhikari, S. P., Meng, S., Wu, Y.-J., Mao, Y.-P., Ye, R.-X., Wang, Q.-Z., Sun, C., Sylvia, S., Rozelle, S., Raat, H., & Zhou, H. (2020). Epidemiology, causes, clinical manifestation and diagnosis, prevention and control of coronavirus disease (COVID-19) during the early outbreak period: A scoping review. Infectious Diseases of Poverty 9(1), 29. 16(1):69. doi : https://doi.org/10.1186/s40249-020-00646-x

Aquilani R, Boselli M, D'Antona G, et al. (2014). Unaffected arm muscle hypercatabolism in dysphagic subacute stroke patients: the effects of essential amino acid supplementation. Biomed Res Int. doi: https://doi.org/10.1155/2014/964365

Aquilani R, Emilio B, Dossena M, Baiardi P, Testa A, Boschi F, Viglio S, Iadarola P, Pasini E, Verri M. (2015). Correlation of deglutition in subacute ischemic stroke patients with peripheral blood adaptive immunity: essential amino acid improvement. Int J Immunopathol Pharmacol 28(4):576–583.doi : https://doi.org/10.1177/0394632015608249

Bosch BJ, van der Zee R, de Haan CA, Rottier PJ. (2003) The coronavirus spike protein is a class I virus fusion protein: structural and functional characterization of the fusion core complex. J Virol ;77: 8801e11. doi : https://doi.org/10.1128/JVI.77.16.8801-8811.2003

Buondonno I, Sassi F, Carignano G, Dutto F, Ferreri C, Pili FG, Massaia M, Nisoli E, Ruocco C, Porrino P, Ravetta C, Riganti C, Isaia GC, D'Amelio P. (2020). From mitochondria to healthy aging: the role of branched-chain amino acids treatment: MATeR a randomized study. Clin Nutr. 39:2080–2091. doi : https://doi.org/10.1016/j.clnu.2019.10.013

Chen N, Zhou M, Dong X, Qu J, Gong F, Han Y, et al. (2020). Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. Lancet ;395:507–13. doi: https://doi.org/10.1016/s0140-6736(20)30211-7

Chen YP, Cheng YF, Li XH, Yang WL, Wen C, Zhuang S, Zhou YM. (2017). Effects of threonine supplementation on the growth performance, immunity, oxidative status, intestinal integrity, and barrier function of broilers at the early age. Poult Sci. doi : https://doi.org/10.3382/ps/pew240

Chill L, Rudi A, Aknin M, Loya S, Hizi A, Kashman Y, et al. (2004). New sesterterpenes from Madagascan Lendenfeldia sponges. Tetrahedron, 60, 10619-10626. doi: https://doi.org/10.5681/bi.2011.029

Clive D and Jian Wang. (2003). Stereospecific Total Synthesis of the Antiviral Agent Hamigeran B—Use of Large Silyl Groups to Enforce Facial Selectivity and to Suppress Hydrogenolysis. Angew. Chem. Int. Ed. 42, 3406 – 3409. doi : https://doi.org/10.1002/anie.200351519

Crumpacker CS. (2004). Use of antiviral drugs to prevent herpes virus transmission. New England Journal of Medicine 350:67-68. doi : https://doi.org/10.1056/NEJMe038189

Cui J, Li F, Shi Z-L. (2019). Origin and evolution of pathogenic coronaviruses. Nat Rev Microbiol ;17:181–92. doi : https://doi.org/10.1038/s41579-018-0118-9

Detering C, Varani G. (2004). Validation of automated docking programs for docking and database screening against RNA drug targets. J. Med. Chem ;47:4188–4201. doi: https://doi.org/10.1021/jm030650o

Duan H.Q., Zhang Y.D., Fan K., Suo Z.W., Hu G., Mu X. (2007). Anti-inflammatory mechanism of esculetin. Chin. J. Vet. Med 43:45–46. doi: https://doi.org/10.3390/molecules22030387

Ge XY, Li JL, Yang XL, Chmura AA, Zhu G, Epstein JH, et al. (2013). Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor. Nature 2013;503:535e8. doi : https://doi.org/10.1038/nature12711

Guedes IA, de Magalhães CS, Dardenne LE. (2014). Receptor-ligand molecular docking. Biophysical Reviews 6: 75-87. doi : https://doi.org/10.1007/s12551-013-0130-2

Han DP, Penn-Nicholson A, Cho MW. (2006). Identifification of critical determinants on ACE2 for SARS-CoV entry and development of a potent entry inhibitor. Virology ;350:15e25. doi : https://doi.org/10.1016/j.virol.2006.01.029

Hoffmann M, Kleine-Weber H, Schroeder S, Krüger N, Herrler T, Erichsen S, Schiergens TS, Herrler G, Wu NH, Nitsche A, Müller MA, Drosten C, Pöhlmann S. (2020). SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell. doi : https://doi.org//10.1016/j.cell.2020.02.052

Huang C, Wang Y, Li X, Ren L, Zhao J, Hu Y, et al. (2020). Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. The Lancet ;395:497e506. doi: https://doi.org/10.1016/S0140-6736(20)30183-5

In 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 H. (2020). Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors. Nature, (7811), 289–293. doi : https://doi.org/10.1038/s41586-020-2223-y

Kannan S, Shaik Syed Ali P, Sheeza A, Hemalatha K. (2020). COVID-19 (Novel Coronavirus 2019)– recent trends. European Review for Medical and Pharmacological Sciences 24:2006-2011. doi : https://doi.org/10.26355/eurrev_202002_20378

Lin X, Li X, Lin X. (2020). A Review on Applications of Computational Methods in Drug Screening and Design. Molecules. doi : https://doi.org/10.3390/molecules25061375

Lira Simone P, Mirna H. R. Seleghim,a David E. Williams,b Frederic Marion,b Pamela Hamill,c François Jean,c Raymond J. Andersen,b Eduardo Hajdud and Roberto G. S. Berlinck. (2007). A SARS-Coronovirus 3CL Protease Inhibitor Isolated from the Marine Sponge Axinella cf. corrugata: Structure Elucidation and Synthesis. J. Braz. Chem. Soc., Vol. 18, No. 2, 440-443. doi : https://doi.org/10.1590/S0103-50532007000200030

Liu W., Morse J.S., Lalonde, T. Xu S. (2020). Learning from the Past: Possible Urgent Prevention and Treatment Options for Severe Acute Respiratory Infections Caused by 2019-nCoV. ChemBioChem 21, 730–738. doi: https://doi.org/10.1002/cbic.202000047

Li W, Moore MJ, Vasilieva N, Sui J, Wong SK, Berne MA, et al. (2003). Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus. Nature ;426:450e4. doi : https://doi.org/10.1038/nature02145

Loya Shoshana, Amira Rudi, Yoel Kashman, and Amnon Hizi. (2002). Mode of inhibition of HIV-1 reverse transcriptase by polyacetylenetriol, a novel inhibitor of RNA- and DNA-directed DNA polymerases. Biochem J 15; 362(Pt 3): 685–692. doi : https://doi.org/10.1042/0264-6021:3620685

McConkey BJ, Sobolev V, Edelman M. (2002). The performance of current methods in ligand-protein docking. Current Science 83:845–855. Corpus ID: 15115681

Moitessier N, Englebienne P, Lee D, Lawandi J, Corbeil C. (2007). Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go. Br. J. Pharmacol ;153:S7– S26. doi : https://doi.org/10.1038/sj.bjp.0707515

Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ. (1998). Automated Docking Using a Lamarkian Genetic Algorithm and an Empirical Binding Free Energy Function. J. Comput. Chem ;19:1639–1662. doi: https://doi.org/10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B

Muller W, Bohm M, Batel R, De Rosa S, Tommonaro G, Muller I, Schroder H. (2000). Application of cell culture for the production of bioactive compounds from sponges: synthesis of avarol by primmorphs from Dysidea avara. J. Nat. Prod 63:1077–1081. doi : https://doi.org/10.1021/np000003p

Nannou C, Ofrydopoulou A, Evgenidou E, Heath D, Heath E, Lambropoulou D. (2020). Antiviral drugs in aquatic environment and wastewater treatment plants: A review on occurrence, fate, removal and ecotoxicity. Sci Total Environ 699:134322. doi : https://doi.org/10.1016/j.scitotenv.2019.134322

Natalia Bailon-Moscoso, Gabriela Cevallos-Solorzano, Juan Carlos Romero-Benavides, and Maria Isabel Ramirez Orellana. (2017). Natural Compounds as Modulators of Cell Cycle Arrest: Application for Anticancer Chemotherapies. Current Genomics 18, 106-131. doi : https://doi.org/10.2174/1389202917666160808125645

Omrani AS, Saad MM, Baig K, Bahloul A, Abdul-Matin M, Alaidaroos AY, et al. (2014). Ribavirin and interferon alfa-2a for severe Middle East respiratory syndrome coronavirus infection: a retrospective cohort study. Lancet Infect Dis ;14:1090e5. doi : https://doi.org/10.1016/S1473-3099(14)70920-X

Park H, Lee J, Lee S. (2006). Critical assessment of the automated AutoDock as a new docking tool for virtual screening. Proteins ;65:549–554. doi : https://doi.org/10.1002/prot.21183

Patrick A. Holt, Jonathan B. Chaires, and John O. Trent. (2008). J Chem Inf Model; 48(8): 1602–1615. doi: https://doi.org/10.1021/ci800063v

Peiris JS, Guan Y, Yuen KY. (2004). Severe acute respiratory syndrome. Nature Medicine 10(12 Suppl):S88-97. doi : https://doi.org/10.1038/nm1143

Pillaiyar, Thanigaimalai, Manoj Manickam, Vigneshwaran Namasivayam, Yoshio Hayashi and Sang-Hun Jung. (2016). An Overview of Severe Acute Respiratory Syndrome−Coronavirus (SARS-CoV) 3CL Protease Inhibitors: Peptidomimetics and Small Molecule Chemotherapy. J. Med. Chem. 59, 6595−6628. doi: https://doi.org/10.1021/acs.jmedchem.5b01461

Rabaan AA, Al-Ahmed SH, Sah R, Tiwari R, Yatoo MI, Patel SK, Pathak M, Malik YS, Dhama K, Singh KP, Bonilla-Aldana DK. (2020). SARS-CoV-2/COVID-19 and advances in developing potential therapeutics and vaccines to counter this emerging pandemic virus–a review. Preprints, 2020040075.recent trends. European Review for Medical and Pharmacological Sciences 24:2006-2011. doi : https://doi.org/10.20944/preprints202004.0075.v1

Rohs R, Bloch I, Sklenar H, Shakked Z. (2005). Molecular flexibility in ab-initio drug docking to DNA: binding-site and binding-mode transitions in all-atom Monte Carlo simulations. Nucl Acids Res 33: 7048-7057. doi : https://doi.org/10.1093/nar/gki1008

Sagar, S., Kaur, M., and Minneman, K. P. (2010). Antiviral lead compounds from marine sponges. Mar. Drugs 8, 2619–2638. doi : https://doi.org/10.3390/md8102619

Sampangi-Ramaiah MH, Vishwakarma R, Shaanker RU. (2020). Molecular docking analysis of selected natural products from plants for inhibition of SARS-CoV-2 main protease. Curr Sci. 118(7):1087. Shaghaghi N. Molecular Docking study of novel COVID-19 Protease with low risk Terpenoides Compounds of Plants. ChemRxiv. doi: https://doi.org/10.18520/cs/v118/i7/1087-1092

Schoeman D, Fielding BC. (2019). Coronavirus envelope protein: current knowledge. Virol J 16, 69 (2019). doi : https://doi.org/10.1186/s12985-019-1182-0

Solerte SB, Gazzaruso C, Bonacasa R, Rondanelli M, Zamboni M, Basso C, Locatelli E, Schifino N, Giustina A, Fioravanti M. (2008). Nutritional supplements with oral amino acid mixtures increases whole-body lean mass and insulin sensitivity in elderly subjects with sarcopenia. Am J Cardiol 101(11A):69E–77E. doi: https://doi.org/10.1016/j.amjcard.2008.03.004

Uzair B, Mahmood Z, Tabassum S. (2011). Antiviral activity of natural products extracted from marine organisms. BioImpacts: BI. 1(4):203. doi : https://doi.org/10.5681/bi.2011.029

Varun, Sonam and Rita Kakkar. (2019). Isatin and its derivatives: a survey of recent syntheses, reactions, and applications. Med. Chem. Commun., 10, 351. doi : https://doi.org/10.1039/C8MD00585K

Vijayaraj, R., Altaff, K., Rosita, A. S., Ramadevi, S., & Revathy, J. (2020). Bioactive compounds from marine resources against novel corona virus (2019-nCoV): in silico study for corona viral drug. Natural Product Research, 1–5. doi : https://doi.org/10.1080/14786419.2020.1791115

Wellington K.D., Cambie R.C., Rutledge P.S., Bergquist P.R. (2000). Chemistry of sponges, 19: novel bioactive metabolites from Hamigera tarangaensis. J. Nat. Prod. 63:79–85. doi : https://doi.org/10.1021/np9903494

World Health Organization. (2020). WHO Coronavirus Disease (COVID-19). World. Health Organization. Retrieved from https://covid19.who.int/

Xuan-Yu Meng Hong-Xing Zhang, Mihaly Mezei, and Meng Cui. (2011). Molecular Docking: A powerful approach for structure-based drug discovery. Curr Comput Aided Drug Des 1; 7(2): 146–157. doi: https://doi.org/10.2174/157340911795677602

Xu, H.; Lv, M. (2009). Developments of Indoles as Anti-HIV-1 Inhibitors. Curr. Pharm. Des. 15. 2120–2148. doi : https://doi.org/10.2174/138161209788489168

Zaki A.M., van Boheemen S., Bestebroer T.M. (2012). Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. The New England Journal of Medicine 367:1814–1820. doi : https://doi.org/10.1056/NEJMoa1211721

Zappe A, M.E. Snell B., M.J. Bossard. (2008). PEGylation of cyanovirin–N, an entry inhibitor of HIV. Advanced Drug Delivery Reviews 60 79–87. doi : https://doi.org/10.1016/j.addr.2007.05.016

Zhang, L., Lin, D., Kusov, Y., Nian, Y., Ma, Q., Wang, J., von Brunn, A., Leyssen, P., Lanko, K., Neyts, J., de Wilde, A., Snijder, E. J., Liu, H., & Hilgenfeld, R. (2020.). α-Ketoamides as broad-spectrum inhibitors of coronavirus and enterovirus replication: Structure-based design, synthesis, and activity assessment. Journal of Medicinal Chemistry, 63(9), 4562–4578. doi : 10.1021/acs.jmedchem.9b01828

Zhou Y, Hou Y, Shen J, Huang Y, Martin W, Cheng F. (2020). Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2. Cell Discovery. doi : https://doi.org/10.1038/s41421-020-0153-3

Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, Zhao X, Huang B, Shi W, Lu R, Niu P, Zhan F, Ma X, Wang D, Xu W, Wu G, Gao GF, Tan W. (2020). A Novel Coronavirus from Patients with Pneumonia in China, 2019. N Engl J Med. 382, 727-733. doi : https://doi.org/10.1056/NEJMoa2001017

Zumla, A.; Chan, J.F.W.; Azhar, E.I.; Hui, D.S.C.; Yuen, K.-Y. (2016). Coronaviruses—Drug discovery and therapeutic options. Nat. Rev. Drug Discov. 15, 327–347. doi https://doi.org/10.1038/nrd.2015.37

Author Biography

Fitri Lianingsih, Institut Teknologi Sepuluh Nopember Surabaya

Department of Biology, Faculty of Science and Data Analytics

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How to Cite

Lianingsih, F. (2021). In silico analysis of Trisindoline 1 compound against Mpro SARS-CoV-2 as novel potential drugs candidate. Sasambo Journal of Pharmacy, 2(2), 42–50. https://doi.org/10.29303/sjp.v2i2.87