In Silico Analysis of Sponges Compound Against Mpro COVID-19: A Review
Keywords:
Keywords: COVID-19, in silico, Mpro, spongesAbstract
Abstract. The novel coronavirus 2019 (COVID-19) is one of the viruses that can infect humans and cause high mortality worldwide. The protease (Mpro) is a key 2019-nCoV enzyme mediate viral replication and transcription. Mpro is currently used as the candidate for the COVID-19 vaccine but yet the interaction of the protein is to be determined. The Mpro can be a target protein to design the drug of COVID19. The drug design from natural products that are considered to have low toxicity is needed against the virus. The aim of this study to determine the potential of some marine compounds against COVID-19 in silico and to find the potential amino acid residues between interaction ligandprotein receptors. The methods of this study use virtual screening of Autodock Vina and study literature to find the action mechanism between ligand and protein receptors. The result of this study was the selected marine compound which may have the potential for 2019-nCoV to be future drugs. The interaction between the best ligand-protein predominant by glutamine and threonine amino acid. The role of glutamine as immune nutrition for recovery patients for some disease and maintain the body back to the homeostasis. Threonine could contribute to inflammatory responses against foreign substances.
Downloads
Download data is not yet available.
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 (COVID19) during the early outbreak period: A scoping review. Infectious Diseases of Poverty 9(1), 29. 16(1):69. 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. 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. 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. 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 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. 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. 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. 2003, 42, 3406 – 3409. Crumpacker CS. 2004. Use of antiviral drugs to prevent herpes virus transmission. New England Journal of Medicine 350:67-68.
Cui J, Li F, Shi Z-L. 2019. Origin and evolution of pathogenic coronaviruses. Nat Rev Microbiol ;17:181–92. Duan H.Q., Zhang Y.D., Fan K., Suo Z.W., Hu G., Mu X. 2007. Antiinflammatory mechanism of esculetin. Chin. J. Vet. Med 43:45– 46 Guedes IA, de Magalhães CS, Dardenne LE. 2014. Receptor-ligand molecular docking. Biophysical Reviews 6: 75-87. 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. Jin, Z., Du, X., Xu, Y. et al. Structure of Mpro from COVID-19 virus and discovery of its inhibitors. 2020. Nature 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. Lin X, Li X, Lin X. 2020. A Review on Applications of Computational Methods in Drug Screening and Design. Molecules. 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. 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. Loya S, 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 J15; 362(Pt 3): 685–692. McConkey BJ, Sobolev V, Edelman M. 2002. The performance of current methods in ligand-protein docking. Current Science 83:845–855. 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. 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. 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. Peiris JS, Guan Y, Yuen KY. 2004. Severe acute respiratory syndrome. Nature Medicine 10(12 Suppl):S88-97. 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. 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. Sagar, S., Kaur, M., and Minneman, K. P. 2010. Antiviral lead compounds from marine sponges. Mar. Drugs 8, 2619–2638. 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. Schoeman D, Fielding BC. 2019. Coronavirus envelope protein: current knowledge. Virology Journal 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 Uzair B, Mahmood Z, Tabassum S. 2011. Antiviral activity of natural products extracted from marine organisms. BioImpacts: BI. 1(4):203 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. 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. World Health Organization. 2020. WHO Coronavirus Disease (COVID-19). World. Health Organization. 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. 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. 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. Zhou Y, Hou Y, Shen J, Huang Y, Martin W, Cheng F. 2020. Networkbased drug repurposing for novel coronavirus 2019-nCoV/SARSCoV-2. Cell Discovery. 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. 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.
Z., Sun, C., Sylvia, S., Rozelle, S., Raat, H., & Zhou, H. 2020. Epidemiology, causes, clinical manifestation and diagnosis, prevention and control of coronavirus disease (COVID19) during the early outbreak period: A scoping review. Infectious Diseases of Poverty 9(1), 29. 16(1):69. 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. 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. 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. 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 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. 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. 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. 2003, 42, 3406 – 3409. Crumpacker CS. 2004. Use of antiviral drugs to prevent herpes virus transmission. New England Journal of Medicine 350:67-68.
Cui J, Li F, Shi Z-L. 2019. Origin and evolution of pathogenic coronaviruses. Nat Rev Microbiol ;17:181–92. Duan H.Q., Zhang Y.D., Fan K., Suo Z.W., Hu G., Mu X. 2007. Antiinflammatory mechanism of esculetin. Chin. J. Vet. Med 43:45– 46 Guedes IA, de Magalhães CS, Dardenne LE. 2014. Receptor-ligand molecular docking. Biophysical Reviews 6: 75-87. 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. Jin, Z., Du, X., Xu, Y. et al. Structure of Mpro from COVID-19 virus and discovery of its inhibitors. 2020. Nature 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. Lin X, Li X, Lin X. 2020. A Review on Applications of Computational Methods in Drug Screening and Design. Molecules. 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. 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. Loya S, 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 J15; 362(Pt 3): 685–692. McConkey BJ, Sobolev V, Edelman M. 2002. The performance of current methods in ligand-protein docking. Current Science 83:845–855. 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. 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. 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. Peiris JS, Guan Y, Yuen KY. 2004. Severe acute respiratory syndrome. Nature Medicine 10(12 Suppl):S88-97. 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. 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. Sagar, S., Kaur, M., and Minneman, K. P. 2010. Antiviral lead compounds from marine sponges. Mar. Drugs 8, 2619–2638. 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. Schoeman D, Fielding BC. 2019. Coronavirus envelope protein: current knowledge. Virology Journal 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 Uzair B, Mahmood Z, Tabassum S. 2011. Antiviral activity of natural products extracted from marine organisms. BioImpacts: BI. 1(4):203 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. 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. World Health Organization. 2020. WHO Coronavirus Disease (COVID-19). World. Health Organization. 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. 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. 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. Zhou Y, Hou Y, Shen J, Huang Y, Martin W, Cheng F. 2020. Networkbased drug repurposing for novel coronavirus 2019-nCoV/SARSCoV-2. Cell Discovery. 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. 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.
Downloads
Published
2021-02-28
How to Cite
Lianingsih, F. (2021). In Silico Analysis of Sponges Compound Against Mpro COVID-19: A Review. Proceeding International Conference on Science and Engineering, 4, 296–300. Retrieved from http://sunankalijaga.org/prosiding/index.php/icse/article/view/673
Issue
Section
Articles
