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Research Article

Pharmacoinformatics and molecular dynamics simulation approach to identify anti-diarrheal potentials of Centella asiatica (L.) Urb. against Vibrio cholerae

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Pages 14730-14743 | Received 13 Dec 2022, Accepted 07 Mar 2023, Published online: 16 Mar 2023

References

  • Abdelli, I., Hassani, F., Bekkel Brikci, S., & Ghalem, S. (2021). In silico study the inhibition of angiotensin converting enzyme 2 receptor of COVID-19 by Ammoides verticillata components harvested from Western Algeria. Journal of Biomolecular Structure & Dynamics, 39(9), 3263–3276. https://doi.org/10.1080/07391102.2020.1763199
  • Ahmed, S. S., Rahman, M. O., Alqahtani, A. S., Sultana, N., Almarfadi, O. M., Ali, M. A., & Lee, J. (2023). Anticancer potential of phytochemicals from Oroxylum indicum targeting Lactate Dehydrogenase A through bioinformatic approach. Toxicology Reports, 10, 56–75. https://doi.org/10.1016/j.toxrep.2022.12.007
  • Alsamhary, K., Al-Enazi, N., Alshehri, W. A., & Ameen, F. (2020). Gold nanoparticles synthesised by flavonoid tricetin as a potential antibacterial nanomedicine to treat respiratory infections causing opportunistic bacterial pathogens. Microbial Pathogenesis, 139, 103928. https://doi.org/10.1016/j.micpath.2019.103928
  • Antibacterial and Antifungal Activities of Several Extracts of Centella asiatica L. against Some Human Pathogenic Microbes | Semantic Scholar. (n.d.). Retrieved February 9 (2023). from https://www.semanticscholar.org/paper/Antibacterial-and-Antifungal-Activities-of-Several-Dash-Faruquee/89d295f1151e20d0df5fc8a08c8e7854d6efd968
  • B, M. (2004). An in vitro study of the effect of Centella asiatica [Indian pennywort] on enteric pathogens. Indian Journal of Pharmacology, 36(1), 41.
  • Balani, S. K., Miwa, G. T., Gan, L.-S., Wu, J.-T., & Lee, F. W. (2005). Strategy of utilizing in vitro and in vivo ADME tools for lead optimization and drug candidate selection. Current Topics in Medicinal Chemistry, 5(11), 1033–1038. https://doi.org/10.2174/156802605774297038
  • Biswas, D., Mandal, S., Chatterjee Saha, S., Tudu, C. K., Nandy, S., Batiha, G. E.-S., Shekhawat, M. S., Pandey, D. K., & Dey, A. (2021). Ethnobotany, phytochemistry, pharmacology, and toxicity of Centella asiatica (L.) Urban: A comprehensive review. Phytotherapy Research, 35(12), 6624–6654. https://doi.org/10.1002/ptr.7248
  • Chatterjee, A., Dutta, P. K., & Chowdhury, R. (2007). Effect of Fatty Acids and Cholesterol Present in Bile on Expression of Virulence Factors and Motility of Vibrio cholerae. Infection and Immunity, 75(4), 1946–1953. https://doi.org/10.1128/IAI.01435-06
  • Colwell, R. R., & Huq, A. (1994). Vibrios in the environment: Viable but nonculturable Vibrio cholerae. In Vibrio cholerae and Cholera (pp. 117–133). John Wiley & Sons, Ltd. https://doi.org/10.1128/9781555818364.ch9
  • Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7(1), 42717. Article 1. https://doi.org/10.1038/srep42717
  • Daina, A., Michielin, O., & Zoete, V. (2019). SwissTargetPrediction: Updated data and new features for efficient prediction of protein targets of small molecules. Nucleic Acids Research, 47(W1), W357–W364. https://doi.org/10.1093/nar/gkz382
  • Daina, A., & Zoete, V. (2016). A BOILED-Egg To Predict Gastrointestinal Absorption and Brain Penetration of Small Molecules. ChemMedChem. 11(11), 1117–1121. https://doi.org/10.1002/cmdc.201600182
  • Dallakyan, S., & Olson, A. J. (2015). Small-molecule library screening by docking with PyRx. Methods in Molecular Biology (Clifton, N.J.), 1263, 243–250. https://doi.org/10.1007/978-1-4939-2269-7_19
  • Du, Y.-Q., Su, T., Hao, J.-Y., Wang, B.-M., Chen, M.-H., Li, Y.-M., Tang, C.-W., Gong, Y.-F., Man, X.-H., Gao, L., Cai, Q.-C., & Li, Z.-S. (2012). Gastro-protecting effect of gefarnate on chronic erosive gastritis with dyspeptic symptoms. Chinese Medical Journal, 125(16), 2878–2884.
  • Dutkiewicz, Z., & Mikstacka, R. (2018). Structure-Based Drug Design for Cytochrome P450 Family 1 Inhibitors. Bioinorganic Chemistry and Applications, 2018, e3924608. https://doi.org/10.1155/2018/3924608
  • Faruque, S. M., Albert, M. J., & Mekalanos, J. J. (1998). Epidemiology, genetics, and ecology of toxigenic Vibrio cholerae. Microbiology and Molecular Biology Reviews, 62(4), 1301–1314. https://doi.org/10.1128/MMBR.62.4.1301-1314.1998
  • Faruque, S. M., Chowdhury, N., Kamruzzaman, M., Ahmad, Q. S., Faruque, A. S. G., Salam, M. A., Ramamurthy, T., Nair, G. B., Weintraub, A., & Sack, D. A. (2003). Reemergence of Epidemic Vibrio cholerae O139, Bangladesh. Emerging Infectious Diseases, 9(9), 1116–1122. https://doi.org/10.3201/eid0909.020443
  • Gangopadhyay, A., & Datta, A. (2015). Identification of inhibitors against the potential ligandable sites in the active cholera toxin. Computational Biology and Chemistry, 55, 37–48. https://doi.org/10.1016/j.compbiolchem.2015.02.011
  • Gohil, K. J., Patel, J. A., & Gajjar, A. K. (2010). Pharmacological review on Centella asiatica: A potential herbal cure-all. Indian Journal of Pharmaceutical Sciences, 72(5), 546–556. https://doi.org/10.4103/0250-474X.78519
  • Guex, N., Peitsch, M. C., & Schwede, T. (2009). Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: A historical perspective. Electrophoresis, 30 Suppl 1(Suppl 1), S162–S173. https://doi.org/10.1002/elps.200900140
  • Hanwell, M. D., Curtis, D. E., Lonie, D. C., Vandermeersch, T., Zurek, E., & Hutchison, G. R. (2012). Avogadro: An advanced semantic chemical editor, visualization, and analysis platform. Journal of Cheminformatics, 4(1), 17. https://doi.org/10.1186/1758-2946-4-17
  • Haus-Cheymol, R., Theodose, R., Quilici, M. L., Chevallier, G., Liautaud, B., Ktari, F., Garcia, J., de Laval, F., & Migliani, R. (2012). A cluster of acute diarrhea suspected to be cholera in French travelers in Haiti, December 2010. Journal of Travel Medicine, 19(3), 189–191. https://doi.org/10.1111/j.1708-8305.2012.00607.x
  • Helgren, T. R., & Hagen, T. J. (2017). Demonstration of AutoDock as an Educational Tool for Drug Discovery. Journal of Chemical Education, 94(3), 345–349. https://doi.org/10.1021/acs.jchemed.6b00555
  • Jain, M., Kumar, P., Goel, A. K., Kamboj, D. V., & Singh, L. (2008). Class 1 integrons and SXT elements conferring multidrug resistance in Vibrio cholerae O1 strains associated with a recent large cholera outbreak in Orissa, Eastern India. International Journal of Antimicrobial Agents, 32(5), 459–460. https://doi.org/10.1016/j.ijantimicag.2008.05.003
  • Junaid, M., Alam, M. J., Hossain, M. K., Halim, M. A., & Ullah, M. O. (2018). Molecular docking and dynamics of Nickel-Schiff base complexes for inhibiting β-lactamase of Mycobacterium tuberculosis. In Silico Pharmacology, 6(1), 6. https://doi.org/10.1007/s40203-018-0044-6
  • Karuvantevida, N., Gnanasekar, S., Iratni, R., & Sivaramakrishnan, S. (2022). Fabrication of g-C3N4 nanosheets reinforced with myricetin functionalized AgNPs for its potential bactericidal effect. Bulletin of Environment, Pharmacology and Life Sciences, 11, 129–136.
  • Khan, W. A., Bennish, M. L., Seas, C., Khan, E. H., Ronan, A., Dhar, U., Busch, W., & Salam, M. A. (1996). Randomised controlled comparison of single-dose ciprofloxacin and doxycycline for cholera caused by Vibrio cholerae 01 or 0139. Lancet (London, England), 348(9023), 296–300. https://doi.org/10.1016/s0140-6736(96)01180-4
  • Krukonis, E. S., Yu, R. R., & Dirita, V. J. (2000). The Vibrio cholerae ToxR/TcpP/ToxT virulence cascade: Distinct roles for two membrane-localized transcriptional activators on a single promoter. Molecular Microbiology, 38(1), 67–84. https://doi.org/10.1046/j.1365-2958.2000.02111.x
  • Kumar, P., Jain, M., Goel, A. K., Kamboj, D. V., & Kumar, O. (2012). Tetracycline resistant V. cholerae O1 biotype El Tor serotype Ogawa with classical ctxB from a recent cholera outbreak in Orissa, Eastern India. Journal of Infection and Public Health, 5(2), 217–219. https://doi.org/10.1016/j.jiph.2011.09.007
  • Cholera Working Group, International Centre for Diarrhoeal Diseases Research, Bangladesh. (1993). Large epidemic of cholera-like disease in Bangladesh caused by Vibrio cholerae O139 synonym Bengal. Lancet (London, England), 342(8868), 387–390.
  • Leite-Sampaio, N. F., Gondim, C. N. F. L., Martins, R. A. A., Siyadatpanah, A., Norouzi, R., Kim, B., Sobral-Souza, C. E., Gondim, G. E. C., Ribeiro-Filho, J., & Coutinho, H. D. M. (2022). Potentiation of the Activity of Antibiotics against ATCC and MDR Bacterial Strains with (+)-α-Pinene and (-)-Borneol. BioMed Research International, 2022, e8217380. https://doi.org/10.1155/2022/8217380
  • Lipinski, C. A. (2004). Lead- and drug-like compounds: The rule-of-five revolution. Drug Discovery Today. Technologies, 1(4), 337–341. https://doi.org/10.1016/j.ddtec.2004.11.007
  • Maltarollo, V. G., Gertrudes, J. C., Oliveira, P. R., & Honorio, K. M. (2015). Applying machine learning techniques for ADME-Tox prediction: A review. Expert Opinion on Drug Metabolism & Toxicology, 11(2), 259–271. https://doi.org/10.1517/17425255.2015.980814
  • McKerrow, J. H., & Lipinski, C. A. (2017). The rule of five should not impede anti-parasitic drug development. International Journal for Parasitology. Drugs and Drug Resistance, 7(2), 248–249. https://doi.org/10.1016/j.ijpddr.2017.05.003
  • Mwansa, J. C. L., Mwaba, J., Lukwesa, C., Bhuiyan, N. A., Ansaruzzaman, M., Ramamurthy, T., Alam, M., & Balakrish Nair, G. (2007). Multiply antibiotic-resistant Vibrio cholerae O1 biotype El Tor strains emerge during cholera outbreaks in Zambia. Epidemiology and Infection, 135(5), 847–853. https://doi.org/10.1017/S0950268806007254
  • Optimized Hydrophobic Interactions and Hydrogen Bonding at the Target-Ligand Interface Leads the Pathways of Drug-Designing | PLOS ONE. (n.d.). Retrieved February 10 (2023). from https://doi.org/10.1371/journal.pone.0012029
  • Pires, D. E. V., Blundell, T. L., & Ascher, D. B. (2015). pkCSM: Predicting Small-Molecule Pharmacokinetic and Toxicity Properties Using Graph-Based Signatures. Journal of Medicinal Chemistry, 58(9), 4066–4072. https://doi.org/10.1021/acs.jmedchem.5b00104
  • Podlipnik, Č., & Reina, J. J. (2012). Structure Based Design of Cholera Toxin Antagonists. In S. Gowder (Ed.), Cholera. InTechOpen. https://doi.org/10.5772/37635
  • Rahman, M. O., & Ahmed, S. S. (2022). Anti-angiogenic potential of bioactive phytochemicals from Helicteres isora targeting VEGFR-2 to fight cancer through molecular docking and molecular dynamics simulation. Journal of Biomolecular Structure and Dynamics, 0(0), 1–16. https://doi.org/10.1080/07391102.2022.2122568
  • Ramamurthy, T., Garg, S., Sharma, R., Bhattacharya, S. K., Nair, G. B., Shimada, T., Takeda, T., Karasawa, T., Kurazano, H., & Pal, A. (1993). Emergence of novel strain of Vibrio cholerae with epidemic potential in southern and eastern India. Lancet (London, England), 341(8846), 703–704. https://doi.org/10.1016/0140-6736(93)90480-5
  • Rashed, S. M., Iqbal, A., Mannan, S. B., Islam, T., Rashid, M., Johura, F., Watanabe, H., Hasan, N. A., Huq, A., Stine, O. C., Sack, R. B., Colwell, R. R., & Alam, M. (2013). Vibrio cholerae O1 El Tor and O139 Bengal Strains Carrying ctxBET, Bangladesh. Emerging Infectious Diseases, 19(10), 1713–1715. https://doi.org/10.3201/eid1910.130626
  • Rashed, S. M., Mannan, S. B., Johura, F., Islam, M. T., Sadique, A., Watanabe, H., Sack, R. B., Huq, A., Colwell, R. R., Cravioto, A., & Alam, M. (2012). Genetic characteristics of drug-resistant Vibrio cholerae O1 causing endemic cholera in Dhaka, 2006–2011. Journal of Medical Microbiology, 61(Pt 12), 1736–1745. https://doi.org/10.1099/jmm.0.049635-0
  • Ren, J., Yuan, L., Wang, W., Zhang, M., Wang, Q., Li, S., Zhang, L., & Hu, K. (2019). Tricetin protects against 6-OHDA-induced neurotoxicity in Parkinson’s disease model by activating Nrf2/HO-1 signaling pathway and preventing mitochondria-dependent apoptosis pathway. Toxicology and Applied Pharmacology, 378, 114617. https://doi.org/10.1016/j.taap.2019.114617
  • Rose, P. W., Prlić, A., Altunkaya, A., Bi, C., Bradley, A. R., Christie, C. H., Costanzo, L. D., Duarte, J. M., Dutta, S., Feng, Z., Green, R. K., Goodsell, D. S., Hudson, B., Kalro, T., Lowe, R., Peisach, E., Randle, C., Rose, A. S., Shao, C., … Burley, S. K. (2017). The RCSB protein data bank: Integrative view of protein, gene and 3D structural information. Nucleic Acids Research, 45(D1), D271–D281. https://doi.org/10.1093/nar/gkw1000
  • Samanta, S. (2023). Chapter 66—Mechanisms of gastrointestinal pathogenesis and landscape of intestinal immunity. In D. Bagchi, A. Das, & B. W. Downs (Eds.), Viral, Parasitic, Bacterial, and Fungal Infections. (pp. 863–913). Academic Press. https://doi.org/10.1016/B978-0-323-85730-7.00023-0
  • Sarma, K., Borkakoty, B., Parida, P., Bora, S., Mohapatra, P., Biswas, D., & Mahanta, J. (2016). Identification of natural lead molecules of Centella asiatica and Azadirachta indica targeting cholera toxin through structure based drug design. Indo American Journal of Pharmaceutical Research, 6(08), 6418–6429.
  • Seenivasagan, R., Kasimani, R., Rajakumar, S., Kalidoss, R., & Ayyasamy, P. M. (2016). Comparative modelling and molecular docking of nitrate reductase from Bacillus weihenstephanensis (DS45). Journal of Taibah University for Science, 10(4), 621–630. https://doi.org/10.1016/j.jtusci.2016.02.006
  • Seevaratnam, V., Banumathi, P., Premalatha, M. R., Sundaram, S., & Arumugam, T. (2012). Functional properties of Centella asiatica (L.): A reviEw. 4.
  • Sharif Siam, M. K., Sarker, A., & Sayeem, M. M. S. (2021). In silico drug design and molecular docking studies targeting Akt1 (RAC-alpha serine/threonine-protein kinase) and Akt2 (RAC-beta serine/threonine-protein kinase) proteins and investigation of CYP (cytochrome P450) inhibitors against MAOB (monoamine oxidase B) for OSCC (oral squamous cell carcinoma) treatment. Journal of Biomolecular Structure & Dynamics, 39(17), 6467–6479. https://doi.org/10.1080/07391102.2020.1802335
  • Shrestha, A. B., Khatroth, S., Malreddy, A., Issa, F. A., Shrestha, S., & Shrestha, S. (2022). Cholera amid COVID-19: Call from three nations; India, Bangladesh, and Nepal. Annals of Medicine and Surgery (2012), 84, 104936. https://doi.org/10.1016/j.amsu.2022.104936
  • Taheri, Y., Suleria, H. A. R., Martins, N., Sytar, O., Beyatli, A., Yeskaliyeva, B., Seitimova, G., Salehi, B., Semwal, P., Painuli, S., Kumar, A., Azzini, E., Martorell, M., Setzer, W. N., Maroyi, A., & Sharifi-Rad, J. (2020). Myricetin bioactive effects: Moving from preclinical evidence to potential clinical applications. BMC Complementary Medicine and Therapies, 20(1), 241. https://doi.org/10.1186/s12906-020-03033-z
  • The Ecology of Vibrio cholerae | SpringerLink. (n.d.). Retrieved February 9 (2023). from https://doi.org/10.1007/978-1-4757-9688-9_6
  • Trott, O., & Olson, A. J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading. Journal of Computational Chemistry, 31(2), 455–461. https://doi.org/10.1002/jcc.21334
  • Vasanth, S., Mohanraj, R. S., & Mandal, J. (2021). In-vitro study of the effect of Centella asiatica on cholera toxin production and the gene expression level of ctxA gene in Vibrio cholerae isolates. Journal of Ethnopharmacology, 279, 113930. https://doi.org/10.1016/j.jep.2021.113930
  • Vidya, N., Vadivukkarasi, B., Manivannan, G., & Anbarasu, K. (2008). Molecular modeling and docking studies of glutamate racemase in Vibrio vulnificus CMCP6. In Silico Biology, 8(5–6), 471–483.
  • Wade, R. C., & Goodford, P. J. (1989). The role of hydrogen-bonds in drug binding. Progress in Clinical and Biological Research, 289, 433–444.
  • Wei, L. S., Musa, N., Sengm, C. T., Wee, W., & Shazili, N. A. M. (2008). Antimicrobial properties of tropical plants against 12 pathogenic bacteria isolated from aquatic organisms. African Journal of Biotechnology, 7(13), Article 13. https://doi.org/10.4314/ajb.v7i13.58974
  • Weil, A. A., Khan, A. I., Chowdhury, F., Larocque, R. C., Faruque, A. S. G., Ryan, E. T., Calderwood, S. B., Qadri, F., & Harris, J. B. (2009). Clinical outcomes in household contacts of patients with cholera in Bangladesh. Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America, 49(10), 1473–1479. https://doi.org/10.1086/644779
  • Yuan, X., Li, Y., Vaziri, A. Z., Kaviar, V. H., Jin, Y., Jin, Y., Maleki, A., Omidi, N., & Kouhsari, E. (2022). Global status of antimicrobial resistance among environmental isolates of Vibrio cholerae O1/O139: A systematic review and meta-analysis. Antimicrobial Resistance and Infection Control, 11(1), 62. https://doi.org/10.1186/s13756-022-01100-3
  • Zuckerman, J. N., Rombo, L., & Fisch, A. (2007). The true burden and risk of cholera: Implications for prevention and control. The Lancet. Infectious Diseases, 7(8), 521–530. https://doi.org/10.1016/S1473-3099(07)70138-X

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