In-silico screening and identification of phytochemicals from Centella asiatica as potential inhibitors of sodium-glucose co-transporter 2 for treating diabetes

References

• Athanasiadis, E., Cournia, Z., & Spyrou, G. (2012). ChemBioServer: A web-based pipeline for filtering, clustering and visualization of chemical compounds used in drug discovery. Bioinformatics (Oxford, England), 28(22), 3002–3003. https://doi.org/10.1093/bioinformatics/bts551
   PubMed Web of Science ®Google Scholar
• Benson, N. C., & Daggett, V. (2012). A comparison of multiscale methods for the analysis of molecular dynamics simulations. The Journal of Physical Chemistry B, 116(29), 8722–8731. https://doi.org/10.1021/jp302103t
   PubMed Web of Science ®Google Scholar
• Bersales, L. G. (2018). Deaths in the Philippines, 2016. Philippine Statistics Authority [WWW Document]. Retrieved October 17, 2020 from https://psa.gov.ph/content/deaths-philippines-2016
   Google Scholar
• Centers for Disease Control and Prevention. (2020). National diabetes statistics report, 2020. Centers for Disease Control and Prevention, US Department of Health and Human Services.
   Google Scholar
• Chauhan, P. K., Pandey, I. P., & Dhatwalia, V. K. (2010). Evaluation of the anti-diabetic effect of ethanolic and methanolic extracts of Centella asiatica leaves extract on alloxan induced diabetic rats. Advances in Biological Research, 4, 27–30.
   Google Scholar
• Choi, C.-I. (2016). Sodium-glucose cotransporter 2 (SGLT2) inhibitors from natural products: Discovery of next-generation antihyperglycemic agents. Molecules, 21(9), 1136. https://doi.org/10.3390/molecules21091136
   PubMed Web of Science ®Google Scholar
• Dash, B. K., Faruquee, H. M., Biswas, S. K., Alam, M. K., Sisir, S. M., & Prodhan, U. K. (2011). Antibacterial and antifungal activities of several extracts of Centella asiatica L. against some human pathogenic microbes. Life Sciences and Medicine Research, 2011, 1–5.
   Google Scholar
• de Freitas, R. F., & Schapira, M. (2017). A systematic analysis of atomic protein–ligand interactions in the PDB. MedChemComm, 8(10), 1970–1981. https://doi.org/10.1039/C7MD00381A
   PubMed Web of Science ®Google Scholar
• Deng, D., Xu, C., Sun, P., Wu, J., Yan, C., Hu, M., & Yan, N. (2014). Crystal structure of the human glucose transporter GLUT1. Nature, 510(7503), 121–125.
   PubMed Web of Science ®Google Scholar
• Fitrianda, E., Sukandar, E. Y., Elfahmi, E., & Adnyana, I. K. (2017). Antidiabetic activity of extract, fractions, and asiaticoside compound isolated from Centella asiatica Linn. Leaves in alloxan-induced diabetic mice. Asian Journal of Pharmaceutical and Clinical Research, 10(10), 268–272. https://doi.org/10.22159/ajpcr.2017.v10i10.20419
   Google Scholar
• Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 10(5), 449–461. https://doi.org/10.1517/17460441.2015.1032936
   PubMed Web of Science ®Google Scholar
• George, M., & Joseph, L. (2009). Anti-allergic, anti-pruritic, and anti-inflammatory activities of Centella asiatica extracts. African Journal of Traditional, Complementary and Alternative Medicines, 6(4), 554–559. https://doi.org/10.4314/ajtcam.v6i4.57206.
   PubMedGoogle Scholar
• 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
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Hashim, P., Sidek, H., Helan, M., Sabery, A., Palanisamy, U. D., & Ilham, M. (2011). Triterpene composition and bioactivities of Centella asiatica. Molecules (Basel, Switzerland), 16(2), 1310–1322. https://doi.org/10.3390/molecules16021310
   PubMed Web of Science ®Google Scholar
• Hsia, D. S., Grove, O., & Cefalu, W. T. (2017). An update on SGLT2 inhibitors for the treatment of diabetes mellitus. Current Opinion in Endocrinology, Diabetes, and Obesity, 24, 73.
   PubMedGoogle Scholar
• Hung, H.-Y., Qian, K., Morris-Natschke, S. L., Hsu, C.-S., & Lee, K.-H. (2012). Recent discovery of plant-derived anti-diabetic natural products. Natural Product Reports, 29(5), 580–606. https://doi.org/10.1039/c2np00074a
   PubMed Web of Science ®Google Scholar
• Izairi, R., & Kamberaj, H. (2017). Comparison study of polar and nonpolar contributions to solvation free energy. Journal of Chemical Information and Modeling, 57(10), 2539–2553. https://doi.org/10.1021/acs.jcim.7b00368
   PubMed Web of Science ®Google Scholar
• Jugran, A. K., Rawat, S., Devkota, H. P., Bhatt, I. D., & Rawal, R. S. (2020). Diabetes and plant-derived natural products: From ethnopharmacological approaches to their potential for modern drug discovery and development. PhytotherapyResearch,5(1), 223–245. https://doi.org/10.1002/ptr.6821
   Google Scholar
• Kabir, A. U., Samad, M. B., D’Costa, N. M., Akhter, F., Ahmed, A., & Hannan, J. M. A. (2014). Anti-hyperglycemic activity of Centella asiatica is partly mediated by carbohydrase inhibition and glucose-fiber binding. BMC Complementary and Alternative Medicine, 14(1), 1–14. https://doi.org/10.1186/1472-6882-14-31
   PubMedGoogle Scholar
• Kalra, S. (2014). Sodium glucose co-transporter-2 (SGLT2) inhibitors: A review of their basic and clinical pharmacology. Diabetes Therapy: Research, Treatment and Education of Diabetes and Related Disorders, 5(2), 355–366. https://doi.org/10.1007/s13300-014-0089-4
   PubMed Web of Science ®Google Scholar
• Kim, S., Thiessen, P. A., Bolton, E. E., Chen, J., Fu, G., Gindulyte, A., Han, L., He, J., He, S., Shoemaker, B. A., Wang, J., Yu, B., Zhang, J., & Bryant, S. H. (2016). PubChem substance and compound databases. Nucleic Acids Research, 44(D1), D1202–D1213. https://doi.org/10.1093/nar/gkv951
   PubMed Web of Science ®Google Scholar
• Kumari, R., Kumar, R., Consortium, O. S. D. D., & Lynn, A. (2014). g_mmpbsa-a GROMACS tool for high-throughput MM-PBSA calculations . Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/10.1021/ci500020m
   PubMed Web of Science ®Google Scholar
• Lemkul, J. (2018). From proteins to perturbed hamiltonians: A suite of tutorials for the GROMACS-2018 molecular simulation package [Article v1. 0]. Living Journal of Computational Molecular Science, 1, 5068.
   Google Scholar
• Li, J., Liu, Z., Zhao, Y., Zhu, X., Yu, R., Dong, S., & Wu, H. (2018). Novel natural angiotensin converting enzyme (ACE)-inhibitory peptides derived from sea cucumber-modified hydrolysates by adding exogenous proline and a study of their structure–activity relationship. Marine Drugs, 16(8), 271. https://doi.org/10.3390/md16080271
   PubMed Web of Science ®Google Scholar
• 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
   PubMedGoogle Scholar
• Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/10.1002/jcc.21256
   PubMed Web of Science ®Google Scholar
• Molsoft, L. L. C. (2018). Drug-Likeness and molecular property prediction. http://molsoft.com/mprop/ (Accessed on May 16, 2021)
   Google Scholar
• Petit, J., Meurice, N., Kaiser, C., & Maggiora, G. (2012). Softening the rule of Five-where to draw the line? Bioorganic & Medicinal Chemistry, 20(18), 5343–5351. https://doi.org/10.1016/j.bmc.2011.11.064
   PubMed Web of Science ®Google Scholar
• Pittella, F., Dutra, R. C., Junior, D. D., Lopes, M. T., & Barbosa, N. R. (2009). Antioxidant and cytotoxic activities of Centella asiatica (L) Urb. International Journal of Molecular Sciences, 10(9), 3713–3721. https://doi.org/10.3390/ijms10093713
   PubMed Web of Science ®Google Scholar
• Rizvi, S., Shakil, S., Biswas, D., Shakil, S., Shaikh, S., Bagga, P., & Kamal, M. A. (2013). Invokana (Canagliflozin) as a dual inhibitor of AChE and SGLT2: Advancement in Alzheimer’s disease-diabetes type 2 linkage via an enzoinformatics study. CNS Neurol Disord Drug Targets, 18, 18.
   Google Scholar
• Roglic, G. (2016). WHO global report on diabetes: A summary. International Journal of Noncommunicable Diseases, 1(1), 3. https://doi.org/10.4103/2468-8827.184853
   Google Scholar
• 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. (2016). 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.
   Web of Science ®Google Scholar
• Schrödinger. (2020a). Schrödinger release 2020-3: Maestro. Schrödinger, LLC.
   Google Scholar
• Schrödinger. (2020b). Schrödinger release 2020-3: QikProp. Schrödinger, LLC.
   Google Scholar
• Sha, S., Polidori, D., Farrell, K., Ghosh, A., Natarajan, J., Vaccaro, N., Pinheiro, J., Rothenberg, P., & Plum-Mörschel, L. (2015). Pharmacodynamic differences between canagliflozin and dapagliflozin: Results of a randomized, double-blind, crossover study. Diabetes, Obesity and Metabolism, 17(2), 188–197. https://doi.org/10.1111/dom.12418
   PubMed Web of Science ®Google Scholar
• Shaikh, F., & Siu, S. W. (2016). Identification of novel natural compound inhibitors for human complement component 5a receptor by homology modeling and virtual screening. Medicinal Chemistry Research: An International Journal for Rapid Communications on Design and Mechanisms of Action of Biologically Active Agents, 25, 1564–1573. https://doi.org/10.1007/s00044-016-1591-1
   PubMed Web of Science ®Google Scholar
• Singh, M., & Kumar, A. (2018). Risks associated with SGLT2 inhibitors: An overview. Current Drug Safety, 13(2), 84–91. https://doi.org/10.2174/1574886313666180226103408
   PubMed Web of Science ®Google Scholar
• Supkamonseni, N., Thinkratok, A., Meksuriyen, D., & Srisawat, R. (2014). Hypolipidemic and hypoglycemic effects of Centella asiatica (L.) extract in vitro and in vivo. Indian Journal of Experimental Biology, 52, 965–971.
   Google Scholar
• Tamura, Y., Miyagawa, H., Yoshida, T., & Chuman, H. (2015). Binding interaction of SGLT with sugar and thiosugar by the molecular dynamics simulation. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1848(11), 2799–2804. https://doi.org/10.1016/j.bbamem.2015.08.001
   PubMed Web of Science ®Google Scholar
• Tentolouris, A., Vlachakis, P., Tzeravini, E., Eleftheriadou, I., & Tentolouris, N. (2019). SGLT2 inhibitors: A review of their antidiabetic and cardioprotective effects. International Journal of Environmental Research and Public Health, 16(16), 2965. https://doi.org/10.3390/ijerph16162965
   PubMed Web of Science ®Google Scholar
• Thompson, D. C., Humblet, C., & Joseph-McCarthy, D. (2008). Investigation of MM-PBSA rescoring of docking poses. Journal of Chemical Information and Modeling, 48(5), 1081–1091. https://doi.org/10.1021/ci700470c
   PubMed Web of Science ®Google Scholar
• Vanommeslaeghe, K., Hatcher, E., Acharya, C., Kundu, S., Zhong, S., Shim, J., Darian, E., Guvench, O., Lopes, P., Vorobyov, I., & Mackerell, A. D. (2010). CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. Journal of Computational Chemistry, 31(4), 671–690. https://doi.org/10.1002/jcc.21367
   PubMed Web of Science ®Google Scholar
• Veeresham, C. (2012). Natural products derived from plants as a source of drugs. Journal of Advanced Pharmaceutical Technology & Research, 3(4), 200–201. https://doi.org/10.4103/2231-4040.104709
   PubMedGoogle Scholar
• Wang, X., Wu, S., Xu, D., Xie, D., & Guo, H. (2011). Inhibitor and substrate binding by angiotensin-converting enzyme: Quantum mechanical/molecular mechanical molecular dynamics studies. Journal of Chemical Information and Modeling, 51(5), 1074–1082. https://doi.org/10.1021/ci200083f
   PubMed Web of Science ®Google Scholar
• Watanabe, A., Choe, S., Chaptal, V., Rosenberg, J. M., Wright, E. M., Grabe, M., & Abramson, J. (2010). The mechanism of sodium and substrate release from the binding pocket of vSGLT. Nature, 468(7326), 988–991. https://doi.org/10.1038/nature09580
   Google Scholar
• Wright, E. M., Loo, D. D., & Hirayama, B. A. (2011). Biology of human sodium glucose transporters. Physiological Reviews, 91(2), 733–794. https://doi.org/10.1152/physrev.00055.2009
   PubMed Web of Science ®Google Scholar
• Zhang, M.-Q., & Wilkinson, B. (2007). Drug discovery beyond the 'rule-of-five' . Current Opinion in Biotechnology, 18(6), 478–488. https://doi.org/10.1016/j.copbio.2007.10.005
   PubMed Web of Science ®Google Scholar