CONSTRUCTION OF THREE DIMENSIONAL STRUCTURES OF PHYTOESTROGENS CONVERTED FROM SMILES STRING REPRESENTATIONS FOR SIMULATIONS USING PLANTS DOCKING SOFTWARE

https://doi.org/10.22146/tradmedj.12820

Enade Perdana Istyastono, Nunung Yuniarti,

(1) Division of Drug Design and Discovery, Faculty of Pharmacy, Sanata Dharma University
(2) Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Gadjah Mada

Abstract


Phytoestrogens have some important biological effects and could be employed as medicinal resources, for example as cancer chemopreventive agents. Phytoestrogen is defined as a phytochemical that has estrogenic or anti estrogenic effects. However, there is no database providing comprehensive list of phytoestrogen structures. In computer-aided drug discovery, the database is required to perform virtual screening for retrospective validation and structure-based drug design. The research presented in this article attempted to collect a comprehensive list of phytoestrogen structures. Subsequently, the structures were prepared in their three dimensional structures using SPORES1.3 for molecular docking simulations using PLANTS1.2. The ready-to-dock structures were then stored online as phytoestrogens.zip and could be downloaded from http://molmod.org/phytoestrogens.zip. This database contains 30 ready-to-dock unique phytoestrogens with total of 53 different configurations.

Keywords


Phytoestrogen, database, drug discovery, molecular docking

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References

Ali, S. and Coombes, R.C. 2000. Estrogen receptor alpha in human breast cancer: occurrence and significance. J. Mammary Gland Biol. Neoplasia 5: 271–281.

Anita, Y., Radifar, M., Kardono, L., Hanafi, M. and Istyastono, E.P. 2012. Structure-based design of eugenol analogs as potential estrogen receptor antagonists. Bioinformation 8: 901–906.

Anita, Y., Sundowo, A., Dewi, N.L.P., Filailla, E., Mulyani, H., Risdian, C., Banjarnahor, S., Hanafi, M. and Istyastono, E.P. 2015. Biotransformation of eugenol to dehydroeugenol catalyzed by Brassica juncea peroxidase and its cytotoxicity activities. Procedia Chem. 16: 265–271.

Balunas, M.J., Su, B., Brueggemeier, R.W. and Kinghorn, A.D. 2008. Xanthones from the botanical dietary supplement mangosteen (Garcinia mangostana) with aromatase inhibitory activity. J. Nat. Prod. 71: 1161–1166.

Bento, A.P., Gaulton, A., Hersey, A., Bellis, L.J., Chambers, J., Davies, M., Krüger, F.A., Light, Y., Mak, L., McGlinchey, S., Nowotka, M., Papadatos, G., Santos, R. and Overington, J.P. 2014. The ChEMBL bioactivity database: An update. Nucl. Acids Res. 42: 1083–1090.

Brusotti, G., Cesari, I., Dentamaro, A., Caccialanza, G. and Massolini, G. 2014. Isolation and characterization of bioactive compounds from plant resources: The role of analysis in the ethnopharmacological approach. J. Pharm. Biomed. Anal. 87: 218–228.

Cardoso, F. and Senkus, E., 2015. Breast cancer in 2014: A call back to reality! Nat. Rev. Clin. Oncol. 12, 67–68.

Dixon, R.A. 2004. Phytoestrogens. Annu. Rev. Plant Biol. 55: 225–261.

Efferth, T. and Koch, E. 2011. Complex interactions between phytochemicals. The multi-target therapeutic concept of phytotherapy. Curr. Drug Targets 12: 122–132.

Helferich, W.G., Andrade, J.E. and Hoagland, M.S. 2008. Phytoestrogens and breast cancer: a complex story. Inflammopharmacology 16: 219–26.

Irwin, J.J., Sterling, T., Mysinger, M.M., Bolstad, E.S. and Coleman, R.G., 2012. ZINC: A free tool to discover chemistry for biology. J. Chem. Inf. Model. 52: 1757–1768.

Istyastono, E.P. 2015. Employing recursive partition and regression tree method to increase the quality of structure-based virtual screening in the estrogen receptor alpha ligands identification. Asian J. Pharm. Clin. Res. 8: 21–24.

Istyastono, E.P., Kooistra, A.J., Vischer, H., Kuijer, M., Roumen, L., Nijmeijer, S., Smits, R., de Esch, I., Leurs, R. and de Graaf, C., 2015a. Structure-based virtual screening for fragment-like ligands of the G protein-coupled histamine H4 receptor. Med. Chem. Commun. 6: 1003–1017.

Istyastono, E.P., Riswanto, F.D.O., and Yuliani, S.H. 2015b. Computer-aided drug repurposing: a cyclooxygenase-2 inhibitor celecoxib as a ligand for estrogen receptor alpha. Indones. J. Chem. 15: 274–280.

Istyastono, E.P. and Setyaningsih, D., 2015. Construction and retrospective validation of structure-based virtual screening protocols to identify potent ligands for human adrenergic β2 receptor. Indones. J. Pharm. 26: 20–28.

Korb, O., Stützle, T. and Exner, T.E., 2007. An ant colony optimization approach to flexible protein–ligand docking. Proc. IEEE Swarm Intell. Symp. 1: 115–134.

Korb, O., Stützle, T. and Exner, T.E., 2009. Empirical scoring functions for advanced protein-ligand docking with PLANTS. J. Chem. Inf. Model. 49: 84–96.

Kufareva, I., Katritch, V., Stevens, R.C. and Abagyan, R. 2014. Advances in GPCR modeling evaluated by the GPCR DOCK 2013 assessment: Meeting new challenges. Structure 22: 1120–1139.

Lill, M.A. and Danielson, M.L. 2011. Computer-aided drug design platform using PyMOL. J. Comput. Aided Mol. Des. 25: 13–19.

Matsuda, H., Shimoda, H., Morikawa, T. and Yoshikawa, M. 2001. Phytoestrogens from the roots of Polygonum cuspidatum (Polygonaceae): Structure-requirement of hydroxyanthraquinones for estrogenic activity. Bioorg. Med. Chem. Lett. 11: 1839–1842.

Mysinger, M.M., Carchia, M., Irwin, J.J. and Shoichet, B.K. 2012. Directory of Useful Decoys, Enhanced (DUD-E): Better ligands and decoys for better benchmarking. J. Med. Chem. 55: 6582–6594.

O’Boyle, N.M., Banck, M., James, C.A., Morley, C., Vandermeersch, T., and Hutchison, G.R. 2011. Open Babel: An open chemical toolbox. J. Cheminform. 3: 33–47.

Pathania, S., Ramakrishnan, S.M. and Bagler, G. 2015. Phytochemica: A platform to explore phytochemicals of medicinal plants. Database 10.1093/database/bav075: 1–8.

Radifar, M., Yuniarti, N., Istyastono, E.P. 2013. PyPLIF: Python-based protein-ligand interaction fingerprinting. Bioinformation 9: 325–328.

Setiawati, A., Riswanto, F.D.O., Yuliani, S.H. and Istyastono, E.P. 2014a. Retrospective validation of a structure-based virtual screening protocol to identify ligands for estrogen receptor alpha and its application to identify the alpha-mangostin binding pose. Indo. J. Chem. 14: 103–108.

Setiawati, A., Riswanto, F.O.D., Yuliani, S.H. and Istyastono, E.P. 2014b. Anticancer activity of mangosteen pericarp dry extract against MCF-7 breast cancer cell line though estrogen receptor-α. Indones. J. Pharm. 25: 119–124.

Shiau, A.K., Barstad, D., Loria, P.M., Cheng, L., Kushner, P.J., Agard, D.A. and Greene, G.L. 1998. The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by tamoxifen. Cell 95: 927–937.

Shibata, M.-A., Iinuma, M., Morimoto, J., Kurose, H., Akamatsu, K., Okuno, Y., Akao, Y. and Otsuki, Y. 2011. α-Mangostin extracted from the pericarp of the mangosteen (Garcinia mangostana Linn) reduces tumor growth and lymph node metastasis in an immunocompetent xenograft model of metastatic mammary cancer carrying a p53 mutation. BMC Med. 9: 69.

ten Brink, T. and Exner, T.E., 2009. Influence of protonation, tautomeric, and stereoisomeric states on protein-ligand docking results. J. Chem. Inf. Model. 49: 1535–1546.

Varinska, L., Gal, P., Mojzisova, G., Mirossay, L. and Mojzis, J. 2015. Soy and breast cancer: Focus on angiogenesis. Int. J. Mol. Sci. 16: 11728–11749.

Vidhya, N. and Devaraj, S.N. 2011. Induction of apoptosis by eugenol in human breast cancer cells. Indian J. Exp. Biol. 49: 871–878.



DOI: https://doi.org/10.22146/tradmedj.12820

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