265
Views
5
CrossRef citations to date
0
Altmetric
Research Articles

Molecular insights into a mechanism of resveratrol action using hybrid computational docking/CoMFA and machine learning approach

, , , , &
Pages 8286-8300 | Received 25 Jun 2020, Accepted 25 Mar 2021, Published online: 08 Apr 2021

References

  • American Cancer Society Report (2018). Global Burden of Cancer in Women. Available from: https://www.cancer.org/content/dam/cancer-org/research/cancer-facts-and-statistics/global-cancer-facts-and-figures/global-burden-of-cancer-in-women.pdf
  • BIOVIA, Dassault Systèmes (2015). Discovery Studio, v 3.1, San Diego.
  • Blumen, H., Fitch, K., & Polkus, V. (2016). Comparison of treatment costs for breast cancer, by tumor stage and type of service. American Health & Drug Benefits, 9(1), 23–32. pmid: 27066193
  • Bingke, L., Li, H., Ying, X., Min, Y., Long, H., Zhentao, Z., Jialei, L., & Guowei, D. (2019). Prediction of matrix metal proteinases-12 inhibitors by machine learning approaches. Journal of Biomolecular Structure & Dynamics, 37(10), 2627–2640. https://doi.org/10.1080/07391102.2018.1492460
  • Buryanovskyy, L., Fu, Y., Boyd, M., Ma, Y., Hsieh, T. C., Wu, J. M., & Zhang, Z. (2004). Crystal structure of quinone reductase 2 in complex with resveratrol. Biochemistry, 43(36), 11417–11426. https://doi.org/10.1021/bi049162o
  • Chao, W. R., Yean, D., Amin, K., Green, C., & Jong, L. (2007). Computer-aided rational drug design: A novel agent (SR13668) designed to mimic the unique anticancer mechanisms of dietary indole-3-carbinol to block Akt signaling. Journal of Medicinal Chemistry, 50(15), 3412–3415. https://doi.org/10.1021/jm070040e
  • Chen, J. C., Hanson, B. L., Fisher, S. Z., Langan, P., & Kovalevsky, A. Y. (2012). Direct observation of hydrogen atom dynamics and interactions by ultrahigh resolution neutron protein crystallography. Proceedings of the National Academy of Sciences of the United States of America, 109(38), 15301–15306. https://doi.org/10.1073/pnas.1208341109
  • Cramer, R. D., Patterson, D. E., & Bunce, J. D. (1988). Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier r proteins. Journal of the American Chemical Society, 110(18), 5959–5967. https://doi.org/10.1021/ja00226a005
  • Deller, M. C., & Rupp, B. (2015). Models of protein-ligand crystal structures: trust, but verify. Journal of Computer-Aided Molecular Design, 29(9), 817–836. https://doi.org/10.1007/s10822-015-9833-8
  • Ferraz da Costa, D. C., Casanova, F. A., Quarti, J., Malheiros, M. S., Sanches, D., Dos Santos, P. S., Fialho, E., & Silva, J. L. (2012). Transient transfection of a wild-type p53 gene triggers resveratrol-induced apoptosis in cancer cells. PLoS One, 7(11), e48746. https://doi.org/10.1371/journal.pone.0048746
  • Florio, P., Folli, C., Cianci, M., Del Rio, D., Zanotti, G., & Berni, R. (2015). Transthyretin binding heterogeneity and anti-amyloidogenic activity of natural polyphenols and their metabolites. Journal of Biological Chemistry, 290(50), 29769–29780. https://doi.org/10.1074/jbc.M115.690172
  • Gahtori, P., Ghosh, S. K., Parida, P., Prakash, A., Gogoi, K., Bhat, H. R., & Singh, U. P. (2012). Antimalarial evaluation and docking studies of hybrid phenylthiazolyl-1,3,5-triazine derivatives: a novel and potential antifolate lead for Pf-DHFR-TS inhibition. Experimental Parasitology, 130(3), 292–299. https://doi.org/10.1016/j.exppara.2011.12.014
  • Gahtori, P., Pandey, R., Kumar, V., Ghosh, S. K., Das, A., Kalita, J. M., Sahu, S., Prakash, A., & Bhattacharyya, D. R. (2016). Toward resistance‐compromised DHFR inhibitors part 1: Combined structure/ligand‐based virtual screenings and ADME‐Tox profiling. Journal of Chemometrics, 30(8), 462–481. https://doi.org/10.1002/cem.2814
  • Golbraikh, A., & Tropsha, A. (2002). Beware of q2!. Journal of Molecular Graphics and Modelling, 20(4), 269–276. https://doi.org/10.1016/S1093-3263(01)00123-1
  • Goldschmidt, L., Teng, P. K., Riek, R., & Eisenberg, D. (2010). Identifying the amylome, proteins capable of forming amyloid-like fibrils. Proceedings of the National Academy of Sciences of the United States of America, 107(8), 3487–3492. https://doi.org/10.1073/pnas.0915166107
  • Gu, S., Chen, C., Jiang, X., & Zhang, Z. (2015). Resveratrol synergistically triggers apoptotic cell death with arsenic trioxide via oxidative stress in human lung adenocarcinoma A549 cells. Biological Trace Element Research, 163(1–2), 112–123. https://doi.org/10.1007/s12011-014-0186-2
  • Guariento, S., Franchini, S., Tonelli, M., Fossa, P., Sorbi, C., Cichero, E., & Brasili, L. J. (2017). Exhaustive CoMFA and CoMSIA analyses around different chemical entities: A ligand-based study exploring the affinity and selectivity profiles of 5-HT1A ligands. Journal of Enzyme Inhibition and Medicinal Chemistry, 32(1), 214–230. https://doi.org/10.1080/14756366.2016.1247057
  • Gupta, A. K., & Saxena, A. K. (2011). 3D-QSAR CoMFA and CoMSIA studies on a set of diverse α1a-adrenergic receptor antagonists. Medicinal Chemistry Research, 20(9), 1455–1464. https://doi.org/10.1007/s00044-010-9379-1
  • Harbeck, N., & Gnant, M. (2017). Breast cancer. The Lancet, 389(10074), 1134–1150. https://doi.org/10.1016/S0140-6736(16)31891-8
  • Hattotuwagama, C. K., Doytchinova, I. A., & Flower, D. R. (2005). In silico prediction of peptide binding affinity to class i mouse major histocompatibility complexes: A comparative molecular similarity index analysis (CoMSIA) Study. Journal of Chemical Information and Modeling, 45(5), 1415–1423. https://doi.org/10.1021/ci049667l
  • Jang, M., Cai, L., Udeani, G. O., Slowing, K. V., Thomas, C. F., Beecher, C. W., Fong, H. H., Farnsworth, N. R., Kinghorn, A. D., Mehta, R. G., Moon, R. C., & Pezzuto, J. M. (1997). Cancer chemopreventive activity of Resveratrol, a natural product derived from grapes. Science (New York, N.Y.), 275(5297), 218–220. https://doi.org/10.1126/science.275.5297.218
  • Klebe, G., & Abraham, U. (1999). Comparative molecular similarity index analysis (CoMSIA) to study hydrogen-bonding properties and to score combinatorial libraries. Journal of Computer-Aided Molecular Design, 13(1), 1–10. doi: 10.1023/A:1008047919606
  • Klebe, G., Abraham, U., & Mietzner, T. (1994). Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity. Journal of Medicinal Chemistry, 37(24), 4130–4146. https://doi.org/10.1021/jm00050a010
  • Kussie, P. H., Gorina, S., Marechal, V., Elenbaas, B., Moreau, J., Levine, A. J., & Pavletich, N. P. (1996). Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain. Science (New York, N.Y.), 274(5289), 948–953. https://doi.org/10.1126/science.274.5289.948
  • Mayo, L. D., Turchi, J. J., & Berberich, S. J. (1997). Mdm-2 phosphorylation by DNA-dependent protein kinase prevents interaction with p53. Cancer Research, 57(22), 5013–5016. pmid: 9371494
  • Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). Autodock4 and AutoDockTools 4: Automated docking with selective receptor flexiblity. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/10.1002/jcc.21256
  • Pavletich, N. P., Chambers, K. A., & Pabo, C. O. (1993). The DNA-binding domain of p53 contains the four conserved regions and the major mutation hot spots. Genes & Development, 7(12B), 2556–2564. https://doi.org/10.1101/gad.7.12b.2556
  • Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF chimera-a visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084
  • Pettit, G. R., & Anderson, C. R. (2009). Stilbene derivatives and methods of inhibiting cancer cell growth and microbial growth. U.S. Patent No. 20090221666A1. WO2006124511A2.
  • Pettit, G. R., Anderson, C. R., Herald, D. L., Jung, M. K., Lee, D. J., Hamel, E., & Pettit, R. K. (2003). Antineoplastic agents. 487. Synthesis and biological evaluation of the antineoplastic agent 3,4-methylenedioxy-5,4′-dimethoxy-3′-amino-Z-stilbene and derived amino acid amides. Journal of Medicinal Chemistry, 46(4), 525–531. https://doi.org/10.1021/jm020204l
  • Pettit, G. R., Grealish, M. P., Jung, M. K., Hamel, E., Pettit, R. K., Chapuis, J. C., & Schmidt, J. M. (2002). Antineoplastic agents. 465. Structural modification of resveratrol: Sodium resverastatin phosphate. Journal of Medicinal Chemistry, 45(12), 2534–2542. https://doi.org/10.1021/jm010119y
  • Pettit, G. R., Melody, N., Thornhill, A., Knight, J. C., Groy, T. L., & Herald, C. L. (2009a). Antineoplastic agents. 579. Synthesis and cancer cell growth evaluation of E-Stilstatin 3: A resveratrol structural modification. Journal of Natural Products, 72(9), 1637–1642. https://doi.org/10.1021/np9002146
  • Pettit, R. K., Pettit, G. R., Hamel, E., Hogan, F., Moser, B. R., Wolf, S., Pon, S., Chapuis, J. C., & Schmidt, J. M. (2009b). E-Combretastatinand E-Resveratrolstructural modifications: Antimicrobial and cancer cell growth inhibitory β-E-nitrostyrenes. Bioorganic and Medicinal Chemistry., 17(18), 6606–6612. https://doi.org/10.1016/j.bmc.2009.07.076
  • Powell, M. J. D. (1977). Restart procedures for the conjugate gradient method. Mathematical Programming., 12(1), 241–254. https://doi.org/10.1007/BF01593790
  • Rizvi, S. M., Shakil, S., & Haneef, M. (2013). A simple click by click protocol to perform docking: AutoDock 4.2 made easy for non-bioinformaticians. EXCLI Journal, 12, 831–857. PMID: 26648810.
  • Ruotolo, R., Calani, L., Fietta, E., Brighenti, F., Crozier, A., Meda, C., Maggi, A., Ottonello, S., & Del Rio, D. (2013). Anti-estrogenic activity of a human resveratrol metabolite. Nutrition, Metabolism, and Cardiovascular Diseases: NMCD, 23(11), 1086–1092. doi: 10.1016/j.bios.2014.01.024
  • Scharl, A., Kühn, T., Papathemelis, T., & Salterberg, A. (2015). The right treatment for the right patient – Personalised treatment of breast cancer. Geburtshilfe und Frauenheilkunde, 75(7), 683–691. https://doi.org/10.1055/s-0035-1546270
  • Schuhmacher, A., Gassmann, O., & Hinder, M. (2016). Changing R&D models in research-based pharmaceutical companies. Journal of Translational Medicine, 14(1), 105. https://doi.org/10.1186/s12967-016-0838-4
  • Serriere, J., Boutin, J. A., Isabet, T., Antoine, M., Ferry, G. (2015). Crystal structure of fad quinonereductase 2 in complex with Resveratrolat 1.6Å. Unpublished. https://www.rcsb.org/structure/4QOH
  • Singh, C. K., Ndiaye, M. A., & Ahmad, N. (2015). Resveratrol and cancer: Challenges for clinical translation. Biochimica et Biophysica Acta, 1852(6), 1178–1185. https://doi.org/10.1016/j.bbadis.2014.11.004
  • Singh, N. P., Singh, U. P., Hegde, V. L., Guan, H., Hofseth, L., Nagarkatti, M., & Nagarkatti, P. S. (2011). Resveratrol (trans-3,5,4′-trihydroxystilbene) suppresses EL4 tumor growth by induction of apoptosis involving reciprocal regulation of SIRT1 and NF-κB. Molecular Nutrition & Food Research, 55(8), 1207–1218. https://doi.org/10.1002/mnfr.201000576
  • Sliwoski, G., Kothiwale, S., Meiler, J., & Lowe, E. W. J. (2014). Computational methods in drug discovery. Pharmacological Reviews, 66(1), 334–395. https://doi.org/10.1124/pr.112.007336
  • Talevi, A. (2015). Multi-target pharmacology: Possibilities and limitations of the “skeleton key approach” from a medicinal chemist perspective. Frontiers in Pharmacology, 6, 205. https://doi.org/10.3389/fphar.2015.00205
  • Torre, L. A., Bray, F., Siegel, R. L., Ferlay, J., Lortet-Tieulent, J., & Jemal, A. (2015). Global cancer statistics, 2012. CA: A Cancer Journal of Clinicians, 65(2), 87–108. https://doi.org/10.3322/caac.21262
  • Tsubaki, M., Tomii, K., & Sese, J. (2019). Compound-protein interaction prediction with end-to-end learning of neural networks for graphs and sequences. Bioinformatics (Oxford, England), 35(2), 309–318. https://doi.org/10.1093/bioinformatics/bty535
  • Watson, G. M., Gunzburg, M. J., Ambaye, N. D., Lucas, W. A., Traore, D. A., Kulkarni, K., Cergol, K. M., Payne, R. J., Panjikar, S., Pero, S. C., Perlmutter, P., Wilce, M. C., & Wilce, J. A. (2015). Cyclic peptides incorporating phosphotyrosine mimetics as potent and specific inhibitors of the Grb7 breast cancer target. Journal of Medicinal Chemistry, 58(19), 7707–7718. https://doi.org/10.1021/acs.jmedchem.5b00609
  • Wójcikowski, M., Ballester, P. J., & Siedlecki, P. (2017). Performance of machine-learning scoring functions in structure-based virtual screening. Scientific Reports, 7, 46710. https://doi.org/10.1038/srep46710
  • Wong, J. C., & Fiscus, R. R. (2015). Resveratrolat anti-angiogenesis/anticancer concentrations suppresses protein kinase G signaling and decreases IAPs expression in HUVECs. Anticancer Research, 35(1), 273–281.
  • Zhang, L., Sedykh, A., Tripathi, A., Zhu, H., Afantitis, A., Mouchlis, V. D., Melagraki, G., Rusyn, I., & Tropsha, A. (2013). Identification of putative estrogen receptor-mediated endocrine disrupting chemicals using Qsar- and structure-based virtual screening approaches. Toxicology and Applied Pharmacology., 272(1), 67–76. https://doi.org/10.1016/j.taap.2013.04.032
  • Zhang, L., Yang, F., Cai, J. Y., Yang, P. H., & Liang, Z. H. (2014a). In-situ detection of resveratrol inhibition effect on epidermal growth factor receptor of living MCF-7 cells by atomic force microscopy. Biosensors & Bioelectronics, 56, 271–277. https://doi.org/10.1016/j.bios.2014.01.024
  • Zhang, Q., Zeng, S. X., & Lu, H. (2014b). Targeting p53-MDM2-MDMX loop for cancer therapy. Sub-Cellular Biochemistry, 85, 281–319. https://doi.org/10.1007/978-94-017-9211-0_16

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.