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Research Articles

Computational investigation reveals Picrasidine C as selective PPARα lead: binding pattern, selectivity mechanism and ADME/tox profile

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Pages 5401-5418 | Received 23 Aug 2019, Accepted 27 Nov 2019, Published online: 12 Dec 2019

References

  • Allen, B. K., Mehta, S., Ember, S. W. J., Zhu, J.-Y., Schönbrunn, E., Ayad, N. G., & Schürer, S. C. (2017). Identification of a novel class of brd4 inhibitors by computational screening and binding simulations. ACS Omega, 2(8), 4760–4771. doi:10.1021/acsomega.7b00553
  • Ashkenazy, H., Erez, E., Martz, E., Pupko, T., & Ben-Tal, N. (2010). ConSurf 2010: Calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Research, 38, W529–W533. doi:10.1093/nar/gkq399
  • Chen, J., Li, W., Yao, H., & Xu, J. (2015). Insights into drug discovery from natural products through structural modification. Fitoterapia, 103, 231–241. doi:10.1016/j.fitote.2015.04.012
  • Chohan, T. A., Chen, J. J., Qian, H. Y., Pan, Y. L., & Chen, J. Z. (2016). Molecular modeling studies to characterize N-phenylpyrimidin-2-amine selectivity for CDK2 and CDK4 through 3D-QSAR and molecular dynamics simulations. Molecular Biosystems, 12(4), 1250–1268. doi:10.1039/C5MB00860C
  • 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. doi:10.1038/srep42717
  • de la Rosa Rodriguez, M. A., & Kersten, S. (2017). Regulation of lipid droplet-associated proteins by peroxisome proliferator-activated receptors. Biochimica et Biophysica Acta (Bba)—Molecular and Cell Biology of Lipids, 1862(10), 1212–1220. doi:10.1016/j.bbalip.2017.07.007
  • Ellenbarger, J. F., Krieger, I. V., Huang, H-L., Gómez-Coca, S., Ioerger, T. R., Sacchettini, J. C., … Dunbar, K. R. (2018). Anion-pi interactions in computer-aided drug design: Modeling the inhibition of malate synthase by phenyl-diketo acids. Journal of Chemical Information and Modeling, 58(10), 2085–2091. doi:10.1021/acs.jcim.8b00417
  • Ertl, P., Rohde, B., & Selzer, P. (2000). Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties. Journal of Medicinal Chemistry, 43(20), 3714–3717. doi:10.1021/jm000942e
  • Friesner, R. A., Murphy, R. B., Repasky, M. P., Frye, L. L., Greenwood, J. R., Halgren, T. A., … Mainz, D. T. (2006). Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. Journal of Medicinal Chemistry, 49(21), 6177–6196. doi:10.1021/jm051256o
  • Hadianawala, M., Mahapatra, A. D., Yadav, J. K., & Datta, B. (2018). Molecular docking, molecular modeling, and molecular dynamics studies of azaisoflavone as dual COX-2 inhibitors and TP receptor antagonists. Journal of Molecular Modeling, 24(3), 69. doi:10.1007/s00894-018-3620-0
  • Iqbal, S., Anantha Krishnan, D., & Gunasekaran, K. (2018). Identification of potential PKC inhibitors through pharmacophore designing, 3D-QSAR and molecular dynamics simulations targeting Alzheimer's disease. Journal of Biomolecular Structure and Dynamics, 36(15), 4029–4044. doi:10.1080/07391102.2017.1406824
  • Ji, C. G., & Zhang, J. Z. (2008). Protein polarization is critical to stabilizing AF-2 and helix-2' domains in ligand binding to PPAR-gamma. Journal of the American Chemical Society, 130(50), 17129–17133. doi:10.1021/ja807374x
  • Kayikci, M., Venkatakrishnan, A. J., Scott-Brown, J., Ravarani, C. N. J., Flock, T., & Babu, M. M. (2018). Visualization and analysis of non-covalent contacts using the protein contacts atlas. Nature Structural & Molecular Biology, 25(2), 185–194. doi:10.1038/s41594-017-0019-z
  • Khalaf, R. A. (2016). Exploring natural products as a source for antidiabetic lead compounds and possible lead optimization. Current Topics in Medicinal Chemistry, 16(23), 2549–2561. doi:10.2174/1568026616666160414123602
  • Kingston, D. G. (2011). Modern natural products drug discovery and its relevance to biodiversity conservation. Journal of Natural Products, 74(3), 496–511. doi:10.1021/np100550t
  • Koonrungsesomboon, N., & Karbwang, J. (2016). Ethical considerations in clinical research on herbal medicine for prevention of cardiovascular disease in the ageing. Phytomedicine, 23(11), 1090–1094. doi:10.1016/j.phymed.2015.10.017
  • Kozakov, D., Hall, D. R., Napoleon, R. L., Yueh, C., Whitty, A., & Vajda, S. (2015). New frontiers in druggability. Journal of Medicinal Chemistry, 58(23), 9063–9088. doi:10.1021/acs.jmedchem.5b00586
  • Li, J., Kennedy, L. J., Shi, Y., Tao, S., Ye, X.-Y., Chen, S. Y., … Tino, J. A. (2010). Discovery of an oxybenzylglycine based peroxisome proliferator activated receptor alpha selective agonist 2-((3-((2-(4-chlorophenyl)-5-methyloxazol-4-yl)methoxy)benzyl)(methoxycarbonyl)am ino)acetic acid (BMS-687453). Journal of Medicinal Chemistry, 53(7), 2854–2864. doi:10.1021/jm9016812
  • Li, R. J., Wang, Y. L., Wang, Q. H., Wang, J., & Cheng, M. S. (2015). In silico design of human IMPDH inhibitors using pharmacophore mapping and molecular docking approaches. Computational and Mathematical Methods in Medicine, 2015, 1. doi:10.1155/2015/418767
  • Llorach-Pares, L., Nonell-Canals, A., Avila, C., & Sanchez-Martinez, M. (2018). Kororamides, convolutamines, and indole derivatives as possible tau and dual-specificity kinase inhibitors for Alzheimer's disease: A computational study. Marine Drugs, 16(10), 386. doi:10.3390/md16100386
  • Miller III, B. R., McGee Jr., T. D., Swails, J. M., Homeyer, N., Gohlke, H., & Roitberg, A. E. (2012). MMPBSA.py: An efficient program for end-state free energy calculations. Journal of Chemical Theory and Computation, 8(9), 3314–3321. doi:10.1021/ct300418h
  • Nolte, R. T., Wisely, G. B., Westin, S., Cobb, J. E., Lambert, M. H., Kurokawa, R., … Milburn, M. V. (1998). Ligand binding and co-activator assembly of the peroxisome proliferator-activated receptor-gamma. Nature, 395(6698), 137–143. doi:10.1038/25931
  • Pires, D. E., 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. doi:10.1021/acs.jmedchem.5b00104
  • Pollinger, J., Gellrich, L., Schierle, S., Kilu, W., Schmidt, J., Kalinowsky, L., … Merk, D. (2019). Tuning nuclear receptor selectivity of Wy14,643 towards selective retinoid X receptor modulation. Journal of Medicinal Chemistry, 62(4), 2112–2126. doi:10.1021/acs.jmedchem.8b01848
  • Rodrigues, T., Reker, D., Schneider, P., & Schneider, G. (2016). Counting on natural products for drug design. Nature Chemistry, 8(6), 531–541. doi:10.1038/nchem.2479
  • Shivakumar, D., Williams, J., Wu, Y., Damm, W., Shelley, J., & Sherman, W. (2010). Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field. Journal of Chemical Theory and Computation, 6(5), 1509–1519. doi:10.1021/ct900587b
  • Sun, M., Zhang, X., Gao, Z., Liu, T., Luo, C., Zhao, Y., … Sun, J. (2019). Probing a dipeptide-based supramolecular assembly as an efficient camptothecin delivering carrier for cancer therapy: Computational simulations and experimental validations. Nanoscale, 11(9), 3864–3876. doi:10.1039/C8NR07014H
  • Tian, S., Li, Y., Li, D., Xu, X., Wang, J., Zhang, Q., & Hou, T. (2013). Modeling compound-target interaction network of traditional Chinese medicines for type II diabetes mellitus: Insight for polypharmacology and drug design. Journal of Chemical Information and Modeling, 53(7), 1787–1803. doi:10.1021/ci400146u
  • Wang, M., Wang, Y., Kong, D., Jiang, H., Wang, J., & Cheng, M. (2018). In silico exploration of aryl sulfonamide analogs as voltage-gated sodium channel 1.7 inhibitors by using 3D-QSAR, molecular docking study, and molecular dynamics simulations. Computational Biology and Chemistry, 77, 214–225. doi:10.1016/j.compbiolchem.2018.10.009
  • Wang, Y., Yang, L., Hou, J., Zou, Q., Gao, Q., Yao, W., … Zhang, J. (2019). Hierarchical virtual screening of the dual MMP-2/HDAC-6 inhibitors from natural products based on pharmacophore models and molecular docking. Journal of Biomolecular Structure and Dynamics, 37(3), 649–670. doi:10.1080/07391102.2018.1434833
  • Wolber, G., & Langer, T. (2005). LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters. Journal of Chemical Information and Modeling, 45(1), 160–169. doi:10.1021/ci049885e
  • Wu, J.-S., Lin, S.-Y., Liao, F.-Y., Hsiao, W.-C., Lee, L.-C., Peng, Y.-H., … Wu, S.-Y. (2015). Identification of substituted naphthotriazolediones as novel tryptophan 2,3-dioxygenase (TDO) inhibitors through structure-based virtual screening. Journal of Medicinal Chemistry, 58(19), 7807–7819. doi:10.1021/acs.jmedchem.5b00921
  • Yamashita, S., Masuda, D., & Matsuzawa, Y. (2019). Clinical applications of a novel selective PPARalpha modulator, pemafibrate, in dyslipidemia and metabolic diseases. Journal of Atherosclerosis and Thrombosis, 26(5), 389–402. doi:10.5551/jat.48918
  • Ylilauri, M., & Pentikainen, O. T. (2013). MMGBSA as a tool to understand the binding affinities of filamin-peptide interactions. Journal of Chemical Information and Modeling, 53(10), 2626–2633. doi:10.1021/ci4002475
  • Ynigez-Gutierrez, A. E., & Bachmann, B. O. (2019). Fixing the unfixable: The art of optimizing natural products for human medicine. Journal of Medicinal Chemistry, 62(18), 8412–8428. doi:10.1021/acs.jmedchem.9b00246
  • You, W. J., Fan, Y. F., Xu, Y. H., Wu, K., & Tan, X. Y. (2017). Molecular characterization and functional analysis of PPARalpha promoter in yellow catfish Pelteobagrus fulvidraco. Gene, 627, 106–113. doi:10.1016/j.gene.2017.06.022
  • Yu, X. H., Zheng, X. L., & Tang, C. K. (2015). Peroxisome proliferator-activated receptor alpha in lipid metabolism and atherosclerosis. Advances in Clinical Chemistry, 71, 171–203. doi:10.1016/bs.acc.2015.06.005[. https://doi.org/26411415
  • Zang, L.-L., Wang, X.-J., Li, X.-B., Wang, S.-Q., Xu, W.-R., Xie, X.-B., … Wang, R.-L. (2014). SAHA-based novel HDAC inhibitor design by core hopping method. Journal of Molecular Graphics and Modelling, 54, 10–18. doi:10.1016/j.jmgm.2014.08.005
  • Zhao, S., Kanno, Y., Li, W., Sasaki, T., Zhang, X., Wang, J., … Li, H. (2016). Identification of picrasidine C as a subtype-selective PPARalpha agonist. Journal of Natural Products, 79(12), 3127–3133. doi:10.1021/acs.jnatprod.6b00883

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