In silico identification of potential drug compound against Peroxisome proliferator-activated receptor-gamma by virtual screening and toxicity studies for the treatment of Diabetic Nephropathy

References

• Abraham, M. J. , Murtola, T. , Schulz, R. , Páll, S. , Smith, J. C. , Hess, B. , & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX , 1–2, 19–25.10.1016/j.softx.2015.06.001
   Google Scholar
• Ahmadian, M. , Suh, J. M. , Hah, N. , Liddle, C. , Atkins, A. R. , Downes, M. , & Evans, R. M. (2013). PPARγ signaling and metabolism: the good, the bad and the future. Nature Medicine , 99 , 557–566. doi:10.1038/nm.3159
   Web of Science ®Google Scholar
• Balakumar, P. , Rose, M. , & Singh, M. (2007). PPAR Ligands: Are They Potential Agents for Cardiovascular Disorders? Pharmacology , 80 , 1–10. doi:10.1159/000102594
   PubMed Web of Science ®Google Scholar
• Brun, R. P. , Tontonoz, P. , Forman, B. M. , Ellis, R. , Chen, J. , Evans, R. M. , & Spiegelman, B. M. (1996). Differential activation of adipogenesis by multiple PPAR isoforms. Genes & Development , 10 , 974–984.10.1101/gad.10.8.974
   PubMed Web of Science ®Google Scholar
• Chang, P. C. , Chen, T. H. , Chang, C. J. , Hou, C. C. , Chan, P. , & Lee, H. M. (2004). Advanced glycosylation end products induce inducible nitric oxide synthase (iNOS) expression via a p38 MAPK-dependent pathway. Kidney International , 65 , 1664–1675. doi:10.1111/j.1523-1755.2004.00602.x
   PubMed Web of Science ®Google Scholar
• Chen, K. C. , & Chen, C. Y. (2014). In Silico Identification of Potent PPAR-γ Agonists from Traditional Chinese Medicine: Bioactivity Prediction, Virtual Screening, and Molecular Dynamics Study. Evidence Based Complementary and Alternative Medicine , 192452 , 1–19. doi:10.1155/2014/192452
   Web of Science ®Google Scholar
• Cheng, A. , & Merz, K. M. (2003). Prediction of aqueous solubility of a diverse set of compounds using quantitative structure-property relationships. Journal of Medicinal Chemistry , 46 , 3572–3580. doi:10.1021/jm020266b
   PubMed Web of Science ®Google Scholar
• Choubey, S. K. , Prabhu, D. , Nachiappan, M. , Biswal, J. , & Jeyakanthan, J. (2016). Molecular modeling, dynamics studies and density functional theory approaches to identify potential inhibitors of SIRT4 protein from Homo sapiens : a novel target for the treatment of type2 diabetes. Journal of Biomolecular Structure and Dynamics , doi:10.1080/07391102.2016.1254117
   PubMed Web of Science ®Google Scholar
• Dallakyan, S. & Olson, A. J. (2015). Small-molecule library screening by docking with PyRx. Methods in Molecular Biology , 1263 , 243–250. doi:10.1007/978-1-4939-2269-7_19
   PubMedGoogle Scholar
• Erickson, J. A. , Jalaie, M. , Robertson, D. H. , Lewis, R. A. , & Vieth, M. (2004). Lessons in Molecular Recognition:  The Effects of Ligand and Protein Flexibility on Molecular Docking Accuracy. Journal of Medicinal Chemistry , 47 , 45–55. doi:10.1021/jm030209y
   PubMed Web of Science ®Google Scholar
• Gahoi, S. , Mandal, R. S. , Ivanisenko, N. , Shrivastava, P. , Jain, S. , Singh, A. K. , Raghunandanan, M. V. , …. Kanchan, S. (2013). Computational screening for new inhibitors of M. tuberculosis mycolyltransferases antigen 85 group of proteins as potential drug targets. Journal of Biomolecular Structure and Dynamics , 31 , 30–43. doi:10.1080/07391102.2012.691343
   PubMed Web of Science ®Google Scholar
• Giaginis, C. , Theocharis, S. , & Tsantili-Kakoulidou, A. (2009). A QSAR Study on Indole-Based PPAR-γ Agonists in Respect to Receptor Binding and Gene Transactivation Data. QSAR and Combinatorial Science , 28 , 802–805. doi:10.1002/qsar.200860185
   Google Scholar
• Gurnell, M. , Wentworth, J. M. , Agostini, M. , Adams, M. , Collingwood, T. N. , Provenzano, C. , & Browne, Paul O. (2000). A Dominant-negative Peroxisome Proliferator-activated Receptor γ (PPARγ) Mutant Is a Constitutive Repressor and Inhibits PPARγ-mediated Adipogenesis. Journal of Biological Chemistry , 275 , 5754–5759.10.1074/jbc.275.8.5754
   PubMed Web of Science ®Google Scholar
• Hsu, K. C. , Chen, Y. F. , Lin, S. R. , & Yang, J. M. (2011). iGEMDOCK: a graphical environment of enhancing GEMDOCK using pharmacological interactions and post-screening analysis. BMC Bioinformatics , 12 (Suppl 1), S33. doi:10.1186/1471-2105-12-S1-S33
   PubMed Web of Science ®Google Scholar
• Huang, W. , Lin, Z. , & van Gunsteren, W. F. (2011). Validation of the GROMOS 54A7 Force Field with Respect to β-Peptide Folding. Journal of Chemical Theory and Computation , 7 , 1237–1243. doi:10.1021/ct100747y
   PubMed Web of Science ®Google Scholar
• Islam, M. A. , Bhayye, S. , Adeniyi, A. A. , Soliman, M. E. , & Pillay, T. S. (2017). Diabetes mellitus caused by mutations in human insulin: analysis of impaired receptor binding of insulins Wakayama, Los Angeles and Chicago using pharmacoinformatics. Journal of Biomolecular Structure and Dynamics , 35 , 724–737. doi:10.1080/07391102.2016.1160258
   PubMed Web of Science ®Google Scholar
• Jia, Z. , Sun, Y. , Yang, G. , Zhang, A. , Huang, S. , Heiney, K. M. , & Zhang, Y. (2014). New Insights into the PPAR gamma Agonists for the Treatment of Diabetic Nephropathy. PPAR Research , 2014 , 818530. doi:10.1155/2014/818530
   PubMed Web of Science ®Google Scholar
• Kumar, S. , Prange, A. , Schulze, J. , Lettis, S. , & Barnett, A. H. (1998). Troglitazone, an insulin action enhancer, improves glycaemic control and insulin sensitivity in elderly Type 2 diabetic patients. Diabetic Medicine , 15 , 772–779.10.1002/(ISSN)1096-9136
   PubMed Web of Science ®Google Scholar
• Kumar, A. , Roy, S. , Tripathi, S. , & Sharma, A. (2016). Molecular docking based virtual screening of natural compounds as potential BACE1 inhibitors: 3D QSAR pharmacophore mapping and molecular dynamics analysis. Journal of Biomolecular Structure and Dynamics , 34 , 239–249. doi:10.1080/07391102.2015.1022603
   PubMed Web of Science ®Google Scholar
• Kung, J. , & Henry, R. R. (2012). Thiazolidinedione safety. Expert Opinion on Drug Safety , 11 , 565–579. doi:10.1517/14740338.2012.691963
   PubMed Web of Science ®Google Scholar
• Lehrke, M. , & Lazar, M. A. (2005). The Many Faces of PPARγ. Cell , 123 , 993–999. doi:10.1016/j.cell.2005.11.026
   PubMed Web of Science ®Google Scholar
• Liberato, M. V. , Nascimento, A. S. , Ayers, S. D. , Lin, J. Z. , Cvoro, A. , Silveira, R. L. , Martínez, L. , Souza, P. C. T. , Saidemberg, D. , Deng, T. , Amato, A. A. , Togashi, M. , ... Hsueh, Willa A. (2012). Medium Chain Fatty Acids Are Selective Peroxisome Proliferator Activated Receptor (PPAR) γ Activators and Pan-PPAR Partial Agonists. PLoS ONE , 7 , e36297. doi:10.1371/journal.pone.0036297
   PubMed Web of Science ®Google Scholar
• Lipinski, C. A. , Lombardo, F. , Dominy, B. W. , & Feeney, P. J. (2001). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings1PII of original article: S0169-409X(96)00423-1. The article was originally published in Advanced Drug Delivery Reviews 23 (1997) 3–25.1. Advanced Drug Delivery Reviews , 46 , 3–26.10.1016/S0169-409X(00)00129-0
   PubMed Web of Science ®Google Scholar
• Lowell, B. B. (1999). An Essential Regulator of Adipogenesis and Modulator of Fat Cell Function: PPARγ. Cell , 99 , 239–242.10.1016/S0092-8674(00)81654-2
   PubMed Web of Science ®Google Scholar
• Malde, A. K. , Zuo, L. , Breeze, M. , Stroet, M. , Poger, D. , Nair, P. C. , Oostenbrink, C. , & Mark, A. E. (2011). An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0. Journal of Chemical Theory and Computation , 7 , 4026–4037. doi:10.1021/ct200196 m
   PubMed Web of Science ®Google Scholar
• Maltarollo, V. G. , Togashi, M. , Nascimento, A. S. , & Honorio, K. M. (2015). Structure-Based Virtual Screening and Discovery of New PPARδ/γ Dual Agonist and PPARδ and γ Agonists. PLOS ONE , 10 , e0118790. doi:10.1371/journal.pone.0118790
   PubMed Web of Science ®Google Scholar
• Miceli, I. , Burt, D. , Tarabra, E. , Camussi, G. , Perin, P. C. , & Gruden, G. (2010). Stretch reduces nephrin expression via an angiotensin II-AT1-dependent mechanism in human podocytes: effect of rosiglitazone. AJP: Renal Physiology , 298 , F381–F390. doi:10.1152/ajprenal.90423.2008
   Google Scholar
• Miyazaki, Y. , Cersosimo, E. , Triplitt, C. , & DeFronzo, R. A. (2007). Rosiglitazone decreases albuminuria in type 2 diabetic patients. Kidney International , 72 , 1367–1373. doi:10.1038/sj.ki.5002516
   PubMed Web of Science ®Google Scholar
• Muthusamy, K. & Krishnasamy, G. (2016). A computational study on role of 6-(hydroxymethyl)-3-[3,4,5-trihydroxy-6-[(3,4,5-trihydroxyoxan-2-yl)oxymethyl]oxan-2-yl]oxyoxane-2,4,5-triol in the regulation of blood glucose level. Journal of Biomolecular Structure and Dynamics , 34 , 2599–2618. doi:10.1080/07391102.2015.1124289
   PubMed Web of Science ®Google Scholar
• Nascimento, A. S. (2010). Structural requirement for PPARγ binding revealed by a meta analysis of holo-crystal structures. Biochimie , 92 , 499–506. doi:10.1016/j.biochi.2010.01.018
   PubMed Web of Science ®Google Scholar
• Nissen, S. E. & Wolski, K. (2007). Effect of Rosiglitazone on the Risk of Myocardial Infarction and Death from Cardiovascular Causes. New England Journal of Medicine , 356 , 2457–2471. doi:10.1056/NEJMoa072761
   PubMed Web of Science ®Google Scholar
• Okada, T. , Wada, J. , Hida, K. , Eguchi, J. , Hashimoto, I. , Baba, M. , … Yasuhara, A. (2006). Thiazolidinediones Ameliorate Diabetic Nephropathy via Cell Cycle-Dependent Mechanisms. Diabetes , 55 , 1666–1677. doi:10.2337/db05-1285
   PubMed Web of Science ®Google Scholar
• Onozaki, A. , Midorikawa, S. , Sanada, H. , Hayashi, Y. , Baba, T. , Katoh, T. , & Watanabe, T. (2004). Rapid change of glucose concentration promotes mesangial cell proliferation via VEGF: inhibitory effects of thiazolidinedione. Biochemical and Biophysical Research Communications , 317 , 24–29. doi:10.1016/j.bbrc.2004.02.175
   PubMed Web of Science ®Google Scholar
• Reutens, A. T. , Prentice, L. , & Atkins, R. (2008). The Epidemiology of Diabetic Kidney Disease. In: The Epidemiology of Diabetes. Mellitus Ekoe. J. (ed), pp. 499–518. Chichester: Wiley.
   Google Scholar
• Sarafidis, P. A. , Stafylas, P. C. , Georgianos, P. I. , Saratzis, A. N. , & Lasaridis, A. N. (2010). Effect of Thiazolidinediones on Albuminuria and Proteinuria in Diabetes: A Meta-analysis. American Journal of Kidney Diseases , 55 , 835–847. doi:10.1053/j.ajkd.2009.11.013
   PubMed Web of Science ®Google Scholar
• Schüttelkopf, A. W. , & van Aalten, D. M. (2004). PRODRG : a tool for high-throughput crystallography of protein–ligand complexes. Acta Crystallographica Section D Biological Crystallography , 60 , 1355–1363. doi:10.1107/S0907444904011679
   PubMed Web of Science ®Google Scholar
• 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 , 455–461. doi:10.1002/jcc.21334
   PubMed Web of Science ®Google Scholar
• Velec, H. F. , Gohlke, H. , & Klebe, G. (2005). DrugScore CSD Knowledge-Based Scoring Function Derived from Small Molecule Crystal Data with Superior Recognition Rate of Near-Native Ligand Poses and Better Affinity Prediction. Journal of Medicinal Chemistry , 48 , 6296–6303. doi:10.1021/jm050436v
   PubMed Web of Science ®Google Scholar
• Vyas, V. K. , Dabasia, M. , Qureshi, G. , Patel, P. , & Ghate, M. (2016). Molecular modeling study for the design of novel acetyl- CoA carboxylase inhibitors using 3DQSAR, molecular docking and dynamic simulations. Journal of Biomolecular Structure and Dynamics ,. doi:10.1080/07391102.2016.1204945
   PubMed Web of Science ®Google Scholar
• Wang, R. , Lu, Y. , & Wang, S. (2003). Comparative Evaluation of 11 Scoring Functions for Molecular Docking. Journal of Medicinal Chemistry , 46 , 2287–2303. doi:10.1021/jm0203783
   PubMed Web of Science ®Google Scholar
• Wild, S. , Roglic, G. , Green, A. , Sicree, R. , & King, H. (2004). Global Prevalence of Diabetes: Estimates for the year 2000 and projections for 2030. Diabetes Care , 27 , 1047–1053.10.2337/diacare.27.5.1047
   PubMed Web of Science ®Google Scholar
• Xu, Y. , Lee, J. , Park, Y. D. , Yang, J. M. , Zheng, J. , & Zhang, Q. (2017). Molecular dynamics simulation integrating the inhibition kinetics of hydroxysafflor yellow A on α-glucosidase. Journal of Biomolecular Structure and Dynamics ,. doi:10.1080/07391102.2017.1300544
   Web of Science ®Google Scholar
• Yang, H. C. , Ma, L. J. , Ma, J. , & Fogo, A. B. (2006). Peroxisome proliferator-activated receptor-gamma agonist is protective in podocyte injury-associated sclerosis. Kidney International , 69 , 1756–1764. doi:10.1038/sj.ki.5000336
   PubMed Web of Science ®Google Scholar
• Zhang, C. , Liu, S. , Zhu, Q. , & Zhou, Y. (2005). A Knowledge-Based Energy Function for Protein−Ligand, Protein−Protein, and Protein−DNA Complexes. Journal of Medicinal Chemistry , 48 , 2325–2335. doi:10.1021/jm049314d
   PubMed Web of Science ®Google Scholar
• Zheng, F. , & Guan, Y. (2007). Thiazolidinediones: A novel class of drugs for the prevention of diabetic nephropathy? Kidney International , 72 , 1301–1303. doi:10.1038/sj.ki.5002557
   PubMed Web of Science ®Google Scholar