247
Views
4
CrossRef citations to date
0
Altmetric
Research Articles

In-silico identification of peroxisome proliferator-activated receptor (PPAR)α/γ agonists from Ligand Expo Components database

, , , &
Pages 1853-1864 | Received 16 Oct 2019, Accepted 02 Mar 2020, Published online: 01 Apr 2020

References

  • Ahmad, A., Ahmad, A., Sudhakar, R., Varshney, H., Subbarao, N., Ansari, S., Rauf, A., & Khan, A. U. (2017). Designing, synthesis, and antimicrobial action of oxazoline and thiazoline derivatives of fatty acid esters. Journal of Biomolecular Structure & Dynamics, 35(15), 3412–3431. doi:10.1080/07391102.2016.1255260
  • Ahmed, R., Jain, S. K., & Shukla, P. K. (2013). in-silico characterization of beta-(1, 3)-endoglucanase (ENGL1) from Aspergillus fumigatus by homology modeling and docking studies. Bioinformation, 9(16), 802–807. doi:10.6026/97320630009802
  • Aziz, T. A., Hussain, S. A., Mahwi, T. O., Ahmed, Z. A., Rahman, H. S., & Rasedee, A. (2018). The efficacy and safety of Ginkgo biloba extract as an adjuvant in type 2 diabetes mellitus patients ineffectively managed with metformin: A double-blind, randomized, placebo-controlled trial. Drug Design, Development and Therapy, 12, 735–742.
  • Baby, S. T., Sharma, S., Enaganti, S., & Cherian, P. R. (2016). Molecular docking and pharmacophore studies of heterocyclic compounds as Heat shock protein 90 (Hsp90) inhibitors. Bioinformation, 12(3), 149–155. doi:10.6026/97320630012149
  • Cho, N. H., Shaw, J. E., Karuranga, S., Huang, Y., da Rocha Fernandes, J. D., Ohlrogge, A. W., & Malanda, B. (2018). IDF diabetes atlas: Global estimates of diabetes prevalence for 2017 and projections for 2045. Diabetes Research and Clinical Practice, 138, 271–281. doi:10.1016/j.diabres.2018.02.023
  • Cronet, P., Petersen, J. F., Folmer, R., Blomberg, N., Sjöblom, K., Karlsson, U., Lindstedt, E. L., & Bamberg, K. (2001). Structure of the PPARalpha and -gamma ligand binding domain in complex with AZ 242; ligand selectivity and agonist activation in the PPAR family. Structure ( Structure), 9(8), 699–706. doi:10.1016/S0969-2126(01)00634-7
  • Engwa, G. A., Nwalo, F. N., Chiezey, V. O., Unachukwu, M. N., Ojo, O. O., & Ubi, B. E. (2018). Assessment of the Pro12Ala polymorphism in the PPAR-gamma2 gene among type 2 diabetes patients in a Nigerian population. J Clin Med, 7(4), 69.
  • Farshadpour, F., Taherkhani, R., Ravanbod, M. R., & Eghbali, S. S. (2018). Prevalence and genotype distribution of hepatitis C virus infection among patients with type 2 diabetes mellitus. Medical Principles and Practice : Practice, 27(4), 308–316. doi:10.1159/000488985
  • Gholami, S., Bordbar, A. K., & Lohrasebi, A. (2017). Identifying binding modes of two synthetic derivatives of adrenalin to the alpha2C-adrenoceptor by using molecular modeling; insights into the alpha2C-adrenoceptor activation. Biophysical Chemistry, 223, 17–24. doi:10.1016/j.bpc.2017.01.005
  • Hasan, M. A., Mazumder, M. H., Chowdhury, A. S., Datta, A., & Khan, M. A. (2015). Molecular-docking study of malaria drug target enzyme transketolase in Plasmodium falciparum 3D7 portends the novel approach to its treatment. Source Code for Biology and Medicine, 10, 7.
  • Higuchi, T., Takeuchi, A., Munesue, S., Yamamoto, N., Hayashi, K., Kimura, H., Miwa, S., Inatani, H., Shimozaki, S., Kato, T., Aoki, Y., Abe, K., Taniguchi, Y., Aiba, H., Murakami, H., Harashima, A., Yamamoto, Y., & Tsuchiya, H. (2018). Anti-tumor effects of a nonsteroidal anti-inflammatory drug zaltoprofen on chondrosarcoma via activating peroxisome proliferator-activated receptor gamma and suppressing matrix metalloproteinase-2 expression. Cancer Medicine, 7(5), 1944–1954. doi:10.1002/cam4.1438
  • Hong, O.-Y., Youn, H. J., Jang, H.-Y., Jung, S. H., Noh, E.-M., Chae, H. S., Jeong, Y.-J., Kim, W., Kim, C.-H., & Kim, J.-S. (2018). Troglitazone inhibits matrix metalloproteinase-9 expression and invasion of breast cancer cell through a peroxisome proliferator-activated receptor gamma-dependent mechanism. Journal of Breast Cancer, 21(1), 28–36. doi:10.4048/jbc.2018.21.1.28
  • Hossain, M. U., Khan, M. A., Rakib-Uz-Zaman, S. M., Ali, M. T., Islam, M. S., Keya, C. A., & Salimullah, M. (2016). Treating diabetes mellitus: Pharmacophore based designing of potential drugs from Gymnema sylvestre against insulin receptor protein. BioMed Research International, 2016, 3187647. doi:10.1155/2016/3187647
  • Jia, W.-Q., Jing, Z., Liu, X., Feng, X.-Y., Liu, Y.-Y., Wang, S.-Q., Xu, W.-R., Liu, J.-W., & Cheng, X.-C. (2018). Virtual identification of novel PPARalpha/gamma dual agonists by scaffold hopping of saroglitazar. Journal of Biomolecular Structure & Dynamics, 36(13), 3496–3512. doi:10.1080/07391102.2017.1392363
  • Joung, K. H., Ju, S. H., Kim, J. M., Choung, S., Lee, J. M., Park, K. S., Kim, H. J., & Ku, B. J. (2018). Clinical Implications of using post-challenge plasma glucose levels for early diagnosis of type 2 diabetes mellitus in older individuals. Diabetes & Metabolism Journal, 42(2), 147–154. doi:10.4093/dmj.2018.42.2.147
  • Julin, J., Napari, I., & Vehkamaki, H. (2007). Comparative study on methodology in molecular dynamics simulation of nucleation. The Journal of Chemical Physics, 126(22), 224517. doi:10.1063/1.2740269
  • Kalathiya, U., Padariya, M., & Baginski, M. (2016). Identification of 1H-indene-(1,3,5,6)-tetrol derivatives as potent pancreatic lipase inhibitors using molecular docking and molecular dynamics approach. Biotechnology and Applied Biochemistry, 63(6), 765–778. doi:10.1002/bab.1432
  • Katari, S. K., Natarajan, P., Swargam, S., Kanipakam, H., Pasala, C., & Umamaheswari, A. (2016). Inhibitor design against JNK1 through e-pharmacophore modeling docking and molecular dynamics simulations. Journal of Receptor and Signal Transduction Research, 36(6), 558–571. doi:10.3109/10799893.2016.1141955
  • Kaul, U., Parmar, D., Manjunath, K., Shah, M., Parmar, K., Patil, K. P., & Jaiswal, A. (2019). New dual peroxisome proliferator activated receptor agonist-Saroglitazar in diabetic dyslipidemia and non-alcoholic fatty liver disease: Integrated analysis of the real world evidence. Cardiovascular Diabetology, 18(1), 80. doi:10.1186/s12933-019-0884-3
  • Kirubakaran, P., Kothapalli, R., Singh Kh, D., Nagamani, S., Arjunan, S., & Muthusamy, K. (2011). In silico studies on marine actinomycetes as potential inhibitors for Glioblastoma multiforme. Bioinformation, 6(3), 100–106. doi:10.6026/97320630006100
  • Kumar, S., Saini, V., Maurya, I. K., Sindhu, J., Kumari, M., Kataria, R., & Kumar, V. (2018). Design, synthesis, DFT, docking studies and ADME prediction of some new coumarinyl linked pyrazolylthiazoles: Potential standalone or adjuvant antimicrobial agents. PLoS One, 13(4), e0196016. doi:10.1371/journal.pone.0196016
  • Lamichane, S., Dahal Lamichane, B., & Kwon, S. M. (2018). Pivotal roles of peroxisome proliferator-activated receptors (PPARs) and their signal cascade for cellular and whole-body energy homeostasis. International Journal of Molecular Sciences., 19(4), 949.
  • Lee, Y. H., Kim, J. H., Kim, S. R., Jin, H. Y., Rhee, E. J., Cho, Y. M., & Lee, B. W. (2017). Lobeglitazone, a novel thiazolidinedione, improves non-alcoholic fatty liver disease in type 2 diabetes: Its efficacy and predictive factors related to responsiveness. Journal of Korean Medical Science, 32(1), 60–69. doi:10.3346/jkms.2017.32.1.60
  • Li, R., Du, Y., Gao, Z., & Shen, J. (2018). Molecular modeling studies on carbazole carboxamide based BTK inhibitors using docking and structure-based 3D-QSAR. International Journal of Molecular Sciences., 19(4), 1244.
  • Liu, X., Jing, Z., Jia, W.-Q., Wang, S.-Q., Ma, Y., Xu, W.-R., Liu, J.-W., & Cheng, X.-C. (2018). Identification of novel PPARalpha/gamma dual agonists by virtual screening, ADMET prediction and molecular dynamics simulations. Journal of Biomolecular Structure & Dynamics, 36(11), 2988–3002. doi:10.1080/07391102.2017.1373706
  • Mahmoodian, R., Salimian, M., Hamidpour, M., Khadem-Maboudi, A. A., & Gharehbaghian, A. (2019). The effect of mild agonist stimulation on the platelet reactivity in patients with type 2 diabetes mellitus. BMC Endocrine Disorders, 19(1), 62.
  • Mondal, S., Mandal, S. M., Mondal, T. K., & Sinha, C. (2015). Structural characterization of new Schiff bases of sulfamethoxazole and sulfathiazole, their antibacterial activity and docking computation with DHPS protein structure. Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy, 150, 268–279.
  • Narayanaswamy, R., Isha, A., Wai, L. K., & Ismail, I. S. (2016). Molecular docking analysis of selected Clinacanthus nutans constituents as xanthine oxidase, nitric oxide synthase, human neutrophil elastase, matrix metalloproteinase 2, matrix metalloproteinase 9 and squalene synthase inhibitors. Pharmacognosy Magazine, 12(Suppl 1), S21–S26.
  • Nolte, R. T., Wisely, G. B., Westin, S., Cobb, J. E., Lambert, M. H., Kurokawa, R., Rosenfeld, M. G., Willson, T. M., Glass, C. K., & 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
  • Norinder, U., & Bergstrom, C. A. (2006). Prediction of ADMET properties. ChemMedChem., 1(9), 920–937. doi:10.1002/cmdc.200600155
  • Patronov, A., Dimitrov, I., Flower, D. R., & Doytchinova, I. (2012). Peptide binding to HLA-DP proteins at pH 5.0 and pH 7.0: A quantitative molecular docking study. BMC Structural Biology, 12, 20. doi:10.1186/1472-6807-12-20
  • Pradhan, D., Priyadarshini, V., Munikumar, M., Swargam, S., Umamaheswari, A., & Bitla, A. (2014). Para-(benzoyl)-phenylalanine as a potential inhibitor against LpxC of Leptospira spp.: Homology modeling, docking, and molecular dynamics study. Journal of Biomolecular Structure & Dynamics, 32(2), 171–185. doi:10.1080/07391102.2012.758056
  • Puratchikody, A., Sriram, D., Umamaheswari, A., & Irfan, N. (2016). 3-D structural interactions and quantitative structural toxicity studies of tyrosine derivatives intended for safe potent inflammation treatment. Chemistry Central Journal, 10, 24.
  • Rajamanikandan, S., Jeyakanthan, J., & Srinivasan, P. (2017). Molecular docking, molecular dynamics simulations, computational screening to design quorum sensing inhibitors targeting LuxP of vibrio harveyi and its biological evaluation. Applied Biochemistry and Biotechnology, 181(1), 192–218. doi:10.1007/s12010-016-2207-4
  • Rajamanikandan, S., & Srinivasan, P. (2016). Pharmacophore modeling and structure-based virtual screening to identify potent inhibitors targeting LuxP of Vibrio harveyi. Journal of Receptor and Signal Transduction Research, 36(6), 617–632. doi:10.3109/10799893.2016.1155063
  • Sastry, G. M., Adzhigirey, M., Day, T., Annabhimoju, R., & Sherman, W. (2013). Protein and ligand preparation: Parameters, protocols, and influence on virtual screening enrichments. Journal of Computer-Aided Molecular Design, 27(3), 221–234. doi:10.1007/s10822-013-9644-8
  • Shan, Y., Kim, E. T., Eastwood, M. P., Dror, R. O., Seeliger, M. A., & Shaw, D. E. (2011). How does a drug molecule find its target binding site? Journal of the American Chemical Society, 133(24), 9181–9183. doi:10.1021/ja202726y
  • Shi, R., Zhao, L., & Qi, Y. (2018). The effect of fenofibrate on early retinal nerve fiber layer loss in type 2 diabetic patients: A case-control study. BMC Ophthalmology, 18(1), 100. doi:10.1186/s12886-018-0769-3
  • Singh, K. D., & Muthusamy, K. (2013). Molecular modeling, quantum polarized ligand docking and structure-based 3D-QSAR analysis of the imidazole series as dual AT(1) and ET(A) receptor antagonists. Acta Pharmacologica Sinica, 34(12), 1592–1606. doi:10.1038/aps.2013.129
  • Sosale, A., Saboo, B., & Sosale, B. (2015). Saroglitazar for the treatment of hypertrig-lyceridemia in patients with type 2 diabetes: Current evidence. Diabetes, Metabolic Syndrome and Obesity : targets and Therapy, 8, 189–196.
  • Wang, X. J., Zhang, J., Wang, S. Q., Xu, W. R., Cheng, X. C., & Wang, R. L. (2014). Identification of novel multitargeted PPARalpha/gamma/delta pan agonists by core hopping of rosiglitazone. Drug Design, Development and Therapy, 8, 2255–2262.
  • Xu, S., & Xu, X. (2018). Research advances in the correlation between peroxisome proliferator-activated receptor-gamma and digestive cancers. PPAR Research, 2018, 5289859. doi:10.1155/2018/5289859
  • Yadava, U., Gupta, H., & Roychoudhury, M. (2015). Stabilization of microtubules by taxane diterpenoids: Insight from docking and MD simulations. Journal of Biological Physics, 41(2), 117–133. doi:10.1007/s10867-014-9369-5
  • Yadava, U., Shukla, B. K., Roychoudhury, M., & Kumar, D. (2015). Pyrazolo[3,4-d]pyrimidines as novel inhibitors of O-acetyl-L-serine sulfhydrylase of Entamoeba histolytica: An in silico study. Journal of Molecular Modeling, 21(4), 96. doi:10.1007/s00894-015-2631-3
  • Yokoyama, M., Fujisaki, S., Shirakura, M., Watanabe, S., Odagiri, T., Ito, K., & Sato, H. (2017). Molecular dynamics simulation of the influenza A(H3N2) hemagglutinin trimer reveals the structural basis for adaptive evolution of the recent epidemic clade 3C.2a. Frontiers in Microbiology, 8, 584.
  • Yun, S. H., Han, S. H., & Park, J. I. (2018). Peroxisome proliferator-activated receptor gamma and PGC-1alpha in cancer: Dual actions as tumor promoter and suppressor. PPAR Research, 2018, 6727421. doi:10.1155/2018/6727421
  • Zhang, D., & Lazim, R. (2017). Application of conventional molecular dynamics simulation in evaluating the stability of apomyoglobin in urea solution. Scientific Reports, 7, 44651. doi:10.1038/srep44651

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.