218
Views
4
CrossRef citations to date
0
Altmetric
Research Articles

Design, synthesis, biological evaluation and molecular dynamics simulation studies of (R)-5-methylthiazolidin-4-One derivatives as megakaryocyte protein tyrosine phosphatase 2 (PTP-MEG2) inhibitors for the treatment of type 2 diabetes

ORCID Icon, , , &
Pages 3156-3165 | Received 10 Jul 2019, Accepted 29 Jul 2019, Published online: 22 Aug 2019

References

  • Aier, I., Varadwaj, P. K., & Raj, U. (2016). Structural insights into conformational stability of both wild-type and mutant EZH2 receptor. Scientific Reports, 6(1). doi:10.1038/srep34984
  • Böhm, H.-J. (1992). The computer program LUDI: A new method for the de novo design of enzyme inhibitors. Journal of Computer-Aided Molecular Design, 6, 61–78.
  • Balmith, M., & Soliman, M. E. (2017). Non-active site mutations disturb the loop dynamics, dimerization, viral budding and egress of VP40 of the Ebola virus. Molecular Biosystems, 13(3), 585–597. doi:10.1039/C6MB00803H
  • Barr, A. J., Ugochukwu, E., Lee, W. H., King, O. N., Filippakopoulos, P., Alfano, I., … Knapp, S. (2009). Large-scale structural analysis of the classical human protein tyrosine phosphatome. Cell, 136(2), 352–363. doi:10.1016/j.cell.2008.11.038
  • Berhanu, W. M., & Masunov, A. E. (2014). Full length amylin oligomer aggregation: Insights from molecular dynamics simulations and implications for design of aggregation inhibitors. Journal of Biomolecular Structure and Dynamics, 32(10), 1651–1669. doi:10.1080/07391102.2013.832635
  • Berman, H. M., Battistuz, T., Bhat, T., Bluhm, W. F., Bourne, P. E., Burkhardt, K., … Jain, S. (2002). The protein data bank. Acta Crystallographica Section D Biological Crystallography, 58(6), 899–907. doi:10.1107/S0907444902003451
  • Buslaev, P., Gordeliy, V., Grudinin, S., & Gushchin, I. (2016). Principal component analysis of lipid molecule conformational changes in molecular dynamics simulations. Journal of Chemical Theory and Computation, 12(3), 1019–1028. doi:10.1021/acs.jctc.5b01106
  • Chatterjee, S., Khunti, K., & Davies, M. J. (2017). Type 2 diabetes. Lancet (London, England)), 389(10085), 2239–2251.
  • Cheng, X. C., Wang, R. L., Dong, Z. K., Li, J., Li, Y. Y., & Li, R. R. (2012). Design, synthesis and evaluation of novel metalloproteinase inhibitors based on L-tyrosine scaffold. Bioorganic & Medicinal Chemistry, 20(19), 5738–5744. doi:10.1016/j.bmc.2012.08.014
  • Cho, C. Y., Koo, S.-H., Wang, Y., Callaway, S., Hedrick, S., Mak, P. A., … Montminy, M. (2006). Identification of the tyrosine phosphatase PTP-MEG2 as an antagonist of hepatic insulin signaling. Cell Metabolism, 3(5), 367–378.
  • Diller, D. J., & Merz, K. M. (2001). High throughput docking for library design and library prioritization. Proteins: Structure, Function, and Genetics, 43(2), 113–124. doi:10.1002/1097-0134(20010501)43:2<113::AID-PROT1023>3.0.CO;2-T
  • Fakhar, Z., Govender, T., Maguire, G. E. M., Lamichhane, G., Walker, R. C., Kruger, H. G., & Honarparvar, B. (2017). Differential flap dynamics in l,d-transpeptidase2 from mycobacterium tuberculosis revealed by molecular dynamics. Molecular Biosystems, 13(6), 1223–1234. doi:10.1039/C7MB00110J
  • Foster, C. A., & West, A. H. (2017). Use of restrained molecular dynamics to predict the conformations of phosphorylated receiver domains in two-component signaling systems. Proteins, 85(1), 155–176. doi:10.1002/prot.25207
  • Gurzov, E. N., Stanley, W. J., Brodnicki, T. C., & Thomas, H. E. (2015). Protein tyrosine phosphatases: Molecular switches in metabolism and diabetes. Trends in Endocrinology & Metabolism, 26(1), 30–39. doi:10.1016/j.tem.2014.10.004
  • He, R., Zeng, L. F., He, Y., Zhang, S., & Zhang, Z. Y. (2013). Small molecule tools for functional interrogation of protein tyrosine phosphatases. FEBS Journal, 280(2), 731–750. doi:10.1111/j.1742-4658.2012.08718.x
  • Hendriks, W., Bourgonje, A., Leenders, W., & Pulido, R. (2018). Proteinaceous regulators and inhibitors of protein tyrosine phosphatases. Molecules, 23(2), 395. doi:10.3390/molecules23020395
  • Hendriks, W. J., Elson, A., Harroch, S., Pulido, R., Stoker, A., & den Hertog, J. (2013). Protein tyrosine phosphatases in health and disease. The FEBS Journal, 280(2), 708–730.
  • Huynh, H., Wang, X., Li, W., Bottini, N., Williams, S., Nika, K., … Mustelin, T. (2003). Homotypic secretory vesicle fusion induced by the protein tyrosine phosphatase MEG2 depends on polyphosphoinositides in T cells. The Journal of Immunology, 171(12), 6661–6671. doi:10.4049/jimmunol.171.12.6661
  • Irwin, J. J., & Shoichet, B. K. (2005). ZINC − a free database of commercially available compounds for virtual screening. Journal of Chemical Information and Modeling, 45(1), 177–182. doi:10.1021/ci049714+
  • Law, R., Barker, O., Barker, J. J., Hesterkamp, T., Godemann, R., Andersen, O., … Whittaker, M. (2009). The multiple roles of computational chemistry in fragment-based drug design. Journal of Computer-Aided Molecular Design, 23(8), 459–473. doi:10.1007/s10822-009-9284-1
  • Lee, H., Yi, J.-S., Lawan, A., Min, K., & Bennett, A. M. (2015). Mining the function of protein tyrosine phosphatases in health and disease. Seminars in Cell & Developmental Biology, doi:10.1016/j.semcdb.2014.09.021
  • Li, H., Huang, J., Chen, L., Liu, X., Chen, T., Zhu, J., … Hilgenfeld, R. (2009). Identification of novel falcipain-2 inhibitors as potential antimalarial agents through structure-based virtual screening. Journal of Medicinal Chemistry, 52(15), 4936–4940. doi:10.1021/jm801622x
  • Li, H. L., Ma, Y., Zheng, C. J., Jin, W. Y., Liu, W. S., & Wang, R. L. (2018). Exploring the effect of D61G mutation on SHP2 cause gain of function activity by a molecular dynamics study. Journal of Biomolecular Structure and Dynamics, 36(14), 3856–3868. doi:10.1080/07391102.2017.1402709
  • Liu, X., Dong, G., Zhang, J., Qi, J., Zheng, C., Zhou, Y., … Lü, J. (2011). Discovery of novel human acrosin inhibitors by virtual screening. Journal of Computer-Aided Molecular Design, 25(10), 977–985. doi:10.1007/s10822-011-9476-3
  • Loving, K., Alberts, I., & Sherman, W. (2010). Computational approaches for fragment-based and de novo design. Current Topics in Medicinal Chemistry, 10(1), 14–32. doi:10.2174/156802610790232305
  • Lukman, S., Lane, D. P., & Verma, C. S. (2013). Mapping the structural and dynamical features of multiple p53 DNA binding domains: Insights into loop 1 intrinsic dynamics. PLoS One, 8(11), e80221. doi:10.1371/journal.pone.0080221
  • Ma, Y., Wang, S. Q., Xu, W. R., Wang, R. L., & Chou, K. C. (2012). Design novel dual agonists for treating type-2 diabetes by targeting peroxisome proliferator-activated receptors with core hopping approach. PLoS One, 7(6), e38546. doi:10.1371/journal.pone.0038546
  • MacKerell, A. D., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., … Karplus, M. (1998). All-atom empirical potential for molecular modeling and dynamics studies of proteins. The Journal of Physical Chemistry B, 102(18), 3586–3616. doi:10.1021/jp973084f
  • Ndagi, U., Mhlongo, N. N., & Soliman, M. E. (2017). The impact of Thr91 mutation on c-Src resistance to UM-164: Molecular dynamics study revealed a new opportunity for drug design. Molecular Biosystems, 13(6), 1157–1171. doi:10.1039/C6MB00848H
  • Niu, Y. Z., Shi, D. F., Li, L. L., Guo, J. Y., Liu, H. X., & Yao, X. J. (2017). Revealing inhibition difference between PFI-2 enantiomers against SETD7 by molecular dynamics simulations, binding free energy calculations and unbinding pathway analysis. Scientific Reports, 7, 46547. doi:10.1038/srep46547
  • Piovesan, D., Minervini, G., & Tosatto, S. C. (2016). The RING 2.0 web server for high quality residue interaction networks. Nucleic Acids Research, 44(W1), W367–374. doi:10.1093/nar/gkw315
  • Qi, Y., Zhao, R., Cao, H., Sui, X., Krantz, S. B., & Zhao, Z. J. (2002). Purification and characterization of protein tyrosine phosphatase PTP‐MEG2. Journal of Cellular Biochemistry, 86(1), 79–89. doi:10.1002/jcb.10195
  • Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., … Ideker, T. (2003). Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research, 13(11), 2498–2504. doi:10.1101/gr.1239303
  • Shoichet, B. K. (2004). Virtual screening of chemical libraries. Nature, 432(7019), 862–865.
  • Sittel, F., Jain, A., & Stock, G. (2014). Principal component analysis of molecular dynamics: On the use of Cartesian vs. internal coordinates. Journal of Chemical Physics, 141
  • Wang, D., Cheng, Z., Zhao, M., Jiao, C., Meng, Q., Pan, H., … Wang, W. (2019). PTPN9 induces cell apoptosis by mitigating the activation of Stat3 and acts as a tumor suppressor in colorectal cancer. Cancer Management and Research, 11, 1309. doi:10.2147/CMAR.S187001
  • Wu, J-W., Yin, L., Liu, Y-Q., Zhang, H., Xie, Y-F., Wang, R-L., & Zhao, G-L. (2019). Synthesis, biological evaluation and 3D-QSAR studies of 1, 2, 4-triazole-5-substituted carboxylic acid bioisosteres as uric acid transporter 1 (URAT1) inhibitors for the treatment of hyperuricemia associated with gout. Bioorganic & Medicinal Chemistry Letters, 29(3), 383–388.
  • Wu, J.-W., Zhang, H., Duan, Y.-Q., Dong, W.-L., Cheng, X.-C., Wang, S.-Q., & Wang, R.-L. (2014). Design novel inhibitors for treating cancer by targeting Cdc25B catalytic domain with de novo design. Combinatorial Chemistry & High Throughput Screening, 17, 837–847. doi:10.2174/1386207317666141029223505
  • Zhang, L. S., Wang, S. Q., Xu, W. R., Wang, R. L., & Wang, J. F. (2012). Scaffold-based pan-agonist design for the PPARalpha, PPARbeta and PPARgamma receptors. PLoS One, 7(10), e48453.
  • Zhang, S., Chen, L., Luo, Y., Gunawan, A., Lawrence, D. S., & Zhang, Z.-Y. (2009). Acquisition of a potent and selective TC-PTP inhibitor via a stepwise fluorophore-tagged combinatorial synthesis and screening strategy. Journal of the American Chemical Society, 131(36), 13072–13079. doi:10.1021/ja903733z
  • Zhang, S., Liu, S., Tao, R., Wei, D., Chen, L., Shen, W., … Zhang, Z. Y. (2012). A highly selective and potent PTP-MEG2 inhibitor with therapeutic potential for type 2 diabetes. Journal of the American Chemical Society, 134(43), 18116–18124. doi:10.1021/ja308212y
  • Zhang, X., Wu, J., Liu, Y., Xie, Y., Liu, C., Wang, J., & Zhao, G. (2017). Facile synthetic approaches to 1-thiocyclopropanecarboxylates. Phosphorus, Sulfur, and Silicon and the Related Elements, 192(7), 799–811. doi:10.1080/10426507.2017.1286492
  • Zhang, Z.-Y. (2001). Protein tyrosine phosphatases: Prospects for therapeutics. Current Opinion in Chemical Biology, 5(4), 416–423. doi:10.1016/S1367-5931(00)00223-4

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.