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Research Articles

Design potential selective inhibitors for human leukocyte common antigen-related (PTP-LAR) with fragment replace approach

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Pages 5338-5348 | Received 07 Nov 2019, Accepted 25 Nov 2019, Published online: 09 Dec 2019

Reference

  • Ahmad, F., & Goldstein, B. J. (1997). Functional association between the insulin receptor and the transmembrane protein-tyrosine phosphatase LAR in intact cells. Journal of Biological Chemistry, 272(1), 448–457. doi:10.1074/jbc.272.1.448
  • Ajay, D., & Sobhia, M. E. (2012). Identification of novel, less toxic PTP-LAR inhibitors using in silico strategies: Pharmacophore modeling, SADMET-based virtual screening and docking. Journal of Molecular Modeling, 18(1), 187–201. doi:10.1007/s00894-011-1037-0
  • Andrew, S., Kahn, S. D., & Steven, L. T. (1995a). Analysis of conformational coverage. 1. validation and estimation of coverage. Journal of Chemical Information and Computer Sciences, 35, 285–294.
  • Andrew, S., Kahn, S. D., & Steven, L. T. (1995b). Analysis of conformational coverage. 2. applications of conformational models. Journal of Chemical Information and Computer Sciences, 35, 295–304
  • Andrew, S., Teig, S. L., & Peter, T. (1995). Poling: promoting conformational variation. Journal of Computational Chemistry, 16, 171–187.
  • Baker, N. A., Sept, D., Joseph, S., Holst, M. J., & McCammon, J. A. (2001). Electrostatics of nanosystems: Application to microtubules and the ribosome. Proceedings of the National Academy of Sciences, 98(18), 10037–10041. doi:10.1073/pnas.181342398
  • Berman, H. M., Battistuz, T., Bhat, T. N., Bluhm, W. F., Bourne, P. E., Burkhardt, K., … Zardecki, C. (2002). The protein data bank. Acta Crystallographica Section D Biological Crystallography, 58(6), 899–907. doi:10.1107/S0907444902003451
  • Chagnon, M. J., Uetani, N., & Tremblay, M. L. (2004). Functional significance of the LAR receptor protein tyrosine phosphatase family in development and diseases. Biochemistry and Cell Biology, 82(6), 664–675. doi:10.1139/o04-120
  • Cheng, A., & Dixon, S. L. (2003). In silico models for the prediction of dose-dependent human hepatotoxicity. Journal of Computer-Aided Molecular Design, 17(12), 811–823. doi:10.1023/B:JCAM.0000021834.50768.c6
  • Cheng, A., & Merz, K. M. Jr.(2003). Prediction of aqueous solubility of a diverse set of compounds using quantitative structure-property relationships. Journal of Medicinal Chemistry, 46(17), 3572–3580. doi:10.1021/jm020266b
  • Dixon, S. L., & Merz, K. M. Jr. (2001). One-dimensional molecular representations and similarity calculations: Methodology and validation. Journal of Medicinal Chemistry, 44(23), 3795–3809. doi:10.1021/jm010137f
  • Egan, W. J., & Lauri, G. (2002). Prediction of intestinal permeability. Advanced Drug Delivery Reviews, 54(3), 273–289. doi:10.1016/S0169-409X(02)00004-2
  • Egan, W. J., Merz, K. M., Jr., & Baldwin, J. J. (2000). Prediction of drug absorption using multivariate statistics. Journal of Medicinal Chemistry, 43(21), 3867–3877. doi:10.1021/jm000292e
  • Egan, W. J., Walters, W. P., & Murcko, M. A. (2002). Guiding molecules towards drug-likeness. Current Opinion in Drug Discovery & Development, 5(4), 540–549.
  • Elchebly, M., Cheng, A., & Tremblay, M. L. (2000). Modulation of insulin signaling by protein tyrosine phosphatases. Journal of Molecular Medicine , 78(9), 473–482. (Berl) doi:10.1007/s001090000141
  • Ftanik, J., & Horvath, I. I. (1989). Computations of energy levels and wave functions of ground and excited states by the steepest-descent method. Phys Rev D Part Fields, 40, 642–649.
  • Guan, K. L., & Dixon, J. E. (1991). Evidence for protein-tyrosine-phosphatase catalysis proceeding via a cysteine-phosphate intermediate. J Biol Chem, 266(26), 17026–17030.
  • Hashimoto, N., Feener, E. P., Zhang, W. R., & Goldstein, B. J. (1992). Insulin receptor protein-tyrosine phosphatases. Leukocyte common antigen-related phosphatase rapidly deactivates the insulin receptor kinase by preferential dephosphorylation of the receptor regulatory domain. J Biol Chem, 267(20), 13811–13814.
  • Hess, B. (2008). P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation. Journal of Chemical Theory and Computation, 4(1), 116–122. doi:10.1021/ct700200b
  • Hess, B., Kutzner, C., van der Spoel, D., & Lindahl, E. (2008). GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4(3), 435–447. doi:10.1021/ct700301q
  • Irwin, J. J., & Shoichet, B. K. (2005). ZINC–a free database of commercially available compounds for virtual screening. J Chem Inf Model, 45(1), 177–182. doi:10.1021/ci049714+
  • Konerding, D. E., Cheatham, T. E., Kollman, P. A., & James, T. L. (1999). Restrained molecular dynamics of solvated duplex DNA using the particle mesh Ewald method. Journal of Biomolecular NMR, 13(2), 119–131.
  • Kulas, D. T., Zhang, W. R., Goldstein, B. J., Furlanetto, R. W., & Mooney, R. A. (1995). Insulin receptor signaling is augmented by antisense inhibition of the protein tyrosine phosphatase LAR. Journal of Biological Chemistry, 270(6), 2435–2438. doi:10.1074/jbc.270.6.2435
  • Kumari, R., Kumar, R., Open Source Drug Discovery Consortium, & Lynn, A. (2014).g_mmpbsa–a GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling , 54(7), 1951–1962. doi:10.1021/ci500020m
  • Lipinski, C. A. (2016). Rule of five in 2015 and beyond: Target and ligand structural limitations, ligand chemistry structure and drug discovery project decisions. Advanced Drug Delivery Reviews, 101, 34–41. doi:10.1016/j.addr.2016.04.029
  • 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 settings. Advanced Drug Delivery Reviews, 46(1–3), 3–26. doi:10.1016/j.addr.2012.09.019
  • Lombardo, F., Gifford, E., & Shalaeva, M. Y. (2003). In silico ADME prediction: Data, models, facts and myths. Mini Reviews in Medicinal Chemistry, 3(8), 861–875. doi:10.2174/1389557033487629
  • MacKerell, A. D., Banavali, N., & Foloppe, N. (2001). Development and current status of the CHARMM force field for nucleic acids. Biopolymers, 56(4), 257–265. doi:10.1002/1097-0282(2000)56:4<257::AID-BIP10029>3.0.CO;2-W
  • Markovic, R., Baranac, M., Dzambaski, Z., Stojanovic, M., & Steel, P. J. (2003). High regioselectivity in the heterocyclization of beta-oxonitriles to 4-oxothiazolidines: X-ray structure proof. Tetrahedron, 59, 7803–7810. doi:10.1016/S0040-4020(03)01146-3
  • Markovic, R., Pergal, M. M., Baranac, M., Stanisavljev, D., & Stojanovic, M. (2006). An expedient solvent-free synthesis of (Z)-2-alkylidene-4-oxothiazolidine derivatives under microwave irradiation. Arkivoc, 2006, 83–90.
  • Mediavilla Bravo, J. J. (2014). Guidelines for the management of diabetes mellitus type 2]. Semergen - Medicina de Familia, 40, 11–18. [ Suppl 4:
  • Michigan Dental, A. (2007). Patient fact sheet. Diabetes and your oral health. Journal of the Michigan Dental Association, 89: 17
  • Nam, H. J., Poy, F., Krueger, N. X., Saito, H., & Frederick, C. A. (1999). Crystal structure of the tandem phosphatase domains of RPTP LAR. Cell, 97(4), 449–457. doi:10.1016/S0092-8674(00)80755-2
  • Norberto de Souza, O., & Ornstein, R. L. (1999). Molecular dynamics simulations of a protein-protein dimer: Particle-mesh Ewald electrostatic model yields far superior results to standard cutoff model. Journal of Biomolecular Structure and Dynamics, 16, 1205–1218. doi:10.1080/07391102.1999.10508328
  • Pol-Fachin, L., Fernandes, C. L., & Verli, H. (2009). GROMOS96 43a1 performance on the characterization of glycoprotein conformational ensembles through molecular dynamics simulations. Carbohydrate Research, 344(4), 491–500. doi:10.1016/j.carres.2008.12.025
  • Premnath, P. N., Liu, S., Perkins, T., Abbott, J., Anderson, E., & McInnes, C. (2014). Fragment based discovery of arginine isosteres through REPLACE: Towards non-ATP competitive CDK inhibitors. Bioorganic & Medicinal Chemistry, 22, 616–622. doi:10.1016/j.bmc.2013.10.039
  • Pulido, R., Serra-Pages, C., Tang, M., & Streuli, M. (1995). The LAR/PTP delta/PTP sigma subfamily of transmembrane protein-tyrosine-phosphatases: Multiple human LAR, PTP delta, and PTP sigma isoforms are expressed in a tissue-specific manner and associate with the LAR-interacting protein LIP.1. Proceedings of the National Academy of Sciences, 92(25), 11686–11690. doi:10.1073/pnas.92.25.11686
  • Rathmann, W., & Giani, G. (2004). Global prevalence of diabetes: Estimates for the year 2000 and projections for 2030. Diabetes Care, 27(10), 2568–2569; author reply 2569. doi:10.2337/diacare.27.10.2568
  • Ren, J. M., Li, P. M., Zhang, W. R., Sweet, L. J., Cline, G., Shulman, G. I., … Goldstein, B. J. (1998). Transgenic mice deficient in the LAR protein-tyrosine phosphatase exhibit profound defects in glucose homeostasis. Diabetes, 47(3), 493–497. doi:10.2337/diabetes.47.3.493
  • Roper, D., Spinderella, D. J., Webb, R. (2014). Let's talk about … diabetes. Diabetes Forecast, 67, 50–53.
  • Susnow, R. G., & Dixon, S. L. (2003). Use of robust classification techniques for the prediction of human cytochrome P450 2D6 inhibition. Journal of Chemical Information and Computer Sciences, 43(4), 1308–1315. doi:10.1021/ci030283p
  • Tsujikawa, K., Kawakami, N., Uchino, Y., Ichijo, T., Furukawa, T., Saito, H., & Yamamoto, H. (2001). Distinct functions of the two protein tyrosine phosphatase domains of LAR (leukocyte common antigen-related) on tyrosine dephosphorylation of insulin receptor. Molecular Endocrinology, 15(2), 271–280. doi:10.1210/mend.15.2.0592
  • van Aalten, D. M., Bywater, R., Findlay, J. B., Hendlich, M., Hooft, R. W., & Vriend, G. (1996). PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules. Journal of Computer-Aided Molecular Design, 10(3), 255–262. doi:10.1007/BF00355047
  • Viswanathan, V., & Sathyamurthy, S. (2015). Global increase in the prevalence of diabetes with special reference to the Middle East and Asia. Diabetes Technology & Therapeutics, 17(10), 676–678. doi:10.1089/dia.2015.0197
  • Votano, J. R., Parham, M., Hall, L. M., Hall, L. H., Kier, L. B., Oloff, S., & Tropsha, A. (2006). QSAR modeling of human serum protein binding with several modeling techniques utilizing structure-information representation. Journal of Medicinal Chemistry, 49(24), 7169–7181. doi:10.1021/jm051245v
  • Walters, W. P. (2012). Going further than Lipinski's rule in drug design. Expert Opinion on Drug Discovery, 7(2), 99–107. doi:10.1517/17460441.2012.648612
  • Wesson, L., & Eisenberg, D. (1992). Atomic solvation parameters applied to molecular dynamics of proteins in solution. Protein Science, 1(2), 227–235. doi:10.1002/pro.5560010204
  • 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(5), 1047–1053. doi:10.2337/diacare.27.5.1047
  • Wu, J., Sun, Y., Zhou, H., Ma, Y., & Wang, R. (2019). 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. Journal of Biomolecular Structure and Dynamics, 1–10. doi:10.1080/07391102.2019.1654410
  • 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. doi:10.1016/j.bmcl.2018.12.036
  • Xia, X., Maliski, E. G., Gallant, P., & Rogers, D. (2004). Classification of kinase inhibitors using a Bayesian model. Journal of Medicinal Chemistry, 47(18), 4463–4470. doi:10.1021/jm0303195
  • Xu, E., Schwab, M., & Marette, A. (2014). Role of protein tyrosine phosphatases in the modulation of insulin signaling and their implication in the pathogenesis of obesity-linked insulin resistance. Reviews in Endocrine and Metabolic Disorders, 15(1), 79–97. doi:10.1007/s11154-013-9282-4
  • Zabolotny, J. M., Kim, Y. B., Peroni, O. D., Kim, J. K., Pani, M. A., Boss, O., … Neel, B. G. (2001). Overexpression of the LAR (leukocyte antigen-related) protein-tyrosine phosphatase in muscle causes insulin resistance. Proceedings of the National Academy of Sciences, 98(9), 5187–5192. doi:10.1073/pnas.071050398
  • Zhang, W. R., Li, P. M., Oswald, M. A., & Goldstein, B. J. (1996). Modulation of insulin signal transduction by eutopic overexpression of the receptor-type protein-tyrosine phosphatase LAR. Molecular Endocrinology, 10, 575–584. doi:10.1210/me.10.5.575
  • Zhu, Y., & Zhang, C. (2016). Prevalence of Gestational Diabetes and Risk of Progression to Type 2 Diabetes: A Global Perspective. Current Diabetes Reports, 16(1), 7. doi:10.1007/s11892-015-0699-x

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