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 type 2 diabetes

References

• Ahuja, N., Schwer, B., Carobbio, S., Waltregny, D., North, B. J., Castronovo, V., … Verdin, E. (2007). Regulation of insulin secretion by SIRT4, a mitochondrial ADP-ribosyltransferase. Journal of Biological Chemistry, 282, 33583–33592.10.1074/jbc.M705488200
   PubMed Web of Science ®Google Scholar
• Banks, J. L. (2005). Integrated modeling program, applied chemical theory (IMPACT). Journal of Computational Chemistry, 26, 1752–1780.10.1002/(ISSN)1096-987X
   PubMed Web of Science ®Google Scholar
• Becke, A. D. (1993). Density-functional thermochemistry. III. The role of exact exchange. The Journal of Chemical Physics, 98, 5648–5652.10.1063/1.464913
   Web of Science ®Google Scholar
• Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. Journal of Chemical Physics, 81, 3684–3690.
   Web of Science ®Google Scholar
• Bowie, J. U., Luthy, R., & Eisenberg, D. (1991). A method to identify protein sequences that fold into a known three-dimensional structure. Science, 253, 164–170.10.1126/science.1853201
   PubMed Web of Science ®Google Scholar
• Bussi, G., Donadio, D., & Parrinello, M. (2007). Canonical sampling through velocity rescaling. The Journal of Chemical Physics, 126, 014101.10.1063/1.2408420
   PubMed Web of Science ®Google Scholar
• Choubey, S. K., Mariadasse, R., Rajendran, S., & Jeyaraman, J. (2016). Identification of novel histone deacetylase 1 inhibitors by combined pharmacophore modeling, 3D-QSAR analysis, in silico screening and density functional theory (DFT) approaches. Journal of Molecular Structure, 1125, 391–404.10.1016/j.molstruc.2016.06.082
   Web of Science ®Google Scholar
• Colovos, C., & Yeates, T. O. (1993). Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Science, 2, 1511–1519.10.1002/pro.v2:9
   PubMed Web of Science ®Google Scholar
• Cramer, C. J., & Truhlar, D. G. (1999). Implicit solvation models:  Equilibria, structure, spectra, and dynamics. Chemical Reviews, 99, 2161–2200.10.1021/cr960149m
   PubMed Web of Science ®Google Scholar
• Forouhi, N. G., & Wareham, N. J. (2014). Epidemiology of diabetes. Medicine (Abingdon), 42, 698–702.
   PubMedGoogle Scholar
• Frye, R. A. (1999). Characterization of five human cDNAs with homology to the yeast SIR2 gene: Sir2-like proteins (Sirtuins) metabolize NAD and may have protein ADP-ribosyltransferase activity. Biochemical and Biophysical Research Communications, 260, 273–279.10.1006/bbrc.1999.0897
   PubMed Web of Science ®Google Scholar
• Gill, P. M. W., Johnson, B. G., Pople, J. A., & Frisch, M. J. (1992). The performance of the Becke – Lee – Yang – Parr (B – LYP) density functional theory with various basis sets. Chemical Physics Letters, 197, 499–505.10.1016/0009-2614(92)85807-M
   Web of Science ®Google Scholar
• Haigis, M. C., Mostoslavsky, R., Haigis, K. M., Fahie, K., Christodoulou, D. C., Murphy, A. J., … Guarente, L. (2006). SIRT4 inhibits glutamate dehydrogenase and opposes the effects of calorie restriction in pancreatic β cells. Cell, 126, 941–954.10.1016/j.cell.2006.06.057
   PubMed Web of Science ®Google Scholar
• Kaminski, G. A., Friesner, R. A., Tirado-Rives, J., & Jorgensen, W. L. (2001). Evaluation and reparametrization of the OPLS-aa force field for proteins via comparison with accurate quantum chemical calculations on peptides. Journal of Physical Chemistry, 105, 6474–6487.
   Web of Science ®Google Scholar
• Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993). PROCHECK-a program to check the stereochemical quality of protein structures. Journal of Applied Crystallography, 26, 283–291.
   Web of Science ®Google Scholar
• Laurent, G., de Boer, V. C., Finley, L. W., Sweeney, M., Lu, H., Schug, T. T., … Haigis, M. C. (2013). SIRT4 represses peroxisome proliferator-activated receptor α activity to suppress hepatic fat oxidation. Molecular and Cellular Biology, 33, 4552–4561.10.1128/MCB.00087-13
   PubMed Web of Science ®Google Scholar
• Lu, B. Z., Zhou, Y. C., Holst, M. J., & McCammon, J. A. (2008). Recent progress in numerical methods for the Poisson-Boltzmann equation in biophysical applications. Communication in Computational physics, 3, 973–1009.
   Web of Science ®Google Scholar
• Lüthy, R., Bowie, J. U., & Eisenberg, D. (1992). Assessment of protein models with three- dimensional profiles. Nature, 356, 83–85.10.1038/356083a0
   PubMed Web of Science ®Google Scholar
• Mariadasse, R., Biswal, J., Jayaprakash, P., Rao, G. R., Choubey, S. K., Rajendran, S., & Jeyakanthan, J. (2016). Mechanical insights of oxythiamine compound as potent inhibitor for human transketolase-like protein 1 (TKTL1 protein). Journal of Receptors and Signal Transduction, 36, 233–242.10.3109/10799893.2015.1080272
   PubMed Web of Science ®Google Scholar
• Matysiak, J. (2007). Evaluation of electronic, lipophilic and membrane affinity effects on antiproliferative activity of 5-substituted-2-(2, 4- dihydroxyphenyl)-1, 3, 4- thiadiazoles against various human cancer cells. European Journal of Medicinal Chemistry, 42, 940–947.10.1016/j.ejmech.2006.12.033
   PubMed Web of Science ®Google Scholar
• Nasrin, N., Wu, X., Fortier, E., Feng, Y., Bare, O. C., Chen, S., … Bordone, L. (2010). SIRT4 regulates fatty acid oxidation and mitochondrial gene expression in liver and muscle cells. Journal of Biological Chemistry, 285, 31995–32002.10.1074/jbc.M110.124164
   PubMed Web of Science ®Google Scholar
• Nosé, S., & Klein, M. L. (1983). Constant pressure molecular dynamics for molecular systems. Molecular Physics, 50, 1055–1076.10.1080/00268978300102851
   Web of Science ®Google Scholar
• Oostenbrink, C., Villa, A., Mark, A. E., & Van Gunsteren, W. F. (2004). A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. Journal of Computational Chemistry, 25, 1656–1676.10.1002/(ISSN)1096-987X
   PubMed Web of Science ®Google Scholar
• Parrinello, M., & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52, 7182–7190.10.1063/1.328693
   Web of Science ®Google Scholar
• Pronk, S., Pall, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., …, Lindahl, E.. (2013). Bioinformatics, 29, 845–854.
   PubMed Web of Science ®Google Scholar
• QM-Polarized Ligand Docking Protocol. Glide (Version 6.6), Jaguar (Version 8.7), QSite (Version 6.6). (2015). New York, NY: Schrödinger, LLC.
   Google Scholar
• Robert, X., & Gouet, P. (2014). Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Research, 42, 320–324.
   PubMed Web of Science ®Google Scholar
• Roy, A., Kucukural, A., & Zhang, Y. (2010). I-TASSER: A unified platform for automated protein structure and function prediction. Nature Protocols, 5, 725–738.10.1038/nprot.2010.5
   PubMed Web of Science ®Google Scholar
• Ruderman, N. B., Carling, D., Prentki, M., & Cacicedo, J. M. (2013). AMPK, insulin resistance, and the metabolic syndrome. Journal of Clinical Investigation, 123, 2764–2772.
   PubMed Web of Science ®Google Scholar
• Ruderman, N. B., & Dean, D. (1998). Malonyl CoA, long chain fatty Acyl CoA and insulin resistance in skeletal muscle. Journal of Basic and Clinical Physiology and Pharmacology, 9, 295–308.10.1515/JBCPP.1998.9.2-4.295
   PubMedGoogle Scholar
• Schrödinger Release 2015-1: LigPrep (Version 3.3). (2015). New York, NY: Schrödinger, LLC.
   Google Scholar
• Schrödinger Release 2015-1: Maestro (Version 10.1). (2015). New York, NY: Schrödinger, LLC.
   Google Scholar
• Schrödinger Release 2015-1: Prime (Version 3.9). (2015). New York, NY: Schrödinger, LLC.
   Google Scholar
• Singh, K. D., Kirubakaran, P., Nagarajan, S., Sugunadevi, S., Karthikeyan, M., & Jeyakanthan, J. (2012). Homology modeling, molecular dynamics, e-pharmacophore mapping and docking study of Chikungunya Virus nsP2 protease. Journal of molecular modeling, 18, 39–51.
   PubMed Web of Science ®Google Scholar
• Sippl, M. J. (1993). Recognition of errors in three-dimensional structures of proteins. Proteins: Structure, Function, and Genetics, 17, 355–362.10.1002/(ISSN)1097-0134
   PubMed Web of Science ®Google Scholar
• Srivastava, R. A. K., Pinkosky, S. L., Filippov, S., Hanselman, J. C., Cramer, C. T., & Newton, R. S. (2012). AMP-activated protein kinase: An emerging drug target to regulate imbalances in lipid and carbohydrate metabolism to treat cardio-metabolic diseases. Jornal of Lipid Research, 53, 2490–2614.
   PubMed Web of Science ®Google Scholar
• Stephens, P. J., Devlin, F. J., Chabalowski, C. F., & Frisch, M. J. (1994). Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields. Journal of Physical Chemistry, 98, 11623–11627.
   Web of Science ®Google Scholar
• Tomasi, J., Mennucci, B., & Cammi, R. (2005). Quantum mechanical continuum solvation models. Chemical Reviews, 105, 2999–3094.10.1021/cr9904009
   PubMed Web of Science ®Google Scholar
• 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, 255–262.10.1007/BF00355047
   PubMed Web of Science ®Google Scholar
• Wiederstein, M., & Sippl, M. J. (2007). ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, 35, 407–410.
   PubMed Web of Science ®Google Scholar
• Yang, Y., Faraggi, E., Zhao, H., & Zhou, Y. (2011). Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of the query and corresponding native properties of templates. Bioinformatics, 27, 2076–2082.
   PubMed Web of Science ®Google Scholar
• Zhan, C. G., Nichols, J. A., & Dixon, D. A. (2005). Ionization potential, electron affinity, electronegativity, hardness, and electron excitation energy: Molecular properties from density functional theory orbital energies. Journal of Physical Chemistry, 107, 4184–4195.
   Web of Science ®Google Scholar
• Zhang, Y. (2008). I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9, 1–8.
   PubMed Web of Science ®Google Scholar
• Zheng, Y., Zheng, M., Ling, X., Liu, Y., Xue, Y., An, L., … Jin, M. (2013). Design, synthesis, quantum chemical studies and biological activity evaluation of pyrazole-benzimidazole derivatives as potent Aurora A/B kinase inhibitors. Bioorganic and Medicinal Chemistry Letters, 23, 3523–3530.10.1016/j.bmcl.2013.04.039
   PubMed Web of Science ®Google Scholar