Identification of novel flavonoid inhibitor of Catechol-O-Methyltransferase enzyme by molecular screening, quantum mechanics/molecular mechanics and molecular dynamics simulations

References

• Baker, D. J., Wijshake, T., Tchkonia, T., LeBrasseur, N. K., Childs, B. G., van de Sluis, B., … van Deursen, J. M. (2011). Clearance of p16 Ink4a-positive senescent cells delays ageing-associated disorders. Nature, 479(7372), 232–236. doi:10.1038/nature10600
   PubMed 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. The Journal of Chemical Physics, 81(8), 3684–3690. doi:10.1063/1.448118
   Web of Science ®Google Scholar
• Bowers, K. J., Chow, E., Xu, H., Dror, R. O., Eastwood, M. P., Gregersen, B. A., …., Shaw, D. E. (2006, November). Scalable algorithms for molecular dynamics simulations on commodity clusters. In SC'06: Proceedings of the 2006 ACM/IEEE Conference on Supercomputing (pp. 43-43). IEEE. doi:10.1145/1188455.1188544.
   Google Scholar
• Boyd, R. J. (2007). The development of computational chemistry in Canada. Reviews in Computational Chemistry, 15, 213–299. doi:10.1002/9780470125922.ch4.
   Google Scholar
• Brandt, W., Manke, K., & Vogt, T. (2015). A catalytic triad - Lys-Asn-Asp - Is essential for the catalysis of the methyl transfer in plant cation-dependent O-methyltransferases. Phytochemistry, 113, 130–139. doi:10.1016/j.phytochem.2014.12.018
   PubMed Web of Science ®Google Scholar
• Brooijmans, N., & Kuntz, I. D. (2003). Molecular recognition and docking algorithms. Annual Review of Biophysics and Biomolecular Structure, 32(1), 335–373. doi:10.1146/annurev.biophys.32.110601.142532
   PubMedGoogle Scholar
• Bunker, A., Männistö, P. T., Pierre, J.-F. S., Róg, T., Pomorski, P., Stimson, L., & Karttunen, M. (2008). Molecular dynamics simulations of the enzyme Catechol-O-Methyltransferase: Methodological issues. SAR and QSAR in Environmental Research, 19(1–2), 179–189. doi:10.1080/10629360701843318
   PubMed Web of Science ®Google Scholar
• Case, D. A., Babin, V., Berryman, J., Betz, R., Cai, Q., Cerutti, D., … Kollman, P. A. (2014). Amber 14. San Francisco, CA: University of California. Retrieved from http://www.ambermd.org
   Google Scholar
• Chen, D., Wang, C. Y., Lambert, J. D., Ai, N., Welsh, W. J., & Yang, C. S. (2005). Inhibition of human liver catechol-O-methyltransferase by tea catechins and their metabolites: Structure-activity relationship and molecular-modeling studies. Biochemical Pharmacology, 69(10), 1523–1531. doi:10.1016/j.bcp.2005.01.024
   PubMed Web of Science ®Google Scholar
• DeLano, W. (2002). PyMOL: An open-oource molecular graphics tool. CCP4 Newsletter On Protein Crystallography. Retrieved from http://www.ccp4.ac.uk/newsletters/newsletter40.pdf#page=44
   Google Scholar
• Farid, R., Day, T., Friesner, A., & Pearlstein, R. A. (2006). New insights about HERG blockade obtained from protein modeling, potential energy mapping, and docking studies. 14, 3160–3173. doi:10.1016/j.bmc.2005.12.032
   Google Scholar
• Flensburg, C., Larsen, S., & Stewart, R. F. (1995). Experimental charge density study of methylammonium hydrogen succinate monohydrate. A salt with a very short O-H-O hydrogen bond. The Journal of Physical Chemistry, 99(25), 10130–10141. doi:10.1021/j100025a013
   Web of Science ®Google Scholar
• Friesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., … Shenkin, P. S. (2004). Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. Journal of medicinal chemistry, 47(7), 1739–1749.
   Google Scholar
• Friesner, R. A., Murphy, R. B., Repasky, M. P., Frye, L. L., Greenwood, J. R., Halgren, T. A., Sanschagrin, P. C., & Mainz, D. T. (2006). Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. Journal of Medicinal Chemistry, 49(21), 6177–6196. doi:10.1021/jm051256o
   PubMed Web of Science ®Google Scholar
• Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., … Pople, J. A. (2005). Gaussian 03, Revision D.1. Wallingford, CT: Gaussian, Inc.
   Google Scholar
• Ghaedi, M., Hassanzadeh, A., & Kokhdan, S. N. (2011). Multiwalled carbon nanotubes as adsorbents for the kinetic and equilibrium study of the removal of Alizarin red S and morin. Journal of Chemical & Engineering Data, 56(5), 2511–2520. doi:10.1021/je2000414
   Web of Science ®Google Scholar
• Goedert, M., Spillantini, M. G., Del Tredici, K., & Braak, H. (2013). 100 years of Lewy pathology. Nature Reviews Neurology, 9(1), 13–24. doi:10.1038/nrneurol.2012.242
   PubMed Web of Science ®Google Scholar
• Halgren, T. A. (2009). Identifying and characterizing binding sites and assessing druggability. Journal of Chemical Information and Modeling, 49(2), 377–389. doi:10.1021/ci800324m
   PubMed Web of Science ®Google Scholar
• Harrach, M. F., & Drossel, B. (2014). Structure and dynamics of TIP3P, TIP4P, and TIP5P water near smooth and atomistic walls of different hydroaffinity. Journal of Chemical Physics, 140(17), 174501. doi:10.1063/1.4872239.
   PubMed Web of Science ®Google Scholar
• Hornykiewicz, O. (1966). Dopamine (3-hydroxytyramine) and brain function. Pharmacological Reviews, 18(2), 925–964. doi:10.1109/RTUCON.2016.7763107.
   PubMed Web of Science ®Google Scholar
• Humphrey, W., Dalke, A., Schulten, K., (1996). Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. doi:10.1016/0263-7855(96)00018-5
   PubMedGoogle Scholar
• Ilari, A., Lalle, M., Botta, M., Mori, M., Fiorillo, A., & Cau, Y. (2015). Molecular dynamics simulations and structural analysis of giardia duodenalis 14-3-3 protein–protein interactions. Journal of Chemical Information and Modeling, 55(12), 2611–2622. doi:10.1021/acs.jcim.5b00452
   PubMed Web of Science ®Google Scholar
• Jacobson, M. P., Pincus, D. L., Rapp, C. S., Day, T. J. F., Honig, B., Shaw, D. E., & Friesner, R. A. (2004). A hierarchical approach to all-atom protein loop prediction. Proteins: Structure, Function, and Bioinformatics, 55(2), 351–367. doi:10.1002/prot.10613
   PubMed Web of Science ®Google Scholar
• Jones, A., & Leimkuhler, B. (2011). Adaptive stochastic methods for sampling driven molecular systems. Journal of Chemical Physics, 135(8), 084125. doi:10.1063/1.3626941.
   PubMed Web of Science ®Google Scholar
• Jorgensen, W. L., Maxwell, D. S., & Tirado-Rives, J. (1996). Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. 7863(15), 11225–11236. doi:10.1021/ja9621760
   Google Scholar
• Kadowaki, M., Ootani, E., Sugiha, N., & Furuno, K. (2005). Inhibitory effects of catechin gallates on o -methyltranslation of protocatechuic acid in rat liver cytosolic preparations and cultured hepatocytes. Biological & Pharmaceutical Bulletin, 28(8), 1509–1513. doi:10.1248/bpb.28.1509
   PubMed Web of Science ®Google Scholar
• Kinnings, S. L., Liu, N., Buchmeier, N., Tonge, P. J., Xie, L., & Bourne, P. E. (2009). Drug discovery using chemical systems biology: Repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis. PLoS Computational Biology, 5(7), e1000423. doi:10.1371/journal.pcbi.1000423
   PubMed Web of Science ®Google Scholar
• Kitchen, D. B., Decornez, H., Furr, J. R., & Bajorath, J. (2004). Docking and scoring in virtual screening for drug discovery: Methods and applications. Nature Reviews Drug Discovery, 3(11), 935–949. doi:10.1038/nrd1549
   PubMed Web of Science ®Google Scholar
• Liu, W., & Guo, R. (2008). Effects of Triton X-100 nanoaggregates on dimerization and antioxidant activity of morin. Molecular Pharmaceutics, 5(4), 588–597. doi:10.1021/mp7001413
   PubMed Web of Science ®Google Scholar
• Maier, J. A., Simmerling, C., Wickstrom, L., Hauser, K. E., Martinez, C., & Kasavajhala, K. (2015). ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB. Journal of Chemical Theory and Computation, 11(8), 3696–3713. doi:10.1021/acs.jctc.5b00255
   PubMed Web of Science ®Google Scholar
• Mark, P., & Nilsson, L. (2001). Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K. The Journal of Physical Chemistry A, 105(43), 9954–9960. doi:10.1021/jp003020w
   Web of Science ®Google Scholar
• Martyna, G. J., Hughes, A., & Tuckerman, M. E. (1999). Molecular dynamics algorithms for path integrals at constant pressure. The Journal of Chemical Physics, 110(7), 3275–3290. doi:10.1063/1.478193
   Web of Science ®Google Scholar
• Naudts, J., & Van Der Straeten, E. (2006). A generalized quantum microcanonical ensemble. Journal of Statistical Mechanics: Theory and Experiment, 2006(6), P06015. doi:10.1088/1742-5468/2006/06/P06015
   Google Scholar
• Nemanashi, M., & Meijboom, R. (2015). Catalytic behavior of different sizes of dendrimer-encapsulated Aun nanoparticles in the oxidative degradation of morin with H2O2. Langmuir, 31(33), 9041–9053. doi:10.1021/acs.langmuir.5b02020
   PubMed Web of Science ®Google Scholar
• Nuno Palma, P., João Bonifácio, M., Isabel Loureiro, A., & Soares-Da-Silva, P. (2012). Computation of the binding affinities of catechol-O-methyltransferase inhibitors: Multisubstate relative free energy calculations. Journal of Computational Chemistry, 33(9), 970–986. doi:10.1002/jcc.22926
   PubMed Web of Science ®Google Scholar
• Para, M., Cao, Y., Chen, Z., Jiang, H., & Chen, J. (2014). Computational studies of the regioselectivities of COMT-catalyzed meta-/para-O methylations of luteolin and quercetin. The Journal of Physical Chemistry B, 118(2), 470–481.
   PubMed Web of Science ®Google Scholar
• Parkinsons Disease Foundation. (2014). MEDICINES IN DEVELOPMENT Parkinson’s Disease. Parkinson’s Disease, 1–12. Retrieved from http://www.phrma.org/sites/default/files/pdf/2014-parkinsons-report.pdf
   Google Scholar
• Paul J Turner and ACE/gr development team, & team, P. J. T. and A. development. (1998). Xmgr: List of changes. 1–11. Retrieved from http://plasma-gate.weizmann.ac.il/Xmgr/doc/CHANGES.html
   Google Scholar
• Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera - A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. doi:10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Renuga Parameswari, A., Rajalakshmi, G., & Kumaradhas, P. (2015). A combined molecular docking and charge density analysis is a new approach for medicinal research to understand drug-receptor interaction: Curcumin-AChE model. Chemico-Biological Interactions, 225(October), 21–31. doi:10.1016/j.cbi.2014.09.011
   PubMedGoogle Scholar
• Roe, D. R., & Cheatham, T. E. (2013). PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data. Journal of Chemical Theory and Computation, 9(7), 3084–3095. doi:10.1021/ct400341p
   PubMed Web of Science ®Google Scholar
• Rutherford, K., Le Trong, I., Stenkamp, R. E., & Parson, W. W. (2008). Crystal structures of human 108V and 108M catechol O-methyltransferase. Journal of Molecular Biology, 380(1), 120–130. doi:10.1016/j.jmb.2008.04.040
   PubMed Web of Science ®Google Scholar
• Ryckaert, J. P., Ciccotti, G., & Berendsen, H. J. C. (1977). Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. Journal of Computational Physics, 23(3), 327–341. doi:10.1016/0021-9991(77)90098-5
   Web of Science ®Google Scholar
• Saravanan, K., Sivanandam, M., Hunday, G., Mathiyalagan, L., & Kumaradhas, P. (2018). Investigation of intermolecular interactions and stability of verubecestat in the active site of BACE1: Development of first model from QM/MM-based charge density and MD analysis. Journal of Biomolecular Structure and Dynamics, 37(9), 2339–2354. doi:10.1080/07391102.2018.1479661
   PubMed Web of Science ®Google Scholar
• Sastry, G. M., Adzhigirey, M., & 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
   PubMed Web of Science ®Google Scholar
• Sherman, W., Beard, H. S., & Farid, R. (2006). Use of an induced fit receptor structure in virtual screening. Chemical Biology & Drug Design, 67(1), 83–84. doi:10.1111/j.1747-0285.2005.00327.x
   PubMed Web of Science ®Google Scholar
• Sherman, W., Day, T., Jacobson, M. P., Friesner, R. A., & Farid, R. (2006). Novel procedure for modeling ligand/receptor induced fit effects. Journal of Medicinal Chemistry, 49(2), 534–553. doi:10.1021/jm050540c
   PubMed Web of Science ®Google Scholar
• Sinnokrot, M. O., Valeev, E. F., & Sherrill, C. D. (2002). Estimates of the ab initio limit for π-π interactions: The benzene dimer. Journal of the American Chemical Society, 124(36), 10887–10893. doi:10.1021/ja025896h
   PubMed Web of Science ®Google Scholar
• Sivanandam, M., Saravanan, K., & Kumaradhas, P. (2017). Insights into intermolecular interactions, electrostatic properties and the stability of C646 in the binding pocket of p300 histone acetyltransferase enzyme: A combined molecular dynamics and charge density study. Journal of Biomolecular Structure and Dynamics, 1102(October), 1–19. doi:10.1080/07391102.2017.1384761
   Google Scholar
• Tamer, Ö., Avci, D., & Atalay, Y. (2014). Quantum chemical characterization of N-(2-hydroxybenzylidene)acetohydrazide (HBAH): A detailed vibrational and NLO analysis. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 117, 78–86. doi:10.1016/j.saa.2013.07.112
   PubMed Web of Science ®Google Scholar
• Tordai, H., Leveles, I., & Hegedűs, T. (2017). Molecular dynamics of the cryo-EM CFTR structure. Biochemical and Biophysical Research Communications, 491(4), 986–993. doi:10.1016/j.bbrc.2017.07.165
   PubMed Web of Science ®Google Scholar
• Tsuji, E., Okazaki, K., & Takeda, K. (2009). Crystal structures of rat catechol-O-methyltransferase complexed with coumarine-based inhibitor. Biochemical and Biophysical Research Communications, 378(3), 494–497. doi:10.1016/j.bbrc.2008.11.085
   PubMed Web of Science ®Google Scholar
• Venkateswarlu, D. (2014). Structural insights into the interaction of blood coagulation co-factor VIIIa with factor IXa: A computational protein-protein docking and molecular dynamics refinement study. Biochemical and Biophysical Research Communications, 452(3), 408–414. doi:10.1016/j.bbrc.2014.08.078
   PubMed Web of Science ®Google Scholar
• Vidgren, J., Svensson, L. A., & Liljas, A. (1994). Crystal structure of catechol O-methyltransferase. Nature, 368(6469), 354–358. doi:10.1038/368354a0
   PubMed Web of Science ®Google Scholar
• Wallace, A. C., Laskowski, R. A., & Thornton, J. M. (1995). LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Engineering, Design and Selection, 8(2), 127–134 doi:10.1093/protein/8.2.127
   Web of Science ®Google Scholar
• Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Development and testing of a general Amber force field. Journal of Computational Chemistry, 25(9), 1157–1174. doi:10.1002/jcc.20035
   PubMed Web of Science ®Google Scholar
• Wang, L., & Yan, F. (2019). Exploring the role of active site Mn 2+ ions in the binding of protein phosphatase 5 with its substrate using molecular dynamics simulations. Biochemical and Biophysical Research Communications), 511(3), 612–618. doi:10.1016/j.bbrc.2019.02.113
   PubMed Web of Science ®Google Scholar
• Wauer, T., & Komander, D. (2013). Structure of the human Parkin ligase domain in an autoinhibited state. The Embo Journal, 32(15), 2099–2112. doi:10.1038/emboj.2013.125
   PubMed Web of Science ®Google Scholar
• Yao, S. C., Hart, A. D., & Terzella, M. J. (2013). An evidence-based osteopathic approach to Parkinson disease. Osteopathic Family Physician, 5(3), 96–101. doi:10.1016/j.osfp.2013.01.003
   Google Scholar