The signaling pathway of dopamine D2 receptor (D2R) activation using normal mode analysis (NMA) and the construction of pharmacophore models for D2R ligands

References

• Attwood, T. K., & Findlay, J. B. C. (1994). Fingerprinting G-protein-coupled receptors. Protein Engineering, Design and Selection, 7, 195–203. doi:10.1093/protein/7.2.195
   Web of Science ®Google Scholar
• Bahar, I., Lezon, T. R., Bakan, A., & Shrivastava, I. H. (2010). Normal mode analysis of biomolecular structures: Functional mechanisms of membrane proteins. Chemical Reviews, 110, 1463–1497. doi:10.1021/cr900095e
   PubMed Web of Science ®Google Scholar
• Bahar, I., & Rader, A. J. (2005). Coarse-grained normal mode analysis in structural biology. Current Opinion in Structural Biology, 15, 586–592. doi:10.1016/j.sbi.2005.08.007
   PubMed Web of Science ®Google Scholar
• Brooks, B., & Karplus, M. (1983). Harmonic dynamics of proteins: Normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proceedings of the National Academy of Sciences, 80, 6571–6575. doi:10.1073/pnas.80.21.6571
   PubMed Web of Science ®Google Scholar
• Case, D. A. (1994). Normal mode analysis of protein dynamics. Current Opinion in Structural Biology, 4, 285–290. doi:10.1016/S0959-440X(94)90321-2
   Web of Science ®Google Scholar
• Congreve, M., & Marshall, F. (2010). The impact of GPCR structures on pharmacology and structure-based drug design. British Journal of Pharmacology, 159, 986–996. doi:10.1111/j.1476-5381.2009.00476.x
   PubMed Web of Science ®Google Scholar
• Creese, I., Burt, D. R., & Snyder, S. H. (1996). Dopamine receptor binding predicts clinical and pharmacological potencies of antischizophrenic drugs. The Journal of Neuropsychiatry and Clinical Neurosciences, 8, 223–226. doi:10.1126/science.3854
   PubMed Web of Science ®Google Scholar
• Cui, Q., & Bahar, I. (2005). Normal mode analysis: Theory and applications to biological and chemical systems. Chapman and Hall/CRC. Retrieved from http://www.crcpress.com/product/isbn/978158488472910.1201/CHMTHCOMBIO
   Google Scholar
• Dixon, S. L., Smondyrev, A. M., Knoll, E. H., Rao, S. N., Shaw, D. E., & Friesner, R. A. (2006). PHASE: A new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results. Journal of Computer-Aided Molecular Design, 20, 647–671. doi:10.1007/s10822-006-9087-6
   PubMed Web of Science ®Google Scholar
• Durdagi, S., Duff, H. J., & Noskov, S. Y. (2011). Combined receptor and ligand-based approach to the universal pharmacophore model development for studies of drug blockade to the hERG1 pore domain. Journal of Chemical Information and Modeling, 51, 463–474. doi:10.1021/ci100409y
   PubMed Web of Science ®Google Scholar
• Durdagi, S., Kapou, A., Kourouli, T., Andreou, T., Nikas, S. P., Nahmias, V. R., … Mavromoustakos, T. (2007). The application of 3D-QSAR studies for novel cannabinoid ligands substituted at the C1’ position of the alkyl side chain on the structural requirements for binding to cannabinoid receptors CB1 and CB2. Journal of Medicinal Chemistry, 50, 2875–2885. doi:10.1021/jm0610705
   PubMed Web of Science ®Google Scholar
• Durdagi, S., Salmas, R. E., Stein, M., Yurtsever, M., & Seeman, P. (2015). Binding interactions of dopamine and apomorphine in D2high and D2low states of human dopamine D2 receptor (D2R) using computational and experimental techniques. ACS Chemical Neuroscience, 7, 185–195. doi:10.1021/acschemneuro.5b00271
   PubMed Web of Science ®Google Scholar
• Foord, S. M., Bonner, T. O. M. I., Neubig, R. R., Rosser, E. M., Pin, J., Davenport, A. P., … Harmar, A. J. (2005). International union of pharmacology. XLVI. G protein-coupled receptor list. Pharmacological Reviews, 57, 279–288. doi:10.1124/pr.57.2.5.2
   PubMed Web of Science ®Google Scholar
• Fu, D., Ballesteros, J. A., Weinstein, H., Chen, J., & Javitch, J. A. (1996). Residues in the seventh membrane-spanning segment of the dopamine D2 receptor accessible in the binding-site crevice. Biochemistry, 35, 11278–11285. doi:10.1021/bi960928x
   PubMed Web of Science ®Google Scholar
• Grant, B. J., Rodrigues, A. P. C., ElSawy, K. M., McCammon, J. A., & Caves, L. S. D. (2006). Bio3d: An R package for the comparative analysis of protein structures. Bioinformatics, 22, 2695–2696. doi:10.1093/bioinformatics/btl461
   PubMed Web of Science ®Google Scholar
• Haga, K., Kruse, A. C., Asada, H., Yurugi-Kobayashi, T., Shiroishi, M., Zhang, C., … Kobayashi, T. (2012). Structure of the human M2 muscarinic acetylcholine receptor bound to an antagonist. Nature, 482, 547–551. doi:10.1038/nature10753
   PubMed Web of Science ®Google Scholar
• Irwin, J. J., Sterling, T., Mysinger, M. M., Bolstad, E. S., & Coleman, R. G. (2012). ZINC: A free tool to discover chemistry for biology. Journal of Chemical Information and Modeling, 52, 1757–1768. doi:10.1021/ci3001277
   PubMed Web of Science ®Google Scholar
• Jaakola, V. P., Griffith, M. T., Hanson, M. A., Cherezov, V., Chien, E. Y., Lane, J. R., … Stevens, R. C. (2008). The 2.6 Å crystal structure of a human A2A adenosine receptor bound to an antagonist. Science, 322, 1211–1217. doi:10.1126/science.1164772
   PubMed Web of Science ®Google Scholar
• Javitch, J. A., Ballesteros, J. A., Weinstein, H., & Chen, J. (1998). A cluster of aromatic residues in the sixth membrane-spanning segment of the dopamine D2 receptor is accessible in the binding-site crevice. Biochemistry, 37, 998–1006. doi:10.1021/bi972241y
   PubMed Web of Science ®Google Scholar
• Javitch, J. A., Fu, D., & Chen, J. (1995). Residues in the fifth membrane-spanning segment of the dopamine D2 receptor exposed in the binding-site crevice. Biochemistry, 34, 16433–16439. doi:10.1021/bi00050a026
   PubMed Web of Science ®Google Scholar
• Kapou, A., Benetis, N.-P., Durdagi, S., Nikolaropoulos, S., & Mavromoustakos, T. (2008). 3D QSAR/CoMFA and CoMSIA studies on antileukemic steroidal esters coupled with conformationally flexible nitrogen mustards. Journal of Chemical Information and Modeling, 48, 2254–2264. doi:10.1021/ci800240 m
   PubMed Web of Science ®Google Scholar
• Kolakowski, L. F. J. (1994). GCRDb: A G-protein-coupled receptor database. Receptors & Channels, 2, 1–7.
   PubMedGoogle Scholar
• Lagerström, M. C., & Schiöth, H. B. (2008). Structural diversity of G protein-coupled receptors and significance for drug discovery. Nature Reviews. Drug Discovery, 7, 339–357. doi:10.1038/nrd2518
   PubMed Web of Science ®Google Scholar
• Laruelle, M., Abi-Dargham, A., van Dyck, C. H., Gil, R., D’Souza, C. D., Erdos, J., … Innis, R. B. (1996). Single photon emission computerized tomography imaging of amphetamine-induced dopamine release in drug-free schizophrenic subjects. Proceedings of the National Academy of Sciences of the United States of America, 93, 9235–9240. doi:10.1073/pnas.93.17.9235
   PubMed Web of Science ®Google Scholar
• Leach, A. R. (2001). Molecular modelling: Principles and applications (2nd ed.). Upper Saddle River, NJ: Prentice Hall.
   Google Scholar
• Mavromoustakos, T., Durdagi, S., Koukoulitsa, C., Simcic, M., Papadopoulos, M. G., Hodoscek, M., & Golic Grdadolnik, S. (2011). Strategies in the rational drug design. Current Medicinal Chemistry, 18, 2517–2530. doi:10.2174/092986711795933731
   PubMed Web of Science ®Google Scholar
• Miloshevsky, G. V., & Jordan, P. C. (2006). The open state gating mechanism of gramicidin a requires relative opposed monomer rotation and simultaneous lateral displacement. Structure, 14, 1241–1249. doi:10.1016/j.str.2006.06.007
   PubMed Web of Science ®Google Scholar
• Overington, J. P., Al-Lazikani, B., & Hopkins, A. L. (2006). How many drug targets are there? Nature Reviews. Drug Discovery, 5, 993–996. doi:10.1038/nrd2199
   PubMed Web of Science ®Google Scholar
• Park, J. H., Scheerer, P., Hofmann, K. P., Choe, H.-W., & Ernst, O. P. (2008). Crystal structure of the ligand-free G-protein-coupled receptor opsin. Nature, 454, 183–187. doi:10.1038/nature07063
   PubMed Web of Science ®Google Scholar
• Politi, A., Durdagi, S., Moutevelis-Minakakis, P., Kokotos, G., Papadopoulos, M. G., & Mavromoustakos, T. (2009). Application of 3D QSAR CoMFA/CoMSIA and in silico docking studies on novel renin inhibitors against cardiovascular diseases. European Journal of Medicinal Chemistry, 44, 3703–3711. doi:10.1016/j.ejmech.2009.03.040
   PubMed Web of Science ®Google Scholar
• Rasmussen, S. G. F., DeVree, B. T., Zou, Y., Kruse, A. C., Chung, K. Y., Kobilka, T. S., … Kobilka, B. K. (2011). Crystal structure of the β2 adrenergic receptor-Gs protein complex. Nature, 477, 549–555. doi:10.1038/nature10361
   PubMed Web of Science ®Google Scholar
• Rompler, H., Staubert, C., Thor, D., Schulz, A., Hofreiter, M., & Schoneberg, T. (2007). G Protein-coupled time travel: Evolutionary aspects of GPCR research. Molecular Interventions, 7, 17–25. doi:10.1124/mi.7.1.5
   PubMed Web of Science ®Google Scholar
• Salmas, R. E, Yurtsever, M., & Durdagi, S. (in press). Atomistic molecular dynamics simulations of typical and atypical antipsychotic drugs at the dopamine D2 receptor (D2R) elucidates their inhibition mechanism. Journal of Bimolecular Structure and Dynamics, 1–17. doi:10.1080/07391102.2016.1159986
   PubMed Web of Science ®Google Scholar
• Salmas, R. E., Yurtsever, M., Stein, M., & Durdagi, S. (2015). Modeling and protein engineering studies of active and inactive states of human dopamine D2 receptor (D2R) and investigation of drug/receptor interactions. Molecular Diversity, 19, 321–332. doi:10.1007/s11030-015-9569-3
   PubMed Web of Science ®Google Scholar
• Scheerer, P., Park, J. H., Hildebrand, P. W., Kim, Y. J., Krauß, N., Choe, H.-W., … Ernst, O. P. (2008). Crystal structure of opsin in its G-protein-interacting conformation. Nature, 455, 497–502. doi:10.1038/nature07330
   PubMed Web of Science ®Google Scholar
• Schrödinger Release 2015-4. (2015). LigPrep, version 3.6. New York, NY: Schrödinger, LLC.
   Google Scholar
• Schrödinger Release 2015-4. (2015). MacroModel, version 11.0. New York, NY: Schrödinger, LLC.
   Google Scholar
• Seeman, P. (2006). Targeting the dopamine D2 receptor in schizophrenia. Expert Opinion on Therapeutic Targets, 10, 515–531. doi:10.1517/14728222.10.4.515
   PubMed Web of Science ®Google Scholar
• Seeman, P., & Lee, T. (1975). Antipsychotic drugs: Direct correlation between clinical potency and presynaptic action on dopamine neurons. Science, 188, 1217–1219. doi:10.1126/science.1145194
   PubMed Web of Science ®Google Scholar
• Seeman, P., Lee, T., Chau-Wong, M., & Wong, K. (1976). Antipsychotic drug doses and neuroleptic/dopamine receptors. Nature, 261, 717–719. doi:10.1038/261717a0
   PubMed Web of Science ®Google Scholar
• Siu, S. W. I., Pluhackova, K., & Böckmann, R. A. (2012). Optimization of the OPLS-AA force field for long hydrocarbons. Journal of Chemical Theory and Computation, 8, 1459–1470. doi:10.1021/ct200908r
   PubMed Web of Science ®Google Scholar
• Skjaerven, L., Martinez, A., & Reuter, N. (2011). Principal component and normal mode analysis of proteins; a quantitative comparison using the GroEL subunit. Proteins, 79, 232–243. doi:10.1002/prot.22875
   PubMed Web of Science ®Google Scholar
• Su, P. C., Tsai, C. C., Mehboob, S., Hevener, K. E., & Johnson, M. E. (2015). Comparison of radii sets, entropy, QM methods, and sampling on MM-PBSA, MM-GBSA, and QM/MM-GBSA ligand binding energies of F. tularensis enoyl-ACP reductase (FabI). Journal of Computational Chemistry, 36, 1859–1873. doi:10.1002/jcc.24011
   PubMed Web of Science ®Google Scholar
• Yang, H. Y., Seo, Y. W., Kim, Y. J., Im, H. Y., Choi, G. D., Cho, H., … Pae, A. N. (2013). Novel pyrimidoazepine analogs as serotonin 5-HT2A and 5-HT2C receptor ligands for the treatment of obesity. European Journal of Medicinal Chemistry, 63, 558–569. doi:10.1016/j.ejmech.2013.02.020
   PubMed Web of Science ®Google Scholar
• Zhu, T., Cao, S., Su, P.-C., Patel, R., Shah, D., Chokshi, H. B., … Hevener, K. E. (2013). Hit identification and optimization in virtual screening: Practical recommendations based on a critical literature analysis. Journal of Medicinal Chemistry, 56, 6560–6572. doi:10.1021/jm301916b
   PubMed Web of Science ®Google Scholar