A QM protein–ligand investigation of antipsychotic drugs with the dopamine D2 Receptor (D2R)

References

• Apweiler, R. (2004). UniProt: The universal protein knowledgebase. Nucleic Acids Research, 32, D115–D119. doi:10.1093/nar/gkh131
   PubMed Web of Science ®Google Scholar
• Björklund, A., & Dunnett, S. B. (2007). Dopamine neuron systems in the brain: An update. Trends in Neurosciences, 30, 194–202. doi:10.1016/j.tins.2007.03.006
   PubMed Web of Science ®Google Scholar
• Boys, S. F., & Bernardi, F. (1970). The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors. Molecular Physics, 19, 553–566. doi:10.1080/00268977000101561
   Web of Science ®Google Scholar
• Chenna, R., Sugawara, H., Koike, T., Lopez, R., Gibson, T. J., Higgins, D. G., & Thompson, J. D. (2003). Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Research, 31, 3497–3500. doi:10.1093/nar/gkg500
   PubMed Web of Science ®Google Scholar
• Contreras, F., Fouillioux, C., Bolívar, A., Simonovis, N., Hernández-Hernández, R., Armas-Hernandez, M. J., & Velasco, M. (2002). Dopamine, hypertension and obesity. Journal of Human Hypertension, 16, S13–S17. doi:10.1016/S0531-5131(01)00579-9
   PubMed Web of Science ®Google Scholar
• Creese, I., Burt, D. R., & Snyder, S. H. (1976). Dopamine receptor binding predicts clinical and pharmacological potencies of antischizophrenic drugs. Science, 192, 481–483. doi:10.1126/science.3854
   PubMed Web of Science ®Google Scholar
• Das, R., & Baker, D. (2008). Macromolecular modeling with rosetta. Annual Review of Biochemistry, 77, 363–382. doi:10.1146/annurev.biochem.77.062906.171838
   PubMed Web of Science ®Google Scholar
• Daulat, A. M., Maurice, P., & Jockers, R. (2009). Recent methodological advances in the discovery of GPCR-associated protein complexes. Trends in Pharmacological Sciences, 30, 72–78. doi:10.1016/j.tips.2008.10.009
   PubMed Web of Science ®Google Scholar
• Ditchfield, R., Hehre, W. J., & Pople, J. A. (1971). Self-consistent molecular-orbital methods. IX. An extended Gaussian-type basis for molecular-orbital studies of organic molecules. The Journal of Chemical Physics, 54, 724–728. doi:10.1063/1.1674902
   Web of Science ®Google Scholar
• Durdagi, S., Salmas, R. E., Stein, M., Yurtsever, M., & Seeman, P. (2016). Binding interactions of dopamine and apomorphine in D2 high and D2 low states of human dopamine D2 Receptor using computational and experimental techniques. ACS Chemical Neuroscience, 7, 185–195. doi:10.1021/acschemneuro.5b00271
   PubMed Web of Science ®Google Scholar
• Ehrlich, S., Göller, A. H., & Grimme, S. (2017). Towards full quantum-mechanics-based protein-ligand binding affinities. ChemPhysChem, 18, 898–905.10.1002/cphc.201700082
   PubMed Web of Science ®Google Scholar
• Eswar, N., Webb, B., Marti-Renom, M. A., Madhusudhan, M., Eramian, D., Shen, M., … Sali, A. (2007). Comparative protein structure modeling using MODELLER. Current Protocols in Protein Science, 50, 2.9.1–2.9.31. doi:10.1002/0471140864.ps0209s50
   Google Scholar
• Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., … Fox, D. J. (2016). Gaussian 09, Revision A.02. Wallingford, CT: Gaussian.
   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
• Ghosh, J., Marru, S., Singh, N., Vanomesslaeghe, K., Fan, Y., & Pamidighantam, S. (2011). Molecular parameter optimization gateway (ParamChem). Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery, 35. doi:10.1145/2016741.2016779
   Google Scholar
• Grimme, S. (2011). Density functional theory with London dispersion corrections. Wiley Interdisciplinary Reviews: Computational Molecular Science, 1, 211–228. doi:10.1002/wcms.30
   Web of Science ®Google Scholar
• Hanson, M. A., Cherezov, V., Griffith, M. T., Roth, C. B., Jaakola, V. P., Chien, E. Y. T., … Stevens, R. C. (2008). A specific cholesterol binding site is established by the 2.8 Å structure of the human β 2-adrenergic receptor. Structure, 16, 897–905. doi:10.1016/j.str.2008.05.001
   PubMed Web of Science ®Google Scholar
• Huang, J., & MacKerell, A. (2013). CHARMM36 all atom additive protein force field: Validation based on comparison to NMR data. Journal of Computational Chemistry, 34, 2135–2145. Retrieved from http://onlinelibrary.wiley.com/doi/10.1002/jcc.23354/full10.1002/jcc.23354
   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., Li, X., Kaback, J., & Karlin, a. (1994). A cysteine residue in the third membrane-spanning segment of the human D2 dopamine receptor is exposed in the binding-site crevice. Proceedings of the National Academy of Sciences of the United States of America, 91, 10355–10359. doi:10.1073/pnas.91.22.10355
   PubMed Web of Science ®Google Scholar
• Klamt, A., & Schüürmann, G. (1993). COSMO: A new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient. Journal of the Chemical Society, Perkin Transactions, 2, 799–805. doi:10.1039/P29930000799
   Google 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
• Muddana, H. S., & Gilson, M. K. (2012). Calculation of host–guest binding affinities using a quantum-mechanical energy model. Journal of Chemical Theory and Computation, 8, 2023–2033. doi:10.1021/ct3002738
   PubMed Web of Science ®Google Scholar
• Nelson, M. T., Humphrey, W., Gursoy, A., Dalke, A., Kale, L. V., Skeel, R. D., & Schulten, K. (1996). NAMD: A parallel, object-oriented molecular dynamics program. International Journal of High Performance Computing Applications, 10, 251–268. doi:10.1177/109434209601000401
   Web of Science ®Google Scholar
• Newcomer, J. W. (2005). Second-generation (atypical) antipsychotics and metabolic effects: A comprehensive literature review. CNS Drugs, 19(1), 1–93. doi:10.2165/00023210-200519010-00001
   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.Crystal
   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
• Ryde, U., & Soderhjelm, P. (2016). Ligand-binding affinity estimates supported by quantum-mechanical methods. Chemical Reviews, 116, 5520–5566. doi:10.1021/acs.chemrev.5b00630
   PubMed Web of Science ®Google Scholar
• Salmas, R. E., Seeman, P., Aksoydan, E. E., Kantarcioglu, K. B., Stein, M., Yurtsever, M., & Durdagi, S. (2017a). Analysis of the glutamate agonist LY404,039 binding to non-static dopamine receptor D2 dimer structures and consensus docking. ACS Chemical Neuroscience, 8, 1404–1415. doi:10.1021/acschemneuro.7b00070
   PubMed Web of Science ®Google Scholar
• Salmas, R. E., Seeman, P., Aksoydan, B., Stein, M., Yurtsever, M., & Durdagi, S. (2017b). Biological insights of the dopaminergic stabilizer ACR16 at the binding pocket of dopamine D2 Receptor. ACS Chemical Neuroscience, 8, 826–836.10.1021/acschemneuro.6b00396
   PubMed Web of Science ®Google Scholar
• Salmas, R. E., Yurtsever, M., & Durdagi, S. (2016). Atomistic molecular dynamics simulations of typical and atypical antipsychotic drugs at the dopamine D2 receptor (D2R) elucidates their inhibition mechanism. Journal of Biomolecular Structure & Dynamics, 35, 738–754. 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
• 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
• Shaikh, S., Hodgkinson, S., Pilowsky, L., Van Os, J., Vallada, H., Collier, D., & Gill, M. (1994). Analysis of the conserved Asp(114) residue of the dopamine D2 receptor in schizophrenic patients. Psychiatric Genetics, 4, 211–214. doi:10.1097/00041444-199400440-00004
   PubMedGoogle 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, 534–553. doi:10.1021/jm050540c
   PubMed Web of Science ®Google Scholar
• Trzaskowski, B., Latek, D., Yuan, S., Ghoshdastider, U., Debinski, a., & Filipek, S. (2012). Action of molecular switches in GPCRs – theoretical and experimental studies. Current Medicinal Chemistry, 19, 1090–1109. doi:10.2174/092986712799320556
   PubMed Web of Science ®Google Scholar
• TURBOMOLE V6.5, a development of University of Karlsruhe and Forschungszentrum Karlsruhe GmbH. (1989–2007). TURBOMOLE GmbH, since 2007. Retrieved from https://www.turbomole.com
   Google Scholar
• Walker, M., Harvey, A. J. A., Sen, A., & Dessent, C. E. H. (2013). Performance of M06, M06-2X, and M06-HF density functionals for conformationally flexible anionic clusters: M06 functionals perform better than B3LYP for a model system with dispersion and ionic hydrogen-bonding interactions. The Journal of Physical Chemistry A, 117, 12590–12600.10.1021/jp408166 m
   PubMed Web of Science ®Google Scholar
• Weigend, F., Furche, F., & Ahlrichs, R. (2003). Gaussian basis sets of quadruple zeta valence quality for atoms H-Kr. Journal of Chemical Physics, 119, 12753–12762. doi:10.1063/1.1627293
   Web of Science ®Google Scholar
• Wiens, B. L., Nelson, C. S., & Neve, K. a. (1998). Contribution of serine residues to constitutive and agonist-induced signaling via the D2S dopamine receptor: Evidence for multiple, agonist-specific active conformations. Molecular Pharmacology, 54, 435–444. doi:10.1124/mol.54.2.435
   PubMed Web of Science ®Google Scholar
• Zhao, Y., & Truhlar, D. G. (2008). The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: Two new functionals and systematic testing of four M06-class functionals and 12 other function. Theoretical Chemistry Accounts, 120, 215–241. doi:10.1007/s00214-007-0310-x
   Web of Science ®Google Scholar