A novel identification approach for discovery of 5-HydroxyTriptamine 2A antagonists: combination of 2D/3D similarity screening, molecular docking and molecular dynamics

References

• Altschuler, E. L., & Kast, R. E. (2005). The atypical antipsychotic agents zisprasidone, risperdone and olanzapine as treatment for and prophylaxis against progressive multifocal leukoencephalopathy. Medical Hypotheses, 65(3), 585–586. doi:10.1016/j.mehy.2005.01.037. Retrieved from https://www.ncbi.nlm.nih.gov/pubmed/16004936
   Google Scholar
• Baell, J. B., & Holloway, G. A. (2010). New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays. Journal of Medicinal Chemistry, 53(7), 2719–2740. doi:10.1021/jm901137j
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Berger, M., Gray, J. A., & Roth, B. L. (2009). The expanded biology of serotonin. Annual Review of Medicine, 60, 355–366. doi:10.1146/annurev.med.60.042307.110802
   PubMed Web of Science ®Google Scholar
• Böckmann, R. A., Hac, A., Heimburg, T., & Grubmüller, H. (2003). Effect of sodium chloride on a lipid bilayer. Biophysical Journal, 85(3), 1647–1655. Retrieved from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1303338/10.1016/S0006-3495(03)74594-9
   Google Scholar
• Braden, M. R., Parrish, J. C., Naylor, J. C., & Nichols, D. E. (2006). Molecular interaction of serotonin 5-HT2A receptor residues Phe339(6.51) and Phe340(6.52) with superpotent N-benzyl phenethylamine agonists. Molecular Pharmacology, 70(6), 1956–1964. doi:10.1124/mol.106.028720
   PubMed Web of Science ®Google Scholar
• Carr, M., & MacPhee, C. E. (2015). Membrainy: A ‘smart’, unified membrane analysis tool. Source Code for Biology and Medicine, 10(1), 1–10. doi:10.1186/s13029-015-0033-7
   PubMedGoogle Scholar
• Celada, P., Puig, M. V., Amargós-Bosch, M., Adell, A., & Artigas, F. (2004). The therapeutic role of 5-HT(1A) and 5-HT(2A) receptors in depression. Journal of Psychiatry and Neuroscience, 29(4), 252–265 . Retrieved from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC446220/
   Google Scholar
• Cheng, M. H., Liu, L. T., Saladino, A. C., Xu, Y., & Tang, P. (2007). Molecular dynamics simulations of ternary membrane mixture: Phosphatidylcholine, phosphatidic acid, and cholesterol. The Journal of Physical Chemistry. B, 111(51), 14186–14192. doi:10.1021/jp075467b. Retrieved from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3286516/
   Google Scholar
• Cherezov, V., Rosenbaum, D. M., Hanson, M. A., Rasmussen, S. G., Thian, F. S., Kobilka, T. S., … Stevens, R. C. (2007). High-resolution crystal structure of an engineered human  2-adrenergic G protein-coupled receptor. Science, 318(5854), 1258–1265. doi:10.1126/science.1150577
   PubMed Web of Science ®Google Scholar
• Chiu, H.-Y., Chan, M.-H., Lee, M.-Y., Chen, S.-T., Zhan, Z.-Y., & Chen, H.-H. (2014). Long-lasting alterations in 5-HT2A receptor after a binge regimen of methamphetamine in mice. The International Journal of Neuropsychopharmacology, 17(10), 1647–1658. doi:10.1017/s1461145714000455
   PubMed Web of Science ®Google Scholar
• Clark, D. E. (2008). What has virtual screening ever done for drug discovery? Expert Opinion on Drug Discovery, 3(8), 841–851. doi:10.1517/17460441.3.8.841
   PubMed Web of Science ®Google Scholar
• Colovos, C., & Yeates, T. O. (1993). Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Science, 2(9), 1511–1519. doi:10.1002/pro.5560020916. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/8401235
   PubMed Web of Science ®Google Scholar
• Costanzi, S., & Vilar, S. (2012). In Silico screening for agonists and blockers of the β2 adrenergic receptor: Implications of inactive and activated state structures. Journal of Computational Chemistry, 33(5), 561–572. doi:10.1002/jcc.22893. Retrieved from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3265623/
   Google Scholar
• Cowen, P. J. (1991). Serotonin receptor subtypes: Implications for psychopharmacology. British Journal Psychiatry Supplement, 159(12), 7–14.
   Google Scholar
• Dobi, K., Flachner, B., Pukáncsik, M., Máthé, E., Bognár, M., Szaszkó, M., … Dorman, G. (2015). Combination of pharmacophore matching, 2D similarity search, and in vitro biological assays in the selection of potential 5-HT 6 antagonists from large commercial repositories. Chemical Biology & Drug Design, 86(4), 864–880. doi:10.1111/cbdd.12563
   PubMed Web of Science ®Google Scholar
• Dobi, K., Hajdú, I., Flachner, B., Fabó, G., Szaszkó, M., Bognár, M., … Dorman, G. (2014). Combination of 2D/3D ligand-based similarity search in rapid virtual screening from multimillion compound repositories. Selection and biological evaluation of potential PDE4 and PDE5 inhibitors. Molecules, 19(12), 7008–7039. doi:10.3390/molecules19067008
   PubMedGoogle Scholar
• Fink, K. B., & Gothert, M. (2007). 5-HT receptor regulation of neurotransmitter release. Pharmacological Reviews, 59(4), 360–417. doi:10.1124/pr.107.07103
   PubMed Web of Science ®Google Scholar
• Fozard, J. R. (1984). Neuronal 5-HT receptors in the periphery. Neuropharmacology, 23(12), 1473–1486.10.1016/0028-3908(84)90091-1
   PubMedGoogle Scholar
• Gandhimathi, A., & Sowdhamini, R. (2015). Molecular modelling of human 5-hydroxytryptamine receptor (5-HT) and virtual screening studies towards the identification of agonist and antagonist molecules. Journal of Biomolecular Structure & Dynamics, 34(5), 952–970.
   PubMed Web of Science ®Google Scholar
• Green, D. V. S. (2008). Virtual screening of chemical libraries for drug discovery. Expert Opinion on Drug Discovery, 3(9), 1011–1026. doi:10.1517/17460441.3.9.1011
   PubMed Web of Science ®Google Scholar
• Ichikawa, J., Ishii, H., Bonaccorso, S., Fowler, W. L., O’Laughlin, I. A., & Meltzer, H. Y. (2001). 5-HT2A and D2 receptor blockade increases cortical DA release via 5-HT1A receptor activation: A possible mechanism of atypical antipsychotic-induced cortical dopamine release. Journal of Neurochemistry, 76(5), 1521–1531. doi:10.1046/j.1471-4159.2001.00154.x
   PubMed Web of Science ®Google Scholar
• Jing, Z., Tao, Q., & Jing, W. (2012). Homology modeling and antagonist binding site study of the human histamine H2 receptor. Medicinal Chemistry, 8(6), 1084–1092. doi:10.2174/1573406411208061084. Retrieved from http://www.eurekaselect.com/node/103171/article
   Google Scholar
• Kalászi, A., Szisz, D., Imre, G., & Polgár, T. (2014). Screen3D: A novel fully flexible high-throughput shape-similarity search method. Journal of Chemical Information and Modeling, 54(4), 1036–1049. doi:10.1021/ci400620f
   PubMed Web of Science ®Google Scholar
• Kanagarajadurai, K., Malini, M., Bhattacharya, A., Panicker, M. M., & Sowdhamini, R. (2009). Molecular modeling and docking studies of human 5-hydroxytryptamine 2A (5-HT2A) receptor for the identification of hotspots for ligand binding. Molecular BioSystems, 5(12), 1877–1888. doi:10.1039/b906391a
   PubMed Web of Science ®Google Scholar
• Koroglu, A., & Akten, E. D. (2015). Transmembrane helix 6 observed at the interface of β 2 AR homodimers in blind docking studies. Journal of Biomolecular Structure and Dynamics, 33(7), 1503–1515. doi:10.1080/07391102.2014.962094
   PubMed 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(2), 283–291. doi:10.1107/S0021889892009944
   Web of Science ®Google Scholar
• Marti-Solano, M., Iglesias, A., de Fabritiis, G., Sanz, F., Brea, J., Loza, M. I., … Selent, J. (2015). Detection of new biased agonists for the serotonin 5-HT2A receptor: Modeling and experimental validation. Molecular Pharmacology, 87(4), 740–746. doi:10.1124/mol.114.097022
   PubMed Web of Science ®Google Scholar
• Metwally, K. A., Dukat, M., Egan, C. T., Smith, C., DuPre, A., Gauthier, C. B., … Glennon, R. A. (1998). Spiperone: Influence of spiro ring substituents on 5-HT 2A serotonin receptor binding. Journal of Medicinal Chemistry, 41(25), 5084–5093. doi:10.1021/jm980452a
   PubMed Web of Science ®Google Scholar
• O’Hara, B. A., & Atwood, W. J. (2008). Interferon β1-a and selective anti-5HT2a receptor antagonists inhibit infection of human glial cells by JC virus. Virus Research, 132(1–2), 97–103. doi:10.1016/j.virusres.2007.11.002. Retrieved from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2350230/
   Google Scholar
• Paissoni, C., Spiliotopoulos, D., Musco, G., & Spitaleri, A. (2014). GMXPBSA 2.0: A GROMACS tool to perform MM/PBSA and computational alanine scanning. Computer Physics Communications, 185(11), 2920–2929. doi:10.1016/j.cpc.2014.06.019. Retrieved from http://www.sciencedirect.com/science/article/pii/S0010465514002240
   Google Scholar
• Pauwels, P. J. (2003). 5-HT receptors and their ligands. Neuropharmacology, 1083, 38–50.
   Google Scholar
• Ramakrishnan, C., Mary Thangakani, A., Velmurugan, D., Anantha Krishnan, D., Sekijima, M., Akiyama, Y., & Gromiha, M. M. (2017). Identification of type I and type II inhibitors of c-Yes kinase using in silico and experimental techniques. Journal of Biomolecular Structure and Dynamics, 8, 1–11. doi:10.1080/07391102.2017.1329098
   Google Scholar
• Reynolds, C. H., Druker, R., & Pfahler, L. B. (1998). Lead discovery using stochastic cluster analysis (SCA):  A new method for clustering structurally similar compounds. Journal of Chemical Information and Computer Sciences, 38(2), 305–312. doi:10.1021/ci970056l
   Google Scholar
• Runyon, S. P., Mosier, P. D., Roth, B. L., Glennon, R. A., & Westkaemper, R. B. (2008). Potential modes of interaction of 9-aminomethyl-9,10-dihydroanthracene (AMDA) derivatives with the 5-HT 2A receptor: A ligand structure-affinity relationship, receptor mutagenesis and receptor modeling investigation. Journal of Medicinal Chemistry, 51(21), 6808–6828. doi:10.1021/jm800771x. Retrieved from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3088499/
   Google Scholar
• Salentin, S., Schreiber, S., Haupt, V. J., Adasme, M. F., & Schroeder, M. (2015). PLIP: Fully automated protein–ligand interaction profiler. Nucleic Acids Research, 43(W1), W443–W447. doi:10.1093/nar/gkv315
   PubMed Web of Science ®Google Scholar
• Schmidt, T. H., & Kandt, C. (2012). LAMBADA and InflateGRO2: Efficient membrane alignment and insertion of membrane proteins for molecular dynamics simulations. Journal of Chemical Information and Modeling, 52(10), 2657–2669. doi:10.1021/ci3000453
   PubMed Web of Science ®Google Scholar
• Schüttelkopf, A. W., & van Aalten, D. M. (2004). PRODRG: A tool for high-throughput crystallography of protein–ligand complexes. Acta Crystallographica Section D Biological Crystallography, 60(8), 1355–1363. doi:10.1107/s0907444904011679
   PubMedGoogle Scholar
• Shapiro, D. A., Kristiansen, K., Kroeze, W. K., & Roth, B. L. (2000). Differential modes of agonist binding to 5-hydroxytryptamine 2A serotonin receptors revealed by mutation and molecular modeling of conserved residues in transmembrane region 5. Molecular Pharmacology, 58(5), 877–886.10.1124/mol.58.5.877
   PubMed Web of Science ®Google Scholar
• Su, P.-C. (2016, February 17). Cheminformatics and data mining in drug discovery targeting bacterial enoyl-ACP reductase. Chicago: University of Illinois at Chicago.
   Google Scholar
• Su, P.-C., & Johnson, M. E. (2016). Evaluating thermodynamic integration performance of the new amber molecular dynamics package and assess potential halogen bonds of enoyl-ACP reductase (FabI) benzimidazole inhibitors. Journal of Computational Chemistry, 37(9), 836–847. doi:10.1002/jcc.24274
   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(25), 1859–1873. doi:10.1002/jcc.24011. Retrieved from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4688044/
   Google Scholar
• Thompson, A. J., & Lummis, S. C. R. (2006). 5-HT3 receptors. Current pharmaceutical design, 12(28), 3615–3630 . Retrieved from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2664614/10.2174/138161206778522029
   Google Scholar
• Wang, Y., Bolton, E., Dracheva, S., Karapetyan, K., Shoemaker, B. A., Suzek, T. O., … Bryant, S. H. (2010). An overview of the PubChem bioassay resource. Nucleic Acids Research, 38(suppl_1), D255–D266. doi:10.1093/nar/gkp965. Retrieved from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808922/
   Google Scholar
• Wang, C. D., Gallaher, T. K., & Shih, J. C. (1993). Site-directed mutagenesis of the serotonin 5-hydroxytrypamine2 receptor: Identification of amino acids necessary for ligand binding and receptor activation. Molecular Pharmacology, 43(6), 931–940.
   PubMed Web of Science ®Google Scholar
• Wang, R., Lai, L., & Wang, S. (2002). Further development and validation of empirical scoring functions for structure-based binding affinity prediction. Journal of Computer-Aided Molecular Design, 16(1), 11–26.10.1023/A:1016357811882
   PubMed Web of Science ®Google Scholar
• Xie, X.-Q. S. (2010). Exploiting PubChem for virtual screening. Expert Opinion on Drug Discovery, 5(12), 1205–1220. doi:10.1517/17460441.2010.524924
   PubMed Web of Science ®Google Scholar
• Zhang, G., & Stackman, R. W. (2015). The role of serotonin 5-HT(2A) receptors in memory and cognition. Frontiers in Pharmacology, 6, 225. doi:10.3389/fphar.2015.00225. Retrieved from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4594018/
   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(17), 6560–6572. doi:10.1021/jm301916b
   PubMed Web of Science ®Google Scholar