Theoretical investigation of selective ligand binding mode of galanin receptors

References

• Abramov, U., Florén, A., Echevarria, D. J., Brewer, A., Manuzon, H., Robinson, J. K., Bartfai, T., Vasar, E., & Langel, Ü. (2004). Regulation of feeding by galnon. Neuropeptides, 38(1), 55–61. https://doi.org/10.1016/j.npep.2004.01.001
   PubMed Web of Science ®Google Scholar
• Bartfai, T., Lu, X., Badie-Mahdavi, H., Barr, A. M., Mazarati, A., Hua, X.-Y., Yaksh, T., Haberhauer, G., Ceide, S. C., Trembleau, L., Somogyi, L., Kröck, L., & Rebek, J. (2004). Galmic, a nonpeptide galanin receptor agonist, affects behaviors in seizure, pain, and forced-swim tests. Proceedings of the National Academy of Sciences of the United States of America, 101(28), 10470–10475. https://doi.org/10.1073/pnas.0403802101
   PubMed Web of Science ®Google Scholar
• Berthold, M., Kahl, U., Juréus, A., Kask, K., Nordvall, G., Langel, Ü., & Bartfai, T. (1997). Mutagenesis and ligand modification studies on galanin binding to its GTP-binding-protein-coupled receptor GalR1. European Journal of Biochemistry, 249(2), 601–606. https://doi.org/10.1111/j.1432-1033.1997.00601.x
   PubMedGoogle Scholar
• Ceide, S. C., Trembleau, L., Haberhauer, G., Somogyi, L., Lu, X., Bartfai, T., & Rebek, J. (2004). Synthesis of galmic: A nonpeptide galanin receptor agonist. Proceedings of the National Academy of Sciences of the United States of America, 101(48), 16727–16732. https://doi.org/10.1073/pnas.0407543101
   PubMed Web of Science ®Google Scholar
• Chu, M., Mierzwa, R., Truumees, I., King, A., Sapidou, E., Barrabee, E., Terracciano, J., Patel, M. G., Gullo, V. P., Burrier, R., Das, P. R., Mittelman, S., & Puar, M. S. (1997). A new fungal metabolite, Sch 202596, with inhibitory activity in the galanin receptor GALR1 assay. Tetrahedron Letters, 38(35), 6111–6114. https://doi.org/10.1016/S0040-4039(97)01385-3
   Web of Science ®Google Scholar
• Church, W. B., Jones, K. A., Kuiper, D. A., Shine, J., & Iismaa, T. P. (2002). Molecular modelling and site-directed mutagenesis of human GALR1 galanin receptor defines determinants of receptor subtype specificity. Protein Engineering, 15(4), 313–323. https://doi.org/10.1093/protein/15.4.313
   PubMedGoogle Scholar
• Colovos, C., & Yeates, T. O. (1993). Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Science: A Publication of the Protein Society, 2(9), 1511–1519. https://doi.org/10.1002/pro.5560020916
   PubMed Web of Science ®Google Scholar
• Counts, S. E., Perez, S. E., & Mufson, E. J. (2008). Galanin in Alzheimer's disease: Neuroinhibitory or neuroprotective? Cellular and Molecular Life Sciences: CMLS, 65(12), 1842–1853. https://doi.org/10.1007/s00018-008-8159-2
   PubMed Web of Science ®Google Scholar
• Demsie, D. G., Altaye, B. M., Weldekidan, E., Gebremedhin, H., Alema, N. M., Tefera, M. M., & Bantie, A. T. (2020). Galanin receptors as drug target for novel antidepressants: Review. Biologics: Targets & Therapy, 14, 37–45. https://doi.org/10.2147/BTT.S240715
   PubMedGoogle Scholar
• Eisenberg, D., Lüthy, R., & Bowie, J. U. (1997). VERIFY3D: Assessment of protein models with three-dimensional profiles. Methods in Enzymology, 277, 396–404.
   Google Scholar
• Fredriksson, R., Lagerström, M. C., Lundin, L. G., & Schiöth, H. B. (2003). The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints. Molecular Pharmacology, 63(6), 1256–1272. https://doi.org/10.1124/mol.63.6.1256
   PubMed Web of Science ®Google Scholar
• Freimann, K., Kurrikoff, K., & Langel, Ü. (2015). Galanin receptors as a potential target for neurological disease. Expert Opinion on Therapeutic Targets, 19(12), 1665–1676. https://doi.org/10.1517/14728222.2015.1072513
   PubMed Web of Science ®Google Scholar
• Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 10(5), 449–461. https://doi.org/10.1517/17460441.2015.1032936
   PubMed Web of Science ®Google Scholar
• Goddard, W. A., & Abrol, R. (2007). 3-dimensional structures of G protein-coupled receptors and binding sites of agonists and antagonists. The Journal of Nutrition, 137(6 Suppl 1), 1528S–1538S. https://doi.org/10.1093/jn/137.6.1528S
   PubMed Web of Science ®Google Scholar
• Guipponi, M., Chentouf, A., Webling, K. E. B., Freimann, K., Crespel, A., Nobile, C., Lemke, J. R., Hansen, J., Dorn, T., Lesca, G., Ryvlin, P., Hirsch, E., Rudolf, G., Rosenberg, D. S., Weber, Y., Becker, F., Helbig, I., Muhle, H., Salzmann, A. … Antonarakis, E. (2015). Galanin pathogenic mutations in temporal lobe epilepsy. Human Molecular Genetics, 24(11), 3082–3091.
   PubMed Web of Science ®Google Scholar
• Hooft, R. W. W., Sander, C., & Vriend, G. (1997). Objectively judging the quality of a protein structure from a Ramachandran plot. Computer Applications in the Biosciences: CABIOS, 13(4), 425–430. https://doi.org/10.1093/bioinformatics/13.4.425
   PubMedGoogle Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. https://doi.org/10.1016/0263-7855(96)00018-5
   PubMedGoogle Scholar
• Kaushik, A. C., Kumar, A., Rehman, A. U., Junaid, M., Khan, A., Bharadwaj, S., Sahi, S., & Wei, D.-Q. (2018). Deciphering G-protein-coupled receptor 119 agonists as promising strategy against type 2 diabetes using systems biology approach. ACS Omega, 3(12), 18214–18226. https://doi.org/10.1021/acsomega.8b01941
   Web of Science ®Google Scholar
• Kolodny, R., & Kosloff, M. (2013). From protein structure to function via computational tools and approaches. Israel Journal of Chemistry, 53(3-4), 147–156. https://doi.org/10.1002/ijch.201200078
   Web of Science ®Google Scholar
• Lundström, L., Elmquist, A., Bartfai, T., & Langel, Ü. (2005). Galanin and its receptors in neurological disorders. Neuromolecular Medicine, 7(1-2), 157–180. https://doi.org/10.1385/NMM:7:1-2:157
   PubMed Web of Science ®Google Scholar
• Lundström, L., Sollenberg, U. E., Bartfai, T., & Langel, Ü. (2007). Molecular characterization of the ligand binding site of the human galanin receptor type 2, identifying subtype selective interactions. Journal of Neurochemistry, 103(5), 1774–1784. https://doi.org/10.1111/j.1471-4159.2007.04959.x
   PubMed Web of Science ®Google Scholar
• Mazarati, A. M. (2004). Galanin and galanin receptors in epilepsy. Neuropeptides, 38(6), 331–343. https://doi.org/10.1016/j.npep.2004.07.006
   PubMed Web of Science ®Google Scholar
• McMillan, P. J., Peskind, E., Raskind, M. A., & Leverenz, J. B. (2004). Increased galanin receptor occupancy in Alzheimer's disease. Neurobiology of Aging, 25(10), 1309–1314. https://doi.org/10.1016/j.neurobiolaging.2004.01.004
   PubMed Web of Science ®Google Scholar
• Nath, V., Ahuja, R., & Kumar, V. (2019). Identification of novel G-protein-coupled receptor 40 (GPR40) agonists by hybrid in silico-screening techniques and molecular dynamics simulations thereof. Journal of Biomolecular Structure & Dynamics, 37(14), 3764–3787.
   PubMed Web of Science ®Google Scholar
• Parker, J. L., & Newstead, S. (2016). Membrane protein crystallisation: Current trends and future perspectives. Advances in Experimental Medicine and Biology, 922, 61–72. https://doi.org/10.1007/978-3-319-35072-1_5
   PubMed Web of Science ®Google Scholar
• Pérez, S., Basile, M., Mash, D. C., & Mufson, E. J. (2002). Galanin receptor over-expression within the amygdala in early Alzheimer’s disease: An in vitro autoradiographic analysis. Journal of Chemical Neuroanatomy, 24(2), 109–116. https://doi.org/10.1016/S0891-0618(02)00034-0
   PubMed Web of Science ®Google Scholar
• Rajarao, S. J. R., Platt, B., Sukoff, S. J., Lin, Q., Bender, C. N., Nieuwenhuijsen, B. W., Ring, R. H., Schechter, L. E., Rosenzweig-Lipson, S., & Beyer, C. E. (2007). Anxiolytic-like activity of the non-selective galanin receptor agonist, galnon. Neuropeptides, 41(5), 307–320. https://doi.org/10.1016/j.npep.2007.05.001
   PubMed Web of Science ®Google Scholar
• Rinne, M., Tanoli, Z. U. R., Khan, A., & Xhaard, H. (2019). Cartography of rhodopsin-like G protein-coupled receptors across vertebrate genomes. Scientific Reports, 9(1), 7058–7016. https://doi.org/10.1038/s41598-018-33120-8
   PubMedGoogle Scholar
• Runesson, J., Sollenberg, U. E., Jurkowski, W., Yazdi, S., Eriksson, E. E., Elofsson, A., & Langel, Ü. (2010). Determining receptor-ligand interaction of human galanin receptor type 3. Neurochemistry International, 57(7), 804–811. https://doi.org/10.1016/j.neuint.2010.08.018
   PubMed Web of Science ®Google Scholar
• Scott, M. K., Ross, T. M., Lee, D. H. S., Wang, H. Y., Shank, R. P., Wild, K. D., Davis, C. B., Crooke, J. J., Potocki, A. C., & Reitz, A. B. (2000). 2,3-Dihydro-dithiin and -dithiepine-1,1,4,4-tetroxides: Small molecule non-peptide antagonists of the human galanin hGAL-1 receptor. Bioorganic & Medicinal Chemistry, 8(6), 1383–1391. https://doi.org/10.1016/S0968-0896(00)00062-6
   PubMed Web of Science ®Google Scholar
• Šípková, J., Kramáriková, I., Hynie, S., & Klenerová, V. (2017). The galanin and galanin receptor subtypes, its regulatory role in the biological and pathological functions. Physiological Research, 66(5), 729–740. https://doi.org/10.33549/physiolres.933576
   PubMed Web of Science ®Google Scholar
• Swanson, C. J., Blackburn, T. P., Zhang, X., Zheng, K., Xu, Z. Q. D., Hökfelt, T., Wolinsky, T. D., Konkel, M. J., Chen, H., Zhong, H., Walker, M. W., Craig, D. A., Gerald, C. P. G., & Branchek, T. A. (2005). Anxiolytic- and antidepressant-like profiles of the galanin-3 receptor (Gal3) antagonists SNAP 37889 and SNAP 398299. Proceedings of the National Academy of Sciences of the United States of America, 102(48), 17489–17494. https://doi.org/10.1073/pnas.0508970102
   PubMed Web of Science ®Google Scholar
• Tobergte, D. R., & Curtis, S. (2013). MOE molecular operating environment. Journal of Chemical Information and Modeling, 53(9), 1689–1699.
   PubMedGoogle Scholar
• Torres, R., & Polymeropoulos, M. H. (1998). Genomic organization and localization of the human CRMP-1 gene. DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes, 5(6), 393–395. https://doi.org/10.1093/dnares/5.6.393
   PubMedGoogle Scholar
• Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. C. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718.
   PubMed Web of Science ®Google Scholar
• Veulens, A. D. L. N., & Rodríguez, R. (2009). G protein-coupled receptors as targets for drug design. Biotecnologia Aplicada, 26(1), 24–33.
   Google Scholar
• Volkamer, A., Kuhn, D., Rippmann, F., & Rarey, M. (2012). DoGSiteScorer: A web server for automatic binding site prediction, analysis and druggability assessment. Bioinformatics (Oxford, England), 28(15), 2074–2075.
   PubMed 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. https://doi.org/10.1002/jcc.20035
   PubMed Web of Science ®Google Scholar
• Wu, E. L., Cheng, X., Jo, S., Rui, H., Song, K. C., Dávila-Contreras, E. M., Qi, Y., Lee, J., Monje-Galvan, V., Venable, R. M., Klauda, J. B., & Im, W. (2014). CHARMM-GUI membrane builder toward realistic biological membrane simulations. Journal of Computational Chemistry, 35(27), 1997–2004. https://doi.org/10.1002/jcc.23702
   PubMed Web of Science ®Google Scholar
• Wu, W. P., Hao, J. X., Lundström, L., Wiesenfeld-Hallin, Z., Langel, Ü., Bartfai, T., & Xu, X. J. (2003). Systemic galnon, a low-molecular weight galanin receptor agonist, reduces heat hyperalgesia in rats with nerve injury. European Journal of Pharmacology, 482(1-3), 133–137. https://doi.org/10.1016/j.ejphar.2003.09.018
   PubMed Web of Science ®Google Scholar
• Zhang, Y. (2008). I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9(1), 40. https://doi.org/10.1186/1471-2105-9-40
   PubMed Web of Science ®Google Scholar