AMPA GluA2 subunit competitive inhibitors for PICK1 PDZ domain: Pharmacophore-based virtual screening, molecular docking, molecular dynamics simulation, and ADME studies

References

• Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindah, E. (2015). Gromacs: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1–2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
   Google Scholar
• Alfonso, S., Kessels, H. W., Banos, C. C., Chan, T. R., Lin, E. T., Kumaravel, G., Scannevin, R. H., Rhodes, K. J., Huganir, R., Guckian, K. M., Dunah, A. W., & Malinow, R. (2014). Synapto-depressive effects of amyloid beta require PICK1. The European Journal of Neuroscience, 39(7), 1225–1233. https://doi.org/10.1111/ejn.12499
   PubMed Web of Science ®Google Scholar
• Allouche, A. (2011). Software news and updates Gabedit — A graphical user interface for computational chemistry softwares. Journal of Computational Chemistry, 32(1), 174–182. https://doi.org/10.1002/jcc https://doi.org/10.1002/jcc.21600
   PubMed Web of Science ®Google Scholar
• Arkin, M. M. R., & Wells, J. A. (2004). Small-molecule inhibitors of protein-protein interactions: Progressing towards the dream. Nature Reviews. Drug Discovery, 3(4), 301–317. https://doi.org/10.1038/nrd1343
   PubMed Web of Science ®Google Scholar
• Arnott, J. A., & Planey, S. L. (2012). The influence of lipophilicity in drug discovery and design. Expert Opinion on Drug Discovery, 7(10), 863–875. https://doi.org/10.1517/17460441.2012.714363
   PubMed Web of Science ®Google Scholar
• Bach, A., Clausen, B. H., Møller, M., Vestergaard, B., Chi, C. N., Round, A., Sørensen, P. L., Nissen, K. B., Kastrup, J. S., Gajhede, M., Jemth, P., Kristensen, A. S., Lundström, P., Lambertsen, K. L., & Strømgaard, K. (2012). A high-affinity, dimeric inhibitor of PSD-95 bivalently interacts with PDZ1-2 and protects against ischemic brain damage. Proceedings of the National Academy of Sciences of the United States of America, 109(9), 3317–3322. https://doi.org/10.1073/pnas.1113761109
   PubMed Web of Science ®Google Scholar
• Bach, A., Stuhr-Hansen, N., Thorsen, T. S., Bork, N., Moreira, I. S., Frydenvang, K., Padrah, S., Christensen, S. B., Madsen, K. L., Weinstein, H., Gether, U., & Strømgaard, K. (2010). Structure-activity relationships of a small-molecule inhibitor of the PDZ domain of PICK1. Organic & Biomolecular Chemistry, 8(19), 4281–4288. https://doi.org/10.1039/c0ob00025f
   PubMed Web of Science ®Google Scholar
• Bell, J. D., Park, E., Ai, J., & Baker, A. J. (2009). PICK1-mediated GluR2 endocytosis contributes to cellular injury after neuronal trauma. Cell Death and Differentiation, 16(12), 1665–1680. https://doi.org/10.1038/cdd.2009.106
   PubMed Web of Science ®Google Scholar
• Bellone, C., & Lüscher, C. (2006). Cocaine triggered AMPA receptor redistribution is reversed in vivo by mGluR-dependent long-term depression. Nature Neuroscience, 9(5), 636–641. https://doi.org/10.1038/nn1682
   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. https://doi.org/10.1063/1.448118
   Web of Science ®Google Scholar
• Berg, T. (2008). Small-molecule inhibitors of protein-protein interactions. Current Opinion in Drug Discovery & Development, 11(5), 666–674. https://europepmc.org/article/med/18729018
   PubMedGoogle Scholar
• Bergström, C. A. S., & Larsson, P. (2018). Computational prediction of drug solubility in water-based systems: Qualitative and quantitative approaches used in the current drug discovery and development setting. International Journal of Pharmaceutics, 540(1–2), 185–193. https://doi.org/10.1016/j.ijpharm.2018.01.044
   PubMed Web of Science ®Google Scholar
• Best, R. B., Zhu, X., Shim, J., Lopes, P. E. M., Mittal, J., Feig, M., & MacKerell, A. D. (2012). Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles. Journal of Chemical Theory and Computation, 8(9), 3257–3273. https://doi.org/10.1021/ct300400x
   PubMed Web of Science ®Google Scholar
• Blazer, L. L., & Neubig, R. R. (2009). Small molecule protein-protein interaction inhibitors as CNS therapeutic agents: Current progress and future hurdles. Neuropsychopharmacology: Official Publication of the American College of Neuropsychopharmacology, 34(1), 126–141. https://doi.org/10.1038/npp.2008.151
   PubMed Web of Science ®Google Scholar
• Chen, C., Huang, Y., Ji, X., & Xiao, Y. (2013). Efficiently finding the minimum free energy path from steepest descent path. Journal of Chemical Physics, 138(16), 1–9. https://doi.org/10.1063/1.4799236
   Web of Science ®Google Scholar
• Cheng, T., Zhao, Y., Li, X., Lin, F., Xu, Y., Zhang, X., Li, Y., Wang, R., & Lai, L. (2007). Computation of octanol-water partition coefficients by guiding an additive model with knowledge. Journal of Chemical Information and Modeling, 47(6), 2140–2148. https://doi.org/10.1021/ci700257y
   PubMed Web of Science ®Google Scholar
• Christensen, N. R., Čalyševa, J., Fernandes, E. F. A., Lüchow, S., Clemmensen, L. S., Haugaard-Kedström, L. M., & Strømgaard, K. (2019). PDZ domains as drug targets. Advanced Therapeutics, 2(7), 1800143. https://doi.org/10.1002/adtp.201800143
   PubMedGoogle Scholar
• Constantinescu, T., Lungu, C. N., & Lung, I. (2019). Lipophilicity as a central component of drug-like properties of chalchones and flavonoid derivatives. Molecules, 24(8), 1505–1511. https://doi.org/10.3390/molecules24081505
   PubMed Web of Science ®Google Scholar
• Daina, A., & Zoete, V. (2016). A BOILED-egg to predict gastrointestinal absorption and brain penetration of small molecules. ChemMedChem, 11(11), 1117–1121. https://doi.org/10.1002/cmdc.201600182
   PubMed Web of Science ®Google Scholar
• Daina, A., Michielin, O., & Zoete, V. (2014). iLOGP: A simple, robust, and efficient description of n-octanol/water partition coefficient for drug design using the GB/SA approach. Journal of Chemical Information and Modeling, 54(12), 3284–3301. https://doi.org/10.1021/ci500467k
   PubMed Web of Science ®Google Scholar
• Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7, 42717. https://doi.org/10.1038/srep42717
   PubMed Web of Science ®Google Scholar
• Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. https://doi.org/10.1063/1.464397
   Web of Science ®Google Scholar
• Daw, M. I., Chittajallu, R., Bortolotto, Z. A., Dev, K. K., Duprat, F., Henley, J. M., Collingridge, G. L., & Isaac, J. T. R. (2000). PDZ proteins interacting with C-terminal GluR2/3 are involved in a PKC-dependent regulation of AMPA receptors at hippocampal synapses. Neuron, 28(3), 873–886. https://doi.org/10.1016/S0896-6273(00)00160-4
   PubMed Web of Science ®Google Scholar
• Delaney, J. S. (2004). ESOL: Estimating aqueous solubility directly from molecular structure. Journal of Chemical Information and Computer Sciences, 44(3), 1000–1005. https://doi.org/10.1021/ci034243x
   PubMedGoogle Scholar
• Dev, K. K. (2004). Making protein interactions druggable: Targeting PDZ domains. Nature Reviews. Drug Discovery, 3(12), 1047–1056. https://doi.org/10.1038/nrd1578
   PubMed Web of Science ®Google Scholar
• Dixon, R. M., Mellor, J. R., & Hanley, J. G. (2009). PICK1-mediated glutamate receptor subunit 2 (GluR2) trafficking contributes to cell death in oxygen/glucose-deprived hippocampal neurons . The Journal of Biological Chemistry, 284(21), 14230–14235. https://doi.org/10.1074/jbc.M901203200
   PubMed Web of Science ®Google Scholar
• Ducki, S., & Bennett, E. (2009). Protein-protein interactions: Recent progress in the development of selective PDZ inhibitors. Current Chemical Biology, 3(2), 146–158. https://doi.org/10.2174/2212796810903020146
   Google Scholar
• Erlendsson, S., Rathje, M., Heidarsson, P. O., Poulsen, F. M., Madsen, K. L., Teilum, K., & Gether, U. (2014). Protein interacting with C-kinase 1 (PICK1) binding promiscuity relies on unconventional PSD-95/discs-large/ZO-1 homology (PDZ) binding modes for nonclass II PDZ ligands. The Journal of Biological Chemistry, 289(36), 25327–25340. https://doi.org/10.1074/jbc.M114.548743
   PubMed Web of Science ®Google Scholar
• Gardner, S. M., Takamiya, K., Xia, J., Suh, J. G., Johnson, R., Yu, S., & Huganir, R. L. (2005). Calcium-permeable AMPA receptor plasticity is mediated by subunit-specific interactions with PICK1 and NSF. Neuron, 45(6), 903–915. https://doi.org/10.1016/j.neuron.2005.02.026
   PubMed Web of Science ®Google Scholar
• Garry, E. M., Moss, A., Rosie, R., Delaney, A., Mitchell, R., & Fleetwood-Walker, S. M. (2003). Specific involvement in neuropathic pain of AMPA receptors and adapter proteins for the GluR2 subunit. Molecular and Cellular Neurosciences, 24(1), 10–22. https://doi.org/10.1016/S1044-7431(03)00134-9
   PubMed Web of Science ®Google Scholar
• Halgren, T. A. (1996). Performance of MMFF94*. Journal of Computational Chemistry, 17(5–6), 490–519. http://journals.wiley.com/jcc https://doi.org/10.1002/(SICI)1096-987X(199604)17:6<490::AID-JCC1>3.3.CO;2-V
   Web of Science ®Google Scholar
• Hanley, J. G., & Henley, J. M. (2005). PICK1 is a calcium-sensor for NMDA-induced AMPA receptor trafficking. The EMBO Journal, 24(18), 3266–3278. https://doi.org/10.1038/sj.emboj.7600801
   PubMed Web of Science ®Google Scholar
• Hanwell, M. D., Curtis, D. E., Lonie, D. C., Vandermeersch, T., Zurek, E., & Hutchison, G. R. (2012). Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. Journal of Cheminformatics, 4(1), 17. https://doi.org/10.1186/1758-2946-4-17
   PubMed Web of Science ®Google Scholar
• Herlo, R., Lund, V. K., Lycas, M. D., Jansen, A. M., Khelashvili, G., Andersen, R. C., Bhatia, V., Pedersen, T. S., Albornoz, P. B. C., Johner, N., Ammendrup-Johnsen, I., Christensen, N. R., Erlendsson, S., Stoklund, M., Larsen, J. B., Weinstein, H., Kjaerulff, O., Stamou, D., Gether, U., & Madsen, K. L. (2018). An amphipathic helix directs cellular membrane curvature sensing and function of the BAR domain protein PICK1. Cell Reports, 23(7), 2056–2069. https://doi.org/10.1016/j.celrep.2018.04.074
   PubMed Web of Science ®Google Scholar
• Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). LINCS: A Linear Constraint Solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. https://doi.org/10.1002/(SICI)1096-987X(199709)18:12 < 1463::AID-JCC4 > 3.0.CO;2-H
   Web of Science ®Google Scholar
• Houslay, M. D. (2009). Disrupting specific PDZ domain-mediated interactions for therapeutic benefit. British Journal of Pharmacology, 158(2), 483–485. https://doi.org/10.1111/j.1476-5381.2009.00359.x
   PubMed Web of Science ®Google Scholar
• Hsieh, H., Boehm, J., Sato, C., Iwatsubo, T., Tomita, T., Sisodia, S., & Malinow, R. (2006). AMPAR Removal Underlies Abeta-induced synaptic depression and dendritic spine loss . Neuron, 52(5), 831–843. https://doi.org/10.1016/j.neuron.2006.10.035
   PubMed Web of Science ®Google Scholar
• Jang, G. R., Harris, R. Z., & Lau, D. T. (2001). Pharmacokinetics and its role in small molecule drug discovery research. Medicinal Research Reviews, 21(5), 382–396. https://doi.org/10.1002/med.1015
   PubMed Web of Science ®Google Scholar
• Johnson, A. W. (1998). Invitation to organic chemistry (pp. 243). Jones & Bartlett Publishers, Inc (Verlag)..
   Google Scholar
• Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926–935. https://doi.org/10.1063/1.445869
   Web of Science ®Google Scholar
• Khan, Z., & Lafon, M. (2014). PDZ domain-mediated protein interactions: therapeutic targets in neurological disorders. Current Medicinal Chemistry, 21(23), 2632–2641. https://doi.org/10.2174/0929867321666140303145312
   PubMed Web of Science ®Google Scholar
• Kim, C. H., Chung, H. J., Lee, H. K., & Huganir, R. L. (2001). Interaction of the AMPA receptor subunit GluR2/3 with PDZ domains regulates hippocampal long-term depression. Proceedings of the National Academy of Sciences of the United States of America, 98(20), 11725–11730. https://doi.org/10.1073/pnas.211132798
   PubMed Web of Science ®Google Scholar
• Kim, E., Niethammer, M., Rothschild, A., Jan, Y. N., & Sheng, M. (1995). Clustering of Shaker-type K + channels by interaction with a family of membrane-associated guanylate kinases. Nature, 378(6552), 85–88. https://doi.org/10.1038/378085a0
   PubMed Web of Science ®Google Scholar
• Kornau, H., Schenker, L. T., Kennedy, M. B., & Seeburg, P. H. (1993). 4-S]s variant expression appears to be develop-mentally regulated, with the CI cassette-containing splice variants exhibiting in. 28–31. www.sciencemag.org
   Google Scholar
• Li, Y. H., Zhang, N., Wang, Y. N., Shen, Y., & Wang, Y. (2016). Multiple faces of protein interacting with C kinase 1 (PICK1): Structure, function, and diseases. Neurochemistry International, 98, 115–121. https://doi.org/10.1016/j.neuint.2016.03.001
   PubMed Web of Science ®Google Scholar
• Lin, E. Y. S., Silvian, L. F., Marcotte, D. J., Banos, C. C., Jow, F., Chan, T. R., Arduini, R. M., Qian, F., Baker, D. P., Bergeron, C., Hession, C. A., Huganir, R. L., Borenstein, C. F., Enyedy, I., Zou, J., Rohde, E., Wittmann, M., Kumaravel, G., Rhodes, K. J., … Guckian, K. M. (2018). Potent PDZ-domain PICK1 inhibitors that modulate amyloid beta-mediated synaptic dysfunction. Scientific Reports, 8(1), 1–10. https://doi.org/10.1038/s41598-018-31680-3
   PubMed Web of Science ®Google Scholar
• Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (2012). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 64(SUPPL), 4–17. https://doi.org/10.1016/j.addr.2012.09.019
   Google Scholar
• Lippert, R. A., Bowers, K. J., Dror, R. O., Eastwood, M. P., Gregersen, B. A., Klepeis, J. L., Kolossvary, I., & Shaw, D. E. (2007). A common, avoidable source of error in molecular dynamics integrators. Journal of Chemical Physics, 126(4), 2006–2008. https://doi.org/10.1063/1.2431176
   Web of Science ®Google Scholar
• MacKerell, A. D., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F. T., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., … Karplus, M. (1998). All-atom empirical potential for molecular modeling and dynamics studies of proteins. The Journal of Physical Chemistry. B, 102(18), 3586–3616. https://doi.org/10.1021/jp973084f
   PubMed Web of Science ®Google Scholar
• Marcotte, D. J., Hus, J. C., Banos, C. C., Wildes, C., Arduini, R., Bergeron, C., Hession, C. A., Baker, D. P., Lin, E., Guckian, K. M., Dunah, A. W., & Silvian, L. F. (2018). Lock and chop: A novel method for the generation of a PICK1 PDZ domain and piperidine-based inhibitor co-crystal structure. Protein Science : a Publication of the Protein Society, 27(3), 672–680. https://doi.org/10.1002/pro.3361
   PubMed Web of Science ®Google Scholar
• Marsault, E., Benakli, K., Beaubien, S., Saint-Louis, C., Déziel, R., & Fraser, G. (2007). Potent macrocyclic antagonists to the motilin receptor presenting novel unnatural amino acids. Bioorganic & Medicinal Chemistry Letters, 17(15), 4187–4190. https://doi.org/10.1016/j.bmcl.2007.05.043
   PubMed Web of Science ®Google Scholar
• Martin, Y. C. (2005). A bioavailability score. Journal of Medicinal Chemistry, 48(9), 3164–3170. https://doi.org/10.1021/jm0492002
   PubMed Web of Science ®Google Scholar
• Moriguchi, I., Hirono, S., Liu, Q., Nakagome, I., & Matsushita, Y. (1992). Simple method of calculating octanol/water partition coefficient. Chemical and Pharmaceutical Bulletin, 40(1), 127–130. https://doi.org/10.1248/cpb.40.127
   Web of Science ®Google Scholar
• Pan, L., Wu, H., Shen, C., Shi, Y., Jin, W., Xia, J., & Zhang, M. (2007). Clustering and synaptic targeting of PICK1 requires direct interaction between the PDZ domain and lipid membranes. The EMBO Journal, 26(21), 4576–4587. https://doi.org/10.1038/sj.emboj.7601860
   PubMed Web of Science ®Google Scholar
• Pant, R., Joshi, A., Maiti, P., Nand, M., Pande, V., & Chandra, S. (2020). Identification of potential Mycolyltransferase Ag85C inhibitors of Mycobacterium tuberculosis H37Rv via Virtual High Throughput Screening and Binding free energy studies. Journal of Molecular Graphics & Modelling, 98, 107584. https://doi.org/10.1016/j.jmgm.2020.107584
   PubMed Web of Science ®Google Scholar
• Parrinello, M., & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52(12), 7182–7190. https://doi.org/10.1063/1.328693
   Web of Science ®Google Scholar
• Pires, D. E. V., Blundell, T. L., & Ascher, D. B. (2015). pkCSM: Predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. Journal of Medicinal Chemistry, 58(9), 4066–4072. https://doi.org/10.1021/acs.jmedchem.5b00104
   PubMed Web of Science ®Google Scholar
• Potts, R. O., & Guy, R. H. (1992). Predicting skin permeability. Pharmaceutical Research, 9(5), 663–669. https://doi.org/10.1023/A:1015810312465
   PubMed Web of Science ®Google Scholar
• Santos, K. B., Guedes, I. A., Karl, A. L. M., & Dardenne, L. E. (2020). Highly flexible ligand docking: Benchmarking of the DockThor Program on the LEADS-PEP protein-peptide data set. Journal of Chemical Information and Modeling, 60(2), 667–683. https://doi.org/10.1021/acs.jcim.9b00905
   PubMed Web of Science ®Google Scholar
• Savjani, K. T., Gajjar, A. K., & Savjani, J. K. (2012). Drug solubility: Importance and enhancement techniques. ISRN Pharmaceutics, 2012(100 mL), 195727. https://doi.org/10.5402/2012/195727
   PubMedGoogle Scholar
• Schrödinger LLC. (2010). The PyMOL molecular graphics system. Version 2.4.1.
   Google Scholar
• Schyman, P., Liu, R., Desai, V., & Wallqvist, A. (2017). vNN web server for ADMET predictions. Frontiers in Pharmacology, 8, 889. https://doi.org/10.3389/fphar.2017.00889
   PubMed Web of Science ®Google Scholar
• Sharma, T., & Siddiqi, M. I. (2019). In silico identification and design of potent peptide inhibitors against PDZ-3 domain of Postsynaptic Density Protein (PSD-95). Journal of Biomolecular Structure & Dynamics, 37(5), 1241–1253. https://doi.org/10.1080/07391102.2018.1454851
   PubMed Web of Science ®Google Scholar
• Singh, R., Ganeshpurkar, A., Kumar, D., Kumar, D., Kumar, A., & Singh, S. K. (2020). Identifying potential GluN2B subunit containing N-Methyl-D-aspartate receptor inhibitors: an integrative in silico and molecular modeling approach. Journal of Biomolecular Structure & Dynamics, 38(9), 2533–2545. https://doi.org/10.1080/07391102.2019.1635530
   PubMed Web of Science ®Google Scholar
• Songyang, Z., Fanning, A. S., Fu, C., Xu, J., Marfatia, S. M., Chishti, A. H., Crompton, A., Chan, A. C., Anderson, J. M., & Cantley, L. C. (1997). Recognition of unique carboxyl-terminal motifs by distinct PDZ domains. Science (New York, NY), 275(5296), 73–77. https://doi.org/10.1126/science.275.5296.73
   Google Scholar
• Sunseri, J., & Koes, D. R. (2016). Pharmit: interactive exploration of chemical space. Nucleic Acids Research, 44(W1), W442–W448. https://doi.org/10.1093/nar/gkw287
   PubMed Web of Science ®Google Scholar
• Szakács, G., Váradi, A., Özvegy-Laczka, C., & Sarkadi, B. (2008). The role of ABC transporters in drug absorption, distribution, metabolism, excretion and toxicity (ADME-Tox). Drug Discovery Today, 13(9–10), 379–393. https://doi.org/10.1016/j.drudis.2007.12.010
   PubMed Web of Science ®Google Scholar
• Terashima, A., Pelkey, K. A., Rah, J. C., Suh, Y. H., Roche, K. W., Collingridge, G. L. L., McBain, C. J., & Isaac, J. T. R. (2008). An essential role for PICK1 in NMDA receptor-dependent bidirectional synaptic plasticity. Neuron, 57(6), 872–882. https://doi.org/10.1016/j.neuron.2008.01.028
   PubMed Web of Science ®Google Scholar
• Testa, B., & Krämer, S. D. (2007). The biochemistry of drug metabolism-an introduction: Part 2. Redox reactions and their enzymes. Chemistry & Biodiversity, 4(3), 257–405. https://doi.org/10.1002/cbdv.200790032
   PubMed Web of Science ®Google Scholar
• Thorsen, T. S., Madsen, K. L., Dyhring, T., Bach, A., Peters, D., Strømgaard, K., Rønn, L. C. B., & Gether, U. (2011). A fluorescence polarization based screening assay for identification of small molecule inhibitors of the PICK1 PDZ Domain. Combinatorial Chemistry & High Throughput Screening, 14(7), 590–600. https://doi.org/10.2174/138620711796367201
   PubMed Web of Science ®Google Scholar
• Thorsen, T. S., Madsen, K. L., Rebola, N., Rathje, M., Anggono, V., Bach, A., Moreira, I. S., Stuhr-Hansen, N., Dyhring, T., Peters, D., Beuming, T., Huganir, R., Weinstein, H., Mulle, C., Strømgaard, K., Rønn, L. C. B., & Gether, U. (2010). Identification of a small-molecule inhibitor of the PICK1 PDZ domain that inhibits hippocampal LTP and LTD. Proceedings of the National Academy of Sciences of the United States of America, 107(1), 413–418. https://doi.org/10.1073/pnas.0902225107
   PubMed Web of Science ®Google Scholar
• Velázquez-Libera, J. L., Durán-Verdugo, F., Valdés-Jiménez, A., Valdés-Jiménez, A., Núñez-Vivanco, G., & Caballero, J. (2020). LigRMSD: A web server for automatic structure matching and RMSD calculations among identical and similar compounds in protein-ligand docking. Bioinformatics (Oxford, England), 36(9), 2912–2914. https://doi.org/10.1093/bioinformatics/btaa018
   PubMed Web of Science ®Google Scholar
• Verlet, L. (1967). Computer “Experiments” on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules. Physical Review, 159(1), 98–103. https://doi.org/10.1103/PhysRev.159.98
   Web of Science ®Google Scholar
• Wang, G., Zhang, X., Pan, X., & Xiao, Y. (2021). FSC231 can alleviate paclitaxel-induced neuralgia by inhibiting PICK1 and affecting related factors. Neuroscience Letters, 741(39), 135471. https://doi.org/10.1016/j.neulet.2020.135471
   PubMedGoogle Scholar
• Webb, B., & Sali, A. (2016). Comparative protein structure modeling using MODELLER. Current Protocols in Bioinformatics, 54(1), 5.6.1–5.6.37. https://doi.org/10.1002/cpbi.3
   PubMedGoogle Scholar
• Wells, J. A., & McClendon, C. L. (2007). Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature, 450(7172), 1001–1009. https://doi.org/10.1038/nature06526
   PubMed Web of Science ®Google Scholar
• Wildman, S. A., & Crippen, G. M. (1999). Prediction of physicochemical parameters by atomic contributions. Journal of Chemical Information and Computer Sciences, 39(5), 868–873. https://doi.org/10.1021/ci990307l
   Google Scholar
• Xia, J., Chung, H. J., Wihler, C., Huganir, R. L., & Linden, D. J. (2000). Cerebellar long-term depression requires PKC-regulated interactions between GluR2/3 and PDZ domain-containing proteins. Neuron, 28(2), 499–510. https://doi.org/10.1016/S0896-6273(00)00128-8
   PubMed Web of Science ®Google Scholar
• Xu, J., & Xia, J. (2007). Structure and function of PICK1. Neuro-Signals, 15(4), 190–201. https://doi.org/10.1159/000098482
   Google Scholar
• Yang, H., Sun, L., Wang, Z., Li, W., Liu, G., & Tang, Y. (2018). ADMETopt: A web server for ADMET optimization in drug design via Scaffold Hopping. Journal of Chemical Information and Modeling, 58(10), 2051–2056. https://doi.org/10.1021/acs.jcim.8b00532
   PubMed Web of Science ®Google Scholar
• Yu, W., He, X., Vanommeslaeghe, K., & MacKerell, A. D. (2012). Extension of the CHARMM general force field to sulfonyl-containing compounds and its utility in biomolecular simulations. Journal of Computational Chemistry, 33(31), 2451–2468. https://doi.org/10.1002/jcc.23067
   PubMed Web of Science ®Google Scholar
• Zhou, P., Jin, B., Li, H., & Huang, S. Y. (2018). HPEPDOCK: A web server for blind peptide-protein docking based on a hierarchical algorithm. Nucleic Acids Research, 46(W1), W443–W450. https://doi.org/10.1093/nar/gky357
   PubMed Web of Science ®Google Scholar