Identification of Novel TRPC5 Inhibitors by Pharmacophore-Based and Structure-Based Approaches

Computational Biology and Chemistry - Tập 87 - Trang 107302 - 2020
Shuxiang Li1,2, Shuqun Zhang2, Dingyuan Chen2, Xuan Jiang1, Bin Liu2, Hongbin Zhang1, Munikishore Rachakunta2, Zhili Zuo1,2
1Key Laboratory of Medicinal Chemistry for Natural Resources, Ministry of Education and Yunnan Province, School of Chemical Science and Technology, Yunnan University, Kunming, China
2State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China

Tài liệu tham khảo

Bon, 2013, In pursuit of small molecule chemistry for calcium-permeable non-selective TRPC channels -- mirage or pot of gold?, Br J Pharmacol, 170, 459, 10.1111/bph.12274 Ramsey, 2006, An introduction to TRP channels, Annual Review of Physiology, 68, 619, 10.1146/annurev.physiol.68.040204.100431 Clapham, 2003, TRP channels as cellular sensors, Nature, 426, 517, 10.1038/nature02196 Montell, 2002, A unified nomenclature for the superfamily of TRP cation channels, Molecular cell, 9, 229, 10.1016/S1097-2765(02)00448-3 Montell, 2005, The TRP superfamily of cation channels, Sci STKE, 2005, re3, 10.1126/stke.2722005re3 Vannier, 1999, Mouse trp2, the homologue of the human trpc2 pseudogene, encodes mTrp2, a store depletion-activated capacitative Ca2+ entry channel, Proceedings of the National Academy of Sciences of the United States of America, 96, 2060, 10.1073/pnas.96.5.2060 Riccio, 2002, mRNA distribution analysis of human TRPC family in CNS and peripheral tissues, Molecular Brain Research, 109, 95, 10.1016/S0169-328X(02)00527-2 Yang, 2015, Acute Treatment with a Novel TRPC4/C5 Channel Inhibitor Produces Antidepressant and Anxiolytic-Like Effects in Mice, PLOS ONE, 10 Phelan, 2013, Canonical Transient Receptor Channel 5 (TRPC5) and TRPC1/4 Contribute to Seizure and Excitotoxicity by Distinct Cellular Mechanisms, Molecular Pharmacology, 83, 429, 10.1124/mol.112.082271 Wei, 2015, Regulation of neuropathic pain behavior by amygdaloid TRPC4/C5 channels, Neuroscience letters, 608, 12, 10.1016/j.neulet.2015.09.033 Bröker‐Lai, 2017, Heteromeric channels formed by TRPC1, TRPC4 and TRPC5 define hippocampal synaptic transmission and working memory, The EMBO Journal, 36, 10.15252/embj.201696369 Hill, 2016, Global Prevalence of Chronic Kidney Disease – A Systematic Review and Meta-Analysis, PLOS ONE, 11, 10.1371/journal.pone.0158765 Go, 2004, Chronic kidney disease and the risks of death, cardiovascular events, and hospitalization, N Engl J Med, 351, 1296, 10.1056/NEJMoa041031 Thomas, 2013, Inhibition of the TRPC5 ion channel protects the kidney filter, Journal of Clinical Investigation, 123, 5298, 10.1172/JCI71165 Sharma, 2019, Design, synthesis and characterization of novel N-heterocyclic-1-benzyl-1H-benzo[d]imidazole-2-amines as selective TRPC5 inhibitors leading to the identification of the selective compound, AC1903, Bioorganic & Medicinal Chemistry Letters, 29, 155, 10.1016/j.bmcl.2018.12.007 Yu, 2019, Discovery of a Potent and Selective TRPC5 Inhibitor, Efficacious in a Focal Segmental Glomerulosclerosis Model, ACS Medicinal Chemistry Letters, 10, 1579, 10.1021/acsmedchemlett.9b00430 Rubaiy, 2017, Picomolar, selective, and subtype-specific small-molecule inhibition of TRPC1/4/5 channels, Journal of Biological Chemistry, 292, 8158, 10.1074/jbc.M116.773556 Just, 2018, Treatment with HC-070, a potent inhibitor of TRPC4 and TRPC5, leads to anxiolytic and antidepressant effects in mice, PLOS ONE, 13, 10.1371/journal.pone.0191225 Richter, 2014, Clemizole hydrochloride is a novel and potent inhibitor of transient receptor potential channel TRPC5, Molecular pharmacology, 86, 514, 10.1124/mol.114.093229 Miller, 2011, Vol. 286 Zhu, 2015, Identification and optimization of 2-aminobenzimidazole derivatives as novel inhibitors of TRPC4 and TRPC5 channels, British Journal of Pharmacology, 172, 3495, 10.1111/bph.13140 Naylor, 2016, Natural and synthetic flavonoid modulation of TRPC5 channels, British Journal of Pharmacology, 173, 562, 10.1111/bph.13387 Muraki, 2017, Na+ entry through heteromeric TRPC4/C1 channels mediates (−)Englerin A-induced cytotoxicity in synovial sarcoma cells, Scientific Reports, 7, 16988, 10.1038/s41598-017-17303-3 Zhou, 2017, Vol. 358 Minard, 2018, Remarkable Progress with Small-Molecule Modulation of TRPC1/4/5 Channels: Implications for Understanding the Channels in Health and Disease, Cells, 7, 52, 10.3390/cells7060052 Rubaiy, 2017, Pico145 - powerful new tool for TRPC1/4/5 channels, Channels (Austin), 11, 362, 10.1080/19336950.2017.1317485 Chenard, B. L., Gallaschun, R. J. Pyrido[2,3-d]pyrimidine-2,4(1H,3H)-dione derivatives as TRPC5 modulators and their preparation. WO2016023830A1 (2016a). Chenard, B. L., Gallaschun, R. J. Thieno- and furo[2,3-d]pyrimidine-2,4[1H,3H]-dione derivatives as TRPC5 modulators and their preparation. US20160039841A1 (2016b). Chenard, B. L., Gallaschun, R. J. Pyrrolo[3,2-d]pyrimidine-2,4[3H,5H]-dione derivatives as TRPC5 modulators and their preparation. US20160039831A1 (2016c). Chenard, B. L.,Gallaschun, R. J. Quinazoline-2,4(1H,3H)-dione derivatives as TRPC5 modulators and their preparation. US20160039772A1 (2016d). Chenard, B. L., Gallaschun, R. J., Kimball, S. D. Substituted xanthines as TRPC5 ion channel inhibitor and their preparation. US20140275528A1 (2014). Gerlach, K., Eickmaier, C., Sauer, A., Just, S., Chenard, B. L. Preparation of novel substituted xanthine derivatives as TRPC5 inhibitors. WO2019011802A1 (2019). Gasteiger, 1981, Prediction of proton magnetic resonance shifts: The dependence on hydrogen charges obtained by iterative partial equalization of orbital electronegativity, Organic Magnetic Resonance, 15, 353, 10.1002/mrc.1270150408 Lipinski, 1997, Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings, Advanced Drug Delivery Reviews, 23, 3, 10.1016/S0169-409X(96)00423-1 Veber, 2002, Molecular Properties That Influence the Oral Bioavailability of Drug Candidates, J Med Chem, 45, 2615, 10.1021/jm020017n Athar, 2016, Pharmacophore model prediction, 3D-QSAR and molecular docking studies on vinyl sulfones targeting Nrf2-mediated gene transcription intended for anti-Parkinson drug design, Journal of Biomolecular Structure and Dynamics, 34, 1282, 10.1080/07391102.2015.1077343 Baell, 2010, New Substructure Filters for Removal of Pan Assay Interference Compounds (PAINS) from Screening Libraries and for Their Exclusion in Bioassays, J Med Chem, 53, 2719, 10.1021/jm901137j Barnum, 1996, Identification of Common Functional Configurations Among Molecules, Journal of Chemical Information and Computer Sciences, 36, 563, 10.1021/ci950273r Mysinger, 2012, Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking, J Med Chem, 55, 6582, 10.1021/jm300687e Lone, 2017, Identification of Mycobacterium tuberculosis enoyl-acyl carrier protein reductase inhibitors: A combined in-silico and in-vitro analysis, Journal of Molecular Graphics and Modelling, 76, 172, 10.1016/j.jmgm.2017.07.005 Schuster, 2006, Pharmacophore Modeling and in Silico Screening for New P450 19 (Aromatase) Inhibitors, Journal of Chemical Information and Modeling, 46, 1301, 10.1021/ci050237k Kurogi, 2001, Pharmacophore Modeling and Three-dimensional Database Searching for Drug Design Using Catalyst, Current Medicinal Chemistry, 8, 1035, 10.2174/0929867013372481 Paliwal, 2012, Ligand-based drug design studies using predictive pharmacophore model generation on 4H-1,2,4-triazoles as AT1 receptor antagonists, Medicinal Chemistry Research, 21, 2307, 10.1007/s00044-011-9756-4 Tromelin, 2003, Use of Catalyst in a 3D-QSAR Study of the Interactions between Flavor Compounds and β-Lactoglobulin, Journal of Agricultural and Food Chemistry, 51, 1977, 10.1021/jf0207981 Chopra, 2008, Molecular modeling study on chemically diverse series of cyclooxygenase-2 selective inhibitors: generation of predictive pharmacophore model using Catalyst, Journal of Molecular Modeling, 14, 1087, 10.1007/s00894-008-0350-8 Xiao, 2004, Modeling of p38 mitogen-activated protein kinase inhibitors using the Catalyst™ HypoGen and k-nearest neighbor QSAR methods, Journal of Molecular Graphics and Modelling, 23, 129, 10.1016/j.jmgm.2004.05.001 Sterling, 2015, ZINC 15--Ligand Discovery for Everyone, Journal of Chemical Information and Modeling, 55, 2324, 10.1021/acs.jcim.5b00559 Güner, 2000, Vol. 2 Johnson, 1990 Šali, 1993, Comparative Protein Modelling by Satisfaction of Spatial Restraints, Journal of Molecular Biology, 234, 779, 10.1006/jmbi.1993.1626 Laskowski, 1996, AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR, Journal of Biomolecular NMR, 8, 477, 10.1007/BF00228148 Lüthy, 1992, VERIFY3D: assessment of protein models with three-dimensional profiles, Nature, 356, 83, 10.1038/356083a0 Wiederstein, 2007, ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins, Nucleic Acids Research, 35, W407, 10.1093/nar/gkm290 Van Der Spoel, 2005, GROMACS: fast, flexible, and free, Journal of computational chemistry, 26, 1701, 10.1002/jcc.20291 Li, 2018, Pharmacophore modeling, molecular docking and molecular dynamics simulations toward identifying lead compounds for Chk1, Computational Biology and Chemistry, 76, 53, 10.1016/j.compbiolchem.2018.06.001 Capra, 2007, Predicting functionally important residues from sequence conservation, Bioinformatics, 23, 1875, 10.1093/bioinformatics/btm270 Volkamer, 2012, DoGSiteScorer: a web server for automatic binding site prediction, analysis and druggability assessment, Bioinformatics (Oxford, England), 28, 2074, 10.1093/bioinformatics/bts310 Chojnacki, 2017, Programmatic access to bioinformatics tools from EMBL-EBI update: 2017, Nucleic Acids Research, 45, W550, 10.1093/nar/gkx273 Korb, 2009, Empirical Scoring Functions for Advanced Protein−Ligand Docking with PLANTS, Journal of Chemical Information and Modeling, 49, 84, 10.1021/ci800298z Biniashvili, 2012, Improving Classical Substructure-Based Virtual Screening to Handle Extrapolation Challenges, Journal of Chemical Information and Modeling, 52, 678, 10.1021/ci200472s Tang, 2018, Structure of the receptor-activated human TRPC6 and TRPC3 ion channels, Cell Research, 28, 746, 10.1038/s41422-018-0038-2