Combining experimental strategies for successful target deconvolution

Drug Discovery Today - Tập 25 - Trang 1998-2005 - 2020
Isabel V.L. Wilkinson1, Georg C. Terstappen2, Angela J. Russell1,2
1Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
2Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3PQ, UK

Tài liệu tham khảo

Terstappen, 2007, Target deconvolution strategies in drug discovery, Nat. Rev. Drug Discov., 6, 891, 10.1038/nrd2410 Trosset, 2019, In silico drug–target profiling, Methods Mol. Biol., 1953, 89, 10.1007/978-1-4939-9145-7_6 Backman, 2017, Large-scale bioactivity analysis of the small-molecule assayed proteome, PLoS One, 12, e0171413, 10.1371/journal.pone.0171413 Ramsay, 2018, A perspective on multi-target drug discovery and design for complex diseases, Clin. Transl. Med., 7, 3, 10.1186/s40169-017-0181-2 Wall, 2020, The Qi site of cytochrome b is a promiscuous drug target in Trypanosoma cruzi and Leishmania donovani, ACS Infect. Dis., 6, 515, 10.1021/acsinfecdis.9b00426 Madhusudhan, 2020, Target discovery of selective non-small-cell lung cancer toxins reveals inhibitors of mitochondrial complex i, ACS Chem. Biol., 15, 10.1021/acschembio.9b00734 Byrne, 2019, In silico target prediction for small molecules, Methods Mol. Biol., 1888, 273, 10.1007/978-1-4939-8891-4_16 Ezzat, 2019, Computational prediction of drug-target interactions using chemogenomic approaches: an empirical survey, Brief Bioinform., 20, 1337, 10.1093/bib/bby002 Lee, 2016, Using reverse docking for target identification and its applications for drug discovery, Expert Opin. Drug Discov., 11, 707, 10.1080/17460441.2016.1190706 Wu, 2018, Network-based methods for prediction of drug-target interactions, Front Pharmacol., 9, 1134, 10.3389/fphar.2018.01134 Zeng, 2020, Target identification among known drugs by deep learning from heterogeneous networks, Chem. Sci., 11, 1775, 10.1039/C9SC04336E Chen, 2018, Machine learning for drug-target interaction prediction, Molecules, 23, 2208, 10.3390/molecules23092208 Chen, 2016, Drug–target interaction prediction: databases, web servers and computational models, Brief Bioinform., 17, 696, 10.1093/bib/bbv066 Subramanian, 2017, A next generation connectivity map: L1000 Platform and the First 1,000,000 profiles, Cell, 171, 1437, 10.1016/j.cell.2017.10.049 Musa, 2018, A review of connectivity map and computational approaches in pharmacogenomics, Brief Bioinform., 19, 506 Comess, 2018, Emerging approaches for the identification of protein targets of small molecules - a practitioners’ perspective, J. Med. Chem., 61, 8504, 10.1021/acs.jmedchem.7b01921 Ho, 2011, Combining functional genomics and chemical biology to identify targets of bioactive compounds, Curr. Opin. Chem. Biol., 15, 66, 10.1016/j.cbpa.2010.10.023 Pries, 2018, Target identification and mechanism of action of picolinamide and benzamide chemotypes with antifungal properties, Cell Chem. Biol., 25, 279, 10.1016/j.chembiol.2017.12.007 Bullock, 2020, Whole-genome approach to understanding the mechanism of action of a histatin 5-derived peptide, Antimicrob. Agents Chemother., 64, 10.1128/AAC.01698-19 Deans, 2016, Parallel shRNA and CRISPR-Cas9 screens enable antiviral drug target identification, Nat. Chem. Biol., 12, 361, 10.1038/nchembio.2050 Jost, 2017, Combined CRISPRi/a-based chemical genetic screens reveal that rigosertib is a microtubule-destabilizing agent, Mol. Cell., 68, 210, 10.1016/j.molcel.2017.09.012 Jost, 2018, CRISPR approaches to small molecule target identification, ACS Chem. Biol., 13, 366, 10.1021/acschembio.7b00965 Neggers, 2018, Target identification of small molecules using large-scale CRISPR-Cas mutagenesis scanning of essential genes, Nat. Commun., 9, 502, 10.1038/s41467-017-02349-8 Horn, 2018, Unbiased compound-protein interface mapping and prediction of chemoresistance loci through forward genetics in haploid stem cells, Oncotarget, 9, 9838, 10.18632/oncotarget.24305 Smith, 2017, Tapinarof is a natural AhR agonist that resolves skin inflammation in mice and humans, J. Invest Dermatol., 137, 2110, 10.1016/j.jid.2017.05.004 Tulloch, 2018, Direct and indirect approaches to identify drug modes of action, IUBMB Life., 70, 9, 10.1002/iub.1697 Tu, 2020, Proteome interrogation using gold nanoprobes to identify targets of arctigenin in fish parasites, J. Nanobiotechnol., 18, 32, 10.1186/s12951-020-00591-9 Kitamura, 2018, Target identification of Yaku’amide B and its two distinct activities against mitochondrial FoF1-ATP synthase, J. Am. Chem. Soc., 140, 12189, 10.1021/jacs.8b07339 Friese, 2019, Chemical genetics reveals a role of dCTP pyrophosphatase 1 in Wnt signaling, Angew. Chemie. Int. Ed., 58, 13009, 10.1002/anie.201905977 Keller, 2020, Activity-based protein profiling in bacteria: applications for identification of therapeutic targets and characterization of microbial communities, Curr. Opin. Chem. Biol., 54, 45, 10.1016/j.cbpa.2019.10.007 Zanon, 2020, Isotopically labeled desthiobiotin azide (isoDTB) tags enable global profiling of the bacterial cysteinome, Angew. Chemie. Int. Ed., 59, 2829, 10.1002/anie.201912075 Parker, 2020, Click chemistry in proteomic investigations, Cell, 180, 605, 10.1016/j.cell.2020.01.025 Shi, 2012, Cell-based proteome profiling of potential dasatinib targets by use of affinity-based probes, J. Am. Chem. Soc., 134, 3001, 10.1021/ja208518u Smith, 2015, Photoaffinity labeling in target- and binding-site identification, Fut. Med. Chem., 7, 159, 10.4155/fmc.14.152 Ge, 2018, Current advances of carbene-mediated photoaffinity labeling in medicinal chemistry, RSC Adv., 8, 29428, 10.1039/C8RA03538E Tamura, 2018, Rapid labelling and covalent inhibition of intracellular native proteins using ligand-directed N-Acyl-N-Alkyl sulfonamide, Nat. Commun., 9, 1, 10.1038/s41467-018-04343-0 Park, 2019, Label-free target identification in drug discovery via phenotypic screening, Curr. Opin. Chem. Biol., 50, 66, 10.1016/j.cbpa.2019.02.006 Dai, 2019, Horizontal cell biology: monitoring global changes of protein interaction states with the proteome-wide cellular thermal shift assay (CETSA), Annu. Rev. Biochem., 88, 383, 10.1146/annurev-biochem-062917-012837 Peuget, 2020, Thermal proteome profiling identifies oxidative-dependent inhibition of the transcription of major oncogenes as a new therapeutic mechanism for select anticancer compounds, Cancer Res., 80, 1538, 10.1158/0008-5472.CAN-19-2069 Dziekan, 2019, Identifying purine nucleoside phosphorylase as the target of quinine using cellular thermal shift assay, Sci. Transl. Med., 11, eaau3174, 10.1126/scitranslmed.aau3174 Shaw, 2018, Determining direct binders of the androgen receptor using a high-throughput cellular thermal shift assay, Sci. Rep., 8, 1, 10.1038/s41598-017-18650-x Gaetani, 2019, Proteome integral solubility alteration: a high-throughput proteomics assay for target deconvolution, J. Proteome. Res., 18, 4027, 10.1021/acs.jproteome.9b00500 Perrin, 2020, Identifying drug targets in tissues and whole blood with thermal-shift profiling, Nat. Biotechnol., 38, 303, 10.1038/s41587-019-0388-4 Chernobrovkin, 2015, Functional identification of target by expression proteomics (FITExP) reveals protein targets and highlights mechanisms of action of small molecule drugs, Sci. Rep., 5, 1, 10.1038/srep11176 Saei, 2020, Comprehensive chemical proteomics for target deconvolution of the redox active drug auranofin, Redox Biol., 32, 101491, 10.1016/j.redox.2020.101491 Ohki, 2019, Perturbation-based proteomic correlation profiling as a target deconvolution methodology, Cell Chem. Biol., 26, 137, 10.1016/j.chembiol.2018.10.012 Gray, 2012, Amphotericin primarily kills yeast by simply binding ergosterol, Proc. Natl. Acad. Sci. U. S. A., 109, 2234, 10.1073/pnas.1117280109 Erwin, 2016, Genome-wide mapping of drug-DNA interactions in cells with COSMIC (Crosslinking of Small Molecules to Isolate Chromatin), J. Vis. Exp., 2016, e53510 Disney, 2019, Targeting RNA with small molecules to capture opportunities at the intersection of chemistry, biology, and medicine, J. Am. Chem. Soc., 141, 6776, 10.1021/jacs.8b13419 Verga, 2014, Photo-cross-linking probes for trapping G-quadruplex DNA, Angew. Chem., 126, 1012, 10.1002/ange.201307413 Yang, 2018, Transcriptome-wide identification of transient RNA G-quadruplexes in human cells, Nat. Commun., 9, 1, 10.1038/s41467-018-07224-8 Wang, 2018, Mechanistic studies of a small-molecule modulator of SMN2 splicing, Proc. Natl. Acad. Sci. U. S. A., 115, E4604, 10.1073/pnas.1800260115 Laraia, 2020, Image‐based morphological profiling identifies a lysosomotropic, iron‐sequestering autophagy inhibitor, Angew. Chemie. Int. Ed., 59, 5721, 10.1002/anie.201913712 Bray, 2016, Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes, Nat. Protoc., 11, 1757, 10.1038/nprot.2016.105 Schneidewind, 2020, Morphological profiling enables the identification of common mode of action for small molecules with different targets, ChemBioChem, 10.1002/cbic.202000734 Ball, 2020, An isothermal shift assay for proteome scale drug-target identification, Commun. Biol., 3, 75, 10.1038/s42003-020-0795-6 Bergamini, 2012, A selective inhibitor reveals PI3Kγ dependence of TH17 cell differentiation, Nat. Chem. Biol., 8, 576, 10.1038/nchembio.957 Yang, 2019, Discovery, optimization, and target identification of novel potent broad-spectrum antiviral inhibitors, J. Med. Chem., 62, 4056, 10.1021/acs.jmedchem.9b00091 Renaud, 2016, Biophysics in drug discovery: impact, challenges and opportunities, Nat. Rev. Drug Discov., 15, 1, 10.1038/nrd.2016.123 Schürmann, 2016, Small-molecule target engagement in cells, Cell Chem. Biol., 23, 435, 10.1016/j.chembiol.2016.03.008 Gleissner, 2019, Neocarzilin A is a potent inhibitor of cancer cell motility targeting VAT-1 controlled pathways, ACS Cent. Sci., 5, 1170, 10.1021/acscentsci.9b00266 Piazza, 2020, A machine learning-based chemoproteomic approach to identify drug targets and binding sites in complex proteomes, Nat. Commun., 11, 4200, 10.1038/s41467-020-18071-x Chen, 2019, Advances in MS based strategies for probing ligand-target interactions: focus on soft ionization mass spectrometric techniques, Front. Chem., 7, 703, 10.3389/fchem.2019.00703 Flaxman, 2019, Small molecule interactome mapping by photo‐affinity labeling (SIM‐PAL) to identify binding sites of small molecules on a proteome‐wide scale, Curr. Protoc. Chem. Biol., 11, e75, 10.1002/cpch.75 Bunnage, 2015, Know your target, know your molecule, Nat. Chem. Biol., 11, 368, 10.1038/nchembio.1813 Erb, 2017, Transcription control by the ENL YEATS domain in acute leukaemia, Nature, 543, 270, 10.1038/nature21688 Kim, 2020, Identification and validation of VEGFR2 kinase as a target of voacangine by a systematic combination of DARTS and MSI, Biomolecules, 10, 508, 10.3390/biom10040508 Wilkinson, 2020, Chemical proteomics and phenotypic profiling identifies the aryl hydrocarbon receptor as a molecular target of the utrophin modulator ezutromid, Angew. Chem. Int. Ed., 59, 2420, 10.1002/anie.201912392 FDA, 2020 Pammolli, 2020, The endless frontier? The recent increase of R&D productivity in pharmaceuticals, J. Transl. Med., 18, 162, 10.1186/s12967-020-02313-z Lu, 2020, Plasmodium chaperonin TRiC/CCT identified as a target of the antihistamine clemastine using parallel chemoproteomic strategy, Proc. Natl. Acad. Sci. U. S. A., 117, 5810, 10.1073/pnas.1913525117 Bruno, 2020, The primary mechanism of cytotoxicity of the chemotherapeutic agent CX-5461 is topoisomerase II poisoning, Proc. Natl. Acad. Sci. U. S. A., 117, 4053, 10.1073/pnas.1921649117 Wyllie, 2018, Cyclin-dependent kinase 12 is a drug target for visceral leishmaniasis, Nature, 560, 192, 10.1038/s41586-018-0356-z Xu, 2020, Phenotypic screening of chemical libraries enriched by molecular docking to multiple targets selected from glioblastoma genomic data, ACS Chem. Biol., 15, 1424, 10.1021/acschembio.0c00078 Ross, 2020, CPSF3-dependent pre-mRNA processing as a druggable node in AML and Ewing’s sarcoma, Nat. Chem. Biol., 16, 50, 10.1038/s41589-019-0424-1 Brand, 2018, Combined proteomic and in silico target identification reveal a role for 5-lipoxygenase in developmental signaling pathways, Cell Chem. Biol., 25, 1095, 10.1016/j.chembiol.2018.05.016 Phillips, 2019, Target identification reveals lanosterol synthase as a vulnerability in glioma, Proc. Natl. Acad. Sci. U. S. A., 116, 7957, 10.1073/pnas.1820989116