In silico Druggability Assessment of the NUDIX Hydrolase Protein Family as a Workflow for Target Prioritization
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Abdelraheim, 2003, Mammalian NADH diphosphatases of the nudix family: cloning and characterization of the human peroxisomal NUDT12 protein, Biochem. J., 374, 329, 10.1042/bj20030441
An, 2018, Small-molecule PROTACs: an emerging and promising approach for the development of targeted therapy drugs, EBioMedicine, 36, 553, 10.1016/j.ebiom.2018.09.005
Aretz, 2018, Allosteric inhibition of a mammalian lectin, J. Am. Chem. Soc, 140, 14915, 10.1021/jacs.8b08644
Aretz, 2014, Computational and experimental prediction of human C-type lectin receptor druggability, Front. Immunol., 5, 323, 10.3389/fimmu.2014.00323
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
Barford, 1994, Crystal structure of human protein tyrosine phosphatase 1B, Science, 263, 1397, 10.1126/science.8128219
Baykov, 1988, A malachite green procedure for orthophosphate determination and its use in alkaline phosphatase-based enzyme immunoassay, Anal. Biochem., 171, 266, 10.1016/0003-2697(88)90484-8
Berthold, 2008, “KNIME: The Konstanz Information Miner,”, Data Analysis, Machine Learning and Applications; Studies in Classification, Data Analysis, and Knowledge Organization, 319
Caffrey, 1999, The human and rat forms of multiple inositol polyphosphate phosphatase: functional homology with a histidine acid phosphatase up-regulated during endochondral ossification, FEBS Lett., 442, 99, 10.1016/S0014-5793(98)01636-6
Caffrey, 2000, Discovery of molecular and catalytic diversity among human diphosphoinositol-polyphosphate phosphohydrolases. an expanding nudt family, J. Biol. Chem., 275, 12730, 10.1074/jbc.275.17.12730
Carreras-Puigvert, 2017, A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family, Nat. Commun, 8, 1541, 10.1038/s41467-017-01642-w
Carter, 2015, Crystal structure, biochemical and cellular activities demonstrate separate functions of MTH1 and MTH2, Nat. Commun., 6, 7871, 10.1038/ncomms8871
Choi, 2011, Analysis of Differentially Expressed Genes in Human rectal carcinoma using suppression subtractive hybridization, Clin. Exp. Med., 11, 219, 10.1007/s10238-010-0130-5
Cimermancic, 2016, CryptoSite: expanding the druggable proteome by characterization and prediction of cryptic binding sites, J. Mol. Biol., 428, 709, 10.1016/j.jmb.2016.01.029
Coseno, 2008, Crystal structure of the 25 KDa subunit of human cleavage factor Im, Nucleic Acids Res, 36, 3474, 10.1093/nar/gkn079
Costa, 2011, Entropy and Mg2+ control ligand affinity and specificity in the malachite green binding RNA aptamer, Mol. BioSyst., 7, 2156, 10.1039/c1mb05075c
DubianokY. CollinsP. KrojerT. FairheadM. MacLeanE. DiazS. LPDB 6gru Structure Summary ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI2018
Ellermann, 2017, Novel class of potent and cellularly active inhibitors devalidates MTH1 as broad-spectrum cancer target, ACS Chem. Biol, 12, 1986, 10.1021/acschembio.7b00370
Farand, 2020, Discovery of potent and selective MTH1 inhibitors for oncology: enabling rapid target (In)validation, ACS Med. Chem. Lett, 11, 358, 10.1021/acsmedchemlett.9b00420
Friesner, 2004, Glide: a new approach for rapid, accurate docking and scoring. 1. method and assessment of docking accuracy, J. Med. Chem., 47, 1739, 10.1021/jm0306430
Friesner, 2006, Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein–ligand complexes, J. Med. Chem., 49, 6177, 10.1021/jm051256o
Gad, 2014, MTH1 inhibition eradicates cancer by preventing sanitation of the DNTP pool, Nature, 508, 215, 10.1038/nature13181
Ge, 2013, Crystal structure of wild-type and mutant human Ap4A hydrolase, Biochem. Biophys. Res. Commun., 432, 16, 10.1016/j.bbrc.2013.01.095
Greenwood, 2010, Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution, J. Comput. Aided Mol. Des, 24, 591, 10.1007/s10822-010-9349-1
Halgren, 2007, New method for fast and accurate binding-site identification and analysis, Chem Biol Drug Des, 69, 146, 10.1111/j.1747-0285.2007.00483.x
Halgren, 2009, Identifying and characterizing binding sites and assessing druggability, J. Chem. Inf. Model, 49, 377, 10.1021/ci800324m
Halgren, 2004, Glide: a new approach for rapid, accurate docking and scoring. 2. enrichment factors in database screening, J. Med. Chem., 47, 1750, 10.1021/jm030644s
Huber, 2014, Stereospecific targeting of MTH1 by (S)-crizotinib as an anticancer strategy, Nature, 508, 222, 10.1038/nature13194
Irwin, 2012, ZINC: a free tool to discover chemistry for biology, J. Chem. Inf. Model, 52, 1757, 10.1021/ci3001277
Kettle, 2016, Potent and selective inhibitors of MTH1 probe its role in cancer cell survival, J. Med. Chem., 59, 2346, 10.1021/acs.jmedchem.5b01760
Kozakov, 2015, The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins, Nat. Protoc., 10, 733, 10.1038/nprot.2015.043
Krishnan, 2018, A potent, selective, and orally bioavailable inhibitor of the protein-tyrosine phosphatase PTP1B improves insulin and leptin signaling in animal models, J. Biol. Chem., 293, 1517, 10.1074/jbc.C117.819110
Llona-Minguez, 2016, Discovery of the first potent and selective inhibitors of human DCTP pyrophosphatase 1, J. Med. Chem., 59, 1140, 10.1021/acs.jmedchem.5b01741
MatheaS. SalahE. VelupillaiS. TallantC. PikeA. C. W. BushellS. R. PDB 5mp0 Structure Summary ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI
MatheaS. TallantC. SalahE. WangD. VelupillaiS. NowakR. PDB 5lf8 Structure Summary ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI
Michel, 2019, Computational and experimental druggability assessment of human DNA glycosylases, ACS Omega, 4, 11642, 10.1021/acsomega.9b00162
Mullard, 2018, Phosphatases start shedding their stigma of undruggability, Nat. Rev. Drug Discov., 17, 847, 10.1038/nrd.2018.201
Niesen, 2007, The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability, Nat. Protoc., 2, 2212, 10.1038/nprot.2007.321
Page, 2018, Targeted NUDT5 inhibitors block hormone signaling in breast cancer cells, Nat. Commun, 9, 250, 10.1038/s41467-017-02293-7
Petrocchi, 2016, Identification of potent and selective MTH1 inhibitors, Bioorg. Med. Chem. Lett., 26, 1503, 10.1016/j.bmcl.2016.02.026
Resnick, 2019, Rapid covalent-probe discovery by electrophile-fragment screening, J. Am. Chem. Soc., 141, 8951, 10.1021/jacs.9b02822
Samaranayake, 2017, MTH1 as a chemotherapeutic target: the elephant in the room, Cancers, 9, 47, 10.3390/cancers9050047
Shelley, 2007, Epik: a software program for PK prediction and protonation state generation for drug-like molecules, J. Comput. Aided. Mol. Des, 21, 681, 10.1007/s10822-007-9133-z
Shen, 2003, The crystal structure and mutational analysis of human NUDT9, J. Mol. Biol., 332, 385, 10.1016/S0022-2836(03)00954-9
SrikannathasanV. NunezC. A. TallantC. SiejkaP. MatheaS. KopecJ. PDB 5t3p Structure Summary ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI
SrikannathasanV. NunezC. A. TallantC. SiejkaP. MatheaS. NewmanJ. PDB 5ltu Structure Summary ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI
TallantC. SiejkaP. MatheaS. ShresthaL. KrojerT. SrikannathasanV. PDB 5lf9 structure summary ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI2017
Thorsell, 2009, Crystal structure of human diphosphoinositol phosphatase 1, Proteins, 77, 242, 10.1002/prot.22489
Trésaugues, 2015, Structural basis for the specificity of human nudt16 and its regulation by inosine monophosphate, PLoS ONE, 10, e0131507, 10.1371/journal.pone.0131507
TresauguesL. MocheM. ArrowsmithC. H. BerglundH. BountraC. CollinsmR. PDB 3h95 Structure Summary ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI
TresauguesL. MocheM. ArrowsmithC. H. BerglundH. BusamR. D. CollinsR. PDB 3cou Structure Summary ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI2008
TresauguesL. SiponenM. I. ArrowsmithC. H. BerglundH. BountraC. CollinsR. PDB 3q93 structure summary ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI
TresauguesL. SiponenM. I. ArrowsmithC. H. BerglundH. BountraC. CollinsR. PDB 3q91 Structure Summary ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI
TresauguesL. SiponenM. I. LehtioL. ArrowsmithC. H. BerglundH. BountraC. PDB 3gg6 Structure Summary ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI
TresauguesL. WelinM. ArrowsmithC. H. BerglundH. BountraC. CollinsR. PDB 3mcf structure summary ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI2010
Tsuzuki, 2001, Analysis of MTH1 gene function in mice with targeted mutagenesis, Mutat. Res., 477, 71, 10.1016/S0027-5107(01)00108-7
Vajda, 2018, Cryptic binding sites on proteins: definition, detection, and druggability, Curr. Opin. Chem. Biol., 44, 1, 10.1016/j.cbpa.2018.05.003
Vardakou, 2014, Comparative analysis and validation of the malachite green assay for the high throughput biochemical characterization of terpene synthases, MethodsX, 1, 187, 10.1016/j.mex.2014.08.007
Volkamer, 2012, DoGSiteScorer: a web server for automatic binding site prediction, analysis and druggability assessment, Bioinformatics, 28, 2074, 10.1093/bioinformatics/bts310
Walters, 2002, Prediction of “drug-likeness”, Adv. Drug Deliv. Rev., 54, 255, 10.1016/S0169-409X(02)00003-0
Warpman Berglund, 2016, Validation and development of MTH1 inhibitors for treatment of cancer, Ann. Oncol., 27, 2275, 10.1093/annonc/mdw429
Wenthur, 2014, Drugs for allosteric sites on receptors, Annu Rev Pharmacol Toxicol, 54, 165, 10.1146/annurev-pharmtox-010611-134525
Wright, 2016, ADP-ribose-derived nuclear ATP synthesis by NUDIX5 is required for chromatin remodeling, Science, 352, 1221, 10.1126/science.aad9335
Wu, 2019, Decapping enzyme NUDT12 partners with BLMH for cytoplasmic surveillance of NAD-capped RNAs, Cell Rep., 29, 4422, 10.1016/j.celrep.2019.11.108
Yueh, 2019, Kinase atlas: druggability analysis of potential allosteric sites in kinases, J. Med. Chem., 62, 6512, 10.1021/acs.jmedchem.9b00089
Zhang, 2007, PTP1B as a drug target: recent developments in PTP1B inhibitor discovery, Drug Discov. Today, 12, 373, 10.1016/j.drudis.2007.03.011