Objective, Quantitative, Data-Driven Assessment of Chemical Probes

Cell Chemical Biology

Volumn 25, Issue 2, 2018, Pages 194-205.e5

  Antolin, Albert A ^a   Tym, Joseph E ^a   Komianou, Angeliki ^a   Collins, Ian ^a   Workman, Paul ^a   Al Lazikani, Bissan ^a  

^a INSTITUTE OF CANCER RESEARCH   (United Kingdom)

Author keywords

chemical probes; chemical tools; large scale; objective quantitative assessment; online public resource; target validation

Indexed keywords

ABC TRANSPORTER; CHECKPOINT KINASE 2; KAPPA OPIATE RECEPTOR; NICOTINAMIDE ADENINE DINUCLEOTIDE ADENOSINE DIPHOSPHATE RIBOSYLTRANSFERASE 1; PROTEOME;

ARTICLE; CHEMICAL ANALYSIS; CHEMICAL PROBE; DATA ANALYSIS; MEDICAL RESEARCH; MOLECULAR PROBE; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; CHEMISTRY; HUMAN; MEDICINAL CHEMISTRY; MOLECULAR LIBRARY;

CHEMISTRY, PHARMACEUTICAL; HUMANS; MOLECULAR PROBES; SMALL MOLECULE LIBRARIES;

EID: 85039435630     PISSN: 24519456     EISSN: 24519448     Source Type: Journal    
DOI: 10.1016/j.chembiol.2017.11.004     Document Type: Article

References (35)

1. Andrs, M., Korabecny, J., Jun, D., Hodny, Z., Bartek, J., Kuca, K., Phosphatidylinositol 3-kinase (PI3K) and phosphatidylinositol 3-kinase-related kinase (PIKK) inhibitors: importance of the morpholine ring. J. Med. Chem. 58 (2015), 41–71.
2. Antolín, A.A., Mestres, J., Linking off-target kinase pharmacology to the differential cellular effects observed among PARP inhibitors. Oncotarget 5 (2014), 1–6.
3. Arrowsmith, C.H., Audia, J.E., Austin, C., Baell, J., Bennett, J., Blagg, J., Bountra, C., Brennan, P.E., Brown, P.J., Bunnage, M.E., et al. The promise and peril of chemical probes. Nat. Chem. Biol. 11 (2015), 536–541.
4. Baell, J., Walters, M.A., Chemical con artists foil drug discovery. Nature 513 (2014), 481–483.
5. Blagg, J., Workman, P., Chemical biology approaches to target validation in cancer. Curr. Opin. Pharmacol. 17 (2014), 87–100.
6. Blagg, J., Workman, P., Choose and use your chemical probe wisely to explore cancer biology. Cancer Cell 32 (2017), 9–25.
7. Bulusu, K.C., Tym, J.E., Coker, E.A., Schierz, A.C., Al-Lazikani, B., CanSAR: updated cancer research and drug discovery knowledgebase. Nucleic Acids Res. 42 (2014), 1040–1047.
8. Bunnage, M.E., Chekler, E.L.P., Jones, L.H., Target validation using chemical probes. Nat. Chem. Biol. 9 (2013), 195–199.
9. Caldwell, J.J., Welsh, E.J., Matijssen, C., Anderson, V.E., Antoni, L., Boxall, K., Urban, F., Hayes, A., Raynaud, F.I., Rigoreau, L.J.M., et al. Structure-based design of potent and selective 2-(quinazolin-2-yl)phenol inhibitors of checkpoint kinase 2. J. Med. Chem. 54 (2011), 580–590.
10. Capuzzi, S.J., Muratov, E.N., Tropsha, A., Phantom PAINS: problems with the utility of alerts for Pan-Assay INterference CompoundS. J. Chem. Inf. Model. 57 (2017), 417–427.
11. Chambers, J., Davies, M., Gaulton, A., Hersey, A., Velankar, S., Petryszak, R., Hastings, J., Bellis, L., McGlinchey, S., Overington, J.P., UniChem: a unified chemical structure cross-referencing and identifier tracking system. J. Cheminform. 5 (2013), 1–9.
12. Coghlan, M.J., Carroll, W.A., Gopalakrishnan, M., Recent developments in the biology and medicinal chemistry of potassium channel modulators: update from a decade of progress. J. Med. Chem. 44 (2001), 1627–1653.
13. Edwards, A.M., Isserlin, R., Bader, G.D., Frye, S.V., Willson, T.M., Yu, F.H., Too many roads not taken. Nature 470 (2011), 163–165.
14. Fedorov, O., Müller, S., Knapp, S., The (un)targeted cancer kinome. Nat. Chem. Biol. 6 (2010), 166–169.
15. Finan, A.C., Gaulton, A., Kruger, F.A., Lumbers, T., Shah, T., Engmann, J., Galver, L., Kelley, R., Karlsson, A., Santos, R., et al. The druggable genome and support for target identification and validation in drug development. Sci. Transl. Med., 9, 2017, 383.
16. Folkes, A.J., Ahmadi, K., Alderton, W.K., Alix, S., Baker, S.J., Box, G., Chuckowree, I.S., Clarke, P.A., Depledge, P., Eccles, S.A., et al. The identification of 2-(1H-indazol-4-yl)-6-(4-methanesulfonyl-piperazin-1-ylmethyl)-4-morpholin-4-yl-thieno[3,2-d]pyrimidine (GDC-0941) as a potent, selective, orally bioavailable inhibitor of class I PI3 kinase for the treatment of cancer. J. Med. Chem. 51 (2008), 5522–5532.
17. Frye, S.V., The art of the chemical probe. Nat. Chem. Biol. 6 (2010), 159–161.
18. Gaulton, A., Hersey, A., Nowotka, M., Bento, A.P., Chambers, J., Mendez, D., Mutowo, P., Atkinson, F., Bellis, L.J., Cibrián-Uhalte, E., et al. The ChEMBL database in 2017. Nucleic Acids Res., 45, 2016, gkw1074.
19. Gilson, M.K., Liu, T., Baitaluk, M., Nicola, G., Hwang, L., Chong, J., BindingDB in 2015: a public database for medicinal chemistry, computational chemistry and systems pharmacology. Nucleic Acids Res. 44 (2016), D1045–D1053.
20. Hopkins, A.L., Keserü G.M., Leeson, P.D., Rees, D.C., Reynolds, C.H., The role of ligand efficiency metrics in drug discovery. Nat. Rev. Drug Discov. 13 (2014), 105–121.
21. Huggins, D.J., Venkitaraman, A.R., Spring, D.R., Rational methods for the selection of diverse screening compounds. ACS Chem. Biol. 6 (2011), 208–217.
22. Langdon, S.R., Brown, N., Blagg, J., Scaffold diversity of exemplified medicinal chemistry space. J. Chem. Inf. Model. 51 (2011), 2174–2185.
23. Mateo, J., Ganji, G., Lemech, C., Burris, H.A., Han, S.-W., Swales, K.E., Decordova, S., DeYoung, M.P., Smith, D.A., Kalyana-Sundaram, S., et al. A first-time-in-human study of GSK2636771, a phosphoinositide 3 kinase beta-selective inhibitor, in patients with advanced solid tumors. Clin. Cancer Res. 23 (2017), 5981–5992.
24. McGonigle, S., Chen, Z., Wu, J., Chang, P., Kolber-Simonds, D., Ackermann, K., Twine, N.C., Shie, J.-L., Miu, J.T., Huang, K.-C., et al. E7449: a dual inhibitor of PARP1/2 and tankyrase1/2 inhibits growth of DNA repair deficient tumors and antagonizes Wnt signaling. Oncotarget 6 (2015), 41307–41323.
25. Oprea, T.I., Bologa, C.G., Boyer, S., Curpan, R.F., Glen, R.C., Hopkins, A.L., Lipinski, C.A., Marshall, G.R., Martin, Y.C., Ostopovici-Halip, L., et al. A crowdsourcing evaluation of the NIH chemical probes. Nat. Chem. Biol. 5 (2009), 441–447.
26. Papeo, G., Posteri, H., Borghi, D., Busel, A.A., Caprera, F., Casale, E., Ciomei, M., Cirla, A., Corti, E., D'Anello, M., et al. Discovery of 2-[1-(4,4-difluorocyclohexyl)piperidin-4-yl]-6-fluoro-3-oxo-2,3-dihydro-1H-isoindole-4-carboxamide (NMS-P118): a potent, orally available, and highly selective PARP-1 inhibitor for cancer therapy. J. Med. Chem. 58 (2015), 6875–6898.
27. Raynaud, F.I., Eccles, S., Clarke, P.A., Hayes, A., Nutley, B., Alix, S., Henley, A., Di-Stefano, F., Ahmad, Z., Guillard, S., et al. Pharmacologic characterization of a potent inhibitor of class I phosphatidylinositide 3-kinases. Cancer Res. 67 (2007), 5840–5850.
28. Rubio-Perez, C., Tamborero, D., Schroeder, M.P., Antolín, A.A., Deu-Pons, J., Perez-Llamas, C., Mestres, J., Gonzalez-Perez, A., Lopez-Bigas, N., In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals targeting opportunities. Cancer Cell 27 (2015), 382–396.
29. Sanchez, R.M., Erhard, K., Hardwicke, M.A., Lin, H., McSurdy-Freed, J., Plant, R., Raha, K., Rominger, C.M., Schaber, M.D., Spengler, M.D., et al. Synthesis and structure–activity relationships of 1,2,4-triazolo[1,5-a]pyrimidin-7(3H)-ones as novel series of potent β isoform selective phosphatidylinositol 3-kinase inhibitors. Bioorg. Med. Chem. Lett. 22 (2012), 3198–3202.
30. Schreiber, S.L., Small molecules: the missing link in the central dogma. Nat. Chem. Biol. 1 (2005), 64–66.
31. The UniProt Consortium. UniProt: the universal protein knowledgebase. Nucleic Acids Res. 45 (2017), 158–169.
32. Tym, J.E., Mitsopoulos, C., Coker, E.A., Parisa, R., Schierz, A.C., Antolin, A.A., Al-Lazikani, B., CanSAR: an updated cancer research and drug discovery knowledgebase. Nucleic Acids Res. 44 (2016), 938–943.
33. Wang, Y., Cornett, A., King, F.J., Mao, Y., Nigsch, F., Paris, C.G., McAllister, G., Jenkins, J.L., Evidence-based and quantitative prioritization of tool compounds in phenotypic drug discovery. Cell Chem. Biol. 23 (2016), 862–874.
34. Weerawarna, S.A., Davis, R.D., Nelson, W.L., Isothiocyanate-substituted/c-selective opioid receptor ligands derived from N-Me thyl-N-[(1s)-1-phenyl-2-(1-pyrrolidinyl)ethyl] phenylace tamide. J. Med. Chem. 13 (1994), 2856–2864.
35. Workman, P., Collins, I., Probing the probes: fitness factors for small molecule tools. Chem. Biol. 17 (2010), 561–577.