Abstract
The discovery of molecular toxicity in a clinical drug candidate can have a significant impact on both the cost and timeline of the drug discovery process. Early identification of potentially toxic compounds during screening library preparation or, alternatively, during the hit validation process, is critical to ensure that valuable time and resources are not spent pursuing compounds that may possess a high propensity for human toxicity. This chapter focuses on the application of computational molecular filters, applied either prescreening or postscreening, to identify and remove known reactive and/or potentially toxic compounds from consideration in drug discovery campaigns.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Waring MJ, Arrowsmith J, Leach AR, Leeson PD, Mandrell S, Owen RM, Pairaudeau G, Pennie WD, Pickett SD, Wang J, Wallace O, Weir A (2015) An analysis of the attrition of drug candidates from four major pharmaceutical companies. Nat Rev Drug Discov 14:475–486
Hughes JD, Blagg J, Price DA, Bailey S, Decrescenzo GA, Devraj RV, Ellsworth E, Fobian YM, Gibbs ME, Gilles RW, Greene N, Huang E, Krieger-Burke T, Loesel J, Wager T, Whiteley L, Zhang Y (2008) Physiochemical drug properties associated with in vivo toxicological outcomes. Bioorg Med Chem Lett 18:4872–4875
Price DA, Blagg J, Jones L, Greene N, Wager T (2009) Physicochemical drug properties associated with in vivo toxicological outcomes: a review. Expert Opin Drug Metab Toxicol 5:921–931
Barratt MD (2000) Prediction of toxicity from chemical structure. Cell Biol Toxicol 16:1–13
Rishton GM (1997) Reactive compounds and in vitro false positives in HTS. Drug Discov Today 2:382–384
Bruns RF, Watson IA (2012) Rules for identifying potentially reactive or promiscuous compounds. J Med Chem 55:9763–9772
Goh GB, Hodas NO, Vishnu A (2017) Deep learning for computational chemistry. J Comput Chem 38:1291–1307
Gawehn E, Hiss JA, Schneider G (2016) Deep learning in drug discovery. Mol Inform 35:3–14
van de Waterbeemd H, Gifford E (2003) ADMET in silico modelling: towards prediction paradise? Nat Rev Drug Discov 2:192–204
Bugrim A, Nikolskaya T, Nikolsky Y (2004) Early prediction of drug metabolism and toxicity: systems biology approach and modeling. Drug Discov Today 9:127–135
Segall MD, Barber C (2014) Addressing toxicity risk when designing and selecting compounds in early drug discovery. Drug Discov Today 19:688–693
Gertrudes JC, Maltarollo VG, Silva RA, Oliveira PR, Honorio KM, da Silva AB (2012) Machine learning techniques and drug design. Curr Med Chem 19:4289–4297
Moroy G, Martiny VY, Vayer P, Villoutreix BO, Miteva MA (2012) Toward in silico structure-based ADMET prediction in drug discovery. Drug Discov Today 17:44–55
Gini G (2016) QSAR methods. Methods Mol Biol 1425:1–20
Singh PK, Negi A, Gupta PK, Chauhan M, Kumar R (2016) Toxicophore exploration as a screening technology for drug design and discovery: techniques, scope and limitations. Arch Toxicol 90:1785–1802
Rishton GM (2003) Nonleadlikeness and leadlikeness in biochemical screening. Drug Discov Today 8:86–96
Pearce BC, Sofia MJ, Good AC, Drexler DM, Stock DA (2006) An empirical process for the design of high-throughput screening deck filters. J Chem Inf Model 46:1060–1068
Walters WP, Ajay, Murcko MA (1999) Recognizing molecules with drug-like properties. Curr Opin Chem Biol 3:384–387
Cumming JG, Davis AM, Muresan S, Haeberlein M, Chen H (2013) Chemical predictive modelling to improve compound quality. Nat Rev Drug Discov 12:948–962
Sushko I, Salmina E, Potemkin VA, Poda G, Tetko IV (2012) ToxAlerts: a Web server of structural alerts for toxic chemicals and compounds with potential adverse reactions. J Chem Inf Model 52:2310–2316
Lipinski CA (2000) Drug-like properties and the causes of poor solubility and poor permeability. J Pharmacol Toxicol Methods 44:235–249
Veber DF, Johnson SR, Cheng HY, Smith BR, Ward KW, Kopple KD (2002) Molecular properties that influence the oral bioavailability of drug candidates. J Med Chem 45:2615–2623
Teague SJ, Davis AM, Leeson PD, Oprea T (1999) The design of leadlike combinatorial libraries. Angew Chem Int Ed Engl 38:3743–3748
Baell JB, Holloway GA (2010) New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays. J Med Chem 53:2719–2740
Dahlin JL, Nissink JW, Strasser JM, Francis S, Higgins L, Zhou H, Zhang Z, Walters MA (2015) PAINS in the assay: chemical mechanisms of assay interference and promiscuous enzymatic inhibition observed during a sulfhydryl-scavenging HTS. J Med Chem 58:2091–2113
Dolle RE (2011) Historical overview of chemical library design. Methods Mol Biol 685:3–25
Lagorce D, Sperandio O, Baell JB, Miteva MA, Villoutreix BO (2015) FAF-Drugs3: a web server for compound property calculation and chemical library design. Nucleic Acids Res 43(W1):W200–W207
Sterling T, Irwin JJ (2015) ZINC 15 – ligand discovery for everyone. J Chem Inf Model 55(11):2324–2337
Abreu RM, Froufe HJ, Daniel PO, Queiroz MJ, Ferreira IC (2011) ChemT, an open-source software for building template-based chemical libraries. SAR QSAR Environ Res 22:603–610
Sanz F, Carrio P, Lopez O, Capoferri L, Kooi DP, Vermeulen NP, Geerke DP, Montanari F, Ecker GF, Schwab CH, Kleinoder T, Magdziarz T, Pastor M (2015) Integrative modeling strategies for predicting drug toxicities at the eTOX project. Mol Inform 34:477–484
Fowler S, Schnall JG (2014) TOXNET: information on toxicology and environmental health. Am J Nurs 114:61–63
Wexler P (2001) TOXNET: an evolving web resource for toxicology and environmental health information. Toxicology 157:3–10
Zhu T, Cao S, Su PC, Patel R, Shah D, Chokshi HB, Szukala R, Johnson ME, Hevener KE (2013) Hit identification and optimization in virtual screening: practical recommendations based on a critical literature analysis. J Med Chem 56:6560–6572
Blagg J (2010) Structural alerts for toxicity. In: Abraham DJ, Rotella DP (eds) Burger’s medicinal chemistry and drug discovery, 7th edn. Wiley, Hoboken, pp 301–334
Smith GF (2011) Designing drugs to avoid toxicity. Prog Med Chem 50:1–47
Kazius J, McGuire R, Bursi R (2005) Derivation and validation of toxicophores for mutagenicity prediction. J Med Chem 48:312–320
SMARTS – a language for describing molecular patterns. Daylight Chemical Information Systems, Inc. http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html. Accessed 20 Dec 2017
Walters WP, Stahl MT, Murcko MA (1998) Virtual screening - an overview. Drug Discov Today 3:160–178
Williams DP, Naisbitt DJ (2002) Toxicophores: groups and metabolic routes associated with increased safety risk. Curr Opin Drug Discov Dev 5:104–115
Hakimelahi GH, Khodarahmi GA (2005) The identification of toxicophores for the prediction of mutagenicity, hepatotoxicity and cardiotoxicity. J Iran Chem Soc 2:244–267
Acknowledgments
This work was supported by NIH grant AI126755 and faculty development program funding from UTHSC College of Pharmacy to K.E.H.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Hevener, K.E. (2018). Computational Toxicology Methods in Chemical Library Design and High-Throughput Screening Hit Validation. In: Nicolotti, O. (eds) Computational Toxicology. Methods in Molecular Biology, vol 1800. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7899-1_13
Download citation
DOI: https://doi.org/10.1007/978-1-4939-7899-1_13
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-7898-4
Online ISBN: 978-1-4939-7899-1
eBook Packages: Springer Protocols