Abstract
Quantitative structure–activity relationship (QSAR) has been used in the scientific research community for many decades and applied to drug discovery and development in the industry. QSAR technologies are advancing fast and attracting possible applications in regulatory science. To facilitate the development of reliable QSAR models, the FDA had invested a lot of efforts in constructing chemical databases with a variety of efficacy and safety endpoint data, as well as in the development of computational algorithms. In this chapter, we briefly describe some of the often used databases developed at the FDA such as EDKB (Endocrine Disruptor Knowledge Base), EADB (Estrogenic Activity Database), LTKB (Liver Toxicity Knowledge Base), and CERES (Chemical Evaluation and Risk Estimation System) and the technologies adopted by the agency such as Mold2 program for calculation of a large and diverse set of molecular descriptors and decision forest algorithm for QSAR model development. We also summarize some QSAR models that have been developed for safety evaluation of the FDA-regulated products.
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References
Brown AC, Fraser TR (1868) On the connection between chemical constitution and physiological action; with special reference to the physiological action of the salts of the ammonium bases derived from strychnia, brucia, thebaia, codeia, morphia, and nicotia. J Anat Physiol 2(2):224–242
Richardson BW (1869) Lectures on experimental and practical medicine. Physiological research on alcohols. Med Times Gaz 2 (1869):703–706
Hansch C, Muir RM, Fujita T, Maloney PP, Geiger F, Streich M (1963) The correlation of biological activity of plant growth regulators and chloromycetin derivatives with Hammett constants and partition coefficients. J Am Chem Soc 85(18):2817–2824
Taft RW, Lewis IC (1959) Evaluation of resonance effects on reactivity by application of the linear inductive energy relationship. V. Concerning a σR scale of resonance effects 1,2. J Am Chem Soc 81(20):5343–5352
Shen J, Xu L, Fang H, Richard AM, Bray JD, Judson RS et al (2013) EADB: an estrogenic activity database for assessing potential endocrine activity. Toxicol Sci 135(2):277–291
Ding D, Xu L, Fang H, Hong H, Perkins R, Harris S et al (2010) The EDKB: an established knowledge base for endocrine disrupting chemicals. BMC Bioinformatics 11(Suppl 6):S5
Shi L, Tong W, Fang H, Xie Q, Hong H, Perkins R et al (2002) An integrated “4-phase” approach for setting endocrine disruption screening priorities –phase I and II predictions of estrogen receptor binding affinity. SAR QSAR Environ Res 13(1):69–88
Tong W, Fang H, Hong H, Xie Q, Perkins R, Anson J et al (2003) Regulatory application of SAR/QSAR for priority setting of endocrine disruptors: a perspective*. Pure Appl Chem 75(11):2375–2388
Tong W, Hong H, Xie Q, Shi L, Fang H, Perkins R (2005) Assessing QSAR limitations-A regulatory perspective. Curr Comput Aided Drug Des 1(2):195–205
Tong W, Perkins R, Fang H, Hong H, Xie Q, Branham W et al (2002) Development of quantitative structure-activity relationships (QSARs) and their use for priority setting in the testing strategy of endocrine disruptors. Regul Res Perspect 1(3):1–13
Hong H, Neamati N, Wang S, Nicklaus MC, Mazumder A, Zhao H et al (1997) Discovery of HIV-1 integrase inhibitors by pharmacophore searching. J Med Chem 40(6):930–936
Hong H, Neamati N, Winslow HE, Christensen JL, Orr A, Pommier Y et al (1998) Identification of HIV-1 integrase inhibitors based on a four-point pharmacophore. Antivir Chem Chemother 9(6):461–472
Neamati N, Hong H, Sunder S, Milne GW, Pommier Y (1997) Potent inhibitors of human immunodeficiency virus type 1 integrase: identification of a novel four-point pharmacophore and tetracyclines as novel inhibitors. Mol Pharmacol 52(6):1041–1055
Neamati N, Hong H, Mazumder A, Wang S, Sunder S, Nicklaus MC et al (1997) Depsides and depsidones as inhibitors of HIV-1 integrase: discovery of novel inhibitors through 3D database searching. J Med Chem 40(6):942–951
Nicklaus MC, Neamati N, Hong H, Mazumder A, Sunder S, Chen J et al (1997) HIV-1 integrase pharmacophore: discovery of inhibitors through three-dimensional database searching. J Med Chem 40(6):920–929
Ng HW, Zhang W, Shu M, Luo H, Ge W, Perkins R et al (2014) Competitive molecular docking approach for predicting estrogen receptor subtype alpha agonists and antagonists. BMC Bioinformatics 15(Suppl 11):S4
Shen J, Zhang W, Fang H, Perkins R, Tong W, Hong H (2013) Homology modeling, molecular docking, and molecular dynamics simulations elucidated alpha-fetoprotein binding modes. BMC Bioinformatics 14(Suppl 14):S6
Tie Y, McPhail B, Hong H, Pearce BA, Schnackenberg LK, Ge W et al (2012) Modeling chemical interaction profiles: II. Molecular docking, spectral data-activity relationship, and structure-activity relationship models for potent and weak inhibitors of cytochrome P450 CYP3A4 isozyme. Molecules 17(3):3407
Hong H, Fang H, Xie Q, Perkins R, Sheehan DM, Tong W (2003) Comparative molecular field analysis (CoMFA) model using a large diverse set of natural, synthetic and environmental chemicals for binding to the androgen receptor. SAR QSAR Environ Res 14(5–6):373–388
Hong H, Tong W, Fang H, Shi L, Xie Q, Wu J et al (2002) Prediction of estrogen receptor binding for 58,000 chemicals using an integrated system of a tree-based model with structural alerts. Environ Health Perspect 110(1):29–36
Tong W, Hong H, Fang H, Xie Q, Perkins R (2003) Decision forest: combining the predictions of multiple independent decision tree models. J Chem Inf Comput Sci 43(2):525–531
Tong W, Xie Q, Hong H, Shi L, Fang H, Perkins R et al (2004) Using decision forest to classify prostate cancer samples on the basis of SELDI-TOF MS data: assessing chance correlation and prediction confidence. Environ Health Perspect 112(16):1622–1627
Hong H, Tong W, Perkins R, Fang H, Xie Q, Shi L (2004) Multiclass decision forest-a novel pattern recognition method for multiclass classification in microarray data analysis. DNA Cell Biol 23(10):685–694
Xie Q, Ratnasinghe LD, Hong H, Perkins R, Tang ZZ, Hu N et al (2005) Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel method. BMC Bioinformatics 6(Suppl 2):S4
Hong H, Tong W, Xie Q, Fang H, Perkins R (2005) An in silico ensemble method for lead discovery: decision forest. SAR QSAR Environ Res 16(4):339–347
McPhail B, Tie Y, Hong H, Pearce BA, Schnackenberg LK, Ge W et al (2012) Modeling chemical interaction profiles: I. Spectral data-activity relationship and structure-activity relationship models for inhibitors and non-inhibitors of cytochrome P450 CYP3A4 and CYP2D6 isozymes. Molecules 17(3):3383–3406
Chen M, Hong H, Fang H, Kelly R, Zhou G, Borlak J et al (2013) Quantitative structure-activity relationship models for predicting drug-induced liver injury based on FDA-approved drug labeling annotation and using a large collection of drugs. Toxicol Sci 136(1):242–249
Liu J, Mansouri K, Judson RS, Martin MT, Hong H, Chen M et al (2015) Predicting hepatotoxicity using toxcast in vitro bioactivity and chemical structure. Chem Res Toxicol 28(4):738–751
Blair RM, Fang H, Branham WS, Hass BS, Dial SL, Moland CL et al (2000) The estrogen receptor relative binding affinities of 188 natural and xenochemicals: structural diversity of ligands. Toxicol Sci 54(1):138–153
Fang H, Tong W, Branham WS, Moland CL, Dial SL, Hong H et al (2003) Study of 202 natural, synthetic, and environmental chemicals for binding to the androgen receptor. Chem Res Toxicol 16(10):1338–1358
Zhang M, Chen M, Tong W (2012) Is toxicogenomics a more reliable and sensitive biomarker than conventional indicators from rats to predict drug-induced liver injury in humans? Chem Res Toxicol 25(1):122–129
Chen M, Bisgin H, Tong L, Hong H, Fang H, Borlak J et al (2014) Toward predictive models for drug-induced liver injury in humans: are we there yet? Biomark Med 8(2):201–213
Chen M, Borlak J, Tong W (2014) Predicting idiosyncratic drug-induced liver injury – some recent advances. Expert Rev Gastroenterol Hepatol 8(7):721–723
Chen M, Zhang J, Wang Y, Liu Z, Kelly R, Zhou G et al (2013) The liver toxicity knowledge base: a systems approach to a complex end point. Clin Pharmacol Ther 93(5):409–412
Chen M, Vijay V, Shi Q, Liu Z, Fang H, Tong W (2011) FDA-approved drug labeling for the study of drug-induced liver injury. Drug Discov Today 16(15–16):697–703
Chen M, Zhang M, Borlak J, Tong W (2012) A decade of toxicogenomic research and its contribution to toxicological science. Toxicol Sci 130(2):217–228
Chen M, Borlak J, Tong W (2013) High lipophilicity and high daily dose of oral medications are associated with significant risk for drug-induced liver injury. Hepatology 58(1):388–396
Yu K, Geng X, Chen M, Zhang J, Wang B, Ilic K et al (2014) High daily dose and being a substrate of cytochrome P450 enzymes are two important predictors of drug-induced liver injury. Drug Metab Dispos 42(4):744–750
Chen M, Tung CW, Shi Q, Guo L, Shi L, Fang H et al (2014) A testing strategy to predict risk for drug-induced liver injury in humans using high-content screen assays and the “rule-of-two” model. Arch Toxicol 88(7):1439–1449
Chen M, Shi L, Kelly R, Perkins R, Fang H, Tong W (2011) Selecting a single model or combining multiple models for microarray-based classifier development? – a comparative analysis based on large and diverse datasets generated from the MAQC-II project. BMC Bioinformatics 12(Suppl 10):S3
Yang Z-Z, Wang C-S (2003) Atom-bond electronegativity equalization method and its applications based on density functional theory. J Theor Comput Chem 2(02):273–299
Arulmozhiraja S, Morita M (2004) Structure-activity relationships for the toxicity of polychlorinated dibenzofurans: approach through density functional theory-based descriptors. Chem Res Toxicol 17(3):348–356
Liu SS, Cui SH, Yin DQ, Shi YY, Wang LS (2003) QSAR studies on the COX-2 inhibition by 3, 4-diarylcycloxazolones based on MEDV descriptor. Chin J Chem 21(11):1510–1516
Chiu T-L, So S-S (2004) Development of neural network QSPR models for Hansch substituent constants. 1. Method and validations. J Chem Inf Comput Sci 44(1):147–153
Chiu T-L, So S-S (2004) Development of neural network QSPR models for hansch substituent constants. 2. Applications in QSAR studies of HIV-1 reverse transcriptase and dihydrofolate reductase inhibitors. J Chem Inf Comput Sci 44(1):154–160
Zhihua L, Yuzhang W, Xuejun Q, Yuegang Z, Bing N, Ying W (2002) Use of a novel electrotopological descriptor for the prediction of biological activity of peptide analogues. Lett Pept Sci 9(6):273–281
Agrawal V, Mishra K, Khadikar P (2003) Multivariate analysis for modelling some antibacterial agents. Oxid Commun 26(1):14–21
McGregor MJ, Pallai PV (1997) Clustering of large databases of compounds: using the MDL “Keys” as structural descriptors. J Chem Inf Comput Sci 37(3):443–448
Brown RD, Martin YC (1997) The information content of 2D and 3D structural descriptors relevant to ligand-receptor binding. J Chem Inf Comput Sci 37(1):1–9
Matter H, Pötter T (1999) Comparing 3D pharmacophore triplets and 2D fingerprints for selecting diverse compound subsets. J Chem Inf Comput Sci 39(6):1211–1225
Hong H, Xie Q, Ge W, Qian F, Fang H, Shi L et al (2008) Mold(2), molecular descriptors from 2D structures for chemoinformatics and toxicoinformatics. J Chem Inf Model 48(7):1337–1344
Draper NR, Smith H, Pownell E (1966) Applied regression analysis. Wiley, New York
Leffler J, Grunwald E (1963) Rates and equilibrium constants of organic reaction. Wiley, New York
Stanton DT, Jurs PC (1990) Development and use of charged partial surface area structural descriptors in computer-assisted quantitative structure-property relationship studies. Anal Chem 62(21):2323–2329
Rohrbaugh RH, Jurs PC (1987) Descriptions of molecular shape applied in studies of structure/activity and structure/property relationships. Anal Chim Acta 199:99–109
Nishihara T, Takatori S, Kitagawa Y, Hori S (2000) Estrogenic activities of 517 chemicals by yeast two-hybrid assay. J Health Sci
Safe S, Kim K (2008) Non-classical genomic estrogen receptor (ER)/specificity protein and ER/activating protein-1 signaling pathways. J Mol Endocrinol 41(5):263–275
Lathe R, Kotelevtsev Y (2014) Steroid signaling: ligand-binding promiscuity, molecular symmetry, and the need for gating. Steroids 82c:14–22
Ng HW, Perkins R, Tong W, Hong H (2014) Versatility or promiscuity: the estrogen receptors, control of ligand selectivity and an update on subtype selective ligands. Int J Env Res Public Health 11(9):8709–8742
Schug TT, Janesick A, Blumberg B, Heindel JJ (2011) Endocrine disrupting chemicals and disease susceptibility. J Steroid Biochem Mol Biol 127(3–5):204–215
Falconer IR, Chapman HF, Moore MR, Ranmuthugala G (2006) Endocrine-disrupting compounds: a review of their challenge to sustainable and safe water supply and water reuse. Environ Toxicol 21(2):181–191
Kitchen DB, Decornez H, Furr JR, Bajorath J (2004) Docking and scoring in virtual screening for drug discovery: methods and applications. Nat Rev Drug Discov 3(11):935–949
Huang N, Shoichet BK, Irwin JJ (2006) Benchmarking sets for molecular docking. J Med Chem 49(23):6789–6801
Kola I, Landis J (2004) Can the pharmaceutical industry reduce attrition rates? Nat Rev Drug Discov 3(8):711–716
Merlot C (2010) Computational toxicology – a tool for early safety evaluation. Drug Discov Today 15(1):16–22
Xu JJ, Kalgutkar AS, Will Y, Dykens J, Tengstrand E, Hsieh F (2009) Predicting drug-induced hepatotoxicity in vitro, in silico and in vivo approach. In: Faller B, Urban L (eds) Hit and lead profiling. pp 345–85
Greene N, Fisk L, Naven RT, Note RR, Patel ML, Pelletier DJ (2010) Developing structure–activity relationships for the prediction of hepatotoxicity. Chem Res Toxicol 23(7):1215–1222
Breiman L (2001) Random forests. Mach Learn 45(1):5–32
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Hong, H., Chen, M., Ng, H.W., Tong, W. (2016). QSAR Models at the US FDA/NCTR. In: Benfenati, E. (eds) In Silico Methods for Predicting Drug Toxicity. Methods in Molecular Biology, vol 1425. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3609-0_18
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DOI: https://doi.org/10.1007/978-1-4939-3609-0_18
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