A multiparametric organ toxicity predictor for drug discovery

References

• Aarsland D, Marsh L, Schrag A. 2009. Neuropsychiatric symptoms in Parkinson's disease. Mov Disord. 24(15):2175–2186.
   PubMed Web of Science ®Google Scholar
• Amur S, LaVange L, Zineh I, Buckman ‐Garner S, Woodcock J. 2015. Biomarker qualification: toward a multiple stakeholder framework for biomarker development, regulatory acceptance, and utilization. Clin Pharmacol Ther. 98(1):34–46.
   PubMed Web of Science ®Google Scholar
• Attene-Ramos MS, Miller N, Huang R, Michael S, Itkin M, Kavlock RJ, Austin CP, Shinn P, Simeonov A, Tice RR, et al. 2013. The Tox21 robotic platform for the assessment of environmental chemicals–from vision to reality. Drug Discov Today. 18(15–16):716–723.
   PubMed Web of Science ®Google Scholar
• Barabási A-L, Gulbahce N, Loscalzo J. 2011. Network medicine: a network-based approach to human disease. Nat Rev Genet. 12(1):56–68.
   PubMed Web of Science ®Google Scholar
• Beatty C, Basinger G, Dully C, Bocek R. 1966. Comparison of red and white voluntary skeletal muscles of several species of primates. J Histochem Cytochem. 14(8):590–600.
   Web of Science ®Google Scholar
• Bessey OA, Lowry OH, Brock MJ. 1946. A method for the rapid determination of alkaline phosphatase with five cubic millimeters of serum. J Biol Chem. 164:321–329.
   PubMed Web of Science ®Google Scholar
• Blaauboer BJ, Boekelheide K, Clewell HJ, Daneshian M, Dingemans MM, Goldberg AM, Leist M. 2012. The use of biomarkers of toxicity for integrating in vitro hazard estimates into risk assessment for humans. Altex. 29(4):411–425.
   PubMedGoogle Scholar
• Bolten BM, DeGregorio T. 2002. Trends in development cycles. Nat Rev Drug Discov. 1(5):335–336.
   PubMed Web of Science ®Google Scholar
• Borenfreund E, Babich H, Martin-Alguacil N. 1988. Comparisons of two in vitro cytotoxicity assays—the neutral red (NR) and tetrazolium MTT tests. Toxicol In Vitro. 2(1):1–6.
   PubMed Web of Science ®Google Scholar
• Bowen WJ, Kerwin TD. 1956. A simple method for assaying adenosine triphosphate and adenosine diphosphate in mixtures. J Biol Chem. 220(1):9–14.
   PubMed Web of Science ®Google Scholar
• Brennan FR, Baumann A, Blaich G, de Haan L, Fagg R, Kiessling A, Kronenberg S, Locher M, Milton M, Tibbitts J, et al. 2015. Nonclinical safety testing of biopharmaceuticals–Addressing current challenges of these novel and emerging therapies. Regul Toxicol Pharm. 73(1):265–275.
   PubMed Web of Science ®Google Scholar
• Bugrim A, Nikolskaya T, Nikolsky Y. 2004. Early prediction of drug metabolism and toxicity: systems biology approach and modeling. Drug Discov Today. 9(3):127–135.
   PubMed Web of Science ®Google Scholar
• Bussiere JL, Martin P, Horner M, Couch J, Flaherty M, Andrews L, Beyer J, Horvath C. 2009. Alternative strategies for toxicity testing of species-specific biopharmaceuticals. Int J Toxicol. 28(3):230–253.
   PubMed Web of Science ®Google Scholar
• Chen C. 2004. Humidity in plant tissue culture vessels. Biosyst Eng. 88(2):231–241.
   Web of Science ®Google Scholar
• Chen B, Butte AJ. 2013. Network medicine in disease analysis and therapeutics. Clin Pharmacol Ther. 94(6):627–629.
   PubMed Web of Science ®Google Scholar
• Collins FS, Gray GM, Bucher JR. 2008. Transforming environmental health protection. Science (New York, NY). 319(5865):906.
   Google Scholar
• Cragg GM, Newman DJ, Snader KM. 1997. Natural products in drug discovery and development. J Nat Prod. 60(1):52–60.
   PubMed Web of Science ®Google Scholar
• Cronin MT, Jaworska JS, Walker JD, Comber MH, Watts CD, Worth AP. 2003. Use of QSARs in international decision-making frameworks to predict health effects of chemical substances. Environ Health Persp. 111(10):1391. p
   PubMed Web of Science ®Google Scholar
• De Logu A, Borgna R, Uda P, Sanna A, Pellerano ML, Saddi B. 2003. The 2, 3-bis (2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide (XTT) assay as rapid colorimetric method for determination of antibiotic susceptibility of clinical Mycobacterium tuberculosis isolates in liquid medium. Clin Lab. 49(7–8):357–365.
   PubMedGoogle Scholar
• DeFina PA, Moser RS, Glenn M, Lichtenstein JD, Fellus J. 2013. Alzheimer's disease clinical and research update for health care practitioners. J Aging Res. 2013:1–9.
   Google Scholar
• Dix DJ, Houck KA, Martin MT, Richard AM, Setzer RW, Kavlock RJ. 2007. The ToxCast program for prioritizing toxicity testing of environmental chemicals. Toxicol Sci. 95(1):5–12.
   PubMed Web of Science ®Google Scholar
• Dixit R, Boelsterli UA. 2007. Healthy animals and animal models of human disease (s) in safety assessment of human pharmaceuticals, including therapeutic antibodies. Drug Discov Today. 12(7–8):336–342.
   PubMed Web of Science ®Google Scholar
• Dominguez-Urban I. 1997. Harmonization in the regulation of pharmaceutical research and human rights: the need to think globally. Cornell Int'l LJ. 30:245.
   PubMed Web of Science ®Google Scholar
• Ekins S. 2007. Computational toxicology: risk assessment for pharmaceutical and environmental chemicals. Hoboken (NJ): John Wiley & Sons.
   Google Scholar
• Engkvist O, Wrede P, Rester U. 2003. Prediction of CNS activity of compound libraries using substructure analysis. J Chem Inf Comput Sci. 43(1):155–160.
   PubMedGoogle Scholar
• Freimoser FM, Jakob CA, Aebi M, Tuor U. 1999. The MTT [3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide] assay is a fast and reliable method for colorimetric determination of fungal cell densities. Appl Environ Microb. 65(8):3727–3729.
   PubMed Web of Science ®Google Scholar
• Frings CS, Fendley TW, Dunn RT, Queen CA. 1972. Improved determination of total serum lipids by the sulfo-phospho-vanillin reaction. Clin Chem. 18(7):673–674.
   PubMed Web of Science ®Google Scholar
• Garg P, Verma J. 2006. In silico prediction of blood brain barrier permeability: an artificial neural network model. J Chem Inf Model. 46(1):289–297.
   PubMed Web of Science ®Google Scholar
• Giles KW, Myers A. 1965. An improved diphenylamine method for the estimation of deoxyribonucleic acid. Nature. 206(4979):93–93.
   PubMed Web of Science ®Google Scholar
• Grunert R, Phillips P. 1951. A modification of the nitroprusside method of analysis for glutathione. Arch Biochem. 30(2):217–225.
   PubMedGoogle Scholar
• Hartung T. 2018. Perspectives on in vitro to in vivo extrapolations. Appl Vitro Tox. 4(4):305–316.
   PubMedGoogle Scholar
• Hartung T, Van Vliet E, Jaworska J, Bonilla L, Skinner N, Thomas R. 2012. Systems toxicology. ALTEX-Altern Anim Ex. 29(2):119–128.
   PubMed Web of Science ®Google Scholar
• Hasan A, Chakrobarty S, Chakrovorty R, Nabi A. 2014. Application of biotechnology and bioinformatics in drug designing and discovery. DOI:10.1201/b17104–15.
   Google Scholar
• Huang R, Xia M, Cho M-H, Sakamuru S, Shinn P, Houck KA, Dix DJ, Judson RS, Witt KL, Kavlock RJ, et al. 2011. Chemical genomics profiling of environmental chemical modulation of human nuclear receptors. Environ Health Persp. 119(8):1142.
   PubMed Web of Science ®Google Scholar
• Huang R, Xia M, Sakamuru S, Zhao J, Shahane SA, Attene-Ramos M, Zhao T, Austin CP, Simeonov A. 2016. Modelling the Tox21 10 K chemical profiles for in vivo toxicity prediction and mechanism characterization. Nat Commun. 7(1):10425.
   PubMedGoogle Scholar
• Humphreys WG, Will Y, Guengerich FP. 2016. Toxicology strategies for drug Discovery-Present and future: introduction. Washington, DC: ACS Publications.
   Google Scholar
• Ivanov SM, Lagunin AA, Rudik AV, Filimonov DA, Poroikov VV. 2017. ADVERPred–Web service for prediction of adverse effects of drugs. J Chem Inf Model. 58(1):8–11.
   Google Scholar
• Kakkar P, Das B, Viswanathan PN. 1984. A modified spectrophotometric assay of superoxide dismutase. Indian J Biochem Biophys. 21(2):130–2.
   Google Scholar
• Kavlock RJ, Ankley G, Blancato J, Breen M, Conolly R, Dix D, Houck K, Hubal E, Judson R, Rabinowitz J, et al. 2008. Computational toxicology—a state of the science mini review. Toxicol Sci. 103(1):14–27.
   PubMed Web of Science ®Google Scholar
• Kaznessis YN, Snow ME, Blankley CJ. 2001. Prediction of blood-brain partitioning using Monte Carlo simulations of molecules in water. J Comput Aid Mol Des. 15(8):697–708.
   PubMed Web of Science ®Google Scholar
• Klaeger S, Heinzlmeir S, Wilhelm M, Polzer H, Vick B, Koenig P-A, Reinecke M, Ruprecht B, Petzoldt S, Meng C, et al. 2017. The target landscape of clinical kinase drugs. Science. 358(6367):eaan4368.
   PubMed Web of Science ®Google Scholar
• Kohonen T. 2006. Self-organizing neural projections. Neural Netw. 19(6–7):723–733.
   PubMed Web of Science ®Google Scholar
• Lednicer D. 2006. New drug discovery and development. Hoboken (NJ): John Wiley & Sons.
   Google Scholar
• Lima BS, Videira MA. 2018. Toxicology and biodistribution: the clinical value of animal biodistribution studies. Mol Ther. 8:183–197.
   Web of Science ®Google Scholar
• Lowry OH, Rosebrough NJ, Farr AL, Randall RJ. 1951. Protein measurement with the Folin phenol reagent. J Biol Chem. 193(1):265–275.
   PubMed Web of Science ®Google Scholar
• Luck H, Peroxidase I. 1963. Of Enzymatic Analysis: New York (NY): Academic Press Inc.
   Google Scholar
• Malich G, Markovic B, Winder C. 1997. The sensitivity and specificity of the MTS tetrazolium assay for detecting the in vitro cytotoxicity of 20 chemicals using human cell lines. Toxicology. 124(3):179–192.
   PubMed Web of Science ®Google Scholar
• Matheis K, Laurie D, Andriamandroso C, Arber N, Badimon L, Benain X, Bendjama K, Clavier I, Colman P, Firat H, et al. 2011. A generic operational strategy to qualify translational safety biomarkers. Drug Discov Today. 16(13–14):600–608.
   PubMed Web of Science ®Google Scholar
• Matthews EJ, Benz RD, Contrera JF. 2000. Use of toxicological information in drug design. J Mol Graph Model. 18(6):605–15.
   Google Scholar
• Mavis RD, Stellwagen E. 1968. Purification and subunit structure of glutathione reductase from bakers' yeast. J Biol Chem. 243(4):809–814.
   PubMed Web of Science ®Google Scholar
• Mehta N, Ozick L, Gbadehan E. 2010. Drug-induced hepatotoxicity. State U New-York Med J. (7):51–57.
   Google Scholar
• Merlot C. 2010. Computational toxicology—a tool for early safety evaluation. Drug Discov Today. 15(1–2):16–22.
   PubMed Web of Science ®Google Scholar
• Mezbaum W. 1939. Estimation of RNA by orcinol method. J Physiol Chem. 258:117–120.
   Google Scholar
• Murphy RF. 2011. An active role for machine learning in drug development. Nat Chem Biol. 7(6):327.
   PubMed Web of Science ®Google Scholar
• Muster W, Breidenbach A, Fischer H, Kirchner S, Müller L, Pähler A. 2008. Computational toxicology in drug development. Drug Discov Today. 13(7–8):303–310.
   PubMed Web of Science ®Google Scholar
• Ohkawa H, Ohishi N, Yagi K. 1979. Assay for lipid peroxides in animal tissues by thiobarbituric acid reaction. Anal Biochem. 95(2):351–358.
   PubMed Web of Science ®Google Scholar
• Paglia DE, Valentine WN. 1967. Studies on the quantitative and qualitative characterization of erythrocyte glutathione peroxidase. J Lab Clin Med. 70(1):158–169.
   PubMed Web of Science ®Google Scholar
• Pai VB, Nahata MC. 2000. Cardiotoxicity of chemotherapeutic agents: incidence, treatment and prevention. Drug Saf. 22(4):263–302.
   PubMed Web of Science ®Google Scholar
• Park N. 2013. Last Updated November 3, 2014 Name: Linda S. Birnbaum.
   Google Scholar
• Patlewicz G, Rodford R, Walker JD. 2003. Quantitative structure‐activity relationships for predicting mutagenicity and carcinogenicity. Environ Toxicol Chem. 22(8):1885–1893.
   PubMed Web of Science ®Google Scholar
• Piotrowski PL, Sumpter BG, Malling HV, Wassom JS, Lu PY, Brothers RA, Sega GA, Martin SA, Parang M. 2007. A toxicity evaluation and predictive system based on neural networks and wavelets. J Chem Inf Model. 47(2):676–685.
   PubMed Web of Science ®Google Scholar
• Pognan F. 2018. Detection, elimination, mitigation, and prediction of drug-induced liver injury in drug discovery Drug-Induced Liver Toxicity. Berlin (Germany): Springer. p. 21–43.
   Google Scholar
• Quinn P, White I. 1968. Distribution of adenosinetriphosphatase activity in ram and bull spermatozoa. J Reprod Fertil. 15(3):449–452.
   PubMedGoogle Scholar
• Rägo L, Santoso B. 2008. Drug regulation: history, present and future. Drug Benefits Risks: Int Textbook Clin Phar. 2:65–77.
   Google Scholar
• Reitz C. 2014. Genomic insights into the etiology of Alzheimer’s disease: a review. Advances in genomics & genetics. 4:59–66.
   Google Scholar
• Romano JD, Tatonetti NP. 2019. Informatics and computational methods in natural product drug discovery: a review and perspectives. Front Genet. 10:368.
   PubMed Web of Science ®Google Scholar
• Rose K, Hall LH, Kier LB. 2002. Modeling blood-brain barrier partitioning using the electrotopological state. J Chem Inf Comp Sci. 42(3):651–666.
   PubMedGoogle Scholar
• Shukla SJ, Huang R, Austin CP, Xia M. 2010. The future of toxicity testing: a focus on in vitro methods using a quantitative high-throughput screening platform. Drug Discov Today. 15(23–24):997–1007.
   PubMed Web of Science ®Google Scholar
• Suke SG, Kosta P, Negi H. 2015. Role of pharmacovigilance in India: An overview. Online J Public Health Inform. 7(2):e223.
   PubMedGoogle Scholar
• Tice RR, Austin CP, Kavlock RJ, Bucher JR. 2013. Improving the human hazard characterization of chemicals: a Tox21 update. Environ Health Persp. 121(7):756.
   PubMed Web of Science ®Google Scholar
• Tong W, Cao X, Harris S, Sun H, Fang H, Fuscoe J, Harris A, Hong H, Xie Q, Perkins R, et al. 2003. ArrayTrack–supporting toxicogenomic research at the US food and drug administration national center for toxicological research. Environ Health Persp. 111(15):1819.
   PubMed Web of Science ®Google Scholar
• Ukeda H, Kawana D, Maeda S, Sawamura M. 1999. Spectrophotometric assay for superoxide dismutase based on the reduction of highly water-soluble tetrazolium salts by xanthine-xanthine oxidase. Biosci Biotech Bioch. 63(3):485–488.
   PubMed Web of Science ®Google Scholar
• Valerio LG. 2011. In silico toxicology models and databases as FDA Critical Path Initiative toolkits. Hum Genomics. 5(3):200.
   PubMedGoogle Scholar
• Vashishtha SC, Hawes EM, McCann DJ, Ghosheh O, Hogg L. 2002. Quaternary ammonium-linked glucuronidation of 1-substituted imidazoles by liver microsomes: interspecies differences and structure-metabolism relationships. Drug Metab Dispos. 30(10):1070–1076.
   PubMed Web of Science ®Google Scholar
• Worth AP, Cronin MT. 2003. The use of discriminant analysis, logistic regression and classification tree analysis in the development of classification models for human health effects. J Mol Struct. 622(1–2):97–111.
   Web of Science ®Google Scholar
• Yolken RH. 1978. ELISA: enzyme-linked immunosorbent assay. Hosp Pract. 13(12):121–127.
   PubMed Web of Science ®Google Scholar
• Zheng X, Ekins S, Raufman J-P, Polli JE. 2009. Computational models for drug inhibition of the human apical sodium-dependent bile acid transporter. Mol Pharmaceut. 6(5):1591–1603.
   PubMed Web of Science ®Google Scholar
• Zlatkis A, Zak B, Boyle AJ. 1953. A new method for the direct determination of serum cholesterol. Transl Res. 41(3):486–492.
   Google Scholar