Enhancing global and local decision making for chemical safety assessments through increasing the availability of data

References

• Amberg A, Harvey JS, Czich A, Spirkl H-P, Robinson S, White A, Elder DP. 2015. Do carboxylic/sulfonic acid halides really present a mutagenic and carcinogenic risk as impurities in final drug products? Org Process Res Dev. 19(11):1495–1506.
   Web of Science ®Google Scholar
• Ankley GT, Bennett RS, Erickson RJ, Hoff DJ, Hornung MW, Johnson RD, Mount DR, Nichols JW, Russom CL, Schmieder PK, et al. 2010. Adverse outcome pathways: a conceptual framework to support ecotoxicology research and risk assessment. Environ Toxicol Chem. 29(3):730–741.
   PubMed Web of Science ®Google Scholar
• AOPwiki. 2022. Type II iodothyronine deiodinase (DIO2) inhibition leading to altered amphibian metamorphosis [Internet]. [accessed 2022 Sep 30]. https://aopwiki.org/aops/190.
   Google Scholar
• Baran S, Brown P, Baudy A, Fitzpatrick SC, Frantz C, Fullerton A, Gan J, Hardwick RN, Hillgren KM, Kopec AK, et al. 2022. Perspectives on the evaluation and adoption of complex in vitro models in drug development: workshop with the FDA and the pharmaceutical industry (IQ MPS Affiliate). ALTEX. 39:297–314.
   Google Scholar
• Barber C, Cayley A, Hanser T, Harding A, Heghes C, Vessey JD, Werner S, Weiner SK, Wichard J, Giddings A, et al. 2016. Evaluation of a statistics-based Ames mutagenicity QSAR model and interpretation of the results obtained. Regul Toxicol Pharmacol. 76:7–20.
   PubMed Web of Science ®Google Scholar
• Barber C, Hanser T, Judson P, Williams R. 2017. Distinguishing between expert and statistical systems for application under ICH M7. Regul Toxicol Pharmacol. 84:124–130.
   PubMed Web of Science ®Google Scholar
• Basketter DA, Clewell H, Kimber I, Rossi A, Blaauboer B, Burrier R, Daneshian M, Eskes C, Goldberg A, Hasiwa N, et al. 2012. A roadmap for the development of alternative (non-animal) methods for systemic toxicity testing. ALTEX. 29(1):3–91.
   PubMedGoogle Scholar
• Bercu JP, Galloway SM, Parris P, Teasdale A, Masuda-Herrera M, Dobo K, Heard P, Kenyon M, Nicolette J, Vock E, et al. 2018. Potential impurities in drug substances: compound-specific toxicology limits for 20 synthetic reagents and by-products, and a class-specific toxicology limit for alkyl bromides. Regul Toxicol Pharmacol. 94:172–182.
   PubMed Web of Science ®Google Scholar
• Boobis A, Brown P, Cronin MTD, Edwards J, Galli CL, Goodman J, Jacobs A, Kirkland D, Luijten M, Marsaux C, et al. 2017. Origin of the TTC values for compounds that are genotoxic and/or carcinogenic and an approach for their re-evaluation. Crit Rev Toxicol. 47(8):710–732.
   Web of Science ®Google Scholar
• Bowes J, Brown AJ, Hamon J, Jarolimek W, Sridhar A, Waldron G, Whitebread S. 2012. Reducing safety-related drug attrition: the use of in vitro pharmacological profiling. Nat Rev Drug Discov. 11(12):909–922.
   PubMed Web of Science ®Google Scholar
• Cayley A, Foster R, Hill E, Kane S, Kocks G, Myden A, Newman D, Stalford S, Vessey J, Zarei R, et al. 2022. Development of a network of carcinogenicity adverse outcome pathways and its employment as an evidence framework for safety assessment. ALTEX. https://doi.org/10.14573/altex.2201311.
   Google Scholar
• Cheeseman MA, Machuga EJ, Bailey AB. 1999. A tiered approach to threshold of regulation. Food Chem Toxicol. 37(4):387–412.
   PubMed Web of Science ®Google Scholar
• FDA. 2017. FDA’s predictive toxicology roadmap [Internet]. [accessed 2022 Jul 26]. https://www.fda.gov/science-research/about-science-research-fda/fdas-predictive-toxicology-roadmap.
   Google Scholar
• Fischer I, Milton C, Wallace H. 2020. Toxicity testing is evolving!. Toxicol Res. 9(2):67–80.
   Web of Science ®Google Scholar
• Gold LS, Sawyer CB, Magaw R, Backman GM, De Veciana M, Levinson R, Hooper NK, Havender WR, Bernstein L, Peto R. 1984. A carcinogenic potency database of the standardized results of animal bioassays. Environ Health Perspect. 58:9–319.
   PubMed Web of Science ®Google Scholar
• Graham JC, Trejo-Martin A, Chilton ML, Kostal J, Bercu J, Beutner GL, Bruen US, Dolan DG, Gomez S, Hillegass J, et al. 2022. An evaluation of the occupational health hazards of peptide couplers. Chem Res Toxicol. 35(6):1011–1022.
   PubMed Web of Science ®Google Scholar
• Gunther WC, Kenyon MO, Cheung JR, Dugger RW, Dobo KL. 2017. Resolution of contradiction between in silico predictions and Ames test results for four pharmaceutically relevant impurities. Regul Toxicol Pharmacol. 91:68–76.
   PubMed Web of Science ®Google Scholar
• Chen S, Xue D, Chuai G, Yang Q, Liu Q. 2021. FL-QSAR: a federated learning-based QSAR prototype for collaborative drug discovery. Bioinform. 36:5492–5498.
   Google Scholar
• Hanser T, Barber C, Rosser E, Vessey JD, Webb SJ, Werner S. 2014. Self organising hypothesis networks: a new approach for representing and structuring SAR knowledge. J Cheminform. 6(1):21.
   PubMedGoogle Scholar
• Hasselgren C, Bercu J, Cayley A, Cross K, Glowienke S, Kruhlak N, Muster W, Nicolette J, Reddy MV, Saiakhov R, et al. 2020. Management of pharmaceutical ICH M7 (Q)SAR predictions – the impact of model updates. Regul Toxicol Pharmacol. 118:104807.
   PubMed Web of Science ®Google Scholar
• ICCVAM. 2018. A strategic roadmap for establishing new approaches to evaluate the safety of chemicals and medical products in the United States [Internet]. [accessed 2022 Jul 26]. https://ntp.niehs.nih.gov/go/natl-strategy.
   Google Scholar
• ICH. 2017. ICH M7 guidelines [Internet]. [accessed 2022 Sep 23]. https://database.ich.org/sites/default/files/M7_R1_Guideline.pdf.
   Google Scholar
• Jayasekara PS, Skanchy SK, Kim MT, Kumaran G, Mugabe BE, Woodard LE, Yang J, Zych AJ, Kruhlak NL. 2021. Assessing the impact of expert knowledge on ICH M7 (Q)SAR predictions. Is expert review still needed? Regul Toxicol Pharmacol. 125:105006.
   PubMed Web of Science ®Google Scholar
• Judson PN, Marchant CA, Vessey JD. 2003. Using argumentation for absolute reasoning about the potential toxicity of chemicals. J Chem Inf Comput Sci. 43(5):1364–1370.
   PubMedGoogle Scholar
• Karmaus AL, Mansouri K, To KT, Blake B, Fitzpatrick J, Strickland J, Patlewicz G, Allen D, Casey W, Kleinstreuer N. 2022. Evaluation of variability across rat acute oral systemic toxicity studies. Toxicol Sci. 188(1):34–47.
   PubMed Web of Science ®Google Scholar
• Knapen D, Angrish MM, Fortin MC, Katsiadaki I, Leonard M, Margiotta-Casaluci L, Munn S, O'Brien JM, Pollesch N, Smith LC, et al. 2018. Adverse outcome pathway networks I: development and applications: advancing adverse outcome pathway networks. Environ Toxicol Chem. 37(6):1723–1733.
   PubMed Web of Science ®Google Scholar
• Landsiedel R, Birk B, Funk-Weyer D. 2022. The evolution of regulatory toxicology: where is the gardener? Altern Lab Anim. 50(4):255–262.
   PubMed Web of Science ®Google Scholar
• Lhasa Limited. 2022. Collaboration & data sharing initiatives [Internet]. [accessed 2022 Sep 30]. https://www.lhasalimited.org/Initiatives/.
   Google Scholar
• Lhasa Limited Carcinogenicity Database. 2022. [accessed 2022 Jul 11]. https://carcdb.lhasalimited.org/.
   Google Scholar
• López-Rodríguez R, McManus JA, Murphy NS, Ott MA, Burns MJ. 2020. Pathways for N -nitroso compound formation: secondary amines and beyond. Org Process Res Dev. 24(9):1558–1585.
   Web of Science ®Google Scholar
• Macmillan DS, Chilton ML, Gao Y, Kern PS, Schneider SN. 2022. How to resolve inconclusive predictions from defined approaches for skin sensitisation in OECD Guideline No. 497. Regul Toxicol Pharmacol. 135:105248.
   PubMed Web of Science ®Google Scholar
• Macmillan DS, Chilton ML, Hillegass J. 2022. Improvements to in silico skin sensitisation predictions through privacy-preserving data sharing. Regul Toxicol Pharmacol. 137:105292.
   PubMed Web of Science ®Google Scholar
• Munro IC, Ford RA, Kennepohl E, Sprenger JG. 1996. Correlation of structural class with no-observed-effect levels: a proposal for establishing a threshold of concern. Food Chem Toxicol. 34(9):829–867.
   PubMed Web of Science ®Google Scholar
• Natsch A. 2021. A triangular approach for the validation of new approach methods for skin sensitization. ALTEX. 38:669–677.
   PubMedGoogle Scholar
• NIH. 2022. Carcinogenic potency database (CPDB) [Internet]. [accessed 2022 Jul 11]. https://www.nlm.nih.gov/databases/download/cpdb.html.
   Google Scholar
• OECD. 2017. Guidance document for the use of adverse outcome pathways in developing integrated approaches to testing and assessment (IATA) [Internet]. [place unknown]: OECD.
   Google Scholar
• OECD. 2021. Guideline no. 497: defined approaches on skin sensitisation [Internet]. [place unknown]: OECD.
   Google Scholar
• Parish ST, Aschner M, Casey W, Corvaro M, Embry MR, Fitzpatrick S, Kidd D, Kleinstreuer NC, Lima BS, Settivari RS, et al. 2020. An evaluation framework for new approach methodologies (NAMs) for human health safety assessment. Regul Toxicol Pharmacol. 112:104592.
   PubMed Web of Science ®Google Scholar
• Patel M, Kranz M, Munoz-Muriedas J, Harvey JS, Giddings A, Swallow S, Fellows M, Naven R, Werner A-L, Yeo DJ, et al. 2018. A pharma-wide approach to address the genotoxicity prediction of primary aromatic amines. Comput Toxicol. 7:27–35.
   Google Scholar
• Pellizzaro ML, Covey-Crump EM, Fisher J, Werner A-LD, Williams RV. 2015. Investigating a relationship between the mutagenicity of arylboronic acids and 11 B NMR chemical shifts. Chem Res Toxicol. 28(7):1422–1426.
   PubMed Web of Science ®Google Scholar
• Peto R, Pike MC, Bernstein L, Gold LS, Ames BN. 1984. The TD50: a proposed general convention for the numerical description of the carcinogenic potency of chemicals in chronic-exposure animal experiments. Environ Health Perspect. 58:1–8.
   PubMed Web of Science ®Google Scholar
• Ponting DJ, Burns MJ, Foster RS, Hemingway R, Kocks G, MacMillan DS, Shannon-Little AL, Tennant RE, Tidmarsh JR, Yeo DJ. 2022. Use of Lhasa Limited products for the in silico prediction of drug toxicity. In: Benfenati E, editor. In silico methods for predicting drug toxicity [Internet]. Vol. 2425. New York (NY): Springer US; p. 435–478.
   Google Scholar
• Ram RN, Gadaleta D, Allen TEH. 2022. The role of ‘big data’ and ‘in silico’ New Approach Methodologies (NAMs) in ending animal use – a commentary on progress. Comput Toxicol. 23:100232.
   Google Scholar
• Robinson S, Delongeas J-L, Donald E, Dreher D, Festag M, Kervyn S, Lampo A, Nahas K, Nogues V, Ockert D, et al. 2008. A European pharmaceutical company initiative challenging the regulatory requirement for acute toxicity studies in pharmaceutical drug development. Regul Toxicol Pharmacol. 50(3):345–352.
   PubMed Web of Science ®Google Scholar
• SAAOP. 2022. AOP-Wiki [Internet]. [accessed 2022 Jun 9]. http://aopwiki.org.
   Google Scholar
• Stalford SA, Cayley AN, de Oliveira AAF. 2021. Employing an adverse outcome pathway framework for weight-of-evidence assessment with application to the ICH S1B guidance addendum. Regul Toxicol Pharmacol. 127:105071.
   PubMed Web of Science ®Google Scholar
• Thresher A, Gosling JP, Williams R. 2019. Generation of TD50 values for carcinogenicity study data. Toxicol Res. 8(5):696–703.
   Web of Science ®Google Scholar
• UK Home Office. 2021. Statistics of scientific procedures on living animals [Internet]. Great Britain; [accessed 2022 Sep 30]. https://www.gov.uk/government/statistics/statistics-of-scientific-procedures-on-living-animals-great-britain-2021.
   Google Scholar
• US EPA. 2022. Exploring ToxCast data: downloadable data [Internet]. [accessed 2022 Sep 30]. https://www.epa.gov/chemical-research/exploring-toxcast-data-downloadable-data.
   Google Scholar
• WikiKaptis. 2022. [accessed 2022 Jul 11]. https://wikikaptis.lhasacloud.org/.
   Google Scholar
• Wilkinson MD, Dumontier M, Aalbersberg I, Appleton G, Axton M, Baak A, Blomberg N, Boiten J-W, da Silva Santos LB, Bourne PE, et al. 2016. The FAIR guiding principles for scientific data management and stewardship. Sci Data. 3(1):160018.
   PubMed Web of Science ®Google Scholar
• Williams RV, DeMarini DM, Stankowski LF, Escobar PA, Zeiger E, Howe J, Elespuru R, Cross KP. 2019. Are all bacterial strains required by OECD mutagenicity test guideline TG471 needed? Mutat Res Genet Toxicol Environ Mutagen. 848:503081.
   PubMed Web of Science ®Google Scholar