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Understanding the metabolism of a compound by identifying which metabolites are formed during in vitro or in vivo studies—that is, “metabolite profiling”—is a critical part of the drug discovery and development process, from assisting in lead optimization to better understanding the pharmacology, pharmacokinetics, and toxicology of drug candidates. Regulatory authorities encourage the identification of differences in drug metabolism between and among preclinical animal species as early as possible during the drug development process; indeed, the discovery of a disproportionate, pharmacologically active, and/or toxic drug metabolite late in drug development can cause delays in development, approval, and marketing. Metabolite profiling is at an interesting interdisciplinary intersection with organic synthesis, experimental biology, bio-analytical chemistry, informatics, toxicology, intellectual property, regulatory science, business considerations, and more. The present chapter provides an overview of the rationale for metabolite profiling, with attention given to special aspects such as in silico metabolite prediction, quantitation of unknown metabolites, metabolite synthesis, profiling of enantioselective metabolite pathways, the future of metabolite profiling, and more.

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