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Wang S, Ballard TE, Christopher LJ, Foti RS, Gu C, Khojasteh SC, Liu J, Ma S, Ma B, Obach RS, Schadt S, Zhang Z, Zhang D. The Importance of Tracking "Missing" Metabolites: How and Why? J Med Chem 2023; 66:15586-15612. [PMID: 37769129 DOI: 10.1021/acs.jmedchem.3c01293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
Technologies currently employed to find and identify drug metabolites in complex biological matrices generally yield results that offer a comprehensive picture of the drug metabolite profile. However, drug metabolites can be missed or are captured only late in the drug development process. This could be due to a variety of factors, such as metabolism that results in partial loss of the molecule, covalent bonding to macromolecules, the drug being metabolized in specific human tissues, or poor ionization in a mass spectrometer. These scenarios often draw a great deal of attention from chemistry, safety assessment, and pharmacology. This review will summarize scenarios of missing metabolites, why they are missing, and associated uncovering strategies from deeper investigations. Uncovering previously missed metabolites can have ramifications in drug development with toxicological and pharmacological consequences, and knowledge of these can help in the design of new drugs.
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Affiliation(s)
- Shuai Wang
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - T Eric Ballard
- Takeda Development Center Americas, Inc., 35 Landsdowne St, Cambridge, Massachusetts 02139, United States
| | - Lisa J Christopher
- Department of Clinical Pharmacology, Pharmacometrics, Disposition & Bioanalysis, Bristol-Myers Squibb, Route 206 & Province Line Road, Princeton, New Jersey 08543, United States
| | - Robert S Foti
- Preclinical Development, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Chungang Gu
- Drug Metabolism and Pharmacokinetics, Biogen Inc., 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - S Cyrus Khojasteh
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Joyce Liu
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Shuguang Ma
- Drug Metabolism and Pharmacokinetics, Pliant Therapeutics, 260 Littlefield Avenue, South San Francisco, California 94080, United States
| | - Bin Ma
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - R Scott Obach
- Pharmacokinetics, Dynamics, and Metabolism, Pfizer, Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Simone Schadt
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacher Strasse 124, 4070 Basel, Switzerland
| | - Zhoupeng Zhang
- DMPK Oncology R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Donglu Zhang
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
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Takahashi RH, Grandner JM, Bobba S, Liu Y, Beroza P, Zhang D, Ma S. Novel Homodimer Metabolites of GDC-0994 via Cytochrome P450-Catalyzed Radical Coupling. Drug Metab Dispos 2020; 48:521-527. [PMID: 32234735 DOI: 10.1124/dmd.119.090019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 03/04/2020] [Indexed: 01/11/2023] Open
Abstract
Two novel homodimer metabolites were identified in rat samples collected during the in vivo study of GDC-0994. In this study, we investigated the mechanism of the formation of these metabolites. We generated and isolated the dimer metabolites using a biomimetic oxidation system for NMR structure elucidation to identify a symmetric dimer formed via carbon-carbon bond between two pyrazoles and an asymmetric dimer formed via an aminopyrazole-nitrogen to pyrazole-carbon bond. In vitro experiments demonstrated formation of these dimers was catalyzed by cytochrome P450 enzymes (P450s) with CYP3A4/5 being the most efficient. Using density functional theory, we determined these metabolites share a mechanism of formation, initiated by an N-H hydrogen atom abstraction by the catalytically active iron-oxo of P450s. Molecular modeling studies also show these dimer metabolites fit in the CYP3A4 binding site in low energy conformations with minimal protein rearrangement. Collectively, the results of these experiments suggest that formation of these two homodimer metabolites is mediated by CYP3A, likely involving activation of two GDC-0994 molecules by a single P450 enzyme and proceeding through a radical coupling mechanism. SIGNIFICANCE STATEMENT: These studies identified structures and enzymology for two distinct homodimer metabolites and indicate a novel biotransformation reaction mediated by CYP3A. In it, two molecules may bind within the active site and combine through radical coupling. The mechanism of dimerization was elucidated using density functional theory computations and supported by molecular modeling.
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Affiliation(s)
- Ryan H Takahashi
- Drug Metabolism and Pharmacokinetics (R.H.T., S.B., D.Z., S.M.) and Discovery Chemistry (J.M.G., Y.L., P.B.), Genentech, Inc., South San Francisco, California
| | - Jessica M Grandner
- Drug Metabolism and Pharmacokinetics (R.H.T., S.B., D.Z., S.M.) and Discovery Chemistry (J.M.G., Y.L., P.B.), Genentech, Inc., South San Francisco, California
| | - Sudheer Bobba
- Drug Metabolism and Pharmacokinetics (R.H.T., S.B., D.Z., S.M.) and Discovery Chemistry (J.M.G., Y.L., P.B.), Genentech, Inc., South San Francisco, California
| | - Yanzhou Liu
- Drug Metabolism and Pharmacokinetics (R.H.T., S.B., D.Z., S.M.) and Discovery Chemistry (J.M.G., Y.L., P.B.), Genentech, Inc., South San Francisco, California
| | - Paul Beroza
- Drug Metabolism and Pharmacokinetics (R.H.T., S.B., D.Z., S.M.) and Discovery Chemistry (J.M.G., Y.L., P.B.), Genentech, Inc., South San Francisco, California
| | - Donglu Zhang
- Drug Metabolism and Pharmacokinetics (R.H.T., S.B., D.Z., S.M.) and Discovery Chemistry (J.M.G., Y.L., P.B.), Genentech, Inc., South San Francisco, California
| | - Shuguang Ma
- Drug Metabolism and Pharmacokinetics (R.H.T., S.B., D.Z., S.M.) and Discovery Chemistry (J.M.G., Y.L., P.B.), Genentech, Inc., South San Francisco, California
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Lim HK, Yang M, Lam W, Xu F, Chen J, Xu Y, Shetty HU, Yang K, Silva J, Evans DC. Free radical metabolism of raloxifene in human liver microsomes. Xenobiotica 2013; 42:737-47. [PMID: 22375838 DOI: 10.3109/00498254.2012.662306] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Raloxifene was metabolized predominantly by CYP3A4 in human liver microsomes to a pair of carbon-carbon (RD1–2) and ether (RD3–4) linked homodimers in an nicotinamide adenine dinucleotide phosphate-dependent manner. The major homodimer formed by human liver microsomes (RD3) was different from the major homodimer formed by peroxidases (RD1). RD1, 3 and 4 were identified by both mass spectrometry (MS) and nuclear magnetic resonance (NMR) as symmetrical carbon-carbon (both carbon 7 from benzo[b]thiopen-6-ol) linked homodimer, asymmetrical ether (oxygen from 4-hydroxyphenyl and carbon 7 from benzo[b]thiopen-6-ol) linked homodimer and asymmetrical ether (oxygen and carbon 7 from benzo[b]thiopen-6-ol) linked homodimer, respectively. The structures of the homodimers RD1, 3 and 4 provided evidence for free radical metabolism of raloxifene by predominantly CYP3A4 in human liver microsomes to oxygen-centered phenoxy radicals from 4-hydroxyphenyl and benzo[b]thiopen-6-ol moieties. Further delocalization to ortho carbon-centered radical was only observed for benzo[b]thiopen-6-ol derived phenoxy radical.
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Affiliation(s)
- Heng-Keang Lim
- Drug Metabolism and Pharmacokinetics, Drug Safety Sciences, Janssen Research and Development, 1000 Route 202 South, Raritan, NJ 08869, USA.
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Niwa T, Murayama N, Yamazaki H. Comparison of the Contributions of Cytochromes P450 3A4 and 3A5 in Drug Oxidation Rates and Substrate Inhibition. ACTA ACUST UNITED AC 2010. [DOI: 10.1248/jhs.56.239] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Toshiro Niwa
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University
| | - Norie Murayama
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University
| | - Hiroshi Yamazaki
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University
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