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Watanabe R, Kawata T, Ueda S, Shinbo T, Higashimori M, Natsume-Kitatani Y, Mizuguchi K. Prediction of the Contribution Ratio of a Target Metabolic Enzyme to Clearance from Chemical Structure Information. Mol Pharm 2023; 20:419-426. [PMID: 36538346 PMCID: PMC9812024 DOI: 10.1021/acs.molpharmaceut.2c00698] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/22/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022]
Abstract
The contribution ratio of metabolic enzymes such as cytochrome P450 to in vivo clearance (fraction metabolized: fm) is a pharmacokinetic index that is particularly important for the quantitative evaluation of drug-drug interactions. Since obtaining experimental in vivo fm values is challenging, those derived from in vitro experiments have often been used alternatively. This study aimed to explore the possibility of constructing machine learning models for predicting in vivo fm using chemical structure information alone. We collected in vivo fm values and chemical structures of 319 compounds from a public database with careful manual curation and constructed predictive models using several machine learning methods. The results showed that in vivo fm values can be obtained from structural information alone with a performance comparable to that based on in vitro experimental values and that the prediction accuracy for the compounds involved in CYP induction or inhibition is significantly higher than that by using in vitro values. Our new approach to predicting in vivo fm values in the early stages of drug discovery should help improve the efficiency of the drug optimization process.
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Affiliation(s)
- Reiko Watanabe
- Artificial
Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health
and Nutrition, Osaka 567-0085, Japan
- Institute
for Protein Research, Osaka University, Osaka 567-0085, Japan
| | - Toshio Kawata
- Science
Enablement Department, Data Science & Innovation Division, Research
& Development, AstraZeneca K.K., Osaka 530-0011, Japan
| | - Shinya Ueda
- Science
Enablement Department, Data Science & Innovation Division, Research
& Development, AstraZeneca K.K., Osaka 530-0011, Japan
| | - Takumi Shinbo
- Science
Enablement Department, Data Science & Innovation Division, Research
& Development, AstraZeneca K.K., Osaka 530-0011, Japan
| | - Mitsuo Higashimori
- Science
Enablement Department, Data Science & Innovation Division, Research
& Development, AstraZeneca K.K., Osaka 530-0011, Japan
| | - Yayoi Natsume-Kitatani
- Artificial
Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health
and Nutrition, Osaka 567-0085, Japan
- Institute
of Advanced Medical Sciences, Tokushima
University, Tokushima 567-0085, Japan
| | - Kenji Mizuguchi
- Artificial
Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health
and Nutrition, Osaka 567-0085, Japan
- Institute
for Protein Research, Osaka University, Osaka 567-0085, Japan
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Insulin Controls Triacylglycerol Synthesis through Control of Glycerol Metabolism and Despite Increased Lipogenesis. Nutrients 2019; 11:nu11030513. [PMID: 30823376 PMCID: PMC6470968 DOI: 10.3390/nu11030513] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 02/22/2019] [Accepted: 02/22/2019] [Indexed: 12/12/2022] Open
Abstract
Under normoxic conditions, adipocytes in primary culture convert huge amounts of glucose to lactate and glycerol. This “wasting” of glucose may help to diminish hyperglycemia. Given the importance of insulin in the metabolism, we have studied how it affects adipocyte response to varying glucose levels, and whether the high basal conversion of glucose to 3-carbon fragments is affected by insulin. Rat fat cells were incubated for 24 h in the presence or absence of 175 nM insulin and 3.5, 7, or 14 mM glucose; half of the wells contained 14C-glucose. We analyzed glucose label fate, medium metabolites, and the expression of key genes controlling glucose and lipid metabolism. Insulin increased both glucose uptake and the flow of carbon through glycolysis and lipogenesis. Lactate excretion was related to medium glucose levels, which agrees with the purported role of disposing excess (circulating) glucose. When medium glucose was low, most basal glycerol came from lipolysis, but when glucose was high, release of glycerol via breakup of glycerol-3P was predominant. Although insulin promotes lipogenesis, it also limited the synthesis of glycerol-3P from glucose and its incorporation into acyl-glycerols. We assume that this is a mechanism of adipose tissue defense to avoid crippling fat accumulation which has not yet been described.
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Ho-Palma AC, Rotondo F, Romero MDM, Fernández-López JA, Remesar X, Alemany M. Use of 14C-glucose by primary cultures of mature rat epididymal adipocytes. Marked release of lactate and glycerol, but limited lipogenesis in the absence of external stimuli. Adipocyte 2018; 7:204-217. [PMID: 29708458 DOI: 10.1080/21623945.2018.1460020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
White adipose tissue can metabolize large amounts of glucose to glycerol and lactate. We quantitatively traced glucose label to lactate, glycerol and fats in primary cultures of mature rat epididymal adipocytes. Cells were incubated with 7/14 mM 14C-glucose for 24/48 h. Medium metabolites and the label in them and in cells' components were measured. Gene expression analysis was done using parallel incubations. Glucose concentration did not affect lactate efflux and most parameters. Glycerol efflux increased after 24 h, coinciding with arrested lipogenesis. Steady production of lactate was maintained in parallel to glycerogenesis. Changes in adipocyte metabolism were paralleled by gene expression. Glucose use for lipogenesis was minimal, and stopped (24 h-onwards) when glycerol efflux increased because of triacylglycerol turnover. Lactate steady efflux showed that anaerobic glycolysis was the main adipocyte source of energy. We can assume that adipose tissue may play a quantitatively significant effect on glycaemia, returning 3C fragments thus minimizing lipogenesis.
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Affiliation(s)
- Ana Cecilia Ho-Palma
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Floriana Rotondo
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - María del Mar Romero
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Institute of Biomedicine, University of Barcelona, Barcelona, Spain
- CIBER-OBN Research Web, Barcelona, Spain
| | - José Antonio Fernández-López
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Institute of Biomedicine, University of Barcelona, Barcelona, Spain
- CIBER-OBN Research Web, Barcelona, Spain
| | - Xavier Remesar
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Institute of Biomedicine, University of Barcelona, Barcelona, Spain
- CIBER-OBN Research Web, Barcelona, Spain
| | - Marià Alemany
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Institute of Biomedicine, University of Barcelona, Barcelona, Spain
- CIBER-OBN Research Web, Barcelona, Spain
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Glycerol is synthesized and secreted by adipocytes to dispose of excess glucose, via glycerogenesis and increased acyl-glycerol turnover. Sci Rep 2017; 7:8983. [PMID: 28827624 PMCID: PMC5567128 DOI: 10.1038/s41598-017-09450-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 07/26/2017] [Indexed: 01/11/2023] Open
Abstract
White adipose tissue (WAT) produces large amounts of lactate and glycerol from glucose. We used mature epididymal adipocytes to analyse the relative importance of glycolytic versus lipogenic glycerol in adipocytes devoid of external stimuli. Cells were incubated (24/48 h) with 7/14 mM glucose; half of the wells contained 14C-glucose. We analysed glucose label fate, medium metabolites, and the expression of key genes coding for proteins controlling glycerol metabolism. The effects of initial glucose levels were small, but time of incubation increased cell activity and modified its metabolic focus. The massive efflux of lactate was uniform with time and unrelated to glucose concentration; however, glycerol-3P synthesis was higher in the second day of incubation, being largely incorporated into the glycerides-glycerol fraction. Glycerophosphatase expression was not affected by incubation. The stimulation of glycerogenic enzymes’ expression was mirrored in lipases. The result was a shift from medium glycolytic to lipolytic glycerol released as a consequence of increased triacylglycerol turnover, in which most fatty acids were recycled. Production of glycerol seems to be an important primary function of adipocytes, maintained both by glycerogenesis and acyl-glycerol turnover. Production of 3C fragments may also contribute to convert excess glucose into smaller, more readily usable, 3C metabolites.
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