Reactions and enzymes in the metabolism of drugs and other xenobiotics

ADMET in silico modelling: towards prediction paradise?

Waterbeemd, H. V. D., & Gifford, E. (2003) · Nature Reviews Drug Discovery · doi:10.1038/nrd1032 · Cited by 1,894 · see citing works

Prodrugs: design and clinical applications

Rautio, J., Kumpulainen, H., Heimbach, T., Oliyai, R., Oh, D.-M., Järvinen, T., & Savolainen, J. (2008) · Nature Reviews Drug Discovery · doi:10.1038/nrd2468 · Cited by 1,645 · see citing works

DRUG-DRUG INTERACTIONS FOR UDP-GLUCURONOSYLTRANSFERASE SUBSTRATES: A PHARMACOKINETIC EXPLANATION FOR TYPICALLY OBSERVED LOW EXPOSURE (AUCI/AUC) RATIOS

Williams, J. A., Hyland, R., Jones, B., Smith, D. A., Hurst, S. I., Goosen, T. C., Peterkin, V. C., Koup, J. R., & Ball, S. E. (2004) · Drug Metabolism and Disposition · doi:10.1124/dmd.104.000794 · Cited by 929 · see citing works

Predicting in vivo drug interactions from in vitro drug discovery data

Wienkers, L. C., & Heath, T. G. (2005) · Nature Reviews Drug Discovery · doi:10.1038/nrd1851 · Cited by 910 · see citing works

Summary of information on human CYP enzymes: human P450 metabolism data

Rendić, S. (2002) · Drug Metabolism Reviews · doi:10.1081/dmr-120001392 · Cited by 819 · see citing works

DETOXICATION MECHANISMS

Browning, E. (1960) · BMJ · doi:10.1136/bmj.1.5189.1868-b · Cited by 763 · see citing works

A Comprehensive Listing of Bioactivation Pathways of Organic Functional Groups

Kalgutkar, A. S. S., Gardner, I. B., Obach, R. S., Shaffer, C. L., Callegari, E., Henne, K. R., Mutlib, A. E., Dalvie, D., Lee, J. S., Nakai, Y., et al. (2005) · Current Drug Metabolism · doi:10.2174/1389200054021799 · Cited by 623 · see citing works

Evolution of the P450 gene superfamily:

Gonzalez, F. J., & Nebert, D. W. (1990) · Trends in Genetics · doi:10.1016/0168-9525(90)90174-5 · Cited by 514 · see citing works

MetaSite: Understanding Metabolism in Human Cytochromes from the Perspective of the Chemist

Cruciani, G., Carosati, E., Boeck, B. D., Ethirajulu, K., Mackie, C. E., Howe, T. J., & Vianello, R. (2005) · Journal of Medicinal Chemistry · doi:10.1021/jm050529c · Cited by 497 · see citing works

The enzymes of detoxication.

Jakoby, W. B., & Ziegler, D. M. (1990) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)45272-0 · Cited by 415 · see citing works

In silicopharmacology for drug discovery: applications to targets and beyond

Ekins, S., Mestres, J., & Testa, B. (2007) · British Journal of Pharmacology · doi:10.1038/sj.bjp.0707306 · Cited by 367 · see citing works

Drug research: myths, hype and reality

Kubinyi, H. (2003) · Nature Reviews Drug Discovery · doi:10.1038/nrd1156 · Cited by 348 · see citing works

The Practice of Medicinal Chemistry

Wermuth, C. G. (2008) · Elsevier eBooks · doi:10.1016/b978-0-12-374194-3.x0001-7 · Cited by 345 · see citing works

In Silico Tools for Sharing Data and Knowledge on Toxicity and Metabolism: Derek for Windows, Meteor, and Vitic

Marchant, C. A., Briggs, K. A., & Long, A. (2008) · Toxicology Mechanisms and Methods · doi:10.1080/15376510701857320 · Cited by 344 · see citing works

Role of Drug Disposition in Drug Hypersensitivity: A Chemical, Molecular, and Clinical Perspective

Park, B. K., Pirmohamed, M., & Kitteringham, N. R. (1998) · Chemical Research in Toxicology · doi:10.1021/tx980058f · Cited by 267 · see citing works

Enzyme Nomenclature. Recommendations 1992

Tipton, K. F. (1994) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1994.tb18960.x · Cited by 260 · see citing works

Applying Mechanisms of Chemical Toxicity to Predict Drug Safety

Guengerich, F. P., & MacDonald, J. S. (2007) · Chemical Research in Toxicology · doi:10.1021/tx600260a · Cited by 230 · see citing works

Pharmacophore and three-dimensional quantitative structure activity relationship methods for modeling cytochrome p450 active sites.

Ekins, S., de Groot, M. J., & Jones, J. P. (2001) · PubMed · Cited by 202 · see citing works

Drug Development: From Concept to Marketing!

Tamimi, N., & Ellis, P. (2009) · Nephron Clinical Practice · doi:10.1159/000232592 · Cited by 172 · see citing works

Burger's medicinal chemistry, drug discovery, and development

Burger, A., Abraham, D. J., & Rotella, D. P. (2010) · Wiley eBooks · Cited by 164 · see citing works

Detoxication Mechanisms

BOYLAND, E. (1948) · Nature · doi:10.1038/162127a0 · Cited by 161 · see citing works

The future of drug development: advancing clinical trial design

Orloff, J. J., Douglas, F. L., Pinheiro, J. C., Levinson, S. L., Branson, M., Chaturvedi, P. R., Ette, E., Gallo, P. P., Hirsch, G., Mehta, C. R., et al. (2009) · Nature Reviews Drug Discovery · doi:10.1038/nrd3025 · Cited by 158 · see citing works

Discovering Drugs through Biological Transformation: Role of Pharmacologically Active Metabolites in Drug Discovery

Fura, A., Shu, Y., Zhu, M., Hanson, R. L., Roongta, V. A., & Humphreys, W. G. (2004) · Journal of Medicinal Chemistry · doi:10.1021/jm040066v · Cited by 151 · see citing works

Designing better drugs: predicting cytochrome P450 metabolism

de Groot, M. J. (2006) · Drug Discovery Today · doi:10.1016/j.drudis.2006.05.001 · Cited by 122 · see citing works

Update Information on Drug Metabolism Systems— 2009, Part II. Summary of Information on the Effects of Diseases and Environmental Factors on Human Cytochrome P450 (CYP) Enzymes and Transporters

Rendić, S., & Guengerich, F. P. (2010) · Current Drug Metabolism · doi:10.2174/138920010791110917 · Cited by 109 · see citing works

Structural Alerts, Reactive Metabolites, and Protein Covalent Binding: How Reliable Are These Attributes as Predictors of Drug Toxicity?

Kalgutkar, A. S. S., & Didiuk, M. T. (2009) · Chemistry & Biodiversity · doi:10.1002/cbdv.200900055 · Cited by 103 · see citing works

Prodrugs: bridging pharmacodynamic/pharmacokinetic gaps

Testa, B. (2009) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2009.04.620 · Cited by 97 · see citing works

Computational prediction of human drug metabolism

Ekins, S., Andreyev, S., Ryabov, A., Kirillov, E., Rakhmatulin, E. A., Bugrim, A. E., & Nikolskaya, T. (2005) · Expert Opinion on Drug Metabolism & Toxicology · doi:10.1517/17425255.1.2.303 · Cited by 86 · see citing works

Predicting Drug Metabolism - An Evaluation of the Expert SystemMETEOR

Testa, B., Balmat, A.-L., Long, A., & Judson, P. N. (2005) · Chemistry & Biodiversity · doi:10.1002/cbdv.200590064 · Cited by 78 · see citing works

Metabolic bioactivation and drug-related adverse effects: current status and future directions from a pharmaceutical research perspective

Tang, W., & Lu, A. Y. H. (2009) · Drug Metabolism Reviews · doi:10.3109/03602530903401658 · Cited by 77 · see citing works

Exploratory drug safety: A discovery strategy to reduce attrition in development

Bass, A. S., Cartwright, M. E., Mahon, C., Morrison, R. A., Snyder, R. D., McNamara, P., Bradley, P. K., Zhou, Y., & Hunter, J. (2009) · Journal of Pharmacological and Toxicological Methods · doi:10.1016/j.vascn.2009.04.194 · Cited by 77 · see citing works

The Evolving Role of Drug Metabolism in Drug Discovery and Development

Yengi, L. G., Leung, L. Y., & Kao, J. (2007) · Pharmaceutical Research · doi:10.1007/s11095-006-9217-9 · Cited by 76 · see citing works

The Biochemistry of Drug Metabolism – An Introduction

Testa, B., & Krämer, S. D. (2009) · Chemistry & Biodiversity · doi:10.1002/cbdv.200900022 · Cited by 75 · see citing works

Role of Biotransformation Studies in Minimizing Metabolism-Related Liabilities in Drug Discovery

Shu, Y., Johnson, B. M., & Yang, T. J. (2008) · The AAPS Journal · doi:10.1208/s12248-008-9016-9 · Cited by 74 · see citing works

Using Absolute and Relative Reasoning in the Prediction of the Potential Metabolism of Xenobiotics

Button, W. G., Judson, P. N., Long, A., & Vessey, J. D. (2003) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci0202739 · Cited by 73 · see citing works

Addressing Metabolic Activation as an Integral Component of Drug Design

Doss, G. A., & Baillie, T. A. (2006) · Drug Metabolism Reviews · doi:10.1080/03602530600959466 · Cited by 72 · see citing works

Comprehensive Assessment of ADMET Risks in Drug Discovery

Wang, J. (2009) · Current Pharmaceutical Design · doi:10.2174/138161209788682514 · Cited by 70 · see citing works

Analytical strategies for the screening and evaluation of chemically reactive drug metabolites

Wen, B., & Fitch, W. L. (2008) · Expert Opinion on Drug Metabolism & Toxicology · doi:10.1517/17425250802665706 · Cited by 52 · see citing works

Why do metabolites circulate?

Smith, D. A., & Dalvie, D. (2011) · Xenobiotica · doi:10.3109/00498254.2011.630110 · Cited by 49 · see citing works

The Role of Metabolites in Bioequivalence

Midha, K. K., Rawson, M. J., & Hubbard, J. W. (2004) · Pharmaceutical Research · doi:10.1023/b:pham.0000036906.65263.da · Cited by 48 · see citing works

Minimizing metabolic activation during pharmaceutical lead optimization: progress, knowledge gaps and future directions.

Kumar, S., Kassahun, K., Tschirret-Guth, R. A., Mitra, K., & Baillie, T. A. (2008) · PubMed · Cited by 48 · see citing works

Xenobiotic lipids: The inclusion of xenobiotic compounds in pathways of lipid biosynthesis

Dodds, P. F. (1995) · Progress in Lipid Research · doi:10.1016/0163-7827(95)00007-m · Cited by 42 · see citing works

Biotransformations Leading to Toxic Metabolites

Macherey, A., & Dansette, P. M. (2008) · Elsevier eBooks · doi:10.1016/b978-0-12-374194-3.00033-0 · Cited by 38 · see citing works

Exploratory Safety Pharmacology: a new safety paradigm to de-risk drug candidates prior to selection for regulatory science investigations

Cavero, I. (2009) · Expert Opinion on Drug Safety · doi:10.1517/14740330903362422 · Cited by 37 · see citing works

Predicting the Oxidative Metabolism of Statins: An Application of the MetaSite® Algorithm

Caron, G., Ermondi, G., & Testa, B. (2007) · Pharmaceutical Research · doi:10.1007/s11095-006-9199-7 · Cited by 37 · see citing works

MultiCASE Expert Systems and the REACH Initiative

Saiakhov, R., & Klopman, G. (2008) · Toxicology Mechanisms and Methods · doi:10.1080/15376510701857460 · Cited by 35 · see citing works

Drug Metabolism for the Perplexed Medicinal Chemist

Testa, B. (2009) · Chemistry & Biodiversity · doi:10.1002/cbdv.200900052 · Cited by 32 · see citing works

Predicting drug metabolism: Concepts and challenges

Testa, B., Balmat, A.-L., & Long, A. (2004) · Pure and Applied Chemistry · doi:10.1351/pac200476050907 · Cited by 29 · see citing works

Novel Drug Metabolites Produced by Functionalization Reactions: Chemistry and Toxicology

Testa, B., & Jenner, P. G. (1978) · Drug Metabolism Reviews · doi:10.3109/03602537808993771 · Cited by 28 · see citing works

Mechanisms of Toxification and Detoxification which Challenge Drug Candidates and Drugs

Oesch‐Bartlomowicz, B., & Oesch, F. (2007) · Elsevier eBooks · doi:10.1016/b0-08-045044-x/00124-3 · Cited by 26 · see citing works

Identification of phenacetin metabolites in human urine after administration of phenacetin-C2H3: Measurement of futile metabolic deacetylation via HPLC/MS-SPE-NMR and HPLC-ToF MS

Nicholls, A. W., Wilson, I. D., Godejohann, M., Nicholson, J. K., & Shockcor, J. P. (2006) · Xenobiotica · doi:10.1080/00498250600711113 · Cited by 26 · see citing works

Importance of Early Assessment of Bioactivation in Drug Discovery

Hop, C. E. C. A., Kalgutkar, A. S. S., & Soglia, J. R. (2006) · Annual reports in medicinal chemistry · doi:10.1016/s0065-7743(06)41025-3 · Cited by 18 · see citing works

The Biochemistry of Drug Metabolism: Conjugations, Consequences of Metabolism, Influencing Factors

Testa, B. (2010) · Cited by 16 · see citing works

Nonenzymatic Contributions to Xenobiotic Metabolism

Testa, B. (1982) · Drug Metabolism Reviews · doi:10.3109/03602538209002230 · Cited by 14 · see citing works

Principles of Drug Metabolism

Testa, B. (2010) · Burger's Medicinal Chemistry and Drug Discovery · doi:10.1002/0471266949.bmc033.pub2 · Cited by 14 · see citing works

Drug-metabolizing Enzymes as Evolutionary Probes

Jondorf, W. R. (1981) · Drug Metabolism Reviews · doi:10.3109/03602538108994038 · Cited by 11 · see citing works

Immunotoxicology

Esser, C. (2007) · Elsevier eBooks · doi:10.1016/b0-08-045044-x/00282-0 · Cited by 8 · see citing works

Nature's pesticides

Ames, B. N., & Profet, M. (1992) · Natural Toxins · doi:10.1002/nt.2620010103 · Cited by 6 · see citing works

The behaviour of foreign substances in the human body

Albert, A. (1987) · Trends in Pharmacological Sciences · doi:10.1016/0165-6147(87)90198-2 · Cited by 2 · see citing works

Bioinformatics Modernization and the Critical Path to Improved Benefit-Risk Assessment of Drugs

Oliva, A., Levin, R., Behrman, R. E., & Woodcock, J. (2008) · Drug Information Journal · doi:10.1177/009286150804200309 · Cited by 2 · see citing works

Improving drug safety using computational biology.

Cook, D. R. (2010) · PubMed · Cited by 2 · see citing works

QSAR Modeling: Where have you been? Where are you going to?

Cherkasov, A., Muratov, E. N., Fourches, D., Varnek, A., Baskin, I. I., Cronin, M., Dearden, J., Gramatica, P., Martin, Y. C., Todeschini, R., et al. (2014) · Journal of Medicinal Chemistry · doi:10.1021/jm4004285 · Cited by 2,164 · see citing works

Cytochrome P450 Enzymes and Drug Metabolism in Humans

Zhao, M., Ma, J., Li, M., Zhang, Y., Jiang, B., Zhao, X., Huai, C., Shen, L., Zhang, N., He, L., et al. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms222312808 · Cited by 1,070 · see citing works

Formation and Biological Targets of Quinones: Cytotoxic versus Cytoprotective Effects

Bolton, J. L., & Dunlap, T. L. (2016) · Chemical Research in Toxicology · doi:10.1021/acs.chemrestox.6b00256 · Cited by 528 · see citing works

The food metabolome: a window over dietary exposure

Scalbert, A., Brennan, L., Manach, C., Andres-Lacueva, C., Dragsted, L. O., Draper, J., Rappaport, S. M., van der Hooft, J. J., & Wishart, D. S. (2014) · The American Journal of Clinical Nutrition · doi:10.3945/ajcn.113.076133 · Cited by 519 · see citing works

BioTransformer: a comprehensive computational tool for small molecule metabolism prediction and metabolite identification

Djoumbou-Feunang, Y., Fiamoncini, J., Gil-de-la-Fuente, A., Greiner, R., Manach, C., & Wishart, D. S. (2019) · Journal of Cheminformatics · doi:10.1186/s13321-018-0324-5 · Cited by 516 · see citing works

Predicting drug metabolism: experiment and/or computation?

Kirchmair, J., Göller, A. H., Lang, D. H., Kunze, J., Testa, B., Wilson, I. D., Glen, R. C., & Schneider, G. (2015) · Nature Reviews Drug Discovery · doi:10.1038/nrd4581 · Cited by 507 · see citing works

A review of the biotransformations of priority pharmaceuticals in biological wastewater treatment processes

Nguyen, P. Y., Carvalho, G., Reis, M. A. M., & Oehmen, A. (2020) · Water Research · doi:10.1016/j.watres.2020.116446 · Cited by 247 · see citing works

Computational methods and tools to predict cytochrome P450 metabolism for drug discovery

Tyzack, J. D., & Kirchmair, J. (2018) · Chemical Biology & Drug Design · doi:10.1111/cbdd.13445 · Cited by 209 · see citing works

Modeling Epoxidation of Drug-like Molecules with a Deep Machine Learning Network

Hughes, T. B., Miller, G. P., & Swamidass, S. J. (2015) · ACS Central Science · doi:10.1021/acscentsci.5b00131 · Cited by 203 · see citing works

Polyphenols as Antioxidant/Pro-Oxidant Compounds and Donors of Reducing Species: Relationship with Human Antioxidant Metabolism

Andrés, C. M. C., de la Lastra, J. M. P., Andrés, C., Plou, F. J., & Pérez‐Lebeña, E. (2023) · Processes · doi:10.3390/pr11092771 · Cited by 193 · see citing works

Removal of Antibiotics in Biological Wastewater Treatment Systems—A Critical Assessment Using the Activated Sludge Modeling Framework for Xenobiotics (ASM-X)

Polesel, F., Andersen, H. R., Trapp, S., & Plósz, B. G. (2016) · Environmental Science & Technology · doi:10.1021/acs.est.6b01899 · Cited by 183 · see citing works

Decoding the Role of CYP450 Enzymes in Metabolism and Disease: A Comprehensive Review

Abdelmonem, B. H., Abdelaal, N. M., Anwer, E. K. E., Rashwan, A. A., Hussein, M. A., Ahmed, Y. F., Khashana, R., Hanna, M. M., & Abdelnaser, A. (2024) · Biomedicines · doi:10.3390/biomedicines12071467 · Cited by 175 · see citing works

GLORYx: Prediction of the Metabolites Resulting from Phase 1 and Phase 2 Biotransformations of Xenobiotics

Kops, C. D. B., Šícho, M., Mazzolari, A., & Kirchmair, J. (2020) · Chemical Research in Toxicology · doi:10.1021/acs.chemrestox.0c00224 · Cited by 162 · see citing works

FAME 3: Predicting the Sites of Metabolism in Synthetic Compounds and Natural Products for Phase 1 and Phase 2 Metabolic Enzymes

Šícho, M., Stork, C., Mazzolari, A., Kops, C. D. B., Pedretti, A., Testa, B., Vistoli, G., Svozil, D., & Kirchmair, J. (2019) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.9b00376 · Cited by 133 · see citing works

Quaternary Ammonium Compounds: Bioaccumulation Potentials in Humans and Levels in Blood before and during the Covid-19 Pandemic

Zheng, G., Webster, T. F., & Salamova, A. (2021) · Environmental Science & Technology · doi:10.1021/acs.est.1c01654 · Cited by 133 · see citing works

A cocktail approach for assessing the in vitro activity of human cytochrome P450s: An overview of current methodologies

Spaggiari, D., Geiser, L., Daali, Y., & Rudaz, S. L. (2014) · Journal of Pharmaceutical and Biomedical Analysis · doi:10.1016/j.jpba.2014.03.018 · Cited by 100 · see citing works

Artificial Intelligence in Drug Metabolism and Excretion Prediction: Recent Advances, Challenges, and Future Perspectives

Tran, T. T. V., Tayara, H., & Chong, K. T. (2023) · Pharmaceutics · doi:10.3390/pharmaceutics15041260 · Cited by 98 · see citing works

Biotransformation in vitro: An essential consideration in the quantitative in vitro-to-in vivo extrapolation (QIVIVE) of toxicity data

Wilk–Zasadna, I., Bernasconi, C., Pelkonen, O., & Coecke, S. (2014) · Toxicology · doi:10.1016/j.tox.2014.10.006 · Cited by 89 · see citing works

Deep Learning to Predict the Formation of Quinone Species in Drug Metabolism

Hughes, T. B., & Swamidass, S. J. (2017) · Chemical Research in Toxicology · doi:10.1021/acs.chemrestox.6b00385 · Cited by 84 · see citing works

Modeling of interactions between xenobiotics and cytochrome P450 (CYP) enzymes

Raunio, H., Kuusisto, M., Juvonen, R. O., & Pentikäinen, O. T. (2015) · Frontiers in Pharmacology · doi:10.3389/fphar.2015.00123 · Cited by 84 · see citing works

The Influence of Bioisosteres in Drug Design: Tactical Applications to Address Developability Problems

Meanwell, N. A. (2013) · Topics in medicinal chemistry · doi:10.1007/7355_2013_29 · Cited by 86 · see citing works

GLORY: Generator of the Structures of Likely Cytochrome P450 Metabolites Based on Predicted Sites of Metabolism

Kops, C. D. B., Stork, C., Šícho, M., Kochev, N. T., Svozil, D., Jeliazkova, N., & Kirchmair, J. (2019) · Frontiers in Chemistry · doi:10.3389/fchem.2019.00402 · Cited by 79 · see citing works

A review on analytical methods for pharmaceutical and personal care products and their transformation products

Meng, Y., Liu, W., Liu, X., Zhang, J., Peng, M., & Zhang, T. (2020) · Journal of Environmental Sciences · doi:10.1016/j.jes.2020.08.025 · Cited by 74 · see citing works

The Metabolic Rainbow: Deep Learning Phase I Metabolism in Five Colors

Dang, N. L., Matlock, M. K., Hughes, T. B., & Swamidass, S. J. (2020) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.9b00836 · Cited by 68 · see citing works

Circadian Clock–Controlled Drug Metabolism: Implications for Chronotherapeutics

Lu, D., Zhao, M., Chen, M., & Wu, B. (2020) · Drug Metabolism and Disposition · doi:10.1124/dmd.120.090472 · Cited by 64 · see citing works

FAME 2: Simple and Effective Machine Learning Model of Cytochrome P450 Regioselectivity

Šícho, M., Kops, C. D. B., Stork, C., Svozil, D., & Kirchmair, J. (2017) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.7b00250 · Cited by 64 · see citing works

CYPlebrity: Machine learning models for the prediction of inhibitors of cytochrome P450 enzymes

Płonka, W., Stork, C., Šícho, M., & Kirchmair, J. (2021) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2021.116388 · Cited by 63 · see citing works

Computational Tools And Resources For Metabolism-Related Property Predictions. 1. Overview Of Publicly Available (Free And Commercial) Databases And Software

Peach, M. L., Zakharov, A. V., Liu, R., Pugliese, A., Tawa, G. J., Wallqvist, A., & Nicklaus, M. C. (2012) · Future Medicinal Chemistry · doi:10.4155/fmc.12.150 · Cited by 63 · see citing works

A UGT2B10 Splicing Polymorphism Common in African Populations May Greatly Increase Drug Exposure

Fowler, S. M., Kletzl, H., Finel, M., Manevski, N., Schmid, P., Tuerck, D., Norcross, R. D., Hoener, M. C., Spleiss, O., & Iglesias, V. A. (2014) · Journal of Pharmacology and Experimental Therapeutics · doi:10.1124/jpet.114.220194 · Cited by 59 · see citing works

Prediction of drug metabolites using neural machine translation

Litsa, E. E., Das, P., & Kavraki, L. E. (2020) · Chemical Science · doi:10.1039/d0sc02639e · Cited by 58 · see citing works

A comprehensive review on pharmacokinetic mechanism of herb-herb/drug interactions in Chinese herbal formula

Li, M., Wang, Y., Chen, Y., Dong, L., Liu, J., Dong, Y., Yang, Q., Cai, W., Li, Q., Peng, B., et al. (2024) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2024.108728 · Cited by 58 · see citing works

Triptolide Induces hepatotoxicity via inhibition of CYP450s in Rat liver microsomes

Lu, Y., Xie, T., Zhang, Y., Zhou, F., Ruan, J., Zhu, W., Zhu, H., Feng, Z., & Zhou, X. (2017) · BMC Complementary and Alternative Medicine · doi:10.1186/s12906-016-1504-3 · Cited by 58 · see citing works

Human Enzymes for Organic Synthesis

Winkler, M., Geier, M., Hanlon, S. P., Nidetzky, B., & Glieder, A. (2018) · Angewandte Chemie International Edition · doi:10.1002/anie.201800678 · Cited by 55 · see citing works

Emerging Metabolic Profiles of Sulfonamide Antibiotics by Cytochromes P450: A Computational–Experimental Synergy Study on Emerging Pollutants

Zhang, H., Wang, X., Song, R., Ding, W., Li, F., & Ji, L. (2023) · Environmental Science & Technology · doi:10.1021/acs.est.3c00071 · Cited by 55 · see citing works

Coumarin-Based Profluorescent and Fluorescent Substrates for Determining Xenobiotic-Metabolizing Enzyme Activities In Vitro

Raunio, H., Pentikäinen, O. T., & Juvonen, R. O. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21134708 · Cited by 54 · see citing works

Genetic and Nongenetic Factors Associated with Protein Abundance of Flavin-Containing Monooxygenase 3 in Human Liver

Xu, M., Bhatt, D. K., Yeung, C. K., Claw, K. G., Chaudhry, A. S., Gaedigk, A., Pearce, R. E., Broeckel, U., Gaedigk, R., Nickerson, D. A., et al. (2017) · Journal of Pharmacology and Experimental Therapeutics · doi:10.1124/jpet.117.243113 · Cited by 54 · see citing works

Computational Approach to Structural Alerts: Furans, Phenols, Nitroaromatics, and Thiophenes

Dang, N. L., Hughes, T. B., Miller, G. P., & Swamidass, S. J. (2017) · Chemical Research in Toxicology · doi:10.1021/acs.chemrestox.6b00336 · Cited by 50 · see citing works

Exposition and reactivity optimization to predict sites of metabolism in chemicals

Cruciani, G., Baroni, M., Benedetti, P., Goracci, L., & Fortuna, C. G. (2012) · Drug Discovery Today Technologies · doi:10.1016/j.ddtec.2012.11.001 · Cited by 46 · see citing works

Metabolomics in chemical risk analysis – A review

Hernández‐Mesa, M., Bizec, B. L., & Dervilly, G. (2021) · Analytica Chimica Acta · doi:10.1016/j.aca.2021.338298 · Cited by 45 · see citing works

Comparison of liquid chromatography and supercritical fluid chromatography coupled to compact single quadrupole mass spectrometer for targeted in vitro metabolism assay

Spaggiari, D., Mehl, F., Desfontaine, V., Perrenoud, A. G., Fekete, S., Rudaz, S. L., & Guillarme, D. (2014) · Journal of Chromatography A · doi:10.1016/j.chroma.2014.10.055 · Cited by 44 · see citing works

Formation of hydroxylated and methoxylated polychlorinated biphenyls by Bacillus subtilis: New insights into microbial metabolism

Sun, J., Pan, L., & Zhu, L. (2017) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2017.09.063 · Cited by 44 · see citing works

Precision Biotransformation of Emerging Pollutants by Human Cytochrome P450 Using Computational–Experimental Synergy: A Case Study of Tris(1,3-dichloro-2-propyl) Phosphate

Chai, L., Zhang, H., Song, R., Yang, H., Yu, H., Paneth, P., Kepp, K. P., Akamatsu, M., & Ji, L. (2021) · Environmental Science & Technology · doi:10.1021/acs.est.1c03036 · Cited by 44 · see citing works

Computational and artificial intelligence-based approaches for drug metabolism and transport prediction

Dudás, B., & Miteva, M. A. (2023) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2023.11.001 · Cited by 42 · see citing works

Flavin Monooxygenase Metabolism: Why Medicinal Chemists Should Matter

Cruciani, G., Valeri, A., Goracci, L., Pellegrino, R. M., Buonerba, F., & Baroni, M. (2014) · Journal of Medicinal Chemistry · doi:10.1021/jm5007098 · Cited by 42 · see citing works

Transformation Products of Emerging Pollutants Explored Using Non-Target Screening: Perspective in the Transformation Pathway and Toxicity Mechanism—A Review

Suman, T. Y., Kim, S., Yeom, D., & Jeon, J. (2022) · Toxics · doi:10.3390/toxics10020054 · Cited by 41 · see citing works

Current High-Throughput Approaches of Screening Modulatory Effects of Xenobiotics on Cytochrome P450 (CYP) Enzymes

Ung, Y. T., Ong, C. E., & Pan, Y. (2018) · Microarrays · doi:10.3390/ht7040029 · Cited by 40 · see citing works

Metabolic profile and safety of piperlongumine

Moreira, F. D. L., Habenschus, M. D., Barth, T., Marques, L. M. M., Pilon, A. C., Bolzani, V. D. S., Vessecchi, R., Lopes, N. P., & de Oliveira, A. R. M. (2016) · Scientific Reports · doi:10.1038/srep33646 · Cited by 39 · see citing works

Quantitative monitoring of tamoxifen in human plasma extended to 40 metabolites using liquid-chromatography high-resolution mass spectrometry: new investigation capabilities for clinical pharmacology

Dahmane, E., Boccard, J., Csajka, C., Rudaz, S. L., Decosterd, L. A., Genin, E., Duretz, B., Bromirski, M., Zaman, K., Testa, B., et al. (2014) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-014-7682-2 · Cited by 39 · see citing works

Circadian clock-controlled drug metabolism and transport

Zhao, M., Xing, H., Chen, M., Dong, D., & Wu, B. (2019) · Xenobiotica · doi:10.1080/00498254.2019.1672120 · Cited by 38 · see citing works

Recent advances in the prediction of non‐ CYP450 ‐mediated drug metabolism

Dixit, V. A., Lal, L. A., & Agrawal, S. R. (2017) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.1323 · Cited by 36 · see citing works

MetaQSAR: An Integrated Database Engine to Manage and Analyze Metabolic Data

Pedretti, A., Mazzolari, A., Vistoli, G., & Testa, B. (2017) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.7b01473 · Cited by 36 · see citing works

In Silico Prediction of Human Sulfotransferase 1E1 Activity Guided by Pharmacophores from Molecular Dynamics Simulations

Rakers, C., Schumacher, F., Meinl, W., Glatt, H. R., Kleuser, B., & Wolber, G. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.685610 · Cited by 35 · see citing works

MetScore: Site of Metabolism Prediction Beyond Cytochrome P450 Enzymes

Finkelmann, A. R., Goldmann, D., Schneider, G., & Göller, A. H. (2018) · ChemMedChem · doi:10.1002/cmdc.201800309 · Cited by 35 · see citing works

Biotransformation and Oxidative Stress Responses in Captive Nile Crocodile (Crocodylus niloticus) Exposed to Organic Contaminants from the Natural Environment in South Africa

Arukwe, A., Røsbak, R., Adeogun, A. O., Langberg, H. A., Venter, A., Myburgh, J. G., Botha, C. J., Benedetti, M., & Regoli, F. (2015) · PLoS ONE · doi:10.1371/journal.pone.0130002 · Cited by 35 · see citing works

Binding Space Concept: A New Approach To Enhance the Reliability of Docking Scores and Its Application to Predicting Butyrylcholinesterase Hydrolytic Activity

Vistoli, G., Mazzolari, A., Testa, B., & Pedretti, A. (2017) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.7b00121 · Cited by 34 · see citing works

Molecular determinants of protein evolvability

Buda, K., Miton, C. M., Fan, X. C., & Tokuriki, N. (2023) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2023.05.009 · Cited by 33 · see citing works

Coupling ultra-high-pressure liquid chromatography with mass spectrometry for in-vitro drug-metabolism studies

Spaggiari, D., Geiser, L., & Rudaz, S. L. (2014) · TrAC Trends in Analytical Chemistry · doi:10.1016/j.trac.2014.06.021 · Cited by 33 · see citing works

Flavin Containing Monooxygenases and Metabolism of Xenobiotics

Başaran, R., & Eke, B. C. (2017) · Turkish Journal of Pharmaceutical Sciences · doi:10.4274/tjps.30592 · Cited by 33 · see citing works

Preclinical toxicity of innovative molecules: In vitro, in vivo and metabolism prediction

Tonholo, D. R., Maltarollo, V. G., Kronenberger, T., SILVA, I. R. M., de Azevedo, P. O., de Oliveira, R. B., de Souza, L. C. R., & Tagliati, C. A. (2019) · Chemico-Biological Interactions · doi:10.1016/j.cbi.2019.108896 · Cited by 33 · see citing works

Using Free Computational Resources To Illustrate the Drug Design Process in an Undergraduate Medicinal Chemistry Course

Rodrigues, R. P., de Andrade, S. F., Mantoani, S. P., Eifler-Lima, V. L., da Silva, V. B., & Kawano, D. F. (2015) · Journal of Chemical Education · doi:10.1021/ed500195d · Cited by 32 · see citing works

Machine learning models in the prediction of drug metabolism: challenges and future perspectives

Litsa, E. E., Das, P., & Kavraki, L. E. (2021) · Expert Opinion on Drug Metabolism & Toxicology · doi:10.1080/17425255.2021.1998454 · Cited by 32 · see citing works

Metabolomic Approaches to Study Chemical Exposure-Related Metabolism Alterations in Mammalian Cell Cultures

Balcerczyk, A., Damblon, C., Elena‐Herrmann, B., Panthu, B., & Rautureau, G. J. P. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21186843 · Cited by 31 · see citing works

Phenotyping of CYP450 in human liver microsomes using the cocktail approach

Spaggiari, D., Geiser, L., Daali, Y., & Rudaz, S. L. (2014) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-014-7915-4 · Cited by 31 · see citing works

Site of Metabolism Prediction Based on ab initio Derived Atom Representations

Finkelmann, A. R., Göller, A. H., & Schneider, G. (2017) · ChemMedChem · doi:10.1002/cmdc.201700097 · Cited by 31 · see citing works

Occurrence of Pharmaceutically Active Compounds and Potential Ecological Risks in Wastewater from Hospitals and Receiving Waters in Sri Lanka

Goswami, P., Guruge, K. S., Tanoue, R., Tamamura, Y. A., Jinadasa, K., Nomiyama, K., Kunisue, T., & Tanabe, S. (2021) · Environmental Toxicology and Chemistry · doi:10.1002/etc.5212 · Cited by 25 · see citing works

Recent advances in circadian-regulated pharmacokinetics and its implications for chronotherapy

Yu, F., Liu, Y., Zhang, R., Zhu, L., Zhang, T., & Shi, Y. (2022) · Biochemical Pharmacology · doi:10.1016/j.bcp.2022.115185 · Cited by 29 · see citing works

Monoamine oxidase A and B substrates: probing the pathway for drug development.

Chajkowski-Scarry, S., & Rimoldi, J. (2014) · Future Medicinal Chemistry · doi:10.4155/fmc.14.23 · Cited by 27 · see citing works

Phytocannabinoid drug-drug interactions and their clinical implications

Silva, D. A., Pate, D. W., Clark, R. D., Davies, N. M., El‐Kadi, A. O. S., & Löbenberg, R. (2020) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2020.107621 · Cited by 28 · see citing works

Using graph neural networks for site-of-metabolism prediction and its applications to ranking promiscuous enzymatic products

Porokhin, V. O., Liu, L., & Hassoun, S. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btad089 · Cited by 28 · see citing works

In Silico Mechanistic Profiling to Probe Small Molecule Binding to Sulfotransferases

Martiny, V. Y., Carbonell, P., Lagorce, D., Villoutreix, B. O., Moroy, G., & Miteva, M. A. (2013) · PLoS ONE · doi:10.1371/journal.pone.0073587 · Cited by 28 · see citing works

Drawing a Line: Where Might the Cohort of Concern End?

Ponting, D. J., & Foster, R. S. (2023) · Organic Process Research & Development · doi:10.1021/acs.oprd.3c00008 · Cited by 27 · see citing works

From Medicinal Chemistry to Human Health: Current Approaches to Drug Discovery for Cancer and Neglected Tropical Diseases

Ferreira, L. L. G., Oliva, G., & Andricopulo, A. D. (2018) · Anais da Academia Brasileira de Ciências · doi:10.1590/0001-3765201820170505 · Cited by 26 · see citing works

CYPstrate: A Set of Machine Learning Models for the Accurate Classification of Cytochrome P450 Enzyme Substrates and Non-Substrates

Holmer, M., Kops, C. D. B., Stork, C., & Kirchmair, J. (2021) · Molecules · doi:10.3390/molecules26154678 · Cited by 26 · see citing works

MetaPredictor: in silico prediction of drug metabolites based on deep language models with prompt engineering

Zhu, K., Huang, M., Wang, Y., Gu, Y., Li, W., Liu, G., & Tang, Y. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae374 · Cited by 25 · see citing works

Identification of position isomers by energy‐resolved mass spectrometry

Menacherry, S. P. M., Laprévôte, O., Nguyen, T. P. N., Aravind, U. K., Pramod, G., & Aravindakumar, C. T. (2015) · Journal of Mass Spectrometry · doi:10.1002/jms.3607 · Cited by 25 · see citing works

Inhibition of human CYP1 enzymes by a classical inhibitor α‐naphthoflavone and a novel inhibitor N‐(3, 5‐dichlorophenyl)cyclopropanecarboxamide: An in vitro and in silico study

Juvonen, R. O., Jokinen, E. M., Javaid, A., Lehtonen, M., Raunio, H., & Pentikäinen, O. T. (2020) · Chemical Biology & Drug Design · doi:10.1111/cbdd.13669 · Cited by 25 · see citing works

Insights into the substrate binding mechanism of SULT1A1 through molecular dynamics with excited normal modes simulations

Dudás, B., Tóth, D. J., Pérahia, D., Nicot, A. B., Balog, E., & Miteva, M. A. (2021) · Scientific Reports · doi:10.1038/s41598-021-92480-w · Cited by 25 · see citing works

Drug‐drug interaction and doping, part 1: An in vitro study on the effect of non‐prohibited drugs on the phase I metabolic profile of toremifene

Mazzarino, M., de la Torre, X., Fiacco, I., Palermo, A., & Botrè, F. (2014) · Drug Testing and Analysis · doi:10.1002/dta.1592 · Cited by 24 · see citing works

Pharmacokinetic Benefits of 3,4-Dimethoxy Substitution of a Phenyl Ring and Design of Isosteres Yielding Orally Available Cathepsin K Inhibitors

Crawford, J. J., Kenny, P. W., Bowyer, J., Cook, C., Finlayson, J., Heyes, C., Highton, A. J., Hudson, J. A., Jestel, A., Krapp, S., et al. (2012) · Journal of Medicinal Chemistry · doi:10.1021/jm301119s · Cited by 24 · see citing works

Modelling the fate of micropollutants in integrated urban wastewater systems: Extending the applicability to pharmaceuticals

Compagni, R. D., Polesel, F., von Borries, K. J. F., Zhang, Z., Turolla, A., Antonelli, M., & Vezzaro, L. (2020) · Water Research · doi:10.1016/j.watres.2020.116097 · Cited by 24 · see citing works

Evidence for the formation of 6PPD-quinone from antioxidant 6PPD by cytochrome P450

Jin, L., Cheng, S., Ge, M., & Ji, L. (2024) · Journal of Hazardous Materials · doi:10.1016/j.jhazmat.2024.136273 · Cited by 23 · see citing works

Palladium-Catalyzed Cross-Coupling Reaction of Trialkylbismuthines with 2-Haloazines and Diazines

Gagnon, A., & Petiot, P. (2013) · Heterocycles · doi:10.3987/com-13-s(s)114 · Cited by 23 · see citing works

Frequency of Important CYP450 Enzyme Gene Polymorphisms in the Iranian Population in Comparison with Other Major Populations: A Comprehensive Review of the Human Data

Neyshaburinezhad, N., Ghasim, H., Rouini, M. R., Daali, Y., & Ardakani, Y. H. (2021) · Journal of Personalized Medicine · doi:10.3390/jpm11080804 · Cited by 21 · see citing works

Neurotherapeutic Effects of Quercetin and Its Metabolite Compounds on Cognitive Impairment and Parkinson’s Disease: An In Silico Study

Nguyen, H. D. (2023) · European Journal of Drug Metabolism and Pharmacokinetics · doi:10.1007/s13318-023-00816-w · Cited by 22 · see citing works

Evaluation of a new standardized enzymatic isolation protocol for human umbilical cord-derived stem cells

Buyl, K., Vanhaecke, T., Desmae, T., Lagneaux, L., Rogiers, V., Najar, M., & Kock, J. D. (2014) · Toxicology in Vitro · doi:10.1016/j.tiv.2014.12.008 · Cited by 22 · see citing works

Utility of Chimeric Mice with Humanized Liver for Predicting Human Pharmacokinetics in Drug Discovery: Comparison with in Vitro–in Vivo Extrapolation and Allometric Scaling

Naritomi, Y., Sanoh, S., & Ohta, S. (2019) · Biological and Pharmaceutical Bulletin · doi:10.1248/bpb.b18-00754 · Cited by 22 · see citing works

Development of new Coumarin-based profluorescent substrates for human cytochrome P450 enzymes

Juvonen, R. O., Ahinko, M., Huuskonen, J., Raunio, H., & Pentikäinen, O. T. (2018) · Xenobiotica · doi:10.1080/00498254.2018.1530399 · Cited by 21 · see citing works

Ion Mobility Spectrometry–Mass Spectrometry Analysis for the Site of Aromatic Hydroxylation

Shimizu, A., & Chiba, M. (2013) · Drug Metabolism and Disposition · doi:10.1124/dmd.113.051953 · Cited by 20 · see citing works

Emerging procedures and solvents in biological sample pre-treatment

Greco, V., Giuffrida, A., Locatelli, M., Savini, F., de Grazia, U., Ciriolo, L., Perrucci, M., Kabir, A., Ulusoy, H. İ., D’Ovidio, C., et al. (2023) · Advances in Sample Preparation · doi:10.1016/j.sampre.2023.100066 · Cited by 20 · see citing works

Dual mechanisms suppress meloxicam bioactivation relative to sudoxicam

Barnette, D. A., Schleiff, M. A., Osborn, L. R., Flynn, N. R., Matlock, M. K., Swamidass, S. J., & Miller, G. P. (2020) · Toxicology · doi:10.1016/j.tox.2020.152478 · Cited by 20 · see citing works

In silico prediction of UGT-mediated metabolism in drug-like molecules via graph neural network

Huang, M., Lou, C., Wu, Z., Li, W., Lee, P. W., Tang, Y., & Liu, G. (2022) · Journal of Cheminformatics · doi:10.1186/s13321-022-00626-3 · Cited by 19 · see citing works

A Robust Machine Learning Framework Built Upon Molecular Representations Predicts CYP450 Inhibition: Toward Precision in Drug Repurposing

Ouzounis, S., Panagiotopoulos, V., Bafiti, V., Zoumpoulakis, P. G., Cavouras, D., Kalatzis, I. K., Matsoukas, M., & Κάτσιλα, Θ. (2023) · OMICS A Journal of Integrative Biology · doi:10.1089/omi.2023.0075 · Cited by 19 · see citing works

Biotransformation Reactions and their Enzymes

Testa, B., & Clement, B. (2015) · Elsevier eBooks · doi:10.1016/b978-0-12-417205-0.00024-9 · Cited by 19 · see citing works

XenoNet: Inference and Likelihood of Intermediate Metabolite Formation

Flynn, N. R., Dang, N. L., Ward, M. D., & Swamidass, S. J. (2020) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.0c00361 · Cited by 19 · see citing works

Regioselective Hydroxylation of Phloretin, a Bioactive Compound from Apples, by Human Cytochrome P450 Enzymes

Nguyen, N.-A., Cao, N. T., Nguyen, T., Le, T., Cha, G., Choi, S.-K., Pan, J., Yeom, S., Kang, H., & Yun, C. (2020) · Pharmaceuticals · doi:10.3390/ph13110330 · Cited by 19 · see citing works

Metabolic Forest: Predicting the Diverse Structures of Drug Metabolites

Hughes, T. B., Dang, N. L., Kumar, A., Flynn, N. R., & Swamidass, S. J. (2020) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.0c00360 · Cited by 18 · see citing works

Machine learning for metabolomics research in drug discovery

Martinelli, D. D. (2023) · Intelligence-Based Medicine · doi:10.1016/j.ibmed.2023.100101 · Cited by 19 · see citing works

Pollutant profile complexity governs wastewater removal of recalcitrant pharmaceuticals

Suleiman, M., Lay, N. L., Demaria, F., Kolvenbach, B. A., Cretoiu, M. S., Petchey, O. L., Jousset, A., & Corvini, P. F.-X. (2024) · The ISME Journal · doi:10.1093/ismejo/wrae033 · Cited by 18 · see citing works

Identification and characterization of metabolites of ASP015K, a novel oral Janus kinase inhibitor, in rats, chimeric mice with humanized liver, and humans

Nakada, N., & Oda, K. (2015) · Xenobiotica · doi:10.3109/00498254.2015.1019594 · Cited by 18 · see citing works

Synergy between Experiments and Computations: A Green Channel for Revealing Metabolic Mechanism of Xenobiotics in Chemical Toxicology

Ji, L. (2020) · Chemical Research in Toxicology · doi:10.1021/acs.chemrestox.9b00448 · Cited by 17 · see citing works

Chapter 32. Mechanistic Aspects of Xenobiotic Metabolism as Related to Drug Design

Armstrong, R. N. (1988) · Annual reports in medicinal chemistry · doi:10.1016/s0065-7743(08)60860-x · Cited by 1 · see citing works

Xenobiotic Metabolising Enzymes: Impact on Pathologic Conditions, Drug Interactions and Drug Design

Rekka, E. A., Kourounakis, P. N., & Pantelidou, M. (2019) · Current Topics in Medicinal Chemistry · doi:10.2174/1568026619666190129122727 · Cited by 26 · see citing works

CYP 450 Enzymes in Drug Discovery and Development: An Overview

Xu, L. S., Das, B., & Prakash, C. (2012) · Encyclopedia of Drug Metabolism and Interactions · doi:10.1002/9780470921920.edm117 · Cited by 7 · see citing works

Chapter 12 Cytochrome p450 (cyp) and udp-glucuronosyltransferase (ugt) enzymes: role in drug metabolism, polymorphism, and identification of their involvement in drug metabolism

Ghosal, A., Ramanathan, R., Kishnani, N. S., Chowdhury, S. K., & Alton, K. B. (2005) · Progress in pharmaceutical and biomedical analysis · doi:10.1016/s1464-3456(05)80014-6 · Cited by 2 · see citing works

Role of drug-metabolizing enzymes in biotransformation of drugs

Yaqoob, A., Rehman, Q., Rehman, K., Akash, M. S. H., Hussain, I., & Ahmad, R. (2022) · Elsevier eBooks · doi:10.1016/b978-0-323-95120-3.00013-0 · Cited by 8 · see citing works