Definition and research guide
This page combines a MeSH definition, publication statistics and selected research abstracts. It is a starting point for reading the literature, not a medical textbook or a systematic evidence review.
Content available: 4 complete abstracts (747 words), 10 references. Full article text is not stored or reproduced here; follow the PMID, DOI or PMC links to read the original sources and their access terms.
Definition
The chemical alteration of an exogenous substance by or in a biological system. The alteration may inactivate the compound or it may result in the production of an active metabolite of an inactive parent compound. The alterations may be divided into metabolic detoxication, phase I and metabolic detoxication, phase II.
Definition: NLM Medical Subject Headings (MeSH) scope note (Public domain (U.S. National Library of Medicine); attribution requested). View the MeSH record.
Where it fits in the MeSH classification
- Broader topics
- Metabolism; Pharmacokinetics
- Narrower topics
- Activation, Metabolic; Inactivation, Metabolic
Related concepts
- Metabolic Detoxication
- Phase
Research landscape
PubMed indexes 42,982 records tagged with the MeSH heading “Biotransformation” (counts retrieved 2026-10-29). 3,649 of them (8.5%) were published from 2020 onward, and the busiest period so far is through 1999 with 21,230 records.
Reviews account for 5,380 records (12.5%) and meta-analyses for 31. Randomized controlled trials number 490 (1.1%) as a share of all records on the topic. Randomized trials make up only a small share of this literature, so much of what is known comes from laboratory, observational or descriptive work.
Show the data
| Period | Records |
|---|---|
| through 1999 | 21,230 |
| 2000-2009 | 7,561 |
| 2010-2019 | 10,542 |
| 2020 onward | 3,649 |
Publication-type chart data
| Type | Records | Share |
|---|---|---|
| Reviews | 5,380 | 12.5% |
| Meta-analyses | 31 | 0.1% |
| Randomized controlled trials | 490 | 1.1% |
Method: PubMed query "Biotransformation"[MeSH Terms] with publication-type and date filters, retrieved 2026-10-29.
Reading the evidence in pharmacology
Drug evidence builds in layers: laboratory pharmacology describes how a compound acts, pharmacokinetic studies describe how the body handles it, and randomized trials test whether it helps and what harms it causes. Post-marketing surveillance and observational studies reveal rarer adverse effects but cannot prove causation. This page is educational and is not a recommendation to start, stop or change any medicine; decisions about treatment belong with a qualified clinician.
Evidence from open-access studies
These open-access studies come from PubMed’s best-match results for this heading (papers whose main topic it is), ranked here by citation count, with one recent addition. Each abstract is reproduced in full under its recorded open licence so that you can read the authors’ own words. They illustrate the literature; they are not a systematic summary of it. Citation counts measure attention, not reliability or clinical benefit.
| Study / authors | Year | Source label / design | Europe PMC citations | Licence / source |
|---|---|---|---|---|
| Cytochrome P450 Enzymes and Drug Metabolism in Humans | 2021 | Review article Design not recorded in structured metadata | 671 | cc by PMID 34884615 · DOI · PMC8657965 |
| Gut microbiota mediate caffeine detoxification in the primary insect pest of coffee | 2015 | Research article Design not recorded in structured metadata | 342 | cc by PMID 26173063 · DOI · PMC4510693 |
| Heavy metal stress and some mechanisms of plant defense response | 2015 | Review article Design not recorded in structured metadata | 341 | cc by PMID 25688377 · DOI · PMC4321847 |
| Biotransformation of Coumarins: Mechanisms and Pharmaceutical Potential | 2026 | Review article Design not recorded in structured metadata | 0 | cc by PMID 42588434 · DOI · PMC13468388 |
Cytochrome P450 Enzymes and Drug Metabolism in Humans [1]
Abstract reading summary — source excerpts
- Opening excerpt
- Human cytochrome P450 (CYP) enzymes, as membrane-bound hemoproteins, play important roles in the detoxification of drugs, cellular metabolism, and homeostasis.
- Closing excerpt
- Additionally, genetic and epigenetic factors, as well as several intrinsic and extrinsic factors that contribute to interindividual variation in drug response are also reviewed, to reveal the multifarious and important roles of CYP-mediated metabolism and elimination in drug therapy.
- Interpretation limits
- Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (196 words)
Human cytochrome P450 (CYP) enzymes, as membrane-bound hemoproteins, play important roles in the detoxification of drugs, cellular metabolism, and homeostasis. In humans, almost 80% of oxidative metabolism and approximately 50% of the overall elimination of common clinical drugs can be attributed to one or more of the various CYPs, from the CYP families 1-3. In addition to the basic metabolic effects for elimination, CYPs are also capable of affecting drug responses by influencing drug action, safety, bioavailability, and drug resistance through metabolism, in both metabolic organs and local sites of action. Structures of CYPs have recently provided new insights into both understanding the mechanisms of drug metabolism and exploiting CYPs as drug targets. Genetic polymorphisms and epigenetic changes in CYP genes and environmental factors may be responsible for interethnic and interindividual variations in the therapeutic efficacy of drugs. In this review, we summarize and highlight the structural knowledge about CYPs and the major CYPs in drug metabolism. Additionally, genetic and epigenetic factors, as well as several intrinsic and extrinsic factors that contribute to interindividual variation in drug response are also reviewed, to reveal the multifarious and important roles of CYP-mediated metabolism and elimination in drug therapy.
Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 34884615 · DOI · PMC8657965
Gut microbiota mediate caffeine detoxification in the primary insect pest of coffee [2]
Abstract reading summary — source excerpts
- Opening excerpt
- The coffee berry borer (Hypothenemus hampei) is the most devastating insect pest of coffee worldwide with its infestations decreasing crop yield by up to 80%.
- Closing excerpt
- hampei, and re-inoculation of antibiotic-treated insects with an isolated Pseudomonas strain reinstates caffeine-degradation ability confirming their key role.
- Interpretation limits
- Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (146 words)
The coffee berry borer (Hypothenemus hampei) is the most devastating insect pest of coffee worldwide with its infestations decreasing crop yield by up to 80%. Caffeine is an alkaloid that can be toxic to insects and is hypothesized to act as a defence mechanism to inhibit herbivory. Here we show that caffeine is degraded in the gut of H. hampei, and that experimental inactivation of the gut microbiota eliminates this activity. We demonstrate that gut microbiota in H. hampei specimens from seven major coffee-producing countries and laboratory-reared colonies share a core of microorganisms. Globally ubiquitous members of the gut microbiota, including prominent Pseudomonas species, subsist on caffeine as a sole source of carbon and nitrogen. Pseudomonas caffeine demethylase genes are expressed in vivo in the gut of H. hampei, and re-inoculation of antibiotic-treated insects with an isolated Pseudomonas strain reinstates caffeine-degradation ability confirming their key role.
Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 26173063 · DOI · PMC4510693
Heavy metal stress and some mechanisms of plant defense response [3]
Abstract reading summary — source excerpts
- Opening excerpt
- Unprecedented bioaccumulation and biomagnification of heavy metals (HMs) in the environment have become a dilemma for all living organisms including plants.
- Closing excerpt
- Additionally, AM fungi can enhance activities of antioxidant defense machinery of plants.
- Interpretation limits
- Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (199 words)
Unprecedented bioaccumulation and biomagnification of heavy metals (HMs) in the environment have become a dilemma for all living organisms including plants. HMs at toxic levels have the capability to interact with several vital cellular biomolecules such as nuclear proteins and DNA, leading to excessive augmentation of reactive oxygen species (ROS). This would inflict serious morphological, metabolic, and physiological anomalies in plants ranging from chlorosis of shoot to lipid peroxidation and protein degradation. In response, plants are equipped with a repertoire of mechanisms to counteract heavy metal (HM) toxicity. The key elements of these are chelating metals by forming phytochelatins (PCs) or metallothioneins (MTs) metal complex at the intra- and intercellular level, which is followed by the removal of HM ions from sensitive sites or vacuolar sequestration of ligand-metal complex. Nonenzymatically synthesized compounds such as proline (Pro) are able to strengthen metal-detoxification capacity of intracellular antioxidant enzymes. Another important additive component of plant defense system is symbiotic association with arbuscular mycorrhizal (AM) fungi. AM can effectively immobilize HMs and reduce their uptake by host plants via binding metal ions to hyphal cell wall and excreting several extracellular biomolecules. Additionally, AM fungi can enhance activities of antioxidant defense machinery of plants.
Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 25688377 · DOI · PMC4321847
Biotransformation of Coumarins: Mechanisms and Pharmaceutical Potential [4]
Abstract reading summary — source excerpts
- Opening excerpt
- Coumarins are compounds that are naturally found in various plants and are known for their potential pharmacological characteristics, such as anti-inflammatory, antibacterial, antiparasitic, and anticoagulant activities.
- Closing excerpt
- This review provides a comprehensive overview of the microbial transformation of coumarins, highlighting the role of various microorganisms, enzymatic mechanisms, and the transformation processes.
- Interpretation limits
- Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (206 words)
Coumarins are compounds that are naturally found in various plants and are known for their potential pharmacological characteristics, such as anti-inflammatory, antibacterial, antiparasitic, and anticoagulant activities. Despite the potential pharmacological properties, structural modification of coumarins is important to enhance the biological activity, solubility, bioavailability, and various therapeutic characteristics. Microbial transformation is a promising method to modify coumarins since this method offers regioselective and stereospecific transformation, which is challenging to obtain through chemical synthesis. Various microorganisms, including bacteria and fungi, play an essential role in the microbial transformation of coumarins. These microorganisms employ enzymatic mechanisms involving various enzymes to catalyze several reactions, such as hydroxylation, oxidation, reduction, and demethylation. Among these microbial transformation processes, the demethylation process is a significant mechanism for altering the bioactivity of coumarins by converting methoxy groups into hydroxyl groups. Despite all the advantages, microbial transformation also has limitations such as low substrate specificity, contamination during inoculation, variable enzymatic activity, and challenges to scale up the production of bioactive coumarins. These challenges can be addressed through the optimization of the bioprocess to enhance the efficiency of microbial coumarin metabolism. This review provides a comprehensive overview of the microbial transformation of coumarins, highlighting the role of various microorganisms, enzymatic mechanisms, and the transformation processes.
Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 42588434 · DOI · PMC13468388
Key reviews and meta-analyses
The most cited review-type papers among PubMed’s best-match results for this heading, listed with bibliographic details only. Follow the links for the full text and access terms.
- Research article Recent advances in 2D and 3D in vitro systems using primary hepatocytes, alternative hepatocyte sources and non-parenchymal liver cells and their use in investigating mechanisms of hepatotoxicity, cell signaling and ADME [5]
- Research article Clinical importance of the cytochromes P450 [6]
- Research article Emerging roles of Nrf2 and phase II antioxidant enzymes in neuroprotection [7]
- Research article Drug Metabolism in the Liver [8]
- Research article Circadian rhythms: mechanisms and therapeutic implications [9]
- Research article Phase II drug metabolizing enzymes [10]
References
- Zhao M, Ma J, Li M, Zhang Y, Jiang B, Zhao X, et al.. Cytochrome P450 Enzymes and Drug Metabolism in Humans. . 2021. PMID 34884615 · DOI · PMC8657965
- Ceja-Navarro JA, Vega FE, Karaoz U, Hao Z, Jenkins S, Lim HC, et al.. Gut microbiota mediate caffeine detoxification in the primary insect pest of coffee. . 2015. PMID 26173063 · DOI · PMC4510693
- Emamverdian A, Ding Y, Mokhberdoran F, Xie Y. Heavy metal stress and some mechanisms of plant defense response. . 2015. PMID 25688377 · DOI · PMC4321847
- Saragih M, Szczepańska E, Olejniczak T. Biotransformation of Coumarins: Mechanisms and Pharmaceutical Potential. . 2026. PMID 42588434 · DOI · PMC13468388
- Godoy P, Hewitt NJ, Albrecht U, Andersen ME, Ansari N, Bhattacharya S, et al.. Recent advances in 2D and 3D in vitro systems using primary hepatocytes, alternative hepatocyte sources and non-parenchymal liver cells and their use in investigating mechanisms of hepatotoxicity, cell signaling and ADME. Arch Toxicol. 2013. PMID 23974980 · DOI · PMC3753504
- Nebert DW, Russell DW. Clinical importance of the cytochromes P450. Lancet. 2002. PMID 12387968 · DOI
- Zhang M, An C, Gao Y, Leak RK, Chen J, Zhang F. Emerging roles of Nrf2 and phase II antioxidant enzymes in neuroprotection. Prog Neurobiol. 2013. PMID 23025925 · DOI · PMC3623606
- Almazroo OA, Miah MK, Venkataramanan R. Drug Metabolism in the Liver. Clin Liver Dis. 2017. PMID 27842765 · DOI
- Levi F, Schibler U. Circadian rhythms: mechanisms and therapeutic implications. Annu Rev Pharmacol Toxicol. 2007. PMID 17209800 · DOI
- Jancova P, Anzenbacher P, Anzenbacherova E. Phase II drug metabolizing enzymes. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub. 2010. PMID 20668491 · DOI
About this article
- Sources
- NLM Medical Subject Headings (definition, synonyms); NCBI PubMed (counts, identifiers); Europe PMC (open-access abstracts and citation counts).
- Verification
- Every reference was resolved against PubMed on 2026-10-31; title, year and DOI matched.
- Review state
- automated source verified; no human expert review has been recorded yet.
- Version
- 1, last updated 2026-10-29.
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Evidence strength
EvidenceHelix's computed view of the study designs behind this topic: how common meta-analyses, randomized trials and reviews are, how recent the literature is, and a plain-language reading. It describes the design mix of the literature. It is not a quality appraisal of any study, and it is not medical advice.