• Human Microbiome and Direct Effects on Drug Metabolism

  "Sites and Types of Metabolism for Drugs Following Oral or Intravenous Administration"21 Attribution: Slightly modified from Figure 1 in reference 21 (Wilson ID Nicholson JK Gut Microbiome Interactions with Drug Metabolism, Efficacy and Toxicity Trans Res 2017 January; 179:204-222 https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5718288&blobtype=pdf ) The gut microbiota is associated with a very large number of enzymes which may participate in metabolizing drugs and xenobiotics generally as well as altering pharmacological effects.22  As noted earlier, the gut microbiota is associated with about 3.3 million unique genes or about 150 times more than those comprising the human genome. The major human gut bacterial phyla include mainly: Firmicutes Bacteroidetes Actinobacteria Proteobacteria Verrucomicrobia22 A screening study considered 76 intestinal bacteria with respect to their capability of metabolizing 271 oral drugs.22,23  About two-thirds of screen drugs were metabolized by at least one bacterial strain.23  Analysis of gene sequenced gut microorganisms verified the presence of enzyme classes associated with xenobiotic metabolism.22 These classes include:22  Hydrolases  Transferases Oxidoreductases Lyases  Although the gut microbiota exhibits the enzymatic capability to catalyze a variety of reactions, the most significant biotransformations center around reductive metabolism and hydrolysis (typically conjugation reactions).21 An example of gut microbiome mediated reductive metabolism is the reduction of azo-"antibacterial pro-drugs" related to sulfanilamide (prontosil and neoprontosil). Reductive metabolism yields the active aminosalicylic agent, derived from compounds such as olsalazine (Dipentum), ipsalazide, balsalazide, and sulfasalazine (Azulfidine).21 Other microbiome-mediated biotransformations include demethylation reactions involving methamphetamine and 4'-hydroxymethamphetamine. An example of a deamination reaction is the conversion of 5-fluorocytosine to 5-fluorouracil. Conversion of 5-Fluorocytosine to 5-fluorouracil24 Attribution: Rooseboom M Commandeur JNM Vermeulen NPE Enzyme-Catalyzed Activation of Anticancer Prodrugs Pharmacological reviews (2004)56. 53-102 https://pubmed.ncbi.nlm.nih.gov/15001663/   Reduction Reactions Associated with the Microbiome15 The anti-inflammatory agent sulfasalazine is activated by a reduction reaction. Microbial enzymes that participate in this process include: Bacterioides fragilis Streptococcus faecium Streptococcus faecalis. The antibiotic chloramphenicol is involved in a deactivation reaction (nitroreduction) that is associated with several microbiome microbes including: Escherichia coli Haemophilus influenzae Neisseria meningitidis Bacterioides fragilis. Digoxin, a digitalis class cardiac positive inotrope, is subject to deactivation by a reduction reaction catalyzed by enzymes synthesized by Eggerthella lenta. Fluorouracil categorized as an anti-neoplastic (anticancer) agent may be deactivated by microbiome-mediated reduction reaction. Omeprazole, a proton-pump inhibitor used in treating stomach disorders, is deactivated by sulfoxide reduction they can be catalyzed by enzymes elaborated from Bacillus megaterium. Attribution:  Derived from Table 6-1, reference 15   Other drugs undergoing Reduction Reactions Associated with the Microbiome:  Table 1 reference 21 (Many more examples are listed!) Wilson ID Nicholson JK Gut Microbiome Interactions with Drug Metabolism, Efficacy and Toxicity Trans Res 2017 January; 179:204-222 (Table 1, page 28 of the pdf)  https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5718288&blobtype=pdf     Some Acylation Reactions Associated with the Microbiome15 Tobramycin is an example antibiotic that is modified by acylation reactions (proprionylation). Tobramycin is classified as aminoglycoside-type antibiotic derived from the bacteria Streptomyces tenebrarius. This antibiotic is especially useful in treating gram-negative infections such as some species of Pseudomonas (Pseudomonas aeruginosa), often in the context of cystic fibrosis patient management. Although tobramycin is generally very poorly metabolized, microbes that metabolize tobramycin have been described in "culture cystic fibrosis communities" Tobramycin (Stick Model) Attribution: Fvasconcellos (talk · contribs), Public domain, via Wikimedia Commons https://commons.wikimedia.org/wiki/File:Tobramycin_1lc4.png     Kanamycin A15,25  An example of an aminoglycoside, kanamycin A, is modified through acetylation. Within the microbiome, the microbe identified as capable of inactivating the parent aminoglycoside drug is Mycobacterium tuberculosis. Kanamycin although not a first-line treatment, may be used to manage tuberculosis and severe bacterial infection on a short-term basis (7-10 days). This antibiotic was originally isolated from the bacterium Streptomyces kanamyceticus and is no longer marketed in the United States.  Kanamycin A Attribution: NEUROtiker, Public domain, via Wikimedia Commons https://commons.wikimedia.org/wiki/File:Kanamycin_A.sv     Simvastatin15,26  Simvastatin (Zocor) is an anti-cholesterol agent. Simvastatin and other "statin" drugs act by inhibiting HMG-CoA reductase (3-hydroxy-3-methyl-glutaryl-coenzyme A reductase). Simvastatin is made from Aspergillus terreus and the drug remains widely prescribed in the United States. The drug is deactivated by a hydroxylation mechanism and such deactivation can be noted in cultured gut community (microbiome). Simvastatin Attribution: CC BY-SA 3.0 <https://creativecommons.org/licenses/by-sa/3.0>, via Wikimedia Commons https://commons.wikimedia.org/wiki/File:Simvastatin.svg Attribution: CC BY-SA 3.0 <https://creativecommons.org/licenses/by-sa/3.0>, via Wikimedia Commons https://commons.wikimedia.org/wiki/File:Simvastatin3Dan.gif     Some Hydrolysis Reactions Associated with the Microbiome15  Lovastatin (Mevacor)15, 28 Lovastatin (Mevacor) is used for treating dyslipidemia, especially elevated cholesterol levels. The mechanism of lovastatin action is inhibition of the enzyme HMG-CoA reductase. Lovastatin itself is metabolized by the cytochrome P450 hepatic microsomal enzymes system. CYP3A4 is the P450 isoform primarily responsible for lovastatin metabolism. Lovastatin itself is a "pro-drug," requiring hydrolysis by carboxylesterases for activation. In humans, at least three esterases exist which catalyzes reaction: one in plasma and two in the liver.27 The human microbiome also supports ester hydrolysis thus contributing to lovastatin activation.15 Lovastatin (Mevacor) Attribution: Panoramix303, CC BY-SA 3.0 <https://creativecommons.org/licenses/by-sa/3.0>, via Wikimedia Commons https://commons.wikimedia.org/wiki/File:Lovastatin.svg     Irinotecan (Camptosar):29 Irinotecan (Camptosar), an antineoplastic agent, is a prodrug converted by carboxylesterase-converting enzyme (hepatic and other tissues) to the active anticancer metabolite, SN-38. Irinotecan is FDA approved for treating metastatic colorectal cancer, given in combination with 5- fluorouracil / leukovorin. Irinotecan, given as a single agent, is classified as a second-line treatment for progressive colorectal cancer following 5-fluorouracil-based treatment. Irinotecan has also been used in combination with carboplatin or cisplatin in small-cell lung cancer (extensive disease). A partial list of other uses include refractory esophageal cancer, gastric cancer, anaplastic gliomas, and glioblastomas. Inactivation of the active SN-38 metabolite is catalyzed by a phase II reaction, glucuronidation, resulting in the formation of SN-38-glucuronide. The anticancer mechanism of action of irinotecan (SN-38) is based on topoisomerase inhibition which leads to blockade of DNA replication. Irinotecan induced toxicities (e.g. diarrhea and neutropenia) are potentially life-threatening and appear caused by SN-38. E. coli associated with the intestinal microbiome produce the enzyme beta-glucuronidase which converts SN-38-glucuronide (inactive) back to the active form, SN-38 which may increase the likelihood of diarrhea as well as localized injury.18 Other microbiome bacteria which may participate in the reactivation SN-38-glucuronide through deglucuronidation include: Lactobacillus rhamnosus Ruminococcus gnavus Faecalibacterium prausnitzii.15   Irinotecan (Camptosar) Attribution: "Ball-and-stick model of irinotecan molecule. The structures taken from ChemSpider ID 54825" MarinaVladivostok, CC0, via Wikimedia Commons https://commons.wikimedia.org/wiki/File:Irinotecan_ball-and-stick.png       Diltiazem (Cardizem)30: Diltiazem (Cardizem) is classified as a calcium channel blocker useful in managing hypertension, angina inappropriate for use in certain cardiac arrhythmias. The mechanism of action of diltiazem involves smooth muscle relaxation in arterial walls by blocking calcium entry. Diltiazem is metabolized through deacetylation as well as other pathways involving O-demethylation, N-oxidation and oxidative deamination. "Diltiazem Metabolic Pathways in Humans"31 Attribution:  Figure 1 from reference below (31): Kurokawa T Fukami T Nakajima M Characterization of Species Differences in Tissue Diltiazem Deacetylation Identifies Ces2A as a Rat-Specific Diltiazem Deacetylase. Drug Metabolism and Disposition August 2015, 43(8) 1218-1225. https://dmd.aspetjournals.org/content/43/8/1218/tab-figures-data   Diltiazem (Cardizem) Attribution: MarinaVladivostok, CC0, via Wikimedia Commons https://commons.wikimedia.org/wiki/File:Diltiazem_ball-and-stick.png The microbiome bacteria, Bacterioides thetaiotamicron, promotes the deacetylation step and in part accounts for diminished diltiazem activity.15     Example Demethylation Reaction Associated with the Microbiome15 Altretamine (Hexalen, hexamethylmelamine) is classified as an antineoplastic drug approved over 30 years ago by the FDA. It may be used as palliation in individuals with recurrent ovarian cancer subsequent to first-line treatment with cisplatin and/or and alkylating agent-based combination protocol. Altretamine is described as an alkylating class anticancer drug.32 Altretamine is converted to formaldehyde, considered to be a weak alkylating agent which is formed as a result of a demethylation reaction (N-demethylation). Following oral administration altretamine exhibits notable first pass effects resulting in both mono-and didemethylated derivatives.32  As a consequence of these observations, demethylation reactions may be described as activating. Altretamine Attribution: Jynto, CC0, via Wikimedia Commons https://commons.wikimedia.org/wiki/File:Altretamine-3D-balls.png Demethylation reactions, in addition to those catalyzed by liver enzymes, are also associated with "pooled fecal microbial culture" bacteria.15   Example Decarboxylation Reaction Associated with the Microbiome15  Another example in which the gut microbiome may modify a drug involves the enzyme tyrosine decarboxylase and inactivation of the Parkinson's disease drug levodopa (L-DOPA). Tyrosine decarboxylase is expressed by Enterococcus and Lactobacillus and more generally in "cultured gut community."15 Extended treatment with L-DOPA appears to increase tyrosine decarboxylase gene expression consistent with reduced L-DOPA treatment effectiveness over time.19   Primary Sources for Table 6-1 Attribution:  Derived from Table 6-1, reference 15: Tsunoda SM Dorrestein PC Knight Rob Chapter 6 The Gastrointestinal Microbiome and Drug Response in Goodman & Gilman's The Pharmacological Basis of Therapeutics (Brunton LL Knollmann BC, eds) 14e McGraw-Hill 2023. Primary sources: Wilson ID Nicholson JK Metformin alters the gut microbiome of individuals with treatment-naïve type 2 diabetes, contributing to the therapeutic effects of the drug. Nat Med, 2017, 23:850-858.`https://pubmed.ncbi.nlm.nih.gov/28530702/ Guthrie L, et al. The human gut chemical landscape predicts microbe-mediated by transformation of foods and drugs. Elife, 2019, 8:e 42866. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6559788/ Letertre MPM, et al. A two-way interaction between methotrexate  and the gut microbiota to improve drug outcomes. Cell Host Microbe, 2019, 19:3326-3339. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7426014/ Aura AM et al. Drug metabolome of the simvastatin formed by human intestinal microbiota in vitro. Mol Biosyst, 2011, 7: 437-446. https://pubmed.ncbi.nlm.nih.gov/21060933/ Swanson HI Drug metabolism by the host in gut microbiota: a partnership or rivalry? Drug Metab Dispos, 2015, 43: 1499-1504. https://pubmed.ncbi.nlm.nih.gov/26261284/ Pellock SJ Redinbo MR Glucuronides in the gut:  sugar-driven symbioses between microbe in host. J Biol Chem, 2017, 292:8569-8576. https://pubmed.ncbi.nlm.nih.gov/28389557/ Biernat KA, et al. Structure, function and inhibition of drug reactivating human gut microbial β-glucuronidases. Sci Rep, 2019, 9: 825. https://www.nature.com/articles/s41598-018-36069-w.pdf Tsodikov OV, et al. A random sequential mechanism of aminoglycoside acetylation by Mycobacterium tuberculosis Eis protein. PLos ONE, 2014, 9: e92370. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0092370 Jarmusch AK, et al. Enhanced characterization of drug metabolism and the influence of the intestinal microbiome: a pharmacokinetic, microbiome, and untargeted metabolomics study. Clin Transl Sci, 220, 13:972-984. https://ascpt.onlinelibrary.wiley.com/doi/full/10.1111/cts.12785 Jang HH, et al. Regioselective C-H hydroxylation of omeprazole sulfide by Bacillus megaterium  CYP102A1 to produce a human metabolite. Biotechnol Lett, 2017, 39:105-112. https://pubmed.ncbi.nlm.nih.gov/27640009/ Guo Y, et al. Gut microbiota in reductive drug metabolism. Prog Mol Biol Transl Sci , 220, 171:63-93.  https://pubmed.ncbi.nlm.nih.gov/32475528/ Zimmermanm M, et al. Mapping human microbiome drug metabolism by gut bacteria in their genes. Nature, 2019, 570:462-467. https://pubmed.ncbi.nlm.nih.gov/31158845/ Clark G, et al. Gut reactions: breaking down xenobiotic-microbiome interactions. Pharmacol Rev, 2019, 71:198- 224. https://pharmrev.aspetjournals.org/content/71/2/198 Guthrie L Kelly L Bringing microbiome-drug interaction research into the clinic. EBioMedicine, 2019, 44:708-715. https://pubmed.ncbi.nlm.nih.gov/31151933/ Koppel N, et al. Chemical transformation of xenobiotics by the human gut microbiota. Science, 2017, 356 (6344): eaag2770. https://www.science.org/doi/10.1126/science.aag2770 Sun C. et al. Mechanisms of gastrointestinal microflora drug metabolism in clinical practice. Saudi Pharm J, 2019, 27:1146-1156.  https://www.researchgate.net/publication/336789262_Mechanisms_of_gastrointestinal_microflora_on_drug_metabolism_in_clinical_practice

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