INNER WORKINGS

Microbiota munch onmedications, causing bigeffects on drug activityJyoti Madhusoodanan, Science Writer

Millions of patients with Parkinson’s disease rely onthe drug Levodopa for relief from tremors, slowedmovement, and other motor symptoms. But manypatients experience side effects such as cardiac ar-rhythmias, nausea, and gastrointestinal problems.Levodopa’s side effects and benefits vary widelyamong patients. Those puzzling disparities, it turnsout, have a lot to do with the microbes in their guts.

Earlier this year, chemist Emily Balskus and hercolleagues at Harvard University in Cambridge, MA,found that many side effects were the result of abacterial decarboxylase enzyme, produced by the gutmicrobe Enterococcus faecalis. Levodopa is an inac-tive form of the neurotransmitter dopamine and must

be activated by a human decarboxylase enzyme towork. Activate the medicine too soon—before itcrosses the blood–brain barrier—and side effects willoccur. To block this premature activation, drug makershave long added an enzyme inhibitor known as carbo-dopa to Levodopa. But Balskus and her colleaguesfound that although carbodopa works on human en-zymes, it does not inhibit bacterial decarboxylase. Infact, the bacterial enzyme acts on the drug in the in-testines before it crosses the blood–brain barrier, trig-gering problematic symptoms (1).

Balskus and others are learning that the interac-tions among our microbes and medications are farmore complex than previously assumed, potentially

Researchers have found that many side effects of the Parkinson’s drug Levodopa were the result of a bacterialdecarboxylase enzyme, produced by the commensal gut microbe E. faecalis (pictured in colored-scanning electronmicrograph). Image credit: ScienceSource/Dennis Kunkel Microscopy.

Published under the PNAS license.First published April 8, 2020.

www.pnas.org/cgi/doi/10.1073/pnas.2003785117 PNAS | April 28, 2020 | vol. 117 | no. 17 | 9135–9137

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causing toxic side effects or altering drugs’ activity.Medications left unabsorbed in the body are usuallymarked for removal in the liver and then transportedto the gut. Although human cells no longer recognizethese excretory products, intestinal bacteria can act oninactivated drug molecules. This stage could be la-beled the “fourth phase of drug metabolism,” sayschemist Matthew Redinbo of the University of NorthCarolina at Chapel Hill. “Bacteria perform incrediblysophisticated chemical reactions that no human sys-tems are able to do.”

Using a combination of chemistry and genomics,researchers are now beginning to identify thesemechanisms. As they do, they’re uncovering ways toinhibit the microbial enzymes that cause distressingside effects. The end result could be drugs that areless toxic, as well as better predictions about how pa-tients respond to medications.

Potent PathwaysMicrobes’ drug-altering abilities have been known fornearly a century. In the preantibiotic era, German re-searchers discovered that the antimicrobial drugprontosil—once it was digested by enzymes in theliver and kidney as well as by gut bacteria—became apotent sulfanilamide, effective against many gram-positive bacteria (2).

Then there’s the case of the antiviral drug sor-ivudine. The drug turned deadly in 18 cancer patients,triggering its removal just two months after FDA ap-proval in the 1990s. Mouse studies later suggestedthat intestinal microbes had likely digested sorivudineinto a product that blocked the liver enzymes neededto metabolize the common cancer drug 5-fluorouracil(5-FU)—leading to a lethal buildup of 5-FU (3).

Only recently have researchers begun to systemati-cally dissect the pathways involved in such unexpectedinteractions. Microbiologist Andrew Goodman of theYale School of Medicine was studying the links betweendietary chemicals and gut bacteria when he discoveredthat certain species depended on specific vitamins fortheir survival. Remove the chemical, and the commensal

bacteria die out. “It was really in the process of trying tounderstand that conversation between commensals andthe host diet that we started thinking about other smallmolecules that gut microbes might be recognizing andthen transforming for their own purposes,” Goodmansays. “That’s what led us to think about medical drugs.”

In a recent study, Goodman and his colleaguesmeasured how 76 different species of human gutbacteria digested 271 common drugs that are takenorally. They found that even when 80% of a medica-tion dose quickly entered circulation, microbial en-zymes could act on the remaining 20% to producetoxic metabolites. Although the team chose drugs thatwere chemically very different from one another, theyfound that at least two-thirds of the molecules weremetabolized by at least one gut microbe studied (4).“The capacity of these microbes to metabolize thesedrugs was much broader than we had expected,”Goodman says.

It wasn’t easy to predict precisely which medica-tions would be metabolized. “Drugs with chemicalstructures that look like perfect bait for microbes wereuntouched for some reason,” Goodman says. “Anddrugs that didn’t have anything that looked like amicrobe might recognize it were very efficientlydegraded.”

In experiments with human microbiota samples,the researchers have begun to spot the enzymes thatcan help predict which bacterial communities arelikely to metabolize drugs. The work is “just the be-ginning of understanding the degree to which almosteverything in our bodies is subject to transformationby microbes,” Redinbo says.

Redinbo and others want to understand the mi-crobial enzymes that act on drug molecules. Typically,the unabsorbed remnants of orally consumed drugsare transported to the liver, where enzymes inactivatethem and add tags such as glucuronic acid to mark themolecules for excretion. Then they are transported tothe intestines via bile acids. The chemical tags makeinactivated drugs unusable by human cells.

A person’s microbiome can determine whether they will experience a drug's benefits, side effects, toxicity, or somecombination. Image credit: From ref. 7. Reprinted with permission from AAAS.

9136 | www.pnas.org/cgi/doi/10.1073/pnas.2003785117 Madhusoodanan

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But gut bacteria see themolecules as food sources,and they carry enzymes known as β-glucuronidasesthat can chomp up the glucuronic acid for energyand toss the drug molecule—now reactivated—backinto the intestines. Redinbo’s studies began with theanticancer drug irinotecan, which can cause intense,delayed diarrhea as a result of this bacterial activity.They also found that a molecule they named SBX-1inhibited these microbial enzymes and thus couldblock these toxic effects (5). “That was really the firstdemonstration that the microbiota contained drug-gable targets, and that they could be targeted for aclinical outcome,” Redinbo says.

Targeting Bacterial EnzymesThe team is also working to identify analogs of SBX-1 that might prove effective against other bacterialenzymes. Approximately 25% of clinical drugs, in-cluding several nonsteroidal inflammatory drugs, aretargeted by bacterial glucuronidases. So enzyme in-hibitors that block this activity could potentially re-duce the toxic side effects of various other drugs.

In a similar vein, Stanley Hazen of the ClevelandClinic in Ohio and his team are working on drugs thatcan block gut microbes from synthesizing trimethyl-amine N-oxide (TMAO), a potentially undesirablemolecule that’s produced from fatty foods such as eggyolks, meat, and dairy. TMAO accelerates the buildupof plaque on artery walls and can lead to cardiovas-cular diseases. In animal studies, the researchers havefound that blocking microbial TMAO synthesis re-duced fatty deposits and could serve as a route totreating cardiac and metabolic disorders (6).

Thanks to recent genomic advances, drug devel-opers are finding ways to tailor molecules to specificvariants in the human genome. These so-calledpharmacogenomic approaches allow patients tochoose from amongst a few different drugs based onthe person’s genetic profile. But if no good optionsexist, it may soon be feasible to tweak the patient’smicrobiome instead, Goodman says. “We have theopportunity to alter a person’s microbiome in a waythat we really wouldn’t think about altering their ge-nome to improve their response to a drug.”

Matching Meds and MicrobesTo perfect drug-modulating microbiome interven-tions, researchers will need to better characterize drugfunction and better gauge the effects of diet and gutcommunity on microbial enzymes, says microbiologistPeter Turnbaugh of the University of California, SanFrancisco.

“We don’t have a simple rule to say this drug won’tbe metabolized and that one will,” Turnbaugh says.“And even assuming yourmicrobiome has some enzymethat affects a compound, we really don’t understandwhatdetermines whether or not those enzymes are active.”

Elucidating these data could also boost the pro-cess of drug development. Many potential drugs arediscarded early in development because of toxic sideeffects. But if those effects are the result of microbialmeddling—and if researchers can identify the sourcesof such interference—the rewards could be signifi-cant: older drugs resurrected, and perhaps new onestailored to patients based on their gut microbiota.“The idea that the microbiome would be used inpreclinical drug development is still sort of contro-versial, and definitely not the standard for drugs onthe market,” Turnbaugh says.

Nonetheless, given the mounting evidence for themicrobiota’s drug-regulating effects, he suggests thatmicrobial activity should be factored into drug designand clinical trials. “I’m not trying to argue that themicrobiome is more important than the human ge-nome,” Turnbaugh says. “But just as people look atspecific human genes or mutations that might matterto a drug’s activity, we need to be at the same pointwith the microbiome.”

1 V. Maini Rekdal, E. N. Bess, J. E. Bisanz, P. J. Turnbaugh, E. P. Balskus, Discovery and inhibition of an interspecies gut bacterial pathwayfor Levodopa metabolism. Science 364, eaau6323 (2019).

2 D. H. Kim, Gut microbiota-mediated drug-antibiotic interactions. Drug Metab. Dispos. 43, 1581–1589 (2015).3 H. Okuda, K. Ogura, A. Kato, H. Takubo, T. Watabe, A possible mechanism of eighteen patient deaths caused by interactions ofsorivudine, a new antiviral drug, with oral 5-fluorouracil prodrugs. J. Pharmacol. Exp. Ther. 287, 791–799 (1998).

4 M. Zimmermann, M. Zimmermann-Kogadeeva, R. Wegmann, A. L. Goodman, Mapping human microbiome drug metabolism by gutbacteria and their genes. Nature 570, 462–467 (2019).

5 B. D. Wallace et al., Alleviating cancer drug toxicity by inhibiting a bacterial enzyme. Science 330, 831–835 (2010).6 Z. Wang et al., Non-lethal inhibition of gut microbial trimethylamine production for the treatment of atherosclerosis. Cell 163, 1585–1595 (2015).

7 S. Devkota, Prescription drugs obscure microbiome analyses. Science 351, 452–453 (2016).

“The idea that the microbiome would be used inpreclinical drug development is still sort ofcontroversial, and definitely not the standard for drugson the market.”

–Peter Turnbaugh

Madhusoodanan PNAS | April 28, 2020 | vol. 117 | no. 17 | 9137

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