Review
The gastrointestinal microbiota as a site for the biotransformation of drugs

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Abstract

There are 100 trillion microbes in the human gastrointestinal tract with numbers increasing distally. These microbiota secrete a diverse array of enzymes (primarily for carbohydrate and protein fermentation) giving them substantial metabolic potential which can have major implications for drug stability. At least thirty drugs which are, or have been, available commercially, were subsequently shown to be substrates for these bacterial enzymes, and with increasing numbers of new and existing drugs having the potential for contact with the distal gut (through modified release systems or poor solubility/permeability), many more are expected to be discovered. The major concern with bacterial drug degradation is the behaviour of the metabolite; is it more or less active than the parent compound, or has toxicity resulted? For example, there were eighteen deaths in 1993 due to a drug interaction in which a toxic drug metabolite was produced by bacterial fermentation. Thus, the objective of this review is the provision of a comprehensive overview of this area; the gastrointestinal microbiota, their drug substrates and metabolic mechanisms, and approaches to studying this further are discussed.

Introduction

The oral route is the preferred route for drug administration with 84% of the fifty bestselling pharmaceutical products in the US and European markets given by mouth (Lennernäs and Abrahamsson, 2005). However, oral administration is arguably the most complex route of drug delivery. For an orally administered drug to be effective it must (a) dissolve in the fluids of the gastrointestinal (GI) tract (b) remain intact in the lumen (c) cross the epithelial membrane and (d) undergo minimal first-pass metabolism. Oral bioavailability is therefore a multi-factorial process dependent on the solubility, stability, permeability and metabolism of the drug molecule.

While much has been written on the role of dissolution, permeability and first-pass metabolism on oral drug bioavailability (Lindahl et al., 1997, Dressman et al., 1998, Amidon et al., 1995, Lennernäs and Abrahamsson, 2005, McConnell et al., 2008a), less attention has been paid to the stability of the drug in the intestinal lumen. Instability is often associated with pH and/or enzyme mediated degradation in the upper gut. These can be overcome by formulation approaches such as enteric coating. A major stability factor that is often overlooked is the effect of the microbiota in the gastrointestinal tract.

The gastrointestinal tract is populated with large numbers of bacteria that contribute to normal digestive function. Most of these bacteria reside in the large intestine and their primary function is to ferment carbohydrate and protein that escape digestion in the upper gut into absorbable energy. In addition, the metabolic reactions performed by these bacteria and their respective enzymes have the ability to metabolise drugs and other xenobiotics far more extensively than any other part of the body (Scheline, 1973, Abu Shamat, 1993, Mikov, 1994). Scheline has even suggested that the gastrointestinal microbiota has the ability to act as an organ with a metabolic potential at least equal to the liver (Scheline, 1973). There are, however, important differences between hepatic and bacterial metabolism. The liver is primarily responsible for metabolism via oxidation and conjugation producing polar high molecular weight metabolites, while the gastrointestinal microbiota is involved in reductive and hydrolytic reactions generating non-polar low molecular weight byproducts. Furthermore, all drugs that are delivered to, or absorbed into, the blood stream, are subject to hepatic metabolism. However, rate and extent of bacterial metabolism will be influenced by the amount of drug that reaches the distal gut.

The majority of drugs are rapidly and completely absorbed in the upper gut and have minimal contact with intestinal bacteria. This goes someway towards explaining why over the last forty years only thirty or so marketed drugs have been identified as substrates for intestinal bacteria. However, the biopharmaceutical complexity of new drug candidates is providing an increasing number of compounds that suffer from low solubility, low permeability or both (Davis, 2005). Drugs that display these properties will reach the lower confines of the gastrointestinal tract, presenting themselves to the host microbiota. Furthermore, drugs that are delivered via the intravenous route or that are fully absorbed from the upper parts of the gastrointestinal tract may still reach the lower gut by secretion or diffusion from the systemic circulation into the intestinal lumen, or may be excreted in the bile, possibly as conjugates following a recycling process known as enterohepatic recirculation. There is an increasing trend to develop modified release preparations (colon specific or extended release systems) to improve therapy via the oral route (Basit, 2005, Rubinstein, 2005, Ibekwe et al., 2006, Tiwari and Rajabi-Siahboomi, 2008, Ibekwe et al., 2008). In such cases, most if not all the entire drug load will be deposited in the large intestine, providing further opportunity for exposure to the microbiota. Drugs can also come in direct contact with bacteria via rectal administration in the form of suppositories or enemas. Given all this it is expected that opportunities for microbiota-mediated metabolism will increase and drug stability assessment in the presence of intestinal bacteria becomes of increasing importance.

The stability of a drug to the microbiota is clinically relevant: metabolism can render a drug pharmacologically active, inactive or toxic. An important example of the significance of this was seen in Japan in 1993 when sorivudine, a promising antiviral drug was introduced into the Japanese market. This was later discovered to be transformed by gut microbiota into (E)-5-(2-bromovinyl)uracil which can inhibit the metabolism of the anti-cancer drug 5-fluorouracil leading to toxic levels of this drug. Within forty days of reaching the Japanese market this bacterially-metabolized interaction was responsible for the death of eighteen patients who were co-administered sorivudine with oral 5-fluouracil prodrugs (Okuda et al., 1998). Sorivudine was withdrawn from the market a few weeks after these deaths. This highlights the importance of studying metabolism by the microbiota, and this has come to the attention of the pharmceutical industry. For example, AstraZeneca has now started to examine the stability of drugs in early development when relevant using an in vitro colonic model (based on an inoculum of human faecal bacteria). New molecules can be screened to assess whether there will be development issues with an extended release formulation option later in the programme. Significantly, of the fifty-one molecules examined since 2004, nineteen underwent degradation in the colonic in vitro model.

In light of the significant issue of bacterial drug metabolism, the purpose of this review is to describe the in vitro and in vivo methods used to assess drug metabolism in the presence of gastrointestinal bacteria and their relative merits. Detailed information on those drug molecules known to be susceptible to bacterial metabolism are also presented with a summary of the metabolic reactions involved. Knowledge of the individual drugs, and drug classes, should be useful for initial identification of chemical groups that are potential substrates: these data could be extrapolated to new drug molecules for further investigation.

Section snippets

The human gastrointestinal microbiota and its function

The term microflora has been used to describe microorganisms residing on body surfaces including the gastrointestinal tract. This is because these microorganisms were originally thought to be plants and were incorrectly classified as “flora”. Since this denomination is scientifically inaccurate and misleading, the term microbiota is preferred. We often consider the members of the human intestinal microbiota as key players in maintaining human health and well-being: they are implicated in

Models to study intestinal bacteria-related drug metabolism

Since the majority of gut bacteria are found in the large intestine this is the main site for biotransformation for endogenous and exogenous molecules. However, the inaccessibility of the human colon prevents the direct examination of the metabolic and ecological activity of the microbiota. Human and animal experiments to study this region are costly and have ethical drawbacks. Toxicity issues also render the use of human in vivo methodologies unviable in early drug development. The use of in

Drug metabolic reactions performed by the gastrointestinal microbiota

The following section highlights over 30 drug substrates for the gastrointestinal microbiota. A detailed understanding of the metabolic reactions involved and the types of studies to confirm a role for gut microbiota in metabolism is also presented (summarised in Table 4). The section is subdivided according to the class of reaction.

Conclusions

The human intestinal microbiota can have a major impact on drug metabolism and ultimately on oral bioavailability. More than 30 drugs that made it onto the market were subsequently identified as substrates for colonic bacteria. However, these examples are merely the tip of the iceberg as the next generation of drugs have a higher probability of being presented to the microbiota in the lower gut, either through poor solubility/permeability properties or formulation development strategies. The

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