Article first published in Drug Discovery World online: https://www.ddw-online.com/unlocking-the-microbiome
By David Weinkove, CEO Magnitude Biosciences
The human microbiome is an important emerging field for drug discovery that harbours an array of life-changing medicines for patients. Whilst it is increasingly acknowledged that the human microbiome holds great promise for healthcare, its potential is still largely untapped. This article outlines how a novel drug discovery approach using the tiny nematode Caenorhabditis elegans could help unlock new therapies.
A large body of evidence has established clear links between the human microbiome and health, with our gut microbiota implicated in a range of pathologies including obesity, gastrointestinal diseases, and ageing1. For example, many studies have linked age-associated shifts in the gut microbiome to increased predisposition in aged individuals to certain diseases2. Recently, COVID-19 severity has been linked to gut microbiota in patients and its associations with levels of cytokines and inflammatory disease markers3. The microbiome has consequently become an important target for improving our health and quality of life, through two key approaches.
The first is the development of non-clinical health supplements. These include supplements that add living strains of beneficial microbes into the body (probiotics) and those that add non-living natural compounds into the body to induce the growth of beneficial microbes (prebiotics). However, for those supplements that seem to have beneficial effects, there are few accessible options available to study the mechanisms by which they improve health. The second approach is the development of clinical therapeutics that target the microbiome.
Developers are nevertheless still challenged by the microbiome’s vast complexity and a lack of understanding about the molecular mechanisms. The trillions of microbes that make up the human microbiome, including thousands of different species and strains of bacteria that vary widely between individual people, make it extremely challenging for drug developers to find specific targets and elucidate the mode of action.
An alternative approach that can overcome this problem is to measure the overall biochemical function of the microbiome, rather than its ecology. Once this biochemical framework is in place, drug developers can then use a simple ‘one animal-one microbe’ system in which a controllable animal (C. elegans) feeds on a single microbe. Drugs are used to modulate the microbe and the effects on the worms’ health can then be measured, quickly and easily. If the data captured by such a system is of a rich quality then it has huge potential to transform the development of microbiome therapeutics.
While small molecules have yet to be approved as clinical therapeutics for the microbiome, live bacterial therapeutics (LBT) have been developed to achieve beneficial clinical outcomes.
A relatively crude but effective approach is faecal microbiota transplantation (FMT), an FDA-approved treatment for Clostridioides difficile infection, which works by repopulating the patient’s microbiome with diverse microorganisms from healthy faeces that competitively exclude C. difficile. Seres Therapeutics has recently developed a more precise alternative using a formulation of purified Firmicutes spores (SER-109), which recently obtained Breakthrough Therapy and Orphan Drug designations from the FDA and has the potential to become a first-in-class FDA-approved microbiome drug.
Other Seres microbiome therapeutics in the pipeline are also showing encouraging results. For example, a consortium of multiple bacterial spores developed for the treatment of ulcerative colitis (SER-287) has successfully reached late-stage clinical trials.
Additional microbiome therapeutics in development are targeting other diseases, such as cancer4. In a collaboration with Cancer Research UK and Cambridge University Hospitals NHS Foundation Trust, Microbiotica has identified gut bacterial signatures predictive of responses to immune checkpoint inhibitor therapy and, based on this, has now advanced an LBT to early-stage clinical trials.
Although this progress is encouraging, the molecular mechanisms are still unclear and drug developers are still challenged by the complexity of the microbiome. One solution that can simplify the process is to measure the overall biochemical function of the microbiome (i.e. the sum of the biochemical output of all microbes in the body). Thus, while two people may harbour completely different gut microbes, the effect of a drug on their biochemistry will be the same, thereby offering an easily measurable outcome without having to target specific microbe species or strains. For example, as many gut microbe-derived metabolites can be found in the blood, researchers are starting to use microbiome-driven drug metabolites as indicators of efficacy and toxicity5.
In the development of microbiome therapeutics, the complexity of the microbiome means that it can be prohibitively difficult to pinpoint and measure suitable drug targets, which can limit the progression of candidate drugs to the next stage of development. Moreover, when candidates are advanced into late-stage whole organism testing, traditional mammalian models can be overly complex, time-consuming, and expensive.
C. elegans assays could help overcome these barriers. Now recognised as a powerful biosensor to study microbe-host interactions and underlying molecular mechanisms6, C. elegans can be used to quickly assess how microbes affect host health. By creating germ-free worms that can be added to specific bacteria (for example, E. coli), it provides a system in which the E. coli they feed on can be manipulated, either genetically, by changing nutrition, or with compounds. For example, research has shown that limiting folate synthesis in E. coli with a sulfonamide drug increases longevity in C. elegans, indicating that bacterial folate synthesis may be a key target to slow chronic disease in animals7.
Another recent example of C. elegans research showed that strains of pathogenic bacteria enhance protein aggregation in a C. elegans model of neurodegenerative disease. Intriguingly, this effect was reversed by adding butyrate, a compound generated in the human intestine by bacteria metabolising complex carbohydrates8.
One valuable characteristic of C. elegans is its amenability to high-throughput screening. Its short life cycle (~3 days) and lifespan (~15 days at 25°C) offers a rapid, natural ageing model for accelerating target identification and other aspects of the drug discovery process. Moreover, as the nematode worm is an appropriate in vivo whole-organism model with multiple organs and a physiology with parallels to humans, but without the ethical regulations that involve mammalian models, C. elegans can offer a similarly robust but quicker and more cost-effective ‘sense check’ between in vitro and in vivo testing in lab rodents that can save time and focus resources on priority compounds.
The availability of genetically modified strains and high gene conservation also means that C. elegans can provide a highly flexible and amenable experimental tool to understand the mechanism of action and can be applied to several stages of the drug discovery process.
C. elegans assays are not yet commonplace in industrial drug discovery, primarily because few companies have invested in applying a model that has been historically used solely in academia. Broadly speaking, biotechnology and pharmaceutical companies are more accustomed to working with in vitro models and other types of animal models, so making C. elegans fit-for-purpose requires deep knowledge and expertise not only of C. elegans but also of the workings of industrial research.
Some companies are now however taking this leap and developing C. elegans approaches that directly address the challenges and demands of industrial drug discovery. For example, a specialist C. elegans Contract Research Organisation, Magnitude Biosciences, has developed an approach to quantify the effect of microbes on the health and ageing of C. elegans. They can assess compounds that modulate microbial metabolism to help predict their impact on human health, or to identify molecular mechanisms by which microbes influence health.
This advanced C. elegans approach uses an automated technology which enables exhaustive and rich data acquisition to provide the high degree of both reproducibility and sensitivity required for drug development. The quantitative data produced allows users to distinguish the function of specific microbial molecules and genes. For those developing microbiome therapies, this data can be compared to their extensive in-house data sets associated with human disease states, to allow assignment of biochemical function or identify useful disease-specific biomarkers.
The ability to customise automated C. elegans assays is also valuable for drug developers. With the appropriate expertise, it can be applied at any stage of the drug discovery process, ranging from target identification and detecting toxicity and efficacy to providing qualitative readouts.
In order to uncover microbiome-targeted therapeutics, we must first understand the molecular basis of why such therapeutics improve our health and find better ways of measuring downstream effects on the host. Future progress involves tackling complex problems through interdisciplinary collaboration and the adoption of new approaches tailored for the specific requirements of each individual drug discovery project.
As in our ongoing battle with COVID-19, industrial drug development must sometimes turn to non-traditional technologies and approaches. C. elegans is a highly-amenable, less complex, reliable and cost-effective whole animal model well-suited to high-throughput screening that can accelerate and facilitate the progress of compounds from in vitro to in vivo testing. Adopting C. elegans into drug discovery workflows is now more feasible than ever before, since innovative automated technologies – and the expertise to go with them – are now available and poised to overcome the limitations that may have put drug developers off in the past.
Implementing a C. elegans approach will allow the quick and easy identification of targets, and the elucidation of molecular mechanisms of action, thereby unlocking our ability to rationally modulate the microbiome and potentially change patients’ lives.
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