Pushing the Limits
It is widely recognized that many drug candidates fail during development due to ancillary toxicity. Uwe Sauer, Ph.D., professor, and Nicola Zamboni, Ph.D., researcher, both at the Eidgenössische Technische Hochschule, Zürich (ETH Zürich), are applying high-throughput intracellular metabolomics to understand the basis of these unfortunate events and head them off early in the course of drug discovery.
“Since metabolism is at the core of drug toxicity, we developed a platform for measurement of 50–100 targeted metabolites by a high-throughput system consisting of flow injection coupled to tandem mass spectrometry.”
Using this approach, Dr. Sauer’s team focused on the central metabolism of the yeast Saccharomyces cerevisiae, reasoning that this core network would be most susceptible to potential drug toxicity. Screening approximately 41 drugs that were administered at seven concentrations over three orders of magnitude, they observed changes in metabolome patterns at much lower drug concentrations without attendant physiological toxicity.
The group carried out statistical modeling of about 60 metabolite profiles for each drug they evaluated. This data allowed the construction of a “profile effect map” in which the influence of each drug on metabolite levels can be followed, including off-target effects, which provide an indirect measure of the possible side effects of the various drugs.
“We have found that this approach is at least 100 times as fast as other omics screening platforms,” Dr. Sauer says. “Some drugs, including many anticancer agents, disrupt metabolism long before affecting growth.”
Furthermore, they used the principle of 13C-based flux analysis, in which metabolites labeled with 13C are used to follow the utilization of metabolic pathways in the cell. These 13C-determined intracellular responses of metabolic fluxes to drug treatment demonstrate the functional performance of the network to be rather robust, leading Dr. Sauer to the conclusion that the phenotypic vigor he observes to drug challenges is achieved by a flexible make up of the metabolome.
Dr. Sauer is confident that it will be possible to expand the scope of these investigations to hundreds of thousands of samples per study. This will allow answers to the questions of how cells establish a stable functioning network in the face of inevitable concentration fluctuations.