Metabolomics Tools in Antiviral Research

Direct-acting antivirals (DAAs) and therapeutics must achieve two goals to effectively assist with disease mitigation. They must reduce viral replication and dissemination as well as reduce tissue damage caused by viral infection and/or the resulting immune response. They are generally “chemically modified mimics” of naturally occurring small molecules/metabolites that are intermediates or products of active biochemical pathways in the cell. However, as opposed to the naturally occurring metabolites, in a disease state, DAAs and therapeutics will divert biochemical pathways toward a more desirable outcome. Mass spectrometry (MS)-based metabolomics can detect and quantify small-molecule metabolites in cells, organs, or biofluids and provide a library of molecules that can be developed into novel chemical inhibitors or activators. However, measuring the metabolome requires consideration of various analytical challenges. Expansive chemical diversity inhibits the development of a catch-all metabolomics workflow, so various workflows must be used to measure specific molecular classes within the metabolome. A wide range of metabolite concentrations requires measurement technologies with a high dynamic range, and the temporal nature of metabolic intermediates and reactivity of certain molecular classes necessitates care with sample handling. Additionally, structural characterization and identification of metabolites are difficult due to the chemical and structural heterogeneity of the metabolome. Thus, metabolomics discovery experiments require careful consideration of study design and choice of analytical technologies with follow-up experiments for confident metabolite identification. In this chapter, we focus on the criteria that need to be considered when designing a metabolomics experiment such that quality and interpretability of data are maximized.