Exploring Metabolic Pathways and Regulation through Functional Chemoproteomic and Metabolomic Platforms

Abstract

Genome sequencing efforts have revealed a strikingly large number of uncharacterized genes, including poorly or uncharacterized metabolic enzymes, metabolites, and metabolic networks that operate in normal physiology, and also those enzymes and pathways that may be rewired under pathological conditions. Though deciphering the functions of the uncharacterized metabolic genome is a challenging prospect, it also presents an opportunity for identifying novel metabolic nodes that may be important in disease therapy. In this review, we will discuss the chemoproteomic and metabolomic platforms employed in identifying, characterizing, and targeting nodal metabolic pathways important in physiology and disease, describing an integrated workflow for functional mapping of metabolic enzymes.

In vivo Reprogramming of Cancer Metabolism by MYC

“…One particularly important consideration is the difference between “snap-shot” strategies of studying metabolism vs. kinetic flux analyses, and how the use of chemically labeled metabolites factors into both approaches. The most common snap-shot method for studying metabolism is mass spectrometry-based metabolomics, which can be “targeted” for known metabolites or “untargeted” for unbiased detection of all metabolites present within a particular sample, and does not require any labeled metabolite (Medina-Cleghorn and Nomura, 2014 ). A second snap-shot strategy is 13 C tracer analysis, in which a 13 C-labeled metabolite is infused or fed to the subject, and mass spectrometry is used to identify downstream metabolite labeling patterns (Buescher et al, 2015 ).…”

“…Understanding the differences between these methods, and the conclusions that can be drawn from them, is vital. In particular, snap-shot metabolomics is often used to prematurely draw conclusions about the activity of a metabolic pathway, when the elevation or decrease of a particular metabolite does not necessarily reflect activation or inhibition of an entire pathway (Medina-Cleghorn and Nomura, 2014 ; Buescher et al, 2015 ). Moreover, interpretation and validation of metabolic data is critical, as for example, accumulation of a particular metabolite could have multiple potential interpretations (i.e., increased activity of an upstream anabolic pathway or decreased activity of a downstream catabolic pathway).…”

The Microbiome in Autoimmune Liver Diseases: Metagenomic and Metabolomic Changes

“…Changes in the composition or function of the gut microbiota lead to metabolite alterations. Through metabolomics, specific bacterial metabolic pathways and metabolites can be defined (Medina-Cleghorn and Nomura, 2014). Apparently, the microbiome is a rising star in the exploration for the prevention, diagnosis, and treatment of AILDs.…”

Mapping proteome-wide interactions of reactive chemicals using chemoproteomic platforms

“…ABPP uses activity-based chemical probes that directly bind to the active sites of large numbers of enzymes, thus providing a functional readout of enzyme activities en masse directly in complex proteomes [12,13]. Because these activity-based probes bind to the active-sites of enzymes, small-molecule inhibitors can be competed against probe-binding, therefore enabling the development of small-molecules for both characterized and uncharacterized enzymes.…”