One goal of metabolic research is to decipher the complex interplay between small molecules, metabolites and enzymes that influences chemical reactions, biochemical networks and organismal physiology. A previous Focus issue1 three years ago noted the importance of high-resolution chemical tools to interrogate and manipulate metabolic pathways. Since that time, exciting new advances and insights have enhanced the existing interplay of physiology, chemical biology and metabolism. In this issue of Nature Chemical Biology, we present a mini-collection of Reviews and Perspectives that discuss the continued importance of chemical biology research for understanding metabolic regulation.

Alterations or dysregulation in particular classes of lipids are linked to metabolic disorders such as diabetes, obesity and aging. Liquid chromatography–tandem mass spectrometry-based untargeted lipidomics2 can enable visualization of the changing global lipid microenvironment or lipidome and also aid in the identification of unique classes of physiologically relevant bioactive lipids. For example, lipidomic analysis of the aging mouse brain tissue identified a class of lipids called 3-sulfogalactosyl diacylglycerols3 that exhibit anti-inflammatory activity and whose abundance decreased in aging brains. Lipidomic analysis of mice over-expressing the adipose-selective glucose transporter led to the discovery of fatty acid esters of hydroxyl fatty acids (FAHFAs)4, which were shown to promote metabolic health in mice and humans but exhibit structural and functional complexity. In this issue, a Review from Tan and Saghatelian provides an up-to date overview of the analytical methods to identify and characterize FAHFAs, the enzymes involved in their synthesis and metabolism, and the various mechanisms by which they may alter physiology.

Similar to lipidomics, untargeted metabolomics provides a snapshot of the metabolome populated with a large number of uncharacterized metabolites. Functional and mechanistic characterization of these compounds has revealed that some of them are highly reactive and can directly modify defined protein residues in a post-translational manner. This has led to the proposal of a proteome–metabolome crosstalk model whereby fluctuations in metabolic levels can alter gene expression and protein function. A Perspective from Zhang and Schroeder describes the emerging landscape of metabolite-driven protein modifications that function through enzymatic and non-enzymatic mechanisms. One type of modification is lipoylation, whereby an eight-carbon lipid cofactor (lipoate) is attached to specific lysine residues to facilitate catalysis. Lipoylation of metabolic complexes such as the oxoglutarate dehydrogenase complex and pyruvate dehydrogenase complex (PDHC) are required for tricarboxylic acid (TCA) cycle function. A mitochondrial localized NAD+ kinase (NADK2) was recently found to promote lipoylation through NADPH-dependent regulation of the mitochondrial fatty acid synthase enzyme mitochondrial trans-2-enoyl-CoA reductase5. The Perspective also noted that these metabolic post-translational modifications can be further modified, resulting in structural and potentially functional complexity. One recent example showed that reactive nitrogen species-produced nitrosylated CoA could modify the lipoate arm of PDHC in a non-enzymatic manner to inhibit PDHC activity6.

There remains a debate about whether these reactive metabolite-mediated modifications are beneficial or detrimental. Glycolytic byproducts such as methylglyoxal can engage in a non-enzymatic post-translational modification called glycation that was historically thought to be a toxic byproduct of carbohydrate metabolism and was negatively associated with diabetes and aging7. However, a Comment from Trujillo and Galligan8 argues that glycation may have a homeostatic role by modifying histone and transcriptional proteins that are responsive to regulatory feedback. Resolving the beneficial or detrimental roles of protein glycation remains difficult owing to the lack of chemical and analytical tools. A Review by Scheck and colleagues9 discussed the recent chemical understanding of these modifications and the current and future tools that can elucidate the biological roles of these modifications in more detail.

Careful disposal of non-specific metabolites or waste products is necessary to avoid disruption of cellular processes and signaling. Recycling and detoxification pathways have been identified to remove these damaging side products. In an Article by Griffith et al., and highlighted in a News & Views article by Chatoff and Snyder, citrate lyase beta-like protein was identified as a recycling enzyme that removes malyl-coenzyme A, a reactive byproduct of the TCA cycle. High levels of malyl-coenzyme A can block the activity of vitamin B12, which is an essential cofactor for DNA synthesis and amino acid metabolism.

Mitochondria are the primary site of energy metabolism and ATP generation, and proteins required for the assembly of the electron transport chain are largely transcribed from the mitochondrial genome. Alterations in mitochondrial genome function and gene expression are likely to have profound effects on respiration. A recent Article from Hao et al. identified a splicing variant of the methyl-CpG-binding domain, a core component of the nucleosome remodeling and histone deacetylation complex, designated as MBD2c. MBD2c was localized in the mitochondria and enhanced mitochondrial DNA (mtDNA) transcription and respiration through regulation of a mitochondrial transcription factor TFAM. The interplay between mtDNA regulation and respiration has inspired the search for small molecules that can rescue mtDNA defects observed in pathological disorders. Valenzuela et al. identified small molecules that can rescue mutations in DNA polymerase γ, which is required for mtDNA replication10. These compounds can increase mtDNA synthesis and enhance oxidative phosphorylation activity, supporting this crucial interplay between mtDNA regulation and metabolism. Respiratory activity also requires assembly of large super-complexes that have been characterized using blue-native gel electrophoresis and mass spectroscopy, but elucidating the identity of proteins within these complexes remains difficult. Two new databases called MARIGOLD and MitoCIAO enable the identification of proteins in a particular mitochondrial super-complex and predict their potential partners within the complex11.

In vitro chemical screening for metabolic regulators has been effective in identifying candidates to ameliorate pathological conditions such as cancer and diabetes. A chemical screen in a beta cell line identified a checkpoint kinase 2 (CHEK2) inhibitor, AZD776212, that stimulated insulin secretion in human and cynomolgus macaque islets through activation of the pentose phosphate pathway. Despite the successes with in vitro screening, whole animal screening remains preferable to examine systemic effects but remains problematic owing to cost-effectiveness. The zebrafish offers a compelling vehicle as it is easy to screen, shares strong gene conservation with higher order vertebrates, and has been successfully used to identify compounds that enhance pancreatic beta cell regeneration. A Review from Karampelias et al. discusses the recent progress in chemical-biological approaches to identify compounds that stimulate beta cell regeneration through enhanced proliferation or trans-differentiation from related cell types. For example, Karampelias et al.13 elucidated the mechanism of action for a beta cell regeneration candidate, CID661578, that acted through a MAPK-interacting serine/threonine kinase–eIF4G axis at the translational initiation complex to enhance protein synthesis.

We hope that this mini-Focus highlights some of the exciting current trends in metabolism research and will inform and inspire our readers. At Nature Chemical Biology, we look forward to new developments in metabolism and are confident that chemical biology will continue to have a crucial role in advancing the field.