Structural requirements of 2-oxoglutaric acid analogues to mimic its signaling function

SAR insights into TET2 catalytic domain inhibition: Synthesis of 2-Hydroxy-4-Methylene-pentanedicarboxylates

The TET (Ten-Eleven Translocation) dioxygenase enzyme family comprising 3 members, TET1-3, play key roles in DNA demethylation. These processes regulate transcription programs that determine cell lineage, survival, proliferation, and differentiation. The impetus for our investigations described here is derived from the need to develop illuminating small molecule probes for TET enzymes with cellular activity and specificity. The studies were done so in the context of the importance of TET2 in the hematopoietic system and the preponderance of loss of function somatic TET2 mutations in myeloid diseases. We have identified that 2-hydroxy-4-methylene-pentanedicarboxylic acid 2a reversibly competes with the co-substrate α-KG in the TET2 catalytic domain and inhibits the dioxygenase activity with an IC₅₀ = 11.0 ± 0.9 μM at 10 μM α-KG in a cell free system and binds in the TET2 catalytic domain with K_d = 0.3 ± 0.12 μM.

Recent advances in the catalytic cyclopropanation of unsaturated compounds with diazomethane

The main achievements and development trends of the past 10–15 years related to the catalytic cyclopropanation of unsaturated compounds with diazomethane are integrated and analyzed. The attention is focused on the most efficient catalysts based on palladium compounds. Data on the effects of substrate structure and nature of catalyst components on the regio- and stereoselectivity of these reactions are systematized. Characteristic features of safe methods for diazomethane generation are considered, including the use of membrane technologies and continuous-flow and in situ preparation methods, which have prospects for industrial application.

The bibliography includes 281 references.

A Therapeutic Strategy for Preferential Targeting of TET2 Mutant and TET-dioxygenase Deficient Cells in Myeloid Neoplasms

TET2 is frequently mutated in myeloid neoplasms. Genetic TET2 deficiency leads to skewed myeloid differentiation and clonal expansion, but minimal residual TET activity is critical for survival of neoplastic progenitor and stem cells. Consistent with mutual exclusivity of TET2 and neomorphic IDH1/2 mutations, here we report that IDH1/2 mutant-derived 2-hydroxyglutarate is synthetically lethal to TET-dioxygenase deficient cells. In addition, a TET-selective small molecule inhibitor decreased cytosine hydroxymethylation and restricted clonal outgrowth of TET2 mutant, but not normal hematopoietic precursor cells in vitro and in vivo. While TET-inhibitor phenocopied somatic TET2 mutations, its pharmacologic effects on normal stem cells were, unlike mutations, reversible. Treatment with TET inhibitor suppressed the clonal evolution of TET2 mutant cells in murine models and TET2-mutated human leukemia xenografts. These results suggest that TET inhibitors may constitute a new class of targeted agents in TET2 mutant neoplasia.

Synthesis of 2-oxoglutarate derivatives and their evaluation as cosubstrates and inhibitors of human aspartate/asparagine-β-hydroxylase

2-Oxoglutarate (2OG) is involved in biological processes including oxidations catalyzed by 2OG oxygenases for which it is a cosubstrate. Eukaryotic 2OG oxygenases have roles in collagen biosynthesis, lipid metabolism, DNA/RNA modification, transcriptional regulation, and the hypoxic response. Aspartate/asparagine-β-hydroxylase (AspH) is a human 2OG oxygenase catalyzing post-translational hydroxylation of Asp/Asn-residues in epidermal growth factor-like domains (EGFDs) in the endoplasmic reticulum. AspH is of chemical interest, because its Fe(ii) cofactor is complexed by two rather than the typical three residues. AspH is upregulated in hypoxia and is a prognostic marker on the surface of cancer cells. We describe studies on how derivatives of its natural 2OG cosubstrate modulate AspH activity. An efficient synthesis of C3- and/or C4-substituted 2OG derivatives, proceeding via cyanosulfur ylid intermediates, is reported. Mass spectrometry-based AspH assays with >30 2OG derivatives reveal that some efficiently inhibit AspH via competing with 2OG as evidenced by crystallographic and solution analyses. Other 2OG derivatives can substitute for 2OG enabling substrate hydroxylation. The results show that subtle changes, e.g. methyl- to ethyl-substitution, can significantly alter the balance between catalysis and inhibition. 3-Methyl-2OG, a natural product present in human nutrition, was the most efficient alternative cosubstrate identified; crystallographic analyses reveal the binding mode of (R)-3-methyl-2OG and other 2OG derivatives to AspH and inform on the balance between turnover and inhibition. The results will enable the use of 2OG derivatives as mechanistic probes for other 2OG utilizing enzymes and suggest 2-oxoacids other than 2OG may be employed by some 2OG oxygenases in vivo.

Metabolic profiling reveals local and systemic responses of kiwifruit to Pseudomonas syringae pv. actinidiae

Pseudomonas syringae pv. actinidiae (Psa), a bacterial pathogen, causes bacterial canker disease in kiwifruit. To elucidate the local and systemic influences of Psa infection on kiwifruit, comprehensive analyses were conducted by combining metabolomic and physiological approach under Psa-infected treatment and mock-inoculated control in leaves, stems, and bleeding saps. Our results show that Psa infection stimulated kiwifruit metabolic reprogramming. Levels of many sugars, fumarate, and malic acid were decreased in Psa-infected leaves and stems, accompanied by the increased level of amino acids (AAs), which implies the anaplerotic reaction to replenish the TCA cycle generating energy and intermediates for defense-related metabolic pathways, such as phenylpropanoid metabolism. The inconsistent results were observed in bleeding saps, which may be attributed to the induced phloem transport of carbon (C) out of leaves and such a transport benefits bacterium movement. Arg, Gln, and pyroglutamic acid systematically were accumulated in long-distance leaves, which probably confers to systemic acquired resistance (SAR) and Psa inoculation accelerated the nitrogen (N) cycling in kiwifruit. Moreover, Psa infection specifically affected the content of phenolic compounds and lignin. Phenolic compounds were negatively and lignin was positively related to kiwifruit Psa resistance, respectively. Our results first reveal that Psa enhances infection by manipulating C/N metabolism and sweet immunity, and that host lignin synthesis is a major physical barrier for restricting bacterial infection. This study provides an insight into the complex remodeling of plant metabolic response to Psa stress.

Carbon/Nitrogen Metabolic Balance: Lessons from Cyanobacteria

Carbon and nitrogen are the two most abundant nutrient elements for all living organisms, and their metabolism is tightly coupled. What are the signaling mechanisms that cells use to sense and control the carbon/nitrogen (C/N) metabolic balance following environmental changes? Based on studies in cyanobacteria, it was found that 2-phosphoglycolate derived from the oxygenase activity of Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) and 2-oxoglutarate from the Krebs cycle act as the carbon- and nitrogen-starvation signals, respectively, and their concentration ratio likely reflects the status of the C/N metabolic balance. We will present and discuss the regulatory principles underlying the signaling mechanisms, which are likely to be conserved in other photosynthetic organisms. These concepts may also contribute to developments in the field of biofuel engineering or improvements in crop productivity.

The Emergence of 2-Oxoglutarate as a Master Regulator Metabolite

The metabolite 2-oxoglutarate (also known as α-ketoglutarate, 2-ketoglutaric acid, or oxoglutaric acid) lies at the intersection between the carbon and nitrogen metabolic pathways. This compound is a key intermediate of one of the most fundamental biochemical pathways in carbon metabolism, the tricarboxylic acid (TCA) cycle. In addition, 2-oxoglutarate also acts as the major carbon skeleton for nitrogen-assimilatory reactions. Experimental data support the conclusion that intracellular levels of 2-oxoglutarate fluctuate according to nitrogen and carbon availability. This review summarizes how nature has capitalized on the ability of 2-oxoglutarate to reflect cellular nutritional status through evolution of a variety of 2-oxoglutarate-sensing regulatory proteins. The number of metabolic pathways known to be regulated by 2-oxoglutarate levels has increased significantly in recent years. The signaling properties of 2-oxoglutarate are highlighted by the fact that this metabolite regulates the synthesis of the well-established master signaling molecule, cyclic AMP (cAMP), in Escherichia coli.

Mimicking the 2-oxoglutaric acid signalling function using molecular probes: insights from structural and functional investigations

2-Oxoglutaric acid (2-OG) has gained considerable attention because of its newly discovered signalling role in addition to its established metabolic functions. With the aim of further exploring the signalling function of 2-OG, here we present a structure-activity relationship study using 2-OG probes bearing different carbon chain lengths and terminal groups. Our results highlight the importance of the five-membered carbon molecular skeleton and of the two carboxylic terminals in maintaining the signalling functions of the parent molecule 2-OG. These findings provide valuable information for designing new, effective molecular probes able to dissect and discriminate the newly discovered, complex signalling role of 2-OG from its canonical activity in metabolism.

A “click” chemistry constructed affinity system for 2-oxoglutaric acid receptors and binding proteins

An ingenious and robust affinity resin to capture the 2-oxoglutaric acid binding proteins was constructed via “click” chemistry and validated using a known 2-OG receptor in cell lysate.