Synthesis of phosphoenol pyruvate (PEP) analogues and evaluation as inhibitors of PEP-utilizing enzymes

An Inhibitor-in-Pieces Approach to DAHP Synthase Inhibition: Potent Enzyme and Bacterial Growth Inhibition

3-Deoxy-d-arabinoheptulosonate-7-phosphate (DAHP) synthase catalyzes the first step in the shikimate biosynthetic pathway and is an antimicrobial target. We used an inhibitor-in-pieces approach, based on the previously reported inhibitor DAHP oxime, to screen inhibitor fragments in the presence and absence of glycerol 3-phosphate to occupy the distal end of the active site. This led to DAHP hydrazone, the most potent inhibitor to date, K_i = 10 ± 1 nM. Three trifluoropyruvate (TFP)-based inhibitor fragments were efficient inhibitors with ligand efficiencies of up to 0.7 kcal mol^-1/atom compared with 0.2 kcal mol^-1/atom for a typical good inhibitor. The crystal structures showed the TFP-based inhibitors binding upside down in the active site relative to DAHP oxime, providing new avenues for inhibitor development. The ethyl esters of TFP oxime and TFP semicarbazone prevented E. coli growth in culture with IC₅₀ = 0.21 ± 0.01 and 0.77 ± 0.08 mg mL^-1, respectively. Overexpressing DAHP synthase relieved growth inhibition, demonstrating that DAHP synthase was the target. Growth inhibition occurred in media containing aromatic amino acids, suggesting that growth inhibition was due to depletion of some other product(s) of the shikimate pathway, possibly folate.

Phosphoenolpyruvate carboxylase identified as a key enzyme in erythrocytic Plasmodium falciparum carbon metabolism

Phospoenolpyruvate carboxylase (PEPC) is absent from humans but encoded in the Plasmodium falciparum genome, suggesting that PEPC has a parasite-specific function. To investigate its importance in P. falciparum, we generated a pepc null mutant (D10^Δpepc), which was only achievable when malate, a reduction product of oxaloacetate, was added to the growth medium. D10^Δpepc had a severe growth defect in vitro, which was partially reversed by addition of malate or fumarate, suggesting that pepc may be essential in vivo. Targeted metabolomics using ¹³C-U-D-glucose and ¹³C-bicarbonate showed that the conversion of glycolytically-derived PEP into malate, fumarate, aspartate and citrate was abolished in D10^Δpepc and that pentose phosphate pathway metabolites and glycerol 3-phosphate were present at increased levels. In contrast, metabolism of the carbon skeleton of ¹³C,¹⁵N-U-glutamine was similar in both parasite lines, although the flux was lower in D10^Δpepc; it also confirmed the operation of a complete forward TCA cycle in the wild type parasite. Overall, these data confirm the CO₂ fixing activity of PEPC and suggest that it provides metabolites essential for TCA cycle anaplerosis and the maintenance of cytosolic and mitochondrial redox balance. Moreover, these findings imply that PEPC may be an exploitable target for future drug discovery.

The genome of the human malaria parasite Plasmodium falciparum encodes a protein called phosphoenolpyruvate carboxylase (PEPC) absent from the human host. PEPC is known to fix CO₂ to generate metabolites used for energy metabolism in plants and bacteria, but its function in malaria parasites remained an enigma. Our study aimed to elucidate the role and importance of PEPC in P. falciparum in its host red blood cell by generating a gene deletion mutant in P. falciparum. This was only achievable in the presence of high concentrations of malate were added to the culture medium. The mutant generated (D10^Δpepc) had a severe growth defect, which was rescued partially by malate or fumarate (but not any other downstream metabolites), suggesting that they feed into the same metabolic pathway. Using heavy isotope labelled ¹³C-U-D-glucose and ¹³C-bicarbonate we showed that PECP has an important role in intermediary carbon metabolism and is vital for the maintenance of cytosolic and mitochondrial redox balance. Together these findings imply that PEPC may be an exploitable target for future drug discovery.

Anticancer agents that counteract tumor glycolysis

Can we consider cancer to be a "metabolic disease"? Tumors are the result of a metabolic selection, forming tissues composed of heterogeneous cells that generally express an overactive metabolism as a common feature. In fact, cancer cells have increased needs for both energy and biosynthetic intermediates to support their growth and invasiveness. However, their high proliferation rate often generates regions that are insufficiently oxygenated. Therefore, their carbohydrate metabolism must rely mostly on a glycolytic process that is uncoupled from oxidative phosphorylation. This metabolic switch, also known as the Warburg effect, constitutes a fundamental adaptation of tumor cells to a relatively hostile environment, and supports the evolution of aggressive and metastatic phenotypes. As a result, tumor glycolysis may constitute an attractive target for cancer therapy. This approach has often raised concerns that antiglycolytic agents may cause serious side effects toward normal cells. The key to selective action against cancer cells can be found in their hyperbolic addiction to glycolysis, which may be exploited to generate new anticancer drugs with minimal toxicity. There is growing evidence to support many glycolytic enzymes and transporters as suitable candidate targets for cancer therapy. Herein we review some of the most relevant antiglycolytic agents that have been investigated thus far for the treatment of cancer.

The pivotal roles of mitochondria in cancer: Warburg and beyond and encouraging prospects for effective therapies

Tumors usurp established metabolic steps used by normal tissues for glucose utilization and ATP production that rely heavily on mitochondria and employ a route that, although involving mitochondria, includes a much greater dependency on glycolysis. First described by Otto Warburg almost nine decades ago [1], this aberrant phenotype becomes more pronounced with increased tumor malignancy [2]. Thus, while maintaining their capacity for respiration, tumors "turn more parasitic" by enhancing their ability to scavenge glucose from their surroundings. With excess glucose at hand, tumors shunt their metabolic flux more toward glycolysis than do their normal cells of origin, a strategy that allows for their survival when oxygen is limiting while providing them a mechanism to poison their extra-cellular environment with acid, thus paving the way for invasion and metastasis. Significantly, tumors harness a crucial enzyme to regulate and support this destructive path--to entrap and channel glucose toward glycolysis. This enzyme is an isoform of hexokinase, referred to as hexokinase type II, and also in abbreviated form as HK-2 or HK II. Due to many-faceted molecular features at genetic, epigenetic, transcriptional, and enzymatic levels, including sub-cellular localization to mitochondria, HK-2 facilitates and promotes the high glycolytic tumor phenotype [3]. Thus, HK-2 represents a pivotal model gene or enzyme that tumors "select for" during tumorigenesis in order to facilitate their destructive path. In this review, we examine the roles played by mitochondrial bound HK-2 within the context of the highly choreographed metabolic roulette of malignant tumors. Recent studies that outline how the aberrant glycolytic flux can be subverted toward a more "normal" metabolic phenotype, and how the glycolytic flux affects the tumor microenvironment to facilitate tumor dissemination are also described, including how these very features can be harnessed in new metabolic targeting strategies to selectively debilitate tumors.

Cross-talk between type three secretion system and metabolism in Yersinia

Pathogenic yersiniae utilize a type three secretion system (T3SS) to inject Yop proteins into host cells in order to undermine their immune response. YscM1 and YscM2 proteins have been reported to be functionally equivalent regulators of the T3SS in Yersinia enterocolitica. Here, we show by affinity purification, native gel electrophoresis and small angle x-ray scattering that both YscM1 and YscM2 bind to phosphoenolpyruvate carboxylase (PEPC) of Y. enterocolitica. Under in vitro conditions, YscM1, but not YscM2, was found to inhibit PEPC with an apparent IC(50) of 4 mum (K(i) = 1 mum). To analyze the functional roles of PEPC, YscM1, and YscM2 in Yop-producing bacteria, cultures of Y. enterocolitica wild type and mutants defective in the formation of PEPC, YscM1, or YscM2, respectively, were grown under low calcium conditions in the presence of [U-(13)C(6)]glucose. The isotope compositions of secreted Yop proteins and nine amino acids from cellular proteins were analyzed by mass spectrometry. The data indicate that a considerable fraction of oxaloacetate used as precursor for amino acids was derived from [(13)C(3)]phosphoenolpyruvate by the catalytic action of PEPC in the wild-type strain but not in the PEPC(-) mutant. The data imply that PEPC is critically involved in replenishing the oxaloacetate pool in the citrate cycle under virulence conditions. In the YscM1(-) and YscM2(-) mutants, increased rates of pyruvate formation via glycolysis or the Entner-Doudoroff pathway, of oxaloacetate formation via the citrate cycle, and of amino acid biosynthesis suggest that both regulators trigger the central metabolism of Y. enterocolitica. We propose a "load-and-shoot cycle" model to account for the cross-talk between T3SS and metabolism in pathogenic yersiniae.

Analysis of oligomeric proteins during unfolding by pH and temperature

During thermal transition and variation of pH, structural properties of 35 proteins and their complexes (bound with substrate and co-factor) were analyzed in detail. During pH alteration, these proteins were shown to have substantial differences in conformations. pH conformers were analyzed in detail. Free energy and other energy parameters were also estimated for these proteins at various pH and temperatures. Detailed structural analysis and binding interfaces of various substrates, inhibitors and cofactor of these proteins were also investigated using docking and molecular dynamic simulation.

Synaptic vesicle-bound pyruvate kinase can support vesicular glutamate uptake

Glucose metabolism is essential for normal brain function and plays a vital role in synaptic transmission. Recent evidence suggests that ATP synthesized locally by glycolysis, particularly via glyceraldehyde 3-phosphate dehydrogenase/3-phosphoglycerate kinase, is critical for synaptic transmission. We present evidence that ATP generated by synaptic vesicle-associated pyruvate kinase is harnessed to transport glutamate into synaptic vesicles. Isolated synaptic vesicles incorporated [(3)H]glutamate in the presence of phosphoenolpyruvate (PEP) and ADP. Pyruvate kinase activators and inhibitors stimulated and reduced PEP/ADP-dependent glutamate uptake, respectively. Membrane potential was also formed in the presence of pyruvate kinase activators. "ATP-trapping" experiments using hexokinase and glucose suggest that ATP produced by vesicle-associated pyruvate kinase is more readily used than exogenously added ATP. Other neurotransmitters such as GABA, dopamine, and serotonin were also taken up into crude synaptic vesicles in a PEP/ADP-dependent manner. The possibility that ATP locally generated by glycolysis supports vesicular accumulation of neurotransmitters is discussed.