Modeling of Isotope Effects on Binding Oxamate to Lactic Dehydrogenase

Świderek, Katarzyna; Panczakiewicz, Artur; Bujacz, A.; Bujacz, G.; Paneth, Piotr

doi:10.1021/jp903579x

Cited by 37 publications

(46 citation statements)

References 53 publications

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“…The results obtained for the monomer of 3H3F 37 with a closed loop conformation, listed in Table 2, reveal a reaction mechanism with a TS with a slightly less advanced hydride transfer than in the previous TSs located with the open loop conformation, while the proton is also found still bonded to His192. Interestingly, some of the observations of the TSs structures located in the present work can be compared with those families of TS structures of the closed loop conformation of Bacillus stearothermophilus LDH published before where the carbonyl bond of pyruvate was polarized basically through an interaction with an asparagine residue (Asn140 in Bacillus stearothermophilus LDH and Asn137 in the present study) of the active site 18 .…”

Section: Resultsmentioning

confidence: 80%

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Protein Conformational Landscapes and Catalysis. Influence of Active Site Conformations in the Reaction Catalyzed by L-Lactate Dehydrogenase

et al. 2015

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In the last decade L-Lactate Dehydrogenase (LDH) has become an extremely useful marker in both clinical diagnosis and in monitoring the course of many human diseases. It has been assumed from the 80s that the full catalytic process of LDH starts with the binding of the cofactor and the substrate followed by the enclosure of the active site by a mobile loop of the protein before the reaction to take place. In this paper we show that the chemical step of the LDH catalyzed reaction can proceed within the open loop conformation, and the different reactivity of the different protein conformations would be in agreement with the broad range of rate constants measured in single molecule spectrometry studies. Starting from a recently solved X-ray diffraction structure that presented an open loop conformation in two of the four chains of the tetramer, QM/MM free energy surfaces have been obtained at different levels of theory. Depending on the level of theory used to describe the electronic structure, the free energy barrier for the transformation of pyruvate into lactate with the open conformation of the protein varies between 12.9 and 16.3 kcal/mol, after quantizing the vibrations and adding the contributions of recrossing and tunneling effects. These values are very close to the experimentally deduced one (14.2 kcal·mol−1) and ~2 kcal·mol−1 smaller than the ones obtained with the closed loop conformer. Calculation of primary KIEs and IR spectra in both protein conformations are also consistent with our hypothesis and in agreement with experimental data. Our calculations suggest that the closure of the active site is mainly required for the inverse process; the oxidation of lactate to pyruvate. According to this hypothesis H4 type LDH enzyme molecules, where it has been propose that lactate is transformed into pyruvate, should have a better ability to close the mobile loop than the M4 type LDH molecules.

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Section: Resultsmentioning

confidence: 80%

“…37 Since the biologically active form of the enzyme is a tetramer only one tetramer was taken into consideration. Moreover, the use of the full tetramer was shown to be crucial to get reliable results in previous computational studies on LDH.…”

Section: Theoretical Methodsmentioning

confidence: 99%

Protein Conformational Landscapes and Catalysis. Influence of Active Site Conformations in the Reaction Catalyzed by L-Lactate Dehydrogenase

et al. 2015

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“…Both data sets were collected at 100 K. The structures were solved by molecular replacement (PHASER) using coordinates for rabbit muscle L-LDH in which all ligands and water molecules were removed (PDB code 3H3F (ref. 62)). The structures were refined using PHENIX and ligands built into density using COOT.…”

Section: Methodsmentioning

confidence: 99%

The self-inhibitory nature of metabolic networks and its alleviation through compartmentalization

et al. 2017

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Metabolites can inhibit the enzymes that generate them. To explore the general nature of metabolic self-inhibition, we surveyed enzymological data accrued from a century of experimentation and generated a genome-scale enzyme-inhibition network. Enzyme inhibition is often driven by essential metabolites, affects the majority of biochemical processes, and is executed by a structured network whose topological organization is reflecting chemical similarities that exist between metabolites. Most inhibitory interactions are competitive, emerge in the close neighbourhood of the inhibited enzymes, and result from structural similarities between substrate and inhibitors. Structural constraints also explain one-third of allosteric inhibitors, a finding rationalized by crystallographic analysis of allosterically inhibited L-lactate dehydrogenase. Our findings suggest that the primary cause of metabolic enzyme inhibition is not the evolution of regulatory metabolite–enzyme interactions, but a finite structural diversity prevalent within the metabolome. In eukaryotes, compartmentalization minimizes inevitable enzyme inhibition and alleviates constraints that self-inhibition places on metabolism.

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“…48 In order to obtain an open loop conformation form of the protein, the loop structure from A96 to K118 was taken from the open conformation of the rabbit muscle L-LDH M chain (PDB code 3H3F). 49 The structure was directly replaced, since between the two loop sequences there is 100% identity.…”

Section: -Methyl-3-nitro-5-(trifluoromethyl)biphenyl (2j) Iodo-arylmentioning

confidence: 99%

Discovery of N-Hydroxyindole-Based Inhibitors of Human Lactate Dehydrogenase Isoform A (LDH-A) as Starvation Agents against Cancer Cells

Granchi¹,

Roy²,

Giacomelli³

et al. 2011

J. Med. Chem.

201

167

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Highly invasive tumor cells are characterized by a metabolic switch, known as the Warburg effect, from "normal" oxidative phosphorylation to increased glycolysis even under sufficiently oxygenated conditions. This dependence on glycolysis also confers a growth advantage to cells present in hypoxic regions of the tumor. One of the key enzymes involved in glycolysis, the muscle isoform of lactate dehydrogenase (LDH-A), is overexpressed by metastatic cancer cells and is linked to the vitality of tumors in hypoxia. This enzyme may be considered as a potential target for new anticancer agents, since its inhibition cuts cancer energetic and anabolic supply, thus reducing the metastatic and invasive potential of cancer cells. We have discovered new and efficient N-hydroxyindole-based inhibitors of LDH-A, which are isoform-selective (over LDH-B) and competitive with both the substrate (pyruvate) and the cofactor (NADH). The antiproliferative activity of these compounds was confirmed on a series of cancer cell lines, and they proved to be particularly effective under hypoxic conditions. Moreover, NMR experiments showed that these compounds are able to reduce the glucose-to-lactate conversion inside the cell.

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Modeling of Isotope Effects on Binding Oxamate to Lactic Dehydrogenase

Cited by 37 publications

References 53 publications

Protein Conformational Landscapes and Catalysis. Influence of Active Site Conformations in the Reaction Catalyzed by L-Lactate Dehydrogenase

Protein Conformational Landscapes and Catalysis. Influence of Active Site Conformations in the Reaction Catalyzed by L-Lactate Dehydrogenase

The self-inhibitory nature of metabolic networks and its alleviation through compartmentalization

Discovery of N-Hydroxyindole-Based Inhibitors of Human Lactate Dehydrogenase Isoform A (LDH-A) as Starvation Agents against Cancer Cells

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