Kinetic Characterization and Allosteric Inhibition of the Yersinia pestis 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (MEP Synthase)

1-Deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) is the first committed enzyme in the 2-methyl-D-erythritol 4-phosphate (MEP) terpenoid biosynthetic pathway and is also a validated antimicrobial target. Theaflavins, which are polyphenolic compounds isolated from fermented tea, possess a wide range of pharmacological activities, especially an antibacterial effect, but little has been reported on their modes of antimicrobial action. To uncover the antibacterial mechanism of theaflavins and to seek new DXR inhibitors from natural sources, the DXR inhibitory activity of theaflavins were investigated in this study. The results show that all four theaflavin compounds could specifically suppress the activity of DXR, with theaflavin displaying the lowest effect against DXR (IC50 162.1 μM) and theaflavin-3,3′-digallate exhibiting the highest (IC50 14.9 μM). Moreover, determination of inhibition kinetics of the theaflavins demonstrates that they are non-competitive inhibitors of DXR against 1-deoxy-D-xylulose 5-phosphate (DXP) and un-competitive inhibitors with respect to NADPH. The possible interactions between DXR and the theaflavins were simulated via docking experiments.

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“…3A, the insert) with an IC 50 of 0.27 μM. These data are in good agreement with the previously published results515.…”

Section: Resultssupporting

confidence: 92%

Antimicrobial mechanism of theaflavins: They target 1-deoxy-D-xylulose 5-phosphate reductoisomerase, the key enzyme of the MEP terpenoid biosynthetic pathway

Xian

Qiao

Zhang

et al. 2016

Sci Rep

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“…3). These data are in good agreement with previously published results [23]. Thus it is obvious that the pre-column derivatization HPLC method is good enough for the measurement of the DXR inhibitory activity of the GTE and the catechins.…”

Section: Evaluation Of the Pre-column Derivatization Hplc Methods For supporting

confidence: 92%

Inhibition of green tea and the catechins against 1-deoxy-d-xylulose 5-phosphate reductoisomerase, the key enzyme of the MEP terpenoid biosynthetic pathway

et al. 2016

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1-Deoxy-d-xylulose 5-phosphate reductoisomerase (DXR) is the first committed enzyme in the MEP terpenoid biosynthetic pathway and also a validated antimicrobial target. Green tea which is rich in polyphenolic components such as the catechins, possesses a plenty of pharmacological activities, in particular an antibacterial effect. To uncover the antibacterial mechanism of green tea and to seek new DXR inhibitors from natural sources, the DXR inhibitory activity of green tea and its main antimicrobial catechins were investigated in this study. The results show that the raw extract of green tea and its ethyl acetate fraction are able to suppress DXR activity explicitly. Further determination of the DXR inhibitory capacity of eight catechin compounds demonstrates that the most active compound is gallocatechin gallate that is able to inhibit around 50% activity of DXR at 25μM. Based on these data, the primary structure-activity relationship of the catechins against DXR is discussed. This study would be very helpful to elucidate the antimicrobial mechanism of green tea and the catechins and also would be very useful to direct the rational utilization of them as food additives.

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“…Koppisch et al 46 measured the steady-state kinetic constant k cat for the reduction of DXP to MEP catalyzed by EcDXR, which is 116 ± 8 s −1 (or 33 s −1 , most recently demonstrated by Haymond et al 67 ). This is translated to a complex reaction barrier 14.6 (or 15.4) kcal/mol based on Eyring's transition state theory.…”

Section: Acs Catalysismentioning

confidence: 97%

Proton-Shuttle-Assisted Heterolytic Carbon–Carbon Bond Cleavage and Formation

Zhou

Wang

et al. 2015

ACS Catal.

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The conversion of 1-deoxy-D-xylulose 5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP) catalyzed by DXP reductoisomerase (DXR) is the committing step in the biosynthesis of terpenoids. This MEP pathway is essential for most pathogenic bacteria but absent in human, and thus, it is an attractive target for the development of novel antibiotics. To this end, it is critical to elucidate the conversion mechanism and identify the transition state, as many drugs are transition-state analogues. Here we performed extensive combined quantum mechanical (density functional theory B3LYP/6-31G*) and molecular mechanical molecular dynamics simulations to elucidate the catalytic mechanism. Computations confirmed the transient existence of two metastable fragments of DXP by the heterolytic C3−C4 bond cleavage, namely, 1-propene-1,2-diol and glycoaldehyde phosphate, in accord with the most recent kinetic isotope effect (KIE) experiments. Significantly, the heterolytic C3−C4 bond cleavage and C2−C4 bond formation are accompanied by proton shuttles, which significantly lower their reaction barriers to only 8.2−6.0 kcal/mol, compared with the normal single carbon−carbon bond energy 83 kcal/mol. This mechanism thus opens a novel way for the design of catalysts in the cleavage or formation of aliphatic carbon−carbon bonds.

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Kinetic Characterization and Allosteric Inhibition of the Yersinia pestis 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (MEP Synthase)

Cited by 19 publications

References 82 publications

Antimicrobial mechanism of theaflavins: They target 1-deoxy-D-xylulose 5-phosphate reductoisomerase, the key enzyme of the MEP terpenoid biosynthetic pathway

Antimicrobial mechanism of theaflavins: They target 1-deoxy-D-xylulose 5-phosphate reductoisomerase, the key enzyme of the MEP terpenoid biosynthetic pathway

Inhibition of green tea and the catechins against 1-deoxy-d-xylulose 5-phosphate reductoisomerase, the key enzyme of the MEP terpenoid biosynthetic pathway

Proton-Shuttle-Assisted Heterolytic Carbon–Carbon Bond Cleavage and Formation

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