Targeting the Unique Mechanism of Bacterial 1-deoxy-D-xylulose 5-phosphate (DXP) Synthase

David Bartee, Caren L Meyers

Research output: Contribution to journalArticle

Abstract

The bacterial metabolite 1-deoxy-D-xyulose-5-phosphate (DXP) is essential in bacterial central metabolism feeding into isoprenoid, thiamin diphosphate (ThDP), and pyridoxal phosphate de novo biosynthesis. Halting its production through the inhibition of DXP synthase is an attractive strategy for the development of novel antibiotics. Recent work has revealed that DXP synthase utilizes a unique random sequential mechanism which requires ternary complex formation between pyruvate-derived C2α-lactylthiamin diphosphate (LThDP), D-glyceraldehyde-3-phosphate (D-GAP) and enzyme, setting it apart from all other known ThDP-dependent enzymes. Herein, we describe the development of bisubstrate inhibitors bearing an acetylphosphonate (AP) pyruvate mimic and a distal negative charge mimicking the phosphoryl group of D-GAP, designed to target the unique form of DXP synthase that binds LThDP and D-GAP in a ternary complex. A D-phenylalanine-derived triazole acetylphosphonate (D-PheTrAP) emerged as the most potent inhibitor in this series, displaying slow-tight-binding inhibition with Ki∗ of 90 ± 10 nM, forward (k1) and reverse (k2) isomerization rates of 1.1 and 0.14 min-1, respectively, and exquisite selectivity (>15,000-fold) for DXP synthase over mammalian pyruvate dehydrogenase. D-PheTrAP is the most potent, selective DXP synthase inhibitor described to date and represents the first inhibitor class designed specifically to exploit the unique E-LThDP-GAP ternary complex in ThDP enzymology.

Original languageEnglish (US)
JournalBiochemistry
DOIs
StateAccepted/In press - May 14 2018

Fingerprint

Glyceraldehyde 3-Phosphate
Thiamine Pyrophosphate
Diphosphates
Pyruvic Acid
Triazoles
Phenylalanine
Bearings (structural)
Pyridoxal Phosphate
Tocopherols
Biosynthesis
Terpenes
Enzymes
Metabolites
Isomerization
Metabolism
Oxidoreductases
Phosphates
deoxyxylulose-5-phosphate synthase
Anti-Bacterial Agents
phosphonoacetaldehyde

ASJC Scopus subject areas

  • Biochemistry

Cite this

Targeting the Unique Mechanism of Bacterial 1-deoxy-D-xylulose 5-phosphate (DXP) Synthase. / Bartee, David; Meyers, Caren L.

In: Biochemistry, 14.05.2018.

Research output: Contribution to journalArticle

@article{c830576130004434bc443177b914dbff,
title = "Targeting the Unique Mechanism of Bacterial 1-deoxy-D-xylulose 5-phosphate (DXP) Synthase",
abstract = "The bacterial metabolite 1-deoxy-D-xyulose-5-phosphate (DXP) is essential in bacterial central metabolism feeding into isoprenoid, thiamin diphosphate (ThDP), and pyridoxal phosphate de novo biosynthesis. Halting its production through the inhibition of DXP synthase is an attractive strategy for the development of novel antibiotics. Recent work has revealed that DXP synthase utilizes a unique random sequential mechanism which requires ternary complex formation between pyruvate-derived C2α-lactylthiamin diphosphate (LThDP), D-glyceraldehyde-3-phosphate (D-GAP) and enzyme, setting it apart from all other known ThDP-dependent enzymes. Herein, we describe the development of bisubstrate inhibitors bearing an acetylphosphonate (AP) pyruvate mimic and a distal negative charge mimicking the phosphoryl group of D-GAP, designed to target the unique form of DXP synthase that binds LThDP and D-GAP in a ternary complex. A D-phenylalanine-derived triazole acetylphosphonate (D-PheTrAP) emerged as the most potent inhibitor in this series, displaying slow-tight-binding inhibition with Ki∗ of 90 ± 10 nM, forward (k1) and reverse (k2) isomerization rates of 1.1 and 0.14 min-1, respectively, and exquisite selectivity (>15,000-fold) for DXP synthase over mammalian pyruvate dehydrogenase. D-PheTrAP is the most potent, selective DXP synthase inhibitor described to date and represents the first inhibitor class designed specifically to exploit the unique E-LThDP-GAP ternary complex in ThDP enzymology.",
author = "David Bartee and Meyers, {Caren L}",
year = "2018",
month = "5",
day = "14",
doi = "10.1021/acs.biochem.8b00548",
language = "English (US)",
journal = "Biochemistry",
issn = "0006-2960",
publisher = "American Chemical Society",

}

TY - JOUR

T1 - Targeting the Unique Mechanism of Bacterial 1-deoxy-D-xylulose 5-phosphate (DXP) Synthase

AU - Bartee, David

AU - Meyers, Caren L

PY - 2018/5/14

Y1 - 2018/5/14

N2 - The bacterial metabolite 1-deoxy-D-xyulose-5-phosphate (DXP) is essential in bacterial central metabolism feeding into isoprenoid, thiamin diphosphate (ThDP), and pyridoxal phosphate de novo biosynthesis. Halting its production through the inhibition of DXP synthase is an attractive strategy for the development of novel antibiotics. Recent work has revealed that DXP synthase utilizes a unique random sequential mechanism which requires ternary complex formation between pyruvate-derived C2α-lactylthiamin diphosphate (LThDP), D-glyceraldehyde-3-phosphate (D-GAP) and enzyme, setting it apart from all other known ThDP-dependent enzymes. Herein, we describe the development of bisubstrate inhibitors bearing an acetylphosphonate (AP) pyruvate mimic and a distal negative charge mimicking the phosphoryl group of D-GAP, designed to target the unique form of DXP synthase that binds LThDP and D-GAP in a ternary complex. A D-phenylalanine-derived triazole acetylphosphonate (D-PheTrAP) emerged as the most potent inhibitor in this series, displaying slow-tight-binding inhibition with Ki∗ of 90 ± 10 nM, forward (k1) and reverse (k2) isomerization rates of 1.1 and 0.14 min-1, respectively, and exquisite selectivity (>15,000-fold) for DXP synthase over mammalian pyruvate dehydrogenase. D-PheTrAP is the most potent, selective DXP synthase inhibitor described to date and represents the first inhibitor class designed specifically to exploit the unique E-LThDP-GAP ternary complex in ThDP enzymology.

AB - The bacterial metabolite 1-deoxy-D-xyulose-5-phosphate (DXP) is essential in bacterial central metabolism feeding into isoprenoid, thiamin diphosphate (ThDP), and pyridoxal phosphate de novo biosynthesis. Halting its production through the inhibition of DXP synthase is an attractive strategy for the development of novel antibiotics. Recent work has revealed that DXP synthase utilizes a unique random sequential mechanism which requires ternary complex formation between pyruvate-derived C2α-lactylthiamin diphosphate (LThDP), D-glyceraldehyde-3-phosphate (D-GAP) and enzyme, setting it apart from all other known ThDP-dependent enzymes. Herein, we describe the development of bisubstrate inhibitors bearing an acetylphosphonate (AP) pyruvate mimic and a distal negative charge mimicking the phosphoryl group of D-GAP, designed to target the unique form of DXP synthase that binds LThDP and D-GAP in a ternary complex. A D-phenylalanine-derived triazole acetylphosphonate (D-PheTrAP) emerged as the most potent inhibitor in this series, displaying slow-tight-binding inhibition with Ki∗ of 90 ± 10 nM, forward (k1) and reverse (k2) isomerization rates of 1.1 and 0.14 min-1, respectively, and exquisite selectivity (>15,000-fold) for DXP synthase over mammalian pyruvate dehydrogenase. D-PheTrAP is the most potent, selective DXP synthase inhibitor described to date and represents the first inhibitor class designed specifically to exploit the unique E-LThDP-GAP ternary complex in ThDP enzymology.

UR - http://www.scopus.com/inward/record.url?scp=85049259335&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85049259335&partnerID=8YFLogxK

U2 - 10.1021/acs.biochem.8b00548

DO - 10.1021/acs.biochem.8b00548

M3 - Article

JO - Biochemistry

JF - Biochemistry

SN - 0006-2960

ER -