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Functional and structural basis of E. coli enolase inhibition by SF2312: a mimic of the carbanion intermediate.

ABSTRACT: Many years ago, the natural secondary metabolite SF2312, produced by the actinomycete Micromonospora, was reported to display broad spectrum antibacterial properties against both Gram-positive and Gram-negative bacteria. Recent studies have revealed that SF2312, a natural phosphonic acid, functions as a potent inhibitor of human enolase. The mechanism of SF2312 inhibition of bacterial enolase and its role in bacterial growth and reproduction, however, have remained elusive. In this work, we detail a structural analysis of E. coli enolase bound to both SF2312 and its oxidized imide-form. Our studies support a model in which SF2312 acts as an analog of a high energy intermediate formed during the catalytic process. Biochemical, biophysical, computational and kinetic characterization of these compounds confirm that altering features characteristic of a putative carbanion (enolate) intermediate significantly reduces the potency of enzyme inhibition. When SF2312 is combined with fosfomycin in the presence of glucose-6 phosphate, significant synergy is observed. This suggests the two agents could be used as a potent combination, targeting distinct cellular mechanism for the treatment of bacterial infections. Together, our studies rationalize the structure-activity relationships for these phosphonates and validate enolase as a promising target for antibiotic discovery.

SUBMITTER: Krucinska J

PROVIDER: S-EPMC6863902 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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Functional and structural basis of E. coli enolase inhibition by SF2312: a mimic of the carbanion intermediate.

Krucinska Jolanta J Lombardo Michael N MN Erlandsen Heidi H Hazeen Akram A Duay Searle S SS Pattis Jason G JG Robinson Victoria L VL May Eric R ER Wright Dennis L DL

Scientific reports 20191119 1

Many years ago, the natural secondary metabolite SF2312, produced by the actinomycete Micromonospora, was reported to display broad spectrum antibacterial properties against both Gram-positive and Gram-negative bacteria. Recent studies have revealed that SF2312, a natural phosphonic acid, functions as a potent inhibitor of human enolase. The mechanism of SF2312 inhibition of bacterial enolase and its role in bacterial growth and reproduction, however, have remained elusive. In this work, we deta ...[more]

PMID: 31745118

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Project description:The pentadentate ligand (n)Bu-P2DA (2(b), (n)Bu-P2DA = N-(1',1'-bis(2-pyridyl)pentyl)iminodiacetate) was designed to bind an iron center in a carboxylate-rich environment similar to that found in the active sites of TauD and other α-ketoglutarate-dependent mononuclear non-heme iron enzymes. The iron(II) complex (n)Bu(4)N[Fe(II)(Cl)((n)Bu-P2DA)] (3(b)-Cl) was synthesized and crystallographically characterized to have a 2-pyridine-2-carboxylate donor set in the plane perpendicular to the Fe-Cl bond. Reaction of 3(b)-Cl with N-heterocyclic amines such as pyridine or imidazole yielded the N-heterocyclic amine adducts [Fe(II)(N)((n)Bu-P2DA)]. These adducts in turn reacted with oxo-transfer reagents at -95 °C to afford a short-lived oxoiron(IV) complex [Fe(IV)(O)((n)Bu-P2DA)] (5(b)) in yields as high as 90% depending on the heterocycle used. Complex 5(b) exhibits near-IR absorption features (λ(max) = 770 nm) and Mossbauer parameters (δ = 0.04 mm/s; ΔE(Q) = 1.13 mm/s; D = 27±2 cm(-1)) characteristic of an S = 1 oxoiron(IV) species. Direct evidence for an Fe=O bond of 1.66 Å was found from EXAFS analysis. DFT calculations on 5(b) in its S =1 spin state afforded a geometry-optimized structure consistent with the EXAFS data. They further demonstrated that the replacement of two pyridine donors in [Fe(IV)(O)(N4Py)](2+) (N4Py = N,N-(bis(2-pyridyl)methyl)N-bis(2-pyridylmethyl)amine) with carboxylate donors in 5(b) decreased the energy gap between the ground S = 1 and the excited S = 2 states, reflecting the weaker equatorial ligand field of 5(b) and accounting for its larger D value. Complex 5(b) reacted readily with dihydrotoluene, methyldiphenylphosphine and ferrocene at -60 °C, and in all cases was approximately a 5-fold more reactive oxidant than [Fe(IV)(O)(N4Py)](2+). The reactivity differences between these two complexes may arise from a combination of electronic and steric factors. Carboxylate-rich 5(b) represents the closest structural mimic reported thus far of the oxoiron(IV) intermediate ('J') found in TauD and provides us with vital insights into the role carboxylate ligands play in modulating the spectroscopic and reactivity properties of the non-heme oxoiron(IV) moiety.

Dataset Information

Functional and structural basis of E. coli enolase inhibition by SF2312: a mimic of the carbanion intermediate.

Publications

Functional and structural basis of E. coli enolase inhibition by SF2312: a mimic of the carbanion intermediate.

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