Structural basis for antibiotic action of the B1 antivitamin 2′-methoxy-thiamine

Abstract

The natural antivitamin 2′-methoxy-thiamine (MTh) is implicated in the suppression of microbial growth. However, its mode of action and enzyme-selective inhibition mechanism have remained elusive. Intriguingly, MTh inhibits some thiamine diphosphate (ThDP) enzymes, while being coenzymatically active in others. Here we report the strong inhibition of Escherichia coli transketolase activity by MTh and unravel its mode of action and the structural basis thereof. The unique 2′-methoxy group of MTh diphosphate (MThDP) clashes with a canonical glutamate required for cofactor activation in ThDP-dependent enzymes. This glutamate is forced into a stable, anticatalytic low-barrier hydrogen bond with a neighboring glutamate, disrupting cofactor activation. Molecular dynamics simulations of transketolases and other ThDP enzymes identify active-site flexibility and the topology of the cofactor-binding locale as key determinants for enzyme-selective inhibition. Human enzymes either retain enzymatic activity with MThDP or preferentially bind authentic ThDP over MThDP, while core bacterial metabolic enzymes are inhibited, demonstrating therapeutic potential.

A lysine–cysteine redox switch with an NOS bridge regulates enzyme function

“…Although we found that the catalytic Lys138 is disordered in the oxidized, inactive state, it becomes ordered upon reduction and activation. It is known for this enzyme, and for many other classes of enzyme, that orbital steering is critical for catalysis, and that small structural changes can lead to large changes in catalytic competence 24,26,27 .…”

Simulations of Pathogenic E1α Variants: Allostery and Impact on Pyruvate Dehydrogenase Complex-E1 Structure and Function

“…45 The coordinate and the topology files of the samples were prepared after the hydrogenation of the samples using the tLEaP module of AmberTools21. 46 The force field parameters for TPP were prepared using Antechamber program of AmberTools21 46,47 while the partial charges were obtained from literature 44 . The systems were modeled with a Mg +2 metal ion that anchors the diphosphate group of TPP that has the net charge of −2.…”

“…The protonation states of all amino acids were identified with pKa calculations using pKa-ANI 43 in conjunction with the reported protonation states in the literature 44 . The systems were described using Ambers ff14SB force field parameters for proteins.…”

Antivitamins: A Silver Lining in the Era of Antimicrobial Resistance

“…11 The potential applications of each of these thiamine antivitamins are discussed. Source: Modified and adopted from Tylicki et al 6 and Rabe von Pappenheim et al 7…”

“…Some examples of synthetic thiamine antivitamins include oxythiamine, amprolium, pyrithiamine, and 3-deazathiamine. 6 Recently, a natural antivitamin of thiamine was discovered known as 2′-methoxy-thiamine 7 (Figure 1). The biosynthesis of TPP has been an appealing target for developing antibiotics against bacteria.…”