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

Abstract

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.