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.

Combined QM(DFT)/MM molecular dynamics simulations of the deamination of cytosine by yeast cytosine deaminase (yCD)

“…The final configuration was served as the initial Michaelis complex for the subsequent QM(DFT)/MM computations. We note that the above procedure is similar to previous studies on other enzyme systems …”

“…A successfully proved way to consider both the accuracy of QM methods and the efficiency of MM methods is to mix QM and MM methods such that a small portion (i.e., the active site) of the whole system is treated explicitly at the QM level, while the rest majority is approximated with a MM method . Combined QM/MM methods have been one of the most significant advances in computational chemistry during the past two decades . The accuracy of this method largely relies on the partition of QM and MM parts, the quality of the classical potential functions (or force fields), and the theoretical level of the QM computations.…”

Enzymatic Plasticity Inspired by the Diterpene Cyclase CotB2

“…Finally, the WHAM program , was employed to calculate the free energy profile. The whole protocol is similar to our previous studies and has been carefully validated. − A more detailed computational protocol is described in the Supporting Information.…”

Double Proton Transfer during a Novel Tertiary α-Ketol Rearrangement in Ketol-Acid Reductoisomerase: A Water-Mediated, Metal-Catalyzed, Base-Induced Mechanism

“…A similar rearrangement has been reported in the 1-deoxy-Dxylulose-5-phosphate (DXP) pathway, where DXP reductoisomerase (DXR) catalyzes the biosynthesis of 2-C-methyl-Derythritol 4-phosphate. 18,19 From a detailed analysis of the pH-dependence of the kinetic parameters and kinetic isotope effects, Calvo and co-workers 20 proposed a base-catalyzed proton shuttle mechanism for the αketol rearrangement, where a base in the enzyme deprotonates the OH group on C2 and also shuttles the proton to the CO group on C3. The alkyl migration occurs from C2 to C3 in concert with the proton shuttle.…”