1.But-3-ene-1,2-diol: a mechanism-based active site inhibitor for coenzyme B12-dependent glycerol dehydratase.
Pierik AJ1, Graf T, Pemberton L, Golding BT, Rétey J. Chembiochem. 2008 Sep 22;9(14):2268-75. doi: 10.1002/cbic.200800213.
Coenzyme B(12)-dependent glycerol dehydratase is a radical enzyme that catalyses the conversion of glycerol into 3-hydroxypropanal and propane-1,2-diol into propanal via enzyme-bound intermediate radicals. The substrate analogue but-3-ene-1,2-diol was studied in the expectation that it would lead to the 4,4-dihydroxylbut-2-en-1-yl radical, which is stabilised (allylic) and not reactive enough to retrieve a hydrogen atom from 5'-deoxyadenosine, thereby interrupting the catalytic cycle. Racemic and enantiomerically pure but-3-ene-1,2-diols and their [1,1-(2)H(2)], [2-(2)H] and [4,4-(2)H(2)] isotopomers were synthesised and characterised by NMR spectroscopy. (S)-[4-(14)C]but-3-ene-1,2-diol was also prepared. Kinetic measurements showed but-3-ene-1,2-diol to be a competitive inhibitor of glycerol dehydratase (K(i)=0.21 mM, k(i)=5.0x10(-2) s(-1)). With [4-(14)C]but-3-ene-1,2-diol it was demonstrated that species derived from the diol become tightly bound to the enzyme's active site, but not covalently bound, because the radioactivity could be removed upon denaturation of the enzyme.
2.Mechanisms of formation of adducts from reactions of glycidaldehyde with 2'-deoxyguanosine and/or guanosine.
Golding BT1, Slaich PK, Kennedy G, Bleasdale C, Watson WP. Chem Res Toxicol. 1996 Jan-Feb;9(1):147-57.
Convenient synthesis of rac-glycidaldehyde from rac-but-3-ene-1,2-diol and (R)-glycidaldehyde from D-mannitol are described. (R)-Glycidaldehyde (1) reacts with guanosine in water (pH 4-11, faster reaction at higher pH) to give initially 6(S)-hydroxy-7(S)-(hydroxymethyl)-3-(beta-D-ribofuranosyl)-5,6,7- trihydroimidazo[1,2-alpha]purin-9(3H)-one (7a) and 6(S),7(R)-dihydroxy-3-(beta-D-ribofuranosyl)-5,6,7,8- tetrahydropyrimido[1,2- alpha]purin-10(3H)-one (8a). The former decomposes to 7-(hydroxymethyl)-5,9-dihydro-9-oxo-3-(beta-D-ribofuranosyl)imidazo[1,2- alpha]purine (3a), 5,9-dihydro-9-oxo-3-(beta-D-ribofuranosyl)imidazo[1,2-alpha]purine (5a, 1,N2-ethenoguanosine), and formaldehyde, while the latter adduct is relatively stable. The position of the hydroxymethyl group on the imidazo ring of 7-(hydroxymethyl)-5,9-dihydro-9-oxo-3-(beta-D-ribofuranosyl)imidazo-[1,2 - alpha]purine was proved by 13C NMR analysis of adducts derived from [1-15N]guanosine and [amino-15N]guanosine.
3.On the reaction of glycerol dehydratase with but-3-ene-1,2-diol.
Sandala GM1, Kovacević B, Barić D, Smith DM, Radom L. Chemistry. 2009;15(19):4865-73. doi: 10.1002/chem.200802640.
High-level conventional ab initio and density functional theory (DFT) calculations have been performed to examine the fate of the native substrate glycerol (1) and its analogue but-3-ene-1,2-diol (7) in the coenzyme B(12)-dependent enzyme glycerol dehydratase (GDH). Experimental studies find that 7 irreversibly inactivates GDH, though the mechanism for the inactivation remains unknown. Interestingly, the EPR data suggest that the spin density for an observed radical is located in the vicinity of the C1 atom, which has been interpreted to indicate termination of the pathway at the substrate-derived radical 8. Our calculations show that if analogue 7 were to follow a similar mechanistic pathway to that followed by 1, then the reaction would be unlikely to stop at 8 but would rather proceed to the highly stabilized product-related radical 9. However, the EPR characteristics of 9 would not be consistent with the observed EPR data. Calculations involving an initial H-atom abstraction from the C2 position of 7 identify alternative radicals that might account for the EPR data, though they are of relatively high energy.
