The Effects of Sulfur Substitution for the Nucleophile and Bridging Oxygen Atoms in Reactions of Hydroxyalkyl Phosphate Esters

Abstract

The effects of sulfur substitution on the reactions of hydroxyalkyl phosphate esters are examined. These compounds are models for the intramolecular phosphoryl transfer reaction involved in the cleavage of the internucleotide bond in RNA. The models studied here lack the ribose ring and their conformational flexibility results in greater stability and the availability of different reaction pathways. Sulfur in the nucleophilic position shows no nucleophilic reaction at phosphorus, instead rapidly attacking at the beta carbon atom, forming thiirane with departure of a phosphomonoester. Sulfur substitution at either of the two bridging positions leads to cleavage of the diester via formation of a cyclic intermediate, but with significant rate acceleration when compared to the oxygen analogues. The bridge-substituted models react substantially slower than the analogous ribose compounds with sulfur substitution at comparable positions. Kinetic isotope effects reveal significant differences in the transition state depending on which bridging position sulfur occupies. When sulfur is in the scissile bridging position, a highly associative transition state is indicated, with a largely formed bond to the nucleophile and the scissile P-S bond is little changed. When sulfur occupies the other bridging position, the isotope effects imply a very early transition state in a concerted reaction.

Altered (transition) states: mechanisms of solution and enzyme catalyzed RNA 2′-O-transphosphorylation

“…Nucleophile KIEs ( 18 k NUC ) can range from normal to inverse for early versus late TSs because they reflect both participation in reaction coordinate motion as well as differences in bonding in the TS compared to the ground state [22,25]. A normal nucleophile KIE of 1.0327 is observed for hydroxypropyl- p -nitrophenol phosphate (HPpNP) reactions consistent with minimal contribution from 2′O-P bond formation.…”

In Vitro Cysteine Reactivates Organophosphate Insecticide Dichlorvos-Inhibited Human Cholinesterases

“…Cysteine is a weak nucleophile and the phosphorus-sulfur bond is much weaker than a phosphorus-oxygen bond and therefore easier to break; however, the concentration of the reactants, namely cysteine and OP, seems to play a critical role in this reaction. 28,29 On the basis of collision theory, a higher concentration of reactants increases the probability of effective collisions, consequently resulting in the formation of a product. 30 However, to be effective, collisions should occur in a particular molecular orientation.…”

Synthesis, Properties, and Applications of Oligonucleotides Containing an RNA Dinucleotide Phosphorothiolate Linkage

“…31 Attack of the hydroxyl group of S-3′mNB (Figure 8) on phosphorus mimics the reaction of 6 to form 36 (Scheme 9), while the analogous reaction of S-5′mNB mimics the reaction of 14 to form 39 (Scheme 10). The similar, large leaving group KIEs for r(UpG) and U-3′mNB suggest that m -nitrobenzylalcohol provides a reasonable mimic of the nucleoside leaving group.…”