Hydrolytic Glycosidic Bond Cleavage in RNA Nucleosides: Effects of the 2′-Hydroxy Group and Acid–Base Catalysis

Abstract

Despite the inherent stability of glycosidic linkages in nucleic acids that connect the nucleobases to sugar-phosphate backbones, cleavage of these bonds is often essential for organism survival. The current study uses DFT (B3LYP) to provide a fundamental understanding of the hydrolytic deglycosylation of the natural RNA nucleosides (A, C, G, and U), offers a comparison to DNA hydrolysis, and examines the effects of acid, base, or simultaneous acid-base catalysis on RNA deglycosylation. By initially examining HCOO···HO mediated deglycosylation, the barriers for RNA hydrolysis were determined to be 30-38 kJ mol higher than the corresponding DNA barriers, indicating that the 2'-OH group stabilizes the glycosidic bond. Although the presence of HCOO as the base (i.e., to activate the water nucleophile) reduces the barrier for uncatalyzed RNA hydrolysis (i.e., unactivated HO nucleophile) by ∼15-20 kJ mol, the extreme of base catalysis as modeled using a fully deprotonated water molecule (i.e., OH nucleophile) decreases the uncatalyzed barriers by up to 65 kJ mol. Acid catalysis was subsequently examined by selectively protonating the hydrogen-bond acceptor sites of the RNA nucleobases, which results in an up to ∼80 kJ mol barrier reduction relative to the corresponding uncatalyzed pathway. Interestingly, the nucleobase proton acceptor sites that result in the greatest barrier reductions match sites typically targeted in enzyme-catalyzed reactions. Nevertheless, simultaneous acid and base catalysis is the most beneficial way to enhance the reactivity of the glycosidic bonds in RNA, with the individual effects of each catalytic approach being weakened, additive, or synergistic depending on the strength of the base (i.e., degree of water nucleophile activation), the nucleobase, and the hydrogen-bonding acceptor site on the nucleobase. Together, the current contribution provides a greater understanding of the reactivity of the glycosidic bond in natural RNA nucleosides, and has fundamental implications for the function of RNA-targeting enzymes.

Can Cyanuric Acid and 2,4,6‐Triaminopyrimidine Containing Ribonucleosides be Components of Prebiotic RNA? Insights from QM Calculations and MD Simulations

“…To gain this information, we first analyzed the conformations of the isolated α and β C1′‐anomers of CA and TAP rNs using (free) rN models containing an unconstrained 5′‐OH group. However, to better analyze the rN conformations in RNA‐like polymers, models were also considered with the 5′‐oxygen capped by a methyl group (denoted polymer model), which mimics the steric bulk of the 5′‐phosphate and prevents hydrogen‐bonding interactions involving the 5′‐OH that cannot occur in polymeric assemblies . The conformational preferences of the TAP‐ and CA‐containing rNs were then analyzed by characterizing the potential energy surface (PES) as a function of the χ glycosidic torsion angle (∠(O4′‐C1′‐C1‐C2) and (∠(O4′‐C1′‐N1‐C2), respectively, Figure ).…”

“…However, to better analyze the rN conformations in RNA-like polymers, models were also considered with the 5'-oxygen capped by a methyl group (denoted polymer model), which mimics the steric bulk of the 5'-phosphate and prevents hydrogen-bonding interactions involving the 5'-OH that cannot occur in polymeric assemblies. [60] The conformational preferences of the TAP-and CA-containing rNs were then analyzed by characterizing the potential energy surface (PES) as a function of the χ glycosidic torsion angle (ff(O4'-C1'-C1-C2) and (ff(O4'-C1'-N1-C2), respectively, Figure 1). We note that the χ conformation was defined in an analogous manner to that of the canonical pyrimidines (i. e. χ = 90°À 270°for the anti conformation; and χ = 0°À 90°a nd 270°À 360°for the syn conformation).…”

The evolution of antiviral nucleoside analogues: A review for chemists and non-chemists. Part II: Complex modifications to the nucleoside scaffold

“…In general, the glycosidic bond is stable under physiological conditions, however, cleavage of this bond can occur and is dependent on various factors including pH, type of nucleobase, and 1′-substituents ( Cho et al, 2012 ; Temburnikar and Seley-Radtke, 2018 ; Rios et al, 2015 ; Lindahl and Karlström, 1973 ; Levy and Miller, 1998 ). Since the glycosidic bond cleavage occurs either by nucleophilic attack on the 1′ carbon of the sugar or by stabilization of the leaving group, changing the substituent from a hydrogen to any other group at the 1′ position could have a profound effect on glycosidic bond cleavage, either through steric or electronic effects ( Temburnikar and Seley-Radtke, 2018 ; Berti and McCann, 2006 ; Lenz et al, 2016 ). Scientists reasoned however, that if they replaced the hemiaminal (O—C—N) glycosidic bond with the O—C—C bond found in C-nucleosides, then they would be able to add 1′ substituents without compromising the integrity of the glycosidic bond ( Temburnikar and Seley-Radtke, 2018 ; De Clercq, 2016 ; Stambaský et al, 2009 ; Siegel et al, 2017 ).…”

Recent advances in synthetic approaches for medicinal chemistry of C-nucleosides

“…Moreover, the glycosidic bond in 2'-deoxy ribonucleosides has a higher susceptibility to cleavage than in the corresponding ribonucleosides [ 38 – 41 43 ]. The rate of glycosidic (C–N) bond cleavage is enhanced by decreasing pH and enzymes, which modify the localized acid–base environment [ 31 , 35 – 36 ]. The C–N bond cleavage proceeds either by activation of a nucleophile that attacks C1' or by stabilization of the leaving group, which could either be the nucleobase or an oxocarbenium ion [ 31 , 36 ].…”

“…The rate of glycosidic (C–N) bond cleavage is enhanced by decreasing pH and enzymes, which modify the localized acid–base environment [ 31 , 35 – 36 ]. The C–N bond cleavage proceeds either by activation of a nucleophile that attacks C1' or by stabilization of the leaving group, which could either be the nucleobase or an oxocarbenium ion [ 31 , 36 ]. As such, the oxocarbenium ion is a species formed during the glycosidic bond cleavage, which may be present as an intermediate or a transition state depending upon the accumulation of the positive charge on the sugar ring ( Fig.…”