Contrasting Behavior of Conformationally Locked Carbocyclic Nucleosides of Adenosine and Cytidine as Substrates for Deaminases

Abstract

In addition to the already known differences between adenosine deaminase (ADA) and cytidine deaminase (CDA) in terms of their tertiary structure, the sphere of Zn +2 coordination, and their reverse stereochemical preference, we present evidence that the enzymes also differ significantly in terms of the North/South conformational preferences for their substrates and the extent to which the lack of the O(4') oxygen affects the kinetics of the enzymatic deamination of carbocyclic substrates. The carbocyclic nucleoside substrates used in this study have either a flexible cyclopentane ring or a rigid bicyclo[3.1.0]hexane scaffold.

Effects of Substitutions at the 4′ and 2 Positions on the Bioactivity of 4′-Ethynyl-2-Fluoro-2′-Deoxyadenosine

“…The activity of ADA is affected by the structural determinants of its substrates. While we have previously demonstrated (Marquez and colleagues) that this enzyme efficiently deaminates nucleoside analogs in the north conformation (43)(44)(45)(46), the kinetic analysis of ADA that we report here shows that the presence of a substituent at the 2 position of the adenine base makes these derivatives poor substrates for ADA. These results agree with previous studies reporting that 2-halo-substituted compounds are not efficiently deaminated by ADA (29,(31)(32)(33).…”

“…In contrast, host cell kinases appear to prefer the sugar ring in the south conformation; compounds that favor the north conformation are generally phosphorylated inefficiently (41,42). Sugar ring conformation has also been reported to play an important role in ADA recognition; the enzyme has been reported to deaminate nucleosides biased toward the north conformation up to 65-fold faster than those biased toward the south conformation (43)(44)(45)(46). Additionally, 2-fluoro-2=-deoxyadenosine (FdA) analogs are somewhat resistant to ADA-mediated catabolism due to the electron withdrawing properties of the 2-fluoro group (47,48), and we have previously reported that EFdA is poorly deaminated by ADA because of the 2-fluoro group (21).…”

Selective Phosphorylation of South and North-Cytidine and Adenosine Methanocarba-Nucleosides by Human Nucleoside and Nucleotide Kinases Correlates with Their Growth Inhibitory Effects on Cultured Cells

“…On the other hand, the deamination of S-MCdC by CDA is 10-fold faster than that of N-MCdC. Comparing the rates of deamination of the S and N analogues of dCyd relative to the natural substrate, the S-MCdC is nearly 100,000 times less efficient than dCyd [5].…”

“…Using this type of conformationally locked nucleosides, the conformational preferences of a number of enzymes were determined, including cytidine and adenosine deaminase (CDA and ADA) [4][5][6], HIV reverse transcriptase [7], DNA (cytosine-C5) methyl transferase [8] and several subtypes of adenosine receptors [9][10][11].…”

Synthesis of Conformationally North-Locked Pyrimidine Nucleosides Built on an Oxabicyclo[3.1.0]hexane Scaffold

“…1 However, in some enzymes, such as adenosine and cytidine deaminases, the degree of North/South discrimination occurs with a significant loss in binding affinity, even for the preferred rigid conformer. 2,3 This drop in affinity has been attributed to the missing oxygen, which could either interact with key amino acids at the active site through hydrogen bonding or participate in important electronic interaction with the base through the anomeric effect. 3,4 …”