Acidic-Amino-Acid-Conjugated Dinucleosides as Ribonuclease A Inhibitors: Rational Design and Effect of Backbone Chirality on Enzyme Inhibition

Carboxymethyl tethered poly(disubstituted)triazoles built on nucleoside skeletons: A unique class of ribonuclease A inhibitors designed using chemical logic

Molecular docking of N-1,4-disubstituted-1,2,3-triazole tethered carboxymethylated thymidine and uridine with ribonuclease A, indicated their possible binding with the P₁, B₁ and P₂ subsites with varied efficiencies. This theoretical study in combination of our earlier experimental observations was used as the guiding principles for designing a range of 1,4-disubstituted 1, 2, 3- triazole tethered carboxymethylated pyrimidine nucleosides. Triazoles are biologically important molecules and at the same time easily accessible through less complicated synthetic routes as reported about two decades back in the context of "click" reactions. Regioselective propargylation of the nucleosides under controlled conditions followed by the use of CuAAC strategy afforded mono-, bis-, tris- and tetratriazolyl pyrimidine nucleosides. Although the characteristics of nucleosides were lost in these densely functionalized polyheterocycles, the catalytic efficiency of ribonuclease A was significantly reduced by these molecules which were investigated experimentally and by docking studies. Triazoles as linkers helped one or more acidic groups to reach the P₁ subsite of ribonuclease A. Enzyme kinetics showed that the efficiency of inhibition reached the highest point with an optimum number of functional groups and were not linearly dependent on the number of triazole tethered carboxymethyl groups. The location of the triazole ring in the molecule affected the efficiency and nature of inhibition which were the result of the overall structure of the modified nucleosides. Thus, the tris-triazolylated thymidine derivative (T-3', 5', N-tris-CH₂TzCH₂COOH) as opposed to tetra-triazolylated uridine (U-2', 3', 5', N-tetrakis-CH₂TzCH₂COOH) emerged as the best inhibitor with an inhibition constant value of 2.3 ± 0.05 µM.

Sulfonic nucleic acids (SNAs): a new class of substrate mimics for ribonuclease A inhibition

Sulfonic nucleic acids were identified as inhibitors of ribonuclease A (RNase A). The incorporation of a strongly acidic group (sulfonic, -SO₃H) at the 3'-end of pyrimidine nucleosides thymidine and uridine was prompted by the low inhibition constant (K_i) values recorded for carboxymethylsulfonyl (-SO₂CH₂CO₂H) and -CO₂H functionalized nucleosides. It was envisaged that the sulfonic acid-modified pyrimidines would bind effectively with the positively charged P₁ site of ribonuclease A. Typical harsh conditions used for SO₃H incorporation were replaced with milder reaction conditions. The uridine analogue showing a K_i value of 0.96 μM elicited a better result than the thymidine-modified inhibitor. Notably, it was also the best result among all modified non-phosphate acidic nucleosides reported and screened so far as RNase A inhibitors.