Morpholino, piperidino, and pyrrolidino derivatives of pyrimidine nucleosides as inhibitors of ribonuclease A: synthesis, biochemical, and crystallographic evaluation

J Med Chem. 2009 Feb 26;52(4):932-42. doi: 10.1021/jm800724t.


Six 5'-deoxy-5'-morpholine, piperidine, and pyrrolidine of pyrimidine nucleosides have been synthesized and characterized. Their inhibitory action to ribonuclease A has been studied by biochemical analysis and X-ray crystallography. These compounds are moderate inhibitors of RNase A with mid-to-upper micromolar inhibition constants (K(i)). The high resolution X-ray crystal structures of the RNase A-inhibitor complexes have shown that all inhibitors bind at the enzyme catalytic cleft with the pyrimidine nucleobase at the B(1)R(2) subsites while the 5' group binds away from the main subsite P(1), where P-O(5') bond cleavage occurs, toward the solvent close to subsite P(0). Structure-activity relationship analysis has demonstrated that the compounds with the larger group in the 5' position are more potent. Comparative structural analysis of these RNase A complexes with other similar RNase A-ligand complexes provides a structural explanation of their potency and suggests ways to improve their efficiency and selectivity. These inhibitors can be the starting point for the development of compounds that can be used as pharmaceuticals against pathologies associated with RNase A homologues such as human angiogenin, which is implicated in tumor induced neovascularization.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Catalytic Domain
  • Crystallography, X-Ray
  • Humans
  • Morpholines
  • Neovascularization, Pathologic / drug therapy
  • Piperidines
  • Protein Binding
  • Protein Conformation
  • Pyrimidine Nucleosides / chemical synthesis*
  • Pyrimidine Nucleosides / chemistry
  • Pyrimidine Nucleosides / pharmacology
  • Pyrrolidines
  • Ribonuclease, Pancreatic / antagonists & inhibitors*
  • Structure-Activity Relationship


  • Morpholines
  • Piperidines
  • Pyrimidine Nucleosides
  • Pyrrolidines
  • angiogenin
  • Ribonuclease, Pancreatic

Associated data

  • PDB/3D6O
  • PDB/3D6P
  • PDB/3D6Q
  • PDB/3D7B
  • PDB/3D8Y
  • PDB/3D8Z