Journal of Computer-Aided Molecular Design

, Volume 24, Issue 12, pp 961–970

Prodrugs of aza nucleosides based on proton transfer reaction


DOI: 10.1007/s10822-010-9389-6

Cite this article as:
Karaman, R. J Comput Aided Mol Des (2010) 24: 961. doi:10.1007/s10822-010-9389-6


DFT calculation results for intramolecular proton transfer reactions in Kirby’s enzyme models 17 reveal that the reaction rate is quite responsive to geometric disposition, especially to distance between the two reactive centers, rGM, and the angle of attack, α (the hydrogen bonding angle). Hence, the study on the systems reported herein could provide a good basis for designing aza nucleoside prodrug systems that are less hydrophilic than their parental drugs and can be used, in different dosage forms, to release the parent drug in a controlled manner. For example, based on the calculated log EM, the cleavage process for prodrug 1ProD is predicted to be about 1010 times faster than that for prodrug 7ProD and about 104 times faster than prodrug 3ProD: rate1ProD > rate3ProD > rate7ProD. Hence, the rate by which the prodrug releases the aza nucleoside drug can be determined according to the structural features of the linker (Kirby’s enzyme model).


Aza nucleosides prodrugsDecitabine prodrugsDFT calculationsProton transfer reactionKirby’s enzyme modelEffective molarity (EM)

Supplementary material

10822_2010_9389_MOESM1_ESM.doc (100 kb)
Xyz Cartesian coordinates for the calculated GM and TS optimized structures in processes 1–7 (DOC 100 kb)

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  1. 1.Faculty of PharmacyAl-Quds UniversityJerusalemPalestine