Understanding How the Herpes Thymidine Kinase Orchestrates Optimal Sugar and Nucleobase Conformations To Accommodate Its Substrate at the Active Site: A Chemical Approach

The herpes virus thymidine kinase (HSV-tk) is a critical enzyme for the activation of anti-HSV
nucleosides. However, a successful therapeutic outcome depends not only on the activity of this enzyme
but also on the ability of the compound(s) to interact effectively with cellular kinases and with the target
viral or cellular DNA polymerases. Herein, we describe the synthesis and study of two nucleoside analogues
built on a conformationally locked bicyclo[3.1.0]hexane template designed to investigate the conformational
preferences of HSV-tk for the 2‘-deoxyribose ring. Intimately associated with the conformation of the 2‘-deoxyribose ring is the value of the C−N torsion angle χ, which positions the nucleobase into two different
domains (syn or anti). The often-conflicting sugar and nucleobase conformational parameters were studied
using North and South methanocarbadeoxythymidine analogues (6 and 7), which forced HSV-tk to make
a clear choice in the conformation of the substrate. The results provide new insights into the mechanism
of action of this enzyme, which cannot be gleaned from a static X-ray crystal structure.