title: Understanding how the herpes thymidine kinase orchestrates optimal sugar and nucleobase conformations to accommodate its substrate at the active site: a chemical approach.
abstract: 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 chi, 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.
authors.affiliation: Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA. marquezv@dc37a.nci.nih.gov
authors.forename: Victor E
authors.initials: VE
authors.lastname: Marquez
authors.forename: Yongseok
authors.initials: Y
authors.lastname: Choi
authors.forename: Maria Julieta
authors.initials: MJ
authors.lastname: Comin
authors.forename: Pamela
authors.initials: P
authors.lastname: Russ
authors.forename: Clifford
authors.initials: C
authors.lastname: George
authors.forename: Mahmoud
authors.initials: M
authors.lastname: Huleihel
authors.forename: Tsipi
authors.initials: T
authors.lastname: Ben-Kasus
authors.forename: Riad
authors.initials: R
authors.lastname: Agbaria
mesh_terms: D000998:Antiviral Agents / Q000737:chemistry / Q000494:pharmacology; D001665:Binding Sites; D001643:Bridged Bicyclo Compounds / Q000737:chemistry; D002241:Carbohydrates / Q000737:chemistry*; D018360:Crystallography, X-Ray; D003855:Deoxyribose / Q000737:chemistry; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000494:pharmacology; D006561:Herpes Simplex / Q000201:enzymology*; D008968:Molecular Conformation; D009705:Nucleosides / Q000737:chemistry*; D013379:Substrate Specificity; D013936:Thymidine / Q000737:chemistry; D013937:Thymidine Kinase / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000378:metabolism
chemical_list: D000998:Antiviral Agents; D001643:Bridged Bicyclo Compounds; D002241:Carbohydrates; D004791:Enzyme Inhibitors; D009705:Nucleosides; C046059:bicyclo(3.1.0)hexane; D003855:Deoxyribose; D013937:Thymidine Kinase; D013936:Thymidine