Structural basis for activation of the therapeutic L-nucleoside analogs 3TC and troxacitabine by human deoxycytidine kinase.
L-nucleoside analogs represent an important class of small molecules for treating both viral infections and cancers. These pro-drugs achieve pharmacological activity only after enzyme-catalyzed conversion to their tri-phosphorylated forms. Herein, we report the crystal structures of human deoxycytidine kinase (dCK) in complex with the L-nucleosides (-)-beta-2',3'-dideoxy-3'-thiacytidine (3TC)--an approved anti-human immunodeficiency virus (HIV) agent--and troxacitabine (TRO)--an experimental anti-neoplastic agent. The first step in activating these agents is catalyzed by dCK. Our studies reveal how dCK, which normally catalyzes phosphorylation of the natural D-nucleosides, can efficiently phosphorylate substrates with non-physiologic chirality. The capability of dCK to phosphorylate both D- and L-nucleosides and nucleoside analogs derives from structural properties of both the enzyme and the substrates themselves. First, the nucleoside-binding site tolerates substrates with different chiral configurations by maintaining virtually all of the protein-ligand interactions responsible for productive substrate positioning. Second, the pseudo-symmetry of nucleosides and nucleoside analogs in combination with their conformational flexibility allows the L- and D-enantiomeric forms to adopt similar shapes when bound to the enzyme. This is the first analysis of the structural basis for activation of L-nucleoside analogs, providing further impetus for discovery and clinical development of new agents in this molecular class.
Sabini
Elisabetta
E
Department of Biochemistry and Molecular Genetics, University of Illinois Chicago, 900 S. Ashland (M/C 669), Chicago, IL 60607, USA.
Hazra
Saugata
S
Konrad
Manfred
M
Burley
Stephen K
SK
Lavie
Arnon
A
D019380:Anti-HIV Agents / Q000737:chemistry*; D000970:Antineoplastic Agents / Q000737:chemistry*; D018360:Crystallography, X-Ray; D003596:Cytosine / Q000031:analogs & derivatives* / Q000737:chemistry; D003842:Deoxycytidine Kinase / Q000737:chemistry*; D004148:Dioxolanes / Q000737:chemistry*; D006801:Humans; D019259:Lamivudine / Q000737:chemistry*; D008958:Models, Molecular; D011355:Prodrugs / Q000737:chemistry / Q000378:metabolism; D013237:Stereoisomerism; D013379:Substrate Specificity
D019380:Anti-HIV Agents; D000970:Antineoplastic Agents; D004148:Dioxolanes; D011355:Prodrugs; D019259:Lamivudine; C074908:troxacitabine; D003596:Cytosine; D003842:Deoxycytidine Kinase