The structure of human deoxycytidine kinase in complex with clofarabine reveals key interactions for prodrug activation

• Published in: Acta crystallographica. Section D, Biological crystallography. Vol. 62; no. 2; pp. 133 - 139
• Main Authors: Zhang, Yan, Secrist III, John A., Ealick, Steven E.
• Format: Journal Article
• Language: English
• Published: 5 Abbey Square, Chester, Cheshire CH1 2HU, England Munksgaard International Publishers 01.02.2006
• Subjects: Adenine Nucleotides; Adenosine Diphosphate - metabolism; Adenosine Triphosphate - metabolism; Arabinonucleosides - metabolism; Binding Sites; Catalysis; clofarabine; deoxycytidine kinase; Deoxycytidine Kinase - chemistry; Deoxycytidine Kinase - isolation & purification; Deoxycytidine Kinase - metabolism; drug design; Humans; Models, Molecular; prodrug; Protein Conformation; Structure-Activity Relationship
• ISSN: 1399-0047; 0907-4449; 1399-0047
• DOI: 10.1107/S0907444905034293

Clofarabine [2‐chloro‐9‐(2‐deoxy‐2‐fluoro‐β‐d‐arabinofuranosyl)‐9H‐purin‐6‐amine] is a hybrid of the widely used anticancer drugs cladribine and fludarabine. It is the precursor of an effective chemotherapeutic agent for leukemias and other hematological malignancies and received accelerated approval by the FDA for the treatment of pediatric patients with relapsed or refractory acute lymphoblastic leukemia. Clofarabine is phosphorylated intracellularly by human deoxycytidine kinase (dCK) to the 5′‐monophosphate, which is the rate‐limiting step in activation of the prodrug. dCK has a broad substrate specificity, with a much higher activity to deoxycytidine than to deoxyadenosine and deoxyguanosine. As a purine‐nucleoside analog, clofarabine is a better substrate of dCK than deoxycytidine. The crystal structure of dCK has been solved previously in complex with pyrimidine nucleosides and ADP [Sabini et al. (2003), Nature Struct. Biol.10, 513–519]. In the current study, the crystal structure of clofarabine‐ and ADP‐bound dCK was solved to 2.55 Å by molecular replacement. It appears that the enzyme takes the same conformation as in the structures of the pyrimidine nucleoside‐bound complexes. The interactions between 2‐Cl and its surrounding hydrophobic residues contribute to the high catalytic efficiency of dCK for clofarabine.