Selective inhibition of DNA replicase assembly by a non-natural nucleotide: exploiting the structural diversity of ATP-binding sites.
DNA synthesis is catalyzed by an ensemble of proteins designated the replicase. The efficient assembly of this multiprotein complex is essential for the continuity of DNA replication and is mediated by clamp-loading accessory proteins that use ATP binding and hydrolysis to coordinate these events. As a consequence, the ability to selectively inhibit the activity of these accessory proteins provides a rational approach to regulate DNA synthesis. Toward this goal, we tested the ability of several non-natural nucleotides to inhibit ATP-dependent enzymes associated with DNA replicase assembly. Kinetic and biophysical studies identified 5-nitro-indolyl-2'-deoxyribose-5'-triphosphate as a unique non-natural nucleotide capable of selectively inhibiting the bacteriophage T4 clamp loader versus the homologous enzyme from Escherichia coli. Modeling studies highlight the structural diversity between the ATP-binding site of each enzyme and provide a mechanism accounting for the differences in potencies for various substituted indolyl-2'-deoxyribose-5'-triphosphates. An in vivo assay measuring plaque formation demonstrates the efficacy and selectivity of 5-nitro-indolyl-2'-deoxyribose as a cytostatic agent against T4 bacteriophage while leaving viability of the E. coli host unaffected. This strategy provides a novel approach to develop agents that selectively inhibit ATP-dependent enzymes that are required for efficient DNA replication.
Eng
Kevin
K
Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106, USA.
Scouten-Ponticelli
Sarah K
SK
Sutton
Mark
M
Berdis
Anthony
A
D000255:Adenosine Triphosphate / Q000378:metabolism*; D001665:Binding Sites; D004261:DNA Replication / Q000187:drug effects*; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry / Q000378:metabolism; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000494:pharmacology*; D004926:Escherichia coli / Q000201:enzymology; D019384:Nucleic Acid Synthesis Inhibitors / Q000737:chemistry / Q000494:pharmacology*; D009711:Nucleotides / Q000737:chemistry / Q000494:pharmacology*; D011487:Protein Conformation; D014764:Viral Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism
C524003:5-nitro-1-indolyl-2'-deoxyriboside-5'-triphosphate; D004791:Enzyme Inhibitors; D019384:Nucleic Acid Synthesis Inhibitors; D009711:Nucleotides; D014764:Viral Proteins; C074855:gene 44 protein, Enterobacteria phage T4; D000255:Adenosine Triphosphate; C023140:DNA replicase; D004259:DNA-Directed DNA Polymerase