Identification of DNA primase inhibitors via a combined fragment-based and virtual screening.
The structural differences between bacterial and human primases render the former an excellent target for drug design. Here we describe a technique for selecting small molecule inhibitors of the activity of T7 DNA primase, an ideal model for bacterial primases due to their common structural and functional features. Using NMR screening, fragment molecules that bind T7 primase were identified and then exploited in virtual filtration to select larger molecules from the ZINC database. The molecules were docked to the primase active site using the available primase crystal structure and ranked based on their predicted binding energies to identify the best candidates for functional and structural investigations. Biochemical assays revealed that some of the molecules inhibit T7 primase-dependent DNA replication. The binding mechanism was delineated via NMR spectroscopy. Our approach, which combines fragment based and virtual screening, is rapid and cost effective and can be applied to other targets.
Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel.
Stefan
S
Ilic
Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel.|Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave., Boston, Massachusetts 02115, USA.
Sabine R
SR
Akabayov
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave., Boston, Massachusetts 02115, USA.
Haribabu
H
Arthanari
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave., Boston, Massachusetts 02115, USA.
Gerhard
G
Wagner
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave., Boston, Massachusetts 02115, USA.
Charles C
CC
Richardson
Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel.
Barak
B
Akabayov
D017123:Bacteriophage T7 / Q000201:enzymology*; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D019915:DNA Primase / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000378:metabolism; D004261:DNA Replication / Q000187:drug effects; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000494:pharmacology*; D006801:Humans; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D019906:Nuclear Magnetic Resonance, Biomolecular; D054852:Small Molecule Libraries / Q000737:chemistry / Q000494:pharmacology*; D014764:Viral Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry
D004791:Enzyme Inhibitors; D054852:Small Molecule Libraries; D014764:Viral Proteins; D019915:DNA Primase