Novel inhibitors of anthrax edema factor.
Several pathogenic bacteria produce adenylyl cyclase toxins, such as the edema factor (EF) of Bacillus anthracis. These disturb cellular metabolism by catalyzing production of excessive amounts of the regulatory molecule cAMP. Here, a structure-based method, where a 3D-pharmacophore that fit the active site of EF was constructed from fragments, was used to identify non-nucleotide inhibitors of EF. A library of small molecule fragments was docked to the EF-active site in existing crystal structures, and those with the highest HINT scores were assembled into a 3D-pharmacophore. About 10,000 compounds, from over 2.7 million compounds in the ZINC database, had a similar molecular framework. These were ranked according to their docking scores, using methodology that was shown to achieve maximum accuracy (i.e., how well the docked position matched the experimentally determined site for ATP analogues in crystal structures of the complex). Finally, 19 diverse compounds with the best AutoDock binding/docking scores were assayed in a cell-based assay for their ability to reduce cAMP secretion induced by EF. Four of the test compounds, from different structural groups, inhibited in the low micromolar range. One of these has a core structure common to phosphatase inhibitors previously identified by high-throughput assays of a diversity library. Thus, the fragment-based pharmacophore identified a small number of diverse compounds for assay, and greatly enhanced the selection process of advanced lead compounds for combinatorial design.
Chen
Deliang
D
Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-0857, USA.
Misra
Milind
M
Sower
Laurie
L
Peterson
Johnny W
JW
Kellogg
Glen E
GE
Schein
Catherine H
CH
D000067956:Adenylyl Cyclase Inhibitors; D000818:Animals; D000942:Antigens, Bacterial; D001427:Bacterial Toxins; D001681:Biological Assay; D002460:Cell Line; D020650:Combinatorial Chemistry Techniques; D015195:Drug Design; D008264:Macrophages / Q000187:drug effects; D008958:Models, Molecular; D015394:Molecular Structure; D011485:Protein Binding; D013329:Structure-Activity Relationship
D000067956:Adenylyl Cyclase Inhibitors; D000942:Antigens, Bacterial; D001427:Bacterial Toxins; C030325:anthrax toxin