In Silico Docking of Small-Molecule Inhibitors to the Escherichia coli Type III Secretion System EscN ATPase

摘要

The type III secretion system (T3SS) is a supermolecular construct that allows many Gram-negative pathogens to translocate effector virulence proteins directly into host cells in a process requiring adenosine triphosphate (ATP) hydrolysis. We used in silico molecular modeling and computational chemistry to determine the conformations of three different small-molecule compounds when bound to EscN, the T3SS ATPase of enteropathogenic Escherichia coli. Each compound was shown to separately bind EscN within or very close to its active site and to effectively inhibit catalytic activity. Two structurally related compounds were observed to adopt extended conformations in the active- site cleft and essentially occupied the entire cleft, which obstructed the ATP binding including the formation of ATP-EscN non-covalent interactions and hydrogen bonds. Both compounds appeared to span the region in the active site with Phe355 and Gln426, residues that are essential for forming -stacking interactions and hydrogen bonds with the adenosine base of the ATP substrate. In contrast, the third compound appeared to fold upon itself in the EscN active- site cleft to adopt a very compact conformation that occupied only one side of the cleft. Our goal was to determine the three-dimensional structures of the compound EscN complexes for designing lead compounds and ultimately develop broad-spectrum therapeutics against T3SS pathogens.