Molecular dynamics and docking simulations as a proof of high flexibility in E. coli FabH and its relevance for accurate inhibitor modeling

Abstract

Bacterial β-ketoacyl-acyl carrier protein synthase III (FabH) has become an attractive target for the development of new antibacterial agents which can overcome the increased resistance of these pathogens to antibiotics in clinical use. Despite several efforts have been dedicated to find inhibitors for this enzyme, it is not a straightforward task, mainly due its high flexibility which makes difficult the structure-based design of FabH inhibitors. Here, we present for the first time a Molecular Dynamics (MD) study of the E. colil FabH enzyme to explore its conformational space. We compare the flexibility of this enzyme for the unliganded protein and an enzyme-inhibitor complex and find a correspondence between our modeling results and the experimental evidence previously reported for this enzyme. Furthermore, through a 100 ns MD simulation of the unliganded enzyme we extract useful information related to the concerted motions that take place along the principal components of displacement. We also establish a relation between the presence of water molecules in the oxyanion hole with the conformational stability of structural important loops. Representative conformations of the binding pocket along the whole trajectory of the unliganded protein are selected through cluster analysis and we find that they contain a conformational diversity which is not provided by the X-ray structures of ecFabH. As a proof of this last hypothesis, we use a set of 10 FabH inhibitors and show that they cannot be correctly modeled in any available X-ray structure, while by using our set of conformations extracted from the MD simulations, this task can be accomplish. Finally, we show the ability of short MD simulations for the refinement of the docking binding poses and for MM-PBSA calculations to predict stable protein-inhibitor complexes in this enzyme.

Regulation of cell size in response to nutrient availability by fatty acid biosynthesis in Escherichia coli

“…In any event, the current model for type II FA biosynthesis in E. coli needs revision. In addition, these findings have important implications for whether FabH is an effective target for antibiotic intervention (55,(66)(67)(68)(69). At the moment, whether any of the condensing enzymes involved in FA elongation (FabF/B) can substitute for FabH in E. coli is unknown.…”

Enzyme Stability and Activity in Non-Aqueous Reaction Systems: A Mini Review

“…Fasoli et al [21] also revealed that the flexibility of subtilisin from Bacillus licheniformis in octane (log P = 4.183) was lower than in acetonitrile (log P =´0.334). As discussing the flexibility of the enzyme, it was worthily noted that enyzme flexibility was usually determined from MD simulations and it is measured by the relative calculated B-factors [22].…”

Molecular basis of HHQ biosynthesis: molecular dynamics simulations, enzyme kinetic and surface plasmon resonance studies

“…Knowledge of the kinetics and of the conformational flexibility of an enzyme can significantly contribute to a successful rational drug design [27-29]. Herein we study the molecular basis of PqsD and the HHQ biosynthesis combining experimental and in silico methods.…”