“An important kinetic parameter for drug efficacy is the residence time of a compound at a drug target, which is related to the dissociation rate constant k(off). For the essential antimyco-bacterial target InhA, this parameter is most likely governed by the ordering of the flexible substrate binding loop (SBL). Whereas
the diphenyl ether inhibitors 6PP and triclosan (TCL) do not show loop ordering and thus, no slow-binding inhibition and high k(off) values, the slightly modified PT70 leads to an ordered loop and a residence time of 24 minutes. To assess the structural differences of the complexes from a dynamic point of view, molecular check details dynamics (MD) simulations with a total sampling time of 3.0 mu s were performed for three ligand-bound and two ligand-free (perturbed) InhA systems. The individual simulations show comparable Selleckchem LCL161 conformational features with
respect to both the binding pocket and the SBL, allowing to define five recurring conformational families. Based on their different occurrence frequencies in the simulated systems, the conformational preferences could be linked to structural differences of the respective ligands to reveal important determinants of residence time. The most abundant conformation besides the stable EI* state is characterized by a shift of IIe202 and Val203 toward the hydrophobic pocket of InhA. The analyses revealed potential CT99021 PI3K/Akt/mTOR inhibitor directions for avoiding this conformational change and, thus, hindering rapid dissociation: (1) an anchor group in 2′-position of the B-ring for scaffold stabilization, (2) proper occupation of the hydrophobic pocket, and (3) the introduction of a barricade sub-stituent in 5′-position of the diphenyl ether B-ring.”
dehalogenases (2-HADs) catalyse the hydrolytic dehalogenation of 2-haloalkanoic acids, cleaving the carbon-halide bond at the C-alpha-atom position and releasing a halogen atom. These enzymes are of interest for their potential use in bioremediation and in the synthesis of industrial chemicals. Here, the crystal structure of 2-HAD from Pseudomonas syringae pv. tomato DC3000 (ps-2-HAD) at 1.98 angstrom resolution solved using the single-wavelength anomalous dispersion method is reported. The ps-2-HAD molecule consists of two structurally distinct domains: the core domain and the subdomain. Enzymatic activity analysis of ps-2-HAD revealed its capacity to catalyse the dehalogenation of both L- and D-substrates; however, the structure of ps-2-HAD is completely different from that of DehI, which is the only DL-2-HAD enzyme that has been structurally characterized, but shows similar overall folding to L-HADs. Single mutations of four amino-acid residues at the putative active site showed that they are related to its enzymatic activity, yet three of them are nonconserved among HADs.