Structure–activity relationship for extracellular block of K+ channels by tetraalkylammonium ions

AbstractExternal tetraalkylammonium ion binding to potassium channels is studied using microscopic molecular modelling methods and the experimental structure of the KcsA channel. Relative binding free energies of the KcsA complexes with Me4N+, Et4N+, and n-Pr4N+ are calculated with the molecular dynamics free energy perturbation approach together with automated ligand docking. The four-fold symmetry of the entrance cavity formed by the Tyr82 residues is found to provide stronger binding for the D2d than for the S4 conformation of the ligands. In agreement with experiment the Et4N+ blocker shows several kcal/mol better binding than the other tetraalkylammonium ions

Computational and NMR study of quaternary ammonium ion conformations in solution

Conformations around C–N bonds at the quaternary centre in tetraalkylammonium ions in water solution are investigated. Structures of Me4N+, Et4N+, n-Pr4N+, n-Bu4N+, and n-Pe4N+ are calculated using quantum mechanical HF and DFT methods together with the PCM solvent model. Relative solvation free energies of tetraalkylammonium ions are further estimated from microscopic molecular dynamics free energy perturbation simulations using the Gromos-87 and Amber-95 force fields. The predicted free energy difference in solution between two stable conformations of Et4N+, D2d and S4, is 0.6–1.0 kcal mol−1 (in favour of D2d), which is in quantitative agreement with the recent Raman spectroscopy results. The energies of the g+g− conformations of Et4N+ are 3.6–4.0 kcal mol−1 higher. The ions with longer hydrocarbon chains show quite similar energy gap between D2d and S4. The torsion barrier for a two-step interconversion between the D2d and S4 structures is 9.5 kcal mol−1 (HF/6-31G(d) calculations). The computational results are augmented by NMR measurements of the Et4N+–I− salt in aqueous solution, which predict a symmetric structure of Et4N+ in water. However, the D2d and S4 conformers are not discernible due to presumably high similarity of chemical shifts. The calculated conformational energetics in solution together with previously observed D2d, S4 and high-energy g+g−-type structures of Et4N+, n-Pr4N+, and n-Bu4N+ in the solid state indicate that the carbon chain conformations at the quaternary ammonium centre sensitively depend on the actual microenvironment

Ligand Binding to the Voltage-Gated Kv1.5 Potassium Channel in the Open State—Docking and Computer Simulations of a Homology Model☆

The binding of blockers to the human voltage-gated Kv1.5 potassium ion channel is investigated using a three-step procedure consisting of homology modeling, automated docking, and binding free energy calculations from molecular dynamics simulations, in combination with the linear interaction energy method. A reliable homology model of Kv1.5 is constructed using the recently published crystal structure of the Kv1.2 channel as a template. This model is expected to be significantly more accurate than earlier ones based on less similar templates. Using the three-dimensional homology model, a series of blockers with known affinities are docked into the cavity of the ion channel and their free energies of binding are calculated. The predicted binding free energies are in very good agreement with experimental data and the binding is predicted to be mainly achieved through nonpolar interactions, whereas the relatively small differences in the polar contribution determine the specificity. Apart from confirming the importance of residues V505, I508, V512, and V516 for ligand binding in the cavity, the results also show that A509 and P513 contribute significantly to the nonpolar binding interactions. Furthermore, we find that pharmacophore models based only on optimized free ligand conformations may not necessarily capture the geometric features of ligands bound to the channel cavity. The calculations herein give a detailed structural and energetic picture of blocker binding to Kv1.5 and this model should thus be useful for further ligand design efforts

Novel Type of Tetranitrosyl Iron Salt: Synthesis, Structure and Antibacterial Activity of Complex [FeL’₂(NO)₂][FeL’L”(NO)₂] with L’-thiobenzamide and L”-thiosulfate

In this work a new donor of nitric oxide (NO) with antibacterial properties, namely nitrosyl iron complex of [Fe(C6H5C-SNH2)2(NO)2][Fe(C6H5C-SNH2)(S2O3)(NO)2] composition (complex I), has been synthesized and studied. Complex I was produced by the reduction of the aqueous solution of [Fe2(S2O3)2(NO)2]2− dianion by the thiosulfate, with the further treatment of the mixture by the acidified alcohol solution of thiobenzamide. Based on the structural study of I (X-ray analysis, quantum chemical calculations by NBO and QTAIM methods in the frame of DFT), the data were obtained on the presence of the NO…NO interactions, which stabilize the DNIC dimer in the solid phase. The conformation properties, electronic structure and free energies of complex I hydration were studied using B3LYP functional and the set of 6–31 + G(d,p) basis functions. The effect of an aquatic surrounding was taken into account in the frame of a polarized continuous model (PCM). The NO-donating activity of complex I was studied by the amperometry method using an “amiNO-700” sensor electrode of the “inNO Nitric Oxide Measuring System”. The antibacterial activity of I was studied on gram-negative (Escherichia coli) and gram-positive (Micrococcus luteus) bacteria. Cytotoxicity was studied using Vero cells. Complex I was found to exhibit antibacterial activity comparable to that of antibiotics, and moderate toxicity to Vero cells