Binding Sites Of Water Molecules Research Articles

Preparation of single crystals of palmatine-sulfophenyl acids pharmaceutical salts by substituting Cl− in palmatine chloride to improve hygroscopic stability and antibacterial activity of palmatine and to preserve its solubility

To enhance the hygroscopic stability of palmatine chloride (PMTCl) while maintaining its solubility, several unexplored pharmaceutical salts of palmatine (PMT) were synthesised using benzenesulfonic acid (PMT-BSA), p-toluenesulfonic acid (PMT-PTSA), and aminobenzenesulfonic acid (PMT-SUL). These novel salts were thoroughly characterized using techniques such as single-crystal X-ray diffraction, powder X-ray diffraction (PXRD), infrared spectroscopy (IR), and Hirshfeld surface analysis to determine their structural properties. Surprisingly, it was discovered that these salts exhibited improved antibacterial activity in addition to their enhanced hygroscopic stability. As anticipated, all three pharmaceutical salts demonstrated improved hygroscopic stability. This improvement might be attributed, to some extent, to the introduction of safe, stable, and less electronegative anions (BSA, PTSA, and SUL) to replace the more electronegative chloride (Cl−) in PMTCl. The replacement of Cl− hindered the binding of the pharmaceutical with external water molecules, thus increasing its resistance to moisture. Moreover, the interaction between PMT and the anions from the benzenesulfonic acid group via hydrogen bonding might have played a role in the improved hygroscopic stability. The crystal structure formed by the PMT molecules exhibited long-range order, while the benzenesulfonic acid anions cleverly avoided potential binding sites for water molecules. Additionally, the antibacterial activities of all three pharmaceutical salts were enhanced. This improvement can be attributed to the alteration of electron cloud density (ρe) in the isoquinoline group of PMT upon the introduction of benzenesulfonate anions to form the pharmaceutical salts. This hypothesis was supported by analyzing the molecular electrostatic potential, electron cloud density, and Hirshfeld surface. The successful outcome of this study suggests that modifying the ρe of the isoquinoline group in protoberberines through the introduction of benzenesulfonic acid anions to form pharmaceutical salts can potentially alter their physicochemical properties and biological activities. This finding paves the way for future research on improving the physicochemical properties of protoberberines-based pharmaceuticals.

Potassium and sodium ion complexes with a partial peptide of the selectivity filter in K+ channels studied by cold ion trap infrared spectroscopy: the effect of hydration.

Potassium channels allow K+ to rapidly diffuse, while the selectivity filter (SF) actively blocks Na+. The presence of water in the SF during ion translocation remains under debate due to the experimental and computational challenges in characterizing the interactions between water, ions, and the SF. Our bottom-up approach has been applied to a system composed of a partial peptide of the SF (Ac-tyrosine-NHMe) with a metal ion and a single water molecule to probe these interactions. The IR photodissociation spectra of M+Ac-tyrosine-NHMe(H2O) (M = Na, K) combined with quantum chemical calculations revealed that the water molecule binding sites are ion-dependent. In addition, the ion-peptide distances are elongated significantly for the K+ complex in comparison to the Na+ complex by the addition of a single water molecule. This striking structural difference with the water molecule is discussed in relation to ion selectivity and translocation within the K+ channel.

On the hydration of DOPE in solution.

The atomic-scale hydration structure around the 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) headgroup in a chloroform/water solution has been investigated using neutron diffraction enhanced by isotopic substitution and NMR, coupled with empirical potential structure refinement and molecular dynamics simulations. The results obtained show the preferential binding sites for water molecules on the DOPE headgroups, with the most predominant interactions being with the ammonium and phosphate groups. Interestingly, the level of hydration, as well as the association of DOPE molecules, varies according to the simulation method used. The results here suggest the presence of a tight water network around these lipid headgroups that could affect the permeability of the membrane for lipid-mediated diffusion.

Rapid and Accurate Prediction and Scoring of Water Molecules in Protein Binding Sites

Water plays a critical role in ligand-protein interactions. However, it is still challenging to predict accurately not only where water molecules prefer to bind, but also which of those water molecules might be displaceable. The latter is often seen as a route to optimizing affinity of potential drug candidates. Using a protocol we call WaterDock, we show that the freely available AutoDock Vina tool can be used to predict accurately the binding sites of water molecules. WaterDock was validated using data from X-ray crystallography, neutron diffraction and molecular dynamics simulations and correctly predicted 97% of the water molecules in the test set. In addition, we combined data-mining, heuristic and machine learning techniques to develop probabilistic water molecule classifiers. When applied to WaterDock predictions in the Astex Diverse Set of protein ligand complexes, we could identify whether a water molecule was conserved or displaced to an accuracy of 75%. A second model predicted whether water molecules were displaced by polar groups or by non-polar groups to an accuracy of 80%. These results should prove useful for anyone wishing to undertake rational design of new compounds where the displacement of water molecules is being considered as a route to improved affinity.

Hydration Isomers of Protonated Phenylalanine and Derivatives: Relative Stabilities from Infrared Photodissociation

The binding sites of water molecules to protonated Phe and its derivatives are investigated using infrared photodissociation (IRPD) spectroscopy and kinetics as well as by computational chemistry. Calculated relative energies for hydration of PheH(+) at various sites on the N- and C-termini depend on the type of theory and basis set used, and no one hydration site was consistently calculated to be most favorable. Infrared photodissociation (IRPD) spectra between approximately 2650 and 3850 cm(-1) are reported for PheH(+)(H(2)O)(1-4) at 133 K and compared to calculated absorption spectra of low-energy hydration isomers, which do not resemble the IRPD spectra closely enough to unambiguously assign spectral bands. The IRPD spectra of PheH(+)(H(2)O)(1-4) are instead compared to those of N,N-Me(2)PheH(+)(H(2)O)(1,2), N-MePheH(+)(H(2)O)(1-3), and PheOMeH(+)(H(2)O)(1-3) at 133 K, which makes possible systematic band assignments. A unique band associated with a binding site not previously reported for PheH(+)(H(2)O), in which the water molecule accepts a hydrogen bond from the N-terminus of PheH(+) and donates a weak hydrogen bond to the pi-system of the side chain, is identified in the IRPD spectra. IRPD kinetics at laser frequencies resonant with specific hydration isomers are found to be biexponential for N,N-Me(2)PheH(+)(H(2)O), N-MePheH(+)(H(2)O), and PheH(+)(H(2)O). Relative populations of ions with water molecules attached at various binding sites are determined from fitting these kinetic data, and relative energies for hydration of these competitive binding sites at 133 K are obtained from these experimental values.

Stacking of Bacteriochlorophyll c Macrocycles in Chlorosome from Chlorobium limicola As Revealed by Intermolecular 13C Magnetic-Dipole Correlation, X-Ray Diffraction, and Quadrupole Coupling in 25Mg NMR

The stacking of the bacteriochlorophyll (BChl) c macrocycles and the role of water in forming an aggregate sheet, in chlorosome, were examined by means of (13)C NMR spectroscopy, the measurement of the X-ray diffraction pattern, and (25)Mg NMR spectroscopy. (1) The stacking of the macrocycles, i.e., weakly overlapped dimers forming displaced layers, was selected out of six different kinds of stacking so far identified in the aggregates of isomeric BChl c in solution and in the solid aggregate of an isomeric mixture of BChl c extracted from Chlorobium limicola. The selection was based on the comparison of the intermolecular (13)C...(13)C magnetic-dipole correlations with the nearest-neighbor carbon-to-carbon close contacts simulated for the above six different stackings. It has turned out that the stacking of the macrocycles in chlorosome is basically the same as that in the in vitro solid aggregate. (2) The crucial role of water in stabilizing the aggregate structure in chlorosome was shown by tracing the dehydration processes and by comparison with the solid aggregate using the X-ray diffraction pattern. Possible binding sites of water molecules were located, by structural simulation, based on the particular stacking structure. (3) The dimer-based stacking of the macrocycles was evidenced by (25)Mg NMR spectroscopy, which exhibited a pair of signals showing different quadrupole coupling, due to the presence or absence of a water molecule in the axial position.

Metahybrid Density Functional Theory and Correlated ab Initio Studies on Microhydrated Adenine−Thymine Base Pairs

Monohydrated and dihydrated adenine-thymine base pairs are characterized using metahybrid density functional theory and correlated ab initio approaches. The motivation of this work is twofold. First, the high-level geometries and interaction energies computed for different complexes serve as a reference for the testing of recently developed density functional theory (DFT) with respect to its ability to correctly describe the balance between the electrostatic and the dispersion contributions that bind these complexes. Second, these studies of nucleic acid base pairs are important for finding binding sites of water molecules around bases and for a better understanding of the influence of the solvent on the stability of the structure of DNA duplexes.

Infrared spectroscopy of anionic hydrated fluorobenzenes

We investigate the structural motifs of anionic hydrated fluorobenzenes by infrared photodissociation spectroscopy and density functional theory. Our calculations show that all fluorobenzene anions under investigation are strongly distorted from the neutral planar molecular geometries. In the anions, different F atoms are no longer equivalent, providing structurally different binding sites for water molecules and giving rise to a multitude of low-lying isomers. The absorption bands for hexa- and pentafluorobenzene show that only one isomer for the respective monohydrate complexes is populated in our experiment. For C6F6.-H2O, we can assign these bands to an isomer where water forms a weak double ionic hydrogen bond with two F atoms in the ion, in accord with the results of Bowen et al. [J. Chem. Phys. 127, 014312 (2007), following paper.] The spectroscopic motif of the binary complexes changes slightly with decreasing fluorination of the aromatic anion. For dihydrated hexafluorobenzene anions, several isomers are populated in our experiments, some of which may be due to hydrogen bonding between water molecules.

Potential Energy Surfaces of the Microhydrated Guanine⋅⋅⋅Cytosine Base Pair and its Methylated Analogue

A complete scan of the potential and free-energy surfaces of monohydrated and dihydrated guanine...cytosine and 9-methylguanine...1-methylcytosine base pairs was realized by the molecular dynamics/quenching technique using the force field of Cornell et al. implemented in the AMBER7 program. The most stable and populated structures localized were further fully reoptimized at the correlated ab initio level employing the resolution of identity Møller-Plesset method with a large basis set. A systematic study of microhydration of these systems using a high-level correlated ab initio approach is presented for the first time. The different behavior of guanine...cytosine and adenine...thymine complexes is also discussed. These studies of nucleic acid base pairs are important for finding binding sites of water molecules around bases and for better understanding of the influence of the solvent on the stability of the structure of DNA.

The structural variation and probability redistribution in alanine dipeptide conformers by hydration

The effects on structural variation and relative stability caused by hydration of alanine dipeptide in the C eq 7, C ax 7, C 5, α R and P II conformations were investigated by the method of the SUMSL (secant-type unconstrained minimization solver) energy-minimization technique, using the empirical potential energy function of the solute and the ST2 water model. The binding sites of water molecules in the solute were selected from spherical interaction energy maps. As a function of the number of added water molecules, we traced the structural variations mainly in the (ø,ψ) torsion angle space, and calculated the total internal energies of each solute-water system to evaluate the relative probabilities between those five conformers. The results indicate that the conformers having no intramolecular hydrogen bonds, such as α R, C 5 and P II, show larger structural variations than the C ax 7 and C eq 7 conformers which have intramolecular hydrogen bonds. The torsion angle, ψ, fluctuated more than ø for all the examined conformers. The energetically dominant conformation is shifted from C eq 7 to α R as the hydration progresses.