Water structure theory and some implications for drug design

Structurally Dynamic Monocyte-Liposome Hybrid Vesicles as an Anticancer Drug Delivery Vehicle: A Crucial Correlation of Microscopic Elasticity and Ultrafast Dynamics

A biomimetic cell-based carrier system based on monocyte membranes and liposomes has been designed to create a hybrid "Monocyte-LP" which inherits the surface antigens of the monocytes along with the drug encapsulation property of the liposome. Förster resonance energy transfer (FRET) and polarization gated anisotropy measurements show the stiffness of the vesicles obtained from monocyte membranes (Mons), phosphatidylcholine membranes (LP), and Monocyte-LP to follow an increasing order of Mons > Monocyte-LP > LP. The dynamics of interface bound water molecules plays a key role in the elasticity of the vesicles, which in turn imparts higher delivery efficacy to the hybrid Monocyte-LP for a model anticancer drug doxorubicin than the other two vesicles, indicating a critical balance between flexibility and rigidity for an efficient cellular uptake. The present work provides insight on the influence of elasticity of delivery vehicles for enhanced drug delivery.

Inconsistent hydrogen bond-mediated vibrational coupling of amide I

Using infrared spectroscopy and density functional theory (DFT) calculations, we scrutinized an amide (dimethylformamide) as a "model" compound to interpret the interactions of amide 1 with different phenol derivatives (para-chlorophenol (PCP) and para-cresol (CP)) as "model guest molecules". We established the involvement of amide I in vibrational coupling with symmetric and asymmetric C[double bond, length as m-dash]C modes of different phenolic derivatives and how their coupling was dependent upon different guest aromatic phenolic compounds. Interestingly, substitution of phenol perturbed the pattern of vibrational coupling with amide I. The symmetric and asymmetric C[double bond, length as m-dash]C modes of PC were coupled significantly with amide 1. For PCP, the symmetric C[double bond, length as m-dash]C mode coupled significantly, but the asymmetric mode coupled negligibly, with amide I. Here, we reveal the nature of vibrational coupling based on the structure of a guest molecule hydrogen-bonded with amide I. Our conclusions could be valuable for depiction of the unusual dynamics of coupled amide-I modes as well as the dependency of vibrational coupling on altered factors.

Network Pharmacology and Transcriptomics Reveal the Mechanism of GuaLouQuMaiWan in Treatment of Type 2 Diabetes and Its Active Small Molecular Compound

The main pathophysiological abnormalities in type 2 diabetes (T2D) include pancreatic β-cell dysfunction and insulin resistance. Due to hyperglycemia, patients receive long-term treatment. However, side effects and drug tolerance usually lead to treatment failure. GuaLouQuMaiWan (GLQMW), a common traditional Chinese medicine (TCM) prescription, has positive effects on controlling blood sugar and improving quality of life, but the mechanism is still unclear. To decipher their molecular mechanisms, we used a novel computational systems pharmacology-based approach consisting of bioinformatics analysis, network pharmacology, and drug similarity comparison. We divided the participants into nondisease (ND), impaired glucose tolerance (IGT), and type 2 diabetes groups according to the WHO's recommendations for diabetes. By analyzing the gene expression profile of the ND-IGT-T2D (ND to IGT to T2D) process, we found that the function of downregulated genes in the whole process was mainly related to insulin secretion, while the upregulated genes were related to inflammation. Furthermore, other genes in the ND-IGT (ND to IGT) process are mainly related to inflammation and lipid metabolic disorders. We speculate that 17 genes with a consistent trend may play a key role in the process of ND-IGT-T2D. We further performed target prediction for 50 compounds in GLQMW that met the screening criteria and intersected the differentially expressed genes of the T2D process with the compounds of GLQMW; a total of 18 proteins proved potential targets for GLQMW. Among these, RBP4 is considerably related to insulin resistance. GO/KEGG enrichment analyses of the target genes of GLQMW showed enrichment in inflammation- and T2D therapy-related pathways. Based on the RDKit tool and the DrugBank database, we speculate that (-)-taxifolin, dialoside A_qt, spinasterol, isofucosterol, and 11,14-eicosadienoic acid can be used as potential drugs for T2D via molecular docking and drug similarity comparison.

Nuclear Magnetic Resonance with Fast Field-Cycling Setup: A Valid Tool for Soil Quality Investigation

Nuclear magnetic resonance (NMR) techniques are largely employed in several fields. As an example, NMR spectroscopy is used to provide structural and conformational information on pure systems, while affording quantitative evaluation on the number of nuclei in a given chemical environment. When dealing with relaxation, NMR allows understanding of molecular dynamics, i.e., the time evolution of molecular motions. The analysis of relaxation times conducted on complex liquid–liquid and solid–liquid mixtures is directly related to the nature of the interactions among the components of the mixture. In the present review paper, the peculiarities of low resolution fast field-cycling (FFC) NMR relaxometry in soil science are reported. In particular, the general aspects of the typical FFC NMR relaxometry experiment are firstly provided. Afterwards, a discussion on the main mathematical models to be used to “read” and interpret experimental data on soils is given. Following this, an overview on the main results in soil science is supplied. Finally, new FFC NMR-based hypotheses on nutrient dynamics in soils are described

Glow Discharge Plasma as a Cause of Changes in Aqueous Solutions: The Mass Spectrometry Study of Solvation Processes of Ions

A new apparatus for inducing changes in the properties of water in closed dielectric vessel by subjecting it to pulsed direct current glow discharge plasma is designed and constructed. It has been hypothesized that the action of plasma on the structure of water consists in resonance excitation of water aggregates. As a result of resonance excitation, aggregates of high molar masses are broken down into low molecular mass aggregates. Analysis of the ESI MS spectra revealed that in all tested aqueous solutions after exposure to plasma, the concentration of low-molecular solvated ions [M(H2O)]+ and [M(H2O)2]+ significantly increased, while the concentration of the ions of high molecular masses [M(H2O)6-10]+ solvated by water aggregates decreased, relative to their concentrations in the water solutions not subjected to plasma irradiation. According to our measurements also a significant change in pH occurs. The presented results clearly show that it is possible to process a liquid that changes its structure without involving high processing energy and, unexpectedly, the obtained change of parameters is significant and stable over time.

Flavonoids as Putative Epi-Modulators: Insight into Their Binding Mode with BRD4 Bromodomains Using Molecular Docking and Dynamics

Flavonoids are widely recognized as natural polydrugs, given their anti-inflammatory, antioxidant, sedative, and antineoplastic activities. Recently, different studies showed that flavonoids have the potential to inhibit bromodomain and extraterminal (BET) bromodomains. Previous reports suggested that flavonoids bind between the Z and A loops of the bromodomain (ZA channel) due to their orientation and interactions with P86, V87, L92, L94, and N140. Herein, a comprehensive characterization of the binding modes of fisetin and the biflavonoid, amentoflavone, is discussed. To this end, both compounds were docked with BET bromodomain 4 (BRD4) using four docking programs. The results were post-processed with protein–ligand interaction fingerprints. To gain further insight into the binding mode of the two natural products, the docking results were further analyzed with molecular dynamics simulations. The results showed that amentoflavone makes numerous contacts in the ZA channel, as previously described for flavonoids and kinase inhibitors. It was also found that amentoflavone can potentially make contacts with non-canonical residues for BET inhibition. Most of these contacts were not observed with fisetin. Based on these results, amentoflavone was experimentally tested for BRD4 inhibition, showing activity in the micromolar range. This work may serve as the basis for scaffold optimization and the further characterization of flavonoids as BET inhibitors.

Effects of ions on water structure: a low-field ¹H T₁ NMR relaxometry approach

Aqueous salt solutions play an important role in nature because of their effects on environmental biogeochemical processes and on structural properties of biomolecules. Upon dissolution, salts split in ions that are solvated. Water in hydration shells is subjected to molecular motions that can be monitored by (1)H T1 NMR relaxometry. This technique allowed the evaluation of the nature of the interactions between water and ions via variable temperature experiments. Examination of relaxometry properties of aqueous solutions at variable salt concentrations allowed acknowledgement of the role played by ions in either structuring or destructuring water aggregates. A mathematical model has been applied on six environmentally relevant salts: NaCl, KCl, CaCl2, CaCO3, NaNO3, and NH4NO3. It was linear only for the concentration dependence of KCl-R1. This model accorded with the one reported in literature where it has been considered valid only for diluted solutions. However, in the present study, the range of linearity for KCl was extended up to the saturation point. The model was modified for NaCl, CaCl2, and CaCO3 by using it as an exponential form in order to account for the nonlinearity of the R1-versus-concentration curves. Nonlinearity was explained by the nonnegligible ion-ion interactions occurring as concentration was increased. Finally, further modification was needed to account for the asymmetric distribution of water around nitrate (in NaNO3 and NH4NO3) and ammonium (in NH4NO3). This study is preliminary to the comprehension of the diffusion mechanisms of ions in water solutions at the equilibrium condition with solid surfaces such as soils and biochar-amended soils.

Orientational order as the origin of the long-range hydrophobic effect

The long range attractive force between two hydrophobic surfaces immersed in water is observed to decrease exponentially with their separation-this distance-dependence of effective force is known as the hydrophobic force law (HFL). We explore the microscopic origin of HFL by studying distance-dependent attraction between two parallel rods immersed in 2D Mercedes Benz model of water. This model is found to exhibit a well-defined HFL. Although the phenomenon is conventionally explained by density-dependent theories, we identify orientation, rather than density, as the relevant order parameter. The range of density variation is noticeably shorter than that of orientational heterogeneity. The latter is comparable to the observed distances of hydrophobic force. At large separation, attraction between the rods arises primarily from a destructive interference among the inwardly propagating oppositely oriented heterogeneity generated in water by the two rods. As the rods are brought closer, the interference increases leading to a decrease in heterogeneity and concomitant decrease in free energy of the system, giving rise to the effective attraction. We notice formation of hexagonal ice-like structures at the onset of attractive region which suggests that metastable free energy minimum may play a role in the origin of HFL.

Temperature perturbed water structure modification by d(−)-fructose at different concentrations

Temperature dependence of water structure modification has been studied at different d(−)-fructose concentrations by near-infrared (NIR) spectroscopy.

Mapping the hydration dynamics of ubiquitin

The nature of water's interaction with biomolecules such as proteins has been difficult to examine in detail at atomic resolution. Solution NMR spectroscopy is potentially a powerful method for characterizing both the structural and temporal aspects of protein hydration but has been plagued by artifacts. Encapsulation of the protein of interest within the aqueous core of a reverse micelle particle results in a general slowing of water dynamics, significant reduction in hydrogen exchange chemistry and elimination of contributions from bulk water thereby enabling the use of nuclear Overhauser effects to quantify interactions between the protein surface and hydration water. Here we extend this approach to allow use of dipolar interactions between hydration water and hydrogens bonded to protein carbon atoms. By manipulating the molecular reorientation time of the reverse micelle particle through use of low viscosity liquid propane, the T(1ρ) relaxation time constants of (1)H bonded to (13)C were sufficiently lengthened to allow high quality rotating frame nuclear Overhauser effects to be obtained. These data supplement previous results obtained from dipolar interactions between the protein and hydrogens bonded to nitrogen and in aggregate cover the majority of the molecular surface of the protein. A wide range of hydration dynamics is observed. Clustering of hydration dynamics on the molecular surface is also seen. Regions of long-lived hydration water correspond with regions of the protein that participate in molecular recognition of binding partners suggesting that the contribution of the solvent entropy to the entropy of binding has been maximized through evolution.

AcquaAlta: a directional approach to the solvation of ligand-protein complexes

Water molecules mediating polar interactions in ligand-protein complexes can substantially contribute to binding affinity and specificity. To account for such water molecules in computer-aided drug design, we performed an extensive search in the Cambridge Structural Database (CSD) to identify the geometrical criteria defining interactions of water molecules with ligand and protein. In addition, with ab initio calculations the propensity of ligand hydration was evaluated. Based on this information, we developed an algorithm (AcquaAlta) to reproduce water molecules bridging polar interactions between ligand and protein moieties. This approach was validated with 20 crystal structures and yielded a match of 76% between experimental and calculated water positions. When water molecules establishing only weak interactions with the protein were neglected, the match could be improved to 88%. Supported by a pharmacophore-based alignment tool, the solvation algorithm was then applied to the docking of oligopeptides to the periplasmic oligopeptide binding protein A (OppA). Calculated waters based on the crystal poses matched an average of 66% of the experimental waters. With water molecules calculated based on the docked ligands, the average match with the experimental waters dropped to 53%.

Quantification of binding data using capillary electrophoresis

The design of new DNA-targeted molecules, primarily for use in the therapy of diseases such as cancer, relies on the assessment of both affinity for DNA and selectivity of binding to chosen base pair sequences. Capillary electrophoresis, with a polymer added to the running buffer, is very well suited to the separation of oligonucleotides in the range 12-20 base pairs, with the separation based on length rather than base pair sequence. In this way, it is possible to conduct competition experiments using mixtures of up to four oligonucleotides and giving a direct measure of the relative affinity of high-affinity ligands, specifically those binding in the minor groove with slow on-off rates. The relative affinities can be securely quantified, even where the affinities are very high. Working from first principles, it is shown that the measurement of absolute affinities presents various problems, not least that the concentration of DNA and ligand used in the experiment will affect the magnitude of K(d), which is not constant.

The role of water in drug–receptor interactions

The idea that liquid water is not a uniform and random arrangement of molecules has been taken very seriously by the scientific community. Many experimental and computational investigations show that clathrate- or ice-like structures probably exist at a short time scale in solution. We have designed a new program to simulate water structure around solutes. Our model is based on the geometrical constraints of hydrogen bonding in order to be capable of producing clathrate-like structures. Simulations with small molecules and bio-molecules, using the new software, produce networks of water with specific patterns made of small water rings. The water structures built are consistent with the classification of molecules in terms of structure breaking and making. This approach may give insight into, and a more accurate description of, drug-receptor interactions. The results also suggest that water structure may impart sufficient energy to modify the conformational space of organic molecules through hydrogen bonding.

Coupling of complex aromatic ring vibrations to solvent through hydrogen bonds: effect of varied on-ring and off-ring hydrogen-bonding substitutions

In this study, we examine the coupling of a complex ring vibration to solvent through hydrogen-bonding interactions. We compare phenylalanine, tyrosine, l-dopa, dopamine, norepinephrine, epinephrine, and hydroxyl-dl-dopa, a group of physiologically important small molecules that vary by single differences in H-bonding substitution. By examination of the temperature dependence of infrared absorptions of these molecules, we show that complex, many-atom vibrations can be coupled to solvent through hydrogen bonds and that the extent of that coupling is dependent on the degree of both on- and off-ring H-bonding substitution. The coupling is seen as a temperature-dependent frequency shift in infrared spectra, but the determination of the physical origin of that shift is based on additional data from temperature-dependent optical experiments and ab initio calculations. The optical experiments show that these small molecules are most sensitive to their immediate H-bonding environment rather than to bulk solvent properties. Ab initio calculations demonstrate H-bond-mediated vibrational coupling for the system of interest and also show that the overall small molecule solvent dependence is determined by a complex interplay of specific interactions and bulk solvation characteristics. Our findings indicate that a full understanding of biomolecule vibrational properties must include consideration of explicit hydrogen-bonding interactions with the surrounding microenvironment.

Effects of Cyclodextrins on Drug Delivery Through Biological Membranes

Cyclodextrins have proven themselves to be useful functional excipients. Cyclodextrin derivatives can be hydrophilic or relatively lipophilic based on their substitution and these properties can give insight into their ability to act as permeability enhancers. Lipophilic cyclodextrins such as the methylated derivatives are thought to increase drug flux by altering barrier properties of the membrane through component extraction or fluidization. The hydrophilic cyclodextrin family also modulate drug flux through membranes but via different mechanisms. The current effort seeks to provide various explanations for these observations based on interactions of hydrophilic cyclodextrins with the unstirred water layer that separates the bulk media from biological membranes such as the gastric mucosa, cornea and reproductive tract. Theories on the serial nature of resistances to drug flux are used to explain why hydrophilic cyclodextrins can enhance drug uptake in some situation (i.e., for lipophilic material) but not in others. In addition, the nature of secondary equilibria and competition between cyclodextrins and rheologically important biopolymers such as mucin are assessed to give a complete picture of the effect of these starch derivatives. This information can be useful not only in understanding the actions of cyclodextrin but also in expanding their application and uses.

Water and Polymer Dynamics in Chemically Cross-Linked Hydrogels of Poly(vinyl alcohol): A Molecular Dynamics Simulation Study

A topologically extended model of a chemically cross-linked hydrogel of poly(vinyl alcohol) (PVA) at high hydration degree has been developed for a molecular dynamics simulation with atomic detail at 323 K. The analysis of the 5 ns trajectory discloses structural and dynamic aspects of polymer solvation and elucidates the water hydrogen bonding and diffusion in the network. The features of local polymer dynamics indicate that PVA mobility is not affected by structural constraints of chemical junctions at the investigated cross-linking density, with a prevailing dumping effect due to water interaction. Simulation results are validated by a favorable comparison with findings of an incoherent quasi-elastic neutron scattering study of the same hydrogel system.

Structured water layers adjacent to biological membranes

Water amid the restricted space of crowded biological macromolecules and at membrane interfaces is essential for cell function, though the structure and function of this "biological water" itself remains poorly defined. The force required to remove strongly bound water is referred to as the hydration force and due to its widespread importance, it has been studied in numerous systems. Here, by using a highly sensitive dynamic atomic force microscope technique in conjunction with a carbon nanotube probe, we reveal a hydration force with an oscillatory profile that reflects the removal of up to five structured water layers from between the probe and biological membrane surface. Further, we find that the hydration force can be modified by changing the membrane fluidity. For 1,2-dipalmitoyl-sn-glycero-3-phosphocholine gel (Lbeta) phase bilayers, each oscillation in the force profile indicates the force required to displace a single layer of water molecules from between the probe and bilayer. In contrast, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine fluid (Lalpha) phase bilayers at 60 degrees C and 1,2-dioleoyl-sn-glycero-3-phosphocholine fluid (Lalpha) phase bilayers at 24 degrees C seriously disrupt the molecular ordering of the water and result predominantly in a monotonic force profile.

The origin of long-range attraction between hydrophobes in water

When water-coated hydrophobic surfaces meet, direct contacts form between the surfaces, driving water out. However, long-range attractive forces first bring those surfaces close. This analysis reveals the source and strength of the long-range attraction between water-coated hydrophobic surfaces. The origin is in the polarization field produced by the strong correlation and coupling of the dipoles of the water molecules at the surfaces. We show that this polarization field gives rise to dipoles on the surface of the hydrophobic solutes that generate long-range hydrophobic attractions. Thus, hydrophobic aggregation begins with a step in which water-coated nonpolar solutes approach one another due to long-range electrostatic forces. This precursor regime occurs before the entropy increase of releasing the water layers and the short-range van der Waals attraction provide the driving force to "dry out" the contact surface. The effective force of attraction is derived from basic molecular principles, without assumptions of the structure of the hydrophobe-water interaction. The strength of this force can be measured directly from atomic force microscopy images of a hydrophobic molecule tethered to a surface but extending into water, and another hydrophobe attached to an atomic force probe. The phenomenon can be observed in the transverse relaxation rates in water proton magnetic resonance as well. The results shed light on the way water mediates chemical and biological self-assembly, a long outstanding problem.

The Cytomatrix as a Cooperative System of Macromolecular and Water Networks

Water was called by Szent-Gyorgi "life's mater and matrix, mother and medium." This chapter considers both aspects of his statement. Many astrobiologists argue that some, if not all, of Earth's water arrived during cometary bombardments. Amorphous water ices of comets possibly facilitated organization of complex organic molecules, kick-starting prebiotic evolution. In Gaian theory, Earth retains its water as a consequence of biological activity. The cell cytomatrix is a proteinaceous matrix/lattice incorporating the cytoskeleton, a pervasive, holistic superstructural network that integrates metabolic pathways. Enzymes of metabolic pathways are ordered in supramolecular clusters (metabolons) associated with cytoskeleton and/or membranes. Metabolic intermediates are microchanneled through metabolons without entering a bulk aqueous phase. Rather than being free in solution, even major signaling ions are probably clustered in association with the cytomatrix. Chloroplasts and mitochondria, like bacteria and archaea, also contain a cytoskeletal lattice, metabolons, and channel metabolites. Eukaryotic metabolism is mathematically a scale-free or small-world network. Enzyme clusters of bacterial origin are incorporated at a pathway level that is architecturally archaean. The eucaryotic cell may be a product of serial endosymbiosis, a chimera. Cell cytoplasm is approximately 80% water. Water is indisputably a conserved structural element of proteins, essential to their folding, specificity, ligand binding, and to enzyme catalysis. The vast literature of organized cell water has long argued that the cytomatrix and cell water are an entire system, a continuum, or gestalt. Alternatives are offered to mainstream explanations of cell electric potentials, ion channel, enzyme, and motor protein function, in terms of high-order cooperative systems of ions, water, and macromolecules. This chapter describes some prominent concepts of organized cell water, including vicinal water network theory, the association-induction hypothesis, wave-cluster theory, phase-gel transition theories, and theories of low- and high-density water polymorphs.

Kosmotropes and chaotropes: modelling preferential exclusion, binding and aggregate stability

Kosmotropic cosolvents added to an aqueous solution promote the aggregation of hydrophobic solute particles, while chaotropic cosolvents act to destabilise such aggregates. We discuss the mechanism for these phenomena within an adapted version of the two-state Muller-Lee-Graziano model for water, which provides a complete description of the ternary water/cosolvent/solute system for small solute particles. This model contains the dominant effect of a kosmotropic substance, which is to enhance the formation of water structure. The consequent preferential exclusion both of cosolvent molecules from the solvation shell of hydrophobic particles and of these particles from the solution leads to a stabilisation of aggregates. By contrast, chaotropic substances disrupt the formation of water structure, are themselves preferentially excluded from the solution, and thereby contribute to solvation of hydrophobic particles. We use Monte Carlo simulations to demonstrate at the molecular level the preferential exclusion or binding of cosolvent molecules in the solvation shell of hydrophobic particles, and the consequent enhancement or suppression of aggregate formation. We illustrate the influence of structure-changing cosolvents on effective hydrophobic interactions by modelling qualitatively the kosmotropic effect of sodium chloride and the chaotropic effect of urea.

Structure and interactions in simple solutions

Neutron scattering with hydrogen/deuterium isotopic substitution techniques has been used to investigate the full range of structural interactions in a dilute 0.02 mol fraction solution of tertiary butanol in water, both in the absence and in the presence of a small amount of sodium chloride. Emphasis is given to the detailed pictures of the intermolecular interactions that have been derived using the empirical potential structure refinement technique. Analysis has been performed to the level of the spatial density distribution functions that illustrate the orientational dependence of the intermolecular interactions between all combinations of molecular and ionic components. The results show the key structural motifs involved in the interactions between the various components in a complex aqueous system. They underline the structural versatility of the water molecule in accommodating a range of different kinds of interactions while retaining its characteristic first-neighbour interaction geometry. Within this framework, the results highlight the complex interplay between the polar, non-polar and charged molecular interactions that exist in the system.