Kinetic and Thermodynamic Solubility Values of Some Bioactive Compounds

Thermodynamic solubility is a decisive physicochemical property in drug development. The Chasing Equilibrium method offers an alternative to the classical procedures to measure the solubility of compounds with acid–base properties. The method is fast and yields accurate results. In this work, the solubility of several compounds including acids and bases was determined through the Chasing Equilibrium approach. A study of experimental conditions in terms of sample weight was performed to measure solubilities. The study shows that only a limited range of weights, depending on the nature and solubility of the compounds, is adequate to obtain reliable results.     

Solubility of Saturated Fatty Acids in Water at Elevated Temperatures

The solubility in water of saturated fatty acids with even carbon numbers from 8 to 18 was measured in the temperature range of 60 to 230°C and at a pressure of 5 or 15 MPa. The pressure had no significant effect on the solubility. The solubility of the fatty acids increased with increasing temperature. At temperatures higher than about 160°C, the logarithm of the solubility in mole fraction was linearly related to the reciprocal of the absolute temperature for each fatty acid, indicating that the water containing solubilized fatty acid molecules formed a regular solution at the higher temperatures. The enthalpy of a solution of the fatty acids in water, which was evaluated from the linear relationship at the given temperatures, increased linearly with the carbon number of the fatty acid.     

Discrimination in resolving systems. III: Pseudoephedrine-mandelic acid

(+)-(1S;2S)-Pseudoephedrine and racemic mandelic acid form three distinct diastereomeric salts from solutions in 95% ethanol. The least-soluble phase, a hemihydrate, contains the (2R)-mandelate. A salt phase of intermediate solubility is the unsolvated double salt, containing both the (2R)- and the (2S)-mandelate. The most-soluble salt phase contains the (2S)-mandelate. Mandelate configuration and order of solubility (based on the heats of fusion) is inverted from that found in the same system synthesized from chiral base and acid, and then crystallized from benzene solution. The (2R)-mandelate hemihydrate (−H₂O at 349.5K, mp 391K), monoclinic, P2₁, a = 6.788(5), b = 29.415(35), c = 9.488(10)Å, β = 108.91(8)°, Z = 4 (2 ion-pairs/asymmetric unit). Intermediate double salt (2S)- and (2R)-mandelate, mp 377.6K, anorthic, P1, a = 7.758(4), b = 9.966(5), c = 13.366(6)Å, α = 72.99(4), β = 79.98(4), γ = 70.51(4)°, Z = 1 (2 ion-pairs/asymmetric unit). The (2S)-mandelate (mp 386.2K), orthorhombic, P2₁2₁2₁, a = 7.079(6), b = 13.443(10), c = 18.820(14)Å, Z = 4 is identical to a salt made from a combination of enantiomeric moieties from benzene solution. While differing from ephedrine mandelates in configuration at one center, solubilities of pseudoephedrine mandelates in 95% ethanol are much larger. A comparison of molecular structure (non-polar and H-bonding) regions of pseudoephedrine and ephedrine mandelates shows similarities and differences that are tentatively linked to crystal properties. This study reemphasizes the necessity for consistency in solvent use in resolution and in phase identification and comparison because the phases produced are frequently dependent upon the solvent. Chirality 10:325–337, 1998. © 1998 Wiley-Liss, Inc.     

Affinity to the Nicotinic Acetylcholine Receptor and Insecticidal Activity of Chiral Imidacloprid Derivatives with a Methylated Imidazolidine Ring

Four imidacloprid derivatives with an asymmetrically methylated imidazolidine ring were synthesized. Their affinity to the nicotinic acetylcholine receptor of housefly Musca domestica and insecticidal activity against the housefly were measured. The compound with a 5R-methylated imidazolidine ring demonstrated intrinsic activity comparable to that of the unsubstituted compound. Most of the compounds were synergized by oxygenase inhibitors.     

Relation between Electronic Structure and Hydroxylation of Aromatic Compounds by Microorganisms

The π-electron distribution of various aromatic compounds has been calculated by a molecular orbital method.

The reaction of hydroxylation was assumed to be radical type.

Relation between electronic structures and mono-hydroxylation of aromatic compounds by microorganisms was investigated.

A distinct parallelism was ruled out between the electronic structure and hydroxylation of aromatic compounds.

Hydroxylation of aromatic compounds occurred where the superdelocalizability Sr (R) showed large value.     

Insights of interaction between small and large subunits of ADP-glucose pyrophosphorylase from bread wheat (Triticum aestivum L.)

Lack of knowledge of three dimensional structures of small and large subunits of ADP- glucose pyrophosphorylase (AGPase) in wheat has hindered efforts to understand the binding specifities of substrate and catalytic mechanism. Thus, to understand the structure activity relationship, 3D structures were built by homology modelling based on crystal structure of potato tuber ADP-glucose pyrophosphorylase. Selected models were refined by energy minimization and further validated by Procheck and Prosa-web analysis. Ramachandran plot showed that overall main chain and side chain parameters are favourable. Moreover, Z-score of the models from Prosa-web analysis gave the conformation that they are in the range of the template. Interaction analysis depicts the involvement of six amino acids in hydrogen bonding (AGP-SThr422-AGP-LMet138, AGP- SArg420-AGP-LGly47, AGP-SSer259-AGP-LSer306, AGP-SGlu241-AGP-LIle311, AGPSGln113- AGP-LGlu286 and AGP-SGln70-AGP-LLys291). Fifteen amino acids of small subunit were able to make hydrophobic contacts with seventeen amino acids of large subunit. Furthermore, decrease in the solvent accessible surface area in the amino acids involved in interaction were also reported. All the distances were formed in between 2.27 to 3.78Å. The present study focussed on heterodimeric structure of (AGPase). This predicted complex not only enhance our understanding of the interaction mechanism between these subunits (AGP-L and AGP-S) but also enable to further study to obtain better variants of this enzyme for the improvement of the plant yield.     

Thermodynamics of site-specific small molecular ion interactions with DNA duplex: a molecular dynamics study

The stability and dynamics of a double-stranded DNA (dsDNA) is affected by the preferential occupancy of small monovalent molecular ions. Small metal and molecular ions such as sodium and alkyl ammonium have crucial biological functions in human body, affect the thermodynamic stability of the duplex DNA and exhibit preferential binding. Here, using atomistic molecular dynamics simulations, we investigate the preferential binding of metal ion such as Na⁺ and molecular ions such as tetramethyl ammonium (TMA⁺) and 2-hydroxy-N,N,N-trimethylethanaminium (CHO⁺) to double-stranded DNA. The thermodynamic driving force for a particular molecular ion-DNA interaction is determined by decomposing the free energy of binding into its entropic and enthalpic contributions. Our simulations show that each of these molecular ions preferentially binds to the minor groove of the DNA and the extent of binding is highest for CHO⁺. The ion binding processes are found to be entropically favourable. In addition, the contribution of hydrophobic effects towards the entropic stabilisation (in case of TMA⁺) and the effect of hydrogen bonding contributing to enthalpic stabilisation (in case of CHO⁺) have also been investigated.     

Internal Water Molecules as Mobile Polar Groups for Light-Induced Proton Translocation in Bacteriorhodopsin and Rhodopsin as Studied by Difference FTIR Spectroscopy

FTIR spectroscopy is advantageous for detecting changes in polar chemical bonds that participate in bacteriorhodopsin function. Changes in H-bonding of Asp85, Asp96, the Schiff base, and internal water molecules around these residues upon the formation of the L, M, and N photo-intermediates of bacteriorhodopsin were investigated by difference FTIR spectroscopy. The locations and the interactions of these water molecules with the amino acid residues were further revealed by use of mutant pigments. The internal water molecules in the cytoplasmic domain probably work as mobile polar groups in an otherwise apolar environment and act to stabilize the L intermediate, and carrying a proton between the Schiff base and the proton acceptor or donor. Similar internal water molecules were shown to be present in bovine rhodopsin.     

Conserved positions for ribose recognition: importance of water bridging interactions among ATP,ADP and FAD-protein complexes

Analysis of the spatial arrangement of protein and water atoms that form polar interactions with ribose has been performed for a structurally non-redundant dataset of ATP, ADP and FAD-protein complexes. The 26 ligand-protein structures were separated into two groups corresponding to the most populated furanose ring conformations (N and S-domains). Four conserved positions were found for S-domain protein-ligand complexes and five for N-domain complexes. Multiple protein folds and secondary structural elements were represented at a single conserved position. The following novel points were revealed: (i) Two complementary positions sometimes combine to describe a putative atomic spatial location for a specific conserved binding spot. (ii) More than one third of the interactions scored were water-mediated. Thus, conserved spatial positions rich in water atoms are a significant feature of ribose-protein complexes.     

PMR Study on the Absolute Structure of Kanamycins and Related Compounds

The antioxidant behaviors of vitamin E and its analogues, 2, 2, 5, 7, 8-pentamethyl-6-hydroxychroman and l, 2-diacyl-sn-glycero-3-phospho-2?-(hydroxyethyl)-2?, 5?, 7?, 8?-tetramethyl-6?-hydroxychro-man, were studied in unilamellar vesicles. The two analogues scavenged aqueous radicals generated from azo compounds more efficiently than vitamin E. On the other hand, vitamin E scavenged the lipid peroxyl radicals preferentially. It is concluded that the superior antioxidant activity of vitamin E is attributed to its location suitable for breaking the chain propagation reaction.     

The Influence of Organic Matter and pH on DDT Aqueous Solubility

We have studied the concentrations of DDT in ground water samples at field locations with DDT-polluted topsoil and concentrations and solubility in samples prepared from deionized water with different types and concentration of organic acids. The solubility of DDT increased with increasing concentration of humic acid when the pH of the samples was low (adjusted to about 5.5). The effect flutters in the humic acid concentration range from 200 to 300?mg/L, in accordance with humic acid hydrophobicity, operationally measured as liquid surface tension. The findings correspond to trends previously reported in the literature. The trend of increasing solubility was not found using fulvic acid or low-molecular-weight aliphatic acids. No trend was found adding humic acid without adjusting the pH. The mechanism of enhanced solubility due to humic compounds can explain relatively high levels of DDT in ground water. The ground water samples, however, had a moderately high concentration of maximum 6?µg/L compared with a maximum of about 2300?µg/L in the water samples with humic acid in pure water.     

Structure,stability and water permeation of ([D-Leu-L-Lys-(D-Gln-L-Ala)3]) cyclic peptide nanotube: a molecular dynamics study

The structural stability of 8 × ([D-Leu-L-Lys-(D-Gln-L-Ala)₃]) cyclic peptide nanotube (CPN) in water and different phospholipid bilayers were explored by 100 ns independent molecular dynamics (MD) simulations. The role of non-bonded interaction energy between the side and main chains of cyclic peptide rings in different membrane environments assessed, wherein the repulsive electrostatic interaction energy between neighbouring cyclic peptide rings was found adequate to break hydrogen bond energy thereby to crumple CPN. Further, the water permeation across the CPN channel was studied in four types of phospholipid bilayers- DMPG (1,2-Dimyristoyl-sn-glycero-3-phosphorylglycerol), DMPS (1,2-Dimyristoyl-sn-glycero-3-phosphoserine), POPC (1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) and POPE (1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine) from MD simulations. DMPS membrane shows higher non-bonded interaction energies (?1913.06 kJ/mol of electrostatic interaction energy and ?994.13 kJ/mol of van der Waals interaction energy) with CPN due to the presence of polar molecules in lipid structure. Thusly, the non-bonded interaction energies were essential towards the stability of CPN than hydrogen bonds between the nearby cyclic peptides. The result also reveals the role of side chains, hydrogen bonds and non-bonded interaction energies in an aqueous environment. The diffusion coefficient of water obtained from means square deviation calculation shows similar coefficients irrespective of the lipid surroundings. However, the permeation coefficients demonstrate water flow in the channel relies upon the environment.     

Dissociation of Abeta(16-22) amyloid fibrils probed by molecular dynamics

The mechanisms of deposition and dissociation are implicated in the assembly of amyloid fibrils. To investigate the kinetics of unbinding of Abeta(16-22) monomers from preformed fibrils, we use molecular dynamics (MD) simulations and the structures for Abeta(16-22) amyloid fibrils. Consistent with experimental studies, the dissociation of Abeta(16-22) peptides involves two main stages, locked and docked, after which peptides unbind. The lifetime of the locked state, in which a peptide retains fibril-like structure and interactions, extends up to 0.5 micros under normal physiological conditions. Upon cooperative rupture of all fibril-like hydrogen bonds (HBs) with the fibril, a peptide enters a docked state. This state is populated by disordered random coil conformations and its lifetime ranges from approximately 10 to 200 ns. The docked state is stabilized by hydrophobic side chain interactions, while the contribution from HBs is small. Our simulations also suggest that the peptides located on fibril edges may form stable beta-strand conformations distinct from the fibril "bulk". We propose that such edge peptides can act as fibril caps, which impede fibril elongation. Our results indicate that the interactions between unbinding peptides constitute the molecular basis for cooperativity of peptide dissociation. The kinetics of fibril growth is reconstructed from unbinding assuming the reversibility of deposition/dissociation pathways. The relation of in silica dissociation kinetics to experimental observations is discussed.     

Nano-Scale Pollutants: Fate in Irish Surface and Drinking Water Regulatory Systems

Nano-functionalized products such as UV protective paints additives, antimicrobial food packaging, and fuel additives offering reduced CO₂ emissions have the potential to secure a significant Irish market share in the near future. This scoping study gives a first estimation of nanomaterial surface water concentrations and population ingestional exposure through drinking water resulting from these products. As nanomaterial behavior in wastewater treatment plants (WWTPs) and water treatment plants (WTPs) is currently unclear, bridging data relating to potentially relevant materials (pharmaceuticals and metal removal efficiencies in WWTPs; pathogen removal efficiencies in WTPs) are employed in this study. Mean nanomaterial removal efficiencies of 59.8% and 70.2% were predicted for Irish WWTPs, between 96.95% and 0% for Irish WTPs. Predicted nano-scale TiO₂ concentrations in surface waters (resulting from exterior paints) were 2 orders of magnitude greater than that of Ag (resulting from food packaging) and CeO₂ (resulting from fuel additives), respectively. Predicted surface and drinking water concentrations were unlikely to pose any ecotoxicological or human health risk, although nano-scale TiO₂ and Ag may warrant monitoring as part of standard surface water monitoring schemes. Future research should be directed toward characterizing the behavior of different categories of nanomaterials within WWTP processes.     

Cytochrome P450 52A3: Modelling of 3D Structure and Surface Mutations

Abstract

Earlier W.-H. Schunck et al. [1] have prepared a water soluble enzymatically active fragment of cytochrome P450 52A3 (CYP52A3) which is lack of 66 amino acid residues, existed as a dimer in aqueous solution. Now we propose 3D structure of the fragment, which is based on multiple sequence alignment of the CYP52A3 with its homologues proteins of known 3D structure: CYP101, 102, 107A1 and 108. The structural model have been optimised and used as a prototype for computer simulation of point mutations. These mutations should bring some changes in the surface properties, interfering dimer formation. For this aim the point of 22 hydrophobic amino acid residues have been sequentially replaced with that of charged amino acids (GLU, ASP, ARG and LYS). The scoring of “mutants” was conducted based on the changes of protein surface hydrophobicity and protein-solvent interaction energy. An analysis of the surface hydrophobicity and protein-solvent interactions permit to select most sensitive three sites (171, 352 and particularly 164 amino acid residues). The dimerization of the following “mutant” fragments must be investigated experimentally.     

Antifungal Activity of Isothiocyanates and Related Compounds: III. Derivatives of Diphenyl, Stilbene, Azobenzene, and Several Polycondensed Aromatic Hydrocarbons

This paper presents the results of a study on the antifungal activity of isothiocyanates-derivatives of biphenyl (group "A"), of stilbene ("B"), of azobenzene and benzeneazonaphthalene ("C"), of naphthalene ("D"), and of further polycondensed aromatic hydrocarbons ("E"). From a total of 48 investigated compounds, antifungal activity was observed only in A and D group compounds. B, C, and E group derivatives are extremely insoluble in water, and the molecules are very large; as a result, they probably cannot pass into spores or mycelium of fungi. Thus, the -NCS group cannot manifest its reactivity.