Ph4Dock: pharmacophore-based protein-ligand docking

The development and validation of the program Ph4Dock is presented. Ph4Dock is a novel automated ligand docking program that makes best use of pharmacophoric features both in a ligand and at concave portions of a protein. By mapping of pharmacophores of the ligand to the pharmacophoric features that represent the concaves of the target protein, Ph4Dock realizes an efficient and accurate prediction of the binding modes between the ligand and the protein. To validate the potential of this unique docking algorithm, we have selected 43 reliable crystal structures of protein-ligand complexes. All of the ligands are druglike, and they are varied in nature. The diffraction-component precision index (DPI) originally used in crystallography was applied in this study in order to evaluate the docking results quantitatively. The root-mean-square deviation (rmsd) between non-hydrogen atoms of the ligand in the prediction and experimental results were analyzed using DPI. The rmsd values for 25 structures, consisting of almost 60% of the dataset, are less than three times of the corresponding DPI values. It means that the precision of docking results obtained by Ph4Dock is mostly equivalent to the experimental error in these cases. The present study has demonstrated that Ph4Dock can accurately reproduce the experimentally determined docking modes if the reliable crystal structures are used. Normally the success rate of the docking is judged using rmsd < or = 2.0 A as the criterion. The Ph4Dock marked an appreciably good success rate of 86% based on this criterion.

Prediction of Solubility of Drugs by Conductor-Like Screening Model for Real Solvents

The solubility of drugs in solvents is fundamentally important for drug development and manufacturing. As the experimental measurements of the solubility are extremely laborious tasks, reliable prediction methods are highly required. We have employed the conductor-like screening model for real solvents (COSMO-RS) in predicting the solubility of drugs and drug-like compounds in various solvent systems. We also evaluated the salt effect on the solubility of caffeine using this method. The present results demonstrated that COSMO-RS has reasonably reproduced the experimental data and have proved that this method is generally available in predicting the solubility of drugs.

Prediction of Solvents Suitable for Crystallization of Small Organic Molecules

Selection of suitable solvent is essential for crystallization of pharmaceuticals. Based on chemical structures of 6397 compounds and 15 single solvents that were used to obtain their single crystals, correlations between the molecular characteristics and the solvents have been investigated by cheminformatics methods. Decision-tree and Bayesian-probability methods have been applied to make classification models. These two models are complementary in character in the present case. It has been proven that the prediction of the solvent rankings for particular compounds by use of the classification models is satisfactory from the practical point of view. The present study has demonstrated that cheminformatics methods could greatly help rational crystallization of small organic molecules such as pharmaceuticals.

Molecular mechanism of dielectrically controlled optical resolution (DCR)

We have recently found the first example of dielectrically controlled optical resolution (DCR). By adjusting the dielectric constant of the solvent used in the resolution process, each optical isomer of (R,S)-alpha-amino-epsilon-caprolactam can be selectively obtained using N-tosyl-(S)-phenylalanine as a chiral selector. The molecular mechanism of DCR has been investigated by comparing the molecular and crystal structures of the optical selector, its target substrate and their diastereomeric salts. Strong hydrophobic interactions between the phenyl rings of the optical selector govern the molecular aggregation of the selectors and form a hydrophilic layer in which molecular recognition takes place. The recognition site in the hydrophilic layer can inherently identify both of the isomers. The dielectric constant of the solvent used in the discrimination process controls the intermolecular interaction which determines the isomer to be selected. The molecular mechanism of DCR disclosed in this study strongly suggests that DCR is not a specific but a general phenomenon. This method can be applicable to a large variety of optical resolution processes.

Interactions of arsenic with human metallothionein-2

Arsenic is a toxic element that is found in the atmosphere, as well as in aquatic and terrestrial environments. We have demonstrated that As(3+) binds to human metallothionein-2 (hMT-2) by UV absorption spectroscopy, inductively coupled plasma-atomic emission spectrometry (ICP-AES), and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS). MALDI-TOF-MS revealed that the structure of the adduct formed by arsenic and hMT-2 (As-hMT-2) was not homogeneous. The maximum molar ratio of arsenic to hMT-2 was found to be more than 6:1 on ICP-AES, UV absorption spectroscopy and MALDI-TOF-MS. The ratio of the number of sulfhydryl groups in hMT-2 that bound arsenic was 3:1, which is the same as the ratios reported previously for arsenic-glutathione and arsenic-phytochelatin complexes.

Alteration of substrate specificity of cholesterol oxidase from Streptomyces sp. by site-directed mutagenesis

Despite the structural similarities between cholesterol oxidase from Streptomyces and that from Brevibacterium, both enzymes exhibit different characteristics, such as catalytic activity, optimum pH and temperature. In attempts to define the molecular basis of differences in catalytic activity or stability, substitutions at six amino acid residues were introduced into cholesterol oxidase using site-directed mutagenesis of its gene. The amino acid substitutions chosen were based on structural comparisons of cholesterol oxidases from Streptomyces and BREVIBACTERIUM: Seven mutant enzymes were constructed with the following amino acid substitutions: L117P, L119A, L119F, V145Q, Q286R, P357N and S379T. All the mutant enzymes exhibited activity with the exception of that with the L117P mutation. The resulting V145Q mutant enzyme has low activities for all substrates examined and the S379T mutant enzyme showed markedly altered substrate specificity compared with the wild-type enzyme. To evaluate the role of V145 and S379 residues in the reaction, mutants with two additional substitutions in V145 and four in S379 were constructed. The mutant enzymes created by the replacement of V145 by Asp and Glu had much lower catalytic efficiency for cholesterol and pregnenolone as substrates than the wild-type enzyme. From previous studies and this study, the V145 residue seems to be important for the stability and substrate binding of the cholesterol oxidase. In contrast, the catalytic efficiencies (k(cat)/K(m)) of the S379T mutant enzyme for cholesterol and pregnenolone were 1.8- and 6.0-fold higher, respectively, than those of the wild-type enzyme. The enhanced catalytic efficiency of the S379T mutant enzyme for pregnenolone was due to a slightly high k(cat) value and a low K(m) value. These findings will provide several ideas for the design of more powerful enzymes that can be applied to clinical determination of serum cholesterol levels and as sterol probes.

Synthesis and antiallergic activity of 11-(aminoalkylidene)-6,11-dihydrodibenz[b,e]oxepin derivatives

A new series of 11-substituted 6,11-dihydrodibenz[b,e]oxepin-2-carboxylic acid derivatives was synthesized and demonstrated to be orally active antiallergic agents. These compounds are structurally related to 1 (KW-4994), which we had reported previously to be a new antiallergic agent. Most compounds synthesized exhibited potent inhibitory effects on 48-h homologous passive cutaneous anaphylaxis (PCA) in rats and on IgG1-mediated bronchoconstriction in guinea pigs. Additionally, compounds possessing a terminal carboxyl group at the 2-position of the dibenz[b,e]oxepin ring system exhibited inhibitory effects on specific [3H]pyrilamine binding to guinea pig cerebellum histamine H1 receptors, whereas these demonstrated negligible effects on specific [3H]QNB binding to rat striatum muscarinic acetylcholine M1 receptors. Structure-activity relationship studies revealed that the following key elements were required for enhanced antiallergic activities: (1) a 3-(dimethylamino)propylidene group as the side chain at the 11-position, (2) a terminal carboxyl moiety at the 2-position, and (3) a dibenzoxepin ring system. Among the compounds synthesized, (Z)-11-[3-(dimethylamino)propylidene]-6,11-dihydrodibenz [b,e]oxepin-2-acetic acid hydrochloride (16) was selected for further evaluation. It had an ED50 value of 0.049 mg/kg po in the PCA test in rats and an ID50 value of 0.030 mg/kg po in inhibiting anaphylactic bronchoconstriction in guinea pigs. Furthermore, it had a Ki value of 16 +/- 0.35 nM for the histamine H1 receptor, while it exhibited negligible CNS side effects up to a dose of 600 mg/kg po. Compound 16 is now under clinical evaluation as KW-4679.

Origin of Ca2+ necessary for carbachol-induced contraction in longitudinal muscle of the proximal colon of rats

The origin of Ca2+ necessary for carbachol (CCh)-induced contraction of longitudinal muscle of the proximal colon of rats was studied. CCh induced contraction of the muscle consisting of two phases, phasic and tonic phases, with a concomitant biphasic increase in [Ca2+]i. After removal of Ca2+ from the bathing solution of the colonic segments, CCh-induced contraction was rapidly inhibited; there was almost complete inhibition 1 min after the removal. Nicardipine, a blocker of voltage-dependent calcium channel, also significantly inhibited CCh-induced contraction. On the other hand, treatment of the colonic segments with thapsigargin, an inhibitor of sarcoplasmic reticulum (SR) Ca2+-ATPase, did not significantly affect the contraction except causing a slight decrease in the rate of contraction. These results suggest that Ca> entering through voltage-dependent calcium channels, but not released from SR, is essential for CCh-induced contraction of longitudinal muscle of the proximal colon of rats. This strict dependency of the CCh-induced contraction on extracellular Ca2+ was discussed in relation to the results obtained in the fundus of rats.

Effect of chromatic aberration on contrast sensitivity in pseudophakic eyes

OBJECTIVE

To evaluate the effect of chromatic aberrations in pseudophakic eyes with various types of intraocular lenses (IOLs).

PATIENTS AND METHODS

The study included 51 eyes of 33 patients who underwent cataract surgery. The eyes were divided into 3 groups according to the material from which their IOL was made: group 1, polymethyl methacrylate; group 2, silicone; and group 3, an acrylate/methacrylate copolymer. Ten normal phakic control eyes (group 4) underwent the same examination. Best-corrected distance visual acuity and contrast sensitivity were measured under white light and monochromatic light with wavelengths of 470 nm, 549 nm, and 630 nm, with the best correction under white light.

RESULTS

There were no significant differences in best-corrected visual acuity and contrast sensitivity under the 549-nm monochromatic light in any group. However, under both white multichromatic light and 470- and 630-nm monochromatic light, the mean contrast sensitivity in group 3 tended to be lower, sometimes significantly, than in the other IOL groups.

CONCLUSIONS

Our results showed that longitudinal chromatic aberrations of some IOLs may degrade the quality of the retinal image. Attention must be paid to the detailed optical performance of IOL materials to achieve good visual function.

X-ray crystallographic approach to the design of phenolic schiff base reagents for the mutual separation of lanthanoids

A novel mutual selectivity of lanthanoids in the N,N'-bis(5-nitrosalicylidene)ethylenediamine (H2Nsalen)-KCl and N,N'-bis(5-nitrosalicylidene)-o-phenylenediamine (H2Nsaloph)-KCl extraction systems was evaluated by the X-ray analysis of similar model complexes for extracted species. Cerium(IV) complexes with N,N'-bis(5-chlorosalicylidene)ethylenediamine (H2Clsalen), N,N'-bis(salicylidene)-o-phenylenediamine (H2saloph) and N,N'-bis(3,5-dibromosalicylidene)-o-phenylenediamine (H2Br2saloph) were selected as the models. The result of the X-ray analysis suggested that [Ln(III)(Nsalen)2]- and [Ln(III)(Nsaloph)2]- are meridional type (two ligands are oriented perpendicular to each other) and sandwich type (two ligands are oriented parallel to each other), respectively. It was suggested that the selectivity of the meridional structure is superior to that of the sandwich structure in these extraction systems.