Novel pH-dependent regulation of human cytosolic sialidase 2 (NEU2) activities by siastatin B and structural prediction of NEU2/siastatin B complex


Binding interaction of SGLT with sugar and thiosugar by the molecular dynamics simulation

The human sodium-glucose co-transporter 2 (hSGLT2) is a transporter responsible for reabsorption of glucose in the proximal convoluted tubule of the kidney. hSGLT2 inhibitors, including luseogliflozin, have been developed as drugs for type 2 diabetes mellitus. Only luseogliflozin contains a thiosugar ring in its chemical structure, while other hSGLT2 inhibitors contain glucose rings. Consequently, we focused on the binding interactions of hSGLT2 with sugars and thiosugars. We first revealed that the binding affinities of thiosugars are stronger than those of sugars through molecular dynamics simulations of Vibrio parahaemolyticus, sodium-galactose co-transporter, and human hSGLT2. We then demonstrated that Na(+) dissociates from the protein to the cytoplasmic solution more slowly in the thiosugar system than in the sugar system. These differences between sugars and thiosugars are discussed on the basis of the different binding modes due to the atom at the 5-position of the sugar and thiosugar rings. Finally, as a result of Na(+) dissociation, we suggest that the dissociation of thiosugars is slower than that of sugars.

Biochimica et Biophysica Acta (BBA) - Biomembranes


A simple and efficient dispersion correction to the Hartree-Fock theory (2): Incorporation of a geometrical correction for the basis set superposition error

One of the most challenging problems in computer-aided drug discovery is the accurate prediction of the binding energy between a ligand and a protein. For accurate estimation of net binding energy Ebind in the framework of the Hartree-Fock (HF) theory, it is necessary to estimate two additional energy terms; the dispersion interaction energy (Edisp) and the basis set superposition error (BSSE). We previously reported a simple and efficient dispersion correction, Edisp, to the Hartree-Fock theory (HF-Dtq). In the present study, an approximation procedure for estimating BSSE proposed by Kruse and Grimme, a geometrical counterpoise correction (gCP), was incorporated into HF-Dtq (HF-Dtq-gCP). The relative weights of the Edisp (Dtq) and BSSE (gCP) terms were determined to reproduce Ebind calculated with CCSD(T)/CBS or /aug-cc-pVTZ (HF-Dtq-gCP (scaled)). The performance of HF-Dtq-gCP (scaled) was compared with that of B3LYP-D3(BJ)-bCP (dispersion corrected B3LYP with the Boys and Bernadi counterpoise correction (bCP)), by taking Ebind (CCSD(T)-bCP) of small non-covalent complexes as 'a golden standard'. As a critical test, HF-Dtq-gCP (scaled)/6-31G(d) and B3LYP-D3(BJ)-bCP/6-31G(d) were applied to the complex model for HIV-1 protease and its potent inhibitor, KNI-10033. The present results demonstrate that HF-Dtq-gCP (scaled) is a useful and powerful remedy for accurately and promptly predicting Ebind between a ligand and a protein, albeit it is a simple correction procedure.

Bioorganic & Medicinal Chemistry Letters


Molecular dynamics and density functional studies on the metabolic selectivity of antipsychotic thioridazine by cytochrome P450 2D6: Connection with crystallographic and metabolic results

CYP2D6, a cytochrome P450 isoform, significantly contributes to the metabolism of many clinically important drugs. Thioridazine (THD) is one of the phenothiazine-type antipsychotics, which exhibit dopamine D2 antagonistic activity. THD shows characteristic metabolic profiles compared to other phenothiazine-type antipsychotics such as chlorpromazine. The sulfur atom attached to the phenothiazine ring is preferentially oxidized mainly by CYP2D6, that is, the 2-sulfoxide is a major metabolite, and interestingly this metabolite shows more potent activity against dopamine D2 receptors than THD. On the other hand, the formation of this metabolite causes many serious problems for its clinical use. Wójcikowski et al. (Drug Metab. Dispos. 2006, 34, 471) reported a kinetic study of THD formed by CYP2D6. Recently, Wang et al. (J. Biol. Chem. 2012, 287, 10834 and J. Biol. Chem. 2015, 290, 5092) revealed the crystallographic structure of THD with CYP2D6. In the current study, the binding and reaction mechanisms at the atomic and electronic levels were computationally examined based on the assumption as to whether or not the different crystallographic binding poses correspond to the different metabolites. The binding and oxidative reaction steps in the whole metabolic process were investigated using molecular dynamics and density functional theory calculations, respectively. The current study demonstrated the essential importance of the orientation of the substrate in the reaction center of CYP2D6 for the metabolic reaction.


A QSAR Study on the Inhibition Mechanism of Matrix Metalloproteinase-12 by Arylsulfone Analogs Based on Molecular Orbital Calculations

A binding mechanism between human matrix metalloproteinase-12 (MMP-12) and eight arylsulfone analogs having two types of carboxylic and hydroxamic acids as the most representative zinc binding group is investigated using a quantitative structure-activity relationship (QSAR) analysis based on a linear expression by representative energy terms (LERE). The LERE-QSAR analysis quantitatively reveals that the variation in the observed (experimental) inhibitory potency among the arylsulfone analogs is decisively governed by those in the intrinsic binding and dispersion interaction energies. The results show that the LERE-QSAR analysis not only can excellently reproduce the observed overall free-energy change but also can determine the contributions of representative free-energy changes. An inter-fragment interaction energy difference (IFIED) analysis based on the fragment molecular orbital (FMO) method (FMO-IFIED) leads to the identification of key residues governing the variation in the inhibitory potency as well as to the understanding of the difference between the interactions of the carboxylic and hydroxamic acid zinc binding groups. The current results that have led to the optimization of the inhibitory potency of arylsulfone analogs toward MMP-12 to be used in the treatment of chronic obstructive pulmonary disease may be useful for the development of a new potent MMP-12 inhibitor.


A simple and efficient dispersion correction to the Hartree-Fock theory (3): A comprehensive performance comparison of HF-DtqwithMP2 and DFT-Ds

Accurate prediction of the intermolecular interaction energy (ΔEbind) has been a challenging and serious problem. Current in silico drug screening demands efficient and accurate evaluation of ΔEbind for ligands and their target proteins. It is desirable that ΔEbind including the dispersion interaction energy (Edisp) is calculated using a post-Hartree-Fock (HF) theory, such as the high-order coupled-cluster one, with a larger basis set. However, it remains computationally too expensive to apply such a one to large molecular systems. As another problem, it is necessary to consider the contribution of the basis set superposition error (BSSE) in calculation of ΔEbind. In Bioorg. Med. Chem. Lett. 2014 and 2015, we proposed simple and efficient corrections of dispersion and BSSE for the HF theory, which is not able to express the dispersion interaction energy correctly. The current Letter, as the final one in the series, aims to verify the HF theory enhanced by the dispersion correction (HF-Dtq) in the light of reproducibility of 'accurate' intermolecular ligand-protein interaction energy values, with comprehensive comparison with the MP2 and recently proposed various DFT-D theories. Taking ΔEbind calculated with the coupled-cluster theory coupled with a complete basis set as a reference, ΔEbind of over a hundred small sized noncovalent complexes as well as real ligand-protein complexes models was systematically examined in terms of accuracy and computational cost. The comprehensive comparison in the current work showed that HF-Dtq is a practical and reliable approach for in silico drug screening and quantitative structure-activity relationships.


Connecting Classical QSAR and LERE Analyses Using Modern Molecular Calculations, LERE-QSAR (VI): Hydrolysis of Substituted Hippuric Acid Phenyl Esters by Trypsin


A simple and efficient dispersion correction to the HartreeFock theory

One of the most challenging problems in computational chemistry and in drug discovery is the accurate prediction of the binding energy between a ligand and a protein receptor. It is well known that the binding energy calculated with the Hartree-Fock molecular orbital theory (HF) lacks the dispersion interaction energy that significantly affects the accuracy of the total binding energy of a large molecular system. We propose a simple and efficient dispersion energy correction to the HF theory (HF-Dtq). The performance of HF-Dtq was compared with those of several recently proposed dispersion corrected density functional theory methods (DFT-Ds) as to the binding energies of 68 small non-covalent complexes. The overall performance of HF-Dtq was found to be nearly equivalent to that of more sophisticated B3LYP-D3. HF-Dtq will thus be a useful and powerful method for accurately predicting the binding energy between a ligand and a protein, albeit it is a simple correction procedure based on HF.


Binding Free-Energy Calculation is a Powerful Tool for Drug Optimization - Calculation and Measurement of Binding Free Energy for 7-Azaindole Derivatives to Glycogen Synthase Kinase-3

Present computational lead (drug)-optimization is lacking in thermodynamic tactics. To examine whether calculation of binding free-energy change (ΔG) is effective for the lead-optimization process, binding ΔGs of 7-azaindole derivatives to the ATP binding site of glycogen synthase kinase-3β (GSK-3β) were calculated. The result was a significant correlation coefficient of r = 0.895 between calculated and observed ΔGs. This indicates that calculated ΔG reflects the inhibitory activities of 7-azaindole derivatives. In addition to quantitative estimation of activity, ΔG calculation characterizes the thermodynamic behavior of 7-azaindole derivatives, providing also useful information for inhibitor optimization on affinity to water molecules.

Journal of Chemical Information and Modeling


Revisiting the Hansch-Fujita Approach and Development of a Fundamental QSAR


Modeling of Human Neuraminidase-1 and Its Validation by LERE-Correlation Analysis

Four human neuraminidases (hNEUs1-4) have been identified. Among them, hNEU1 has been studied extensively as a target for sialidosis. It has been desired to understand the biological functions of hNEU1 at the molecular and atomic levels. The three-dimensional structure of hNEU1 is not known at present. In the present work, we constructed a three-dimensional structure of hNEU1 by homology modeling, and then performed correlation analyses between observed and calculated free-energy changes (quantitative structure-activity relationship (QSAR) analyses), coupled with LERE (linear expression by representative energy terms) procedure using the modeled three-dimensional structure in order to confirm the validity of the modeled structure. The atomic coordinates of all atoms in the verified model of hNEU1 are available. The proposed structure of hNEU1 will be useful and helpful for further studies concerning the biological and chemical functions of hNEU1. The present article is one of continuous works derived from the one that won the CBI Award for the best presentation in the CBI/JSBi 2011 Joint Conference (presented by Seiji Hitaoka).


Combined QM/MM (ONIOM) and QSAR Approach to the Study of Complex Formation of Matrix Metalloproteinase-9 with a Series of Biphenylsulfonamides - LERE-QSAR Analysis (V)

We previously proposed a novel QSAR (quantitative structure-activity relationship) procedure called LERE (linear expression by representative energy terms)-QSAR involving molecular calculations such as an ab initio fragment molecular orbital ones. In the present work, we applied LERE-QSAR to complex formation of matrix metalloproteinase-9 (MMP-9) with a series of substituted biphenylsulfonamides. The results shows that the overall free-energy change accompanying complex formation is due to predominantly the contribution from the electrostatic interaction with the zinc atom in the active site of MMP-9. Carbonic anhydrase (CA) belongs to the zinc-containing protease family. In contrast to the current case of MMP-9, the overall free-energy change during complex formation of CA with a series of benzenesulfonamides is due to the contributions from the solvation and dissociation free-energy changes, as previously reported. Comparison of the two sets of results indicates quantitative differences in the relative contributions of free-energy components to the overall free-energy change between the two data sets, corresponding with those in the respective classical QSAR equations. The LERE-QSAR procedure was demonstrated to quantitatively reveal differences in the binding mechanisms between the two cases involving similar but different zinc-containing proteins at the electronic and atomic levels.


Reassessment of Hammett sigma as an effective parameter representing intermolecular interaction energy - links between traditional and modern QSAR approaches

The Hammett constant has for a long time been known to be one of most important linear free-energy related parameters that correlate with biological activity. It is a conventionally used electronic parameter in studies of enzymatic quantitative structure-activity relationships (QSAR). However, it is not necessarily obvious why represents variations in the free-energy change associated with the complex formation between a congeneric series of ligands with their target protein. So far, several powerful molecular calculations, such as the ab initio fragment molecular orbital (FMO) one, that are directly applicable to ligand-protein complexes have emerged. In this study, we comprehensively reevaluate experimentally derived parameter confirming it represents intermolecular interaction energy terms, by applying molecular orbital (MO) calculations to a simple ligand-protein complex model. The current results provide a rational and quantitative basis for bridging the gap between the traditional QSAR approach and 'the modern QSAR one', which involves the molecular calculations to evaluate the overall free-energy change for complex formation.

Bioorganic & Medicinal Chemistry Letters


Correlation Analyses on Binding Affinity of Sialic Acid Analogues and Antiinfluenza Drugs with Human Neuraminidase Using ab Initio MO Calculations on Their Complex Structures - LERE-QSAR Analysis (IV)

We carried out full ab initio fragment molecular orbital (FMO) calculations for complexes comprising human neuraminidase-2 (hNEU2) and sialic acid analogues including anti-influenza drugs zanamivir (Relenza) and oseltamivir (Tamiflu) in order to examine the variation in the observed inhibitory activity toward hNEU2 at the atomic and electronic levels. We recently proposed the LERE (linear expression by representative energy terms)-QSAR (quantitative structure-activity relationship) procedure. LERE-QSAR analysis quantitatively revealed that the complex formation is driven by hydrogen-bonding and electrostatic interaction of hNEU2 with sialic acid analogues. The most potent inhibitory activity, that of zanamivir, is attributable to the strong electrostatic interaction of a positively charged guanidino group in zanamivir with negatively charged amino acid residues in hNEU2. After we confirmed that the variation in the observed inhibitory activity among sialic acid analogues is excellently reproducible with the LERE-QSAR equation, we examined the reason for the remarkable difference between the inhibitory potencies of oseltamivir as to hNEU2 and influenza A virus neuraminidase-1 (N1-NA). Several amino acid residues in close contact with a positively charged amino group in oseltamivir are different between hNEU2 and N1-NA. FMO-IFIE (interfragment interaction energy) analysis showed that the difference in amino acid residues causes a remarkably large difference between the overall interaction energies of oseltamivir with hNEU2 and N1-NA. The current results will be useful for the development of new anti-influenza drugs with high selectivity and without the risk of adverse side effects.


Density Functional Theory Study of Hydrogen Atom Abstraction form a Series of para-Substituted Phenols: Why is the Hammett sigma p+ Constant Able to Represent Radical Reaction Rates?

The rate of hydrogen atom abstraction from phenolic compounds by a radical is known to be often linear with the Hammett substitution constant (+), defined using the S(N)1 solvolysis rates of substituted cumyl chlorides. Nevertheless, a physicochemical reason for the above "empirical fact" has not been fully revealed. The transition states of complexes between the 2,2-diphenyl-1-picrylhydrazyl radical (dpph·) and a series of para-substituted phenols were determined by DFT (Density Functional Theory) calculations, and then the activation energy as well as the homolytic bond dissociation energy of the O-H bond and charge distribution in the transition state were calculated. The heterolytic bond dissociation energy of the C-Cl bond and charge distribution in the corresponding para-substituted cumyl chlorides were calculated in parallel. Excellent correlations among (+), charge distribution, and activation and bond dissociation energies revealed quantitatively that there is a strong similarity between the two reactions, showing that the electron-deficiency of the -electron system conjugated with a substituent plays a crucial role in determining rates of the two reactions. The results provide a new insight into and physicochemical understanding of (+) in the hydrogen abstraction from substituted phenols by a radical.


Correlation analyses on binding affinity of substituted benzenesulfonamides with carbonic anhydrase using ab Initio MO calculations on their complex structures (II)

We proposed a novel QSAR (quantitative structure-activity relationship) procedure called LERE (linear expression by representative energy terms)-QSAR involving molecular calculations such as ab initio fragment molecular orbital and generalized Born/surface area ones. We applied LERE-QSAR to two datasets for the free-energy changes during complex formation between carbonic anhydrase and a series of substituted benzenesulfonamides. The first compound set (Set I) and the second one (Set II) include relatively small substituents and alkyl chains of different lengths in the benzene ring, respectively. Variation of the inhibitory activity in Set I is expressed as the combination of Hammett and the hydrophobic substituent constant in classical QSAR, and variation in Set II only by . LERE-QSAR analyses clearly revealed that effects of and on the activity variations in Sets I and II are consistently explainable with the energy terms in the LERE formulation, and provide more detailed and direct information as to the binding mechanism. The proposed procedure was demonstrated to provide a quantitative basis for understanding ligand-protein interactions at the electronic and atomic levels.


Correlation Analyses on Binding Affinity of Sialic Acid Analogues with Influenza Virus Neuraminidase-1 Using ab Initio MO Calculations on Their Complex Structures

We carried out full ab initio molecular orbital calculations on complexes between neuraminidase-1 (N1-NA) in the influenza A virus and a series of eight sialic acid analogues including oseltamivir (Tamiflu) in order to quantitatively examine the binding mechanism and variation in the inhibitory potency at the atomic and electronic levels. FMO-MP2-IFIE (interfragment interaction energy at the MP2 level of ab initio fragment molecular orbital calculations) analyses quantitatively revealed (1) that the complex formation is driven by strong electrostatic interactions of charged functional groups in the analogues with ionized amino acid residues and water molecules in the active site of N1-NA, and (2) that the variation in the inhibitory potency among the eight analogues is determined by the dispersion and/or hydrophobic interaction energies of the 3-pentyl ether and charged amino moieties in oseltamivir with certain residues and water molecules in the active site of N1-NA. The current results will be useful for the development of new antiinfluenza drugs with high potency against various subtypes of wild-type and drug-resistant NAs.

Journal of Chemical Information and Modeling


Correlation Analyses on Binding Affinity of Substituted Benzenesulfonamides with Carbonic Anhydrase Using ab Initio MO Calculations on Their Complex Structures

Quantitative structure-activity relationship analyses on the free energy change during complex formation between substituted benzenesulfonamides (BSAs) and bovine carbonic anhydrase II (bCA II) were performed using generilized Born/surface area (GB/SA) and ab initio fragment molecular orbital (FMO) calculations for the whole complex structures. The result shows that the overall free energy change is governed by the contribution from solvation and dissociation free energy changes accompanying by complex formation. The FMO-IFIE (interfragment interaction energy) analysis quantitatively revealed that the intrinsic interaction energy of bCA II with BSAs is mostly from interactions with amino acid residues in the active site of bCA II. The "Zn block" (Zn(2+) and three histidine residues coordinated to Zn(2+)) in the active site shows the lowest interaction energy and the greatest variance of interaction energy with BSAs through their coordination interaction. The proposed procedure was demonstrated to provide a quantitative basis for understanding a ligand-protein interaction at electronic and atomic levels.


Assessment of Free Energy Expression in RISM Integral Equation Theory: Theoretical Prediction of Partition Coefficients Revisited.


Expression and molecular dynamics studies on effect of amino acid substitutions at Arg344 in human cathepsin A on the protein local conformation.

Human lysosomal protective protein/cathepsin A (CathA) is a multifunctional protein that exhibits not only protective functions as to lysosomal glycosidases, i.e., neuraminidase 1 (NEU1) and beta-galactosidase (GLB), but also its own serine carboxypeptidase activity, and exhibits conserved structural similarity to yeast and wheat homologs (CPY and CPW). Our previous study revealed that the R344 (Arg344) residue in CathA could contribute to the binding and recognition of the serine peptidase inhibitor chymostatin. We examined here the effects of substitution of R344 with other amino acids, including A, D, E, G, I, K, M, N, P, Q, S, and V, denoted as R344X, including the wild-type CathA, on expression of CathA activity and intracellular processing. Among the mutant gene products, the 54-kDa precursor/zymogen with the R344D substitution was not processed to the 32/20-kDa mature form with CathA activity in a fibroblastic cell line derived from a galactosialidosis patient. Molecular dynamics (MD) simulations on the total twelve R344X mutants and the wild-type revealed that only R344D takes on a significantly different conformation of S293-D295 in the excision peptide (M285-R298) compared to the other R344X mutants; the side chains of S293 and D295 in R344D are exposed on the molecular surface, although those in the other twelve R344X mutants are buried inside the protein. The results of the current work strongly suggest that the distinct conformational change of the S293-D295 region in the R344D protein causes the processing defect of the 54-kDa precursor of the R344D mutant gene product in cultured cells.

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics


Novel Quantitative Structure-Activity Studies of HIV-1 Protease Inhibitors of the Cyclic Urea Type Using Descriptors Derived from Molecular Dynamics and Molecular Orbital Calculations


Quantitative Structure-Activity Relationship for Inhibition of CYP2B6 and CYP3A4 by Azole Compounds - Comparison with Their Binding Affinity


Flavonoids as Substrates and Inhibitors of Myeloperoxidase : Molecular Actions of Aglycone and Metabolites

Myeloperoxidase (MPO), secreted by activated neutrophils and macrophages at the site of inflammation, may be implicated in the oxidation of protein/lipoprotein during the development of cardiovascular diseases. Flavonoids have been suggested to act as antioxidative and anti-inflammatory agents in vivo; however, their molecular actions have not yet been fully understood. In this study, we examined the molecular basis of the inhibitory effects of dietary flavonoids, such as quercetin, and their metabolites on the catalytic reaction of MPO using a combination of biological assays and theoretical calculation studies. Immunohistochemical staining showed that a quercetin metabolite was colocalized with macrophages, MPO, and dityrosine, an MPO-derived oxidation product of tyrosine, in human atherosclerotic aorta. Quercetin and the plasma metabolites inhibited the formation of dityrosine catalyzed by the MPO enzyme and HL-60 cells in a dose-dependent manner. Spectrometric analysis indicated that quercetin might act as a cosubstrate of MPO resulting in the formation of the oxidized quercetin. Quantitative structure-activity relationship studies showed that the inhibitory actions of flavonoids strongly depended not only on radical scavenging activity but also on hydrophobicity (log P). The requirement of a set of hydroxyl groups at the 3, 5, and 4'-positions and C2-C3 double bond was suggested for the inhibitory effect. The binding of quercetin and the metabolites to a hydrophobic region at the entrance to the distal heme pocket of MPO was also proposed by a computer docking simulation. The current study provides the structure-activity relationships for flavonoids as the anti-inflammatory dietary constituents targeting the MPO-derived oxidative reactions in vivo.


Simple computational models of type I / type II cells in Fas signaling-induced apoptosis

Distinct apoptotic response of the type I/type II cells against Fas-ligand stimulation is considered to arise from the difference in dominant signaling pathways involved. In the type I cells, apoptotic signaling predominantly takes place via the direct activation of caspase-3 by activated caspase-8 (D channel) while mitochondrial pathway (M channel) plays a major role in the type II cells. To elucidate the selection mechanism of dominant pathway, we carried out systematic model analysis of the Fas signaling-induced apoptosis network. An increase in the expression level of caspase-8 induced a switch of dominant pathway from M- to D-channel (M-D transition), showing a phenotypic change from type II to type I cells. With the aid of sensitivity analysis and kinetic considerations, we succeeded in constructing a minimal network model relevant for the M-D transition, which revealed that mechanistic origin of the transition lies in the competition between the activated forms of caspase-8 and caspase-9 for their common substrate caspase-3. The pathway dominance was found to be primarily controlled by the balance between the activation rate of caspase-8 and the initial level of caspase-9. In the full network model, we showed that differential formation ability of the death-inducing signaling complex (DISC) can also induce M-D transition, in accordance with the experimental observations.


QSAR Study of Cyclic Urea Type HIV-1 PR Inhibitors Using Ab Initio MO Calculation of Their Complex Structures with HIV-1 PR


Toward basic understanding of the partition coefficient log P and its application in QSAR


A New Type of Imido Group Donor: Synthesis and Characterization of Sulfonylimino-λ3-bromane that Acts as a Nitrenoid in the Aziridination of Olefins at Room Temperature under Metal-Free Conditions

Journal of the American Chemical Society


医薬品安全性情報コミュニティ·データベースシステム:妊娠と薬に関する安全性情報の共有に向けて

Journal of Information Processing and Management


A structural similarity evaluation by SimScore in a teratogenicity information sharing system

Many efforts have been devoted to the development of computer-aided prediction of drug toxicity over the decades, but at present, systems and programs available for predicting teratogenicity from chemical structures do not always give satisfactory answers yet, mainly because of the complex and unknown mechanism of reproductive and developmental toxicity. We developed a novel algorithm and implemented in the program "SimScore" to evaluate quantitatively the structural similarity score of a target compound with the teratogenic drugs which are defined as serious human teratogens by the United States Food and Drug Administration. In SimScore, a molecular structure is divided into its skeletal and substituent parts in order to perform similarity comparison for these parts independently. This idea is based on that compounds with the same or similar skeleton show a similar biological activity, but their activity strengths depend on the variation of substituents. We demonstrated the usefulness of SimScore by applying it to an example.SimScore will be used in our web-based information system about teratogenicity to predict the potential risk of query compounds.


Quantitative structure - activity relationship study of binding affinity of azole compounds with CYP2B and CYP3A


Effect of a conjugated quercetin metabolite, quercetin 3-glucuronide, on lipid hydroperoxide-dependent formation of reactive oxygen species in differentiated PC-12 cells

To assess the efficacy of conjugated quercetin metabolites as attenuators for oxidative stress in the central nervous system, we measured the 13-hydroperoxyoctadecadienoic acid (13-HPODE)-dependent formation of reactive oxygen species (ROS) in pheochromocytoma PC-12 cells in the presence of quercetin 3-O-beta-glucuronide (Q3GA) and related compounds. A 2',7'-dichlorofluorescin (DCFH) assay showed that Q3GA significantly suppressed the formation of ROS, when it was coincubated with 13-HPODE (coincubation system). However, it was less effective than quercetin aglycon in the concentration range from 0.5 to 10 microM. In an experiment in which the cells were incubated with the test compounds for 24 h before being exposed to 13-HPODE, Q3GA was also effective in suppressing the formation of ROS in spite that little Q3GA was taken up into the cells. These results suggest that antioxidative metabolites of quercetin are capable of protecting nerve cells from attack of lipid hydroperoxides.


「妊娠と薬」に関する意識調査-薬剤師, 薬学生, 研究者の場合

「妊娠と薬」に関する意識調査-薬剤師, 薬学生, 研究者の場合

The aim of this study was to assess the awareness of pharmacists, pharmacy students and researchers regarding "Drugs and Pregnancy". In order to do this, a questionnaire was given to 211 attendees of a symposium held under a pharmacists' education program held at the University of Tokushima. The response rate was 108/211 (51%) and the breakdown of the respondents was students 46%, pharmacists 36% and researchers 9%. Among the 36 persons with experience of delivery, 67% had taken medicine during pregnancy, and 42% of them were worried about the embryotoxic effects of drugs. Persons with no experience of delivery were more worried about such effects than those who had experienced delivery. Before being given a prescription, 71% of the respondents had been asked about the possibility of pregnancy by a physician. On the other hand, no respondent had been asked about this by a pharmacist, suggesting that pharmacists are passive with regard to providing information about drugs and pregnancy. Information on drugs and pregnancy was mainly obtained from drug package inserts, books and pharmaceutical companies. The majority of the respondents (96%) were interested in a web site from which they could retrieve information on drug safety during pregnancy. They showed a willingness to cooperate with regard to recording medicines used during the pregnancy as well as the outcome of their pregnancies. Eighty-nine percent of the researchers and 78% of the students wanted to use teratogenicity information in drug design. All of the researchers answered that it was beneficial to share information on reproductive and developmental toxicity. The results of our questionnaire survey showed that many people desired drug safety information during pregnancy, and were willing to share such information.

Japanese Journal of Pharmaceutical Health Care and Sciences


Comparative Analysis of Binding Energy of Chymostatin with Human Cathepsin A and Its Homologous Proteins by Molecular Orbital Calculation

Cathepsin A is a mammalian lysosomal enzyme that catalyzes the hydrolysis of the carboxy-terminal amino acids of polypeptides and also regulates beta-galactosidase and neuraminidase-1 activities through the formation of a multienzymic complex in lysosomes. Human cathepsin A (hCathA), yeast carboxypeptidase (CPY), and wheat carboxypeptidase II (CPW) belong to the alpha/beta-hydrolase fold family. They have structurally similar active-site clefts, but there are small differences in the amino acid residues comprising their active sites that might determine the substrate specificity and sensitivity to microbial inhibitors including chymostatin. To examine the selectivity and binding mechanism of chymostatin as to hCathA, CPY, and CPW at the atomic level, we analyzed the interaction energy between chymostatin and each protein quantitatively by semiempirical molecular orbital calculation AM1 with the continuum solvent model. We predicted the electrostatic repulsion between the P3 cyclic arginine residue of the inhibitor and the Arg344 in the S3 active subsite of hCathA. Genetic conversion of Arg344 of the wild-type hCathA to Ile also caused an increase in its sensitivity to chymostatin, which was correlated with the decrease in the interaction energy calculated with the molecular orbital method. The present results suggest that such molecular calculation should be useful for evaluating the interactions between ligands, including inhibitors and homologous enzymes, in their docking models.

Journal of Chemical Information and Modeling


Pharmacotherapy During Pregnancy-Influence on both the Mother and the Fetus-

妊娠期の薬物療法∼その実態と母児への影響∼


Screening for New Antidepressant Leads of Multiple Activities by Support Vector Machines

Virtual screening was carried out against 21 biological targets related to depression by support vector machine classification using the same atom-type descriptors. The models were effective as 0.2-0.8 of theoretical enrichments of the external test data sets could be achieved, depending on the target. The set of predicted active molecules had large diversity and contained examples with high dissimilarity to the compounds of training sets. Filtering the database of known antidepressants by all 21 models it was found that on average compounds were classified active for 2.3 targets.


Flavonoids are polyphenolic compounds that occur ubiquitously in foods of plant origin. Some of these molecules exhibit various physiological activities. Among existing drugs, there are a huge number of compounds bearing a flavonoid-related skeleton. Because of the relevance for pharmaceutical research, it would be beneficial to collect these compounds into a database. Recently, various databases of chemicals were compiled to help biological and/or chemical research, but no comprehensive database of flavonoids with chemical structures and physicochemical parameters, supposedly related to their activity, is available yet. The aim of this research was to merge the information about flavonoids of plant origin and flavonoids used as medicines into a database. Moreover, predictions of activities against various targets were performed using a virtual screening procedure to demonstrate a possible application of the database for pharmaceutical research.


Virtual screening models for finding novel antidepressants

Virtual screening was carried out against various biological targets related to depression by support vector machine classification using the atom-type descriptors. The models were effective as over 75 and 95% of the molecules in external test datasets could be correctly classified, depending on target. Antidepressant compounds had predicted activity against 2.3 targets, on average. An introduction is given to virtual screening and the results of classification experiments are presented.

The Journal of Medical Investigation : JMI


Determination of solute lipophilicity by reversed-phase high-performance liquid chromatography (RP-HPLC)

Lipophilicity was evaluated by the high-throughput RP-HPLC method. A set of 40 solutes with well-defined solvatochromic parameters were selected in this study. The chromatographic results show that, under the conditions of study, the lipophilicity index log kw was highly correlated with the experimental log Poct.


Construction of a novel database for flavonoids

Flavonoids are polyphenolic compounds that exist ubiquitously in foods of plant origin. Flavonoids show various interesting biological activities, such as removal of oxygen radical, anti-cancer action, improvement of high blood pressure, antibacterial, antibiotic and anti-allergy actions. So far, over 4000 structurally unique flavonoids have been isolated from plant sources. Recently, databases of chemicals have been utilized in to help chemical and biological researches, however the comprehensive database of flavonoids with information about structural, biological and physicochemical properties not yet available. We have constructed the integrated database of flavonoids for nutrition research.


VISCAN: Visualized Cluster Analysis of Protein-Ligand Interaction Based on the ab initio Fragment Molecular Orbital Method for Virtual Ligand Screening

We have developed a visualized cluster analysis of protein-ligand interaction (VISCANA) that analyzes the pattern of the interaction of the receptor and ligand on the basis of quantum theory for virtual ligand screening. Kitaura et al. (Chem. Phys. Lett. 1999, 312, 319-324.) have proposed an ab initio fragment molecular orbital (FMO) method by which large molecules such as proteins can be easily treated with chemical accuracy. In the FMO method, a total energy of the molecule is evaluated by summation of fragment energies and interfragment interaction energies (IFIEs). In this paper, we have proposed a cluster analysis using the dissimilarity that is defined as the squared Euclidean distance between IFIEs of two ligands. Although the result of an ordered table by clustering is still a massive collection of numbers, we combine a clustering method with a graphical representation of the IFIEs by representing each data point with colors that quantitatively and qualitatively reflect the IFIEs. We applied VISCANA to a docking study of pharmacophores of the human estrogen receptor alpha ligand-binding domain (57 amino acid residues). By using VISCANA, we could classify even structurally different ligands into functionally similar clusters according to the interaction pattern of a ligand and amino acid residues of the receptor protein. In addition, VISCANA could estimate the correct docking conformation by analyzing patterns of the receptor-ligand interactions of some conformations through the docking calculation.


Determination of lipophilicity by reversed-phase high-performance liquid chromatography: Influence of 1-octanol in the mobile phase

Lipophilicity was evaluated using a novel RP-HPLC stationary phase (Discovery-RP-Amide-C16) with and without 1-octanol added to the mobile phase. A set of 46 drugs and flavonoids characterized by a broad structural diversity and a wide log Poct range (-0.69 to 5.70) was selected for this study. This set consists of neutral solutes and solutes with acidic or ampholytic functionalities which were maintained neutral at pH 2.5 or 4. In our conditions, the addition of 1-octanol in the mobile phase proved a key factor to derive a lipophilicity index log k(w) highly correlated with log Poct for all investigated solutes. 1-Octanol improved the correlation between log Poct and log k(w) mainly by influencing the retention behavior of the solutes with log Poct values below +3. This study brings additional evidence that under proper experimental conditions of stationary and mobile phases, RP-HPLC is a very useful method to obtain log Poct values.


Clinical QSAR study on the prediction of drug excretion into human breast milk


Comparative Study on Solvation Free Energy Expressions in Reference Interaction Site Model Integral Equation Theory

The performance of the recently proposed partial wave (PW) free energy functional is compared with those of two previous expressions, Gaussian fluctuation (GF) and hypernetted chain (HNC), within the reference interaction site model framework. The applications to the calculations of ambient and supercritical water, solvation free energies of organic molecules, and partition coefficients clearly show that the PW and GF free energy expressions provide more reliable results than the HNC functional, indicating rather associative situations of geometry in ordinary liquids of medium-sized molecules.


Approach to novel functional foods for stress control 1.Toward structure-activity relationship and data mining of food compounds by chemoinformatics

Over the past several decades, thousands of natural organic compounds have been isolated from foods, and the information about their structures and biological activities has been accumulated. Despite the long research history of food products and their potential great promise as a medicine and functional food, the systematic research and development have not been carried out extensively. For understanding of the comprehensive structure-activity relationship, we have developed the database system of flavonoids, which are frequently found in vegetables and fruits. We also plan to execute a virtual screening of flavonoids with antidepressant activity by using the database and an advanced chemoinformatic tool. In this section, we will briefly describe (1) flavonoid database and (2) virtual screening of antidepressant compounds.


Connecting Traditional QSAR and Molecular Simulations of Papain Hydrolysis-Importance of Charge Transfer

Molecular dynamics and full structure LocalSCF semi-empirical quantum mechanics calculations of receptor-ligand complexes were carried out to investigate structure-activity relationship for the papain hydrolysis of a series of N-benzoylglycine esters and reinterpret traditional QSAR descriptors using detailed structural information. A correlation of r(2)=0.694 was obtained and it was shown that the pattern of charge distribution on the ester group is different if charges of free or complex ligands or are analyzed. The results can help to understand how traditional QSAR descriptors, such as F or sigma, interacts with other electronic effects during complex formation.


Application of a Stepwise Flow Ratiometry without Phase Separation to the Determination of the Chloroform/Water Distribution Coefficients of Volatile Diazines

The chloroform/water distribution coefficients (K(D)) of sixteen diazine compounds were determined by a stepwise flow ratiometry. An aqueous solution of analyte was delivered and merged with chloroform. The flow rate ratio of both the phases was varied stepwise under a constant total (chloroform+aqueous) flow rate. The analyte was extracted to chloroform while both the phases, which were segmented by each other, were passing through an extraction coil. The segmented stream was then led to a UV/Vis detector directly without phase-separation. The absorbance of the chloroform and aqueous phases (A(o) and A(a), respectively) was each measured at the maximum absorption wavelength of the analyte. The plots of A(-1) against R(f), (AR(f))(-1) against R(f)(-1), and AR(f) against A gave straight lines, where A was A(o), A(a) or the sum of them (A(S)). The K(D) of the analyte was calculated from the slopes and intercepts of the plots. The log K(D) values obtained for the analytes (-0.5-1.4) were agreed well with the values measured by a shake-flask method. The present method is simple, rapid (5 min/determination) and applicable to the volatile compounds with reasonable precision (standard deviation of log K(D)<0.07).


Analyses of the Partition Coefficient, Log P, using Ab Initio MO Parameter and Accessible Surface Area of Solute Molecules

To analyze the log P(sol/w) values (sol: n-octanol or chloroform, w: water) in the framework of the molecular orbital (MO) procedure, we selected solute descriptors such as the solvation energy difference between aqueous and organic solvent phases and the "surface" area of solute molecules to which water molecules are accessible. The solvation energy of solute molecules in their minimum free-energy conformation was calculated using the ab initio self-consistent reaction field-MO method with the conductor-like screening model. The experimentally measured log P(sol/w) value of various solutes except for those of amphiprotics was shown to be analyzable reasonably well by the MO model with additional descriptors for the hydrogen-bonding patterns in the solute-solvent interactions.


Stress is a pervasive factor in everyday life that critically affects development and functioning. Severe and prolonged stress exposure impairs homeostatic mechanisms, particularly associated with the onset of depressive illness. Brain food is aimed at preventing as well as treating a growing number of stress-related mental disorders. Some topics on the association of stress and nutrition is reviewed. (1) An increased activity of serotonergic neurons in the brain is an established consequence of stress. An increase in brain tryptophan levels on the order of that produced by eating a carbohydrate-rich/protein-poor meal causes parallel increases in the amounts of serotonin released into synapses. (2) Eating is thought to be suppressed during stress, due to anorectic effects of corticotrophin releasing hormone, and increased during recovery from stress, due to appetite stimulating effects of residual cortisol. (3) A strong inverse association between coffee intake and risk of suicide. (4) Night eating syndrome has been found to occur during periods of stress and is associated with poor results at attempts to lose weight and disturbances in the hypothalamic-pituitary-adrenal axis. (5) Dietary antioxidants present in fruits and vegetables may improve cognitive function. Therefore, it is concluded that the establishment of functional foods that correctly regulate stress response must be firmly based upon scientific knowledge and legal regulation.

The Journal of Medical Investigation : JMI


医薬品安全性情報コミュニティの構築にむけて

医薬品安全性情報コミュニティの構築にむけて


超高速計算環境での生体関連分子の活性·機能予測システムの構築:HIVプロテアーゼ阻害剤の解析への応用


Construction of a drug safety information community in Japan


Lipophilicity measurement by reversed-phase high-performance liquid chromatography (RP-HPLC): A comparison of two stationary phases based on retention mechanisms


Determination of dissociation constants of weak acids by feedback-based flow ratiometry


Construction of a Growing Information-Community for Teratogenic Agents

双方向·成長型薬物催奇形性情報コミュニテイの構築

Congenital malformations or birth defects are a major public concern. However, lack of proper information may panic a pregnant woman who had taken medicines without noticing the pregnancy, and thus may result in an unnecessary abortion. We have undertaken a new research/development project to create an information-community for teratogenic agents, consisting of pregnant women, pharmacists, physicians and research scientists working on medicinal products. We have designed a trial database system for teratogenic agents. The database performs not only retrieval of teratogenic information and chemical structures of drugs/medicinal products, but also registration of clinical case reports and teratogenic information on various chemicals. Our system will be useful for clinical risk-assessment of teratogenic exposures in pregnant women and for the development of new drugs based on chemical information and computer science.

薬物が原因で起こる胎児奇形は，頻度は低いが薬物治療において決して起こしてはならない副作用である．しかし，わが国には，妊娠に気づかずクスリを服用したとして過度の不安を抱いている妊婦に対する適切な情報提供システムがない．また，開発の中断された医薬品候補化合物の生殖・発生毒性情報は，公開され有効に利用されることなく企業の研究室に眠っているのが実状である．そこで，我々は，インターネット上に情報提供・収集システムを構築し，妊婦(市民)・医療関係者・研究者に情報コミュニティの場を提供することを目指している．先導研究として，Web上で医薬品催奇形性情報と化学構造式に関する条件検索が可能で，さらにクライアント側からも臨床症例登録のできる双方向・成長型の試用データベースを作成した．薬物催奇形性情報コミュニティの実現は，妊婦に対する根拠に基づいた薬物治療の実践と，情報化学的解析手法を用いた効率的な医薬品研究開発に資するものと期待される．


Determination of the Chloroform/Water Distribution Coefficient of Weak Acids by a Stepwise Flow Ratiomwtry


Prediction of the 1-Octanol/H2O Partition Coefficient, Log P, by Ab Initio MO Calculations: Hydrogen-Bonding Effect of Organic solutes on Log P

To predict the 1-octanol/H2O partition coefficient, log P, based on molecular structures, we calculated the solvent accessible surface area and the solvation energy difference of 166 organic molecules between 1-octanol and water environments with the ab initio molecular orbital self-consistent reaction field method, and then analyzed the relationships among the measured log P values with these two structural quantities by multiple linear-regression analyses. Physicochemically meaningful correlations were obtained, suggesting that non-hydrogen bonding and hydrogen-acceptor molecules behave similarly to each other in partitioning, but that hydrogen-donor molecules behave differently from the former molecules. The results provide a new computational approach for predicting log P.


How does the mitochondrial ADP/ATP carrier distinguish transportable ATP and ADP from untransportable AMP and GTP? Dynamic modeling of the recognition/translocation process in the major substrate binding region

To understand the transport mechanism of the bovine heart mitochondrial ADP/ATP carrier at the atomic level, we studied the four-dimensional features of the interaction of various purine nucleotides with the adenine nucleotide binding region (ABR) consisting of Arg(151)-Asp(167) in the second loop facing the matrix side. After three-dimensional modeling of ABR based on the experimental results, its structural changes on interaction with purine nucleotides were examined by molecular dynamics computation at 300 K. ATP/ADP were translocated to a considerable degree from the matrix side to the inner membrane region accompanied by significant backbone conformational changes, whereas neither appreciable translocation nor a significant conformational change was observed with the untransportable nucleotides AMP/GTP. The results suggested that binding of the terminal phosphate group and the adenine ring of ATP/ADP with Arg(151) and Lys(162), respectively, and subsequent interaction of a phosphate group(s) other than the terminal phosphate with Lys(162) triggered the expansion and subsequent contraction of the backbone conformation of ABR, leading to the translocation of ATP/ADP. Based on a simplified molecular dynamic simulation, we propose a dynamic model for the initial recognition process of ATP/ADP with the carrier.

Biochimica et Biophysica Acta (BBA) - Molecular Cell Research


Quantitative estimation of interaction between carbohydrates and concanavalin A by surface plasmon resonance biosensor

We measured the affinity of more than 20 sugars with concanavalin A (ConA) by an optical biosensor (surface plasmon resonance sensor) using asialofetuin (ASF) as an immobilized binding partner of ConA. We determined kinetic parameters of the effects of sugars on the dissociation of ConA from ASF quantitatively, and the structural requirements of the functional groups of sugars for binding with ConA. We found that the affinity of ConA for sugars is dependent on its conformation induced by interaction with the binding partner. In addition, the results showed that optical biosensor system is well mimics the interaction of ConA with sugars in biomembrane.


Determination of the Distribution Coefficients of Phenol Derivatives and Others Based on a Volume Ratiometry Coupled with a Shake-Flask Method


Remarkable Discrepancy in the Predominant Structures of Acyl(or Thioacyl)aminothiadiazoles, Acyl(or Thioazyl)aminooxadiazoles and Related Compounds Having the Potential for Rotational, Geometrical and Tautomeric Isomerism


Determination of Distribution Coefficient by Flow Ratiometry


Three-Dimensional Structure-Activity Relationships of Synthetic Pyrethroids: 2. Three-Dimensional and Classical QSAR Studies


Three-Dimensional Structure-Activity Relationships of Synthetic Pyrethroids: 1. Similarity in Bioactive Conformations and Their Structure-Activity Pattern


Structure-Activity Relationships of the Azole Fungicide Metconazole and its Related Azolylmethylcycloalkanols

Metconazole, (1RS, 5RS; 1RS, 5SR)-5-(4-chlorobenzyl)-2, 2-dimethyl-1-(1H-1, 2, 4-triazol-1-ylmethyl)cyclopentanol, is a novel triazole fungicide containing a cyclopentane ring. The related compounds, cyclopentanol, cyclohexanol and cycloheptanol derivatives having none or gem-dimethyl groups at the 2-position on the cycloalkane ring were synthesized, and their fungicidal activities were compared. The gem-dimethyl groups at the 2-position on the cyclohexane and cycloheptane rings were important for fungicidal activity as well as the case of the cyclopentanols. The cis-isomers of the cyclopentanols and the cycloheptanols showed higher fungicidal activities than the trans-isomers of them. On the contrary, the trans-isomers of the cyclohexanols were more active than the cis-isomers of them, but less active than the cis-isomers of the cyclopentanols and the cycloheptanols. Among the cis-cycloalkanols, the cyclopentanols and the cycloheptanols showed higher activities than the cyclohexanols. The conformational analysis of these cycloalkanols indicated that the relative three-dimensional orientation of the two important aromatic rings, triazole and benzene, of the cycloalkanols affected their fungicidal activities.

シクロペンタン環を基本骨格とするアゾール系殺菌剤メトコナゾール, (1RS, 5RS; 1RS, 5SR)-5-(4-クロロベンジル)-2,2-ジメチル-1-(1H-1,2,4-トリアゾール-1-イルメチル) シクロペンタノールの誘導体として, シクロアルカンの2位が無置換あるいは gem-ジメチル基を有するシクロペンタノール, シクロヘキサノール, シクロヘプタノール類を合成し, 構造と殺菌活性について検討した. その結果, シクロアルカン2位に置換したジメチル基はいずれも活性の向上に大きく寄与した. ジアステレオマー間の比較では, シクロペンタノール類とシクロヘプタノール類ではシス体がトランス体より活性が高く, 一方シクロヘキサノール類の場合はトランス体がシス体より活性が高かった. シス体間の活性比較では, シクロペンタノール類とシクロヘプタノール類は高い活性を示したが, シクロヘキサノール類は前2者に比べて低かった. 環の員数の違いによる活性の差を, コンポメーション解析から検討した結果, シクロアルカン構造に起因するベンゼン環とトリアゾール環の3次元空間配置と殺菌活性に相関があることが示唆された.


Exhaustive Parallel Conformational Search of Pyrethroids and Structure Similarity Study

ピレスロイド系殺虫化合物の大規模並列配座解析と構造類似性の評価


A Novel Tree Dimensional Procedure: Voronoi Field Analysis


Enantiometric Structure-Activity Relationships of the Azole Fungicide, Ipconazole, and its Related Compounds: Antifungal and Plant Growth Regulatory Activities


Constructing a web-based drug-teratogenicity information sharing system, anzen-drug com


Estimating potential risks of pharmaceuticals human fetuses by SimScore in a teratogenicity information sharing system


薬物の胎盤通過性と母乳移行性予測-Clinical QSAR

薬物の胎盤通過性と母乳移行性予測-Clinical QSAR