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At least 667 records · Page 37Linked to original sources
PubMed2000

Synthesis and evaluation of 4-(N,N-diarylamino)piperidines with high selectivity to the delta-opioid receptor: a combined 3D-QSAR and ligand docking study.

A series of 4-(N,N-diarylamino)piperidines are synthesized and evaluated for high affinity binding and selectivity to the delta-opioid receptor using a combination of 3D-QSAR and molecular docking techniques. Based on experimental ligand binding data to both mu- and delta- opioid receptors, CoMFA fields are generated and applied to identify potential ligand modifications to further optimize lead compounds. Molecular docking experiments to the delta-receptor are also reported that explain the CoMFA trends predicted as well as the differential binding and selectivity displayed by various compounds in the series. An analysis of the binding site model proposed indicates the piperidines take advantage of 3 key sites or binding domains within the delta-receptor. These include an aromatic pocket (approximately 1/3 into the receptor cavity), an aspartic acid residue (which serves as a docking point for the piperidinyl cationic amine) and a hydrophobic pocket at the extracellular boundary of the receptor cavity. Links are established between ligand modification and amino acid composition at these sites in mu and delta, providing new insight to the structural basis to binding and selectivity across the series and for related piperazines (i.e. SNC80 and BW373U86). Results are also presented that indicate delta- and mu-selectivity may be determined at alternate sites, suggesting opioid receptors may display multiple binding domains. The model is further supported by comparisons with opiate binding modes and site directed mutagenesis studies and is finally applied to suggest new strategies in ligand design.

Amino Acid Sequence↗
PubMed2000

DARWIN: a program for docking flexible molecules.

A new program named "DARWIN" has been developed to perform docking calculations with proteins and other biological molecules. The program uses the Genetic Algorithm to optimize the molecule's conformation and orientation under the selective pressure of minimizing the potential energy of the complex. A unique feature of DARWIN is that it communicates with the molecular mechanics program CHARMM to make the energy calculations. A second important feature is its parallel interface, which allows simultaneous use of multiple stand-alone copies of CHARMM to rapidly evaluate large numbers of potential solutions. This permits an "accuracy first" approach to docking, which avoids many of the common assumptions and shortcuts often made to reduce computation time. The method was applied to three protein-carbohydrate complexes: the crystallographically determined structures of Concanavalin A and Fab Se155-4; and a model structure for Fab ME36.1. Conformations close to the crystal structures were obtained with this approach, but some "false positive" solutions were also selected. Many of these could be eliminated by introducing different methods for simulating solvent effects. An effective screening method for docking a database of compounds to a single target enzyme using DARWIN is also presented.

Algorithms↗
PubMed1999

Results of screening for cancer in Japanese in the prime of life--an analysis of nationwide MHTS and human dry dock statistics--Preventive Medicine Committee of the Japan Hospital Association.

The nationwide survey of institutions with MHTS and human dry dock capabilities was analyzed and the following results have been obtained. 1) The relative rates of cancer detection by sex and organ were the stomach > colon > rectum > lung > kidney > esophagus for men and the stomach > breast > uterus > colon > thyroid > lung for women. 2) Gastric cancer takes first place in the ranking of rates of cancer detection in the population of both sexes, followed by colon cancer. The difference in rate of detection between these cancers has been narrowed from year to year. In 1997, the ratio of gastric to colon cancers was 10:7. 3) Early cancers account for 74% of gastric cancer patients and 75% of colon cancer patients. 4) Since gastric and colon cancers are detected early, the proportions of persons with gastrointestinal symptoms are as low as 28% for gastric cancer patients and 26% for colon cancer patients. 5) The relative rates of cancer detection by the degree obesity are normal > obese > lean person. The rates of gastric and colon cancers are 2- and 3-fold higher for obese persons than for lean persons, respectively. Gastric and colon cancers are detected with higher frequency in well-nourished persons. The present review of the national MHTS and human dry dock statistics has confirmed the efficacy of MHTS and human dry dock, especially in the examination for gastrointestinal cancers.

Adult↗
PubMed1995

Comparison of voice stress reactivity under psychological stress test and simulated Mir docking manoeuvre.

The relation between the results of laboratory tests and results of the interesting professional work is a very difficult one. The same is true for the relation between training and real performance. The pilot controlled MIR-docking manoeuvre is in reality a very seldom but very important one. The training of this manoeuvre is a very special professional work and only for cosmonauts available. But the objective estimation of the performance and the used objective and subjective needs is nevertheless necessary. Even for the subjective "stress"-feelings during task solving it is often impossible to get reliable data without any physiological measurements. The use of electrodes, cables and equipments is hardly limited during real work. Sometimes only the voice is available over more or less quality communication channels. So it is the case during the training and the real pilot controlled MIR-docking manoeuvre. Based on findings in the literature and own experiments analyzing the relation between fundamental voice frequency (F0) and subjective stress feelings we tested the hypothesis that a on-line measurement of F0 can be used for stress evaluation during standardised training sessions of MIR-docking manoeuvres.

Astronauts↗
PubMed2002

Screened charge electrostatic model in protein-protein docking simulations.

A new method for considering solvation when calculating electrostatics for protein docking is proposed. The solvent-exposed charges are attenuated by induced solvent polarization charges. Modified charges are pre-calculated and the correction doesn't affect the speed of the actual simulation. The new Screened Charge Electrostatic Model (SChEM) results in an improved discrimination of near-native solutions from false positives in docking simulations as compared to conventional 'non-solvated' charge assignment. A series of protein-protein complexes were analyzed by running automated rigid-body Monte-Carlo docking simulations using the 3-D coordinates of the unbound components. In all but one case, the use of solvation screened charges for electrostatic calculations helped to improve the rank of the near-native solution after rigid-body simulations. The SChEM also drastically improved the results of the subsequent refinement of the interface side-chains. In all cases the final lowest energy solution was found within 3.0 A r.m.s.d. of the crystal structure.

Animals↗
PubMed2003

A soft docking algorithm for predicting the structures of protein-protein complexes.

An efficient soft docking algorithm is described to predict the mode of binding between two proteins based on the three-dimensional structures of molecules. The molecular model used in this work was grounded on the "simplified protein" model used in Janin's docking algorithm. The side chain flexibility of the amino acid residues Arg, Lys, Asp, Glu and Met at the protein surface was considered through softening the molecular surface. A double filtering technique was used to eliminate most of the unlike binding modes. The energy minimization was performed on the retained structures, and then these structures were evaluated with the scoring function which included electrostatic, desolvation and van der Waals energy terms. The 26 complexes were used to test this docking algorithm and good results were obtained. The native-like conformations of all the complexes were all found, of which 20 were ranked in the top 10.

Algorithms↗
PubMed2000

The Role of the Human Dry Dock in Smoking Cessation in Japan.

The human dry dock, a Japanese system of detailed health check-ups for middle-aged and elderly people was originally set up for the purpose of secondary prevention, but it is now expected to increasingly play a role in primary prevention. A series of our studies of smoking cessation in the human dry dock setting showed that the abstinence rate increased from 5-6% for non-advised smokers to 9-10% for those who were advised. Thoracic CT screening participants were found to be more likely to quit smoking. It can be estimated that an additional seventy thousand male smokers would quit smoking every year if advice on smoking cessation was routinely given in every dock in Japan.

Journal Article↗
PubMed2005

Prediction of HIV-1 protease inhibitor resistance using a protein-inhibitor flexible docking approach.

Emergence of drug resistance remains one of the most challenging issues in the treatment of HIV-1 infection. Here we focus on resistance to HIV-1 protease inhibitors (PIs) at a molecular level, which can be analysed genotypically or phenotypically. Genotypic assays are based on the analysis of mutations associated with reduced drug susceptibility, but are problematic because of the numerous mutations and mutational patterns that confer drug resistance. Phenotypic resistance or susceptibility can be experimentally evaluated by measuring the amount of free drug bound to HIV-1 protease molecules, but this procedure is expensive and time-consuming. To overcome these problems, we have developed a docking protocol that takes protein-inhibitor flexibility into account to predict phenotypic drug resistance. For six FDA-approved Pls and a total of 1792 HIV-1 protease sequence mutants, we used a combination of inhibitor flexible docking and molecular dynamics (MD) simulations to calculate protein-inhibitor binding energies. Prediction results were expressed as fold changes of the calculated inhibitory constant (Ki), and the samples predicted to have fold-increase in calculated Ki above the fixed cut-off were defined as drug resistant. Our combined docking and MD protocol achieved accuracies ranging from 72-83% in predicting resistance/susceptibility for five of the six drugs evaluated. Evaluating the method only on samples where our predictions concurred with established knowledge-based methods resulted in increased accuracies of 83-94% for the six drugs. The results suggest that a physics-based approach, which is readily applicable to any novel PI and/or mutant, can be used judiciously with knowledge-based approaches that require experimental training data to devise accurate models of HIV-1 Pl resistance prediction.

Binding Sites↗
PubMed2006

Demonstration of in silico docking at a large scale on grid infrastructure.

WISDOM stands for World-wide In Silico Docking On Malaria. First step toward enabling the in silico drug discovery pipeline on a grid infrastructure, this CPU consuming application generating large data flows was deployed successfully on EGEE, the largest grid infrastructure in the world, during the summer 2005. 46 million docking scores were computed in 6 weeks. The proposed demonstration presents the submission of in silico docking jobs at a large scale on the grid. The demonstration will use the new middleware stack gLite developed within the EGEE project.

Europe↗
PubMed2005

A fast protein-protein docking algorithm using series expansion in terms of spherical basis functions.

We describe a fast protein-protein docking algorithm using a series expansion in terms of newly designed bases to efficiently search the entire six-dimensional conformational space of rigid body molecules. This algorithm is an ab initio docking algorithm designed to list candidates of putative conformations from a global conformational space for unbound docking. In our algorithm, a scoring function is constructed from terms that are the inner products of two scalar fields expressing individual molecules. The mapping from a molecule to a scalar field can be arbitrarily defined to express an energy term. Since this scoring scheme has the same expressiveness as that of a method using a fast Fourier transform (FFT), it has the flexibility to introduce various physicochemical energies. Currently, we are using scalar fields that approximate desolvation free energy and steric hindrance energy. Fast calculation of the scoring function for each conformation of the six-dimensional search space is realized by expansion of the fields in terms of basis functions which are combinations of spherical harmonics and modified Legendre polynomials, and the use of only low-order terms, which carry most of the information on the scalar field. We have implemented this algorithm and evaluated the computation time and precision by using actual protein structure data of complexes and their monomers. This paper presents the results for six unbound cases and in all the cases we obtained at least one conformation close to the native structures (interface RMSD < 3.0 A) within the top 1000 candidates with about 40 seconds of computation time using a single Pentium4 2.4 GHz CPU.

Algorithms↗
PubMed1989

Effects of tail docking and castration on behaviour and plasma cortisol concentrations in young lambs.

Behavioural and cortisol responses of lambs to the usual husbandry practices of castration and, or, tail docking using tight rubber rings were investigated between birth and seven days old. There were four treatments: control handling and blood sampling (n = 52), tail-docking (T) (n = 57), castration plus tail-docking (CT) (n = 54) and intravenous adrenocorticotrophin injection (ACTH) (n = 52). After treatment there was a transient rise in plasma cortisol concentration, the magnitude and duration of which increased in the following order; control, T, CT and ACTH. Behavioural characteristics indicative of distress included restlessness (standing up and lying down frequently, rolling, kicking, stamping), lateral recumbency, immobility with neck extension and hyperventilation. Using changes in cortisol concentrations and behaviour the lamb responses were characterised as reflecting 'mild disturbance without distress' (control, ACTH), 'mild distress' (T) and 'marked distress' (CT). The mild distress lasted for about 30 minutes in T lambs and marked distress for about 60 minutes in CT lambs.

Adrenocorticotropic Hormone↗
PubMed1996

STK/RON receptor tyrosine kinase mediates both apoptotic and growth signals via the multifunctional docking site conserved among the HGF receptor family.

STK/RON tyrosine kinase, a member of the hepatocyte growth factor (HGF) receptor family, is a receptor for macrophage-stimulating protein (MSP). To examine the STK/RON signalling pathway, we generated STK/ RON transfectants showing opposite features in growth. STK/RON-expressing Ba/F3 pro-B cells (BaF/STK) exhibited MSP-dependent growth, whereas STK/ RON-expressing mouse erythroleukaemia cells (MEL/ STK) displayed MSP-induced apoptosis. This apoptosis was accompanied by the prolonged activation of c-Jun N-terminal kinase (JNK), which has recently been implicated in the initiation of apoptosis. Co-immunoprecipitation analyses showed that autophosphorylated STK/RON associated with PLC-gamma, P13-kinase, Shc and Grb2 in both transfectants. However, major tyrosine-phosphorylated proteins, p61 and p65, specifically associated with STK/RON in MEL/STK cells. Mutations at two C-terminal tyrosine residues, Y1330 and Y1337, in the counterpart of the multifunctional docking site of the HGF receptor abolished both MSP-induced growth and apoptosis. Analyses of these mutants and in vitro association revealed that signalling proteins including p61 and p65 directly bound to the phosphotyrosines in the multifunctional docking site. These results demonstrate that positive or negative signals toward cell growth are generated through the multifunctional docking site and suggest the involvement of p61 and p65 as well as JNK in apoptosis. Our findings provide the first evidence for apoptosis via a receptor tyrosine kinase.

Amino Acid Sequence↗
PubMed1997

High resolution fast quantitative docking using Fourier domain correlation techniques.

A 'docking' method based on finite grid forcefield sampling is proposed for fast evaluation of interaction energies between macromolecules and ligands. Forcefield used to calculate interaction energies utilizes a potential energy function composed of a 1/r-dependent electrostatic term and a (6-12) Lennard-Jones term for van der Waals interactions. Fast evaluation makes use of the convolution theorem allowing a point-by-point N-dimensional correlation in direct space to be replaced by a simple multiplication in spatial frequency space. Predictive accuracy was assessed by using seven protein-ligand complexes available from the Brookhaven Data Bank and determined crystallographically to high resolution. Successful prediction of ligand position and determination of ligand-protein interaction enthalpy was dependent on forecefield sampling grid size. Minimum interaction enthalpy calculated for four protein-ligand complexes coincided with crystallographic structures that used sampling grid sizes of 0.25 A resolution and was independent of ligand starting position and orientation. Successful docking was obtained for the remaining complexes at same grid resolution provided ligand starting positions were not randomized. Sensitivity of the docking algorithm to starting orientation was a consequence of tight fit of respective ligand structures with their protein target sites for these three cases and can be circumvented by using finer rotational sampling grids for the ligand. Boltzmann statistics derived from calculated interaction energies successfully extracted the observed ribonuclease A cytidylic acid complex from a manifold of similar interaction energies. The proposed method was able to reproduce the observed crystallographic complex by using a dynamical description of ligand.

Algorithms↗
PubMed1997

Automated docking of glucosyl disaccharides in the glucoamylase active site.

To better understand the molecular basis of glucomylase selectivity, low-energy conformers of glucosyl disaccharides obtained from relaxed-residue conformational mapping were flexibly docked into the glucoamylase active site using AutoDock 2.2. This procedure ensures that significant conformational space is searched and can produce bound structures comparable to those obtained by protein crystallography. alpha-Linked glucosyl disaccharides except alpha,alpha-trehalose dock easily into the active site while exclusively beta-linked disaccharides do not, explaining why only the former are glucoamylase substrates. The optimized docking modes are similar at the nonreducing end of the different substrates. Individual atomic energies of intermolecular interaction allow the definite identification of key hydroxyl groups for each substrate. This approach confirmed the versatility of the second subsite of the glucoamylase active site in binding different substrates.

Binding Sites↗
PubMed1997

Evaluation of GRAMM low-resolution docking methodology on the hemagglutinin-antibody complex.

A single protein-protein pair, the complex of the influenza virus hemagglutinin with an antibody (Fab BH151), was suggested for prediction at the second experiment on the Critical Assessment of Techniques for Protein Structure Prediction. To predict the structure of the complex, we applied our docking program GRAMM at a decreased resolution (to accommodate the conformational inaccuracies). The lowest-energy match showed a remarkable "low-resolution" surface complementarity between the molecular structures. After receiving the experimental structure of the complex we had a chance to verify our assumptions and results. The analysis of the hemagglutinin-antibody interface revealed several significant conformational changes in the side chains, which resulted in deep interpenetrations of the hemagglutinin and the antibody structures. This confirmed our initial assumption that the structural changes will be beyond the tolerance of high-resolution rigid-body docking. The comparison of the predicted low-resolution match, submitted as the solution, and the experimentally determined complex showed significant structural discrepancies in the orientation of the antibody, due to the low-resolution character of the docking. Because of the severe structural errors, no residue-residue contacts were predicted correctly. However, a significant part of the antigenic site was determined. This illustrates the practical value of the present methodology for the initial prediction of the binding site, as well as points out the problem of transition from the low-resolution predictions of protein-protein complexes to the accurate structure.

Antibodies, Viral↗
PubMed1998

NSF function in neurotransmitter release involves rearrangement of the SNARE complex downstream of synaptic vesicle docking.

The SNARE hypothesis has been proposed to explain both constitutive and regulated vesicular transport in eukaryotic cells, including release of neurotransmitter at synapses. According to this model, a vesicle targeting/docking complex consisting primarily of vesicle- and target-membrane proteins, known as SNAREs, serves as a receptor for the cytosolic N-ethylmaleimide-sensitive fusion protein (NSF). NSF-dependent hydrolysis of ATP disassembles the SNARE complex in a step postulated to initiate membrane fusion. While features of this model remain tenable, recent studies have challenged fundamental aspects of the SNARE hypothesis, indicating that further analysis of these components is needed to fully understand their roles in neurotransmitter release. We have addressed this issue by using the temperature-sensitive Drosophila NSF mutant comatose (comt) to study the function of NSF in neurotransmitter release in vivo. Synaptic electrophysiology and ultrastructure in comt mutants have recently defined a role for NSF after docking in the priming of synaptic vesicles for fast calcium-triggered fusion. Here we report that an SDS-resistant neural SNARE complex, composed of the SNARE polypeptides syntaxin, n-synaptobrevin, and SNAP-25, accumulates in comt mutants at restrictive temperature. Subcellular fractionation experiments indicate that these SNARE complexes are distributed predominantly in fractions containing plasma membrane and docked synaptic vesicles. Together with the electrophysiological and ultrastructural analyses of comt mutants, these results indicate that NSF functions to disassemble or otherwise rearrange a SNARE complex after vesicle docking and that this rearrangement is required to maintain the readily releasable pool of synaptic vesicles.

Adenosine Triphosphatases↗
PubMed1999

Multiple docking sites on substrate proteins form a modular system that mediates recognition by ERK MAP kinase.

MAP kinases phosphorylate specific groups of substrate proteins. Here we show that the amino acid sequence FXFP is an evolutionarily conserved docking site that mediates ERK MAP kinase binding to substrates in multiple protein families. FXFP and the D box, a different docking site, form a modular recognition system, as they can function independently or in combination. FXFP is specific for ERK, whereas the D box mediates binding to ERK and JNK MAP kinase, suggesting that the partially overlapping substrate specificities of ERK and JNK result from recognition of shared and unique docking sites. These findings enabled us to predict new ERK substrates and design peptide inhibitors of ERK that functioned in vitro and in vivo.

3T3 Cells↗
PubMed2026

Multitarget interactions of bisphenol A in polycystic ovary syndrome: evidence from integrated network toxicology, mendelian randomization, and molecular docking.

OBJECTIVE: To study the potential pathogenic mechanisms of bisphenol A (BPA) in polycystic ovary syndrome (PCOS) using an integrative computational strategy. DESIGN: Integrative computational study combining network toxicology, Mendelian randomization (MR), and molecular docking. SUBJECTS: For MR analysis, genetic data were sourced from large European-ancestry cohorts, including plasma protein quantitative trait loci data and genome-wide association study summary statistics for PCOS (3,045 cases and 267,780 controls). EXPOSURE: In silico exposure to BPA for target prediction; genetically predicted plasma protein levels for causal inference. MAIN OUTCOME MEASURES: Identification of overlapping targets between BPA and PCOS; functional enrichment pathways; causal effects of prioritized proteins on PCOS risk (odds ratios with 95% confidence intervals); binding affinities between BPA and core targets (kcal/mol). RESULTS: Network toxicology identified 310 overlapping targets between BPA and PCOS. Enrichment analyses revealed significant involvement in endocrine signaling, inflammatory pathways (eg, IL-17), and cellular processes. MR demonstrated that genetically elevated levels of RET, CXCL8, HTR6, MMP1, MMP9, NTRK1, and TNNI2 were significantly associated with increased PCOS risk, whereas higher PSAP and SHBG levels were protective. Molecular docking confirmed stable binding between BPA and all nine key targets, with strongest affinity for SHBG (-8.4 kcal/mol), followed by NTRK1, TNNI2, and RET. CONCLUSION: This integrative investigation suggests that BPA may contribute to PCOS pathogenesis through multitarget interactions involving inflammatory mediators, endocrine regulators, and tissue remodeling proteins. The findings provide prioritized targets and mechanistic insights for future experimental validation and environmental risk assessment.

Female↗