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At least 163 records · Page 9Linked to original sources

PubMed2006

Molecular modeling of some 1H-benzimidazole derivatives with biological activity against Entamoeba histolytica: a comparative molecular field analysis study.

Comparative molecular field analysis (CoMFA) was performed on a set of 1H-benzimidazole derivatives. Molecular modeling and 3D-QSAR were employed to determine the tautomeric form that would probably fit a target receptor in Entamoeba histolytica. CoMFA results suggest that the antiamoebic activity is favored with steric bulk at position 5 of the benzimidazole ring and low electron density on the group at position 2. To the best of our knowledge this is the first 3D-QSAR study performed for benzimidazoles as antiamoebic agents. The CoMFA models derived will be very valuable to design new and more potent compounds against E. histolytica.

Algorithms↗

PubMed2002

Molecular modeling of wild-type and antifolate resistant mutant Plasmodium falciparum DHFR.

The development of drug resistance is reducing the efficiency of antifolates as antimalarials. This phenomenon has been linked to the occurrence of mutations in the parasite's dihydrofolate reductase (DHFR). In this way, the resistance to pyrimethamine and cycloguanil, two potent inhibitors of P. falciparum DHFR, is mainly related to mutations (single and crossed) at residues 16, 51, 59, 108 and 164 of the enzyme. In this work, we have refined a recently proposed homology-model of P. falciparum DHFR, and the resulting structure was used to obtain models for 14 mutant enzymes, employing molecular modeling. Ternary complexes of the mutant enzymes with these inhibitors have been superimposed to equivalent ternary complexes of the wild-type enzyme, allowing the proposition of hypotheses for the role of each mutation in drug resistance. Based on these results, possible reasons for antifolate resistance have been proposed.

Animals↗

PubMed2003

Molecular modeling of syringyl and p-hydroxyphenyl beta-O-4 dimers. Comparative study of the computed and experimental conformational properties of lignin beta-O-4 model compounds.

As a new approach for the study of the ultrastructure of lignin, the conformational preferences of lignin beta-O-4 model compounds have been investigated by molecular modeling. The computed results have been compared with the experimental data (X-ray crystal structures and (3)J(H)(alpha)(H)(beta) NMR coupling constant values) reported in the literature. This comparison has led to an improved understanding of the influence of the structure, stereochemistry, and intramolecular H-bonding upon the conformational properties of the beta-O-4 dimers. A large number of low-energy conformations have been predicted for the structures. It has also appeared that the conformational features are predominantly governed by local steric interactions rather than by differences in the H-bonding interactions. The threo and erythro forms differ significantly in their conformational features, with a preferential extended overall shape for the threo form in which the bulky aromatic groups are distant from each other.

Anisoles↗

PubMed1996

Molecular modeling and design of invariant chain peptides with altered dissociation kinetics from class II MHC.

We have used molecular modeling to design substitutions in an invariant chain-derived peptide (CLIP), so as to alter the stability of its complex with class II major histocompatibility complex (MHC) proteins. We sought first to test whether CLIP binds in the same way to different class II MHC proteins. We designed destabilizing substitutions of two residues (Met 91 and Met 99) previously predicted to act as the major anchor residues for binding to all class II MHC and measured their effect on CLIP's dissociation rate from a series of three murine I-A MHC proteins. Even a conservative substitution preserving size and hydrophobicity but reducing flexibility (leucine, a branched residue) caused large accelerations in dissociation rates (up to 25-fold) at either position in all three MHC alleles, supporting the consistent role of these positions as the major anchors for MHC binding. These data also support the view that the special flexibility of the methionine side chains at these positions is essential for binding to diverse MHC molecules. We also used molecular modeling to design allele-specific enhancements of peptide binding. Designed substitutions of CLIP Pro 96 by Ala (for Ad), Glu (Ak), and Tyr (Au) each yielded strong enhancement of binding (up to 128-fold) for their targeted allele and only moderate or destabilizing effects to the other alleles. These results demonstrate the accuracy of the molecular models and the predictive value of this modeling. Moreover, they provide strong evidence for the proposed general model of invariant chain association, indicating that it binds to all class II MHC in the same conformation.

Alleles↗

PubMed1987

A general theory of chemical cytotoxicity based on a molecular model of the living cell, the Bhopalator.

To define the molecular processes underlying toxicological manifestations experimentally measured on the cellular level, it is essential to have available a molecular model of the living cell itself. The Bhopalator is a molecular model of the living cell formulated by integrating the three major branches of biology within a coherent theoretical framework - the Watson-Crick molecular genetics, the conformon theory of enzymic catalysis, and the theory of dissipative structures developed by I. Prigogine. According to this model, the living cell is a self-moving, self-thinking and self-reproducing machine (automaton) that receives information and energy from its environment, processes them according to the genetic programs stored in DNA, and generates output signals to environment in order to realize teleonomically designed functions. The Bhopalator suggests a set of general statements useful in toxicological research, and these statements have been utilized to provide possible answers to several fundamental questions raised by recent experimental findings on chemically-induced cell injury and death.

Animals↗

PubMed1975

Molecular model of postsynaptic potential.

A molecular model of the excitatory postsynaptic membrane is given in terms of two biochemical cycles intimately associated: an acetylcholine cycle and a calcium cycle. The acetylcholine controls the Na ionophores while calcium ions control the tk ionophore. The two ionophores are spatially separated but interact in such a way that the variation in K conductance precedes that in Na conductance. Digital simulation shows that our model accounts quantitatively for both the evolution of excitatory postsynaptic potential and current in a variety of experimental conditions.

Acetylcholine↗

PubMed1994

Computational molecular modeling in peptide drug design.

The review concentrates on practical applications of computer molecular modeling in peptide drug design. The examples of the predictions (successful or not) made by computational modeling before synthesis of peptide analogs, not the explanations provided after synthesis and biological testing of peptides, are discussed. The review spans over 20 years of predictions made by computer molecular modeling for bradykinin, angiotensin, thyrotropin-releasing factor, tuftsin, substance P, CCK-related peptides, luliberin, alpha-melanotropin and opioid peptides. The described examples are discussed in terms of finding the optimal way to use computer modeling for peptide design. The step-by-step 'technology' of peptide design is outlined in detail.

Amino Acid Sequence↗

PubMed1994

Determinants of the factor IX mutational spectrum in haemophilia B: an analysis of missense mutations using a multi-domain molecular model of the activated protein.

A multi-domain molecular model of factor IXa was constructed by comparative methods. The quaternary structure of the protein was assembled by docking individual domains through consideration of their shape complementarity, polaric properties and the location of cross-reacting material positive/negative (CRM+/-) variants on domain surfaces. Some 217 different missense mutations in the factor IX (F9) gene were then selected for study. Using maximum likelihood analysis, missense mutations affecting highly conserved amino acid residues of factor IX were shown to be 15-20 times more likely to result in haemophilia B than those affecting non-conserved residues. However, about one quarter of this increase in likelihood of clinical observation could be attributed to the magnitude of the amino acid exchange. Missense mutations in structurally conserved residues were found to be 2.1-fold more likely to come to clinical attention than those in structurally variable residues. Missense mutations in residues whose side chains were inwardly pointing were 3.6-fold more likely to be observed than those in surface residues. These observations imply a complex hierarchy of sequence/structure conservation in the protein. The severity of the clinical phenotype correlated with both the extent of the evolutionary sequence conservation of the residue at the site of mutation and the magnitude of the amino acid exchange. Further, the substitution of residues exhibiting minimal side chain solvent accessibility was associated disproportionately with severe haemophilia compared with that of surface residues. Clusters of CRM+ mutations were observed at factor IX-specific residues on the surface of the molecule. These clusters may reflect factor IX-specific docking interactions. The likelihood that a given factor IX mutation will come to clinical attention is therefore a complex function of the sequence characteristics of the F9 gene, the nature of the amino acid substitution, its precise location and immediate environment within the protein molecule, and its resulting effects on the structure and function of the protein.

Factor IX↗

PubMed1994

Polymer chain packing analysis using molecular modeling.

This article describes the methodology used in applying molecular modeling to investigate the chain packing of polymers. Models for polyethylene and trans-polyacetylene were developed in order to study the cell packing energy as a function of the chain setting angles. This approach was found to yield chain setting angle values that corresponded to those determined experimentally by other authors. The limitations of the method are also discussed.

Acetylene↗

PubMed2006

Binding analysis of glycyrrhetinic acid to human serum albumin: fluorescence spectroscopy, FTIR, and molecular modeling.

Fluorescence spectroscopy, Fourier transform infrared spectroscopy (FTIR), and molecular modeling methods were employed to analyze the binding of glycyrrhetinic acid (GEA) to human serum albumin (HSA) under physiological conditions with GEA concentrations from 4.0x10(-6) to 4.5x10(-5) mol L(-1). The binding of GEA to HSA was via two types of sites: the numbers of binding site for the first type was near 0.45 and for the second type it was approximately 0.75. The binding constants of the second type binding site were lower than those of the first type binding site at corresponding temperatures, the results suggesting that the first type of binding site had high affinity and the second binding site involved other sites with lower binding affinity and selectivity. The fluorescence titration results indicated that GEA quenched the fluorescence intensity of HSA through static mechanism. The FTIR spectra evidence showed that the protein secondary structure changed with reduction of alpha-helices about 26.2% at the drug to protein molar ratio of 3. Thermodynamic analysis showed that hydrogen bonds were the mainly binding force in the first type of binding site, and hydrophobic interactions might play a main role in the second type of binding site. Furthermore, the study of computational modeling indicated that GEA could bind to the site I of HSA and hydrophobic interaction was the major acting force for the second type of binding site, which was in agreement with the thermodynamic analysis.

Glycyrrhetinic Acid↗

PubMed2001

New hypotheses for the GPCR 3D arrangement based on a molecular model of the human sweet-taste receptor.

A molecular model of the human sweet-taste receptor has been inferred from superpositions of 3D maps of sweetener interaction sites (themselves previously deduced from extensive structure-activity relationship studies on highly potent sweeteners) onto three well-known G protein-coupled receptors (GPCRs)-rhodopsin, beta(2)- and alpha(2A)-adrenergic receptors-assumed to be linked by common evolutionary origins. The model gives new answers to old questions on the GPCR 3D structure, such as on the orientation and arrangement of the binding helices, their interaxial distances, radial orientations and relative heights. The model should be useful as a new approach to the rational design of drugs.

Amino Acid Sequence↗

PubMed2003

Molecular model of the alpha(IIb)beta(3) integrin.

A molecular model of the alpha(IIb)beta(3) integrin has been developed utilizing (i). the crystal structure of alpha(v)beta(3), (ii). homology model of the alpha(IIb) subdomain, and (iii). the docking of alpha(IIb)beta(3)/alpha(v)beta(3) dual and selective inhibitors into the putative binding sites of alpha(IIb)beta(3) and alpha(v)beta(3). Since the binding sites of these integrins are located at the interface between the two heads of the individual subunits, only the alpha(IIb)beta(3) head region is modeled. The 3D conformations of two loops in alpha(IIb), whose residues have been implicated in non-peptide ligand binding, could not be determined from homology with alpha(v) alone. Mutagenesis data and the modeling of small ligand binding contributed to the rational design of these loop conformations. The final energy minimized loop conformations exhibit permissible phi/psi angles and contribute to a binding site model of alpha(IIb)beta(3) that is consistent with both the known mutagenesis studies and in-house structure-activity relationships. The charged residues alpha(IIb):E117 and beta(3):R214 are found to dominate the ligand-protein binding interaction. The previously identified "exosite" is also identified as a hydrogen bond, hydrophobic or pi-pi interaction with Y190, similar to the recently proposed binding model of alpha(v)beta(3).

Amino Acid Sequence↗

PubMed2003

Molecular modelling probes: docking and scoring.

A general introduction to molecular modelling techniques in the area of protein-ligand interactions is given. Methods covered range from binding-site analysis to statistical treatment of sets of ligands. The main focus of this paper is on docking and scoring. After an outline of the main concepts, two specific application examples are given.

Algorithms↗

PubMed2001

Virtual reality system using force feedback device for molecular modeling.

We designed two new concept of computer aided molecular modeling system using virtual reality technologies. Although it is still a prototype, the most characteristic function of the system is enabling its user to "touch" and feel the electrostatic potential field of a protein or a drug molecule. User can scan surface of a protein using a globular probe, which is given an electrostatic charge, controlled by a force feedback devise. The electrostatic force between the protein and the probe is calculated in real time, and immediately fed back into the force feedback device. The user can easily search interactively for positions where the probe is strongly attracted to the force field. Such positions can be regarded as candidate sites where small chemical groups corresponding to the probe, functional parts of lead compounds, can bind to the target protein. We also developed a binding simulator which we can bind a small molecule (drug) to a large molecule (protein). In this system, we placed a camera, so that we can not only "feel" but also "see" how drug fits into the binding site. Our prototype system has the potential to serve as a new application method as well as being applicable to conventional VR technologies, especially to force feedback technologies.

Computer Simulation↗

PubMed2004

Elastic energy storage in unmineralized and mineralized extracellular matrices (ECMs): a comparison between molecular modeling and experimental measurements.

In order to facilitate locomotion and limb movement many animals store energy elastically in their tendons. In the turkey, much of the force generated by the gastrocnemius muscle is stored as elastic energy during tendon deformation and not within the muscle. As limbs move, the tendons are strained causing the collagen fibers in the extracellular matrices to be strained. During growth, avian tendons mineralize in the portions distal to the muscle and show increased tensile strength, modulus, and energy stored per unit strain as a result. In this study the energy stored in unmineralized and mineralized collagen fibers was measured and compared to the amount of energy stored in molecular models. Elastic energy storage values calculated using the molecular model were slightly higher than those obtained from collagen fibers, but display the same increases in slope as the fiber data. We hypothesize that these increases in slope are due to a change from the stretching of flexible regions of the collagen molecule to the stretching of less flexible regions. The elastic modulus obtained from the unmineralized molecular model correlates well with elastic moduli of unmineralized collagen from other studies. This study demonstrates the potential importance of molecular modeling in the design of new biomaterials.

Animals↗

PubMed1990

Calculation of drug-melanin binding energy using molecular modeling.

Conformational analysis and molecular graphics are used to model a representative melanin structure to estimate a chemical's in vitro affinity for melanin. The modelling data fit to a simple linear equation relative to a logarithmic transformation of the experimentally-derived binding data (r = 0.901). The goodness of fit, as evidenced by the F-statistic, F (1,14) = 60.09 (p = 0.000002), for the regression indicates that this technique gives an accurate representation of the interaction of these chemicals with melanin in vitro.

Animals↗

PubMed1996

Molecular modeling of the flexible cell wall polysaccharide of Streptococcus mitis J22 on the basis of heteronuclear NMR coupling constants.

A method for constructing conformational models of flexible complex polysaccharides on the basis of NMR data and molecular modeling is described and is applied to a polysaccharide which is a lectin-binding receptor important in coaggregation of oral bacteria. The method involves uniform biosynthetic enrichment of the polysaccharide with 13C which allows accurate measurements of heteronuclear coupling constants from a three-dimensional coupled HMQC-NOESY spectrum. The improved resolution of the 3D spectrum also provides a large number of accurate values of NOE cross peak volumes in a decoupled HMQC-NOESY spectrum. While it was not possible to construct a model for the flexible polysaccharide directly from the NOE data, a model was successfully built from the coupling constant data. Possible values of glycosidic dihedral angles were extracted from the 3JCH data to build models which were evaluated by molecular modeling calculations. A simple average over a linear combination of low-energy conformations was selected which matched the experimental 3JCH data within experimental error. Simulation of the NOE data for this same combination of conformers gave excellent agreement with experimental NOESY data. Molecular dynamics trajectories both with and without coupling constant constraints do not represent the experimental NOE and 3JCH data as well as the linear combination model. While the polysaccharide has some flexibility in the antigenic site, the lectin-binding site, which contains a furanoside with (1-->6)-linkages, provides a more flexible hinge in the polysaccharide.

Carbohydrate Conformation↗

PubMed1999

Radioprotection of DNA by spermine: a molecular modelling approach.

PURPOSE: To observe and explain the sequence-dependence of DNA radioprotection by spermine. MATERIALS AND METHODS: Sequencing gel electrophoresis was used to analyse the probability of frank strand break (FSB) induction at each nucleotide site. Molecular modelling of complexes of DNA with spermine molecules and of a curved electrically null DNA has been performed. RESULTS: The effect of spermine on radiation-induced strand breakage varied significantly along the studied fragment. At low spermine concentration, some sequences were protected while others were unprotected. Molecular modelling calculations show that the most electro-negative sites are located in the minor or in the major groove of DNA. The positively charged spermine (Z=+4) should preferentially bind to such sites. When bound in the minor groove, spermine triggers a reduction of the accessibility of radiolytic attack sites to OH* radicals. This is due to induced structural modifications and to the masking of attack sites. In the case of major groove binding, no reduction of accessibility occurs. This type of binding can explain the lack of protection of sequences with electro-negative sites in the major groove. At high spermine concentration, the fragment is strongly protected. A nucleosome-like pattern of breakage with periodically distributed regions of protection was observed. Molecular modelling calculations show that the accessibility of the attack sites in a curved electrically null DNA is also periodically reduced. CONCLUSIONS: Molecular modelling of DNA-spermine complexes that takes into account the electrostatic properties of DNA, allows an explanation of the experimentally observed effects of spermine on DNA radiosensitivity.

Base Sequence↗