Molecular Modeling Software Research Articles

Effective removal of rhodamine B from contaminated water using non-covalent imprinted microspheres designed by computational approach

Molecular dynamics simulations and computational screening were used to identify functional monomers capable of interacting with rhodamine B (RhB). A library of 24 kinds of common functional monomers for preparing molecular imprinted polymer (MIP) was built and their interactions with RhB in acetonitrile were calculated using the molecular dynamics software (Gromacs 3.3). It was anticipated that the monomers giving the highest binding energy are suitable for preparing the affinity polymers. According to the theoretical calculation results, the MIP microspheres with RhB as template was prepared by reverse microemulsion polymerization method using acrylamide (AAm) as functional monomer and divinylbenzene as cross-linker in acetonitrile. Microspheres have been characterized by scanning electron microscopy (SEM). The proper adsorption and selective recognition ability of the MIP were studied by an equilibrium-adsorption method. The MIP showed outstanding affinity towards RhB in aqueous solution and the optimum pH value for binding has been found around neutral range. The molecular recognition of RhB was analyzed in detail by using molecular modeling software (Gaussian03). In addition, the MIP reusability without obviously deterioration in performance was demonstrated at least five repeated cycles.

QSAR study of substituted 2-pyridinyl guanidines as selective urokinase-type plasminogen activator (uPA) inhibitors

A quantitative structure–activity relationship analysis was conducted on two different series of pyridinylguanidines acting as inhibitors of urokinase-type plasminogen activator using QuaSAR descriptors of molecular modeling software MOE. Multiple linear regression analysis following a stepwise scheme was employed to generate QSARs that relate molecular descriptors to uPA inhibitory activity data of the title compounds. Among the several QSARs generated by MLR analysis, the best models were selected on the basis of their statistical significance and predictive potential. The interpretation of the selected QSAR models suggest that uPA inhibitory activity of compounds in series 1 is influenced by their molecular shape, molecular flexibility and halogen atoms in the molecule whereas the uPA inhibitory potency of compounds in series 2 is dependent on molecular lipophilicity, number of double bonds and spatial orientation of bulky substituents in the molecule.

Structural basis of aspartylglucosaminuria

To elucidate the basis of aspartylglucosaminuria (AGU) from the viewpoint of enzyme structure, we constructed structural models of mutant aspartylglucosaminidase (AGA) proteins using molecular modeling software, TINKER. We classified the amino acid substitutions responsible for AGU and divided them into three groups based on the biochemical phenotype. Then, we examined the structural changes in the AGA protein for each group by calculating the solvent-accessible surface area (ASA), the number of atoms affected, and the root-mean-square deviation (RMSD). Our results revealed that the structural changes in group 1, which exhibits folding/transport defects and a complete deficiency of AGA activity, were generally large and located in the core region of the enzyme molecule. In group 2, exhibiting the mature AGA protein but no AGA activity, the functionally important region of the enzyme molecule was seriously affected. In group 3 exhibiting residual AGA activity, the structural changes in AGA were small and localized near the surface of the enzyme molecule. Coloring of affected atoms based on the distances between the wild-type and mutant ones revealed the characteristic structural changes in the AGA protein geographically and semi-quantitatively. Structural investigation provides us with a deeper insight into the basis of AGU.

The Laser Synthesis of Linear Polyynes: The Particle in a Box Revisited

In this experiment, linear polyynes are synthesized and then the predictions of a one-dimensional, particle in a box are used to calculate the quantum mechanical box length for the polyynes. A solution of graphite in ethanol is irradiated with a Nd:YAG laser (532 nm) and the resulting solution is filtered and analyzed. Data from gas chromatography–mass spectrometry shows that linear polyynes, C6H2 and C8H2, are produced. The absorbance spectrum of the reaction mixture is obtained and the wavelengths are used to calculate the length of the conjugated pi system for each polyyne. The calculated box lengths for C6H2 and C8H2 are 9.23 Å and 10.82 Å, respectively. Although these values differ (47% and 22% larger) from the molecular lengths determined from the summation of bond lengths and from molecular modeling software, the experiment provides students with an opportunity to enrich their understanding of the predictions and limitations of the one-dimensional, particle in a box. The experiment is suitable for inclusion in a standard physical chemistry course or other upper-level laboratory where the principles of quantum mechanics are studied.

His-311 and Arg-559 Are Key Residues Involved in Fatty Acid Oxygenation in Pathogen-inducible Oxygenase

Pathogen-inducible oxygenase (PIOX) oxygenates fatty acids into 2R-hydroperoxides. PIOX belongs to the fatty acid alpha-dioxygenase family, which exhibits homology to cyclooxygenase enzymes (COX-1 and COX-2). Although these enzymes share common catalytic features, including the use of a tyrosine radical during catalysis, little is known about other residues involved in the dioxygenase reaction of PIOX. We generated a model of linoleic acid (LA) bound to PIOX based on computational sequence alignment and secondary structure predictions with COX-1 and experimental observations that governed the placement of carbon-2 of LA below the catalytic Tyr-379. Examination of the model identified His-311, Arg-558, and Arg-559 as potential molecular determinants of the dioxygenase reaction. Substitutions at His-311 and Arg-559 resulted in mutant constructs that retained virtually no oxygenase activity, whereas substitutions of Arg-558 caused only moderate decreases in activity. Arg-559 mutant constructs exhibited increases of greater than 140-fold in Km, whereas no substantial change in Km was observed for His-311 or Arg-558 mutant constructs. Thermal shift assays used to measure ligand binding affinity show that the binding of LA is significantly reduced in a Y379F/R559A mutant construct compared with that observed for Y379F/R558A construct. Although Oryza sativa PIOX exhibited oxygenase activity against a variety of 14-20-carbon fatty acids, the enzyme did not oxygenate substrates containing modifications at the carboxylate, carbon-1, or carbon-2. Taken together, these data suggest that Arg-559 is required for high affinity binding of substrates to PIOX, whereas His-311 is involved in optimally aligning carbon-2 below Tyr-379 for catalysis.

Molecular modelling simulations to predict density and solubility parameters of ionic liquids

Molecular modelling simulations are one of the most convenient tools to predict solvent properties of ionic liquids, which are otherwise difficult to predict or measure by experimental means. Ionic liquids have emerged as effective and desirable alternative solvents during the last decade. Their use is greatly favoured because of their ‘green’ characteristics: low vapour pressure, non-flammability and chemical stability. An enormous variety of ionic liquids are potentially available and thus the design of task-specific ionic liquids is gaining importance. Traditional solvents are often evaluated based on their multi-component solubility parameters to assess their compatibility with different solutes. The analogous parameter values for ionic liquids are also useful, though their availability is often limited. Consequently, solvent design and pre-screening of candidates by molecular modelling tools are attractive alternatives. In this work, the density and two-component solubility parameter of a variety of ionic liquids were investigated using atomistic level molecular modelling and the commercially available Materials Studio® software package. The ionic liquids chosen consisted of ethyl, butyl and hexyl imidazolium cations in conjunction with four anions (Cl− , [(CN)2N] − , [CF3CO2]− and [Tf2N]− ). The goal was to develop appropriate computational protocols and carry out calculations, which are able to predict densities and two-component solubility parameters for these ionic liquids, as well as to evaluate the usefulness and accuracy of the currently available commercial molecular modelling software for these applications. It was found that the density of ionic liquids comprised of all possible combinations of these cations and anions could be calculated with satisfactory accuracy with the exception of systems containing the Cl− anion. A Hess cycle-based protocol was developed to correct cohesive energy densities and solubility parameters as calculated in Materials Studio to take into account ion pair interactions to successfully reproduce the experimental results. It was found that both the cation and the anion of the ionic liquid had a strong impact on the components of the solubility parameter.

Small Molecule Antagonizes Autoinhibition and Activates AMP-activated Protein Kinase in Cells

AMP-activated protein kinase (AMPK) serves as an energy sensor and is considered a promising drug target for treatment of type II diabetes and obesity. A previous report has shown that mammalian AMPK alpha1 catalytic subunit including autoinhibitory domain was inactive. To test the hypothesis that small molecules can activate AMPK through antagonizing the autoinhibition in alpha subunits, we screened a chemical library with inactive human alpha1(394) (alpha1, residues 1-394) and found a novel small-molecule activator, PT1, which dose-dependently activated AMPK alpha1(394), alpha1(335), alpha2(398), and even heterotrimer alpha1beta1gamma1. Based on PT1-docked AMPK alpha1 subunit structure model and different mutations, we found PT1 might interact with Glu-96 and Lys-156 residues near the autoinhibitory domain and directly relieve autoinhibition. Further studies using L6 myotubes showed that the phosphorylation of AMPK and its downstream substrate, acetyl-CoA carboxylase, were dose-dependently and time-dependently increased by PT1 with-out an increase in cellular AMP:ATP ratio. Moreover, in HeLa cells deficient in LKB1, PT1 enhanced AMPK phosphorylation, which can be inhibited by the calcium/calmodulin-dependent protein kinase kinases inhibitor STO-609 and AMPK inhibitor compound C. PT1 also lowered hepatic lipid content in a dose-dependent manner through AMPK activation in HepG2 cells, and this effect was diminished by compound C. Taken together, these data indicate that this small-molecule activator may directly activate AMPK via antagonizing the autoinhibition in vitro and in cells. This compound highlights the effort to discover novel AMPK activators and can be a useful tool for elucidating the mechanism responsible for conformational change and autoinhibitory regulation of AMPK.

Crystal Structures of F420-dependent Glucose-6-phosphate Dehydrogenase FGD1 Involved in the Activation of the Anti-tuberculosis Drug Candidate PA-824 Reveal the Basis of Coenzyme and Substrate Binding

The modified flavin coenzyme F(420) is found in a restricted number of microorganisms. It is widely distributed in mycobacteria, however, where it is important in energy metabolism, and in Mycobacterium tuberculosis (Mtb) is implicated in redox processes related to non-replicating persistence. In Mtb, the F(420)-dependent glucose-6-phosphate dehydrogenase FGD1 provides reduced F(420) for the in vivo activation of the nitroimidazopyran prodrug PA-824, currently being developed for anti-tuberculosis therapy against both replicating and persistent bacteria. The structure of M. tuberculosis FGD1 has been determined by x-ray crystallography both in its apo state and in complex with F(420) and citrate at resolutions of 1.90 and 1.95 A(,) respectively. The structure reveals a highly specific F(420) binding mode, which is shared with several other F(420)-dependent enzymes. Citrate occupies the substrate binding pocket adjacent to F(420) and is shown to be a competitive inhibitor (IC(50) 43 microm). Modeling of the binding of the glucose 6-phosphate (G6P) substrate identifies a positively charged phosphate binding pocket and shows that G6P, like citrate, packs against the isoalloxazine moiety of F(420) and helps promote a butterfly bend conformation that facilitates F(420) reduction and catalysis.

Henry’s Law Constants of Some Aromatic Aldehydes and Ketones Measured by an Internal Standard Method

Dimensionless Henry’s law constants kH (air−water partition coefficients) for a series of aromatic aldehydes and ketones were measured by using an internal standard method. It was demonstrated that the technique works well for both liquid and solid species. The kH values of these compounds, which usually are difficult to be determined experimentally, are in the order of 10−6 to 10−3. The measurements were carried out under atmospheric pressure and at various temperatures [(273 to 298) K]. The temperature dependence of kH was also studied, and the van’t Hoff parameters were calculated. All the data are reported with the corresponding standard deviations and uncertainties at the 95 % confidence level. The theoretical dipole moments in the gas phase were computed by utilizing Cerius(2) molecular modeling software to justify the discrepancies among the kH values of the isomers. These calculations exhibit linear relationships between the dipole moment and kH within each isomer series.

Screening of rationally designed oligopeptides for Listeria monocytogenes detection by means of a high density colorimetric microarray

The aim of this work was to optimize, by means of molecular modeling software, biomimetic-based traps for pathogen detection suitable for analytical applications like screening or pre-analytical methods. The pathogen prototype system chosen was Listeria monocytogenes because of the large number of X ray and NMR structures available. 298 oligopeptides were computationally designed mimicking the binding pocket of the mammalian protein E-cadherin, the target of Listeria monocytogenes adhesion, internalin A. The contribution of individual peptides to bind was investigated using FRED, a protein-ligand docking program. Ten peptides were selected for experimental analysis taking as selection parameters the length, the position in the docking pocket and the score of simulated binding energy. A series of competition assays were carried out using high density colorimetric microarray using various bacteria species (Listeria monocytogenes, Listeria monocytogenes genetically modified without internalin A, Listeria innocua and Lactococcus lactis) in solution with computationally selected peptides. The data demonstrated that peptides could be able to distinguish Listeria monocytogenes with an EC50 up to 107cfu × mL−1. In particular the peptide with the best calculated binding score gave the highest statistically unambiguous response toward Listeria monocytogenes compared to other bacteria, demonstrating that rationally simulated approach can be useful as preliminary screening in the choice of biomimetic ligands.

Differentiable, multi-dimensional, knowledge-based energy terms for torsion angle probabilities and propensities

Rotatable torsion angles are the major degrees of freedom in proteins. Adjacent angles are highly correlated and energy terms that rely on these correlations are intensively used in molecular modeling. However, the utility of torsion based terms is not yet fully exploited. Many of these terms do not capture the full scale of the correlations. Other terms, which rely on lookup tables, cannot be used in the context of force-driven algorithms because they are not fully differentiable. This study aims to extend the usability of torsion terms by presenting a set of high-dimensional and fully-differentiable energy terms that are derived from high-resolution structures. The set includes terms that describe backbone conformational probabilities and propensities, side-chain rotamer probabilities, and an elaborate term that couples all the torsion angles within the same residue. The terms are constructed by cubic spline interpolation with periodic boundary conditions that enable full differentiability and high computational efficiency. We show that the spline implementation does not compromise the accuracy of the original database statistics. We further show that the side-chain relevant terms are compatible with established rotamer probabilities. Despite their very local characteristics, the new terms are often able to identify native and native-like structures within decoy sets. Finally, force-based minimization of NMR structures with the new terms improves their torsion angle statistics with minor structural distortion (0.5 A RMSD on average). The new terms are freely available in the MESHI molecular modeling package. The spline coefficients are also available as a documented MATLAB file.

Adsorption of carbaryl using molecularly imprinted microspheres prepared by precipitation polymerization

AbstractTo obtain the desired specific adsorbents for carbaryl to enrichment, separation, and analysis of trace pesticide residues in environmental water, molecularly imprinted polymer (MIP) microspheres were prepared by precipitation polymerization using carbaryl, methacrylic acid (MAA), ethylene glycol dimethacrylate (EGDMA), azobisisobutyronitrile (AIBN), and acetonitrile as template, functional monomer, cross‐linker, initiator, and porogen, respectively. Molecular modeling software was used to compute rational interaction between the template molecule and function monomer. The adsorption properties of carbaryl in acetonitrile for imprinted microspheres were evaluated by equilibrium rebinding experiments. Scatchard plot analysis revealed that there was one class of binding sites populated in the imprinted polymer microspheres with dissociation constants of 3.3 × 10−2 mol/l and an apparent maximum number of 1.95 µmol/g. The specificity of the imprinted microspheres was investigated by binding analysis using carbaryl and structurally related carbamate pesticides. The results indicated that the obtained imprinted microspheres showed a good selectivity for carbaryl. Copyright © 2007 John Wiley & Sons, Ltd.

QSAR analysis of some phthalimide analogues based inhibitors of HIV-1 integrase

A quantitative structure activity relationship (QSAR) study has been performed on phthalimide analogues based inhibitors of HIV-1 integrase to understand the structural features influencing the affinity of these inhibitors towards the enzyme. The compounds in the selected series were characterized by molecular descriptors calculated using the QSAR software Dragon and molecular modeling software ChemOffice 2001. QSAR models were derived by stepwise multiple regression analysis employing the method of least squares. The best QSAR model describing the HIV-1 integrase inhibitory activity of phthalimide analogues was selected on the basis of statistical significance and predictive ability as gauged by cross-validation procedure and external test-set method. The generated QSAR models revealed that increased HIV-1 inhibitory potency of tricyclic phthalimide derivatives could be achieved by increasing the overall lipophilicity of the molecules and by incorporating halogen substituents in the benzylic aromatic ring attached to the phthalimido nitrogen atom. Additionally, the model also suggests that the increase in the molecular flexibility by incorporation of rotatable bonds is conducive for HIV-1 inhibitory activity of phthalimide derivatives whereas increase in molecular branching appears to be detrimental to the activity.

Conformational Sampling of Bioactive Molecules: A Comparative Study

The necessity to generate conformations that sample the entire conformational space accessible to a given molecule is ubiquitous in the field of computer-aided drug design. Protein-ligand docking, 3D database searching, and 3D QSAR are three commonly used techniques that depend critically upon the quality and diversity of the generated conformers. Although there are a wide range of conformational search algorithms available, the extent to which they sample conformational space is often unclear. To address this question, we conducted a robust comparison of the search algorithms implemented in several widely used molecular modeling packages, including Catalyst, Macromodel, Omega, MOE, and Rubicon as well as our own method, stochastic proximity embedding (SPE). We found that SPE used in conjunction with conformational boosting, a heuristic for biasing conformational search toward more extended or compact geometries, along with Catalyst, are significantly more effective in sampling the full range of conformational space compared to the other methods, which show distinct preferences for either more extended or more compact geometries.

Characterization of High Explosives and Other Energetic Compounds by Computational Chemistry and Molecular Modeling

Four experiments suitable for use in the undergraduate instructional laboratory are described. These experiments demonstrate the use of computational chemistry and molecular-modeling procedures to calculate selected physical and chemical properties of several high explosives and other energetic compounds. The first experiment focuses on familiarizing the student with computational chemistry and molecular modeling software and is suitable for an introductory chemistry course. A semiempirical experiment then compares the ability of three procedures, the Austin Model 1 (AM1), Modified Neglect of Differential Overlap (MNDO), and the Parametric Model 3 (PM3), to predict heats of formation. In a third experiment the use of older group additivity procedures to predict heats of formation is also assessed. Experiments two and three are suitable for an organic chemistry course. Finally, a fourth experiment, suitable for an advanced course, demonstrates how an isodesmic approach coupled with density functional theor...

French Fries, Dialysis Tubing & Computer Models: Teaching Diffusion & Osmosis Through Inquiry & Modeling

an eating large amounts of sugarless candy and gum lead to diarrhea? How does Milk of Magnesia® work? How does penicillin kill bacteria? These are some of the questions that students answer in this series of lessons on diffusion and osmosis. T o begin the unit, students predict the results of a demonstration involving the relationship between soaking French fries in salt water and crispiness. T o understand this relationship, students investigate the permeability of cell membranes by designing their own investigations using dialysis tubing. This investigation is a revised, inquiry version of the traditional lab found in many high school textbooks. To visualize the movement of molecules and the resulting effect on the cellular level, students use the innovative molecular modeling software, Molecular Workbench (available online at http://molo.concord.org at no cost). In the Molecular Workbench activities, students interact with dynamic computer models of diffusion, osmosis, and 3-D representations of molecules; observe the interactions and the net flow of molecules in air, in cells, and across a cell’s semi-permeable membrane; and learn about the properties of the molecules. Students then apply their knowledge of osmosis to the novel situations listed above.

Rational Design of Analyte Channels of the Green Fluorescent Protein for Biosensor Applications

A novel solvent-exposed analyte channel, generated by F165G substitution, on the surface of green fluorescent protein (designated His(6)GFPuv/F165G) was successfully discovered by the aid of molecular modeling software (PyMOL) in conjunction with site-directed mutagenesis. Regarding the high predictive performance of PyMOL, two pore-containing mutants namely His(6)GFPuv/H148G and His(6)GFPuv/H148G/F165G were also revealed. The pore sizes of F165G, H148G, and the double mutant H148G/F165G were in the order of 4, 4.5 and 5.5 A, respectively. These mutants were subjected to further investigation on the effect of small analytes (e.g. metal ions and hydrogen peroxide) as elucidated by fluorescence quenching experiments. Results revealed that the F165G mutant exhibited the highest metal sensitivity at physiological pH. Meanwhile, the other 2 mutants lacking histidine at position 148 had lower sensitivity against Zn(2+) and Cu(2+) than those of the template protein (His(6)GFPuv). Hence, a significant role of this histidine residue in mediating metal transfer toward the GFP chromophore was proposed and evidently demonstrated by testing in acidic condition. Results revealed that at pH 6.5 the order of metal sensitivity was found to be inverted whereby the H148G/F165G became the most sensitive mutant. The dissociation constants (K(d)) to metal ions were in the order of 4.88 x 10(-6) M, 16.67 x 10(-6) M, 25 x 10(-6) M, and 33.33 x 10(-6) M for His(6)GFPuv/F165G, His(6)GFPuv, His(6)GFPuv/H148G/F165G and His(6)GFPuv/H148G, respectively. Sensitivity against hydrogen peroxide was in the order of H148G/F165G > H148G > F165G indicating the crucial role of pore diameters. However, it should be mentioned that H148G substitution caused a markedly decrease in pH- and thermo-stability. Taken together, our findings rendered the novel pore of GFP as formed by F165G substitution to be a high impact channel without adversely affecting the intrinsic fluorescent properties. This opens up a great potential of using F165G mutant in enhancing the sensitivity of GFP in future development of biosensors.

Comparison of properties of tumor necrosis factor-α converting enzyme (TACE) and some matrix metalloproteases (MMPs) in catalytic domains

The crystal structural data of TACE, MMP-1, MMP-2, MMP-3 and MMP-9 were obtained from PDB database, and then their catalytic domains' properties including conformation, molecular surface hydrophobicity and electrostatic potential were analyzed and compared by using Insight II molecular modeling software. It was found that the conformation and molecular surface hydrophobicity of catalytic domains of TACE and MMPs were not obviously different, but the molecular surface electrostatic potential of catalytic domain of TACE and MMPs had obvious differences. The findings are helpful in the Rational Drug Design of TACE selective inhibitor.

PEGylation and Multimerization of the Anti-p185HER-2 Single Chain Fv Fragment 4D5

A major goal in antibody design for cancer therapy is to tailor the pharmacokinetic properties of the molecule according to specific treatment requirements. Key parameters determining the pharmacokinetics of therapeutic antibodies are target specificity, affinity, stability, and size. Using the p185HER-2 (HER-2)-specific scFv 4D5 as model system, we analyzed how changes in molecular weight and valency independently affect antigen binding and tumor localization. By employing multimerization and PEGylation, four different antibody formats were generated and compared with the scFv 4D5. First, dimeric and tetrameric miniantibodies were constructed by fusion of self-associating, disulfide-linked peptides to the scFv 4D5. Second, we attached a 20-kDa PEG moiety to the monovalent scFv and to the divalent miniantibody at the respective C terminus. In all formats, serum stability and full binding reactivity of the scFv 4D5 were retained. Functional affinity, however, did change. An avidity increase was achieved by multimerization, whereas PEGylation resulted in a 5-fold decreased affinity. Nevertheless, the PEGylated monomer showed an 8.5-fold, and the PEGylated dimer even a 14.5-fold higher tumor accumulation than the corresponding scFv, 48 h post-injection, because of a significantly longer serum half-life. In comparison, the non-PEGylated bivalent and tetravalent miniantibodies showed only a moderate increase in tumor localization compared with the scFv, which correlated with the degree of multimerization. However, these non-PEGylated formats resulted in higher tumor-to-blood ratios. Both multimerization and PEGylation represent thus useful strategies to tailor the pharmacokinetic properties of therapeutic antibodies and their combined use can additively improve tumor targeting.

Skin Constituents as Cosmetic Ingredients. Part III: A Molecular Modeling Study of Bio‐Mimetic Monoglycerides Behavior at the Squalene‐Water Interface

The molecular modeling study described here revisits the experimental work that focused on the interfacial properties of different monoglycerides at the squalene/water interface.12 The use of molecular modeling software programs allowed the determination of new parameters and provided a better understanding of the behavior of those amphiphilic molecules at the interface of the two non‐miscible liquids. Each monoglyceride studied has been characterized by an HLVB value; the curvature radius, Rc; the area of the droplets formed, AG; the number of monoglyceride molecules required to form a droplet, N; and the distance separating surfactant molecules at the interface, d. The analysis of those different parameters shows that short hydrocarbon chain monoglycerides, such as those having one or more unsaturations and those having a grafted hydroxyl function in the middle of their chain, are excellent surfactants. These configurations promote the efficient reduction of surface tension existing at the squalene/water interface.