Modeling the interaction of a neutral polymer with small ions in solution. A theoretical study of ion binding to a neutral polymer

The interaction between NaCl and 1,2-dimethoxyethylene is used to model ion binding to a neutral polymer. The relative binding energies involving different ion-polymer structures were calculated using minimal basis STO-3G and split valence 3-21Gab-initio and CNDO/2 semi-empirical wavefunctions. The results obtained are consistent with an adsorption model in which the cation is primarily adsorbed on the oxygen sites. The counter ion is then bound by the charged polymer in a form consistent with an ion pair structure. These results are consistent with recent experimental studies on polyoxyethylene (POE). Additional calculations were performed to include specific interactions with the liquid environment. Electrostatic solvation effects, introduced through the self-consistent reaction field (SCRF) model, appear to be significant in the stabilization of a solvent-separated ion-pair structure. However, the global stabilization produced by both specific and electrostatic solvations predicts the preferential stabilization of an externally hydrated intimate ion pair.Dedicated to the memory of the late Professor Luis Sepulveda (1988).CMCA Contribution No 3.     

48 NMR study of the interaction between G-quadruplexes and small molecules

Guanine-rich oligonucleotides are able to adopt secondary DNA structures, known as G-quadruplexes. Such G-rich sequences are found in human telomeres, promoter regions of oncogenes, 5′ untranslated regions (UTRs) of mRNAs and human intronic sequences. Studies have shown that small molecules can induce anti-cancer effect through stabilizing or promoting G-quadruplex formation. In order to design and develop a potent drug, structural details on the interaction between small molecules and G-quadruplexes are invaluable. In this study, we seek to understand the structural determinants involved in the interaction between G-quadruplexes and small molecules. NMR spectroscopy is employed to resolve the structures of two intramolecular G-quadruplexes bound to small molecules. These resolved complexes allow us to structurally design new potent drugs for their application in anti-cancer therapy.     

Cooperative effects in the transport of small molecules through an amorphous polymer matrix

The transport of small molecules (penetrants) through polymer materials proceeds by a hopping mechanism: A peneprant typically dwells in a cavity of the polymer for a while and then performs a quick jump into an adjacent cavity. In this article we investigate a jump event in detail. Molecular graphics is used to identify if and how the motion of the penetrant is aided by the fluctuations of the polymer matrix. We employ both traditional molecular graphics techniques to show atomic motion and surface rendering methods to display the redistribution of penetrant-accessible volume in the polymer.     

The interaction between small molecules and nucleic acids studied by circular dichroism

The circular dichroism (CD) spectra of complexes between aromatic hydrocarbons and quinolines with DNA and complexes between proflavine and nucleic acids have been measured.     

Theory of the toroidal compact form of DNA in a polymer solution

A diagram of the states of single long rigid DNA macromolecule in solution of short flexible polymer was plotted. It has been shown that the compacting effect of the polymer solvent on DNA can be interpreted as hydrostatic pressure of coils gas on impermeable "walls" of the DNA globule. Conditions were found for the existence of compact (globular) states in the form of a sphere (stable for a very long DNA) and tore (for a relatively short one). Possibility of intramolecular liquidcrystalline orderliness of DNA segments in a globule was analyzed. Regions of realization of both regimes were studied: when compression with an added polymer was equalized by the forces of steric repulsion of DNA segments and when it was balanced by the elasticity of the DNA chain bendings.     

Prediction of interaction between enzymes and small molecules in metabolic pathways through integrating multiple classifiers

Information about interactions between enzymes and small molecules is important for understanding various metabolic bioprocesses. In this article we applied a majority voting system to predict the interactions between enzymes and small molecules in the metabolic pathways, by combining several classifiers including AdaBoost, Bagging and KNN together. The advantage of such a strategy is based on the principle that a predictor based majority voting systems usually provide more reliable results than any single classifier. The prediction accuracies thus obtained on a training dataset and an independent testing dataset were 82.8% and 84.8%, respectively. The prediction accuracy for the networking couples in the independent testing dataset was 75.5%, which is about 4% higher than that reported in a previous study. The web-server for the prediction method presented in this paper is available at http://chemdata.shu.edu.cn/small-enz.     

A method for the determination of diffusion coefficients for small molecules in aqueous solution

A method is described for determining the diffusion coefficients of small solutes in limited volumes (approximately equal to 4-9 ml) of fluid. Diffusion is measured in a three-chamber diffusion cell across a central unstirred compartment. Compartments are separated by nitrocellulose membranes. The instantaneous concentration gradient and the instantaneous flux of solute into the dilute end compartment are derived from changes in the concentration of solute in the two stirred end compartments through time. The diffusion coefficient is calculated from the slope of the least-squares regression line relating the magnitude of the instantaneous solute flux to that of the instantaneous concentration gradient. The apparatus is calibrated with a solute of known diffusivity (KCl). Diffusion coefficients thus determined in water at 25 degrees C for CaCl2 (7.54 X 10(-6) cm2.s-1), Na2-ATP (7.01 X 10(-6) cm2.s-1), 2-deoxyglucose (5.31 X 10(-6) cm2.s-1), and D-Na-lactate (5.62 X 10(-6) cm2.s-1) differed by an average of 3.7% from literature values. The method described results in accurate estimates of diffusion coefficients by a simple and relatively rapid procedure.     

Label-enhanced surface plasmon resonance applied to label-free interaction analysis of small molecules and fragments

Surface plasmon resonance (SPR) is a well-established method for studying interactions between small molecules and biomolecules. In particular, SPR is being increasingly applied within fragment-based drug discovery; however, within this application area, the limited sensitivity of SPR may constitute a problem. This problem can be circumvented by the use of label-enhanced SPR that shows a 100-fold higher sensitivity as compared with conventional SPR. Truly label-free interaction data for small molecules can be obtained by applying label-enhanced SPR in a surface competition assay format. The enhanced sensitivity is accompanied by an increased specificity and inertness toward disturbances (e.g., bulk refractive index disturbances). Label-enhanced SPR can be used for fragment screening in a competitive assay format; the competitive format has the added advantage of confirming the specificity of the molecular interaction. In addition, label-enhanced SPR extends the accessible kinetic regime of SPR to the analysis of very fast fragment binding kinetics. In this article, we demonstrate the working principles and benchmark the performance of label-enhanced SPR in a model system—the interaction between carbonic anhydrase II and a number of small-molecule sulfonamide-based inhibitors.     

Thermodynamics of ligand binding on dilute polymer molecules in solution: Complementary monomers and oligomers on polynucleotides

Previous work on the thermodynamics of small systems is applied to the binding of ligands on dilute polymer molecules in solution, and especially to the binding of complementary monomers and oligomers on polynucleotides. Topics emphasized are: binding isotherms, optical melting curves, calorimetric melting and mixing studies, role of the activity of the ligand, quasi phase transitions, the polymer phase diagram, and interrelations between these subjects. The one-dimensional Ising model (linear and circular) is used to illustrate some of the thermodynamics. An Appendix shows how the ligand activity in salt solution may be found from vapor pressure osmometry measurements.     

Use of organic solvents and small molecules for locating binding sites on proteins in solution*

Application of a modified ePHOGSY and other novel NMR experiments to an H2O-DMSO solution of the protein FKBP12 identified the presence of one molecule of DMSO bound in the substrate binding site. It occupies the same spatial region occupied by the pipecolidine moiety of the immunosuppressive drugs FK506 and Rapamycin complexed to the protein. The binding constant KD for this DMSO molecule was only 275 mM. A substructure search of small molecules similar to DMSO resulted in the identification of molecules with improved binding affinity. This work represents a clear example of the powerful interplay of molecular modelling and NMR.     

A novel mechanism for the modulation of the Ras-effector interaction by small molecules

When proteins require different conformations for their biological function, all these functional states have to coexist simultaneously in solution. However, the corresponding Gibbs free energy differences are usually rather high and thus the conformation with lowest energy predominates in solution whereas the populations of the states with higher energy (excited states) are very small. A stabilization of these excited states can be used as a novel principle to influence the activity of proteins by small molecules. For a proof of this principle, we selected the Ras protein that was shown by (31)P NMR spectroscopy to exist in solution in at least two different conformational states in its GTP form. One of these states shows a drastically reduced affinity to effectors. With Zn(2+)-cyclen we found a small molecule which selectively stabilizes the weak-binding state. It may serve as lead compound for the development of a new type of Ras-inhibitors.     

Cellular proteins which can specifically associate with simian virus 40 small t antigen.

When crude, radiolabeled extracts of various cells were applied to homogeneous simian virus 40 small t antigen-Sepharose adsorbents, three cell proteins (57, 32, and 20 kilodaltons [kDa]) bound specifically. Each also bound to an insoluble, truncated t derivative composed of the COOH-terminal 123 residues of the protein. The binding of these proteins was greatly inhibited after reduction and alkylation of the t ligand. Therefore, some element of native conformation, but not all of the primary structure of t, is necessary for this binding property, which may constitute a discrete, in vitro biochemical function of this protein. Results of cell fractionation experiments suggested that the 57- and 32-kDa proteins are nonnuclear cell constituents, whereas the 20-kDa protein was closely associated with a detergent-washed nuclear fraction. Specific immunoblotting and comparative partial proteolytic digestion analyses indicated that the 57-kDa protein is tubulin, a major component of the cytoskeleton. In this regard, t and tubulin were observed to coimmunoprecipitate from crude cell extracts after incubation with monospecific anti-t antibody. Therefore, it is possible that t and tubulin interact in vivo.     

The synthetic genetic interaction network reveals small molecules that target specific pathways in Sacchromyces cerevisiae

High-throughput elucidation of synthetic genetic interactions (SGIs) has contributed to a systems-level understanding of genetic robustness and fault-tolerance encoded in the genome. Pathway targets of various compounds have been predicted by comparing chemical-genetic synthetic interactions to a network of SGIs. We demonstrate that the SGI network can also be used in a powerful reverse pathway-to-drug approach for identifying compounds that target specific pathways of interest. Using the SGI network, the method identifies an indicator gene that may serve as a good candidate for screening a library of compounds. The indicator gene is selected so that compounds found to produce sensitivity in mutants deleted for the indicator gene are likely to abrogate the target pathway. We tested the utility of the SGI network for pathway-to-drug discovery using the DNA damage checkpoint as the target pathway. An analysis of the compendium of synthetic lethal interactions in yeast showed that superoxide dismutase 1 (SOD1) has significant SGI connectivity with a large subset of DNA damage checkpoint and repair (DDCR) genes in Saccharomyces cerevisiae, and minimal SGIs with non-DDCR genes. We screened a sod1Δ strain against three National Cancer Institute (NCI) compound libraries using a soft agar high-throughput halo assay. Fifteen compounds out of ～3100 screened showed selective toxicity toward sod1Δ relative to the isogenic wild type (wt) strain. One of these, 1A08, caused a transient increase in growth in the presence of sublethal doses of DNA damaging agents, suggesting that 1A08 inhibits DDCR signaling in yeast. Genome-wide screening of 1A08 against the library of viable homozygous deletion mutants further supported DDCR as the relevant targeted pathway of 1A08. When assayed in human HCT-116 colorectal cancer cells, 1A08 caused DNA-damage resistant DNA synthesis and blocked the DNA-damage checkpoint selectively in S-phase.     

Stabilization of the bio-membrane by small molecules: interaction of trehalose with the phospholipid bilayer

Anhydrobiotic organisms undergo periods of acute dehydration during their life cycle. It is of interest to understand how the biomembrane remains intact through such stress. A disaccharide, trehalose, which is metabolised during anhydrobiosis is found to prevent disruption of model membrane systems. Molecular modelling techniques are used to investigate the possible mode of interaction of trehalose with a model monolayer. The objective is to maximise hydrogen bonding between the two systems. A phospholipid matrix consisting of 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC) is chosen to represent the monolayer. The crystal structure of DMPC reveals that there are two distinct conformers designated as A and B. An expansion of the monolayer, coplanar with its surface, results in the trehalose molecule being accommodated in a pocket formed by four B conformers. One glucose ring of the sugar rests on the hydrophobic patch provided by the choline methyls of an A conformer. Five hydrogen bonds are formed involving the phosphate oxygens of three of the surrounding B conformers. The model will be discussed with reference to relevant experimental data on the interaction.     

Nucleic acid and prion protein interaction produces spherical amyloids which can function in vivo as coats of spongiform encephalopathy agent

The infectious agent of transmissible spongiform encephalopathies (TSE) has been considered to be PrP(SC), a structural isoform of cellular prion protein PrP(C). PrP(SC) can exist as oligomers and/or as amyloid polymers. Nucleic acids induce structural conversion of recombinant prion protein PrP and PrP(C) to PrP(SC) form in solution and in vitro. Here, we report that nucleic acids, by interacting with PrP in solution, produce amyloid fibril and fibres of different morphologies, similar to those identified in the diseased brains. In addition, the same interaction produces polymer lattices and spherical amyloids of different dimensions (15-150 nm in diameters). The polymer lattices show apparent morphological similarity to the two-dimensional amyloid crystals obtained from linear amyloids isolated in vivo. The spherical amyloids structurally resemble "spherical particles" observed in natural spongiform encephalopathy (SE) and in scrapie-infected brains (TSE). We suggest that spherical amyloids, PrP(SC)-amylospheroids, are probable constituents of the coat of the spherical particles found in vivo and the latter can act as protective coats of the SE and TSE agents in vivo.