Functional nanoparticle based on β-cyclodextrin

Aminoethylcarbamoyl-β-cyclodextrin (AEC-β-CD)-based nanoparticle is prepared by an interfacial polyaddition reaction. The nanoparticle has high β-CD content and many amino groups on the surface. The β-CD cavity of this particle forms inclusion complexes with aromatic molecules, where the uptake ability significantly depends on physicochemical factors such as hydrophobicity, ionic charge, size, and shape of guest molecules.     

Structural details,pathways, and energetics of unfolding apomyoglobin

Protein folding is often difficult to characterize experimentally because of the transience of intermediate states, and the complexity of the protein-solvent system. Atomistic simulations, which could provide more detailed information, have had to employ highly simplified models or high temperatures, to cope with the long time scales of unfolding; direct simulation of folding is even more problematic. We report a fully atomistic simulation of the acid-induced unfolding of apomyoglobin in which the protonation of acidic side-chains to simulate low pH is sufficient to induce unfolding at room temperature with no added biasing forces or other unusual conditions; and the trajectory is validated by comparison to experimental characterization of intermediate states. Novel insights provided by their analysis include: characterization of a dry swollen globule state forming a barrier to initial unfolding or final folding; observation of cooperativity in secondary and tertiary structure formation and its explanation in terms of dielectric environments; and structural details of the intermediate and the completely unfolded states. These insights involve time scales and levels of structural detail that are presently beyond the range of experiment, but come within reach through the simulation methods described here. An implicit solvation model is used to analyze the energetics of protein folding at various pH and ionic strength values, and a reasonable estimate of folding free energy is obtained. Electrostatic interactions are found to disfavor folding.     

Oxytocin receptor mimetics prepared by molecular imprinting

Summary Oxytocin receptor mimetics were prepared by molecular imprinting using Z-oxytocin as the template. Comparative binding studies with reference polymers showed that the imprinted polymers recognized both Z-oxytocin and unprotected oxytocin selectively. The dissociation constants were 47 μM and 102 μM, respectively, and the density of binding sites was 12 μmol/g. The synthetic oxytocin receptors were easily prepared, possessed high mechanical and chemical stability, and were reused without loss of selectivity and capacity after regeneration by extraction. Abbreviations: B_max, number of binding sites; CLEAR, Cross-Linked Ethoxylate Acrylate Resin; EDMA, ethylene glycol dimethacrylate; FABMS, fast atom bombardment mass spectrometry; Fmoc, 9-fluorenylmethyloxycarbonyl; HPLC, high-performance liquid chromatography; K_D, dissociation constant; MAA, methacrylic acid; MIP, molecularly imprinted polymer; SPPS, solid-phase peptide synthesis; TRIM, trimethylolpropane trimethacrylate; Z, benzyloxycarbonyl. Abbreviations used for amino acids and the designation of peptides follow the rules of the IUPAC-IUB Commission of Biochemical Nomenclature [J. Biol. Chem., 247 (1972) 977–983]. All amino acids were of thel-configuration.     

Oxytocin receptor mimetics prepared by molecular imprinting

Oxytocin receptor mimetics were prepared by molecularimprinting using Z-oxytocin as the template. Comparative binding studies with reference polymersshowed that the imprinted polymers recognized bothZ-oxytocin and unprotected oxytocin selectively. Thedissociation constants were 47 M and 102 M,respectively, and the density of binding sites was12 mol/g. The synthetic oxytocin receptors wereeasily prepared, possessed high mechanical andchemical stability, and were reused without loss ofselectivity and capacity after regeneration byextraction.     

Molecular electrostatic potential as a factor of drug-receptor recognition

When a drug molecule approaches a non-specific acceptor both molecules are in electrostatic fields of equal sign which prevents drug-acceptor complex formation. At the same time, the drug-acceptor system does not achieve the thermodynamic global minimum. Otherwise, when a certain drug interacts with its specific receptor, mutual compensation of their molecular electrostatic potentials takes place. Then separate atoms and groups of the drug molecule can bind to the receptor. We show that the fundamental role of molecular electrostatic potential in the process of drug-receptor recognition consists in fast correction of errors.     

Saturation fluorescence labeling of proteins for proteomic analyses

We present here an optimized and cost-effective approach to saturation fluorescence labeling of protein thiols for proteomic analysis. We investigated a number of conditions and reagent concentrations, including the disulfide reducing agent tris(2-carboxyethyl)phosphine (TCEP), pH, incubation time, linearity of labeling, and saturating dye/protein thiol ratio with protein standards to gauge specific and nonspecific labeling. Efficacy of labeling under these conditions was quantified using specific fluorescence estimation, defined as the ratio of fluorescence pixel intensities and Coomassie-stained pixel intensities of bands after digital imaging. Factors leading to specific versus nonspecific labeling in the presence of thiourea are also discussed. We found that reproducible saturation of available Cys residues of the proteins used as labeling standards (human carbonic anhydrase I, enolase, and α-lactalbumin) is achieved at 50- to 100-fold excess of the uncharged maleimide-functionalized BODIPY dyes over Cys. We confirmed our previous findings, and those of others, that the maleimide dyes are not affected by the presence of 2 M thiourea. Moreover, we established that 2 mM TCEP used as reductant is optimal. We also established that labeling is optimal at pH 7.5 and complete after 30 min. Low nonspecific labeling was gauged by the inclusion of non-Cys-containing proteins (horse myoglobin and bovine carbonic anhydrase) to the labeling mixture. We also showed that the dye exhibits little to no effect on the two-dimensional mobilities of labeled proteins derived from cells.     

糖皮质激素受体的光亲和标记

利用[~3H]去炎松缩酮([~3H]TA)进行了糖皮质激素受体(GCR)的光亲和标记。[~3H]TA和GCR共价交联的证据有:(1)光照后,10％的三氯醋酸不能使[~3H]TA和GCR解离;(2)SDS-聚丙烯酰胺凝胶电泳时,有单一的放射活性峰;(3)用地塞米松保护后,GCR不被标记。采用本方法测定的GCR分子量为94000±3000 dalton,该方法可用于GCR分子量的测定、提纯和配基结合区的分析。     

Discovery of human autophagy initiation kinase ULK1 inhibitors by multi-directional in silico screening strategies

Autophagy is a self-catabolic mechanism employed by cancer cells to acquire nutrients and energy in times of stress conditions, thereby leading to its progression and survival. Thus, autophagy inhibition has emerged as a new paradigm in the area of cancer treatment. Here, we leverage multi-dimensional screening campaigns aim to identify potent inhibitors against an early and an essential autophagic kinase, ULK1 from DrugBank database. In particular, receptor-based hypothesis, pharmacophore hypothesis, e-pharmacophore hypothesis and shape similarity-based screening algorithm were employed. Of note, the results of the different algorithm were then integrated to eliminate the false positive prediction. Moreover, the inhibitory activities and PK/PD parameters of the leads were tested by Glide and Qikprop algorithm. This resulted in a set of four hits namely; DB12686, DB08341, DB07936, and DB07163. Finally, molecular dynamics simulation was performed using the GROMACS package, to validate the binding kinetics of the hit compound. The compound activity in vitro was assessed by PASS algorithm, highlights the anti-cancer activities of the hits. The structural insights reveal existence of functional moieties such as piperidine carboxamide, benzenesulfonamide, benzamide, and isoindolone in the resultant hits which plays a major role in the anti-cancer activity. Overall, we strongly believe that these ULK1 antagonists could be novel and potent drug candidates for future cancer therapeutics.     

Fluorescence and molecular dynamics studies of the acetylcholine receptor γM4 transmembrane peptide in reconstituted systems

A combination of fluorescence spectroscopy and molecular dynamics (MD) is applied to assess the conformational dynamics of a peptide making up the outermost ring of the nicotinic acetylcholine receptor (AChR) transmembrane region and the effect of membrane thickness and cholesterol on the hydrophobic matching of this peptide. The fluorescence studies exploit the intrinsic fluorescence of the only tryptophan residue in a synthetic peptide corresponding to the fourth transmembrane domain of the AChR γ subunit (γM4-Trp⁶) reconstituted in lipid bilayers of varying thickness, and combine this information with quenching studies using depth-sensitive phosphatidylcholine spin-labeled probes and acrylamide, polarization of fluorescence, and generalized polarization of Laurdan. A direct correlation was found between bilayer width and the depth of insertion of Trp⁶. We further extend our recent MD study of the conformational dynamics of the AChR channel to focus on the crosstalk between M4 and the lipid-belt region. The isolated γM4 peptide is shown to possess considerable orientational flexibility while maintaining a linear α-helical structure, and to vary its tilt depending on bilayer width and cholesterol (Chol) content. MD studies also show that γM4 also establishes contacts with the other TM peptides on its inner face, stabilizing a shorter TM length that is still highly sensitive to the lipid environment. In the native membrane the topology of the M4 ring is likely to exhibit a similar behavior, dynamically modifying its tilt to match the hydrophobic thickness of the bilayer.     

Photoaffinity Labeling of the 5-HydroxytryptamineIA Receptor in Rat Hippocampus

1-[2-(4-Azidophenyl)ethyl]-4-(3-trifluoromethylphenyl)piperazine (p-azido-PAPP) inhibits [3H]5-hydroxytryptamine [( 3H]5-HT) binding to 5-HT1A and 5-HT1B sites in rat brain with equilibrium dissociation constants (KD) of 0.9 nM and 230 nM, respectively. [3H]p-Azido-PAPP was synthesized and its reversible and irreversible binding properties to the hippocampal 5-HT1A site characterized. [3H]p-Azido-PAPP labeled a single class of sites in rat hippocampal membranes with a KD of 1 nM and a maximal binding density of 370 fmol/mg protein. The pharmacological profile of [3H]p-azido-PAPP binding was consistent with the radioligand's selective interaction with the 5-HT1A receptor. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of membranes preincubated with [3H]p-azido-PAPP and irradiated showed a major band of incorporation of radioactivity at approximately 55,000 daltons. This incorporation could be blocked when membranes were incubated with 1 microM of several agents that have high affinity for 5-HT1A sites [5-HT, 8-hydroxy-2-(di-n-propylamino)tetraline, TVX Q 7821, spiperone, buspirone, d-lysergic acid diethylamide, metergoline]. The results indicate that on photolysis [3H]p-azido-PAPP irreversibly labels a polypeptide that is, or is a subunit of, the 5-HT1A receptor in rat hippocampus.