Molecular view of water dynamics near model peptides

Incoherent quasi-elastic neutron scattering (QENS) has been used to measure the dynamics of water molecules in solutions of a model protein backbone, N-acetyl-glycine-methylamide (NAGMA), as a function of concentration, for comparison with results for water dynamics in aqueous solutions of the N-acetyl-leucine-methylamide (NALMA) hydrophobic peptide at comparable concentrations. From the analysis of the elastic incoherent structure factor, we find significant fractions of elastic intensity at high and low concentrations for both solutes, which corresponds to a greater population of protons with rotational time scales outside the experimental resolution (>13 ps). The higher-concentration solutions show a component of the elastic fraction that we propose is due to water motions that are strongly coupled to the solute motions, while for low-concentration solutions an additional component is activated due to dynamic coupling between inner and outer hydration layers. An important difference between the solute types at the highest concentration studied is found from stretched exponential fits to their experimental intermediate scattering functions, showing more pronounced anomalous diffusion signatures for NALMA, including a smaller stretched exponent beta and a longer structural relaxation time tau than those found for NAGMA. The more normal water diffusion exhibited near the hydrophilic NAGMA provides experimental support for an explanation of the origin of the anomalous diffusion behavior of NALMA as arising from frustrated interactions between water molecules when a chemical interface is formed upon addition of a hydrophobic side chain, inducing spatial heterogeneity in the hydration dynamics in the two types of regions of the NALMA peptide. We place our QENS measurements on model biological solutes in the context of other spectroscopic techniques and provide both confirming as well as complementary dynamic information that attempts to give a unifying molecular view of hydration dynamics signatures near peptides and proteins.     

Novel feature extraction technique for fuzzy relational clustering of a flexible dopamine reuptake inhibitor

This paper describes a novel clustering methodology for classifying over 700 conformations of a flexible analogue of GBR 12909, a dopamine reuptake inhibitor that has completed phase I clinical trials as a treatment for cocaine abuse. The major aspect of the clustering methodology includes an efficient data-conditioning scheme where a systematic feature extraction procedure based on the structural properties of the molecule was used to reduce the associated feature space. This allowed region-specific clustering that focused on individual pharmacophore elements of the molecule. For clustering of the reduced feature set, the fuzzy clustering partitional method was utilized. Due to the relational nature of the feature data, fuzzy relational clustering was employed, and it successfully detected natural groups defined by rotational minima around N(sp(3))-C(sp(3)), O(sp(3))-C(sp(3)), and C(sp(3))-C(sp(2)) bonds. The proposed clustering methodology also employed several cluster validity measures, which corroborated the partitions produced by the clustering technique and agreed with the results of hierarchical clustering using the XCluster program. Representative structures which exhibited a reasonable spread of energies and showed good spatial coverage of the conformational space were identified for use as putative bioactive conformations in a future Comparative Molecular Field Analysis of GBR 12909 analogues. The clustering methodology developed here is capable of handling other computational chemistry problems, and the feature extraction technique can be easily generalized to other molecules.     

Regioselective nucleophilic ring-opening reaction of chiral epoxyallyl alcohols: a ready access to the pyran core of macrolactin 3

Herein we report the synthetic strategy towards the pyran core of macrolactin 3 via Sharpless epoxidation, titanium(IV) mediated regioselective ring-opening reaction of epoxyallyl alcohol/epoxy alcohol and oxa-Michael addition as the key steps.     

Population Balance Modeling with Coupled Agglomeration and Disintegration Processes for TiO2 Nanoparticles Formation and Experimental Validation

Particle size distribution of nanoparticles plays an important role in modelling many scientific and engineering problems. In this article, we proposed a Finite Volume Method (FVM) to model TiO₂ nanoparticles formation using population balance equations (PBEs) by incorporating the simultaneous agglomeration and disintegration processes. The superposition of the PBEs for agglomeration and disintegration with different kernels leads to a system of partial-integro differential equations, which are numerically solved by using FVM. The precipitation of TiO₂ nanoparticles in the batch reactor is studied experimentally as well as by numerical simulations based on Austin and Diemer disintegration kernels and Shear agglomeration kernel. Finally, the capability of the precipitation model is evaluated and the experimental results on particle sizes are compared with the numerical results.

     

Solvent‐assisted anionic ring opening polymerization of glycidol: Toward medium and high molecular weight hyperbranched polyglycerols

Hyperbranched polyglycerols (HPGs) are globular structures with a large number of functionalizable hydroxyl groups and have excellent in vitro and in vivo biocompatibility profiles comparable to polyethylene glycol. This work introduces a facile method for the synthesis of medium molecular weights (M_ws) (50–300 kDa) HPGs, which has been difficult to synthesize with low polydispersity, with the assistance of solvents by ring opening polymerization. The influence of different solvents (1,4‐dioxane, tetrahydropyran (THP), ethylene glycol diethyl ether (EGDE) and decane), solvent to glycidol ratio, concentration of glycidol and the time of polymerization on M_w and polydispersity of HPGs has been studied. The M_w and polydispersity of HPGs are significantly affected by the nature of the polymerization phase (homogeneous or heterogeneous) and chemical structure of the solvent. The differences in the solvation of the potassium cations and change in the nucleophilicity of the alkoxide anion in various solvents may be responsible for the changes in M_w and PDI of the HPG. The M_w of the HPG decreases in the order 1,4‐dioxane > THP > EGDE >decane. The microstructure, solution and thermal properties of the HPG do not depend on the nature of solvent. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013, 51, 2614–2621     

Biomolecular docking,antimicrobial and cytotoxic studies on new bidentate schiff base ligand derived metal (II) complexes

Three new metal complexes [Cu(L)₂] (1), [Co(L)₂] (2) and [Zn(L)₂] (3) have been prepared by the reaction of hydrated salts of metal (II) acetate with new Schiff base ligand HL, [2‐((4‐(dimethylamino)phenylimino)methyl)‐4,6‐di‐t‐butylphenol] and characterized by different physico‐chemical analyses such as elemental analysis, single XRD, ¹H NMR, FTIR and UV–Vis spectroscopic techniques. Their biomolecular docking, antimicrobial and cytotoxicity studies have also been demonstrated. The proposed structure of Schiff base ligand HL and complex 2 are confirmed by Single crystal X‐ray crystallography study. This analysis revealed that metal (II) complexes remain in distorted tetrahedral coordination environments. The electronic properties such as HOMO and LUMO energies are carried out by gaseous phase DFT/B3LYP calculations using Gaussian 09 program. Complex 1 showed a good binding propensity to the DNA and HSA, during the assessment of docking studies. Schiff base ligand HL and its metal (II) complexes, 1–3 screened for their in vitro antimicrobial activities using the disc diffusion method against selected microbes. Complex 1 shows higher antimicrobial activity than complexes 2, 3 and Schiff base ligand HL. According to the results obtained from the cytotoxic studies, Schiff base ligand HL and its metal (II) complexes 1–3 have better cytotoxicity against MCF‐7 cell lines with potency higher than the currently used chemotherapeutic agent cyclophosphamide.     

Enantioselective LC‐ESI‐MS/MS determination of dropropizine enantiomers in rat plasma and application to a pharmacokinetic study

We developed and validated a simple, sensitive, selective and reliable LC–ESI‐MS/MS method for direct quantitation of dropropizine enantiomers namely levodropropizine (LDP) and dextrodropropizine (DDP) in rat plasma without the need for derivatization as per regulatory guidelines. Dropropizine enantiomers and carbamazepine (internal standard) were extracted from 50 μL rat plasma using ethyl acetate. LDP and DDP resolved with good baseline separation (R_s = 4.45) on a Chiralpak IG‐3 column. The mobile phase consisted of methanol with 0.05% diethylamine pumped at a flow rate of 0.5 mL/min. Detection and quantitation were done in multiple reaction monitoring mode following the transitions m/z 237 → 160 and 237 → 194 for dropropizine enantiomers and the internal standard, respectively, in the positive ionization mode. The proposed method provided accurate and reproducible results over the linearity range of 3.23–2022 ng/mL for each enantiomer. The intra‐ and inter‐day precisions were in the ranges of 3.38–13.6 and 5.11–13.8 for LDP and 4.19–11.8 and 8.89–10.1 for DDP. Both LDP and DDP were found to be stable under different stability conditions. The method was successfully used in a stereoselective pharmacokinetic study of dropropizine enantiomers in rats following oral administration of racemate dropropizine at 100 mg/kg. The pharmacokinetic results indicate that the disposition of dropropizine enantiomers is not stereoselective and chiral inversion does not occur in rats.