Structural basis of the inhibition of Golgi alpha-mannosidase II by mannostatin A and the role of the thiomethyl moiety in ligand-protein interactions

The X-ray crystal structures of mannose trimming enzyme drosophila Golgi alpha-mannosidase II (dGMII) complexed with the inhibitors mannostatin A (1) and an N-benzyl analogue (2) have been determined. Molecular dynamics simulations and NMR studies have shown that the five-membered ring of mannostatin A is rather flexible occupying pseudorotational itineraries between 2T3 and 5E, and 2T3 and 4E. In the bound state, mannostatin A adopts a 2T1 twist envelope conformation, which is not significantly populated in solution. Possible conformations of the mannosyl oxacarbenium ion and an enzyme-linked intermediate have been compared to the conformation of mannostatin A in the cocrystal structure with dGMII. It has been found that mannostatin A best mimics the covalent linked mannosyl intermediate, which adopts a 1S5 skew boat conformation. The thiomethyl group, which is critical for high affinity, superimposes with the C-6 hydroxyl of the covalent linked intermediate. This functionality is able to make a number of additional polar and nonpolar interactions increasing the affinity for dGMII. Furthermore, the X-ray structures show that the environment surrounding the thiomethyl group of 1 is remarkably similar to the arrangements around the methionine residues in the protein. Collectively, our studies contradict the long held view that potent inhibitors of glycosidases must mimic an oxacarbenium ion like transition state.     

Rapid one-pot iterative diselenide–selenoester ligation using a novel coumarin-based photolabile protecting group

The development of an iterative one-pot peptide ligation strategy is described that capitalises on the rapid and efficient nature of the diselenide–selenoester ligation reaction, together with photodeselenisation chemistry. This ligation strategy hinged on the development of a novel photolabile protecting group for the side chain of selenocysteine, namely the 7-diethylamino-3-methyl coumarin (DEAMC) moiety. Deprotection of this DEAMC group can be effected in a mild, reagent-free manner using visible light (λ = 450 nm) without deleterious deselenisation of selenocysteine residues, thus enabling a subsequent ligation reaction without purification. The use of this DEAMC-protected selenocysteine in iterative DSL chemistry is highlighted through the efficient one-pot syntheses of 60- and 80-residue fragments of mucin-1 as well as apolipoprotein CIII in just 2–4 hours.

A method for the rapid one-pot iterative assembly of proteins via diselenide–selenoester ligation (DSL) chemistry is described that capitalises on a novel coumarin-based photolabile protecting group for selenocysteine.     

A quantum pseudodot system with two-dimensional pseudoharmonic oscillator in external magnetic and Aharonov-Bohm fields

Using the Nikiforov–Uvarov (NU) method, the energy levels and the wave functions of an electron confined in a two-dimensional (2D) pseudoharmonic quantum dot are calculated under the influence of temperature and an external magnetic field inside dot and Aharonov–Bohm (AB) field inside a pseudodot. The exact solutions for energy eigenvalues and wave functions are computed as functions of the chemical potential parameters, applied magnetic field strength, AB flux field, magnetic quantum number and temperature. Analytical expression for the light interband absorption coefficient and absorption threshold frequency are found as functions of applied magnetic field and geometrical size of quantum pseudodot. The temperature dependence energy levels for GaAs semiconductor are also calculated.     

Reversal of Klein reflection by magnetic barriers in bilayer graphene

Massless Dirac fermions in monolayer graphene exhibit total transmission when normally incident on a scalar potential barrier, a consequence of the Klein paradox originally predicted by O Klein for relativistic electrons obeying the 3 + 1 dimensional Dirac equation. For bilayer graphene, charge carriers are massive Dirac fermions and, due to different chiralities, electron and hole states are not coupled to each other. Therefore, the wavefunction of an incident particle decays inside a barrier as for the non-relativistic Schr?dinger equation. This leads to exponentially small transmission upon normal incidence. We show that, in the presence of magnetic barriers, such massive Dirac fermions can have transmission even at normal incidence. The general consequences of this behavior for multilayer graphene consisting of massless and massive modes are mentioned. We also briefly discuss the effect of a bias voltage on such magnetotransport.     

Binding site characterization of G protein-coupled receptor by alanine-scanning mutagenesis using molecular dynamics and binding free energy approach: application to C-C chemokine receptor-2 (CCR2)

The C-C chemokine receptor 2 (CCR2) was proved as a multidrug target in many diseases like diabetes, inflammation and AIDS, but rational drug design on this target is still lagging behind as the information on the exact binding site and the crystal structure is not yet available. Therefore, for a successful structure-based drug design, an accurate receptor model in ligand-bound state is necessary. In this study, binding-site residues of CCR2 was determined using in silico alanine scanning mutagenesis and the interactions between TAK-779 and the developed homology model of CCR2. Molecular dynamic simulation and Molecular Mechanics-Generalized Born Solvent Area method was applied to calculate binding free energy difference between the template and mutated protein. Upon mutating 29 amino acids of template protein and comparison of binding free energy with wild type, six residues were identified as putative hot spots of CCR2.     

Relativistic New Yukawa-Like Potential and Tensor Coupling

We approximately solve the Dirac equation for a new suggested generalized inversely quadratic Yukawa potential including a Coulomb-like tensor interaction with arbitrary spin-orbit coupling quantum number ${\kappa}$ . In the framework of the spin and pseudospin (p-spin) symmetry, we obtain the energy eigenvalue equation and the corresponding eigenfunctions, in closed form, by using the parametric Nikiforov–Uvarov method. The numerical results show that the Coulomb-like tensor interaction, ?T/r, removes degeneracies between spin and p-spin state doublets. The Dirac solutions in the presence of exact spin symmetry are reduced to Schr?dinger solutions for Yukawa and inversely quadratic Yukawa potentials.     

Development and validation of a UV-spectrophotometric method for the determination of pheniramine maleate and its stability studies

A sensitive, precise, and cost-effective UV-spectrophotometric method is described for the determination of pheniramine maleate (PAM) in bulk drug and tablets. The method is based on the measurement of absorbance of a PAM solution in 0.1 N HCl at 264 nm. As per the International Conference on Harmonization (ICH) guidelines, the method was validated for linearity, accuracy, precision, limits of detection (LOD) and quantification (LOQ), and robustness and ruggedness. A linear relationship between absorbance and concentration of PAM in the range of 2–40 μg/ml with a correlation coefficient (r) of 0.9998 was obtained. The LOD and LOQ values were found to be 0.18 and 0.39 μg/ml PAM, respectively. The precision of the method was satisfactory: the value of relative standard deviation (RSD) did not exceed 3.47%. The proposed method was applied successfully to the determination of PAM in tablets with good accuracy and precision. Percentages of the label claims ranged from 101.8 to 102.01% with the standard deviation (SD) from 0.64 to 0.72%. The accuracy of the method was further ascertained by recovery studies via a standard addition procedure. In addition, the forced degradation of PAM was conducted in accordance with the ICH guidelines. Acidic and basic hydrolysis, thermal stress, peroxide, and photolytic degradation were used to assess the stability-indicating power of the method. A substantial degradation was observed during oxidative and alkaline degradations. No degradation was observed under other stress conditions.     

Ligand free,highly efficient synthesis of diaryl ether over copper fluorapatite as heterogeneous reusable catalyst

A novel ligand-free, highly efficient, and an inexpensive method has been developed by using ecofriendly, heterogeneous reusable copper fluorapatite (CuFAP) catalyst for the synthesis of diaryl ethers from the cross coupling reaction of the various substituted aryl halides (fluoride, chloride, bromide, and iodide) with the potassium salts of various substituted phenols in the presence of N-methyl 2-pyrrolidone (NMP) as a solvent at 120 °C. The protocol obtained the corresponding cross coupling products in good to excellent yield. The CuFAP catalyst was recovered by simple filtration from the reaction mixture and reused several times without the loss of catalytic activity.     

Effects of external fields on a two-dimensional Klein-Gordon particle under pseudo-harmonic oscillator interaction

We study the effects of the perpendicular magnetic and Aharonov-Bohm(AB) flux fields on the energy levels of a two-dimensional(2D) Klein-Gordon(KG) particle subjected to an equal scalar and vector pseudo-harmonic oscillator(PHO).We calculate the exact energy eigenvalues and normalized wave functions in terms of chemical potential parameter,magnetic field strength,AB flux field,and magnetic quantum number by means of the Nikiforov-Uvarov(NU) method.The non-relativistic limit,PHO,and harmonic oscillator solutions in the existence and absence of external fields are also obtained.