Phosphorylation mapping of laminin α1-chain: Kinases in association with active sites

Laminin­111 is a trimeric glycoprotein of the extracellular matrix (ECM) that holds a significant role in cell adhesion, migration and differentiation. Laminin­111 is the most studied laminin isoform, composed of three chains; α1, β1 and γ1. Phosphorylation is the most common eukaryotic post ­ translational modification and has regulatory effect on protein function. Using bioinformatic tools we computationally predicted all the possible phosphorylation sites on human laminin α1-chain sequence (LAMA1) according to kinases binding motifs. Thus, we predicted, for the first time, the possibly responsible kinases for fifteen of the nineteen already published experimentally observed phosphorylated residues in LAMA1. Searching the literature extensively, we recorded all the known functional sites (active sites) in LAMA1. We combined the experimentally observed and predicted phosphorylated residues as well as the active sites in LAMA1, generating an analytic phosphorylation map of human laminin α1-chain, which is useful for further analysis. Our results indicated fourteen kinases that might be important for the phosphorylation of human laminin α1-chain, out of which three kinases with reported ecto-phosphorylation activity (PKA, PKC and CKII) were suggested to have a more significant role. Six cancer associated-active sites were correlated with kinases, three out which were correlated with only the above ecto ­ kinases.     

Alkylation of 2-Sulfanylbenzoxazole with α-Iodoketones in the Absence of Bases

Reaction of 2-sulfanylbenzoxazole with 1-iodopropan-2-one, 2-iodo-1-phenylethanone, and 2-iodo-1-(thiophen-2-yl)ethanone without solvent and bases afforded bis(benzoxazol-2-yl)disulfonium derivatives in a single preparative stage. The reaction proceeds as a domino-process and includes the alkylation of a sulfanyl group of benzoxazole, the reduction of iodoketone with hydrogen iodide, the oxidation of 2-sulfanylbenzoxazole to disulfide, the alkylation of disulfide atoms of sulfur, and the formation of triiodideanions. The yield of disulfonium derivatives increases twice in the presence of equimolar amount of iodine.     

Screening of fibrillogenesis inhibitors of β2-microglobulin: integrated strategies by mass spectrometry capillary electrophoresis and in silico simulations

The challenging search of ligands for the amyloidogenic protein β₂-microglobulin led us to set up an integrated strategy that combines analytical techniques and molecular modelling. Using a chemical library composed of 90 sulphonated molecules and a novel MS screening approach, we initially single out a few new binders. To check for anti-amyloid activity, the best hit obtained was thoroughly studied by docking analysis, affinity and refolding experiments by capillary electrophoresis and in vitro fibrillogenesis Thioflavin T test. Correlative analysis of the overall results obtained from the MS screening led to develop an equation able to identify the key factors of the affinity for β₂-microglobulin and to predict the affinity for novel derivatives. The proposed equation was then used for a virtual screening of a large compound database. Studies on the new hit thus retrieved confirm the predictive potential of both the equation on affinity and of docking analysis on anti-amyloid activity.     

Molecular dynamic study of the mechanism of formation of 2D carbon nanostructures in a solid Al–C nanocomposite grain

The behavior of graphene fragments in the structural fcc grains of aluminum was studied by molecular dynamics. In the course of structural relaxation, the graphene sheets united, twisted, and shifted toward the grain boundaries. The structure of the formed nanocomposite grain was studied in detail by statistical geometry. The distributions of Voronoi polyhedra according to the number of faces and of faces according to the number of sides were determined, including those after elimination of small-scale thermal fluctuations from the model. The angular distributions of the nearest geometrical neighbors were calculated, and the selfdiffusion coefficients were determined.     

New benzoxazole-based sulphonamide hybrids analogs as potent inhibitors of α-amylase and α-glucosidase: Synthesis and in vitro evaluation along with in silico study

The development of drugs resistance in diabetes mellitus is a growing clinical problem, creates many challenges for patient. To overcome these problems, there is a serious deficiency of anti-diabetic agents, may be synthesized that inhibit alpha amylase and alpha glucosidase activity. Here, we have design and synthesized benzoxazole based sulphonamide derivatives and evaluated for their anti-diabetic activity. Twenty-two benzoxazole based sulphonamide derivatives were synthesized by reacting 2-aminophenol with carbon disulphide in the presence of base (Et3N) to obtained 2-marcapto benzoxazole which was further dissolved in ethanol by slow addition of different substituted phenacyl bromide in the presence of triethylamine, afforded varied S-substituted benzoxazole products. These products were dissolved in ethanol and hydrazine hydrate was added an excess in the presence of acetic acid to gives Schiff base. This Schiff base products were further dissolved in THF along with different substituted benzene sulphonyl chloride followed by addition of few drops of Et3N, yielded benzoxazole based sulphonamide derivatives (1–22). Moreover, SAR was established for the synthesized compounds and molecular docking studies were conducted for the potent moieties in order to explore the binding modalities of analogs. Among the tested series few analogues were found few folds better potential than standard drug but analog 1 (IC₅₀ = 1.10 ± 0.20 µM, 1.20 ± 0.30 µM), showed promising anti-diabetic activity against α-amylase and α-glucosidase (11.12 ± 0.15 µM and 11.29 ± 0.07 µM respectively).     

Implementations of Nosé-Hoover and Nosé-Poincaré thermostats in mesoscopic dynamic simulations with the united-residue model of a polypeptide chain

Molecular dynamics (MD) simulations generate a canonical ensemble only when integration of the equations of motion is coupled to a thermostat. Three extended phase space thermostats, one version of Nose-Hoover and two versions of Nose-Poincare, are compared with each other and with the Berendsen thermostat and Langevin stochastic dynamics. Implementation of extended phase space thermostats was first tested on a model Lennard-Jones fluid system; subsequently, they were implemented with our physics-based protein united-residue (UNRES) force field MD. The thermostats were also implemented and tested for the multiple-time-step reversible reference system propagator (RESPA). The velocity and temperature distributions were analyzed to confirm that the proper canonical distribution is generated by each simulation. The value of the artificial mass constant, Q, of the thermostat has a large influence on the distribution of the temperatures sampled during UNRES simulations (the velocity distributions were affected only slightly). The numerical stabilities of all three algorithms were compared with each other and with that of microcanonical MD. Both Nose-Poincare thermostats, which are symplectic, were not very stable for both the Lennard-Jones fluid and UNRES MD simulations started from nonequilibrated structures which implies major changes of the potential energy throughout a trajectory. Even though the Nose-Hoover thermostat does not have a canonical symplectic structure, it is the most stable algorithm for UNRES MD simulations. For UNRES with RESPA, the "extended system inside-reference system propagator algorithm" of the RESPA implementation of the Nose-Hoover thermostat was the only stable algorithm, and enabled us to increase the integration time step.     

Interaction of naproxen with α-, β-, and γ-hydroxypropyl cyclodextrins in solution and in the solid state

Solid combinations of naproxen with amorphous hydroxypropyl derivatives of -, -, and -cyclodextrin with an average substitution degree per anhydroglucose unit of 0.6 were investigated for thermal behaviour (differential scanning calorimetry), drug crystallinity (X-ray diffractometry), and dissolution rate (dispersed amount and rotating disc methods). Phase-solubility analysis and computer-aided molecular modelling were carried out to study the inclusion complexation of naproxen with hydroxypropyl cyclodextrins. The cavity size of the host is a selective factor for the solubilizing effect, complexing ability, and dissolution rate enhancement on naproxen, hydroxypropyl -cyclodextrin being markedly the most effective derivative. No relationship was found between the decrease in crystallinity of the drug dispersed in the amorphous carrier matrix and the geometrical features of the cyclodextrin macrocycle.     

Application of the oscillator strength of “hypersensitive” transitions to the investigation of complex equilibria of lanthanide ions—II: Spectroscopy,stability and thermodynamics of lanthanide complexes with monocarboxylic and α-hydroxyacids

Stability constants and thermodynamic parameters of Nd³⁺, Ho³⁺ and Er³⁺ complexes with acetates, propionates, glycolates, lactates and α-hydroxyisobutyrates were determined by a spectroscopic method based upon the measurements of the variation of oscillator strengths of “hypersensitive” 4f-4f-transitions [2].The sets of β_n values at 21°C are in a good agreement with those found potentiometrically [3–8]. The stability constants of the complexes evaluated at 5 different temperatures were used for the calculation of ΔG, ΔH, ΔS values. The evaluated thermodynamic parameters are in a satisfactory agreement with those found calorimetrically [5,8]. The thermodynamic parameters calculated from two independent “hypersensitive” transitions of the Er³⁺ ion are also consistent.     

First example of the coupling of α-diazoketones with thiourea: a novel route for the synthesis of 2-aminothiazoles

α-Diazoketones undergo smooth coupling with thiourea in the presence of 10 mol % of copper(II) triflate to produce the corresponding 2-aminothiazoles in excellent yields with high selectivity. The use of copper(II) triflate makes this method simple, convenient and practical. This method works well with both aryl and alkyl diazoketones to furnish a wide range of 2-aminothiazoles.     

Study of the structure and binding site features of FaEXPA2, an α-expansin protein involved in strawberry fruit softening

Tissue softening accompanies the ripening of many fruits and initiates the processes of irreversible deterioration. Expansins are plant cell wall proteins that have been proposed to disrupt hydrogen bonds within the cell wall polymer matrix. Several authors have shown that FaEXPA2 is a key gene that shows an increased expression level during ripening and softening of the strawberry fruit. For this reason, FaEXPA2 is frequently used as a molecular marker of softening in strawberry fruit, and changes in its relative expression have been related to changes in fruit firmness. In this context, we previously reported that FaEXPA2 has a high accumulation rate during fruit ripening in four different strawberry cultivars; however, the molecular mechanism of FaEXPA2 or expansins in general is not yet clear. Herein, a 3D model of the FaEXPA2 protein was built by comparative modeling to understand how FaEXPA2 interacts with different cell wall components at the molecular level. First, the structure was shown to display two domains characteristic of the other expansins that were previously described. The protein-ligand interaction was evaluated by molecular dynamic (MD) simulation using four different long ligands (a cellulose fiber, two of the more important xyloglucan (XG) fibers found in strawberry (XXXG and XXFG type), and a pectin (homogalacturonic acid type)). The results showed that FaEXPA2 formed a more stable complex with cellulose than other ligands via the different residues present in the open groove surface of its two domains, while FaEXPA2 did not interact with the pectin ligand.     

Structures of the crystalline supramolecular associates of imidazole with 1,1′-binaphthyl-8,8′-dicarboxylic acid and 2,2′-dihydroxy-1,1′-binaphthyl. Spatial similarity of the acid associate crystal packing to the active site of a serine protease

Abstract

Crystal structure analysis of the imidazole associates with 1,1′-binaphthyl-8,8′-dicarboxylic acid (1), [1a, triclinic, P1, a = 7.569(4), b = 8.393(2), c = 8.634(1) Å, α = 93.21(2), β = 106.88(3), γ = 105.17(3)°, D_c = 1.36 g/cm³, Z = 1, R = 0.045 for 1031 data] and with 2,2′-dihydroxy-1,1′-binaphthyl (2), [2a, tetragonal P4₁2₁2, a = 8.519(1), c = 29.821(2), D_c = 1.30 g/cm³, Z = 4, R = 0.051 for 1236 reflections] revealed 1:1 and 1:2 stoichiometry, respectively. Spontaneous resolution occur during crystallization in both compound crystals. 1a is a salt-like associate with hydrogen bonds between the carboxylate and imidazolium ion pairs while the neutral 2a has also well defined hydrogen bonds between host and guest molecules. In a modeling experiment corresponding Brookhaven Protein Data Bank atomic coordinates from the active site of the bacterial serine protease enzyme Subtilisin BPN were fitted to the crystal packing of the small molecule associate 1a crystal. The relative displacement of the ion pair components and a symmetry related carboxyl function in 1a has fair steric resemblance to similar moieties in the active site of Subtilisin (Δ_ave = 0.24 Å for 9 fitted atoms). The agreement in the results of two fully independent and totally different (i.e. a native protein active site and an artificial small molecule associate) crystal structure determinations underlines the assumed conceptual similarity of crystals (“giant supramolecules”) to protein sequences optimized through evolution.     

Highly enantioselective alkynylation of trifluoropyruvate with alkynylsilanes catalyzed by the BINAP-Pd complex: access to α-trifluoromethyl-substituted tertiary alcohols

A highly enantioselective alkynylation catalyzed by the dicationic (S)-BINAP-Pd complex with a variety of alkynylsilanes and trifluoropyruvate is described. The catalytic reaction is applicable to highly enantioselective addition of polyyne to trifluoropyruvate to construct α-trifluoromethyl-substituted tertiary alcohols as enantiomerically enriched forms. The alkynyl products can be converted into a chiral allene bearing a trifluoromethyl group.     

The nature of the catalytically active species in olefin dioxygenation with PhI(OAc)2: metal or proton?

Evidence for the protiocatalytic nature of the diacetoxylation of alkenes using PhI(OAc)(2) as oxidant is presented. Systematic studies into the catalytic activity in the presence of proton-trapping and metal-complexing agents indicate that protons act as catalysts in the reaction. Using triflic acid as catalyst, the selectivity and reaction rate of the conversion is similar or superior to most efficient metal-based catalysts. Metal cations, such as Pd(II) and Cu(II), may interact with the oxidant in the initiation phase of the catalytic transformation; however, 1 equiv of strong acid is produced in the first cycle which then functions as the active catalyst. Based on a kinetic study as well as in situ mass spectrometry, a mechanistic cycle for the proton-catalyzed reaction, which is consistent with all experimental data presented in this work, is proposed.     

Interaction and reaction of the hydroxyl ion with β-d-galactose and its hydrated complex: an ab initio molecular dynamics study

The interaction of OH(-) with the sugar β-d-galactose is studied computationally, with Ab Initio Molecular Dynamics (AIMD) as the prime tool. The main findings are: (1) the OH(-) abstracts a proton from the sugar in a barrier-less process, yielding H(2)O and a Deprotonated beta-d-Galactose anion, (Dep-beta-d-G)(-). (2) This reaction can be reversed when two additional H(2)O molecules are present in the sugar. (3) At 500 K, a ring-opening reaction occurs in (Dep-beta-d-G)(-) within a timescale of 10 ps. The (neutral) sugar itself is stable over this timescale, and well beyond. This indicates that OH(-) can catalyze the degradation of β-d-galactose. Implications of this process are briefly discussed.     

Complexation of new active antibacterial adamantan derivatives with β CD: Preparation and characterization of complexes study of the thermotropic properties of pure and complex form with dipalmitoyl phosphatidylcholine bilayers

-Cyclodextrin (CD) complexes of I1-8, I1-10, I1-12, were prepared, isolated and characterized in solid and liquid form. Their thermotropic effects were studied by inserting them in DPPC bilayers both in pure and complexed forms. The results have shown that the presence of I1-8 causes spliting, broadening and lowering of the phase transition of DPPC bilayers. Their effects are more significant when I1-0 and I1-12 are inserted. These differential effects are eliminated when the above studied three molecules are incorporated in a complex form with CD in DPPC bilayers. The obtained results suggest that the bromine salts in the bilayer are likely to remain in the complex form rather than released in the membrane.     

An insight into the disorder properties of the α-cyclodextrin polyiodide inclusion complex with Sr2+ ion: dielectric,DSC and FT-Raman spectroscopy studies

At T < 250 K, the polyiodide inclusion complex (α-cyclodextrin)₂·Sr_0.5·I₅·17H₂O displays two separate relaxation processes due to both the frozen-in proton motions in an otherwise ordered H-bonding network and the order–disorder transition of some normal H-bonds to flip-flop ones. At T>250 K, the AC-conductivity is dominated by the combinational contributions of the disordered water network, the mobile Sr²⁺ ions, the polyiodide charge-transfer interactions and the dehydration process. The evolution of the Raman spectroscopic data with temperature reveals the coexistence of four discrete pentaiodide forms. In form (I) (I^?  ₃·I₂ ? I₂·I^?  ₃), the occupancy ratio (x/y) of the central I^?  ion differs from 50/50. In form (IIa) (I₂·I^? ·I₂) x/y = 50/50, whereas in its equivalent form (IIb) (I₂·I^? ·I₂) ^* as well as in form (III) (I^?  ₃·I₂), x/y = 100/0 (indicative of full occupancy). Through slow cooling and heating, the inverse transformations (I) → (IIa) and (IIa) → (I) occur, respectively.