Modifications in Trypsin Digestion Protocol for Increasing the Efficiency and Coverage

Standard trypsin digestion protocol of proteins followed by MALDI-MS analysis has been realized as an important tool for the identification and characterization of proteins. In this article, we proposed the elimination of the step of `staining/de-staining of gel pieces' in in-gel digestion protocol in order to improve the efficiency of trypsin digestion. Coomassie dye is known to interfere with digestion of proteins by trypsin and the procedure of staining-de-staining could result in loss of photoaffinity probe, post translational modifications and catalytic activities of enzymes. Further, we studied parameters like hydrophobicity and isoelectric point, and attempted to quantitatively relate it to the efficiency of trypsin digestion. We suggest that properties of proteins should be considered and trypsin digestion protocol should be appropriately modified as per sequence and other information.

A gap theorem for Ricci-flat 4-manifolds

Let (M, g) be a compact Ricci-fiat 4-manifold. For p is an element of M let K-max(P) (respectively K-min(p)) denote the maximum (respectively the minimum) of sectional curvatures at p. We prove that if K-max(p) <= -cK(min)(P) for all p is an element of M, for some constant c with 0 <= c < 2+root 6/4 then (M, g) is fiat. We prove a similar result for compact Ricci-flat Kahler surfaces. Let (M, g) be such a surface and for p is an element of M let H-max(p) (respectively H-min(P)) denote the maximum (respectively the minimum) of holomorphic sectional curvatures at p. If H-max(P) <= -cH(min)(P) for all p is an element of M, for some constant c with 0 <= c < 1+root 3/2, then (M, g) is flat. (C) 2015 Elsevier B.V. All rights reserved.

Conformational Stability and Intramolecular Hydrogen Bonding in 1,2-Ethanediol and 1,4-Butanediol

The gas-phase infrared spectra of 1,2-ED and 1,4-BD have been, recorded at three different temperatures using a multipass gas cell of 6 m optical path length. DFT calculation has also been carried out using 6-311++G** and aug-cc-pVDZ basis sets to look for the existence of intramolecular hydrogen bonding, in them from the red shift and infrared absorption intensity enhancement of the bonded O-H band compared to that of the free O-H hand. Equilibrium population analysis With 10 conformers of 1,2-ED and 1,4-BD at experimental temperatures were-carried out for the reconstruction of the Observed vibrational spectra at that temperature,using standard statistical relationships. The most abundant conformer at experimental temperatures, was identified. In 1,2-ED a red shift of 45 cm(-1) in the intramolecularly interacting O-H stretching vibrational band position and no significant intensity enhancement compared to that of-the free O-H have been observed. On the contrary, in one of the hydrogen bonded conformers of 1,4-BD, a 124 cm(-1) red shift in the O-H stretching frequency and 8.5 times-intensity enhancement for the ``bonded'' O-H compared to that of the ``free'' O-H is seen. On the basis of this comparative study, we have concluded that strong intramolecular hydrogen bonding exists in 1,4-BD. But there appears, to be weak intramolecular hydrogen bonding in 1,2-ED at temperatures of 303, 313, and 323 Km the gas phase We have found that most stable hydrogen-bonded conformers of 1,4-BD are less populated than some of the non-hydrogen-bonded conformers. Even for the 1,4-BD, the relative population of the g'GG'Gt conformer, which has a strong intramolecular,hydrogen bond, is less than what is predicted. Perhaps the intramolecular hydrogen bond plays a less Significant role in the relative stability,of the various Conformers than what has been predicted from calculations and prevails in the literature.

DNA intercalative 4-butylaminopyrimido4',5':4,5]thieno(2,3-b)quinoline induces cell cycle arrest and apoptosis in leukemia cells

DNA intercalators are one of the interesting groups in cancer chemotherapy. The development of novel anticancer small molecule has gained remarkable interest over the last decade. In this study, we synthesized and investigated the ability of a tetracyclic-condensed quinoline compound, 4-butylaminopyrimido4',5':4,5]thieno(2,3-b)quinoline (BPTQ), to interact with double-stranded DNA and inhibit cancer cell proliferation. Circular dichroism, topological studies, molecular docking, absorbance, and fluorescence spectral titrations were employed to study the interaction of BPTQ with DNA. Cytotoxicity was studied by performing 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and lactate dehydrogenase (LDH) assay. Further, cell cycle analysis by flow cytometry, annexin V staining, mitochondrial membrane potential assay, DNA fragmentation, and western blot analysis were used to elucidate the mechanism of action of BPTQ at the cellular level. Spectral, topological, and docking studies confirmed that BPTQ is a typical intercalator of DNA. BPTQ induces dose-dependent inhibitory effect on the proliferation of cancer cells by arresting cells at S and G2/M phase. Further, BPTQ activates the mitochondria-mediated apoptosis pathway, as explicated by a decrease in mitochondrial membrane potential, increase in the Bax:Bcl-2 ratio, and activation of caspases. These results confirmed that BPTQ is a DNA intercalative anticancer molecule, which could aid in the development of future cancer therapeutic agents.

One-step synthesis of a cyclic 2,17-dioxo3,3](4,4 `)biphenylophane and first preparation of a microporous polymer network from a macrocyclic precursor by cyclotrimerization

One-step synthesis of a cyclic 2,17-dioxo3,3](4,4') biphenylophane (MC) was achieved in high yield; its structure was verified by single crystal X-ray analysis. As a first example, a microporous polymer network was formed from macrocycle MC via acid-catalysed cyclotrimerization yielding a BET surface area of ca. 570 m(2) g(-1).

Solid state structure of p-bromo phenyl 4,5,7-tri-O-benzyl-beta-D-glycero-D-talo-septanoside and an analysis of non-covalent interactions

The solid state structure of a new seven-membered sugar oxepane derivative, namely, p-bromo phenyl 4,5,7-tri-O-benzyl-beta-D-glycero-D-talo-septanoside is discussed, as determined through single crystal X-ray structural determination and in relation to their conformational features. The molecule adopts twist-chair as the preferred conformation, with conformational descriptor (TC2,3)-T-0,1. The solid state packing of molecules is governed by a rich network of non-covalent bonding originating from O-H center dot center dot center dot O, C-H center dot center dot center dot pi, C-H center dot center dot center dot Br and aromatic pi center dot center dot center dot pi interactions that stabilize the packing of molecules in the crystal. (C) 2015 Elsevier Ltd. All rights reserved.

Disappearance of electron-hole asymmetry in nanoparticles of Nd1-xCaxMnO3(x=0.6, 0.4): magnetization and electron paramagnetic resonance evidence

We study and compare magnetic and electron paramagnetic resonance behaviors of bulk and nanoparticles of Nd1-xCaxMnO3 in hole doped (x = 0.4; NCMOH) and electron doped (x = 0.6; NCMOE) samples. NCMOH in bulk form shows a complex temperature dependence of magnetization M(T), with a charge ordering transition at similar to 250 K, an antiferromagnetic (AFM) transition at similar to 150 K, and a transition to a canted AFM phase/mixed phase at similar to 80 K. Bulk NCMOE behaves quite differently with just a charge ordering transition at similar to 280 K, thus providing a striking example of the so called electron-hole asymmetry. While our magnetization data on bulk samples are consistent with the earlier reports, the new results on the nanoparticles bring out drastic effects of size reduction. They show that M(T) behaviors of the two nanosamples are essentially similar in addition to the absence of the charge order in them thus providing strong evidence for vanishing of the electron-hole asymmetry in nanomanganites. This conclusion is further corroborated by electron paramagnetic resonance studies which show that the large difference in the ``g'' values and their temperature dependences found for the two bulk samples disappears as they approach a common behavior in the corresponding nanosamples. (C) 2015 AIP Publishing LLC.

Crystal landscape in the orcinol:4,4 `-bipyridine system: synthon modularity, polymorphism and transferability of multipole charge density parameters

Polymorphism in the orcinol: 4,4'-bipyridine cocrystal system is analyzed in terms of a robust convergent modular phenol...pyridine supramolecular synthon. Employing the Synthon Based Fragments Approach (SBFA) to transfer the multipole charge density parameters, it is demonstrated that the crystal landscape can be quantified in terms of intermolecular interaction energies in the five crystal forms so far isolated in this complex system. There are five crystal forms. The first has an open, divergent O-H...N based structure with alternating orcinol and bipyridine molecules. The other four polymorphs have different three-dimensional packing but all of them are similar at an interaction level, and are based on a modular O-H...N mediated supramolecular synthon that consists of two orcinol and two bipyridine molecules in a closed, convergent structure. The SBFA method, which depends on the modularity of synthons, provides good agreement between experiment and theory because it takes into account the supramolecular contribution to charge density. The existence of five crystal forms in this system shows that polymorphism in cocrystals need not be considered to be an unusual phenomenon. Studies of the crystal landscape could lead to an understanding of the kinetic pathways that control the crystallization processes, in other words the valleys in the landscape. These pathways are traditionally not considered in exercises pertaining to computational crystal structure prediction, which rather monitors the thermodynamics of the various stable forms in the system, in other words the peaks in the landscape.

A novel DNA intercalator, 8-methoxy pyrimido4 `,5 `:4,5]thieno (2,3-b)quinoline-4(3H)-one induces apoptosis in cancer cells, inhibits the tumor progression and enhances lifespan in mice with tumor

Polycyclic aromatic molecules such as ellipticine intercalate into double-stranded DNA and interfere with physiological functions. In the present study, we evaluate the chemotherapeutic potential of MPTQ on animal models and its mode of action. In order to test the antitumor activity, monohydrochloride of MPTQ was orally administered in mice bearing tumor. Results showed a significant inhibition of tumor growth compared to that of untreated controls. More importantly, mean lifespan of tumor bearing animals treated with MPTQ was significantly higher as compared to that of untreated tumor bearing mice suggesting that the treatment affected viability of cancerous cells, but not of normal cells. Consistent with this, we find that administration of MPTQ to normal mice did not cause any major side effects as observed upon hematological and serum profiling. We also found that MPTQ induces cytotoxicity in cancer cell lines, by activating apoptosis both by intrinsic and extrinsic pathways. Thus, MPTQ could be used as a potential cancer therapeutic agent. (c) 2011 Wiley Periodicals, Inc.

Synthesis and evaluation of 2,5-di(4-aryloylaryloxymethyl)-1,3,4-oxadiazoles as anti-cancer agents

A series of 2,5-di(4-aryloylaryloxymethyl)-1,3,4-oxadiazoles 9a-j were obtained via multistep synthesis from hydroxybenzophenones 4a-e. The cytotoxicity of compounds 9a-j was evaluated against human leukemia cell lilies (K562 and CEM). The compounds exhibited moderate to good anti-cancer activity with compounds 9b and 9i having a chloro group exhibiting the best activity (IC50 = 10 mu M). Compound 9i exhibited activity against both the cell lines and 9b only exhibited activity against CEM. Further, a lactate dehydrogenase (LDH) assay and DNA fragmentation studies of the compounds 9a-j were also performed. (C) 2013 Elsevier Masson SAS. All rights reserved.

Antiproliferative and tumor inhibitory studies of 2,3 disubstituted 4-thiazolidinone derivatives

4-Thiazolidinone derivatives were synthesized using T3P (R)-DMSO media as a cyclodehydrating agent. All the molecules were tested for their cytotoxicity against leukemic cell lines. The compound 3-(4-bromophenyl)-2-(4-(dimethylamino)phenyl)thiazolidin-4-one (4e) with electron donating substituent at para position of phenyl ring displayed considerable cytotoxicity against Reh and Nalm6 cells with an IC50 value of 11.9 and 13.5 mu M, respectively. Furthermore, the compound 4e tested for tumor regression studies induced by EAC in Swiss albino mouse. Both in vitro and in vivo results suggested significant antiproliferative activity of compound 4e in Reh cells and mouse tumor tissue treated with compound 4e showed multifocal areas of necrosis and numerous number of apoptotic cells. (C) 2015 Elsevier Ltd. All rights reserved.

Dual Stress and Thermally Driven Mechanical Properties of the Same Organic Crystal: 2,6-Dichlorobenzylidene-4-fluoro-3-nitroaniline

An elastic organic crystal, 2,6-dichlorobenzylidine-4-fluoro-3-nitroaniline (DFNA), which also shows thermosalient behavior, is studied. The presence of these two distinct properties in the same crystal is unusual and unprecedented because they follow respectively from isotropy and anisotropy in the crystal packing. Therefore, while both properties lead from the crystal structure, the mechanisms for bending and thermosalience are quite independent of one another. Crystals of the low-temperature (a) form of the title compound are bent easily without any signs of fracture with the application of deforming stress, and this bending is within the elastic limit. The crystal structure of the a-form was determined (P2(1)/c, Z = 4, a = 3.927(7) angstrom, b = 21.98(4) angstrom, c = 15.32(3) angstrom). There is an irreversible phase transition at 138 degrees C of this form to the high-temperature beta-form followed by melting at 140 degrees C. Variable-temperature X-ray powder diffraction was used to investigate the structural changes across the phase transition and, along with an FTIR study, establishes the structure of the beta-form. A possible rationale for strain build-up is given. Thermosalient behavior arises from anisotropic changes in the three unit cell parameters across the phase transition, notably an increase in the b axis parameter from 21.98 to 22.30 angstrom. A rationale is provided for the existence of both elasticity and thermosalience in the same crystal. FTIR studies across the phase transition reveal important mechanistic insights: (i) increased pi...pi repulsions along 100] lead to expansion along the a axis; (ii) change in alignment of C-Cl and NO2 groups result from density changes; and (iii) competition between short-range repulsive (pi...pi) interactions and long-range attractive dipolar interactions (C-Cl and NO2) could lie at the origin of the existence of two distinctive properties.

Halogen Bonding and Chalcogen Bonding in 4,7-Dibromo-5, 6-dinitro-2,1,3-benzothiadiazole

An organic solid, 4,7-dibromo-5,6-dinitro-2,1,3-benzothiadiazole, has been designed to serve as an illustrative example to quantitatively evaluate the relative merits of halogen and chalcogen bonding in terms of charge density features. The compound displays two polymorphic modifications, one crystallizing in a non-centrosymmetric space group (Z' = 1) and the other in a centrosymmetric space group with two molecules in the asymmetric unit (Z' = 2). Topological analysis based on QTAIM clearly brings out the dominance of the chalcogen bond over the halogen bond along with an indication that halogen bonds are more directional compared to chalcogen bonds. The cohesive energies calculated with the absence of both strong and weak hydrogen bonds as well as stacking interaction are indicative of the stabilities associated with the polymorphic forms.

Catalytic Enantioselective 1,4-lodofunctionalizations of Conjugated Dienes

The first catalytic enantioselective 1,4-iodofunctionalizations of conjugated dienes have been developed. Starting from beta,gamma,delta,epsilon-unsaturated oximes and 4-Ns hydrazones, these N-iodosuccinimide-mediated reactions are catalyzed by newly modified tertiary aminothiourea derivatives and furnish Delta(2)-isoxazoline and Delta(2)-pyrazoline derivatives, respectively, containing an (E)-allyl iodide group at the quaternary stereogenic center generally in high yield and with excellent enantioselectivity (up to 98.5:1.5 er).

Synthesis of Novel Benzofuran-Gathered C-2,4,6-substituted Pyrimidine Derivatives Conjugated by Sulfonyl Chlorides: Orally Bioavailable, Selective, Effective Antioxidants and Antimicrobials Drug Candidates

In the present study, we have made an effort to develop the novel synthetic antioxidants and antimicrobials with improved potency. The novel benzofuran-gathered C-2,4,6-substituted pyrimidine derivatives 5a, 5b, 5c, 5d, 5e, 5f, 6a, 6b, 6c, 6d, 6e, 6f, 7a, 7b, 7c, 7d, 7e, 7f, 8a, 8b, 8c, 8d, 8e, 8f, 9a, 9b, 9c, 9d, 9e, 9f were synthesized by simple and efficient four-step reaction pathway. Initially, o-alkyl derivative of salicylaldehyde readily furnish corresponding 2-acetyl benzofuran 2 in good yield, upon the treatment with potassium tertiary butoxide in the presence of molecular sieves. Further, Claisen-Schmidt condensation with aromatic aldehydes via treatment with thiourea followed by coupling reaction with different sulfonyl chlorides afforded target compounds. The structures of newly synthesized compounds were confirmed by IR, H-1 NMR, C-13 NMR, mass, and elemental analysis and further screened for their antioxidant and antimicrobial activities. The results showed that the synthesized compounds 8b, 8e, 9b, and 9e produced significant antioxidant activity with 50% inhibitory concentration higher than that of reference, whereas compounds 7d and 7c produced dominant antimicrobial activity at concentrations 1.0 and 0.5mg/mL compared with standard Gentamicin and Nystatin, respectively.