Synthesis, NMR kinetics and dynamic structure of a 17-mer heptaloop RNA hairpin carrying a 3--methyluridine nucleotide residue in the loop region.

A 17-mer RNA hairpin (5'GGGAGUAGCGGCUCCC3') carrying 3--methyluridine (m3U) at position (m3U7-RNA), designed to represent the anticodon stem-loop (ACSL) region of tRNAs to study an open loop state (O-state), was synthesized, purified by HPLC, and characterized by MALDI-ToF_MS and NMR methods. H-NMR data revealed primary (P-state in 56.1%), secondary (S-state in 43.

Cross Referencing 2D-LC Determination of Intact Gliptins in Urine.

Dipeptidyl peptidase-4 inhibitors, so-called gliptins, constitute a fairly novel class of oral hypoglycemic agents. The development and validation of an automated online SPE-LC-UV method to determine intact sitagliptin, saxagliptin, vildagliptin and metformin simultaneously in human urine samples were performed. For the two-dimensional chromatographic separation, a Gemini C18 (250.

Quinoline-based promising anticancer and antibacterial agents, and some metabolic enzyme inhibitors.

A series of substituted quinolines was screened for their antiproliferative, cytotoxic, antibacterial activities, DNA/protein binding affinity, and anticholinergic properties by using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide cell proliferation, lactate dehydrogenase cytotoxicity, and microdilution assays, the Wolfe-Shimmer equality method, the Ellman method, and the esterase assay, respectively. The results of the cytotoxic and anticancer activities of the compounds displayed that 6-bromotetrahydroquinoline (2), 6,8-dibromotetrahydroquinoline (3), 8-bromo-6-cyanoquinoline (10), 5-bromo-6,8-dimethoxyquinoline (12), the novel N-nitrated 6,8-dimethoxyquinoline (13), and 5,7-dibromo-8-hydroxyquinoline (17) showed a significant antiproliferative potency against the A549, HeLa, HT29, Hep3B, and MCF7 cancer cell lines (IC  = 2-50 μg/ml) and low cytotoxicity (∼7-35%) as the controls, 5-fluorouracil and cisplatin. The compound-DNA linkages are hyperchromic or hypochromic, causing variations in their spectra.

Molecular dynamics, thermodynamic, and mutational binding studies for tumor-specific LyP-1 in complex with p32.

Recent studies in tumor homing peptides have shown the specificity of LyP-1 (CGNKRTRGC) to tumor lymphatics. In this present work, we evaluated the possible interactions between cyclic LyP-1 and its receptor, p32, with molecular dynamics and docking studies in order to lead the design of novel LyP-1 derivatives, which could bind to p32 more effectively and perform enhanced antitumor effect. The total binding enthalpy energies have been obtained by MM-PBSA thermodynamic computations and the favorability of p32.

Seroprevalence of Crimean-Congo Hemorrhagic Fever in Turkey's Van Province.

Crimean-Congo hemorrhagic fever (CCHF) is an endemic tick-borne viral disease that affects both animals and humans. This study aims to determine the seroprevalence of CCHF in Turkey's Van province using analysis of blood samples obtained from people living in the region. Blood specimens were taken from healthy subjects living in Van province and some of the surrounding villages between January and July 2012.

Characterisation of drug resistance of nosocomial ESBL-producing E. coli isolates obtained from a Turkish university hospital between 2009 and 2012 by pulsed field gel electrophoresis and antibiotic resistance tests.

In this study, drug resistance of 28 ESBL-producing Escherichia coli isolates obtained from 144 patients hospitalized at the Yüzüncüyil University Hospital at Van (YUH), Turkey, between 2009 and 2012 were characterized by pulsed field gel electrophoresis and antibiotic susceptibility tests. Antibiotic resistance profile was determined by Phoenix automated system (BD, USA). The ratio of ESBL-producing E.

Compressed images for affinity prediction-2 (CIFAP-2): an improved machine learning methodology on protein-ligand interactions based on a study on caspase 3 inhibitors.

The aim of this study is to propose an improved computational methodology, which is called Compressed Images for Affinity Prediction-2 (CIFAP-2) to predict binding affinities of structurally related protein-ligand complexes. CIFAP-2 method is established based on a protein-ligand model from which computational affinity information is obtained by utilizing 2D electrostatic potential images determined for the binding site of protein-ligand complexes. The quality of the prediction of the CIFAP-2 algorithm was tested using partial least squares regression (PLSR) as well as support vector regression (SVR) and adaptive neuro-fuzzy ınference system (ANFIS), which are highly promising prediction methods in drug design.

Synthesis, anticancer activities and molecular modeling studies of novel indole retinoid derivatives.

In this study, novel (E)-3-(5-substituted-1H-indol-3-yl)-1-(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)prop-2-en-1-one (5(a-e)) derivatives were synthesized and their anticancer effects were determined in vitro. Novel indole retinoid compounds except 5e have anti-proliferative capacity in liver, breast and colon cancer cell lines. This anti-proliferative effect was further analyzed in breast cancer cell line panel by using the most potent compound 5a.

Use of the parmbsc0 force field and trajectory analysis to study the binding of netropsin to the DNA fragment (5'CCAATTGG)(2) in the presence of excess NaCl salt in aqueous solution.

The parmbsc0 force field was applied to study in detail the binding of netropsin, at a salt concentration of 0.28M Na(+), to the minor groove of an 8-mer (5'CCAATTGG)(2) DNA duplex forming a netropsin·DNA complex which previously has been characterized by X-ray crystallography, albeit with the use of closely related DNA duplexes. The X-ray structure revealed that the terminal guanidinium and amidinium groups of netropsin interact with the extreme ends of the palindromic AATT sequence of the receptor DNA.

NMR and amber analysis of the neamine pharmacophore for the design of novel aminoglycoside antibiotics.

The dependence of the solution structure of neamine on pH was determined by NMR and AMBER molecular dynamics methods at pD 3.3, pD 6.5, and pD 7.

Molecular recognition-based detoxification of aluminum in human plasma.

Molecular recognition-based Al(3+)-imprinted poly(hydroxyethyl methacrylate-N-methacryloyl-L-glutamic acid) (PHEMAGA-Al(3+)) beads were prepared to be used in selective removal of Al(3+) out of human plasma overdosed with Al(3+) cations. The PHEMAGA-Al(3+) beads were synthesized by suspension polymerization in the presence of a template-monomer complex (MAGA-Al(3+)). The specific surface area of PHEMAGA-Al(3+) beads was found to be 55.

Predicting the binding properties of cibacron blue F3GA in affinity separation systems.

The binding properties of cibacron blue F3GA (CB-F3GA) bound to a model NAD(P)H/FAD(H2)-dependent protein system, namely cytosolic quinone reductase (QR), was characterized by AMBER in an attempt to address the binding properties of immobilized CB-F3GA used in the separation of serum albumin. A favorable binding free energy of -4.52kcal/mol (KD=5.