Synthesis of 2′-O-[2-[(N,N-dialkylamino)oxy]ethyl]-modified oligonucleotides: hybridization affinity, resistance to nuclease, and protein binding characteristics

Synthesis of a series of 2′-O-[2-[(N,N-dialkylamino)oxy]ethyl]-modified 5-methyluridine nucleoside phosphoramidites and solid supports are described. Using these monomers, modified oligonucleotides containing phosphodiester linkages were synthesized in high yields. These modified oligonucleotides showed enhanced binding affinity to the complementary RNA (and not to DNA) and excellent nuclease stability with t_1/2>24 h. The human serum albumin binding properties of modified oligonucleotides have been evaluated to assess their transport and toxicity properties.     

Thermochemical investigations of nearly idial binary solvents. 6. Solubilities of iodine and benzil in systems of nonspecific interactions

Solubilities have been determined at 25°C for iodine in binary mixtures of carbon tetrachloride with cyclohexane, n-hexane, n-heptane, and octamethylcyclotetrasiloxane (OMCTS) and in mixtures of cyclohexane with n-hexane and OMCTS; and for benzil in binary mixtures of carbon tetrachloride with cyclohexane, n-hexane, and n-heptane, mixtures of n-hexane with cyclohexane and n-heptane, and mixtures of benzene with cyclohexane and toluene. With the exception of the benzene+cyclohexane system, the nearly ideal binary solvent model predicts these solubilities with a maximum deviation of 6% and an overall standard deviation of 2.4%. The model correctly predicts minima for solubility (mole fraction) of iodine in the OMCTS systems, and predicts solubilities within 4% for benzil in the carbon tetrachloride+n-hexane system, in which the solubility changes by a factor of 14. The failure of the model for predicting solubilities of benzil in mixtures of benzene and cyclohexane (maximum error of 25% for and 18-fold range of solubilities) is possibly due to specific interactions between benzil and benzene.     

Detection and characterization of nonspecific,sparsely populated binding modes in the early stages of complexation

A method is proposed to study protein–ligand binding in a system governed by specific and nonspecific interactions. Strong associations lead to narrow distributions in the proteins configuration space; weak and ultraweak associations lead instead to broader distributions, a manifestation of nonspecific, sparsely populated binding modes with multiple interfaces. The method is based on the notion that a discrete set of preferential first‐encounter modes are metastable states from which stable (prerelaxation) complexes at equilibrium evolve. The method can be used to explore alternative pathways of complexation with statistical significance and can be integrated into a general algorithm to study protein interaction networks. The method is applied to a peptide–protein complex. The peptide adopts several low‐population conformers and binds in a variety of modes with a broad range of affinities. The system is thus well suited to analyze general features of binding, including conformational selection, multiplicity of binding modes, and nonspecific interactions, and to illustrate how the method can be applied to study these problems systematically. The equilibrium distributions can be used to generate biasing functions for simulations of multiprotein systems from which bulk thermodynamic quantities can be calculated. © 2015 Wiley Periodicals, Inc.     

Computational study of ligand binding in lipid transfer proteins: Structures,interfaces, and free energies of protein‐lipid complexes

Plant nonspecific lipid transfer proteins (nsLTPs) bind a wide variety of lipids, which allows them to perform disparate functions. Recent reports on their multifunctionality in plant growth processes have posed new questions on the versatile binding abilities of these proteins. The lack of binding specificity has been customarily explained in qualitative terms on the basis of a supposed structural flexibility and nonspecificity of hydrophobic protein‐ligand interactions. We present here a computational study of protein‐ligand complexes formed between five nsLTPs and seven lipids bound in two different ways in every receptor protein. After optimizing geometries in molecular dynamics calculations, we computed Poisson‐Boltzmann electrostatic potentials, solvation energies, properties of the protein‐ligand interfaces, and estimates of binding free energies of the resulting complexes. Our results provide the first quantitative information on the ligand abilities of nsLTPs, shed new light into protein‐lipid interactions, and reveal new features which supplement commonly held assumptions on their lack of binding specificity. © 2012 Wiley Periodicals, Inc.     

Conformational study of a guaiacyl beta-O-4 lignin model compound by NMR. Examination of intramolecular hydrogen bonding interactions and conformational flexibility in solution

Intramolecular H-bonding interactions were investigated in solution for the threo and erythro diastereomeric forms of a guaiacyl beta-O-4 lignin model compound by using the NMR data obtained from hydroxyl protons. Temperature coefficients of the chemical shifts (ddelta/dT) and coupling constants (3J(HCOH)) were measured in aprotic and protic solutions: DMSO-d6, acetone-d6 and acetone-d6-water. The NMR parameters do not support the existence of strong and persistent intramolecular H-bonds that could participate in the stabilization of the guaiacyl beta-O-4 structure in solution, but instead indicate that intermolecular H-bonds to solvent predominate. 1D NOE experiments nevertheless revealed the presence of a direct chemical exchange between the hydroxyl protons, suggesting the possible existence of weak and transient intramolecular H-bonding interactions. The conformational flexibility of the threo structure was also investigated in acetone solution from the measurement of long-range 1H, 1H and 1H, 13C coupling constants and from NOESY experiments. The NMR data are not consistent with any single conformation, indicating that different conformers co-exist in solution. The experimental results support the conformational flexibility predicted by molecular dynamics simulations performed in a previous study. Finally, both experimental and theoretical approaches indicate that weak intramolecular H-bonds can exist transiently in solution, breaking and reforming as the beta-O-4 molecule undergoes conformational interconversion, but cannot be invoked as possible means of conferring rigidity to the beta-O-4 structure.     

An approach to estimate the energy and strength of the intramolecular hydrogen bond in different conformers of 4‐methylamino‐3‐penten‐2‐one

The molecular structure and intramolecular hydrogen bond energy of 32 conformers of 4‐methylamino‐3‐penten‐2‐one were investigated at MP2 and B3LYP levels of theory using the standard 6–31G** basis set and AIM analyses. Furthermore, calculations for all the possible conformations of 4‐methylamino‐3‐penten‐2‐one in water solution were also carried out at B3LYP/6–31G** level of theory. The calculated geometrical parameters and conformational analyses in gas phase and water solution show that the ketoamine conformers of this compound are more stable than the other conformers (i.e., enolimine and ketoimine). This stability is mainly due to the formation of a strong N? H···O intramolecular hydrogen bond, which is assisted by π‐electrons resonance. Hydrogen bond energies for all conformers of 4‐methylamino‐3‐penten‐2‐one were obtained from the related rotamers method. The nature of intramolecular hydrogen bond existing within 4‐methylamino‐3‐penten‐2‐one has been investigated by means of the Bader theory of atoms in molecules, which is based on topological properties of the electron density. The results of these calculations support the results which obtained by related rotamers method. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Spectral and molecular docking studies of nucleic acids/protein binding interactions of a novel organometallic palladium (II) complex containing bioactive PTA ligands: Its synthesis,anticancer effects and encapsulation in albumin nanoparticles

The organometallic palladium complex with nitrogen-containing heterocycles is a potent antitumor agent. Coordination of phosphorus ligands to organometallic complexes increases their hydrophilicity, promotes ligand−DNA interactions and damage level to cancer cells, and blocks division in target cells. In this study, a phosphaadamantane palladium complex ([Pd{(C,N)- (C₁₂H₈NH₂)} (PTA) Cl], PTA = 1,3,5-Triaza-7-phosphaadamantane) ( 2 ) was synthesized via the reaction of biologically active PTA with binuclear palladacycles [Pd₂{(C,N)-(C₁₂H₈NH₂)}₂(μ-Cl)₂] ( 1 ). In vitro studies of the complex with DNA (calf-thymus) explored by UV–Vis, emission titration, circular dichroism and helix melting methods showed that the complex interacts with DNA via an intercalative mechanism. Furthermore, competitive binding studies using warfarin, digoxin and ibuprofen site markers containing definite binding sites revealed the binding of the complex to site I on bovine serum albumin. The in vitro release mechanism of the palladium complex exhibited a biphasic pattern characterized by an initial burst release followed by a slower sustained release. Ultimately, in vitro evaluation of cytotoxicity and cell death showed that the complexes were able to decrease the viability of human cancer cell lines (MCF-7 and Jurkat) in a dose-dependent manner, but lower decreases were observed in the viability of normal fibroblast cells ASF-4 at the dosages evaluated. Finally, the order of in vitro anticancer activities was found to be consistent with the DNA-binding affinities.     

Fluorescence,ion binding,and viscosity properties of poly[2‐ and 4‐vinylpyridine]s in methanol and in sulfuric acid

Fluorescence intensities of poly(2‐vinylpyridine) (P2VP) and poly(4‐vinylpyridine) (P4VP) in H₂SO₄/H₂O solutions were increased with increasing acid concentration. The intensities for P2VP were found to be six times stronger than that of P4VP. These differences were accounted for by the microenvironment of protonated pyridinium group. The ion binding properties of 4‐methylpyridine (4MP), P2VP, and P4VP were investigated in methanol using Tb³⁺ as a fluorescence probe. The increase of fluorescence intensity of Tb³⁺ in [P2VP–Tb³⁺] and [P4VP–Tb³⁺] complexes is due to both the replacement of the inner coordinated methanol molecules and ligand‐to‐metal energy transfer. The model compound 4MP was inefficient from this point of view, and the results were attributed to the polymer cooperative effect. Reduced viscosities of poly(vinylpyridine)s (PVP) in methanol were similar to nonionic polymers; however, when TbCl₃ was added into the solution, the viscosities increased upon dilution. These results also indicated that PVP form complexes with Tb³⁺ in methanol. When diluted, the counterions Cl⁻ are allowed to dissociate and the charged polymer expands. Consequently, the solution's viscosity increases. © 1999 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 37: 1341–1345, 1999     

Assessment of pharmacokinetics,bioavailability and protein binding of anacetrapib in rats by a simple high‐performance liquid chromatography–tandem mass spectrometry method

Anacetrapib is a potent and selective CETP inhibitor and is undergoing phase III clinical trials for the treatment of dyslipidemia. A simple and sensitive high‐performance liquid chromatography–tandem mass spectrometry (HPLC–MS/MS) method for the quantification of anacetrapib in rat plasma was developed and validated using an easily purchasable compound, chlorpropamide, as an internal standard (IS). A minimal volume of rat plasma sample (20 μL) was prepared by a single‐step deproteinization procedure with 80 μL of acetonitrile. Chromatographic separation was performed using Kinetex C₁₈ column with a gradient mobile phase consisting of water and acetonitrile containing 0.1% formic acid at a flow rate of 0.3 mL/min. Mass spectrometric detection was performed using selected reaction monitoring modes at the mass/charge transitions m/z 638 → 283 for anacetrapib and m/z 277 → 175 for IS. The assay was validated to demonstrate the selectivity, linearity, precision, accuracy, recovery, matrix effect and stability. The lower limit of quantification was 5 ng/mL. This LC‐MS/MS assay was successfully applied in the rat plasma protein binding and pharmacokinetic studies of anacetrapib. The fraction of unbound anacetrapib was determined to be low (ranging from 5.66 to 12.3%), and the absolute oral bioavailability of anacetrapib was 32.7%.     

Synthesis,structure and in vitro antiproliferative activities of oxamido‐bridged dicopper(II) complexes: A comparative study of experimental evidence and molecular docking of DNA/protein binding

Two μ‐oxamido‐bridged dicopper(II) complexes, namely [Cu₂(hmpoxd)(H₂O)(phen)](ClO₄) ( 1 ) and [Cu₂(papo)(H₂O)(phen)](ClO₄)·2H₂O ( 2 ), where H₃hmpoxd and H₃papo represent N‐(2‐hydroxy‐5‐methylphenyl)‐N′‐[3‐(dimethylamino)propyl]oxamide and N‐(2‐hydroxylphenyl)‐N′‐(3‐aminopropyl)oxamide, respectively, and phen represents 1,10‐phenanthroline, were synthesized. Single‐crystal X‐ray crystallography and other methods revealed that the two copper(II) ions in complex 1 are bridged by the cis‐hmpoxd^3? with Cu···Cu separation of 5.1896(7) Å, in which the inner (Cu1) and outer (Cu2) copper(II) atoms are located in square‐planar and square‐pyramidal geometries, respectively. To evaluate the effects of bridging ligand hydrophobicity on DNA/protein binding and potential anticancer activities, comparative studies of the reactivity towards herring sperm DNA and protein bovine serum albumin (BSA) as well as cytotoxicity of complex 1 with our previously reported complex 2 were conducted theoretically and experimentally. The results indicate that the two complexes can interact interactively with DNA, and bind to BSA via the binding sites Trp213 for 1 and Trp134 for 2 . Interestingly, the in vitro anticancer activities and DNA/protein binding affinities consistently follow the order of 1 > 2 .     

Pharmacokinetics,protein binding and metabolism of a quinoxaline urea analog as an NF‐κB inhibitor in mice and rats by LC‐MS/MS

13–197 is a novel NF‐κB inhibitor that shows promising in vitro efficacy data against pancreatic cancer. In this study, we characterized the pharmacokinetics, tissue distribution, protein binding and metabolism of 13–197 in mice and rats. A valid, sensitive and selective LC‐MS/MS method was developed. This method was validated for the quantification of 13–197, in the range of 0.1 or 0.2‐500 ng/mL in mouse plasma, liver, kidney, lung, heart, spleen, brain, urine and feces. 13–197 has low bioavailability of 3 and 16% in mice and rats, respectively. It has faster absorption in mice with 12‐fold shorter T_max than in rats. Tissue concentrations were 1.3–69.2‐fold higher in mice than in rats at 72 h after intravenous administration. 13–197 is well distributed to the peripheral tissues and has relatively high tissue–plasma concentration ratios, ranging from 1.8 to 3634, in both mice and rats. It also demonstrated more than 99% binding to plasma proteins in both mice and rats. Finally, <1% of 13–197 is excreted unchanged in urine and feces, and metabolite profiling studies detected more than 20 metabolites in mouse and rat plasma, urine and feces, which indicates that 13–197 is extensively metabolized and primarily eliminated by metabolism rather than by excretion. Copyright © 2013 John Wiley & Sons, Ltd.