1H NMR study of complexation of ethidium bromide with single-stranded noncomplementary desoxytetranucleotide 5′-d(GpApApG) in aqueous solution

Complication of the ethidium bromide dye (3,8-diamino-6-phenyl-5-ethylphenanthridine) with single-stranded noncomplementary desaxytetranucleotide 5′-d(GpApApG) in aqueous salt solution was studied by one- and two-dimensional¹H NMR (500 and 600 MHz). The concentration dependences of the proton chemical shifts of the reactant molecules were measured at different temperatures (T₁ = 298 K, T₂ = 308 K). Investigations of self-association of the tetranucleotide showed that duplices can hardly form in solution. Therefore, dye complexes with single-stranded tetranucleotide play a major role in the equilibrium in solution; this makes it possible to analyze the specifics of interactions of aromatic ligands with single-stranded DNA. Various schemes of complexation are discussed; the equilibrium constants and the limiting values of the proton chemical shifts of ethidium bromide in the complexes are determined. The constants of dye binding to the single-stranded tetranucleotide 5′-d(GAAG) involving only purine bases is approximately an order of magnitude lower than the constants of ethidium bromide complexation with desaxytetranucleotide monomers whose sequences contain alternating types of base in the chain. The relative contents of complexes of different types are analyzed, and peculiarities of dynamic equilibrium, depending on the ratio of concentrations between the dye and the tetranucleotide, are revealed. Based on the data obtained it is concluded that the binding between ethidium bromide and the single-stranded nucleotide is sequence-specific. The estimated values of the induced chemical shifts of the dye protons are used to establish the most probable structures of the 1:1 and 2:1 complexes of ethidium bromide with single-stranded desaxytetranucleotide. Translated fromZhumal Struktumoi Khimii, Vol. 39, No. 5, pp. 808–820, September–October, 1998. This work was supported by INTAS grant NUD 7200.     

Asymmetric conjugate reductions with samarium diiodide: asymmetric synthesis of (2S,3R)- and (2S,3S)-[2-2H,3-2H]-leucine-(S)-phenylalanine dipeptides and (2S,3R)-[2-(2)H,3-2H]-phenylalanine methyl ester

The highly diastereoselective samarium diiodide and D(2)O-promoted conjugate reduction of homochiral (E)- and (Z)-benzylidene and isobutylidene diketopiperazines (E)-5,7 and (Z)-6,8 has been demonstrated. This methodology allows the asymmetric synthesis of methyl (2S,3R)-dideuteriophenylalanine 27 in > or = 95% de and >98% ee, and (2S,3R)- or (2S,3S)-dideuterioleucine-(S)-phenylalanine dipeptides 37 and 38 in moderate de, 66% and 74% respectively. A mechanism is proposed to account for this process.     

1H NMR study of self-association of actinomycin D in an aqueous solution

This paper presents the results of a proton magnetic resonance study (500 MHz) of self-association of actinomycin D (AMD) antibiotic in an aqueous solution. The equailibrium constants and thermo-dynamic parameters (ΔH, ΔS) of molecular association as well as the limiting values of proton chemical shifts of associate molecules were determined from the concentration and temperature dependences of¹H NMR chemical shifts of AMD. The results were analyzed using dimeric and infinite-dimensional cooperative models of molecular self-association. The value of the cooperativity parameter indicates that AMD self-association is anticooperative, i.e., formation of aggregates larger than dimers is energetically unfavorable. The values of induced proton chemical shifts were used to determine the most probable mutual orientation of chromophores in AMD structure. Sevastopol State Technical University. Berkbeck College, London University. Translated fromZhurnal Struktumoi Khimii, Vol. 36, No. 1, pp. 81–88, January–February, 1995. Translated by L. Smolina     

Assessing the role of polarization in docking

We describe a strategy for including ligand and protein polarization in docking that is based on the conversion of induced dipoles to induced charges. Induced charges have a distinct advantage in that they are readily implemented into a number of different computer programs, including many docking programs and hybrid QM/MM programs; induced charges are also more readily interpreted. In this study, the ligand was treated quantum mechanically to avoid parametrization issues and was polarized by the target protein, which was treated as a set of point charges. The induced dipole at a given target atom, due to polarization by the ligand and neighboring residues, was reformulated as induced charges at the given atom and its bonded neighbors, and these were allowed to repolarize the ligand in an iterative manner. The final set of polarized charges was evaluated in docking using AutoDock 4.0 on 12 protein-ligand systems against the default empirical Gasteiger charges, and against nonpolarized and partially polarized potential-derived charges. One advantage of AutoDock is that the best rmsd structure can be identified not only from the lowest energy pose but also from the largest cluster of poses. Inclusion of polarization does not always lead to the lowest energy pose having a lower rmsd, because docking is designed by necessity to be rapid rather than accurate. However, whenever an improvement in methodology, corresponding to a more thorough treatment of polarization, resulted in an increased cluster size, then there was also a corresponding decrease in the rmsd. The options for implementing polarization within a purely classical docking framework are discussed.     

Predicting human intestinal absorption in the presence of bile salt with micellar liquid chromatography

Understanding intestinal absorption for pharmaceutical compounds is vital to estimate the bioavailability and therefore the in vivo potential of a drug. This study considers the application of micellar liquid chromatography (MLC) to predict passive intestinal absorption with a selection of model compounds. MLC is already known to aid prediction of absorption using simple surfactant systems; however, with this study the focus was on the presence of a more complex, bile salt surfactant, as would be encountered in the in vivo environment. As a result, MLC using a specific bile salt has been confirmed as an ideal in vitro system to predict the intestinal permeability for a wide range of drugs, through the development of a quantitative partition–absorption relationship. MLC offers many benefits including environmental, economic, time‐saving and ethical advantages compared with the traditional techniques employed to obtain passive intestinal absorption values. Copyright © 2016 John Wiley & Sons, Ltd.     

Bond‐Forming Reactions of Small Triply Charged Cations with Neutral Molecules

Time‐of‐flight mass spectrometry reveals that atomic and small molecular triply charged cations exhibit extensive bond‐forming chemistry, following gas‐phase collisions with neutral molecules. These experiments show that at collision energies of a few eV, I³⁺ reacts with a variety of small molecules to generate molecular monocations and molecular dications containing iodine. Xe³⁺ and CS₂³⁺ react in a similar manner to I³⁺, undergoing bond‐forming reactions with neutrals. A simple model, involving relative product energetics and electrostatic interaction potentials, is used to account for the observed reactivity.     

Closed loop folding units from structural alignments: Experimental foldons revisited

Nonoverlapping closed loops of around 25–35 amino acids formed via nonlocal interactions at the loop ends have been proposed as an important unit of protein structure. This hypothesis is significant as such short loops can fold quickly and so would not be bound by the Leventhal paradox, giving insight into the possible nature of the funnel in protein folding. Previously, these closed loops have been identified either by sequence analysis (conservation and autocorrelation) or studies of the geometry of individual proteins. Given the potential significance of the closed loop hypothesis, we have explored a new strategy for determining closed loops from the insertions identified by the structural alignment of proteins sharing the same overall fold. We determined the locations of the closed loops in 37 pairs of proteins and obtained excellent agreement with previously published closed loops. The relevance of NMR structures to closed loop determination is briefly discussed. For cytochrome c, cytochrome b₅₆₂ and triosephophate isomerase, independent folding units have been determined on the basis of hydrogen exchange experiments and misincorporation proton‐alkyl exchange experiments. The correspondence between these experimentally derived foldons and the theoretically derived closed loops indicates that the closed loop hypothesis may provide a useful framework for analyzing such experimental data. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010