Molecular Modeling Study on the Enantioselective Binding of S- and R-Ofloxacin to Various DNA Sequences

Abstract

The complex formation of S- and R-ofloxacin with the self-complementary oligonucleotides, namely d[ATAGCGCTAT]₂, d[GCGATATCGC]₂ and d[ATAICICTAT]₂, were investigated by the molecular dynamics (MD) simulation. Four starting positions, including two intercalation positions with different insertion directions and two minor groove binding positions, were considered. The total energy of both S- and R-ofloxacin-d[ATAGCGCTAT]₂ complex, in which ofloxacin binds in the minor groove of the oligonucleotide, were lower than any intercalation binding mode. For both enantiomers, formation of the complex with GC oligonucleotide is more favorable than AT and IC oligonucleotides. When S- and R-ofloxacin are compared, the S-enantiomer exhibits more favorable total energy and torsion angles in the complex formation. This result is in agreement with the experimental observation [Hwangbo et al., Eur J Pharm Sci 18, 197 (2003)]. In the complex, both enantiomers form two hydrogen bonds: one between the carbonyl group of ofloxacin and the amine group of G16 and the other between the fluorine group and the G6 amine for S-ofloxacin. However, only one hydrogen bond is formed between endocyclic hydrogen atom at the C2 position of adenine and inosine base and carbonyl group of ofloxacin, which may be the reason for the GC preferentiality of ofloxacin.     

Circadian Rhythm in Muscarinic Receptor Subtypes in Rat Forebrain

The binding of different ligands to muscarinic receptors in the centra) nervous system is regulated by several factors. Among these are the administration of drugs, disease, ontogeny or aging. Studies carried out in rat brains have demonstrated changes in the density of the muscarinic receptors at different times of the day. These changes might be related to variations in the circadian rhythms. In this work we have studied the binding of the [3H]-N-methyl-escopolamine, the agonist carbachol and the antagonist pirenzepine to muscarinic receptors in rat forebrains at 10.00,14.00,18.00,22.00,02.00 and 06.00 hr. We have observed changes in the density of muscarinic receptors but not changes in affinity to the radioligand. The Bmax values obtained by saturation studies were maximum at 14.00 hr and minimum at 02.00 hr (p < 0.05 Mann-Whitney's test). Inhibition studies in the presence of the non-selective agonist carbachol and the selective antagonist pirenzepine, at the same time-points, did not show statistically significant changes in the Bmax values. These data indicate that changes in the Bmax values are only observed in the total population of muscarinic receptors and are not due to modifications in the subtypes of muscarinic receptors nor to the different affinity states of agonist binding.     

Resistance ofHER2/neu-overexpressing tumor targets to lymphokine-activated-killer-cell-mediated lysis: evidence for deficiency of binding and post-binding events

HER2/neu-overexpressing tumor cell lines are relatively resistant to lymphokine-activated killer (LAK) cell cytotoxicity when compared toHER2/neu-nonexpressing lines.HER2/neu ⁺ targets were also resistant to binding by LAK large granular lymphocytes (LGL) as shown by visualization at the single-cell level, a target monolayer binding assay and in cold target inhibition experiments.HER2/neu ⁺ LAK-resistant ovarian cell lines demonstrated an absence of ICAM-1 expression while expression of LFA-3, N-CAM, laminin and ₁ integrins was comparable to that ofHER2/neu ^– targets. In contrast, theHER2/neu ⁺ breast cell line, SKBR-3, which was also resistant to lysis and binding by LAK LGL, demonstrated normal expression of ICAM-1. Anti-ICAM-1 antibodies blocked binding and lysis ofHER2/neu ^– carcinoma targets by LAK cells, further supporting the notion that lack of ICAM-1 expression onHER2/neu ⁺ cells contributes to their resistance. The modest binding and lysis ofHER2/neu ⁺ targets by LAK cells was significantly inhibited by anti-LFA-1 antibodies, suggesting the existence of another counter-receptor for LFA-1 onHER2/neu ⁺ targets. The following also supported deficiencies in post-binding events whenHER2/neu ⁺ cells resisted the lytic activity of LAK cells: (a) when the relative resistance to effector cell binding was overcome by exogenous lectin,HER2/neu ⁺ cell lines were still resistant to LAK cytolysis, and (b)HER2/neu ⁺ targets were resistant to perforin-containing granule extracts obtained from the CTLL-R8 cytotoxic lymphocyte cell line. These results indicate that deficiency in effector binding as well as post-binding events contributes to the resistance ofHER2/neu-overexpressing tumor targets to LAK-cell-mediated lysis.Supported by research funds of the Veteran's Administration, the California Institute for Cancer Research and Jonsson Cancer Center core grant CA 16042 funded by NIH     

Glycoconjugates for the recognition of Bacillus spores

Carbohydrates act as ligands in many biological processes, including the folding and secretion of proteins, cell-cell recognition, adhesion, and sporulation in the Bacillus genus. Fluorescent-labeled disaccharide glycoconjugates have been applied to evaluate binding to bacterial spores assuming that the spore surface is covered with carbohydrates. This study has shown that specific recognition of bacterial spores is based on interactions between disaccharide glycoconjugates acting as ligands and monosaccharide units expressed on the exterior of bacterial spores. Using fluorophore-assisted carbohydrate electrophoresis (FACE), carbohydrates that are expressed on the exterior of the spores were enumerated. The findings have an impact on how to improve ligand selection, essential for sensor development. In addition, the findings provide new information for inhibition of bacterial spores, and in general, demonstrate how carbohydrates function as recognition signals in nature.     

Binding Interactions of Leukemia Inhibitory Factor and Ciliary Neurotrophic Factor with the Different Subunits of Their High Affinity Receptors

Abstract: Leukemia inhibitory factor (LIF) and ciliary neurotrophic factor (CNTF) share common components in their multimeric receptors. Both cytokine receptors contain gp130/interleukin-6-receptor transducer as well as gp190/low-affinity LIF receptor. For CNTF, addition of a third subunit, or α subunit, defines the high-affinity CNTF receptor. In the present study, we analyzed the binding interactions of LIF and CNTF in human cell lines and showed a mutual displacement for LIF and CNTF toward the trimeric high-affinity CNTF receptor. Similar results were obtained in the JEG cell line, which only expressed the gp130/gp190 high-affinity LIF receptor, by adding a soluble form of the αCNTF receptor to the system to reconstitute the high-affinity-type CNTF receptor. The different receptor subunits were then expressed separately in transfected cells and their binding capacities analyzed. The results showed that the heterocomplex CNTF/αCNTF receptor bound to gp130 with an affinity of 3–5 × 10⁻¹⁰ M , whereas LIF interacted mainly with gp190. In summary, the observed competition between LIF and CNTF does not result from the binding to a common site or receptor subunit, but rather to the interaction of the three receptor components to create a conformational site common to both LIF and CNTF.     

Pancreatic Polypeptide Is Recognized by Two Hydrophobic Domains of the Human Y4 Receptor Binding Pocket

Structural characterization of the human Y₄ receptor (hY₄R) interaction with human pancreatic polypeptide (hPP) is crucial, not only for understanding its biological function but also for testing treatment strategies for obesity that target this interaction. Here, the interaction of receptor mutants with pancreatic polypeptide analogs was studied through double-cycle mutagenesis. To guide mutagenesis and interpret results, a three-dimensional comparative model of the hY₄R-hPP complex was constructed based on all available class A G protein-coupled receptor crystal structures and refined using experimental data. Our study reveals that residues of the hPP and the hY₄R form a complex network consisting of ionic interactions, hydrophobic interactions, and hydrogen binding. Residues Tyr^2.64, Asp^2.68, Asn^6.55, Asn^7.32, and Phe^7.35 of Y₄R are found to be important in receptor activation by hPP. Specifically, Tyr^2.64 interacts with Tyr²⁷ of hPP through hydrophobic contacts. Asn^7.32 is affected by modifications on position Arg³³ of hPP, suggesting a hydrogen bond between these two residues. Likewise, we find that Phe^7.35 is affected by modifications of hPP at positions 33 and 36, indicating interactions between these three amino acids. Taken together, we demonstrate that the top of transmembrane helix 2 (TM2) and the top of transmembrane helices 6 and 7 (TM6–TM7) form the core of the peptide binding pocket. These findings will contribute to the rational design of ligands that bind the receptor more effectively to produce an enhanced agonistic or antagonistic effect.     

Comparative molecular dynamics simulation analysis of G20 and C92 mutations in c-di-GMP I riboswitch and the wild type with docked c-di-GMP ligand

Riboswitch, a bacterial regulatory RNA consists of an aptamer (specific ligand binding unit) and an expression platform (gene expression modulation unit), which act as a potential drug target as it regulates critical genes. Therefore, it is of interest to glean information on the binding of c-di-GMP ligand to mutated conserved G20 and C92 residues of cyclic diguanosine monophosphate I (c-di-GMP I) riboswitch using molecular dynamics simulation. The result shows that the binding energy of wild/native type riboswitch-ligand complex (3IRW) is lower than the mutant complexes suggesting that the binding affinity for c-di-GMP ligand decreases in case of mutant riboswitches. The hydrogen bonding interactions analysis also showed a high number of hydrogen bonds formation in the wild type riboswitch-ligand complex as compared to the mutant complexes illustrating stronger interaction of ligand to wild type riboswitch than the mutants. The simulation result shows that the mutations affected riboswitch-ligand interactions. The residues G14, G21, C46, A47, and U92 were identified as the key residues which contributed effectively to the binding of c-di-GMP I riboswitch with the natural ligand.     

Study the interactions between human serum albumin and two antifungal drugs: Fluconazole and its analogue DTP

Binding affinities of fluconazole and its analogue 2-(2,4-dichlorophenyl)-1,3-di(1H-1,2,4-triazol-yl)-2-propanol (DTP) to human serum albumin (HSA) were investigated under approximately human physiological conditions. The obtained result indicated that HSA could generate fluorescent quenching by fluconazole and DTP because of the formation of non-fluorescent ground-state complexes. Binding parameters calculated from the Stern–Volmer and the Scatchard equations showed that fluconazole and DTP bind to HSA with binding affinities of the order 10⁴ L/mol. The thermodynamic parameters revealed that the binding was characterized by negative enthalpy and positive entropy changes, suggesting that the binding reaction was exothermic. Hydrogen bonds and hydrophobic interaction were found to be the predominant intermolecular forces stabilizing the drug–protein. The effect of metal ions on the binding constants of fluconazole–HSA complex suggested that the presence of Mg²⁺ and Zn²⁺ ions could decrease the free drug level and extend the half-life in the systematic circulation. Docking experiments revealed that fluconazole and DTP binds in HSA mainly by hydrophobic interaction with the possibility of hydrogen bonds formation between the drugs and the residues Arg 222, Lys 199 and Lys 195 in HSA.     

Interaction of the DNA bases and their mononucleotides with pyridine-2-carbaldehyde thiosemicarbazonecopper(II) complexes. Structure of the cytosine derivative

Experimental studies of the binding interactions of [CuL(NO₃)] and [{CuL′(NO₃)}₂] (HL = pyridine-2-carbaldehyde thiosemicarbazone, and HL′ = pyridine-2-carbaldehyde 4N-methylthiosemicarbazone) with adenine, guanine, cytosine, thymine and their mononucleotides (dNMP), 2-deoxyadenosine-5′-monophosphate, (dAMP), 2′-deoxyguanosine-5′-monophosphate, (dGMP), 2′-deoxycytidine-5′-monophpsphate (dCMP), and thymidine-5′-monophosphate (dTMP) have been carried out in aqueous solution at pH 6.0, I = 0.1 M (NaClO₄) and T = 25 °C. The complexation constants of these compounds, calculated by Hildebrand-Benesi plots for the dye binding, D, ([CuL] or [CuL′]) to the nucleobases or nucleotides (P), have shown two linear stretches in adenine, guanine, dAMP and dGMP. The data were analyzed in terms of formation of 1:1 DP and 1:2 DP₂ complexes with increasing purine base or nucleotide content. For cytosine and dCMP only 1:1 complexes have been observed, whereas for thymine and dTMP such complex structures were not observed. The [CuL(Hcyt)](ClO₄) cytosine derivative has been isolated and characterized. The crystal structure consists of perchlorate ions and [CuL(Hcyt)]⁺ monomers attached by hydrogen bond, chelate π−ring and anion-π interactions. The Cu²⁺ ions bind to the NNS chelating moiety of the thiosemicarbazone ligand and the cytosine N13 site (N3, most common notation) yielding a square-planar geometry. A pseudocoordination to the cytosine O12 site (=O2) can also be considered.     

A model for the development of the tandem repeat units in the EBV ori-P region and a discussion of their possible function

Summary This paper presents an analysis of the repeat units of the ori-P region of the Epstein-Barr virus (EBV) genome. These repeat units are well-conserved palindromes. The pattern of these repeats, their lengths, phases, and the distribution of the relatively few substitutions are explained by a scenario that gives a reasonable course for the evolutionary development of the pattern. The scenario suggests a model for the production of an initiating 3/2 palindrome from a moderately lengthy sequence. The palindromic units are then multiplied in judicious combinations by mechanisms of unequal crossing-over events associated with some point substitutions and a few instances of slippage replication. The potential secondary structures of the two separated tandem palindromic repeat regions in ori-P are contrasted. Possible modes of binding of Epstein-Barr nuclear antigen (EBNA) 1 protein to these hairpins are discussed. A number of possibilities for the origin and development of the ori-P region in relation to viral and cellular function are considered.