Two-prong inhibitors for human carbonic anhydrase II

The enzyme inhibitors are usually designed by taking into consideration the overall dimensions of the enzyme's active site pockets. This conventional approach often fails to produce desirable affinities of inhibitors for their cognate enzymes. To circumvent such constraints, we contemplated enhancing the binding affinities of inhibitors by attaching tether groups, which would interact with the surface exposed amino acid residues. This strategy has been tested for the inhibition of human carbonic anhydrase II. Benzenesulfonamide serves as a weak inhibitor for the enzyme, but when it is conjugated to iminodiacetate-Cu2+ (which interacts with the surface-exposed His residues) via a spacer group, its binding affinity is enhanced by about 2 orders of magnitude. This "two-prong" approach is expected to serve as a general strategy for converting weak inhibitors of enzymes into tight-binding inhibitors.     

C2 symmetrical double chromophores: cooperativity effects in lanthanide ion complexation

We describe the synthesis and characterization of C(2) symmetrical double chromophores, in which two identical chromophores are linked through ethylene glycol spacers of increasing lengths. The complexation ability of the trans stereopure form for each diastereoisomeric pair showed how the two chromophores, when the spacer unit is comprised of a diethylene or a triethylene glycol moiety, are able to interact in a positive way, stabilizing the resulting complexes when compared with single chromophore analogous compounds.     

New syntheses for 11-(mercaptoundecyl)triethylene glycol and mercaptododecyltriethyleneoxy biotin amide

Novel syntheses for mercaptododecyltriethyleneoxy biotin amide and 11-(mercaptoundecyl)triethylene glycol are presented here. Such alkyl thiols are popular components in creating monolayers capable of specifically binding proteins. The development of a variety of functionalized alkyl thiol compounds has a great impact on biosensor substrate design. In our synthesis of mercaptododecyltriethyleneoxy biotin amide, we couple aminotriethyleneoxydodecane disulfide to the NHS-activated biotin; this technique is amenable to attaching a carboxylated molecule of interest in order to create the functionalized alkyl thiol of choice. The 11-(mercaptoundecyl)triethylene glycol synthesis presented here is an alternative method easily completed in three steps.     

Hemoglobin binding from human blood hemolysate with poly(glycidyl methacrylate) beads

Metal-chelating affinity beads have attracted increasing interest in recent years for protein purification. In this study, iminodiacetic acid (IDA) was covalently attached to the poly(glycidyl methacrylate) [PGMA] beads (1.6 μm in diameter). Cu(2+) ions were chelated via IDA groups on PGMA beads for affinity binding of hemoglobin (Hb) from human blood hemolysate. The PGMA beads were characterized by scanning electron microscopy (SEM). The PGMA-Cu(2+) beads (628 μmol/g) were used in the Hb binding-elution studies. The effects of Hb concentration, pH and temperature on the binding efficiency of PGMA-Cu(2+) beads were performed in a batch system. Non-specific binding of Hb to PGMA beads in the absence of Cu(2+) ions was very low (0.39 mg/g). The maximum Hb binding was 130.3 mg/g. The equilibrium Hb binding increased with increasing temperature. The negative change in Gibbs free energy (ΔG°<0) indicated that the binding of Hb on the PGMA-Cu(2+) beads was a thermodynamically favorable process. The ΔS and ΔH values were 102.2 J/mol K and -2.02 kJ/mol, respectively. Significant amount of the bound Hb (up to 95.8%) was eluted in the elution medium containing 1.0 M NaCl in 1 h. The binding followed Langmuir isotherm model with monolayer binding capacity of 80.3-135.7 mg/g. Consecutive binding-elution experiments showed that the PGMA-Cu(2+) beads can be reused almost without any loss in the Hb binding capacity. To test the efficiency of Hb depletion from blood hemolysate, eluted portion was analyzed by fast protein liquid chromatography. The depletion efficiency for Hb was above 97.5%. This study determined that the PGMA-Cu(2+) beads had a superior binding capacity for Hb compared to the other carriers within this study.     

Surface grafting of glycidyl methacrylate on silica gel and polyethylene beads

Surface grafting of glycidyl methacrylate (GMA) on silica gel and a polyethylene bead was performed by radical polymerization and radiation-induced polymerization, respectively, in order to improve softness. Subsequently, diethylene triamine (DETA), triethylene tetraamine (TETA), and iminodiacetic acid (IDA) were introduced to the grafted GMA for use as affinity columns. The efficiency of the affinity column was investigated by use of bovine serum albumin (BSA) and hemoglobin (Hb) as model proteins. The affinity degree of BSA was higher than Hb for the DETA and TETA column, whereas the affinity degree of Hb was higher than BSA for the IDA column supported by silica gel. The affinity degree of BSA was higher than Hb for the DETA and TTA column supported by polyethylene (PE) beads.     

新型5-溴嘧啶衍生物的选择性合成

对甲苯磺酰氯与三甘醇单甲酯完成酯化反应,再与对溴苯酚缩合制得对溴苯基三甘醇单甲醚(3);3与硼酸甲酯完成取代反应、酸解后在Pd(PPh3)4催化下与5-溴-2-碘嘧啶(5)在甲苯中通过Suzuki偶联反应选择性地合成了5-溴-2-对(甲基三甘醇基)苯基嘧啶(1a),收率73%。以1-十二烯和5为主要原料,通过Suzuki偶联反应,一锅法选择性地合成了5-溴-2-十二烷基嘧啶(1b),收率82%。1a和1b未见文献报道,其结构经1HNMR,13C NMR和MS表征。     

Is [N+-H...O] hydrogen bonding the most important noncovalent interaction in macrocycle-dibenzylammonium ion complexes?

We report a new host molecule in which one diethylene glycol chain (i.e., a loop possessing only three oxygen atoms) incorporated along with two phenolic aromatic rings is linked by a xylene spacer into a macroring. The design of the molecular structure of this macrocycle "amplifies" any potential [cation...pi], [N+-H...pi], and [N+C-H...pi] interactions between the dibenzylammonium (DBA+) ion and the phenolic rings of the macrocycle; as such, these species display a very strong binding affinity in CD3NO2 (Ka = 15,000 M(-1)). The macroring also coordinates to bipyridinium ions in a [2]pseudorotaxane fashion, which makes it the smallest macrocycle (i.e., a 25-membered ring) known to complex both DBA+ and bipyridinium ions in solution. To confirm unambiguously that these pseudorotaxanes exist in solution, we synthesized their corresponding interlocked molecules, namely rotaxanes and catenanes.     

Colorimetric response to mercury-induced abstraction of triethylene glycol ligands from a gold nanoparticle surface

A simple method for specific colorimetric sensing of aqueous mercury(ii) has been developed by using a gold nanoparticle supported by triethylene glycol ligand (Au:S-EG(3)). The unusual kinetic behavior of the sensing process of Hg(2+) and the TEM images of the Au core, as well as the electrospray ionization mass spectroscopic analysis of the analyte solution, have led us to propose a new color changing mechanism that involves ligand abstraction from a gold surface by Hg(2+).     

Predicting the coordination geometry for Mg2+ in the p53 DNA-binding domain: insights from computational studies

Zn(2+) in the tumor-suppressor protein p53 DNA-binding domain (DBD) is essential for its structural stability and DNA-binding specificity. Mg(2+) has also been recently reported to bind to the p53DBD and influence its DNA-binding activity. In this contribution, the binding geometry of Mg(2+) in the p53DBD and the mechanism of how Mg(2+) affects its DNA-binding activity were investigated using density functional theory (DFT) calculations and molecular dynamics (MD) simulations. Various possible coordination geometries of Mg(2+) binding to histidines (His), cysteines (Cys), and water molecules were studied at the B3LYP/6-311+g** level of theory. The protonation state of Cys and the environment were taken into account to explore the factors governing the coordination geometry. The free energy of the reaction to form the Mg(2+) complexes was estimated, suggesting that the favorable binding mode changes from a four- to six-coordinated geometry as the number of the protonated Cys increases. Furthermore, MD simulations were employed to explore the binding modes of Mg(2+) in the active site of the p53DBD. The simulation results of the Mg(2+) system and the native Zn(2+) system show that the binding affinity of Mg(2+)to the p53DBD is weaker than that of Zn(2+), in agreement with the DFT calculation results and experiments. In addition, the two metal ions are found to make a significant contribution to maintain a favorable orientation for Arg248 to interact with putative DNA, which is critically important to the sequence-specific DNA-binding activity of the p53DBD. However, the effect of Mg(2+) is less marked. Additionally, analysis of the natural bond orbital (NBO) charge transfer reveals that Mg(2+) has a higher net positive charge than Zn(2+), leading to a stronger electrostatic attractive interaction between Mg(2+) and putative DNA. This may partly explain the higher sequence-independent DNA-binding affinity of p53DBD-Mg(2+) compared to p53DBD-Zn(2+) observed in experiment.     

An indicator-displacement assay for naked-eye detection and quantification of histidine in human urine

A simple and efficient colorimetric method for the naked-eye detection and quantification of histidine in biological fluids was developed based on an indicator-displacement assay (IDA) and the Ni(2+)-histidine affinity pair. In this IDA approach, a commercially available dye, murexide, was used as the indicator and the selective detection of histidine was achieved based on the competition between indicator and histidine for the binding with Ni(2+). The competition of histidine with murexide for Ni(2+) resulted in an obvious color change of the solution from yellow to purple, and the permitted naked-eye detection of trace histidine. The developed bioassay allows the rapid, sensitive and selective detection of histidine in urine samples, and does not need complicated sample pretreatment. The detection limit was 0.4 μM with a linear range from 2 to 30 μM. The relative standard deviation for 11 replicate detections of 8 μM histidine was 2.0%. The developed sensor was successfully applied to the determination of histidine in human urine samples with recoveries from 97 to 105%.     

Synthesis of the sialyl Lewis X epitope attached to glycolipids with different core structures and their selectin-binding characteristics in a dynamic test system

Sialyl Lewis X (sLeX)/selectin-mediated leukocyte rolling along endothelial cells has recently gained wide interest. In this paper the influence of the spacer length of laterally clustered neoglycolipids 1a-d on cell rolling in a dynamic test system is investigated. The required di-O-hexadecyl glycerols with none, and with three, six, or nine ethylene glycol units as spacer groups (compounds 4a-d) could be readily obtained. The synthesis of 1-O-thexyldimethylsilyl-protected sLeX 24 was based on sialylation of 2,3,4-O-unprotected galactose derivative 11 with sialyl phosphite 8 as donor; this afforded the desired disaccharide 12, which was transformed into trichloroacetimidate 14 as disaccharide donor. Reaction of 3-O-unprotected glucosamine derivative 18 with fucosyl donor 20 afforded disaccharide 21, which was transformed into the 4-O-unprotected derivative 23. Reaction of 14 with 23 furnished the desired tetrasaccharide 24 in good yield. Transformation of 24 into the trichloroacetimidate 26 as donor, followed by the reaction with 4a-d as acceptor gave, after deprotection, the target molecules 1a-d. For comparison, 4d was also connected with a sialyl residue (-->31) and with an N-acetylglucosamine residue (-->34). Compounds 1c and 1d with a hexaethylene glycol and a nonaethylene glycol spacer, respectively, were much more efficient in mediating selectin-dependent cell rolling in the dynamic test system than compounds 1a and 1b, which had no spacer (1a), or only a triethylene glycol spacer (1b).     

Catalytic effects of galactose oxidase on micelle-forming galactolipids

Catalytic effects of galactose oxidase on the oxidation of beta-D-galactose-carrying lipids with an oligo-ethylene glycol spacer (number of ethylene glycol units (n)=1, 2, 3, 6, 9, 13, and 20) were examined. The affinity of galactose oxidase for the galactose residue in the amphiphile (estimated by the inverse of the Michaelis constant, K(m)) was much higher than those for free D-galactose and small beta-D-galactopyranosides, and dependent on the length of the ethylene glycol spacer. That is, both below and above the critical micellar concentration, the 1/K(m) values decreased with an increase in the n value. The effectiveness of the enzyme, which can be estimated by the k(cat)/K(m) value, showed the same tendency as the 1/K(m) value. These results could be attributed to the role of the nonpolar environment around the galactose residue in the binding by the enzyme. A significant enhancement of the enzymatic oxidation of galactose residue on the liposome surface was also observed.     

In Silico Molecular Docking and Simulation Studies of Protein HBx Involved in the Pathogenesis of Hepatitis B Virus-HBV

Current drug discovery involves finding leading drug candidates for further development. New scientific approaches include molecular docking, ADMET studies, and molecular dynamic simulation to determine targets and lead compounds. Hepatitis B is a disease of concern that is a life-threatening liver infection. The protein considered for the study was HBx. The hepatitis B X-interacting protein crystal structure was obtained from the PDB database (PDB ID-3MSH). Twenty ligands were chosen from the PubChem database for further in silico studies. The present study focused on in silico molecular docking studies using iGEMDOCK. The triethylene glycol monoethyl ether derivative showed an optimum binding affinity with the molecular target HBx, with a high negative affinity binding energy of −59.02 kcal/mol. Lipinski’s rule of five, Veber, and Ghose were followed in subsequent ADMET studies. Molecular dynamic simulation was performed to confirm the docking studies and to analyze the stability of the structure. In these respects, the triethylene glycol monoethyl ether derivative may be a promising molecule to prepare future hepatitis B drug candidates. Substantial research effort to find a promising drug for hepatitis B is warranted in the future.     

Synthesis and characterization of bisphenol-A imprinted polymer as a selective recognition receptor

Molecularly imprinted polymers (MIPs) are currently used to provide selectivity in chemical sensors. In this context, a non-covalent bisphenol-A (BPA)-imprinted polymer using 4-vinylpyridine (4-Vpy) as the functional monomer, ethylene glycol dimethacrylate (EGDMA) as crosslinker and a low volatile solvent, triethylene glycol dimethyl ether (TRIGLYME), in combination with a non-reactive linear polymer, poly (vinyl acetate) (PVAc), as porogen, was synthesized with a simple polymerization procedure. Batch rebinding experiments were carried out to evaluate the binding and selectivity properties of the BPA-MIP. The experimental adsorption isotherms were fitted and a heterogeneous distribution of the binding sites was found. The selectivity of MIP demonstrated higher affinity for target BPA and BPA-analogues over other common water pollutants. The adsorption kinetics followed the pseudo-second-order kinetic model so that the specific adsorption in the imprinted cavities by two strong hydrogen bonds could be described as a chemisorption process. The diffusion mechanism was determined by the intra-particle diffusion and Boyd models, both of them revealing that the adsorption was mainly governed by intra-particle diffusion. MIP was shown to be promising for regeneration without significant loss in adsorption capacity.     

A new family of Ru(II) polypyridyl complexes containing open-chain crown ether for Mg2+ and Ca2+ probing

Six polypyridyl bridging ligands BL(1-6) containing open-chain crown ether, where BL(1-3) formed by the condensation of 4,5-diazafluoren-9-hydrazine with 1,7-bis-(4-formylphenyl)-1,4,7-trioxaheptane, 1,10-bis-(4-formylphenyl)-1,4,7,10-tetraoxadecane, and 1,13-bis-(4-formylphenyl)-1,4,7,10,13-pentaoxatridecane, respectively, BL(4-6) formed by the reaction of 9-(4-hydroxy)phenylimino-4,5-diazafluorene with diethylene glycol di-p-tosylate, triethylene glycol di-p-tosylate, and tetraethylene glycol di-p-tosylate, respectively, have been synthesized. Reaction of Ru(bpy)(2)Cl(2).2H(2)O with BL(1-6), respectively, afforded six bimetallic complexes [(bpy)(2)RuBL(1-6)Ru(bpy)(2)](4+) as PF(6)(-) salts. Cyclic voltammetry of these complexes is consistent with one Ru(II)-centered oxidation around 1.32V and three ligand-centered reductions. These complexes show metal-to-ligand charge transfer absorption at 413-444 nm and emission at 570 nm. Binding behavior of complexes with alkali and alkaline-earth metal ions are investigated by UV-vis absorption, fluorescence, and cyclic voltammetry. Addition of alkali and alkaline-earth metal ions to the solution of [(bpy)(2)RuBL(1-6)Ru(bpy)(2)](PF(6))(4) all result in a progressive quenching of fluorescence, a hyperchromic effect of UV-vis absorption, and a progressive cathodal shift of Ru(II)-centered E(1/2). Ru-BL(2) and Ru-BL(5) show the highest binding ability toward Mg(2+) among the five cations examined while Ru-BL(3) and Ru-BL(6) exhibit good selective recognition ability to Ca(2+).     

Modification of capillary electrophoresis capillaries by poly(hydroxyethyl methacrylate), poly(diethylene glycol monomethacrylate) and poly(triethylene glycol monomethacrylate)

Modification of capillary electrophoresis (CE) capillaries by poly(hydroxyethyl methacrylate) (poly(HEMA), poly(diethylene glycol monomethacrylate) (poly(DEGMA) and poly(triethylene glycol monomethacrylate) (poly(TEGMA), was studied. Methods based on physical adsorption of the modifier and on its chemical binding were compared on the basis of the electroosmotic flow (EOF) reproducibility, the EOF dependence on the pH, the symmetry of the peak of positively charged tyramine, the stability of the coating and the separation of standard and milk proteins in the modified capillaries. Reproducible coatings were obtained by chemical binding of the polymers to the capillary walls and by coating with a solution of a polymer, as also demonstrated by the atomic force microscopy.     

Synthesis and molecular tumbling properties of sialyl Lewis X and derived neoglycolipids

The sialyl Lewis X (sLeX) epitope has become a prominent target for biological studies because of its role in inflammation through binding to selectins. This epitope is located at the terminal end in glycosphingolipids and a lactose unit serves as spacer to the ceramide moiety. This paper focuses on the influence of the spacer structure and spacer length in regard to the mobility of the sLeX epitope. To this end sLex neoglycolipids 1a-c, with one, two, or three lactose units as spacer between the sLeX tetrasaccharide epitope and the membrane anchor, were synthesized. The synthetic strategy was also applied to the synthesis of the corresponding Lewis X (LeX) derivatives. The glycolipids were inserted in model membranes, and the tumbling frequencies of the sLex tetrasaccharide epitopes were then analysed by NMR spectroscopy. A nonaethylene glycol spacer decouples the carbohydrate moiety from the membrane mobility while (oligo-)lactoses act as more rigid distance keepers between the Lewis epitope and the surface of the membrane. Quantification of the different degrees of decoupling was possible by analysis of rotational correlation times.     

Studies on carbohydrates. Part 33: Synthesis of spacer-armed 2-acetamido-2-deoxy-4-O-β-d-galactopyranosyl-α-d-mannosides and their dimers

The mixture of 3,6-di-O-acetyl-4-O-(2,3,4,6-tetra-O-acetyl-β-d-galactopyranosyl)-2-azido-2-deoxy-d-glucopyranosyl 1-acetates or 1-trichloroacetates and the corresponding mannose type glycosyl donors reacted with the spacer arms di- and triethylene glycol, in dichloromethane solution with BF₃·OEt₂ and TMSOTf as promotors at room temperature to give highly selective products. Only the mannose type products were obtained.     

Optimization of tether length in nonglycosidically linked bivalent ligands that target sites 2 and 1 of a Shiga-like toxin

A series of bivalent ligands for a Shiga-like toxin have been synthesized, their experimentally determined inhibitory activities were compared with a simplified thermodynamic model, and computer simulations were used to predict the optimal tether length in bivalent ligands. The design of the inhibitors exploits the proximity of the C-2' hydroxyl groups of two P(k)-trisaccharides when bound to two different, neighboring carbohydrate recognizing binding sites located on the surface of Shiga-like toxin. NMR studies of the complex between the toxin and bivalent ligands show that site 2 and site 1 of a single B subunit are simultaneously occupied by a tethered P(k)-trisaccharide dimer. A simplified thermodynamic treatment provides the intrinsic affinities and binding energies for the intermolecular and intramolecular association events and permits the deconvolution of the contributions to the relative binding energies for the set of bivalent ligands. Conformational analysis based on MD simulations for bivalent galabioside dimers containing different tethers demonstrated that the calculated local concentrations of the pendant ligand at the second binding site correlate with the experimentally determined relative affinity values of the respective bivalent ligands, thereby providing a predictive method to optimize tether length.     

The influence of linker geometry in bis(3-hydroxy-N-methyl-pyridin-2-one) ligands on solution phase uranyl affinity

Seven water-soluble, tetradentate bis(3-hydroxy-N-methyl-pyridin-2-one) (bis-Me-3,2-HOPO) ligands were synthesized that vary only in linker geometry and rigidity. Solution-phase thermodynamic measurements were conducted between pH 1.6 and pH 9.0 to determine the effects of these variations on proton and uranyl cation affinity. Proton affinity decreases by introduction of the solubilizing triethylene glycol group as compared to unsubstituted reference ligands. Uranyl affinity was found to follow no discernable trends with incremental geometric modification. The butyl-linked 4 li-Me-3,2-HOPO ligand exhibited the highest uranyl affinity, consistent with prior in vivo decorporation results. Of the rigidly-linked ligands, the o-phenylene linker imparted the best uranyl affinity to the bis-Me-3,2-HOPO ligand platform.