Quantitative study of stereospecific binding of monoclonal antibody to anti-benzo(a)pyrene diol epoxide-N-dG adducts by capillary electrophoresis immunoassay

The stereospecific binding of monoclonal antibody (mAb) 8E11 to anti-benzo(a)pyrene diol epoxide (BPDE)-dG adducts in single nucleoside, long oligonucleotide, and genomic DNA were quantitatively evaluated using noncompetitive and competitive capillary electrophoresis (CE) immunoassays. Two single-stranded TMR-BPDE-90mers containing a single anti-BPDE-dG adduct with defined stereochemistry and a fluorescent label at 5′-end were used as fluorescent probes for competitive CE immunoassay. To quantitatively evaluate the binding affinity through competitive CE immunoassays, a series of equations were derived according to the binding stoichiometry. The binding of mAb 8E11 to trans-(+)-anti-BPDE-dG displays strongest affinity (K_b: 3.57 × 10⁸ M⁻¹) among all four investigated anti-BPDE-dG mononucleoside adducts, and the cis-(−)-anti-BPDE-dG displays lowest affinity (K_b: 1.14 ×10⁷ M⁻¹). The binding of monoclonal antibody (mAb) 8E11 to BPDE-dG adducts in long DNA (90mer) preferentially forms the complex with a stoichiometry of 1:1, and that mAb 8E11 displays a slightly higher affinity with trans-(+)-anti-BPDE-90mers (K_b: 6.36 ± 0.54 × 10⁸ M⁻¹) than trans-(−)-anti-BPDE-90mers (K_b: 4.52 ± 0.52 × 10⁸ M⁻¹). The mAb 8E11 also displays high affinity with BPDE-dG adducts in genomic DNA (K_b: 3.74 × 10⁸ M⁻¹), indicating its promising applications for sensitive immuno-detection of BPDE-DNA adducts in genomic DNA.     

The interaction between some ethyl esters of aminoacids and acetic acid in carbon tetrachloride

The dimerization constant, K₁ of acetic acid in CCl₄ is determined by an IR spectrometric method and is found to have a value of 2252M⁻¹ at 20°. The association constants, K₂, for the interaction between the acetic acid monomer and some aminoacid ethyl esters are determined by the same method and found to have the values given (in M⁻¹ at 20°) for the esters of the following aminoacids: glycine (282 ± 24), dl-alanine (236 ± 33), dl-α-aminobutyric acid (139 ± 11), α-aminoisobutyric acid (172 ± 18). dl-norvaline (104 ± 13), dl-valine (150 ± 8), dl-leucine (108 ± 18) and 3-phenyl-dl-alanine (140 ± 21). A correlation of these experimental values with some structural parameters related to the steric effect of the substituents on the esters is proposed.     

Synthesis, spectrophotometric pH titrations and DNA binding properties of a cyclometalated iridium(III) complex of tetrapyrido[3,2-a:2′,3′-c:3″,2″-h:2?,3?-j]phenazine

A new cyclometalated iridium(III) complex [Ir(ppy)₂(tpphz)]Cl {Hppy = 2-phenylpyridine and tpphz = tetrapyrido[3,2-a:2′,3′-c:3″,2″-h:2?,3?-j]phenazine} has been synthesized and characterized. The pH effects on UV-vis absorption spectra have been studied, and three ground-state acidity ionization constant values have been derived. The calf thymus (ct) DNA binding properties of the complex have also been investigated with UV-vis absorption spectrophotometric titrations, DNA competitive binding with ethidium bromide, DNA melting experiments, viscosity measurements, and density functional theory calculations. The complex was demonstrated to act as a DNA intercalator with a binding constant of (9.29 ± 1.26) × 10⁵ M⁻¹ more than one order of magnitude greater than that previously reported for DNA intercalator of [Ir(ppy)₂(dppz)]⁺.     

Rationally designed chromogenic chemosensor that detects cysteine in aqueous solution with remarkable selectivity

A sensing ensemble for cysteine was assembled conveniently by simply mixing N,N,N′,N′-tetra-(2-pyridylmethyl)-p-xylylenediamine (TPXD), cadmium perchlorate, and pyrocatechol violet in an 1:2:1 molar ratio in water of neutral pH. In the ensemble, [Cd₂(TPXD)]⁴⁺ formed from TPXD and cadmium perchlorate serves as the receptor, and pyrocatechol violet functions as the indicator in sensing the analyte. The detection can be made either spectroscopically from the decrease of the UV-visible absorbance at 665 nm or visually from the color change to yellow upon addition of an aqueous solution of the analyte to the solution of the ensemble. The association constant (K_ass) for the binding of the indicator to the receptor was determined with an isothermal titration calorimeter to be (2.77±0.98)×10⁵ M⁻¹ and that for the binding of cysteine to the receptor was obtained to have (1.62±0.97)×10⁷ M⁻¹ by the non-linear regression analysis of the titration curve obtained by titration of the solution of the ensemble with cysteine solution. The chemosensor showed excellent selectivity for cysteine over other amino acids including homocysteine.     

In vitro binding studies of organotin(IV) complexes of 1,2-bis(1H-benzimidazol-2-yl)ethane-1,2-diol with CT-DNA and nucleotides (5′-GMP and 5′-TMP): Effect of the ancillary ligand on the binding propensity

The chiral benzimidazole ligand, 1,2-Bis(1H-benzimidazol-2-yl)ethane-1,2-diol, L, exhibiting coordination mode with an oxygen atom of alcohol group directed towards the metal ion and another -OH group with different molecular axis directed away from the metal center was utilized as a building block for organotin complexes [C₁₈H₁₉N₄O₂SnCl], [C₂₈H₂₃N₄O₂SnCl] and [C₅₂H₄₂N₄O₂Sn₂] (1-3). Complexes 1 and 3 exhibit a pentacoordinate geometry while the complex 2 reveals hexacoordinated environment around the Sn(IV) metal ions as evidenced by ¹¹⁹Sn NMR studies. The DNA binding ability of benzimidazole ligand and their organotin(IV) complexes 1-3 were examined by employing different biophysical methods. The absorption titration of the complexes with CT-DNA reveal significant hyperchromic effect together with strong bathochromic shift of 4-5 nm which infer substantial binding of the complexes with CT-DNA. The intrinsic binding constant K_b values of the complexes 1-3 were found to be 2.16 ± 0.04 × 10⁴, 3.47 ± 0.04 × 10⁴ and 4.60 ± 0.04 × 10³ M⁻¹, respectively, suggesting pronounced binding of complex 2 with DNA double helix. The mechanism of binding of the complexes was further ascertained by the interaction studies of these complexes with nucleotides (5′-GMP and 5′-TMP) using absorption spectroscopy suggesting a clear preference for 5′-GMP binding which was further authenticated by NMR (¹H and ³¹P NMR) studies.     

Biindolyl-based molecular clefts that bind anions by hydrogen-bonding interactions

Molecular clefts were synthesized from 2,2′-biindolyl scaffold that contains good hydrogen bond donors of two indole NHs. The molecular clefts were systematically modified in two different manners to increase binding affinities toward chloride. The association constant dramatically increased when additional hydrogen-bonding sites of two benzamide units were incorporated to the biindolyl scaffold. For example, the association constants of 1a and 1b are 5.1 × 10³ and 1.4 × 10⁴ M⁻¹ in CH₃CN at 22 ± 1 °C, while reference molecule 10 having only two indole NHs showed the association constant of 340 M⁻¹ under the same conditions. When the biindolyl backbone was structurally preorganized, the binding affinities toward anions were further increased with additional stabilization energy (−ΔΔG) of 2.0 ± 0.2 kcal/mol).     

A novel strapped porphyrin receptor for molecular recognition

A novel strapped porphyrin receptor Zn1, in which two electron-rich bis(p-phenylene)-34-crown ether-10 units are incorporated, has been designed and synthesized from the newly developed intermediate 7 for investigating new chemistry of molecular recognition. ¹H NMR and UV-Vis studies revealed that Zn1 displays relatively weak binding abilities to neutral electron deficient naphthalene-1,8,4,5-tetracarboxydiimide (NDI) derivatives 13 (no simple complexing stoichiometry was observed), 19 (K_a=48(±5) M⁻¹) and 30 (K_a=46(±5) M⁻¹) in chloroform-d, strong binding ability to pyridine derivative 25, (K_a=1.5(±0.12)×10³ M⁻¹) in chloroform, moderately strong binding ability to tetracationic compound 35·4PF₆ (K_a=475(±50) M⁻¹) in acetone-d₆, and very strong binding affinity to compound 22 (K_a=6.5(±0.7)×10⁵ M⁻¹), which consists of one pyridine and two NDI units, in chloroform. Remarkable cooperative effect of the intermolecular metal-ligand coordination and donor-acceptor interactions in complex Zn1·22 was observed by comparing the complexing behaviors between Zn1 and the appropriately designed guests. Complex Zn1·22 possesses an unique three-dimensional tri-site binding feature. For comparison, the complexing affinity of 1 toward compounds 13, 19, and 30 in chloroform-d and 35·4PF₆ in acetone-d₆ has also been investigated and the binding patterns in different complexes were explored. The results demonstrate that strapped porphyrin derivatives are ideal precursors for constructing new generation of three-dimensional multi-site artificial receptors for molecular recognition and host-guest chemistry.     

Macrocycles with two exclusive hydrogen-bonding modes

A series of large, 44-membered macrocycles 7a-e were synthesized and characterized, which display two different diagonal binding modes. The unsubstituted macrocycle 7a strongly binds naphthalene-2,6-dicarboxylate through hydrogen bonds with the association constant (K_a ± 15%) of 4500 M⁻¹ in 40% (v/v) CD₃CN/CDCl₃ at 23 ± 1 °C. Introduction of an electron-withdrawing substituent (Cl) at all four corners increases the binding affinity (22,000 M⁻¹ for 7b), while that of an electron-donating substituent (pyrrolidinyl) greatly decreases it (150 M⁻¹ for 7c). The same propensity has been observed with macrocycles 7d and 7e bearing different substituents at two diagonal corners, suggesting that the relative population of the binding modes would be modulated by controlling the electron density of the aromatic ring.     

Solubility products for aminocarboxylate ligands: determination, validation and speciation uses

A method combining glass electrode potentiometry and computer simulation of speciation is described and used to determine the solubility product for S,S′-ethylenediamine disuccinate (EDDS) (also known as ethylenediiminodibutanedioic acid). This previously unpublished constant is validated by re-measuring K_sp for isomeric EDTA⁴⁻·H₄⁺ and by a linear free energy relationship. For EDDS⁴⁻·H₄⁺, log K_sp=−25.75±0.30.     

Enthalpy change and mechanism of oxidation of o-phenylenediamine by hydrogen peroxide catalyzed by horseradish peroxidase

The hydrogen peroxide-oxidation of o-phenylenediamine (OPD) catalyzed by horseradish peroxidase (HRP) at 37 °C in 50 mM phosphate buffer (pH 7.0) was studied by calorimetry. The apparent molar reaction enthalpy with respect to OPD and hydrogen peroxide were −447 ± 8 kJ mol⁻¹ and −298 ± 9 kJ mol⁻¹, respectively. Oxidation of OPD by H₂O₂ catalyzed by HRP (1.25 nM) at pH 7.0 and 37 °C follows a ping-pong mechanism. The maximum rate V_max (0.91 ± 0.05 μM s⁻¹), Michaelis constant for OPD K_m,S (51 ± 3 μM), Michaelis constant for hydrogen peroxide Km,H₂O₂ (136 ± 8 μM), the catalytic constant k_cat (364 ± 18 s⁻¹) and the second-order rate constants k₊₁ = (2.7 ± 0.3) × 10⁶ M⁻¹ s⁻¹ and k₊₅ = (7.1 ± 0.8) × 10⁶ M⁻¹ s⁻¹ were obtained by the initial rate method.     

Bisphenol A-recognition polymers prepared by covalent molecular imprinting

A specific recognition material for bisphenol A (BPA) was prepared by using a covalent imprinting technique. A chloroform solution containing bisphenol A dimethacrylate as a template, ethylene glycol dimethacrylate as a cross-linking agent and 2,2′-azobis(isobutyronitrile) as an initiator was polymerized by UV initiation. When BPA was removed from the resulting polymer by hydrolysis of the ester bonds with aqueous sodium hydroxide, carboxylic acid residues were generated in the polymer. After the polymer was packed into a stainless steel column, retention factors of BPA and related compounds were measured. The imprinted polymer adsorbed BPA and structurally related compounds such as 4,4′-dihydroxybenzophenone, bis(4-hydroxyphenyl)sulfone and 4,4′-dihydroxybiphenyl. A typical association constant (K_a) was calculated to be 1.72×10⁵ M⁻¹ by Scatchard analysis. Interestingly, 17α- and 17β-estradiol were also bound to the imprinted polymer (K_a=1.68×10⁵ M⁻¹), indicating that the polymer could be used as artificial receptors for screening the compounds having estrogenic action.     

Molecular imprinted Nylon-6 as a recognition material of amino acids

Nylon-6 was functionalized by phase inversion molecular imprinting technique to introduce l-glutamine recognition property. For imprinting l-glutamine in the polymer, 20 wt.% of Nylon-6-formic acid solution with 8 wt.% of l-glutamine template was used for the phase inversion process in water. The resulted polymer including the template molecule was washed with acetic acid solution to extract the template from the polymer. The substrate binding experiments of the l-glutamine imprinted polymer were examined in aqueous l-glutamine, d-glutamine, l-glutamic acid, and d-glutamic acid solution. The binding of l-glutamine increased with the increase of the amino acid concentration from 5 to 20 μM. The value of equilibrium binding constant for l-glutamine, K_E=4.9×10⁵ M⁻¹, was larger than that for d-glutamine, K_E=1.5×10⁵ M⁻¹. The recognition experiments were extended to membrane filtration and quartz-crystal microbalance response by using the imprinted Nylon-6. Evidence was also presented by FT-IR analysis that the amide-hydrogen-bonding interaction between the imprinted Nylon-6 and template was originated for the amino acid recognition.     

Study of binding and denaturation dynamics of IgG and anti-IgG using dual color fluorescence correlation spectroscopy

In this article, we present a systematic study on IgG and Fab fragment of anti-IgG molecules using fluorescence auto- and cross-correlation spectroscopy to investigate their diffusion characteristics, binding kinetics, and the effect of small organic molecule, urea on their binding. Through our analysis, we found that the diffusion coefficient for IgG and Fab fragment of anti-IgG molecules were 37 ± 2 μm² s⁻¹ and 56 ± 2 μm² s⁻¹, respectively. From the binding kinetics study, the respective forward (k_a) and backward (k_d) reaction rates were (5.25 ± 0.25) × 10⁶ M⁻¹ s⁻¹ and 0.08 ± 0.005 s⁻¹, respectively and the corresponding dissociation binding constant (K_D) was 15 ± 2 nM. We also found that urea inhibits the binding of these molecules at 4 M concentration due to denaturation.     

Synthesis and anion binding studies of a new crown ether containing 2,2′-biimidazole

A novel crown ether which incorporates the 2,2′-biimidazole moiety was prepared by cyclization of 1,1′-dibenzyl-1H,1′H-[2,2′]biimidazolyl-4,4′-dicarboxylic acid and 4,7,10-trioxa-1,13-tridecanediamine followed by removal of the benzyl groups. The diacid has been obtained by hydrolysis of the diester previously prepared by alcoholysis of the corresponding dicyano biimidazole. The cyano group is introduced by a palladium-catalyzed procedure starting from the corresponding dibromo biimidazole. The macrocyclic structure of the N-dibenzylated derivative of the receptor has been studied by X-ray diffraction. Binding constants for 1:1 biimidazole–anion complexation (K_assoc) are on the order of 10⁵ M⁻¹ for H₂PO₄⁻ and Cl⁻.     

Copper(II) complexes of N4 tetradentate ligands with flexible alkyl spacers: Crystal structure,DNA binding and cleavage studies

Mononuclear copper(II) complexes, [Cu L1] (ClO₄)₂ (1), [Cu L2] (ClO₄)₂ (2) and [Cu L3] (ClO₄)₂ (3) with quadridentate Schiff base ligands L1 (N,N′-bis-pyridin-2-ylmethyl-butane-1,4-diimine), L2 (N,N′-bis-pyridin-2-ylmethyl-pentane-1,5-diimine) and L3 (N,N′-bis-pyridin-2-ylmethyl-hexane-1,6-diimine) have been synthesized and characterized. The crystal structure data of 1 reveals the existence of the complex in two different geometries, namely a square pyramid and a distorted octahedron, which eventually leads to the packing of the molecule into helical and anti-parallel structures respectively. Absorption titration studies with calf thymus DNA for all three complexes are suggestive of groove binding with binding constant values for 1, 2 and 3 being 2.6 ± 0.2 × 10⁴ M⁻¹, 11.5 ± 0.2 × 10⁴ M⁻¹ and 1.83 ± 0.2 × 10⁴ M⁻¹ respectively. Control cleavage experiments using pBR 322 plasmid DNA and distamycin suggest minor groove binding for these complexes. In the presence of ascorbic acid, the complexes show efficient DNA cleavage, the order of efficiency being 1 > 2 ≅ 3.     

Cellular uptake, cytotoxicity, apoptosis, antioxidant activity and DNA binding of polypyridyl ruthenium(II) complexes

Ruthenium(II) polypyridyl complexes [Ru(phen)₂(APIP)](ClO₄)₂1 and [Ru(phen)₂(HAPIP)](ClO₄)₂2 have been synthesized and characterized. The DNA-binding behaviors were investigated by electronic absorption titration, luminescence spectra, viscosity measurements, thermal denaturation and photoactivated cleavage. The DNA-binding constants K_b for complexes 1 and 2 were determined to be 3.38 (±0.42) × 10⁵ M⁻¹ (s = 1.48) and 3.93 (±0.60) × 10⁵ M⁻¹ (s = 3.14), respectively. The studies on the photocleavage demonstrated that the effects of cleavage are concentration-dependent. The results showed that complexes 1 and 2 interact with CT-DNA by intercalative mode. The cytotoxicity of complexes 1 and 2 has been evaluated by MTT method. The apoptosis assay was carried out with acridine orange/ethidium bromide (AO/EB) staining methods. The cellular uptake showed that complexes can enter into the cytoplasm and accumulate in the nuclei. The antioxidant activity studies suggested that the ligands and complexes may be potential drugs to eliminate the radical.     

Molecular docking analysis and spectroscopic investigations of zinc(II), nickel(II) N-phthaloyl-β-alanine complexes for DNA binding: Evaluation of antibacterial and antitumor activities

Herein, computational molecular docking, UV/visible and fluorescence spectroscopic techniques have been used to explore the DNA binding interactions of N-phthaloyl-β-alanine (NPA) ligand and its Zn(II) and Ni(II) complexes (NPAZn, NPANi). The compounds were further tested for anti-bacterial and anti-tumor activities. Docking analysis depicted that ligand NPA interacted with DNA via intercalation, while its metal complexes showed mixed mode of interactions. Spectroscopic experiments for DNA binding studies were run under physiological conditions of pH (stomach; 4.7, blood; 7.4) and temperature (37 °C). Based on changes in spectral responses, binding parameters for all the compounds were obtained which showed comparatively greater binding constant values (K_b: UV; 1.16 × 10⁵ M⁻¹, Flu; 1.35 × 10⁵ M⁻¹) and more negative free energy changes (ΔG: UV; −30.00 kJ mol⁻¹, Flu; −30.44 kJ mol⁻¹) for NPAZn at pH 4.7. The overall, binding results were also found more significant at stomach pH. Dynamic “K_D” and bimolecular “K_B” constants were evaluated, and the values affirmed the participation of static process for each compound–DNA binding. The greater binding site size values (n > 1) of metal complexes NPAZn and NPANi indicated other sites availability of intercalative compounds. DNA viscosity variation by increasing compound’s concentration further verified the compound–DNA interaction. Antibacterial and tumor inhibitory activities were observed significant for both metal complexes, while ligand has shown no activity. The greater binding affinity of metal complexes, as evaluated both computationally and spectroscopically, further validated the lower IC50 values of complexes as compared to ligand.     

Complexes of benzo-15-crown-5 with protonated primary amines and diamines

Three complexes of benzo-15-crown-5 (B15C5) with protonated primary amines [PhCH₂NH₃(B15C5)](ClO₄), [p-C₆H₄(CH₂NH₃)₂(B15C5)₂](ClO₄)₂, and [(CH₂)₄(NH₃)₂(B15C5)₂](SCN)₂ were isolated and studied in acetonitrile solutions by NMR, and in the solid state by X-ray crystallography. In all complexes, one B15C5 molecule was bound with each R-NH₃⁺ moiety with characteristic small separation of 1.84-1.86 Å between the nitrogen of the R-NH₃⁺ group and the O₅ mean plane of the crown residue. No sandwich-type complexes with a 1:2 R-NH₃⁺/B15C5 stoichiometry were observed. Binding affinities of B15C5 in acetonitrile were similar for all ammonium cations studied: K₁=550±10 M⁻¹ for [PhCH₂NH₃]⁺; K₁=1100±100 and K₂=400±30 M⁻¹ for [p-C₆H₄(CH₂NH₃)₂]²⁺; and K₁=1100±100 and K₂=300±30 M⁻¹ for [H₃N(CH₂)₄NH₃]²⁺. The complexation is primarily enthalpy-driven (ΔH°=−4.9±0.5 kcal/mol, ΔS°=−3.8±1.0 eu for PhCH₂NH₃⁺-B15C5), as determined by variable temperature ¹H NMR titrations.     

Kinetic determination of cysteine and thiosulphate by inhibition of Hg(II) catalyzed ligand substitution reaction

The sulphur containing inhibitors (I), cysteine (Cys) and sodium thiosulphate (THS), have been found to inhibit Hg(II) catalyzed exchange of cyanide in hexacyanoferrate(II) by nitroso-R-salt (NRS). The inhibitory effect of both the ligands are attributed to their binding tendencies with Hg(II) leading to the formation of catalyst-inhibitor (C-I) complex. The reactions have been followed spectrophotometrically in aqueous medium at 720 nm by noting the increase in absorbance of the green colour product, [Fe(CN)₅NRS]³⁻ at pH 6.50 ± 0.02, temp 25.0 ± 0.1 °C and ionic strength (μ) 0.1 M (KNO₃). A most plausible mechanistic scheme involving the role of analytes (inhibitors) has been proposed. The values of equilibrium constants for complex formation between catalyst-inhibitor (K_CI), catalyst-substrate (K_S) and Mechaelis-Menton constant (K_m) have been computed from the kinetic data. The linear calibration curves have been established between absorbance and inhibitor concentrations under specified conditions. Cys and THS have been determined in the range 1-5 × 10^− 7 M and 4.9-16.9 × 10^− 7 M respectively. The detection limits have been computed to be 1 × 10^− 7 M and 4.9 × 10^− 7 M for Cys and THS, respectively.     

Kinetic investigation of a PC(sp)P pincer palladium (II) complex in the Heck reaction

An investigation of the kinetics of the Heck reaction between 4-iodoanisole and styrene catalysed by {cis-1,3-bis[(di-tert-butylphosphino)methyl]-cyclohexane} palladium (II) iodide (1) has been performed in DMF-d₇ solution. Based on mercury poisoning experiments a heterogeneous palladium catalyst formed from the pre-catalyst is proposed. Saturation behaviour with respect to the olefin concentration suggests a mechanism consisting of a pre-equilibrium association of the olefin followed by a rate determining reaction with aryl halide. The equilibrium constant for the olefin association, K₁, and the rate constant for the subsequent oxidative addition step, k₂, were determined to (5.7 ± 2.5) × 10⁻³ and 18.4 ± 2.7 M⁻¹ s⁻¹, respectively.