Binding constant

Phospholipase A2 is potentially an important target for structure-based rational drug design. In order to determine the involvement of phospholipase A2 in the action of non-steroidal anti-inflammatory drugs (NSAIDs), the crystal structure of the complex formed between ...

The anthraquinoid dye, Alizarin Red S, forms an anionic moiety in aqueous solution. The complex formation of this dye was studied with the cationic surfactant, cetyltrimethylammonium bromide, in an aqueous environment at low surfactant concentrations. The complex was studied with the help of ultraviolet–visible spectroscopy. A method of continuous variation was applied to confirm the complex formation and showed that a 1:1 complex was evident from the experimental results. The equilibrium constant for the formation of the complex was determined at various temperatures. Different thermodynamic parameters, free energy of binding, enthalpy of binding and entropy of binding were calculated.

The quantitative structure-activity relationship (QSPR) model was formulated to quantify values of the binding constant (lnK) of a series of ligands to beta-cyclodextrin (β-CD). For this purpose, the multivariate adaptive regression splines (MARSplines) methodology was adopted with molecular descriptors derived from the simplified molecular input line entry specification (SMILES) strings. This approach allows discovery of regression equations consisting of new non-linear components (basis functions) being combinations of molecular descriptors. The model was subjected to the standard internal and external validation procedures, which indicated its high predictive power. The appearance of polarity-related descriptors, such as XlogP, confirms the hydrophobic nature of the cyclodextrin cavity. The model can be used for predicting the affinity of new ligands to β-CD.

"Alzheimer’s disease (AD) is a progressive, neurodegenerative disorder characterized by the deposition of amyloid plaque. The plaque is primarily composed of insoluble beta-amyloid (Aβ) peptide fibrils and elevated metal concentrations, namely copper, iron, and zinc. In a human brain, the neurotoxicity of the plaque has been linked to a Fenton-like reaction wherein the Aβ-metal complex(es) is(are) involved in the generation of reactive oxygen species (ROS), such as hydrogen peroxide and possibly hydroxyl radicals, which are believed to be responsible for the oxidative stress that forms in an AD-affected brain. To date, the majority of studies have focused on Aβ-copper interactions, and to a lesser degree, Aβ-zinc, but Aβ-iron complexes have yet to be studied in detail. As such, the objective of this research is to determine whether an in vitro Aβ-Fe complex can form, and if so, can it facilitate the production of hydrogen peroxide.

Matrix assisted laser desorption/ionization quadrupole time-of-flight mass spectrometry and fluorescence spectroscopy confirmed the formation of a significant amount of Aβ-Fe complex in the presence of Fe3+ but not Fe2+. Additionally, the equilibrium for the reaction (Kd = 4.499 x 10-4 M and Kb = 0.223 x 104 M-1) was found to favor the reactants, although, hydrolysis may have greatly affected these findings.

When a potential was applied to the complex, the resulting reversible cyclic voltammogram (Delta Ep  ~ 60mV) suggests that the complex is redox-active, and thermodynamically capable of reducing O2 to H2O2 (E o ~ 0.48 V vs. Ag/AgCl) based on a calculated formal potential of ~ 0.195 V vs. Ag/AgCl, which is being reported for the first time. However, this reaction was not detected given the reduction wave of oxygen by the complex was not observed. This may be due to fouling of the electrode surface by the hydrolyzed Fe3+ product and/or the kinetically unfavored nature of the reaction given the time frame of the CV experiment. Further study employing other techniques are need to better discern whether this reaction does in fact proceed.

Lastly, when the complex was exposed to excess amounts of 1,10-phenanthroline, a chelating Fe2+ indicator, the absence of a ferrion induced UV-vis absorption band at ~ 530 nm implies that the oxidation state of the complexed iron is 3+.

Taken together, these data present strong evidence for the in vitro complexation of A and Fe3+ to form a redox-active species, Aβ-Fe3+. This species does not appear to participate in the Fenton-like redox cycling of the complexed iron and reduction of oxygen to produce hydrogen peroxide, as previously proposed by Bush and coworkers [Huang, X., et al. (1999) Biochemistry 38, 7609-7616]. However, given the existence of antioxidants in the brain, such as ascorbic acid, which are capable of reducing the Aβ-Fe3+,complex to Aβ-Fe2+, the catalytic reduction of oxygen by Aβ-Fe2+ to produce ROS may be possible."

Human serum albumin (HSA) is a predominant protein in the blood. Most drugs can bind to HSA and be transported to target locations of the body. For this study, we have extracted 3-trans-feruloyl maslinic acid (FMA) from the medicinal plant Tetracera asiatica, its a non-fluorescent derivative have potent anti-cancer, anti-HIV, anti-diabetic, and anti-inflammatory activities. The binding constant of the compound with HSA, calculated from fluorescence data, was found as KFMA = 1.42 ± 0.01 × 108 M−1, which corresponds to 10.9 kcal M−1 of free energy. Furthermore, microTOF-Q mass spectrometry data showed binding of FMA at nanomolar concentrations of FMA to free HSA. The study detected a mass increase from 66,560 Da (free HSA) to 67,919 Da (HSA + drug). This indicated a strong binding of FMA to HSA, resulting in an increase of the protein’s absorbance and fluorescence. The secondary structure of HSA + FMA (0.1 mM) complexes showed the protein secondary structure became partially unfolded upon interaction of FMA with HSA, as well as indicating that HSA–FMA complexes were formed. Docking experiments uncovered the binding mode of FMA in HSA molecule. It was found that FMA binds strongly in different places with hydrogen bonding at IB domain of Arg 114, Leu 115 and Asp 173.

Six transition metal-salen complexes (metal = Fe, Mn
and Cr) 1-6 have been synthesized and characterized using
different spectroscopic and electrochemical techniques. The
binding studies of natural antioxidant, curcumin with the
complexes (1-6) have been carried out by electronic absorption
spectroscopic technique. The substantial shift in the absorption
maximum of complexes (1-6) when they bind to curcumin
indicated that there was a strong binding between them. The
binding constant calculated ranges from 20 to 2.46 X 104 M
-1
s
-1
.
To the best of our knowledge, this is the first report for studying
binding nature of curcumin, the natural antioxidant with these
biologicallly relevant metal-salen complexes.

We present here a tutorial review on the electrospray mass spectrometry technique and its applications to the study of drug-nucleic acid non-covalent complexes. Particular emphasis has been made on the basic principles of the technique, to allow even the non-specialist to design fit-for-purpose mass spectrometry experiments and interpret the results. Standard applications will be described in detail, including the determination of stoichiometries and equilibrium binding constants of non-covalent complexes, the study of binding kinetics, and the development of ligand screening assays. We also outline the potentials of more advanced and/or more recent MS-based techniques (tandem mass spectrometry, ion mobility spectrometry and gas-phase spectroscopy) for the study of the nucleic acid-ligand complexes.

In this paper, we report the analysis of seven benzopyridoindole and benzopyridoquinoxaline drugs binding to different duplex DNA and triple helical DNA, using an approach combining electrospray ionization mass spectrometry (ESI-MS), tandem mass spectrometry (MS/MS), and molecular modeling. The ligands were ranked according to the collision energy (CE50) necessary to dissociate 50% of the complex with the duplex or the triplex in tandem MS. To determine the probable ligand binding site and binding mode, molecular modeling was used to calculate relative ligand binding energies in different binding sites and binding modes. For duplex DNA binding, the ligand-DNA interaction energies are roughly correlated with the experimental CE50, with the two benzopyridoindole ligands more tightly bound than the benzopyridoquinoxaline ligands. There is, however, no marked AT versus GC base preference in binding, as supported both by the ESI-MS and the calculated ligand binding energies. Product ion spectra of the complexes with triplex DNA show only loss of neutral ligand for the benzopyridoquinoxalines, and loss of the third strand for the benzopyridoindoles, the ligand remaining on the duplex part. This indicates a higher binding energy of the benzopyridoindoles, and also shows that the ligands interact with the triplex via the duplex. The ranking of the ligand interaction energies compared with the CE50 values obtained by MS/MS on the complexes with the triplex clearly indicates that the ligands intercalate via the minor groove of the Watson-Crick duplex. Regarding triplex versus duplex selectivity, our experiments have demonstrated that the most selective drugs for triplex share the same heteroaromatic core.

The interactions of caffeine and theophylline with potassium+, cobalt2+ and nickel2+ ions were studied in aqueous solution at physiological pH with constant ligand concentration and various metal ion contents. Fourier Transform infrared spectroscopy and absorption spectra were used to determine the cation binding mode and association constants. Spectroscopic results showed direct and indirect cation interactions for Co2+, Ni2+ and K+ through O6 and N9 atoms (caffeine) and O6, N9 and N7 atoms (theophylline). The overall binding constants were, K(Co–caffeine)=6.92×104 M−1, K(Ni–caffeine)=2.22×104 M−1, K(K–caffeine)=5.08×103 M−1, K(Co–theophylline)=5.06×104 M−1, K(Ni–theophylline)=4.84×104 M−1 and K(K–theophylline)=2.13×103 M−1. The association constants showed weaker interaction for monovalent cation than divalent metal ions.

In this paper, we report the analysis of seven benzopyridoindole and benzopyridoquinoxaline drugs binding to different duplex DNA and triple helical DNA, using an approach combining electrospray ionization mass spectrometry (ESI-MS), tandem mass spectrometry (MS/MS), and molecular modeling. The ligands were ranked according to the collision energy (CE(50)) necessary to dissociate 50% of the complex with the duplex or the triplex in tandem MS. To determine the probable ligand binding site and binding mode, molecular modeling was used to calculate relative ligand binding energies in different binding sites and binding modes. For duplex DNA binding, the ligand-DNA interaction energies are roughly correlated with the experimental CE(50), with the two benzopyridoindole ligands more tightly bound than the benzopyridoquinoxaline ligands. There is, however, no marked AT versus GC base preference in binding, as supported both by the ESI-MS and the calculated ligand binding energies. Product ...