On the application of Job's method of continuous variation to the stoichiometry of protein-ligand complexes

A Simple Live Cell Imaging "Turn-On" Fluorescence Probe for the Selective and Sensitive Detection of Aqueous Hg2+ Ions

A simple, efficient, and reversible fluorescent sensor probe, PBA (2,6-dimethyl pyrone barbituric acid conjugate), comprised of a pro-aromatic donor conjugated with a barbituric acid, was developed for the detection of highly toxic mercuric ions. The probe showed high selectivity and "Turn-On" fluorescence response towards Hg2+ among various metal cations such as Na+, Mg2+, Ca2+, Mn2+, Fe2+, Co2+, Ni2+, Cu2+, Zn2+, Cd2+, Ba2+, Hg2+, and Pb2+, in both homogeneous and microheterogeneous micelle medium sodium dodecyl sulphate (SDS). The binding stoichiometry, limit of detection (LOD), and binding constant for the PBA-Hg complex were determined. The mechanism of binding was ascertained using the N,N'-dimethylbarbituric acid conjugate of 2,6-dimethylpyran (PDMBA), where no binding interaction by deprotonation is possible. In the presence of cysteamine hydrochloride and trifluoroacetic acid (TFA), the complexation of Hg2+ with PBA was demonstrated to be reversible, indicating its potential for the development of reusable sensors. Moreover, the practical applicability of PBA in monitoring Hg2+ in living cells was also evaluated.

Shedding light on the use of graphene oxide-thiosemicarbazone hybrids towards the rapid immobilisation of methylene blue and functional coumarins

Coumarins, methylene blue derivatives, as well as related functional organic dyes have become prevalent tools in life sciences and biomedicine. Their intense blue fluorescence emission makes them ideal agents for a range of applications, yet an unwanted facet of the interesting biological properties of such probes presents a simultaneous environmental threat due to inherent toxicity and persistence in aqueous media. As such, significant research efforts now ought to focus on their removal from the environment, and the sustainable trapping onto widely available, water dispersible and processable adsorbent structures such as graphene oxides could be advantageous. Additionally, flat and aromatic bis(thiosemicarbazones) (BTSCs) have shown biocompatibility and chemotherapeutic potential, as well as intrinsic fluorescence, hence traceability in the environment and in living systems. A new palette of graphene oxide-based hierarchical supramolecular materials incorporating BTSCs were prepared, characterised, and reported hereby. We report on the supramolecular entrapping of several flat, aromatic fluorogenic molecules onto graphene oxide on basis of non-covalent interactions, by virtue of their structural features with potential to form aromatic stacks and H-bonds. The evaluations of the binding interactions in solution by between organic dyes (methylene blue and functional coumarins) and new graphene oxide-anchored Zn(ii) derivatised bis(thiosemicarbazones) nanohybrids were carried out by UV-Vis and fluorescence spectroscopies.

Reinforcing Protein Biochemistry: A Two-Week Experiment Studying Iron(III) Binding by the Transferrin Protein through Stoichiometric Determination, Stability Analysis, and Visualization of the Binding Site

The two-week protein biochemistry experience described herein focuses on reinforcing key biochemical concepts and achieving significant learning domain accomplishments for students (Content Knowledge, Logical Mathematical Reasoning, Visualization, Information Literacy, and Knowledge Integration) and valuable teaching opportunities for instructors. The experience encompasses an exploration of the transport protein serum transferrin as an important regulator of Fe(III) biochemistry and incorporates techniques to assess protein-metal stoichiometry and protein stability and to perform molecular visualization. Students gain practical experience in utilizing spectrophotometric analysis for constructing stoichiometric curves, in performing urea-PAGE, and in applying the PyMOL program to evaluate metal coordination at a protein binding site and the associated protein structural change. The learning and teaching accomplishments provide valuable skills that can be extended into research and translated to other teaching formats.

Chalcone-based Turn-Off Chemosensor for Selective and Susceptible Detection of Fe2+ Ions: Spectroscopic and DFT Investigations

Herein, in this report we are introducing newly synthesized chalcone derivative, "(E)-1-phenyl-3-(4-((5-(((Z)-thiophen-2-ylmethylene)amino)-1,3,4-thiadiazol-2-yl)thio)phenyl)prop-2-en-1-one" (5), as a chemosensor to detect Fe2+ metal ions in HEPES buffer solution of pH 7.5. Spectroscopic techniques were used to confirm the synthesized sensor. To determine the chemical reactivity and molecular stability of the probe, a frontier molecular orbitals investigation was carried out. A molecular electrostatic potential map was investigated to know the binding site of 5 for metal ion coordination. The theoretical absorption and fluorescence emission properties were estimated and correlated with the experimental observations. The sensor showed excellent selectivity for Fe2+ compared to all other studied metal ions. The fluorescence binding studies were carried out by adding different amounts of Fe2+ ions for a fixed concentration of probe 5. The inclusion of Fe2+ ions resulted in a decrease in fluorescence intensity with a bathochromic shift of emission wavelength of 5 due to the 5-Fe2+ complexation. The binding affinity value for the probe was found to be 576.2 M-1 with the help of the Stern-Volmer plot. The Job's plot and mass spectra supported the 2:1 (5: Fe2+) stoichiometry of complex formation. The detection limit and limit of quantification of 5 for Fe2+ were calculated to be 4.79 × 10-5 M and 14.54 × 10-5 M. Further, in addition to this, the photophysical parameters such as fluorescence lifetime of 5 and 5-Fe2+ complex measured to be 0.1439 and 0.1574 ns. The quantum yield of 5 and 5-Fe2+ was found to be 0.0398 and 0.0376. All these experimental findings revealed that probe 5 has excellent selectivity and sensitivity for Fe2+ ions.

Fluorene-Chloroquine Hybrids: Synthesis, in vitro Antiplasmodial Activity, and Inhibition of Heme Detoxification Machinery of Plasmodium falciparum

Fluorene-chloroquine hybrids have been identified as a new promising class of antiplasmodial agents. The most active compound 9d exhibited good in vitro antiplasmodial activity against a chloroquine-sensitive NF54 strain of the human malaria parasite Plasmodium falciparum with an IC50 value of 139 nM. UV-visible absorption, FTIR spectral and 1H NMR titration data corroborated the binding of 9d to monomeric and µ-oxodimeric heme as well as inhibition of β-hematin formation, which collectively supported the inhibition of heme detoxification machinery in P. falciparum. In silico docking studies revealed the binding interactions of the hybrids in the active site of the wild type as well as quadruple mutant of Pf-DHFR-TS dihydrofolate enzyme. Further, the ADMET parameters were predicted and were in good agreement with the expected values, suggesting the drug likeness of the synthesized hybrid molecules.Introduction.

Modifying electron injection kinetics for selective photoreduction of nitroarenes into cyclic and asymmetric azo compounds

Modifying the reactivity of substrates by encapsulation is essential for microenvironment catalysts. Herein, we report an alternative strategy that modifies the entry behaviour of reactants into the microenvironment and substrate inclusion thermodynamics related to the capsule to control the electron injection kinetics and the selectivity of products from the nitroarenes photoreduction. The strategy includes the orchestration of capsule openings to control the electron injection kinetics of electron donors, and the capsule’s pocket to encapsulate more than one nitroarene molecules, facilitating a condensation reaction between the in situ formed azanol and nitroso species to produce azo product. The conceptual microenvironment catalyst endows selective conversion of asymmetric azo products from different nitroarenes, wherein, the estimated diameter and inclusion Gibbs free energy of substrates are used to control and predict the selectivity of products. Inhibition experiments confirm a typical enzymatic conversion, paving a new avenue for rational design of photocatalysts toward green chemistry.

Spectroscopic Determination of Fluoride Using Eriochrome Black T (EBT) as a Spectrophotometric Reagent from Groundwater

Fluoride health problem is a great concern worldwide, most often as a result of groundwater intake. Thus, determination of fluoride is vital to take appropriate measures upon fluoride contamination of water. Potentiometric method of analysis is reliable for the determination of fluoride in various samples. In addition, spectroscopic methods are found important to quantify fluoride levels from water; however, several factors hinder its easier determination. Among the bottlenecks, the use of toxic chemicals and tedious steps in preparing chemicals (e.g., SPADNS method) are to mention a few. In this study, a spectrophotometric method was developed for the determination of fluoride from groundwater using Eriochrome Black T (EBT) as a spectroscopic reagent. Experimental parameters that influence the determination of fluoride including ligand type, kinetics, pH, and ligand-to-metal ratio were assayed. Evaluation of fluoride levels showed that Beer–Lambert's law is obeyed in the range of 0.3–5.0 mg/L at 544 nm. The calibration curve, resulting in good linearity (R² = 0.9997), was considered during quantitative analysis of the samples and in the spiking analysis. The limits of detection (LOD) and quantification (LOQ) of the method were found to be 0.19 and 0.64 mg/L, respectively. The precision studied in terms of intraday and interday at three concentration levels showed less than 5.4% RSD. Applicability of the method was investigated by analyzing groundwater samples spiked with fluoride standards, and satisfactory recoveries in the range of 98.18–111.4 were demonstrated. The developed spectrophotometric method has been successfully applied for fluoride determinations in groundwater samples. Thus, it could be used as an attractive alternative for the determination of fluoride from groundwater.

Cannabidiol Inhibits Tau Aggregation In Vitro

A hallmark of Alzheimer’s disease (AD) is the accumulation of tau protein in the brain. Compelling evidence indicates that the presence of tau aggregates causes irreversible neuronal destruction, eventually leading to synaptic loss. So far, the inhibition of tau aggregation has been recognized as one of the most effective therapeutic strategies. Cannabidiol (CBD), a major component found in Cannabis sativa L., has antioxidant activities as well as numerous neuroprotective features. Therefore, we hypothesize that CBD may serve as a potent substance to hamper tau aggregation in AD. In this study, we aim to investigate the CBD effect on the aggregation of recombinant human tau protein 1N/4R isoform using biochemical methods in vitro and in silico. Using Thioflavin T (ThT) assay, circular dichroism (CD), and atomic force microscopy (AFM), we demonstrated that CBD can suppress tau fibrils formation. Moreover, by quenching assay, docking, and job’s plot, we further demonstrated that one molecule of CBD interacts with one molecule of tau protein through a spontaneous binding. Experiments performed by quenching assay, docking, and Thioflavin T assay further established that the main forces are hydrogen Van der Waals and some non-negligible hydrophobic forces, affecting the lag phase of tau protein kinetics. Taken together, this study provides new insights about a natural substance, CBD, for tau therapy which may offer new hope for the treatment of AD.

Hydroxy-neo-Clerodanes and 5,10-seco-neo-Clerodanes from Salvia decora

Preliminary analysis of the mass spectrometric (MS) and NMR spectroscopic data of the primary fractions from the biologically active extract of Salvia decora revealed spectra that are characteristic for neo-clerodane-type diterpenoids. MS-guided isolation of the bioactive fractions led to the isolation of three new chemical entities, including two hydroxy-neo-clerodanes (1 and 2) and one acylated 5,10-seco-neo-clerodane (3), along with three known diterpenoids (4-6), ursolic acid (7), and eupatorin (8). The structures of the new compounds were established by analysis of the 1D and 2D NMR and MS data, whereas their absolute configuration was deduced using a combination of experimental and theoretical ECD data and confirmed by X-ray crystallography (1 and 4). Furthermore, compounds 1, 3, 4, and 6-8 were evaluated as hPTP1B_1-400 (human protein tyrosine phosphatase) inhibitors, where 7 showed the best activity, with an IC₅₀ value in the lower μM range. Additionally, compound 7 was evaluated as an α-glucosidase inhibitor. The affinity constant of the 7-hPTP1B_1-400 complex was determined by quenching fluorescence experiments (k_a = 1.3 × 10⁴ M^-1), while the stoichiometry ratio (1:1 protein-ligand) was determined by a continuous variation method.

Spectroscopic studies of Thioflavin-T binding to c-Myc G-quadruplex DNA

G-quadruplexes are well-known DNA secondary structures which can be formed both within the DNA and the RNA sequences of the human genome. While many functions of G-quadruplex during cell regulatory events are still unknown, a number of reports have established their role in finding new cancer therapies. In this report, we provide a detailed account of Thioflavin T (ThT) interacting with a promoter gene (c-Myc) which has relevance in several types of human cancers. Using a variety of spectroscopic techniques, we have shown that the binding of ThT is selective to c-Myc G-quadruplex only, having poor interactions with the duplex DNA sequences. UV-Visible titration experiments show that binding involves stacking interactions which were further corroborated by CD experiments. Fluorescence studies showed that the binding of ThT to c-Myc G-quadruplex results in a large increase in the fluorescence emission spectrum of c-Myc G-quadruplex while the same to duplex DNAs was much poor. Binding of ThT to c-Myc G-quadruplex results in thermal stabilization of the quadruplex DNA by up to 7.4 °C and Job plot experiments demonstrated the presence of 1:1 and 2:1 ligand to quadruplex complexes. Finally, the docking study suggested that ThT stacks with the guanine bases in one of the grooves which is in agreement with the CD studies. These results are expected to provide leads into the design of new ThT analogs and derivatives for enhancing the stability and selectivity of new G-quadruplex targeting ligands.

Kaempferol Binding to Zinc(II), Efficient Radical Scavenging through Increased Phenol Acidity

Zinc(II) enhances radical scavenging of the flavonoid kaempferol (Kaem) most significantly for the 1:1 Zn(II)-Kaem complex in equilibrium with the 1:2 Zn(II)-Kaem complex both with high affinity at 3-hydroxyl and 4-carboxyl coordination. In methanol/chloroform (7/3, v/v), 1:1 Zn(II)-Kaem complex reduces β-carotene radical cation, β-Car^•+, with a second-order rate constant, 1.88 × 10⁸ L·mol^-1·s^-1, while both Kaem and 1:2 Zn(II)-Kaem complex are nonreactive, as determined by laser flash photolysis. In ethanol, 1:1 Zn(II)-Kaem complex reduces the 2,2-diphenyl-1-picrylhydrazyl radical, DPPH^•, with a second-order rate constant, 2.48 × 10⁴ L·mol^-1·s^-1, 16 times and 2 times as efficient as Kaem and 1:2 Zn(II)-Kaem complex, respectively, as determined by stopped-flow spectroscopy. Density functional theory calculation results indicate significantly increased acidity of Kaem as ligand in 1:1 Zn(II)-Kaem complex other than in 1:2 Zn(II)-Kaem complex. Kaem in 1:1 Zn(II)-Kaem complex loses two protons (one from 3-hydroxyl and one from phenolic hydroxyl) forming 1:1 Zn(II)-(Kaem-2H) during binding with Zn(II), while Kaem in 1:2 Zn(II)-Kaem complex loses one proton in each ligand forming Zn(II)-(Kaem-H)₂, as confirmed by UV-vis absorption spectroscopy. Zn(II)-(Kaem-2H) is a far stronger reductant than Kaem and Zn(II)-(Kaem-H)₂ as determined by cyclic voltammetry. Significant rate increases for the 1:1 complex in both β-Car^•+ scavenging by electron transfer and DPPH^• scavenging by hydrogen atom transfer were ascribed to decreases of ionization potential and of bond dissociation energy of 4'-OH for deprotonated Zn(II)-(Kaem-2H), respectively. Increased phenol acidity of plant polyphenols by 1:1 coordination with Zn(II) may explain the unique function of Zn(II) as a biological antioxidant and may help to design nontoxic metal-based drugs derived from natural bioactive molecules.

Coassembly of Peptides Derived from β-Sheet Regions of β-Amyloid

In this paper, we investigate the coassembly of peptides derived from the central and C-terminal regions of the β-amyloid peptide (Aβ). In the preceding paper, J. Am. Chem. Soc.2016, DOI: 10.1021/jacs.6b06000, we established that peptides containing residues 17–23 (LVFFAED) from the central region of Aβ and residues 30–36 (AIIGLMV) from the C-terminal region of Aβ assemble to form homotetramers consisting of two hydrogen-bonded dimers. Here, we mix these tetramer-forming peptides and determine how they coassemble. Incorporation of a single ¹⁵N isotopic label into each peptide provides a spectroscopic probe with which to elucidate the coassembly of the peptides by ¹H,¹⁵N HSQC. Job’s method of continuous variation and nonlinear least-squares fitting reveal that the peptides form a mixture of heterotetramers in 3:1, 2:2, and 1:3 stoichiometries, in addition to the homotetramers. These studies also establish the relative stability of each tetramer and show that the 2:2 heterotetramer predominates. ¹⁵N-Edited NOESY shows the 2:2 heterotetramer comprises two different homodimers, rather than two heterodimers. The peptides within the heterotetramer segregate in forming the homodimer subunits, but the two homodimers coassemble in forming the heterotetramer. These studies show that the central and C-terminal regions of Aβ can preferentially segregate within β-sheets and that the resulting segregated β-sheets can further coassemble.

Recognizing the Limited Applicability of Job Plots in Studying Host-Guest Interactions in Supramolecular Chemistry

Continuous variation method, known as Job plot, is the most commonly applied method for the determination of stoichiometry of complex chemical entities for over 100 years. Although, the method was proven successful in the analysis of very stable metal-ligand complexes, we demonstrate that its use in supramolecular chemistry often provides false results. We support this statement with multiple simulations as well as cases studies of several real host-guest systems. We propose an alternative, general method relying on the analysis of residual distribution in titration data fitting. The latter method is more convenient compared to the Job plot and unlike it gives correct results in all real cases studied.

Spectroscopic, biological, and molecular modeling studies on the interactions of [Fe(III)-meloxicam] with G-quadruplex DNA and investigation of its release from bovine serum albumin (BSA) nanoparticles

The guanine-rich sequence, specifically in DNA, telomeric DNA, is a potential target of anticancer drugs. In this work, a mononuclear Fe(III) complex containing two meloxicam ligands was synthesized as a G-quadruplex stabilizer. The interaction between the Fe(III) complex and G-quadruplex with sequence of 5'-G3(T2AG3)3-3' (HTG21) was investigated using spectroscopic methods, molecular modeling, and polymerase chain reaction (PCR) assays. The spectroscopic methods of UV-vis, fluorescence, and circular dichroism showed that the metal complex can effectively induce and stabilize G-quadruplex structure in the G-rich 21-mer sequence. Also, the binding constant between the Fe(III) complex and G-quadruplex was measured by these methods and it was found to be 4.53(±0.30) × 10(5) M(-1)). The PCR stop assay indicated that the Fe(III) complex inhibits DNA amplification. The cell viability assay showed that the complex has significant antitumor activities against Hela cells. According to the UV-vis results, the interaction of the Fe(III) complex with duplex DNA is an order of magnitude lower than G-quadruplex. Furthermore, the release of the complex incorporated in bovine serum albumin nanoparticles was also investigated in physiological conditions. The release of the complex followed a bi-phasic release pattern with high and low releasing rates at the first and second phases, respectively. Also, in order to obtain the binding mode of the Fe(III) complex with G-quadruplex, molecular modeling was performed. The molecular docking results showed that the Fe(III) complex was docked to the end-stacked of the G-quadruplex with a π-π interaction, created between the meloxicam ligand and the guanine bases of the G-quadruplex.

β-Cyclodextrin assisted solubilization of Cu and Cr complexes of flavonoids in aqueous medium: a DNA-interaction study

Cu and Cr complexes of three flavonoids (morin, quercetin and 6-hydroxyflavone) were synthesized and included in beta-cyclodextrin (βCD) with the objective of improving their pharmacokinetic profiles. Then binding with ds.DNA was studied to monitor their interactive tendencies at physiological conditions. The binding constants and other thermodynamic data from UV-vis spectroscopy and cyclic voltammetry revealed Cr-flavonoid-βCD to interact with ds.DNA at pH-7.4 through electrostatic mode of binding while Cu-flavonoid-βCD can intercalate into DNA. The strong binding propensity of Cu-flavonoid-βCD with ds.DNA encourages their application as anticancerous agent.

The promiscuous protein binding ability of erythrosine B studied by metachromasy (metachromasia)

The present study aims to elucidate aspects of the protein binding ability of erythrosine B (ErB), a poly-iodinated xanthene dye and an FDA-approved food colorant (FD&C Red No. 3), which we have identified recently as a promiscuous inhibitor of protein-protein interactions (PPIs) with a remarkably consistent median inhibitory concentration (IC50 ) in the 5- to 30-μM range. Because ErB exhibits metachromasy, that is, color change upon binding to several proteins, we exploited this property to quantify its binding to proteins such as bovine serum albumin (BSA) and CD40L (CD154) and to determine the corresponding binding constants (Kd ) and stoichiometry (nb ) using spectrophotometric methods. Binding was reversible, and the estimated affinities for both protein targets obtained here (Kd values of 14 and 20 μM for BSA and CD40L, respectively) were in good agreement with that expected from the PPI inhibitory activity of ErB. A stoichiometry greater than one was observed both for CD40L and BSA binding (nb of 5-6 and 8-9 for BSA and CD40L, respectively), indicating the possibility of nonspecific binding of the flat and rigid ErB molecule at multiple sites, which could explain the promiscuous PPI inhibitory activity if some of these overlap with the binding site of the protein partner and interfere with the binding.

NMR spectroscopic detection of chirality and enantiopurity in referenced systems without formation of diastereomers

Enantiomeric excess of chiral compounds is a key parameter that determines their activity or therapeutic action. The current paradigm for rapid measurement of enantiomeric excess using NMR is based on the formation of diastereomeric complexes between the chiral analyte and a chiral resolving agent, leading to (at least) two species with no symmetry relationship. Here we report an effective method of enantiomeric excess determination using a symmetrical achiral molecule as the resolving agent, which is based on the complexation with analyte (in the fast exchange regime) without the formation of diastereomers. The use of N,N'-disubstituted oxoporphyrinogen as the resolving agent makes this novel method extremely versatile, and appropriate for various chiral analytes including carboxylic acids, esters, alcohols and protected amino acids using the same achiral molecule. The model of sensing mechanism exhibits a fundamental linear response between enantiomeric excess and the observed magnitude of induced chemical shift non-equivalence in the (1)H NMR spectra.

Synthesis, computational, spectroscopic, thermal and antimicrobial activity studies on some metal-urate complexes

New sixteen uric acid metal complexes of different stoichiometry, stereo-chemistries and modes of interactions were synthesized using different metals Cr, Mn, Fe, Co, Ni, Cu, Cd, UO(2), Na and K. The synthesized complexes were characterized by elemental analysis, spectral (IR, UV-Vis and ESR) methods, thermal analysis (TG, DTA and DSC) and magnetic susceptibility studies. Molecular modeling calculations were used to characterize the ligation sites of the free ligand. Furthermore, quantum chemical parameters of uric acid such as the energies of highest occupied molecular orbital (E(HOMO)), energies of lowest unoccupied molecular orbital (E(LUMO)), the separation energy (ΔE=E(LUMO)-E(HOMO)), the absolute electronegativity, χ, the chemical potential, P(i), the absolute hardness, η and the softness (σ) were obtained for uric acid. Eight different microbial categories were used to study the antimicrobial activity of the free ligand and ten of its complexes. The results indicate that the ligand and its metal complexes possess antimicrobial properties. The stoichiometry of iron-uric acid complex was studied by using different spectrophotometric methods.

2-Aminopyrimidine based 4-aminoquinoline anti-plasmodial agents. Synthesis, biological activity, structure-activity relationship and mode of action studies

2-Aminopyrimidine based 4-aminoquinolines were synthesized using an efficacious protocol. Some of the compounds showed in vitro anti-plasmodial activity against drug-sensitive CQ(S) (3D7) and drug-resistant CQ(R) (K1) strains of Plasmodium falciparum in the nM range. In particular, 5-isopropyloxycarbonyl-6-methyl-4-(2-nitrophenyl)-2-[(7-chloroquinolin-4-ylamino)butylamino] pyrimidine depicted the lowest IC(50) (3.6 nM) value (56-fold less than CQ) against CQ(R) strain. Structure-activity profile and binding with heme, μ-oxo-heme have been studied. Binding assays with DNA revealed better binding with target parasite type AT rich pUC18 DNA. Most compounds were somewhat cytotoxic, but especially cytostatic. Molecular docking analysis with Pf DHFR allowed identification of stabilizing interactions.

Incorporation of basic side chains into cryptolepine scaffold: structure-antimalarial activity relationships and mechanistic studies

The synthesis of cryptolepine derivatives containing basic side-chains at the C-11 position and their evaluations for antiplasmodial and cytotoxicity properties are reported. Propyl, butyl, and cycloalkyl diamine side chains significantly increased activity against chloroquine-resistant Plasmodium falciparum strains while reducing cytotoxicity when compared with the parent compound. Localization studies inside parasite blood stages by fluorescence microscopy showed that these derivatives accumulate inside the nucleus, indicating that the incorporation of a basic side chain is not sufficient enough to promote selective accumulation in the acidic digestive vacuole of the parasite. Most of the compounds within this series showed the ability to bind to a double-stranded DNA duplex as well to monomeric hematin, suggesting that these are possible targets associated with the observed antimalarial activity. Overall, these novel cryptolepine analogues with substantially improved antiplasmodial activity and selectivity index provide a promising starting point for development of potent and highly selective agents against drug-resistant malaria parasites.

Effect of Ionic Strength on Porphyrin Drugs Interaction with Quadruplex DNA Formed by the Promoter Region of C-myc and Bcl2 Oncogenes

C-myc and Bcl2 are well characterized oncogenes that are capable of forming G-quadruplex structures. Promoter regions of C-myc and Bcl2 forming G-quadruplex structures are chemically synthesized and G-quadruplex structure is formed in presence of 100 mM potassium ion. Three different porphyrin drugs, namely TMPyP2, TMPyP3, and TMPyP4 are allowed to interact with quadruplex DNA complex and the site and nature of interaction are studied. Drug interactions with quadruplex DNA were carried out in different potassium ionic strengths using fluorescence spectroscopy. It is found that fluorescence hypochromicity decreases with an increase in ionic strength in the case of TMPyP4, TMPyP3, and TMPyP2. Fluorescence titration studies and Job plots indicate that four molecules of TMPyP4, two molecules of TMPyP3 and TMPyP2 are interacting with one molecule of quadruplex DNA.

Evidence for the binding mode of porphyrins to G-quadruplex DNA

Interactions of porphyrin derivatives 5,10,15,20-tetrakis(N-methylpyridinium-4-yl)-21H,23H-porphyrin (TMPyP4) and 5,10,15,20-tetrakis(N-propylpyridinium-4-yl)-21H,23H-porphyrin (TPrPyP4) with human telomeric AG(3)(T(2)AG(3))(3) G-quadruplex DNAs in 150 mM K(+)-containing buffer in the presence or absence of 40% molecular crowding agent poly(ethylene glycol) (PEG 200) were studied by absorption titration fitting and time-resolved fluorescence spectroscopy. The results show that two TMPyP4 (or TPrPyP4) molecules bind to antiparallel/parallel hybrid structure of AG(3)(T(2)AG(3))(3) G-quadruplex by end-stacking and outside groove binding modes in the absence of PEG. Interestingly, in the presence of PEG one porphyrin molecule is stacked between two parallel AG(3)(T(2)AG(3))(3) G- quadruplexes to form a sandwich structure, another porphyrin molecule is bound to the groove of the G-quadruplex. The interactions of TMPyP4 with different structures of AG(3)(T(2)AG(3))(3) G-quadruplex are non cooperative, the binding constants of two independent binding sites are 1.07 x 10(6) and 4.42 x 10(8) M(-1) for an antiparallel/parallel hybrid structure of AG(3)(T(2)AG(3))(3), 8.67 x 10(5) and 2.26 x 10(8) M(-1) for parallel-stranded AG(3)(T(2)AG(3))(3) G-quadruplex. Conversely, the two binding sites are cooperative for TPrPyP4, the apparent association constants are 5.58 x 10(6) and 1.24 x 10(7) M(-1) for parallel-stranded and antiparallel/parallel hybrid structures of AG(3)(T(2)AG(3))(3) G-quadruplex, respectively.

Resolution of multiple substrate binding sites in cytochrome P450 3A4: the stoichiometry of the enzyme-substrate complexes probed by FRET and Job's titration

To explore the mechanism of homotropic cooperativity in human cytochrome P450 3A4 (CYP3A4) we studied the interactions of the enzyme with 1-pyrenebutanol (1-PB), 1-pyrenemethylamine (PMA), and bromocriptine by FRET from the substrate fluorophore to the heme, and by absorbance spectroscopy. These approaches combined with an innovative setup of titration-by-dilution and continuous variation (Job's titration) experiments allowed us to probe the relationship between substrate binding and the subsequent spin transition caused by 1-PB or bromocriptine or the type-II spectral changes caused by PMA. The 1-PB-induced spin shift in CYP3A4 reveals prominent homotropic cooperativity, which is characterized by a Hill coefficient of 1.8 +/- 0.3 (S50 = 8.0 +/- 1.1 microM). In contrast, the interactions of CYP3A4 with bromocriptine or PMA reveal no cooperativity, exhibiting KD values of 0.31 +/- 0.08 microM and 7.1 +/- 2.3 microM, respectively. The binding of all three substrates monitored by FRET in titration-by-dilution experiments at an enzyme:substrate ratio of 1 reveals a simple bimolecular interaction with KD values of 0.16 +/- 0.09, 4.8 +/- 1.4, and 0.18 +/- 0.09 microM for 1-PB, PMA, and bromocriptine, respectively. Correspondingly, Job's titration experiments showed that the 1-PB-induced spin shift reflects the formation of a complex of the enzyme with two substrate molecules, while bromocriptine and PMA exhibit 1:1 binding stoichiometry. Combining the results of Job's titrations with the value of KD obtained in our FRET experiments, we demonstrate that the interactions of CYP3A4 with 1-PB obey a sequential binding mechanism, where the spin transition is triggered by the binding of 1-PB to the low-affinity site, which becomes possible only upon saturation of the high-affinity site.

Variable path length and counter-flow continuous variation methods for the study of the formation of high-affinity complexes by absorbance spectroscopy. An application to the studies of substrate binding in cytochrome P450

Studies of the equilibrium of protein-ligand interactions and determination of the stoichiometry of protein complexes constitute an important element of routine biochemical practice. In this paper we describe two innovative modifications of Job's method of continuous variation, which allow us to analyze tight interactions and determine stoichiometry in multi-site binding systems, including cases where the absorbance of the ligand overlaps with that of the enzyme-ligand complex. Our results on the interactions of cytochromes P450 3A4 and P450eryF with substrates illustrate the applicability of these approaches to the studies of substrate binding in enzymes that exhibit homotropic cooperativity.

Interactions of some modified mono- and bis-β-cyclodextrins with bovine serum albumin

Two mono-substituted beta-cyclodextrins and two bridged bis-beta-cyclodextrins, that is, mono(6-(2-aminoethylamino)-6-deoxy)-beta-cyclodextrin (1), mono(6-(2-(2-aminoethylamino)ethylamino)-6-deoxy)-beta-cyclodextrin (2), ethylene-1,2-diamino bis-6-(6-deoxy-beta-cyclodextrin) (3), and iminodiethylene-2,2'-diamino bis-6-(6-deoxy-beta-cyclodextrin) (4), were prepared from beta-cyclodextrin. Their binding ability with bovine serum albumin as a model protein was investigated through proton magnetic resonance (1H NMR), ultraviolet visible spectroscopy (UV-vis), circular dichroism (CD), and fluorescence spectroscopy. In the 1H NMR spectra of the modified cyclodextrins, the resolution of proton signals decreases after the addition of BSA. From the UV and CD spectra, it is found that both the UV absorption and the alpha-helix content of BSA increase with the concentration of the modified cyclodextrins. The protein-ligand interactions cause a fluorescence quenching. The quenching constants are determined using the Stern-Volmer equation to provide an observation of the binding affinity between modified cyclodextrins and BSA. All these results indicate that the modified cyclodextrins can interact with BSA and the bridged bis(beta-cyclodextrin)s (3 and 4) have much stronger interactions than the mono-substituted beta-cyclodextrins (1 and 2). The strong binding stability of bis-cyclodextrins should be attributed to the cooperative effect of two adjacent cyclodextrin moieties. Job's plot shows that the complex stoichiometries of BSA to the modified cyclodextrins were 1:4 for 1 and 2, as well as 1:3 for 3 and 4, respectively.

The identification of hydrophobic sites on the surface of proteins using absorption difference spectroscopy of bromophenol blue

Hydrophobic sites on the surface of protein molecules are thought to have important functional roles. The identification of such sites can provide information about the function and mode of interaction with other cellular components. While the fluorescence enhancement of polarity-sensitive dyes has been useful in identifying hydrophobic sites on a number of targets, strong intrinsic quenching of Nile red and ANSA dye fluorescence is observed on binding to a cytochrome c('). Fluorescence quenching is also observed to take place in the presence of a variety of other biologically important molecules which can compromise the quantitative determination of binding constants. Absorption difference spectroscopy is shown not to be sensitive to the presence of fluorescence quenchers but sensitive enough to measure binding constants. The dye BPB is shown to bind to the same hydrophobic sites on proteins as polarity-sensitive fluorescence probes. The absorption spectrum of BPB is also observed to be polarity sensitive. A binding constant of 3x10(6)M(-1) for BPB to BSA has been measured by absorption difference spectroscopy. An empirical correlation is observed between the shape of the absorption difference spectrum of BPB and the polarity of the environment. The results indicate that absorption difference spectroscopy of BPB provides a valuable supplement to fluorescence for determining the presence of hydrophobic sites on the surface of proteins as well as a method for measuring binding constants.

4,4(')-Dianilino-1,1(')-binaphthyl-5,5(')-disulfonate: report on non-beta-sheet conformers of Alzheimer's peptide beta(1-40)

The venerable fluorescent probe of protein hydrophobic regions, 4,4(')-dianilino-1,1(')-binaphthyl-5,5(')-disulfonate (bis-ANS), unexpectedly increases in fluorescence with soluble beta(1-40) in acidic buffer solutions but reacts weakly with amyloid fibrils while other hydrophobic probes react with the fibrils. CD analysis correlates reaction with the probe with random coil/mixed conformations and alpha-helical forms of beta(1-40) in buffer solutions but less so with soluble beta-sheet forms or amyloid fibrils. The kinetics of the fluoroalcohol-induced interconversion of conformers can be followed by changes in bis-ANS fluorescence. Formation of the beta-sheet form in aqueous buffer is limited by a slow component (minutes) while fluoroalcohol-promoted changes between beta-sheet and alpha-helix occur over seconds. Variants of beta(1-40) such as beta(1-42) or the Dutch E22Q mutation of beta(1-40) and fragments beta(1-28), beta(12-28), beta(10-20 amide), and beta(10-35 amide) react with bis-ANS under conditions that do not support fibril formation. Primary amino acid sequence is important as beta(1-11) does not cause bis-ANS fluorescence while beta(1-16) does, but hydrophobicity is not as beta(25-35) and beta(15-20 amide) are unreactive. bis-ANS is a useful biophysical tool for characterizing particular, but not all, soluble Abeta conformations distinct from the fibrillar form of amyloid peptides detected by Thioflavin T.

Reactions of dysprosium with adenine nucleotides

Dysprosium catalyzes a rapid hydrolysis of both ATP and ADP, at ambient temperatures, pH 7.0, where no hydroxide precipitates. The reactive complexes, at pH 6.7, were found to contain 2Dy:1ATP and 3Dy:2ADP. AMP forms an insoluble complex containing 1Dy:2AMP, which does not hydrolyze. ATP also forms a soluble 1Dy:1ATP complex, which does not react. Dysprosium only catalyzes the hydrolysis of ATP above pH 5.8, where it has been titrated to the hydroxide. At the optimum pH (pH 7) the stoichiometric composition is Dy2.ATP.(OH)2, indicating that the active complex is neutral, whereas at pH 5.8 the stoichiometric composition is Dy2.ATP.(OH)+, indicating an inactive cationic complex. The mechanism proposed for the hydrolysis is consistent with those proposed for other in vitro systems known to catalyze the hydrolysis of ATP.