Development of tBu-phenyl acetamide appended thiacalix[4]arene as “Turn-ON” Fluorescent Probe For Selective Recognition of Hg(II) Ions

Herein, a novel N-(4-(tert-butyl)-phenyl)-2-chloroacetamide functionalized thiacalix[4]arene architecture, viz TCAN2PA has been synthesized and the sensing behaviour towards metal ions was explored. The probe, TCAN2PA displayed a “Turn-ON” fluorescence response towards Hg(II) ions in acetonitrile over a series of competing common metal ions. A bathochromic shift in absorption band along with a significant “Turn-ON” fluorescence behaviour of TCAN2PA was observed upon interaction with Hg(II) ions. The lower rim modification of thiacalixarene with N-(4-(tert-butyl)-phenyl)-2-chloroacetamide actively contributes toward the fluorescence property due to the presence of strong electron-donating aryl amido substituent. Fluorescence titration experiments were conducted to find out the limit of detection and to understand binding stoichiometry as well. The electron transfer interactions between the electron-rich TCAN2PA host with Hg(II) ions have been postulated which is also supported by computational modelling insights.

2,6-Bis(E)-4-Methylbenzylidine)-Cyclohexan-1-One As A Fluorescent-On Sensor For Ultra-Selective Detection Of Chromium Ion In Aqueous Media

In current decade, curcumin and its analogues have been broadly used in biological field. However, there are relatively fewer studies regarding their fluorescence based applications for chromium ion sensing in water samples. This article, hereby, reports the synthesis, FTIR and 1H-NMR spectroscopic analyses and optical description of 2,6-bis(E)-4-methylbenzylidine)-cyclohexan-1-one (sensor C), as a fluorescence-on sensor for trace level sensing of chromium. The sensor C exhibited an ultra-selective response to chromium among the tested heavy metal ions. Different parameters were optimized like pH, effect of concentration of sensor C, metal ion and contact time. The binding stoichiometry of C :Cr3+ was calculated to be 2:1 (Job’s plot) with a significantly low detection limit of 2.3×10− 9 M. Sensor C were practically employed for detection of chromium in spiked water samples.

Thermodynamic properties of hydroxypropyl-β-cyclodextrin/guest interaction: a survey of recent studies

For many years, cyclodextrins (CDs) have been the object of attention for their capability of improving the stability, solubility and bioavailability of numerous molecules of interest, including drugs and nutraceuticals. They have low toxicity and for this reason have been employed for different routes of administration, including oral, ocular, nasal and parenteral. Among them, the hydroxypropyl-β-cyclodextrin (HP-β-CD) is the least toxic. Several physicochemical methodologies have been employed for studying cyclodextrin/guest interaction, but isothermal titration calorimetry (ITC) is the only one capable of simultaneously providing the binding constant, ΔH°, ΔS°, ΔG° and the binding stoichiometry. Here, we present the state of the art of ITC studies applied to HP-β-CD/guest complexes, discussing selected publications of the last five years, highlighting the thermodynamic factors that are decisive for optimal encapsulation.

Biophysical and X-ray structural studies of the (GGGTT)3GGG G-quadruplex in complex with N-methyl mesoporphyrin IX

The G-quadruplex (GQ) is a well-studied non-canonical DNA structure formed by G-rich sequences found at telomeres and gene promoters. Biological studies suggest that GQs may play roles in regulating gene expression, DNA replication, and DNA repair. Small molecule ligands were shown to alter GQ structure and stability and thereby serve as novel therapies, particularly against cancer. In this work, we investigate the interaction of a G-rich sequence, 5’-GGGTTGGGTTGGGTTGGG-3’ (T1), with a water-soluble porphyrin, N-methyl mesoporphyrin IX (NMM) via biophysical and X-ray crystallographic studies. UV-vis and fluorescence titrations, as well as a Job plot, revealed a 1:1 binding stoichiometry with an impressively tight binding constant of 30–50 μM-1 and ΔG298 of -10.3 kcal/mol. Eight extended variants of T1 (named T2 –T9) were fully characterized and T7 was identified as a suitable candidate for crystallographic studies. We solved the crystal structures of the T1- and T7-NMM complexes at 2.39 and 2.34 Å resolution, respectively. Both complexes form a 5’-5’ dimer of parallel GQs capped by NMM at the 3’ G-quartet, supporting the 1:1 binding stoichiometry. Our work provides invaluable details about GQ-ligand binding interactions and informs the design of novel anticancer drugs that selectively recognize specific GQs and modulate their stability for therapeutic purposes.

Purification of a heterodimeric Reelin construct to investigate binding stoichiometry

Reelin is a secreted glycoprotein that is integral in neocortex development and synaptic function. Reelin exists as a homodimer with two chains linked by a disulfide bond at cysteine 2101, a feature that is vital to the protein’s function. This is highlighted by the fact that only dimeric Reelin can elicit efficient, canonical signaling, even though a mutated (C2101A) monomeric construct of Reelin retains the capacity to bind to its receptors. Receptor clustering has been shown to be important in the signaling pathway, however direct evidence regarding the stoichiometry of Reelin-receptor binding interaction is lacking. Here we describe the construction and purification of a heterodimeric Reelin construct to investigate the stoichiometry of Reelin-receptor binding and how it affects Reelin pathway signaling. We have devised different strategies and have finalized a protocol to produce a heterodimer of Reelin’s central fragment using differential tagging and tandem affinity chromatography, such that chain A is wild type in amino acid sequence whereas chain B includes a receptor binding site mutation (K2467A). We also validate that the heterodimer is capable of binding to the extracellular domain of one of Reelin’s known receptors, calculating the KD of the interaction. This heterodimeric construct will enable us to understand in greater detail the mechanism by which Reelin interacts with its known receptors and initiates pathway signaling.

Assembly and symmetry of the fungal E3BP-containing core of the Pyruvate Dehydrogenase Complex

The pyruvate dehydrogenase complex (PDC) is a central component of all aerobic respiration, connecting glycolysis to mitochondrial oxidation of pyruvate. Despite its central metabolic role, its precise composition and means of regulation remain unknown. To explain the variation in stoichiometry reported for the E3-recruiting protein X (PX) in the fungal PDC, we established cryo-EM reconstructions of the native and recombinant PDC from the filamentous fungus and model organism Neurospora crassa. We find that the PX C-terminal domain localizes interior to the E2 core. Critically, we show that two distinct arrangements of a trimeric oligomer exists, which both result in strict tetrahedral symmetry of the PDC core interior. Both oligomerization and volume occlusion of the PDC interior by PX appears to limit its binding stoichiometry, which explains the variety of stoichiometries found previously for S. cerevisiae. This also suggests that the PX oligomer stability and size are potential mechanisms to dynamically adjust PDC compostion in response to external cues. Moreover, we find that the site where PX binds is conserved within fungi but not mammals, suggesting that it could be therapeutically targeted. To this end, we also show that a PX knockout results in loss of activity through dysfunctional E3 recruitment, leading to severely impaired N. crassa growth on sucrose. The fungal PDC is thus shown to be fundamentally similar to the mammalian PDC in function but subject to other conditions of possible regulation, conditioned by a steric restrictions imposed by the symmetry of the PDC and its components.

Green Synthesis of Triazole-Based Chemosensors and their Efficacy Towards Mercury Sensing

Background: The synthesis of small organic molecules based Hg2+ ions receptors have gained considerable attention because it is one of the most prevalent toxic metals which is continuously discharged into the environment by different natural and industrial activities. 1,4-Disubstituted 1,2,3-triazoles have been reported as good chemosensors for the detection of various metal ions including Hg2+ ions. Methods: The synthesis of 1,2,3-triazoles (4a-4c) was achieved by Cu(I)-catalyzed azide-alkyne cycloaddition, and their binding affinity towards various metal ions and anions were studied by UVVisible titration experiments. The perchlorate salts of metal ions and tetrabutylammonium salts of anions were utilized for the UV-Visible experiments. DFT studies were performed to understand the binding and mechanism on the sensing of 4a toward Hg2+ using the B3LYP/6-311G(d,p) method for 4a and B3LYP/LANL2DZ for 4a-Hg2+ species on the Gaussian 09W program. Results: The UV-visible experiments indicated that the compounds 4a-4c show a selective response towards Hg2+ ion in UV-Visible spectra, while other ions did not display such changes in the absorption spectra. The binding stoichiometry was evaluated by Job’s plot which indicated the 1:1 binding stoichiometry between receptors (4a-4c) and Hg2+ ion. The detection limit of 4a, 4b and 4c for the Hg2+ ions was found to be 29.1 nM, 3.5 μM and 1.34 μM, respectively. Conclusion: Some 1,2,3-triazole derivatives were synthesized (4a-4c) exhibiting high selectively and sensitivity towards Hg2+ ions in preference to other ions. Compound 4a has a low detection limit of 29.1 nM and the binding constant of 2.3×106 M-1. Similarly, 4b and 4c also showed selective sensing towards Hg2+ ions in the μM range. The observed experimental results were corroborated by density functional theory (DFT) calculations.

Kinetic Exclusion Assay of Biomolecules by Aptamer Capture

DNA aptamers are short nucleotide oligomers selected to bind a target ligand with affinity and specificity rivaling that of antibodies. These remarkable features recommend aptamers as candidates for analytical and therapeutic applications that traditionally use antibodies as biorecognition elements. Numerous traditional and emerging analytical techniques have been proposed and successfully implemented to utilize aptamers for sensing purposes. In this work, we exploited the analytical capabilities offered by the kinetic exclusion assay technology to measure the affinity of fluorescent aptamers for their thrombin target and quantify the concentration of analyte in solution. Standard binding curves constructed by using equilibrated mixtures of aptamers titrated with thrombin were fitted with a 1:1 binding model and provided an effective Kd of the binding in the sub-nanomolar range. However, our experimental results suggest that this simple model does not satisfactorily describe the binding process; therefore, the possibility that the aptamer is composed of a mixture of two or more distinct Kd populations is discussed. The same standard curves, together with a four-parameter logistic equation, were used to determine “unknown” concentrations of thrombin in mock samples. The ability to identify and characterize complex binding stoichiometry, together with the determination of target analyte concentrations in the pM–nM range, supports the adoption of this technology for kinetics, equilibrium, and analytical purposes by employing aptamers as biorecognition elements.

A copper complex formed with neurokinin B: binding stoichiometry, redox properties, self-assembly and cytotoxicity

This work reveals the binding stoichiometry, redox properties, self-assembly and cytotoxicity of the copper complex formed with neurokinin B.

Long-cavity [Pd2L4]4+ cages and designer 1,8-naphthalimide sulfonate guests: rich variation in affinity and differentiated binding stoichiometry

Long cavity dual domain [Pd2L4]4+ cages bind long, dual domain guests, with tunable binding affinities and stoichiometries.