General-base catalysed hydrolysis and nucleophilic substitution of activated amides in aqueous solutions

The reactivity of 1-benzoyl-3-phenyl-1,2,4-triazole (1a) was studied in the presence of a range of weak bases in aqueous solution. A change in mechanism is observed from general-base catalysed hydrolysis to nucleophilic substitution and general-base catalysed nucleophilic substitution. A slight tendency is also observed for the more hydrophobic general bases to show higher reactivity towards 1a. Aspartame is an effective nucleophile, possibly because nucleophilic substitution is subject to intramolecular general-base catalysis. A general conclusion derived from the present results is that unexpected rate effects can only be rationalised provided that the detailed reaction mechanisms are well understood. Copyright (C) 2003 John Wiley Sons, Ltd.</p

A water-soluble tetraazaperopyrene dye as strong G-quadruplex DNA binder

The interactions of the water-soluble tetraazaperopyrene dye 1 with ct-DNA, duplex-[(dAdT)12⋅(dAdT)12], duplex-[(dGdC)12⋅(dGdC)12] as well as with two G-quadruplex-forming sequences, namely the human telomeric 22AG and the promotor sequence c-myc, were investigated by means of UV/visible and fluorescence spectroscopy, isothermal titration calorimetry (ITC) and molecular docking studies. Dye 1 exhibits a high affinity for G-quadruplex structures over duplex DNA structures. Furthermore, the ligand shows promising G-quadruplex discrimination, with an affinity towards c-myc of 2×107 m−1 (i.e., Kd=50 nm), which is higher than for 22AG (4×106 m−1). The ITC data reveal that compound 1 interacts with c-myc in a stoichiometric ratio of 1:1 but also indicate the presence of two identical lower affinity secondary binding sites per quadruplex. In 22AG, there are two high affinity binding sites per quadruplex, that is, one on each side, with a further four weaker binding sites. For both quadruplex structures, the high affinity interactions between compound 1 and the quadruplex-forming nucleic acid structures are weakly endothermic. Molecular docking studies suggest an end-stacking binding mode for compound 1 interacting with quadruplex structures, and a higher affinity for the parallel conformation of c-myc than for the mixed-hybrid conformation of 22AG. In addition, docking studies also suggest that the reduced affinity for duplex DNA structures is due to the non-viability of an intercalative binding mode

A focus on computer vision for non-contact monitoring of catalyst degradation and product formation kinetics

Chemists know the value of looking at a reaction for clues about reaction progress and success, but what-it-looks-like has never been quantified. Reid and co-workers (C. Yan, M. Cowie, C. Howcutt, K. M. P. Wheelhouse, N. S. Hodnett, M. Kollie, M. Gildea, M. H. Goodfellow and M. Reid, Chem. Sci., 2023, 14, 5323–5331, https://doi.org/10.1039/d2sc05702f) have developed an approach that uses camera footage of reactions to obtain quantitative descriptors of changes in reaction mixtures to support kinetic analysis

Investigation of the interactions between methylene blue and intramolecular G-quadruplexes: an explicit distinction in electrochemical behavior

G-quadruplex sequences exist in eukaryotic organisms and prokaryotes, and the investigation of interactions between G-quadruplexes and small molecule ligands is important for gene therapy, biosensor fabrication, fluorescence imaging and so on. Here, we investigated the behaviour of methylene blue (MB), an electroactive molecule, in the presence of different intramolecular G-quadruplexes by electrochemical method using a miniaturized electrochemical device based on its intrinsic electrochemical property. Although the effects of MB on different intramolecular G-quadruplex structures are not obvious by circular dichroism spectroscopy, distinct differences in binding affinities of MB with different intramolecular G-quadruplexes were fast and easily observed by the electrochemical technique. At the same time, for the human telomerase G-rich sequence (HT), the diffusion current of MB changed sensitively under different ion conditions due to the formation of different conformations of HT, which indicated that our electrochemical method has the potential to study the influence of metal ions on the conformations of the G-quadruplexes with simplicity, rapid response and low cost. From all these, new stacking mechanism and rule were obtained, which were also validated by docking studies and isothermal titration calorimetry (ITC)

The problem of racemization in drug discovery and tools to predict it

Introduction: Racemization has long been an ignored risk in drug development, probably because of a lack of convenient access to good tools for its detection and an absence of methods to predict racemization risk. As a result, the potential effects of racemization have been systematically underestimated. Areas covered: Herein, the potential effects of racemization are discussed through a review of drugs for which activity and side effects for both enantiomers are known. Subsequently, drugs known to racemize are discussed and the authors review methods to predict racemization risk. Application of a method quantitatively predicting racemization risk to databases of compounds from the medicinal chemistry literature shows that success in clinical trials is negatively correlated with racemization risk. Expert opinion: It is envisioned that a quantitative method of predicting racemization risk will remove a blind spot from the drug development pipeline. Removal of the blind spot will make drug development more efficient and result in less late-stage attrition of the drug pipeline

Racemisation in chemistry and biology

The two enantiomers of a compound often have profoundly different biological properties and so their liability to racemisation in aqueous solutions is an important piece of information. We have reviewed the available data concerning the process of racemisation in vivo, in the presence biological molecules (e.g. racemase enzymes, serum albumin, cofactors and derivatives) and under purely chemical but aqueous conditions (acid, base and other aqueous systems). Mechanistic studies are described critically in light of reported kinetic data. The types of experimental measurement that can be used to effectively determine rate constants of racemisation in various conditions are discussed and the data they provide is summarised. The proposed origins of enzymatic racemisation are presented and suggest ways to promote the process that are different from processes taking place in bulk water. Experimental and computational studies that provide understanding and quantitative predictions of racemisation risk are also presented

Targeted cell imaging properties of a deep red luminescent iridium(III) complex conjugated with a c-Myc signal peptide

A nuclear localisation sequence (NLS) peptide, PAAKRVKLD, derived from the human c-Myc regulator gene, has been functionalised with a long wavelength (λex = 550 nm; λem = 677 nm) cyclometalated organometallic iridium(III) complex to give the conjugate Ir-CMYC. Confocal fluorescence microscopy studies on human fibroblast cells imaged after 18–24 h incubation show that Ir-CMYC concentrations of 80–100 μM promote good cell uptake and nuclear localisation, which was confirmed though co-localisation studies using Hoechst 33342. In comparison, a structurally related, photophysically analogous iridium(III) complex lacking the peptide sequence, Ir-PYR, showed very different biological behaviour, with no evidence of nuclear, lysosomal or autophagic vesicle localisation and significantly increased toxicity to the cells at concentrations >10 μM that induced mitochondrial dysfunction. Supporting UV-visible and circular dichroism spectroscopic studies show that Ir-PYR and Ir-CMYC display similarly low affinities for DNA (ca. 103 M−1), consistent with electrostatic binding. Therefore the translocation and nuclear uptake properties of Ir-CMYC are attributed to the presence of the PAAKRVKLD nuclear localisation sequence in this complex

A novel cobalt complex for enhancing amperometric and impedimetric DNA detection

In this work we present a novel cobalt complex, [Co(GA)2(aqphen)]Cl that is water-soluble, redox-active and binds to dsDNA. We report that this complex can be used as a signal enhancer when detecting DNA hybridisation using electrochemical impedance spectroscopy (EIS) and differential pulse voltammetry (DPV). The compound mediates its EIS signal enhancement by causing an increase in charge transfer resistance (Rct) when bound to dsDNA. Increased peak currents are also observed with DPV when the compound is incubated with dsDNA as compared with ssDNA. We believe that this compound intercalates specifically with dsDNA and alters the DNA structure to affect the electrostatic barrier to charged redox markers in solution. To our knowledge this is the first example of a single compound that can enhance both amperometric and impedimetric signals for DNA detection. Our findings enable the development of a label-free and multi-modal approach to improve the sensitivity, accuracy and speed of electrochemical DNA detection