Recent research and development of DYRK1A inhibitors

Dual specificity tyrosine phosphorylation regulated kinase 1 A(DYRK1 A) is an evolutionarily conserved protein kinase belonging to the CMGC kinase family, which is closely related to Down syndrome(DS)and Alzheimer’s disease(AD). In recent years, not only the treatment of diabetes, but also the treatment of cancer gradually focuses on targeting DYRK1 A. Therefore, a series of DYRK1 A inhibitors have been developed to treat relevant diseases and clarify their treatment mechanism furtherly. DYRK1 A...     

Straightforward Access to a New Class of Dual DYRK1A/CLK1 Inhibitors Possessing a Simple Dihydroquinoline Core

The DYRK (Dual-specificity tyrosine phosphorylation-regulated kinase) family of protein kinases is involved in the pathogenesis of several neurodegenerative diseases. Among them, the DYRK1A protein kinase is thought to be implicated in Alzheimer’s disease (AD) and Down syndrome, and as such, has emerged as an appealing therapeutic target. DYRKs are a subset of the CMGC (CDK, MAPKK, GSK3 and CLK) group of kinases. Within this group of kinases, the CDC2-like kinases (CLKs), such as CLK1, are closely related to DYRKs and have also sparked great interest as potential therapeutic targets for AD. Based on inhibitors previously described in the literature (namely TG003 and INDY), we report in this work a new class of dihydroquinolines exhibiting inhibitory activities in the nanomolar range on hDYRK1A and hCLK1. Moreover, there is overwhelming evidence that oxidative stress plays an important role in AD. Pleasingly, the most potent dual kinase inhibitor 1p exhibited antioxidant and radical scavenging properties. Finally, drug-likeness and molecular docking studies of this new class of DYRK1A/CLK1 inhibitors are also discussed in this article.     

Identification of Pharmacophoric Fragments of DYRK1A Inhibitors Using Machine Learning Classification Models

Dual-specific tyrosine phosphorylation regulated kinase 1 (DYRK1A) has been regarded as a potential therapeutic target of neurodegenerative diseases, and considerable progress has been made in the discovery of DYRK1A inhibitors. Identification of pharmacophoric fragments provides valuable information for structure- and fragment-based design of potent and selective DYRK1A inhibitors. In this study, seven machine learning methods along with five molecular fingerprints were employed to develop qualitative classification models of DYRK1A inhibitors, which were evaluated by cross-validation, test set, and external validation set with four performance indicators of predictive classification accuracy (CA), the area under receiver operating characteristic (AUC), Matthews correlation coefficient (MCC), and balanced accuracy (BA). The PubChem fingerprint-support vector machine model (CA = 0.909, AUC = 0.933, MCC = 0.717, BA = 0.855) and PubChem fingerprint along with the artificial neural model (CA = 0.862, AUC = 0.911, MCC = 0.705, BA = 0.870) were considered as the optimal modes for training set and test set, respectively. A hybrid data balancing method SMOTETL, a combination of synthetic minority over-sampling technique (SMOTE) and Tomek link (TL) algorithms, was applied to explore the impact of balanced learning on the performance of models. Based on the frequency analysis and information gain, pharmacophoric fragments related to DYRK1A inhibition were also identified. All the results will provide theoretical supports and clues for the screening and design of novel DYRK1A inhibitors.     

A convenient new method to construct 1-alkynyl cyclopropanol and its synthetic application to prepare trisubstituted dienones

A new synthetic route was developed via the nucleophilic addition of lithium alkynylide to 1-arylsulfonyl cyclopropanol 1 to afford 1-alkynyl cyclopropanol, which then reacted with aryl iodide to construct trisubstituted cross-conjugated dienones through a palladium-catalyzed process, where the key steps included the regioselective carbopalladation of arylpalladium(II) intermediate across the triple bond of 1-alkynyl cyclopropanol and the ring opening of the cyclopropyl group.     

Trajectory on-the-fly molecular dynamics approach to tunneling splitting in the electronic excited state: A case of tropolone

The semiclassical tunneling method is applied to evaluate the tunneling splitting of tropolone due to the intramolecular proton transfer in the electronic excited state, first time, in a framework of the trajectory on-the-fly molecular dynamics (TOF-MD) approach. To prevent unphysical zero-point vibrational energy transfer among the normal modes of vibration, quantum zero-point vibrational energies are assigned only to the vibrational modes related to intramolecular proton transfer, whereas the remaining modes are treated as bath modes. Practical ways to determine the tunnel-initiating points and tunneling path are introduced. It is shown that the tunneling splitting decreases as the bath-mode energy increases. The experimental tunneling splitting value is well reproduced by the present TOF-MD approach based on the Wentzel-Kramers-Brillouin (WKB) approximation.     

A complexity-based measure and its application to phylogenetic analysis

In this article, we propose two well-defined distance metrics of biological sequences based on a universal complexity profile. To illustrate our metrics, phylogenetic trees of 18 Eutherian mammals from comparison of their mtDNA sequences and 24 coronaviruses using the whole genomes are constructed. The resulting monophyletic clusters agree well with the established taxonomic groups.     

A new aromaticity index and its application to five-membered ring heterocycles

A new index of aromatic character has been devised based upon a statistical evaluation of the deviations in peripheral bond orders. The latter can be derived readily from experimentally determined bond lengths. The utility of this index is exemplified by its application to five-membered ring heterocycles and their mesoionic derivatives.     

A vidicon spectrometer and its application to the analysis of gold

A TV camera which is attached to a monochromator, is used for the photoelectric measurement of optical spectra. The properties of this detection system and its application to the analysis of trace metals in high purity gold with d.c. arc excitation are described. Problems which originate from this application are discussed and results are compared with those obtained with different analytical methods.     

A simultaneous correlation of vapour pressures and thermal data: application to 1-alkanols

R∪žička, K. and Majer, V., 1986. A simultaneous correlation of vapour pressures and thermal data: application to 1-alkanols. Fluid Phase Equilibria, 28: 253-264Possibilities of simultaneous correlation of vapour pressures and thermal data (enthalpy of vaporization and difference between heat capacity of idea gas and liquid) are investigated. This approach permits a reliable evaluation of vapour pressures and/or enthalpies of vaporization far below the normal boiling point and can serve also as a consistency test of experimental data. A simple procedure using smoothed input data is proposed which can be implemented in a software of the data bank of thermodynamic properties. The method is demonstrated on a group of eight 1-alkanols.     

A new laccase-catalyzed domino process and its application to the efficient synthesis of 2-aryl-1H-benzimidazoles

The laccase-catalyzed domino reaction of o-phenylenediamine and benzaldehydes with aerial oxygen as the oxidant exclusively yields 2-aryl-1H-benzimidazoles in good to very good yields. It is easy to perform under very mild reaction conditions.     

ANLIZE: A molecular mechanics force field visualization tool and its application to 18-crown-6

We describe a software tool that allows one to visualize and analyze the importance of each individual steric interaction in a molecular mechanics force field. ANLIZE is presently implemented for the Dreiding force field for use with the Cerius2 software package, but could be implemented in any molecular mechanics package with a graphical user interface. ANLIZE calculates individual interactions in the force field, sorts them by size, and displays them in several ways from a menu of choices. This allows the user to scan through selected interactions to visualize which interactions are the primary determinants of preferred conformations. The features of ANLIZE are illustrated using 18-crown-6 as an example, and the factors governing conformational preference in 18-crown-6 are demonstrated. Users of molecular mechanics packages are encouraged to demand this functionality from commercial software producers.     

A reusable liposome array and its application to assay of growth-hormone-related peptides

We describe a reusable liposome array based on the formation of cleavable disulfide cross-links between liposomes and the surface of a glass slip. The N-succinimidyl 3-(2-pyridyldithio)-propionate (SPDP)-modified liposomes encapsulating a pH-sensitive fluorescence dye were immobilized on a 3-mercaptopropyltrimethoxysilane (MTS)-modified glass slip through the formation of disulfide bonds. The regeneration of a used slip was performed by the lysis of immobilized liposomes with Triton X-100 and the cleavage of disulfide bonds by reduction with TCEP, followed by immobilization of SPDP-modified liposomes. The regeneration steps did not affect the fluorescence intensity of re-immobilized liposomes. The liposome array was applied to simultaneous quantification of growth hormone related peptides, i.e., GHRF and somatostatin, in a mixture. After optimizing the assay condition, the method allowed quantification of GHRF and somatostatin in concentration ranges from 0.5 × 10⁻⁹ to 0.5 × 10⁻⁷ g/mL with detection limits of 2 × 10⁻¹⁰ and 3 × 10⁻¹⁰ g/mL, respectively.     

A self-polishing platinum ring voltammetric sensor and its application to complex media

A self-polishing voltammetric sensor was recently developed and has been applied to samples of urea, milk and sewage water. The polishing device continuously grinds a platinum ring electrode, offering a reproducible and clean electrode surface. Principal component analysis (PCA) and partial least squares (PLS) techniques were applied to interpret the data and to build prediction models. In an evaluation of samples with different urea concentrations, the grinding step allows for repeatable measurements, similar to those after electrochemical cleaning. Furthermore, for the determination of sewage water concentrations in drinking water and for the evaluation of different fat contents in milk samples, the polishing eliminates sensor drift produced by electrode fouling. The results show that the application of a self-polishing unit offers a promising tool for electrochemical studies of difficult analytes and complex media.     

A unified equation for matter transport: its derivation and application

The patterns formed by the limit to the range of (1) rill spacings on a given soil type, and (2) impact spacings of any two sets of waterdrops which differ minimally in pressure, obey the same boundary rules as any two consecutive natural numbers (CNN). The coefficients and exponents of the boundary rules can be multiplied so as to produce a unified equation for matter transport (UEMT). Subsequently, the UEMT can be used to determine the equivalents of environmental lapse rate, vertical wind velocities and temperatures above and below the earth for each of the seven independent co-ordinate systems of the earth. The rill field values agree closely with those measured from matching standard regions.     

Carbon-coated mesoporous silica incorporating organoruthenium complexes and its application to hydrosilylation of 1-hexyne

Research on Chemical Intermediates - The present article describes the construction of the organoruthenium complex catalyst within carbon-coated mesoporous silica and its application to a...     

A fast new approach to pharmacophore mapping and its application to dopaminergic and benzodiazepine agonists

Summary In the absence of a 3D structure of the target biomolecule, to propose the 3D requirements for a small molecule to exhibit a particular bioactivity, one must supply both a bioactive conformation and a superposition rule for every active compound. Our strategy identifies both simultaneously. We first generate and optimize all low-energy conformations by any suitable method. For each conformation we then use ALAD-DIN to calculate the location of points to be considered as part of the superposition. These points include atoms in the molecule and projections from the molecule to hydrogen-bond donors and acceptors or charged groups in the binding site. These positions and the relative energy of each conformation are the input to our new program DISCO. It uses a clique-detection method to find superpositions that contain a least one conformation of each molecule and user-specified numbers of point types and chirality. DISCO is fast; for example, it takes about 1 min CPU to propose pharmacophores from 21 conformations of seven molecules. We typically run DISCO several times to compare alternative pharmacophore maps. For D₂ dopamine agonists DISCO shows that the newer 2-aminothiazoles fit the traditional pharmacophore. Using site points correctly identifies the bioactive enantiomers of indoles to compare with catechols whereas using only ligand points leads to selecting the inactive enantiomer for the pharmacophore map. In addition, DISCO reproduces pharmacophore maps of benzodiazepines in the literature and proposes subtle improvements. Our experience suggests that clique-detection methods will find many applications in computational chemistry and computer-assisted molecular design.