5 research outputs found
Fragment-based drug design of small molecule EPHA4 kinase inhibitors
Get PDFLeurs, R. [Promotor]Esch, I.J.P. de [Copromotor
Regiochemistry of the condensation of 2-aroyl-cyclohexanones and 2-cyanoacetamide: 13C-labeling studies and semi-empirical MO calculations
No full textHydroxy-aryl-5,6,7,8-tetrahydroisoquinoline-4-carbonitriles represent interesting chemical scaffolds, but synthetic access to these compounds is limited. The reaction of 2-aroyl-cyclohexanones with 2-cyanoacetamide and base in ethanol has been reported to lead to the formation of the tetrahydroisoquinoline isomer. We show that depending on the electronic nature of the para-substituent on the aryl ring, formation of the regioisomeric tetrahydroquinoline isomer can significantly compete. The electron-donating or -withdrawing properties of the para-substituent of the aryl ring determines the ratio of product isomers. A series of 2-aroyl-cyclohexanones, with para-substituents ranging from electron-donating to electron-withdrawing, were reacted with [2
KLIFS: a structural kinase-ligand interaction database.
No full textProtein kinases play a crucial role in cell signaling and are important drug targets in several therapeutic areas. The KLIFS database contains detailed structural kinase-ligand interaction information derived from all (>2900) structures of catalytic domains of human and mouse protein kinases deposited in the Protein Data Bank in order to provide insights into the structural determinants of kinase-ligand binding and selectivity. The kinase structures have been processed in a consistent manner by systematically analyzing the structural features and molecular interaction fingerprints (IFPs) of a predefined set of 85 binding site residues with bound ligands. KLIFS has been completely rebuilt and extended (>65% more structures) since its first release as a data set, including: novel automated annotation methods for (i) the assessment of ligand-targeted subpockets and the analysis of (ii) DFG and (iii) αC-helix conformations; improved and automated protocols for (iv) the generation of sequence/structure alignments, (v) the curation of ligand atom and bond typing for accurate IFP analysis and (vi) weekly database updates. KLIFS is now accessible via a website (http://klifs.vucompmedchem.nl) that provides a comprehensive visual presentation of different types of chemical, biological and structural chemogenomics data, and allows the user to easily access, compare, search and download the data
Fragment-based lead discovery of small molecule inhibitors for the EPHA4 receptor tyrosine kinase
No full textThe in silico identification, optimization and crystallographic characterization of a 6,7,8,9-tetrahydro-3H-pyrazolo[3,4-c]isoquinolin-1-amine scaffold as an inhibitor for the EPHA4 receptor tyrosine kinase is described. A database containing commercially available compounds was subjected to an in silico screening procedure which was focused on finding novel, EPHA4 hinge binding fragments. This resulted in the identification of 6,7,8,9-tetrahydro-3H- pyrazolo[3,4-c]isoquinolin-1-amine derivatives as EPHA4 inhibitors. Hit exploration yielded a compound with 2 μM (I
KLIFS: A Knowledge-Based Structural Database To Navigate Kinase–Ligand Interaction Space
No full text<p>The Kinase-Ligand Interaction Fingerprints and Structure database (KLIFS) contains a consistent structural alignment and deconstruction of the kinase domains from over 1734 PDB structures covering 190 different human kinases. </p>
<p>Every crystal structure was structurally aligned in a consistent manner, subsequently broken down from the full complex into separate structural parts: the protein, the orthosteric ligand-binding pocket (85 aligned residues covering the catalytic cleft), orthosteric and allosteric ligand(s), ions, organometallics, cofactors, and waters. By combining the pocket with the orthosteric ligand all interactions are annotated using Interactions FingerPrints (IFPs) for systematic comparison.</p>This dataset is part of a 2013 publication in Journal of Medicinal Chemistry (doi: 10.1021/jm400378w). For the new, web-based, and automatically updated version of KLIFS please go to http://klifs.vu-compmedchem.nl as published in the 2016 database issue of Nucleic Acids Research (doi: 10.1093/nar/gkv1082)
