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Steinau an der Straße, Germany

Krotzky T.,University of Marburg | Grunwald C.,BioCrea GmbH | Egerland U.,BioCrea GmbH | Klebe G.,University of Marburg
Journal of Chemical Information and Modeling | Year: 2015

Determination of structural similarities between protein binding pockets is an important challenge in in silico drug design. It can help to understand selectivity considerations, predict unexpected ligand cross-reactivity, and support the putative annotation of function to orphan proteins. To this end, Cavbase was developed as a tool for the automated detection, storage, and classification of putative protein binding sites. In this context, binding sites are characterized as sets of pseudocenters, which denote surface-exposed physicochemical properties, and can be used to enable mutual binding site comparisons. However, these comparisons tend to be computationally very demanding and often lead to very slow computations of the similarity measures. In this study, we propose RAPMAD (RApid Pocket MAtching using Distances), a new evaluation formalism for Cavbase entries that allows for ultrafast similarity comparisons. Protein binding sites are represented by sets of distance histograms that are both generated and compared with linear complexity. Attaining a speed of more than 20 000 comparisons per second, screenings across large data sets and even entire databases become easily feasible. We demonstrate the discriminative power and the short runtime by performing several classification and retrieval experiments. RAPMAD attains better success rates than the comparison formalism originally implemented into Cavbase or several alternative approaches developed in recent time, while requiring only a fraction of their runtime. The pratical use of our method is finally proven by a successful prospective virtual screening study that aims for the identification of novel inhibitors of the NMDA receptor. © 2014 American Chemical Society. Source

Wagner S.,Helmholtz Center Dresden | Scheunemann M.,Helmholtz Center Dresden | Dipper K.,Helmholtz Center Dresden | Egerland U.,BioCrea GmbH | And 3 more authors.
European Journal of Medicinal Chemistry | Year: 2016

Herein we report the synthesis of fluorinated inhibitors of phosphodiesterase 10A (PDE10A) which can be used potentially as lead structure for the development of a 18F-labeled PDE10A imaging agent for positron emission tomography. The use of ortho-fluoropyridines as residues could potentially enable the introduction of 18F through nucleophilic substitution for radiolabeling purposes. 2-Fluoropyridines are introduced by a Suzuki coupling at different positions of the molecule. The reference compounds, 1,8-dipyridinylimidazo[1,5-a]quinoxalines and 1-pyridinylimidazo[1,5-a]quinoxalines, show inhibitory potencies at best in the subnanomolar range and selectivity factors greater than 38 against other PDE's. 1,8-Dipyridinylimidazo[1,5-a]quinoxalines are more potent inhibitors than 1-pyridinylimidazo[1,5-a]quinoxalines. Using 2-fluoro-3-pyridinyl as residue provided the most potent inhibitors 16 (IC50 Combining double low line 0.12 nM), 17 (IC50 Combining double low line 0.048 nM) and 32 (IC50 Combining double low line 0.037 nM). © 2015 Published by Elsevier Masson SAS. Source

Langen B.,BioCrea GmbH | Dost R.,BioCrea GmbH
ADHD Attention Deficit and Hyperactivity Disorders | Year: 2011

Spontaneously hypertensive rats (SHR) and its counterpart, the Wistar-Kyoto rats (WKY), are probably the most often used animal model of ADHD. However, SHR as model of ADHD have also been criticised partly because of not differing to outbred rat strains. In the present study, adolescent SHR, WKY and Wistar rats from Charles River were tested in open-field, elevated plus maze and novel object recognition and on gastrointestinal transport to more intensively evaluate the strain characteristics. Non-habituated SHR and Wistar rats were more active than WKY rats but contrary to Wistar rats SHR stay hyperactive in a familiar environment. SHR were more sensitive to the alpha2-adrenoceptor agonist guanfacine and the dopamine D1 agonist A-68930 than WKY and Wistar rats, whereas amphetamine, the D1/D5 agonist ABT431 and the D2 agonist quinpirole, similarly affected open-field activity in all strains. In the elevated plus maze, SHR and Wistar rats showed less anxiety-related behaviour than WKY rats. Guanfacine and amphetamine induced an anxiolytic-like activity in SHR but not in WKY and Wistar rats. SHR showed the highest long-term memory in the novel object recognition. Gastrointestinal transport was similar and comparably affected by guanfacine in all rat strains. The present study shows clear differences in the behaviour of SHR and Wistar rats but also of WKY and Wistar rats. The use of SHR as animal model of ADHD is supported. © 2010 Springer-Verlag. Source

Lojewski X.,Massachusetts General Hospital | Lojewski X.,TU Dresden | Lojewski X.,BioCrea GmbH | Staropoli J.F.,Massachusetts General Hospital | And 24 more authors.
Human Molecular Genetics | Year: 2014

Neuronal ceroid lipofuscinosis (NCL) comprises ̃13 genetically distinct lysosomal disorders primarily affecting the central nervous system. Here we report successful reprograming of patient fibroblasts into induced pluripotent stem cells (iPSCs) for the two most common NCL subtypes: classic late-infantile NCL, caused by TPP1(CLN2) mutation, and juvenile NCL, caused by CLN3 mutation. CLN2/TPP1- and CLN3-iPSCs displayed overlapping but distinct biochemical and morphological abnormalities within the endosomal-lysosomal system. In neuronal derivatives, further abnormalities were observed in mitochondria, Golgi and endoplasmic reticulum. While lysosomal storage was undetectable in iPSCs, progressive disease subtype-specific storage material was evident upon neural differentiation and was rescued by reintroducing the non-mutated NCL proteins. In proof-of-concept studies, we further documented differential effects of potential small molecule TPP1 activity inducers. Fenofibrate and gemfibrozil, previously reported to induce TPP1 activity in control cells, failed to increase TPP1 activity in patient iPSC-derived neural progenitor cells. Conversely, nonsense suppression by PTC124 resulted in both an increase of TPP1 activity and attenuation of neuropathology in patient iPSC-derived neural progenitor cells. This study therefore documents the high value of this powerful new set of tools for improved drug screening and for investigating early mechanisms driving NCL pathogenesis. © The Author 2013. Published by Oxford University Press. All rights reserved. Source

Schwan G.,University of Leipzig | Barbar Asskar G.,University of Leipzig | Hofgen N.,BioCrea GmbH | Kubicova L.,University of Leipzig | And 9 more authors.
ChemMedChem | Year: 2014

Based on the potent phosphodiesterase 10 A (PDE10A) inhibitor PQ-10, we synthesized 32 derivatives to determine relationships between their molecular structure and binding properties. Their roles as potential positron emission tomography (PET) ligands were evaluated, as well as their inhibitory potency toward PDE10A and other PDEs, and their metabolic stability was determined in vitro. According to our findings, halo-alkyl substituents at position 2 of the quinazoline moiety and/or halo-alkyloxy substituents at positions 6 or 7 affect not only the compounds′ affinity, but also their selectivity toward PDE10A. As a result of substituting the methoxy group for a monofluoroethoxy or difluoroethoxy group at position 6 of the quinazoline ring, the selectivity for PDE10A over PDE3A increased. The same result was obtained by 6,7-difluoride substitution on the quinoxaline moiety. Finally, fluorinated compounds (R)-7-(fluoromethoxy)-6-methoxy-4-(3-(quinoxaline-2-yloxy)pyrrolidine-1-yl) quinazoline (16 a), 19 a-d, (R)-tert-butyl-3-(6-fluoroquinoxalin-2-yloxy) pyrrolidine-1-carboxylate (29), and 35 (IC50 PDE10A 11-65 nM) showed the highest inhibitory potential. Further, fluoroethoxy substitution at position 7 of the quinazoline ring improved metabolic stability over that of the lead structure PQ-10. Fluor your health: Phosphodiesterase 10 A (PDE10A) has emerged as an attractive target for the development of 18F-labelled brain imaging agents for positron emission tomography. A series of fluorinated dialkoxybiaryl compounds were synthesized and evaluated as PDE10A inhibitors, assisted by QSAR docking studies. The 7-fluoromethoxy derivative appears to be a promising candidate for further development. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Source

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