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Theoretical Investigations on the Interactions of Small Compounds with their Molecular Environments
(2015)
In the first part of this work, a combination of theoretical methods for the rational design of covalent inhibitor is presented. Starting from the crystal structure of the covalent complex of a lead compound, quantum mechanical and QM/MM calculations were used to derive the exact geometry of the preceeding non-covalent enzyme inhibitor complex. The geometry of the latter mainly determines the reactivity of the inhibitor against its target enzyme concerning the formation of the covalent bond towards an active site residue. Therefore, this geometry was used as starting point for the optimization of the substitution pattern of the inhibitor such as to increase its binding affinity without loosing its ability to covalently bind to the target protein. The optimization of the chemical structure was supported by using docking procedures, which are best suited to estimate binding affinities that arise from the introduced changes. A screening of the novel substitution patterns resulted in a first generation of model compounds which were further tested for their reactivity against the target. Dynamic simulations on the novel compounds revealed that the orientation that compounds adopt within the active site are such that a covalent interaction with the enzyme is no longer possible. Hence, the chemical structure was further modified, including not only changes in the substituents but also within the core of the molecule. Docking experiments have been conducted to assure sufficiently high binding affinities and to obtain the most favored binding poses. Those have then again been used for dynamic simulations which resulted in structures, for which the bond formation process appeared feasible. A final series of QM/MM calculations considering various protonation states was computed to estimate the reaction energies for the covalent attachment of the inhibitor to the enzyme. The theoretical results indicate a reasonable high inhibition potency of the novel compounds.
The second part concentrates on the environmental influences on the electron density of an inhibitor molecule. Therefore, a vinylsulfone-based model compound was selected for which an experimental crystal structure for the pure compound as well as a theoretically determined enzyme-inhibitor complex have been available. To provide reference data for the larger systems, the conformational space of the isolated molecule was screened for favorable geometries which were later compared to those within the crystal and protein surrounding. The geometry of the crystal structure could readily be taken from the experimental data whereas calculations on the protein complex revealed four potential non-covalent complexes exhibiting different arrangements of the molecule within the active site of the protein as well as two possible protonation states of the catalytic dyad. Hence, all four protein complexes have been compared to the crystal structure of the molecule as well as against the more favorable geometries of the isolated molecule being determined within vacuum or aqueous surrounding. Whereas the molecule itself was found to adopt comparable geometries within all investigated environments, the interactions pattern between the crystal surrounding and the protein differed largely from each other. The favorable formation of dimers within the crystal has a strong stabilizing effect and explains the extraordinarily good quality of the crystal. Within the protein however, repulsive forces have been found between the protein and the inhibitor. The origin of the repulsion could be traced back to effect of on of the substituents to the vinyl scaffold. The difference in the chemical structure in comparison to a well known inhibitor might also explain the experimentally found loss of activity for the model compound in comparison to K11777.
Background: Dual phosphatidylinositol-3-kinase (PI3K)/mammalian target of rapamycin (mTOR) inhibition offers an attractive therapeutic strategy in anaplastic large cell lymphoma depending on oncogenic nucleophosmin-anaplastic lymphoma kinase (NPM-ALK) signaling. We tested the efficacy of a novel dual PI3K/mTOR inhibitor, NVP-BGT226 (BGT226), in two anaplastic large cell lymphoma cell lines in vitro and in vivo and performed an early response evaluation with positron emission tomography (PET) imaging using the standard tracer, 2-deoxy-2-[F-18] fluoro-D-glucose (FDG) and the thymidine analog, 3'-deoxy-3'-[F-18] fluorothymidine (FLT).
Methods: The biological effects of BGT226 were determined in vitro in the NPM-ALK positive cell lines SU-DHL-1 and Karpas299 by 3-[4,5-Dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide assay, propidium iodide staining, and biochemical analysis of PI3K and mTOR downstream signaling. FDG-PET and FLT-PET were performed in immunodeficient mice bearing either SU-DHL-1 or Karpas299 xenografts at baseline and 7 days after initiation of treatment with BGT226. Lymphomas were removed for immunohistochemical analysis of proliferation and apoptosis to correlate PET findings with in vivo treatment effects.
Results: SU-DHL-1 cells showed sensitivity to BGT226 in vitro, with cell cycle arrest in G0/G1 phase and an IC50 in the low nanomolar range, in contrast with Karpas299 cells, which were mainly resistant to BGT226. In vivo, both FDG-PET and FLT-PET discriminated sensitive from resistant lymphoma, as indicated by a significant reduction of tumor-to-background ratios on day 7 in treated SU-DHL-1 lymphoma-bearing animals compared with the control group, but not in animals with Karpas299 xenografts. Imaging results correlated with a marked decrease in the proliferation marker Ki67, and a slight increase in the apoptotic marker, cleaved caspase 3, as revealed by immunostaining of explanted lymphoma tissue.
Conclusion: Dual PI3K/mTOR inhibition using BGT226 is effective in ALK-positive anaplastic large cell lymphoma and can be monitored with both FDG-PET and FLT-PET early on in the course of therapy.
Background: The Ikkα kinase, a subunit of the NF-kappa B-activating IKK complex, has emerged as an important regulator of inflammatory gene expression. However, the role of Ikkα-mediated phosphorylation in haematopoiesis and atherogenesis remains unexplored. In this study, we investigated the effect of a bone marrow (BM)-specific activation-resistant Ikk alpha mutant knock-in on haematopoiesis and atherosclerosis in mice.
Methods and Results: Apolipoprotein E (Apoe)-deficient mice were transplanted with BM carrying an activation-resistant Ikkα gene (Ikkα(AA/AA) Apoe(-/-)) or with Ikkα(+/+) Apoe(-/-) BM as control and were fed a high-cholesterol diet for 8 or 13 weeks. Interestingly, haematopoietic profiling by flow cytometry revealed a significant decrease in B-cells, regulatory T-cells and effector memory T-cells in Ikkα(AA/AA) Apoe(-/-) BM-chimeras, whereas the naive T-cell population was increased. Surprisingly, no differences were observed in the size, stage or cellular composition of atherosclerotic lesions in the aorta and aortic root of Ikkα(AA/AA) Apoe(-/-) vs Ikkα(+/+) Apoe(-/-) BM-transplanted mice, as shown by histological and immunofluorescent stainings. Necrotic core sizes, apoptosis, and intracellular lipid deposits in aortic root lesions were unaltered. In vitro, BM-derived macrophages from Ikkα(AA/AA) Apoe(-/-) vs Ikkα(+/+) Apoe(-/-) mice did not show significant differences in the uptake of oxidized low-density lipoproteins (oxLDL), and, with the exception of Il-12, the secretion of inflammatory proteins in conditions of Tnf-α or oxLDL stimulation was not significantly altered. Furthermore, serum levels of inflammatory proteins as measured with a cytokine bead array were comparable.
Conclusion: Our data reveal an important and previously unrecognized role of haematopoietic Ikkα kinase activation in the homeostasis of B-cells and regulatory T-cells. However, transplantation of Ikkα AA mutant BM did not affect atherosclerosis in Apoe(-/-) mice. This suggests that the diverse functions of Ikkα in haematopoietic cells may counterbalance each other or may not be strong enough to influence atherogenesis, and reveals that targeting haematopoietic Ikkα kinase activity alone does not represent a therapeutic approach.
The maximum of the brain electrical field after NoGo stimuli is located more anteriorly than that after stimuli that tells participants to respond. The difference in topography was called NoGo-Anteriorization (NGA). Recently, there was a debate, whether the NGA is related to a central inhibitory process or not. However, experiments showed that the NGA is not the result of motor potentials during Go trials, the NGA does not represent higher response conflict and or higher mental effort in NoGo trials, and the NGA is not based on less cognitive response selection in NoGo trials. Therefore, the experiments support the assumption that the NGA is connected to an inhibitory mechanism in NoGo conditions.
Der organische Kationentransport im proximalen Tubulus der Niere spielt eine wichtige Rolle bei der Aufrechterhaltung der Homöostase der Körperflüssigkeiten und der Ausschleusung von toxischen organischen Kationen. Der Transport von organischen Kationen wird an der Bürstensaummembran durch den H+/organische Kationen-Austauscher vermittelt, während bei dem Transport von organischen Kationen an der basolateralen Membran das nach innen gerichtete negative Membranpotential eine treibende Kraft darstellt. Durch Expressionsklonierung wurde der erste organische Kationentransporter, rOCT1, aus der Rattenniere isoliert. Kurz darauf wurde im Rahmen dieser Arbeit ein zweiter organischer Kationentransporter ebenfalls aus der Ratenniere kloniert. rOCT2 besteht aus 593 Aminosäuren und besitzt 12 putative Transmembrandomänen. Zum funktionellen Vergleich zwischen rOCT1 und rOCT2 wurde das Oozytenexpressionssystem verwendet. In der vorliegenden Arbeit wurde ein pharmakologisches Profil von rOCT2 erstellt. Das Substratsprektrum von rOCT2 ist dem von rOCT1 sehr ähnlich. Die Affinitäten von rOCT2 gegenüber verschiedenen Substanzen wurden direkt mit denen von rOCT1 verglichen. Einerseits fanden wir bei einigen Substraten Unterschiede in den Km- und Vmax-Werten, aber andererseits auch viele Ähnlichkeiten zwischen beiden Transportern. Anionen (z. B. p-Aminohippurat) wurden als neue Gruppe von Inhibitoren für den durch rOCT1- und rOCT2-vermittelten Transport identifiziert. Die Potentialdifferenz ist die treibende Kraft des rOCT1- und rOCT2-vermittelten Transportes. Wir konnten potentialabhängige Veränderungen der Km-Werte von Cholin-induzierten Einwärtsströmen zeigen. Bei dem Austausch von Na+-Ionen gegen K+-Ionen im Reaktionspuffer wurde die Aufnahme von Cholin und MPP durch rOCT2 erniedrigt. Der bidirektionale Transport von MPP wurde gezeigt und trans-Stimulationsexperimente für MPP-Influx und MPP-Efflux durchgeführt, um die Asymmetrie des Transporters zu studieren. Darüberhinaus wurde in der vorliegenden Arbeit die Interaktion von verschiedenen Substraten mit rOCT1 und rOCT2 untersucht und ein kompetitver und nicht-kompetitiver Hemmtyp bei der TEA-Aufnahme gefunden.