Exploring NMR ensembles of calcium binding proteins: Perspectives to design inhibitors of protein-protein interactions

<p>Abstract</p> <p>Background</p> <p>Disrupting protein-protein interactions by small organic molecules is nowadays a promising strategy employed to block protein targets involved in different pathologies. However, structural changes occurring at the binding interfaces make difficult drug discovery processes using structure-based drug design/virtual screening approaches. Here we focused on two homologous calcium binding proteins, calmodulin and human centrin 2, involved in different cellular functions via protein-protein interactions, and known to undergo important conformational changes upon ligand binding.</p> <p>Results</p> <p>In order to find suitable protein conformations of calmodulin and centrin for further structure-based drug design/virtual screening, we performed <it>in silico </it>structural/energetic analysis and molecular docking of terphenyl (a mimicking alpha-helical molecule known to inhibit protein-protein interactions of calmodulin) into X-ray and NMR ensembles of calmodulin and centrin. We employed several scoring methods in order to find the best protein conformations. Our results show that docking on NMR structures of calmodulin and centrin can be very helpful to take into account conformational changes occurring at protein-protein interfaces.</p> <p>Conclusions</p> <p>NMR structures of protein-protein complexes nowadays available could efficiently be exploited for further structure-based drug design/virtual screening processes employed to design small molecule inhibitors of protein-protein interactions.</p

DYRK1A, a Novel Determinant of the Methionine-Homocysteine Cycle in Different Mouse Models Overexpressing this Down-Syndrome-Associated Kinase

BACKGROUND:Hyperhomocysteinemia, characterized by increased plasma homocysteine level, is associated with an increased risk of atherosclerosis. On the contrary, patients with Down syndrome appear to be protected from the development of atherosclerosis. We previously found a deleterious effect of hyperhomocysteinemia on expression of DYRK1A, a Down-syndrome-associated kinase. As increased expression of DYRK1A and low plasma homocysteine level have been associated with Down syndrome, we aimed to analyze the effect of its over-expression on homocysteine metabolism in mice. METHODOLOGY/PRINCIPAL FINDINGS:Effects of DYRK1A over-expression were examined by biochemical analysis of methionine metabolites, real-time quantitative reverse-transcription polymerase chain reaction, and enzyme activities. We found that over-expression of Dyrk1a increased the hepatic NAD(P)H:quinone oxidoreductase and S-adenosylhomocysteine hydrolase activities, concomitant with decreased level of plasma homocysteine in three mice models overexpressing Dyrk1a. Moreover, these effects were abolished by treatment with harmine, the most potent and specific inhibitor of Dyrk1a. The increased NAD(P)H:quinone oxidoreductase and S-adenosylhomocysteine hydrolase activities were also found in lymphoblastoid cell lines from patients with Down syndrome. CONCLUSIONS/SIGNIFICANCE:Our results might give clues to understand the protective effect of Down syndrome against vascular defect through a decrease of homocysteine level by DYRK1A over-expression. They reveal a link between the Dyrk1a signaling pathway and the homocysteine cycle

A first-in-human study investigating biodistribution, safety and recommended dose of a new radiolabeled MAb targeting FZD10 in metastatic synovial sarcoma patients

Background: Synovial Sarcomas (SS) are rare tumors occurring predominantly in adolescent and young adults with a dismal prognosis in advanced phases. We report a first-in-human phase I of monoclonal antibody (OTSA-101) targeting FZD10, overexpressed in most SS but not present in normal tissues, labelled with radioisotopes and used as a molecular vehicle to specifically deliver radiation to FZD10 expressing SS lesions. Methods: Patients with progressive advanced SS were included. In the first step of this trial, OTSA-101 in vivo biodistribution and lesions uptake were evaluated by repeated whole body planar and SPECT-CT scintigraphies from H1 till H144 after IV injection of 187 MBq of 111In-OTSA-101. A 2D dosimetry study also evaluated the liver absorbed dose when using 90Y-OTSA-101. In the second step, those patients with significant tumor uptake were randomized between 370 MBq (Arm A) and 1110 MBq (Arm B) of 90Y-OTSA-101 for radionuclide therapy. Results: From January 2012 to June 2015, 20 pts. (median age 43 years [21–67]) with advanced SS were enrolled. Even though 111In-OTSA-101 liver uptake appeared to be intense, estimated absorbed liver dose was less than 20 Gy for each patient. Tracer intensity was greater than mediastinum in 10 patients consistent with sufficient tumor uptake to proceed to treatment with 90Y-OTSA-101: 8 were randomized (Arm A: 3 patients and Arm B: 5 patients) and 2 were not randomized due to worsening PS. The most common Grade ≥ 3 AEs were reversible hematological disorders, which were more frequent in Arm B. No objective response was observed. Best response was stable disease in 3/8 patients lasting up to 21 weeks for 1 patient. Conclusions: Radioimmunotherapy targeting FZD10 is feasible in SS patients as all patients presented at least one lesion with 111In-OTSA-101 uptake. Tumor uptake was heterogeneous but sufficient to select 50% of pts. for 90Y-OTSA-101 treatment. The recommended activity for further clinical investigations is 1110 MBq of 90Y-OTSA-101. However, because of hematological toxicity, less energetic particle emitter radioisopotes such as Lutetium 177 may be a better option to wider the therapeutic index. Trial registration: The study was registered on the NCT01469975 ( https://clinicaltrials.gov/ct2/show/NCT01469975 ) website with a registration code NCT01469975 on November the third, 2011

ASPR, amélioration du service pharmaceutique rendu (mesure de satisfaction et optimisation)

LYON1-BU Santé (693882101) / SudocSudocFranceF

Arbres de régression pour l'analyse de séries chaotiques

L'analyse non paramétrique des données (ou des séries) issues de modèles statistiques non additifs a été introduite par Sonquist et Morgan ([1]) puis reprise par Breiman, Friedman, Olshen et Stone ([2]). Nous présentons ici une méthode de prédiction non linéaire reposant sur une partition adaptative de l'espace des phases (reconstruit) du système étudié. La partition est obtenue par une méthode de segmentation récursive de l'espace, dirigée par un critère de maximum d'entropie. Nous illustrons l'intérêt de cette approche pour la prédiction de signaux chaotiques, pour lesquels les algorithmes de prédiction linéaire ne sont pas satisfaisants. Nous montrons que l'erreur de prédiction peut être utilisée pour déterminer les paramètres de reconstruction de l'espace des phases. Les résultats obtenus sont comparés à ceux issus d'autres tests

Synthetic lethals in HIV: ways to avoid drug resistance: Running title: Preventing HIV resistance

International audienceBackground : RNA viruses rapidly accumulate genetic variation, which can give rise to synthetic lethal (SL) and deleterious (SD) mutations. Synthetic lethal mutations (non-lethal when alone but lethal when combined in one genome) have been studied to develop cancer therapies. This principle can also be used against fast-evolving RNA-viruses. Indeed, targeting protein sites involved in SD + SL interactions with a drug would render any mutation of such sites, lethal. Results : Here, we set up a strategy to detect intragenic pairs of SL and SD at the surface of the protein to predict less escapable drug target sites. For this, we detected SD + SL, studying HIV protease (PR) and reverse transcriptase (RT) sequence alignments from two groups of VIH+ individuals: treated with drugs (T) or not (NT). Using a series of statistical approaches, we were able to propose bona fide SD + SL couples. When focusing on spatially close co-variant SD + SL couples at the surface of the protein, we found 5 SD + SL groups (2 in the protease and 3 in the reverse transcriptase), which could be good candidates to form pockets to accommodate potential drugs. Conclusions : Thus, designing drugs targeting these specific SD + SL groups would not allow the virus to mutate any residue involved in such groups without losing an essential function. Moreover, we also show that the selection pressure induced by the treatment leads to the appearance of new mutations, which change the mutational landscape of the protein. This drives the existence of differential SD + SL couples between the drug-treated and non-treated groups. Thus, new anti-viral drugs should be designed differently to target such groups

Exploration of the Structural Asymmetry Induced by the Intrinsic Flexibility of HIV-2 Protease

HIV-2 protease (PR2) is a homodimer targeted by drugs in the treatment of HIV-2 infections. This dimer is often considered symmetric. However, exploration of crystallographic structures showed that the two chains of PR2 exhibit different conformations. This study presents the first analysis of the structural asymmetry of PR2 induced by its intrinsic flexibility. We followed the structural asymmetry of PR2 throughout a molecular dynamics (MD) simulation of 1 microsecond. To do so, we quantified the global and local structural asymmetries of 1001 structures extracted from the MD simulation using the root mean square deviation (RMSD) between the two chains in each structure. We then analyzed the links between global and local asymmetry and PR2 flexibility. Our results showed that the global asymmetry of PR2 evolves over time and that it is not explained by the asymmetry of only one region of PR2. We noted that the most flexible regions of PR2 are the most asymmetric regions, revealing that the structural asymmetry of a region is induced by its intrinsic flexibility. Using multivariate analysis methods, we identified six asymmetric profiles varying from structures exhibiting weak asymmetry to structures with extreme asymmetry in at least eight different regions. The analysis of transitions between the different profiles in the MD simulation showed that two consecutive structures often exhibit similar asymmetric profiles, revealing small deformations. To conclude, this study provides insights which help to better understand PR2’s structure, dynamics, and deformations

Tree Structured Non-linear Signal Modeling and Prediction

In this paper we develop a regression tree approach toidenti cation and prediction of signals which evolve according to an unknown non-linear state space model. In this approach a tree is recursively constructed which partitions the p-dimensional state space into a collection of piecewise homogeneous regions utilizing a 2 p-ary splitting rule with an entropy-based node impurity criterion. On this partition the joint density of the state is approximately piecewise constant leading to a non-linear predictor that nearly attains minimum mean square error. This process decomposition is closely related to a generalized version of the thresholded AR signal model (ART) which we call piecewise constant AR (PCAR). We illustrate the method for two cases where classical linear prediction is ine ective: achaotic &quot;double-scroll&quot; signal measured at the output of a Chua-type electronic circuit, and a second order ART model. We show that the prediction errors are comparable to the nearest neighbor approach to non-linear prediction but with greatly reduced complexity