Protein-protein interactions in epidermal growth factor receptors through molecular dynamics

Tesis doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Química Física Aplicada. Fecha de lectura: 23-01-2015Los Receptores de Factor de Crecimiento Epidérmico (EGFR, en inglés) son esencialmente cuatro proteínas: EGFR/ErbB1, ErbB2, ErbB3 y ErbB4. Estas están asociadas con determinados procesos biolóicos y cada vez son reconocidas como dianas terapéuticas importantes contra el cáncer. En esta tesis, se proporcionan modelos basados en homología para los dominios extracelulares (ectodomio, ECD en inglés) de ErbB3 y ErbB4 en sus conformaciones activas, incluyendo el ligando heregulin, seguido de un posterior refinamiento de los modelos a través de dinámica molecular a una resolución atomística (AA). Un modelo construído para la ErbB2 basado en información cristalográfica permitió el análisis de las caracterís ticas comunes observadas entre los miembros de esta familia, concretamente, el movimiento de periscopio del brazo de dimerización y el movimiento de bisagra del subdominio IV. Adicionalmente a esta parte, se proporciona un modelo re - nado para la interacción en las regiones ECD correspondientes al heterodímero ErbB2/ErbB3. Este heterodímero es ampliamente reconocido por tener un alto impacto en el desarrollo del cáncer. El receptor ErbB2 es considerado como una onco-proteína transmembranal que está sobre-expresada en el cáncer de mama. Un tratamiento terapéutico exitoso está basado en el uso de un anticuerpo monoclonal llamado Trastuzumab el cual se sabe que interactúa con el dominio extracelular (ECD-ErbB2). Un mejor entendimiento de la estructura de forma detallada, en la interacción receptor{ anticuerpo es de primordial interés en el diseño de terapias anticáncer más efectivas. Con el fin de discutir la exibilidad del complejo ECD-ErbB2/Trastuzumab, se han hecho tanto una simulación de dinámica molecular de multi-segundos como una análisis de componentes principales (PCA, en inglés) de este sistema. Con el propósito de validar estas simulaciones, se ha realizado un análisis detallado de las interacciones entre el dominio variable del anticuerpo y el subdominio IV de ECD-ErbB2. Esta estructura ha sido elucidada estáticamente mediante cristalografía de Rayos-X. Ciertamente, los resultados de la simulación están en excelente concordancia con la información experimental disponible durante toda la trayectoria. Los resultados de PCA muestran actuaciones colectivas asociadas a un movimiento de bisagra, en el cual, el subdominio II y el dominio constante (CH) se acercan entre sí . Este movimiento es probablemente estabilizado por la fomaci ón de puentes de hidrógeno y puentes salinos entre residuos del brazo de dimerización en el subdominio II y residuos localizados en el dominio constante CH del anticuerpo Trastuzumab. Finalmente, en este punto, se discutió la exibilidad del modelo descrito por dinámica molecular en relación con la estructura cristalográfica. Se ha reportado por primera vez un movimiento del anticuerpo hacia el dominio de dimerización del receptor ErbB2. Este hallazgo podrá tener consecuencias importantes en la acción biológica del anticuerpo monoclonal. Además de lo anteriormente mencionado en modelos puramente atómicos, se ha validado un mapeo desde la resolución AA hacia una resolución de grano{ grueso (Coarse{Grained, CG, en inglés). De esta manera, AA MD sobre el complejo ECD-ErbB2/Trastuzumab-Fab ha sido usada para comparar con simulaciones CG MD. Específicamente, se ha comparado el campo de fuerzas CG Martini con el AA OPLS. Se ha analizado la exibilidad conformacional y las interacciones entre el anticuerpo y el receptor. En esta tesis han sido examinados los siguientes parámetros en los algoritmos de MD para llevar a cabo las simulaciones con Martini: el método de cálculo de interacciones no-enlazantes para la descripción de las interacciones electrostáticas, el valor del radio cut-off de la lista de vecinos (rlist) y el método de Redes Elásticas (Elastic Network, EN, en inglés). Los resultados muestran que en simulaciones de CG MD los modelos basados en domElNeDyn (redes elásticas por dominios), PME y un rlist de 1.4 nm, son comparables a los modelos AA. Los resultados proporcionan una luz para validar el campo de fuerzas Martini tanto en las interacciones proteína-proteína como en la predicción de estructura. Siguiendo este formalismo se han aplicado simulaciones CG MD han sido aplicadas para estudiar la infuencia del Trastuzumab en la estructura y dinámica del dímero ErbB2 entero, incluyendo la bicapa lipídica. El uso de modelos CG para estudiar tales complejos es al menos de momento, obligatorio, debido al gran tamaño del sistema entero. El modelo Martini lo hace satisfactoriamente bien, arrojando resultados a la par con aquellos obtenidos por modelos AA, como también con la información experimental existente sobre receptores homólogos. Por ejemplo, los dominios ECD e intracelular se aproximan a la superficie de la bicapa lipídica en sendos casos, el monómero y el dímero. El Trastuzumab- Fab dificulta la interacción de los receptores con la bicapa lipídica. Otro efecto interesante del anticuerpo es la alteración de la disposición anti-paralela de los segmentos yuxtamembrana en el caso del dímero. Estos hallazgos ayudan a entender el efecto del anticuerpo sobre la bioactividad del receptor.The family of epidermal growth factor receptors (EGFR) is composed by four members: EGFR/ErbB1, ErbB2, ErbB3 and ErbB4. They are associated with a number of biological processes and are becoming increasingly recognized as important therapeutic targets against cancer. In this thesis, some models, based on homology, there are provided for the extracellular domains (ectodomain, ECD) of ErbB3 and ErbB4 in their active conformations, including a heregulin ligand, followed by further re nement of the models by molecular dynamics (MD) simulations at atomistic (AA) resolution. A model built for ErbB2 based on crystallographic information allowed an analysis of the common features observed among members of the family, namely, the periscope movement of the dimerization arm and the hinge displacement of subdomain IV. In addition, a re ned model for the interaction of the ECD corresponding to a ErbB2/ErbB3 heterodimer is given. This heterodimer is widely recognized to have a high impact in cancer development. The ErbB2 receptor is a transmembrane oncoprotein that is over expressed in breast cancer. A successful therapeutic treatment is a monoclonal antibody called Trastuzumab which interacts with the ErbB2 extracellular domain (ECD-ErbB2). A better understanding of the detailed structure of the receptor-antibody interaction is indeed of prime interest for the design of more e ective anticancer therapies. To analyze the exibility of the complex ECD-ErbB2/Trastuzumab, a multinanosecond MD simulation together with an analysis of uctuations through a principal component analysis (PCA) of this system, was carried out. For validating the simulations, a detailed analysis of the variable antibody domain interactions with the extracellular subdomain IV of ErbB2 was performed. This structure has been statically elucidated by X-ray crystallography. Indeed, the simulation results are in excellent agreement with the available experimental information. The PCA shows collective uctuations resulting in a hinge motion in which subdomain II and constant domain (CH) approach each other. This movement is likely stabilized by the formation of H-bonds and salt bridge interactions between residues of the dimerization arm in the subdomain II and the Summary antibody Trastuzumab residues located in the CH domain. Finally, the exibility of the molecular dynamics model in relation with the static X-ray structure was discussed. A movement of the antibody towards the dimerization domain of the ErbB2 receptor is reported for the rst time. This nding could have relevant consequences on the biological action of the monoclonal antibody. In addition to the above mentioned pure atomistic models, a mapping from AA to coarse-grained (CG) resolution has been validated. In this manner AA MD on ECD-ErbB2/Trastuzumab-Fab has been used to compare with CG MD simulations. Speci cally, the CG Martini force eld has been compared with the AA OPLS representation. The conformational exibility and interactions between the antibody and the receptor have been analyzed. In this thesis the following parameters have been tested in the MD algorithms to carry out the Martini simulations: the non-bonded interactions methods to calculate the electrostatic interactions, the value of the neighbor lists cut-o radius (rlist) and the Elastic Network method. The results show that when used in MD simulations domElNeDyn models, PME and an rlist of 1.4 nm, are comparable to the AA protein models. The results shed light to validate the Martini force eld in the protein{protein interactions and towards protein prediction structure. Therefore, CG MD simulations have been applied to study the in uence of the Trastuzumab monoclonal antibody on the structure and dynamics of the full-length ErbB2 receptor dimer, including the lipid bilayer. The usage of CG models to study such complexes is almost mandatory, at present, due to the large size of the whole system. The Martini model performs satisfactorily well, giving results well-matched with those obtained by AA models as well as with the experimental information existing on homologous receptors. For example, the ecto and intracellular domains approach the bilayer surface in both the monomer and dimer cases. The Trastuzumab-Fab hinders the interaction of the receptors with the lipid bilayer. Another interesting e ect of the antibody is the disruption of the antiparallel arrangement of the juxtamembrane segments in the dimer case. These ndings might help to understand the e ect of the antibody on the receptor bioactivity

Morphology and ion diffusion in PEDOT:Tos. A coarse grained molecular dynamics simulation

A Martini coarse-grained Molecular Dynamics (MD) model for the doped conducting polymer poly(3,4-ethylenedioxythiophene) (PEDOT) is developed. The morphology of PEDOT:Tos (i.e. PEDOT doped with molecular tosylate) and its crystallization in aqueous solution for different oxidation levels were calculated using the developed method and compared with corresponding all atomistic MD simulations. The diffusion coefficients of Na+ and Cl- ions in PEDOT:Tos are studied using the developed coarse-grained MD approach. It is shown that the diffusion coefficients decrease exponentially as the hydration level is reduced. It is also predicted that the diffusion coefficients decrease when the doping level of PEDOT is increased. The observed behavior is related to the evolution of water clusters and trapping of ions around the polymer matrix as the hydration level changes. The predicted behavior of the ionic diffusion coefficients can be tested experimentally, and we believe that molecular picture of ionic diffusion in PEDOT unraveled in the present study is instrumental for the design of polymeric materials and devices for better and enhanced performance.This work was supported by the Troëdssons foundation (896/16), Knut and Alice Wallenberg Foundation through the project The Tail of the Sun, and the Swedish Research Council via ‘‘Research Environment grant’’ on ‘‘Disposable paper fuel cells’’ (201605990). IZ thanks the Advanced Functional Material center at Linköping University for financial support

Charge transport and structure in semimetallic polymers

Owing to changes in their chemistry and structure, polymers can be fabricated to demonstrate vastly different electrical conductivities over many orders of magnitude. At the high end of conductivity is the class of conducting polymers, which are ideal candidates for many applications in low-cost electronics. Here, we report the influence of the nature of the doping anion at high doping levels within the semi-metallic conducting polymer poly(3,4-ethylenedioxythiophene) (PEDOT) on its electronic transport properties. Hall effect measurements on a variety of PEDOT samples show that the choice of doping anion can lead to an order of magnitude enhancement in the charge carrier mobility > 3 cm2/Vs at conductivities approaching 3000 S/cm under ambient conditions. Grazing Incidence Wide Angle X-ray Scattering, Density Functional Theory calculations, and Molecular Dynamics simulations indicate that the chosen doping anion modifies the way PEDOT chains stack together. This link between structure and specific anion doping at high doping levels has ramifications for the fabrication of conducting polymer-based devices. © 2017 The Authors. Journal of Polymer Science Part B: Polymer Physics Published by Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2018, 56, 97–104.The authors acknowledge the European Research Council (ERC-starting-grant 307596), the Swedish foundation for strategic research (project: “Nano-material and Scalable TE materials”), the Knut and Alice Wallenberg foundation (project “Power Paper” and “Tail of the Sun”), The Swedish Energy Agency (3833221), the Swedish Research Council via “Research Environment grant” on “Disposable paper fuel cells” (2016205990), and the Advanced Functional Materials Center at Link€oping University. The authors thank Masatsugu Yamashita from the THz Sensing & Imaging Lab at RIKEN in Japan for conducting the THz reflectance spectroscopy experiments. D.R. Evans acknowledges the support of the Australian Research Council through the Future Fellowship scheme (FT160100300). J.W. Andreasen acknowledges the support of the European Research Council (ERC-consolidator-grant 681881)

UFR2709, a nicotinic acetylcholine receptor antagonist, decreases ethanol intake in alcohol-preferring rats

Brain nicotinic acetylcholine receptors (nAChRs), a heterogeneous family of pentameric acetylcholine-gated cation channels, have been suggested as molecular targets for the treatment of alcohol abuse and dependence. Here, we examined the effect of the competitive nAChR antagonist UFR2709 on the alcohol consumption of high-alcohol-drinking UChB rats. UChB rats were given free access to ethanol for 24-h periods in a two-bottle free-choice paradigm and their ethanol and water intake were measured. The animals were i.p injected daily for 17 days with a 10, 5, 2.5 or 1 mg/kg dose of UFR2709. Potential confounding motor effects of UFR2709 were assessed by examining the locomotor activity of animals administered the highest dose of UR2709 tested (10 mg/kg i.p.). UFR2709 reduced ethanol consumption and ethanol preference and increased water consumption in a dose-dependent manner. The most effective dose of UFR2709 was 2.5 mg/kg, which induced a 56% reduction in alcohol consumption. Administration of UFR2709 did not affect the weight or locomotor activity of the rats, suggesting that its effects on alcohol consumption and preference were mediated by specific nAChRs

Quid: observatorio de medios

El informe está dividido en cuatro apartados: “Derecho a la información y transparencia”, “La televisión mexicana”, “Empresas y prácticas periodísticas” y “Los que se fueron”. En el primero de ellos se presenta un texto que ayuda a entender cuál es el momento en el que se encuentran las propuestas legislativas para regular a los medios y las telecomunicaciones en México, y una evaluación de los primeros cinco años del Instituto de Transparencia e Información Pública de Jalisco. El segundo apartado del informe es ecléctico, pues se compone de artículos que trabajan distintas temáticas de la televisión:la estructura y oferta de la televisión en nuestro país (en particular en la ciudad de Guadalajara), la televisión por cable (enfatizando el caso de Megacable), un recuento de cómo se gestó el Canal 44 y de sus prospectivas en 2011, y los mundiales de futbol. La tercera parte del informe documenta algunas de las situaciones más importantes que se viven en el periodismo local: estos trabajos presentan sistemas en crisis (alta vulnerabilidad de los periodistas mexicanos ante un clima de violencia que lejos de disminuir va en aumento, y la participación, por acción u omisión, del Estado mexicano en la sistemática violación de los derechos de quienes dedican su vida al trabajo periodístico. Los siguientes artículos tratan sobre las transformaciones de las empresas periodísticas, particularmente las del sector de la prensa escrita: la rápida e inexorable desaparición de los suplementos culturales, y una radiografía sobre las formas de producción de algunas secciones internacionales de los periódicos tapatíos. Al final se presentan las semblanzas de José Galindo, Raúl Mora Lomelí, S.J., Tomás Eloy Martínez y Juan Pablo Rosell.ITESO, A.C

Impact of operatoŕs experience on peri-procedural outcomes with Watchman FLX: Insights from the FLX-SPA registry

Background: The Watchman FLX is a device upgrade of the Watchman 2.5 that incorporates several design enhancements intended to simplify left atrial appendage occlusion (LAAO) and improve procedural outcomes. This study compares peri-procedural results of LAAO with Watchman FLX (Boston Scientific, Marlborough, Massachusetts) in centers with varying degrees of experience with the Watchman 2.5 and Watchman FLX. Methods: Prospective, multicenter, 'real-world' registry including consecutive patients undergoing LAAO with the Watchman FLX at 26 Spanish sites (FLX-SPA registry). Implanting centers were classified according to the center's prior experience with the Watchman 2.5. A further division of centers according to whether or not they had performed ≤ 10 or > 10Watchman FLX implants was prespecified at the beginning of the study. Procedural outcomes of institutions stratified according to their experience with the Watchman 2.5 and FLX devices were compared. Results: 359 patients [mean age 75.5 (SD8.1), CHA2DS2-VASc 4.4 (SD1.4), HAS-BLED 3.8(SD0.9)] were included. Global success rate was 98.6%, successful LAAO with the first selected device size was achieved in 95.5% patients and the device was implanted at first attempt in 78.6% cases. There were only 9(2.5%) major peri-procedural complications. No differences in efficacy or safety results according to the centeŕs previous experience with Watchman 2.5 and procedural volume with Watchman FLX existed. Conclusions: The Watchman FLX attains high procedural success rates with complete LAA sealing in unselected, real-world patients, along with a low incidence of peri-procedural complications, regardless of operatoŕs experience with its previous device iteration or the number of Watchman FLX devices implanted

Corrigendum to ‘a horizon scan exercise for aquatic invasive alien species in Iberian inland waters’

info:eu-repo/semantics/publishedVersio

Effectiveness of an intervention for improving drug prescription in primary care patients with multimorbidity and polypharmacy:Study protocol of a cluster randomized clinical trial (Multi-PAP project)

This study was funded by the Fondo de Investigaciones Sanitarias ISCIII (Grant Numbers PI15/00276, PI15/00572, PI15/00996), REDISSEC (Project Numbers RD12/0001/0012, RD16/0001/0005), and the European Regional Development Fund ("A way to build Europe").Background: Multimorbidity is associated with negative effects both on people's health and on healthcare systems. A key problem linked to multimorbidity is polypharmacy, which in turn is associated with increased risk of partly preventable adverse effects, including mortality. The Ariadne principles describe a model of care based on a thorough assessment of diseases, treatments (and potential interactions), clinical status, context and preferences of patients with multimorbidity, with the aim of prioritizing and sharing realistic treatment goals that guide an individualized management. The aim of this study is to evaluate the effectiveness of a complex intervention that implements the Ariadne principles in a population of young-old patients with multimorbidity and polypharmacy. The intervention seeks to improve the appropriateness of prescribing in primary care (PC), as measured by the medication appropriateness index (MAI) score at 6 and 12months, as compared with usual care. Methods/Design: Design:pragmatic cluster randomized clinical trial. Unit of randomization: family physician (FP). Unit of analysis: patient. Scope: PC health centres in three autonomous communities: Aragon, Madrid, and Andalusia (Spain). Population: patients aged 65-74years with multimorbidity (≥3 chronic diseases) and polypharmacy (≥5 drugs prescribed in ≥3months). Sample size: n=400 (200 per study arm). Intervention: complex intervention based on the implementation of the Ariadne principles with two components: (1) FP training and (2) FP-patient interview. Outcomes: MAI score, health services use, quality of life (Euroqol 5D-5L), pharmacotherapy and adherence to treatment (Morisky-Green, Haynes-Sackett), and clinical and socio-demographic variables. Statistical analysis: primary outcome is the difference in MAI score between T0 and T1 and corresponding 95% confidence interval. Adjustment for confounding factors will be performed by multilevel analysis. All analyses will be carried out in accordance with the intention-to-treat principle. Discussion: It is essential to provide evidence concerning interventions on PC patients with polypharmacy and multimorbidity, conducted in the context of routine clinical practice, and involving young-old patients with significant potential for preventing negative health outcomes. Trial registration: Clinicaltrials.gov, NCT02866799Publisher PDFPeer reviewe

Clustering COVID-19 ARDS patients through the first days of ICU admission. An analysis of the CIBERESUCICOVID Cohort

Background Acute respiratory distress syndrome (ARDS) can be classified into sub-phenotypes according to different inflammatory/clinical status. Prognostic enrichment was achieved by grouping patients into hypoinflammatory or hyperinflammatory sub-phenotypes, even though the time of analysis may change the classification according to treatment response or disease evolution. We aimed to evaluate when patients can be clustered in more than 1 group, and how they may change the clustering of patients using data of baseline or day 3, and the prognosis of patients according to their evolution by changing or not the cluster.Methods Multicenter, observational prospective, and retrospective study of patients admitted due to ARDS related to COVID-19 infection in Spain. Patients were grouped according to a clustering mixed-type data algorithm (k-prototypes) using continuous and categorical readily available variables at baseline and day 3.Results Of 6205 patients, 3743 (60%) were included in the study. According to silhouette analysis, patients were grouped in two clusters. At baseline, 1402 (37%) patients were included in cluster 1 and 2341(63%) in cluster 2. On day 3, 1557(42%) patients were included in cluster 1 and 2086 (57%) in cluster 2. The patients included in cluster 2 were older and more frequently hypertensive and had a higher prevalence of shock, organ dysfunction, inflammatory biomarkers, and worst respiratory indexes at both time points. The 90-day mortality was higher in cluster 2 at both clustering processes (43.8% [n = 1025] versus 27.3% [n = 383] at baseline, and 49% [n = 1023] versus 20.6% [n = 321] on day 3). Four hundred and fifty-eight (33%) patients clustered in the first group were clustered in the second group on day 3. In contrast, 638 (27%) patients clustered in the second group were clustered in the first group on day 3.Conclusions During the first days, patients can be clustered into two groups and the process of clustering patients may change as they continue to evolve. This means that despite a vast majority of patients remaining in the same cluster, a minority reaching 33% of patients analyzed may be re-categorized into different clusters based on their progress. Such changes can significantly impact their prognosis

Treatment with tocilizumab or corticosteroids for COVID-19 patients with hyperinflammatory state: a multicentre cohort study (SAM-COVID-19)

Objectives: The objective of this study was to estimate the association between tocilizumab or corticosteroids and the risk of intubation or death in patients with coronavirus disease 19 (COVID-19) with a hyperinflammatory state according to clinical and laboratory parameters. Methods: A cohort study was performed in 60 Spanish hospitals including 778 patients with COVID-19 and clinical and laboratory data indicative of a hyperinflammatory state. Treatment was mainly with tocilizumab, an intermediate-high dose of corticosteroids (IHDC), a pulse dose of corticosteroids (PDC), combination therapy, or no treatment. Primary outcome was intubation or death; follow-up was 21 days. Propensity score-adjusted estimations using Cox regression (logistic regression if needed) were calculated. Propensity scores were used as confounders, matching variables and for the inverse probability of treatment weights (IPTWs). Results: In all, 88, 117, 78 and 151 patients treated with tocilizumab, IHDC, PDC, and combination therapy, respectively, were compared with 344 untreated patients. The primary endpoint occurred in 10 (11.4%), 27 (23.1%), 12 (15.4%), 40 (25.6%) and 69 (21.1%), respectively. The IPTW-based hazard ratios (odds ratio for combination therapy) for the primary endpoint were 0.32 (95%CI 0.22-0.47; p < 0.001) for tocilizumab, 0.82 (0.71-1.30; p 0.82) for IHDC, 0.61 (0.43-0.86; p 0.006) for PDC, and 1.17 (0.86-1.58; p 0.30) for combination therapy. Other applications of the propensity score provided similar results, but were not significant for PDC. Tocilizumab was also associated with lower hazard of death alone in IPTW analysis (0.07; 0.02-0.17; p < 0.001). Conclusions: Tocilizumab might be useful in COVID-19 patients with a hyperinflammatory state and should be prioritized for randomized trials in this situatio