Unveiling the Secrets of the Ancestral PI3 Kinase Vps34

Vps34 is the primordial member of the PI3 kinase family involved in vesicular trafficking, nutrient signaling, and autophagy. A report in Science unveils the Vps34 structure, providing new insights into the catalytic mechanism, explaining why Vsp34 is so difficult to inhibit, and facilitating design of chemical tools and potential drugs

Current perspectives in fragment based lead discovery (FBLD)

It is over 20 years since the first fragment-based discovery projects were disclosed. The methods are now mature for most ‘conventional’ targets in drug discovery such as enzymes (kinases and proteases) but there has also been growing success on more challenging targets, such as disruption of protein–protein interactions. The main application is to identify tractable chemical startpoints that non-covalently modulate the activity of a biological molecule. In this essay, we overview current practice in the methods and discuss how they have had an impact in lead discovery – generating a large number of fragment-derived compounds that are in clinical trials and two medicines treating patients. In addition, we discuss some of the more recent applications of the methods in chemical biology – providing chemical tools to investigate biological molecules, mechanisms and systems

Targeting HSP70: The second potentially druggable heat shock protein and molecular chaperone?

Introducción: A pesar de que la televisión abierta es el principal medio de comunicación en México, su oferta informativa en el ámbito político es limitada; puesto que sus noticieros tienden a destacar la versión oficial por encima de otras fuentes de información. Metodología: Para demostrar lo anterior, se recurrió a un análisis de contenido en el que se midió cuáles son los personajes de la política nacional que destacan dichos programas, qué tan diversos son y con qué frecuencia son presentados. Además del tratamiento estadístico común en esta técnica, los resultados fueron sometidos al Índice Gini, que mide el grado de desigualdad en la distribución – en este caso – del tiempo otorgado a cada actor político. Resultados: Los resultados que se discutirán a lo largo de este texto indican que los personajes mayormente representados pertenecen al Gobierno Federal y, en menor medida, al Poder Legislativo y al Gobierno Estatal. Asimismo, y dado que es el partido gobernante, el Partido Revolucionario Institucional es el que mayor presencia tiene en comparación con los otros institutos políticos. Por tanto, no resulta inesperado que los principales temas abordados en las noticias hayan sido la economía, seguridad y política; puesto que son justamente los temas incluidos en la agenda de los actores políticos. Conclusiones: Esta situación refuerza la tesis de la falta de modernización del periodismo mexicano, caracterizado por la ausencia de investigación periodística y por ceder el control de la agenda al gobierno, principalmente el federal

The structure of an energy-coupling protein from bacteria, IIBcellobiose, reveals similarity to eukaryotic protein tyrosine phosphatases

Background: The bacterial phosphoenolpyruvate-dependent phosphotransferase system (PTS) mediates the energy-driven uptake of carbohydrates and their concomitant phosphorylation. In addition, the PTS is intimately involved in the regulation of a variety of metabolic and transcriptional processes in the bacterium. The multiprotein PTS consists of a membrane channel and at least four cytoplasmic proteins or protein domains that sequentially transfer a phosphoryl group from phosphoenolpyruvate to the transported carbohydrate. Determination of the three-dimensional structure of the IIB enzymes within the multiprotein complex would provide insights into the mechanisms by which they promote efficient transport by the membrane channel IIC protein and phosphorylate the transported carbohydrate on the inside of the cell. Results: The crystal structure of the IIB enzyme specific for cellobiose, IIBcellobiose (molecular weight 11.4 kDa), has been determined to a resolution of 1.8 Å and refined to an R factor of 18.7% (Rfree of 24.1%). The enzyme consists of a single four-stranded parallel β sheet flanked by helices on both sides. The phosphorylation site (Cys10) is located at the C-terminal end of the first β strand. No positively charged residues, which could assist in phosphoryl-transfer, can be found in or near the active site. The fold of IIBcellobiose is remarkably similar to that of the mammalian low molecular weight protein tyrosine phosphatases. Conclusions: A comparison between IIBcellobiose and the structurally similar low molecular weight protein tyrosine phosphatases provides insight into the mechanism of the phosphoryltransfer reactions in which IIBcellobiose is involved. The differences in tertiary structure and active-site composition between IIBcellobiose and the glucose-specific IIBglucose give a structural explanation why the carbohydrate-specific components of different families cannot complement each other.

Crystallization of Enzyme IIB of the Cellobiose-specific Phosphotransferase System of Escherichia coli

Crystals of enzyme IIB of the cellobiose-specific phosphotransferase system have been obtained from 15% polyethylene glycol 4000 using both streak-seeding and macroseeding techniques at 4°. Crystals were grown with the hanging drop method of vapour diffusion. Addition of 2-propanol and benzamidine/HCl proved essential to obtain single crystals suitable for X-ray analysis. The crystals diffract to 1.8 Å resolution and have the monoclinic space group P21, with cell dimensions a = 53.6 Å, b = 31.7 Å, c = 60.0 Å and β = 101.7°. From a self-rotation function it seems likely that there are two molecules in the asymmetric unit related by a non-crystallographic 2-fold axis.

Insights into the Conformational Variability and Regulation of Human Nek2 Kinase

The Nek family of serine/threonine kinases regulates centrosome and cilia function; in addition, several of its members are potential targets for drug discovery. Nek2 is dimeric, is cell cycle regulated and functions in the separation of centrosomes at G2/M. Here, we report the crystal structures of wild-type human Nek2 kinase domain bound to ADP at 1.55-Å resolution and T175A mutant in apo form as well as that bound to a non-hydrolyzable ATP analog. These show that regions of the Nek2 structure around the nucleotide-binding site can adopt several different but well-defined conformations. None of the conformations was the same as that observed for the previously reported inhibitor-bound structure, and the two nucleotides stabilized two conformations. The structures suggest mechanisms for the auto-inhibition of Nek2 that we have tested by mutagenesis. Comparison of the structures with Aurora-A and Cdk2 gives insight into the structural mechanism of Nek2 activation. The production of specific inhibitors that target individual kinases of the human genome is an urgent challenge in drug discovery, and Nek2 is especially promising as a cancer target. We not only identify potential challenges to the task of producing Nek2 inhibitors but also propose that the conformational variability provides an opportunity for the design of Nek2 selective inhibitors because one of the conformations may provide a unique target