3 research outputs found
Comprehensive structural and functional characterization of the human kinome by protein structure modeling and ligand virtual screening
The growing interest in the identification of kinase inhibitors, promising therapeutics in the treatment of many diseases, has created a demand for the structural characterization of the entire human kinome. At the outset of the drug development process, the lead-finding stage, approaches that enrich the screening library with bioactive compounds are needed. Here, protein structure based methods can play an important role, but despite structural genomics efforts, it is unlikely that the three-dimensional structures of the entire kinome will be available soon. Therefore, at the proteome level, structure-based approaches must rely on predicted models, with a key issue being their utility in virtual ligand screening. In this study, we employ the recently developed FINDSITE/Q-Dock ligand homology modeling approach, which is well-suited for proteome-scale applications using predicted structures, to provide extensive structural and functional characterization of the human kinome. Specifically, we construct structure models for the human kinome; these are subsequently subject to virtual screening against a library of more than 2 million compounds. To rank the compounds, we employ a hierarchical approach that combines ligand- and structure-based filters. Modeling accuracy is carefully validated using available experimental data with particularly encouraging results found for the ability to identify, without prior knowledge, specific kinase inhibitors. More generally, the modeling procedure results in a large number of predicted molecular interactions between kinases and small ligands that should be of practical use in the development of novel inhibitors. The data set is freely available to the academic community via a user-friendly Web interface at http://cssb.biology.gatech.edu/kinomelhm/ as well as at the ZINC Web site (http://zinc.docking.org/applications/2010Apr/Brylinski-2010.tar.gz). © 2010 American Chemical Society
Estudio y cribado virtual de compuestos quĂmicos antivirales (VIH). Estudio de la modulaciĂłn alostĂ©rica de agonistas y antagonistas del receptor celular CXCR4
Els mètodes de descobriment de nous fà rmacs han evolucionat recentment grà cies a la resolució de les estructures proteiques que actuen com a dianes terapèutiques responsables de malalties o desregulacions biològiques. Aquestes estructures proteiques tridimensionals, juntament amb el desenvolupament de noves tècniques computacionals permeten el desenvolupament accelerat de nous compostos candidats a esdevenir fà rmacs.
El present treball s’inicia proposant un nou mètode que millora l’elecciĂł de compostos candidats a ser inhibidors d’una “diana difĂcil”, però ben coneguda com Ă©s el receptor VEGFR-2, a partir de la seva estructura tridimensional cristal·litzada, aixĂ com de compostos inhibidors coneguts de l’esmentada diana.
La resolució tridimensional de l’estructura CXCR4 mitjançant cristal•lografia de raigs X a l’any 2010, ha esdevingut un avenç important a l’hora de millorar el disseny de compostos inhibidors del VIH, aixà com compostos antitumorals, malalties en les que intervé de forma determinant el receptor CXCR4. Aixà doncs, els models de cribratge virtual desenvolupats abans del 2010 dins el laboratori de disseny molecular de l’IQS (GEM) han estat generats a partir de models creats per homologia vers a altres proteïnes GPCRs i/o s’han basat solament en la forma de lligands coneguts. D’aquesta forma, a partir de les diferents estructures proteiques publicades de CXCR4, s’ha avaluat quina d’aquestes estructures presenta la conformació que distingeix millor els compostos antagonistes actius dels compostos inactius. A més, s’han avaluat múltiples mètodes de cribratge virtual de CXCR4 basats en l’estructura, en la forma del lligand i mitjançant models farmacofòrics. Una vegada obtinguda la millor estructura de CXCR4 i els millors mètodes de cribratge virtual retrospectiu, es realitzen cribratges virtuals prospectius d’una nova quimioteca generada de forma combinatòria, basada en estructures anà logues prèviament desenvolupades al laboratori de disseny molecular de l’IQS.
Addicionalment, s’ha estudiat el comportament al·lostèric del receptor CXCR4 davant de moduladors antagonistes petits i moduladors al·lostèrics agonistes de naturalesa pèptica. CXCR4 Ă©s qualificada com a una “diana difĂcil” per la gran mida del seu lloc actiu ortostèric, aixĂ com per l’ampli nĂşmero de funcions reguladores en les que intervĂ© el receptor. Per això la modulaciĂł al·lostèrica en CXCR4 s’ha estudiat utilitzant diferents aproximacions com sĂłn el docking cec, docking proteĂŻna-proteĂŻna, docking per subllocs d’uniĂł i dinĂ mica molecular.Los mĂ©todos de descubrimiento de nuevos fármacos han evolucionado recientemente gracias a la resoluciĂłn de las estructuras proteicas las cuales actĂşan como dianas terapĂ©uticas responsables de enfermedades o desregulaciones biolĂłgicas. Estas estructuras proteicas tridimensionales, conjuntamente con el desarrollo de nuevas tĂ©cnicas computacionales están permitiendo el desarrollo acelerado de nuevos compuestos candidatos a convertirse en fármacos.
El presente trabajo se inicia proponiendo un nuevo mĂ©todo que permita mejorar la elecciĂłn de compuestos candidatos a ser inhibidores de una “diana difĂcil” aunque bien conocida, como es el receptor VEGFR-2, partiendo de su estructura tridimensional cristalizada y de compuestos inhibidores conocidos de dicha diana.
La resoluciĂłn tridimensional de la estructura del receptor CXCR4 mediante cristalografĂa de rayos X, en el año 2010, ha supuesto un avance importante de cara a mejorar el diseño de compuestos inhibidores del VIH, asĂ como de compuestos antitumorales, enfermedades en las que interviene de forma determinante el receptor CXCR4. AsĂ pues, los modelos de cribado virtual desarrollados anteriormente al 2010 en el laboratorio de diseño molecular del IQS (GEM) han sido generados a partir de modelos creados por homologĂa a otras proteĂnas GPCRs y/o basados Ăşnicamente en la forma de ligandos conocidos. De este modo, partiendo de las diferentes estructuras proteicas publicadas de CXCR4, se ha evaluado cuál de dichas estructuras presenta la conformaciĂłn que distingue mejor los compuestos antagonistas activos de compuestos inactivos. Además, se han evaluado mĂşltiples mĂ©todos de cribado virtual de CXCR4 basados en la estructura, en la forma del ligando y mediante modelos farmacofĂłricos. Una vez obtenida la mejor estructura de CXCR4 y los mejores mĂ©todos de cribado virtual retrospectivo, se realizan cribados virtuales prospectivos de una nueva quimioteca generada combinatoriamente, basada en análogos de estructuras previamente desarrolladas en el laboratorio de diseño molecular del IQS.
Adicionalmente se ha estudiado el comportamiento alostĂ©rico del receptor CXCR4 frente a moduladores antagonistas de pequeño tamaño y moduladores alostĂ©ricos agonistas de naturaleza peptĂdica. CXCR4 se califica como “diana difĂcil” debido al gran tamaño del sitio activo ortostĂ©rico, juntamente con el amplio nĂşmero de funciones reguladoras en las que interviene el receptor CXCR4. Por ello la modulaciĂłn alostĂ©rica en CXCR4 se ha estudiado utilizando diferentes aproximaciones, como son: docking ciego, docking proteĂna-proteĂna, docking por subsitios y dinámica molecular.: Drug discovery methods have recently emerged thanks to the resolution of protein structures which act as therapeutic targets responsible for diseases or biological deregulations. These three dimensional structures in combination with the development of new computational techniques are accelerating the development of new candidates to become drug compounds.
This work starts with the proposal of a new method that improves the selection of candidates to become inhibitors of a well-known “difficult target” such us VEGFR-2 receptor. This method is based on the crystal structure of the receptor and also by a number of inhibitors known for this target.
CXCR4 crystal structure was solved in 2010 by X-ray crystallography and this has been an important event in order to improve the molecular design of HIV inhibitors, as well as anticancer compounds, diseases where CXCR4 receptor is involved. Therefore, virtual screening models developed in the laboratory of molecular design of IQS (GEM) were generated using homology models from other GPCRs and/or based on ligand shape techniques. In this sense, taking into consideration all published CXCR4 crystal structures, it has been evaluated which of them shows the most suitable conformation to distinguish antagonists actives from inactives. Moreover, different virtual screening methods have also been evaluated such us structure based methods, ligand based methods and pharmacophoric models. Once obtained the most suitable structure and the best retrospective virtual screening methods, a prospective virtual screening has been carried out using a new combinatorial library of chemical structures. This new library is based on analogous structures previously generated in the laboratory of molecular design of IQS (GEM).
In addition, the allosteric behaviour of CXCR4 receptor has been studied versus small antagonist modulators and versus peptidomimetic agonist modulators. CXCR4 is classified as a “difficult target” due to the large size of its extracellular pocket that the orthosteric binding site is placed as well as the diverse number of biochemical regulations where the receptor mediates. Thus, the allosteric modulation of CXCR4 has been studied using different approaches such as blind docking, protein-protein docking, docking by subsites and molecular dynamics