X‐Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A2A Adenosine Receptor Antagonists

We present a robust protocol based on iterations of free energy perturbation (FEP) calculations, chemical synthesis, biophysical mapping and X‐ray crystallography to reveal the binding mode of an antagonist series to the A2A adenosine receptor (AR). Eight A2AAR binding site mutations from biophysical mapping experiments were initially analyzed with sidechain FEP simulations, performed on alternate binding modes. The results distinctively supported one binding mode, which was subsequently used to design new chromone derivatives. Their affinities for the A2AAR were experimentally determined and investigated through a cycle of ligand‐FEP calculations, validating the binding orientation of the different chemical substituents proposed. Subsequent X‐ray crystallography of the A2AAR with a low and a high affinity chromone derivative confirmed the predicted binding orientation. The new molecules and structures here reported were driven by free energy calculations, and provide new insights on antagonist binding to the A2AAR, an emerging target in immuno‐oncologyThis work was financially supported by the Swedish Research Council (Grant 521‐2014‐2118); Consellería de Cultura, Educación e Ordenación Universitaria of the Galician Government (Grant ED431B2017/70); Centro Singular de Investigación de Galicia accreditation 2016–2019 (Grant ED431G/09), and the European Regional Development Fund (ERDF). Additional support from the Swedish strategic research program eSSENCE is acknowledged. The computations were performed on resources provided by the Swedish National Infrastructure for Computing (SNIC). This research program has been developed in the frame of the European COST action ERNEST (Grant CA 18133) and GLISTEN (Grant CA 1207)S

Modelización molecular de los receptores de adenosina y sus ligandos en el marco de diseño de fármacos asistido por ordenador

El objetivo de la presente tesis es el de aportar conocimiento sobre la bioquímica y la farmacología de los receptores de adenosina, así como entender las relaciones entre estructura química y actividad farmacológica de los ligandos existentes para estos receptores. Con este objetivo se han empleado distintas técnicas y metodologías del diseño de fármacos asistido por ordenador. Los resultados presentados en este trabajo incluyen:· El desarrollo de una estrategia original para la selección de una muestra que cubra adecuadamente la diversidad molecular existente en una base de datos de compuestos químicos· La construcción de un modelo de la región transmembrana del receptor A1 humano de adenosina, en el que se ha localizado y caracterizado un sitio de unión de agonistas compatible con los datos experimentales.· Predicciones teóricas de las energías de unión de ligandos, realizadas a partir de los complejos agonista-receptor predichos sobre el modelo mencionado, obteniendo un grado de acuerdo con los datos experimentales que resulta esperanzadorThe goal of the present thesis is to gain knowledge about the biochemistry and pharmacology of adenosine receptors, as well as to understand structure-activity relationships for the existing ligands for this receptors. In order to achieve this goal, we have used several techniques and methodologies from the computer-aided drug design field. Results presented in this work include:· The development of an original strategy of selection of a maximum diversity sample that adequately covers the original molecular diversity contained in a compound database· The building of the transmembrane region of a human A1 adenosine receptor model. In such a model, an agonists binding site has been located and characterized, showing agreement with experimental data.· The resulting ligand-receptor complexes have been studied with computational approaches for the prediction of ligand-binding free energies. A nice correlation with experimental results was observe