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ChemRxivs_Chromones_-2019.pdf (4.64 MB)

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

submitted on 23.12.2019 and posted on 24.12.2019 by Willem Jespers, Grégory Verdon, Jhonny Azuaje, maria majellaro, Henrik Keränen, Xerardo García-Mera, Miles Congreve, Francesca Deflorian, Chris de Graaf, Andrei Zhukov, Andy Dore, Jonathan S. Mason, Johan Åqvist, Robert M. Cooke, Eddy Sotelo, Hugo Gutierrez de Teran

Nowadays, rigorous free energy calculations are routinely considered in pharmaceutical design strategies. One typical sce- nario is the lead-optimization based on well-defined protein-ligand binding modes, inferred by pharmacological data in com- putational models and ultimately revealed by structural data. In this work, we reveal the molecular determinants of antago- nist binding to the adenosine A2A adenosine receptor (AR), an emerging target in immuno-oncology, via a robust protocol that connects structural and pharmacological data through free energy perturbation (FEP) calculations. Eight A2AAR binding site mutations from biophysical mapping experiments were initially analyzed with FEP simulations of each side-chain mutation, performed on alternate binding modes previously proposed in the literature. The results strongly suggested that only one binding mode could explain this experimental data, which was used to subsequently design a series of 11 chromone deriva- tives. The experimental affinities of these new compounds were linked through a cycle of ligand-FEP calculations around selected ligand pairs, which allowed the identification of the optimal positioning of the different chemical substituents in the proposed binding model. Subsequent X-ray crystallography of the A2AAR with a low and high affinity chromone derivative confirmed the predicted binding orientation, and provided new insights in the role of the explored substituents in the chro-

mone scaffold.


Email Address of Submitting Author


Uppsala University



ORCID For Submitting Author


Declaration of Conflict of Interest

No conflict of interest