Structure-Based Design of Potent and Selective Ligands at the Four Adenosine Receptors

Abstract

The four receptors that signal for adenosine, A1, A2A, A2B and A3 ARs, belong to the superfamily of G protein-coupled receptors (GPCRs). They mediate a number of (patho)physiological functions and have attracted the interest of the biopharmaceutical sector for decades as potential drug targets. The many crystal structures of the A2A, and lately the A1 ARs, allow for the use of advanced computational, structure-based ligand design methodologies. Over the last decade, we have assessed the efficient synthesis of novel ligands specifically addressed to each of the four ARs. We herein review and update the results of this program with particular focus on molecular dynamics (MD) and free energy perturbation (FEP) protocols. The first in silico mutagenesis on the A1AR here reported allows understanding the specificity and high affinity of the xanthine-antagonist 8-Cyclopentyl-1,3-dipropylxanthine (DPCPX). On the A2AAR, we demonstrate how FEP simulations can distinguish the conformational selectivity of a recent series of partial agonists. These novel results are complemented with the revision of the first series of enantiospecific antagonists on the A2BAR, and the use of FEP as a tool for bioisosteric design on the A3AR.

Purinergic Signaling: Impact of GPCR Structures on Rational Drug Design

“… [1,8,30‐37] We have collaborated in this effort with Ray Stevens at the University of Southern California and his colleagues. Furthermore, we and others have employed the receptor coordinates in structure‐based drug design (SBDD) of new ligands [1,8,9,38] . At least 57 purinergic GPCR structures are reported in the public Protein Data Bank: [39] 52 for ARs and 5 for P2YRs [5] .…”

“…The MD simulations allowed the recognition modes of key ligands to be analyzed in detail, considering each of the recognition elements [38,57] . The docking poses of the 3′,5′‐bisphosphate antagonist MRS2500 and closely related bisphosphate agonist MRS2268 27 (Figure 3), and of the 5′‐diphosphate agonist 2‐MeSADP 24 , to the hP2Y 1 R were subjected to MD simulation.…”

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

“…[10] There is alarge amount of SAR and SDM data available for these receptors,w hich can be combined with the increasing growth of structural knowledge of many GPCR targets.T he first integrated approach of ligand and residue FEP simulations was published by Boukharta et al to characterize antagonist binding to the Y 1 neuropeptide receptor, [11] which we later expanded to other GPCR families,i ncluding the related neuropeptide receptor Y 2 , [12] the orphan receptor GPR139 [13] and several members of the family of adenosine receptors. [14][15][16] Among the latter, the adenosine A 2A receptor (A 2A AR) was one of the first GPCRs to be crystallized [17] and today stands out as one of the better characterized GPCRs from as tructural perspective.S everal structures of the inactive and active forms of the receptor have been solved within the last decade,and the integration of the available experimental data has strongly aided ligand design programs for this receptor. [18,19] Many A 2A AR antagonists have been developed targeting anumber of pathologies, [20][21][22] including recent clinical candidates in immuno-oncology.Anumber of these antagonists have been co-crystallized with the A 2A AR, providing unique structural information which, in combination with the extensive SDM data available, [23] allow envisaging ligand binding mechanisms and structure-based drug design (SBDD) programs of antagonist molecules.…”

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

“…The first integrated approach of ligand and residue FEP simulations was published by Boukharta et al to characterize antagonist binding to the Y1 neuropeptide receptor, 9 which we later expanded to other GPCR families, including the related neuropeptide receptor Y2, 10 the orphan receptor GPR139 11 and several members of the family of adenosine receptors. [12][13][14] Among the last, the A2A adenosine receptor (A2AAR) was one of the first GPCRs to be crystallized 15 and today stands out as one of the better characterized GPCRs from a structural perspective. Several structures of the inactive and active forms of the receptor have been solved within the last decade, and the integration of the available experimental data has strongly aided ligand design programs for this receptor.…”