Effect of Nitrogen Atom Substitution in A₃ Adenosine Receptor Binding: N-(4,6-Diarylpyridin-2-yl)acetamides as Potent and Selective Antagonists

Abstract

We report the first family of 2-acetamidopyridines as potent and selective A adenosine receptor (AR) antagonists. The computer-assisted design was focused on the bioisosteric replacement of the N1 atom by a CH group in a previous series of diarylpyrimidines. Some of the generated 2-acetamidopyridines elicit an antagonistic effect with excellent affinity (K < 10 nM) and outstanding selectivity profiles, providing an alternative and simpler chemical scaffold to the parent series of diarylpyrimidines. In addition, using molecular dynamics and free energy perturbation simulations, we elucidate the effect of the second nitrogen of the parent diarylpyrimidines, which is revealed as a stabilizer of a water network in the binding site. The discovery of 2,6-diaryl-2-acetamidopyridines represents a step forward in the search of chemically simple, potent, and selective antagonists for the hAAR, and exemplifies the benefits of a joint theoretical-experimental approach to identify novel hAAR antagonists through succinct and efficient synthetic methodologies.

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

“…We here provide further support for the existence of these structural water molecules, by means of an MD exploration of the solvent in the binding site (see methods). The idea is that the structural water molecules, which might favor the binding of ligands, is reflected in a higher occupancy during the MD trajectories, as we recently showed for the A 3 AR (see below and reference [ 30 ]). Figure 4 shows the calculated water density maps at 80% occupancy, supporting the position of the two water molecules discussed above, mediating interactions between the ligand and E170 EL2 as well as the intramolecular interaction between the 2-furan and esther groups of the ligand.…”

“…The 3D-QSAR model suggested a role of this nitrogen in the affinity of these compounds, presumably by interaction with a potentially conserved structural water molecule within ARs linked to Ser271 7.42 , for which evidence in the hA 3 AR homology model was suggested by a GRID analysis with a water probe [ 24 ]. To further explore the complex effect of a “necessary nitrogen” [ 48 ] in the structure–activity (SAR) of these heterocycles, we designed a new series of bioisosteres derived from the 4-acetamidopyrimidine scaffold, i.e., lacking this nitrogen atom [ 30 ] ( Figure 5 ). The most potent pyridines obtained displayed affinity values in the low nanomolar range, comparable to the best pyrimidines of the former series, maintaining the excellent selectivity profile toward the remaining ARs.…”

“…During the last years, our labs have combined FEP and other computational methodologies with high-throughput synthetic methodologies and pharmacological characterization, to develop various series of structurally simple, novel AR ligands [ 23 ]. Our SBDD protocol includes homology modeling, protein–ligand docking, 3D-QSAR, MD and FEP simulations, and was used to assist the design of novel ligands as well as to predict or rationalize their pharmacological profile [ 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 ]. The different series obtained with this strategy, represented in Figure 1 , have been optimized to yield potent and selective antagonists of the different ARs.…”

“…The different series obtained with this strategy, represented in Figure 1 , have been optimized to yield potent and selective antagonists of the different ARs. The first scaffold reported, a 2,4-diarylpyrimidine, was recently followed by a bioisosteric series of 2,4-diarylpyridines, both of them revealing high affinity and selectivity as A 3 AR antagonists [ 24 , 25 , 30 ]. For the A 2B receptor, we have documented the first non-planar, enantioselective antagonists, and disclosed the reasons of their enantiospecificity [ 31 , 32 ].…”

Design and analysis of the 4-anilino-quin(az)oline kinase inhibition profiles of GAK/SLK/STK10 using quantitative structure activity relationships

“…This can be used to increase potency on target and enhance selectivity over other kinases/targets. Cardiac troponin Iinteracting kinase (TNNI3K) [50][51] and Spleen tyrosine kinase (Syk) 52 have both utilised this to increase potency (by 60-160-fold) and selectivity by the addition of a nitrogen (Figure S1).…”