Dual A1/A3 Adenosine Receptor Antagonists: Binding Kinetics and Structure-Activity Relationship Studies Using Mutagenesis and Alchemical Binding Free Energy Calculations

Drugs targeting adenosine receptors (AR) can provide treatment for diseases. We report the identification of 7-(phenylamino)-pyrazolo[3,4-c]pyridines L2-L10, A15, and A17 as low-micromolar to low-nanomolar A(1)R/A(3)R dual antagonists, with 3-phenyl-5-cyano-7-(trimethoxyphenylamino)-pyrazolo[3,4-c] pyridine (A17) displaying the highest affinity at both receptors with a long residence time of binding, as determined using a NanoBRET-based assay. Two binding orientations of A17 produce stable complexes inside the orthosteric binding area of A(1)R in molecular dynamics (MD) simulations, and we selected the most plausible orientation based on the agreement with alanine mutagenesis supported by affinity experiments. Interestingly, for drug design purposes, the mutation of L250(6.51) to alanine increased the binding affinity of A17 at A(1)R. We explored the structure-activity relationships against A(1)R using alchemical binding free energy calculations with the thermodynamic integration coupled with the MD simulation (TI/MD) method, applied on the whole G-protein-coupled receptor-membrane system, which showed a good agreement (r = 0.73) between calculated and experimental relative binding free energies.

Automated summary

This study reports the identification of a new class of compounds, L2-L10, A15, and A17, which act as dual antagonists for A(1)R/A(3)R. Among them, A17 exhibits the highest affinity and a long binding residence time at both receptors. Molecular dynamics simulations and affinity experiments were employed to determine the binding mode of A17. It was found that the mutation of L250(6.51) to alanine enhances the binding affinity of A17 at A(1)R.