Impact of protein–ligand solvation and desolvation on transition state thermodynamic properties of adenosine A2A ligand binding kinetics

Abstract

Ligand-protein binding kinetic rates are growing in importance as parameters to consider in drug discovery and lead optimization. In this study we analysed using surface plasmon resonance (SPR) the transition state (TS) properties of a set of six adenosine A receptor inhibitors, belonging to both the xanthine and the triazolo-triazine scaffolds. SPR highlighted interesting differences among the ligands in the enthalpic and entropic components of the TS energy barriers for the binding and unbinding events. To better understand at a molecular level these differences, we developed suMetaD, a novel molecular dynamics (MD)-based approach combining supervised MD and metadynamics. This method allows simulation of the ligand unbinding and binding events. It also provides the system conformation corresponding to the highest energy barrier the ligand is required to overcome to reach the final state. For the six ligands evaluated in this study their TS thermodynamic properties were linked in particular to the role of water molecules in solvating/desolvating the pocket and the small molecules. suMetaD identified kinetic bottleneck conformations near the bound state position or in the vestibule area. In the first case the barrier is mainly enthalpic, requiring the breaking of strong interactions with the protein. In the vestibule TS location the kinetic bottleneck is instead mainly of entropic nature, linked to the solvent behaviour.

New Insights into Key Determinants for Adenosine 1 Receptor Antagonists Selectivity Using Supervised Molecular Dynamics Simulations

“…Interestingly, A 2A AR bears Ala265 instead of Lys265 on the ECL3, while Lys168 and Lys173 (ECL2) are farther from the binding site, compared to A 1 AR. This is consistent with mutagenesis studies that demonstrated the importance of these lysine residues forthe binding of several A 1 AR ligands [39][40][41]. On A 2A AR, Z48 reachedthe orthosteric site producing the classic interactions fingerprint of the ARs antagonists.…”

“…It is possible that the ligand binds A 1 AR and A 2A AR with the same conformation, but differently interacting with water molecules nearby ECL3. From this standpoint, and in analogy with [41], we propose these "happy" water molecules contribute to the ligand stabilization in A 1 AR ( Figure S16), but not in A 2 AR ( Figure S17). An alternative and unique LC4 binding mechanism was sampled only on A 1 AR, with a metastable state before the final complex formation.…”

Deciphering the Agonist Binding Mechanism to the Adenosine A1 Receptor

“…The (un)binding kinetics have a major impact on both pharmacodynamics [55][56][57] [60][61][62][63] and small changes in either the structure of the ligand or the protein can alter the nature and the position of the transition states along the (un)binding routes 64 .…”

In Silico Drug Design for Purinergic GPCRs: Overview on Molecular Dynamics Applied to Adenosine and P2Y Receptors

“…A method combining SuMD, metadynamics, and suMetaD, enables the investigation of ligand binding and dissociation and retrieval of the transition state conformations of the two processes [146]. This algorithm was applied to A 2A AR and six ligands, three xanthines (XAC, DPCPX, KW3902), and three triazolotriazines (ZMA, Z48, Z80), whose transition state thermodynamics appeared to be connected to the characteristics of water molecules solvating the binding pocket and the compounds.…”