Fragment optimization for GPCRs by molecular dynamics free energy calculations: Probing druggable subpockets of the A2A adenosine receptor binding site

Pierre Matricon,Anirudh Ranganathan,Diego Dal Ben,Gabriella Marucci,Zhan-Guo Gao,Eugene Warnick,Mariama Jaiteh,Kenneth A Jacobson,Aitakin Ezzati,Catia Lambertucci,Axel Rudling,Jens Carlsson

doi:10.1038/s41598-017-04905-0

Abstract

Fragment-based lead discovery is becoming an increasingly popular strategy for drug discovery. Fragment screening identifies weakly binding compounds that require optimization to become high-affinity leads. As design of leads from fragments is challenging, reliable computational methods to guide optimization would be invaluable. We evaluated using molecular dynamics simulations and the free energy perturbation method (MD/FEP) in fragment optimization for the A2A adenosine receptor, a pharmaceutically relevant G protein-coupled receptor. Optimization of fragments exploring two binding site subpockets was probed by calculating relative binding affinities for 23 adenine derivatives, resulting in strong agreement with experimental data (R2 = 0.78). The predictive power of MD/FEP was significantly better than that of an empirical scoring function. We also demonstrated the potential of the MD/FEP to assess multiple binding modes and to tailor the thermodynamic profile of ligands during optimization. Finally, MD/FEP was applied prospectively to optimize three nonpurine fragments, and predictions for 12 compounds were evaluated experimentally. The direction of the change in binding affinity was correctly predicted in a majority of the cases, and agreement with experiment could be improved with rigorous parameter derivation. The results suggest that MD/FEP will become a powerful tool in structure-driven optimization of fragments to lead candidates.

Highlights

Fragment-based lead discovery (FBLD) has rapidly become a well-established technique in early drug development[1]
The utility of Molecular dynamics (MD) combined with alchemical free energy methods in fragment optimization was explored for the human A2A adenosine receptor (A2AAR), a G protein-coupled receptor (GPCR) relevant for drug development[14] against Parkinson’s disease[15] and cancer[16]
Three key results emerged from calculations of relative binding affinities for fragments ligands of the A2AAR, a GPCR that has been intensively studied as a drug target[14]

Summary

Introduction

Fragment-based lead discovery (FBLD) has rapidly become a well-established technique in early drug development[1]. Molecular dynamics (MD) simulations in combination with alchemical free energy methods, which explicitly consider contributions to binding from conformational flexibility and interactions with water molecules, could provide a rigorous approach to guide fragment optimization[13], but this technique has only recently been applied to FBLD10. Accurate predictions of relative binding affinities for analogs to ligands identified by fragment screening could improve the efficiency of FBLD, further establishing this approach as a groundbreaking strategy for early drug development. Multiple high-resolution crystal structures of the A2AAR have recently been determined[17, 18] and numerous fragment-sized ligands have been identified to this target[19,20,21], making it an ideal test case for evaluating a computational approach. In light of the results, the feasibility of using MD simulations in combination with alchemical free energy methods as a tool in fragment-to-lead optimization will be discussed

Methods

Results

Conclusion