Unveiling the KRAS Relationship between Affinity and Dynamics: A Molecular Simulations Study
TL;DR
The thermodynamic reasons for the increased stability of the G12C mutant in the active, GTP-bound state are quantified and the use of Accelerated Enveloping Distribution Sampling (A-EDS) to efficiently screen a small set of fragments with the strongest binding affinity is explored.
Abstract
Kirsten rat sarcoma virus protein (KRAS) is one of the most important targets in current drug discovery. Its intrinsic properties, including a high structural flexibility and a shallow polar pocket, make KRAS extremely difficult to target. In fact, for a long time it was considered undruggable. A better understanding of its structure and dynamics will help to advance drug discovery efforts. KRAS is a GTPase, which is highly relevant for the growth, proliferation, and differentiation of cells. Several oncogenic mutations have been identified, suggesting that KRAS could be an excellent target in the fight against cancer. In this work, we use molecular dynamics simulations to highlight the challenges of this protein in computational drug design. We start from a characterization of the structural flexibility and the diversity in observed molecular interactions. Then we quantify the thermodynamic reasons for the increased stability of the G12C mutant in the active, GTP-bound state. For this we use two thermodynamic cycles and find that the alchemical mutation leads to internally consistent results, in agreement with the biological observations. Furthermore, we explore the use of Accelerated Enveloping Distribution Sampling (A-EDS) to efficiently screen a small set of fragments with the strongest binding affinity. The screening mode of A-EDS already allows for the identification of the most favorable candidate molecules. Subsequently, further optimization of the A-EDS parameters facilitates a quantification of the relative binding affinities in terms of free energies.