Dynamically encoded reactivity of Ras enzymes: opening new frontiers for drug discovery

Abstract

Decoding molecular flexibility in order to understand and predict biological processes-applying the principles of dynamicstructure-activity relationships (DSAR)-becomes a necessity when attempting to design selective and specific inhibitors of a protein that has overlapping interaction surfaces with its upstream and downstream partners along its signaling cascade. Ras proteins are molecular switches that meet this definition perfectly. The close-lying P-loop and the highly flexible switch I and switch II regions are the site of nucleotide-, assisting-, and effector-protein binding. Oncogenic mutations that also appear in this region do not cause easily characterized overall structural changes, due partly to the inherent conformational heterogeneity and pliability of these segments. In this review, we present an overview of the results obtained using approaches targeting Ras dynamics, such as nuclear magnetic resonance (NMR) measurements and experiment-based modeling calculations (mostly molecular dynamics (MD) simulations). These methodologies were successfully used to decipher the mutant-and isoformspecific nature of certain transient states, far-lying allosteric sites, and the internal interaction networks, as well as the interconnectivity of the catalytic and membrane-binding regions. This opens new therapeutic potential: the discovered interaction hotspots present hitherto not targeted, selective sites for drug design efforts in diverse locations of the protein matrix.

Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development

“…Approaches to obtain a better understanding of RAS signaling on the membrane are ongoing, and for instance, a structural model of RAS-RAF signalosome was recently reported by Shaw et al [139]. For further information on RAS-related MD simulations and dynamics, the reader is referred to reviews [122,140,141].…”

Identification of functional substates of KRas during GTP hydrolysis with enhanced sampling simulations

“…8 In recent years, Ras has (re)emerged as a potentially promising drug target 9 for cancer treatment, especially following Amgen's 10 development of a covalent inhibitor of the KRasG12C mutant. Numerous strategies have been proposed for inhibitor design 11–13 targeting Ras, especially for KRas, 14 which include inhibiting the active conformation of RasGTP·Mg 2+ , 15 stabilizing the inactive hydrolysis product RasGDP·Mg 2+ 16 and hindering the GDP/GTP exchange, 17 etc. Considering the conformational flexibility of Ras, to further improve the effectiveness and specificity of inhibitors, 18 it is essential to establish the functionality for every specific conformational state of Ras isoforms.…”

The Importance of Mg2+‐Free State in Nucleotide Exchange of Oncogenic K‐Ras Mutants

“…The C-terminal allosteric lobe (T87-H166) is responsible for the regulation of the effector lobe through allosteric interaction networks, and it is more specific for each family member. [14] As internal motions often participate in the formation of transiently appearing binding sites, communication networks coupled to the regulation of the catalytic cycle, membrane targeting, or determining the pliability of effector-binding regions, [15][16] internal dynamics plays an important role not only in K-Ras function, but also in the potential mechanisms of its inhibition. While experiments characterizing internal dynamics have extensively been carried out for H-Ras, [17][18][19][20][21][22][23][24][25][26][27][28][29][30][31] K-Ras has come into the spotlight more recently due to the huge efforts to find applicable drugs against its oncogenic mutants.…”