Metadynamic calculations for anticancer drug analysis
Protein kinases (PKs) are the principal elements in cell signalling that help in controlling processes such as cell proliferation, differentiation and motility. Their transition between inactive and active state is tightly controlled. PK mutations may lock them in activated state and are associated with many types of cancer. B-Raf is a PK that is part of the RAS-RAF-MEK signalling pathway. It is mutated in 8 % of all cancers, and 80 % of all cases of melanoma have an activating V600E mutation of the protein. Vemurafenib and dabrafenib have been used for successful inhibition of B-Raf with V600E. However, some patients taking the drugs develop secondary tumours with wild-type B-Raf as a result of trans-activation through a dimerisation-dependent mechanism. Wild-type B-Raf requires dimerisation for full activation and previous studies have confirmed that B-Raf inhibitors cause paradoxical activation by binding to the wild-type protein monomer. The goal of the EU-funded KIBINDING (Improving the selectivity of kinase inhibitors: characterizing binding mechanisms of inhibitors targeting inactive states and allosteric sites) project was to determine the effect of the V600E mutation on the conformation of the B-Raf monomer and the mechanism of transactivation at the molecular level. For analysis, scientists adopted computational molecular dynamics (MD) simulations and a state-of-the-art enhanced sampling method, parallel-tempering metadynamics (PT-metaD). MD/PT-metaD application to calculate the free energy surfaces (FES) of the wild-type and mutant B-Raf monomers showed that the active state of the mutant is stabilised by the mutation. The FES also revealed that the mutation increases the barrier for inactivation transition, locking the PK in the active state. The intermediate in the wild-type active to inactive transition could be a potential target in the design of inhibitors for the treatment of cancer. Researchers performed MD on the wild-type dimer, the V600E mutant dimer, and the wild-type dimer with an inhibitor bound in one of the active sites. Component analysis and elastic network analysis were performed to identify residues involved in allosteric communication within the dimer. Obtained results would help to evaluate the effect of the mutation on dimerisation. Since many oncogenic mutations result in a switch to active PK conformation, developing inhibitors targeting this stage could prove to be the key for cancer treatment. MD/PT-metaD analysis enables the investigation of the binding mechanisms of inhibitors targeting the inactive conformation and allosteric sites.
Keywords
Metadynamic calculations, anticancer drug, inhibitor, protein kinase, B-Raf, KIBINDING, free energy surfaces
