Insights Into Interaction Mechanisms Between RAS-Related Inhibitors And PDE?,BRAF By Molecular Dynamics

RAS mutation is among the most important oncogenic drivers in many major cancer types,such as lung,colorectal and pancreatic cancer.However,there is still no effective treatment for RAS mutant cancers.Phosphodiesterase ?(PDE ?)and BRAF are thought to play a key role in the RAS signalling pathway.PDE? protein regulates the binding of RAS to the plasma membrane;RAF kinases(including ARAF,BRAF,and CRAF)are the first to be activated by RAS in the RAF-MEK-ERK pathway,and BRAF protein is the most important role in signal transduction pathway.Therefore,PDE? and BRAF are considered as important targets for treating RAS mutation.Based on this,studying the binding mode and microscopic mechanism of PDE?,BRAF with RAS inhibitors will help to develop and design more effective drugs.In this paper,the mechanism of action of PDE?,BRAF with small molecule inhibitors was studied in detail using the atomic molecular dynamics(MD)simulation method.(1)Exploring binding modes of the selected inhibitors bind to phosphodiesterase delta by all-atom molecular dynamics simulation and free-energy calculationsIt's favorable to alter KRas mutation's location to endomembrane by interfering the binding of PDE?(the prenyl-binding protein phosphodiesterase delta)to KRas.We analyze the role of four small molecules(Deltarasin,allyl analogue,pyrazolopyridazinone derivative and Deltazinone 1)which bind to prenyl-binding pocket of PDE? and explore the binding micro-mechanisms in PDE?/inhibitors binding by comparing the results from all-atom Molecular Dynamic(MD)simulations.Comparisons are made on the basis of the binding free energies,hydrogen bonding,and the conformation of inhibitors after protein binding.The obtained results indicate that main contribution to the total binding free energy is van der Waals energy;especially,the residues R61 and 1129 do importantly contributions to binding free energy in all systems.The conserved hydrogen bonds play crucial roles in anchoring the inhibitors to the exact site for binding.The results for conformational analysis of PDE?/free and PDE?/inhibitors systems show that the structures are more stable after the inhibitors binding to the PDE8.It's found that a3-helix formed by the residues P113-Q116 is disappeared in the PDE?/pyrazolopyridazinone derivative system,which explains that PDE?/pyrazolopyridazinone is the most unstable system among four complexes.This study may provide valuable information for the design of high potency PDE? inhibitors.(2)Exploring binding modes of the pan-RAF inhibitors bind to BRAF by all-atom molecular dynamics simulation and free-energy calculation.Pan-RAF inhibitors inhibit the phosphorylation of downstream MEK and ERK,which is important to alter tumor activities in RAS or BRAF mutant cancers.All-atom molecular dynamics(MD)simulations and Molecular Mechanics Generalized Born surface area(MM/GBSA)energy calculations are performed to investigate the two pan-RAF inhibitors(LY3009120 and RAF709)in wild-type(WT)BRAF as well as in the primary mutant(V600E)BRAF.The obtained results indicate that main contribution to the total binding free energy is van der Waals energy.WT-inhibitor and mutant-inhibitor complexes both have large AEvdw values,which gives a reasonable explanation that the inhibitors have affinity binding with BRAFV600E but also with BRAF WT.Moreover,the V600E mutant has a favorable effect on the electrostatic interactions which is caused by the dramatic changes in electrostatic surface near the binding pocket.This study may provide valuable information for the design of high potency pan-RAF inhibitors.