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BRAF is a key intracellular cascade involved in the regulation of cellular proliferation,survival and differentiation.BRAF is easily activated by RAS and has high basal kinase activity,which provides a reasonable explanation for the mutational activation of BRAF frequently observed in human tumors.The most commom mutation of BRAF,particularly V600E,accounts for over 90 percent of the detected mutations in BRAF,This V600E point mutation results in constitutive kinase activity 500-fold greater than wild type BRAF.Hence,BRAFV600E is an attractive target for cancer therapy and BRAFV600E small-molecule inhibitors have recently received increasing attention as very effective agents for the therapy of cancer,particularly for malignant melanoma.Notebly,Vemurafenib(PLX4032)has been approved by FDA in 2011 for the treatment of melanoma with the BRAFV600E mutation.In the current work,we use different computational approaches,such as molecular dynamics(MD)simulations,MM-PBSA and MM-GBSA free energy calculations,and MM-GBSA free energy decomposition to investigate the binding mechanism of Vemurafenib(PLX4032)and its analogue PLX4720 with BRAFV600E Parameterization for ligands PLX4032 and PLX4720 were performed using the Gaussian03 suite.The MD simulations were carried out using the PMEMD module of AMBER 12 program.MM-PBSA and MM-GBSA binding free energy calculations based on MD simulations reveal that ligands PLX4032 and PLX4720 bind to and stabilize the DFG-in conformation of BRAFV600E.Component analysis of binding free energy revealed that vdWaals interactions play a dominating effect on BRAFV600E inhibition.Furthermore,the MM-GBSA per-residue binding free energy decomposition revealed that the most favorable contribution came from Ile463,Val471,Ala481,Lys483,Leu514 Ile527,Thr529,Gln530,Trp531,Cys532,Phe583,Gly593,and Asp594.These results agree well with experimental data,which provide valuable resources for understanding the inhibition mechanism of BRAFV600E by PLX4032 and PLX4720 and clues for the design of novel potent BRAFV600E inhibitors.