In silico binding mode analysis of andrographolide and its derivatives to mutant and wild-type K-ras

OBJECTIVE To investigate the structural requirements for effective binding of andrographolide(AGP)and its derivatives(SRJ09and SRJ23)to mutant K-ras for inhibition of exchange factor binding viain silico docking simulations.METHODS The molecular docking studies were carried out by using SiteMap v3.4andGlide v6.6modules(Schrdinger,Inc.).Surface mapping on the 3-D X-ray crystal structures of three mutant K-ras proteins-K-rasG12V(PDB ID:4EPX),K-rasG12C(PDB ID:4LDJ),and K-rasG12D(PDB ID:4DSU),as well as wild-type K-ras protein(PDB ID:4LPK),was performed to generate possible sites for ligand binding.Thirty conformers were generated for each of the studied compounds,and these conformers were docked into each possible binding site in both wild-type and mutant K-ras proteins.The free energy of binding of the compounds with the wild-type and mutant K-ras proteins was performed using prime molecular mechanics with generalized Born and solvent accessibility(MM-GBSA)approach.RESULTS The conformers of AGP,SRJ09 and SRJ23that were found to form the most stable complex inside each possible binding siteas indicated by the highest binding free energy,both in wild-type and mutant proteins,were selected.A common binding site between switchⅠ and Ⅱregions,where a pocket surrounded by amino acid residues Lys5,Leu6,Val7,Ser39,Asp54,Leu56,Tyr71,Thr74,and Gly75,was found in all K-rasG12 mutants.This site corresponds to the hydrophobic binding pockets having aliphatic side-chain portionsas found previously for other Ras binders,which are located betweenα-helix 2 and the core β-sheets(between switchⅠ and Ⅱregions).This common binding pocket was not observed in the wild-type K-ras.A binding pocket adjacent to switchⅡregion(amino acid 60-72),where all ligands bind well,was found instead.All compoundsanchor well inside the common binding pocket in each of the K-fasG12 mutants and these compounds showed the strongest binding interactions to K-fasG12 C.SRJ09 and SRJ23 showed stronger binding interactions to both wild-type and mutant K-ras proteins as compared with the parent compound.Overall,the compounds displayed higher binding energies toall three mutant proteins as compared to their wild-type counterpart.CONCLUSION AGP,SRJ09,and SRJ23 are potential K-ras-targeting anti-cancer agents.The compounds target both wild-type and mutant K-ras but they bind to a different binding pocket in the wild-type protein.Both binding pockets found in wild-type and mutant K-ras involve switchⅡ region that binds the guanine nucleotide exchange factor(GEF)such as Son of Sevenless.These suggest a possible inhibition of exchange factor binding to both wild-type and mutant K-ras proteins.Lower binding energies of the compounds to wild-type K-ras protein suggest a transient binding and inhibition.Stronger binding of all compounds to mutant K-ras proteins could lead to more targeted and prolonged inhibition.