title: Molecular dynamics simulation and free energy calculation studies of kinase inhibitors binding to active and inactive conformations of VEGFR-2.
abstract: Vascular endothelial growth factors receptor-2 (VEGFR-2) inhibitors have been proved as very effective anticancer agents. Structurally similar ligands 1 and 2 show almost the same inhibitory activities against VEGFR-2, but they bind to the enzyme in distinct binding mode. Ligand 1 targets DFG-in active conformation of VEGFR-2, known as Type I inhibitor. On the other hand, ligand 2 targets DFG-out inactive conformation of VEGFR-2, known as Type II inhibitor or allosteric kinase inhibitor. Ligand 2 shows high inhibitory activity, while the compound 3, a close analog of 2 with the cyclopropylamide replaced by tert-butylamide, exhibits drastically diminished potency. In this work, molecular dynamics simulations and free energy calculations were performed on inhibitors 1-3 binding to active and inactive conformation of VEGFR-2. Molecular dynamics simulations find that the active conformation binding to Type I inhibitor 1 appears more flexible when compared to the unbound form. In contrast, binding of Type II inhibitor 2 to the inactive conformation helps to stabilize the inactive conformation of the protein. Binding free energy calculations verify that inhibitors 1 and 2 have almost the same activities against VEGFR-2, and that ligand 1 binds to and stabilizes the DFG-in conformation of VEGFR-2, which is in agree with the experimental observation. Molecular dynamics simulations and binding free energy calculations of 3 binding to VEGFR-2 can give a good explanation of the drastically diminished potency. Free energy analysis revealed that van der Waals interactions provided the substantial driving force for the binding process. The important hydrophobic property of the terminal 4-Cl phenyl was required to be Type II inhibitors. Furthermore, per-residue free energy decomposition analysis revealed that the most favorable contribution came from Leu840, Val848, Ala866, Lys868, Leu889, Val899, Thr916, Phe918, Cys919, Leu1035, Cys1045, Asp1046, and Phe1047. These results are expected to be useful for future rational design of novel potent VEGFR-2 inhibitors.
authors.affiliation: School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China. Electronic address: xywugz@163.com.
authors.forename: XiaoYun
authors.initials: X
authors.lastname: Wu
authors.affiliation: School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China.
authors.forename: ShanHe
authors.initials: S
authors.lastname: Wan
authors.affiliation: School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China.
authors.forename: GuangFa
authors.initials: G
authors.lastname: Wang
authors.affiliation: School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China.
authors.forename: Hong
authors.initials: H
authors.lastname: Jin
authors.affiliation: School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China.
authors.forename: ZhongHuang
authors.initials: Z
authors.lastname: Li
authors.affiliation: School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China.
authors.forename: YuanXin
authors.initials: Y
authors.lastname: Tian
authors.affiliation: School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China.
authors.forename: ZhengGuang
authors.initials: Z
authors.lastname: Zhu
authors.affiliation: School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China. Electronic address: zhangjj@smu.edu.cn.
authors.forename: JiaJie
authors.initials: J
authors.lastname: Zhang
mesh_terms: D000494:Allosteric Regulation; D020816:Amino Acid Motifs; D001665:Binding Sites; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D007700:Kinetics; D008024:Ligands; D062105:Molecular Docking Simulation; D008969:Molecular Sequence Data; D011485:Protein Binding; D011487:Protein Conformation; D047428:Protein Kinase Inhibitors / Q000737:chemistry*; D013329:Structure-Activity Relationship; D013816:Thermodynamics; D040301:Vascular Endothelial Growth Factor Receptor-2 / Q000037:antagonists & inhibitors / Q000737:chemistry*
chemical_list: D008024:Ligands; D047428:Protein Kinase Inhibitors; C000588866:KDR protein, human; D040301:Vascular Endothelial Growth Factor Receptor-2
keywords: MM-GBSA; MM-PBSA; Molecular dynamics; Type I inhibitors; Type II inhibitors; VEGFR-2