Exploring binding mechanisms of VEGFR2 with three drugs lenvatinib, sorafenib, and sunitinib by molecular dynamics simulation and free energy calculation

Molecular Dynamics Simulations Revealed the Regulation of Ligands to the Interactions between Androgen Receptor and Its Coactivator

(2018) Na Liu et al.   Journal of Chemical Information and Modeling

Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches

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Importance of protein flexibility on molecular recognition: modeling binding mechanisms of aminopyrazine inhibitors to Nek2

(2018) Xinyi Tang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Assessing the performance of MM/PBSA and MM/GBSA methods. 8. Predicting binding free energies and poses of protein-RNA complexes

(2018) Fu Chen et al.   RNA

VEGFR-2 inhibitors and the therapeutic applications thereof: a patent review (2012-2016)

(2017) Fan-Wei Peng et al.   EXPERT OPINION ON THERAPEUTIC PATENTS

Computational study of the binding mechanism of medium chain acyl-CoA synthetase with substrate in Methanosarcina acetivorans

(2017) Juan Du et al.   JOURNAL OF BIOTECHNOLOGY

Design, synthesis and biological evaluation of phenylpicolinamide sorafenib derivatives as antitumor agents

(2017) Chunjiang Wu et al.   MEDICINAL CHEMISTRY RESEARCH

Mutation L1196M-induced conformational changes and the drug resistant mechanism of anaplastic lymphoma kinase studied by free energy perturbation and umbrella sampling

(2017) Jianzhong Chen et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

How Does the L884P Mutation Confer Resistance to Type-II Inhibitors of JAK2 Kinase: A Comprehensive Molecular Modeling Study

(2017) Xiaotian Kong et al.   Scientific Reports

Revealing the molecular mechanism of different residence times of ERK2 inhibitors via binding free energy calculation and unbinding pathway analysis

(2016) Yuzhen Niu et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

Classification of small molecule protein kinase inhibitors based upon the structures of their drug-enzyme complexes

(2016) Robert Roskoski   PHARMACOLOGICAL RESEARCH

Assessing the performance of the MM/PBSA and MM/GBSA methods. 6. Capability to predict protein–protein binding free energies and re-rank binding poses generated by protein–protein docking

(2016) Fu Chen et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Discovery of vascular endothelial growth factor receptor tyrosine kinase inhibitors by quantitative structure–activity relationships, molecular dynamics simulation and free energy calculation

(2016) Juan Wang et al.   RSC Advances

Importance of protein flexibility in ranking inhibitor affinities: modeling the binding mechanisms of piperidine carboxamides as Type I1/2 ALK inhibitors

(2015) Xiaotian Kong et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Design, Synthesis and AntitumorActivities of Bis-arylureas and Bisarylamides Based on 1H-benzo[d]imidazole Moiety as Novel BRaf V600E/VEGFR2 Dual Inhibitors

(2014) Weimin Yang et al.   Letters in Drug Design & Discovery

Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set

(2014) Huiyong Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring

(2014) Huiyong Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Distinct Binding Mode of Multikinase Inhibitor Lenvatinib Revealed by Biochemical Characterization

(2014) Kiyoshi Okamoto et al.   ACS Medicinal Chemistry Letters

A phase 1b clinical trial of the multi-targeted tyrosine kinase inhibitor lenvatinib (E7080) in combination with everolimus for treatment of metastatic renal cell carcinoma (RCC)

(2013) Ana M. Molina et al.   CANCER CHEMOTHERAPY AND PHARMACOLOGY

Axitinib versus sorafenib as second-line treatment for advanced renal cell carcinoma: overall survival analysis and updated results from a randomised phase 3 trial

(2013) Robert J Motzer et al.   LANCET ONCOLOGY

Study on Docking and Molecular Dynamics Simulation between VEGFR-2 and the Inhibitor Sunitinib

(2012) Kang An et al.   ACTA CHIMICA SINICA

Applying new clinicopathological characteristics to prognostication in advanced thyroid carcinoma

(2012) Maria E Cabanillas et al.   ENDOCRINE-RELATED CANCER

Consensus Induced Fit Docking (cIFD): methodology, validation, and application to the discovery of novel Crm1 inhibitors

(2012) Ori Kalid et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Design and Synthesis of Novel DFG-Out RAF/Vascular Endothelial Growth Factor Receptor 2 (VEGFR2) Inhibitors. 1. Exploration of [5,6]-Fused Bicyclic Scaffolds

(2012) Masanori Okaniwa et al.   JOURNAL OF MEDICINAL CHEMISTRY

Molecular conformations, interactions, and properties associated with drug efficiency and clinical performance among VEGFR TK inhibitors

(2012) M. McTigue et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular modeling study of checkpoint kinase 1 inhibitors by multiple docking strategies and prime/MM-GBSA calculation

(2011) Juan Du et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Suppression of VEGFR2 Expression in Human Endothelial Cells by Dimethylfumarate Treatment: Evidence for Anti-Angiogenic Action

(2011) Markus Meissner et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Molecular mechanisms and clinical applications of angiogenesis

(2011) Peter Carmeliet et al.   NATURE

Design, synthesis, and evaluation of 5-methyl-4-phenoxy-5H-pyrrolo[3,2-d]pyrimidine derivatives: Novel VEGFR2 kinase inhibitors binding to inactive kinase conformation

(2010) Yuya Oguro et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations

(2010) Tingjun Hou et al.   Journal of Chemical Information and Modeling

VEGFs and receptors involved in angiogenesis versus lymphangiogenesis

(2009) Marja Lohela et al.   CURRENT OPINION IN CELL BIOLOGY

Design, Synthesis, and Biological Evaluation of Novel 3-Aryl-4-(1H-indole-3yl)-1,5-dihydro-2H-pyrrole-2-ones as Vascular Endothelial Growth Factor Receptor (VEGF-R) Inhibitors

(2008) Christian Peifer et al.   JOURNAL OF MEDICINAL CHEMISTRY