Study of differences in the VEGFR2 inhibitory activities between semaxanib and SU5205 using 3D-QSAR, docking, and molecular dynamics simulations

Molecular Dynamics Simulation of VEGFR2 with Sorafenib and Other Urea-Substituted Aryloxy Compounds

“…From Supplementary Table 1 we can see that Coulomb interaction contributes less to the whole interaction energy between VEGFR2 and the title compounds. The interaction is governed by van der Waals interactions, which is in accordance with the results of Muñoz et al [9]. Parts A and B have little difference due to same structure for compounds 12-22.…”

“…Thus, there are still needs to develop new VEGFR2 inhibitors. With the development of the computational software and hardware, the usage of in silico methods, such as docking [9], QSAR, pharmacophore modeling [10], and molecular dynamics method [11], has become essential to pharmaceutical research. Abreu et al [12] have studied the VEGFR2-selective side-chain residue flexibility using AutoDock Vina docking software, and they found that Glu885 flexible conformation could present best scores.…”

Development of indazolylpyrimidine derivatives as high-affine EphB4 receptor ligands and potential PET radiotracers

“…Xantphos and Pd 2 (dba) 3 were added in catalytic amounts and the mixture was stirred at stereochemistries, and ring conformations of the sketched ligands. Docking parameters were used as in previous works, 41 in extraprecision (XP) mode during the search. The more energetically favorable conformation was selected as the best pose.…”

Vascular endothelial growth factor receptor-2 (VEGFR-2) inhibitors: development and validation of predictive 3-D QSAR models through extensive ligand- and structure-based approaches

“…VEGFR-2 is a likely target for computational drug design as small molecule inhibitors have been derived from many molecular scaffolds, including quinazolines [14,15], naphtamides [16], furo [2,3-d]pyrimidines [17], pyridinyltriazines [18], pyrimidinyllindazoles [19], and most recently thieno [3,2-d]pyrimidinones and thieno [1][2][3] triazines [20], offering an expansive data set for design and optimization. Using SciFinder Ò as a representative search tool for the literature, 17 publications were identified which used 3-D QSAR methods to study inhibitors of VEGFR-2 [21][22][23][24][25][26][27][28][29][30][31][32][33][34][35][36][37]. Most of these studies built CoMFA/CoMSIA models using SYBYL software [21,22,[28][29][30][31][35][36][37], and all but one simply used these models for pharmacophore modeling and analysis; one study used the 3-D QSAR models as a virtual screening tool to identify novel N-(pyridin-4-ylmethyl)aniline derivates as potential VEGFR-2 inhibitors [37].…”

“…Using SciFinder Ò as a representative search tool for the literature, 17 publications were identified which used 3-D QSAR methods to study inhibitors of VEGFR-2 [21][22][23][24][25][26][27][28][29][30][31][32][33][34][35][36][37]. Most of these studies built CoMFA/CoMSIA models using SYBYL software [21,22,[28][29][30][31][35][36][37], and all but one simply used these models for pharmacophore modeling and analysis; one study used the 3-D QSAR models as a virtual screening tool to identify novel N-(pyridin-4-ylmethyl)aniline derivates as potential VEGFR-2 inhibitors [37]. Many of the studies performed docking studies on the training and test set molecules using a variety of docking software (AutoDock [36], Sybyl [21,37], Surflex-Dock [35], MacroModel [31], GOLD [28] ), but each study made use of only one available crystal structure of VEGFR-2.…”