Pharmacophore modeling and virtual screening studies for new VEGFR-2 kinase inhibitors

Lee, Kyungik; Jeong, Ki-Woong; Lee, Yeonjoo; Song, Ji Yeon; Kim, Maeng Sup; Lee, Gwan Sun; Kim, Yangmee

doi:10.1016/j.ejmech.2010.09.002

Cited by 119 publications

(78 citation statements)

References 30 publications

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“…It has been successfully used to predict high affinity protein ligands (Lee et al, 2010;Park et al, 2009). The molecules of the library are ranked according to their predicted binding affinity for the receptor.…”

Section: Introductionmentioning

confidence: 99%

Consensus virtual screening approaches to predict protein ligands

Kukol

2011

European Journal of Medicinal Chemistry

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-In order to exploit the advantages of receptor-based virtual screening, namely time/cost saving and specificity, it is important to rely on algorithms that predict a high number of active ligands at the top ranks of a small molecule database. Towards that goal consensus methods combining the results of several docking algorithms were developed and compared against the individual algorithms. Furthermore, a recently proposed rescoring method based on drug efficiency indices was evaluated. Among AutoDock Vina 1.0, AutoDock 4.2 and GemDock, AutoDock Vina was the best performing single method in predicting high affinity ligands from a database of known ligands and decoys. The rescoring of predicted binding energies with the water/butanol partition coeffcient did not lead to an improvement averaged over all receptor targets. Various consensus algorithms were investigated and a simple combination of AutoDock and AutoDock Vina results gave the most consistent performance that showed early enrichment of known ligands for all receptor targets investigated. In case a number ligands is known for a specific target, every method proposed in this study should be evaluated.

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Section: Introductionmentioning

confidence: 99%

Consensus virtual screening approaches to predict protein ligands

Kukol

2011

European Journal of Medicinal Chemistry

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“…The pharmacophoric requirements for VEGFR-2 inhibitors have been reported by Lee et al [10] (Fig. 1), which are as follows: In accordance with the structural requirements for the adenine region of ATP, the core structure of most VEGFR-2 kinase inhibitors consists of a flat aromatic ring system with a hydrogen bond acceptor group which will accept hydrogen from the backbone NH of Cys-917.…”

Section: Design Of Novel Moleculesmentioning

confidence: 85%

“…Recently Kyungik et al reported structural requirements for adenine region of ATP binding site of VEGFR-2; the core structure of all VEGFR-2 inhibitors consists of a flat aromatic ring system with the hydrogen bond acceptor group which will accept hydrogen from the backbone NH of Cys-917 [10].…”

Section: Introductionmentioning

confidence: 99%

5-Benzylidene-2,4-thiazolidenedione derivatives: Design, synthesis and evaluation as inhibitors of angiogenesis targeting VEGR-2

Bhanushali

Rajendran²,

Sarma

et al. 2016

Bioorganic Chemistry

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“…3). This cysteine residue, which is unique for VEGFR-2 kinase active site, plays a crucial role in the recognition of ligands [17]. It was also noticed that this pyrimido [4,5-b]indole derivative which possess a relatively small aniline portion compared to the large extended hydrophobic region I.…”

Section: Ligand-receptor Interaction Studies Of Vegfr-2 Kinase Inhibimentioning

confidence: 97%

“…The development of selective VEGFR-2 inhibitors is of interest as they might provide promising anticancer agents with minimal toxicity [1]. Therefore, much effort has been focused on identifying novel VEGFR-2 selective inhibitors [7,[16][17][18]. It is worth noting that efforts exerted to identify selective inhibitors of a particular kinase often begin with the screening of the archived inhibitors that were developed in previous studies.…”

Section: Introductionmentioning

confidence: 99%