2013
DOI: 10.3109/14756366.2013.845816
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Docking and molecular dynamics studies of the binding between Peloruside A and tubulin

Abstract: The molecular docking, MD simulation and binding free energy calculation were performed to explore the probable binding modes between PLA and tubulin. Through docking study, three possible binding sites for PLA were speculated as follows: the taxane site, the alternative site and a new site in a-tubulin. Then, 12.0 ns MD simulations show that these binding modes predicted by docking have been changed more or less, whereas the MD simulations offer more reliable binding details. The MM-PBSA binding free-energy c… Show more

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Cited by 3 publications
(6 citation statements)
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References 27 publications
(35 reference statements)
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“…Going further, Figure shows a new model with two α-tubulins and two β-tubulins (α1β1/α2β2, the minimum representative fragment of two adjacent filaments of a microtubule), to evaluate features of the lateral contacts. Other authors have very recently calculated the interactions of tetramers with 1 , or with 2 via other methods. Our blind docking outcomes in the case of 1 are shown in Figure and the results for 2 in Figure .…”
Section: Results and Discussionmentioning
confidence: 99%
See 3 more Smart Citations
“…Going further, Figure shows a new model with two α-tubulins and two β-tubulins (α1β1/α2β2, the minimum representative fragment of two adjacent filaments of a microtubule), to evaluate features of the lateral contacts. Other authors have very recently calculated the interactions of tetramers with 1 , or with 2 via other methods. Our blind docking outcomes in the case of 1 are shown in Figure and the results for 2 in Figure .…”
Section: Results and Discussionmentioning
confidence: 99%
“…The MD simulations were performed with the periodic boundary conditions in the NPT ensemble using OPLS2005 force field parameters; the ligand−β-tubulin and β-tubulin−β-tubulin interactions turned out to be almost identical to those obtained with AMBER. 2426 The temperature and pressure were kept at 300 K and 1 atm (1013.25 hPa), respectively, using Nose–Hoover temperature coupling and isotropic scaling. Finally, the analysis of the contacts between the two adjacent β-tubulins was done with MDcons.…”
Section: Methodsmentioning
confidence: 99%
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“…They also utilized a quantitative structure activity relationship (QSAR) model to improve the correlation to 0.88, combining affinities from MMPBSA, QM/MMGBSA, and Glide scoring (Slynko et al, 2014 ). There were other attractive targets including indoleamine 2,3-dioxygenase 1 (Zou et al, 2017 ), translationally controlled tumor protein (Kumar R. et al, 2017 ), estrogen receptor (Anbarasu and Jayanthi, 2017 ), MutT homolog 1 (Zhou et al, 2016 ), survivin (Sarvagalla et al, 2016 ), CD44 (Nguyen et al, 2016 ), calmodulin (Gonzalez-Andrade et al, 2016 ), androgen receptor (Liu H. L. et al, 2016 ), human topoisomerase I (Guruge et al, 2016 ), Mcl-1 (Zhao et al, 2015 ), vascular endothelial growth factor receptor-2 (Wu et al, 2015 ), tubulin (Liao et al, 2014a , b ; Santoshi and Naik, 2014 ; Suri and Naik, 2015 ; Suri et al, 2015 ), the Hsp70 protein family (Bhattacharjee et al, 2015 ; Schneider et al, 2016 ), the Hsp90 protein family (Arba et al, 2015 ), glucose 6-phosphate dehydrogenase (Obiol-Pardo et al, 2014 ; Zhao et al, 2014 ), lysozyme (Zhan et al, 2015 ), p53 (Verma S. et al, 2016 ), wheat germ agglutinin (Parasuraman et al, 2014 ), bromodomains (Muvva et al, 2014 ), matrix metalloproteinases (Zhou et al, 2014 ), protein arginine methyltransferases (Hong et al, 2014 ; Yan et al, 2014 ), human arsenic methyltransferase (Abro and Azam, 2016 ), Atox1 proteins (Wang X. L. et al, 2014 ), tyrosyl-DNA phosphodiesterase 2 (Kossmann et al, 2016 ), and urokinase-type plasminogen activator (Sa et al, 2014 ).…”
Section: Applications Of Mmpbsamentioning
confidence: 99%