Journal ArticleDOI
Investigating the binding mechanism of (4-Cyanophenyl)glycine derivatives as reversible LSD1 by 3D-QSAR, molecular docking and molecular dynamics simulations
TLDR
A molecular modeling study on (4-Cyanophenyl)glycine derivatives as reversible LSD1 inhibitors using 3D-QSAR, molecular docking and molecular dynamics simulations revealed the possible binding mechanism of these inhibitors with LSD1 and an important hydrogen bond network was discovered.About:
This article is published in Journal of Molecular Structure.The article was published on 2019-01-05. It has received 12 citations till now. The article focuses on the topics: Docking (molecular) & Molecular model.read more
Citations
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Two-dimensional and Three-dimensional quantitative structure-activity relationship models for the degradation of organophosphate flame retardants during supercritical Water oxidation.
Zhiwen Cheng,Qincheng Chen,Sheila Cervantes,Qingli Tang,Xiaoping Gao,Yujia Tan,Shiqiang Liu,Yuning Ma,Zhemin Shen +8 more
TL;DR: Two-dimensional and three-dimensional quantitative structure-activity relationship models were established to investigate the factors influencing the total carbon degradation rates (kTOC) and generated critical knowledge of influencing factors on OPFRs degradation and yielded theoretical basis for estimating removal behaviors of OP FRs undergoing SCWO process.
Journal ArticleDOI
Molecular docking, 3D-QSAR, and molecular dynamics simulations of thieno[3,2-b]pyrrole derivatives against anticancer targets of KDM1A/LSD1.
TL;DR: A molecular modeling study on a set of 43 thieno[3,2-b]pyrrole competitive inhibitors of LSD1 using three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking and molecular dynamics simulations indicated the good predictive power and statistical reliability of this model.
Journal ArticleDOI
Investigation of pyrimidine analogues as xanthine oxidase inhibitors to treat of hyperuricemia and gout through combined QSAR techniques, molecular docking and molecular dynamics simulations
TL;DR: Contour maps of all models were generated and it was proved by molecular docking studies and molecular dynamics simulation, that the steric, hydrophobic and hydrogen bonding fields are crucial in these models for improving the binding affinity and determine of structure- activity relationship.
Journal ArticleDOI
Rational design of novel pyridine-based drugs candidates for lymphoma therapy
TL;DR: In this paper , an extensive in silico computational study based on pharmacophore QSAR modeling, DFT, Molecular Docking, ADME-Tox, biophysical simulation approaches such as Molecular Dynamics analysis (MD) and comprehensive MM-GBSA free binding energy computations on a novel series of pyridine derivatives as promising MALT1 allosteric inhibitors (PDB code: 4I1R).
Journal ArticleDOI
Investigating the binding mechanism of sphingosine kinase 1/2 inhibitors: Insights into subtype selectivity by homology modeling, molecular dynamics simulation and free energy calculation studies
Jinmiao Zhang,Maoyu Zhang,Jinying Yu,Yanguo Shang,Kaixuan Jiang,Yihe Jia,Jinxin Wang,Kan Yang +7 more
TL;DR: Introducing suitable substituents that insert into the region of Cys533 or designing a flexible polar head that interacts with Leu297 and Ser298 might improve the selectivity towards SPHK2.
References
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David van der Spoel,Erik Lindahl,Berk Hess,Gerrit Groenhof,Alan E. Mark,Herman J. C. Berendsen +5 more
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Iterative partial equalization of orbital electronegativity – a rapid access to atomic charges
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TL;DR: In this article, a method for the rapid calculation of atomic charges in σ-bonded and nonconjugated π-systems is presented, where only the connectivities of the atoms are considered.
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Histone demethylation mediated by the nuclear amine oxidase homolog lsd1
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g_mmpbsa--a GROMACS tool for high-throughput MM-PBSA calculations.
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