Inhibition of Bioconcentration of Pentachlorobenzene in the Aquatic Food Chain Based on 3D-QSAR, Molecular Docking, and Molecular Dynamics Simulation

Sun, Ruihao; Zhang, Wenhui; Li, Qing; Yu, Lie

doi:10.1007/s11270-021-05000-x

Cited by 3 publications

(2 citation statements)

References 26 publications

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“…Subsequently, the experimentally measured IC 50 values were converted into pIC 50 values [19] . The three‐dimensional structures of all compounds were built using the Sybyl‐X2.0 molecular simulation software [20] . Then, the Minimize module was used to apply the Tripos force field and add Gasteiger‐Hückel charges to all 34 compounds [21] .…”

Section: Methodsmentioning

confidence: 99%

“…[19] The three-dimensional structures of all compounds were built using the Sybyl-X2.0 molecular simulation software. [20] Then, the Minimize module was used to apply the Tripos force field and add Gasteiger-Hückel charges to all 34 compounds. [21] The maximum number of iterations was set to 10,000, and when the energy difference did not exceed 0.005 kcal/ mol, it was considered that the iteration had converged.…”

Section: Data Source and Constructionmentioning

confidence: 99%

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Design of New Second‐Generation TRK Inhibitors Targeting Tropomyosin Receptor Kinases by Using Molecular Docking, Molecular Dynamics Simulations and ADMET Properties

Zhao,

Cui,

Tang

et al. 2024

ChemistrySelect

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TRK, as a type of cell surface protein, plays a critical role in various biological processes, particularly as a key target for cancer treatment. We explored the correlation between the structure and activity of indole‐2‐one derivatives through investigations involving 3D‐QSAR molecular modelling, molecular docking, molecular dynamics, and ADMET property research. The statistical data from the CoMFA and CoMSIA models exhibit excellent internal stability (CoMFA: q2=0.622, r2=0.992; CoMSIA: q2=0.740, r2=0.972). Further molecular docking unveiled the interaction mechanism between small molecules and receptor proteins, demonstrating that the hydrogen bonding between amino acids Met590 and Glu592 and small molecules could enhance the ligand‐receptor binding affinity. Based on the 3D‐QSAR model and molecular docking, we designed and predicted the activity of eight new molecules, which displayed high expected activity. Subsequently, through 100 ns MD simulations and binding free energy calculations, we affirmed the stability of the molecular docking results. Finally, we employed ADMET to predict the pharmacokinetic properties of the newly designed molecules, validating their commendable drug‐like characteristics. These research findings provide valuable references for the design and development of novel TRK inhibitors, offering fresh perspectives for subsequent drug design.

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Section: Methodsmentioning

confidence: 99%