Molecular Dynamics Simulation Study of ClF in Water: Halogen Bonding Interaction in Liquid

Ye, Yu-feng; Fu, Cen‐Feng; Tian, Shi‐Kai

doi:10.1063/1674-0068/30/cjcp1608157

Cited by 3 publications

(1 citation statement)

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“…Molecular docking is also a helpful methodology to further study the interaction mechanisms, as it can simulate the vivid interaction picture between a ligand and a receptor [11]. In addition, molecular dynamics simulation studies the interaction mechanism of protein complex with ligands by offering vivid pictures to depict the fluctuations and conformational changes of molecules, and the structural features contributing to the inhibitory activity [12]. Therefore, a combined 3D-QSAR, molecular docking and MD simulation study can provide deep insights into the understanding structural characteristics of ligand-Abl interactions and the binding process.…”

Section: Introductionmentioning

confidence: 99%

Binding Mechanism and Molecular Design of Benzimidazole/Benzothiazole Derivatives as Potent Abl T315I Mutant Inhibitors

Lin

Tan

Zhou

et al. 2017

Chinese Journal of Chemical Physics

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Despite the efficacy of imatinib therapy in chronic myelogenous leukemia, the development of drug-resistant Abl mutants, especially the most difficult overcoming T315I mutant, makes the search for new Abl T315I inhibitors a very interesting challenge in medicinal chemistry. In this work, a multistep computational framework combining the three dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking, molecular dynamics (MD) simulation and binding free energy calculation, was performed to explore the structural requirements for the Abl T315I activities of benzimidazole/benzothiazole derivatives and the binding mechanism between the inhibitors and Abl T315I. The established 3D-QSAR models exhibited satisfactory internal and external predictability. Docking study elucidated the comformations of compounds and the key amino acid residues at the binding pocket, which were confirmed by MD simulation. The binding free energies correlated well with the experimental activities. The MM-GBSA energy decomposition revealed that the van der Waals interaction was the major driving force for the interaction between the ligands and Abl T315I. The hydrogen bond interactions between the inhibitors and Met318 also played an important role in stablizing the binding of compounds to Abl T315I. Finally, four new compounds with rather high Abl T315I activities were designed and presented to experimenters for reference.

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Section: Introductionmentioning

confidence: 99%