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3D-QSAR, molecular docking and molecular dynamics studies of a series of RORγt inhibitors
The 3D-QSAR models and the results of molecular docking, MD simulation, binding free energies corroborate well with each other and further provide insights regarding the development of novel RORγt inhibitors with better activity.
Discovery of High Affinity Receptors for Dityrosine through Inverse Virtual Screening and Docking and Molecular Dynamics
An inverse virtual screening approach was performed to screen possible novel targets for dityrosine using a panel of targets extracted from the potential drug target database (PDTD) to facilitate the prediction of unknown targets for known ligands, and direct future experimental assays.
Toward the identification of a reliable 3D-QSAR model for the protein tyrosine phosphatase 1B inhibitors
Abstract Protein tyrosine phosphatase 1B (PTP1B) is an intracellular non-receptor phosphatase that is implicated in signal transduction of insulin and leptin pathways, thus PTP1B is considered as
Structural Determination of Three Different Series of Compounds as Hsp90 Inhibitors Using 3D-QSAR Modeling, Molecular Docking and Molecular Dynamics Methods
The docking analysis showed that Asp93, Tyr139 and Thr184 in Hsp90 are important for the three series of inhibitors, and the conformation derived from docking is basically consistent with the average structure extracted from MD simulation.
Combined 3D-QSAR, Molecular Docking and Molecular Dynamics Study on Derivatives of Peptide Epoxyketone and Tyropeptin-Boronic Acid as Inhibitors Against the β5 Subunit of Human 20S Proteasome
Three in silico models have been built with two classes of proteasome inhibitors by using 3D-QSAR, homology modeling, molecular docking and molecular dynamics simulations, revealing key structural factors responsible for the activity of these two series of PIs.
Structural analysis of selective agonists of thyroid hormone receptor β using 3D-QSAR and molecular docking
Abstract Selective thyroid hormone receptor β (TRβ) binding over TRα is an important requirement for improved therapeutic profile of TRβ agonists. Since selective compounds might be tolerated at
Structural determinants of benzodiazepinedione/peptide-based p53-HDM2 inhibitors using 3D-QSAR, docking and molecular dynamics
Two optimal 3D-QSAR models were obtained and it is revealed that the electrostatic interactions contributed much larger to the compound binding affinity than the steric effects, which may help facilitate the design of novel potent inhibitors.
Insight into structural requirements of ACE inhibitory dipeptides: QSAR and molecular docking studies
The combination of QSAR studies and molecular docking indicates the requirement of certain physicochemical parameters for better ACE inhibitors.
Development of in silico models for pyrazoles and pyrimidine derivatives as cyclin-dependent kinase 2 inhibitors.
A comparison between 3D-contour map, docking and MD simulation explore in detail the binding modes and the key structural features impacting the interaction of each series of inhibitors with the CDK₂ enzyme, which should be useful to aid the designing of new inhibitors with CDK ₂ improved biological response.
Molecular simulation of a series of benzothiazole PI3Kα inhibitors: probing the relationship between structural features, anti-tumor potency and selectivity
The satisfactory results obtained from this work strongly suggest that the developed 3D-QSAR models and the obtained PI3Kα inhibitor binding structures are reasonable for the prediction of the activity of new inhibitors and be helpful in future PI3kα inhibitor design.