Virtual screening studies reveal linarin as a potential natural inhibitor targeting CDK4 in retinoblastoma.

ABSTRACT:

Objective

To find out whether linarin can be used as a potential natural inhibitor to target CDK4 in retinoblastoma using virtual screening studies.

Materials and methods

In this study, molecular modeling and protein structure optimization was performed for crystal structure of CDK4 (PDB id: 3G33), and was subjected to Molecular Dynamics (MD) simulation for 10 nanoseconds, as a preparatory process for docking. Furthermore, the stable conformation obtained in the MD simulation was utilized for virtual screening against the library of natural compounds in Indian Plant Anticancer Compounds Database (InPACdb) using AutoDock Vina. Finally, best docked ligands were revalidated individually through semi-flexible docking by AutoDock 4.0.

Results

The CDK4 structure was stereoc

SUBMITTER: Sivashanmugam M 

PROVIDER: S-EPMC3826001 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature