Application of Virtual Screening Approaches for the Identification of Small Molecule Inhibitors of the Methyllysine Reader Protein Spindlin1

  • Chiara Luise
  • Dina RobaaEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1824)


Computer-based approaches represent a powerful tool which helps to identify and optimize lead structures in the process of drug discovery. Computer-aided drug design techniques (CADD) encompass a large variety of methods which are subdivided into structure-based (SBDD) and ligand-based drug design (LBDD) methods. Several approaches have been successfully used over the last three decades in different fields. Indeed also in the field of epigenetics, virtual screening (VS) studies and structure-based approaches have been applied to identify novel chemical modulators of epigenetic targets as well as to predict the binding mode of active ligands and to study the protein dynamics.

In this chapter, an iterative VS approach using both SBDD and LBDD methods, which was successful in identifying Spindlin1 inhibitors, will be described. All protocol steps, starting from structure-based pharmacophore modeling, protein and database preparation along with docking and similarity search, will be explained in details.

Key words

Computer-aided drug design Virtual screening Structure-based pharmacophore Docking Database preparation Similarity search Spindlin1 Methyllysine reader proteins Epigenetics 


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Authors and Affiliations

  1. 1.Department of Pharmaceutical ChemistryMartin-Luther University of Halle-WittenbergHalle/SaaleGermany

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