Structure-based drug design, virtual screening

 
  • Structure-based drug design, virtual screening starts with processing the 3D target structural information of interest. The target structure may be derived from experimental data (X-ray, NMR or neutron scattering spectroscopy), homology modeling, or from Molecular Dynamics (MD) simulations. There are numerous fundamental issues that should be examined when considering a biological target for SBVS; for example, the druggability of the receptor, the choice of binding site, the selection of the most relevant protein structure, incorporating receptor flexibility, suitable assignment of protonation states, and consideration of water molecules in a binding site, to name a few. In fact, the identification of ligand binding sites on biological targets is becoming increasingly important. The need for novel modulators of protein/gene function has recently directed the scientific community to pursue druggable allosteric binding pockets. Another consideration for SBVS includes the careful choice of the compound library to be screened in the VS exercise according to the target in question, and the preprocessing of libraries in order to assign the proper stereochemistry, tautomeric, and protonation states.

  • Protein biochemistry
  • Organic synthesis of ligands and inhibitors
  • Drug metabolism
  • Molecular biology and genetic engineering
  • Ligand and structure based drug design

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