Discovery and development of appropriate therapeutic pharmaceuticals has been always regarded as one the major goals of human beings. Finding a molecular structure with desirable pharmacological property may be possibly the most difficult step of drug discovery effort. Within the last centuries, drugs have been discovered via serendipitous methods (me too method). This trend leads to the waste of time and money since no rationality may exist in selection of the assayed compounds. Drug discovery projects may be more efficient, economic and less tedious through "rational drug design" methods that require more information on the therapeutic targets.
The topic "rational design of bioactive molecules" which is known also as "rational drug design" is an extensive scientific branch that is partly attributed to the computer aided drug design (CADD). Modeling of bioactive molecules can be generally performed within two general methods; ligand based drug design and structure based drug design. In the former, techniques such as quantitative structure activity relationship (QSAR), similarity search and molecular modifications on the chemical structure of initial drug substances are applied. The major advantage of such methods is their applicability when no information on 3D structure of bimolecular target is available.
When 3D structural information of the target is accessible, drug design protocols may be conducted on the basis of target structure. In this regard, molecular docking is the most important technique in which effective ligand-receptor interactions may be computationally modeled in the active site of the receptor. This procedure aims at the selection of molecules with the maximum steric fitness in the active site of the receptor and at the same time possessing appropriate free binding energy with the receptor.
The advanced program AutoDock is one of the most recognized docking softwares (1). It has been extensively applied in the field of rational drug design and has also produced several fruitful results. AutoDock estimates the free binding energy of ligand-receptor complex through its efficient force field function. The potential of AutoDock in qualitative and quantitative modeling of ligand-receptor interactions has introduced it as an appropriate simulation medium for the identification of pharmacophoric sites of ligands in the active site of the receptors.
The workshop on "Molecular Docking and its Application in Drug Design" aims at the introduction of modern drug discovery methods and their application in pharmacy via bringing up the researchers and students.
(1) Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ, AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility.J. Comput. Chem., 2009, 30(16): 2785–2791.