Akademik Veri Yönetim Sistemi
IntechOpen, London, 2023
Molecular docking, the first algorithms of which were written in the 1980s, has now
become a routine computational method in the discovery of effective molecules
(high-throughput screening, drug repurposing) for curable and even incurable
diseases. It is used to elucidate receptor–ligand intermolecular interactions at the
atom level and to predict the possible binding conformations of molecular complexes (DNA–protein, RNA–protein, protein-protein, or protein-small molecule)
whose crystal structure is still unknown. Although these are among the routine
uses of molecular docking, from a reductionist scientific point of view, the capacity
of this technique to illuminate different molecular phenomena is limited only by
imagination, and its use in biology and medicine is diversifying day by day.
With the outbreak of the COVID-19 pandemic worldwide, it became clear how this
technique, which made a very rapid entry into the biological sciences in the last
decade, has contributed greatly to new drug discovery and drug development. It has
also made a significant contribution to the identification of new molecular targets
related to COVID-19 treatment. In addition, multiple human protein targets were
determined in the treatment of COVID-19 via the molecular docking technique,
which led to the adoption of the ‘multi-target’ approach in drug screening studies.
Strikingly, although molecular docking is used quite frequently in hit identification
and lead optimization, it has also begun to be used in bioremediation for predicting
pollutants that can be degraded by different enzymes.
Despite molecular docking being a promising technique in biology, biochemistry, and
medicine, the conformation of the obtained molecular complexes and the compatibility of the binding energies with the experimental data is still debatable and, thus,
more refinement of scoring functions is required. Hopefully, with the development
of new docking algorithms and approaches (e.g., flexible docking, solvated docking,
covalent docking, and consensus docking), the prediction of molecular complexes
in accordance with experimental data can now be made more accurately. In addition,
the contribution of molecular dynamics simulations and free energy calculations in
refining the molecular docking binding energy is invaluable and cannot be ignored.
This book presents current studies on computational molecular docking as well as
discusses the fundamentals of the technique. It is designed for researchers of all levels.