Molecular docking: A powerful tool for predicting protein-ligand interactions
Keywords:Molecular docking, Computational biology, Therapeutic development, Molecular interactions
Molecular docking is a computational method used in molecular biology, structural biology and therapeutic discovery to predict how candidate molecules bind with target molecules. While predicting the binding patterns and conformations of the molecules, hardware, software, algorithm, molecule databases and models are widely used. Molecular docking processes consist of the generation and analysis of different possible conformations and orientations of the ligand within the binding site of the receptor/target. The goal is to predict the most favorable binding position or configuration, as well as the strength of the binding affinity between the ligand and receptor. The key elements of molecular docking consist of molecule preparations and using proper scoring parameters. With the help of previous knowledge and advancing technology, it is possible to expand diversity of potent therapeutics with low cost. In this proceeding review, we will focus on molecular docking as a powerful tool to predict protein-ligand interactions.
Biçak, B., Gündüz, S. K., Kökcü, Y., & Özel, A. E., Akyüz, S. (2019). Molecular docking and molecular dynamics studies of L-glycyl-L-glutamic acid dipeptide. Bilge International Journal of Science and Technology Research, 3(1), 1-9. https://doi.org/10.30516/bilgesci.476841
Stanzione, F., Giangreco, I., & Cole, J. C. (2021). Use of molecular docking computational tools in drug discovery. Progress in Medicinal Chemistry, 60, 273-343. https://doi.org/10.1016/bs.pmch.2021.01.004
Hernández-Santoyo, A., Tenorio-Barajas, A. Y., Altuzar, V., Vivanco-Cid, H., & Mendoza-Barrera, C. (2013). Protein-protein and protein-ligand docking. Protein engineering-technology and application, 63-81.
Fan, J., Fu, A., & Zhang, L. (2019). Progress in molecular docking. Quantitative Biology, 7, 83-89. https://doi.org/10.1007/s40484-019-0172-y
Meng, X. Y., Zhang, H. X., Mezei, M., & Cui, M. (2011). Molecular docking: a powerful approach for structure-based drug discovery. Current computer-aided drug design, 7(2), 146-157. https://doi.org/10.2174/157340911795677602
Boehm, H. J., Boehringer, M., Bur, D., Gmuender, H., Huber, W., Klaus, W., ... & Mueller, F. (2000). Novel inhibitors of DNA gyrase: 3D structure based biased needle screening, hit validation by biophysical methods, and 3D guided optimization. A promising alternative to random screening. Journal of medicinal chemistry, 43(14), 2664-2674. https://doi.org/10.1021/jm000017s
Elijah, S., Uba, S., & Uzairu, A. (2019). Molecular docking study for evaluating the binding mode and interaction of 2, 4-disubstituted quiloline and its derivatives as potent anti-tubercular agents against Lipoate protein B (LipB). Turkish Computational and Theoretical Chemistry, 3(1), 17-24. https://doi.org/10.33435/tcandtc.458615