Abstract
One of the most powerful tools for designing drug molecules is an understanding of the target protein’s binding site. Identifying key amino acids and understanding the electronic, steric, and solvation properties of the site enables the design of potent ligands. Of equal importance for the success of a drug discovery program is the evaluation of binding site druggability. Determining, a priori, if a particular binding site has the appropriate character to bind drug-like ligands saves research time and money.
While there are a variety of experimental and computational techniques to identify and characterize binding sites, the focus of this chapter is on Binding Site Analysis (BSA) using virtual fragment simulations. The methodology of the technique is described, along with examples of successful application to drug discovery programs. BSA both indicates if a protein is a viable target for drug discovery and provides a roadmap for designing ligands. Using a computational fragment-based method is a effective means of understanding of a binding site.
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Acknowledgments
The author thanks the following colleagues for their contributions to the Locus technology and this approach to BSA: F. Guarnieri, Z. Konteatis, T. Fujimoto, F. Hollinger, M. Clark, J. Wiseman, A. Klon, J. Zou, S. Meshkat, G. Talbot, K. Milligan, and W. Chiang. The author also thanks D. Ludington and M. Ringuette for their editing assistance.
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Ludington, J.L. (2015). Protein Binding Site Analysis for Drug Discovery Using a Computational Fragment-Based Method. In: Klon, A. (eds) Fragment-Based Methods in Drug Discovery. Methods in Molecular Biology, vol 1289. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2486-8_12
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DOI: https://doi.org/10.1007/978-1-4939-2486-8_12
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