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Hydrogen Bonds in Protein-Ligand Complexes

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Docking Screens for Drug Discovery

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2053))

Abstract

Fast and reliable evaluation of the hydrogen bond potential energy has a significant impact in the drug design and development since it allows the assessment of large databases of organic molecules in virtual screening projects focused on a protein of interest. Semi-empirical force fields implemented in molecular docking programs make it possible the evaluation of protein-ligand binding affinity where the hydrogen bond potential is a common term used in the calculation. In this chapter, we describe the concepts behind the programs used to predict hydrogen bond potential energy employing semi-empirical force fields as the ones available in the programs AMBER, AutoDock4, TreeDock, and ReplicOpter. We described here the 12-10 potential and applied it to evaluate the binding affinity for an ensemble of crystallographic structures for which experimental data about binding affinity are available.

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Acknowledgments

This work was supported by grants from CNPq (Brazil) (308883/2014-4). This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nivel Superior—Brasil (CAPES)—Finance Code 001. GB-F acknowledges support from PUCRS/BPA fellowship. MV-A acknowledges support from PUCRS/IC Jr. WFA is a senior researcher for CNPq (Brazil) (Process Numbers: 308883/2014-4 and 309029/2018-0).

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  1. Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul—PUCRS, Porto Alegre, RS, Brazil

    Gabriela Bitencourt-Ferreira, Martina Veit-Acosta & Walter Filgueira de Azevedo Jr.

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  1. Gabriela Bitencourt-Ferreira
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  2. Martina Veit-Acosta
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  3. Walter Filgueira de Azevedo Jr.
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Correspondence to Walter Filgueira de Azevedo Jr. .

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  1. Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul—PUCRS, Porto Alegre, Rio Grande do Sul, Brazil

    Walter Filgueira de Azevedo Jr.

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Bitencourt-Ferreira, G., Veit-Acosta, M., de Azevedo, W.F. (2019). Hydrogen Bonds in Protein-Ligand Complexes. In: de Azevedo Jr., W. (eds) Docking Screens for Drug Discovery. Methods in Molecular Biology, vol 2053. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9752-7_7

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  • DOI: https://doi.org/10.1007/978-1-4939-9752-7_7

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9751-0

  • Online ISBN: 978-1-4939-9752-7

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