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A Computational Simulation Study of Benzamidine Derivatives Binding to Arginine-Specific Gingipain (HRgpA) from Periodontopathogen Porphyromonas gingivalis

We have shown that the binding free energy calculation from molecular dynamics can be adapted successfully to cysteine proteinases, such as arginine-specific gingipain (HRgpA) from Porphyromonas gingivalis. The binding free energy obtained is in good agreement with the available experimental data fo...

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Detalles Bibliográficos
Autores principales: Kim, Dooil, Lee, Dae-Sil
Formato: Texto
Lenguaje:English
Publicado: Molecular Diversity Preservation International (MDPI) 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2956092/
https://www.ncbi.nlm.nih.gov/pubmed/20957091
http://dx.doi.org/10.3390/ijms11093252
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author Kim, Dooil
Lee, Dae-Sil
author_facet Kim, Dooil
Lee, Dae-Sil
author_sort Kim, Dooil
collection PubMed
description We have shown that the binding free energy calculation from molecular dynamics can be adapted successfully to cysteine proteinases, such as arginine-specific gingipain (HRgpA) from Porphyromonas gingivalis. The binding free energy obtained is in good agreement with the available experimental data for eight benzamidine derivatives including urea and ether linker. The calculations showed that the electrostatic energies between HRgpA and inhibitors were important in determining the relative affinities of the inhibitors to the HRgpA, with an average binding free energy of about −5 kcal/mol. The average structures of the eight complexes suggest that benzamidine inhibitors interact with Asp387, His435, and Cys468 by hydrogen bonding and with Trp508 by hydrophilic interactions that are essential for the activities of benzamidine inhibitors. It can therefore be expected that the method provides a reliable tool for the investigation of new HRgpA inhibitors. This finding could significantly benefit the future design of HRgpA inhibitors.
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spelling pubmed-29560922010-10-18 A Computational Simulation Study of Benzamidine Derivatives Binding to Arginine-Specific Gingipain (HRgpA) from Periodontopathogen Porphyromonas gingivalis Kim, Dooil Lee, Dae-Sil Int J Mol Sci Article We have shown that the binding free energy calculation from molecular dynamics can be adapted successfully to cysteine proteinases, such as arginine-specific gingipain (HRgpA) from Porphyromonas gingivalis. The binding free energy obtained is in good agreement with the available experimental data for eight benzamidine derivatives including urea and ether linker. The calculations showed that the electrostatic energies between HRgpA and inhibitors were important in determining the relative affinities of the inhibitors to the HRgpA, with an average binding free energy of about −5 kcal/mol. The average structures of the eight complexes suggest that benzamidine inhibitors interact with Asp387, His435, and Cys468 by hydrogen bonding and with Trp508 by hydrophilic interactions that are essential for the activities of benzamidine inhibitors. It can therefore be expected that the method provides a reliable tool for the investigation of new HRgpA inhibitors. This finding could significantly benefit the future design of HRgpA inhibitors. Molecular Diversity Preservation International (MDPI) 2010-09-13 /pmc/articles/PMC2956092/ /pubmed/20957091 http://dx.doi.org/10.3390/ijms11093252 Text en © 2010 by the authors; licensee Molecular Diversity Preservation International, Basel, Switzerland. http://creativecommons.org/licenses/by/3.0 This article is an open-access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).
spellingShingle Article
Kim, Dooil
Lee, Dae-Sil
A Computational Simulation Study of Benzamidine Derivatives Binding to Arginine-Specific Gingipain (HRgpA) from Periodontopathogen Porphyromonas gingivalis
title A Computational Simulation Study of Benzamidine Derivatives Binding to Arginine-Specific Gingipain (HRgpA) from Periodontopathogen Porphyromonas gingivalis
title_full A Computational Simulation Study of Benzamidine Derivatives Binding to Arginine-Specific Gingipain (HRgpA) from Periodontopathogen Porphyromonas gingivalis
title_fullStr A Computational Simulation Study of Benzamidine Derivatives Binding to Arginine-Specific Gingipain (HRgpA) from Periodontopathogen Porphyromonas gingivalis
title_full_unstemmed A Computational Simulation Study of Benzamidine Derivatives Binding to Arginine-Specific Gingipain (HRgpA) from Periodontopathogen Porphyromonas gingivalis
title_short A Computational Simulation Study of Benzamidine Derivatives Binding to Arginine-Specific Gingipain (HRgpA) from Periodontopathogen Porphyromonas gingivalis
title_sort computational simulation study of benzamidine derivatives binding to arginine-specific gingipain (hrgpa) from periodontopathogen porphyromonas gingivalis
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2956092/
https://www.ncbi.nlm.nih.gov/pubmed/20957091
http://dx.doi.org/10.3390/ijms11093252
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