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Extension of an Atom–Atom Dispersion Function to Halogen Bonds and Its Use for Rational Design of Drugs and Biocatalysts

[Image: see text] A dispersion function D(as) in the form of a damped atom–atom asymptotic expansion fitted to ab initio dispersion energies from symmetry-adapted perturbation theory was improved and extended to systems containing heavier halogen atoms. To illustrate its performance, the revised D(a...

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Autores principales: Jedwabny, Wiktoria, Dyguda-Kazimierowicz, Edyta, Pernal, Katarzyna, Szalewicz, Krzysztof, Patkowski, Konrad
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2021
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8028329/
https://www.ncbi.nlm.nih.gov/pubmed/33620223
http://dx.doi.org/10.1021/acs.jpca.0c11347
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author Jedwabny, Wiktoria
Dyguda-Kazimierowicz, Edyta
Pernal, Katarzyna
Szalewicz, Krzysztof
Patkowski, Konrad
author_facet Jedwabny, Wiktoria
Dyguda-Kazimierowicz, Edyta
Pernal, Katarzyna
Szalewicz, Krzysztof
Patkowski, Konrad
author_sort Jedwabny, Wiktoria
collection PubMed
description [Image: see text] A dispersion function D(as) in the form of a damped atom–atom asymptotic expansion fitted to ab initio dispersion energies from symmetry-adapted perturbation theory was improved and extended to systems containing heavier halogen atoms. To illustrate its performance, the revised D(as) function was implemented in the multipole first-order electrostatic and second-order dispersion (MED) scoring model. The extension has allowed applications to a much larger set of biocomplexes than it was possible with the original D(as). A reasonable correlation between MED and experimentally determined inhibitory activities was achieved in a number of test cases, including structures featuring nonphysically shortened intermonomer distances, which constitute a particular challenge for binding strength predictions. Since the MED model is also computationally efficient, it can be used for reliable and rapid assessment of the ligand affinity or multidimensional scanning of amino acid side-chain conformations in the process of rational design of novel drugs or biocatalysts.
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spelling pubmed-80283292021-04-08 Extension of an Atom–Atom Dispersion Function to Halogen Bonds and Its Use for Rational Design of Drugs and Biocatalysts Jedwabny, Wiktoria Dyguda-Kazimierowicz, Edyta Pernal, Katarzyna Szalewicz, Krzysztof Patkowski, Konrad J Phys Chem A [Image: see text] A dispersion function D(as) in the form of a damped atom–atom asymptotic expansion fitted to ab initio dispersion energies from symmetry-adapted perturbation theory was improved and extended to systems containing heavier halogen atoms. To illustrate its performance, the revised D(as) function was implemented in the multipole first-order electrostatic and second-order dispersion (MED) scoring model. The extension has allowed applications to a much larger set of biocomplexes than it was possible with the original D(as). A reasonable correlation between MED and experimentally determined inhibitory activities was achieved in a number of test cases, including structures featuring nonphysically shortened intermonomer distances, which constitute a particular challenge for binding strength predictions. Since the MED model is also computationally efficient, it can be used for reliable and rapid assessment of the ligand affinity or multidimensional scanning of amino acid side-chain conformations in the process of rational design of novel drugs or biocatalysts. American Chemical Society 2021-02-23 2021-03-04 /pmc/articles/PMC8028329/ /pubmed/33620223 http://dx.doi.org/10.1021/acs.jpca.0c11347 Text en © 2021 The Authors. Published by American Chemical Society Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Jedwabny, Wiktoria
Dyguda-Kazimierowicz, Edyta
Pernal, Katarzyna
Szalewicz, Krzysztof
Patkowski, Konrad
Extension of an Atom–Atom Dispersion Function to Halogen Bonds and Its Use for Rational Design of Drugs and Biocatalysts
title Extension of an Atom–Atom Dispersion Function to Halogen Bonds and Its Use for Rational Design of Drugs and Biocatalysts
title_full Extension of an Atom–Atom Dispersion Function to Halogen Bonds and Its Use for Rational Design of Drugs and Biocatalysts
title_fullStr Extension of an Atom–Atom Dispersion Function to Halogen Bonds and Its Use for Rational Design of Drugs and Biocatalysts
title_full_unstemmed Extension of an Atom–Atom Dispersion Function to Halogen Bonds and Its Use for Rational Design of Drugs and Biocatalysts
title_short Extension of an Atom–Atom Dispersion Function to Halogen Bonds and Its Use for Rational Design of Drugs and Biocatalysts
title_sort extension of an atom–atom dispersion function to halogen bonds and its use for rational design of drugs and biocatalysts
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8028329/
https://www.ncbi.nlm.nih.gov/pubmed/33620223
http://dx.doi.org/10.1021/acs.jpca.0c11347
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