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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...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical
Society
2021
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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. |
format | Online Article Text |
id | pubmed-8028329 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | American Chemical
Society |
record_format | MEDLINE/PubMed |
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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