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Fragment Linking and Optimization of Inhibitors of the Aspartic Protease Endothiapepsin: Fragment‐Based Drug Design Facilitated by Dynamic Combinatorial Chemistry

Fragment‐based drug design (FBDD) affords active compounds for biological targets. While there are numerous reports on FBDD by fragment growing/optimization, fragment linking has rarely been reported. Dynamic combinatorial chemistry (DCC) has become a powerful hit‐identification strategy for biologi...

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Autores principales: Mondal, Milon, Radeva, Nedyalka, Fanlo‐Virgós, Hugo, Otto, Sijbren, Klebe, Gerhard, Hirsch, Anna K. H.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5113778/
https://www.ncbi.nlm.nih.gov/pubmed/27400756
http://dx.doi.org/10.1002/anie.201603074
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author Mondal, Milon
Radeva, Nedyalka
Fanlo‐Virgós, Hugo
Otto, Sijbren
Klebe, Gerhard
Hirsch, Anna K. H.
author_facet Mondal, Milon
Radeva, Nedyalka
Fanlo‐Virgós, Hugo
Otto, Sijbren
Klebe, Gerhard
Hirsch, Anna K. H.
author_sort Mondal, Milon
collection PubMed
description Fragment‐based drug design (FBDD) affords active compounds for biological targets. While there are numerous reports on FBDD by fragment growing/optimization, fragment linking has rarely been reported. Dynamic combinatorial chemistry (DCC) has become a powerful hit‐identification strategy for biological targets. We report the synergistic combination of fragment linking and DCC to identify inhibitors of the aspartic protease endothiapepsin. Based on X‐ray crystal structures of endothiapepsin in complex with fragments, we designed a library of bis‐acylhydrazones and used DCC to identify potent inhibitors. The most potent inhibitor exhibits an IC(50) value of 54 nm, which represents a 240‐fold improvement in potency compared to the parent hits. Subsequent X‐ray crystallography validated the predicted binding mode, thus demonstrating the efficiency of the combination of fragment linking and DCC as a hit‐identification strategy. This approach could be applied to a range of biological targets, and holds the potential to facilitate hit‐to‐lead optimization.
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spelling pubmed-51137782016-12-02 Fragment Linking and Optimization of Inhibitors of the Aspartic Protease Endothiapepsin: Fragment‐Based Drug Design Facilitated by Dynamic Combinatorial Chemistry Mondal, Milon Radeva, Nedyalka Fanlo‐Virgós, Hugo Otto, Sijbren Klebe, Gerhard Hirsch, Anna K. H. Angew Chem Int Ed Engl Communications Fragment‐based drug design (FBDD) affords active compounds for biological targets. While there are numerous reports on FBDD by fragment growing/optimization, fragment linking has rarely been reported. Dynamic combinatorial chemistry (DCC) has become a powerful hit‐identification strategy for biological targets. We report the synergistic combination of fragment linking and DCC to identify inhibitors of the aspartic protease endothiapepsin. Based on X‐ray crystal structures of endothiapepsin in complex with fragments, we designed a library of bis‐acylhydrazones and used DCC to identify potent inhibitors. The most potent inhibitor exhibits an IC(50) value of 54 nm, which represents a 240‐fold improvement in potency compared to the parent hits. Subsequent X‐ray crystallography validated the predicted binding mode, thus demonstrating the efficiency of the combination of fragment linking and DCC as a hit‐identification strategy. This approach could be applied to a range of biological targets, and holds the potential to facilitate hit‐to‐lead optimization. John Wiley and Sons Inc. 2016-07-12 2016-08-01 /pmc/articles/PMC5113778/ /pubmed/27400756 http://dx.doi.org/10.1002/anie.201603074 Text en © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA. This is an open access article under the terms of the Creative Commons Attribution (http://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Communications
Mondal, Milon
Radeva, Nedyalka
Fanlo‐Virgós, Hugo
Otto, Sijbren
Klebe, Gerhard
Hirsch, Anna K. H.
Fragment Linking and Optimization of Inhibitors of the Aspartic Protease Endothiapepsin: Fragment‐Based Drug Design Facilitated by Dynamic Combinatorial Chemistry
title Fragment Linking and Optimization of Inhibitors of the Aspartic Protease Endothiapepsin: Fragment‐Based Drug Design Facilitated by Dynamic Combinatorial Chemistry
title_full Fragment Linking and Optimization of Inhibitors of the Aspartic Protease Endothiapepsin: Fragment‐Based Drug Design Facilitated by Dynamic Combinatorial Chemistry
title_fullStr Fragment Linking and Optimization of Inhibitors of the Aspartic Protease Endothiapepsin: Fragment‐Based Drug Design Facilitated by Dynamic Combinatorial Chemistry
title_full_unstemmed Fragment Linking and Optimization of Inhibitors of the Aspartic Protease Endothiapepsin: Fragment‐Based Drug Design Facilitated by Dynamic Combinatorial Chemistry
title_short Fragment Linking and Optimization of Inhibitors of the Aspartic Protease Endothiapepsin: Fragment‐Based Drug Design Facilitated by Dynamic Combinatorial Chemistry
title_sort fragment linking and optimization of inhibitors of the aspartic protease endothiapepsin: fragment‐based drug design facilitated by dynamic combinatorial chemistry
topic Communications
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5113778/
https://www.ncbi.nlm.nih.gov/pubmed/27400756
http://dx.doi.org/10.1002/anie.201603074
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