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Search for Novel Lead Inhibitors of Yeast Cytochrome bc1, from Drugbank and COCONUT

In this work we introduce a novel filtering and molecular modeling pipeline based on a fingerprint and descriptor similarity procedure, coupled with molecular docking and molecular dynamics (MD), to select potential novel quoinone outside inhibitors (QoI) of cytochrome bc1 with the aim of determinin...

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Autores principales: Jović, Ozren, Šmuc, Tomislav
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8307329/
https://www.ncbi.nlm.nih.gov/pubmed/34299598
http://dx.doi.org/10.3390/molecules26144323
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author Jović, Ozren
Šmuc, Tomislav
author_facet Jović, Ozren
Šmuc, Tomislav
author_sort Jović, Ozren
collection PubMed
description In this work we introduce a novel filtering and molecular modeling pipeline based on a fingerprint and descriptor similarity procedure, coupled with molecular docking and molecular dynamics (MD), to select potential novel quoinone outside inhibitors (QoI) of cytochrome bc1 with the aim of determining the same or different chromophores to usual. The study was carried out using the yeast cytochrome bc1 complex with its docked ligand (stigmatellin), using all the fungicides from FRAC code C3 mode of action, 8617 Drugbank compounds and 401,624 COCONUT compounds. The introduced drug repurposing pipeline consists of compound similarity with C3 fungicides and molecular docking (MD) simulations with final QM/MM binding energy determination, while aiming for potential novel chromophores and perserving at least an amide (R1HN(C=O)R2) or ester functional group of almost all up to date C3 fungicides. 3D descriptors used for a similarity test were based on the 280 most stable Padel descriptors. Hit compounds that passed fingerprint and 3D descriptor similarity condition and had either an amide or an ester group were submitted to docking where they further had to satisfy both Chemscore fitness and specific conformation constraints. This rigorous selection resulted in a very limited number of candidates that were forwarded to MD simulations and QM/MM binding affinity estimations by the ORCA DFT program. In this final step, stringent criteria based on (a) sufficiently high frequency of H-bonds; (b) high interaction energy between protein and ligand through the whole MD trajectory; and (c) high enough QM/MM binding energy scores were applied to further filter candidate inhibitors. This elaborate search pipeline led finaly to four Drugbank synthetic lead compounds (DrugBank) and seven natural (COCONUT database) lead compounds—tentative new inhibitors of cytochrome bc1. These eleven lead compounds were additionally validated through a comparison of MM/PBSA free binding energy for new leads against those obtatined for 19 QoIs.
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spelling pubmed-83073292021-07-25 Search for Novel Lead Inhibitors of Yeast Cytochrome bc1, from Drugbank and COCONUT Jović, Ozren Šmuc, Tomislav Molecules Article In this work we introduce a novel filtering and molecular modeling pipeline based on a fingerprint and descriptor similarity procedure, coupled with molecular docking and molecular dynamics (MD), to select potential novel quoinone outside inhibitors (QoI) of cytochrome bc1 with the aim of determining the same or different chromophores to usual. The study was carried out using the yeast cytochrome bc1 complex with its docked ligand (stigmatellin), using all the fungicides from FRAC code C3 mode of action, 8617 Drugbank compounds and 401,624 COCONUT compounds. The introduced drug repurposing pipeline consists of compound similarity with C3 fungicides and molecular docking (MD) simulations with final QM/MM binding energy determination, while aiming for potential novel chromophores and perserving at least an amide (R1HN(C=O)R2) or ester functional group of almost all up to date C3 fungicides. 3D descriptors used for a similarity test were based on the 280 most stable Padel descriptors. Hit compounds that passed fingerprint and 3D descriptor similarity condition and had either an amide or an ester group were submitted to docking where they further had to satisfy both Chemscore fitness and specific conformation constraints. This rigorous selection resulted in a very limited number of candidates that were forwarded to MD simulations and QM/MM binding affinity estimations by the ORCA DFT program. In this final step, stringent criteria based on (a) sufficiently high frequency of H-bonds; (b) high interaction energy between protein and ligand through the whole MD trajectory; and (c) high enough QM/MM binding energy scores were applied to further filter candidate inhibitors. This elaborate search pipeline led finaly to four Drugbank synthetic lead compounds (DrugBank) and seven natural (COCONUT database) lead compounds—tentative new inhibitors of cytochrome bc1. These eleven lead compounds were additionally validated through a comparison of MM/PBSA free binding energy for new leads against those obtatined for 19 QoIs. MDPI 2021-07-16 /pmc/articles/PMC8307329/ /pubmed/34299598 http://dx.doi.org/10.3390/molecules26144323 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Jović, Ozren
Šmuc, Tomislav
Search for Novel Lead Inhibitors of Yeast Cytochrome bc1, from Drugbank and COCONUT
title Search for Novel Lead Inhibitors of Yeast Cytochrome bc1, from Drugbank and COCONUT
title_full Search for Novel Lead Inhibitors of Yeast Cytochrome bc1, from Drugbank and COCONUT
title_fullStr Search for Novel Lead Inhibitors of Yeast Cytochrome bc1, from Drugbank and COCONUT
title_full_unstemmed Search for Novel Lead Inhibitors of Yeast Cytochrome bc1, from Drugbank and COCONUT
title_short Search for Novel Lead Inhibitors of Yeast Cytochrome bc1, from Drugbank and COCONUT
title_sort search for novel lead inhibitors of yeast cytochrome bc1, from drugbank and coconut
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8307329/
https://www.ncbi.nlm.nih.gov/pubmed/34299598
http://dx.doi.org/10.3390/molecules26144323
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