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Determining the unbinding events and conserved motions associated with the pyrazinamide release due to resistance mutations of Mycobacterium tuberculosis pyrazinamidase

Pyrazinamide (PZA) is the only first-line antitubercular drug active against latent Mycobacterium tuberculosis (Mtb). It is activated to pyrazinoic acid by the pncA-encoded pyrazinamidase enzyme (PZase). Despite the emergence of PZA drug resistance, the underlying mechanisms of resistance remain unc...

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Autores principales: Sheik Amamuddy, Olivier, Musyoka, Thommas Mutemi, Boateng, Rita Afriyie, Zabo, Sophakama, Tastan Bishop, Özlem
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Research Network of Computational and Structural Biotechnology 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7251373/
https://www.ncbi.nlm.nih.gov/pubmed/32489525
http://dx.doi.org/10.1016/j.csbj.2020.05.009
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author Sheik Amamuddy, Olivier
Musyoka, Thommas Mutemi
Boateng, Rita Afriyie
Zabo, Sophakama
Tastan Bishop, Özlem
author_facet Sheik Amamuddy, Olivier
Musyoka, Thommas Mutemi
Boateng, Rita Afriyie
Zabo, Sophakama
Tastan Bishop, Özlem
author_sort Sheik Amamuddy, Olivier
collection PubMed
description Pyrazinamide (PZA) is the only first-line antitubercular drug active against latent Mycobacterium tuberculosis (Mtb). It is activated to pyrazinoic acid by the pncA-encoded pyrazinamidase enzyme (PZase). Despite the emergence of PZA drug resistance, the underlying mechanisms of resistance remain unclear. This study investigated part of these mechanisms by modelling a PZA-bound wild type and 82 mutant PZase structures before applying molecular dynamics (MD) with an accurate Fe(2+) cofactor coordination geometry. After observing nanosecond-scale PZA unbinding from several PZase mutants, an algorithm was developed to systematically detect ligand release via centre of mass distances (COM) and ligand average speed calculations, before applying the statistically guided network analysis (SGNA) method to investigate conserved protein motions associated with ligand unbinding. Ligand and cofactor perspectives were also investigated. A conserved pair of lid-destabilising motions was found. These consisted of (1) antiparallel lid and side flap motions; (2) the contractions of a flanking region within the same flap and residue 74 towards the core. Mutations affecting the hinge residues (H51 and H71), nearby residues or L19 were found to destabilise the lid. Additionally, other metal binding site (MBS) mutations delocalised the Fe(2+) cofactor, also facilitating lid opening. In the early stages of unbinding, a wider variety of PZA poses were observed, suggesting multiple exit pathways. These findings provide insights into the late events preceding PZA unbinding, which we found to occur in some resistant PZase mutants. Further, the algorithm developed here to identify unbinding events coupled with SGNA can be applicable to other similar problems.
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spelling pubmed-72513732020-06-01 Determining the unbinding events and conserved motions associated with the pyrazinamide release due to resistance mutations of Mycobacterium tuberculosis pyrazinamidase Sheik Amamuddy, Olivier Musyoka, Thommas Mutemi Boateng, Rita Afriyie Zabo, Sophakama Tastan Bishop, Özlem Comput Struct Biotechnol J Research Article Pyrazinamide (PZA) is the only first-line antitubercular drug active against latent Mycobacterium tuberculosis (Mtb). It is activated to pyrazinoic acid by the pncA-encoded pyrazinamidase enzyme (PZase). Despite the emergence of PZA drug resistance, the underlying mechanisms of resistance remain unclear. This study investigated part of these mechanisms by modelling a PZA-bound wild type and 82 mutant PZase structures before applying molecular dynamics (MD) with an accurate Fe(2+) cofactor coordination geometry. After observing nanosecond-scale PZA unbinding from several PZase mutants, an algorithm was developed to systematically detect ligand release via centre of mass distances (COM) and ligand average speed calculations, before applying the statistically guided network analysis (SGNA) method to investigate conserved protein motions associated with ligand unbinding. Ligand and cofactor perspectives were also investigated. A conserved pair of lid-destabilising motions was found. These consisted of (1) antiparallel lid and side flap motions; (2) the contractions of a flanking region within the same flap and residue 74 towards the core. Mutations affecting the hinge residues (H51 and H71), nearby residues or L19 were found to destabilise the lid. Additionally, other metal binding site (MBS) mutations delocalised the Fe(2+) cofactor, also facilitating lid opening. In the early stages of unbinding, a wider variety of PZA poses were observed, suggesting multiple exit pathways. These findings provide insights into the late events preceding PZA unbinding, which we found to occur in some resistant PZase mutants. Further, the algorithm developed here to identify unbinding events coupled with SGNA can be applicable to other similar problems. Research Network of Computational and Structural Biotechnology 2020-05-18 /pmc/articles/PMC7251373/ /pubmed/32489525 http://dx.doi.org/10.1016/j.csbj.2020.05.009 Text en © 2020 The Author(s) http://creativecommons.org/licenses/by-nc-nd/4.0/ This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Research Article
Sheik Amamuddy, Olivier
Musyoka, Thommas Mutemi
Boateng, Rita Afriyie
Zabo, Sophakama
Tastan Bishop, Özlem
Determining the unbinding events and conserved motions associated with the pyrazinamide release due to resistance mutations of Mycobacterium tuberculosis pyrazinamidase
title Determining the unbinding events and conserved motions associated with the pyrazinamide release due to resistance mutations of Mycobacterium tuberculosis pyrazinamidase
title_full Determining the unbinding events and conserved motions associated with the pyrazinamide release due to resistance mutations of Mycobacterium tuberculosis pyrazinamidase
title_fullStr Determining the unbinding events and conserved motions associated with the pyrazinamide release due to resistance mutations of Mycobacterium tuberculosis pyrazinamidase
title_full_unstemmed Determining the unbinding events and conserved motions associated with the pyrazinamide release due to resistance mutations of Mycobacterium tuberculosis pyrazinamidase
title_short Determining the unbinding events and conserved motions associated with the pyrazinamide release due to resistance mutations of Mycobacterium tuberculosis pyrazinamidase
title_sort determining the unbinding events and conserved motions associated with the pyrazinamide release due to resistance mutations of mycobacterium tuberculosis pyrazinamidase
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7251373/
https://www.ncbi.nlm.nih.gov/pubmed/32489525
http://dx.doi.org/10.1016/j.csbj.2020.05.009
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