Examining the role of protein structural dynamics in drug resistance in Mycobacterium tuberculosis

Daniel J. Shaw, Rachel E. Hill, Niall Simpson, Fouad S. Husseini, Kirsty Robb, Gregory M. Greetham, Michael Towrie, Anthony W. Parker, David Robinson, Jonathan D. Hirst, Paul Hoskisson, Neil T. Hunt

Research output: Contribution to journalArticle

Abstract

Antimicrobial resistance represents a growing global health problem. The emergence of novel resistance mechanisms necessitates the development of alternative approaches to investigate the molecular fundamentals of resistance, leading ultimately to new strategies for counteracting them. To gain deeper insight into antibiotic-target interactions, the binding of the frontline anti-tuberculosis drug isoniazid (INH) to a target enzyme, InhA, from Mycobacterium tuberculosis was studied using ultrafast two-dimensional infrared (2D-IR) spectroscopy and molecular simulations. Comparing wild-type InhA with a series of single point mutations, it was found that binding of the INH-NAD inhibitor to susceptible forms of the enzyme increased the vibrational coupling between residues located in the Rossmann fold co-factor binding site of InhA and suppressed dynamic fluctuations of the enzyme structure. The effect correlated with biochemical assay data, being reduced in the INHresistant S94A mutant and absent in the biochemically-inactive P193A control. Molecular dynamics simulations and calculations of inter-residue couplings indicate that the changes in coupling and dynamics are not localised to the co-factor binding site, but permeate much of the protein. We thus propose that the resistant S94A mutation circumvents subtle changes in global structural dynamics caused by INH upon binding to the wild-type enzyme that may impact upon the formation of important protein-protein complexes in the fatty acid synthase pathway of M. tuberculosis.
LanguageEnglish
Number of pages30
JournalChemical Science
Early online date16 Oct 2017
DOIs
StateE-pub ahead of print - 16 Oct 2017

Fingerprint

Structural dynamics
Enzymes
Pharmaceutical Preparations
Infrared spectroscopy
Proteins
Binding Sites
Fatty Acid Synthases
Isoniazid
Medical problems
Molecular dynamics
Assays
Anti-Bacterial Agents
Computer simulation

Keywords

  • antimicrobial resistance
  • antibiotics
  • Mycobacterium tuberculosis

Cite this

Shaw, D. J., Hill, R. E., Simpson, N., Husseini, F. S., Robb, K., Greetham, G. M., ... Hunt, N. T. (2017). Examining the role of protein structural dynamics in drug resistance in Mycobacterium tuberculosis. Chemical Science. DOI: 10.1039/C7SC03336B
Shaw, Daniel J. ; Hill, Rachel E. ; Simpson, Niall ; Husseini, Fouad S. ; Robb, Kirsty ; Greetham, Gregory M. ; Towrie, Michael ; Parker, Anthony W. ; Robinson, David ; Hirst, Jonathan D. ; Hoskisson, Paul ; Hunt, Neil T./ Examining the role of protein structural dynamics in drug resistance in Mycobacterium tuberculosis. In: Chemical Science. 2017
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Shaw, DJ, Hill, RE, Simpson, N, Husseini, FS, Robb, K, Greetham, GM, Towrie, M, Parker, AW, Robinson, D, Hirst, JD, Hoskisson, P & Hunt, NT 2017, 'Examining the role of protein structural dynamics in drug resistance in Mycobacterium tuberculosis' Chemical Science. DOI: 10.1039/C7SC03336B

Examining the role of protein structural dynamics in drug resistance in Mycobacterium tuberculosis. / Shaw, Daniel J.; Hill, Rachel E.; Simpson, Niall; Husseini, Fouad S.; Robb, Kirsty; Greetham, Gregory M.; Towrie, Michael; Parker, Anthony W.; Robinson, David ; Hirst, Jonathan D. ; Hoskisson, Paul; Hunt, Neil T.

In: Chemical Science, 16.10.2017.

Research output: Contribution to journalArticle

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AU - Shaw,Daniel J.

AU - Hill,Rachel E.

AU - Simpson,Niall

AU - Husseini,Fouad S.

AU - Robb,Kirsty

AU - Greetham,Gregory M.

AU - Towrie,Michael

AU - Parker,Anthony W.

AU - Robinson,David

AU - Hirst,Jonathan D.

AU - Hoskisson,Paul

AU - Hunt,Neil T.

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N2 - Antimicrobial resistance represents a growing global health problem. The emergence of novel resistance mechanisms necessitates the development of alternative approaches to investigate the molecular fundamentals of resistance, leading ultimately to new strategies for counteracting them. To gain deeper insight into antibiotic-target interactions, the binding of the frontline anti-tuberculosis drug isoniazid (INH) to a target enzyme, InhA, from Mycobacterium tuberculosis was studied using ultrafast two-dimensional infrared (2D-IR) spectroscopy and molecular simulations. Comparing wild-type InhA with a series of single point mutations, it was found that binding of the INH-NAD inhibitor to susceptible forms of the enzyme increased the vibrational coupling between residues located in the Rossmann fold co-factor binding site of InhA and suppressed dynamic fluctuations of the enzyme structure. The effect correlated with biochemical assay data, being reduced in the INHresistant S94A mutant and absent in the biochemically-inactive P193A control. Molecular dynamics simulations and calculations of inter-residue couplings indicate that the changes in coupling and dynamics are not localised to the co-factor binding site, but permeate much of the protein. We thus propose that the resistant S94A mutation circumvents subtle changes in global structural dynamics caused by INH upon binding to the wild-type enzyme that may impact upon the formation of important protein-protein complexes in the fatty acid synthase pathway of M. tuberculosis.

AB - Antimicrobial resistance represents a growing global health problem. The emergence of novel resistance mechanisms necessitates the development of alternative approaches to investigate the molecular fundamentals of resistance, leading ultimately to new strategies for counteracting them. To gain deeper insight into antibiotic-target interactions, the binding of the frontline anti-tuberculosis drug isoniazid (INH) to a target enzyme, InhA, from Mycobacterium tuberculosis was studied using ultrafast two-dimensional infrared (2D-IR) spectroscopy and molecular simulations. Comparing wild-type InhA with a series of single point mutations, it was found that binding of the INH-NAD inhibitor to susceptible forms of the enzyme increased the vibrational coupling between residues located in the Rossmann fold co-factor binding site of InhA and suppressed dynamic fluctuations of the enzyme structure. The effect correlated with biochemical assay data, being reduced in the INHresistant S94A mutant and absent in the biochemically-inactive P193A control. Molecular dynamics simulations and calculations of inter-residue couplings indicate that the changes in coupling and dynamics are not localised to the co-factor binding site, but permeate much of the protein. We thus propose that the resistant S94A mutation circumvents subtle changes in global structural dynamics caused by INH upon binding to the wild-type enzyme that may impact upon the formation of important protein-protein complexes in the fatty acid synthase pathway of M. tuberculosis.

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JF - Chemical Science

SN - 2041-6520

ER -

Shaw DJ, Hill RE, Simpson N, Husseini FS, Robb K, Greetham GM et al. Examining the role of protein structural dynamics in drug resistance in Mycobacterium tuberculosis. Chemical Science. 2017 Oct 16. Available from, DOI: 10.1039/C7SC03336B