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Asymmetric ligand binding in homodimeric Enterobacter cloacae nitroreductase yields the Michaelis complex for nitroaromatic substrates

Abstract

Nitroreductase enzymes are of interest as antibiotic targets and as activators in enzyme prodrug therapy, but the precise substrate binding orientation and reaction mechanism are poorly understood. In order to design more effective antibiotics and improve enzyme prodrug therapy, an atomistic description of nitroaromatic substrate binding in the active Michaelis complex is highly desirable. Here, using an iterative molecular dynamics (MD) simulation protocol, the binding of p-nitrobenzoic acid (p-NBA) in oxidized and reduced Enterobacter cloacae nitroreductase (NR) was investigated. For the oxidized NR, the MD simulations distinguished between the two possible binding orientations of p-NBA in NR from X-ray crystal structure data. For the reduced NR, a distinct active binding orientation of p-NBA was found when the second active site of the NR homodimer was occupied by a NADH analogue. This model of the active Michaelis complex of p-NBA with NR provides a rationale for the reduction of p-NBA by NR via a hydride transfer reaction mechanism suggested by experimental results, and brings the proposed reaction mechanism from experiment and computational models into agreement.

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Acknowledgments

This research was undertaken using the LIEF HPC-GPGPU Facility (resource grant pRMIT0007) hosted at the University of Melbourne [1], which was established with the assistance of LIEF Grant LE170100200. This research was also undertaken with the assistance of resources and services (resource grant nr3) from the National Computational Infrastructure (NCI), which is supported by the Australian Government, and Melbourne Bioinformatics (resource grant RMIT0003). Drs. E. Hyde, S. White, P. Searle, J. Wilkie, P. Charchar, M. Penna, and Q. Besford are gratefully acknowledged for useful discussions, and Drs. E. Hyde, Q. Besford, and Prof. C. F. McConville for their comments on the manuscript. Prof. I. Yarovsky and Prof. C. F. McConville are gratefully acknowledged for their continued support. The anonymous reviewers are also thanked for helpful and constructive comments.

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Correspondence to Andrew J. Christofferson.

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Christofferson, A.J. Asymmetric ligand binding in homodimeric Enterobacter cloacae nitroreductase yields the Michaelis complex for nitroaromatic substrates. J Mol Model 26, 28 (2020). https://doi.org/10.1007/s00894-020-4288-9

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Keywords

  • Drug design
  • Flavoprotein
  • Molecular dynamics
  • Oxidation-reduction (redox)
  • Protein drug interaction