Essential but Not Vulnerable: Indazole Sulfonamides Targeting Inosine Monophosphate Dehydrogenase as Potential Leads against Mycobacterium tuberculosis

Yumi Park, Angela Pacitto, Tracy Bayliss, Laura A T Cleghorn, Zhe Wang, Travis Hartman, Kriti Arora, Thomas R Ioerger, Jim Sacchettini, Menico Rizzi, Stefano Donini, Tom L Blundell, David B Ascher, Kyu Rhee, Ardala Breda, Nian Zhou, Veronique Dartois, Surendranadha Reddy Jonnala, Laura E Via, Valerie MizrahiOla Epemolu, Laste Stojanovski, Fred Simeons, Maria Osuna-Cabello, Lucy Ellis, Claire J MacKenzie, Alasdair R C Smith, Susan H Davis, Dinakaran Murugesan, Kirsteen I Buchanan, Penelope A Turner, Margaret Huggett, Fabio Zuccotto, Maria Jose Rebollo-Lopez, Maria Jose Lafuente-Monasterio, Olalla Sanz, Gracia Santos Diaz, Joël Lelièvre, Lluis Ballell, Carolyn Selenski, Matthew Axtman, Sonja Ghidelli-Disse, Hannah Pflaumer, Markus Bösche, Gerard Drewes, Gail M Freiberg, Matthew D Kurnick, Myron Srikumaran, Dale J Kempf, Simon R Green, Peter C Ray, Kevin Read, Paul Wyatt, Clifton E Barry, Helena I Boshoff

Research output: Contribution to journalArticle

43 Citations (Scopus)

Abstract

A potent, noncytotoxic indazole sulfonamide was identified by high-throughput screening of >100,000 synthetic compounds for activity against Mycobacterium tuberculosis (Mtb). This noncytotoxic compound did not directly inhibit cell wall biogenesis but triggered a slow lysis of Mtb cells as measured by release of intracellular green fluorescent protein (GFP). Isolation of resistant mutants followed by whole-genome sequencing showed an unusual gene amplification of a 40 gene region spanning from Rv3371 to Rv3411c and in one case a potential promoter mutation upstream of guaB2 (Rv3411c) encoding inosine monophosphate dehydrogenase (IMPDH). Subsequent biochemical validation confirmed direct inhibition of IMPDH by an uncompetitive mode of inhibition, and growth inhibition could be rescued by supplementation with guanine, a bypass mechanism for the IMPDH pathway. Beads containing immobilized indazole sulfonamides specifically interacted with IMPDH in cell lysates. X-ray crystallography of the IMPDH-IMP-inhibitor complex revealed that the primary interactions of these compounds with IMPDH were direct pi-pi interactions with the IMP substrate. Advanced lead compounds in this series with acceptable pharmacokinetic properties failed to show efficacy in acute or chronic murine models of tuberculosis (TB). Time-kill experiments in vitro suggest that sustained exposure to drug concentrations above the minimum inhibitory concentration (MIC) for 24 h were required for a cidal effect, levels that have been difficult to achieve in vivo. Direct measurement of guanine levels in resected lung tissue from tuberculosis-infected animals and patients revealed 0.5-2 mM concentrations in caseum and normal lung tissue. The high lesional levels of guanine and the slow lytic, growth-rate-dependent effect of IMPDH inhibition pose challenges to developing drugs against this target for use in treating TB.

Original languageEnglish
Pages (from-to)18-33
Number of pages16
JournalACS Infectious Diseases
Volume3
Issue number1
Early online date5 Oct 2016
DOIs
Publication statusPublished - 13 Jan 2017

Keywords

  • Animals
  • Antitubercular agents
  • Drug design
  • Drug discovery
  • Drug resistance, Bacterial
  • Gene expression regulation, Bacterial
  • Gene expression regulation, Enzymologic
  • Humans
  • IMP Dehydrogenase
  • Mice
  • Mice, Inbred C57BL
  • Molecular structure
  • Mutation
  • Mycobacterium tuberculosis
  • Protein conformation
  • Rabbits
  • Structure-activity relationship
  • Sulfonamides
  • Tuberculosis
  • Journal article

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    Park, Y., Pacitto, A., Bayliss, T., Cleghorn, L. A. T., Wang, Z., Hartman, T., Arora, K., Ioerger, T. R., Sacchettini, J., Rizzi, M., Donini, S., Blundell, T. L., Ascher, D. B., Rhee, K., Breda, A., Zhou, N., Dartois, V., Jonnala, S. R., Via, L. E., ... Boshoff, H. I. (2017). Essential but Not Vulnerable: Indazole Sulfonamides Targeting Inosine Monophosphate Dehydrogenase as Potential Leads against Mycobacterium tuberculosis. ACS Infectious Diseases, 3(1), 18-33. https://doi.org/10.1021/acsinfecdis.6b00103