DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Indoline-6-Sulfonamide Inhibitors of the Bacterial Enzyme DapE

Abstract

Inhibitors of the bacterial enzyme dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE; EC 3.5.1.18) hold promise as antibiotics with a new mechanism of action. Herein we describe the discovery of a new series of indoline sulfonamide DapE inhibitors from a high-throughput screen and the synthesis of a series of analogs. Inhibitory potency was measured by a ninhydrin-based DapE assay recently developed by our group. Molecular docking experiments suggest active site binding with the sulfonamide acting as a zinc-binding group (ZBG).

Authors:
 [1];  [2];  [2]; ORCiD logo [2];  [2];  [2];  [3];  [2];  [4]; ORCiD logo [2]
  1. Loyola Univ., Chicago, IL (United States); Northwestern Univ., Evanston, IL (United States)
  2. Loyola Univ., Chicago, IL (United States)
  3. Argonne National Lab. (ANL), Argonne, IL (United States)
  4. Colorado School of Mines, Golden, CO (United States)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE; National Institutes of Health (NIH); National Science Foundation (NSF)
OSTI Identifier:
1764848
Grant/Contract Number:  
AC02-06CH11357; HHSN272200700058C; HHSN272201200026C; CHE-1412443
Resource Type:
Accepted Manuscript
Journal Name:
Antibiotics
Additional Journal Information:
Journal Volume: 9; Journal Issue: 9; Journal ID: ISSN 2079-6382
Publisher:
MDPI
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; DapE; antibiotic; diaminopimelate desuccinylase; enzyme inhibition; indoline; ninhydrin enzyme assay; sulfonamide

Citation Formats

Reidl, Cory T., Heath, Tahirah K., Darwish, Iman, Torrez, Rachel M., Moore, Maxwell, Gild, Elliot, Nocek, Boguslaw P., Starus, Anna, Holz, Richard C., and Becker, Daniel P. Indoline-6-Sulfonamide Inhibitors of the Bacterial Enzyme DapE. United States: N. p., 2020. Web. doi:10.3390/antibiotics9090595.
Reidl, Cory T., Heath, Tahirah K., Darwish, Iman, Torrez, Rachel M., Moore, Maxwell, Gild, Elliot, Nocek, Boguslaw P., Starus, Anna, Holz, Richard C., & Becker, Daniel P. Indoline-6-Sulfonamide Inhibitors of the Bacterial Enzyme DapE. United States. https://doi.org/10.3390/antibiotics9090595
Reidl, Cory T., Heath, Tahirah K., Darwish, Iman, Torrez, Rachel M., Moore, Maxwell, Gild, Elliot, Nocek, Boguslaw P., Starus, Anna, Holz, Richard C., and Becker, Daniel P. Fri . "Indoline-6-Sulfonamide Inhibitors of the Bacterial Enzyme DapE". United States. https://doi.org/10.3390/antibiotics9090595. https://www.osti.gov/servlets/purl/1764848.
@article{osti_1764848,
title = {Indoline-6-Sulfonamide Inhibitors of the Bacterial Enzyme DapE},
author = {Reidl, Cory T. and Heath, Tahirah K. and Darwish, Iman and Torrez, Rachel M. and Moore, Maxwell and Gild, Elliot and Nocek, Boguslaw P. and Starus, Anna and Holz, Richard C. and Becker, Daniel P.},
abstractNote = {Inhibitors of the bacterial enzyme dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE; EC 3.5.1.18) hold promise as antibiotics with a new mechanism of action. Herein we describe the discovery of a new series of indoline sulfonamide DapE inhibitors from a high-throughput screen and the synthesis of a series of analogs. Inhibitory potency was measured by a ninhydrin-based DapE assay recently developed by our group. Molecular docking experiments suggest active site binding with the sulfonamide acting as a zinc-binding group (ZBG).},
doi = {10.3390/antibiotics9090595},
journal = {Antibiotics},
number = 9,
volume = 9,
place = {United States},
year = {Fri Sep 11 00:00:00 EDT 2020},
month = {Fri Sep 11 00:00:00 EDT 2020}
}

Works referenced in this record:

Structural analysis of a set of proteins resulting from a bacterial genomics project
journal, July 2005

  • Badger, J.; Sauder, J. M.; Adams, J. M.
  • Proteins: Structure, Function, and Bioinformatics, Vol. 60, Issue 4
  • DOI: 10.1002/prot.20541

Inhibitors of bacterial N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE) and demonstration of in vitro antimicrobial activity
journal, November 2009

  • Gillner, Danuta; Armoush, Nicola; Holz, Richard C.
  • Bioorganic & Medicinal Chemistry Letters, Vol. 19, Issue 22
  • DOI: 10.1016/j.bmcl.2009.09.077

In silico approach towards identification of potential inhibitors of Helicobacter pylori DapE
journal, September 2014


24. The Clinical Development of Lumateperone (ITI-007) for the Treatment of Schizophrenia
journal, March 2017

  • Vanover, Kimberly; Correll, Christoph; Dmitrienko, Alex
  • Schizophrenia Bulletin, Vol. 43, Issue suppl_1
  • DOI: 10.1093/schbul/sbx021.043

Reductive Cleavage of Secondary Sulfonamides: Converting Terminal Functional Groups into Versatile Synthetic Handles
journal, October 2019

  • Fier, Patrick S.; Kim, Suhong; Maloney, Kevin M.
  • Journal of the American Chemical Society, Vol. 141, Issue 46
  • DOI: 10.1021/jacs.9b10985

Inhibition of the dapE -Encoded N -Succinyl- l , l -diaminopimelic Acid Desuccinylase from Neisseria meningitidis by l -Captopril
journal, July 2015


Ruthenium-Catalyzed C7 Amidation of Indoline CH Bonds with Sulfonyl Azides
journal, February 2014

  • Pan, Changduo; Abdukader, Ablimit; Han, Jie
  • Chemistry - A European Journal, Vol. 20, Issue 13
  • DOI: 10.1002/chem.201304236

Vinflunine in the treatment of advanced urothelial cancer: clinical evidence and experience
journal, November 2016

  • Gerullis, Holger; Wawroschek, Friedhelm; Köhne, Claus-Henning
  • Therapeutic Advances in Urology, Vol. 9, Issue 1
  • DOI: 10.1177/1756287216677903

Vancomycin-resistant Staphylococcus aureus
journal, February 1998


Continuous-Flow Technology-A Tool for the Safe Manufacturing of Active Pharmaceutical Ingredients
journal, May 2015

  • Gutmann, Bernhard; Cantillo, David; Kappe, C. Oliver
  • Angewandte Chemie International Edition, Vol. 54, Issue 23
  • DOI: 10.1002/anie.201409318

Data-Mining for Sulfur and Fluorine: An Evaluation of Pharmaceuticals To Reveal Opportunities for Drug Design and Discovery: Miniperspective
journal, October 2013

  • Ilardi, Elizabeth A.; Vitaku, Edon; Njardarson, Jon T.
  • Journal of Medicinal Chemistry, Vol. 57, Issue 7
  • DOI: 10.1021/jm401375q

Beyond C, H, O, and N! Analysis of the Elemental Composition of U.S. FDA Approved Drug Architectures: Miniperspective
journal, October 2014

  • Smith, Brandon R.; Eastman, Candice M.; Njardarson, Jon T.
  • Journal of Medicinal Chemistry, Vol. 57, Issue 23
  • DOI: 10.1021/jm501105n

Structural Basis for Catalysis by the Mono- and Dimetalated Forms of the dapE-Encoded N-succinyl-l,l-Diaminopimelic Acid Desuccinylase
journal, April 2010

  • Nocek, Boguslaw P.; Gillner, Danuta M.; Fan, Yao
  • Journal of Molecular Biology, Vol. 397, Issue 3
  • DOI: 10.1016/j.jmb.2010.01.062

Lysine biosynthesis in bacteria: a metallodesuccinylase as a potential antimicrobial target
journal, December 2012

  • Gillner, Danuta M.; Becker, Daniel P.; Holz, Richard C.
  • JBIC Journal of Biological Inorganic Chemistry, Vol. 18, Issue 2
  • DOI: 10.1007/s00775-012-0965-1

Characterization of Helicobacter pylori dapE and construction of a conditionally lethal dapE mutant.
journal, January 1997


Regioselectivity of electrophilic aromatic substitution: syntheses of 6- and 7-sulfamoylindolines and -indoles
journal, April 1988

  • Borror, Alan L.; Chinoporos, Efthimios; Filosa, Michael P.
  • The Journal of Organic Chemistry, Vol. 53, Issue 9
  • DOI: 10.1021/jo00244a036

Generating enzyme and radical-mediated bisubstrates as tools for investigating Gcn5-related N- acetyltransferases
journal, August 2017


Lumateperone: a new treatment approach for neuropsychiatric disorders
journal, January 2018


Hexahydrochromeno[4,3- b ]pyrrole Derivatives as Acetylcholinesterase Inhibitors
journal, January 2001

  • Bolognesi, Maria L.; Andrisano, Vincenza; Bartolini, Manuela
  • Journal of Medicinal Chemistry, Vol. 44, Issue 1
  • DOI: 10.1021/jm000991r

A Convenient Synthesis of Novel 3-(Heterocyclylsulfonyl)propanoic Acids and Their Amide Derivatives.
journal, May 2005

  • Dorogov, Mikhail V.; Filimonov, Sergey I.; Kobylinsky, Dmitry B.
  • ChemInform, Vol. 36, Issue 19
  • DOI: 10.1002/chin.200519111

Derailing the aspartate pathway of Mycobacterium tuberculosis to eradicate persistent infection
journal, September 2019

  • Hasenoehrl, Erik J.; Rae Sajorda, Dannah; Berney-Meyer, Linda
  • Nature Communications, Vol. 10, Issue 1
  • DOI: 10.1038/s41467-019-12224-3

Facile, Fast and Safe Process Development of Nitration and Bromination Reactions Using Continuous Flow Reactors
journal, July 2009

  • Pelleter, Jacques; Renaud, Fabrice
  • Organic Process Research & Development, Vol. 13, Issue 4
  • DOI: 10.1021/op8002695