The Enzymatic Activity of Inosine 5'-Monophosphate Dehydrogenase May Not Be a Vulnerable Target for Staphylococcus aureus Infections
Abstract
Many bacterial pathogens, including Staphylococcus aureus, require inosine 5'-monophosphate dehydrogenase (IMPDH) for infection, making this enzyme a promising new target for antibiotics. Although potent selective inhibitors of bacterial IMPDHs have been reported, relatively few have displayed antibacterial activity. Here we use structure-informed design to obtain inhibitors of S. aureus IMPDH (SaIMPDH) that have potent antibacterial activity (minimal inhibitory concentrations less than 2 μM) and low cytotoxicity in mammalian cells. The physicochemical properties of the most active compounds were within typical Lipinski/Veber space, suggesting that polarity is not a general requirement for achieving antibacterial activity. In this work, five compounds failed to display activity in mouse models of septicemia and abscess infection. Inhibitor-resistant S. aureus strains readily emerged in vitro. Resistance resulted from substitutions in the cofactor/inhibitor binding site of SaIMPDH, confirming on-target antibacterial activity. These mutations decreased the binding of all inhibitors tested, but also decreased catalytic activity. Nonetheless, the resistant strains had comparable virulence to wild-type bacteria. Surprisingly, strains expressing catalytically inactive SaIMPDH displayed only a mild virulence defect. Collectively these observations question the vulnerability of the enzymatic activity of SaIMPDH as a target for the treatment of S. aureus infections, suggesting other functions of this protein may bemore »
- Authors:
-
more »
- Brandeis Univ., Waltham, MA (United States)
- Univ. of Houston, TX (United States)
- Univ. of Chicago, IL (United States); Argonne National Lab. (ANL), Lemont, IL (United States)
- Dartmouth College, Hanover, NH (United States). Geisel School of Medicine
- BioKin Ltd., Watertown, MA (United States)
- David Rothstein Consulting, LLC, Lexington, MA (United States)
- Publication Date:
- Research Org.:
- Argonne National Lab. (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- National Institutes of Health (NIH); National Institute of Allergy and Infectious Diseases (NIAID); USDOE Office of Science (SC)
- OSTI Identifier:
- 1854352
- Grant/Contract Number:
- AC02-06CH11357; 1R21AI138048; R01AI125362; HHSN272201700060C
- Resource Type:
- Accepted Manuscript
- Journal Name:
- ACS Infectious Diseases
- Additional Journal Information:
- Journal Volume: 7; Journal Issue: 11; Journal ID: ISSN 2373-8227
- Publisher:
- American Chemical Society (ACS)
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 60 APPLIED LIFE SCIENCES; IMPDH; antibiotic space; guaB; guanine nucleotide biosynthesis; target vulnerability; virulenc
Citation Formats
Modi, Gyan, Marqus, Gary M., Vippila, Mohana Rao, Gollapalli, Deviprasad R., Kim, Youngchang, Manna, Adhar C., Chacko, Shibin, Maltseva, Natalia, Wang, Xingyou, Cullinane, Ryan T., Zhang, Yubo, Kotler, Judy L. M., Kuzmic, Petr, Zhang, Minjia, Lawson, Ann P., Joachimiak, Andrzej, Cheung, Ambrose, Snider, Barry B., Rothstein, David M., Cuny, Gregory D., and Hedstrom, Lizbeth. The Enzymatic Activity of Inosine 5'-Monophosphate Dehydrogenase May Not Be a Vulnerable Target for Staphylococcus aureus Infections. United States: N. p., 2021.
Web. doi:10.1021/acsinfecdis.1c00342.
Modi, Gyan, Marqus, Gary M., Vippila, Mohana Rao, Gollapalli, Deviprasad R., Kim, Youngchang, Manna, Adhar C., Chacko, Shibin, Maltseva, Natalia, Wang, Xingyou, Cullinane, Ryan T., Zhang, Yubo, Kotler, Judy L. M., Kuzmic, Petr, Zhang, Minjia, Lawson, Ann P., Joachimiak, Andrzej, Cheung, Ambrose, Snider, Barry B., Rothstein, David M., Cuny, Gregory D., & Hedstrom, Lizbeth. The Enzymatic Activity of Inosine 5'-Monophosphate Dehydrogenase May Not Be a Vulnerable Target for Staphylococcus aureus Infections. United States. https://doi.org/10.1021/acsinfecdis.1c00342
Modi, Gyan, Marqus, Gary M., Vippila, Mohana Rao, Gollapalli, Deviprasad R., Kim, Youngchang, Manna, Adhar C., Chacko, Shibin, Maltseva, Natalia, Wang, Xingyou, Cullinane, Ryan T., Zhang, Yubo, Kotler, Judy L. M., Kuzmic, Petr, Zhang, Minjia, Lawson, Ann P., Joachimiak, Andrzej, Cheung, Ambrose, Snider, Barry B., Rothstein, David M., Cuny, Gregory D., and Hedstrom, Lizbeth. Thu .
"The Enzymatic Activity of Inosine 5'-Monophosphate Dehydrogenase May Not Be a Vulnerable Target for Staphylococcus aureus Infections". United States. https://doi.org/10.1021/acsinfecdis.1c00342. https://www.osti.gov/servlets/purl/1854352.
@article{osti_1854352,
title = {The Enzymatic Activity of Inosine 5'-Monophosphate Dehydrogenase May Not Be a Vulnerable Target for Staphylococcus aureus Infections},
author = {Modi, Gyan and Marqus, Gary M. and Vippila, Mohana Rao and Gollapalli, Deviprasad R. and Kim, Youngchang and Manna, Adhar C. and Chacko, Shibin and Maltseva, Natalia and Wang, Xingyou and Cullinane, Ryan T. and Zhang, Yubo and Kotler, Judy L. M. and Kuzmic, Petr and Zhang, Minjia and Lawson, Ann P. and Joachimiak, Andrzej and Cheung, Ambrose and Snider, Barry B. and Rothstein, David M. and Cuny, Gregory D. and Hedstrom, Lizbeth},
abstractNote = {Many bacterial pathogens, including Staphylococcus aureus, require inosine 5'-monophosphate dehydrogenase (IMPDH) for infection, making this enzyme a promising new target for antibiotics. Although potent selective inhibitors of bacterial IMPDHs have been reported, relatively few have displayed antibacterial activity. Here we use structure-informed design to obtain inhibitors of S. aureus IMPDH (SaIMPDH) that have potent antibacterial activity (minimal inhibitory concentrations less than 2 μM) and low cytotoxicity in mammalian cells. The physicochemical properties of the most active compounds were within typical Lipinski/Veber space, suggesting that polarity is not a general requirement for achieving antibacterial activity. In this work, five compounds failed to display activity in mouse models of septicemia and abscess infection. Inhibitor-resistant S. aureus strains readily emerged in vitro. Resistance resulted from substitutions in the cofactor/inhibitor binding site of SaIMPDH, confirming on-target antibacterial activity. These mutations decreased the binding of all inhibitors tested, but also decreased catalytic activity. Nonetheless, the resistant strains had comparable virulence to wild-type bacteria. Surprisingly, strains expressing catalytically inactive SaIMPDH displayed only a mild virulence defect. Collectively these observations question the vulnerability of the enzymatic activity of SaIMPDH as a target for the treatment of S. aureus infections, suggesting other functions of this protein may be responsible for its role in infection.},
doi = {10.1021/acsinfecdis.1c00342},
journal = {ACS Infectious Diseases},
number = 11,
volume = 7,
place = {United States},
year = {Thu Sep 30 00:00:00 EDT 2021},
month = {Thu Sep 30 00:00:00 EDT 2021}
}
Works referenced in this record:
Fragment-to-Hit-to-Lead Discovery of a Novel Pyridylurea Scaffold of ATP Competitive Dual Targeting Type II Topoisomerase Inhibiting Antibacterial Agents
journal, October 2013
- Basarab, Gregory S.; Manchester, John I.; Bist, Shanta
- Journal of Medicinal Chemistry, Vol. 56, Issue 21
A Regulatory Role of the Bateman Domain of IMP Dehydrogenase in Adenylate Nucleotide Biosynthesis
journal, March 2009
- Pimkin, Maxim; Pimkina, Julia; Markham, George D.
- Journal of Biological Chemistry, Vol. 284, Issue 12
High-Resolution Phenotypic Profiling Defines Genes Essential for Mycobacterial Growth and Cholesterol Catabolism
journal, September 2011
- Griffin, Jennifer E.; Gawronski, Jeffrey D.; DeJesus, Michael A.
- PLoS Pathogens, Vol. 7, Issue 9
Genome-Wide Identification of Acinetobacter baumannii Genes Necessary for Persistence in the Lung
journal, June 2014
- Wang, Nengding; Ozer, Egon A.; Mandel, Mark J.
- mBio, Vol. 5, Issue 3
Synthesis, in Vitro Evaluation and Cocrystal Structure of 4-Oxo-[1]benzopyrano[4,3- c ]pyrazole Cryptosporidium parvum Inosine 5′-Monophosphate Dehydrogenase ( Cp IMPDH) Inhibitors
journal, December 2014
- Sun, Zhuming; Khan, Jihan; Makowska-Grzyska, Magdalena
- Journal of Medicinal Chemistry, Vol. 57, Issue 24
Benzoxazoles, Phthalazinones, and Arylurea-Based Compounds with IMP Dehydrogenase-Independent Antibacterial Activity against Francisella tularensis
journal, October 2017
- Gorla, Suresh Kumar; Zhang, Yan; Rabideau, Meaghan M.
- Antimicrobial Agents and Chemotherapy, Vol. 61, Issue 10
The Structural Basis of Cryptosporidium-Specific IMP Dehydrogenase Inhibitor Selectivity
journal, February 2010
- MacPherson, Iain S.; Kirubakaran, Sivapriya; Gorla, Suresh Kumar
- Journal of the American Chemical Society, Vol. 132, Issue 4
Comprehensive Essentiality Analysis of the Mycobacterium tuberculosis Genome via Saturating Transposon Mutagenesis
journal, January 2017
- DeJesus, Michael A.; Gerrick, Elias R.; Xu, Weizhen
- mBio, Vol. 8, Issue 1
Fragment-Based Approach to Targeting Inosine-5′-monophosphate Dehydrogenase (IMPDH) from Mycobacterium tuberculosis
journal, March 2018
- Trapero, Ana; Pacitto, Angela; Singh, Vinayak
- Journal of Medicinal Chemistry, Vol. 61, Issue 7
Triazole Inhibitors of Cryptosporidium parvum Inosine 5′-Monophosphate Dehydrogenase
journal, August 2009
- Maurya, Sushil K.; Gollapalli, Deviprasad R.; Kirubakaran, Shivapriya
- Journal of Medicinal Chemistry, Vol. 52, Issue 15
IMPDH2 Is an Intracellular Target of the Cyclophilin A and Sanglifehrin A Complex
journal, January 2017
- Pua, Khian Hong; Stiles, Dylan T.; Sowa, Mathew E.
- Cell Reports, Vol. 18, Issue 2
Structural Determinants of Inhibitor Selectivity in Prokaryotic IMP Dehydrogenases
journal, October 2010
- Gollapalli, Deviprasad R.; MacPherson, Iain S.; Liechti, George
- Chemistry & Biology, Vol. 17, Issue 10
The Antibiotic Potential of Prokaryotic IMP Dehydrogenase Inhibitors
journal, May 2011
- Hedstrom, L.; Liechti, G.; B. Goldberg, J.
- Current Medicinal Chemistry, Vol. 18, Issue 13
Phthalazinone inhibitors of inosine-5′-monophosphate dehydrogenase from Cryptosporidium parvum
journal, February 2013
- Johnson, Corey R.; Gorla, Suresh Kumar; Kavitha, Mandapati
- Bioorganic & Medicinal Chemistry Letters, Vol. 23, Issue 4
Metabolite concentrations, fluxes and free energies imply efficient enzyme usage
journal, May 2016
- Park, Junyoung O.; Rubin, Sara A.; Xu, Yi-Fan
- Nature Chemical Biology, Vol. 12, Issue 7
High-performance liquid chromatographic methods for base and nucleoside analysis in extracellular fluids and in cells
journal, December 1981
- Simmonds, R. J.; Harkness, R. A.
- Journal of Chromatography B: Biomedical Sciences and Applications, Vol. 226, Issue 2
Two Classes of Bacterial IMPDHs according to Their Quaternary Structures and Catalytic Properties
journal, February 2015
- Alexandre, Thomas; Rayna, Bertrand; Munier-Lehmann, Hélène
- PLOS ONE, Vol. 10, Issue 2
A fine scale phenotype-genotype virulence map of a bacterial pathogen
journal, July 2012
- van Opijnen, T.; Camilli, A.
- Genome Research, Vol. 22, Issue 12
Evolving medicinal chemistry strategies in antibiotic discovery
journal, December 2016
- Pawlowski, Andrew C.; Johnson, Jarrod W.; Wright, Gerard D.
- Current Opinion in Biotechnology, Vol. 42
Bacillus anthracis Inosine 5′-Monophosphate Dehydrogenase in Action: The First Bacterial Series of Structures of Phosphate Ion-, Substrate-, and Product-Bound Complexes
journal, July 2012
- Makowska-Grzyska, Magdalena; Kim, Youngchang; Wu, Ruiying
- Biochemistry, Vol. 51, Issue 31
The purine biosynthesis regulator PurR moonlights as a virulence regulator in Staphylococcus aureus
journal, June 2019
- Sause, William E.; Balasubramanian, Divya; Irnov, Irnov
- Proceedings of the National Academy of Sciences, Vol. 116, Issue 27
The Inosine Monophosphate Dehydrogenase, GuaB2, Is a Vulnerable New Bactericidal Drug Target for Tuberculosis
journal, September 2016
- Singh, Vinayak; Donini, Stefano; Pacitto, Angela
- ACS Infectious Diseases, Vol. 3, Issue 1
Essential but Not Vulnerable: Indazole Sulfonamides Targeting Inosine Monophosphate Dehydrogenase as Potential Leads against Mycobacterium tuberculosis
journal, October 2016
- Park, Yumi; Pacitto, Angela; Bayliss, Tracy
- ACS Infectious Diseases, Vol. 3, Issue 1
Discovery of a novel azaindole class of antibacterial agents targeting the ATPase domains of DNA gyrase and Topoisomerase IV
journal, August 2012
- Manchester, John I.; Dussault, Daemian D.; Rose, Jonathan A.
- Bioorganic & Medicinal Chemistry Letters, Vol. 22, Issue 15
Efficacy of Novel Rifamycin Derivatives against Rifamycin-Sensitive and -Resistant Staphylococcus aureus Isolates in Murine Models of Infection
journal, November 2006
- Rothstein, David M. ; Farquhar, Ronald S.; Sirokman, Klari
- Antimicrobial Agents and Chemotherapy, Vol. 50, Issue 11
Repurposing Cryptosporidium Inosine 5′-Monophosphate Dehydrogenase Inhibitors as Potential Antibacterial Agents
journal, June 2014
- Mandapati, Kavitha; Gorla, Suresh Kumar; House, Amanda L.
- ACS Medicinal Chemistry Letters, Vol. 5, Issue 8
Carbohydrate-based inducers of cellular stress for targeting cancer cells
journal, March 2016
- Ndombera, Fidelis T.; VanHecke, Garrett C.; Nagi, Shima
- Bioorganic & Medicinal Chemistry Letters, Vol. 26, Issue 5
Structure–activity relationship study of selective benzimidazole-based inhibitors of Cryptosporidium parvum IMPDH
journal, March 2012
- Kirubakaran, Sivapriya; Gorla, Suresh Kumar; Sharling, Lisa
- Bioorganic & Medicinal Chemistry Letters, Vol. 22, Issue 5
A Novel Cofactor-binding Mode in Bacterial IMP Dehydrogenases Explains Inhibitor Selectivity
journal, January 2015
- Makowska-Grzyska, Magdalena; Kim, Youngchang; Maltseva, Natalia
- Journal of Biological Chemistry, Vol. 290, Issue 9
The CBS subdomain of inosine 5′-monophosphate dehydrogenase regulates purine nucleotide turnover: CBS subdomain of IMPDH
journal, February 2008
- Pimkin, Maxim; Markham, George D.
- Molecular Microbiology, Vol. 68, Issue 2
FAF-Drugs4: free ADME-tox filtering computations for chemical biology and early stages drug discovery
journal, July 2017
- Lagorce, David; Bouslama, Lina; Becot, Jerome
- Bioinformatics, Vol. 33, Issue 22
The Bare Essentials of Antibiotic Target Validation
journal, November 2016
- Hedstrom, Lizbeth
- ACS Infectious Diseases, Vol. 3, Issue 1
Optimization of Benzoxazole-Based Inhibitors of Cryptosporidium parvum Inosine 5′-Monophosphate Dehydrogenase
journal, May 2013
- Gorla, Suresh Kumar; Kavitha, Mandapati; Zhang, Minjia
- Journal of Medicinal Chemistry, Vol. 56, Issue 10
Kinetics of the reversible inhibition of enzyme-catalysed reactions by tight-binding inhibitors
journal, August 1969
- Morrison, J. F.
- Biochimica et Biophysica Acta (BBA) - Enzymology, Vol. 185, Issue 2
General and condition-specific essential functions of Pseudomonas aeruginosa
journal, April 2015
- Lee, Samuel A.; Gallagher, Larry A.; Thongdee, Metawee
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 16
Mapping the Protein Interaction Network in Methicillin-Resistant Staphylococcus aureus
journal, March 2011
- Cherkasov, Artem; Hsing, Michael; Zoraghi, Roya
- Journal of Proteome Research, Vol. 10, Issue 3
Characterization of Francisella tularensis Schu S4 defined mutants as live-attenuated vaccine candidates
journal, May 2015
- Santiago, Araceli E.; Mann, Barbara J.; Qin, Aiping
- Pathogens and Disease, Vol. 73, Issue 6
Genome-Wide Identification of Klebsiella pneumoniae Fitness Genes during Lung Infection
journal, July 2015
- Bachman, Michael A.; Breen, Paul; Deornellas, Valerie
- mBio, Vol. 6, Issue 3
Structure of Cryptosporidium IMP dehydrogenase bound to an inhibitor with in vivo antiparasitic activity
journal, April 2015
- Kim, Youngchang; Makowska-Grzyska, Magdalena; Gorla, Suresh Kumar
- Acta Crystallographica Section F Structural Biology Communications, Vol. 71, Issue 5
Expanding Benzoxazole-Based Inosine 5′-Monophosphate Dehydrogenase (IMPDH) Inhibitor Structure–Activity As Potential Antituberculosis Agents
journal, May 2018
- Chacko, Shibin; Boshoff, Helena I. M.; Singh, Vinayak
- Journal of Medicinal Chemistry, Vol. 61, Issue 11
Regulating the Intersection of Metabolism and Pathogenesis in Gram-positive Bacteria
journal, June 2015
- Richardson†, Anthony R.; Somerville†, Greg A.; Sonenshein†, Abraham L.
- Microbiology Spectrum, Vol. 3, Issue 3
Synthesis and Structure–Activity relationship of 1-(5-isoquinolinesulfonyl)piperazine analogues as inhibitors of Mycobacterium tuberculosis IMPDH
journal, July 2019
- Singh, Vinayak; Pacitto, Angela; Donini, Stefano
- European Journal of Medicinal Chemistry, Vol. 174
Mutation of purD and purF genes further attenuates Brucella abortus strain RB51
journal, February 2015
- Truong, Quang Lam; Cho, Youngjae; Barate, Abhijit Kashinath
- Microbial Pathogenesis, Vol. 79
De Novo Guanine Biosynthesis but Not the Riboswitch-Regulated Purine Salvage Pathway Is Required for Staphylococcus aureus Infection In Vivo
journal, July 2016
- Kofoed, Eric M.; Yan, Donghong; Katakam, Anand K.
- Journal of Bacteriology, Vol. 198, Issue 14
Genes Contributing to Staphylococcus aureus Fitness in Abscess- and Infection-Related Ecologies
journal, October 2014
- Valentino, Michael D.; Foulston, Lucy; Sadaka, Ama
- mBio, Vol. 5, Issue 5
Physicochemical Properties of Antibacterial Compounds: Implications for Drug Discovery
journal, May 2008
- O’Shea, Rosemarie; Moser, Heinz E.
- Journal of Medicinal Chemistry, Vol. 51, Issue 10
Identification of novel diphenyl urea inhibitors of Mt-GuaB2 active against Mycobacterium tuberculosis
journal, January 2011
- Usha, Veeraraghavan; Gurcha, Sudagar S.; Lovering, Andrew L.
- Microbiology, Vol. 157, Issue 1
New Vector for Efficient Allelic Replacement in Naturally Nontransformable, Low-GC-Content, Gram-Positive Bacteria
journal, November 2004
- Arnaud, Maryvonne; Chastanet, Arnaud; D�barbouill�, Michel
- Applied and Environmental Microbiology, Vol. 70, Issue 11
Complete Bypass of Restriction Systems for Major Staphylococcus aureus Lineages
journal, May 2015
- Monk, Ian R.; Tree, Jai J.; Howden, Benjamin P.
- mBio, Vol. 6, Issue 3
Physiological concentrations of purines and pyrimidines
journal, January 1994
- Traut, Thomas W.
- Molecular and Cellular Biochemistry, Vol. 140, Issue 1
Genome-Wide Identification of Genes Required for Fitness of Group A Streptococcus in Human Blood
journal, March 2013
- Le Breton, Yoann; Mistry, Pragnesh; Valdes, Kayla M.
- Infection and Immunity, Vol. 81, Issue 3
Selective and Potent Urea Inhibitors of Cryptosporidium parvum Inosine 5′-Monophosphate Dehydrogenase
journal, September 2012
- Gorla, Suresh Kumar; Kavitha, Mandapati; Zhang, Minjia
- Journal of Medicinal Chemistry, Vol. 55, Issue 17
Mycobacterium tuberculosis IMPDH in Complexes with Substrates, Products and Antitubercular Compounds
journal, October 2015
- Makowska-Grzyska, Magdalena; Kim, Youngchang; Gorla, Suresh Kumar
- PLOS ONE, Vol. 10, Issue 10
The identification of the two crystalline N-phenyl-d-ribosylamines (“ribose anilides”) by n.m.r. spectroscopy
journal, September 1981
- Ellis, Gwynn P.; Williams, J. Michael
- Carbohydrate Research, Vol. 95, Issue 2
Trends and Exceptions of Physical Properties on Antibacterial Activity for Gram-Positive and Gram-Negative Pathogens
journal, November 2014
- Brown, Dean G.; May-Dracka, Tricia L.; Gagnon, Moriah M.
- Journal of Medicinal Chemistry, Vol. 57, Issue 23
N.m.r. studies of d-ribosylamines in solution: Derivatives of primary amines
journal, February 1983
- Chavis, Claude; de Gourcy, Chantal; Dumont, Françoise
- Carbohydrate Research, Vol. 113, Issue 1