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Le P, Kunold E, Macsics R, Rox K, Jennings MC, Ugur I, Reinecke M, Chaves-Moreno D, Hackl MW, Fetzer C, Mandl FAM, Lehmann J, Korotkov VS, Hacker SM, Kuster B, Antes I, Pieper DH, Rohde M, Wuest WM, Medina E, Sieber SA. Repurposing human kinase inhibitors to create an antibiotic active against drug-resistant Staphylococcus aureus, persisters and biofilms. Nat Chem 2020; 12:145-158. [PMID: 31844194 PMCID: PMC6994260 DOI: 10.1038/s41557-019-0378-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/15/2019] [Indexed: 12/31/2022]
Abstract
New drugs are desperately needed to combat methicillin-resistant Staphylococcus aureus (MRSA) infections. Here, we report screening commercial kinase inhibitors for antibacterial activity and found the anticancer drug sorafenib as major hit that effectively kills MRSA strains. Varying the key structural features led to the identification of a potent analogue, PK150, that showed antibacterial activity against several pathogenic strains at submicromolar concentrations. Furthermore, this antibiotic eliminated challenging persisters as well as established biofilms. PK150 holds promising therapeutic potential as it did not induce in vitro resistance, and shows oral bioavailability and in vivo efficacy. Analysis of the mode of action using chemical proteomics revealed several targets, which included interference with menaquinone biosynthesis by inhibiting demethylmenaquinone methyltransferase and the stimulation of protein secretion by altering the activity of signal peptidase IB. Reduced endogenous menaquinone levels along with enhanced levels of extracellular proteins of PK150-treated bacteria support this target hypothesis. The associated antibiotic effects, especially the lack of resistance development, probably stem from the compound's polypharmacology.
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Affiliation(s)
- Philipp Le
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Garching bei München, Germany
- Chair of Organic Chemistry II, Technische Universität München, Garching bei München, Germany
| | - Elena Kunold
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Garching bei München, Germany
- Chair of Organic Chemistry II, Technische Universität München, Garching bei München, Germany
- SciLifeLab, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Robert Macsics
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Garching bei München, Germany
- Chair of Organic Chemistry II, Technische Universität München, Garching bei München, Germany
| | - Katharina Rox
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- German Centre for Infection Research, Partner Site Braunschweig-Hannover, Hannover, Germany
| | - Megan C Jennings
- Department of Chemistry, Temple University, Philadelphia, PA, USA
| | - Ilke Ugur
- Center for Integrated Protein Science, TUM School of Life Sciences, Technische Universität München, Freising, Germany
| | - Maria Reinecke
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
- German Cancer Consortium, Partner Site Munich, Munich, Germany
- German Cancer Research Center, Heidelberg, Germany
| | - Diego Chaves-Moreno
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Mathias W Hackl
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Garching bei München, Germany
- Chair of Organic Chemistry II, Technische Universität München, Garching bei München, Germany
| | - Christian Fetzer
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Garching bei München, Germany
- Chair of Organic Chemistry II, Technische Universität München, Garching bei München, Germany
| | - Franziska A M Mandl
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Garching bei München, Germany
- Chair of Organic Chemistry II, Technische Universität München, Garching bei München, Germany
| | - Johannes Lehmann
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Garching bei München, Germany
- Chair of Organic Chemistry II, Technische Universität München, Garching bei München, Germany
| | - Vadim S Korotkov
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Garching bei München, Germany
- Chair of Organic Chemistry II, Technische Universität München, Garching bei München, Germany
| | - Stephan M Hacker
- Department of Chemistry, Technische Universität München, Garching bei München, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
- German Cancer Consortium, Partner Site Munich, Munich, Germany
- German Cancer Research Center, Heidelberg, Germany
- Center for Integrated Protein Science Munich, Garching bei München, Germany
| | - Iris Antes
- Center for Integrated Protein Science, TUM School of Life Sciences, Technische Universität München, Freising, Germany
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - William M Wuest
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Emory Antibiotic Resistance Center, Emory School of Medicine, Atlanta, GA, USA
| | - Eva Medina
- Infection Immunology Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Stephan A Sieber
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Garching bei München, Germany.
- Chair of Organic Chemistry II, Technische Universität München, Garching bei München, Germany.
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, Saarbrücken, Germany.
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Yu D, Liang X. Fragmentation pathways and differentiation of positional isomers of sorafenib and structural analogues by ESI-IT-MS n and ESI-Q-TOF-MS/MS coupled with DFT calculations. J Mass Spectrom 2018; 53:579-589. [PMID: 29673031 DOI: 10.1002/jms.4192] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 03/31/2018] [Accepted: 04/11/2018] [Indexed: 06/08/2023]
Abstract
Sorafenib is an orally active multikinase inhibitor for the treatment of renal cell carcinoma. A series of sorafenib structural analogues were investigated in this work for their gas-phase fragmentation behaviors using electrospray ionization ion trap mass spectrometry and quadrupole time-of-flight mass spectrometry in the positive mode. The possible fragmentation pathways were proposed based on ESI-MS/MS data and theoretical calculation. Different from the typical α-cleavage of amide, consecutive reactions that involved elimination of H2 O and CH3 NC were observed for 2-pyridinecarboxamide derivatives, which were followed by the formation of a stabilized 7-membered ring carbocation by loss of CO. Two possible protonation sites occurred at carbonyl oxygen atoms for aryl-urea derivatives and the α-cleavage of urea was the main fragmentation pathways, which was followed by the formation of stable benzo [d] oxazole ring characteristic to aryl-urea derivatives. The relative abundance of characteristic fragment ions and the energy-resolved breakdown curves were used to distinguish the 4 sets of positional isomers of sorafenib and analogues. The methodology and results of the present work would contribute to the chemical structure identification of other structural analogues and the potential impurities presented in active pharmaceutical ingredients and drug formulations.
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Affiliation(s)
- Dandan Yu
- Key Laboratory for Green Pharmaceutical Technologies and Related Equipment of Ministry of Education, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Xianrui Liang
- Key Laboratory for Green Pharmaceutical Technologies and Related Equipment of Ministry of Education, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
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