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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The mass spectrometry proteomics data have been deposited at the ProteomeXchange Consortium via the PRIDE59 partner repository with the dataset identifier PXD012946. Whole-genome sequencing data and metadata are available on the SRA repository under the Bioproject number PRJNA525411. Bacterial strains and plasmids used in this work are readily available from the authors, or can be purchased commercially as stated in the Supplementary Information.
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We thank the Network on Antimicrobial Resistance in Staphylococcus aureus (NARSA) for the supply of the Nebraska Transposon Mutant Library (NTML). Furthermore, we thank S. Grond for providing arylomycin and F. Romesberg for providing S. aureus N315 ARC0001ΔSpsB. We also thank S. Miami and E. Rubin for determining the antimicrobial activities against M. tuberculosis. We thank A. Klaschwitz, F. Kortmann, S. Hifinger and C. Lierse von Gostomski for the scintillation measurement of radioactively labelled menaquinone. S.A.S. was funded by the Center for Integrated Protein Science Munich (CIPSM), Deutsche Forschungsgemeinschaft SFB1035 and European Research Council (ERC) and the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 725085, CHEMMINE, ERC consolidator grant). E.K. was supported by a doctoral fellowship of the Fonds der Chemischen Industrie. R.M. was supported by a doctoral fellowship of the Boehringer Ingelheim Fonds. K.R. was supported by the German Centre for Infection Research (DZIF) (TTU 09.710). I.A. acknowledges funding by Deutsche Forschungsgemeinschaft SFB1035. W.M.W. was funded by the National Science Foundation (CHE-1454116) and the National Institute of General Medical Sciences (R35 GM119426). M.C.J. acknowledges a National Science Foundation predoctoral grant (DGE-1144462). S.M.H. acknowledges financial support by a Liebig fellowship of the Fonds der Chemischen Industrie. M.W.H., C.F. and F.A.M.M. were funded by the Federal Ministry for Education and Research (BMBF) under the framework programme ‘VIP+’—project ‘aBacter’. We thank D. Mostert for excellent experimental support, M. Wolff, K. Bäuml, K. Gliesche, L. Nguyen and J. Schreiber for excellent technical support and M. Stahl for critical comments on the manuscript.
P.L., E.K. and S.A.S. are co-inventors on a European patent (EP 16 171 906.7) that covers the structure of PK150. All the other authors declare no competing interests.
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Kinase inhibitor and SFN analogues libraries.
Target identification related proteomic data.
Proteome, secretome, surfaceome related proteomic data.
Genome sequencing of SFN-resistant isolates.
Kinobead pull-down related proteomic data.
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Le, P., Kunold, E., Macsics, R. et al. Repurposing human kinase inhibitors to create an antibiotic active against drug-resistant Staphylococcus aureus, persisters and biofilms. Nat. Chem. (2019). https://doi.org/10.1038/s41557-019-0378-7