Repurposing PFM01 as a novel antibacterial agent against Staphylococcus aureus
5 affiliations
- 1School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen University, Shenzhen, China
- 2Department of Infectious Diseases and Shenzhen Key Laboratory for Endogenous Infections, Shenzhen Nanshan People's Hospital, Affiliated Nanshan Hospital of Shenzhen University, Shenzhen, China
- 3School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, China
- 4Department of Critical Care Medicine, Shenzhen Nanshan People's Hospital, Shenzhen University Medical School, Shenzhen, China
- 5Marketing Department of Guangzhou Branch of Varian Medical Equipment Trading (Beijing) Corp, Guangzhou, China
Abstract
Staphylococcus aureus infections pose a significant threat to global human health, particularly with the widespread transmission of methicillin-resistant S. aureus (MRSA) strains, which has created an urgent need for the development of new antimicrobial agents. PFM01 is an N-alkylated derivative of Mirin, an MRE11 endonuclease inhibitor. It was initially discovered to block the repair of double-strand DNA breaks and demonstrated preliminary anti-tumor potential; however, its antimicrobial activity had not yet been explored. Here, the anti-S. aureus activity of PFM01 was determined by broth microdilution minimum inhibitory concentration (MIC) testing and time-kill kinetics. The in vitro cytotoxicity was assessed by CCK-8 assay and hemolysis test. The potential mechanisms were systematically investigated by whole-genome sequencing, drug affinity responsive target stability (DARTS), and molecular docking analyses. PFM01 exhibited potent antibacterial activity against Gram-positive bacteria (including S. aureus, Enterococcus faecalis, Enterococcus faecium, and Streptococcus lactis), with MIC50 values ranging from 6.25 to 12.5 μM (1.83–3.67 μg/mL). Time-kill curve analysis confirmed its bactericidal capacity against free-floating S. aureus (including bacteria in the logarithmic growth phase and stationary phase-retained cells). Furthermore, PFM01 inhibited S. aureus biofilm formation in a concentration-dependent manner and possesses the ability to remove mature biofilms. In vitro cellular safety tests of PFM01 indicated low cytotoxicity and no significant hemolytic activity. Moreover, PFM01 altered the membrane permeability and potential of S. aureus, and its antibacterial activity was counteracted by the exogenous phospholipids. Whole-genome sequencing identified genetic mutations in the rapZ, mupR, mprF, and clpX genes of PFM01-resistant S. aureus strains; however, the antibacterial activity of PFM01 against mprF and clpX knockout S. aureus strains showed no significant change compared with wild-type strains. Proteomic analysis further revealed that PFM01 primarily might interfere with purine metabolism, amino acid biosynthesis, and the phosphotransferase system. DARTS experiments suggested that glycerol-3-phosphate cytidylyltransferase (TarD) might be a potential target, and molecular docking results further confirmed a stable interaction between PFM01 and TarD (binding energy: −7.4 kcal/mol). In summary, PFM01 may exert its antibacterial effect by disrupting the bacterial cell membrane structure and targeting TarD, and holds promise as a therapeutic agent for S. aureus infections.
IMPORTANCE: This study confirms that PFM01 has a broad and strong antibacterial effect against Gram-positive bacteria while also being biologically safe. The antimicrobial mechanism of PFM01 is closely associated with TarD. The advantages of low cytotoxicity against host cells and reduced hemolysis toward red cells were further demonstrated. As a promising repurposed antimicrobial candidate, PFM01 shows potential application for the treatment of infections caused by multidrug-resistant S. aureus.
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BibTeX
@article{li2026repurposing,
title = {{Repurposing PFM01 as a novel antibacterial agent against Staphylococcus aureus}},
author = {Congcong Li and Xuancheng Huang and Kewei Fan and Jintuan Lin and Yong Xiang and Bing Bai and Haigang Zhang and Zhijian Yu and Tieying Hou},
journal = {Microbiology Spectrum},
year = {2026},
month = oct,
doi = {10.1128/spectrum.01372-26},
url = {https://doi.org/10.1128/spectrum.01372-26},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Repurposing PFM01 as a novel antibacterial agent against Staphylococcus aureus
AU - Congcong Li
AU - Xuancheng Huang
AU - Kewei Fan
AU - Jintuan Lin
AU - Yong Xiang
AU - Bing Bai
AU - Haigang Zhang
AU - Zhijian Yu
AU - Tieying Hou
PY - 2026
DA - 2026/10/01
JO - Microbiology Spectrum
DO - 10.1128/spectrum.01372-26
UR - https://doi.org/10.1128/spectrum.01372-26
AB - Staphylococcus aureus infections pose a significant threat to global human health, particularly with the widespread transmission of methicillin-resistant S. aureus (MRSA) strains, which has created an urgent need for the development of new antimicrobial agents. PFM01 is an N-alkylated derivative of Mirin, an MRE11 endonuclease inhibitor. It was initially discovered to block the repair of double-strand DNA breaks and demonstrated preliminary anti-tumor potential; however, its antimicrobial activity had not yet been explored. Here, the anti-S. aureus activity of PFM01 was determined by broth microdilution minimum inhibitory concentration (MIC) testing and time-kill kinetics. The in vitro cytotoxicity was assessed by CCK-8 assay and hemolysis test. The potential mechanisms were systematically investigated by whole-genome sequencing, drug affinity responsive target stability (DARTS), and molecular docking analyses. PFM01 exhibited potent antibacterial activity against Gram-positive bacteria (including S. aureus, Enterococcus faecalis, Enterococcus faecium, and Streptococcus lactis), with MIC50 values ranging from 6.25 to 12.5 μM (1.83–3.67 μg/mL). Time-kill curve analysis confirmed its bactericidal capacity against free-floating S. aureus (including bacteria in the logarithmic growth phase and stationary phase-retained cells). Furthermore, PFM01 inhibited S. aureus biofilm formation in a concentration-dependent manner and possesses the ability to remove mature biofilms. In vitro cellular safety tests of PFM01 indicated low cytotoxicity and no significant hemolytic activity. Moreover, PFM01 altered the membrane permeability and potential of S. aureus, and its antibacterial activity was counteracted by the exogenous phospholipids. Whole-genome sequencing identified genetic mutations in the rapZ, mupR, mprF, and clpX genes of PFM01-resistant S. aureus strains; however, the antibacterial activity of PFM01 against mprF and clpX knockout S. aureus strains showed no significant change compared with wild-type strains. Proteomic analysis further revealed that PFM01 primarily might interfere with purine metabolism, amino acid biosynthesis, and the phosphotransferase system. DARTS experiments suggested that glycerol-3-phosphate cytidylyltransferase (TarD) might be a potential target, and molecular docking results further confirmed a stable interaction between PFM01 and TarD (binding energy: −7.4 kcal/mol). In summary, PFM01 may exert its antibacterial effect by disrupting the bacterial cell membrane structure and targeting TarD, and holds promise as a therapeutic agent for S. aureus infections. IMPORTANCE: This study confirms that PFM01 has a broad and strong antibacterial effect against Gram-positive bacteria while also being biologically safe. The antimicrobial mechanism of PFM01 is closely associated with TarD. The advantages of low cytotoxicity against host cells and reduced hemolysis toward red cells were further demonstrated. As a promising repurposed antimicrobial candidate, PFM01 shows potential application for the treatment of infections caused by multidrug-resistant S. aureus.
SN - 2165-0497
ER -