Identification of a phenyl ester covalent inhibitor of caseinolytic protease and analysis of the ClpP1P2 inhibition in mycobacteria
Abstract The caseinolytic protease complex ClpP1P2 is crucial for protein homeostasis in mycobacteria and stress response and virulence of the pathogens. Its role as a potential drug target for combating tuberculosis (TB) has just begun to be substantiated in drug discovery research. We conducted a...
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2025-04-01
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| Online Access: | https://doi.org/10.1002/mlf2.12169 |
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| author | Genhui Xiao Yumeng Cui Liangliang Zhou Chuya Niu Bing Wang Jinglan Wang Shaoyang Zhou Miaomiao Pan Chi Kin Chan Yan Xia Lan Xu Yu Lu Shawn Chen |
| author_facet | Genhui Xiao Yumeng Cui Liangliang Zhou Chuya Niu Bing Wang Jinglan Wang Shaoyang Zhou Miaomiao Pan Chi Kin Chan Yan Xia Lan Xu Yu Lu Shawn Chen |
| author_sort | Genhui Xiao |
| collection | DOAJ |
| description | Abstract The caseinolytic protease complex ClpP1P2 is crucial for protein homeostasis in mycobacteria and stress response and virulence of the pathogens. Its role as a potential drug target for combating tuberculosis (TB) has just begun to be substantiated in drug discovery research. We conducted a biochemical screening targeting the ClpP1P2 using a library of compounds phenotypically active against Mycobacterium tuberculosis (Mtb). The screening identified a phenyl ester compound GDI‐5755, inhibiting the growth of Mtb and M. bovis BCG, the model organism of mycobacteria. GDI‐5755 covalently modified the active‐site serine residue of ClpP1, rendering the peptidase inactive, which was delineated through protein mass spectrometry and kinetic analyses. GDI‐5755 exerted antibacterial activity by inhibiting ClpP1P2 in the bacteria, which could be demonstrated through a minimum inhibitory concentration (MIC) shift assay with a clpP1 CRISPRi knockdown (clpP1‐KD) mutant GH189. The knockdown also remarkably heightened the mutant's sensitivity to ethionamide and meropenem, but not to many other TB drugs. On the other hand, a comparative proteomic analysis of wild‐type cells exposed to GDI‐5755 revealed the dysregulated proteome, specifically showing changes in the expression levels of multiple TB drug targets, including EthA, LdtMt2, and PanD. Subsequent evaluation confirmed the synergistic activity of GDI‐5755 when combined with the TB drugs to inhibit mycobacterial growth. Our findings indicate that small‐molecule inhibitors targeting ClpP1P2, when used alongside existing TB medications, could represent novel therapeutic strategies. |
| format | Article |
| id | doaj-art-6fcf047db7e74f9580bc3d1c28a55672 |
| institution | Kabale University |
| issn | 2770-100X |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Wiley |
| record_format | Article |
| series | mLife |
| spelling | doaj-art-6fcf047db7e74f9580bc3d1c28a556722025-08-20T03:53:39ZengWileymLife2770-100X2025-04-014215516810.1002/mlf2.12169Identification of a phenyl ester covalent inhibitor of caseinolytic protease and analysis of the ClpP1P2 inhibition in mycobacteriaGenhui Xiao0Yumeng Cui1Liangliang Zhou2Chuya Niu3Bing Wang4Jinglan Wang5Shaoyang Zhou6Miaomiao Pan7Chi Kin Chan8Yan Xia9Lan Xu10Yu Lu11Shawn Chen12Global Health Drug Discovery Institute Beijing ChinaGlobal Health Drug Discovery Institute Beijing ChinaGlobal Health Drug Discovery Institute Beijing ChinaGlobal Health Drug Discovery Institute Beijing ChinaBeijing Key Laboratory of Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, and Beijing Chest Hospital Capital Medical University Beijing ChinaGlobal Health Drug Discovery Institute Beijing ChinaGlobal Health Drug Discovery Institute Beijing ChinaGlobal Health Drug Discovery Institute Beijing ChinaGlobal Health Drug Discovery Institute Beijing ChinaGlobal Health Drug Discovery Institute Beijing ChinaGlobal Health Drug Discovery Institute Beijing ChinaBeijing Key Laboratory of Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, and Beijing Chest Hospital Capital Medical University Beijing ChinaGlobal Health Drug Discovery Institute Beijing ChinaAbstract The caseinolytic protease complex ClpP1P2 is crucial for protein homeostasis in mycobacteria and stress response and virulence of the pathogens. Its role as a potential drug target for combating tuberculosis (TB) has just begun to be substantiated in drug discovery research. We conducted a biochemical screening targeting the ClpP1P2 using a library of compounds phenotypically active against Mycobacterium tuberculosis (Mtb). The screening identified a phenyl ester compound GDI‐5755, inhibiting the growth of Mtb and M. bovis BCG, the model organism of mycobacteria. GDI‐5755 covalently modified the active‐site serine residue of ClpP1, rendering the peptidase inactive, which was delineated through protein mass spectrometry and kinetic analyses. GDI‐5755 exerted antibacterial activity by inhibiting ClpP1P2 in the bacteria, which could be demonstrated through a minimum inhibitory concentration (MIC) shift assay with a clpP1 CRISPRi knockdown (clpP1‐KD) mutant GH189. The knockdown also remarkably heightened the mutant's sensitivity to ethionamide and meropenem, but not to many other TB drugs. On the other hand, a comparative proteomic analysis of wild‐type cells exposed to GDI‐5755 revealed the dysregulated proteome, specifically showing changes in the expression levels of multiple TB drug targets, including EthA, LdtMt2, and PanD. Subsequent evaluation confirmed the synergistic activity of GDI‐5755 when combined with the TB drugs to inhibit mycobacterial growth. Our findings indicate that small‐molecule inhibitors targeting ClpP1P2, when used alongside existing TB medications, could represent novel therapeutic strategies.https://doi.org/10.1002/mlf2.12169caseinolytic proteasechemical–genetic interactiondrug combinationenzyme inhibitormycobacteria |
| spellingShingle | Genhui Xiao Yumeng Cui Liangliang Zhou Chuya Niu Bing Wang Jinglan Wang Shaoyang Zhou Miaomiao Pan Chi Kin Chan Yan Xia Lan Xu Yu Lu Shawn Chen Identification of a phenyl ester covalent inhibitor of caseinolytic protease and analysis of the ClpP1P2 inhibition in mycobacteria mLife caseinolytic protease chemical–genetic interaction drug combination enzyme inhibitor mycobacteria |
| title | Identification of a phenyl ester covalent inhibitor of caseinolytic protease and analysis of the ClpP1P2 inhibition in mycobacteria |
| title_full | Identification of a phenyl ester covalent inhibitor of caseinolytic protease and analysis of the ClpP1P2 inhibition in mycobacteria |
| title_fullStr | Identification of a phenyl ester covalent inhibitor of caseinolytic protease and analysis of the ClpP1P2 inhibition in mycobacteria |
| title_full_unstemmed | Identification of a phenyl ester covalent inhibitor of caseinolytic protease and analysis of the ClpP1P2 inhibition in mycobacteria |
| title_short | Identification of a phenyl ester covalent inhibitor of caseinolytic protease and analysis of the ClpP1P2 inhibition in mycobacteria |
| title_sort | identification of a phenyl ester covalent inhibitor of caseinolytic protease and analysis of the clpp1p2 inhibition in mycobacteria |
| topic | caseinolytic protease chemical–genetic interaction drug combination enzyme inhibitor mycobacteria |
| url | https://doi.org/10.1002/mlf2.12169 |
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