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Dong W, Wang G, Bai Y, Li Y, Zhao L, Lu W, Wang C, Zhang Z, Lu H, Wang X, Chen H, Tan C. Repurposing an Antioxidant to Kill Mycobacterium tuberculosis by Targeting the 50S Subunit of the Ribosome. Biomolecules 2023; 13:1793. [PMID: 38136663 PMCID: PMC10742058 DOI: 10.3390/biom13121793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/01/2023] [Accepted: 12/03/2023] [Indexed: 12/24/2023] Open
Abstract
Tuberculosis and drug-resistant TB remain serious threats to global public health. It is urgent to develop novel anti-TB drugs in order to control it. In addition to redesigning and developing new anti-TB drugs, drug repurposing is also an innovative way to develop antibacterial drugs. Based on this method, we discovered SKQ-1 in the FDA-approved drug library and evaluated its anti-TB activity. In vitro, we demonstrated that SKQ-1 engaged in bactericidal activity against drug-sensitive and -resistant Mtb and confirmed the synergistic effects of SKQ1 with RIF and INH. Moreover, SKQ-1 showed a significant Mtb-killing effect in macrophages. In vivo, both the SKQ-1 treatment alone and the treatment in combination with RIF were able to significantly reduce the bacterial load and improve the survival rate of G. mellonella infected with Mtb. We performed whole-genome sequencing on screened SKQ-1-resistant strains and found that the SNP sites were concentrated in the 50S ribosomal subunit of Mtb. Furthermore, we proved that SKQ-1 can inhibit protein translation. In summary, from the perspective of drug repurposing, we discovered and determined the anti-tuberculosis effect of SKQ-1, revealed its synergistic effects with RIF and INH, and demonstrated its mechanism of action through targeting ribosomes and disrupting protein synthesis, thus making it a potential treatment option for DR-TB.
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Affiliation(s)
- Wenqi Dong
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (W.D.); (G.W.); (Y.B.); (Y.L.); (L.Z.); (W.L.); (C.W.); (Z.Z.); (H.L.); (X.W.); (H.C.)
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Gaoyan Wang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (W.D.); (G.W.); (Y.B.); (Y.L.); (L.Z.); (W.L.); (C.W.); (Z.Z.); (H.L.); (X.W.); (H.C.)
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Yajuan Bai
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (W.D.); (G.W.); (Y.B.); (Y.L.); (L.Z.); (W.L.); (C.W.); (Z.Z.); (H.L.); (X.W.); (H.C.)
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Yuxin Li
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (W.D.); (G.W.); (Y.B.); (Y.L.); (L.Z.); (W.L.); (C.W.); (Z.Z.); (H.L.); (X.W.); (H.C.)
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Liying Zhao
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (W.D.); (G.W.); (Y.B.); (Y.L.); (L.Z.); (W.L.); (C.W.); (Z.Z.); (H.L.); (X.W.); (H.C.)
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Wenjia Lu
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (W.D.); (G.W.); (Y.B.); (Y.L.); (L.Z.); (W.L.); (C.W.); (Z.Z.); (H.L.); (X.W.); (H.C.)
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Chenchen Wang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (W.D.); (G.W.); (Y.B.); (Y.L.); (L.Z.); (W.L.); (C.W.); (Z.Z.); (H.L.); (X.W.); (H.C.)
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Zhaoran Zhang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (W.D.); (G.W.); (Y.B.); (Y.L.); (L.Z.); (W.L.); (C.W.); (Z.Z.); (H.L.); (X.W.); (H.C.)
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Hao Lu
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (W.D.); (G.W.); (Y.B.); (Y.L.); (L.Z.); (W.L.); (C.W.); (Z.Z.); (H.L.); (X.W.); (H.C.)
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Xiangru Wang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (W.D.); (G.W.); (Y.B.); (Y.L.); (L.Z.); (W.L.); (C.W.); (Z.Z.); (H.L.); (X.W.); (H.C.)
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Huanchun Chen
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (W.D.); (G.W.); (Y.B.); (Y.L.); (L.Z.); (W.L.); (C.W.); (Z.Z.); (H.L.); (X.W.); (H.C.)
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Chen Tan
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (W.D.); (G.W.); (Y.B.); (Y.L.); (L.Z.); (W.L.); (C.W.); (Z.Z.); (H.L.); (X.W.); (H.C.)
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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Zhang W, Li Z, Sun Y, Cui P, Liang J, Xing Q, Wu J, Xu Y, Zhang W, Zhang Y, He L, Gao N. Cryo-EM structure of Mycobacterium tuberculosis 50S ribosomal subunit bound with clarithromycin reveals dynamic and specific interactions with macrolides. Emerg Microbes Infect 2021; 11:293-305. [PMID: 34935599 PMCID: PMC8786254 DOI: 10.1080/22221751.2021.2022439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Tuberculosis (TB) is the leading infectious disease caused by Mycobacterium tuberculosis (Mtb). Clarithromycin (CTY), an analog of erythromycin (ERY), is more potent against multidrug-resistance (MDR) TB. ERY and CTY were previously reported to bind to the nascent polypeptide exit tunnel (NPET) near peptidyl transferase center (PTC), but the only available CTY structure in complex with D. radiodurans (Dra) ribosome could be misinterpreted due to resolution limitation. To date, the mechanism of specificity and efficacy of CTY for Mtb remains elusive since the Mtb ribosome-CTY complex structure is still unknown. Here, we employed new sample preparation methods and solved the Mtb ribosome-CTY complex structure at 3.3Å with cryo-EM technique, where the crucial gate site A2062 (E. coli numbering) is located at the CTY binding site within NPET. Two alternative conformations of A2062, a novel syn-conformation as well as a swayed conformation bound with water molecule at interface, may play a role in coordinating the binding of specific drug molecules. The previously overlooked C–H hydrogen bond (H-bond) and π interaction may collectively contribute to the enhanced binding affinity. Together, our structure data provide a structural basis for the dynamic binding as well as the specificity of CTY and explain of how a single methyl group in CTY improves its potency, which provides new evidence to reveal previously unclear mechanism of translational modulation for future drug design and anti-TB therapy. Furthermore, our sample preparation method may facilitate drug discovery based on the complexes with low water solubility drugs by cryo-EM technique.
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Affiliation(s)
- Wen Zhang
- Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - ZhiFei Li
- State Key Laboratory of Membrane Biology, National Biomedical Imaging Center, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, 100871, Beijing, China.,China National Center for Biotechnology Development. 10039, Beijing, China
| | - Yufan Sun
- Department of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Peng Cui
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Jianhua Liang
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China
| | - Qinghe Xing
- Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Jing Wu
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yanhui Xu
- Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Wenhong Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Ying Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200032, China.,State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China
| | - Lin He
- Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China.,Bio-X Institute, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Ning Gao
- State Key Laboratory of Membrane Biology, National Biomedical Imaging Center, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, 100871, Beijing, China
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Choi E, Jeon H, Oh JI, Hwang J. Overexpressed L20 Rescues 50S Ribosomal Subunit Assembly Defects of bipA-Deletion in Escherichia coli. Front Microbiol 2020; 10:2982. [PMID: 31998269 PMCID: PMC6962249 DOI: 10.3389/fmicb.2019.02982] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 12/10/2019] [Indexed: 11/13/2022] Open
Abstract
The BipA (BPI-inducible protein A) protein is highly conserved in a large variety of bacteria and belongs to the translational GTPases, based on sequential and structural similarities. Despite its conservation in bacteria, bipA is not essential for cell growth under normal growth conditions. However, at 20°C, deletion of bipA causes not only severe growth defects but also several phenotypic changes such as capsule production, motility, and ribosome assembly, indicating that it has global regulatory properties. Our recent studies revealed that BipA is a novel ribosome-associating GTPase, whose expression is cold-shock-inducible and involved in the incorporation of the ribosomal protein (r-protein) L6. However, the precise mechanism of BipA in 50S ribosomal subunit assembly is not completely understood. In this study, to demonstrate the role of BipA in the 50S ribosomal subunit and possibly to find an interplaying partner(s), a genomic library was constructed and suppressor screening was conducted. Through screening, we found a suppressor gene, rplT, encoding r-protein L20, which is assembled at the early stage of ribosome assembly and negatively regulates its own expression at the translational level. We demonstrated that the exogenous expression of rplT restored the growth of bipA-deleted strain at low temperature by partially recovering the defects in ribosomal RNA processing and ribosome assembly. Our findings suggest that the function of BipA is pivotal for 50S ribosomal subunit biogenesis at a low temperature and imply that BipA and L20 may exert coordinated actions for proper ribosome assembly under cold-shock conditions.
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Affiliation(s)
- Eunsil Choi
- Department of Microbiology, Pusan National University, Busan, South Korea
| | - Hyerin Jeon
- Department of Microbiology, Pusan National University, Busan, South Korea
| | - Jeong-Il Oh
- Department of Microbiology, Pusan National University, Busan, South Korea
| | - Jihwan Hwang
- Department of Microbiology, Pusan National University, Busan, South Korea
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Vickers A, Mushtaq S, Woodford N, Doumith M, Livermore DM. Activity of RX-04 Pyrrolocytosine Protein Synthesis Inhibitors against Multidrug-Resistant Gram-Negative Bacteria. Antimicrob Agents Chemother 2018; 62:e00689-18. [PMID: 29914946 DOI: 10.1128/AAC.00689-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/08/2018] [Indexed: 01/13/2023] Open
Abstract
Pyrrolocytosines RX-04A to -D are designed to bind to the bacterial 50S ribosomal subunit differently from currently used antibiotics. The four analogs had broad anti-Gram-negative activity: RX-04A-the most active analog-inhibited 94.7% of clinical Enterobacteriaceae, Acinetobacter baumannii, and Pseudomonas aeruginosa at 0.5 to 4 μg/ml, with no MICs of >8 μg/ml. MICs for multidrug-resistant (MDR) carbapenemase producers were up to 2-fold higher than those for control strains; values were highest for one Serratia isolate with porin and efflux lesions. mcr-1 did not affect MICs.
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Gabdulkhakov A, Nikonov S, Garber M. Revisiting the Haloarcula marismortui 50S ribosomal subunit model. Acta Crystallogr D Biol Crystallogr 2013; 69:997-1004. [PMID: 23695244 DOI: 10.1107/s0907444913004745] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Accepted: 02/18/2013] [Indexed: 11/10/2022]
Abstract
The structure of the large ribosomal subunit from the halophilic archaeon Haloarcula marismortui (Hma) is the only crystal structure of an archaeal ribosomal particle that has been determined to date. However, the first model of the Hma 50S ribosomal subunit contained some gaps: the structures of functionally important mobile lateral protuberances were not visualized. Subsequently, some parts of the P (L12) stalk base were visualized at 3.0 Å resolution [Kavran & Steitz (2007), J. Mol. Biol. 371, 1047-1059]: the RNA-binding domain of r-protein P0 (L10), the C-terminal domain of L11 and helices 43 and 44 of the 23 S rRNA. Here, the 2.4 Å resolution electron-density map of the Hma 50S ribosomal subunit was revisited and approximately two-thirds of the P0 protein, residues 1-58 of the N-terminal domains of two P1 protein molecules, residues 130-156 of L11, the full-length r-protein LX, nucleotides 2137-2149 and 2226-2237 of the 23S rRNA helix H76 forming the L1 stalk, nucleotides 2339-2343 of the 23S rRNA (contacting L5 protein) and loops 29-34 and 108-128 of protein L5 could be visualized. Thus, this paper provides a supplemented version of the Hma 50S ribosomal subunit model.
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Affiliation(s)
- Azat Gabdulkhakov
- Institute of Protein Research, RAS, Pushchino, Moscow Region 142290, Russian Federation.
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