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Liu R, Sun J, Li LF, Cheng Y, Li M, Fu L, Li S, Peng G, Wang Y, Liu S, Qu X, Ran J, Li X, Pang E, Qiu HJ, Wang Y, Qi J, Wang H, Gao GF. Structural basis for difunctional mechanism of m-AMSA against African swine fever virus pP1192R. Nucleic Acids Res 2024:gkae703. [PMID: 39166497 DOI: 10.1093/nar/gkae703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 07/24/2024] [Accepted: 08/07/2024] [Indexed: 08/23/2024] Open
Abstract
The African swine fever virus (ASFV) type II topoisomerase (Topo II), pP1192R, is the only known Topo II expressed by mammalian viruses and is essential for ASFV replication in the host cytoplasm. Herein, we report the structures of pP1192R in various enzymatic stages using both X-ray crystallography and single-particle cryo-electron microscopy. Our data structurally define the pP1192R-modulated DNA topology changes. By presenting the A2+-like metal ion at the pre-cleavage site, the pP1192R-DNA-m-AMSA complex structure provides support for the classical two-metal mechanism in Topo II-mediated DNA cleavage and a better explanation for nucleophile formation. The unique inhibitor selectivity of pP1192R and the difunctional mechanism of pP1192R inhibition by m-AMSA highlight the specificity of viral Topo II in the poison binding site. Altogether, this study provides the information applicable to the development of a pP1192R-targeting anti-ASFV strategy.
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Affiliation(s)
- Ruili Liu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province 450046, China
- Beijing Life Science Academy, Beijing 102200, China
| | - Junqing Sun
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, Shanxi Province 030801, China
| | - Lian-Feng Li
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin Province 150069, China
| | - Yingxian Cheng
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province 450046, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Meilin Li
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin Province 150069, China
| | - Lifeng Fu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Su Li
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin Province 150069, China
| | - Guorui Peng
- China/WOAH Reference Laboratory for Classical Swine Fever, China Institute of Veterinary Drug Control, Beijing 100081, China
| | - Yanjin Wang
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin Province 150069, China
| | - Sheng Liu
- SUSTech Cryo-EM Centre, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiao Qu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiaqi Ran
- Department of Biological Sciences, School of life Science, Liaoning University, Shenyang, Liaoning Province 110030, China
| | - Xiaomei Li
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, Shanxi Province 030032, China
| | - Erqi Pang
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, Shanxi Province 030032, China
| | - Hua-Ji Qiu
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin Province 150069, China
| | - Yanli Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Han Wang
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100091, China
| | - George Fu Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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2
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Liu KT, Chen SF, Chan NL. Structural insights into the assembly of type IIA topoisomerase DNA cleavage-religation center. Nucleic Acids Res 2024:gkae657. [PMID: 39077950 DOI: 10.1093/nar/gkae657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 07/09/2024] [Accepted: 07/16/2024] [Indexed: 07/31/2024] Open
Abstract
The ability to catalyze reversible DNA cleavage and religation is central to topoisomerases' role in regulating DNA topology. In type IIA topoisomerases (Top2), the formation of its DNA cleavage-religation center is driven by DNA-binding-induced structural rearrangements. These changes optimally position key catalytic modules, such as the active site tyrosine of the WHD domain and metal ion(s) chelated by the TOPRIM domain, around the scissile phosphodiester bond to perform reversible transesterification. To understand this assembly process in detail, we report the catalytic core structures of human Top2α and Top2β in an on-pathway conformational state. This state features an in trans formation of an interface between the Tower and opposing TOPRIM domain, revealing a groove for accommodating incoming G-segment DNA. Structural superimposition further unveils how subsequent DNA-binding-induced disengagement of the TOPRIM and Tower domains allows a firm grasp of the bound DNA for cleavage/religation. Notably, we identified a previously undocumented protein-DNA interaction, formed between an arginine-capped C-terminus of an α-helix in the TOPRIM domain and the DNA backbone, significantly contributing to Top2 function. This work uncovers a previously unrecognized role of the Tower domain, highlighting its involvement in anchoring and releasing the TOPRIM domain, thus priming Top2 for DNA binding and cleavage.
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Affiliation(s)
- Ko-Ting Liu
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Shin-Fu Chen
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Nei-Li Chan
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
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3
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Kuang W, Zhao Y, Li J, Deng Z. Structure-function analysis of the ATPase domain of African swine fever virus topoisomerase. mBio 2024; 15:e0308623. [PMID: 38411066 PMCID: PMC11005426 DOI: 10.1128/mbio.03086-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/05/2024] [Indexed: 02/28/2024] Open
Abstract
Type II topoisomerase utilizes the energy from ATP hydrolysis to alter DNA topology during genome replication and transcription. The ATPase domain of this enzyme is required for ATP hydrolysis and plays a crucial role in coupling DNA binding and ATP turnover with the DNA strand passage reaction. The African swine fever virus (ASFV) specifically encodes a topoisomerase II (topo II), which is critical for viral replication and an attractive target for antiviral development. Here, we present a high-resolution crystal structure of the ASFV topo II ATPase domain complexed with the substrate analog AMPPNP. Structural comparison reveals that the ASFV topo II ATPase domain shares a conserved overall structure with its homologs from eukaryotes and prokaryotes but also has three characteristic regions, including the intra-molecular interface formed by the ATP-lid and QTK loop as well as helix α9, the K-loop in the transducer domain, and the antennae-like α-helix at the ATP binding domain. Mutating the key residues within these three regions impairs or abolishes the basal and DNA-stimulated ATPase activities and reduces or eliminates the relaxation activity of the holoenzyme. Our data indicate that all three regions are functionally important for the ATPase and relaxation activities and strongly suggest that ATP hydrolysis, DNA binding, and strand passage are highly coupled and managed by the allosteric coordination of multiple domains of the type II topoisomerase. Moreover, we find a promising druggable pocket in the dimeric interface of the ASFV topo II ATPase domain, which will benefit future anti-ASFV drug development. IMPORTANCE The ATPase domain of type II topoisomerase provides energy by hydrolyzing ATP and coordinates with the DNA-binding/cleavage domain to drive and control DNA transport. The precise molecular mechanisms of how these domains respond to DNA binding and ATP hydrolysis signals and communicate with each other remain elusive. We determine the first high-resolution crystal structure of the ATPase domain of African swine fever virus (ASFV) topo II in complex with AMPPNP and biochemically investigate its function in ATPase and DNA relaxation activities. Importantly, we find that mutations at three characteristic regions of the ASFV ATPase domain produce parallel effects on the basal/DNA-stimulated ATPase and relaxation activities, implying the tight coupling of the ATP hydrolysis and strand passage process. Therefore, our data provide important implications for understanding the strand passage mechanism of the type II topoisomerase and the structural basis for developing ATPase domain-targeting antivirals against ASFV.
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Affiliation(s)
- Wenhua Kuang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Antiviral Research, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Yan Zhao
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Antiviral Research, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinyue Li
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Antiviral Research, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Zengqin Deng
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Antiviral Research, Chinese Academy of Sciences, Wuhan, Hubei, China
- Hubei Jiangxia Laboratory, Wuhan, Hubei, China
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4
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Ochoa-Sánchez LE, Martínez JL, Gil-Gil T. Evolution of Resistance against Ciprofloxacin, Tobramycin, and Trimethoprim/Sulfamethoxazole in the Environmental Opportunistic Pathogen Stenotrophomonas maltophilia. Antibiotics (Basel) 2024; 13:330. [PMID: 38667006 PMCID: PMC11047544 DOI: 10.3390/antibiotics13040330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/27/2024] [Accepted: 04/02/2024] [Indexed: 04/29/2024] Open
Abstract
Stenotrophomonas maltophilia is an opportunistic pathogen that produces respiratory infections in immunosuppressed and cystic fibrosis patients. The therapeutic options to treat S. maltophilia infections are limited since it exhibits resistance to a wide variety of antibiotics such as β-lactams, aminoglycosides, tetracyclines, cephalosporins, macrolides, fluoroquinolones, or carbapenems. The antibiotic combination trimethoprim/sulfamethoxazole (SXT) is the treatment of choice to combat infections caused by S. maltophilia, while ceftazidime, ciprofloxacin, or tobramycin are used in most SXT-resistant infections. In the current study, experimental evolution and whole-genome sequencing (WGS) were used to examine the evolutionary trajectories of S. maltophilia towards resistance against tobramycin, ciprofloxacin, and SXT. The genetic changes underlying antibiotic resistance, as well as the evolutionary trajectories toward that resistance, were determined. Our results determine that genomic changes in the efflux pump regulatory genes smeT and soxR are essential to confer resistance to ciprofloxacin, and the mutation in the rplA gene is significant in the resistance to tobramycin. We identified mutations in folP and the efflux pump regulator smeRV as the basis of SXT resistance. Detailed and reliable knowledge of ciprofloxacin, tobramycin, and SXT resistance is essential for safe and effective use in clinical settings. Herein, we were able to prove once again the extraordinary ability that S. maltophilia has to acquire resistance and the importance of looking for alternatives to combat this resistance.
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Affiliation(s)
- Luz Edith Ochoa-Sánchez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Darwin 3, 28049 Madrid, Spain;
| | - José Luis Martínez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Darwin 3, 28049 Madrid, Spain;
| | - Teresa Gil-Gil
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Darwin 3, 28049 Madrid, Spain;
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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5
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Chang CWM, Wang SC, Wang CH, Pang AH, Yang CH, Chang YK, Wu WJ, Tsai MD. A unified view on enzyme catalysis by cryo-EM study of a DNA topoisomerase. Commun Chem 2024; 7:45. [PMID: 38418525 PMCID: PMC10901890 DOI: 10.1038/s42004-024-01129-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/14/2024] [Indexed: 03/01/2024] Open
Abstract
The theories for substrate recognition in enzyme catalysis have evolved from lock-key to induced fit, then conformational selection, and conformational selection followed by induced fit. However, the prevalence and consensus of these theories require further examination. Here we use cryogenic electron microscopy and African swine fever virus type 2 topoisomerase (AsfvTop2) to demonstrate substrate binding theories in a joint and ordered manner: catalytic selection by the enzyme, conformational selection by the substrates, then induced fit. The apo-AsfvTop2 pre-exists in six conformers that comply with the two-gate mechanism directing DNA passage and release in the Top2 catalytic cycle. The structures of AsfvTop2-DNA-inhibitor complexes show that substantial induced-fit changes occur locally from the closed apo-conformer that however is too far-fetched for the open apo-conformer. Furthermore, the ATPase domain of AsfvTop2 in the MgAMP-PNP-bound crystal structures coexist in reduced and oxidized forms involving a disulfide bond, which can regulate the AsfvTop2 function.
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Affiliation(s)
- Chiung-Wen Mary Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
- Institute of Biochemistry and Molecular Biology, China Medical University, Taichung, Taiwan
| | - Shun-Chang Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Chun-Hsiung Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Allan H Pang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Cheng-Han Yang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Yao-Kai Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Wen-Jin Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan.
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 106, Taiwan.
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6
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Salem MG, Abu El-Ata SA, Elsayed EH, Mali SN, Alshwyeh HA, Almaimani G, Almaimani RA, Almasmoum HA, Altwaijry N, Al-Olayan E, Saied EM, Youssef MF. Novel 2-substituted-quinoxaline analogs with potential antiproliferative activity against breast cancer: insights into cell cycle arrest, topoisomerase II, and EGFR activity. RSC Adv 2023; 13:33080-33095. [PMID: 37954422 PMCID: PMC10633821 DOI: 10.1039/d3ra06189b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 10/26/2023] [Indexed: 11/14/2023] Open
Abstract
Breast cancer is a global health concern, with increasing disease burden and disparities in access to healthcare. Late diagnosis and limited treatment options in underserved areas contribute to poor outcomes. In response to this challenge, we developed a novel family of 2-substituted-quinoxaline analogues, combining coumarin and quinoxaline scaffolds known for their anticancer properties. Through a versatile synthetic approach, we designed, synthesized, and characterized a set of 2-substituted quinoxaline derivatives. The antiproliferative activity of the synthesized compounds was assessed toward the MCF-7 breast cancer cells. Our investigations showed that the synthesized compounds exhibit considerable antiproliferative activity toward MCF-7 cells. Notably, compound 3b, among examined compounds, displayed a superior inhibitory effect (IC50 = 1.85 ± 0.11 μM) toward the growth of MCF-7 cells compared to the conventional anticancer drug staurosporine (IC50 = 6.77 ± 0.41 μM) and showed minimal impact on normal cells (MCF-10A cell lines, IC50 = 33.7 ± 2.04 μM). Mechanistic studies revealed that compound 3b induced cell cycle arrest at the G1 transition and triggered apoptosis in MCF-7 cells, as evidenced by increasing the percentage of cells arrested in the G2/M and pre-G1 phases utilizing flow cytometric analysis and Annexin V-FITC/PI analysis. Moreover, compound 3b was found to substantially suppress topoisomerase enzyme activity in MCF-7 cells. Molecular modeling studies further supported the potential of compound 3b as a therapeutic candidate by demonstrating significant binding affinity to the active sites of both topoisomerase II and EGFR proteins. Taken together, the presented 2-substituted-quinoxaline analogues, especially compound 3b, show promise as potential candidates for the development of effective anti-breast cancer drugs.
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Affiliation(s)
- Manar G Salem
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Suez Canal University Ismailia 41522 Egypt
| | - Sara A Abu El-Ata
- Department of Chemistry, Faculty of Science, Port Said University Port Said Egypt
| | - Elsherbiny H Elsayed
- Department of Chemistry, Faculty of Science, Port Said University Port Said Egypt
| | - Suraj N Mali
- Department of Pharmaceutical Sciences and Technology, Birla Institute of Technology Ranchi 835215 India
| | - Hussah Abdullah Alshwyeh
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University Dammam 31441 Saudi Arabia
- Basic & Applied Scientific Research Centre, Imam Abdulrahman Bin Faisal University PO Box 1982 Dammam 31441 Saudi Arabia
| | - Ghassan Almaimani
- Department of Surgery, Faculty of Medicine, Umm Al-Qura University Al Abdeyah, PO Box 7607 Makkah Saudi Arabia
| | - Riyad A Almaimani
- Department of Biochemistry, Faculty of Medicine, Umm Al-Qura University Al Abdeyah, PO Box 7607 Makkah Saudi Arabia
| | - Hussain A Almasmoum
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Umm Al-Qura University Al Abdeyah, PO Box 7607 Makkah Saudi Arabia
| | - Najla Altwaijry
- Department of Pharmaceutical Sciences, Princess Nourah Bint Abdulrahman University PO Box 84428 Riyadh 11671 Saudi Arabia
| | - Ebtesam Al-Olayan
- Department of Zoology, College of Science, King Saud University Riyadh Saudi Arabia
| | - Essa M Saied
- Department of Chemistry (Biochemistry Division), Faculty of Science, Suez Canal University Ismailia 41522 Egypt
- Institute for Chemistry, Humboldt Universität zu Berlin Brook-Taylor-Str. 2 12489 Berlin Germany
| | - Mohamed F Youssef
- Department of Chemistry (Organic Chemistry Division), Faculty of Science, Suez Canal University Ismailia 41522 Egypt
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7
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Pavlin M, Herlah B, Valjavec K, Perdih A. Unveiling the interdomain dynamics of type II DNA topoisomerase through all-atom simulations: Implications for understanding its catalytic cycle. Comput Struct Biotechnol J 2023; 21:3746-3759. [PMID: 37602233 PMCID: PMC10436251 DOI: 10.1016/j.csbj.2023.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 07/01/2023] [Accepted: 07/19/2023] [Indexed: 08/22/2023] Open
Abstract
Type IIA DNA topoisomerases are complex molecular nanomachines that manage topological states of the DNA molecule in the cell and play a crucial role in cellular processes such as cell division and transcription. They are also established targets of cancer chemotherapy. Starting from the available crystal structure of a fully catalytic topoisomerase IIA homodimer from Saccharomyces cerevisiae, we constructed three states of this molecular motor primarily changing the configurations of the DNA segment bound in the DNA gate and performed μs-long all-atom molecular simulations. A comprehensive analysis revealed a sliding motion within the DNA gate and a teamwork between the N-gate and DNA gate that may be associated with the necessary molecular events that allow passage of the T-segment of DNA. The observed movement of the ATPase dimer relative to the DNA domain was reflected in different interaction patterns between the K-loops of the transducer domain and the B-A-B form of the bound DNA. Based on the obtained results, we mapped simulated configurations to the structures in the proposed catalytic cycle through which type IIA topoisomerases exert their function and discussed the possible transition events. The results extend our understanding of the mechanism of action of type IIA topoisomerases and provide an atomistic interpretation of some of the observed features of these molecular motors.
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Affiliation(s)
- Matic Pavlin
- Department of Catalysis and Chemical Reaction Engineering, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Barbara Herlah
- Theory Department, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Katja Valjavec
- Theory Department, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Andrej Perdih
- Theory Department, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
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8
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Gu L, Hickey RJ, Malkas LH. Therapeutic Targeting of DNA Replication Stress in Cancer. Genes (Basel) 2023; 14:1346. [PMID: 37510250 PMCID: PMC10378776 DOI: 10.3390/genes14071346] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 07/30/2023] Open
Abstract
This article reviews the currently used therapeutic strategies to target DNA replication stress for cancer treatment in the clinic, highlighting their effectiveness and limitations due to toxicity and drug resistance. Cancer cells experience enhanced spontaneous DNA damage due to compromised DNA replication machinery, elevated levels of reactive oxygen species, loss of tumor suppressor genes, and/or constitutive activation of oncogenes. Consequently, these cells are addicted to DNA damage response signaling pathways and repair machinery to maintain genome stability and support survival and proliferation. Chemotherapeutic drugs exploit this genetic instability by inducing additional DNA damage to overwhelm the repair system in cancer cells. However, the clinical use of DNA-damaging agents is limited by their toxicity and drug resistance often arises. To address these issues, the article discusses a potential strategy to target the cancer-associated isoform of proliferating cell nuclear antigen (caPCNA), which plays a central role in the DNA replication and damage response network. Small molecule and peptide agents that specifically target caPCNA can selectively target cancer cells without significant toxicity to normal cells or experimental animals.
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Affiliation(s)
- Long Gu
- Department of Molecular Diagnostics & Experimental Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Robert J Hickey
- Department of Cancer Biology & Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Linda H Malkas
- Department of Molecular Diagnostics & Experimental Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
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9
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Shariati A, Arshadi M, Khosrojerdi MA, Abedinzadeh M, Ganjalishahi M, Maleki A, Heidary M, Khoshnood S. The resistance mechanisms of bacteria against ciprofloxacin and new approaches for enhancing the efficacy of this antibiotic. Front Public Health 2022; 10:1025633. [PMID: 36620240 PMCID: PMC9815622 DOI: 10.3389/fpubh.2022.1025633] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022] Open
Abstract
For around three decades, the fluoroquinolone (FQ) antibiotic ciprofloxacin has been used to treat a range of diseases, including chronic otorrhea, endocarditis, lower respiratory tract, gastrointestinal, skin and soft tissue, and urinary tract infections. Ciprofloxacin's main mode of action is to stop DNA replication by blocking the A subunit of DNA gyrase and having an extra impact on the substances in cell walls. Available in intravenous and oral formulations, ciprofloxacin reaches therapeutic concentrations in the majority of tissues and bodily fluids with a low possibility for side effects. Despite the outstanding qualities of this antibiotic, Salmonella typhi, Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa have all shown an increase in ciprofloxacin resistance over time. The rise of infections that are resistant to ciprofloxacin shows that new pharmacological synergisms and derivatives are required. To this end, ciprofloxacin may be more effective against the biofilm community of microorganisms and multi-drug resistant isolates when combined with a variety of antibacterial agents, such as antibiotics from various classes, nanoparticles, natural products, bacteriophages, and photodynamic therapy. This review focuses on the resistance mechanisms of bacteria against ciprofloxacin and new approaches for enhancing its efficacy.
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Affiliation(s)
- Aref Shariati
- Molecular and Medicine Research Center, Khomein University of Medical Sciences, Khomein, Iran
| | - Maniya Arshadi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran,Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | | | - Mostafa Abedinzadeh
- Student Research Committee, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Mahsa Ganjalishahi
- Student Research Committee, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Abbas Maleki
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Mohsen Heidary
- Department of Laboratory Sciences, School of Paramedical Sciences, Sabzevar University of Medical Sciences, Sabzevar, Iran,Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, Iran,*Correspondence: Mohsen Heidary
| | - Saeed Khoshnood
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran,Student Research Committee, Ilam University of Medical Sciences, Ilam, Iran,Saeed Khoshnood
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10
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Goodsell DS. Integrative illustration of a JCVI-syn3A minimal cell. J Integr Bioinform 2022; 19:jib-2022-0013. [PMID: 35749071 PMCID: PMC9377704 DOI: 10.1515/jib-2022-0013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/02/2022] [Indexed: 01/22/2023] Open
Abstract
Data from genomics, proteomics, structural biology and cryo-electron microscopy are integrated into a structural illustration of a cross section through an entire JCVI-syn3.0 minimal cell. The illustration is designed with several goals: to inspire excitement in science, to depict the underlying scientific results accurately, and to be feasible in traditional media. Design choices to achieve these goals include reduction of visual complexity with simplified representations, use of orthographic projection to retain scale relationships, and an approach to color that highlights functional compartments of the cell. Given that this simple cell provides an attractive laboratory for exploring the central processes needed for life, several functional narratives are included in the illustration, including division of the cell and the first depiction of an entire cellular proteome. The illustration lays the foundation for 3D molecular modeling of this cell.
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Affiliation(s)
- David S. Goodsell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037, USA
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ08854, USA
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11
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Brovarets’ OO, Muradova A, Hovorun DM. Novel horizons of the conformationally-tautomeric transformations of the G·T base pairs: quantum-mechanical investigation. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2026510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Ol’ha O. Brovarets’
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Alona Muradova
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Dmytro M. Hovorun
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
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12
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Fisher GL, Bolla JR, Rajasekar KV, Mäkelä J, Baker R, Zhou M, Prince JP, Stracy M, Robinson CV, Arciszewska LK, Sherratt DJ. Competitive binding of MatP and topoisomerase IV to the MukB hinge domain. eLife 2021; 10:70444. [PMID: 34585666 PMCID: PMC8523169 DOI: 10.7554/elife.70444] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 09/21/2021] [Indexed: 11/13/2022] Open
Abstract
Structural Maintenance of Chromosomes (SMC) complexes have ubiquitous roles in compacting DNA linearly, thereby promoting chromosome organization-segregation. Interaction between the Escherichia coli SMC complex, MukBEF, and matS-bound MatP in the chromosome replication termination region, ter, results in depletion of MukBEF from ter, a process essential for efficient daughter chromosome individualization and for preferential association of MukBEF with the replication origin region. Chromosome-associated MukBEF complexes also interact with topoisomerase IV (ParC2E2), so that their chromosome distribution mirrors that of MukBEF. We demonstrate that MatP and ParC have an overlapping binding interface on the MukB hinge, leading to their mutually exclusive binding, which occurs with the same dimer to dimer stoichiometry. Furthermore, we show that matS DNA competes with the MukB hinge for MatP binding. Cells expressing MukBEF complexes that are mutated at the ParC/MatP binding interface are impaired in ParC binding and have a mild defect in MukBEF function. These data highlight competitive binding as a means of globally regulating MukBEF-topoisomerase IV activity in space and time.
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Affiliation(s)
- Gemma Lm Fisher
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Jani R Bolla
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom.,The Kavli Institute for Nanoscience Discovery, Oxford, United Kingdom
| | | | - Jarno Mäkelä
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Rachel Baker
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Man Zhou
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Josh P Prince
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Mathew Stracy
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom.,The Kavli Institute for Nanoscience Discovery, Oxford, United Kingdom
| | | | - David J Sherratt
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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13
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Hirsch J, Klostermeier D. What makes a type IIA topoisomerase a gyrase or a Topo IV? Nucleic Acids Res 2021; 49:6027-6042. [PMID: 33905522 PMCID: PMC8216471 DOI: 10.1093/nar/gkab270] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/26/2021] [Accepted: 04/01/2021] [Indexed: 12/14/2022] Open
Abstract
Type IIA topoisomerases catalyze a variety of different reactions: eukaryotic topoisomerase II relaxes DNA in an ATP-dependent reaction, whereas the bacterial representatives gyrase and topoisomerase IV (Topo IV) preferentially introduce negative supercoils into DNA (gyrase) or decatenate DNA (Topo IV). Gyrase and Topo IV perform separate, dedicated tasks during replication: gyrase removes positive supercoils in front, Topo IV removes pre-catenanes behind the replication fork. Despite their well-separated cellular functions, gyrase and Topo IV have an overlapping activity spectrum: gyrase is also able to catalyze DNA decatenation, although less efficiently than Topo IV. The balance between supercoiling and decatenation activities is different for gyrases from different organisms. Both enzymes consist of a conserved topoisomerase core and structurally divergent C-terminal domains (CTDs). Deletion of the entire CTD, mutation of a conserved motif and even by just a single point mutation within the CTD converts gyrase into a Topo IV-like enzyme, implicating the CTDs as the major determinant for function. Here, we summarize the structural and mechanistic features that make a type IIA topoisomerase a gyrase or a Topo IV, and discuss the implications for type IIA topoisomerase evolution.
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Affiliation(s)
- Jana Hirsch
- University of Muenster, Institute for Physical Chemistry, Corrensstrasse 30, 48149 Muenster, Germany
| | - Dagmar Klostermeier
- University of Muenster, Institute for Physical Chemistry, Corrensstrasse 30, 48149 Muenster, Germany
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14
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Vanden Broeck A, Lotz C, Drillien R, Haas L, Bedez C, Lamour V. Structural basis for allosteric regulation of Human Topoisomerase IIα. Nat Commun 2021; 12:2962. [PMID: 34016969 PMCID: PMC8137924 DOI: 10.1038/s41467-021-23136-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 04/15/2021] [Indexed: 12/01/2022] Open
Abstract
The human type IIA topoisomerases (Top2) are essential enzymes that regulate DNA topology and chromosome organization. The Topo IIα isoform is a prime target for antineoplastic compounds used in cancer therapy that form ternary cleavage complexes with the DNA. Despite extensive studies, structural information on this large dimeric assembly is limited to the catalytic domains, hindering the exploration of allosteric mechanism governing the enzyme activities and the contribution of its non-conserved C-terminal domain (CTD). Herein we present cryo-EM structures of the entire human Topo IIα nucleoprotein complex in different conformations solved at subnanometer resolutions (3.6-7.4 Å). Our data unveils the molecular determinants that fine tune the allosteric connections between the ATPase domain and the DNA binding/cleavage domain. Strikingly, the reconstruction of the DNA-binding/cleavage domain uncovers a linker leading to the CTD, which plays a critical role in modulating the enzyme's activities and opens perspective for the analysis of post-translational modifications.
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Affiliation(s)
- Arnaud Vanden Broeck
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Department of Integrated Structural Biology, IGBMC, Illkirch, France
| | - Christophe Lotz
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Department of Integrated Structural Biology, IGBMC, Illkirch, France
| | - Robert Drillien
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Department of Integrated Structural Biology, IGBMC, Illkirch, France
| | - Léa Haas
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Department of Integrated Structural Biology, IGBMC, Illkirch, France
| | - Claire Bedez
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Department of Integrated Structural Biology, IGBMC, Illkirch, France
| | - Valérie Lamour
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.
- Department of Integrated Structural Biology, IGBMC, Illkirch, France.
- Hôpitaux Universitaires de Strasbourg, Strasbourg, France.
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15
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Mazurek Ł, Ghilarov D, Michalczyk E, Pakosz Z, Metelev M, Czyszczoń W, Wawro K, Behroz I, Dubiley S, Süssmuth RD, Heddle JG. Pentapeptide repeat protein QnrB1 requires ATP hydrolysis to rejuvenate poisoned gyrase complexes. Nucleic Acids Res 2021; 49:1581-1596. [PMID: 33434265 PMCID: PMC7897471 DOI: 10.1093/nar/gkaa1266] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/16/2020] [Accepted: 01/06/2021] [Indexed: 11/14/2022] Open
Abstract
DNA gyrase, a type II topoisomerase found predominantly in bacteria, is the target for a variety of 'poisons', namely natural product toxins (e.g. albicidin, microcin B17) and clinically important synthetic molecules (e.g. fluoroquinolones). Resistance to both groups can be mediated by pentapeptide repeat proteins (PRPs). Despite long-term studies, the mechanism of action of these protective PRPs is not known. We show that a PRP, QnrB1 provides specific protection against fluoroquinolones, which strictly requires ATP hydrolysis by gyrase. QnrB1 binds to the GyrB protein and stimulates ATPase activity of the isolated N-terminal ATPase domain of GyrB (GyrB43). We probed the QnrB1 binding site using site-specific incorporation of a photoreactive amino acid and mapped the crosslinks to the GyrB43 protein. We propose a model in which QnrB1 binding allosterically promotes dissociation of the fluoroquinolone molecule from the cleavage complex.
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Affiliation(s)
- Łukasz Mazurek
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Postgraduate School of Molecular Medicine, Warsaw, Poland
| | - Dmitry Ghilarov
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Zuzanna Pakosz
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Postgraduate School of Molecular Medicine, Warsaw, Poland
| | | | - Wojciech Czyszczoń
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Karolina Wawro
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Iraj Behroz
- Institute of Biological Chemistry, Technische Universität Berlin, Berlin, Germany
| | | | - Roderich D Süssmuth
- Institute of Biological Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Jonathan G Heddle
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
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16
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Zhao M, Bai J, Bu X, Tang Y, Han W, Li D, Wang L, Yang Y, Xu Y. Microwave-assisted aqueous two-phase extraction of phenolic compounds from Ribes nigrum L. and its antibacterial effect on foodborne pathogens. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107449] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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17
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Vidovic N, Vidovic S. Antimicrobial Resistance and Food Animals: Influence of Livestock Environment on the Emergence and Dissemination of Antimicrobial Resistance. Antibiotics (Basel) 2020; 9:antibiotics9020052. [PMID: 32023977 PMCID: PMC7168261 DOI: 10.3390/antibiotics9020052] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 01/26/2020] [Accepted: 01/27/2020] [Indexed: 02/07/2023] Open
Abstract
The emergence and dissemination of antimicrobial resistance among human, animal and zoonotic pathogens pose an enormous threat to human health worldwide. The use of antibiotics in human and veterinary medicine, and especially the use of large quantities of antibiotics in livestock for the purpose of growth promotion of food animals is believed to be contributing to the modern trend of the emergence and spread of bacteria with antibiotic resistant traits. To better control the emergence and spread of antimicrobial resistance several countries from Western Europe implemented a ban for antibiotic use in livestock, specifically the use of antibiotics for growth promotion of food animals. This review article summarizes the recent knowledge of molecular acquisition of antimicrobial resistance and the effects of implementation of antibiotic growth promoter bans on the spread of antimicrobial resistant bacteria in animals and humans. In this article, we also discuss the main zoonotic transmission routes of antimicrobial resistance and novel approaches designed to prevent or slow down the emergence and spread of antimicrobial resistance worldwide. Finally, we provide future perspectives associated with the control and management of the emergence and spread of antimicrobial resistant bacteria.
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Affiliation(s)
- Nikola Vidovic
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, SK S7K 4H3, Canada;
| | - Sinisa Vidovic
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108, USA
- Correspondence:
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18
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Hobson MJ, Berger JM. Caught in the Open: A Domain Insertion of M. tuberculosis Gyrase Suppresses ATPase Dimerization. Structure 2019; 27:561-563. [PMID: 30943386 DOI: 10.1016/j.str.2019.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In this issue of Structure, Petrella et al. (2019) determine the structure of a catalytically competent construct of M. tuberculosis gyrase. Surprisingly, both apo and AMPPNP-bound structures capture a previously unknown enzyme state that is stabilized by a domain insertion unique to Corynebacteriales and appears to help regulate ATPase cycling.
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Affiliation(s)
- Matthew J Hobson
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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19
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Petrella S, Capton E, Raynal B, Giffard C, Thureau A, Bonneté F, Alzari PM, Aubry A, Mayer C. Overall Structures of Mycobacterium tuberculosis DNA Gyrase Reveal the Role of a Corynebacteriales GyrB-Specific Insert in ATPase Activity. Structure 2019; 27:579-589.e5. [PMID: 30744994 DOI: 10.1016/j.str.2019.01.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 10/13/2018] [Accepted: 01/14/2019] [Indexed: 01/03/2023]
Abstract
Despite sharing common features, previous studies have shown that gyrases from different species have been modified throughout evolution to modulate their properties. Here, we report two crystal structures of Mycobacterium tuberculosis DNA gyrase, an apo and AMPPNP-bound form at 2.6-Å and 3.3-Å resolution, respectively. These structures provide high-resolution structural data on the quaternary organization and interdomain connections of a gyrase (full-length GyrB-GyrA57)2 thus providing crucial inputs on this essential drug target. Together with small-angle X-ray scattering studies, they revealed an "extremely open" N-gate state, which persists even in the DNA-free gyrase-AMPPNP complex and an unexpected connection between the ATPase and cleavage core domains mediated by two Corynebacteriales-specific motifs, respectively the C-loop and DEEE-loop. We show that the C-loop participates in the stabilization of this open conformation, explaining why this gyrase has a lower ATPase activity. Our results image a conformational state which might be targeted for drug discovery.
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Affiliation(s)
- Stéphanie Petrella
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France; Université Paris Diderot, Sorbonne Paris Cité, 75724 Paris Cedex 15, France.
| | - Estelle Capton
- Sorbonne Université, Centre d'Immunologie et des Maladies Infectieuses-Paris, Cimi-Paris, INSERM U1135, National Reference Center for Mycobacteria, Laboratoire de Bactériologie-Hygiène, AP-HP, Hôpitaux Universitaires Pitié-Salpêtrière - Charles Foix, 75013 Paris, France
| | - Bertrand Raynal
- Plateforme de Biophysique Moléculaire, Institut Pasteur, CNRS UMR 3528, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Clément Giffard
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France; Université Paris Diderot, Sorbonne Paris Cité, 75724 Paris Cedex 15, France
| | - Aurélien Thureau
- Synchrotron SOLEIL, l'Orme des Merisiers, 91410 Saint Aubin, France
| | - Françoise Bonneté
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique, CNRS UMR7099 and Université Paris Didérot, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Pedro M Alzari
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France; Université Paris Diderot, Sorbonne Paris Cité, 75724 Paris Cedex 15, France
| | - Alexandra Aubry
- Sorbonne Université, Centre d'Immunologie et des Maladies Infectieuses-Paris, Cimi-Paris, INSERM U1135, National Reference Center for Mycobacteria, Laboratoire de Bactériologie-Hygiène, AP-HP, Hôpitaux Universitaires Pitié-Salpêtrière - Charles Foix, 75013 Paris, France.
| | - Claudine Mayer
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France; Université Paris Diderot, Sorbonne Paris Cité, 75724 Paris Cedex 15, France
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20
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Rocha-Roa C, Cossio-Pérez R, Molina D, Patiño J, Cardona N. In silico study of Moxifloxacin derivatives with possible antibacterial activity against a resistant form of DNA gyrase from Porphyromonas gingivalis. Arch Oral Biol 2018; 95:30-39. [DOI: 10.1016/j.archoralbio.2018.07.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 07/18/2018] [Accepted: 07/18/2018] [Indexed: 11/24/2022]
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21
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Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate. Nat Commun 2018; 9:3085. [PMID: 30082834 PMCID: PMC6078968 DOI: 10.1038/s41467-018-05406-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 07/05/2018] [Indexed: 12/11/2022] Open
Abstract
Type IIA topoisomerases (Top2s) manipulate the handedness of DNA crossovers by introducing a transient and protein-linked double-strand break in one DNA duplex, termed the DNA-gate, whose opening allows another DNA segment to be transported through to change the DNA topology. Despite the central importance of this gate-opening event to Top2 function, the DNA-gate in all reported structures of Top2-DNA complexes is in the closed state. Here we present the crystal structure of a human Top2 DNA-gate in an open conformation, which not only reveals structural characteristics of its DNA-conducting path, but also uncovers unexpected yet functionally significant conformational changes associated with gate-opening. This structure further implicates Top2’s preference for a left-handed DNA braid and allows the construction of a model representing the initial entry of another DNA duplex into the DNA-gate. Steered molecular dynamics calculations suggests the Top2-catalyzed DNA passage may be achieved by a rocker-switch-type movement of the DNA-gate. Type II DNA topoisomerases (Top2s) direct the passage of one DNA duplex through another, which is important for resolving DNA entanglements. Here the authors combine X-ray crystallography and MD simulations and present the structure of the human Top2 DNA-gate in an open conformation and discuss mechanistic implications.
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22
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Laponogov I, Pan XS, Veselkov DA, Skamrova GB, Umrekar TR, Fisher LM, Sanderson MR. Trapping of the transport-segment DNA by the ATPase domains of a type II topoisomerase. Nat Commun 2018; 9:2579. [PMID: 29968711 PMCID: PMC6030046 DOI: 10.1038/s41467-018-05005-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 05/25/2018] [Indexed: 11/09/2022] Open
Abstract
Type II topoisomerases alter DNA topology to control DNA supercoiling and chromosome segregation and are targets of clinically important anti-infective and anticancer therapeutics. They act as ATP-operated clamps to trap a DNA helix and transport it through a transient break in a second DNA. Here, we present the first X-ray crystal structure solved at 2.83 Å of a closed clamp complete with trapped T-segment DNA obtained by co-crystallizing the ATPase domain of S. pneumoniae topoisomerase IV with a nonhydrolyzable ATP analogue and 14-mer duplex DNA. The ATPase dimer forms a 22 Å protein hole occupied by the kinked DNA bound asymmetrically through positively charged residues lining the hole, and whose mutagenesis impacts the DNA decatenation, DNA relaxation and DNA-dependent ATPase activities of topo IV. These results and a side-bound DNA-ParE structure help explain how the T-segment DNA is captured and transported by a type II topoisomerase, and reveal a new enzyme-DNA interface for drug discovery.
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Affiliation(s)
- Ivan Laponogov
- Randall Centre for Cell and Molecular Biophysics, 3rd Floor New Hunt's House, Faculty of Life Sciences and Medicine, King's College London, London, SE1 1UL, UK.,Molecular and Clinical Sciences Research Institute, St. George's, University of London, Cranmer Terrace, London, SW17 0RE, UK.,Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, London, SW7 2AZ, UK
| | - Xiao-Su Pan
- Molecular and Clinical Sciences Research Institute, St. George's, University of London, Cranmer Terrace, London, SW17 0RE, UK
| | - Dennis A Veselkov
- Randall Centre for Cell and Molecular Biophysics, 3rd Floor New Hunt's House, Faculty of Life Sciences and Medicine, King's College London, London, SE1 1UL, UK
| | - Galyna B Skamrova
- Randall Centre for Cell and Molecular Biophysics, 3rd Floor New Hunt's House, Faculty of Life Sciences and Medicine, King's College London, London, SE1 1UL, UK
| | - Trishant R Umrekar
- Randall Centre for Cell and Molecular Biophysics, 3rd Floor New Hunt's House, Faculty of Life Sciences and Medicine, King's College London, London, SE1 1UL, UK.,The Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, Malet St., London, WC1E 7HX, UK
| | - L Mark Fisher
- Molecular and Clinical Sciences Research Institute, St. George's, University of London, Cranmer Terrace, London, SW17 0RE, UK.
| | - Mark R Sanderson
- Randall Centre for Cell and Molecular Biophysics, 3rd Floor New Hunt's House, Faculty of Life Sciences and Medicine, King's College London, London, SE1 1UL, UK.
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23
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Directed evolution of multiple genomic loci allows the prediction of antibiotic resistance. Proc Natl Acad Sci U S A 2018; 115:E5726-E5735. [PMID: 29871954 PMCID: PMC6016788 DOI: 10.1073/pnas.1801646115] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Antibiotic development is frequently plagued by the rapid emergence of drug resistance. However, assessing the risk of resistance development in the preclinical stage is difficult. Standard laboratory evolution approaches explore only a small fraction of the sequence space and fail to identify exceedingly rare resistance mutations and combinations thereof. Therefore, new rapid and exhaustive methods are needed to accurately assess the potential of resistance evolution and uncover the underlying mutational mechanisms. Here, we introduce directed evolution with random genomic mutations (DIvERGE), a method that allows an up to million-fold increase in mutation rate along the full lengths of multiple predefined loci in a range of bacterial species. In a single day, DIvERGE generated specific mutation combinations, yielding clinically significant resistance against trimethoprim and ciprofloxacin. Many of these mutations have remained previously undetected or provide resistance in a species-specific manner. These results indicate pathogen-specific resistance mechanisms and the necessity of future narrow-spectrum antibacterial treatments. In contrast to prior claims, we detected the rapid emergence of resistance against gepotidacin, a novel antibiotic currently in clinical trials. Based on these properties, DIvERGE could be applicable to identify less resistance-prone antibiotics at an early stage of drug development. Finally, we discuss potential future applications of DIvERGE in synthetic and evolutionary biology.
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24
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Khan A, Miller WR, Arias CA. Mechanisms of antimicrobial resistance among hospital-associated pathogens. Expert Rev Anti Infect Ther 2018; 16:269-287. [PMID: 29617188 DOI: 10.1080/14787210.2018.1456919] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
INTRODUCTION The introduction of antibiotics revolutionized medicine in the 20th-century permitting the treatment of once incurable infections. Widespread use of antibiotics, however, has led to the development of resistant organisms, particularly in the healthcare setting. Today, the clinician is often faced with pathogens carrying a cadre of resistance determinants that severely limit therapeutic options. The genetic plasticity of microbes allows them to adapt to stressors via genetic mutations, acquisition or sharing of genetic material and modulation of genetic expression leading to resistance to virtually any antimicrobial used in clinical practice. Areas covered: This is a comprehensive review that outlines major mechanisms of resistance in the most common hospital-associated pathogens including bacteria and fungi. Expert commentary: Understanding the genetic and biochemical mechanisms of such antimicrobial adaptation is crucial to tackling the rapid spread of resistance, can expose unconventional therapeutic targets to combat multidrug resistant pathogens and lead to more accurate prediction of antimicrobial susceptibility using rapid molecular diagnostics. Clinicians making treatment decisions based on the molecular basis of resistance may design therapeutic strategies that include de-escalation of broad spectrum antimicrobial usage, more focused therapies or combination therapies. These strategies are likely to improve patient outcomes and decrease the risk of resistance in hospital settings.
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Affiliation(s)
- Ayesha Khan
- a Department of Microbiology and Molecular Genetics , University of Texas McGovern Medical School , Houston , Texas , USA.,b Center for Antimicrobial Resistance and Microbial Genomics , University of Texas Health Science Center , Houston , TX , USA
| | - William R Miller
- b Center for Antimicrobial Resistance and Microbial Genomics , University of Texas Health Science Center , Houston , TX , USA.,c Department of Internal Medicine, Division of Infectious Diseases , McGovern Medical School
| | - Cesar A Arias
- a Department of Microbiology and Molecular Genetics , University of Texas McGovern Medical School , Houston , Texas , USA.,b Center for Antimicrobial Resistance and Microbial Genomics , University of Texas Health Science Center , Houston , TX , USA.,c Department of Internal Medicine, Division of Infectious Diseases , McGovern Medical School.,d Molecular Genetics and Antimicrobial Resistance Unit and International Center for Microbial Genomics , Universidad El Bosque , Bogota , Colombia.,e School of Public Health , UTHealth Center for Infectious Diseases , Houston , TX , USA
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25
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Delgado JL, Hsieh CM, Chan NL, Hiasa H. Topoisomerases as anticancer targets. Biochem J 2018; 475:373-398. [PMID: 29363591 PMCID: PMC6110615 DOI: 10.1042/bcj20160583] [Citation(s) in RCA: 264] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 12/14/2017] [Accepted: 12/21/2017] [Indexed: 12/15/2022]
Abstract
Many cancer type-specific anticancer agents have been developed and significant advances have been made toward precision medicine in cancer treatment. However, traditional or nonspecific anticancer drugs are still important for the treatment of many cancer patients whose cancers either do not respond to or have developed resistance to cancer-specific anticancer agents. DNA topoisomerases, especially type IIA topoisomerases, are proved therapeutic targets of anticancer and antibacterial drugs. Clinically successful topoisomerase-targeting anticancer drugs act through topoisomerase poisoning, which leads to replication fork arrest and double-strand break formation. Unfortunately, this unique mode of action is associated with the development of secondary cancers and cardiotoxicity. Structures of topoisomerase-drug-DNA ternary complexes have revealed the exact binding sites and mechanisms of topoisomerase poisons. Recent advances in the field have suggested a possibility of designing isoform-specific human topoisomerase II poisons, which may be developed as safer anticancer drugs. It may also be possible to design catalytic inhibitors of topoisomerases by targeting certain inactive conformations of these enzymes. Furthermore, identification of various new bacterial topoisomerase inhibitors and regulatory proteins may inspire the discovery of novel human topoisomerase inhibitors. Thus, topoisomerases remain as important therapeutic targets of anticancer agents.
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Affiliation(s)
- Justine L Delgado
- Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, 115 S Grand Ave., S321 Pharmacy Building, Iowa City, IA 52242, U.S.A
| | - Chao-Ming Hsieh
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei City 100, Taiwan
| | - Nei-Li Chan
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei City 100, Taiwan
| | - Hiroshi Hiasa
- Department of Pharmacology, University of Minnesota Medical School, 6-120 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455, U.S.A.
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Ubiquitous Nature of Fluoroquinolones: The Oscillation between Antibacterial and Anticancer Activities. Antibiotics (Basel) 2017; 6:antibiotics6040026. [PMID: 29112154 PMCID: PMC5745469 DOI: 10.3390/antibiotics6040026] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 10/26/2017] [Accepted: 11/03/2017] [Indexed: 12/15/2022] Open
Abstract
Fluoroquinolones are synthetic antibacterial agents that stabilize the ternary complex of prokaryotic topoisomerase II enzymes (gyrase and Topo IV), leading to extensive DNA fragmentation and bacteria death. Despite the similar structural folds within the critical regions of prokaryotic and eukaryotic topoisomerases, clinically relevant fluoroquinolones display a remarkable selectivity for prokaryotic topoisomerase II, with excellent safety records in humans. Typical agents that target human topoisomerases (such as etoposide, doxorubicin and mitoxantrone) are associated with significant toxicities and secondary malignancies, whereas clinically relevant fluoroquinolones are not known to exhibit such propensities. Although many fluoroquinolones have been shown to display topoisomerase-independent antiproliferative effects against various human cancer cells, those that are significantly active against eukaryotic topoisomerase show the same DNA damaging properties as other topoisomerase poisons. Empirical models also show that fluoroquinolones mediate some unique immunomodulatory activities of suppressing pro-inflammatory cytokines and super-inducing interleukin-2. This article reviews the extended roles of fluoroquinolones and their prospects as lead for the unmet needs of "small and safe" multimodal-targeting drug scaffolds.
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Molecular insights on analogs of imidazo[1,2-a]pyridine, azaindole, and pyridylurea towards ParE using pharmacophore modeling, molecular docking, and dynamic simulation. Struct Chem 2017. [DOI: 10.1007/s11224-017-0919-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Plasmid-mediated quinolone resistance in Enterobacteriaceae: a systematic review with a focus on Mediterranean countries. Eur J Clin Microbiol Infect Dis 2016; 36:421-435. [PMID: 27889879 DOI: 10.1007/s10096-016-2847-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/14/2016] [Indexed: 10/20/2022]
Abstract
Quinolones are a family of synthetic broad-spectrum antimicrobial drugs. These molecules have been widely prescribed to treat various infectious diseases and have been classified into several generations based on their spectrum of activity. Quinolones inhibit bacterial DNA synthesis by interfering with the action of DNA gyrase and topoisomerase IV. Mutations in the genes encoding these targets are the most common mechanisms of high-level fluoroquinolone resistance. Moreover, three mechanisms for plasmid-mediated quinolone resistance (PMQR) have been discovered since 1998 and include Qnr proteins, the aminoglycoside acetyltransferase AAC(6')-Ib-cr, and plasmid-mediated efflux pumps QepA and OqxAB. Plasmids with these mechanisms often encode additional antimicrobial resistance (extended spectrum beta-lactamases [ESBLs] and plasmidic AmpC [pAmpC] ß-lactamases) and can transfer multidrug resistance. The PMQR determinants are disseminated in Mediterranean countries with prevalence relatively high depending on the sources and the regions, highlighting the necessity of long-term surveillance for the future monitoring of trends in the occurrence of PMQR genes.
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Jaing CJ, McLoughlin KS, Thissen JB, Zemla A, Gardner SN, Vergez LM, Bourguet F, Mabery S, Fofanov VY, Koshinsky H, Jackson PJ. Identification of Genome-Wide Mutations in Ciprofloxacin-Resistant F. tularensis LVS Using Whole Genome Tiling Arrays and Next Generation Sequencing. PLoS One 2016; 11:e0163458. [PMID: 27668749 PMCID: PMC5036845 DOI: 10.1371/journal.pone.0163458] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 09/08/2016] [Indexed: 11/19/2022] Open
Abstract
Francisella tularensis is classified as a Class A bioterrorism agent by the U.S. government due to its high virulence and the ease with which it can be spread as an aerosol. It is a facultative intracellular pathogen and the causative agent of tularemia. Ciprofloxacin (Cipro) is a broad spectrum antibiotic effective against Gram-positive and Gram-negative bacteria. Increased Cipro resistance in pathogenic microbes is of serious concern when considering options for medical treatment of bacterial infections. Identification of genes and loci that are associated with Ciprofloxacin resistance will help advance the understanding of resistance mechanisms and may, in the future, provide better treatment options for patients. It may also provide information for development of assays that can rapidly identify Cipro-resistant isolates of this pathogen. In this study, we selected a large number of F. tularensis live vaccine strain (LVS) isolates that survived in progressively higher Ciprofloxacin concentrations, screened the isolates using a whole genome F. tularensis LVS tiling microarray and Illumina sequencing, and identified both known and novel mutations associated with resistance. Genes containing mutations encode DNA gyrase subunit A, a hypothetical protein, an asparagine synthase, a sugar transamine/perosamine synthetase and others. Structural modeling performed on these proteins provides insights into the potential function of these proteins and how they might contribute to Cipro resistance mechanisms.
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Affiliation(s)
- Crystal J. Jaing
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
- * E-mail:
| | - Kevin S. McLoughlin
- Computations Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | - James B. Thissen
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | - Adam Zemla
- Computations Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | - Shea N. Gardner
- Computations Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | - Lisa M. Vergez
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | - Feliza Bourguet
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | - Shalini Mabery
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | | | | | - Paul J. Jackson
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
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Laponogov I, Pan XS, Veselkov DA, Cirz RT, Wagman A, Moser HE, Fisher LM, Sanderson MR. Exploring the active site of the Streptococcus pneumoniae topoisomerase IV-DNA cleavage complex with novel 7,8-bridged fluoroquinolones. Open Biol 2016; 6:rsob.160157. [PMID: 27655731 PMCID: PMC5043579 DOI: 10.1098/rsob.160157] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 08/26/2016] [Indexed: 12/16/2022] Open
Abstract
As part of a programme of synthesizing and investigating the biological properties of new fluoroquinolone antibacterials and their targeting of topoisomerase IV from Streptococcus pneumoniae, we have solved the X-ray structure of the complexes of two new 7,8-bridged fluoroquinolones (with restricted C7 group rotation favouring tight binding) in complex with the topoisomerase IV from S. pneumoniae and an 18-base-pair DNA binding site—the E-site—found by our DNA mapping studies to bind drug strongly in the presence of topoisomerase IV (Leo et al. 2005 J. Biol. Chem.280, 14 252–14 263, doi:10.1074/jbc.M500156200). Although the degree of antibiotic resistance towards fluoroquinolones is much lower than that of β-lactams and a range of ribosome-bound antibiotics, there is a pressing need to increase the diversity of members of this successful clinically used class of drugs. The quinolone moiety of the new 7,8-bridged agents ACHN-245 and ACHN-454 binds similarly to that of clinafloxocin, levofloxacin, moxifloxacin and trovofloxacin but the cyclic scaffold offers the possibility of chemical modification to produce interactions with other topoisomerase residues at the active site.
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Affiliation(s)
- Ivan Laponogov
- Randall Division of Cell and Molecular Biophysics, King's College, Guy's Campus, London Bridge, London SE1 1UL, UK Molecular and Clinical Sciences Research Institute, St George's, University of London, Cranmer Terrace, London SW17 0RE, UK
| | - Xiao-Su Pan
- Molecular and Clinical Sciences Research Institute, St George's, University of London, Cranmer Terrace, London SW17 0RE, UK
| | - Dennis A Veselkov
- Randall Division of Cell and Molecular Biophysics, King's College, Guy's Campus, London Bridge, London SE1 1UL, UK
| | - Ryan T Cirz
- Achaogen, 7000 Shoreline Ct. No. 371, San Francisco, CA 94080, USA
| | - Allan Wagman
- Achaogen, 7000 Shoreline Ct. No. 371, San Francisco, CA 94080, USA
| | - Heinz E Moser
- Achaogen, 7000 Shoreline Ct. No. 371, San Francisco, CA 94080, USA
| | - L Mark Fisher
- Molecular and Clinical Sciences Research Institute, St George's, University of London, Cranmer Terrace, London SW17 0RE, UK
| | - Mark R Sanderson
- Randall Division of Cell and Molecular Biophysics, King's College, Guy's Campus, London Bridge, London SE1 1UL, UK
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Hooper DC, Jacoby GA. Topoisomerase Inhibitors: Fluoroquinolone Mechanisms of Action and Resistance. Cold Spring Harb Perspect Med 2016; 6:cshperspect.a025320. [PMID: 27449972 DOI: 10.1101/cshperspect.a025320] [Citation(s) in RCA: 255] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Quinolone antimicrobials are widely used in clinical medicine and are the only current class of agents that directly inhibit bacterial DNA synthesis. Quinolones dually target DNA gyrase and topoisomerase IV binding to specific domains and conformations so as to block DNA strand passage catalysis and stabilize DNA-enzyme complexes that block the DNA replication apparatus and generate double breaks in DNA that underlie their bactericidal activity. Resistance has emerged with clinical use of these agents and is common in some bacterial pathogens. Mechanisms of resistance include mutational alterations in drug target affinity and efflux pump expression and acquisition of resistance-conferring genes. Resistance mutations in one or both of the two drug target enzymes are commonly in a localized domain of the GyrA and ParC subunits of gyrase and topoisomerase IV, respectively, and reduce drug binding to the enzyme-DNA complex. Other resistance mutations occur in regulatory genes that control the expression of native efflux pumps localized in the bacterial membrane(s). These pumps have broad substrate profiles that include other antimicrobials as well as quinolones. Mutations of both types can accumulate with selection pressure and produce highly resistant strains. Resistance genes acquired on plasmids confer low-level resistance that promotes the selection of mutational high-level resistance. Plasmid-encoded resistance is because of Qnr proteins that protect the target enzymes from quinolone action, a mutant aminoglycoside-modifying enzyme that also modifies certain quinolones, and mobile efflux pumps. Plasmids with these mechanisms often encode additional antimicrobial resistances and can transfer multidrug resistance that includes quinolones.
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Affiliation(s)
- David C Hooper
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts 02114
| | - George A Jacoby
- Lahey Hospital and Medical Center, Burlington, Massachusetts 01805
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Veselkov DA, Laponogov I, Pan XS, Selvarajah J, Skamrova GB, Branstrom A, Narasimhan J, Prasad JVNV, Fisher LM, Sanderson MR. Structure of a quinolone-stabilized cleavage complex of topoisomerase IV from Klebsiella pneumoniae and comparison with a related Streptococcus pneumoniae complex. Acta Crystallogr D Struct Biol 2016; 72:488-96. [PMID: 27050128 PMCID: PMC4822561 DOI: 10.1107/s2059798316001212] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 01/19/2016] [Indexed: 11/24/2022] Open
Abstract
Klebsiella pneumoniae is a Gram-negative bacterium that is responsible for a range of common infections, including pulmonary pneumonia, bloodstream infections and meningitis. Certain strains of Klebsiella have become highly resistant to antibiotics. Despite the vast amount of research carried out on this class of bacteria, the molecular structure of its topoisomerase IV, a type II topoisomerase essential for catalysing chromosomal segregation, had remained unknown. In this paper, the structure of its DNA-cleavage complex is reported at 3.35 Å resolution. The complex is comprised of ParC breakage-reunion and ParE TOPRIM domains of K. pneumoniae topoisomerase IV with DNA stabilized by levofloxacin, a broad-spectrum fluoroquinolone antimicrobial agent. This complex is compared with a similar complex from Streptococcus pneumoniae, which has recently been solved.
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Affiliation(s)
- Dennis A. Veselkov
- Randall Division of Cell and Molecular Biophysics, King’s College London, 3rd Floor, New Hunt’s House, Guy’s Campus, London SE1 1UL, England
| | - Ivan Laponogov
- Randall Division of Cell and Molecular Biophysics, King’s College London, 3rd Floor, New Hunt’s House, Guy’s Campus, London SE1 1UL, England
- Cardiovascular and Cell Sciences Research Institute, St George’s, University of London, Cranmer Terrace, London SW17 0RE, England
| | - Xiao-Su Pan
- Cardiovascular and Cell Sciences Research Institute, St George’s, University of London, Cranmer Terrace, London SW17 0RE, England
| | - Jogitha Selvarajah
- Cardiovascular and Cell Sciences Research Institute, St George’s, University of London, Cranmer Terrace, London SW17 0RE, England
| | - Galyna B. Skamrova
- Randall Division of Cell and Molecular Biophysics, King’s College London, 3rd Floor, New Hunt’s House, Guy’s Campus, London SE1 1UL, England
| | - Arthur Branstrom
- PTC Therapeutics Inc., 100 Corporate Court, South Plainfield, NJ 07080, USA
| | - Jana Narasimhan
- PTC Therapeutics Inc., 100 Corporate Court, South Plainfield, NJ 07080, USA
| | | | - L. Mark Fisher
- Cardiovascular and Cell Sciences Research Institute, St George’s, University of London, Cranmer Terrace, London SW17 0RE, England
| | - Mark R. Sanderson
- Randall Division of Cell and Molecular Biophysics, King’s College London, 3rd Floor, New Hunt’s House, Guy’s Campus, London SE1 1UL, England
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Bisacchi GS, Hale MR. A "Double-Edged" Scaffold: Antitumor Power within the Antibacterial Quinolone. Curr Med Chem 2016; 23:520-77. [PMID: 26695512 PMCID: PMC4997924 DOI: 10.2174/0929867323666151223095839] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 11/27/2015] [Accepted: 12/22/2015] [Indexed: 12/22/2022]
Abstract
In the late 1980s, reports emerged describing experimental antibacterial quinolones having significant potency against eukaryotic Type II topoisomerases (topo II) and showing cytotoxic activity against tumor cell lines. As a result, several pharmaceutical companies initiated quinolone anticancer programs to explore the potential of this class in comparison to conventional human topo II inhibiting antitumor drugs such as doxorubicin and etoposide. In this review, we present a modern re-evaluation of the anticancer potential of the quinolone class in the context of today's predominantly pathway-based (rather than cytotoxicity-based) oncology drug R&D environment. The quinolone eukaryotic SAR is comprehensively discussed, contrasted with the corresponding prokaryotic data, and merged with recent structural biology information which is now beginning to help explain the basis for that SAR. Quinolone topo II inhibitors appear to be much less susceptible to efflux-mediated resistance, a current limitation of therapy with conventional agents. Recent advances in the biological understanding of human topo II isoforms suggest that significant progress might now be made in overcoming two other treatment-limiting disadvantages of conventional topo II inhibitors, namely cardiotoxicity and drug-induced secondary leukemias. We propose that quinolone class topo II inhibitors could have a useful future therapeutic role due to the continued need for effective topo II drugs in many cancer treatment settings, and due to the recent biological and structural advances which can now provide, for the first time, specific guidance for the design of a new class of inhibitors potentially superior to existing agents.
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Affiliation(s)
- Gregory S Bisacchi
- Syngene International Ltd., Biocon Park, Jigani Link Road, Bangalore 560099, India.
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Mladenović M, Stanković N, Matić S, Stanić S, Mihailović M, Mihailović V, Katanić J, Boroja T, Vuković N. Newly discovered chroman-2,4-diones neutralize the in vivo DNA damage induced by alkylation through the inhibition of Topoisomerase IIα: A story behind the molecular modeling approach. Biochem Pharmacol 2015; 98:243-66. [PMID: 26319574 DOI: 10.1016/j.bcp.2015.08.106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 08/24/2015] [Indexed: 01/09/2023]
Abstract
Eight chroman-2,4-diones, namely 2a-h, previously investigated as anticoagulants, of which 2a and 2f as the most active, were evaluated as in vivo genotoxic agents in Wistar rat livers and kidneys using the comet assay. Compounds 2a, 2b, and 2f without genotoxic activity were applied prior to ethyl methanesulfonate (EMS) and diminished EMS-induced DNA damage according to the total score and percentage of reduction. EMS produce harmful O(6)-ethylguanine lesion which is incorporated in aberrant genotoxic GT and TG pairing after ATP-dependent DNA strand breaks have been catalyzed by rat Topoisomerase IIα (rTopIIα, EC 5.99.1.3). Therefore, the mechanism of 2a, 2b, and 2f antigenotoxic activity was investigated on the enzyme level using molecular docking and molecular dynamics simulations insamuch as it had been determined that compounds do not intercalate DNA but instead inhibit the ATPase activity. Calculations predicted that compounds inhibit ATP hydrolysis before the DNA-EMS cleavage is being catalyzed by rTopIIα, prevent EMS mutagenic and carcinogenic effects, and beside anticoagulant activity can even be applied in the cancer treatment to control the rate of anticancer alkylation drugs.
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Affiliation(s)
- Milan Mladenović
- Kragujevac Center for Computational Biochemistry, Department of Chemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, PO Box 60, 34000 Kragujevac, Serbia.
| | - Nevena Stanković
- Kragujevac Center for Computational Biochemistry, Department of Chemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, PO Box 60, 34000 Kragujevac, Serbia.
| | - Sanja Matić
- Department of Biology and Ecology, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, PO Box 60, 34000 Kragujevac, Serbia.
| | - Snežana Stanić
- Department of Biology and Ecology, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, PO Box 60, 34000 Kragujevac, Serbia.
| | - Mirjana Mihailović
- Department of Molecular Biology, Institute for Biological Research, University of Belgrade, Bulevar Despota Stefana 142, 11000 Belgrade, Serbia.
| | - Vladimir Mihailović
- Bioactive Natural Products Investigation, Department of Chemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, PO Box 60, 34000 Kragujevac, Serbia.
| | - Jelena Katanić
- Bioactive Natural Products Investigation, Department of Chemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, PO Box 60, 34000 Kragujevac, Serbia.
| | - Tatjana Boroja
- Bioactive Natural Products Investigation, Department of Chemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, PO Box 60, 34000 Kragujevac, Serbia.
| | - Nenad Vuković
- Department of Chemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, PO Box 60, 34000 Kragujevac, Serbia.
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Basarab GS, Doig P, Galullo V, Kern G, Kimzey A, Kutschke A, Newman JP, Morningstar M, Mueller J, Otterson L, Vishwanathan K, Zhou F, Gowravaram M. Discovery of Novel DNA Gyrase Inhibiting Spiropyrimidinetriones: Benzisoxazole Fusion with N-Linked Oxazolidinone Substituents Leading to a Clinical Candidate (ETX0914). J Med Chem 2015; 58:6264-82. [PMID: 26158756 DOI: 10.1021/acs.jmedchem.5b00863] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A novel class of bacterial type-II topoisomerase inhibitor displaying a spiropyrimidinetrione architecture fused to a benzisoxazole scaffold shows potent activity against Gram-positive and fastidious Gram-negative bacteria. Here, we describe a series of N-linked oxazolidinone substituents on the benzisoxazole that improve upon the antibacterial activity of initially described compounds of the class, show favorable PK properties, and demonstrate efficacy in an in vivo Staphylococcus aureus infection model. Inhibition of the topoisomerases DNA gyrase and topoisomerase IV from both Gram-positive and a Gram-negative organisms was demonstrated. Compounds showed a clean in vitro toxicity profile, including no genotoxicity and no bone marrow toxicity at the highest evaluated concentrations or other issues that have been problematic for some fluoroquinolones. Compound 1u was identified for advancement into human clinical trials for treatment of uncomplicated gonorrhea based on a variety of beneficial attributes including the potent activity and the favorable safety profile.
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Abstract
Quinolone antimicrobials are synthetic and widely used in clinical medicine. Resistance emerged with clinical use and became common in some bacterial pathogens. Mechanisms of resistance include two categories of mutation and acquisition of resistance-conferring genes. Resistance mutations in one or both of the two drug target enzymes, DNA gyrase and DNA topoisomerase IV, are commonly in a localized domain of the GyrA and ParE subunits of the respective enzymes and reduce drug binding to the enzyme-DNA complex. Other resistance mutations occur in regulatory genes that control the expression of native efflux pumps localized in the bacterial membrane(s). These pumps have broad substrate profiles that include quinolones as well as other antimicrobials, disinfectants, and dyes. Mutations of both types can accumulate with selection pressure and produce highly resistant strains. Resistance genes acquired on plasmids can confer low-level resistance that promotes the selection of mutational high-level resistance. Plasmid-encoded resistance is due to Qnr proteins that protect the target enzymes from quinolone action, one mutant aminoglycoside-modifying enzyme that also modifies certain quinolones, and mobile efflux pumps. Plasmids with these mechanisms often encode additional antimicrobial resistances and can transfer multidrug resistance that includes quinolones. Thus, the bacterial quinolone resistance armamentarium is large.
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Affiliation(s)
- David C Hooper
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - George A Jacoby
- Lahey Hospital and Medical Center, Burlington, Massachusetts.,Harvard Medical School, Boston, Massachusetts
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Huang NL, Lin JH. Recovery of the poisoned topoisomerase II for DNA religation: coordinated motion of the cleavage core revealed with the microsecond atomistic simulation. Nucleic Acids Res 2015; 43:6772-86. [PMID: 26150421 PMCID: PMC4538842 DOI: 10.1093/nar/gkv672] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 06/19/2015] [Indexed: 01/24/2023] Open
Abstract
Type II topoisomerases resolve topological problems of DNA double helices by passing one duplex through the reversible double-stranded break they generated on another duplex. Despite the wealth of information in the cleaving operation, molecular understanding of the enzymatic DNA ligation remains elusive. Topoisomerase poisons are widely used in anti-cancer and anti-bacterial therapy and have been employed to entrap the intermediates of topoisomerase IIβ with religatable DNA substrate. We removed drug molecules from the structure and conducted molecular dynamics simulations to investigate the enzyme-mediated DNA religation. The drug-unbound intermediate displayed transitions toward the resealing-compliant configuration: closing distance between the cleaved DNA termini, B-to-A transformation of the double helix, and restoration of the metal-binding motif. By mapping the contact configurations and the correlated motions between enzyme and DNA, we identified the indispensable role of the linker preceding winged helix domain (WHD) in coordinating the movements of TOPRIM, the nucleotide-binding motifs, and the bound DNA substrate during gate closure. We observed a nearly vectorial transition in the recovery of the enzyme and identified the previously uncharacterized roles of Asn508 and Arg677 in DNA rejoining. Our findings delineate the dynamic mechanism of the DNA religation conducted by type II topoisomerases.
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Affiliation(s)
- Nan-Lan Huang
- Research Center for Applied Sciences, Academia Sinica, Nangang, Taipei 11529, Taiwan
| | - Jung-Hsin Lin
- Research Center for Applied Sciences, Academia Sinica, Nangang, Taipei 11529, Taiwan Institute of Biomedical Sciences, Academia Sinica, Nangang, Taipei 11529, Taiwan School of Pharmacy, National Taiwan University, Taipei 10050, Taiwan
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38
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Insights into the mechanism of inhibition of novel bacterial topoisomerase inhibitors from characterization of resistant mutants of Staphylococcus aureus. Antimicrob Agents Chemother 2015; 59:5278-87. [PMID: 26077256 DOI: 10.1128/aac.00571-15] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 06/09/2015] [Indexed: 11/20/2022] Open
Abstract
The type II topoisomerases DNA gyrase and topoisomerase IV are clinically validated bacterial targets that catalyze the modulation of DNA topology that is vital to DNA replication, repair, and decatenation. Increasing resistance to fluoroquinolones, which trap the topoisomerase-DNA complex, has led to significant efforts in the discovery of novel inhibitors of these targets. AZ6142 is a member of the class of novel bacterial topoisomerase inhibitors (NBTIs) that utilizes a distinct mechanism to trap the protein-DNA complex. AZ6142 has very potent activity against Gram-positive organisms, including Staphylococcus aureus, Streptococcus pneumoniae, and Streptococcus pyogenes. In this study, we determined the frequencies of resistance to AZ6142 and other representative NBTI compounds in S. aureus and S. pneumoniae. The frequencies of selection of resistant mutants at 4× the MIC were 1.7 × 10(-8) for S. aureus and <5.5 × 10(-10) for S. pneumoniae. To improve our understanding of the NBTI mechanism of inhibition, the resistant S. aureus mutants were characterized and 20 unique substitutions in the topoisomerase subunits were identified. Many of these substitutions were located outside the NBTI binding pocket and impact the susceptibility of AZ6142, resulting in a 4- to 32-fold elevation in the MIC over the wild-type parent strain. Data on cross-resistance with other NBTIs and fluoroquinolones enabled the differentiation of scaffold-specific changes from compound-specific variations. Our results suggest that AZ6142 inhibits both type II topoisomerases in S. aureus but that DNA gyrase is the primary target. Further, the genotype of the resistant mutants suggests that domain conformations and DNA interactions may uniquely impact NBTIs compared to fluoroquinolones.
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Bisacchi GS, Manchester JI. A New-Class Antibacterial-Almost. Lessons in Drug Discovery and Development: A Critical Analysis of More than 50 Years of Effort toward ATPase Inhibitors of DNA Gyrase and Topoisomerase IV. ACS Infect Dis 2015; 1:4-41. [PMID: 27620144 DOI: 10.1021/id500013t] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The introduction into clinical practice of an ATPase inhibitor of bacterial DNA gyrase and topoisomerase IV (topo IV) would represent a new-class agent for the treatment of resistant bacterial infections. Novobiocin, the only historical member of this class, established the clinical proof of concept for this novel mechanism during the late 1950s, but its use declined rapidly and it was eventually withdrawn from the market. Despite significant and prolonged effort across the biopharmaceutical industry to develop other agents of this class, novobiocin remains the only ATPase inhibitor of gyrase and topo IV ever to progress beyond Phase I. In this review, we analyze the historical attempts to discover and develop agents within this class and highlight factors that might have hindered those efforts. Within the last 15 years, however, our technical understanding of the molecular details of the inhibition of the gyrase and topo IV ATPases, the factors governing resistance development to such inhibitors, and our knowledge of the physical properties required for robust clinical drug candidates have all matured to the point wherein the industry may now address this mechanism of action with greater confidence. The antibacterial spectrum within this class has recently been extended to begin to include serious Gram negative pathogens such as Pseudomonas aeruginosa, Acinetobacter baumannii, and Klebsiella pneumoniae. In spite of this recent technical progress, adverse economics associated with antibacterial R&D over the last 20 years has diminished industry's ability to commit the resources and perseverance needed to bring new-class agents to launch. Consequently, a number of recent efforts in the ATPase class have been derailed by organizational rather than scientific factors. Nevertheless, within this context we discuss the unique opportunity for the development of ATPase inhibitors of gyrase and topo IV as new-class antibacterial agents with broad spectrum potential.
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Affiliation(s)
- Gregory S. Bisacchi
- AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - John I. Manchester
- AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
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Abstract
DNA topoisomerases are enzymes that control the topology of DNA in all cells. There are two types, I and II, classified according to whether they make transient single- or double-stranded breaks in DNA. Their reactions generally involve the passage of a single- or double-strand segment of DNA through this transient break, stabilized by DNA-protein covalent bonds. All topoisomerases can relax DNA, but DNA gyrase, present in all bacteria, can also introduce supercoils into DNA. Because of their essentiality in all cells and the fact that their reactions proceed via DNA breaks, topoisomerases have become important drug targets; the bacterial enzymes are key targets for antibacterial agents. This article discusses the structure and mechanism of topoisomerases and their roles in the bacterial cell. Targeting of the bacterial topoisomerases by inhibitors, including antibiotics in clinical use, is also discussed.
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Nagano S, Lin TY, Edula JR, Heddle JG. Unique features of apicoplast DNA gyrases from Toxoplasma gondii and Plasmodium falciparum. BMC Bioinformatics 2014; 15:416. [PMID: 25523502 PMCID: PMC4297366 DOI: 10.1186/s12859-014-0416-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 12/10/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND DNA gyrase, an enzyme once thought to be unique to bacteria, is also found in some eukaryotic plastids including the apicoplast of Apicomplexa such as Plasmodium falciparum and Toxoplasma gondii which are important disease-causing organisms. DNA gyrase is an excellent target for antibacterial drugs, yet such antibacterials seem ineffective against Apicomplexa. Characterisation of the apicoplast gyrases would be a useful step towards understanding why this should be so. While purification of active apicoplast gyrase has proved impossible to date, in silico analyses have allowed us to discover differences in the apicoplast proteins. The resulting predicted structural and functional differences will be a first step towards development of apicoplast-gyrase specific inhibitors. RESULTS We have carried out sequence analysis and structural predictions of the enzymes from the two species and find that P. falciparum gyrase lacks a GyrA box, but T. gondii may retain one. All proteins contained signal/transport peptides for localization to the apicoplast but T. gondii Gyrase B protein lacks the expected hydrophobic region. The most significant difference is in the GyrA C-terminal domain: While the cores of the proteins, including DNA binding and cleavage regions are essentially unchanged, both apicoplast gyrase A proteins have C-terminal domains that are significantly larger than bacterial counterparts and are predicted to have different structures. CONCLUSION The apicoplast gyrases differ significantly from bacterial gyrases while retaining similar core domains. T. gondii Gyrase B may have an unusual or inefficient mechanism of localisation to the apicoplast. P.falciparum gyrase, lacks a GyrA box and is therefore likely to be inefficient in DNA supercoiling. The C-terminal domains of both apicoplast Gyrase A proteins diverge significantly from the bacterial proteins. We predict that an additional structural element is present in the C-terminal domain of both apicoplast Gyrase A proteins, including the possibility of a β-pinwheel with a non-canonical number of blades. These differences undoubtedly will affect the DNA supercoiling mechanism and have perhaps evolved to compensate for the lack of Topoisomerase IV in the apicoplast. These data will be useful first step towards further characterisation and development of inhibitors for apicoplast gyrases.
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Affiliation(s)
- Soshichiro Nagano
- Heddle Initiative Research Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Ting-Yu Lin
- Heddle Initiative Research Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Jyotheeswara Reddy Edula
- Heddle Initiative Research Unit, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. .,Current address: Department of Molecular Protozoology, Research Institute for Microbial Diseases (RIMD), Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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Shah S, Heddle JG. Squaring up to DNA: pentapeptide repeat proteins and DNA mimicry. Appl Microbiol Biotechnol 2014; 98:9545-60. [PMID: 25343976 DOI: 10.1007/s00253-014-6151-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 10/08/2014] [Accepted: 10/09/2014] [Indexed: 02/01/2023]
Abstract
Pentapeptide repeats are a class of proteins characterized by the presence of multiple repeating sequences five amino acids in length. The sequences fold into a right-handed β-helix with a roughly square-shaped cross section. Pentapeptide repeat proteins include a number of examples which are thought to function as structural mimics of DNA and act to competitively bind to the type II topoisomerase DNA gyrase, an important antibacterial target. DNA gyrase-targeting pentapeptide repeat proteins can both inhibit DNA gyrase-a potentially useful therapeutic property-and contribute to resistance to quinolone antibacterials (by acting to prevent them forming a lethal complex with the DNA and enzyme). Pentapeptide repeat proteins are therefore of wide interest not only because of their unusual structure, function, and potential as an antibacterial target, but also because knowledge of their mechanism of action may lead to both a greater understanding of the details of DNA gyrase function as well as being a useful template for the design of new DNA gyrase inhibitors. However, many puzzling aspects as to how these DNA mimics function and indeed even their ability to act as DNA mimics itself remains open to question. This review summarizes the current state of knowledge regarding pentapeptide repeat proteins, focusing on those that are thought to mimic DNA, and speculates on potential structure-function relationships which may account for their differing specificities.
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Affiliation(s)
- Shama Shah
- Heddle Initiative Research Unit, RIKEN, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan
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Ehmann DE, Lahiri SD. Novel compounds targeting bacterial DNA topoisomerase/DNA gyrase. Curr Opin Pharmacol 2014; 18:76-83. [PMID: 25271174 DOI: 10.1016/j.coph.2014.09.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 09/12/2014] [Indexed: 02/08/2023]
Abstract
Among the targets for the development of new antibacterial agents, bacterial topoisomerases remain a vibrant area of discovery. A structurally diverse set of inhibitors that bind to the adenosine 5'-triphosphate (ATP) site of type II topoisomerases have been disclosed recently. Seven compounds with this mechanism are highlighted, focusing on antibacterial potency and spectrum, as well as examples of in vivo efficacy against pathogens including Staphylococcus aureus and Mycobacterium tuberculosis. Five compounds from two structural classes are exemplified that are inhibitors that bind to the catalytic site of DNA gyrase and topoisomerase IV. The pharmacokinetic and pharmacodynamic properties of these molecules, derived from in vivo efficacy against Gram-positive and Gram-negative pathogens, define the potential for these agents with broad-spectrum and targeted-spectrum clinical utilities.
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Affiliation(s)
- David E Ehmann
- Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA.
| | - Sushmita D Lahiri
- Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA
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Vos SM, Lyubimov AY, Hershey DM, Schoeffler AJ, Sengupta S, Nagaraja V, Berger JM. Direct control of type IIA topoisomerase activity by a chromosomally encoded regulatory protein. Genes Dev 2014; 28:1485-97. [PMID: 24990966 PMCID: PMC4083091 DOI: 10.1101/gad.241984.114] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Topoisomerases are central regulators of DNA supercoiling; how these enzymes are regulated to suit specific cellular needs is poorly understood. Vos et al. now report the structure of E. coli gyrase, a type IIA topoisomerase bound to an inhibitor, YacG. YacG represses gyrase through steric occlusion of its DNA-binding site. Further studies show that YacG engages two spatially segregated regions associated with small-molecule inhibitor interactions—fluoroquinolone antibiotics and a gyrase agonist. This study thus defines a new mechanism for the protein-based control of topoisomerases. Precise control of supercoiling homeostasis is critical to DNA-dependent processes such as gene expression, replication, and damage response. Topoisomerases are central regulators of DNA supercoiling commonly thought to act independently in the recognition and modulation of chromosome superstructure; however, recent evidence has indicated that cells tightly regulate topoisomerase activity to support chromosome dynamics, transcriptional response, and replicative events. How topoisomerase control is executed and linked to the internal status of a cell is poorly understood. To investigate these connections, we determined the structure of Escherichia coli gyrase, a type IIA topoisomerase bound to YacG, a recently identified chromosomally encoded inhibitor protein. Phylogenetic analyses indicate that YacG is frequently associated with coenzyme A (CoA) production enzymes, linking the protein to metabolism and stress. The structure, along with supporting solution studies, shows that YacG represses gyrase by sterically occluding the principal DNA-binding site of the enzyme. Unexpectedly, YacG acts by both engaging two spatially segregated regions associated with small-molecule inhibitor interactions (fluoroquinolone antibiotics and the newly reported antagonist GSK299423) and remodeling the gyrase holoenzyme into an inactive, ATP-trapped configuration. This study establishes a new mechanism for the protein-based control of topoisomerases, an approach that may be used to alter supercoiling levels for responding to changes in cellular state.
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Affiliation(s)
| | | | - David M Hershey
- Deparment of Plant and Microbial Biology, University of California at Berkeley, Berkeley, California 94720, USA
| | | | - Sugopa Sengupta
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560 012, India
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Redgrave LS, Sutton SB, Webber MA, Piddock LJV. Fluoroquinolone resistance: mechanisms, impact on bacteria, and role in evolutionary success. Trends Microbiol 2014; 22:438-45. [PMID: 24842194 DOI: 10.1016/j.tim.2014.04.007] [Citation(s) in RCA: 584] [Impact Index Per Article: 58.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 04/11/2014] [Accepted: 04/16/2014] [Indexed: 12/12/2022]
Abstract
Quinolone and fluoroquinolone antibiotics are potent, broad-spectrum agents commonly used to treat a range of infections. Resistance to these agents is multifactorial and can be via one or a combination of target-site gene mutations, increased production of multidrug-resistance (MDR) efflux pumps, modifying enzymes, and/or target-protection proteins. Fluoroquinolone-resistant clinical isolates of bacteria have emerged readily and recent data have shown that resistance to this class of antibiotics can have diverse, species-dependent impacts on host-strain fitness. Here we outline the impacts of quinolone-resistance mutations in relation to the fitness and evolutionary success of mutant strains.
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Affiliation(s)
- Liam S Redgrave
- School of Immunity and Infection, Institute of Microbiology and Infection, Biosciences Building, University Road West, University of Birmingham, Birmingham B15 2TT, UK
| | - Sam B Sutton
- School of Immunity and Infection, Institute of Microbiology and Infection, Biosciences Building, University Road West, University of Birmingham, Birmingham B15 2TT, UK
| | - Mark A Webber
- School of Immunity and Infection, Institute of Microbiology and Infection, Biosciences Building, University Road West, University of Birmingham, Birmingham B15 2TT, UK
| | - Laura J V Piddock
- School of Immunity and Infection, Institute of Microbiology and Infection, Biosciences Building, University Road West, University of Birmingham, Birmingham B15 2TT, UK.
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Abstract
The double helical structure of DNA lends itself to topological constraints. Many DNA-based processes alter the topological state of DNA, generating torsional stress, which is efficiently relieved by topoisomerases. Maintaining this topological balance is crucial to cell survival, as excessive torsional strain risks DNA damage. Here, we review the mechanisms that generate and modulate DNA torsion within the cell. In particular, we discuss how transcription-generated torsional stress affects Pol II kinetics and chromatin dynamics, highlighting an emerging role of DNA torsion as a feedback mediator of torsion-generating processes.
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Affiliation(s)
- Sheila S Teves
- Molecular and Cell Biology; University of California, Berkeley; Berkeley, CA USA
| | - Steven Henikoff
- Basic Sciences Division; Fred Hutchinson Cancer Research Center; Seattle, WA USA; Howard Hughes Medical Institute; Seattle, WA USA
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