1
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Riepl D, Gamiz-Hernandez AP, Kovalova T, Król SM, Mader SL, Sjöstrand D, Högbom M, Brzezinski P, Kaila VRI. Long-range charge transfer mechanism of the III 2IV 2 mycobacterial supercomplex. Nat Commun 2024; 15:5276. [PMID: 38902248 PMCID: PMC11189923 DOI: 10.1038/s41467-024-49628-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 06/12/2024] [Indexed: 06/22/2024] Open
Abstract
Aerobic life is powered by membrane-bound redox enzymes that shuttle electrons to oxygen and transfer protons across a biological membrane. Structural studies suggest that these energy-transducing enzymes operate as higher-order supercomplexes, but their functional role remains poorly understood and highly debated. Here we resolve the functional dynamics of the 0.7 MDa III2IV2 obligate supercomplex from Mycobacterium smegmatis, a close relative of M. tuberculosis, the causative agent of tuberculosis. By combining computational, biochemical, and high-resolution (2.3 Å) cryo-electron microscopy experiments, we show how the mycobacterial supercomplex catalyses long-range charge transport from its menaquinol oxidation site to the binuclear active site for oxygen reduction. Our data reveal proton and electron pathways responsible for the charge transfer reactions, mechanistic principles of the quinone catalysis, and how unique molecular adaptations, water molecules, and lipid interactions enable the proton-coupled electron transfer (PCET) reactions. Our combined findings provide a mechanistic blueprint of mycobacterial supercomplexes and a basis for developing drugs against pathogenic bacteria.
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Affiliation(s)
- Daniel Riepl
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Ana P Gamiz-Hernandez
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Terezia Kovalova
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Sylwia M Król
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Sophie L Mader
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Dan Sjöstrand
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden.
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2
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Zheng W, Chai P, Zhu J, Zhang K. High-resolution in situ structures of mammalian respiratory supercomplexes. Nature 2024:10.1038/s41586-024-07488-9. [PMID: 38811722 DOI: 10.1038/s41586-024-07488-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 04/30/2024] [Indexed: 05/31/2024]
Abstract
Mitochondria play a pivotal part in ATP energy production through oxidative phosphorylation, which occurs within the inner membrane through a series of respiratory complexes1-4. Despite extensive in vitro structural studies, determining the atomic details of their molecular mechanisms in physiological states remains a major challenge, primarily because of loss of the native environment during purification. Here we directly image porcine mitochondria using an in situ cryo-electron microscopy approach. This enables us to determine the structures of various high-order assemblies of respiratory supercomplexes in their native states. We identify four main supercomplex organizations: I1III2IV1, I1III2IV2, I2III2IV2 and I2III4IV2, which potentially expand into higher-order arrays on the inner membranes. These diverse supercomplexes are largely formed by 'protein-lipids-protein' interactions, which in turn have a substantial impact on the local geometry of the surrounding membranes. Our in situ structures also capture numerous reactive intermediates within these respiratory supercomplexes, shedding light on the dynamic processes of the ubiquinone/ubiquinol exchange mechanism in complex I and the Q-cycle in complex III. Structural comparison of supercomplexes from mitochondria treated under different conditions indicates a possible correlation between conformational states of complexes I and III, probably in response to environmental changes. By preserving the native membrane environment, our approach enables structural studies of mitochondrial respiratory supercomplexes in reaction at high resolution across multiple scales, from atomic-level details to the broader subcellular context.
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Affiliation(s)
- Wan Zheng
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Pengxin Chai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jiapeng Zhu
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
| | - Kai Zhang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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3
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Li Z, Chai L, Tang Z, Zhu H, Xue P, Sun F, Lin H, Zhou Y, Lin X. Precursor-Directed Biosynthesis of Neoantimycin Derivatives with Selective Cytotoxicity. JOURNAL OF NATURAL PRODUCTS 2024; 87:1376-1383. [PMID: 38662398 DOI: 10.1021/acs.jnatprod.4c00013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
A precursor-directed biosynthesis approach led to the accumulation of seven new neoantimycin derivatives (1-7) from Streptomyces conglobatus RJ2. Structure elucidation was conducted using NMR and HRESIMS analysis, and the absolute configuration was determined by advanced Marfey's method, Mosher's analysis, and ECD analysis. The obtained compounds revealed selective and significant cytotoxicity, specifically against colorectal cancer cells bearing the K-ras mutation, with IC50 values ranging from 40 nM to 3.5 μM.
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Affiliation(s)
- Zhengyuan Li
- Institute of Marine Drugs, Guangxi Key Laboratory of Marine Drugs, Guangxi University of Chinese Medicine, Nanning 530200, People's Republic of China
| | - Ling Chai
- Guangxi Key Laboratory of Traditional Chinese Medicine Quality Standards, Guangxi Institute of Chinese Medicine and Pharmaceutical Science, Nanning 530022, People's Republic of China
| | - Zhenzhou Tang
- Institute of Marine Drugs, Guangxi Key Laboratory of Marine Drugs, Guangxi University of Chinese Medicine, Nanning 530200, People's Republic of China
| | - Hongrui Zhu
- Research Center for Marine Drugs, Department of Pharmacy, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, People's Republic of China
| | - Peiying Xue
- Institute of Marine Drugs, Guangxi Key Laboratory of Marine Drugs, Guangxi University of Chinese Medicine, Nanning 530200, People's Republic of China
| | - Fan Sun
- Research Center for Marine Drugs, Department of Pharmacy, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, People's Republic of China
| | - Houwen Lin
- Research Center for Marine Drugs, Department of Pharmacy, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, People's Republic of China
| | - Yongjun Zhou
- Research Center for Marine Drugs, Department of Pharmacy, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, People's Republic of China
| | - Xiao Lin
- Institute of Marine Drugs, Guangxi Key Laboratory of Marine Drugs, Guangxi University of Chinese Medicine, Nanning 530200, People's Republic of China
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4
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Alfatah M, Lim JJJ, Zhang Y, Naaz A, Cheng TYN, Yogasundaram S, Faidzinn NA, Lin JJ, Eisenhaber B, Eisenhaber F. Uncharacterized yeast gene YBR238C, an effector of TORC1 signaling in a mitochondrial feedback loop, accelerates cellular aging via HAP4- and RMD9-dependent mechanisms. eLife 2024; 12:RP92178. [PMID: 38713053 PMCID: PMC11076046 DOI: 10.7554/elife.92178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024] Open
Abstract
Uncovering the regulators of cellular aging will unravel the complexity of aging biology and identify potential therapeutic interventions to delay the onset and progress of chronic, aging-related diseases. In this work, we systematically compared genesets involved in regulating the lifespan of Saccharomyces cerevisiae (a powerful model organism to study the cellular aging of humans) and those with expression changes under rapamycin treatment. Among the functionally uncharacterized genes in the overlap set, YBR238C stood out as the only one downregulated by rapamycin and with an increased chronological and replicative lifespan upon deletion. We show that YBR238C and its paralog RMD9 oppositely affect mitochondria and aging. YBR238C deletion increases the cellular lifespan by enhancing mitochondrial function. Its overexpression accelerates cellular aging via mitochondrial dysfunction. We find that the phenotypic effect of YBR238C is largely explained by HAP4- and RMD9-dependent mechanisms. Furthermore, we find that genetic- or chemical-based induction of mitochondrial dysfunction increases TORC1 (Target of Rapamycin Complex 1) activity that, subsequently, accelerates cellular aging. Notably, TORC1 inhibition by rapamycin (or deletion of YBR238C) improves the shortened lifespan under these mitochondrial dysfunction conditions in yeast and human cells. The growth of mutant cells (a proxy of TORC1 activity) with enhanced mitochondrial function is sensitive to rapamycin whereas the growth of defective mitochondrial mutants is largely resistant to rapamycin compared to wild type. Our findings demonstrate a feedback loop between TORC1 and mitochondria (the TORC1-MItochondria-TORC1 (TOMITO) signaling process) that regulates cellular aging processes. Hereby, YBR238C is an effector of TORC1 modulating mitochondrial function.
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Affiliation(s)
- Mohammad Alfatah
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Jolyn Jia Jia Lim
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Yizhong Zhang
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Arshia Naaz
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Trishia Yi Ning Cheng
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Sonia Yogasundaram
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Nashrul Afiq Faidzinn
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Jovian Jing Lin
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Birgit Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- LASA – Lausitz Advanced Scientific Applications gGmbHWeißwasserGermany
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- LASA – Lausitz Advanced Scientific Applications gGmbHWeißwasserGermany
- School of Biological Sciences (SBS), Nanyang Technological University (NTU)SingaporeSingapore
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5
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Zheng W, Chai P, Zhu J, Zhang K. High-resolution In-situ Structures of Mammalian Mitochondrial Respiratory Supercomplexes in Reaction within Native Mitochondria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587796. [PMID: 38617346 PMCID: PMC11014577 DOI: 10.1101/2024.04.02.587796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Mitochondria play a pivotal role in ATP energy production through oxidative phosphorylation, which occurs within the inner membrane via a series of respiratory complexes. Despite extensive in-vitro structural studies, revealing the atomic details of their molecular mechanisms in physiological states remains a major challenge, primarily because of the loss of the native environment during purification. Here, we directly image porcine mitochondria using an in-situ cryo-electron microscopy approach. This enables us to determine the structures of various high-order assemblies of respiratory supercomplexes in their native states, achieving up to 1.8-Å local resolution. We identify four major supercomplex organizations: I1III2IV1, I1III2IV2, I2III2IV2, and I2III4IV2, which can potentially expand into higher-order arrays on the inner membranes. The formation of these diverse supercomplexes is largely contributed by 'protein-lipids-protein' interactions, which in turn dramatically impact the local geometry of the surrounding membranes. Our in-situ structures also capture numerous reactive intermediates within these respiratory supercomplexes, shedding light on the dynamic processes of the ubiquinone/ubiquinol exchange mechanism in complex I and the Q-cycle in complex III. By comparing supercomplex structures from mitochondria treated under distinct conditions, we elucidate how conformational changes and ligand binding states interplay between complexes I and III in response to environmental redox alterations. Our approach, by preserving the native membrane environment, enables structural studies of mitochondrial respiratory supercomplexes in reaction at high resolution across multiple scales, spanning from atomic-level details to the broader subcellular context.
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Affiliation(s)
- Wan Zheng
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06511, USA
| | - Pengxin Chai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06511, USA
| | - Jiapeng Zhu
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Kai Zhang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06511, USA
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6
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Garcia MR, Andrade PB, Lefranc F, Gomes NGM. Marine-Derived Leads as Anticancer Candidates by Disrupting Hypoxic Signaling through Hypoxia-Inducible Factors Inhibition. Mar Drugs 2024; 22:143. [PMID: 38667760 PMCID: PMC11051506 DOI: 10.3390/md22040143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
The inadequate vascularization seen in fast-growing solid tumors gives rise to hypoxic areas, fostering specific changes in gene expression that bolster tumor cell survival and metastasis, ultimately leading to unfavorable clinical prognoses across different cancer types. Hypoxia-inducible factors (HIF-1 and HIF-2) emerge as druggable pivotal players orchestrating tumor metastasis and angiogenesis, thus positioning them as prime targets for cancer treatment. A range of HIF inhibitors, notably natural compounds originating from marine organisms, exhibit encouraging anticancer properties, underscoring their significance as promising therapeutic options. Bioprospection of the marine environment is now a well-settled approach to the discovery and development of anticancer agents that might have their medicinal chemistry developed into clinical candidates. However, despite the massive increase in the number of marine natural products classified as 'anticancer leads,' most of which correspond to general cytotoxic agents, and only a few have been characterized regarding their molecular targets and mechanisms of action. The current review presents a critical analysis of inhibitors of HIF-1 and HIF-2 and hypoxia-selective compounds that have been sourced from marine organisms and that might act as new chemotherapeutic candidates or serve as templates for the development of structurally similar derivatives with improved anticancer efficacy.
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Affiliation(s)
- Maria Rita Garcia
- REQUIMTE/LAQV, Laboratório de Farmacognosia, Departamento de Química, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal; (M.R.G.); (P.B.A.)
- 1H-TOXRUN-Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, 4585-116 Gandra, Portugal
- UCIBIO/REQUIMTE, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Paula B. Andrade
- REQUIMTE/LAQV, Laboratório de Farmacognosia, Departamento de Química, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal; (M.R.G.); (P.B.A.)
| | - Florence Lefranc
- Department of Neurosurgery, Hôpital Universitaire de Bruxelles (H.U.B), CUB Hôpital Erasme, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium;
| | - Nelson G. M. Gomes
- REQUIMTE/LAQV, Laboratório de Farmacognosia, Departamento de Química, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal; (M.R.G.); (P.B.A.)
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7
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Dong Y, Li B, Yin MX, Liu Z, Niu Y, Wu QY, Zhu XL, Yang GF. The Interaction Mechanism of Picolinamide Fungicide Targeting on the Cytochrome bc1 Complex and Its Structural Modification. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:3755-3762. [PMID: 38346446 DOI: 10.1021/acs.jafc.3c05982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Picolinamide fungicides, structurally related to UK-2A and antimycin-A, bind into the Qi-site in the bc1 complex. However, the detailed binding mode of picolinamide fungicides remains unknown. In the present study, antimycin-A and UK-2A were selected to study the binding mode of picolinamide inhibitors with four protonation states in the Qi-site by integrating molecular dynamics simulation, molecular docking, and molecular mechanics Generalized Born surface area (MM/GBSA) calculations. Subsequently, a series of new picolinamide derivatives were designed and synthesized to further understand the effects of substituents on the tail phenyl ring. The computational results indicated that the substituted aromatic rings in antimycin-A and UK-2A were the pharmacophore fragments and made the primary contribution when bound to a protein. Compound 9g-hydrolysis formed H-bonds with Hie201 and Ash228 and showed an IC50 value of 6.05 ± 0.24 μM against the porcine bc1 complex. Compound 9c, with a simpler chemical structure, showed higher control effects than florylpicoxamid against cucumber downy mildew and expanded the fungicidal spectrum of picolinamide fungicides. The structural and mechanistic insights obtained from the present study will provide a valuable clue for the future designing of new promising Qi-site inhibitors.
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Affiliation(s)
- Ying Dong
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health of Ministry of Science and Technology, Central China Normal University, Wuhan 430079, People's Republic of China
| | - Bo Li
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health of Ministry of Science and Technology, Central China Normal University, Wuhan 430079, People's Republic of China
| | - Mao-Xue Yin
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health of Ministry of Science and Technology, Central China Normal University, Wuhan 430079, People's Republic of China
| | - Zheng Liu
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health of Ministry of Science and Technology, Central China Normal University, Wuhan 430079, People's Republic of China
| | - Yan Niu
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health of Ministry of Science and Technology, Central China Normal University, Wuhan 430079, People's Republic of China
| | - Qiong-You Wu
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health of Ministry of Science and Technology, Central China Normal University, Wuhan 430079, People's Republic of China
| | - Xiao-Lei Zhu
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health of Ministry of Science and Technology, Central China Normal University, Wuhan 430079, People's Republic of China
| | - Guang-Fu Yang
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health of Ministry of Science and Technology, Central China Normal University, Wuhan 430079, People's Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300071, People's Republic of China
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8
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Miao J, Gao X, Tang Y, Dai T, Liu X. Characteristics of famoxadone-resistant mutants of Phytophthora litchii and their effect on lychee fruit quality. Int J Food Microbiol 2024; 411:110528. [PMID: 38118356 DOI: 10.1016/j.ijfoodmicro.2023.110528] [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: 08/17/2023] [Revised: 12/03/2023] [Accepted: 12/12/2023] [Indexed: 12/22/2023]
Abstract
Lychee downy blight (LDB), a common disease caused by the oomycete Phytophthora litchii, poses a significant threat to both pre- and post-harvest stages, leading to substantial economic losses. Famoxadone, a quinone outside inhibitor fungicide, was registered for controlling LDB in China in 2002. However, limited information is available regarding the risk, mechanism, and impact on lychee fruit quality associated with famoxadone resistance. In this study, we determined the sensitivity of 133 P. litchii isolates to famoxadone, yielding a mean EC50 value of 0.46 ± 0.21 μg/mL. Through fungicide adaption, we derived resistant mutants with M124I and Y131C substitutions in PlCyt b (Cytochrome b in P. litchii) from wild-type isolates. In vitro assessments revealed that the fitness of the resistant mutants was significantly lower compared to the parental isolates. These laboratory findings demonstrate a moderate resistance risk of P. litchii to famoxadone. Molecular docking analyses indicated that the M124I and Y131C alterations disrupted hydrogen bonds and weakened the binding energy between famoxadone and PlCyt b. This indicates that the M124I and Y131C changes do indeed confer famoxadone resistance in P. litchii. Infection caused by famoxadone-resistant mutants exhibited a decreased or comparable impact on the characteristic traits of lychee fruit compared to the sensitive isolate. For future detection of famoxadone-resistant strains, AS-PCR primers were designed based on the M124I substitution.
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Affiliation(s)
- Jianqiang Miao
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi, China
| | - Xuheng Gao
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi, China
| | - Yidong Tang
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi, China
| | - Tan Dai
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi, China.
| | - Xili Liu
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi, China; Department of Plant Pathology, College of Plant Protection, China Agricultural University, 2 Yuanmingyuanxi Road, Beijing 100193, China.
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9
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Gao X, Li W, Wang S, Xie B, Peng Q, Zhang C, Miao J, Dai T, Liu X. Attributes of Cyazofamid-Resistant Phytophthora litchii Mutants and Its Impact on Quality of Litchi Fruits. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:219-229. [PMID: 38131297 DOI: 10.1021/acs.jafc.3c07325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
In this study, we determined the sensitivity of 148 Phytophthora litchii isolates to cyazofamid, yielding a mean EC50 value of 0.0091 ± 0.0028 μg/mL. Through fungicide adaptation, resistant mutants (RMs) carrying the F220L substitution in PlCyt b were derived from wild-type isolates. Notably, these RMs exhibited a lower fitness compared with the parental isolates. Molecular docking analysis further revealed that the F220L change contributed to a decrease in the binding energy between cyazofamid and PlCyt b. The total phenol and flavonoid contents in the litchi pericarp treated with cyazofamid on day 5 were significantly higher than in other treatments. Overall, the laboratory assessment indicated a moderate risk of cyazofamid resistance in P. litchii, but the emergence of the F220L change could lead to a high level of resistance. Thus, cyazofamid represents a promising agrochemical for controlling postharvest litchi downy blight and extending the shelf life of litchi fruits.
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Affiliation(s)
- Xuheng Gao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi China
| | - Wenhao Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi China
| | - Shuai Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi China
| | - Bowen Xie
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi China
| | - Qin Peng
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi China
| | - Can Zhang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, 2 Yuanmingyuanxi Road, Beijing 100193, China
| | - Jianqiang Miao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi China
| | - Tan Dai
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi China
| | - Xili Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi China
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, 2 Yuanmingyuanxi Road, Beijing 100193, China
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10
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González S, Wall RJ, Thomas J, Braillard S, Brunori G, Díaz IC, Cantizani J, Carvalho S, Castañeda Casado P, Chatelain E, Cotillo I, Fiandor JM, Francisco AF, Grimsditch D, Keenan M, Kelly JM, Kessler A, Luise C, Lyon JJ, MacLean L, Marco M, Martin JJ, Martinez MS, Paterson C, Read KD, Santos-Villarejo A, Zuccotto F, Wyllie S, Miles TJ, De Rycker M. Short-course combination treatment for experimental chronic Chagas disease. Sci Transl Med 2023; 15:eadg8105. [PMID: 38091410 PMCID: PMC7615676 DOI: 10.1126/scitranslmed.adg8105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023]
Abstract
Chagas disease, caused by the protozoan parasite Trypanosoma cruzi, affects millions of people in the Americas and across the world, leading to considerable morbidity and mortality. Current treatment options, benznidazole (BNZ) and nifurtimox, offer limited efficacy and often lead to adverse side effects because of long treatment durations. Better treatment options are therefore urgently required. Here, we describe a pyrrolopyrimidine series, identified through phenotypic screening, that offers an opportunity to improve on current treatments. In vitro cell-based washout assays demonstrate that compounds in the series are incapable of killing all parasites; however, combining these pyrrolopyrimidines with a subefficacious dose of BNZ can clear all parasites in vitro after 5 days. These findings were replicated in a clinically predictive in vivo model of chronic Chagas disease, where 5 days of treatment with the combination was sufficient to prevent parasite relapse. Comprehensive mechanism of action studies, supported by ligand-structure modeling, show that compounds from this pyrrolopyrimidine series inhibit the Qi active site of T. cruzi cytochrome b, part of the cytochrome bc1 complex of the electron transport chain. Knowledge of the molecular target enabled a cascade of assays to be assembled to evaluate selectivity over the human cytochrome b homolog. As a result, a highly selective and efficacious lead compound was identified. The combination of our lead compound with BNZ rapidly clears T. cruzi parasites, both in vitro and in vivo, and shows great potential to overcome key issues associated with currently available treatments.
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Affiliation(s)
- Silvia González
- Global Health Medicines R&D, GSK, Tres Cantos, Madrid, Spain
| | - Richard J. Wall
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | - John Thomas
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | | | | | | | - Juan Cantizani
- Global Health Medicines R&D, GSK, Tres Cantos, Madrid, Spain
| | - Sandra Carvalho
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | | | | | - Ignacio Cotillo
- Global Health Medicines R&D, GSK, Tres Cantos, Madrid, Spain
| | - Jose M. Fiandor
- Global Health Medicines R&D, GSK, Tres Cantos, Madrid, Spain
| | | | | | | | - John M. Kelly
- London School for Hygiene and Tropical Medicine, London, UK
| | - Albane Kessler
- Global Health Medicines R&D, GSK, Tres Cantos, Madrid, Spain
| | - Chiara Luise
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | | | - Lorna MacLean
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | - Maria Marco
- Global Health Medicines R&D, GSK, Tres Cantos, Madrid, Spain
| | - J. Julio Martin
- Global Health Medicines R&D, GSK, Tres Cantos, Madrid, Spain
| | | | - Christy Paterson
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | - Kevin D. Read
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | | | - Fabio Zuccotto
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | - Susan Wyllie
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | - Tim J. Miles
- Global Health Medicines R&D, GSK, Tres Cantos, Madrid, Spain
| | - Manu De Rycker
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
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11
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Dumitrescu A, Maxim C, Badea M, Rostas AM, Ciorîță A, Tirsoaga A, Olar R. Decavanadate-Bearing Guanidine Derivatives Developed as Antimicrobial and Antitumor Species. Int J Mol Sci 2023; 24:17137. [PMID: 38138964 PMCID: PMC10742724 DOI: 10.3390/ijms242417137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/29/2023] [Accepted: 12/02/2023] [Indexed: 12/24/2023] Open
Abstract
To obtain biologically active species, a series of decavanadates (Hpbg)4[H2V10O28]·6H2O (1) (Htbg)4[H2V10O28]·6H2O; (2) (Hgnd)2(Hgnu)4[V10O28]; (3) (Hgnu)6[V10O28]·2H2O; and (4) (pbg = 1-phenyl biguanide, tbg = 1-(o-tolyl)biguanide, gnd = guanidine, and gnu = guanylurea) were synthesized and characterized by several spectroscopic techniques (IR, UV-Vis, and EPR) as well as by single crystal X-ray diffraction. Compound (1) crystallizes in space group P-1 while (3) and (4) adopt the same centrosymmetric space group P21/n. The unusual signal identified by EPR spectroscopy was assigned to a charge-transfer π(O)→d(V) process. Both stability in solution and reactivity towards reactive oxygen species (O2- and OH·) were screened through EPR signal modification. All compounds inhibited the development of Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Enterococcus faecalis bacterial strains in a planktonic state at a micromolar level, the most active being compound (3). However, the experiments conducted at a minimal inhibitory concentration (MIC) indicated that the compounds do not disrupt the biofilm produced by these bacterial strains. The cytotoxicity assayed against A375 human melanoma cells and BJ human fibroblasts by testing the viability, lactate dehydrogenase, and nitric oxide levels indicated compound (1) as the most active in tumor cells.
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Affiliation(s)
- Andreea Dumitrescu
- Department of Inorganic and Organic Chemistry, Biochemistry and Catalysis, Faculty of Chemistry, University of Bucharest, 90-92 Panduri Str., District 5, 050663 Bucharest, Romania; (A.D.); (C.M.); (M.B.)
| | - Catalin Maxim
- Department of Inorganic and Organic Chemistry, Biochemistry and Catalysis, Faculty of Chemistry, University of Bucharest, 90-92 Panduri Str., District 5, 050663 Bucharest, Romania; (A.D.); (C.M.); (M.B.)
| | - Mihaela Badea
- Department of Inorganic and Organic Chemistry, Biochemistry and Catalysis, Faculty of Chemistry, University of Bucharest, 90-92 Panduri Str., District 5, 050663 Bucharest, Romania; (A.D.); (C.M.); (M.B.)
| | - Arpad Mihai Rostas
- Department of Physics of Nanostructured Systems, National Institute for Research and Development of Isotopic and Molecular Technologies, 67-103 Donat Str., 400293 Cluj-Napoca, Romania;
| | - Alexandra Ciorîță
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, 5-7 Clinicilor St., 400001 Cluj-Napoca, Romania
| | - Alina Tirsoaga
- Department of Analytical and Physical Chemistry, Faculty of Chemistry, University of Bucharest, 4-12 Regina Elisabeta Av., District 3, 030018 Bucharest, Romania;
| | - Rodica Olar
- Department of Inorganic and Organic Chemistry, Biochemistry and Catalysis, Faculty of Chemistry, University of Bucharest, 90-92 Panduri Str., District 5, 050663 Bucharest, Romania; (A.D.); (C.M.); (M.B.)
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12
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Galvez-Llompart M, Zanni R, Manyes L, Meca G. Elucidating the mechanism of action of mycotoxins through machine learning-driven QSAR models: Focus on lipid peroxidation. Food Chem Toxicol 2023; 182:114120. [PMID: 37944785 DOI: 10.1016/j.fct.2023.114120] [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: 07/28/2023] [Revised: 10/06/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023]
Abstract
Understanding the mechanisms of mycotoxin toxicity is crucial for establishing effective guidelines and preventive strategies. In this study, machine learning models based on quantitative structure-activity relationship (QSAR) were employed to predict the lipid peroxidation activity of mycotoxins. Two different algorithms using Linear Discriminant Analysis (LDA) and Artificial Neural Networks (ANNs) have been trained using a dataset of 70 mycotoxins. The LDA model had an average correct classification rate of 91%, while the ANN model achieved a perfect 100% classification rate. Following an internal validation process, the models were utilized to predict mycotoxins with known lipid peroxidation activity. The machine learning models achieved an 88% correct classification rate for these mycotoxins. Finally, by utilizing classified algorithms, the study aimed to infer the mechanism of action related to lipid peroxidation for 91 unstudied mycotoxins. These models provide a fast, accurate, and cost-effective means to assess the potential toxicity and mechanism of action of mycotoxins. The findings of this study contribute to a comprehensive understanding of mycotoxin toxicology and assist researchers and toxicologists in evaluating health risks associated with mycotoxin exposure and developing appropriate preventive strategies and potential therapeutic interventions to mitigate the effects of mycotoxins.
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Affiliation(s)
- Maria Galvez-Llompart
- Department of Preventive Medicine and Public Health, Food Science, Toxicology and Forensic Medicine, Faculty of Pharmacy, University of Valencia, 46100, Burjassot, Valencia, Spain; Department of Physical Chemistry, University of Valencia, 46100, Burjassot, Valencia, Spain.
| | - Riccardo Zanni
- Department of Physical Chemistry, University of Valencia, 46100, Burjassot, Valencia, Spain
| | - Lara Manyes
- Department of Preventive Medicine and Public Health, Food Science, Toxicology and Forensic Medicine, Faculty of Pharmacy, University of Valencia, 46100, Burjassot, Valencia, Spain
| | - Giuseppe Meca
- Department of Preventive Medicine and Public Health, Food Science, Toxicology and Forensic Medicine, Faculty of Pharmacy, University of Valencia, 46100, Burjassot, Valencia, Spain
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13
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Borek A, Wójcik-Augustyn A, Kuleta P, Ekiert R, Osyczka A. Identification of hydrogen bonding network for proton transfer at the quinol oxidation site of Rhodobacter capsulatus cytochrome bc 1. J Biol Chem 2023; 299:105249. [PMID: 37714464 PMCID: PMC10583091 DOI: 10.1016/j.jbc.2023.105249] [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: 07/14/2023] [Revised: 09/04/2023] [Accepted: 09/08/2023] [Indexed: 09/17/2023] Open
Abstract
Cytochrome bc1 catalyzes electron transfer from quinol (QH2) to cytochrome c in reactions coupled to proton translocation across the energy-conserving membrane. Energetic efficiency of the catalytic cycle is secured by a two-electron and two-proton bifurcation reaction leading to oxidation of QH2 and reduction of the Rieske cluster and heme bL. The proton paths associated with this reaction remain elusive. Here, we used site-directed mutagenesis and quantum mechanical calculations to analyze the contribution of protonable side chains located at the heme bL side of the QH2 oxidation site in Rhodobacter capsulatus cytochrome bc1. We observe that the proton path is effectively switched off when H276 and E295 are simultaneously mutated to the nonprotonable residues in the H276F/E295V double mutant. The two single mutants, H276F or E295V, are less efficient but still transfer protons at functionally relevant rates. Natural selection exposed two single mutations, N279S and M154T, that restored the functional proton transfers in H276F/E295V. Quantum mechanical calculations indicated that H276F/E295V traps the side chain of Y147 in a position distant from QH2, whereas either N279S or M154T induce local changes releasing Y147 from that position. This shortens the distance between the protonable groups of Y147 and D278 and/or increases mobility of the Y147 side chain, which makes Y147 efficient in transferring protons from QH2 toward D278 in H276F/E295V. Overall, our study identified an extended hydrogen bonding network, build up by E295, H276, D278, and Y147, involved in efficient proton removal from QH2 at the heme bL side of QH2 oxidation site.
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Affiliation(s)
- Arkadiusz Borek
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Anna Wójcik-Augustyn
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Patryk Kuleta
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Robert Ekiert
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Artur Osyczka
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland.
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14
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Ikunishi R, Otani R, Masuya T, Shinzawa-Itoh K, Shiba T, Murai M, Miyoshi H. Respiratory complex I in mitochondrial membrane catalyzes oversized ubiquinones. J Biol Chem 2023; 299:105001. [PMID: 37394006 PMCID: PMC10416054 DOI: 10.1016/j.jbc.2023.105001] [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: 05/08/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/04/2023] Open
Abstract
NADH-ubiquinone (UQ) oxidoreductase (complex I) couples electron transfer from NADH to UQ with proton translocation in its membrane part. The UQ reduction step is key to triggering proton translocation. Structural studies have identified a long, narrow, tunnel-like cavity within complex I, through which UQ may access a deep reaction site. To elucidate the physiological relevance of this UQ-accessing tunnel, we previously investigated whether a series of oversized UQs (OS-UQs), whose tail moiety is too large to enter and transit the narrow tunnel, can be catalytically reduced by complex I using the native enzyme in bovine heart submitochondrial particles (SMPs) and the isolated enzyme reconstituted into liposomes. Nevertheless, the physiological relevance remained unclear because some amphiphilic OS-UQs were reduced in SMPs but not in proteoliposomes, and investigation of extremely hydrophobic OS-UQs was not possible in SMPs. To uniformly assess the electron transfer activities of all OS-UQs with the native complex I, here we present a new assay system using SMPs, which were fused with liposomes incorporating OS-UQ and supplemented with a parasitic quinol oxidase to recycle reduced OS-UQ. In this system, all OS-UQs tested were reduced by the native enzyme, and the reduction was coupled with proton translocation. This finding does not support the canonical tunnel model. We propose that the UQ reaction cavity is flexibly open in the native enzyme to allow OS-UQs to access the reaction site, but their access is obstructed in the isolated enzyme as the cavity is altered by detergent-solubilizing from the mitochondrial membrane.
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Affiliation(s)
- Ryo Ikunishi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Ryohei Otani
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Takahiro Masuya
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kyoko Shinzawa-Itoh
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Hyogo, Japan
| | - Tomoo Shiba
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto, Japan
| | - Masatoshi Murai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hideto Miyoshi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
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15
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Mitchell RJ, Gowda AS, Olivelli AG, Huckaba AJ, Parkin S, Unrine JM, Oza V, Blackburn JS, Ladipo F, Heidary DK, Glazer EC. Triarylphosphine-Coordinated Bipyridyl Ru(II) Complexes Induce Mitochondrial Dysfunction. Inorg Chem 2023; 62:10940-10954. [PMID: 37405779 DOI: 10.1021/acs.inorgchem.3c00736] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
While cancer cells rely heavily upon glycolysis to meet their energetic needs, reducing the importance of mitochondrial oxidative respiration processes, more recent studies have shown that their mitochondria still play an active role in the bioenergetics of metastases. This feature, in combination with the regulatory role of mitochondria in cell death, has made this organelle an attractive anticancer target. Here, we report the synthesis and biological characterization of triarylphosphine-containing bipyridyl ruthenium (Ru(II)) compounds and found distinct differences as a function of the substituents on the bipyridine and phosphine ligands. 4,4'-Dimethylbipyridyl-substituted compound 3 exhibited especially high depolarizing capabilities, and this depolarization was selective for the mitochondrial membrane and occurred within minutes of treatment in cancer cells. The Ru(II) complex 3 exhibited an 8-fold increase in depolarized mitochondrial membranes, as determined by flow cytometry, which compares favorably to the 2-fold increase observed by carbonyl cyanide chlorophenylhydrazone (CCCP), a proton ionophore that shuttles protons across membranes, depositing them into the mitochondrial matrix. Fluorination of the triphenylphosphine ligand provided a scaffold that maintained potency against a range of cancer cells but avoided inducing toxicity in zebrafish embryos at higher concentrations, displaying the potential of these Ru(II) compounds for anticancer applications. This study provides essential information regarding the role of ancillary ligands for the anticancer activity of Ru(II) coordination compounds that induce mitochondrial dysfunction.
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Affiliation(s)
- Richard J Mitchell
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington, Kentucky 40506, United States
| | - Anitha S Gowda
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington, Kentucky 40506, United States
| | - Alexander G Olivelli
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington, Kentucky 40506, United States
| | - Aron J Huckaba
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington, Kentucky 40506, United States
| | - Sean Parkin
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington, Kentucky 40506, United States
| | - Jason M Unrine
- Department of Plant and Soil Sciences, University of Kentucky, 1100 S. Limestone Street, Lexington, Kentucky 40546, United States
| | - Viral Oza
- Department of Molecular and Cell Biology, University of Kentucky, 741 S. Limestone Street, Lexington, Kentucky 40536, United States
| | - Jessica S Blackburn
- Department of Molecular and Cell Biology, University of Kentucky, 741 S. Limestone Street, Lexington, Kentucky 40536, United States
| | - Folami Ladipo
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington, Kentucky 40506, United States
| | - David K Heidary
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington, Kentucky 40506, United States
| | - Edith C Glazer
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington, Kentucky 40506, United States
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16
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Abstract
We present a brief review of the mitochondrial respiratory chain with emphasis on complexes I, III and IV, which contribute to the generation of protonmotive force across the inner mitochondrial membrane, and drive the synthesis of ATP by the process called oxidative phosphorylation. The basic structural and functional details of these complexes are discussed. In addition, we briefly review the information on the so-called supercomplexes, aggregates of complexes I-IV, and summarize basic physiological aspects of cell respiration.
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Affiliation(s)
- Mårten Wikström
- HiLife Institute of Biotechnology, University of Helsinki, Biocenter, Viikinkaari, Helsinki, Finland.
| | - Cristina Pecorilla
- Department of Physics, University of Helsinki, Gustaf Hällströmin katu, Helsinki, Finland
| | - Vivek Sharma
- HiLife Institute of Biotechnology, University of Helsinki, Biocenter, Viikinkaari, Helsinki, Finland; Department of Physics, University of Helsinki, Gustaf Hällströmin katu, Helsinki, Finland
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17
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Gao X, Yuan K, Li X, Liao S, Peng Q, Miao J, Liu X. Resistance Risk and Resistance-Related Point Mutations in Target Protein Cyt b of the Quinone Inside Inhibitor Amisulbrom in Phytophthora litchii. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:6552-6560. [PMID: 37071710 DOI: 10.1021/acs.jafc.2c08860] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Amisulbrom is a novel quinone inside inhibitor, which exhibits excellent inhibitory activity against phytopathogenic oomycetes. However, the resistance risk and mechanism of amisulbrom in Phytophthora litchii are rarely reported. In this study, the sensitivity of 147 P. litchii isolates to amisulbrom was determined, with an average EC50 of 0.24 ± 0.11 μg/mL. The fitness of resistant mutants, obtained by fungicide adaption, was significantly lower than that of the parental isolates in vitro. Cross-resistance was detected between amisulbrom and cyazofamid. Amisulbrom could not inhibit the cytochrome bc1 complex activity with H15Y and G30E + F220L point mutations in cytochrome b (Cyt b) in vitro. Molecular docking indicated that the H15Y or G30E point mutation can decrease the binding energy between amisulbrom and P. litchii Cyt b. In conclusion, P. litchii might have a medium resistance risk to amisulbrom, and a novel point mutation H15Y or G30E in Cyt b could cause high amisulbrom resistance in P. litchii.
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Affiliation(s)
- Xuheng Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi, China
| | - Kang Yuan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi, China
| | - Xinyue Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi, China
| | - Shuailin Liao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi, China
| | - Qin Peng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi, China
| | - Jianqiang Miao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi, China
| | - Xili Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, 3 Taicheng Road, Yangling 712100, Shaanxi, China
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, 2 Yuanmingyuanxi Road, Beijing 100193, China
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18
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Usuki Y, Tanaka Y, Morii M, Satoh T. Total synthesis of isoneoantimycin. Org Biomol Chem 2023; 21:2398-2404. [PMID: 36857695 DOI: 10.1039/d3ob00099k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Antimycins are one of the well-known antifungal metabolites produced by Streptomyces bacteria. Neoantimycin and its analogues, the ring-expanded antimycins featuring a 15-membered tetraester ring, have been shown to be effective regulators of the oncogenic proteins GRP78/BiP and K-Ras. Isoneoantimycin was isolated from Streptomyces fradiae IFO12773 (ISP 5063) as a minor metabolite during the fermentation of neoantimycin and is the first reported antibiotic of the antimycin family without the macrolide core. In this study, we explored the total synthesis and stereochemical assignment of isoneoantimycin as an approach to perform structure-activity studies on neoantimycins. Taking the neoantimycin biosynthesis pathway into account, we presumed that the stereochemistry of isoneoantimycin is the same as that of neoantimycin. The synthesis of our target molecule with the (1S,2R,5S,6S,14R,15R,17S) configuration has been achieved by using chiral-pool building blocks. A comparison of the spectroscopic data between the synthetic and natural samples verified our presumption of the stereochemistry of natural isoneoantimycin.
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Affiliation(s)
- Yoshinosuke Usuki
- Department of Chemistry, Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan.
| | - Yuka Tanaka
- Department of Chemistry, Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan.
| | - Miyu Morii
- Department of Chemistry, Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan.
| | - Tetsuya Satoh
- Department of Chemistry, Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan.
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19
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Rosell-Hidalgo A, Moore AL, Ghafourian T. Prediction of drug-induced mitochondrial dysfunction using succinate-cytochrome c reductase activity, QSAR and molecular docking. Toxicology 2023; 485:153412. [PMID: 36584908 DOI: 10.1016/j.tox.2022.153412] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/15/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022]
Abstract
There is increasing evidence that links mitochondrial off-target effects with organ toxicities. For this reason, predictive strategies need to be developed to identify mitochondrial dysfunction early in the drug discovery process. In this study, as a major mechanism of mitochondrial toxicity, first, the inhibitory activity of 35 compounds against succinate-cytochrome c reductase (SCR) was investigated. This in vitro study led to the generation of consistent experimental data for a diverse range of compounds, including pharmaceutical drugs and fungicides. Next, molecular docking and protein-ligand interaction fingerprinting (PLIF) analysis were used to identify significant residues and protein-ligand interactions for the Qo site of complex III and Q site of complex II. Finally, this data was used for the development of QSAR models using a regression-based approach to highlight structural and chemical features that might be responsible for SCR inhibition. The statistically validated QSAR models from this work highlighted the importance of low aqueous solubility, low ionisation, fewer 6-membered rings and shorter hydrocarbon alkane chains in the molecular structure for increased inhibition of SCR, hence mitochondrial toxicity. PLIF analysis highlighted two key residues for inhibitory activity of the Qo site of complex III: His 161 as H-bond acceptor and Pro 270 for arene interactions. Currently, there are limited structure-activity models published in the scientific literature for the prediction of mitochondrial toxicity. We believe this study helps shed light on the chemical space for the inhibition of mitochondrial electron transport chain (ETC).
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Affiliation(s)
- Alicia Rosell-Hidalgo
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, United Kingdom.
| | - Anthony L Moore
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, United Kingdom
| | - Taravat Ghafourian
- NSU College of Pharmacy, 3200 South University Drive, Ft. Lauderdale, FL 33328-2018, USA.
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20
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Cherrad S, Gillet B, Dellinger J, Bellaton L, Roux P, Hernandez C, Steva H, Perrier L, Vacher S, Hughes S. New insights from short and long reads sequencing to explore cytochrome b variants in Plasmopara viticola populations collected from vineyards and related to resistance to complex III inhibitors. PLoS One 2023; 18:e0268385. [PMID: 36656908 PMCID: PMC9851517 DOI: 10.1371/journal.pone.0268385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 12/27/2022] [Indexed: 01/20/2023] Open
Abstract
Downy mildew is caused by Plasmopara viticola, an obligate oomycete plant pathogen, a devasting disease of grapevine. To protect plants from the disease, complex III inhibitors are among the fungicides widely used. They specifically target the mitochondrial cytochrome b (cytb) of the pathogen to block cellular respiration mechanisms. In the French vineyard, P. viticola has developed resistance against a first group of these fungicides, the Quinone outside Inhibitors (QoI), with a single amino acid substitution G143A in its cytb mitochondrial sequence. The use of QoI was limited and another type of fungicide, the Quinone inside Inhibitors, targeting the same gene and highly effective against oomycetes, was used instead. Recently however, less sensitive P. viticola populations were detected after treatments with some inhibitors, in particular ametoctradin and cyazofamid. By isolating single-sporangia P. viticola strains resistant to these fungicides, we characterized new variants in the cytb sequences associated with cyazofamid resistance: a point mutation (L201S) and more strikingly, two insertions (E203-DE-V204, E203-VE-V204). In parallel with the classical tools, pyrosequencing and qPCR, we then benchmarked short and long-reads NGS technologies (Ion Torrent, Illumina, Oxford Nanopore Technologies) to sequence the complete cytb with a view to detecting and assessing the proportion of resistant variants of P. viticola at the scale of a field population. Eighteen populations collected from French vineyard fields in 2020 were analysed: 12 showed a variable proportion of G143A, 11 of E203-DE-V204 and 7 populations of the S34L variant that confers resistance to ametoctradin. Interestingly, the long reads were able to identify variants, including SNPs, with confidence and to detect a small proportion of P. viticola with multiple variants along the same cytb sequence. Overall, NGS appears to be a promising method for assessing fungicide resistance of pathogens linked to cytb modifications at the field population level. This approach could rapidly become a robust decision support tool for resistance management in the future.
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Affiliation(s)
| | - Benjamin Gillet
- Institut de Génomique Fonctionnelle de Lyon (IGFL), CNRS UMR 5242, Ecole Normale Supérieure de Lyon, INRAE USC 1370, Université Claude Bernard Lyon 1, Lyon, France
| | - Julien Dellinger
- Institut de Génomique Fonctionnelle de Lyon (IGFL), CNRS UMR 5242, Ecole Normale Supérieure de Lyon, INRAE USC 1370, Université Claude Bernard Lyon 1, Lyon, France
| | - Lalie Bellaton
- Institut de Génomique Fonctionnelle de Lyon (IGFL), CNRS UMR 5242, Ecole Normale Supérieure de Lyon, INRAE USC 1370, Université Claude Bernard Lyon 1, Lyon, France
| | - Pascale Roux
- Institut de Génomique Fonctionnelle de Lyon (IGFL), CNRS UMR 5242, Ecole Normale Supérieure de Lyon, INRAE USC 1370, Université Claude Bernard Lyon 1, Lyon, France
| | | | | | | | | | - Sandrine Hughes
- Institut de Génomique Fonctionnelle de Lyon (IGFL), CNRS UMR 5242, Ecole Normale Supérieure de Lyon, INRAE USC 1370, Université Claude Bernard Lyon 1, Lyon, France
- * E-mail: (SH); (SC)
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21
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Zivkovic FG, D-T Nielsen C, Schoenebeck F. Access to N-CF 3 Formamides by Reduction of N-CF 3 Carbamoyl Fluorides. Angew Chem Int Ed Engl 2022; 61:e202213829. [PMID: 36308723 PMCID: PMC10099374 DOI: 10.1002/anie.202213829] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Indexed: 11/06/2022]
Abstract
The departure into unknown chemical space is essential for the discovery of new properties and function. We herein report the first synthetic access to N-trifluoromethylated formamides. The method involves the reduction of bench-stable NCF3 carbamoyl fluorides and is characterized by operational simplicity and mildness, tolerating a broad range of functional groups as well as stereocenters. The newly made N-CF3 formamide motif proved to be highly robust and compatible with diverse chemical transformations, underscoring its potential as building block in complex functional molecules.
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Affiliation(s)
- Filip G Zivkovic
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52074, Aachen, Germany
| | - Christian D-T Nielsen
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52074, Aachen, Germany
| | - Franziska Schoenebeck
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52074, Aachen, Germany
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22
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Laboria M, Lozano R. [And for a few mitochondria more: When the use of nanotubes promotes cancer proliferation]. Med Sci (Paris) 2022; 38:960-962. [PMID: 36448906 DOI: 10.1051/medsci/2022142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Affiliation(s)
- Mélanie Laboria
- M2 Infectiologie, Immunité, Vaccinologie et Biomédicaments, université de Tours, 37000 Tours, France
| | - Romain Lozano
- M2 Infectiologie, Immunité, Vaccinologie et Biomédicaments, université de Tours, 37000 Tours, France
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23
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Blanco-Prieto O, Maside C, Àlex Peña, Ibáñez-Príncep J, Bonet S, Yeste M, Rodríguez-Gil JE. The effects of red LED light on pig sperm function rely upon mitochondrial electron chain activity rather than on a PKC-mediated mechanism. Front Cell Dev Biol 2022; 10:930855. [PMID: 36274839 PMCID: PMC9585505 DOI: 10.3389/fcell.2022.930855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 09/12/2022] [Indexed: 12/04/2022] Open
Abstract
While irradiation with red LED light has been reported to modulate sperm function in different mammalian species, the mechanisms underlying their response are poorly understood. This work sought to provide new insights into whether this effect relies on a direct action upon mitochondrial electron chain and/or on PKC-linked mechanisms such as those related to opsins. For this purpose, pig semen was light-stimulated for 1, 5 or 10 min in the presence/absence of antimycin A, an inhibitor of the mitochondrial electron chain, or PKC 20–28® (PKCi), a PKC inhibitor. Antimycin A completely blocked the effects of light at all the performed irradiation patterns. This effect was linked to a complete immobility of sperm, which was accompanied with a significant (p < 0.05) drop in several markers of mitochondrial activity, such as JC-1 staining and O2 consumption rate. Antimycin A, however, did not affect intracellular ATP levels, intramitochondrial calcium, total ROS, superoxides or cytochrome C oxidase (CCO) activity. In the case of PKCi, it did also counteract the effects of light on motility, O2 consumption rate and CCO activity, but not to the same extent than that observed for antimycin A. Finally, the effects observed when sperm were co-incubated with antimycin A and PKCi were similar to those observed with antimycin A alone. In conclusion, red LED light acts on sperm function via a direct effect on mitochondrial electron chain. Additionally, light-activated PKC pathways have a supplementary effect to that observed in the electron chain, thereby modulating sperm parameters such as motility and CCO activity.
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24
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Smith KLM, Swiderska A, Lock MC, Graham L, Iswari W, Choudhary T, Thomas D, Kowash HM, Desforges M, Cottrell EC, Trafford AW, Giussani DA, Galli GLJ. Chronic developmental hypoxia alters mitochondrial oxidative capacity and reactive oxygen species production in the fetal rat heart in a sex-dependent manner. J Pineal Res 2022; 73:e12821. [PMID: 35941749 PMCID: PMC9540814 DOI: 10.1111/jpi.12821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/28/2022] [Accepted: 08/03/2022] [Indexed: 11/29/2022]
Abstract
Insufficient oxygen supply (hypoxia) during fetal development leads to cardiac remodeling and a predisposition to cardiovascular disease in later life. Previous work has shown hypoxia causes oxidative stress in the fetal heart and alters the activity and expression of mitochondrial proteins in a sex-dependent manner. However, the functional effects of these modifications on mitochondrial respiration remain unknown. Furthermore, while maternal antioxidant treatments are emerging as a promising new strategy to protect the hypoxic fetus, whether these treatments convey similar protection to cardiac mitochondria in the male or female fetus has not been investigated. Therefore, using an established rat model, we measured the sex-dependent effects of gestational hypoxia and maternal melatonin treatment on fetal cardiac mitochondrial respiration, reactive oxygen species (ROS) production, and lipid peroxidation. Pregnant Wistar rats were subjected to normoxia or hypoxia (13% oxygen) during gestational days (GDs) 6-20 (term ~22 days) with or without melatonin treatment (5 µg/ml in maternal drinking water). On GD 20, mitochondrial aerobic respiration and H2 O2 production were measured in fetal heart tissue, together with lipid peroxidation and citrate synthase (CS) activity. Gestational hypoxia reduced maternal body weight gain (p < .01) and increased placental weight (p < .05) but had no effect on fetal weight or litter size. Cardiac mitochondria from male but not female fetuses of hypoxic pregnancy had reduced respiratory capacity at Complex II (CII) (p < .05), and an increase in H2 O2 production/O2 consumption (p < .05) without any changes in lipid peroxidation. CS activity was also unchanged in both sexes. Despite maternal melatonin treatment increasing maternal and fetal plasma melatonin concentration (p < .001), melatonin treatment had no effect on any of the mitochondrial parameters investigated. To conclude, we show that gestational hypoxia leads to ROS generation from the mitochondrial electron transport chain and affects fetal cardiac mitochondrial respiration in a sex-dependent manner. We also show that maternal melatonin treatment had no effect on these relationships, which has implications for the development of future therapies for hypoxic pregnancies.
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Affiliation(s)
- Kerri L. M. Smith
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and HealthUniversity of ManchesterManchesterUK
| | - Agnieszka Swiderska
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and HealthUniversity of ManchesterManchesterUK
| | - Mitchell C. Lock
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and HealthUniversity of ManchesterManchesterUK
| | - Lucia Graham
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and HealthUniversity of ManchesterManchesterUK
| | - Wulan Iswari
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and HealthUniversity of ManchesterManchesterUK
| | - Tashi Choudhary
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and HealthUniversity of ManchesterManchesterUK
| | - Donna Thomas
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and HealthUniversity of ManchesterManchesterUK
| | - Hager M. Kowash
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and HealthUniversity of ManchesterManchesterUK
| | - Michelle Desforges
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and HealthUniversity of ManchesterManchesterUK
| | - Elizabeth C. Cottrell
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and HealthUniversity of ManchesterManchesterUK
| | - Andrew W. Trafford
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and HealthUniversity of ManchesterManchesterUK
| | - Dino A. Giussani
- Department of Physiology Development and NeuroscienceUniversity of CambridgeCambridgeUK
| | - Gina L. J. Galli
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and HealthUniversity of ManchesterManchesterUK
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Zhou S, Xue J, Shan J, Hong Y, Zhu W, Nie Z, Zhang Y, Ji N, Luo X, Zhang T, Ma W. Gut-Flora-Dependent Metabolite Trimethylamine-N-Oxide Promotes Atherosclerosis-Associated Inflammation Responses by Indirect ROS Stimulation and Signaling Involving AMPK and SIRT1. Nutrients 2022; 14:nu14163338. [PMID: 36014845 PMCID: PMC9416570 DOI: 10.3390/nu14163338] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 11/29/2022] Open
Abstract
Trimethylamine-N-oxide (TMAO), a gut-microbiota-dependent metabolite after ingesting dietary choline, has been identified as a novel risk factor for atherosclerosis through inducing vascular inflammation. However, the underlying molecular mechanism is poorly understood. Using an in vitro vascular cellular model, we found that the TMAO-induced inflammation responses were correlated with an elevation of ROS levels and downregulation of SIRT1 expression in VSMCs and HUVECs. The overexpression of SIRT1 could abrogate both the stimulation of ROS and inflammation. Further studies revealed that AMPK was also suppressed by TMAO and was a mediator upstream of SIRT1. Activation of AMPK by AICAR could reduce TMAO-induced ROS and inflammation. Moreover, the GSH precursor NAC could attenuate TMAO-induced inflammation. In vivo studies with mice models also showed that choline-induced production of TMAO and the associated glycolipid metabolic changes leading to atherosclerosis could be relieved by NAC and a probiotic LP8198. Collectively, the present study revealed an unrecognized mechanistic link between TMAO and atherosclerosis risk, and probiotics ameliorated TMAO-induced atherosclerosis through affecting the gut microbiota. Consistent with previous studies, our data confirmed that TMAO could stimulate inflammation by modulating cellular ROS levels. However, this was not due to direct cytotoxicity but through complex signaling pathways involving AMPK and SIRT1.
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Affiliation(s)
- Sa Zhou
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Jiamin Xue
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Jingbo Shan
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yingxiang Hong
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Wenkang Zhu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Zhiyan Nie
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yujie Zhang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Nanxi Ji
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Xuegang Luo
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Tongcun Zhang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
- Institute of Biology and Medicine, Wuhan University of Science and Technology, Wuhan 430081, China
| | - Wenjian Ma
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
- Qilu Institute of Technology, Jinan 250200, China
- Correspondence: ; Tel.: +86-131-1619-7160
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26
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Amporndanai K, Pinthong N, O’Neill PM, Hong WD, Amewu RK, Pidathala C, Berry NG, Leung SC, Ward SA, Biagini GA, Hasnain SS, Antonyuk SV. Targeting the Ubiquinol-Reduction (Q i) Site of the Mitochondrial Cytochrome bc1 Complex for the Development of Next Generation Quinolone Antimalarials. BIOLOGY 2022; 11:biology11081109. [PMID: 35892964 PMCID: PMC9330653 DOI: 10.3390/biology11081109] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/11/2022] [Accepted: 07/18/2022] [Indexed: 11/16/2022]
Abstract
Antimalarials targeting the ubiquinol-oxidation (Qo) site of the Plasmodium falciparum bc1 complex, such as atovaquone, have become less effective due to the rapid emergence of resistance linked to point mutations in the Qo site. Recent findings showed a series of 2-aryl quinolones mediate inhibitions of this complex by binding to the ubiquinone-reduction (Qi) site, which offers a potential advantage in circumventing drug resistance. Since it is essential to understand how 2-aryl quinolone lead compounds bind within the Qi site, here we describe the co-crystallization and structure elucidation of the bovine cytochrome bc1 complex with three different antimalarial 4(1H)-quinolone sub-types, including two 2-aryl quinolone derivatives and a 3-aryl quinolone analogue for comparison. Currently, no structural information is available for Plasmodial cytochrome bc1. Our crystallographic studies have enabled comparison of an in-silico homology docking model of P. falciparum with the mammalian's equivalent, enabling an examination of how binding compares for the 2- versus 3-aryl analogues. Based on crystallographic and computational modeling, key differences in human and P. falciparum Qi sites have been mapped that provide new insights that can be exploited for the development of next-generation antimalarials with greater selective inhibitory activity against the parasite bc1 with improved antimalarial properties.
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Affiliation(s)
- Kangsa Amporndanai
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK; (K.A.); (N.P.); (S.S.H.)
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Nattapon Pinthong
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK; (K.A.); (N.P.); (S.S.H.)
- Department of Protozoology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Paul M. O’Neill
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK; (W.D.H.); (R.K.A.); (C.P.); (N.G.B.); (S.C.L.)
- Correspondence: (P.M.O.); (S.V.A.); Tel.: +44-(0)-1517955145 (S.V.A.); +44-(0)-1517943552 (P.M.O.)
| | - W. David Hong
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK; (W.D.H.); (R.K.A.); (C.P.); (N.G.B.); (S.C.L.)
| | - Richard K. Amewu
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK; (W.D.H.); (R.K.A.); (C.P.); (N.G.B.); (S.C.L.)
- Department of Chemistry, School of Physical and Mathematical Sciences, University of Ghana, Accra P.O. Box LG 586, Ghana
| | - Chandrakala Pidathala
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK; (W.D.H.); (R.K.A.); (C.P.); (N.G.B.); (S.C.L.)
- Composite Interceptive Med-Science Laboratories Pvt. Ltd., Bengaluru 60099, Karnataka, India
| | - Neil G. Berry
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK; (W.D.H.); (R.K.A.); (C.P.); (N.G.B.); (S.C.L.)
| | - Suet C. Leung
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK; (W.D.H.); (R.K.A.); (C.P.); (N.G.B.); (S.C.L.)
| | - Stephen A. Ward
- Centre for Drugs and Diagnostics, Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK; (S.A.W.); (G.A.B.)
| | - Giancarlo A. Biagini
- Centre for Drugs and Diagnostics, Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK; (S.A.W.); (G.A.B.)
| | - S. Samar Hasnain
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK; (K.A.); (N.P.); (S.S.H.)
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK; (K.A.); (N.P.); (S.S.H.)
- Correspondence: (P.M.O.); (S.V.A.); Tel.: +44-(0)-1517955145 (S.V.A.); +44-(0)-1517943552 (P.M.O.)
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27
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Young DH, Meunier B, Wang NX. Interaction of picolinamide fungicide primary metabolites UK-2A and CAS-649 with the cytochrome bc 1 complex Qi site: mutation effects and modelling in Saccharomyces cerevisiae. PEST MANAGEMENT SCIENCE 2022; 78:2657-2666. [PMID: 35355395 DOI: 10.1002/ps.6893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/30/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Fenpicoxamid and florylpicoxamid are picolinamide fungicides targeting the Qi site of the cytochrome bc1 complex, via their primary metabolites UK-2A and CAS-649, respectively. We explore binding interactions and resistance mechanisms for picolinamides, antimycin A and ilicicolin H in yeast by testing effects of cytochrome b amino acid changes on fungicide sensitivity and interpreting results using molecular docking. RESULTS Effects of amino acid changes on sensitivity to UK-2A and CAS-649 were similar, with highest resistance associated with exchanges involving G37 and substitutions N31K and L198F. These changes, as well as K228M, also affected antimycin A, while ilicicolin H was affected by changes at G37 and L198, as well as Q22E. N31 substitution patterns suggest that a lysine at position 31 introduces an electrostatic interaction with neighbouring D229, causing disruption of a key salt-bridge interaction with picolinamides. Changes involving G37 and L198 imply resistance primarily through steric interference. G37 changes also showed differences between CAS-649 and UK-2A or antimycin A with respect to branched versus unbranched amino acids. N31K and substitution of G37 by large amino acids reduced growth rate substantially while L198 substitutions showed little effect on growth. CONCLUSION Binding of UK-2A and CAS-649 at the Qi site involves similar interactions such that general cross-resistance between fenpicoxamid and florylpicoxamid is anticipated in target pathogens. Some resistance mutations reduced growth rate and could carry a fitness penalty in pathogens. However, certain changes involving G37 and L198 carry little or no growth penalty and may pose the greatest risk for resistance development in the field. © 2022 Society of Chemical Industry.
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Affiliation(s)
- David H Young
- Crop Protection Discovery and Development, Corteva Agriscience, Indianapolis, IN, USA
| | - Brigitte Meunier
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Nick X Wang
- Crop Protection Discovery and Development, Corteva Agriscience, Indianapolis, IN, USA
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Quinone binding sites of cyt bc complexes analysed by X-ray crystallography and cryogenic electron microscopy. Biochem Soc Trans 2022; 50:877-893. [PMID: 35356963 PMCID: PMC9162462 DOI: 10.1042/bst20190963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/06/2022] [Accepted: 03/11/2022] [Indexed: 11/17/2022]
Abstract
Cytochrome (cyt) bc1, bcc and b6f complexes, collectively referred to as cyt bc complexes, are homologous isoprenoid quinol oxidising enzymes present in diverse phylogenetic lineages. Cyt bc1 and bcc complexes are constituents of the electron transport chain (ETC) of cellular respiration, and cyt b6f complex is a component of the photosynthetic ETC. Cyt bc complexes share in general the same Mitchellian Q cycle mechanism, with which they accomplish proton translocation and thus contribute to the generation of proton motive force which drives ATP synthesis. They therefore require a quinol oxidation (Qo) and a quinone reduction (Qi) site. Yet, cyt bc complexes evolved to adapt to specific electrochemical properties of different quinone species and exhibit structural diversity. This review summarises structural information on native quinones and quinone-like inhibitors bound in cyt bc complexes resolved by X-ray crystallography and cryo-EM structures. Although the Qi site architecture of cyt bc1 complex and cyt bcc complex differs considerably, quinone molecules were resolved at the respective Qi sites in very similar distance to haem bH. In contrast, more diverse positions of native quinone molecules were resolved at Qo sites, suggesting multiple quinone binding positions or captured snapshots of trajectories toward the catalytic site. A wide spectrum of inhibitors resolved at Qo or Qi site covers fungicides, antimalarial and antituberculosis medications and drug candidates. The impact of these structures for characterising the Q cycle mechanism, as well as their relevance for the development of medications and agrochemicals are discussed.
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29
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Song X, Jiang Z, Li J, Lu X, Han Q, Zhu K, Li H, Ling Y, Duan H. Synthesis, antifungal activity, and molecular dynamics study of novel geranyl aromatic sulfonamide compounds as potential complex III inhibitors. Med Chem Res 2022. [DOI: 10.1007/s00044-022-02864-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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30
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Karki P, Angardi V, Mier JC, Orman MA. A Transient Metabolic State in Melanoma Persister Cells Mediated by Chemotherapeutic Treatments. Front Mol Biosci 2022; 8:780192. [PMID: 35155562 PMCID: PMC8829428 DOI: 10.3389/fmolb.2021.780192] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 12/29/2021] [Indexed: 11/16/2022] Open
Abstract
Persistence is a transient state that poses an important health concern in cancer therapy. The mechanisms associated with persister phenotypes are highly diverse and complex, and many aspects of persister cell physiology remain to be explored. We applied a melanoma cell line and panel of chemotherapeutic agents to show that melanoma persister cells are not necessarily preexisting dormant cells; in fact, they may be induced by cancer chemotherapeutics. Our metabolomics analysis and phenotype microarray assays further demonstrated a transient upregulation in Krebs cycle metabolism in persister cells. We also verified that targeting electron transport chain activity can significantly reduce melanoma persister levels. The reported metabolic remodeling feature seems to be a conserved characteristic of melanoma persistence, as it has been observed in various melanoma persister subpopulations derived from a diverse range of chemotherapeutics. Elucidating a global metabolic mechanism that contributes to persister survival and reversible switching will ultimately foster the development of novel cancer therapeutic strategies.
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31
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Electron transfer via cytochrome b6f complex displays sensitivity to Antimycin A upon STT7 kinase activation. Biochem J 2022; 479:111-127. [PMID: 34981811 DOI: 10.1042/bcj20210802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/23/2021] [Accepted: 01/04/2022] [Indexed: 11/17/2022]
Abstract
The cytochrome b6f complex (b6f) has been initially considered as the ferredoxin-plastoquinone reductase (FQR) during cyclic electron flow (CEF) with photosystem I that is inhibited by antimycin A (AA). The binding of AA to the b6f Qi-site is aggravated by heme-ci, which challenged the FQR function of b6f during CEF. Alternative models suggest that PROTON GRADIENT REGULATION5 (PGR5) is involved in a b6f-independent, AA-sensitive FQR. Here, we show in Chlamydomonas reinhardtii that the b6f is conditionally inhibited by AA in vivo and that the inhibition did not require PGR5. Instead, activation of the STT7 kinase upon anaerobic treatment induced the AA sensitivity of b6f which was absent in stt7-1. However, a lock in State 2 due to persisting phosphorylation in the phosphatase double mutant pph1;pbcp did not increase AA sensitivity of electron transfer. The latter required a redox poise, supporting the view that state transitions and CEF are not coercively coupled. This suggests that the b6f-interacting kinase is required for structure-function modulation of the Qi-site under CEF favoring conditions. We propose that PGR5 and STT7 independently sustain AA-sensitive FQR activity of the b6f. Accordingly, PGR5-mediated electron injection into an STT7-modulated Qi-site drives a Mitchellian Q cycle in CEF conditions.
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Dual targeting of the DNA damage response pathway and BCL-2 in diffuse large B-cell lymphoma. Leukemia 2022; 36:197-209. [PMID: 34304248 PMCID: PMC8727301 DOI: 10.1038/s41375-021-01347-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 06/28/2021] [Accepted: 07/08/2021] [Indexed: 02/07/2023]
Abstract
Standard chemotherapies for diffuse large B-cell lymphoma (DLBCL), based on the induction of exogenous DNA damage and oxidative stress, are often less effective in the presence of increased MYC and BCL-2 levels, especially in the case of double hit (DH) lymphomas harboring rearrangements of the MYC and BCL-2 oncogenes, which enrich for a patient's population characterized by refractoriness to anthracycline-based chemotherapy. Here we hypothesized that adaptive mechanisms to MYC-induced replicative and oxidative stress, consisting in DNA damage response (DDR) activation and BCL-2 overexpression, could represent the biologic basis of the poor prognosis and chemoresistance observed in MYC/BCL-2-positive lymphoma. We first integrated targeted gene expression profiling (T-GEP), fluorescence in situ hybridization (FISH) analysis, and characterization of replicative and oxidative stress biomarkers in two independent DLBCL cohorts. The presence of oxidative DNA damage biomarkers identified a poor prognosis double expresser (DE)-DLBCL subset, characterized by relatively higher BCL-2 gene expression levels and enrichment for DH lymphomas. Based on these findings, we tested therapeutic strategies based on combined DDR and BCL-2 inhibition, confirming efficacy and synergistic interactions in in vitro and in vivo DH-DLBCL models. These data provide the rationale for precision-therapy strategies based on combined DDR and BCL-2 inhibition in DH or DE-DLBCL.
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33
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Kumar R, Jafri MS. Computational Modeling of Mitochondria to Understand the Dynamics of Oxidative Stress. Methods Mol Biol 2022; 2497:363-422. [PMID: 35771458 PMCID: PMC9811848 DOI: 10.1007/978-1-0716-2309-1_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Mitochondria are complex organelles that use catabolic metabolism to produce ATP which is the critical energy source for cell function. Oxidative phosphorylation by the electron transport chain, which receives reducing equivalents (NADH and FADH2) from the tricarboxylic acid cycle, also produces reactive oxygen species (ROS) as a by-product at complex I and III. ROS play a significant role in health and disease. In order to better understand this process, a computational model of mitochondrial energy metabolism and the production of ROS has been developed. The model demonstrates the process regulating ROS production and removal and how different energy substrates can affect ROS production.
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Affiliation(s)
- Rashmi Kumar
- School of Systems Biology, George Mason University, Fairfax, VA, USA
| | - Mohsin S Jafri
- School of Systems Biology, George Mason University, Fairfax, VA, USA.
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, USA.
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34
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35
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Golubewa L, Kulahava T, Timoshchenko I, Shuba M, Svirko Y, Kuzhir P. Rapid and delayed effects of single-walled carbon nanotubes in glioma cells. NANOTECHNOLOGY 2021; 32:505103. [PMID: 34547739 DOI: 10.1088/1361-6528/ac28da] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
Single-walled carbon nanotubes (SWCNTs) demonstrate a strong potential as an optically activated theranostic nano-agent. However, using SWCNTs in theranostics still requires revealing mechanisms of the SWCNT-mediated effects on cellular functions. Even though rapid and delayed cellular responses can differ significantly and may lead to undesirable consequences, understanding of these mechanisms is still incomplete. We demonstrate that introducing short (150-250 nm) SWCNTs into C6 rat glioma cells leads to SWCNT-driven effects that show pronounced time dependence. Accumulation of SWCNTs is carried out due to endocytosis with modification of the actin cytoskeleton but not accompanied with autophagy. Its initial stage launches a rapid cellular response via significantly heightened mitochondrial membrane potential and superoxide anion radical production, satisfying the cell demand of energy for SWCNT transfer inside the cytoplasm. In the long term, SWCNTs agglomerate to micron-sized structures surrounded by highly active mitochondria having parameters return to control values. SWCNTs postponed effects are also manifested themselves in the suppression of the cell proliferative activity with further restoration after five passages. These results demonstrate relative cellular inertness and safety of SWCNTs eliminating possible side effects caused by optically activated theranostic applications.
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Affiliation(s)
- Lena Golubewa
- Department of Molecular Compounds Physics, State Research Institute Center for Physical Sciences and Technology, Saulėtekio av. 3, Vilnius, 10257, Lithuania
- Laboratory of Nanoelectromagnetics, Institute for Nuclear Problems of Belarusian State University, Bobruiskaya str. 11, Minsk, 220006, Belarus
| | - Tatsiana Kulahava
- Laboratory of Nanoelectromagnetics, Institute for Nuclear Problems of Belarusian State University, Bobruiskaya str. 11, Minsk, 220006, Belarus
| | - Igor Timoshchenko
- Laboratory of Nanoelectromagnetics, Institute for Nuclear Problems of Belarusian State University, Bobruiskaya str. 11, Minsk, 220006, Belarus
- Department of Computer Modelling, Physics Faculty, Belarusian State University, Bobruiskaya str. 5, Minsk, 220030, Belarus
| | - Mikhail Shuba
- Laboratory of Nanoelectromagnetics, Institute for Nuclear Problems of Belarusian State University, Bobruiskaya str. 11, Minsk, 220006, Belarus
| | - Yuri Svirko
- Institute of Photonics, Department of Physics and Mathematics, University of Eastern Finland, Yliopistokatu 7, Joensuu, FI-80101, Finland
| | - Polina Kuzhir
- Laboratory of Nanoelectromagnetics, Institute for Nuclear Problems of Belarusian State University, Bobruiskaya str. 11, Minsk, 220006, Belarus
- Institute of Photonics, Department of Physics and Mathematics, University of Eastern Finland, Yliopistokatu 7, Joensuu, FI-80101, Finland
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36
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Yanofsky DJ, Di Trani JM, Król S, Abdelaziz R, Bueler SA, Imming P, Brzezinski P, Rubinstein JL. Structure of mycobacterial CIII 2CIV 2 respiratory supercomplex bound to the tuberculosis drug candidate telacebec (Q203). eLife 2021; 10:e71959. [PMID: 34590581 PMCID: PMC8523172 DOI: 10.7554/elife.71959] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/29/2021] [Indexed: 12/19/2022] Open
Abstract
The imidazopyridine telacebec, also known as Q203, is one of only a few new classes of compounds in more than 50 years with demonstrated antituberculosis activity in humans. Telacebec inhibits the mycobacterial respiratory supercomplex composed of complexes III and IV (CIII2CIV2). In mycobacterial electron transport chains, CIII2CIV2 replaces canonical CIII and CIV, transferring electrons from the intermediate carrier menaquinol to the final acceptor, molecular oxygen, while simultaneously transferring protons across the inner membrane to power ATP synthesis. We show that telacebec inhibits the menaquinol:oxygen oxidoreductase activity of purified Mycobacterium smegmatis CIII2CIV2 at concentrations similar to those needed to inhibit electron transfer in mycobacterial membranes and Mycobacterium tuberculosis growth in culture. We then used electron cryomicroscopy (cryoEM) to determine structures of CIII2CIV2 both in the presence and absence of telacebec. The structures suggest that telacebec prevents menaquinol oxidation by blocking two different menaquinol binding modes to prevent CIII2CIV2 activity.
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Affiliation(s)
- David J Yanofsky
- Molecular Medicine Program, The Hospital for Sick ChildrenTorontoCanada
- Department of Medical Biophysics, The University of TorontoTorontoCanada
| | - Justin M Di Trani
- Molecular Medicine Program, The Hospital for Sick ChildrenTorontoCanada
| | - Sylwia Król
- Department of Biochemistry and Biophysics, Stockholm UniversityStockholmSweden
| | - Rana Abdelaziz
- Department of Pharmaceutical/Medicinal Chemistry and Clinical Pharmacy, Martin-Luther-Universitaet Halle-WittenbergHalle (Saale)Germany
| | | | - Peter Imming
- Department of Pharmaceutical/Medicinal Chemistry and Clinical Pharmacy, Martin-Luther-Universitaet Halle-WittenbergHalle (Saale)Germany
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, Stockholm UniversityStockholmSweden
| | - John L Rubinstein
- Molecular Medicine Program, The Hospital for Sick ChildrenTorontoCanada
- Department of Medical Biophysics, The University of TorontoTorontoCanada
- Department of Biochemistry, The University of TorontoTorontoCanada
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37
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Koumpoura CL, Robert A, Athanassopoulos CM, Baltas M. Antimalarial Inhibitors Targeting Epigenetics or Mitochondria in Plasmodium falciparum: Recent Survey upon Synthesis and Biological Evaluation of Potential Drugs against Malaria. Molecules 2021; 26:molecules26185711. [PMID: 34577183 PMCID: PMC8467436 DOI: 10.3390/molecules26185711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 12/01/2022] Open
Abstract
Despite many efforts, malaria remains among the most problematic infectious diseases worldwide, mainly due to the development of drug resistance by P. falciparum. Over the past decade, new essential pathways have been emerged to fight against malaria. Among them, epigenetic processes and mitochondrial metabolism appear to be important targets. This review will focus on recent evolutions concerning worldwide efforts to conceive, synthesize and evaluate new drug candidates interfering selectively and efficiently with these two targets and pathways. The focus will be on compounds/scaffolds that possess biological/pharmacophoric properties on DNA methyltransferases and HDAC’s for epigenetics, and on cytochrome bc1 and dihydroorotate dehydrogenase for mitochondrion.
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Affiliation(s)
- Christina L. Koumpoura
- CNRS, LCC (Laboratoire de Chimie de Coordination), Université de Toulouse, UPS, INPT, Inserm ERL 1289, 205 Route de Narbonne, BP 44099, CEDEX 4, F-31077 Toulouse, France; (C.L.K.); (A.R.)
| | - Anne Robert
- CNRS, LCC (Laboratoire de Chimie de Coordination), Université de Toulouse, UPS, INPT, Inserm ERL 1289, 205 Route de Narbonne, BP 44099, CEDEX 4, F-31077 Toulouse, France; (C.L.K.); (A.R.)
| | | | - Michel Baltas
- CNRS, LCC (Laboratoire de Chimie de Coordination), Université de Toulouse, UPS, INPT, Inserm ERL 1289, 205 Route de Narbonne, BP 44099, CEDEX 4, F-31077 Toulouse, France; (C.L.K.); (A.R.)
- Correspondence:
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38
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Di Trani JM, Liu Z, Whitesell L, Brzezinski P, Cowen LE, Rubinstein JL. Rieske head domain dynamics and indazole-derivative inhibition of Candida albicans complex III. Structure 2021; 30:129-138.e4. [PMID: 34525326 DOI: 10.1016/j.str.2021.08.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/06/2021] [Accepted: 08/17/2021] [Indexed: 11/26/2022]
Abstract
Electron transfer between respiratory complexes drives transmembrane proton translocation, which powers ATP synthesis and membrane transport. The homodimeric respiratory complex III (CIII2) oxidizes ubiquinol to ubiquinone, transferring electrons to cytochrome c and translocating protons through a mechanism known as the Q cycle. The Q cycle involves ubiquinol oxidation and ubiquinone reduction at two different sites within each CIII monomer, as well as movement of the head domain of the Rieske subunit. We determined structures of Candida albicans CIII2 by cryoelectron microscopy (cryo-EM), revealing endogenous ubiquinone and visualizing the continuum of Rieske head domain conformations. Analysis of these conformations does not indicate cooperativity in the Rieske head domain position or ligand binding in the two CIIIs of the CIII2 dimer. Cryo-EM with the indazole derivative Inz-5, which inhibits fungal CIII2 and is fungicidal when administered with fungistatic azole drugs, showed that Inz-5 inhibition alters the equilibrium of Rieske head domain positions.
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Affiliation(s)
- Justin M Di Trani
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Zhongle Liu
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Luke Whitesell
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Science, Stockholm University, Stockholm, Sweden.
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
| | - John L Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
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39
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Bacle A, Buslaev P, Garcia-Fandino R, Favela-Rosales F, Mendes Ferreira T, Fuchs PFJ, Gushchin I, Javanainen M, Kiirikki AM, Madsen JJ, Melcr J, Milán Rodríguez P, Miettinen MS, Ollila OHS, Papadopoulos CG, Peón A, Piggot TJ, Piñeiro Á, Virtanen SI. Inverse Conformational Selection in Lipid-Protein Binding. J Am Chem Soc 2021; 143:13701-13709. [PMID: 34465095 DOI: 10.1021/jacs.1c05549] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Interest in lipid interactions with proteins and other biomolecules is emerging not only in fundamental biochemistry but also in the field of nanobiotechnology where lipids are commonly used, for example, in carriers of mRNA vaccines. The outward-facing components of cellular membranes and lipid nanoparticles, the lipid headgroups, regulate membrane interactions with approaching substances, such as proteins, drugs, RNA, or viruses. Because lipid headgroup conformational ensembles have not been experimentally determined in physiologically relevant conditions, an essential question about their interactions with other biomolecules remains unanswered: Do headgroups exchange between a few rigid structures, or fluctuate freely across a practically continuous spectrum of conformations? Here, we combine solid-state NMR experiments and molecular dynamics simulations from the NMRlipids Project to resolve the conformational ensembles of headgroups of four key lipid types in various biologically relevant conditions. We find that lipid headgroups sample a wide range of overlapping conformations in both neutral and charged cellular membranes, and that differences in the headgroup chemistry manifest only in probability distributions of conformations. Furthermore, the analysis of 894 protein-bound lipid structures from the Protein Data Bank suggests that lipids can bind to proteins in a wide range of conformations, which are not limited by the headgroup chemistry. We propose that lipids can select a suitable headgroup conformation from the wide range available to them to fit the various binding sites in proteins. The proposed inverse conformational selection model will extend also to lipid binding to targets other than proteins, such as drugs, RNA, and viruses.
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Affiliation(s)
- Amélie Bacle
- Laboratoire Coopératif "Lipotoxicity and Channelopathies - ConicMeds", Université de Poitiers, 1 rue Georges Bonnet, Poitiers 86000, France
| | - Pavel Buslaev
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, P.O. Box 35, Jyväskylä 40014, Finland.,Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Rebeca Garcia-Fandino
- Center for Research in Biological Chemistry and Molecular Materials (CiQUS), Universidade de Santiago de Compostela, Santiago de Compostela E-15782, Spain.,CIQUP, Centro de Investigao em Química, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto 4169-007, Portugal
| | - Fernando Favela-Rosales
- Departamento de Ciencias Básicas, Tecnológico Nacional de México - ITS Zacatecas Occidente, Sombrerete, Zacatecas 99102, México
| | - Tiago Mendes Ferreira
- NMR group - Institute for Physics, Martin Luther University Halle-Wittenberg, Halle (Saale), 06120, Germany
| | - Patrick F J Fuchs
- Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules (LBM), Sorbonne Université, Paris 75005, France.,UFR Sciences du Vivant, Université de Paris, Paris 75013, France
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Matti Javanainen
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, Prague CZ-16610, Czech Republic
| | - Anne M Kiirikki
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Jesper J Madsen
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States.,Global and Planetary Health, College of Public Health, University of South Florida, Tampa, Florida 33612, United States
| | - Josef Melcr
- Groningen Biomolecular Sciences and Biotechnology Institute and The Zernike Institute for Advanced Materials, University of Groningen, Groningen9747 AG, The Netherlands
| | - Paula Milán Rodríguez
- Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules (LBM), Sorbonne Université, Paris 75005, France
| | - Markus S Miettinen
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Potsdam 14424, Germany
| | - O H Samuli Ollila
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Chris G Papadopoulos
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette 91198, France
| | - Antonio Peón
- CIQUP, Centro de Investigao em Química, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto 4169-007, Portugal
| | - Thomas J Piggot
- Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Ángel Piñeiro
- Departamento de Física Aplicada, Facultade de Física, Universidade de Santiago de Compostela, Santiago de Compostela E-15782, Spain
| | - Salla I Virtanen
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
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40
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Santos-Beneit F, Raškevičius V, Skeberdis VA, Bordel S. A metabolic modeling approach reveals promising therapeutic targets and antiviral drugs to combat COVID-19. Sci Rep 2021; 11:11982. [PMID: 34099831 PMCID: PMC8184994 DOI: 10.1038/s41598-021-91526-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 05/26/2021] [Indexed: 02/07/2023] Open
Abstract
In this study we have developed a method based on Flux Balance Analysis to identify human metabolic enzymes which can be targeted for therapeutic intervention against COVID-19. A literature search was carried out in order to identify suitable inhibitors of these enzymes, which were confirmed by docking calculations. In total, 10 targets and 12 bioactive molecules have been predicted. Among the most promising molecules we identified Triacsin C, which inhibits ACSL3, and which has been shown to be very effective against different viruses, including positive-sense single-stranded RNA viruses. Similarly, we also identified the drug Celgosivir, which has been successfully tested in cells infected with different types of viruses such as Dengue, Zika, Hepatitis C and Influenza. Finally, other drugs targeting enzymes of lipid metabolism, carbohydrate metabolism or protein palmitoylation (such as Propylthiouracil, 2-Bromopalmitate, Lipofermata, Tunicamycin, Benzyl Isothiocyanate, Tipifarnib and Lonafarnib) are also proposed.
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Affiliation(s)
| | - Vytautas Raškevičius
- Cell Culture Laboratory, Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Vytenis A Skeberdis
- Cell Culture Laboratory, Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Sergio Bordel
- Institute of Sustainable Processes, Universidad de Valladolid, Valladolid, Spain.
- Cell Culture Laboratory, Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania.
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41
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Ferrando J, Solomon LA. Recent Progress Using De Novo Design to Study Protein Structure, Design and Binding Interactions. Life (Basel) 2021; 11:life11030225. [PMID: 33802210 PMCID: PMC7999464 DOI: 10.3390/life11030225] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/04/2021] [Accepted: 03/05/2021] [Indexed: 12/14/2022] Open
Abstract
De novo protein design is a powerful methodology used to study natural functions in an artificial-protein context. Since its inception, it has been used to reproduce a plethora of reactions and uncover biophysical principles that are often difficult to extract from direct studies of natural proteins. Natural proteins are capable of assuming a variety of different structures and subsequently binding ligands at impressively high levels of both specificity and affinity. Here, we will review recent examples of de novo design studies on binding reactions for small molecules, nucleic acids, and the formation of protein-protein interactions. We will then discuss some new structural advances in the field. Finally, we will discuss some advancements in computational modeling and design approaches and provide an overview of some modern algorithmic tools being used to design these proteins.
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Affiliation(s)
- Juan Ferrando
- Department of Biology, George Mason University, 4400 University Dr, Fairfax, VA 22030, USA;
| | - Lee A. Solomon
- Department of Chemistry and Biochemistry, George Mason University, 10920 George Mason Circle, Manassas, VA 20110, USA
- Correspondence: ; Tel.: +703-993-6418
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42
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Sarewicz M, Pintscher S, Pietras R, Borek A, Bujnowicz Ł, Hanke G, Cramer WA, Finazzi G, Osyczka A. Catalytic Reactions and Energy Conservation in the Cytochrome bc1 and b6f Complexes of Energy-Transducing Membranes. Chem Rev 2021; 121:2020-2108. [PMID: 33464892 PMCID: PMC7908018 DOI: 10.1021/acs.chemrev.0c00712] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Indexed: 12/16/2022]
Abstract
This review focuses on key components of respiratory and photosynthetic energy-transduction systems: the cytochrome bc1 and b6f (Cytbc1/b6f) membranous multisubunit homodimeric complexes. These remarkable molecular machines catalyze electron transfer from membranous quinones to water-soluble electron carriers (such as cytochromes c or plastocyanin), coupling electron flow to proton translocation across the energy-transducing membrane and contributing to the generation of a transmembrane electrochemical potential gradient, which powers cellular metabolism in the majority of living organisms. Cytsbc1/b6f share many similarities but also have significant differences. While decades of research have provided extensive knowledge on these enzymes, several important aspects of their molecular mechanisms remain to be elucidated. We summarize a broad range of structural, mechanistic, and physiological aspects required for function of Cytbc1/b6f, combining textbook fundamentals with new intriguing concepts that have emerged from more recent studies. The discussion covers but is not limited to (i) mechanisms of energy-conserving bifurcation of electron pathway and energy-wasting superoxide generation at the quinol oxidation site, (ii) the mechanism by which semiquinone is stabilized at the quinone reduction site, (iii) interactions with substrates and specific inhibitors, (iv) intermonomer electron transfer and the role of a dimeric complex, and (v) higher levels of organization and regulation that involve Cytsbc1/b6f. In addressing these topics, we point out existing uncertainties and controversies, which, as suggested, will drive further research in this field.
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Affiliation(s)
- Marcin Sarewicz
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Sebastian Pintscher
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Rafał Pietras
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Arkadiusz Borek
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Łukasz Bujnowicz
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Guy Hanke
- School
of Biological and Chemical Sciences, Queen
Mary University of London, London E1 4NS, U.K.
| | - William A. Cramer
- Department
of Biological Sciences, Purdue University, West Lafayette, Indiana 47907 United States
| | - Giovanni Finazzi
- Laboratoire
de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre National Recherche Scientifique,
Commissariat Energie Atomique et Energies Alternatives, Institut National
Recherche l’agriculture, l’alimentation et l’environnement, 38054 Grenoble Cedex 9, France
| | - Artur Osyczka
- Department
of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
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43
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Chebon-Bore L, Sanyanga TA, Manyumwa CV, Khairallah A, Tastan Bishop Ö. Decoding the Molecular Effects of Atovaquone Linked Resistant Mutations on Plasmodium falciparum Cytb-ISP Complex in the Phospholipid Bilayer Membrane. Int J Mol Sci 2021; 22:2138. [PMID: 33670016 PMCID: PMC7926518 DOI: 10.3390/ijms22042138] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/02/2021] [Accepted: 02/07/2021] [Indexed: 12/19/2022] Open
Abstract
Atovaquone (ATQ) is a drug used to prevent and treat malaria that functions by targeting the Plasmodium falciparum cytochrome b (PfCytb) protein. PfCytb catalyzes the transmembrane electron transfer (ET) pathway which maintains the mitochondrial membrane potential. The ubiquinol substrate binding site of the protein has heme bL, heme bH and iron-sulphur [2FE-2S] cluster cofactors that act as redox centers to aid in ET. Recent studies investigating ATQ resistance mechanisms have shown that point mutations of PfCytb confer resistance. Thus, understanding the resistance mechanisms at the molecular level via computational approaches incorporating phospholipid bilayer would help in the design of new efficacious drugs that are also capable of bypassing parasite resistance. With this knowledge gap, this article seeks to explore the effect of three drug resistant mutations Y268C, Y268N and Y268S on the PfCytb structure and function in the presence and absence of ATQ. To draw reliable conclusions, 350 ns all-atom membrane (POPC:POPE phospholipid bilayer) molecular dynamics (MD) simulations with derived metal parameters for the holo and ATQ-bound -proteins were performed. Thereafter, simulation outputs were analyzed using dynamic residue network (DRN) analysis. Across the triplicate MD runs, hydrophobic interactions, reported to be crucial in protein function were assessed. In both, the presence and absence of ATQ and a loss of key active site residue interactions were observed as a result of mutations. These active site residues included: Met 133, Trp136, Val140, Thr142, Ile258, Val259, Pro260 and Phe264. These changes to residue interactions are likely to destabilize the overall intra-protein residue communication network where the proteins' function could be implicated. Protein dynamics of the ATQ-bound mutant complexes showed that they assumed a different pose to the wild-type, resulting in diminished residue interactions in the mutant proteins. In summary, this study presents insights on the possible effect of the mutations on ATQ drug activity causing resistance and describes accurate MD simulations in the presence of the lipid bilayer prior to conducting inhibitory drug discovery for the PfCytb-iron sulphur protein (Cytb-ISP) complex.
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Affiliation(s)
| | | | | | | | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6140, South Africa; (L.C.-B.); (T.A.S.); (C.V.M.); (A.K.)
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The road to the structure of the mitochondrial respiratory chain supercomplex. Biochem Soc Trans 2021; 48:621-629. [PMID: 32311046 PMCID: PMC7200630 DOI: 10.1042/bst20190930] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 03/30/2020] [Accepted: 03/31/2020] [Indexed: 01/04/2023]
Abstract
The four complexes of the mitochondrial respiratory chain are critical for ATP production in most eukaryotic cells. Structural characterisation of these complexes has been critical for understanding the mechanisms underpinning their function. The three proton-pumping complexes, Complexes I, III and IV associate to form stable supercomplexes or respirasomes, the most abundant form containing 80 subunits in mammals. Multiple functions have been proposed for the supercomplexes, including enhancing the diffusion of electron carriers, providing stability for the complexes and protection against reactive oxygen species. Although high-resolution structures for Complexes III and IV were determined by X-ray crystallography in the 1990s, the size of Complex I and the supercomplexes necessitated advances in sample preparation and the development of cryo-electron microscopy techniques. We now enjoy structures for these beautiful complexes isolated from multiple organisms and in multiple states and together they provide important insights into respiratory chain function and the role of the supercomplex. While we as non-structural biologists use these structures for interpreting our own functional data, we need to remind ourselves that they stand on the shoulders of a large body of previous structural studies, many of which are still appropriate for use in understanding our results. In this mini-review, we discuss the history of respiratory chain structural biology studies leading to the structures of the mammalian supercomplexes and beyond.
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Dong X, He Y, Ye F, Zhao Y, Cheng J, Xiao J, Yu W, Zhao J, Sai Y, Dan G, Chen M, Zou Z. Vitamin D3 ameliorates nitrogen mustard-induced cutaneous inflammation by inactivating the NLRP3 inflammasome through the SIRT3-SOD2-mtROS signaling pathway. Clin Transl Med 2021; 11:e312. [PMID: 33634989 PMCID: PMC7882108 DOI: 10.1002/ctm2.312] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 01/18/2021] [Accepted: 01/21/2021] [Indexed: 12/12/2022] Open
Abstract
Nitrogen mustard (NM) causes severe skin injury with an obvious inflammatory response, which is lack of effective and targeted therapies. Vitamin D3 (VD3) has excellent anti-inflammatory properties and is considered as a potential candidate for the treatment of NM-induced dermal toxicity; however, the underlying mechanisms are currently unclear. Cyclooxygenase-2 (COX2; a widely used marker of skin inflammation) plays a key role in NM-induced cutaneous inflammation. Herein, we initially confirmed that NM markedly promoted COX2 expression in vitro and in vivo. NM also increased NOD-like receptor family pyrin domain containing 3 (NLRP3) expression, caspase-1 activity, and interleukin-1β (IL-1β) release. Notably, treatment with a caspase-1 inhibitor (zYVAD-fmk), NLRP3 inhibitor (MCC950), and NLRP3 or caspase-1 siRNA attenuated NM-induced NLRP3 inflammasome activation, with subsequent suppression of COX2 expression and IL-1β release in keratinocytes. Meanwhile, NM increased mitochondrial reactive oxygen species (mtROS) and decreased manganese superoxide dismutase 2 (SOD2) and sirtuin 3 (SIRT3) activities. Mito-TEMPO (a mtROS scavenger) ameliorated NM-caused NLRP3 inflammasome activation in keratinocytes. Moreover, VD3 improved SIRT3 and SOD2 activities, decreased mtROS contents, inactivated the NLRP3 inflammasome, and attenuated cutaneous inflammation induced by NM in vitro and in vivo. The beneficial activity of VD3 against NM-triggered cutaneous inflammation was enhanced by the inhibitors of IL-1, mtROS, NLRP3, caspase-1, and NLRP3 or caspase-1 siRNAs, which was abolished in SIRT3 inhibitor or SIRT3 siRNA-treated keratinocytes and skins from SIRT3-/- mice. In conclusion, VD3 ameliorated NM-induced cutaneous inflammation by inactivating the NLRP3 inflammasome, which was partially mediated through the SIRT3-SOD2-mtROS signaling pathway.
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Affiliation(s)
- Xunhu Dong
- Department of Chemical Defense Medicine, School of Military Preventive MedicineThird Military Medical University (Army Medical University)ChongqingChina
- Institute of Toxicology, School of Military Preventive MedicineThird Military Medical University (Army Medical University)ChongqingChina
| | - Ying He
- Department of UltrasoundXinqiao HospitalThird Military Medical University (Army Medical University)ChongqingChina
| | - Feng Ye
- Department of Chemical Defense Medicine, School of Military Preventive MedicineThird Military Medical University (Army Medical University)ChongqingChina
- Institute of Toxicology, School of Military Preventive MedicineThird Military Medical University (Army Medical University)ChongqingChina
| | - Yuanpeng Zhao
- Department of Chemical Defense Medicine, School of Military Preventive MedicineThird Military Medical University (Army Medical University)ChongqingChina
- Institute of Toxicology, School of Military Preventive MedicineThird Military Medical University (Army Medical University)ChongqingChina
| | - Jin Cheng
- Department of Chemical Defense Medicine, School of Military Preventive MedicineThird Military Medical University (Army Medical University)ChongqingChina
- Institute of Toxicology, School of Military Preventive MedicineThird Military Medical University (Army Medical University)ChongqingChina
| | - Jingsong Xiao
- Department of Chemical Defense Medicine, School of Military Preventive MedicineThird Military Medical University (Army Medical University)ChongqingChina
- Institute of Toxicology, School of Military Preventive MedicineThird Military Medical University (Army Medical University)ChongqingChina
| | - Wenpei Yu
- Department of Chemical Defense Medicine, School of Military Preventive MedicineThird Military Medical University (Army Medical University)ChongqingChina
- Institute of Toxicology, School of Military Preventive MedicineThird Military Medical University (Army Medical University)ChongqingChina
| | - Jiqing Zhao
- Department of Chemical Defense Medicine, School of Military Preventive MedicineThird Military Medical University (Army Medical University)ChongqingChina
- Institute of Toxicology, School of Military Preventive MedicineThird Military Medical University (Army Medical University)ChongqingChina
| | - Yan Sai
- Department of Chemical Defense Medicine, School of Military Preventive MedicineThird Military Medical University (Army Medical University)ChongqingChina
- Institute of Toxicology, School of Military Preventive MedicineThird Military Medical University (Army Medical University)ChongqingChina
| | - Guorong Dan
- Department of Chemical Defense Medicine, School of Military Preventive MedicineThird Military Medical University (Army Medical University)ChongqingChina
- Institute of Toxicology, School of Military Preventive MedicineThird Military Medical University (Army Medical University)ChongqingChina
| | - Mingliang Chen
- Department of Chemical Defense Medicine, School of Military Preventive MedicineThird Military Medical University (Army Medical University)ChongqingChina
- Institute of Toxicology, School of Military Preventive MedicineThird Military Medical University (Army Medical University)ChongqingChina
- Institute of Pathology and Southwest Cancer Centre, Southwest HospitalThird Military Medical University (Army Medical University)ChongqingChina
| | - Zhongmin Zou
- Department of Chemical Defense Medicine, School of Military Preventive MedicineThird Military Medical University (Army Medical University)ChongqingChina
- Institute of Toxicology, School of Military Preventive MedicineThird Military Medical University (Army Medical University)ChongqingChina
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Maldonado M, Guo F, Letts JA. Atomic structures of respiratory complex III 2, complex IV, and supercomplex III 2-IV from vascular plants. eLife 2021; 10:e62047. [PMID: 33463523 PMCID: PMC7815315 DOI: 10.7554/elife.62047] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/25/2020] [Indexed: 12/11/2022] Open
Abstract
Mitochondrial complex III (CIII2) and complex IV (CIV), which can associate into a higher-order supercomplex (SC III2+IV), play key roles in respiration. However, structures of these plant complexes remain unknown. We present atomic models of CIII2, CIV, and SC III2+IV from Vigna radiata determined by single-particle cryoEM. The structures reveal plant-specific differences in the MPP domain of CIII2 and define the subunit composition of CIV. Conformational heterogeneity analysis of CIII2 revealed long-range, coordinated movements across the complex, as well as the motion of CIII2's iron-sulfur head domain. The CIV structure suggests that, in plants, proton translocation does not occur via the H channel. The supercomplex interface differs significantly from that in yeast and bacteria in its interacting subunits, angle of approach and limited interactions in the mitochondrial matrix. These structures challenge long-standing assumptions about the plant complexes and generate new mechanistic hypotheses.
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Affiliation(s)
- Maria Maldonado
- Department of Molecular and Cellular Biology, University of California DavisDavisUnited States
| | - Fei Guo
- Department of Molecular and Cellular Biology, University of California DavisDavisUnited States
- BIOEM Facility, University of California DavisDavisUnited States
| | - James A Letts
- Department of Molecular and Cellular Biology, University of California DavisDavisUnited States
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Peraman R, Sure SK, Dusthackeer VNA, Chilamakuru NB, Yiragamreddy PR, Pokuri C, Kutagulla VK, Chinni S. Insights on recent approaches in drug discovery strategies and untapped drug targets against drug resistance. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2021; 7:56. [PMID: 33686369 PMCID: PMC7928709 DOI: 10.1186/s43094-021-00196-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 02/03/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Despite the various strategies undertaken in the clinical practice, the mortality rate due to antibiotic-resistant microbes has been markedly increasing worldwide. In addition to multidrug-resistant (MDR) microbes, the "ESKAPE" bacteria are also emerging. Of course, the infection caused by ESKAPE cannot be treated even with lethal doses of antibiotics. Now, the drug resistance is also more prevalent in antiviral, anticancer, antimalarial and antifungal chemotherapies. MAIN BODY To date, in the literature, the quantum of research reported on the discovery strategies for new antibiotics is remarkable but the milestone is still far away. Considering the need of the updated strategies and drug discovery approaches in the area of drug resistance among researchers, in this communication, we consolidated the insights pertaining to new drug development against drug-resistant microbes. It includes drug discovery void, gene paradox, transposon mutagenesis, vitamin biosynthesis inhibition, use of non-conventional media, host model, target through quorum sensing, genomic-chemical network, synthetic viability to targets, chemical versus biological space, combinational approach, photosensitization, antimicrobial peptides and transcriptome profiling. Furthermore, we optimally briefed about antievolution drugs, nanotheranostics and antimicrobial adjuvants and then followed by twelve selected new feasible drug targets for new drug design against drug resistance. Finally, we have also tabulated the chemical structures of potent molecules against antimicrobial resistance. CONCLUSION It is highly recommended to execute the anti-drug resistance research as integrated approach where both molecular and genetic research needs to be as integrative objective of drug discovery. This is time to accelerate new drug discovery research with advanced genetic approaches instead of conventional blind screening.
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Affiliation(s)
- Ramalingam Peraman
- RERDS-CPR, Raghavendra Institute of Pharmaceutical Education and Research (RIPER)-Autonomous, Anantapur, Andhra Pradesh India
| | - Sathish Kumar Sure
- RERDS-CPR, Raghavendra Institute of Pharmaceutical Education and Research (RIPER)-Autonomous, Anantapur, Andhra Pradesh India
| | - V. N. Azger Dusthackeer
- grid.417330.20000 0004 1767 6138ICMR-National Institute of Research in Tuberculosis, Chennai, Tamilnadu India
| | - Naresh Babu Chilamakuru
- RERDS-CPR, Raghavendra Institute of Pharmaceutical Education and Research (RIPER)-Autonomous, Anantapur, Andhra Pradesh India
| | - Padmanabha Reddy Yiragamreddy
- RERDS-CPR, Raghavendra Institute of Pharmaceutical Education and Research (RIPER)-Autonomous, Anantapur, Andhra Pradesh India
| | - Chiranjeevi Pokuri
- RERDS-CPR, Raghavendra Institute of Pharmaceutical Education and Research (RIPER)-Autonomous, Anantapur, Andhra Pradesh India
| | - Vinay Kumar Kutagulla
- RERDS-CPR, Raghavendra Institute of Pharmaceutical Education and Research (RIPER)-Autonomous, Anantapur, Andhra Pradesh India
| | - Santhivardhan Chinni
- RERDS-CPR, Raghavendra Institute of Pharmaceutical Education and Research (RIPER)-Autonomous, Anantapur, Andhra Pradesh India
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Ma M, Liu Y, Bai C, Yang Y, Sun Z, Liu X, Zhang S, Han X, Yong JWH. The Physiological Functionality of PGR5/PGRL1-Dependent Cyclic Electron Transport in Sustaining Photosynthesis. FRONTIERS IN PLANT SCIENCE 2021; 12:702196. [PMID: 34305990 PMCID: PMC8294387 DOI: 10.3389/fpls.2021.702196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/07/2021] [Indexed: 05/07/2023]
Abstract
The cyclic electron transport (CET), after the linear electron transport (LET), is another important electron transport pathway during the light reactions of photosynthesis. The proton gradient regulation 5 (PGR5)/PRG5-like photosynthetic phenotype 1 (PGRL1) and the NADH dehydrogenase-like complex pathways are linked to the CET. Recently, the regulation of CET around photosystem I (PSI) has been recognized as crucial for photosynthesis and plant growth. Here, we summarized the main biochemical processes of the PGR5/PGRL1-dependent CET pathway and its physiological significance in protecting the photosystem II and PSI, ATP/NADPH ratio maintenance, and regulating the transitions between LET and CET in order to optimize photosynthesis when encountering unfavorable conditions. A better understanding of the PGR5/PGRL1-mediated CET during photosynthesis might provide novel strategies for improving crop yield in a world facing more extreme weather events with multiple stresses affecting the plants.
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Affiliation(s)
- Mingzhu Ma
- College of Land and Environment, National Key Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Northeast China Plant Nutrition and Fertilization Scientific Observation and Research Center for Ministry of Agriculture and Rural Affairs, Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, Shenyang Agricultural University, Shenyang, China
| | - Yifei Liu
- College of Land and Environment, National Key Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Northeast China Plant Nutrition and Fertilization Scientific Observation and Research Center for Ministry of Agriculture and Rural Affairs, Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, Shenyang Agricultural University, Shenyang, China
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- School of Biological Sciences, The University of Western Australia, Perth, WA, Australia
- School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- *Correspondence: Yifei Liu, ; Xiaori Han,
| | - Chunming Bai
- National Sorghum Improvement Center, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Yunhong Yang
- Professional Technology Innovation Center of Magnesium Nutrition, Yingkou Magnesite Chemical Ind Group Co., Ltd., Yingkou, China
| | - Zhiyu Sun
- College of Land and Environment, National Key Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Northeast China Plant Nutrition and Fertilization Scientific Observation and Research Center for Ministry of Agriculture and Rural Affairs, Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, Shenyang Agricultural University, Shenyang, China
| | - Xinyue Liu
- College of Land and Environment, National Key Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Northeast China Plant Nutrition and Fertilization Scientific Observation and Research Center for Ministry of Agriculture and Rural Affairs, Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, Shenyang Agricultural University, Shenyang, China
| | - Siwei Zhang
- College of Land and Environment, National Key Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Northeast China Plant Nutrition and Fertilization Scientific Observation and Research Center for Ministry of Agriculture and Rural Affairs, Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, Shenyang Agricultural University, Shenyang, China
| | - Xiaori Han
- College of Land and Environment, National Key Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Northeast China Plant Nutrition and Fertilization Scientific Observation and Research Center for Ministry of Agriculture and Rural Affairs, Key Laboratory of Protected Horticulture of Education Ministry and Liaoning Province, Shenyang Agricultural University, Shenyang, China
- *Correspondence: Yifei Liu, ; Xiaori Han,
| | - Jean Wan Hong Yong
- School of Biological Sciences, The University of Western Australia, Perth, WA, Australia
- Department of Biosystems and Technology, Swedish University of Agricultural Sciences, Alnarp, Sweden
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Piłsyk S, Mieczkowski A, Golan MP, Wawrzyniak A, Kruszewska JS. Internalization of the Aspergillus nidulans AstA Transporter into Mitochondria Depends on Growth Conditions, and Affects ATP Levels and Sulfite Oxidase Activity. Int J Mol Sci 2020; 21:ijms21207727. [PMID: 33086570 PMCID: PMC7589619 DOI: 10.3390/ijms21207727] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/13/2020] [Accepted: 10/17/2020] [Indexed: 12/12/2022] Open
Abstract
The astA gene encoding an alternative sulfate transporter was originally cloned from the genome of the Japanese Aspergillus nidulans isolate as a suppressor of sulfate permease-deficient strains. Expression of the astA gene is under the control of the sulfur metabolite repression system. The encoded protein transports sulfate across the cell membrane. In this study we show that AstA, having orthologs in numerous pathogenic or endophytic fungi, has a second function and, depending on growth conditions, can be translocated into mitochondria. This effect is especially pronounced when an astA-overexpressing strain grows on solid medium at 37 °C. AstA is also recruited to the mitochondria in the presence of mitochondria-affecting compounds such as menadione or antimycin A, which are also detrimental to the growth of the astA-overexpressing strain. Disruption of the Hsp70-Porin1 mitochondrial import system either by methylene blue, an Hsp70 inhibitor, or by deletion of the porin1-encoding gene abolishes AstA translocation into the mitochondria. Furthermore, we observed altered ATP levels and sulfite oxidase activity in the astA-overexpressing strain in a manner dependent on sulfur sources. The presented data indicate that AstA is also involved in the mitochondrial sulfur metabolism in some fungi, and thereby indirectly manages redox potential and energy state.
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Affiliation(s)
- Sebastian Piłsyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A str., 02-106 Warsaw, Poland; (A.M.); (J.S.K.)
- Correspondence: ; Tel.: +48-22-5921209; Fax: +48-39-121623
| | - Adam Mieczkowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A str., 02-106 Warsaw, Poland; (A.M.); (J.S.K.)
| | - Maciej P. Golan
- Department of Neuropathology, Institute of Psychiatry and Neurology, Sobieskiego 9 str., 02-957 Warsaw, Poland;
| | - Agata Wawrzyniak
- Morphological Sciences Department, College for Medical Sciences of University of Rzeszów, Leszka Czarnego str. 4, 35-615 Rzeszów, Poland;
| | - Joanna S. Kruszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A str., 02-106 Warsaw, Poland; (A.M.); (J.S.K.)
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50
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Lai B, Bernhardt PV, Krömer JO. Cytochrome c Reductase is a Key Enzyme Involved in the Extracellular Electron Transfer Pathway towards Transition Metal Complexes in Pseudomonas Putida. CHEMSUSCHEM 2020; 13:5308-5317. [PMID: 32678505 PMCID: PMC7589348 DOI: 10.1002/cssc.202001645] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/16/2020] [Indexed: 05/06/2023]
Abstract
Mediator-based extracellular electron transfer (EET) pathways can balance the redox metabolism of microbes. However, such electro-biosynthesis processes are constrained by the unknown underlying EET mechanisms. In this paper, Pseudomonas putida was studied to systematically investigate its EET pathway to transition metal complexes (i. e., [Fe(CN)6 ]3-/4- and [Co(bpy)3 ]3+/2+ ; bpy=2,2'-bipyridyl) under anaerobic conditions. Comparative proteomics showed the aerobic respiratory components were upregulated in a bioelectrochemical system without oxygen, suggesting their potential contribution to EET. Further tests found inhibiting cytochrome c oxidase activity by NaN3 and NADH dehydrogenase by rotenone did not significantly change the current output. However, the EET pathway was completely blocked, while cytochrome c reductase activity was inhibited by antimycin A. Although it cannot be excluded that cytochrome c and the periplasmic subunit of cytochrome c oxidase donate electrons to the transition metal complexes, these results strongly demonstrate that cytochrome c reductase is a key complex for the EET pathway.
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Affiliation(s)
- Bin Lai
- Systems Biotechnology group, Department of Solar MaterialsHelmholtz Centre for Environmental Research - UFZLeipzig04318Germany
- Advanced Water Management CentreThe University of QueenslandBrisbane4072Australia
| | - Paul V. Bernhardt
- School of Chemical and Molecular BiosciencesThe University of QueenslandBrisbane4072Australia
| | - Jens O. Krömer
- Systems Biotechnology group, Department of Solar MaterialsHelmholtz Centre for Environmental Research - UFZLeipzig04318Germany
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