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Zhu L, Weng C, Shen X, Zhu X. Aptly chosen, effectively emphasizing the action and mechanism of antimycin A 1. Front Microbiol 2024; 15:1371850. [PMID: 38633707 PMCID: PMC11021728 DOI: 10.3389/fmicb.2024.1371850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 02/26/2024] [Indexed: 04/19/2024] Open
Abstract
Rhizoctonia solani Kühn, a plant pathogenic fungus that can cause diseases in multiple plant species is considered one of the common and destructive pathogens in many crops. This study investigated the action of antimycin A1, which was isolated from Streptomyces AHF-20 found in the rhizosphere soil of an ancient banyan tree, on Rhizoctonia solani and its mechanism. The inhibitory effect of antimycin A1 on R. solani was assessed using the comparative growth rate method. The results revealed that antimycin A1 exhibited a 92.55% inhibition rate against R. solani at a concentration of 26.66 μg/mL, with an EC50 value of 1.25 μg/mL. To observe the impact of antimycin A1 on mycelial morphology and ultrastructure, the fungal mycelium was treated with 6.66 μg/mL antimycin A1, and scanning electron microscopy (SEM) and transmission electron microscopy (TEM) were employed. SEM analysis demonstrated that antimycin A1 caused mycelial morphology to become stripped, rough, and folded. The mycelium experienced severe distortion and breakage, with incomplete or locally enlarged ends, shortened branches, and reduced numbers. TEM observation revealed thickened cell walls, indistinct organelle boundaries, swollen mitochondria, exosmotic substances in vesicles, slow vesicle fusion, and cavitation. Real-time quantitative PCR and enzyme activity assays were conducted to further investigate the impact of antimycin A1 on mitochondria. The physiological and biochemical results indicated that antimycin A1 inhibited complexes III and IV of the mitochondrial electron transport chain. RT-PCR analysis demonstrated that antimycin A1 controlled the synthesis of relevant enzymes by suppressing the transcription levels of ATP6, ATP8, COX3, QCR6, CytB, ND1, and ND3 genes in mitochondria. Additionally, a metabolomic analysis revealed that antimycin A1 significantly impacted 12 metabolic pathways. These pathways likely experienced alterations in their metabolite profiles due to the inhibitory effects of antimycin A1. Consequently, the findings of this research contribute to the potential development of novel fungicides.
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Affiliation(s)
- Linyan Zhu
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, China
| | - Chenhong Weng
- College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Xiaoman Shen
- College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Xiangdong Zhu
- College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
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2
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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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3
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PGRL2 triggers degradation of PGR5 in the absence of PGRL1. Nat Commun 2021; 12:3941. [PMID: 34168134 PMCID: PMC8225790 DOI: 10.1038/s41467-021-24107-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 06/01/2021] [Indexed: 12/01/2022] Open
Abstract
In plants, inactivation of either of the thylakoid proteins PGR5 and PGRL1 impairs cyclic electron flow (CEF) around photosystem I. Because PGR5 is unstable in the absence of the redox-active PGRL1, but not vice versa, PGRL1 is thought to be essential for CEF. However, we show here that inactivation of PGRL2, a distant homolog of PGRL1, relieves the need for PGRL1 itself. Conversely, high levels of PGRL2 destabilize PGR5 even when PGRL1 is present. In the absence of both PGRL1 and PGRL2, PGR5 alters thylakoid electron flow and impairs plant growth. Consequently, PGR5 can operate in CEF on its own, and is the target of the CEF inhibitor antimycin A, but its activity must be modulated by PGRL1. We conclude that PGRL1 channels PGR5 activity, and that PGRL2 triggers the degradation of PGR5 when the latter cannot productively interact with PGRL1. It is currently thought that the thylakoid proteins PGRL1 and PGR5 form a complex to mediate cyclic electron flow (CEF) around photosystem I. Here the authors show that CEF can in fact be mediated by PGR5 alone and that PGRL1 and the homologous PGRL2 modify the process by modulating PGR5 activity and stability.
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Shen Y, Sun F, Zhang L, Cheng Y, Zhu H, Wang SP, Jiao WH, Leadlay PF, Zhou Y, Lin HW. Biosynthesis of depsipeptides with a 3-hydroxybenzoate moiety and selective anticancer activities involves a chorismatase. J Biol Chem 2020; 295:5509-5518. [PMID: 32165500 PMCID: PMC7170507 DOI: 10.1074/jbc.ra119.010922] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 03/10/2020] [Indexed: 11/18/2022] Open
Abstract
Neoantimycins are anticancer compounds of 15-membered ring antimycin-type depsipeptides. They are biosynthesized by a hybrid multimodular protein complex of nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS), typically from the starting precursor 3-formamidosalicylate. Examining fermentation extracts of Streptomyces conglobatus, here we discovered four new neoantimycin analogs, unantimycins B-E, in which 3-formamidosalicylates are replaced by an unusual 3-hydroxybenzoate (3-HBA) moiety. Unantimycins B-E exhibited levels of anticancer activities similar to those of the chemotherapeutic drug cisplatin in human lung cancer, colorectal cancer, and melanoma cells. Notably, they mostly displayed no significant toxicity toward noncancerous cells, unlike the serious toxicities generally reported for antimycin-type natural products. Using site-directed mutagenesis and heterologous expression, we found that unantimycin productions are correlated with the activity of a chorismatase homolog, the nat-hyg5 gene, from a type I PKS gene cluster. Biochemical analysis confirmed that the catalytic activity of Nat-hyg5 generates 3-HBA from chorismate. Finally, we achieved selective production of unantimycins B and C by engineering a chassis host. On the basis of these findings, we propose that unantimycin biosynthesis is directed by the neoantimycin-producing NRPS-PKS complex and initiated with the starter unit of 3-HBA. The elucidation of the biosynthetic unantimycin pathway reported here paves the way to improve the yield of these compounds for evaluation in oncotherapeutic applications.
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Affiliation(s)
- Yaoyao Shen
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fan Sun
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Liu Zhang
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yijia Cheng
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Hongrui Zhu
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Shu-Ping Wang
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Wei-Hua Jiao
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Peter F. Leadlay
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Yongjun Zhou
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Hou-Wen Lin
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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Bioenergetic and proteomic profiling to screen small molecule inhibitors that target cancer metabolisms. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:28-37. [DOI: 10.1016/j.bbapap.2018.06.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/30/2018] [Accepted: 06/01/2018] [Indexed: 12/14/2022]
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Liu J, Zhu X, Kim SJ, Zhang W. Antimycin-type depsipeptides: discovery, biosynthesis, chemical synthesis, and bioactivities. Nat Prod Rep 2016; 33:1146-65. [DOI: 10.1039/c6np00004e] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This review discusses the isolation, structural variation, biosynthesis, chemical synthesis, and biological activities of antimycin-type depsipeptides.
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Affiliation(s)
- Joyce Liu
- Department of Bioengineering
- University of California
- Berkeley
- USA
| | - Xuejun Zhu
- Department of Chemical and Biomolecular Engineering
- University of California
- Berkeley
- USA
| | - Seong Jong Kim
- Department of Chemical and Biomolecular Engineering
- University of California
- Berkeley
- USA
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering
- University of California
- Berkeley
- USA
- Physical Biosciences Division
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Arsianti A, Fadilah &, Kusmardi &, Tanimoto H, Morimoto T, Kakiuchi K. Design and Molecular Docking Study of Antimycin A<sub>3</sub> Analogues as Inhibitors of Anti-Apoptotic Bcl-2 of Breast Cancer. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/ojmc.2014.43006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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8
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Discovery of potent broad spectrum antivirals derived from marine actinobacteria. PLoS One 2013; 8:e82318. [PMID: 24349254 PMCID: PMC3857800 DOI: 10.1371/journal.pone.0082318] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 10/29/2013] [Indexed: 11/19/2022] Open
Abstract
Natural products provide a vast array of chemical structures to explore in the discovery of new medicines. Although secondary metabolites produced by microbes have been developed to treat a variety of diseases, including bacterial and fungal infections, to date there has been limited investigation of natural products with antiviral activity. In this report, we used a phenotypic cell-based replicon assay coupled with an iterative biochemical fractionation process to identify, purify, and characterize antiviral compounds produced by marine microbes. We isolated a compound from Streptomyces kaviengensis, a novel actinomycetes isolated from marine sediments obtained off the coast of New Ireland, Papua New Guinea, which we identified as antimycin A1a. This compound displays potent activity against western equine encephalitis virus in cultured cells with half-maximal inhibitory concentrations of less than 4 nM and a selectivity index of greater than 550. Our efforts also revealed that several antimycin A analogues display antiviral activity, and mechanism of action studies confirmed that these Streptomyces-derived secondary metabolites function by inhibiting the cellular mitochondrial electron transport chain, thereby suppressing de novo pyrimidine synthesis. Furthermore, we found that antimycin A functions as a broad spectrum agent with activity against a wide range of RNA viruses in cultured cells, including members of the Togaviridae, Flaviviridae, Bunyaviridae, Picornaviridae, and Paramyxoviridae families. Finally, we demonstrate that antimycin A reduces central nervous system viral titers, improves clinical disease severity, and enhances survival in mice given a lethal challenge with western equine encephalitis virus. Our results provide conclusive validation for using natural product resources derived from marine microbes as source material for antiviral drug discovery, and they indicate that host mitochondrial electron transport is a viable target for the continued development of broadly active antiviral compounds.
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9
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Sugimoto K, Okegawa Y, Tohri A, Long TA, Covert SF, Hisabori T, Shikanai T. A Single Amino Acid Alteration in PGR5 Confers Resistance to Antimycin A in Cyclic Electron Transport around PSI. ACTA ACUST UNITED AC 2013; 54:1525-34. [DOI: 10.1093/pcp/pct098] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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10
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Ivanova B, Spiteller M. Coordination ability of silver(I) with antimycins and actinomycins – Properties of the T-shaped chromophores. Polyhedron 2012. [DOI: 10.1016/j.poly.2012.03.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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11
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Natesan S, Wang T, Lukacova V, Bartus V, Khandelwal A, Subramaniam R, Balaz S. Cellular quantitative structure-activity relationship (Cell-QSAR): conceptual dissection of receptor binding and intracellular disposition in antifilarial activities of Selwood antimycins. J Med Chem 2012; 55:3699-712. [PMID: 22468611 PMCID: PMC3338160 DOI: 10.1021/jm201371y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
We present the cellular quantitative structure–activity
relationship (cell-QSAR) concept that adapts ligand-based and receptor-based
3D-QSAR methods for use with cell-level activities. The unknown intracellular
drug disposition is accounted for by the disposition function (DF),
a model-based, nonlinear function of a drug’s lipophilicity,
acidity, and other properties. We conceptually combined the DF with
our multispecies, multimode version of the frequently used ligand-based
comparative molecular field analysis (CoMFA) method, forming a single
correlation function for fitting the cell-level activities. The resulting
cell-QSAR model was applied to the Selwood data on filaricidal activities
of antimycin analogues. Their molecules are flexible, ionize under
physiologic conditions, form different intramolecular H-bonds for
neutral and ionized species, and cross several membranes to reach
unknown receptors. The calibrated cell-QSAR model is significantly
more predictive than other models lacking the disposition part and
provides valuable structure optimization clues by factorizing the
cell-level activity of each compound into the contributions of the
receptor binding and disposition.
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Affiliation(s)
- Senthil Natesan
- Albany College of Pharmacy and Health Sciences, Vermont Campus, Colchester, Vermont 05446, USA
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12
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Arsianti A, Tanimoto H, Morimoto T, Bahtiar A, Takeya T, Kakiuchi K. Synthesis and anticancer activity of polyhydroxylated 18-membered analogue of antimycin A3. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.01.080] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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13
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Kokhan O, Shinkarev VP. All-atom molecular dynamics simulations reveal significant differences in interaction between antimycin and conserved amino acid residues in bovine and bacterial bc1 complexes. Biophys J 2011; 100:720-728. [PMID: 21281587 DOI: 10.1016/j.bpj.2010.12.3705] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Revised: 12/09/2010] [Accepted: 12/13/2010] [Indexed: 11/17/2022] Open
Abstract
Antimycin A is the most frequently used specific and powerful inhibitor of the mitochondrial respiratory chain. We used all-atom molecular dynamics (MD) simulations to study the dynamic aspects of the interaction of antimycin A with the Q(i) site of the bacterial and bovine bc(1) complexes embedded in a membrane. The MD simulations revealed considerable conformational flexibility of antimycin and significant mobility of antimycin, as a whole, inside the Q(i) pocket. We conclude that many of the differences in antimycin binding observed in high-resolution x-ray structures may have a dynamic origin and result from fluctuations of protein and antimycin between multiple conformational states of similar energy separated by low activation barriers, as well as from the mobility of antimycin within the Q(i) pocket. The MD simulations also revealed a significant difference in interaction between antimycin and conserved amino acid residues in bovine and bacterial bc(1) complexes. The strong hydrogen bond between antimycin and conserved Asp-228 (bovine numeration) was observed to be frequently broken in the bacterial bc(1) complex and only rarely in the bovine bc(1) complex. In addition, the distances between antimycin and conserved His-201 and Lys-227 were consistently larger in the bacterial bc(1) complex. The observed differences could be responsible for a weaker interaction of antimycin with the bacterial bc(1) complex.
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Affiliation(s)
- Oleksandr Kokhan
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Vladimir P Shinkarev
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois.
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Djung JF, Mears RJ, Montalbetti CA, Coulter TS, Golebiowski A, Carr AN, Barker O, Greis KD, Zhou S, Dolan E, Davis GF. The synthesis and evaluation of indolylureas as PKCα inhibitors. Bioorg Med Chem 2011; 19:2742-50. [DOI: 10.1016/j.bmc.2011.02.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2011] [Revised: 02/17/2011] [Accepted: 02/21/2011] [Indexed: 10/18/2022]
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15
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Inai M, Nishii T, Tanaka A, Kaku H, Horikawa M, Tsunoda T. Total Synthesis of the (+)-Antimycin A Family. European J Org Chem 2011. [DOI: 10.1002/ejoc.201100034] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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16
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Fath MA, Diers AR, Aykin-Burns N, Simons AL, Hua L, Spitz DR. Mitochondrial electron transport chain blockers enhance 2-deoxy-D-glucose induced oxidative stress and cell killing in human colon carcinoma cells. Cancer Biol Ther 2009; 8:1228-36. [PMID: 19411865 DOI: 10.4161/cbt.8.13.8631] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Increasing evidence suggests that cancer cells (relative to normal cells) have altered mitochondrial electron transport chains (ETC) that are more likely to form reactive oxygen species (ROS; i.e., O(2)(*-) and H(2)O(2)) resulting in a condition of chronic metabolic oxidative stress, that maybe compensated for by increasing glucose and hydroperoxide metabolism. In the current study, the ability of an inhibitor of glucose metabolism, 2-deoxy-D-glucose (2DG), combined with mitochondrial electron transport chain blockers (ETCBs) to enhance oxidative stress and cytotoxicity was determined in human colon cancer cells. Treatment of HT29 and HCT116 cancer cells with Antimycin A (Ant A) or rotenone (Rot) increased carboxy-dichlorodihydrofluorescein diacetate (H2DCFDA) and dihydroethidine (DHE) oxidation, caused the accumulation of glutathione disulfide and enhanced 2DG-induced cell killing. In contrast, Rot did not enhance the toxicity of 2DG in normal human fibroblasts supporting the hypotheses that cancer cells are more susceptible to inhibition of glucose metabolism in the presence of ETCBs. In addition, 2-methoxy-antimycin A (Meth A; an analog of Ant A that does not have ETCB activity) did not enhance 2DG-induced DHE oxidation or cytotoxicity in cancer cells. Finally, in HT29 tumor bearing mice treated with the combination of 2DG (500 mg/kg) + Rot (2 mg/kg) the average rate of tumor growth was significantly slower when compared to control or either drug alone. These results show that 2DG-induced cytotoxicity and oxidative stress can be significantly enhanced by ETCBs in human colon cancer cells both in vitro and in vivo.
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Affiliation(s)
- Melissa A Fath
- Free Radical and Radiation Biology Program, Department of Radiation Oncology, Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, IA 52242, USA.
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17
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On the antibiotic activity of oxazolomycin. Bioorg Med Chem Lett 2008; 18:4081-6. [PMID: 18558487 DOI: 10.1016/j.bmcl.2008.05.105] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2008] [Revised: 05/23/2008] [Accepted: 05/24/2008] [Indexed: 11/24/2022]
Abstract
Structural analysis of oxazolomycin and simpler fragments containing a common 3-hydroxy-2,2-dimethylpropanamide moiety has indicated that a U-shaped conformation is preferred, in some cases stabilised by hydrogen bonding between the N-H and O-H residues, as shown by a combination of molecular modelling, NMR spectroscopic and single crystal X-ray analysis. A direct synthesis of this unit has been established via the opening of beta-lactones by a range of amines, and their antibacterial activity been shown to vary with the hydrophobic character of the substituents.
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18
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Esser L, Elberry M, Zhou F, Yu CA, Yu L, Xia D. Inhibitor-complexed Structures of the Cytochrome bc1 from the Photosynthetic Bacterium Rhodobacter sphaeroides. J Biol Chem 2008; 283:2846-57. [DOI: 10.1074/jbc.m708608200] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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19
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Hudder BN, Morales JG, Stubna A, Münck E, Hendrich MP, Lindahl PA. Electron paramagnetic resonance and Mössbauer spectroscopy of intact mitochondria from respiring Saccharomyces cerevisiae. J Biol Inorg Chem 2007; 12:1029-53. [PMID: 17665226 DOI: 10.1007/s00775-007-0275-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2007] [Accepted: 06/27/2007] [Indexed: 11/30/2022]
Abstract
Mitochondria from respiring cells were isolated under anaerobic conditions. Microscopic images were largely devoid of contaminants, and samples consumed O(2) in an NADH-dependent manner. Protein and metal concentrations of packed mitochondria were determined, as was the percentage of external void volume. Samples were similarly packed into electron paramagnetic resonance tubes, either in the as-isolated state or after exposure to various reagents. Analyses revealed two signals originating from species that could be removed by chelation, including rhombic Fe(3+) (g = 4.3) and aqueous Mn(2+) ions (g = 2.00 with Mn-based hyperfine). Three S = 5/2 signals from Fe(3+) hemes were observed, probably arising from cytochrome c peroxidase and the a(3):Cu(b) site of cytochrome c oxidase. Three Fe/S-based signals were observed, with averaged g values of 1.94, 1.90 and 2.01. These probably arise, respectively, from the [Fe(2)S(2)](+) cluster of succinate dehydrogenase, the [Fe(2)S(2)](+) cluster of the Rieske protein of cytochrome bc (1), and the [Fe(3)S(4)](+) cluster of aconitase, homoaconitase or succinate dehydrogenase. Also observed was a low-intensity isotropic g = 2.00 signal arising from organic-based radicals, and a broad signal with g (ave) = 2.02. Mössbauer spectra of intact mitochondria were dominated by signals from Fe(4)S(4) clusters (60-85% of Fe). The major feature in as-isolated samples, and in samples treated with ethylenebis(oxyethylenenitrilo)tetraacetic acid, dithionite or O(2), was a quadrupole doublet with DeltaE (Q) = 1.15 mm/s and delta = 0.45 mm/s, assigned to [Fe(4)S(4)](2+) clusters. Substantial high-spin non-heme Fe(2+) (up to 20%) and Fe(3+) (up to 15%) species were observed. The distribution of Fe was qualitatively similar to that suggested by the mitochondrial proteome.
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Affiliation(s)
- Brandon N Hudder
- Department of Chemistry, Texas A&M University, College Station, TX 77843-3255, USA
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Yang Z, Gagarin D, Ramezani A, Hawley RG, McCaffrey TA. Resistance to fas-induced apoptosis in cells from human atherosclerotic lesions: elevated Bcl-XL inhibits apoptosis and caspase activation. J Vasc Res 2007; 44:483-94. [PMID: 17657164 DOI: 10.1159/000106466] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2006] [Accepted: 05/09/2007] [Indexed: 01/26/2023] Open
Abstract
The inappropriate survival of cells in the neointima contributes to atherosclerotic plaque progression, while apoptosis in the fibrous cap of lesions contributes to myocardial infarction and stroke. Prior genomic-scale transcript profiling of human carotid artery plaque cells with known sensitivity or resistance to fas-induced apoptosis identified candidate genes involved in lesion cell apoptosis. Retroviral overexpression indicated that several candidate factors were not causative, but that Bcl-X(L) conferred complete resistance to apoptosis induced by fas ligation. Resistant cells failed to efficiently activate caspase 8, an effect which was also observed in Bcl-X(L)-transfected cells. Small-molecule Bcl-2/X(L) inhibitors and siRNA knockdown of Bcl-X(L) markedly sensitized resistant cells to apoptosis, and partially restored caspase 8 activation. Caspase 3, 6 and 9 inhibitors reduced caspase 8 activation and blocked apoptosis. Complete knockdown of caspase 9 did not reduce apoptosis, while knockdown of Bid suppressed apoptosis, suggesting that mitochondrial pathways independent of caspase 9, such as Smac/Diablo or AIF, provide a necessary mitochondrial input to efficient caspase activation. Bcl-X(L) appears to modulate lesion cell apoptosis by suppressing mitochondrial amplification of caspase activation loops. The results may have direct implications for controlling plaque instability/progression, and identify a new class of small molecules to inhibit restenosis.
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Affiliation(s)
- Zhaoqing Yang
- Department of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC 20037, USA
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Huang LS, Cobessi D, Tung EY, Berry EA. Binding of the respiratory chain inhibitor antimycin to the mitochondrial bc1 complex: a new crystal structure reveals an altered intramolecular hydrogen-bonding pattern. J Mol Biol 2005; 351:573-97. [PMID: 16024040 PMCID: PMC1482829 DOI: 10.1016/j.jmb.2005.05.053] [Citation(s) in RCA: 224] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2005] [Revised: 05/10/2005] [Accepted: 05/19/2005] [Indexed: 01/07/2023]
Abstract
Antimycin A (antimycin), one of the first known and most potent inhibitors of the mitochondrial respiratory chain, binds to the quinone reduction site of the cytochrome bc1 complex. Structure-activity relationship studies have shown that the N-formylamino-salicyl-amide group is responsible for most of the binding specificity, and suggested that a low pKa for the phenolic OH group and an intramolecular H-bond between that OH and the carbonyl O of the salicylamide linkage are important. Two previous X-ray structures of antimycin bound to vertebrate bc1 complex gave conflicting results. A new structure reported here of the bovine mitochondrial bc1 complex at 2.28 A resolution with antimycin bound, allows us for the first time to reliably describe the binding of antimycin and shows that the intramolecular hydrogen bond described in solution and in the small-molecule structure is replaced by one involving the NH rather than carbonyl O of the amide linkage, with rotation of the amide group relative to the aromatic ring. The phenolic OH and formylamino N form H-bonds with conserved Asp228 of cytochrome b, and the formylamino O H-bonds via a water molecule to Lys227. A strong density, the right size and shape for a diatomic molecule is found between the other side of the dilactone ring and the alphaA helix.
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Affiliation(s)
| | | | | | - Edward A. Berry
- * corresponding author: Tel: 510 486-4335; Fax: 510 588-4829;
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22
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Kanamori D, Okamura TA, Yamamoto H, Shimizu S, Tsujimoto Y, Ueyama N. Structures of the Small-Molecule Bcl-2 Inhibitor (BH3I-2) and Its Related Simple Model in Protonated and Deprotonated Forms. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2004. [DOI: 10.1246/bcsj.77.2057] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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23
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Total synthesis of the (+)-antimycin A3 family: structure elucidation of (+)-antimycin A3a. Tetrahedron Lett 2003. [DOI: 10.1016/j.tetlet.2003.08.046] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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24
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Hockenbery DM, Giedt CD, O'Neill JW, Manion MK, Banker DE. Mitochondria and apoptosis: new therapeutic targets. Adv Cancer Res 2003; 85:203-42. [PMID: 12374287 DOI: 10.1016/s0065-230x(02)85007-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- David M Hockenbery
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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25
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Huang Z. The chemical biology of apoptosis. Exploring protein-protein interactions and the life and death of cells with small molecules. CHEMISTRY & BIOLOGY 2002; 9:1059-72. [PMID: 12401491 DOI: 10.1016/s1074-5521(02)00247-8] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Apoptosis, a fundamental process for both human health and disease, is initiated and regulated by protein-protein interactions, notable examples of which are the interactions involving Bcl-2 and IAP protein families. This article discusses recent advances in the use of chemical approaches in discovering and studying small molecules targeted to proteins of the Bcl-2 and IAP families. These small molecules and their complexes with receptors provide the tools and model systems to probe the basic mechanism of molecule recognition underling the life and death of cells and develop novel strategies for therapeutic intervention of the dysregulated apoptotic process. The review of these studies highlights the opportunity and challenge in this emerging area of chemical and chemical biological research.
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Affiliation(s)
- Ziwei Huang
- Departments of Biochemistry and Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801,
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26
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Tzung SP, Kim KM, Basañez G, Giedt CD, Simon J, Zimmerberg J, Zhang KY, Hockenbery DM. Antimycin A mimics a cell-death-inducing Bcl-2 homology domain 3. Nat Cell Biol 2001; 3:183-91. [PMID: 11175751 DOI: 10.1038/35055095] [Citation(s) in RCA: 354] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The Bcl-2-related survival proteins confer cellular resistance to a wide range of agents. Bcl-xL-expressing hepatocyte cell lines are resistant to tumour necrosis factor and anti-cancer drugs, but are more sensitive than isogenic control cells to antimycin A, an inhibitor of mitochondrial electron transfer. Computational molecular docking analysis predicted that antimycin A interacts with the Bcl-2 homology domain 3 (BH3)-binding hydrophobic groove of Bcl-xL. We demonstrate that antimycin A and a Bak BH3 peptide bind competitively to recombinant Bcl-2. Antimycin A and BH3 peptide both induce mitochondrial swelling and loss of DeltaPsim on addition to mitochondria expressing Bcl-xL. The 2-methoxy derivative of antimycin A3 is inactive as an inhibitor of cellular respiration but still retains toxicity for Bcl-xL+ cells and mitochondria. Finally, antimycin A inhibits the pore-forming activity of Bcl-x L in synthetic liposomes, demonstrating that a small non-peptide ligand can directly inhibit the function of Bcl-2-related proteins.
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Affiliation(s)
- S P Tzung
- Division of Gastroenterology, Department of Medicine, University of Washington, Seattle, Washington, 98195 USA
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27
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Tsunoda T, Nishii T, Yoshizuka M, Yamasaki C, Suzuki T, Itô S. A total synthesis of (−)-antimycin A3b. Tetrahedron Lett 2000. [DOI: 10.1016/s0040-4039(00)01316-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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28
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Abstract
Mitochondria have long been recognized as the generators of energy for the cell. Like any other power source, however, mitochondria are highly vulnerable to inhibition or uncoupling of the energy harnessing process and run a high risk for catastrophic damage to the cell. The exquisite structural and functional characteristics of mitochondria provide a number of primary targets for xenobiotic-induced bioenergetic failure. They also provide opportunities for selective delivery of drugs to the mitochondrion. In light of the large number of natural, commercial, pharmaceutical, and environmental chemicals that manifest their toxicity by interfering with mitochondrial bioenergetics, it is important to understand the underlying mechanisms. The significance is further underscored by the recent identification of bioenergetic control points for cell replication and differentiation and the realization that mitochondria play a determinant role in cell signaling and apoptotic modes of cell death.
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Affiliation(s)
- K B Wallace
- Department of Biochemistry and Molecular Biology, University of Minnesota School of Medicine, Duluth 55812, USA.
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29
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Kim H, Esser L, Hossain MB, Xia D, Yu CA, Rizo J, van der Helm D, Deisenhofer J. Structure of Antimycin A1, a Specific Electron Transfer Inhibitor of Ubiquinol−Cytochrome c Oxidoreductase. J Am Chem Soc 1999. [DOI: 10.1021/ja990190h] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hoeon Kim
- Department of Biochemistry and Howard Hughes Medical Institute The University of Texas Southwestern Medical Center Dallas, Texas 75235 Department of Chemistry and Biochemistry University of Oklahoma, Norman, Oklahoma 73019 Departments of Biochemistry and Pharmacology The University of Texas Southwestern Medical Center Dallas, Texas 75235 Department of Biochemistry and Molecular Biology University of Oklahoma, Stillwater, Oklahoma 74078
| | - Lothar Esser
- Department of Biochemistry and Howard Hughes Medical Institute The University of Texas Southwestern Medical Center Dallas, Texas 75235 Department of Chemistry and Biochemistry University of Oklahoma, Norman, Oklahoma 73019 Departments of Biochemistry and Pharmacology The University of Texas Southwestern Medical Center Dallas, Texas 75235 Department of Biochemistry and Molecular Biology University of Oklahoma, Stillwater, Oklahoma 74078
| | - M. Bilayet Hossain
- Department of Biochemistry and Howard Hughes Medical Institute The University of Texas Southwestern Medical Center Dallas, Texas 75235 Department of Chemistry and Biochemistry University of Oklahoma, Norman, Oklahoma 73019 Departments of Biochemistry and Pharmacology The University of Texas Southwestern Medical Center Dallas, Texas 75235 Department of Biochemistry and Molecular Biology University of Oklahoma, Stillwater, Oklahoma 74078
| | - Di Xia
- Department of Biochemistry and Howard Hughes Medical Institute The University of Texas Southwestern Medical Center Dallas, Texas 75235 Department of Chemistry and Biochemistry University of Oklahoma, Norman, Oklahoma 73019 Departments of Biochemistry and Pharmacology The University of Texas Southwestern Medical Center Dallas, Texas 75235 Department of Biochemistry and Molecular Biology University of Oklahoma, Stillwater, Oklahoma 74078
| | - Chang-An Yu
- Department of Biochemistry and Howard Hughes Medical Institute The University of Texas Southwestern Medical Center Dallas, Texas 75235 Department of Chemistry and Biochemistry University of Oklahoma, Norman, Oklahoma 73019 Departments of Biochemistry and Pharmacology The University of Texas Southwestern Medical Center Dallas, Texas 75235 Department of Biochemistry and Molecular Biology University of Oklahoma, Stillwater, Oklahoma 74078
| | - Josep Rizo
- Department of Biochemistry and Howard Hughes Medical Institute The University of Texas Southwestern Medical Center Dallas, Texas 75235 Department of Chemistry and Biochemistry University of Oklahoma, Norman, Oklahoma 73019 Departments of Biochemistry and Pharmacology The University of Texas Southwestern Medical Center Dallas, Texas 75235 Department of Biochemistry and Molecular Biology University of Oklahoma, Stillwater, Oklahoma 74078
| | - Dick van der Helm
- Department of Biochemistry and Howard Hughes Medical Institute The University of Texas Southwestern Medical Center Dallas, Texas 75235 Department of Chemistry and Biochemistry University of Oklahoma, Norman, Oklahoma 73019 Departments of Biochemistry and Pharmacology The University of Texas Southwestern Medical Center Dallas, Texas 75235 Department of Biochemistry and Molecular Biology University of Oklahoma, Stillwater, Oklahoma 74078
| | - Johann Deisenhofer
- Department of Biochemistry and Howard Hughes Medical Institute The University of Texas Southwestern Medical Center Dallas, Texas 75235 Department of Chemistry and Biochemistry University of Oklahoma, Norman, Oklahoma 73019 Departments of Biochemistry and Pharmacology The University of Texas Southwestern Medical Center Dallas, Texas 75235 Department of Biochemistry and Molecular Biology University of Oklahoma, Stillwater, Oklahoma 74078
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30
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Total synthesis of the antifungal dilactones UK-2A and UK-3A: The determination of their relative and absolute configurations, analog synthesis and antifungal activities. Tetrahedron 1998. [DOI: 10.1016/s0040-4020(98)00777-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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31
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Miyoshi H, Ohshima M, Shimada H, Akagi T, Iwamura H, McLaughlin JL. Essential structural factors of annonaceous acetogenins as potent inhibitors of mitochondrial complex I. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1365:443-52. [PMID: 9711297 DOI: 10.1016/s0005-2728(98)00097-8] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The annonaceous acetogenins are the most potent of the known inhibitors of bovine heart mitochondrial complex I. These inhibitors act, at the terminal electron transfer step of the enzyme, in a similar way to the usual complex I inhibitors, such as piericidin A and rotenone; however, structural similarities are not apparent between the acetogenins and these known complex I inhibitors. A systematic set of isolated natural acetogenins was prepared and examined for their inhibitory actions with bovine heart mitochondrial complex I to identify the essential structural factors of these inhibitors for the exhibition of potent activity. Despite their very potent activity, the structural requirements of the acetogenins are not particularly rigid and remain somewhat ambiguous. The most common structural units, such as adjacent bis-tetrahydrofuran (THF) rings and hydroxyl groups in the 4- and/or 10-positions, were not essential for exhibiting potent activity. The stereochemistry surrounding the THF rings, surprisingly, seemed to be unimportant, which was corroborated by an exhaustive conformational space search analysis, indicating that the model compounds, with different stereochemical arrangements around the THF moieties, were in fairly good superimposition. Proper length and flexibility of the alkyl spacer moiety, which links the THF and the alpha, beta-unsaturated gamma-lactone ring moieties, were essential for the potent activity. This probably results from some sort of specific conformation of the spacer moiety which regulates the two ring moieties to locate into an optimal spatial position on the enzyme. It is, therefore, suggested that the structural specificity of the acetogenins, required for optimum inhibition, differs significantly from that of the common complex I inhibitors in which essential structural units are compactly arranged and conveniently defined. The structure-activity profile for complex I inhibition is discussed in comparison with those for other biological activities.
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Affiliation(s)
- H Miyoshi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Japan.
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32
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Enantioselective total synthesis of the antifungal dilactone, UK-2A: The determination of the relative and absolute configurations. Tetrahedron Lett 1998. [DOI: 10.1016/s0040-4039(98)00796-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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33
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Satoh T, Miyoshi H, Sakamoto K, Iwamura H. Comparison of the inhibitory action of synthetic capsaicin analogues with various NADH-ubiquinone oxidoreductases. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1273:21-30. [PMID: 8573592 DOI: 10.1016/0005-2728(95)00131-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Capsaicin is a new naturally occurring inhibitor of proton-pumping NADH-ubiquinone oxidoreductase (NDH-1), that competitively acts against ubiquinone. A series of capsaicin analogues was synthesized to examine the structural factors required for the inhibitory action and to probe the structural property of the ubiquinone catalytic site of various NADH-ubiquinone reductases, including non-proton-pumping enzyme (NDH-2), from bovine heart mitochondria, potato tuber (Solanum tuberosum, L) mitochondria and Escherichia coli (GR 19N) plasma membranes. Some synthetic capsaicins were fairly potent inhibitors of each of the three NDH-1 compared with the potent rotenone and piericidin A. Synthetic capsaicin analogues inhibited all three NDH-1 activities in a competitive manner against an exogenous quinone. The modification both of the substitution pattern and of the number of methoxy groups on the benzene ring, which may be superimposable on the quinone ring of ubiquinone, did not drastically affect the inhibitory potency. In addition, alteration of the position of dipolar amide bond unit in the molecule and chemical modifications of this unit did not change the inhibitory potency, particularly with bovine heart and potato tuber NDH-1. These results might be explained assuming that the ubiquinone catalytic site of NDH-1 is spacious enough to accommodate a variety of structurally different capsaicin analogues in a dissimilar manner. Regarding the moiety corresponding to the alkyl side chain, a rigid diphenyl ether structure was more inhibitory than a flexible alkyl chain. Structure-activity studies and molecular orbital calculations suggested that a bent form is the active conformation of capsaicin analogues. On the other hand, poor correlations between the inhibitory potencies determined with the three NDH-1 suggested that the structural similarity of the ubiquinone catalytic sites of these enzymes is rather poor. The sensitivity to the inhibition by synthetic capsaicins remarkably differed between NDH-1 and NDH-2, supporting the notion that the sensitivity against capsaicin inhibition correlates well with the presence of an energy coupling site in the enzyme (Yagi, T. (1990) Arch. Biochem. Biophys. 281, 305-311). It is noteworthy that several synthetic capsaicins discriminated between NDH-1 and NDH-2 much better than natural capsaicin.
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Affiliation(s)
- T Satoh
- Department of Agricultural Chemistry, Kyoto University, Japan
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