1
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Li L, Hui T, Li Y, Wang Y, Gu H, Chen G, Lei P, Gao Y, Feng J. Design, synthesis and antifungal activity of novel α-methylene-γ-butyrolactone derivatives containing benzothiophene moiety. PEST MANAGEMENT SCIENCE 2024. [PMID: 38482986 DOI: 10.1002/ps.8080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/10/2024] [Accepted: 03/14/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND The discovery of agricultural fungicide candidates from natural products is one of the key strategies for developing environment friendly agricultural fungicides with high efficiency, high selectivity and unique modes-of-action. Based on previous work, a series of novel α-methylene-γ-butyrolactone (MBL) derivatives containing benzothiophene moiety were designed and synthesized. RESULTS The majority of the proposed compounds displayed moderate to considerable antifungal efficacy against the tested pathogenic fungi and oomycetes, some exhibiting broad spectrum antifungal activity. Notably, compounds 2 (3-F-Ph) and 7 (4-Cl-Ph) showed excellent antifungal activity against Rhizoctonia with half maximal effective concentration (EC50) values of 0.94 and 0.99 mg L-1, respectively, comparable to the commercial fungicide tebuconazole (EC50 = 0.96 mg L-1), and also displayed significant inhibitory effects against V alsa mali with EC50 values of 2.26 and 1.67 mg L-1, respectively - better than famoxadone and carabrone. The in vivo protective and curative effects against R. solani of compound 2 were 57.2% and 53.7% at 100 mg L-1, respectively, which were equivalent to tebuconazole (51.6% and 52.4%). Further investigations found that compound 2 altered the ultrastructure of R. solani cell, significantly increased the relative conductivity of the cells, and reduced the activity of complex III in a dose-dependent manner. Molecular docking results showed that compound 2 matched well with the Qo pocket. CONCLUSION The results revealed that MBL derivatives containing benzothiophene moiety are promising antifungal candidates and provide a new backbone structure for further optimization of novel fungicides. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Luwei Li
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
- Shaanxi Research Center of Biopesticide Engineering & Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Tuoping Hui
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
- Shaanxi Research Center of Biopesticide Engineering & Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuying Li
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
- Shaanxi Research Center of Biopesticide Engineering & Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yaqiang Wang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
- Shaanxi Research Center of Biopesticide Engineering & Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Huiping Gu
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
- Shaanxi Research Center of Biopesticide Engineering & Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Guangyou Chen
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
- Shaanxi Research Center of Biopesticide Engineering & Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Peng Lei
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
- Shaanxi Research Center of Biopesticide Engineering & Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yanqing Gao
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
- Shaanxi Research Center of Biopesticide Engineering & Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Juntao Feng
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
- Shaanxi Research Center of Biopesticide Engineering & Technology, Northwest A&F University, Yangling, Shaanxi, China
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, Northwest A&F University, Yangling, Shaanxi, China
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2
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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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3
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Esser L, Xia D. Mitochondrial Cytochrome bc1 Complex as Validated Drug Target: A Structural Perspective. Trop Med Infect Dis 2024; 9:39. [PMID: 38393128 PMCID: PMC10892539 DOI: 10.3390/tropicalmed9020039] [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: 12/06/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
Mitochondrial respiratory chain Complex III, also known as cytochrome bc1 complex or cyt bc1, is a validated target not only for antibiotics but also for pesticides and anti-parasitic drugs. Although significant progress has been made in understanding the mechanisms of cyt bc1 function and inhibition by using various natural and synthetic compounds, important issues remain in overcoming drug resistance in agriculture and in evading cytotoxicity in medicine. In this review, we look at these issues from a structural perspective. After a brief description of the essential and common structural features, we point out the differences among various cyt bc1 complexes of different organisms, whose structures have been determined to atomic resolution. We use a few examples of cyt bc1 structures determined via bound inhibitors to illustrate both conformational changes observed and implications to the Q-cycle mechanism of cyt bc1 function. These structures not only offer views of atomic interactions between cyt bc1 complexes and inhibitors, but they also provide explanations for drug resistance when structural details are coupled to sequence changes. Examples are provided for exploiting structural differences in evolutionarily conserved enzymes to develop antifungal drugs for selectivity enhancement, which offer a unique perspective on differential interactions that can be exploited to overcome cytotoxicity in treating human infections.
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Affiliation(s)
| | - Di Xia
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Room 2122C, Bethesda, MD 20892, USA
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4
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Liu Y, Esser L, Bai H, Fu B, Xia D, Zhou Y, Hong S, Yang S, Xiao Y, Qin Z. Synthesis and Antiphytopathogenic Activity of Novel Oxazolidine-2,4-diones Bearing Phenoxypyridine Moiety. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:14199-14210. [PMID: 37728976 DOI: 10.1021/acs.jafc.3c03464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
In the present study, we conducted optimization of pyramoxadone and synthesized a series of novel oxazolidinediones. Antifungal assays showed that these compounds exhibited moderate to excellent antifungal activity against various pathogens. Further SAR analysis revealed that the introduction of substituents to the benzene ring of the phenoxy group or the inclusion of bulky groups, such as tert-butyl, on the aniline moiety, had a detrimental effect on the activity. However, the inclusion of fluorine atoms in the aniline moiety significantly enhanced the antifungal efficacy. Notably, compound 2-4 displayed significantly higher activity compared to both pyramoxadone and famoxadone against R. solani, B. cinerea, S. sclerotiorum, and P. oryzae, where it demonstrated EC50 values of 1.78, 2.47, 2.33, and 2.23 μg/mL, respectively. Furthermore, compound 2-4 exhibited potent protective and curative effects against the tomato gray mold in vivo. A mechanistic investigation revealed that compound 2-4 significantly impacted the mycelial morphology, inhibited spore germination, and impeded mycelial respiration, ultimately leading to the inhibition of pathogenic fungus growth. These findings indicate that compound 2-4 has the potential to serve as a cyt bc1 inhibitor and should be further investigated for development.
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Affiliation(s)
- Yanfei Liu
- College of Science, China Agricultural University, Beijing 100193, China
| | - Lothar Esser
- Structural Biology Section, Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892, United States
| | - Hui Bai
- College of Science, China Agricultural University, Beijing 100193, China
| | - Bin Fu
- College of Science, China Agricultural University, Beijing 100193, China
| | - Di Xia
- Structural Biology Section, Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892, United States
| | - Yihui Zhou
- College of Science, China Agricultural University, Beijing 100193, China
| | - Sai Hong
- College of Science, China Agricultural University, Beijing 100193, China
| | - Sihan Yang
- College of Science, China Agricultural University, Beijing 100193, China
| | - Yumei Xiao
- College of Science, China Agricultural University, Beijing 100193, China
| | - Zhaohai Qin
- College of Science, China Agricultural University, Beijing 100193, China
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5
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Esser L, Zhou F, Zeher A, Wu W, Huang R, Yu CA, Lane KD, Wellems TE, Xia D. Structure of complex III with bound antimalarial agent CK-2-68 provides insights into selective inhibition of Plasmodium cytochrome bc 1 complexes. J Biol Chem 2023; 299:104860. [PMID: 37236355 PMCID: PMC10404626 DOI: 10.1016/j.jbc.2023.104860] [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: 12/19/2022] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
Among the various components of the protozoan Plasmodium mitochondrial respiratory chain, only Complex III is a validated cellular target for antimalarial drugs. The compound CK-2-68 was developed to specifically target the alternate NADH dehydrogenase of the malaria parasite respiratory chain, but the true target for its antimalarial activity has been controversial. Here, we report the cryo-EM structure of mammalian mitochondrial Complex III bound with CK-2-68 and examine the structure-function relationships of the inhibitor's selective action on Plasmodium. We show that CK-2-68 binds specifically to the quinol oxidation site of Complex III, arresting the motion of the iron-sulfur protein subunit, which suggests an inhibition mechanism similar to that of Pf-type Complex III inhibitors such as atovaquone, stigmatellin, and UHDBT. Our results shed light on the mechanisms of observed resistance conferred by mutations, elucidate the molecular basis of the wide therapeutic window of CK-2-68 for selective action of Plasmodium vs. host cytochrome bc1, and provide guidance for future development of antimalarials targeting Complex III.
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Affiliation(s)
- Lothar Esser
- Laboratory of Cell Biology, Center for Cancer Research National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Fei Zhou
- Laboratory of Cell Biology, Center for Cancer Research National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Allison Zeher
- Laboratory of Cell Biology, Center for Cancer Research National Cancer Institute, NIH, Bethesda, Maryland, USA; NIH Intramural Cryo-EM Consortium (NICE), Bethesda, Maryland, USA
| | - Weimin Wu
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, NIH, Frederick, Maryland, USA
| | - Rick Huang
- Laboratory of Cell Biology, Center for Cancer Research National Cancer Institute, NIH, Bethesda, Maryland, USA; NIH Intramural Cryo-EM Consortium (NICE), Bethesda, Maryland, USA
| | - Chang-An Yu
- Department of Biochemistry, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Kristin D Lane
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Thomas E Wellems
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Di Xia
- Laboratory of Cell Biology, Center for Cancer Research National Cancer Institute, NIH, Bethesda, Maryland, USA.
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6
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Li Y, Zhang T, Ma H, Xu L, Zhang Q, He L, Jiang J, Zhang Z, Zhao Z, Wang M. Design, Synthesis, and Antifungal/Antioomycete Activity of Thiohydantoin Analogues Containing Spirocyclic Butenolide. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:6249-6267. [PMID: 37058604 DOI: 10.1021/acs.jafc.2c09144] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Novel fungicidal agents were designed based on the combination of two privileged scaffolds, thiohydantoin and spirocyclic butenolide, which are widely found in natural products. The synthesized compounds were characterized by 1H NMR, 13C NMR, and high-resolution electrospray ionisation mass spectrometry. The in vitro antioomycete activity evaluation showed that most of the compounds exhibited excellent inhibitory activities against different developmental stages in the life cycle of pathogenic oomycete Phytophthora capsici. Compound 5j could inhibit the mycelial growth, sporangium production, zoospore release, and cystospore germination significantly with EC50 values of 0.38, 0.25, 0.11, and 0.026 μg/mL, respectively. The in vivo antifungal/antioomycete bioassay results revealed that the series of compounds generally showed outstanding control efficacies against the pathogenic oomycete Pseudoperonospora cubensis, and compounds 5j, 5l, 7j, 7k, and 7l possessed broad-spectrum antifungal activities against the test phytopathogens. The in vivo protective and curative efficacies against P. capsici of the representative compound 5j were excellent, which were better than those of azoxystrobin. More prominently, 5j significantly promoted the biomass accumulation of the root system and reinforced the cell wall by callose deposition. The pronounced upregulation of immune response-related genes indicated that the active oomycete inhibitor 5j also functioned as a plant elicitor. Transmission electron microscopy observation and the enzyme activity test demonstrated that the mechanism of action of 5j was to bind to the pivotal protein, complex III on the respiratory chain, which resulted in a shortage of energy supply. Molecular docking results exhibited that compound 5j appropriately matched with the Qo pocket and had no interaction with the most commonly mutated site Gly-142, which may be of significant benefit in Qo fungicide resistance management. Compound 5j showed great advantages and potential in oomycete control, resistance management, and induction of disease resistance. A further investigation of 5j with a unique structure might have direct implications for the creation of novel oomycete inhibitors against plant-pathogenic oomycetes.
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Affiliation(s)
- Yihao Li
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Tingting Zhang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Haoyun Ma
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Leichuan Xu
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Qian Zhang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Lei He
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Jiazhen Jiang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Zhenhua Zhang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Zhangwu Zhao
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Mingan Wang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
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7
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Havens J, Su T, Wang Q, Yu CA, Yu L, Durham B, Millett F. Photoinduced electron transfer in cytochrome bc 1: Dynamics of rotation of the Iron-sulfur protein during bifurcated electron transfer from ubiquinol to cytochrome c 1 and cytochrome b L. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148957. [PMID: 36709837 DOI: 10.1016/j.bbabio.2023.148957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 01/12/2023] [Accepted: 01/20/2023] [Indexed: 01/27/2023]
Abstract
The electron transfer reactions within wild-type Rhodobacter sphaeroides cytochrome bc1 (cyt bc1) were studied using a binuclear ruthenium complex to rapidly photooxidize cyt c1. When cyt c1, the iron‑sulfur center Fe2S2, and cyt bH were reduced before the reaction, photooxidation of cyt c1 led to electron transfer from Fe2S2 to cyt c1 with a rate constant of ka = 80,000 s-1, followed by bifurcated reduction of both Fe2S2 and cyt bL by QH2 in the Qo site with a rate constant of k2 = 3000 s-1. The resulting Q then traveled from the Qo site to the Qi site and oxidized one equivalent each of cyt bL and cyt bH with a rate constant of k3 = 340 s-1. The rate constant ka was decreased in a nonlinear fashion by a factor of 53 as the viscosity was increased to 13.7. A mechanism that is consistent with the effect of viscosity involves rotational diffusion of the iron‑sulfur protein from the b state with reduced Fe2S2 close to cyt bL to one or more intermediate states, followed by rotation to the final c1 state with Fe2S2 close to cyt c1, and rapid electron transfer to cyt c1.
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Affiliation(s)
- Jeffrey Havens
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States of America; Vaccines and Therapeutics Division, Chemical and Biological Technologies, Defense Threat Reduction Agency, Fort Belvoir, VA 22060, United States of America
| | - Ting Su
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, United States of America; ABclonal Technology Woburn, MA 01801, United States of America
| | - Qiyu Wang
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, United States of America; Vesigen Therapeutics Cambridge, MA 02139, United States of America
| | - Chang-An Yu
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, United States of America
| | - Linda Yu
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, United States of America
| | - Bill Durham
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States of America
| | - Francis Millett
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, United States of America.
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8
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Zhan J, Xia D. Bcs1, a novel target for fungicide. Front Chem 2023; 11:1146753. [PMID: 36993815 PMCID: PMC10040684 DOI: 10.3389/fchem.2023.1146753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/03/2023] [Indexed: 03/14/2023] Open
Abstract
The mitochondrial respiratory chain has long been a primary target for the development of fungicides for its indispensable role in various cellular functions including energy metabolism. Over the years, a wide range of natural and synthetic fungicides and pesticides targeting the respiratory chain complexes have been discovered or developed and used in agriculture and in medicine, which brought considerable economic gains but was also accompanied by the emergence of resistance to these compounds. To delay and overcome the onset of resistance, novel targets for fungicides development are actively being pursued. Mitochondrial AAA protein Bcs1 is necessary for the biogenesis of respiratory chain Complex III, also known as cyt bc1 complex, by delivering the last essential iron-sulfur protein subunit in its folded form to the cyt bc1 precomplex. Although no report on the phenotypes of knock-out Bcs1 has been reported in animals, pathogenic Bcs1 mutations cause Complex III deficiency and respiratory growth defects, which makes it a promising new target for the development of fungicides. Recent Cryo-EM and X-ray structures of mouse and yeast Bcs1 revealed the basic oligomeric states of Bcs1, shed light on the translocation mechanism of its substrate ISP, and provided the basis for structure-based drug design. This review summarizes the recent progress made on understanding the structure and function of Bcs1, proposes the use of Bcs1 as an antifungal target, and provides novel prospects for fungicides design by targeting Bcs1.
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9
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Wieferig JP, Kühlbrandt W. Analysis of the conformational heterogeneity of the Rieske iron-sulfur protein in complex III 2 by cryo-EM. IUCRJ 2023; 10:27-37. [PMID: 36598500 PMCID: PMC9812224 DOI: 10.1107/s2052252522010570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/02/2022] [Indexed: 06/17/2023]
Abstract
Movement of the Rieske domain of the iron-sulfur protein is essential for intramolecular electron transfer within complex III2 (CIII2) of the respiratory chain as it bridges a gap in the cofactor chain towards the electron acceptor cytochrome c. We present cryo-EM structures of CIII2 from Yarrowia lipolytica at resolutions up to 2.0 Å under different conditions, with different redox states of the cofactors of the high-potential chain. All possible permutations of three primary positions were observed, indicating that the two halves of the dimeric complex act independently. Addition of the substrate analogue decylubiquinone to CIII2 with a reduced high-potential chain increased the occupancy of the Qo site. The extent of Rieske domain interactions through hydrogen bonds to the cytochrome b and cytochrome c1 subunits varied depending on the redox state and substrate. In the absence of quinols, the reduced Rieske domain interacted more closely with cytochrome b and cytochrome c1 than in the oxidized state. Upon addition of the inhibitor antimycin A, the heterogeneity of the cd1-helix and ef-loop increased, which may be indicative of a long-range effect on the Rieske domain.
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Affiliation(s)
- Jan-Philip Wieferig
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
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10
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Kiiskilä JM, Hassinen IE, Kettunen J, Kytövuori L, Mikkola I, Härkönen P, Jokelainen JJ, Keinänen-Kiukaanniemi S, Perola M, Majamaa K. Association between mitochondrial DNA haplogroups J and K, serum branched-chain amino acids and lowered capability for endurance exercise. BMC Sports Sci Med Rehabil 2022; 14:95. [PMID: 35619160 PMCID: PMC9137050 DOI: 10.1186/s13102-022-00485-3] [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: 10/07/2021] [Accepted: 05/17/2022] [Indexed: 11/11/2022]
Abstract
Background Endurance exercise training promotes the catabolism of branched-chain amino acids (BCAAs) in skeletal muscles. We have previously shown that mitochondrial DNA (mtDNA) haplogroups J and K are markers of low responders in endurance training. In this paper, we hypothesize that BCAA catabolism is a surrogate marker of lower respiratory chain activity attributed to these haplogroups. We evaluated whether exercise-induced changes in amino acid concentrations differ between subjects harbouring mtDNA haplogroups J or K and those with non-JK haplogroups. Methods Finnish male conscripts (N = 633) undertook the 12-min Cooper running test at the beginning and end of their military service. The intervention during the service mainly included endurance aerobic exercise and sports-related muscle training. Concentrations of seven amino acids were analysed in the serum using a high-throughput 1H NMR metabolomics platform. Total DNA was extracted from whole blood, and restriction fragment analysis was used to determine mtDNA haplogroups J and K. Results The concentrations of the seven amino acids were higher following the intervention, with the exception of phenylalanine; interestingly, the increase in the concentrations of three BCAAs was larger in subjects with haplogroup J or K than in subjects with non-JK haplogroups (p = 0.029). MtDNA haplogroups J and K share two common nonsynonymous variants. Structural analysis based on crystallographic data on bovine complexes I and III revealed that the Leu18 variant in cytochrome b encoded by m.14798T > C may interfere with ubiquinone binding at the Qi site in complex III. Conclusions The increase in the concentrations of serum BCAAs following exercise intervention differs between subjects harbouring mtDNA haplogroup J or K and those harbouring non-JK haplogroups. Lower response in endurance training and difference in exercise-induced increase in the concentrations of serum BCAAs suggest decreased respiratory chain activity. Haplogroups J and K share m.14798T > C in MT-CYB, which may hamper the function of complex III. Supplementary information The online version contains supplementary material available at 10.1186/s13102-022-00485-3.
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Affiliation(s)
- Jukka M Kiiskilä
- Research Unit of Clinical Neuroscience, University of Oulu, P.O. Box 5000, 90014, Oulu, Finland. .,Department of Neurology and Medical Research Center, Oulu University Hospital, Oulu, Finland.
| | - Ilmo E Hassinen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Johannes Kettunen
- Computational Medicine, Faculty of Medicine, University of Oulu, Oulu, Finland.,Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland.,Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Laura Kytövuori
- Research Unit of Clinical Neuroscience, University of Oulu, P.O. Box 5000, 90014, Oulu, Finland.,Department of Neurology and Medical Research Center, Oulu University Hospital, Oulu, Finland
| | | | - Pirjo Härkönen
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland.,Unit of General Practice, Oulu University Hospital, Oulu, Finland
| | - Jari J Jokelainen
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland.,Unit of General Practice, Oulu University Hospital, Oulu, Finland
| | - Sirkka Keinänen-Kiukaanniemi
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland.,Unit of Primary Health Care, Oulu University Hospital, Oulu, Finland.,Healthcare and Social Services of Selänne, Pyhäjärvi, Finland
| | - Markus Perola
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Kari Majamaa
- Research Unit of Clinical Neuroscience, University of Oulu, P.O. Box 5000, 90014, Oulu, Finland.,Department of Neurology and Medical Research Center, Oulu University Hospital, Oulu, Finland
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11
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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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12
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Tembe N, Machaba KE, Ndagi U, Kumalo HM, Mhlongo NN. Ursolic acid as a potential inhibitor of Mycobacterium tuberculosis cytochrome bc1 oxidase-a molecular modelling perspective. J Mol Model 2022; 28:35. [PMID: 35022913 DOI: 10.1007/s00894-021-04993-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 11/23/2021] [Indexed: 01/05/2023]
Abstract
The escalating burden of tuberculosis disease and drastic effects of current medicine has stimulated a search for alternative drugs. A medicinal plant Warburgia salutaris has been reported to possess inhibitory properties against M. tuberculosis. In this study, we apply computational methods to investigate the probability of W. salutaris compounds as potential inhibitors of M. tuberculosis QcrB protein. We performed molecular docking, molecular dynamics simulations, radius of gyration, principal component analysis (PCA), and molecular mechanics-generalized born surface area (MM-GBSA) binding-free energy calculations in explicit solvent to achieve our objective. The results suggested that ursolic acid (UA) and ursolic acid acetate (UAA) could serve as preferred potential inhibitors of mycobacterial QcrB compared to lansoprazole sulphide (LSPZ) and telacebec (Q203)-UA and UAA have a higher binding affinity to QcrB compared to LSPZ and Q203 drugs. UA binding affinity is attributed to hydrogen bond formation with Val120, Arg364 and Arg366, and largely resonated from van der Waals forces resulting from UA interactions with hydrophobic amino acids in its vicinity. UAA binds to the porphyrin ring binding site with higher binding affinity compared to LSPZ. The binding affinity results primarily from van der Waals forces between UAA and hydrophobic residues of QcrB in the porphyrin ring binding site where UAA binds competitively. UA and UAA formed stable complexes with the protein with reduced overall residue mobility, consequently supporting the magnitude of binding affinity of the respective ligands. UAA could potentially compete with the porphyrin ring for the binding site and deprive the mycobacterial cell from oxygen, consequently disturbing mycobacterial oxygen-dependent metabolic processes. Therefore, discovery of a compound that competes with porphyrin ring for the binding site may be useful in QcrB pharmocological studies. UA proved to be a superior compound, although its estimated toxicity profile revealed UA to be hepatotoxic within acceptable parameters. Although preliminary findings of this report still warrant experimental validation, they could serve as a baseline for the development of new anti-tubercular drugs from natural resources that target QcrB.
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Affiliation(s)
- Ntombikayise Tembe
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Kgothatso E Machaba
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Umar Ndagi
- Africa Centre of Excellence for Mycotoxin and Food Safety, Federal University of Technology, Minna, Nigeria
| | - Hezekiel M Kumalo
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Ndumiso N Mhlongo
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa.
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13
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Sindhu T, Debnath P. Cytochrome bc1-aa3 oxidase supercomplex as emerging and potential drug target against tuberculosis. Curr Mol Pharmacol 2021; 15:380-392. [PMID: 34602044 DOI: 10.2174/1874467214666210928152512] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 03/26/2021] [Accepted: 06/06/2021] [Indexed: 11/22/2022]
Abstract
The cytochrome bc1-aa3 supercomplex plays an essential role in the cellular respiratory system of Mycobacterium Tuberculosis. It transfers electrons from menaquinol to cytochrome aa3 (Complex IV) via cytochrome bc1 (Complex III), which reduces the oxygen. The electron transfer from a variety of donors into oxygen through the respiratory electron transport chain is essential to pump protons across the membrane creating an electrochemical transmembrane gradient (proton motive force, PMF) that regulates the synthesis of ATP via the oxidative phosphorylation process. Cytochrome bc1-aa3 supercomplex in M. tuberculosis is, therefore, a major drug target for antibiotic action. In recent years, several respiratory chain components have been targeted for developing new candidate drugs, illustrating the therapeutic potential of obstructing energy conversion of M. tuberculosis. The recently available cryo-EM structure of mycobacterial cytochrome bc1-aa3 supercomplex with open and closed conformations has opened new avenues for understanding its structure and function for developing more effective, new therapeutics against pulmonary tuberculosis. In this review, we discuss the role and function of several components, subunits, and drug targeting elements of the supercomplex cytochrome bc1-aa3, and its potential inhibitors in detail.
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Affiliation(s)
- Thangaraj Sindhu
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, Karnataka. India
| | - Pal Debnath
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, Karnataka. India
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14
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Search for Novel Lead Inhibitors of Yeast Cytochrome bc1, from Drugbank and COCONUT. Molecules 2021; 26:molecules26144323. [PMID: 34299598 PMCID: PMC8307329 DOI: 10.3390/molecules26144323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 11/17/2022] Open
Abstract
In this work we introduce a novel filtering and molecular modeling pipeline based on a fingerprint and descriptor similarity procedure, coupled with molecular docking and molecular dynamics (MD), to select potential novel quoinone outside inhibitors (QoI) of cytochrome bc1 with the aim of determining the same or different chromophores to usual. The study was carried out using the yeast cytochrome bc1 complex with its docked ligand (stigmatellin), using all the fungicides from FRAC code C3 mode of action, 8617 Drugbank compounds and 401,624 COCONUT compounds. The introduced drug repurposing pipeline consists of compound similarity with C3 fungicides and molecular docking (MD) simulations with final QM/MM binding energy determination, while aiming for potential novel chromophores and perserving at least an amide (R1HN(C=O)R2) or ester functional group of almost all up to date C3 fungicides. 3D descriptors used for a similarity test were based on the 280 most stable Padel descriptors. Hit compounds that passed fingerprint and 3D descriptor similarity condition and had either an amide or an ester group were submitted to docking where they further had to satisfy both Chemscore fitness and specific conformation constraints. This rigorous selection resulted in a very limited number of candidates that were forwarded to MD simulations and QM/MM binding affinity estimations by the ORCA DFT program. In this final step, stringent criteria based on (a) sufficiently high frequency of H-bonds; (b) high interaction energy between protein and ligand through the whole MD trajectory; and (c) high enough QM/MM binding energy scores were applied to further filter candidate inhibitors. This elaborate search pipeline led finaly to four Drugbank synthetic lead compounds (DrugBank) and seven natural (COCONUT database) lead compounds—tentative new inhibitors of cytochrome bc1. These eleven lead compounds were additionally validated through a comparison of MM/PBSA free binding energy for new leads against those obtatined for 19 QoIs.
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15
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Hao Z, Wang W, Yu B, Qi X, Lv Y, Liu X, Chen H, Kalinina TA, Glukhareva TV, Fan Z. Design, Synthesis, and Evaluation of Fungicidal Activity of Novel
Pyrazole‐Containing
Strobilurin Derivatives
†. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202000685] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Zesheng Hao
- State Key Laboratory of Elemento‐Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
| | - Weibo Wang
- State Key Laboratory of Elemento‐Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
| | - Bin Yu
- State Key Laboratory of Elemento‐Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
| | - Xin Qi
- State Key Laboratory of Elemento‐Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
| | - You Lv
- State Key Laboratory of Elemento‐Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
| | - Xiaoyu Liu
- State Key Laboratory of Elemento‐Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
| | - Haoyin Chen
- State Key Laboratory of Elemento‐Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
| | - Tatiana A. Kalinina
- The Ural Federal University Named after the First President of Russia B. N. Yeltsin Yeltsin UrFU 620002 Ekaterinburg Russia
| | - Tatiana V. Glukhareva
- The Ural Federal University Named after the First President of Russia B. N. Yeltsin Yeltsin UrFU 620002 Ekaterinburg Russia
| | - Zhijin Fan
- State Key Laboratory of Elemento‐Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
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16
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Kell DB. A protet-based, protonic charge transfer model of energy coupling in oxidative and photosynthetic phosphorylation. Adv Microb Physiol 2021; 78:1-177. [PMID: 34147184 DOI: 10.1016/bs.ampbs.2021.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Textbooks of biochemistry will explain that the otherwise endergonic reactions of ATP synthesis can be driven by the exergonic reactions of respiratory electron transport, and that these two half-reactions are catalyzed by protein complexes embedded in the same, closed membrane. These views are correct. The textbooks also state that, according to the chemiosmotic coupling hypothesis, a (or the) kinetically and thermodynamically competent intermediate linking the two half-reactions is the electrochemical difference of protons that is in equilibrium with that between the two bulk phases that the coupling membrane serves to separate. This gradient consists of a membrane potential term Δψ and a pH gradient term ΔpH, and is known colloquially as the protonmotive force or pmf. Artificial imposition of a pmf can drive phosphorylation, but only if the pmf exceeds some 150-170mV; to achieve in vivo rates the imposed pmf must reach 200mV. The key question then is 'does the pmf generated by electron transport exceed 200mV, or even 170mV?' The possibly surprising answer, from a great many kinds of experiment and sources of evidence, including direct measurements with microelectrodes, indicates it that it does not. Observable pH changes driven by electron transport are real, and they control various processes; however, compensating ion movements restrict the Δψ component to low values. A protet-based model, that I outline here, can account for all the necessary observations, including all of those inconsistent with chemiosmotic coupling, and provides for a variety of testable hypotheses by which it might be refined.
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Affiliation(s)
- Douglas B Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative, Biology, University of Liverpool, Liverpool, United Kingdom; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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Abdullahi M, Adeniji SE, Arthur DE, Haruna A. Homology modeling and molecular docking simulation of some novel imidazo[1,2-a]pyridine-3-carboxamide (IPA) series as inhibitors of Mycobacterium tuberculosis. J Genet Eng Biotechnol 2021; 19:12. [PMID: 33474593 PMCID: PMC7817721 DOI: 10.1186/s43141-020-00102-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 12/07/2020] [Indexed: 02/05/2023]
Abstract
Background Tuberculosis (TB) remains a serious global health challenge that is caused by Mycobacterium tuberculosis and has killed numerous people. This necessitated the urgent need for the hunt and development of more potent drugs against the fast-emerging extensively drug-resistant (XDR) and multiple-drug-resistant (MDR) M. tuberculosis strains. Mycobacterium tuberculosis cytochrome b subunit of the cytochrome bc1 complex (QcrB) was recognized as a potential drug target in M. tuberculosis (25618/H37Rv) for imidazo[1,2-a]pyridine-3-carboxamides whose crystal strucuture is not yet reported in the Protein Data Bank (PDB). The concept of homology modeling as a powerful and useful computational method can be applied, since the M. tuberculosis QcrB protein sequence data are available. Results The homology model of QcrB protein in M. tuberculosis was built from the X-ray structure of QcrB in M. smegmatis as a template using the Swiss-Model online workspace. The modeled protein was assessed, validated, and prepared for the molecular docking simulation of 35 ligands of N-(2-phenoxy)ethyl imidazo[1,2-a] pyridine-3-carboxamide (IPA) to analyze their theoretical binding affinities and modes. The docking results showed that the binding affinity values ranged from − 6.5 to − 10.1 kcal/mol which confirms their resilience potency when compared with 6.0kcal/mol of isoniazid standard drug. However, ligands 2, 7, 22, 26, and 35 scored higher binding affinity values of − 9.60, − 9.80, − 10.10, − 10.00, and − 10.00 kcal/mol, and are respectively considered as the best ligands among others with better binding modes in the active site of the modeled QcrB protein. Conclusion The information derived in this research revealed some potential hits and paved a route for structure-based drug discovery of new hypothetical imidazo pyridine amide analogs as anti-tubercular drug candidates.
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Affiliation(s)
- Mustapha Abdullahi
- Faculty of Physical sciences, Department of Chemistry, Ahmadu Bello University, P.M.B. 1044, Kaduna State, Zaria, Federal Republic of Nigeria.
| | - Shola Elijah Adeniji
- Faculty of Physical sciences, Department of Chemistry, Ahmadu Bello University, P.M.B. 1044, Kaduna State, Zaria, Federal Republic of Nigeria
| | | | - Abdurrashid Haruna
- Faculty of Physical sciences, Department of Chemistry, Ahmadu Bello University, P.M.B. 1044, Kaduna State, Zaria, Federal Republic of Nigeria
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18
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Malík I, Čižmárik J, Kováč G, Pecháčová M, Hudecova L. Telacebec (Q203): Is there a novel effective and safe anti-tuberculosis drug on the horizon? CESKA A SLOVENSKA FARMACIE : CASOPIS CESKE FARMACEUTICKE SPOLECNOSTI A SLOVENSKE FARMACEUTICKE SPOLECNOSTI 2021; 70:164–171. [PMID: 34875838 DOI: 10.5817/csf2021-5-164] [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] [Indexed: 06/13/2023]
Abstract
High prevalence and stronger emergency of various forms of drug-resistant tuberculosis (DR-TB), including the multidrug-resistant (MDR-TB) as well as extensively drug-resistant (XDR-TB) ones, caused by variously resistant Mycobacterium tuberculosis pathogens, make first-line anti-tuberculosis (anti-TB) agents therapeutically more and more ineffective. Therefore, there is an imperative to develop novel highly efficient (synthetic) agents against both drug-sensitive-TB and DR-TB. The exploration of various heterocycles as prospective core scaffolds for the discovery, development and optimization of anti-TB drugs remains an intriguing scientific endeavour. Telacebec (Q203; TCB), a molecule containing an imidazo[1,2-a]pyridine-3-carboxamide (IPA) structural motif, is considered a novel very promising anti-TB agent showing a unique mechanism of action. The compound blocks oxidative phosphorylation by inhibiting a mycobacterial respiratory chain due to interference with a specific cytochrome b subunit (QcrB) of transmembrane bc1 menaquinol-cytochrome c oxidoreductase as an essential component for transporting electrons across the membrane from menaquinol to other specific subunit, cytochrome c (QcrC). Thus, the ability of mycobacteria to synthesize adenosine-5´-triphosphate is limited and energy generating machinery is disabled. The TCB molecule effectively fights drug-susceptible, MDR as well as XDR M. tuberculosis strains. The article briefly explains a mechanism of an anti-TB action related to the compounds containing a variously substituted IPA scaffold and is focused on their fundamental structure-anti-TB activity relationships as well. Special consideration is paid to TCB indicating the importance of particular structural fragments for maintaining (or even improving) favourable pharmacodynamic, pharmacokinetic and/or toxicological properties. High lipophilicity of TCB might be regarded as one of the key physicochemical properties with positive impact on anti-TB effect of the drug. In January 2021, the TCB molecule was also involved in phase-II clinical trials focused on the treatment of Coronavirus Disease-19 caused by Severe Acute Respiratory Syndrome Coronavirus 2.
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19
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Wang M, Ren X, Wang L, Lu X, Han L, Zhang X, Feng J. A functional analysis of mitochondrial respiratory chain cytochrome bc 1 complex in Gaeumannomyces tritici by RNA silencing as a possible target of carabrone. MOLECULAR PLANT PATHOLOGY 2020; 21:1529-1544. [PMID: 32997435 PMCID: PMC7694678 DOI: 10.1111/mpp.12993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/20/2020] [Accepted: 08/21/2020] [Indexed: 05/05/2023]
Abstract
Gaeumannomyces tritici, an ascomycete soilborne fungus, causes a devastating root disease in wheat. Carabrone, a botanical bicyclic sesquiterpenic lactone, is a promising fungicidal agent that can effectively control G. tritici. However, the mechanism of action of carabrone against G. tritici remains largely unclear. Here, we used immunogold for subcellular localization of carabrone and the results showed that carabrone is subcellularly localized in the mitochondria of G. tritici. We then explored the functional analysis of genes GtCytc1 , GtCytb, and GtIsp of the mitochondrial respiratory chain cytochrome bc1 complex in G. tritici by RNA silencing as a possible target of carabrone. The results showed that the silenced mutant ∆GtIsp is less sensitive to carabrone compared to ∆GtCytc1 and ∆GtCytb. Compared with the control, the activities of complex III in all the strains, except ∆GtIsp and carabrone-resistant isolate 24-HN-1, were significantly decreased following treatment with carabrone at EC20 and EC80 in vitro (40%-50% and 70%-80%, respectively). The activities of mitochondrial respiratory chain complex III and the mitochondrial respiration oxygen consumption rates in all the strains, except ∆GtIsp and 24-HN-1, were higher with respect to the control when treated with carabrone at EC20 in vivo. The rates of mitochondrial respiration of all strains, except ∆GtIsp, were significantly inhibited following treatment with carabrone at EC80 (ranging from 57% to 81%). This study reveals that the targeting of the iron-sulphur protein encoded by GtIsp is highly sensitive to carabrone and provides a direction for the research of carabrone's target.
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Affiliation(s)
- Mei Wang
- Engineering and Research Center of Biological Pesticide of Shaanxi ProvinceNorthwest A&F UniversityYanglingChina
- College of Life SciencesYulin UniversityYulinChina
| | - Xingyu Ren
- Engineering and Research Center of Biological Pesticide of Shaanxi ProvinceNorthwest A&F UniversityYanglingChina
| | - Lanying Wang
- Engineering and Research Center of Biological Pesticide of Shaanxi ProvinceNorthwest A&F UniversityYanglingChina
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and PestsMinistry of EducationHainan UniversityHaikouChina
| | - Xiang Lu
- Engineering and Research Center of Biological Pesticide of Shaanxi ProvinceNorthwest A&F UniversityYanglingChina
| | - Lirong Han
- Engineering and Research Center of Biological Pesticide of Shaanxi ProvinceNorthwest A&F UniversityYanglingChina
| | - Xing Zhang
- Engineering and Research Center of Biological Pesticide of Shaanxi ProvinceNorthwest A&F UniversityYanglingChina
- State Key Laboratory of Crop Stress Biology for Arid AreasNorthwest A&F UniversityYanglingChina
| | - Juntao Feng
- Engineering and Research Center of Biological Pesticide of Shaanxi ProvinceNorthwest A&F UniversityYanglingChina
- State Key Laboratory of Crop Stress Biology for Arid AreasNorthwest A&F UniversityYanglingChina
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20
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Xia D. Structural snapshots of the cellular folded protein translocation machinery Bcs1. FEBS J 2020; 288:2870-2883. [PMID: 32979284 PMCID: PMC7994207 DOI: 10.1111/febs.15576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/05/2020] [Accepted: 09/22/2020] [Indexed: 11/29/2022]
Abstract
Proteins destined to various intra‐ and extra‐cellular locations must traverse membranes most frequently in an unfolded form. When the proteins being translocated need to remain in a folded state, specialized cellular transport machinery is used. One such machine is the membrane‐bound AAA protein Bcs1 (Bcs1), which assists the iron‐sulfur protein, an essential subunit of the respiratory Complex III, across the mitochondrial inner membrane. Recent structure determinations of mouse and yeast Bcs1 in three different nucleotide states reveal its homo‐heptameric association and at least two dramatically different conformations. The apo and ADP‐bound structures are similar, both containing a large substrate‐binding cavity accessible to the mitochondrial matrix space, which contracts by concerted motion of the ATPase domains upon ATP binding, suggesting that bound substrate could then be pushed across the membrane. ATP hydrolysis drives substrate release and resets Bcs1 conformation back to the apo/ADP form. These structures shed new light on the mechanism of folded protein translocation across a membrane, provide better understanding on the assembly process of the respiratory Complex III, and correlate clinical presentations of disease‐associated mutations with their locations in the 3D structure.
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Affiliation(s)
- Di Xia
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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21
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Li X, Yang X, Zheng X, Bai M, Hu D. Review on Structures of Pesticide Targets. Int J Mol Sci 2020; 21:E7144. [PMID: 32998191 PMCID: PMC7582455 DOI: 10.3390/ijms21197144] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/23/2020] [Accepted: 09/25/2020] [Indexed: 12/12/2022] Open
Abstract
Molecular targets play important roles in agrochemical discovery. Numerous pesticides target the key proteins in pathogens, insect, or plants. Investigating ligand-binding pockets and/or active sites in the proteins' structures is usually the first step in designing new green pesticides. Thus, molecular target structures are extremely important for the discovery and development of such pesticides. In this manuscript, we present a review of the molecular target structures, including those of antiviral, fungicidal, bactericidal, insecticidal, herbicidal, and plant growth-regulator targets, currently used in agrochemical research. The data will be helpful in pesticide design and the discovery of new green pesticides.
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Affiliation(s)
- Xiangyang Li
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, China;
| | - Xueqing Yang
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China;
| | - Xiaodong Zheng
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China;
| | - Miao Bai
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China;
| | - Deyu Hu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, China;
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22
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Fisher N, Meunier B, Biagini GA. The cytochrome bc 1 complex as an antipathogenic target. FEBS Lett 2020; 594:2935-2952. [PMID: 32573760 DOI: 10.1002/1873-3468.13868] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/31/2020] [Accepted: 06/10/2020] [Indexed: 12/15/2022]
Abstract
The cytochrome bc1 complex is a key component of the mitochondrial respiratory chains of many eukaryotic microorganisms that are pathogenic for plants or humans, such as fungi responsible for crop diseases and Plasmodium falciparum, which causes human malaria. Cytochrome bc1 is an enzyme that contains two (ubi)quinone/quinol-binding sites, which can be exploited for the development of fungicidal and chemotherapeutic agents. Here, we review recent progress in determination of the structure and mechanism of action of cytochrome bc1 , and the associated development of antimicrobial agents (and associated resistance mechanisms) targeting its activity.
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Affiliation(s)
- Nicholas Fisher
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
| | - Brigitte Meunier
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France
| | - Giancarlo A Biagini
- Parasitology Department, Research Centre for Drugs & Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
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23
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Kamerlin N, Delcey MG, Manzetti S, van der Spoel D. Toward a Computational Ecotoxicity Assay. J Chem Inf Model 2020; 60:3792-3803. [PMID: 32648756 DOI: 10.1021/acs.jcim.0c00574] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thousands of anthropogenic chemicals are released into the environment each year, posing potential hazards to human and environmental health. Toxic chemicals may cause a variety of adverse health effects, triggering immediate symptoms or delayed effects over longer periods of time. It is thus crucial to develop methods that can rapidly screen and predict the toxicity of chemicals to limit the potential harmful impacts of chemical pollutants. Computational methods are being increasingly used in toxicity predictions. Here, the method of molecular docking is assessed for screening potential toxicity of a variety of xenobiotic compounds, including pesticides, pharmaceuticals, pollutants, and toxins derived from the chemical industry. The method predicts the binding energy of pollutants to a set of carefully selected receptors under the assumption that toxicity in many cases is related to interference with biochemical pathways. The strength of the applied method lies in its rapid generation of interaction maps between potential toxins and the targeted enzymes, which could quickly yield molecular-level information and insight into potential perturbation pathways, aiding in the prioritization of chemicals for further tests. Two scoring functions are compared: Autodock Vina and the machine-learning scoring function RF-Score-VS. The results are promising, although hampered by the accuracy of the scoring functions. The strengths and weaknesses of the docking protocol are discussed, as well as future directions for improving the accuracy for the purpose of toxicity predictions.
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Affiliation(s)
- Natasha Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Mickaël G Delcey
- Department of Chemistry-Ångström Laboratory, Uppsala University, SE-75120 Uppsala, Sweden
| | - Sergio Manzetti
- Institute for Science and Technology, Fjordforsk A.S., Midtun, 6894 Vangsnes, Norway
| | - David van der Spoel
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
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Purhonen J, Grigorjev V, Ekiert R, Aho N, Rajendran J, Pietras R, Truvé K, Wikström M, Sharma V, Osyczka A, Fellman V, Kallijärvi J. A spontaneous mitonuclear epistasis converging on Rieske Fe-S protein exacerbates complex III deficiency in mice. Nat Commun 2020; 11:322. [PMID: 31949167 PMCID: PMC6965120 DOI: 10.1038/s41467-019-14201-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 12/17/2019] [Indexed: 12/12/2022] Open
Abstract
We previously observed an unexpected fivefold (35 vs. 200 days) difference in the survival of respiratory chain complex III (CIII) deficient Bcs1lp.S78G mice between two congenic backgrounds. Here, we identify a spontaneous homoplasmic mtDNA variant (m.G14904A, mt-Cybp.D254N), affecting the CIII subunit cytochrome b (MT-CYB), in the background with short survival. We utilize maternal inheritance of mtDNA to confirm this as the causative variant and show that it further decreases the low CIII activity in Bcs1lp.S78G tissues to below survival threshold by 35 days of age. Molecular dynamics simulations predict D254N to restrict the flexibility of MT-CYB ef loop, potentially affecting RISP dynamics. In Rhodobacter cytochrome bc1 complex the equivalent substitution causes a kinetics defect with longer occupancy of RISP head domain towards the quinol oxidation site. These findings represent a unique case of spontaneous mitonuclear epistasis and highlight the role of mtDNA variation as modifier of mitochondrial disease phenotypes.
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Affiliation(s)
- Janne Purhonen
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, P.O. Box 63 (Haartmaninkatu 8), FI-00014, Helsinki, Finland.,Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Vladislav Grigorjev
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, P.O. Box 63 (Haartmaninkatu 8), FI-00014, Helsinki, Finland
| | - Robert Ekiert
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387, Kraków, Poland
| | - Noora Aho
- Department of Physics, University of Helsinki, P.O. Box 64 (Gustaf Hällströmin katu 2), FI-00014, Helsinki, Finland.,Department of Chemistry, University of Jyväskylä, P.O. Box 35 (Survontie 9B), FI-40014, Jyväskylä, Finland
| | - Jayasimman Rajendran
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, P.O. Box 63 (Haartmaninkatu 8), FI-00014, Helsinki, Finland.,Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Rafał Pietras
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387, Kraków, Poland
| | - Katarina Truvé
- Sahlgrenska Academy, University of Gothenburg, P.O. Box 413 (Medicinaregatan 3), 41390, Gothenburg, Sweden
| | - Mårten Wikström
- Institute of Biotechnology, University of Helsinki, PL 56 (Viikinkaari 9), FI-00014, Helsinki, Finland
| | - Vivek Sharma
- Department of Physics, University of Helsinki, P.O. Box 64 (Gustaf Hällströmin katu 2), FI-00014, Helsinki, Finland.,Institute of Biotechnology, University of Helsinki, PL 56 (Viikinkaari 9), FI-00014, Helsinki, Finland
| | - Artur Osyczka
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387, Kraków, Poland
| | - Vineta Fellman
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, P.O. Box 63 (Haartmaninkatu 8), FI-00014, Helsinki, Finland.,Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Clinical Sciences, Pediatrics, BMC F12, Lund University, 221 84, Lund, Sweden.,Children's Hospital, Helsinki University Hospital, P.O. Box 281 (Stenbäckinkatu 11), FI-00029, Helsinki, Finland
| | - Jukka Kallijärvi
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, P.O. Box 63 (Haartmaninkatu 8), FI-00014, Helsinki, Finland. .,Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
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25
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Pan Z, Wang Y, Gu X, Wang J, Cheng M. Refined homology model of cytochrome bcc complex B subunit for virtual screening of potential anti-tuberculosis agents. J Biomol Struct Dyn 2019; 38:4733-4745. [DOI: 10.1080/07391102.2019.1688196] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Zhenhai Pan
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, Liaoning, P. R. China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, P. R. China
| | - Ying Wang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, P. R. China
| | - Xi Gu
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, Liaoning, P. R. China
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning, P. R. China
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, Liaoning, P. R. China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, P. R. China
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, Liaoning, P. R. China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, P. R. China
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26
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Bahuguna A, Rawat DS. An overview of new antitubercular drugs, drug candidates, and their targets. Med Res Rev 2019; 40:263-292. [PMID: 31254295 DOI: 10.1002/med.21602] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 05/16/2019] [Accepted: 05/17/2019] [Indexed: 12/15/2022]
Abstract
The causative agent of tuberculosis (TB), Mycobacterium tuberculosis and more recently totally drug-resistant strains of M. tuberculosis, display unique mechanisms to survive in the host. A four-drug treatment regimen was introduced 40 years ago but the emergence of multidrug-resistance and more recently TDR necessitates the identification of new targets and drugs for the cure of M. tuberculosis infection. The current efforts in the drug development process are insufficient to completely eradicate the TB epidemic. For almost five decades the TB drug development process remained stagnant. The last 10 years have made sudden progress giving some new and highly promising drugs including bedaquiline, delamanid, and pretomanid. Many of the candidates are repurposed compounds, which were developed to treat other infections but later, exhibited anti-TB properties also. Each class of drug has a specific target and a definite mode of action. These targets are either involved in cell wall biosynthesis, protein synthesis, DNA/RNA synthesis, or metabolism. This review discusses recent progress in the discovery of newly developed and Food and Drug Administration approved drugs as well as repurposed drugs, their targets, mode of action, drug-target interactions, and their structure-activity relationship.
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Affiliation(s)
| | - Diwan S Rawat
- Department of Chemistry, University of Delhi, Delhi, India
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27
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Perevoshchikova AN, Eroshenko DV, Dmitriev MV, Grishko VV, Shklyaev YV. Synthesis and Prediction of the Ubiquinol‐cytochrome
c
Reductase Inhibitory Activity of 3,4‐Dihydroisoquinolines and 2‐Azaspiro[4.5]decanes (Spiropyrrolines). J Heterocycl Chem 2019. [DOI: 10.1002/jhet.3551] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Anna N. Perevoshchikova
- Institute of Technical Chemistry of Ural Branch of the Russian Academy of Sciences Academician Korolev Street 3 614013 Perm Russia
| | - Daria V. Eroshenko
- Institute of Technical Chemistry of Ural Branch of the Russian Academy of Sciences Academician Korolev Street 3 614013 Perm Russia
| | - Maksim V. Dmitriev
- Perm State National Research University Bukirev Street 15 614990 Perm Russia
| | - Victoria V. Grishko
- Institute of Technical Chemistry of Ural Branch of the Russian Academy of Sciences Academician Korolev Street 3 614013 Perm Russia
| | - Yurii V. Shklyaev
- Institute of Technical Chemistry of Ural Branch of the Russian Academy of Sciences Academician Korolev Street 3 614013 Perm Russia
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28
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Preparation, characterization, and evaluation of azoxystrobin nanosuspension produced by wet media milling. APPLIED NANOSCIENCE 2018. [DOI: 10.1007/s13204-018-0745-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Abstract
To improve the bioavailability of the poorly water-soluble fungicide, an azoxystrobin nanosuspension was prepared by the wet media milling method. Due to their reduced mean particle size and polydispersity index, 1-Dodecanesulfonic acid sodium salt and polyvinylpyrrolidone K30 were selected from six conventional surfactants, the content only accounting for 15% of the active compound. The mean particle size, polydispersity index, and
$$\zeta$$
ζ
potential of the nanosuspension were determined to be 238.1 ± 1.5 nm, 0.17 ± 0.02 and − 31.8 ± 0.3 mV, respectively. The lyophilized nanosuspension mainly retained crystalline state, with only a little amorphous content as determined by powder X-ray diffraction. Compared to conventional fungicide formulations, the nanosuspension presented an increased retention volume and a reduced contact angle, indicating enhanced wettability and adhesion. In addition, the azoxystrobin nanosuspension showed the highest antifungal activity, with a medial lethal concentration of 1.4243 μg/mL against Fusarium oxysporum. In optical micrographs, hyphal deformations of thinner and intertwined hyphae were detected in the exposed group. Compared to the control group, the total soluble protein content, superoxide dismutase, and catalase activities were initially increased and then decreased with prolonged exposure time. The azoxystrobin nanosuspension reduced the defensive antioxidant capability of Fusarium oxysporum and resulted in the generation of excessive reactive oxygen species. This study provides a novel method for preparing nanosuspension formulation of poorly soluble antifungal agents to enhance the biological activity and decrease the negative environmental impact.
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29
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Fernandez-Vizarra E, Zeviani M. Mitochondrial complex III Rieske Fe-S protein processing and assembly. Cell Cycle 2018; 17:681-687. [PMID: 29243944 DOI: 10.1080/15384101.2017.1417707] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Regulation of the mitochondrial respiratory chain biogenesis is a matter of great interest because of its implications for mitochondrial disease. One of the mitochondrial disease genes recently discovered associated to encephalopathy and mitochondrial complex III (cIII) deficiency is TTC19. Our study of TTC19-deficient human and mouse models, has led us to propose a post-assembly quality control role or 'husbandry' function for this factor that is linked to Rieske Fe-S protein (UQCRFS1). UQCRFS1 is the last incorporated cIII subunit, and its presence is essential for enzymatic activity. During UQCRFS1 assembly, the precursor is cleaved and its N-terminal part remains bound to the complex, between the two core subunits (UQCRC1 and UQCRC2). In the absence of TTC19 there is a prominent accumulation of these UQCRFS1-derived N-terminal fragments that proved to be detrimental for cIII function. In this article we will discuss some ideas around the UQCRFS1 processing and assembly and its importance for the regulation of cIII activity and biogenesis.
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Affiliation(s)
- Erika Fernandez-Vizarra
- a MRC-Mitochondrial Biology Unit , University of Cambridge , Hills Road, CB2 0XY , Cambridge , UK
| | - Massimo Zeviani
- a MRC-Mitochondrial Biology Unit , University of Cambridge , Hills Road, CB2 0XY , Cambridge , UK
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30
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Wang M, Wang L, Han L, Zhang X, Feng J. The effect of carabrone on mitochondrial respiratory chain complexes inGaeumannomyces graminis. J Appl Microbiol 2017; 123:1100-1110. [DOI: 10.1111/jam.13554] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 07/07/2017] [Accepted: 07/27/2017] [Indexed: 01/01/2023]
Affiliation(s)
- M. Wang
- Research and Development Center of Biorational Pesticide; Northwest A&F University; Yangling 712100 Shaanxi China
| | - L. Wang
- Research and Development Center of Biorational Pesticide; Northwest A&F University; Yangling 712100 Shaanxi China
| | - L. Han
- Research and Development Center of Biorational Pesticide; Northwest A&F University; Yangling 712100 Shaanxi China
| | - X. Zhang
- Research and Development Center of Biorational Pesticide; Northwest A&F University; Yangling 712100 Shaanxi China
- Engineering and Research Center of Biological Pesticide of Shaanxi Province; Yangling 712100 Shaanxi China
| | - J. Feng
- Research and Development Center of Biorational Pesticide; Northwest A&F University; Yangling 712100 Shaanxi China
- Engineering and Research Center of Biological Pesticide of Shaanxi Province; Yangling 712100 Shaanxi China
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31
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Amazing structure of respirasome: unveiling the secrets of cell respiration. Protein Cell 2016; 7:854-865. [PMID: 27743346 PMCID: PMC5205662 DOI: 10.1007/s13238-016-0329-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 09/28/2016] [Indexed: 11/02/2022] Open
Abstract
Respirasome, a huge molecular machine that carries out cellular respiration, has gained growing attention since its discovery, because respiration is the most indispensable biological process in almost all living creatures. The concept of respirasome has renewed our understanding of the respiratory chain organization, and most recently, the structure of respirasome solved by Yang's group from Tsinghua University (Gu et al. Nature 237(7622):639-643, 2016) firstly presented the detailed interactions within this huge molecular machine, and provided important information for drug design and screening. However, the study of cellular respiration went through a long history. Here, we briefly showed the detoured history of respiratory chain investigation, and then described the amazing structure of respirasome.
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32
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Esser L, Zhou F, Zhou Y, Xiao Y, Tang WK, Yu CA, Qin Z, Xia D. Hydrogen Bonding to the Substrate Is Not Required for Rieske Iron-Sulfur Protein Docking to the Quinol Oxidation Site of Complex III. J Biol Chem 2016; 291:25019-25031. [PMID: 27758861 DOI: 10.1074/jbc.m116.744391] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 10/05/2016] [Indexed: 11/06/2022] Open
Abstract
Complex III or the cytochrome (cyt) bc1 complex constitutes an integral part of the respiratory chain of most aerobic organisms and of the photosynthetic apparatus of anoxygenic purple bacteria. The function of cyt bc1 is to couple the reaction of electron transfer from ubiquinol to cytochrome c to proton pumping across the membrane. Mechanistically, the electron transfer reaction requires docking of its Rieske iron-sulfur protein (ISP) subunit to the quinol oxidation site (QP) of the complex. Formation of an H-bond between the ISP and the bound substrate was proposed to mediate the docking. Here we show that the binding of oxazolidinedione-type inhibitors famoxadone, jg144, and fenamidone induces docking of the ISP to the QP site in the absence of the H-bond formation both in mitochondrial and bacterial cyt bc1 complexes, demonstrating that ISP docking is independent of the proposed direct ISP-inhibitor interaction. The binding of oxazolidinedione-type inhibitors to cyt bc1 of different species reveals a toxophore that appears to interact optimally with residues in the QP site. The effect of modifications or additions to the toxophore on the binding to cyt bc1 from different species could not be predicted from structure-based sequence alignments, as demonstrated by the altered binding mode of famoxadone to bacterial cyt bc1.
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Affiliation(s)
- Lothar Esser
- From the Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Fei Zhou
- From the Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Yihui Zhou
- From the Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892.,the College of Science, China Agricultural University, Beijing 100193, China, and
| | - Yumei Xiao
- From the Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892.,the College of Science, China Agricultural University, Beijing 100193, China, and
| | - Wai-Kwan Tang
- From the Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Chang-An Yu
- the Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma 74078
| | - Zhaohai Qin
- the College of Science, China Agricultural University, Beijing 100193, China, and
| | - Di Xia
- From the Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892,
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33
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Sarewicz M, Dutka M, Pietras R, Borek A, Osyczka A. Effect of H bond removal and changes in the position of the iron-sulphur head domain on the spin-lattice relaxation properties of the [2Fe-2S](2+) Rieske cluster in cytochrome bc(1). Phys Chem Chem Phys 2016; 17:25297-308. [PMID: 26355649 PMCID: PMC5716461 DOI: 10.1039/c5cp02815a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Here, comparative electron spin–lattice relaxation studies of the 2Fe–2S iron–sulphur (Fe–S) cluster embedded in a large membrane protein complex – cytochrome bc1 – are reported.
Here, comparative electron spin–lattice relaxation studies of the 2Fe–2S iron–sulphur (Fe–S) cluster embedded in a large membrane protein complex – cytochrome bc1 – are reported. Structural modifications of the local environment alone (mutations S158A and Y160W removing specific H bonds between Fe–S and amino acid side chains) or in combination with changes in global protein conformation (mutations/inhibitors changing the position of the Fe–S binding domain within the protein complex) resulted in different redox potentials as well as g-, g-strain and the relaxation rates (T1–1) for the Fe–S cluster. The relaxation rates for T < 25 K were measured directly by inversion recovery, while for T > 60 K they were deduced from simulation of continuous wave EPR spectra of the cluster using a model that included anisotropy of Lorentzian broadening. In all cases, the relaxation rate involved contributions from direct, second-order Raman and Orbach processes, each dominating over different temperature ranges. The analysis of T1–1 (T) over the range 5–120 K yielded the values of the Orbach energy (EOrb), Debye temperature θD and Raman process efficiency CRam for each variant of the protein. As the Orbach energy was generally higher for mutants S158A and Y160W, compared to wild-type protein (WT), it is suggested that H bond removal influences the geometry leading to increased strength of antiferromagnetic coupling between two Fe ions of the cluster. While θD was similar for all variants (∼107 K), the efficiency of the Raman process generally depends on the spin–orbit coupling that is lower for S158A and Y160W mutants, when compared to the WT. However, in several cases CRam did not only correlate with spin–orbit coupling but was also influenced by other factors – possibly the modification of protein rigidity and therefore the vibrational modes around the Fe–S cluster that change upon the movement of the iron–sulphur head domain.
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Affiliation(s)
- Marcin Sarewicz
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland.
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34
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Arnarez C, Marrink SJ, Periole X. Molecular mechanism of cardiolipin-mediated assembly of respiratory chain supercomplexes. Chem Sci 2016; 7:4435-4443. [PMID: 30155091 PMCID: PMC6014297 DOI: 10.1039/c5sc04664e] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/15/2016] [Indexed: 12/22/2022] Open
Abstract
Mitochondria produce most of the ATP consumed by cells through the respiratory chain in their inner membrane. This process involves protein complexes assembled into larger structures, the respiratory supercomplexes (SCs). Cardiolipin (CL), the mitochondrial signature phospholipid, is crucial for the structural and functional integrity of these SCs, but it is as yet unclear by what mechanism it operates. Our data disclose the mechanism for bulk CL in gluing SCs, steering their formation, and suggest how it may stabilize specific interfaces. We describe self-assembly molecular dynamics simulations of 9 cytochrome bc1 (CIII) dimers and 27 cytochrome c oxidase (CIV) monomers from bovine heart mitochondria embedded in a CL-containing model lipid bilayer, aimed at mimicking the crowdedness and complexity of mitochondrial membranes. The simulations reveal a large diversity of interfaces, including those of existing experimental CIII/CIV SC models and an alternative interface with CIV rotated by 180°. SC interfaces enclose 4 to 12 CLs, a ∼10 fold enrichment from the bulk. Half of these CLs glue complexes together using CL binding sites at the surface of both complexes. Free energy calculations demonstrate a larger CL binding strength, compared to other mitochondrial lipids, that is exclusive to these binding sites and results from non-additive electrostatic and van der Waals forces. This study provides a key example of the ability of lipids to selectively mediate protein-protein interactions by altering all ranges of forces, lubricate protein interfaces and act as traffic control agents steering proteins together.
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Affiliation(s)
- C Arnarez
- Groningen Biomolecular Sciences and Biotechnology Institute , Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 7 , 9747 AG Groningen , The Netherlands . ; ; Tel: +31-503632462
| | - S J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute , Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 7 , 9747 AG Groningen , The Netherlands . ; ; Tel: +31-503632462
| | - X Periole
- Groningen Biomolecular Sciences and Biotechnology Institute , Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 7 , 9747 AG Groningen , The Netherlands . ; ; Tel: +31-503632462
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35
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Ko Y, Choi I. Putative 3D Structure of QcrB fromMycobacterium tuberculosisCytochromebc1 Complex, a Novel Drug-Target for New Series of Antituberculosis Agent Q203. B KOREAN CHEM SOC 2016. [DOI: 10.1002/bkcs.10765] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yoonae Ko
- Cheminformatics Group; Institut Pasteur Korea; Gyeonggi-do 13488 Republic of Korea
| | - Inhee Choi
- Cheminformatics Group; Institut Pasteur Korea; Gyeonggi-do 13488 Republic of Korea
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36
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Zhu L, Peigneur S, Gao B, Zhang S, Tytgat J, Zhu S. Target-Driven Positive Selection at Hot Spots of Scorpion Toxins Uncovers Their Potential in Design of Insecticides. Mol Biol Evol 2016; 33:1907-20. [PMID: 27189560 DOI: 10.1093/molbev/msw065] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Positive selection sites (PSSs), a class of amino acid sites with an excess of nonsynonymous to synonymous substitutions, are indicators of adaptive molecular evolution and have been detected in many protein families involved in a diversity of biological processes by statistical approaches. However, few studies are conducted to evaluate their functional significance and the driving force behind the evolution (i.e., agent of selection). Scorpion α-toxins are a class of multigene family of peptide neurotoxins affecting voltage-gated Na(+ )(Nav) channels, whose members exhibit differential potency and preference for insect and mammalian Nav channels. In this study, we undertook a systematical molecular dissection of nearly all the PSSs newly characterized in the Mesobuthus α-toxin family and a two-residue insertion ((19)AlaPhe(20)) located within a positively selected loop via mutational analysis of α-like MeuNaTxα-5, one member affecting both insect and mammalian Nav channels. This allows to identify hot-spot residues on its functional face involved in interaction with the receptor site of Nav channels, which comprises two PSSs (Ile(40) and Leu(41)) and the small insertion, both located on two spatially separated functional loops. Mutations at these hot-spots resulted in a remarkably decreased anti-mammalian activity in MeuNaTxα-5 with partially impaired or enhanced insecticide activity, suggesting the potential of PSSs in designing promising candidate insecticides from scorpion α-like toxins. Based on an experiment-guided toxin-channel complex model and high evolutionary variability in the receptor site of predators and prey of scorpions, we provide new evidence for target-driven adaptive evolution of scorpion toxins to deal with their targets' diversity.
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Affiliation(s)
- Limei Zhu
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects & Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Steve Peigneur
- Laboratory of Toxicology, University of Leuven, Leuven, Belgium
| | - Bin Gao
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects & Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Shangfei Zhang
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects & Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jan Tytgat
- Laboratory of Toxicology, University of Leuven, Leuven, Belgium
| | - Shunyi Zhu
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects & Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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37
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The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part III. {[Fe2S2](Cys)3(X)} (X=Asp, Arg, His) and {[Fe2S2](Cys)2(His)2} proteins. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2015.07.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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38
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Electron Transfer Reactions at the Qo Site of the Cytochrome bc 1 Complex: The Good, the Bad, and the Ugly. ADVANCES IN PHOTOSYNTHESIS AND RESPIRATION 2016. [DOI: 10.1007/978-94-017-7481-9_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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39
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Vladkova R. Chlorophyllais the crucial redox sensor and transmembrane signal transmitter in the cytochromeb6fcomplex. Components and mechanisms of state transitions from the hydrophobic mismatch viewpoint. J Biomol Struct Dyn 2015; 34:824-54. [DOI: 10.1080/07391102.2015.1056551] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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40
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Karunadharma PP, Basisty N, Chiao YA, Dai DF, Drake R, Levy N, Koh WJ, Emond MJ, Kruse S, Marcinek D, Maccoss MJ, Rabinovitch PS. Respiratory chain protein turnover rates in mice are highly heterogeneous but strikingly conserved across tissues, ages, and treatments. FASEB J 2015; 29:3582-92. [PMID: 25977255 DOI: 10.1096/fj.15-272666] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 05/04/2015] [Indexed: 11/11/2022]
Abstract
The mitochondrial respiratory chain (RC) produces most of the cellular ATP and requires strict quality-control mechanisms. To examine RC subunit proteostasis in vivo, we measured RC protein half-lives (HLs) in mice by liquid chromatography-tandem mass spectrometry with metabolic [(2)H3]-leucine heavy isotope labeling under divergent conditions. We studied 7 tissues/fractions of young and old mice on control diet or one of 2 diet regimens (caloric restriction or rapamycin) that altered protein turnover (42 conditions in total). We observed a 6.5-fold difference in mean HL across tissues and an 11.5-fold difference across all conditions. Normalization to the mean HL of each condition showed that relative HLs were conserved across conditions (Spearman's ρ = 0.57; P < 10(-4)), but were highly heterogeneous between subunits, with a 7.3-fold mean range overall, and a 2.2- to 4.6-fold range within each complex. To identify factors regulating this conserved distribution, we performed statistical analyses to study the correlation of HLs to the properties of the subunits. HLs significantly correlated with localization within the mitochondria, evolutionary origin, location of protein-encoding, and ubiquitination levels. These findings challenge the notion that all subunits in a complex turnover at comparable rates and suggest that there are common rules governing the differential proteolysis of RC protein subunits under divergent cellular conditions.
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Affiliation(s)
- Pabalu P Karunadharma
- *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA
| | - Nathan Basisty
- *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA
| | - Ying Ann Chiao
- *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA
| | - Dao-Fu Dai
- *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA
| | - Rachel Drake
- *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA
| | - Nick Levy
- *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA
| | - William J Koh
- *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA
| | - Mary J Emond
- *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA
| | - Shane Kruse
- *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA
| | - David Marcinek
- *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA
| | - Michael J Maccoss
- *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA
| | - Peter S Rabinovitch
- *Department of Pathology, Department of Environmental Health and Biostatistics, Department of Radiology, and Department of Genome Sciences, University of Washington, Seattle, Washington, USA; and The Scripps Research Institute, Jupiter, Florida, USA
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Zhu X, Zhang M, Liu J, Ge J, Yang G. Ametoctradin is a potent Qo site inhibitor of the mitochondrial respiration complex III. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:3377-3386. [PMID: 25784492 DOI: 10.1021/acs.jafc.5b00228] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Ametoctradin is a new Oomycete-specific fungicide under development by BASF. It is a potent inhibitor of the bc1 complex in mitochondrial respiration. However, its detailed action mechanism remains unknown. In the present work, the binding mode of ametoctradin was first uncovered by integrating molecular docking, MD simulations, and MM/PBSA calculations, which showed that ametoctradin should be a Q(o) site inhibitor of bc1 complex. Subsequently, a series of new 1,2,4-triazolo[1,5-a]pyrimidine derivatives were designed and synthesized to further understand the substituent effects on the 5- and 6-position of 1,2,4-triazolo[1,5-a]pyrimidine. The calculated binding free energies (ΔG(cal)) of newly synthesized analogues as Qo site inhibitors correlated very well (R(2) = 0.96) with their experimental binding free energies (ΔG(exp)). Two compounds (4a and 4c) with higher inhibitory activity against porcine SQR than ametoctradin were successfully identified. The structural and mechanistic insights obtained from the present study will provide a valuable clue for future designing of a new promising bc1 inhibitor.
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Affiliation(s)
- Xiaolei Zhu
- †Key Laboratory of Pesticide and Chemical Biology, College of Chemistry, Ministry of Education, Central China Normal University, Wuhan 430079, P.R. China
| | - Mengmeng Zhang
- †Key Laboratory of Pesticide and Chemical Biology, College of Chemistry, Ministry of Education, Central China Normal University, Wuhan 430079, P.R. China
| | - Jingjing Liu
- †Key Laboratory of Pesticide and Chemical Biology, College of Chemistry, Ministry of Education, Central China Normal University, Wuhan 430079, P.R. China
| | - Jingming Ge
- †Key Laboratory of Pesticide and Chemical Biology, College of Chemistry, Ministry of Education, Central China Normal University, Wuhan 430079, P.R. China
| | - Guangfu Yang
- †Key Laboratory of Pesticide and Chemical Biology, College of Chemistry, Ministry of Education, Central China Normal University, Wuhan 430079, P.R. China
- ‡Collaborative Innovation Center of Chemical Science and Engineering, Tianjing 30071, P.R.China
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42
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Reimann J, Jetten MSM, Keltjens JT. Metal enzymes in "impossible" microorganisms catalyzing the anaerobic oxidation of ammonium and methane. Met Ions Life Sci 2015; 15:257-313. [PMID: 25707470 DOI: 10.1007/978-3-319-12415-5_7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ammonium and methane are inert molecules and dedicated enzymes are required to break up the N-H and C-H bonds. Until recently, only aerobic microorganisms were known to grow by the oxidation of ammonium or methane. Apart from respiration, oxygen was specifically utilized to activate the inert substrates. The presumed obligatory need for oxygen may have resisted the search for microorganisms that are capable of the anaerobic oxidation of ammonium and of methane. However extremely slowly growing, these "impossible" organisms exist and they found other means to tackle ammonium and methane. Anaerobic ammonium-oxidizing (anammox) bacteria use the oxidative power of nitric oxide (NO) by forging this molecule to ammonium, thereby making hydrazine (N2H4). Nitrite-dependent anaerobic methane oxidizers (N-DAMO) again take advantage of NO, but now apparently disproportionating the compound into dinitrogen and dioxygen gas. This intracellularly produced dioxygen enables N-DAMO bacteria to adopt an aerobic mechanism for methane oxidation.Although our understanding is only emerging how hydrazine synthase and the NO dismutase act, it seems clear that reactions fully rely on metal-based catalyses known from other enzymes. Metal-dependent conversions not only hold for these key enzymes, but for most other reactions in the central catabolic pathways, again supported by well-studied enzymes from model organisms, but adapted to own specific needs. Remarkably, those accessory catabolic enzymes are not unique for anammox bacteria and N-DAMO. Close homologs are found in protein databases where those homologs derive from (partly) known, but in most cases unknown species that together comprise an only poorly comprehended microbial world.
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Affiliation(s)
- Joachim Reimann
- Department of Microbiology, Institute of Wetland and Water Research (IWWR), Radboud University of Nijmegen, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands,
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43
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Hung V, Zou P, Rhee HW, Udeshi ND, Cracan V, Svinkina T, Carr SA, Mootha VK, Ting AY. Proteomic mapping of the human mitochondrial intermembrane space in live cells via ratiometric APEX tagging. Mol Cell 2014; 55:332-41. [PMID: 25002142 DOI: 10.1016/j.molcel.2014.06.003] [Citation(s) in RCA: 351] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 04/21/2014] [Accepted: 05/20/2014] [Indexed: 12/29/2022]
Abstract
Obtaining complete protein inventories for subcellular regions is a challenge that often limits our understanding of cellular function, especially for regions that are impossible to purify and are therefore inaccessible to traditional proteomic analysis. We recently developed a method to map proteomes in living cells with an engineered peroxidase (APEX) that bypasses the need for organellar purification when applied to membrane-bound compartments; however, it was insufficiently specific when applied to unbounded regions that allow APEX-generated radicals to escape. Here, we combine APEX technology with a SILAC-based ratiometric tagging strategy to substantially reduce unwanted background and achieve nanometer spatial resolution. This is applied to map the proteome of the mitochondrial intermembrane space (IMS), which can freely exchange small molecules with the cytosol. Our IMS proteome of 127 proteins has >94% specificity and includes nine newly discovered mitochondrial proteins. This approach will enable scientists to map proteomes of cellular regions that were previously inaccessible.
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Affiliation(s)
- Victoria Hung
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Peng Zou
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hyun-Woo Rhee
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ulsan National Institute of Science and Technology (UNIST), Ulsan 689-798, Korea
| | | | - Valentin Cracan
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Tanya Svinkina
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vamsi K Mootha
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Alice Y Ting
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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44
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Gao AH, Fu YY, Zhang KZ, Zhang M, Jiang HW, Fan LX, Nan FJ, Yuan CG, Li J, Zhou YB, Li JY. Azoxystrobin, a mitochondrial complex III Qo site inhibitor, exerts beneficial metabolic effects in vivo and in vitro. Biochim Biophys Acta Gen Subj 2014; 1840:2212-21. [DOI: 10.1016/j.bbagen.2014.04.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 04/01/2014] [Accepted: 04/02/2014] [Indexed: 02/08/2023]
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45
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Xia D, Esser L, Tang WK, Zhou F, Zhou Y, Yu L, Yu CA. Structural analysis of cytochrome bc1 complexes: implications to the mechanism of function. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1827:1278-94. [PMID: 23201476 PMCID: PMC3593749 DOI: 10.1016/j.bbabio.2012.11.008] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 11/13/2012] [Accepted: 11/19/2012] [Indexed: 01/18/2023]
Abstract
The cytochrome bc1 complex (bc1) is the mid-segment of the cellular respiratory chain of mitochondria and many aerobic prokaryotic organisms; it is also part of the photosynthetic apparatus of non-oxygenic purple bacteria. The bc1 complex catalyzes the reaction of transferring electrons from the low potential substrate ubiquinol to high potential cytochrome c. Concomitantly, bc1 translocates protons across the membrane, contributing to the proton-motive force essential for a variety of cellular activities such as ATP synthesis. Structural investigations of bc1 have been exceedingly successful, yielding atomic resolution structures of bc1 from various organisms and trapped in different reaction intermediates. These structures have confirmed and unified results of decades of experiments and have contributed to our understanding of the mechanism of bc1 functions as well as its inactivation by respiratory inhibitors. This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes.
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Affiliation(s)
- Di Xia
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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46
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Vennam PR, Fisher N, Krzyaniak MD, Kramer DM, Bowman MK. A caged, destabilized, free radical intermediate in the q-cycle. Chembiochem 2013; 14:1745-53. [PMID: 24009094 PMCID: PMC3951126 DOI: 10.1002/cbic.201300265] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Indexed: 11/12/2022]
Abstract
The Rieske/cytochrome b complexes, also known as cytochrome bc complexes, catalyze a unique oxidant-induced reduction reaction at their quinol oxidase (Qo ) sites, in which substrate hydroquinone reduces two distinct electron transfer chains, one through a series of high-potential electron carriers, the second through low-potential cytochrome b. This reaction is a critical step in energy storage by the Q-cycle. The semiquinone intermediate in this reaction can reduce O2 to produce deleterious superoxide. It is yet unknown how the enzyme controls this reaction, though numerous models have been proposed. In previous work, we trapped a Q-cycle semiquinone anion intermediate, termed SQo , in bacterial cytochrome bc1 by rapid freeze-quenching. In this work, we apply pulsed-EPR techniques to determine the location and properties of SQo in the mitochondrial complex. In contrast to semiquinone intermediates in other enzymes, SQo is not thermodynamically stabilized, and can even be destabilized with respect to solution. It is trapped in Qo at a site that is distinct from previously described inhibitor-binding sites, yet sufficiently close to cytochrome bL to allow rapid electron transfer. The binding site and EPR analyses show that SQo is not stabilized by hydrogen bonds to proteins. The formation of SQo involves "stripping" of both substrate -OH protons during the initial oxidation step, as well as conformational changes of the semiquinone and Qo proteins. The resulting charged radical is kinetically trapped, rather than thermodynamically stabilized (as in most enzymatic semiquinone species), conserving redox energy to drive electron transfer to cytochrome bL while minimizing certain Q-cycle bypass reactions, including oxidation of prereduced cytochrome b and reduction of O2 .
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Affiliation(s)
- Preethi R. Vennam
- Chemistry Department University of Alabama Box 870336, Tuscaloosa, AL 35487, United States
| | - Nicholas Fisher
- Biochemistry and Molecular Biology and the MSU-DOE Plant Research Laboratory Michigan State University East Lansing, MI 48824, United States
| | - Matthew D. Krzyaniak
- Chemistry Department University of Alabama Box 870336, Tuscaloosa, AL 35487, United States
| | - David M. Kramer
- Biochemistry and Molecular Biology and the MSU-DOE Plant Research Laboratory Michigan State University East Lansing, MI 48824, United States
| | - Michael K. Bowman
- Chemistry Department University of Alabama Box 870336, Tuscaloosa, AL 35487, United States
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Sun F, Zhou Q, Pang X, Xu Y, Rao Z. Revealing various coupling of electron transfer and proton pumping in mitochondrial respiratory chain. Curr Opin Struct Biol 2013; 23:526-38. [DOI: 10.1016/j.sbi.2013.06.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 06/13/2013] [Accepted: 06/19/2013] [Indexed: 01/23/2023]
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48
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Berry EA, De Bari H, Huang LS. Unanswered questions about the structure of cytochrome bc1 complexes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1258-77. [PMID: 23624176 DOI: 10.1016/j.bbabio.2013.04.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 03/13/2013] [Accepted: 04/16/2013] [Indexed: 11/25/2022]
Abstract
X-ray crystal structures of bc1 complexes obtained over the last 15 years have provided a firm structural basis for our understanding of the complex. For the most part there is good agreement between structures from different species, different crystal forms, and with different inhibitors bound. In this review we focus on some of the remaining unexplained differences, either between the structures themselves or the interpretations of the structural observations. These include the structural basis for the motion of the Rieske iron-sulfur protein in response to inhibitors, a possible conformational change involving tyrosine132 of cytochrome (cyt) b, the presence of cis-peptides at the beginnings of transmembrane helices C, E, and H, the structural insight into the function of the so-called "Core proteins", different modelings of the retained signal peptide, orientation of the low-potential heme b, and chirality of the Met ligand to heme c1. This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes.
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Affiliation(s)
- Edward A Berry
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA.
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49
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Transmembrane signaling and assembly of the cytochrome b6f-lipidic charge transfer complex. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1295-308. [PMID: 23507619 DOI: 10.1016/j.bbabio.2013.03.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 02/27/2013] [Accepted: 03/06/2013] [Indexed: 12/30/2022]
Abstract
Structure-function properties of the cytochrome b6f complex are sufficiently unique compared to those of the cytochrome bc1 complex that b6f should not be considered a trivially modified bc1 complex. A unique property of the dimeric b6f complex is its involvement in transmembrane signaling associated with the p-side oxidation of plastoquinol. Structure analysis of lipid binding sites in the cyanobacterial b6f complex prepared by hydrophobic chromatography shows that the space occupied by the H transmembrane helix in the cytochrome b subunit of the bc1 complex is mostly filled by a lipid in the b6f crystal structure. It is suggested that this space can be filled by the domain of a transmembrane signaling protein. The identification of lipid sites and likely function defines the intra-membrane conserved central core of the b6f complex, consisting of the seven trans-membrane helices of the cytochrome b and subunit IV polypeptides. The other six TM helices, contributed by cytochrome f, the iron-sulfur protein, and the four peripheral single span subunits, define a peripheral less conserved domain of the complex. The distribution of conserved and non-conserved domains of each monomer of the complex, and the position and inferred function of a number of the lipids, suggests a model for the sequential assembly in the membrane of the eight subunits of the b6f complex, in which the assembly is initiated by formation of the cytochrome b6-subunit IV core sub-complex in a monomer unit. Two conformations of the unique lipidic chlorophyll a, defined in crystal structures, are described, and functions of the outlying β-carotene, a possible 'latch' in supercomplex formation, are discussed. This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes.
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50
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Behrens C, Hartmann K, Sunderhaus S, Braun HP, Eubel H. Approximate calculation and experimental derivation of native isoelectric points of membrane protein complexes of Arabidopsis chloroplasts and mitochondria. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013. [DOI: 10.1016/j.bbamem.2012.11.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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