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Bolling C, Mendez A, Taylor S, Makumire S, Reers A, Zigweid R, Subramanian S, Dranow DM, Staker B, Edwards TE, Tate EW, Bell AS, Myler PJ, Asojo OA, Chakafana G. Ternary structure of Plasmodium vivaxN-myristoyltransferase with myristoyl-CoA and inhibitor IMP-0001173. Acta Crystallogr F Struct Biol Commun 2024; 80:269-277. [PMID: 39291304 PMCID: PMC11448930 DOI: 10.1107/s2053230x24008604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2024] [Accepted: 08/30/2024] [Indexed: 09/19/2024] Open
Abstract
Plasmodium vivax is a major cause of malaria, which poses an increased health burden on approximately one third of the world's population due to climate change. Primaquine, the preferred treatment for P. vivax malaria, is contraindicated in individuals with glucose-6-phosphate dehydrogenase (G6PD) deficiency, a common genetic cause of hemolytic anemia, that affects ∼2.5% of the world's population and ∼8% of the population in areas of the world where P. vivax malaria is endemic. The Seattle Structural Genomics Center for Infectious Disease (SSGCID) conducted a structure-function analysis of P. vivax N-myristoyltransferase (PvNMT) as part of efforts to develop alternative malaria drugs. PvNMT catalyzes the attachment of myristate to the N-terminal glycine of many proteins, and this critical post-translational modification is required for the survival of P. vivax. The first step is the formation of a PvNMT-myristoyl-CoA binary complex that can bind to peptides. Understanding how inhibitors prevent protein binding will facilitate the development of PvNMT as a viable drug target. NMTs are secreted in all life stages of malarial parasites, making them attractive targets, unlike current antimalarials that are only effective during the plasmodial erythrocytic stages. The 2.3 Å resolution crystal structure of the ternary complex of PvNMT with myristoyl-CoA and a novel inhibitor is reported. One asymmetric unit contains two monomers. The structure reveals notable differences between the PvNMT and human enzymes and similarities to other plasmodial NMTs that can be exploited to develop new antimalarials.
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Affiliation(s)
- Cydni Bolling
- Chemistry and Biochemistry Department, Hampton University, 200 William R. Harvey Way, Hampton, VA 23668, USA
| | - Alex Mendez
- Chemistry and Biochemistry Department, Hampton University, 200 William R. Harvey Way, Hampton, VA 23668, USA
| | - Shane Taylor
- Chemistry and Biochemistry Department, Hampton University, 200 William R. Harvey Way, Hampton, VA 23668, USA
| | - Stanley Makumire
- Structural Biology Research Unit, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7C, 90220 Oulu, Finland
| | - Alexandra Reers
- Seattle Structural Genomics Center for Infectious Diseases, Seattle, Washington, USA
| | - Rachael Zigweid
- Seattle Structural Genomics Center for Infectious Diseases, Seattle, Washington, USA
| | - Sandhya Subramanian
- Seattle Structural Genomics Center for Infectious Diseases, Seattle, Washington, USA
| | | | - Bart Staker
- Structural Biology Research Unit, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7C, 90220 Oulu, Finland
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Diseases, Seattle, Washington, USA
| | - Edward W Tate
- Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Andrew S Bell
- Myricx Pharma, 125 Wood Street, London EC2V 7AN, United Kingdom
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Diseases, Seattle, Washington, USA
| | - Oluwatoyin A Asojo
- Dartmouth Cancer Center, Dartmouth College, One Medical Center Drive, Lebanon, NH 03756, USA
| | - Graham Chakafana
- Chemistry and Biochemistry Department, Hampton University, 200 William R. Harvey Way, Hampton, VA 23668, USA
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Chao W, Qiu L, Gao L, Feng J, Liu Y, Yan L, Jiang Y, Lv Q. Antifungal Tetrahydrocarbazole Compound CAR-8 Induces Endoplasmic Reticulum Stress in Candida albicans. ACS Infect Dis 2024; 10:2705-2716. [PMID: 38989983 DOI: 10.1021/acsinfecdis.4c00069] [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] [Indexed: 07/12/2024]
Abstract
The development of new effective antifungal agents is essential to combat fungal infections. Tetrahydrocarbazole has been exploited as a promising skeleton against various pathogenic microorganisms and is used to search for novel active antifungal compounds. In this study, a library composed of small tetrahydrocarbazole compounds was screened, and a potent antifungal agent, CAR-8, was identified with a minimum inhibitory concentration of 2-4 μg/mL against Candida albicans. CAR-8 showed strong fungicidal activities and killed almost all C. albicans within 3 h at a concentration of 16 μg/mL. At concentrations of 2 and 8 μg/mL, CAR-8 significantly inhibited the formation of hyphae and biofilms. Moreover, CAR-8 at 10 and 20 mg/kg reduced the fungal load and improved the survival in the C. albicans infection model in the invertebrate Galleria mellonella. Transcriptome analysis revealed significant changes in the expression of genes associated with protein processing in the endoplasmic reticulum (ER), ER-associated degradation, and unfolded protein response (UPR), which suggested that CAR-8 treatment induced ER stress. Moreover, CAR-8 treatment resulted in various phenotypes similar to tunicamycin, a classical ER stress inducer. These included nonconventional splicing of HAC1 mRNA, the fragmented morphology of ER, the distribution changes of GFP-Snc1 in Saccharomyces cerevisiae, and cell apoptosis probably caused by ER stress. More importantly, the disruption of IRE1 or HAC1 increased the sensitivity of C. albicans to CAR-8, confirming that the UPR signaling pathway was critical for CAR-8 resistance. Overall, our study identifies a potent ER stress-induced antifungal compound that will help the discovery of new antifungal drugs.
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Affiliation(s)
- Wen Chao
- College of Basic Medical Sciences, Naval Medical University, Shanghai 200433, China
| | - Lijuan Qiu
- College of Basic Medical Sciences, Naval Medical University, Shanghai 200433, China
| | - Lu Gao
- Department of Pharmacology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Jia Feng
- Department of Pharmacology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Yu Liu
- School of Pharmacy, Naval Medical University, Shanghai 200433, China
| | - Lan Yan
- School of Pharmacy, Naval Medical University, Shanghai 200433, China
- The Center for Basic Research and Innovation of Medicine and Pharmacy (MOE), School of Pharmacy, Naval Medical University, Shanghai 200433, China
| | - Yuanying Jiang
- Department of Pharmacology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Quanzhen Lv
- School of Pharmacy, Naval Medical University, Shanghai 200433, China
- The Center for Basic Research and Innovation of Medicine and Pharmacy (MOE), School of Pharmacy, Naval Medical University, Shanghai 200433, China
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3
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Fenwick M, Reers AR, Liu Y, Zigweid R, Sankaran B, Shin J, Hulverson MA, Hammerson B, Fernández Álvaro E, Myler PJ, Kaushansky A, Van Voorhis WC, Fan E, Staker BL. Identification of and Structural Insights into Hit Compounds Targeting N-Myristoyltransferase for Cryptosporidium Drug Development. ACS Infect Dis 2023; 9:1821-1833. [PMID: 37722671 PMCID: PMC10580320 DOI: 10.1021/acsinfecdis.3c00151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Indexed: 09/20/2023]
Abstract
Each year, approximately 50,000 children under 5 die as a result of diarrhea caused by Cryptosporidium parvum, a protozoan parasite. There are currently no effective drugs or vaccines available to cure or prevent Cryptosporidium infection, and there are limited tools for identifying and validating targets for drug or vaccine development. We previously reported a high throughput screening (HTS) of a large compound library against Plasmodium N-myristoyltransferase (NMT), a validated drug target in multiple protozoan parasite species. To identify molecules that could be effective against Cryptosporidium, we counter-screened hits from the Plasmodium NMT HTS against Cryptosporidium NMT. We identified two potential hit compounds and validated them against CpNMT to determine if NMT might be an attractive drug target also for Cryptosporidium. We tested the compounds against Cryptosporidium using both cell-based and NMT enzymatic assays. We then determined the crystal structure of CpNMT bound to Myristoyl-Coenzyme A (MyrCoA) and structures of ternary complexes with MyrCoA and the hit compounds to identify the ligand binding modes. The binding site architectures display different conformational states in the presence of the two inhibitors and provide a basis for rational design of selective inhibitors.
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Affiliation(s)
- Michael
K. Fenwick
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
| | - Alexandra R. Reers
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | - Yi Liu
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Rachael Zigweid
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | - Banumathi Sankaran
- Berkeley
Center for Structural Biology, Advanced Light Source, Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Janis Shin
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | - Matthew A. Hulverson
- Center
for Emerging and Re-emerging Infectious Diseases, Division of Allergy
and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington 98109, United States
| | - Bradley Hammerson
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | | | - Peter J. Myler
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
- Department
of Global Health, University of Washington, Seattle, Washington 98195, United States
- Department
of Pediatrics, University of Washington, Seattle, Washington 98195, United States
| | - Alexis Kaushansky
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
- Center
for Emerging and Re-emerging Infectious Diseases, Division of Allergy
and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington 98109, United States
- Department
of Global Health, University of Washington, Seattle, Washington 98195, United States
| | - Wesley C. Van Voorhis
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Emerging and Re-emerging Infectious Diseases, Division of Allergy
and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington 98109, United States
| | - Erkang Fan
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Bart L. Staker
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
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4
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Lai L, Ruan J, Xiao C, Yi P. The putative myristoylome of Physcomitrium patens reveals conserved features of myristoylation in basal land plants. PLANT CELL REPORTS 2023; 42:1107-1124. [PMID: 37052714 DOI: 10.1007/s00299-023-03016-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/03/2023] [Indexed: 05/12/2023]
Abstract
KEYMESSAGE The putative myristoylome of moss P. patens opens an avenue for studying myristoylation substrates in non-canonical model plants. A myristoylation signal was shown sufficient for membrane targeting and useful for membrane dynamics visualization during cell growth. N-myristoylation (MYR) is one form of lipid modification catalyzed by N-myristoyltransferase that enables protein-membrane association. MYR is highly conserved in all eukaryotes. However, the study of MYR is limited to a few models such as yeasts, humans, and Arabidopsis. Here, using prediction tools, we report the characterization of the putative myristoylome of the moss Physcomitrium patens. We show that basal land plants display a similar signature of MYR to Arabidopsis and may have organism-specific substrates. Phylogenetically, MYR signals have mostly co-evolved with protein function but also exhibit variability in an organism-specific manner. We also demonstrate that the MYR motif of a moss brassinosteroid-signaling kinase is an efficient plasma membrane targeting signal and labels lipid-rich domains in tip-growing cells. Our results provide insights into the myristoylome in a basal land plant and lay the foundation for future studies on MYR and its roles in plant evolution.
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Affiliation(s)
- Linyu Lai
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, No. 24 South Section 1, Yihuan Road, Wuhou District, Chengdu, Sichuan, 610064, People's Republic of China
| | - Jingtong Ruan
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, No. 24 South Section 1, Yihuan Road, Wuhou District, Chengdu, Sichuan, 610064, People's Republic of China
| | - Chaowen Xiao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, No. 24 South Section 1, Yihuan Road, Wuhou District, Chengdu, Sichuan, 610064, People's Republic of China
| | - Peishan Yi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, No. 24 South Section 1, Yihuan Road, Wuhou District, Chengdu, Sichuan, 610064, People's Republic of China.
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5
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Rastija V, Vrandečić K, Ćosić J, Kanižai Šarić G, Majić I, Agić D, Šubarić D, Karnaš M, Bešlo D, Brahmbhatt H, Komar M. Antifungal Activities of Fluorinated Pyrazole Aldehydes on Phytopathogenic Fungi, and Their Effect on Entomopathogenic Nematodes, and Soil-Beneficial Bacteria. Int J Mol Sci 2023; 24:ijms24119335. [PMID: 37298285 DOI: 10.3390/ijms24119335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Fluoro-substituted pyrazoles have a wide range of biological activities, such as antibacterial, antiviral, and antifungal activities. The aim of this study was to evaluate the antifungal activities of fluorinated 4,5-dihydro-1H-pyrazole derivatives on four phytopathogenic fungi: Sclerotinia sclerotiorum, Macrophomina phaseolina, Fusarium oxysporum f. sp. lycopersici, and F. culmorum. Moreover, they were tested on two soil beneficial bacteria-Bacillus mycoides and Bradyrhizobium japonicum-as well as two entomopathogenic nematodes (EPNs)-Heterorhabditis bacteriophora and Steinernema feltiae. The molecular docking was performed on the three enzymes responsible for fungal growth, the three plant cell wall-degrading enzymes, and acetylcholinesterase (AChE). The most active compounds against fungi S. sclerotiorum were 2-chlorophenyl derivative (H9) (43.07% of inhibition) and 2,5-dimethoxyphenyl derivative (H7) (42.23% of inhibition), as well as H9 against F. culmorum (46.75% of inhibition). Compounds were shown to be safe for beneficial soil bacteria and nematodes, except for compound H9 on EPN H. bacteriophora (18.75% mortality), which also showed the strongest inhibition against AChE (79.50% of inhibition). The molecular docking study revealed that antifungal activity is possible through the inhibition of proteinase K, and nematicidal activity is possible through the inhibition of AChE. The fluorinated pyrazole aldehydes are promising components of future plant protection products that could be environmentally and toxicologically acceptable.
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Affiliation(s)
- Vesna Rastija
- Faculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, Vladimira Preloga 1, 31000 Osijek, Croatia
| | - Karolina Vrandečić
- Faculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, Vladimira Preloga 1, 31000 Osijek, Croatia
| | - Jasenka Ćosić
- Faculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, Vladimira Preloga 1, 31000 Osijek, Croatia
| | - Gabriella Kanižai Šarić
- Faculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, Vladimira Preloga 1, 31000 Osijek, Croatia
| | - Ivana Majić
- Faculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, Vladimira Preloga 1, 31000 Osijek, Croatia
| | - Dejan Agić
- Faculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, Vladimira Preloga 1, 31000 Osijek, Croatia
| | - Domagoj Šubarić
- Faculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, Vladimira Preloga 1, 31000 Osijek, Croatia
| | - Maja Karnaš
- Faculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, Vladimira Preloga 1, 31000 Osijek, Croatia
| | - Drago Bešlo
- Faculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, Vladimira Preloga 1, 31000 Osijek, Croatia
| | - Harshad Brahmbhatt
- Faculty of Food Technology Osijek, Josip Juraj Strossmayer University, Franje Kuhača 20, 31000 Osijek, Croatia
| | - Mario Komar
- Faculty of Food Technology Osijek, Josip Juraj Strossmayer University, Franje Kuhača 20, 31000 Osijek, Croatia
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6
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Wang Y, Lin R, Liu M, Wang S, Chen H, Zeng W, Nie X, Wang S. N-Myristoyltransferase, a Potential Antifungal Candidate Drug-Target for Aspergillus flavus. Microbiol Spectr 2023; 11:e0421222. [PMID: 36541770 PMCID: PMC9927591 DOI: 10.1128/spectrum.04212-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
The filamentous fungus Aspergillus flavus causes devastating diseases not only to cash crops but also to humans by secreting a series of secondary metabolites called aflatoxins. In the cotranslational or posttranslational process, N-myristoyltransferase (Nmt) is a crucial enzyme that catalyzes the myristate group from myristoyl-coenzyme A (myristoyl-CoA) to the N terminus or internal glycine residue of a protein by forming a covalent bond. Members of the Nmt family execute a diverse range of biological functions across a broad range of fungi. However, the underlying mechanism of AflNmt action in the A. flavus life cycle is unclear, particularly during the growth, development, and secondary metabolic synthesis stages. In the present study, AlfNmt was found to be essential for the development of spore and sclerotia, based on the regulation of the xylose-inducible promoter. AflNmt, located in the cytoplasm of A. flavus, is also involved in modulating aflatoxin (AFB1) in A. flavus, which has not previously been reported in Aspergillus spp. In addition, we purified, characterized, and crystallized the recombinant AflNmt protein (rAflNmt) from the Escherichia coli expression system. Interestingly, the crystal structure of rAlfNmt is moderately different from the models predicted by AlphaFold2 in the N-terminal region, indicating the limitations of machine-learning prediction. In conclusion, these results provide a molecular basis for the functional role of AflNmt in A. flavus and structural insights concerning protein prediction. IMPORTANCE As an opportunistic pathogen, A. flavus causes crop loss due to fungal growth and mycotoxin contamination. Investigating the role of virulence factors during infection and searching for novel drug targets have been popular scientific topics in the field of fungal control. Nmt has become a potential target in some organisms. However, whether Nmt is involved in the developmental stages of A. flavus and aflatoxin synthesis, and whether AlfNmt is an ideal target for structure-based drug design, remains unclear. This study systematically explored and identified the role of AlfNmt in the development of spore and sclerotia, especially in aflatoxin biosynthesis. Moreover, although there is not much difference between the AflNmt model predicted using the AlphaFold2 technique and the structure determined using the X-ray method, current AI prediction models may not be suitable for structure-based drug development. There is still room for further improvements in protein prediction.
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Affiliation(s)
- Yu Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Ranxun Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Mengxin Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Sen Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Hongyu Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Wanlin Zeng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Xinyi Nie
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Shihua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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7
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Monassa P, Rivière F, Dian C, Frottin F, Giglione C, Meinnel T. Biochemical and structural analysis of N-myristoyltransferase mediated protein tagging. Methods Enzymol 2023; 684:135-166. [DOI: 10.1016/bs.mie.2023.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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8
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Meinnel T. Comment on “Binding Affinity Determines Substrate Specificity and Enables Discovery of Substrates for N-Myristoyltransferases”. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01060] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Thierry Meinnel
- Université Paris Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette cedex, France
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9
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Effects of Coumarinyl Schiff Bases against Phytopathogenic Fungi, the Soil-Beneficial Bacteria and Entomopathogenic Nematodes: Deeper Insight into the Mechanism of Action. Molecules 2022; 27:molecules27072196. [PMID: 35408596 PMCID: PMC9000709 DOI: 10.3390/molecules27072196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/24/2022] [Accepted: 03/26/2022] [Indexed: 11/24/2022] Open
Abstract
Coumarin derivatives have been reported as strong antifungal agents against various phytopathogenic fungi. In this study, inhibitory effects of nine coumarinyl Schiff bases were evaluated against the plant pathogenic fungi (Fusarium oxysporum f. sp. lycopersici, Fusarium culmorum, Macrophomina phaseolina and Sclerotinia sclerotiourum). The compounds were demonstrated to be efficient antifungal agents against Macrophomina phaseolina. The results of molecular docking on the six enzymes related to the antifungal activity suggested that the tested compounds act against plant pathogenic fungi, inhibiting plant cell-wall-degrading enzymes such as endoglucanase I and pectinase. Neither compound exhibited inhibitory effects against two beneficial bacteria (Bacillus mycoides and Bradyrhizobium japonicum) and two entomopathogenic nematodes. However, compound 9 was lethal (46.25%) for nematode Heterorhabditis bacteriophora and showed an inhibitory effect against acetylcholinesterase (AChE) (31.45%), confirming the relationship between these two activities. Calculated toxicity and the pesticide-likeness study showed that compound 9 was the least lipophilic compound with the highest aquatic toxicity. A molecular docking study showed that compounds 9 and 8 bind directly to the active site of AChE. Coumarinyl Schiff bases are promising active components of plant protection products, safe for the environment, human health, and nontarget organisms.
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10
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Biological Activities Related to Plant Protection and Environmental Effects of Coumarin Derivatives: QSAR and Molecular Docking Studies. Int J Mol Sci 2021; 22:ijms22147283. [PMID: 34298898 PMCID: PMC8303553 DOI: 10.3390/ijms22147283] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 01/31/2023] Open
Abstract
The aim was to study the inhibitory effects of coumarin derivatives on the plant pathogenic fungi, as well as beneficial bacteria and nematodes. The antifungal assay was performed on four cultures of phytopathogenic fungi by measuring the radial growth of the fungal colonies. Antibacterial activity was determined by the broth microdilution method performed on two beneficial soil organisms. Nematicidal activity was tested on two entomopathogenic nematodes. The quantitative structure-activity relationship (QSAR) model was generated by genetic algorithm, and toxicity was estimated by T.E.S.T. software. The mode of inhibition of enzymes related to the antifungal activity is elucidated by molecular docking. Coumarin derivatives were most effective against Macrophomina phaseolina and Sclerotinia sclerotiorum, but were not harmful against beneficial nematodes and bacteria. A predictive QSAR model was obtained for the activity against M. phaseolina (R2tr = 0.78; R2ext = 0.67; Q2loo = 0.67). A QSAR study showed that multiple electron-withdrawal groups, especially at position C-3, enhanced activities against M. phaseolina, while the hydrophobic benzoyl group at the pyrone ring, and –Br, –OH, –OCH3, at the benzene ring, may increase inhibition of S. sclerotiourum. Tested compounds possibly act inhibitory against plant wall-degrading enzymes, proteinase K. Coumarin derivatives are the potentially active ingredient of environmentally friendly plant-protection products.
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11
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Islinger M, Costello JL, Kors S, Soupene E, Levine TP, Kuypers FA, Schrader M. The diversity of ACBD proteins - From lipid binding to protein modulators and organelle tethers. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2020; 1867:118675. [PMID: 32044385 PMCID: PMC7057175 DOI: 10.1016/j.bbamcr.2020.118675] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/30/2020] [Accepted: 02/05/2020] [Indexed: 12/12/2022]
Abstract
Members of the large multigene family of acyl-CoA binding domain containing proteins (ACBDs) share a conserved motif required for binding of Coenzyme A esterified fatty acids of various chain length. These proteins are present in the three kingdoms of life, and despite their predicted roles in cellular lipid metabolism, knowledge about the precise functions of many ACBD proteins remains scarce. Interestingly, several ACBD proteins are now suggested to function at organelle contact sites, and are recognized as host interaction proteins for different pathogens including viruses and bacteria. Here, we present a thorough phylogenetic analysis of the ACBD family and discuss their structure and evolution. We summarize recent findings on the various functions of animal and fungal ACBDs with particular focus on peroxisomes, the role of ACBD proteins at organelle membranes, and their increasing recognition as targets for pathogens.
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Affiliation(s)
- Markus Islinger
- Institute of Neuroanatomy, Medical Faculty Manheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Joseph L Costello
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter EX4 4QD, Devon, UK
| | - Suzan Kors
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter EX4 4QD, Devon, UK
| | - Eric Soupene
- Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA
| | | | - Frans A Kuypers
- Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA
| | - Michael Schrader
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter EX4 4QD, Devon, UK.
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12
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Dian C, Pérez-Dorado I, Rivière F, Asensio T, Legrand P, Ritzefeld M, Shen M, Cota E, Meinnel T, Tate EW, Giglione C. High-resolution snapshots of human N-myristoyltransferase in action illuminate a mechanism promoting N-terminal Lys and Gly myristoylation. Nat Commun 2020; 11:1132. [PMID: 32111831 PMCID: PMC7048800 DOI: 10.1038/s41467-020-14847-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/04/2020] [Indexed: 01/09/2023] Open
Abstract
The promising drug target N-myristoyltransferase (NMT) catalyses an essential protein modification thought to occur exclusively at N-terminal glycines (Gly). Here, we present high-resolution human NMT1 structures co-crystallised with reactive cognate lipid and peptide substrates, revealing high-resolution snapshots of the entire catalytic mechanism from the initial to final reaction states. Structural comparisons, together with biochemical analysis, provide unforeseen details about how NMT1 reaches a catalytically competent conformation in which the reactive groups are brought into close proximity to enable catalysis. We demonstrate that this mechanism further supports efficient and unprecedented myristoylation of an N-terminal lysine side chain, providing evidence that NMT acts both as N-terminal-lysine and glycine myristoyltransferase.
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Affiliation(s)
- Cyril Dian
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - Inmaculada Pérez-Dorado
- Department of Chemistry, Imperial College, Molecular Sciences Research Hub, Wood Lane, London, W12 0BZ, UK
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, SW7 2AZ, UK
- Evotec Ltd, 114 Innovation Dr, Milton Park, Milton, Abingdon, OX14 4RZ, UK
| | - Frédéric Rivière
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - Thomas Asensio
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - Pierre Legrand
- Synchrotron SOLEIL, Gif-sur-Yvette, Cedex, 91192, France
| | - Markus Ritzefeld
- Department of Chemistry, Imperial College, Molecular Sciences Research Hub, Wood Lane, London, W12 0BZ, UK
- Evotec SE, Essener Bogen 7, Hamburg, 22419, Germany
| | - Mengjie Shen
- Department of Chemistry, Imperial College, Molecular Sciences Research Hub, Wood Lane, London, W12 0BZ, UK
- Oakland Innovation, Mill Rd, Harston, Cambridge, CB22 7GG, UK
| | - Ernesto Cota
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, SW7 2AZ, UK
| | - Thierry Meinnel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France.
| | - Edward W Tate
- Department of Chemistry, Imperial College, Molecular Sciences Research Hub, Wood Lane, London, W12 0BZ, UK.
- The Francis Crick Institute, 1 Midland Rd, London, NW 1AT, UK.
| | - Carmela Giglione
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France.
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13
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Harupa A, De Las Heras L, Colmenarejo G, Lyons-Abbott S, Reers A, Caballero Hernandez I, Chung CW, Charter D, Myler PJ, Fernández-Menéndez RM, Calderón F, Palomo S, Rodríguez B, Berlanga M, Herreros-Avilés E, Staker BL, Fernández Álvaro E, Kaushansky A. Identification of Selective Inhibitors of Plasmodium N-Myristoyltransferase by High-Throughput Screening. J Med Chem 2020; 63:591-600. [PMID: 31850752 DOI: 10.1021/acs.jmedchem.9b01343] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
New drugs that target Plasmodium species, the causative agents of malaria, are needed. The enzyme N-myristoyltransferase (NMT) is an essential protein, which catalyzes the myristoylation of protein substrates, often to mediate membrane targeting. We screened ∼1.8 million small molecules for activity against Plasmodium vivax (P. vivax) NMT. Hits were triaged based on potency and physicochemical properties and further tested against P. vivax and Plasmodium falciparum (P. falciparum) NMTs. We assessed the activity of hits against human NMT1 and NMT2 and discarded compounds with low selectivity indices. We identified 23 chemical classes specific for the inhibition of Plasmodium NMTs over human NMTs, including multiple novel scaffolds. Cocrystallization of P. vivax NMT with one compound revealed peptide binding pocket binding. Other compounds show a range of potential modes of action. Our data provide insight into the activity of a collection of selective inhibitors of Plasmodium NMT and serve as a starting point for subsequent medicinal chemistry efforts.
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Affiliation(s)
- Anke Harupa
- Center for Infectious Disease Research , Seattle , Washington 98109 , United States
- GlaxoSmithKline , Tres Cantos, Madrid 28760 , Spain
- Novartis Institute for Biomedical Research , Emeryville , California 94608 , United States
| | | | | | - Sally Lyons-Abbott
- Center for Infectious Disease Research , Seattle , Washington 98109 , United States
- Seattle Structural Genomics Center for Infectious Disease , Seattle , Washington 98109 , United States
| | - Alexandra Reers
- Center for Infectious Disease Research , Seattle , Washington 98109 , United States
- Seattle Structural Genomics Center for Infectious Disease , Seattle , Washington 98109 , United States
- Seattle Children's Research Institute , Seattle , Washington 98109 , United States
| | | | | | | | - Peter J Myler
- Center for Infectious Disease Research , Seattle , Washington 98109 , United States
- Seattle Structural Genomics Center for Infectious Disease , Seattle , Washington 98109 , United States
- Seattle Children's Research Institute , Seattle , Washington 98109 , United States
| | | | | | - Sara Palomo
- GlaxoSmithKline , Tres Cantos, Madrid 28760 , Spain
| | | | | | | | - Bart L Staker
- Center for Infectious Disease Research , Seattle , Washington 98109 , United States
- Seattle Structural Genomics Center for Infectious Disease , Seattle , Washington 98109 , United States
- Seattle Children's Research Institute , Seattle , Washington 98109 , United States
| | | | - Alexis Kaushansky
- Center for Infectious Disease Research , Seattle , Washington 98109 , United States
- Seattle Children's Research Institute , Seattle , Washington 98109 , United States
- Department of Global Health , University of Washington , Seattle , Washington 98195 , United States
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14
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Salah Ud-Din AIM, Tikhomirova A, Roujeinikova A. Structure and Functional Diversity of GCN5-Related N-Acetyltransferases (GNAT). Int J Mol Sci 2016; 17:E1018. [PMID: 27367672 PMCID: PMC4964394 DOI: 10.3390/ijms17071018] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 06/14/2016] [Accepted: 06/20/2016] [Indexed: 12/17/2022] Open
Abstract
General control non-repressible 5 (GCN5)-related N-acetyltransferases (GNAT) catalyze the transfer of an acyl moiety from acyl coenzyme A (acyl-CoA) to a diverse group of substrates and are widely distributed in all domains of life. This review of the currently available data acquired on GNAT enzymes by a combination of structural, mutagenesis and kinetic methods summarizes the key similarities and differences between several distinctly different families within the GNAT superfamily, with an emphasis on the mechanistic insights obtained from the analysis of the complexes with substrates or inhibitors. It discusses the structural basis for the common acetyltransferase mechanism, outlines the factors important for the substrate recognition, and describes the mechanism of action of inhibitors of these enzymes. It is anticipated that understanding of the structural basis behind the reaction and substrate specificity of the enzymes from this superfamily can be exploited in the development of novel therapeutics to treat human diseases and combat emerging multidrug-resistant microbial infections.
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Affiliation(s)
- Abu Iftiaf Md Salah Ud-Din
- Infection and Immunity Program, Monash Biomedicine Discovery Institute; Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia.
| | - Alexandra Tikhomirova
- Infection and Immunity Program, Monash Biomedicine Discovery Institute; Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia.
| | - Anna Roujeinikova
- Infection and Immunity Program, Monash Biomedicine Discovery Institute; Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia.
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.
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15
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Analyses of the Binding between Water Soluble C60 Derivatives and Potential Drug Targets through a Molecular Docking Approach. PLoS One 2016; 11:e0147761. [PMID: 26829126 PMCID: PMC4735121 DOI: 10.1371/journal.pone.0147761] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 01/07/2016] [Indexed: 11/19/2022] Open
Abstract
Fullerene C60, a unique sphere-shaped molecule consisting of carbon, has been proved to have inhibitory effects on many diseases. However, the applications of C60 in medicine have been severely hindered by its complete insolubility in water and low solubility in almost all organic solvents. In this study, the water-soluble C60 derivatives and the C60 binding protein’s structures were collected from the literature. The selected proteins fall into several groups, including acetylcholinesterase, glutamate racemase, inosine monophosphate dehydrogenase, lumazine synthase, human estrogen receptor alpha, dihydrofolate reductase and N-myristoyltransferase. The C60 derivatives were docked into the binding sites in the proteins. The binding affinities of the C60 derivatives were calculated. The bindings between proteins and their known inhibitors or native ligands were also characterized in the same way. The results show that C60 derivatives form good interactions with the binding sites of different protein targets. In many cases, the binding affinities of C60 derivatives are better than those of known inhibitors and native ligands. This study demonstrates the interaction patterns of C60 derivatives and their binding partners, which will have good impact on the fullerene-based drug discovery.
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16
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Soupene E, Kao J, Cheng DH, Wang D, Greninger AL, Knudsen GM, DeRisi JL, Kuypers FA. Association of NMT2 with the acyl-CoA carrier ACBD6 protects the N-myristoyltransferase reaction from palmitoyl-CoA. J Lipid Res 2016; 57:288-98. [PMID: 26621918 PMCID: PMC4727424 DOI: 10.1194/jlr.m065003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Indexed: 01/13/2023] Open
Abstract
The covalent attachment of a 14-carbon aliphatic tail on a glycine residue of nascent translated peptide chains is catalyzed in human cells by two N-myristoyltransferase (NMT) enzymes using the rare myristoyl-CoA (C(14)-CoA) molecule as fatty acid donor. Although, NMT enzymes can only transfer a myristate group, they lack specificity for C(14)-CoA and can also bind the far more abundant palmitoyl-CoA (C(16)-CoA) molecule. We determined that the acyl-CoA binding protein, acyl-CoA binding domain (ACBD)6, stimulated the NMT reaction of NMT2. This stimulatory effect required interaction between ACBD6 and NMT2, and was enhanced by binding of ACBD6 to its ligand, C(18:2)-CoA. ACBD6 also interacted with the second human NMT enzyme, NMT1. The presence of ACBD6 prevented competition of the NMT reaction by C(16)-CoA. Mutants of ACBD6 that were either deficient in ligand binding to the N-terminal ACBD or unable to interact with NMT2 did not stimulate activity of NMT2, nor could they protect the enzyme from utilizing the competitor C(16)-CoA. These results indicate that ACBD6 can locally sequester C(16)-CoA and prevent its access to the enzyme binding site via interaction with NMT2. Thus, the ligand binding properties of the NMT/ACBD6 complex can explain how the NMT reaction can proceed in the presence of the very abundant competitive substrate, C(16)-CoA.
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Affiliation(s)
- Eric Soupene
- Children's Hospital Oakland Research Institute, Oakland, CA
| | - Joseph Kao
- Children's Hospital Oakland Research Institute, Oakland, CA
| | - Daniel H Cheng
- Children's Hospital Oakland Research Institute, Oakland, CA
| | - Derek Wang
- Children's Hospital Oakland Research Institute, Oakland, CA
| | - Alexander L Greninger
- Department of Biochemistry and Biophysics, University of California at San Francisco and Howard Hughes Medical Institute, San Francisco, CA
| | - Giselle M Knudsen
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California at San Francisco and Howard Hughes Medical Institute, San Francisco, CA
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17
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Kumar S, Sharma RK. N-terminal region of the catalytic domain of human N-myristoyltransferase 1 acts as an inhibitory module. PLoS One 2015; 10:e0127661. [PMID: 26000639 PMCID: PMC4441422 DOI: 10.1371/journal.pone.0127661] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 04/17/2015] [Indexed: 11/18/2022] Open
Abstract
N-myristoyltransferase (NMT) plays critical roles in the modulation of various signaling molecules, however, the regulation of this enzyme in diverse cellular states remains poorly understood. We provide experimental evidence to show for the first time that for the isoform 1 of human NMT (hNMT1), the regulatory roles extend into the catalytic core. In our present study, we expressed, purified, and characterized a truncation mutant devoid of 28 N-terminal amino acids from the catalytic module (Δ28-hNMT1s) and compared its properties to the full-length catalytic domain of hNMT1. The deletion of the N-terminal peptide had no effect on the enzyme stability. Our findings suggest that the N-terminal region in the catalytic module of hNMT1 functions serves as a regulatory control element. The observations of an ~3 fold increase in enzymatic efficiency following removal of the N-terminal peptide of hNMT1s indicates that N-terminal amino acids acts as an inhibitory segment and negatively regulate the enzyme activity. Our findings that the N-terminal region confers control over activity, taken together with the earlier observations that the N-terminal of hNMT1 is differentially processed in diverse cellular states, suggests that the proteolytic processing of the peptide segment containing the inhibitory region provides a molecular mechanism for physiological up-regulation of myristoyltransferase activity.
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Affiliation(s)
- Sujeet Kumar
- Department of Pathology and Laboratory Medicine, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Rajendra K. Sharma
- Department of Pathology and Laboratory Medicine, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- * E-mail: (RKS)
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18
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Shimada T, Suzuki M, Katakura SI. Structure of N-myristoyltransferase from Aspergillus fumigatus. ACTA ACUST UNITED AC 2015; 71:754-61. [PMID: 25849386 DOI: 10.1107/s1399004715000401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Accepted: 01/09/2015] [Indexed: 11/10/2022]
Abstract
N-Myristoyltransferase (NMT) is an enzyme which translocates the 14-carbon saturated fatty acid myristate from myristoyl-CoA to the N-terminal glycine of substrate peptides. This myristoylation process is involved in protein modification in various eukaryotes, including animals and fungi. Furthermore, this enzyme has been shown to be essential to the growth of various species, such as Saccharomyces cerevisiae, which indicates that NMT is an attractive target for the development of a novel antifungal drug. In this study, the crystal structure of a ternary complex of NMT from Aspergillus fumigatus with S-(2-oxo)pentadecyl-CoA, a myristoyl-CoA analogue cofactor, and a synthetic inhibitor is reported at a resolution of 2.1 Å. The results advance the understanding of the specificity of NMT inhibitors and provide valuable information for structure-based drug design.
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Affiliation(s)
- Takashi Shimada
- Drug Discovery and Biomedical Technology Unit, Daiichi Sankyo RD Novare Co. Ltd, 1-16-13 Kita-kasai, Edogawa-ku, Tokyo 134-8630, Japan
| | - Makoto Suzuki
- Drug Discovery and Biomedical Technology Unit, Daiichi Sankyo RD Novare Co. Ltd, 1-16-13 Kita-kasai, Edogawa-ku, Tokyo 134-8630, Japan
| | - Shin-ichi Katakura
- Drug Discovery and Biomedical Technology Unit, Daiichi Sankyo RD Novare Co. Ltd, 1-16-13 Kita-kasai, Edogawa-ku, Tokyo 134-8630, Japan
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19
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Tate EW, Kalesh KA, Lanyon-Hogg T, Storck EM, Thinon E. Global profiling of protein lipidation using chemical proteomic technologies. Curr Opin Chem Biol 2015; 24:48-57. [PMID: 25461723 PMCID: PMC4319709 DOI: 10.1016/j.cbpa.2014.10.016] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 10/23/2014] [Indexed: 01/22/2023]
Abstract
Protein lipidation is unique amongst post-translational modifications (PTMs) in enabling direct interaction with cell membranes, and is found in every form of life. Lipidation is important in normal function and in disease, but its intricate interplay with disease context presents a challenging for drug development. Global whole-proteome profiling of protein lipidation lies beyond the range of standard methods, but is well-suited to metabolic tagging with small 'clickable' chemical reporters that do not disrupt metabolism and function; chemoselective reactions are then used to add multifunctional labels exclusively to tagged-lipidated proteins. This chemical proteomic technology has opened up the first quantitative whole-proteome studies of the known major classes of protein lipidation, and the first insights into their full scope in vivo.
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Affiliation(s)
- Edward W Tate
- Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ, UK.
| | - Karunakaran A Kalesh
- Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ, UK
| | - Thomas Lanyon-Hogg
- Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ, UK
| | - Elisabeth M Storck
- Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ, UK
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20
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Traverso JA, Giglione C, Meinnel T. High-throughput profiling of N-myristoylation substrate specificity across species including pathogens. Proteomics 2013; 13:25-36. [PMID: 23165749 DOI: 10.1002/pmic.201200375] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 10/08/2012] [Accepted: 10/09/2012] [Indexed: 11/10/2022]
Abstract
One of the most critical modifications affecting the N-terminus of proteins is N-myristoylation. This irreversible modification affects the membrane-binding properties of crucial proteins involved in signal transduction cascades. This cotranslational modification, catalyzed by N-myristoyl transferase, occurs both in lower and higher eukaryotes and is a validated therapeutic target for several pathologies. However, this lipidation proves very difficult to be evidenced in vivo even with state-of-the-art proteomics approaches or bioinformatics tools. A large part of N-myristoylated proteins remains to be discovered and the rules of substrate specificity need to be established in each organism. Because the peptide substrate recognition occurs around the first eight residues, short peptides are used for modeling the reaction in vitro. Here, we provide a novel approach including a dedicated peptide array for high-throughput profiling protein N-myristoylation specificity. We show that myristoylation predictive tools need to be fine-tuned to organisms and that their poor accuracy should be significantly enhanced. This should lead to strongly improved knowledge of the number and function of myristoylated proteins occurring in any proteome.
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Affiliation(s)
- José A Traverso
- CNRS, Centre de Recherche de Gif, Institut des Sciences du Végétal, Gif-sur-Yvette, France
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21
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Wang W, Dong G, Gu J, Zhang Y, Wang S, Zhu S, Liu Y, Miao Z, Yao J, Zhang W, Sheng C. Structure–activity relationships of tetrahydrocarbazole derivatives as antifungal lead compounds. MEDCHEMCOMM 2013. [DOI: 10.1039/c2md20211e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Yu Z, Brannigan JA, Moss DK, Brzozowski AM, Wilkinson AJ, Holder AA, Tate EW, Leatherbarrow RJ. Design and synthesis of inhibitors of Plasmodium falciparum N-myristoyltransferase, a promising target for antimalarial drug discovery. J Med Chem 2012; 55:8879-90. [PMID: 23035716 PMCID: PMC3863768 DOI: 10.1021/jm301160h] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Design of inhibitors for N-myristoyltransferase (NMT), an enzyme responsible for protein trafficking in Plasmodium falciparum , the most lethal species of parasites that cause malaria, is described. Chemistry-driven optimization of compound 1 from a focused NMT inhibitor library led to the identification of two early lead compounds 4 and 25, which showed good enzyme and cellular potency and excellent selectivity over human NMT. These molecules provide a valuable starting point for further development.
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Affiliation(s)
- Zhiyong Yu
- Department of Chemistry, Imperial College London, London, SW7 2AZ, U.K
| | - James A. Brannigan
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, U.K
| | - David K. Moss
- Division of Parasitology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, U.K
| | - A. Marek Brzozowski
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, U.K
| | - Anthony J. Wilkinson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, U.K
| | - Anthony A. Holder
- Division of Parasitology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, U.K
| | - Edward W. Tate
- Department of Chemistry, Imperial College London, London, SW7 2AZ, U.K
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23
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Tomašić T, Peterlin Mašič L. Rhodanine as a scaffold in drug discovery: a critical review of its biological activities and mechanisms of target modulation. Expert Opin Drug Discov 2012; 7:549-60. [PMID: 22607309 DOI: 10.1517/17460441.2012.688743] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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24
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Taha MO, Qandil AM, Al-Haraznah T, Khalaf RA, Zalloum H, Al-Bakri AG. Discovery of New Antifungal Leads via Pharmacophore Modeling and QSAR Analysis of Fungal N-Myristoyl Transferase Inhibitors Followed by In Silico Screening. Chem Biol Drug Des 2011; 78:391-407. [PMID: 21679375 DOI: 10.1111/j.1747-0285.2011.01160.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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25
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Taha MO, Habash M, Al-Hadidi Z, Al-Bakri A, Younis K, Sisan S. Docking-based comparative intermolecular contacts analysis as new 3-D QSAR concept for validating docking studies and in silico screening: NMT and GP inhibitors as case studies. J Chem Inf Model 2011; 51:647-69. [PMID: 21370899 DOI: 10.1021/ci100368t] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The significant role played by docking algorithms in drug discovery combined with their serious pitfalls prompted us to envisage a novel concept for validating docking solutions, namely, docking-based comparative intermolecular contacts analysis (dbCICA). This novel approach is based on the number and quality of contacts between docked ligands and amino acid residues within the binding pocket. It assesses a particular docking configuration on the basis of its ability to align a set of ligands within a corresponding binding pocket in such a way that potent ligands come into contact with binding site spots distinct from those approached by low-affinity ligands and vice versa. In other words, dbCICA evaluates the consistency of docking by assessing the correlation between ligands' affinities and their contacts with binding site spots. Optimal dbCICA models can be translated into valid pharmacophore models that can be used as 3-D search queries to mine structural databases for new bioactive compounds. dbCICA was implemented to search for new inhibitors of candida N-myristoyl transferase as potential antifungal agents and glycogen phosphorylase (GP) inhibitors as potential antidiabetic agents. The process culminated in five selective micromolar antifungal leads and nine GP inhibitory leads.
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Affiliation(s)
- Mutasem O Taha
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Jordan, Amman, Jordan.
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Wright MH, Heal WP, Mann DJ, Tate EW. Protein myristoylation in health and disease. J Chem Biol 2010; 3:19-35. [PMID: 19898886 PMCID: PMC2816741 DOI: 10.1007/s12154-009-0032-8] [Citation(s) in RCA: 185] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2009] [Revised: 10/05/2009] [Accepted: 10/19/2009] [Indexed: 02/07/2023] Open
Abstract
N-myristoylation is the attachment of a 14-carbon fatty acid, myristate, onto the N-terminal glycine residue of target proteins, catalysed by N-myristoyltransferase (NMT), a ubiquitous and essential enzyme in eukaryotes. Many of the target proteins of NMT are crucial components of signalling pathways, and myristoylation typically promotes membrane binding that is essential for proper protein localisation or biological function. NMT is a validated therapeutic target in opportunistic infections of humans by fungi or parasitic protozoa. Additionally, NMT is implicated in carcinogenesis, particularly colon cancer, where there is evidence for its upregulation in the early stages of tumour formation. However, the study of myristoylation in all organisms has until recently been hindered by a lack of techniques for detection and identification of myristoylated proteins. Here we introduce the chemistry and biology of N-myristoylation and NMT, and discuss new developments in chemical proteomic technologies that are meeting the challenge of studying this important co-translational modification in living systems.
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Affiliation(s)
- Megan H. Wright
- Chemical Biology Centre, Imperial College London, Exhibition Rd., London, SW72AZ UK
- Department of Chemistry, Imperial College London, Exhibition Rd., London, SW72AZ UK
- Department of Life Sciences, Imperial College London, Exhibition Rd., London, SW72AZ UK
| | - William P. Heal
- Department of Chemistry, Imperial College London, Exhibition Rd., London, SW72AZ UK
- Department of Life Sciences, Imperial College London, Exhibition Rd., London, SW72AZ UK
| | - David J. Mann
- Chemical Biology Centre, Imperial College London, Exhibition Rd., London, SW72AZ UK
- Department of Life Sciences, Imperial College London, Exhibition Rd., London, SW72AZ UK
| | - Edward W. Tate
- Chemical Biology Centre, Imperial College London, Exhibition Rd., London, SW72AZ UK
- Department of Chemistry, Imperial College London, Exhibition Rd., London, SW72AZ UK
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Sheng C, Ji H, Miao Z, Che X, Yao J, Wang W, Dong G, Guo W, Lü J, Zhang W. Homology modeling and molecular dynamics simulation of N-myristoyltransferase from protozoan parasites: active site characterization and insights into rational inhibitor design. J Comput Aided Mol Des 2009; 23:375-89. [PMID: 19370313 DOI: 10.1007/s10822-009-9267-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Accepted: 03/26/2009] [Indexed: 11/25/2022]
Abstract
Myristoyl-CoA:protein N-myristoyltransferase (NMT) is a cytosolic monomeric enzyme that catalyzes the transfer of the myristoyl group from myristoyl-CoA to the N-terminal glycine of a number of eukaryotic cellular and viral proteins. Recent experimental data suggest NMT from parasites could be a promising new target for the design of novel antiparasitic agents with new mode of action. However, the active site topology and inhibitor specificity of these enzymes remain unclear. In this study, three-dimensional models of NMT from Plasmodium falciparum (PfNMT), Leishmania major (LmNMT) and Trypanosoma brucei (TbNMT) were constructed on the basis of the crystal structures of fungal NMTs using homology modeling method. The models were further refined by energy minimization and molecular dynamics simulations. The active sites of PfNMT, LmNMT and TbNMT were characterized by multiple copy simultaneous search (MCSS). MCSS functional maps reveal that PfNMT, LmNMT and TbNMT share a similar active site topology, which is defined by two hydrophobic pockets, a hydrogen-bonding (HB) pocket, a negatively-charged HB pocket and a positively-charged HB pocket. Flexible docking approaches were then employed to dock known inhibitors into the active site of PfNMT. The binding mode, structure-activity relationships and selectivity of inhibitors were investigated in detail. From the results of molecular modeling, the active site architecture and certain key residues responsible for inhibitor binding were identified, which provided insights for the design of novel inhibitors of parasitic NMTs.
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Affiliation(s)
- Chunquan Sheng
- School of Pharmacy, Military Key Laboratory of Medicinal Chemistry, Second Military Medical University, Shanghai, People's Republic of China
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Bowyer PW, Tate EW, Leatherbarrow RJ, Holder AA, Smith DF, Brown KA. N-myristoyltransferase: a prospective drug target for protozoan parasites. ChemMedChem 2008; 3:402-8. [PMID: 18324715 DOI: 10.1002/cmdc.200700301] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Paul W Bowyer
- Division of Cell and Molecular Biology, Centre for Molecular Microbiology and Infection, Imperial College London, London SW7 2AZ, UK
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Current awareness on yeast. Yeast 2008. [DOI: 10.1002/yea.1456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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