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Olasard P, Suksri P, Taneerat C, Rungrassamee W, Sathapondecha P. In silico identification and functional study of long non-coding RNA involved in acute hepatopancreatic necrosis disease caused by Vibrio parahaemolyticus infection in white shrimp, Litopenaeus vannamei. FISH & SHELLFISH IMMUNOLOGY 2024; 152:109768. [PMID: 39013534 DOI: 10.1016/j.fsi.2024.109768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 07/04/2024] [Accepted: 07/13/2024] [Indexed: 07/18/2024]
Abstract
Acute hepatopancreatic necrosis disease (AHPND) caused by toxin-producing Vibrio parahaemolyticus (VpAHPND) has severely affected shrimp production. Long non-coding RNA (lncRNA), a regulatory non-coding RNA, which can play important function in shrimp disease responses. This study aimed to identify and investigate the role of lncRNA involved in VpAHPND infection in Pacific white shrimp, Litopenaeus vannamei. From a total of 368,736 de novo assembled transcripts, 67,559 were identified as putative lncRNAs, and only 72 putative lncRNAs showed differential expression between VpAHPND-infected and normal shrimp. The six candidate lncRNAs were validated for their expression profiles during VpAHPND infection and tissue distribution using RT-qPCR. The role of lnc2088 in response to VpAHPND infection was investigated through RNA interference. The result indicated that the suppression of lnc2088 expression led to an increase in shrimp mortality after VpAHPND infection. To explore the set of genes involved in lnc2088 knockdown, RNA sequencing was performed. A total of 275 differentially expressed transcripts were identified in the hepatopancreas of lnc2088 knockdown shrimp. The expression profiles of five candidate metabolic and immune-related genes were validated in lnc2088 knockdown and VpAHPND-infected shrimp. The result showed that the expression of ChiNAG was significantly increased, while that of NCBP1, WIPF2, and NFKB1 was significantly downregulated in ds2088-injected shrimp. Additionally, the expression of NFKB1, NCBP1 and WIPF2 was significantly increased, whereas that of ChiNAG and CUL5 were significantly decreased after infection with VpAHPND. Our work identified putative lncRNA profiles in L. vannamei in response to VpAHPND infection and investigated the role of lncRNA in shrimp immunity.
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Affiliation(s)
- Praewrung Olasard
- Center for Genomics and Bioinformatics Research, Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Phassorn Suksri
- Center for Genomics and Bioinformatics Research, Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Chanikan Taneerat
- Center for Genomics and Bioinformatics Research, Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Wanilada Rungrassamee
- Biosensing and Bioprospectiing Technology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 111 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathum Thani 12120, Thailand
| | - Ponsit Sathapondecha
- Center for Genomics and Bioinformatics Research, Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand.
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Dutkiewicz Z, Varrot A, Breese KJ, Stubbs KA, Nuschy L, Adduci I, Paschinger K, Wilson IBH. Bioinformatic, Enzymatic, and Structural Characterization of Trichuris suis Hexosaminidase HEX-2. Biochemistry 2024; 63:1941-1954. [PMID: 39058279 PMCID: PMC11308363 DOI: 10.1021/acs.biochem.4c00187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024]
Abstract
Hexosaminidases are key enzymes in glycoconjugate metabolism and occur in all kingdoms of life. Here, we have investigated the phylogeny of the GH20 glycosyl hydrolase family in nematodes and identified a β-hexosaminidase subclade present only in the Dorylaimia. We have expressed one of these, HEX-2 from Trichuris suis, a porcine parasite, and shown that it prefers an aryl β-N-acetylgalactosaminide in vitro. HEX-2 has an almost neutral pH optimum and is best inhibited by GalNAc-isofagomine. Toward N-glycan substrates, it displays a preference for the removal of GalNAc residues from LacdiNAc motifs as well as the GlcNAc attached to the α1,3-linked core mannose. Therefore, it has a broader specificity than insect fused lobe (FDL) hexosaminidases but one narrower than distant homologues from plants. Its X-ray crystal structure, the first of any subfamily 1 GH20 hexosaminidase to be determined, is closest to Streptococcus pneumoniae GH20C and the active site is predicted to be compatible with accommodating both GalNAc and GlcNAc. The new structure extends our knowledge about this large enzyme family, particularly as T. suis HEX-2 also possesses the key glutamate residue found in human hexosaminidases of either GH20 subfamily, including HEXD whose biological function remains elusive.
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Affiliation(s)
- Zuzanna Dutkiewicz
- Institut
für Biochemie, Department für Chemie, Universität für Bodenkultur, Muthgasse 18, Wien 1190, Austria
| | | | - Karen J. Breese
- School
of Molecular Sciences, University of Western
Australia, Crawley, WA 6009, Australia
| | - Keith A. Stubbs
- School
of Molecular Sciences, University of Western
Australia, Crawley, WA 6009, Australia
- ARC
Training Centre for Next-Gen Technologies in Biomedical Analysis,
School of Molecular Sciences, University
of Western Australia, Crawley, WA 6009, Australia
| | - Lena Nuschy
- Institut
für Biochemie, Department für Chemie, Universität für Bodenkultur, Muthgasse 18, Wien 1190, Austria
| | - Isabella Adduci
- Institut
für Parasitologie, Department für Pathobiologie, Veterinärmedizinische Universität Wien, Veterinärplatz 1, Wien A-1210, Austria
| | - Katharina Paschinger
- Institut
für Biochemie, Department für Chemie, Universität für Bodenkultur, Muthgasse 18, Wien 1190, Austria
| | - Iain B. H. Wilson
- Institut
für Biochemie, Department für Chemie, Universität für Bodenkultur, Muthgasse 18, Wien 1190, Austria
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Tahir A, Siddiqi AR, Maryam A, Chaitanya Vedithi S, Blundell TL. Structure-guided computational insecticide discovery targeting β-N-acetyl-D-hexosaminidase of Ostrinia furnacalis. J Biomol Struct Dyn 2023:1-14. [PMID: 37814544 DOI: 10.1080/07391102.2023.2264394] [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: 03/27/2023] [Accepted: 09/20/2023] [Indexed: 10/11/2023]
Abstract
Ostrinia furnacalis is a species of moth in the Crambidae family that is harmful to maize and other corn crops in Southeast Asia and the Western Pacific regions. Ostrinia furnacalis causes devastating losses to economically important corn fields. The β-N-acetyl-D-hexosaminidase is an essential enzyme in O. furnacalis and its substrate binding +1 active site is different from that of the plants and humans β-N-acetyl-D-hexosaminidases. To develop environment-friendly insecticides against OfHex1, we conducted structure-guided computational insecticide discovery to identify potential inhibitors that can bind the active site and inhibit the substrate binding and activity of the enzyme. We adopted a three-pronged strategy to conduct virtual screening using Glide and virtual screening workflow (VSW) in Schrödinger Suite-2022-3, against crystal structures of OfHex1 (PDB Id:3NSN), its homologue in humans (PDB Id: 1NP0) and Alphafold model of β-N-acetyl-D-hexosaminidase from Trichogramma pretiosum, an egg parasitoid that protects the crops from O. furnacalis. A library of 20,313 commercially available and "insecticide-like" compounds was extracted from published literature. LigPrep enabled 44,943 ready-to-dock conformers generation. Glide docking revealed 18 OfHex1-specific hits that were absent in human and T. pretiosum screens. Reference docking was conducted using inhibitors/natural ligands in the crystal structures and hits with better docking scores than the reference were selected for MD simulations using Desmond to understand the stability of hit-target interactions. We noted five compounds that bound to OfHex1 TMX active-site based on their docking scores, consistent binding as noted by MD simulations and their insecticide/pesticide likeliness as noted by the Comprehensive Pesticide Likeness Analysis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Adeena Tahir
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad, Pakistan
| | - Abdul Rauf Siddiqi
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad, Pakistan
| | - Arooma Maryam
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad, Pakistan
| | - Sundeep Chaitanya Vedithi
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Heart and Lung Research Institute (HLRI), Cambridge, United Kingdom
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Heart and Lung Research Institute (HLRI), Cambridge, United Kingdom
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Raj S, Unsworth LD. Targeting active sites of inflammation using inherent properties of tissue-resident mast cells. Acta Biomater 2023; 159:21-37. [PMID: 36657696 DOI: 10.1016/j.actbio.2023.01.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/12/2022] [Accepted: 01/10/2023] [Indexed: 01/18/2023]
Abstract
Mast cells play a pivotal role in initiating and directing host's immune response. They reside in tissues that primarily interface with the external environment. Activated mast cells respond to environmental cues throughout acute and chronic inflammation through releasing immune mediators via rapid degranulation, or long-term de novo expression. Mast cell activation results in the rapid release of a variety of unique enzymes and reactive oxygen species. Furthermore, the increased density of mast cell unique receptors like mas related G protein-coupled receptor X2 also characterizes the inflamed tissues. The presence of these molecules (either released mediators or surface receptors) are particular to the sites of active inflammation, and are a result of mast cell activation. Herein, the molecular design principles for capitalizing on these novel mast cell properties is discussed with the goal of manipulating localized inflammation. STATEMENT OF SIGNIFICANCE: Mast cells are immune regulating cells that play a crucial role in both innate and adaptive immune responses. The activation of mast cells causes the release of multiple unique profiles of biomolecules, which are specific to both tissue and disease. These unique characteristics are tightly regulated and afford a localized stimulus for targeting inflammatory diseases. Herein, these important mast cell attributes are discussed in the frame of highlighting strategies for the design of bioresponsive functional materials to target regions of inflammations.
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Affiliation(s)
- Shammy Raj
- Department of Chemical and Materials Engineering, Donadeo Innovation Centre for Engineering, 9211-116 Street NW, University of Alberta, Edmonton, AB, T6G1H9, Canada
| | - Larry D Unsworth
- Department of Chemical and Materials Engineering, Donadeo Innovation Centre for Engineering, 9211-116 Street NW, University of Alberta, Edmonton, AB, T6G1H9, Canada.
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Zhao D, Liu X, Liu Z, Lu X, Guo W. Identification and functional analysis of two potential RNAi targets for chitin degradation in Holotrichia parallela Motschulsky (Insecta Coleoptera). PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2022; 188:105257. [PMID: 36464362 DOI: 10.1016/j.pestbp.2022.105257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 06/17/2023]
Abstract
Chitin metabolism enzymes are safe and desirable targets for pest management. β-N-acetylglucosaminidase (NAG) and N-acetylglucosamine kinase (NAGK) are involved in chitin degradation. NAG is the main glycosidase that works synergistically with chitinases. NAGK is a key enzyme for the generation of UDP-Nacetylglucosamine (UDP-GlcNAc) and for the conversion of GlcNAc into GlcNAc 6-phosphate (GlcNAc-6-P). In this study, NAG and NAGK genes were identified from Holotrichia parallela, a polyphagous soil pest that causes serious damage to crops. The spatiotemporal expression investigated by RT-qPCR indicated that the two genes are expressed in all larval developmental stages. HpNAG is highly expressed in the integument and HpNAGK overexpressed in the midgut. After injection of dsHpNAG and dsHpNAGK, a significant RNAi effect was found after 72 h and larvae stopped growing. The survival rates of larvae were 13.3% and 16.7%, respectively. RNAi of HpNAG and HpNAGK regulated the expression levels of chitin metabolism-related genes, indicating that these two genes could be critical in the chitin metabolism. Furthermore, silencing HpNAG and HpNAGK reduced the thickness of the cuticle, and decreased its content of chitin. The study will lay a foundation for further clarifying the mechanism of chitin metabolism and provide potential targets for the biological control of H. parallela larvae.
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Affiliation(s)
- Dan Zhao
- College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Xiaomin Liu
- Key Laboratory of Crop Cultivation Physiology and Green Production of Hebei Province, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Zhaorui Liu
- College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Xiujun Lu
- College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Wei Guo
- College of Plant Protection, Hebei Agricultural University, Baoding, China; Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China.
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Design, synthesis, biologically evaluation and molecular docking of C-glycosidic oximino carbamates as novel OfHex1 inhibitors. Carbohydr Res 2022; 520:108629. [PMID: 35849863 DOI: 10.1016/j.carres.2022.108629] [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: 05/31/2022] [Revised: 06/28/2022] [Accepted: 06/28/2022] [Indexed: 11/24/2022]
Abstract
The inhibition of function-specific β-N-acetyl-D-hexosaminidases, such as OfHex1 from the Asian corn borer (Ostrinia furnacalis), is a promising strategy for the development of green pesticides. Among reported OfHex1 inhibitors, glycosyl inhibitors show especially high inhibitory activity. In this study, a series of novel C-glycosidic oximino carbamate derivatives were designed using the OfHex1 crystal structure and synthesized. Among the C-Glycoside derivatives studied, compound 7k exhibited the best inhibitory activity against OfHex1 (IC50 = 47.47 μM). Compound 7k also exhibited excellent larvicidal activity against Plutella xylostella. The potential inhibitory mechanism of 7k was studied using molecular docking. Notably, compound 7k is the first reported C-glycoside inhibitor of OfHex1. These results provide direction for the rational design of novel OfHex1 inhibitors.
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The Role of Chitooligosaccharidolytic β- N-Acetylglucosamindase in the Molting and Wing Development of the Silkworm Bombyx mori. Int J Mol Sci 2022; 23:ijms23073850. [PMID: 35409210 PMCID: PMC8998872 DOI: 10.3390/ijms23073850] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/21/2022] [Accepted: 03/27/2022] [Indexed: 02/01/2023] Open
Abstract
The insect glycoside hydrolase family 20 β-N-acetylhexosaminidases (HEXs) are key enzymes involved in chitin degradation. In this study, nine HEX genes in Bombyx mori were identified by genome-wide analysis. Bioinformatic analysis based on the transcriptome database indicated that each gene had a distinct expression pattern. qRT-PCR was performed to detect the expression pattern of the chitooligosaccharidolytic β-N-acetylglucosaminidase (BmChiNAG). BmChiNAG was highly expressed in chitin-rich tissues, such as the epidermis. In the wing disc and epidermis, BmChiNAG has the highest expression level during the wandering stage. CRISPR/Cas9-mediated BmChiNAG deletion was used to study the function. In the BmChiNAG-knockout line, 39.2% of female heterozygotes had small and curly wings. The ultrastructure of a cross-section showed that the lack of BmChiNAG affected the stratification of the wing membrane and the formation of the correct wing vein structure. The molting process of the homozygotes was severely hindered during the larva to pupa transition. Epidermal sections showed that the endocuticle of the pupa was not degraded in the mutant. These results indicate that BmChiNAG is involved in chitin catabolism and plays an important role in the molting and wing development of the silkworm, which highlights the potential of BmChiNAG as a pest control target.
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Chen T, Li WQ, Liu Z, Jiang W, Liu T, Yang Q, Zhu XL, Yang GF. Discovery of Biphenyl-Sulfonamides as Novel β- N-Acetyl-d-Hexosaminidase Inhibitors via Structure-Based Virtual Screening. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:12039-12047. [PMID: 34587743 DOI: 10.1021/acs.jafc.1c01642] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Novel insecticidal targets are always in demand due to the development of resistance. OfHex1, a β-N-acetyl-d-hexosaminidase identified in Ostrinia furnacalis (Asian corn borer), is involved in insect chitin catabolism and has proven an ideal target for insecticide development. In this study, structure-based virtual screening, structure simplification, and biological evaluation are used to show that compounds with a biphenyl-sulfonamide skeleton have great potential as OfHex1 inhibitors. Specifically, compounds 10k, 10u, and 10v have Ki values of 4.30, 3.72, and 4.56 μM, respectively, and thus, they are more potent than some reported nonglycosyl-based inhibitors such as phlegmacin B1 (Ki = 26 μM), berberine (Ki = 12 μM), 2 (Ki = 11.2 μM), and 3 (Ki = 28.9 μM). Furthermore, inhibitory kinetic assessments reveal that the target compounds are competitive inhibitors with respect substrate, and based on toxicity predictions, most of them have potent drug properties. The obtained results indicate that the biphenyl-sulfonamide skeleton characterized by simple chemical structure, synthetic tractability, potent activity, and low toxicity has potential for further development in pest management targeting OfHex1.
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Affiliation(s)
- Tao Chen
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Chemical Biology Center, Central China Normal University, Wuhan 430079, P.R. China
| | - Wen-Qin Li
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, P.R. China
| | - Zheng Liu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Chemical Biology Center, Central China Normal University, Wuhan 430079, P.R. China
| | - Wen Jiang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Chemical Biology Center, Central China Normal University, Wuhan 430079, P.R. China
| | - Tian Liu
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, P.R. China
| | - Qing Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection and Shenzhen Agricultural Genome Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China
| | - Xiao-Lei Zhu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Chemical Biology Center, Central China Normal University, Wuhan 430079, P.R. China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Chemical Biology Center, Central China Normal University, Wuhan 430079, P.R. China
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Mathew GM, Huang CC, Sindhu R, Binod P, Sirohi R, Awsathi MK, Pillai S, Pandey A. Enzymatic approaches in the bioprocessing of shellfish wastes. 3 Biotech 2021; 11:367. [PMID: 34290950 PMCID: PMC8260653 DOI: 10.1007/s13205-021-02912-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/28/2021] [Indexed: 12/14/2022] Open
Abstract
Several tonnes of shellfish wastes are generated globally due to the mass consumption of shellfish meat from crustaceans like prawn, shrimp, lobster, crab, Antarctic krill, etc. These shellfish wastes are a reservoir of valuable by-products like chitin, protein, calcium carbonate, and pigments. In the present scenario, these wastes are treated chemically to recover chitin by the chitin and chitosan industries, using hazardous chemicals like HCl and NaOH. Although this process is efficient in removing proteins and minerals, the unscientific dumping of harmful effluents is hazardous to the ecosystem. Stringent environmental laws and regulations on waste disposal have encouraged researchers to look for alternate strategies to produce near-zero wastes on shellfish degradation. The role of enzymes in degrading shellfish wastes is advantageous yet has not been explored much, although it produces bioactive rich protein hydrolysates with good quality chitin. The main objective of the review is to discuss the potential of various enzymes involved in shellfish degradation and their opportunities and challenges over chemical processes in chitin recovery.
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Affiliation(s)
- Gincy Marina Mathew
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR- NIIST), Trivandrum, 695019 India
| | - Chieh Chen Huang
- Department of Life Sciences, National Chung Hsing University, No. 145, Xingda Road, South District, Taichung City, 402 Taiwan
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR- NIIST), Trivandrum, 695019 India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR- NIIST), Trivandrum, 695019 India
| | - Ranjna Sirohi
- Department of Chemical and Biological Engineering, Korea University, Seoul, 136713 Republic of Korea
| | - Mukesh Kumar Awsathi
- College of Natural Resources and Environment, Northwest A & F University, Yangling, 712100 Shaanxi China
| | - Santhosh Pillai
- Department of Biotechnology and Food Science, Durban University of Technology, Durban, 4000 South Africa
| | - Ashok Pandey
- Center for Innovation and Translational Research, CSIR- Indian Institute of Toxicology Research (CSIR-IITR), 31 MG Marg, Lucknow, 226001 India
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Morimoto Y, Takahashi S, Isoda Y, Nokami T, Fukamizo T, Suginta W, Ohnuma T. Kinetic and thermodynamic insights into the inhibitory mechanism of TMG-chitotriomycin on Vibrio campbellii GH20 exo-β-N-acetylglucosaminidase. Carbohydr Res 2020; 499:108201. [PMID: 33243428 DOI: 10.1016/j.carres.2020.108201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 12/20/2022]
Abstract
We investigated the inhibition kinetics of VhGlcNAcase, a GH20 exo-β-N-acetylglucosaminidase (GlcNAcase) from the marine bacterium Vibrio campbellii (formerly V. harveyi) ATCC BAA-1116, using TMG-chitotriomycin, a natural enzyme inhibitor specific for GH20 GlcNAcases from chitin-processing organisms, with p-nitrophenyl N-acetyl-β-d-glucosaminide (pNP-GlcNAc) as the substrate. TMG-chitotriomycin inhibited VhGlcNAcase with an IC50 of 3.0 ± 0.7 μM. Using Dixon plots, the inhibition kinetics indicated that TMG-chitotriomycin is a competitive inhibitor, with an inhibition constant Ki of 2.2 ± 0.3 μM. Isothermal titration calorimetry experiments provided the thermodynamic parameters for the binding of TMG-chitotriomycin to VhGlcNAcase and revealed that binding was driven by both favorable enthalpy and entropy changes (ΔH° = -2.5 ± 0.1 kcal/mol and -TΔS° = -5.8 ± 0.3 kcal/mol), resulting in a free energy change, ΔG°, of -8.2 ± 0.2 kcal/mol. Dissection of the entropic term showed that a favorable solvation entropy change (-TΔSsolv° = -16 ± 2 kcal/mol) is the main contributor to the entropic term.
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Affiliation(s)
- Yusuke Morimoto
- Department of Advanced Bioscience, Kindai University, 3327-204 Nakamachi, Nara, 631-8505, Japan
| | - Shuji Takahashi
- Department of Chemistry and Biotechnology, Tottori University, 4-101 Koyama-minami, Tottori, 680-8552, Japan
| | - Yuta Isoda
- Department of Chemistry and Biotechnology, Tottori University, 4-101 Koyama-minami, Tottori, 680-8552, Japan
| | - Toshiki Nokami
- Department of Chemistry and Biotechnology, Tottori University, 4-101 Koyama-minami, Tottori, 680-8552, Japan
| | - Tamo Fukamizo
- Department of Advanced Bioscience, Kindai University, 3327-204 Nakamachi, Nara, 631-8505, Japan; School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Tumbol Payupnai, Wangchan Valley, Rayong, 21210, Thailand
| | - Wipa Suginta
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Tumbol Payupnai, Wangchan Valley, Rayong, 21210, Thailand
| | - Takayuki Ohnuma
- Department of Advanced Bioscience, Kindai University, 3327-204 Nakamachi, Nara, 631-8505, Japan; Agricultural Technology and Innovation Research Institute, Kindai University, Nara, Japan.
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11
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Shen S, Dong L, Lu H, Dong Y, Yang Q, Zhang J. Synthesis of ureido thioglycosides as novel insect β‑N‑acetylhexosaminidase OfHex1 inhibitors. Bioorg Med Chem 2020; 28:115602. [PMID: 32631559 DOI: 10.1016/j.bmc.2020.115602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/07/2020] [Accepted: 06/09/2020] [Indexed: 02/05/2023]
Abstract
The insect β-N-acetylhexosaminidase OfHex1 from Ostrinia furnacalis (one of the most destructive agricultural pests) has been considered as a promising pesticide target. In this study, a series of novel and readily available ureido thioglycosides were designed and synthesized based on the catalytic mechanism and the co-crystal structures of OfHex1 with substrates. After evaluation via enzyme inhibition experiments, thioglycosides 11c and 15k were found to have inhibitory activities against OfHex1 with the Ki values of 25.6 µM and 53.8 µM, respectively. In addition, all these ureido thioglycosides exhibited high selectivity toward OfHex1 over hOGA and HsHexB (Ki > 100 μM). Furthermore, to investigate the inhibitory mechanism, the possible binding modes of 11c and 15k with OfHex1 were deduced based on molecular docking analysis. This work may provide useful structural starting points for further rational design of potent inhibitors of OfHex1.
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Affiliation(s)
- Shengqiang Shen
- Department of Pesticide Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Lili Dong
- Department of Pesticide Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Huizhe Lu
- Department of Pesticide Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Yanhong Dong
- Department of Pesticide Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Qing Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection and Shenzhen Agricultural Genome Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Jianjun Zhang
- Department of Pesticide Chemistry, College of Science, China Agricultural University, Beijing, China.
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12
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Yang H, Qi H, Hao Z, Shao X, Liu T, Yang Q, Qian X. Thiazolylhydrazone dervatives as inhibitors for insect N-acetyl-β-d-hexosaminidase and chitinase. CHINESE CHEM LETT 2020. [DOI: 10.1016/j.cclet.2019.11.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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13
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Shen S, Dong L, Chen W, Wu R, Lu H, Yang Q, Zhang J. Synthesis, Optimization, and Evaluation of Glycosylated Naphthalimide Derivatives as Efficient and Selective Insect β- N-Acetylhexosaminidase OfHex1 Inhibitors. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:6387-6396. [PMID: 31090403 DOI: 10.1021/acs.jafc.9b02281] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Insect chitinolytic β- N-acetylhexosaminidase OfHex1, from the agricultural pest Ostrinia furnacalis (Guenée), is considered as a potential target for green pesticide design. In this study, rational molecular design and optimization led to the synthesis of compounds 15r ( Ki = 5.3 μM) and 15y ( Ki = 2.7 μM) that had superior activity against OfHex1 than previously reported lead compounds. Both compounds 15r and 15y had high selectivity toward OfHex1 over human β- N-acetylhexosaminidase B (HsHexB) and human O-GlcNAcase (hOGA). In addition, to investigate the basis for the potency of glycosylated naphthalimides against OfHex1, molecular docking and molecular dynamics simulations were performed to study possible binding modes. Furthermore, the in vivo biological activity of target compounds with efficient OfHex1 inhibitory potency was assayed against Myzus persicae, Plutella xylostella, and O. furnacalis. This present work indicates that glycosylated naphthalimides can be further developed as potential pest control and management agents targeting OfHex1.
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Affiliation(s)
- Shengqiang Shen
- Department of Applied Chemistry, College of Science , China Agricultural University , Beijing 100193 , People's Republic of China
| | - Lili Dong
- Department of Applied Chemistry, College of Science , China Agricultural University , Beijing 100193 , People's Republic of China
| | - Wei Chen
- Institute of Plant Protection , Chinese Academy of Agricultural Sciences , Beijing 100193 , People's Republic of China
| | - Renjie Wu
- Department of Applied Chemistry, College of Science , China Agricultural University , Beijing 100193 , People's Republic of China
| | - Huizhe Lu
- Department of Applied Chemistry, College of Science , China Agricultural University , Beijing 100193 , People's Republic of China
| | - Qing Yang
- Institute of Plant Protection , Chinese Academy of Agricultural Sciences , Beijing 100193 , People's Republic of China
| | - Jianjun Zhang
- Department of Applied Chemistry, College of Science , China Agricultural University , Beijing 100193 , People's Republic of China
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14
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Dong L, Shen S, Lu H, Jin S, Zhang J. Novel Glycosylated Naphthalimide-Based Activatable Fluorescent Probe: A Tool for the Assessment of Hexosaminidase Activity and Intracellular Hexosaminidase Imaging. ACS Sens 2019; 4:1222-1229. [PMID: 31001975 DOI: 10.1021/acssensors.8b01617] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The development of effective detection methods for hexosaminidase is of great importance for the rapid screening of potential inhibitors in vitro and for the early diagnosis of related diseases ex vivo. In this study, the activatable fluorescent probes that are based on naphthalimide decorated with ethylene glycol units were synthesized using N-acetyl-β-d-glucosaminide as a hexosaminidase-responsive group. When exposed to this enzyme, the glucoside-linked naphthalimide moiety of 1c can be cleaved quickly with significant changes in both color (from colorless to yellow) and fluorescence (from blue to green). Probe 1c shows better water-solubility and fluorescence properties than common substrate 4-methylumbelliferyl N-acetyl-β-d-glucosaminide. Furthermore, the response mechanism of 1c to hexosaminidase was evaluated using HPLC analysis and TD-DFT calculations. Molecular docking was performed to investigate the interaction mode. In addition, 1c has successfully achieved the straightforward rapid discovery of effective hexosaminidase inhibitors. Fluorescence imaging experiments indicate that 1c has good cell safety and can be employed as a useful tool for detecting intracellular hexosaminidase activity.
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Affiliation(s)
- Lili Dong
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, P.R. China
| | - Shengqiang Shen
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, P.R. China
| | - Huizhe Lu
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, P.R. China
| | - Shuhui Jin
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, P.R. China
| | - Jianjun Zhang
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, P.R. China
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15
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Muthukrishnan S, Merzendorfer H, Arakane Y, Yang Q. Chitin Organizing and Modifying Enzymes and Proteins Involved In Remodeling of the Insect Cuticle. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1142:83-114. [DOI: 10.1007/978-981-13-7318-3_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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16
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Naphthalimide and quinoline derivatives as inhibitors for insect N-acetyl-β-d-hexosaminidase. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2019.01.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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17
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Zhang R, Xu S, Li X, Han X, Song Z, Zhou J, Huang Z. Examining the molecular characteristics of glycoside hydrolase family 20 β-N-acetylglucosaminidases with high activity. Bioengineered 2019; 10:71-77. [PMID: 30982422 PMCID: PMC6527067 DOI: 10.1080/21655979.2019.1602427] [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] [Indexed: 11/13/2022] Open
Abstract
β-N-Acetylglucosaminidases (GlcNAcases) possess many important biological functions and are used for promising applications that are often hampered by low-activity enzymes. We previously demonstrated that most GlcNAcases of the glycoside hydrolase (GH) family 20 showed higher activities than those of other GH families, and we presented two novel GH 20 GlcNAcases that showed higher activities than most GlcNAcases. A highly flexible structure, which was attributed to the presence of to a high proportion of random coils and flexible amino acid residues, was presumed to be a factor in the high activity of GH 20 GlcNAcases. In this study, we further hypothesized that two special positions might play a key role in catalytic activity. The increase in GH 20 GlcNAcase activity might correspond to the increased structural flexibility and substrate affinity of the two positions due to an increase in random coils and amino acid residues, notably acidic Asp and Glu.
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Affiliation(s)
- Rui Zhang
- a Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education , Yunnan Normal University , Kunming , P. R. China.,b College of Life Sciences , Yunnan Normal University , Kunming , P. R. China.,c Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment , Yunnan , Kunming , P. R. China.,d Key Laboratory of Enzyme Engineering , Yunnan Normal University , Kunming , P. R. China
| | - Shujing Xu
- b College of Life Sciences , Yunnan Normal University , Kunming , P. R. China
| | - Xinyue Li
- b College of Life Sciences , Yunnan Normal University , Kunming , P. R. China
| | - Xiaowei Han
- b College of Life Sciences , Yunnan Normal University , Kunming , P. R. China
| | - Zhifeng Song
- b College of Life Sciences , Yunnan Normal University , Kunming , P. R. China
| | - Junpei Zhou
- a Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education , Yunnan Normal University , Kunming , P. R. China.,b College of Life Sciences , Yunnan Normal University , Kunming , P. R. China.,c Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment , Yunnan , Kunming , P. R. China.,d Key Laboratory of Enzyme Engineering , Yunnan Normal University , Kunming , P. R. China
| | - Zunxi Huang
- a Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education , Yunnan Normal University , Kunming , P. R. China.,b College of Life Sciences , Yunnan Normal University , Kunming , P. R. China.,c Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment , Yunnan , Kunming , P. R. China.,d Key Laboratory of Enzyme Engineering , Yunnan Normal University , Kunming , P. R. China
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18
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Wang M, Zheng F, Wang T, Lyu YM, Alteen MG, Cai ZP, Cui ZL, Liu L, Voglmeir J. Characterization of Stackebrandtia nassauensis GH 20 Beta-Hexosaminidase, a Versatile Biocatalyst for Chitobiose Degradation. Int J Mol Sci 2019; 20:ijms20051243. [PMID: 30871033 PMCID: PMC6429369 DOI: 10.3390/ijms20051243] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/21/2019] [Accepted: 03/04/2019] [Indexed: 12/31/2022] Open
Abstract
An unstudied β-N-acetylhexosaminidase (SnHex) from the soil bacterium Stackebrandtia nassauensis was successfully cloned and subsequently expressed as a soluble protein in Escherichia coli. Activity tests and the biochemical characterization of the purified protein revealed an optimum pH of 6.0 and a robust thermal stability at 50 °C within 24 h. The addition of urea (1 M) or sodium dodecyl sulfate (1% w/v) reduced the activity of the enzyme by 44% and 58%, respectively, whereas the addition of divalent metal ions had no effect on the enzymatic activity. PUGNAc (O-(2-acetamido-2-deoxy-D-glucopyranosylidene)amino-N-phenylcarbamate) strongly inhibited the enzyme in sub-micromolar concentrations. The β-N-acetylhexosaminidase was able to hydrolyze β1,2-linked, β1,3-linked, β1,4-linked, and β1,6-linked GlcNAc residues from the non-reducing end of various tested glycan standards, including bisecting GlcNAc from one of the tested hybrid-type N-glycan substrates. A mutational study revealed that the amino acids D306 and E307 bear the catalytically relevant side acid/base side chains. When coupled with a chitinase, the β-N-acetylhexosaminidase was able to generate GlcNAc directly from colloidal chitin, which showed the potential of this enzyme for biotechnological applications.
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Affiliation(s)
- Meng Wang
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Feng Zheng
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Ting Wang
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yong-Mei Lyu
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Matthew G Alteen
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
| | - Zhi-Peng Cai
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Zhong-Li Cui
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Li Liu
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Josef Voglmeir
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
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19
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Colgan TJ, Fletcher IK, Arce AN, Gill RJ, Ramos Rodrigues A, Stolle E, Chittka L, Wurm Y. Caste- and pesticide-specific effects of neonicotinoid pesticide exposure on gene expression in bumblebees. Mol Ecol 2019; 28:1964-1974. [PMID: 30843300 PMCID: PMC6563198 DOI: 10.1111/mec.15047] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 01/31/2019] [Accepted: 02/05/2019] [Indexed: 01/10/2023]
Abstract
Social bees are important insect pollinators of wildflowers and agricultural crops, making their reported declines a global concern. A major factor implicated in these declines is the widespread use of neonicotinoid pesticides. Indeed, recent research has demonstrated that exposure to low doses of these neurotoxic pesticides impairs bee behaviours important for colony function and survival. However, our understanding of the molecular-genetic pathways that lead to such effects is limited, as is our knowledge of how effects may differ between colony members. To understand what genes and pathways are affected by exposure of bumblebee workers and queens to neonicotinoid pesticides, we implemented a transcriptome-wide gene expression study. We chronically exposed Bombus terrestriscolonies to either clothianidin or imidacloprid at field-realistic concentrations while controlling for factors including colony social environment and worker age. We reveal that genes involved in important biological processes including mitochondrial function are differentially expressed in response to neonicotinoid exposure. Additionally, clothianidin exposure had stronger effects on gene expression amplitude and alternative splicing than imidacloprid. Finally, exposure affected workers more strongly than queens. Our work demonstrates how RNA-Seq transcriptome profiling can provide detailed novel insight on the mechanisms mediating pesticide toxicity to a key insect pollinator.
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Affiliation(s)
- Thomas J Colgan
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.,School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - Isabel K Fletcher
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Andres N Arce
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - Richard J Gill
- Department of Life Sciences, Imperial College London, Ascot, UK
| | | | - Eckart Stolle
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Lars Chittka
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Yannick Wurm
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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20
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Liu X, Zhang J, Zhu KY. Chitin in Arthropods: Biosynthesis, Modification, and Metabolism. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1142:169-207. [PMID: 31102247 DOI: 10.1007/978-981-13-7318-3_9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Chitin is a structural constituent of extracellular matrices including the cuticle of the exoskeleton and the peritrophic matrix (PM) of the midgut in arthropods. Chitin chains are synthesized through multiple biochemical reactions, organized in several hierarchical levels and associated with various proteins that give their unique physicochemical characteristics of the cuticle and PM. Because, arthropod growth and morphogenesis are dependent on the capability of remodeling chitin-containing structures, chitin biosynthesis and degradation are highly regulated, allowing ecdysis and regeneration of the cuticle and PM. Over the past 20 years, much progress has been made in understanding the physiological functions of chitinous matrices. In this chapter, we mainly discussed the biochemical processes of chitin biosynthesis, modification and degradation, and various enzymes involved in these processes. We also discussed cuticular proteins and PM proteins, which largely determine the physicochemical properties of the cuticle and PM. Although rapid advances in genomics, proteomics, RNA interference, and other technologies have considerably facilitated our research in chitin biosynthesis, modification, and metabolism in recent years, many aspects of these processes are still partially understood. Further research is needed in understanding how the structural organization of chitin synthase in plasma membrane accommodate chitin biosynthesis, transport of chitin chain across the plasma membrane, and release of the chitin chain from the enzyme. Other research is also needed in elucidating the roles of chitin deacetylases in chitin organization and the mechanism controlling the formation of different types of chitin in arthropods.
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Affiliation(s)
- Xiaojian Liu
- Research Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, 030006, China
| | - Jianzhen Zhang
- Research Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, 030006, China.
| | - Kun Yan Zhu
- Department of Entomology, Kansas State University, 123 Waters Hall, Manhattan, KS, 66506, USA.
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21
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Dong L, Shen S, Chen W, Lu H, Xu D, Jin S, Yang Q, Zhang J. Glycosyl triazoles as novel insect β-N-acetylhexosaminidase OfHex1 inhibitors: Design, synthesis, molecular docking and MD simulations. Bioorg Med Chem 2018; 27:2315-2322. [PMID: 30528165 DOI: 10.1016/j.bmc.2018.11.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/16/2018] [Accepted: 11/21/2018] [Indexed: 12/18/2022]
Abstract
The insect enzyme GH20 β-N-acetyl-d-hexosaminidase OfHex1 represents an important chitinolytic enzyme found in the agricultural pest Ostrinia furnacalis (Guenée) and inhibition of this enzyme has been considered a promising strategy for the development of eco-friendly pesticides. In this article, based on the structure of the catalytic domains of OfHex1, a series of novel glycosyl triazoles were designed and synthesized via Cu-catalyzed azide-alkyne [3+2] cycloaddition reaction. To investigate the potency and selectivity of these glycosyl triazoles, the inhibition activities towards OfHex1 and HsHexB (human β-N-acetylhexosaminidase B) were studied. Particularly compound 17c (OfHex1, Ki = 28.68 μM; HsHexB, Ki > 100 μM) exhibited a suitable activity and selectivity against OfHex1. Furthermore, the possible inhibitory mechanisms of 17c with OfHex1 were studied using molecular docking and MD simulations. The structure-activity relationship results as well as the formed binding patterns may provide promising insights into the further development of novel OfHex1 inhibitors.
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Affiliation(s)
- Lili Dong
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Shengqiang Shen
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Wei Chen
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Huizhe Lu
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Dongdong Xu
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Shuhui Jin
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Qing Yang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China; Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jianjun Zhang
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
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22
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Yang H, Liu T, Qi H, Huang Z, Hao Z, Ying J, Yang Q, Qian X. Design and synthesis of thiazolylhydrazone derivatives as inhibitors of chitinolytic N-acetyl-β-d-hexosaminidase. Bioorg Med Chem 2018; 26:5420-5426. [DOI: 10.1016/j.bmc.2018.09.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/12/2018] [Accepted: 09/15/2018] [Indexed: 01/31/2023]
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23
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Wang D, Li A, Han H, Liu T, Yang Q. A potent chitinase from Bacillus subtilis for the efficient bioconversion of chitin-containing wastes. Int J Biol Macromol 2018; 116:863-868. [DOI: 10.1016/j.ijbiomac.2018.05.122] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/04/2018] [Accepted: 05/17/2018] [Indexed: 01/04/2023]
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24
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Revisiting glycoside hydrolase family 20 β-N-acetyl-d-hexosaminidases: Crystal structures, physiological substrates and specific inhibitors. Biotechnol Adv 2018; 36:1127-1138. [DOI: 10.1016/j.biotechadv.2018.03.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 03/18/2018] [Accepted: 03/19/2018] [Indexed: 12/31/2022]
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25
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Wang M, Zhang XY, Guo RR, Cai ZP, Hu XC, Chen H, Wei S, Voglmeir J, Liu L. Cloning, purification and biochemical characterization of two β- N -acetylhexosaminidases from the mucin-degrading gut bacterium Akkermansia muciniphila. Carbohydr Res 2018; 457:1-7. [DOI: 10.1016/j.carres.2017.12.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/13/2017] [Accepted: 12/18/2017] [Indexed: 12/15/2022]
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26
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Liu T, Zhu W, Wang J, Zhou Y, Duan Y, Qu M, Yang Q. The deduced role of a chitinase containing two nonsynergistic catalytic domains. Acta Crystallogr D Struct Biol 2018; 74:30-40. [PMID: 29372897 PMCID: PMC5786006 DOI: 10.1107/s2059798317018289] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 12/21/2017] [Indexed: 01/27/2023] Open
Abstract
The glycoside hydrolase family 18 chitinases degrade or alter chitin. Multiple catalytic domains in a glycoside hydrolase family 18 chitinase function synergistically during chitin degradation. Here, an insect group III chitinase from the agricultural pest Ostrinia furnacalis (OfChtIII) is revealed to be an arthropod-conserved chitinase that contains two nonsynergistic GH18 domains according to its catalytic properties. Both GH18 domains are active towards single-chained chitin substrates, but are inactive towards insoluble chitin substrates. The crystal structures of each unbound GH18 domain, as well as of GH18 domains complexed with hexa-N-acetyl-chitohexaose or penta-N-acetyl-chitopentaose, suggest that the two GH18 domains possess endo-specific activities. Physiological data indicated that the developmental stage-dependent gene-expression pattern of OfChtIII was the same as that of the chitin synthase OfChsA but significantly different from that of the chitinase OfChtI, which is indispensable for cuticular chitin degradation. Additionally, immunological staining indicated that OfChtIII was co-localized with OfChsA. Thus, OfChtIII is most likely to be involved in the chitin-synthesis pathway.
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Affiliation(s)
- Tian Liu
- State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, No. 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
| | - Weixing Zhu
- State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, No. 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
| | - Jing Wang
- State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, No. 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
| | - Yong Zhou
- State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, No. 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
| | - Yanwei Duan
- State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, No. 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
| | - Mingbo Qu
- State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, No. 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
| | - Qing Yang
- State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, No. 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Beijing 100193, People’s Republic of China
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27
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Zhu KY, Merzendorfer H, Zhang W, Zhang J, Muthukrishnan S. Biosynthesis, Turnover, and Functions of Chitin in Insects. ANNUAL REVIEW OF ENTOMOLOGY 2016; 61:177-96. [PMID: 26982439 DOI: 10.1146/annurev-ento-010715-023933] [Citation(s) in RCA: 211] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Chitin is a major component of the exoskeleton and the peritrophic matrix of insects. It forms complex structures in association with different assortments of cuticle and peritrophic matrix proteins to yield biocomposites with a wide range of physicochemical and mechanical properties. The growth and development of insects are intimately coupled with the biosynthesis, turnover, and modification of chitin. The genes encoding numerous enzymes of chitin metabolism and proteins that associate with and organize chitin have been uncovered by bioinformatics analyses. Many of these proteins are encoded by sets of large gene families. There is specialization among members within each family, which function in particular tissues or developmental stages. Chitin-containing matrices are dynamically modified at every developmental stage and are under developmental and/or physiological control. A thorough understanding of the diverse processes associated with the assembly and turnover of these chitinous matrices offers many strategies to achieve selective pest control.
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Affiliation(s)
| | | | - Wenqing Zhang
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China;
| | - Jianzhen Zhang
- Research Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi 030006, China;
| | - Subbaratnam Muthukrishnan
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506; ,
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28
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Xi Y, Pan PL, Zhang CX. The β-N-acetylhexosaminidase gene family in the brown planthopper, Nilaparvata lugens. INSECT MOLECULAR BIOLOGY 2015; 24:601-610. [PMID: 26304035 DOI: 10.1111/imb.12187] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
β-N-Acetylhexosaminidases (HEXs) are enzymes that can degrade the chitin oligosaccharides that are produced by the activity of chitinases on chitin in insects. Using bioinformatic methods based on genome and transcriptome databases, 11 β-N-acetylhexosaminidase genes (NlHexs) in Nilaparvata lugens were identified and characterized. Phylogenetic analysis revealed a six-grouped tree topology. The O-Linked N-acetylglucosaminidase (O-GlcNAcase) group includes NlHex11, which harbours a catalytic domain that differs from that of the other 10 NlHexs. Observations of the expression of NlHexs during different developmental stages revealed that NlHex4 is expressed with periodicity during moulting. Although the tissue-specific expression patterns of most NlHexs were nonspecific, NlHex4 was found to be expressed mainly in the female reproductive system as well as in the integument. RNA interference (RNAi) demonstrated failure to shed the old cuticle only in the nymphs treated with double-stranded RNA (dsRNA) targeting NlHex4, and these nymphs eventually died; no observable morphological abnormalities were found in insects treated with dsRNAs targeting the other 10 NlHexs. Based on this study and our previous analyses, a '5 + 1 + 3' pattern of chitinolytic enzymes is proposed, in which five chitinases, one NlHEX and three chitin deacetylases are required for moulting in N. lugens. A better understanding of chitin metabolism in the hemimetabolous insect, N. lugens, would be achieved by considering three chitinolytic enzyme families: chitinase, chitin deacetylase and β-N-acetylhexosaminidase.
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Affiliation(s)
- Y Xi
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Science, Zhejiang University, Hangzhou, China
| | - P-L Pan
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Science, Zhejiang University, Hangzhou, China
| | - C-X Zhang
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Science, Zhejiang University, Hangzhou, China
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29
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Liu T, Xia M, Zhang H, Zhou H, Wang J, Shen X, Yang Q. Exploring NAG-thiazoline and its derivatives as inhibitors of chitinolytic β-acetylglucosaminidases. FEBS Lett 2014; 589:110-6. [PMID: 25436416 DOI: 10.1016/j.febslet.2014.11.032] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 11/19/2014] [Accepted: 11/20/2014] [Indexed: 10/24/2022]
Abstract
NAG-thiazoline (NGT) and its derivatives are well-known inhibitors against most β-acetylglucosaminidases (β-GlcNAcases) except for insect and bacterial chitinolytic β-GlcNAcases, including the molting-indispensable OfHex1 from the insect Ostrinia furnacalis. Here, we report the co-crystal structure of OfHex1 in complex with NGT. This structure reveals a large active pocket in OfHex1 that may account for the poor inhibitory activity of NGT. To test this hypothesis, a bulky substituent was designed and synthesized on the thiazoline ring of NGT. The resulting compound (NMAGT) was determined to be a submicromolar inhibitor of OfHex1 with a Ki value of 0.13 μM, which is 600-fold lower than Ki value of NGT. Molecular dynamics simulation analysis supported the good fit of NMAGT to the active pocket.
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Affiliation(s)
- Tian Liu
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China
| | - Meng Xia
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China
| | - Haitao Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 200237, China
| | - Hao Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering, School of Food and Environmental Science and Technology, Dalian University of Technology, Panjin 124000, China
| | - Jing Wang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China
| | - Xu Shen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 200237, China
| | - Qing Yang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China.
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A crystal structure-guided rational design switching non-carbohydrate inhibitors' specificity between two β-GlcNAcase homologs. Sci Rep 2014; 4:6188. [PMID: 25155420 PMCID: PMC4143770 DOI: 10.1038/srep06188] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 08/05/2014] [Indexed: 12/16/2022] Open
Abstract
Selective inhibition of function-specific β-GlcNAcase has great potential in terms of drug design and biological research. The symmetrical bis-naphthalimide M-31850 was previously obtained by screening for specificity against human glycoconjugate-lytic β-GlcNAcase. Using protein-ligand co-crystallization and molecular docking, we designed an unsymmetrical dyad of naphthalimide and thiadiazole, Q2, that changes naphthalimide specificity from against a human glycoconjugate-lytic β-GlcNAcase to against insect and bacterial chitinolytic β-GlcNAcases. The crystallographic and in silico studies reveal that the naphthalimide ring can be utilized to bind different parts of these enzyme homologs, providing a new starting point to design specific inhibitors. Moreover, Q2-induced closure of the substrate binding pocket is the structural basis for its 13-fold increment in inhibitory potency. Q2 is the first non-carbohydrate inhibitor against chitinolytic β-GlcNAcases. This study provides a useful example of structure-based rationally designed inhibitors as potential pharmaceuticals or pesticides.
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31
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Qu M, Ma L, Chen P, Yang Q. Proteomic Analysis of Insect Molting Fluid with a Focus on Enzymes Involved in Chitin Degradation. J Proteome Res 2014; 13:2931-40. [DOI: 10.1021/pr5000957] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mingbo Qu
- School
of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China
| | - Li Ma
- Key
Laboratory of Insect Developmental and Evolutionary Biology, Institute
of Plant Physiology and Ecology, Shanghai Institutes for Biological
Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Peng Chen
- School
of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China
| | - Qing Yang
- School
of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China
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32
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Katta S, Ankati S, Podile AR. Chitooligosaccharides are converted to N-acetylglucosamine by N-acetyl-β-hexosaminidase from Stenotrophomonas maltophilia. FEMS Microbiol Lett 2013; 348:19-25. [PMID: 23965017 DOI: 10.1111/1574-6968.12237] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 08/18/2013] [Indexed: 11/29/2022] Open
Abstract
The Stenotrophomonas maltophilia k279a (Stm) Hex gene encodes a polypeptide of 785 amino acid residues, with an N-terminal signal peptide. StmHex was cloned without signal peptide and expressed as an 83.6 kDa soluble protein in Escherichia coli BL21 (DE3). Purified StmHex was optimally active at pH 5.0 and 40 °C. The Vmax, Km and kcat/Km for StmHex towards chitin hexamer were 10.55 nkat (mg protein)(-1), 271 μM and 0.246 s(-1) mM(-1), while the kinetic values with chitobiose were 30.65 nkat (mg protein)(-1), 2365 μM and 0.082 s(-1) mM(-1), respectively. Hydrolytic activity on chitooligosaccharides indicated that StmHex was an exo-acting enzyme and yielded N-acetyl-D-glucosamine (GlcNAc) as the final product. StmHex hydrolysed chitooligosaccharides (up to hexamer) into GlcNAc within 60 min, suggesting that this enzyme has potential for use in large-scale production of GlcNAc from chitooligosaccharides.
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Affiliation(s)
- Suma Katta
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
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Qu M, Liu T, Chen P, Yang Q. A sperm-plasma β-N-acetyl-D-hexosaminidase interacting with a Chitinolytic β-N-Acetyl-D-hexosaminidase in insect molting fluid. PLoS One 2013; 8:e71738. [PMID: 23951233 PMCID: PMC3741120 DOI: 10.1371/journal.pone.0071738] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 07/03/2013] [Indexed: 11/25/2022] Open
Abstract
Insects require molting fluids to shed the old cuticle during molting. β-N-acetyl-D-hexosaminidase, known as Hex1, together with various chitinases, is responsible for degrading the chitin component of the old cuticle. This study showed that another β-N-acetyl-D-hexosaminidase, termed OfHex3, interacted with Hex1 and functioned in the molting fluid, although the homolog of OfHex3 was known as a sperm–plasma enzyme functioning in egg–sperm recognition. OfHex3 is an enzyme cloned from the insect Asian corn borer, Ostrinia furnacalis, which is one of the most destructive pests of maize. The enzymatic activity analysis indicated that OfHex3 was able to degrade chitooligosaccharides, but at a lower rate than that of OfHex1. Because OfHex3 did not have substrate inhibition, we deduced that the presence of OfHex3 might help OfHex1 relieve substrate inhibition during chitin degradation during molting. The expression patterns of OfHex3 during O. furnacalis development were studied by real-time PCR as well as western blot. The results showed that both gene transcription and protein translation levels of OfHex3 were up-regulated during larval–larval molting. The tissue-specific expression pattern analysis indicated that OfHex3 was mostly localized in the fat body and testis. All these data further supported that Hex3 was involved in molting as well as in fertilization. This study may help to understand the complexity of cuticle degradation during insect molting, and may provide a possible target for pest control.
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Affiliation(s)
- Mingbo Qu
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Tian Liu
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Peng Chen
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Qing Yang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
- * E-mail:
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Wu Q, Liu T, Yang Q. Cloning, expression and biocharacterization of OfCht5, the chitinase from the insect Ostrinia furnacalis. INSECT SCIENCE 2013; 20:147-157. [PMID: 23955855 DOI: 10.1111/j.1744-7917.2012.01512.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Chitinase catalyzes β-1,4-glycosidic linkages in chitin and has attracted research interest due to it being a potential pesticide target and an enzymatic tool for preparation of N-acetyl-β-D-glucosamine. An individual insect contains multiple genes encoding chitinases, which vary in domain architectures, expression patterns, physiological roles and biochemical properties. Herein, OfCht5, the glycoside hydrolase family 18 chitinase from the widespread lepidopteran pest Ostrinia furnacalis, was cloned, expressed in the yeast Pichia pastoris and biochemically characterized in an attempt to facilitate both pest control and biomaterial preparation. Complementary DNA sequence analysis indicated that OfCHT5 consisted of an open reading frame of 1 665-bp nucleotides. Phylogenic analysis suggested OfCht5 belongs to the Group I insect chitinases. Expression of OfCht5 in Pichia pastoris resulted in highest specific activity after 120 h of induction with methanol. Through two steps of purification, consisting of ammonium sulfate precipitation and metal chelating chromatography, about 7 mg of the recombinant OfCht5 was purified to homogeneity from 1 L culture supernatant. OfCht5 effectively converted colloidal chitin into chitobiose, but had relatively low activity toward α-chitin. When chitooligosaccharides [(GlcNAc)n , n= 3-6] were used as substrates, OfCht5 was observed to possess the highest catalytic efficiency parameter toward (GlcNAc)4 and predominantely hydrolyzed the second glycosidic bond from the non-reducing end. Together with β-N-acetyl-D-hexosaminidase OfHex1, OfCht5 achieved its highest efficiency in chitin degradation that yielded N-acetyl-β-D-glucosamine, a valuable pharmacological reagent and food supplement, within a molar concentration ratio of OfCht5 versus OfHex1 in the range of 9 : 1-15 : 1. This work provides an alternative to existing preparation of chitinase for pesticides and other applications.
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Affiliation(s)
- Qingyue Wu
- Department of Bioscience and Biotechnology, Dalian University of Technology, Dalian 116024, China
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35
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Liu T, Wu Q, Liu L, Yang Q. Elimination of substrate inhibition of a β-N-acetyl-d-hexosaminidase by single site mutation. Process Biochem 2013. [DOI: 10.1016/j.procbio.2012.11.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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36
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Structural insights into cellulolytic and chitinolytic enzymes revealing crucial residues of insect β-N-acetyl-D-hexosaminidase. PLoS One 2012; 7:e52225. [PMID: 23300622 PMCID: PMC3531433 DOI: 10.1371/journal.pone.0052225] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 11/16/2012] [Indexed: 01/24/2023] Open
Abstract
The chemical similarity of cellulose and chitin supports the idea that their corresponding hydrolytic enzymes would bind β-1,4-linked glucose residues in a similar manner. A structural and mutational analysis was performed for the plant cellulolytic enzyme BGlu1 from Oryza sativa and the insect chitinolytic enzyme OfHex1 from Ostrinia furnacalis. Although BGlu1 shows little amino-acid sequence or topological similarity with OfHex1, three residues (Trp490, Glu328, Val327 in OfHex1, and Trp358, Tyr131 and Ile179 in BGlu1) were identified as being conserved in the +1 sugar binding site. OfHex1 Glu328 together with Trp490 was confirmed to be necessary for substrate binding. The mutant E328A exhibited a 8-fold increment in Km for (GlcNAc)2 and a 42-fold increment in Ki for TMG-chitotriomycin. A crystal structure of E328A in complex with TMG-chitotriomycin was resolved at 2.5 Å, revealing the obvious conformational changes of the catalytic residues (Glu368 and Asp367) and the absence of the hydrogen bond between E328A and the C3-OH of the +1 sugar. V327G exhibited the same activity as the wild-type, but acquired the ability to efficiently hydrolyse β-1,2-linked GlcNAc in contrast to the wild-type. Thus, Glu328 and Val327 were identified as important for substrate-binding and as glycosidic-bond determinants. A structure-based sequence alignment confirmed the spatial conservation of these three residues in most plant cellulolytic, insect and bacterial chitinolytic enzymes.
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37
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Liu F, Liu T, Qu M, Yang Q. Molecular and biochemical characterization of a novel β-N-acetyl-D-hexosaminidase with broad substrate-spectrum from the Aisan corn borer, Ostrinia furnacalis. Int J Biol Sci 2012; 8:1085-96. [PMID: 22991497 PMCID: PMC3445047 DOI: 10.7150/ijbs.4406] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 08/19/2012] [Indexed: 11/21/2022] Open
Abstract
Insect β-N-acetyl-D-hexosaminidases with broad substrate-spectrum (IBS-Hex) are the homologues of human β-N-acetyl-D-hexosaminidase A/B (HsHex A/ B). These enzymes are distributed in most insect species and vary in physiological roles. In this study, the gene encoding an IBS-Hex, OfHEX2, was cloned from the Asian corn borer, Ostrinia furnacalis. Recombinant OfHex2 was expressed in Pichia pastoris and purified to homogeneity. By structure-based sequence alignment, three sequence segments with high diversity among IBS-Hexs were firstly concluded. Furthermore, the residue pair N423-R424/ D452-L453 important for the specificity of human β-N-acetyl-D-hexosaminidase subunits α/β toward charged/ non-charged substrates was not conserved in OfHex2 and other IBS-Hexs. Unlike HsHex A, OfHex2 could not degrade charged substrates such as 4-methylumbelliferyl-6-sulfo-N-acetyl-β-D-glucosaminide, ganglioside GM2 and peptidoglycan. OfHex2 showed a broad substrate-spectrum by hydrolyzing β1-2 linked N-acetyl-D-glucosamines from both α3 and α6 branches of biantennary N-glycan and β1-4 linked GlcNAc from chitooligosaccharides as well as β1-3 linked or β1-4 linked N-acetyl-D-galactosamine from oligosaccharides of glycolipids. Real-time PCR analysis demonstrated that the expression of OfHEX2 was up-regulated in the intermolt stages (both larva and pupa), and mainly occurred in the carcass rather than in the midgut during the feeding stage of fifth (final) instar larva. This study reported a novel IBS-Hex with specific biochemical properties, suggesting biodiversity of this class of enzymes.
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Affiliation(s)
- Fengyi Liu
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
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38
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Konno N, Takahashi H, Nakajima M, Takeda T, Sakamoto Y. Characterization of β-N-acetylhexosaminidase (LeHex20A), a member of glycoside hydrolase family 20, from Lentinula edodes (shiitake mushroom). AMB Express 2012; 2:29. [PMID: 22656067 PMCID: PMC3430601 DOI: 10.1186/2191-0855-2-29] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 05/13/2012] [Indexed: 01/29/2023] Open
Abstract
We purified and cloned a β-N-acetylhexosaminidase, LeHex20A, with a molecular mass of 79 kDa from the fruiting body of Lentinula edodes (shiitake mushroom). The gene lehex20a gene had 1,659 nucleotides, encoding 553 amino acid residues. Sequence analysis indicated that LeHex20A belongs to glycoside hydrolase (GH) family 20, and homologues of lehex20a are broadly represented in the genomes of basidiomycetes. Purified LeHex20A hydrolyzed the terminal monosaccharide residues of β-N-acetylgalactosaminides and β-N-acetylglucosaminides, indicating that LeHex20A is a β-N-acetylhexosaminidase classified into EC 3.2.1.52. The maximum LeHex20A activity was observed at pH 4.0 and 50°C. The kinetic constants were estimated using chitooligosaccharides with degree of polymerization 2-6. GH20 β-N-acetylhexosaminidases generally prefer chitobiose among natural substrates. However, LeHex20A had the highest catalytic efficiency (kcat/Km) for chitotetraose, and the Km values for GlcNAc6 were 3.9-fold lower than for chitobiose. Furthermore, the enzyme partially hydrolyzed amorphous chitin polymers. These results indicate that LeHex20A can produce N-acetylglucosamine from long-chain chitomaterials.
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Affiliation(s)
- Naotake Konno
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami-shi, Iwate 024-0003, Japan
| | - Hideyuki Takahashi
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami-shi, Iwate 024-0003, Japan
| | - Masahiro Nakajima
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami-shi, Iwate 024-0003, Japan
| | - Takumi Takeda
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami-shi, Iwate 024-0003, Japan
| | - Yuichi Sakamoto
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami-shi, Iwate 024-0003, Japan
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Identification of novel potential β-N-acetyl-D-hexosaminidase inhibitors by virtual screening, molecular dynamics simulation and MM-PBSA calculations. Int J Mol Sci 2012; 13:4545-4563. [PMID: 22605995 PMCID: PMC3344231 DOI: 10.3390/ijms13044545] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 03/13/2012] [Accepted: 03/26/2012] [Indexed: 11/16/2022] Open
Abstract
Chitinolytic β-N-acetyl-d-hexosaminidases, as a class of chitin hydrolysis enzyme in insects, are a potential species-specific target for developing environmentally-friendly pesticides. Until now, pesticides targeting chitinolytic β-N-acetyl-d-hexosaminidase have not been developed. This study demonstrates a combination of different theoretical methods for investigating the key structural features of this enzyme responsible for pesticide inhibition, thus allowing for the discovery of novel small molecule inhibitors. Firstly, based on the currently reported crystal structure of this protein (OfHex1.pdb), we conducted a pre-screening of a drug-like compound database with 8 × 106 compounds by using the expanded pesticide-likeness criteria, followed by docking-based screening, obtaining 5 top-ranked compounds with favorable docking conformation into OfHex1. Secondly, molecular docking and molecular dynamics simulations are performed for the five complexes and demonstrate that one main hydrophobic pocket formed by residues Trp424, Trp448 and Trp524, which is significant for stabilization of the ligand–receptor complex, and key residues Asp477 and Trp490, are respectively responsible for forming hydrogen-bonding and π–π stacking interactions with the ligands. Finally, the molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) analysis indicates that van der Waals interactions are the main driving force for the inhibitor binding that agrees with the fact that the binding pocket of OfHex1 is mainly composed of hydrophobic residues. These results suggest that screening the ZINC database can maximize the identification of potential OfHex1 inhibitors and the computational protocol will be valuable for screening potential inhibitors of the binding mode, which is useful for the future rational design of novel, potent OfHex1-specific pesticides.
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40
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Wang Y, Liu T, Yang Q, Li Z, Qian X. A Modeling Study for Structure Features of β-N-acetyl-D-hexosaminidase from Ostrinia furnacalis and its Novel Inhibitor Allosamidin: Species Selectivity and Multi-Target Characteristics. Chem Biol Drug Des 2012; 79:572-82. [DOI: 10.1111/j.1747-0285.2011.01301.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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41
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Active-pocket size differentiating insectile from bacterial chitinolytic β-N-acetyl-D-hexosaminidases. Biochem J 2011; 438:467-74. [PMID: 21692744 DOI: 10.1042/bj20110390] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Chitinolytic β-N-acetyl-D-hexosaminidase is a branch of the GH20 (glycoside hydrolase family 20) β-N-acetyl-D-hexosaminidases that is only distributed in insects and micro-organisms, and is therefore a potential target for the action of insecticides. PUGNAc [O-(2-acetamido-2-deoxy-D-glucopyransylidene)-amino-N-phenylcarbamate] was initially identified as an inhibitor against GH20 β-N-acetyl-D-hexosaminidases. So far no crystal structure of PUGNAc in complex with any GH20 β-N-acetyl-D-hexosaminidase has been reported. We show in the present study that the sensitivities of chitinolytic β-N-acetyl-D-hexosaminidases towards PUGNAc can vary by 100-fold, with the order being OfHex1 (Ostrinia furnacalis β-N-acetyl-D-hexosaminidase)<SmCHB (Serratia marcescens chitobiase)<SpHex (Streptomyces plicatus β-N-acetyl-D-hexosaminidase). To explain this difference, the crystal structures of wild-type OfHex1 as well as mutant OfHex1(V327G) in complex with PUGNAc were determined at 2.0 Å (1 Å=0.1 nm) and 2.3 Å resolutions and aligned with the complex structures of SpHex and SmCHB. The results showed that the sensitivities of these enzymes to PUGNAc were determined by the active pocket size, with OfHex1 having the largest but narrowest entrance, whereas SpHex has the smallest entrance, suitable for holding the inhibitor, and SmCHB has the widest entrance. By widening the size of the active pocket entrance of OfHex1 through replacing the active site Val327 with a glycine residue, the sensitivity of OfHex1 to PUGNAc became similar to that of SmCHB. The structural differences among chitinolytic β-N-acetyl-D-hexosaminidases leading to different sensitivities to PUGNAc may be useful for developing species-specific pesticides and bactericides.
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Liu T, Zhang H, Liu F, Wu Q, Shen X, Yang Q. Structural determinants of an insect beta-N-Acetyl-D-hexosaminidase specialized as a chitinolytic enzyme. J Biol Chem 2010; 286:4049-58. [PMID: 21106526 DOI: 10.1074/jbc.m110.184796] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
β-N-acetyl-D-hexosaminidase has been postulated to have a specialized function. However, the structural basis of this specialization is not yet established. OfHex1, the enzyme from the Asian corn borer Ostrinia furnacalis (one of the most destructive pests) has previously been reported to function merely in chitin degradation. Here the vital role of OfHex1 during the pupation of O. furnacalis was revealed by RNA interference, and the crystal structures of OfHex1 and OfHex1 complexed with TMG-chitotriomycin were determined at 2.1 Å. The mechanism of selective inhibition by TMG-chitotriomycin was related to the existence of the +1 subsite at the active pocket of OfHex1 and a key residue, Trp(490), at this site. Mutation of Trp(490) to Ala led to a 2,277-fold decrease in sensitivity toward TMG-chitotriomycin as well as an 18-fold decrease in binding affinity for the substrate (GlcNAc)(2). Although the overall topology of the catalytic domain of OfHex1 shows a high similarity with the human and bacterial enzymes, OfHex1 is distinguished from these enzymes by large conformational changes linked to an "open-close" mechanism at the entrance of the active site, which is characterized by the "lid" residue, Trp(448). Mutation of Trp(448) to Ala or Phe resulted in a more than 1,000-fold loss in enzyme activity, due mainly to the effect on k(cat). The current work has increased our understanding of the structure-function relationship of OfHex1, shedding light on the structural basis that accounts for the specialized function of β-N-acetyl-D-hexosaminidase as well as making the development of species-specific pesticides a likely reality.
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Affiliation(s)
- Tian Liu
- Department of Bioscience and Biotechnology, Dalian University of Technology, Dalian 116024, China
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Qian X, Lee PW, Cao S. China: forward to the green pesticides via a basic research program. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2010; 58:2613-23. [PMID: 20128592 DOI: 10.1021/jf904098w] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The 973 Program is China's keystone national research program established to support basic research in natural and physical sciences. In addition to promoting the development of core technology and scientific infrastructure needed to enable China to meet the social and economic challenges of the 21st century, the training and mentoring of the new generation of China's young scientists are also important objectives of this national program. The green chemical pesticide research program is a part of the 973 Program. The main objectives of stage 1 of the green chemical pesticide research program (2003-2008) are to establish China's capability to conduct basic research in the discovery of "green" crop protection chemicals that are not only novel in mode of action and highly selective to pest species that are unique to China's agricultural situation but also possess favorable environmental and human hazard and risk potentials. The target-based discovery strategy was selected as the main discovery platform. This strategy not only provided this research program the best chance to discover new products but also provided members of this research team opportunities to establish core technologies in chemoinformatics/computation-aided pesticide design using QSAR, QAAR, sensitive and selective bioassay methodology, combinatorial synthesis, hit to lead optimization, and biological targets that were derived from resistance-AChE, IGR, nAChR, etc. On the basis of the learning from stage 1, stage 2 (2010-2014) of this program will focus on the molecular target-oriented innovation of green chemical pesticides. This commentary presents key learnings and accomplishments from the stage 1 of China's green chemical pesticide research program. It is hoped that this information will stimulate further constructive collaborations between pesticide scientists from China and abroad.
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Affiliation(s)
- Xuhong Qian
- Shanghai Key Laboratory of Chemical Biology, Institute of Pharmaceuticals and Pesticides, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.
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Liu T, Liu F, Yang Q, Yang J. Expression, purification and characterization of the chitinolytic β-N-acetyl-d-hexosaminidase from the insect Ostrinia furnacalis. Protein Expr Purif 2009; 68:99-103. [DOI: 10.1016/j.pep.2009.06.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Revised: 06/03/2009] [Accepted: 06/03/2009] [Indexed: 10/20/2022]
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