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Qi Z, Lei B, Xiong M, Li W, Liao Y, Cai D, Ma X, Zhang R, Chen S. High-level production of chitinase by multi-strategy combination optimization in Bacillus licheniformis. World J Microbiol Biotechnol 2024; 40:181. [PMID: 38668833 DOI: 10.1007/s11274-024-03995-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 04/19/2024] [Indexed: 05/01/2024]
Abstract
In view of the extensive potential applications of chitinase (ChiA) in various fields such as agriculture, environmental protection, medicine, and biotechnology, the development of a high-yielding strain capable of producing chitinase with enhanced activity holds significant importance. The objective of this study was to utilize the extracellular chitinase from Bacillus thuringiensis as the target, and Bacillus licheniformis as the expression host to achieve heterologous expression of ChiA with enhanced activity. Initially, through structural analysis and molecular dynamics simulation, we identified key amino acids to improve the enzymatic performance of chitinase, and the specific activity of chitinase mutant D116N/E118N was 48% higher than that of the natural enzyme, with concomitant enhancements in thermostability and pH stability. Subsequently, the expression elements of ChiA(D116N/E118N) were screened and modified in Bacillus licheniformis, resulting in extracellular ChiA activity reached 89.31 U/mL. Further efforts involved the successful knockout of extracellular protease genes aprE, bprA and epr, along with the gene clusters involved in the synthesis of by-products such as bacitracin and lichenin from Bacillus licheniformis. This led to the development of a recombinant strain, DW2△abelA, which exhibited a remarkable improvement in chitinase activity, reaching 145.56 U/mL. To further improve chitinase activity, a chitinase expression frame was integrated into the genome of DW2△abelA, resulting in a significant increas to 180.26 U/mL. Optimization of fermentation conditions and medium components further boosted shake flask enzyme activity shake flask enzyme activity, achieving 200.28 U/mL, while scale-up fermentation experiments yielded an impressive enzyme activity of 338.79 U/mL. Through host genetic modification, expression optimization and fermentation optimization, a high-yielding ChiA strain was successfully constructed, which will provide a solid foundation for the extracellular production of ChiA.
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Affiliation(s)
- Zhimin Qi
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuhan, Hubei, 430062, PR China
| | - Bo Lei
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuhan, Hubei, 430062, PR China
| | - Min Xiong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuhan, Hubei, 430062, PR China
| | - Weijia Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuhan, Hubei, 430062, PR China
| | - Yongqing Liao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuhan, Hubei, 430062, PR China
| | - Dongbo Cai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuhan, Hubei, 430062, PR China
| | - Xin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuhan, Hubei, 430062, PR China
| | - Ruibin Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuhan, Hubei, 430062, PR China.
| | - Shouwen Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, 368 Youyi Avenue, Wuhan, Hubei, 430062, PR China.
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2
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Niu X, Wang Z, Wang C, Wang H. Dibenzylideneacetone Overcomes Botrytis cinerea Infection in Cherry Tomatoes by Inhibiting Chitinase Activity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:19422-19433. [PMID: 37915214 DOI: 10.1021/acs.jafc.3c05695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Chitinase, a crucial component of the fungal cell wall and septa, plays an important role in fungal germination by hydrolyzing chitin to provide carbon and energy for fungal growth and reproduction. In this study, we initially screened dibenzylideneacetone (DBA), a small molecule with inhibitory activity against Botrytis cinerea Chitinase, exhibiting an IC50 of 13.10 μg/mL. By constructing a three-dimensional (3D) model of the B. cinerea Chitinase and utilizing computational biology approaches, we found DBA bound to the active site pocket and formed strong π-π interactions and hydrophobic interactions with Chitinase, indicative of its competitive inhibitory mode. Site-directed mutagenesis also revealed that TRP-382, TRP-135, and ALA-215 were key amino acid residues involved in DBA binding. Subsequent antifungal assays showed that DBA had an MIC of 32 μg/mL against B. cinerea and EC50 values of 16.29 and 14.64 μg/mL in inhibiting mycelial growth and spore germination, respectively. Importantly, in vivo experiments demonstrated that DBA treatment significantly extended the shelf life of cherry tomatoes by 2-fold. Therefore, DBA represents a promising antifungal agent for fruit preservation applications.
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Affiliation(s)
- Xiaodi Niu
- College of Food Science and Engineering, Jilin University, Changchun 130062, P. R. China
| | - Ziyou Wang
- College of Food Science and Engineering, Jilin University, Changchun 130062, P. R. China
| | - Chenyang Wang
- College of Food Science and Engineering, Jilin University, Changchun 130062, P. R. China
| | - Hongsu Wang
- College of Food Science and Engineering, Jilin University, Changchun 130062, P. R. China
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Liang B, Song W, Xing R, Liu S, Yu H, Li P. The source, activity influencing factors and biological activities for future development of chitin deacetylase. Carbohydr Polym 2023; 321:121335. [PMID: 37739548 DOI: 10.1016/j.carbpol.2023.121335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/24/2023]
Abstract
Chitin deacetylase (CDA), a prominent member of the carbohydrate esterase enzyme family 4 (CE4), is found ubiquitously in bacteria, fungi, insects, and crustaceans. This metalloenzyme plays a pivotal role in recognizing and selectively removing acetyl groups from chitin, thus offering an environmentally friendly and biologically-driven preparation method for chitosan with immense industrial potential. Due to its diverse origins, CDAs sourced from different organisms exhibit unique functions, optimal pH ranges, and temperature preferences. Furthermore, certain organic reagents can induce structural changes in CDAs, influencing their catalytic activity. Leveraging CDA's capabilities extends beyond chitosan biocatalysis, as it demonstrates promising application value in agricultural pest control. In this paper, the source, reaction mechanism, influencing factors, the fermentation methods and applications of CDA are reviewed, which provides theoretical help for the research and application of CDA.
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Affiliation(s)
- Bicheng Liang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Wen Song
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Ronge Xing
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 7 Nanhai Road, Qingdao 266000, China.
| | - Song Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 7 Nanhai Road, Qingdao 266000, China
| | - Huahua Yu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 7 Nanhai Road, Qingdao 266000, China
| | - Pengcheng Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 7 Nanhai Road, Qingdao 266000, China
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4
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Li F, Zhao Z, Chen W, Liu R, Lu H, Dong Y, Yang Q, Zhang J. Design, Synthesis, and Biological Investigations of Novel Carbamoylguanidinyl Nitrobenzoxadiazoles against Chitinolytic Enzymes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:18333-18344. [PMID: 37967522 DOI: 10.1021/acs.jafc.3c06157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
Chitinase has been identified as an important target for insecticides. In this study, a series of novel chitinase inhibitors was designed and synthesized with nitrobenzoxadiazoles. Compound 8d, which contains the N-methylcarbamoylguanidinyl, exhibited high enzyme inhibitory activity and achieved nanomolar inhibition against OfChtI (IC50 = 12.3 nM). Delightfully, it was also found to possess significant inhibitory activity against OfHex1 (IC50 = 1.76 μM). The computational simulation results indicated that compound 8d interacted with OfChtI and OfHex1 in similar modes through hydrogen bonds and hydrophobic and π-π interactions. Insecticidal activity studies revealed that compound 8d showed high mortality against the Lepidoptera Plutella xylostella (mortality rate = 81%) at 200 mg/L. Toxicity studies indicated that compound 8d exhibited negligible toxicity to the natural enemy Trichogramma ostriniae. These results indicate that compound 8d may be a promising candidate for the development of environmentally friendly chitinase inhibitors. Moreover, this study provides a new angle for the design of innovative inhibitors of chitinolytic enzymes.
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Affiliation(s)
- Fang Li
- Department of Applied Chemistry, China Agricultural University, Beijing 100193, China
| | - Zhixiang Zhao
- Department of Applied Chemistry, China Agricultural University, Beijing 100193, China
| | - Wei Chen
- 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, People's Republic of China
| | - Ruiyuan Liu
- Department of Applied Chemistry, China Agricultural University, Beijing 100193, China
| | - Huizhe Lu
- Department of Applied Chemistry, China Agricultural University, Beijing 100193, China
| | - Yanhong Dong
- Department of Applied Chemistry, China Agricultural University, Beijing 100193, 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, People's Republic of China
| | - Jianjun Zhang
- Department of Applied Chemistry, China Agricultural University, Beijing 100193, China
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5
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Zhao Z, Chen W, Dong Y, Yang Q, Lu H, Zhang J. Discovery of Potent N-Methylcarbamoylguanidino Insect Growth Regulators Targeting OfChtI and OfChi-h. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:12431-12439. [PMID: 37556680 DOI: 10.1021/acs.jafc.3c02448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Insect growth regulators (IGRs) are important insecticides that reduce the harm caused by insects to crops by controlling pest population growth. Chitinases are closely associated with insect growth and are among the most important glycoside hydrolases. Thus, Chitinase is an attractive target for the development of novel insecticides. In this study, we designed and synthesized a series of novel and highly potent insecticides targeting OfChtI and OfChi-h in insects. Enzymatic activity tests showed that most compounds exhibited a potent inhibitory activity against OfCh-h. Binding mode analysis revealed that the target compounds bound to the -1 active subsite of Chitinase through the key pharmacophore N-methylcarbamoylguanidino. Compounds 6e, 6g, 6j, and 6o significantly affected the growth and development of Plutella xylostella at 200 mg/L. Our study provides novel insights for the development of potent insecticide-targeted Chitinase combinations based on receptors and ligands.
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Affiliation(s)
- Zhixiang Zhao
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, People's Republic of China
| | - Wei Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China
| | - Yanhong Dong
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, People's Republic of 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, People's Republic of China
| | - Huizhe Lu
- Department of Applied Chemistry, College of Science, China Agricultural University, 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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6
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Zhao Z, Li F, Chen W, Yang Q, Lu H, Zhang J. Discovery of aromatic 2-(3-(methylcarbamoyl) guanidino)-N-aylacetamides as highly potent chitinase inhibitors. Bioorg Med Chem 2023; 80:117172. [PMID: 36709570 DOI: 10.1016/j.bmc.2023.117172] [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: 10/24/2022] [Revised: 12/25/2022] [Accepted: 01/09/2023] [Indexed: 01/13/2023]
Abstract
Chitinases are important glycoside hydrolases that are closely related to bacterial pathogenesis, fungal cell wall remodelling, and insect moulting. Consequently, chitinases have become attractive targets for therapeutic drugs and pesticides. In this study, we designed and synthesised a series of novel chitinase inhibitors based on the N-methylcarbamoylguanidinyl group of the natural product argifin. The most active compound 8h showed strong inhibitory activity against the group I chitinases HsChit1, SmChiB, and OfChi-h, with IC50 values of 0.19 µM, 4.2 nM, and 25 nM, respectively. Binding mode studies revealed that the compound 8h formed π-π stacking/hydrophobic interactions at +1 or +2 subsite of chitinases. In addition, a key hydrogen bond net was formed between the pharmacophore N-methylcarbamoylguanidinyl and key residues at the -1 subsite. Together, the findings of this study provide novel insights into the development of potent small-molecule chitinase inhibitors using a combination of planar structures and N-methylcarbamoylguanidinyl.
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Affiliation(s)
- Zhixiang Zhao
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, People's Republic of China
| | - Fang Li
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, People's Republic of China
| | - Wei Chen
- 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, People's Republic of 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, People's Republic of China.
| | - Huizhe Lu
- Department of Applied Chemistry, College of Science, China Agricultural University, 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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7
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Zhao Z, Chen W, Wang S, Dong Y, Yang Q, Zhang J. Rational Design of N-Methylcarbamoylguanidinyl Derivatives as Highly Potent Dual-Target Chitin Hydrolase Inhibitors for Retarding Growth of Pest Insects. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:2817-2826. [PMID: 36735960 DOI: 10.1021/acs.jafc.2c07605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Chitin degradation is a vital process for the growth of insects. Chitin hydrolase OfChtI and β-N-acetylhexosaminidase OfHex1 are two key enzymes involved in hydrolyzing the chitin of insects' cuticles. Thus, they are considered promising targets for preventing and controlling agricultural pests. In this study, we designed and synthesized a series of compounds bearing N-methylcarbamoylguanidinyl and N-methoxycarbonylguanidinyl as dual-target inhibitors of OfChtI and OfHex1. The most potent dual-target inhibitor, compound 10d, exhibited half-maximal inhibitory concentration (IC50) values of 27.1 and 249.1 nM against OfChtI and OfHex1, respectively. Furthermore, the insecticidal activity studies showed that compounds 10a-c, 10k, and 10l bear significant effects on the growth and development of Plutella xylostella. This work provides a promising method for the development of novel chitin hydrolase inhibitors as potential pest control and management agents.
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Affiliation(s)
- Zhixiang Zhao
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing100193, People's Republic of China
| | - Wei Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing100193, People's Republic of China
| | - Simin Wang
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing100193, People's Republic of China
| | - Yanhong Dong
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing100193, People's Republic of China
| | - Qing Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing100193, People's Republic of China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518120, People's Republic of China
| | - Jianjun Zhang
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing100193, People's Republic of China
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Qiu S, Zhou S, Tan Y, Feng J, Bai Y, He J, Cao H, Che Q, Guo J, Su Z. Biodegradation and Prospect of Polysaccharide from Crustaceans. Mar Drugs 2022; 20:310. [PMID: 35621961 PMCID: PMC9146327 DOI: 10.3390/md20050310] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 04/29/2022] [Accepted: 04/29/2022] [Indexed: 01/27/2023] Open
Abstract
Marine crustacean waste has not been fully utilized and is a rich source of chitin. Enzymatic degradation has attracted the wide attention of researchers due to its unique biocatalytic ability to protect the environment. Chitosan (CTS) and its derivative chitosan oligosaccharides (COSs) with various biological activities can be obtained by the enzymatic degradation of chitin. Many studies have shown that chitosan and its derivatives, chitosan oligosaccharides (COSs), have beneficial properties, including lipid-lowering, anti-inflammatory and antitumor activities, and have important application value in the medical treatment field, the food industry and agriculture. In this review, we describe the classification, biochemical characteristics and catalytic mechanisms of the major degrading enzymes: chitinases, chitin deacetylases (CDAs) and chitosanases. We also introduced the technology for enzymatic design and modification and proposed the current problems and development trends of enzymatic degradation of chitin polysaccharides. The discussion on the characteristics and catalytic mechanism of chitosan-degrading enzymes will help to develop new types of hydrolases by various biotechnology methods and promote their application in chitosan.
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Affiliation(s)
- Shuting Qiu
- Guangdong Engineering Research Center of Natural Products and New Drugs, Guangdong Provincial University Engineering Technology Research Center of Natural Products and Drugs, Guangdong Pharmaceutical University, Guangzhou 510006, China; (S.Q.); (S.Z.); (Y.T.); (J.F.)
- Guangdong Metabolic Disease Research Center of Integrated Chinese and Western Medicine, Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangdong TCM Key Laboratory for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Shipeng Zhou
- Guangdong Engineering Research Center of Natural Products and New Drugs, Guangdong Provincial University Engineering Technology Research Center of Natural Products and Drugs, Guangdong Pharmaceutical University, Guangzhou 510006, China; (S.Q.); (S.Z.); (Y.T.); (J.F.)
- Guangdong Metabolic Disease Research Center of Integrated Chinese and Western Medicine, Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangdong TCM Key Laboratory for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Yue Tan
- Guangdong Engineering Research Center of Natural Products and New Drugs, Guangdong Provincial University Engineering Technology Research Center of Natural Products and Drugs, Guangdong Pharmaceutical University, Guangzhou 510006, China; (S.Q.); (S.Z.); (Y.T.); (J.F.)
- Guangdong Metabolic Disease Research Center of Integrated Chinese and Western Medicine, Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangdong TCM Key Laboratory for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Jiayao Feng
- Guangdong Engineering Research Center of Natural Products and New Drugs, Guangdong Provincial University Engineering Technology Research Center of Natural Products and Drugs, Guangdong Pharmaceutical University, Guangzhou 510006, China; (S.Q.); (S.Z.); (Y.T.); (J.F.)
- Guangdong Metabolic Disease Research Center of Integrated Chinese and Western Medicine, Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangdong TCM Key Laboratory for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Yan Bai
- School of Public Health, Guangdong Pharmaceutical University, Guangzhou 510310, China; (Y.B.); (J.H.)
| | - Jincan He
- School of Public Health, Guangdong Pharmaceutical University, Guangzhou 510310, China; (Y.B.); (J.H.)
| | - Hua Cao
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Zhongshan 528458, China;
| | - Qishi Che
- Guangzhou Rainhome Pharm & Tech Co., Ltd., Science City, Guangzhou 510663, China;
| | - Jiao Guo
- Guangdong Metabolic Disease Research Center of Integrated Chinese and Western Medicine, Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangdong TCM Key Laboratory for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Zhengquan Su
- Guangdong Engineering Research Center of Natural Products and New Drugs, Guangdong Provincial University Engineering Technology Research Center of Natural Products and Drugs, Guangdong Pharmaceutical University, Guangzhou 510006, China; (S.Q.); (S.Z.); (Y.T.); (J.F.)
- Guangdong Metabolic Disease Research Center of Integrated Chinese and Western Medicine, Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangdong TCM Key Laboratory for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou 510006, China
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9
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Liu Y, Ahmed S, Fang Y, Chen M, An J, Yang G, Hou X, Lu J, Ye Q, Zhu R, Liu Q, Liu S. Discovery of Chitin Deacetylase Inhibitors through Structure-Based Virtual Screening and Biological Assays. J Microbiol Biotechnol 2022; 32:504-513. [PMID: 35131956 PMCID: PMC9628821 DOI: 10.4014/jmb.2201.01009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 01/30/2022] [Accepted: 02/03/2022] [Indexed: 12/15/2022]
Abstract
Chitin deacetylase (CDA) inhibitors were developed as novel antifungal agents because CDA participates in critical fungal physiological and metabolic processes and increases virulence in soilborne fungal pathogens. However, few CDA inhibitors have been reported. In this study, 150 candidate CDA inhibitors were selected from the commercial Chemdiv compound library through structure-based virtual screening. The top-ranked 25 compounds were further evaluated for biological activity. The compound J075-4187 had an IC50 of 4.24 ± 0.16 μM for AnCDA. Molecular docking calculations predicted that compound J075-4187 binds to the amino acid residues, including active sites (H101, D48). Furthermore, compound J075-4187 inhibited food spoilage fungi and plant pathogenic fungi, with minimum inhibitory concentration (MIC) at 260 μg/ml and minimum fungicidal concentration (MFC) at 520 μg/ml. Therefore, compound J075-4187 is a good candidate for use in developing antifungal agents for fungi control.
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Affiliation(s)
- Yaodong Liu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, 222005, P.R. China,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, P.R. China
| | - Sibtain Ahmed
- University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Yaowei Fang
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, 222005, P.R. China,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, P.R. China,Jiangsu Marine Resources Development Research Institute, Jiangsu Ocean University, Lianyungang 222000, P.R. China
| | - Meng Chen
- Lianyungang Inspection and Testing Center for Food and Drug Control, P.R. China
| | - Jia An
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, 222005, P.R. China,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, P.R. China
| | - Guang Yang
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, 222005, P.R. China,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, P.R. China
| | - Xiaoyue Hou
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, 222005, P.R. China,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, P.R. China
| | - Jing Lu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, 222005, P.R. China,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, P.R. China
| | - Qinwen Ye
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, 222005, P.R. China,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, P.R. China
| | - Rongjun Zhu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, 222005, P.R. China,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, P.R. China
| | - Qitong Liu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, 222005, P.R. China,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, P.R. China
| | - Shu Liu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, 222005, P.R. China,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, P.R. China,Corresponding author E-mail:
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10
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Zhao Z, Xu Q, Chen W, Wang S, Yang Q, Dong Y, Zhang J. Rational Design, Synthesis, and Biological Investigations of N-Methylcarbamoylguanidinyl Azamacrolides as a Novel Chitinase Inhibitor. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:4889-4898. [PMID: 35416043 DOI: 10.1021/acs.jafc.2c00016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Chitinase is one of the most important glycoside hydrolyases, widely existing in bacteria, fungi, insects, and plants. It is involved in fungal cell wall remodeling and insect molting. Chitinase inhibitors are an effective means of controlling pathogens and pests. Natural product argifin is a 17-membered pentapeptide that exhibits efficient chitinase inhibitory activity. However, the complexity of the synthetic process results in a lot of restrictions for wide range of applications. In this work, we designed a series of azamacrolide chitinase inhibitors based on the structural features of argifin that have high inhibitory activities against bacterial and insectile chitinase. The most potent chitinase inhibitor compound 19c exhibited IC50 values of 56 nM and 110 nM against OfChi-h and SmChiB, respectively. The molecular docking and molecular dynamics simulations revealed that all inhibitors were bound to the -1 subsite of chitinases via N-methylcarbamoylguanidinyl as well as argifin. Finally, a bioactivity assay against pests was carried out. Compound 18a showed 80% mortality for Mythimna separata at a concentration of 50 mg/L. Besides, insecticides 19b and 19c exhibited high mortality against Plutella xylostella (76 and 73% mortalities at 50 mg/L, respectively).
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Affiliation(s)
- Zhixiang Zhao
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, People's Republic of China
| | - Qingbo Xu
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, People's Republic of China
| | - Wei Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Siming Wang
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, People's Republic of China
| | - Qing Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yanhong Dong
- Department of Applied Chemistry, College of Science, China Agricultural University, 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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11
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Discovery of Octahydroisoindolone as a Scaffold for the Selective Inhibition of Chitinase B1 from Aspergillus fumigatus: In Silico Drug Design Studies. Molecules 2021; 26:molecules26247606. [PMID: 34946697 PMCID: PMC8705689 DOI: 10.3390/molecules26247606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/08/2021] [Accepted: 12/13/2021] [Indexed: 11/21/2022] Open
Abstract
Chitinases represent an alternative therapeutic target for opportunistic invasive mycosis since they are necessary for fungal cell wall remodeling. This study presents the design of new chitinase inhibitors from a known hydrolysis intermediate. Firstly, a bioinformatic analysis of Aspergillus fumigatus chitinase B1 (AfChiB1) and chitotriosidase (CHIT1) by length and conservation was done to obtain consensus sequences, and molecular homology models of fungi and human chitinases were built to determine their structural differences. We explored the octahydroisoindolone scaffold as a potential new antifungal series by means of its structural and electronic features. Therefore, we evaluated several synthesis-safe octahydroisoindolone derivatives by molecular docking and evaluated their AfChiB1 interaction profile. Additionally, compounds with the best interaction profile (1–5) were docked within the CHIT1 catalytic site to evaluate their selectivity over AfChiB1. Furthermore, we considered the interaction energy (MolDock score) and a lipophilic parameter (aLogP) for the selection of the best candidates. Based on these descriptors, we constructed a mathematical model for the IC50 prediction of our candidates (60–200 μM), using experimental known inhibitors of AfChiB1. As a final step, ADME characteristics were obtained for all the candidates, showing that 5 is our best designed hit, which possesses the best pharmacodynamic and pharmacokinetic character.
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12
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Jiménez-Ortega E, Kidibule PE, Fernández-Lobato M, Sanz-Aparicio J. Structural inspection and protein motions modelling of a fungal glycoside hydrolase family 18 chitinase by crystallography depicts a dynamic enzymatic mechanism. Comput Struct Biotechnol J 2021; 19:5466-5478. [PMID: 34712392 PMCID: PMC8515301 DOI: 10.1016/j.csbj.2021.09.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/21/2021] [Accepted: 09/26/2021] [Indexed: 12/01/2022] Open
Abstract
Chitinases degrade chitin into low molecular weight chitooligomers, which have a broad range of industrial, agricultural, and medical functions. Understanding the relationship between the diverse characteristics of chitinases and their functions is necessary for the improvement of functional enzymes that meet specific requirements. We report here a full crystallographic analysis of three complexes obtained from the chitinase Chit42 from Trichoderma harzianum, which represent different states along the enzymatic mechanism. The inactive double mutant D169A/E171A was submitted to soaking/crystallization experiments with hexa-N-acetyl-glucosamine (NAG6) or tetra-N-acetyl-glucosamine (NAG4), trapping the enzyme-substrate complex (Chit42-NAG6), the enzyme-products complex (Chit42-NAG4-NAG2) and a someway intermediate state. Structural comparison among the different complexes depicts the determinants defining the different subsites and revealed a previously unobserved dynamic on-off ligand binding process associated with a motion of its insertion domain, which might be accompanying the role or aromatics in processivity. An ensemble refinement performed to extract dynamic details from the diffraction data elucidates the implication of some highly flexible residues in the productive sliding of the substrate and the product release event. These positions were submitted to mutagenesis and the activity of the variants was investigated in the hydrolysis of NAG6, colloidal chitin and two chitosans with different polymerization and acetylation degree. All the changes affected the Chit42 hydrolytic activity therefore confirming the involvement of these positions in catalysis. Furthermore, we found the variants R295S and E316S improving the apparent catalytic efficiency of chitin and NAG6 and, together with E316A, enhancing the specific activity on chitosan. Therefore, our results provide novel insight into the molecular mechanisms underlying the hydrolysis of chitinous material by fungal chitinases, and suggest new targets to address engineering of these biotechnologically important enzymes.
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Affiliation(s)
- Elena Jiménez-Ortega
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, CSIC, 28006 Madrid, Spain
| | - Peter Elias Kidibule
- Department of Molecular Biology, Centre of Molecular Biology Severo Ochoa, CSIC-UAM, 28049 Madrid, Spain
| | - María Fernández-Lobato
- Department of Molecular Biology, Centre of Molecular Biology Severo Ochoa, CSIC-UAM, 28049 Madrid, Spain
| | - Julia Sanz-Aparicio
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, CSIC, 28006 Madrid, Spain
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13
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Jiang Z, Hu S, Ma J, Liu Y, Qiao Z, Yan Q, Gao Y, Yang S. Crystal structure of a chitinase (RmChiA) from the thermophilic fungus Rhizomucor miehei with a real active site tunnel. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140709. [PMID: 34358705 DOI: 10.1016/j.bbapap.2021.140709] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/13/2021] [Accepted: 08/02/2021] [Indexed: 02/05/2023]
Abstract
A chitinase gene (RmChiA) encoding 445 amino acid (aa) residues from a fungus Rhizomucor miehei was cloned and overexpressed in Escherichia coli. Two kinds of RmChiA crystal forms, with space groups P32 2 1 and P1, were obtained by sitting-drop vapor diffusion and the structures were determined by X-ray diffraction. The overall structure of RmChiA monomer, which is the first structure of bacterial-type chitinases from nonpathogenic fungi, adopts a canonical triosephosphate isomerase (TIM) barrel fold with two protruding chitinase insertion domains. RmChiA exhibited a unique NxDxE catalytical motif and a real active site tunnel structure, which are firstly found in GH family 18 chitinases. The motif had high structural homolog with the typical DxDxE motif in other GH family 18 chitinases. The tunnel is formed by two unusual long loops, containing 15 aa and 45 aa respectively, linked by a disulfide bond across the substrate-binding cleft. Mutation experiments found that opening the roof of tunnel structure increased the hydrolysis efficiency of RmChiA, but the thermostability of the mutants decreased. Moreover, the tunnel structure endowed RmChiA with the exo-chitinase character.
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Affiliation(s)
- Zhengqiang Jiang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Songqing Hu
- College of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong 510640, China
| | - Junwen Ma
- Bioresource Utilization Laboratory, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Yuchun Liu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Zhu Qiao
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Qiaojuan Yan
- Bioresource Utilization Laboratory, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Yonggui Gao
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Shaoqing Yang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
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14
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Gomaa EZ. Microbial chitinases: properties, enhancement and potential applications. PROTOPLASMA 2021; 258:695-710. [PMID: 33483852 DOI: 10.1007/s00709-021-01612-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/08/2021] [Indexed: 06/12/2023]
Abstract
Chitinases are a category of hydrolytic enzymes that catalyze chitin and are formed by a wide variety of microorganisms. In nature, microbial chitinases are primarily responsible for chitin decomposition and play a vital role in the balance of carbon and nitrogen ratio in the ecosystem. The physicochemical attributes and the source of chitinase are the main bases that determine their functional characteristics and hydrolyzed products. Several chitinases have been reported and characterized, and they obtain a wider consideration for their utilization in a large number of uses such as in agriculture, food, environment, medicine and pharmaceutical companies. The antifungal and insecticidal impacts of several chitinases have been extensively studied, aiming to protect crops from phytopathogenic fungi and insects. Chitooligosaccharides synthesized by chitin degradation have been shown to improve human health through their antimicrobial, antioxidant, anti-inflammatory and antitumor properties. This review aims at investigating chitinase production, properties and their potential applications in various biotechnological fields.
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Affiliation(s)
- Eman Zakaria Gomaa
- Department of Biological and Geological Sciences, Faculty of Education, Ain Shams University, Cairo, Egypt.
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15
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Glycoside hydrolase family 18 chitinases: The known and the unknown. Biotechnol Adv 2020; 43:107553. [DOI: 10.1016/j.biotechadv.2020.107553] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/09/2020] [Accepted: 04/20/2020] [Indexed: 12/13/2022]
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16
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Silva E Souza E, Barcellos VDA, Sbaraini N, Reuwsaat JCV, Schneider RDO, da Silva AC, Garcia AWA, von Poser GL, Barbosa EG, Lima JPMS, Vainstein MH. A Plumieridine-Rich Fraction From Allamanda polyantha Inhibits Chitinolytic Activity and Exhibits Antifungal Properties Against Cryptococcus neoformans. Front Microbiol 2020; 11:2058. [PMID: 32983042 PMCID: PMC7483551 DOI: 10.3389/fmicb.2020.02058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 08/05/2020] [Indexed: 12/28/2022] Open
Abstract
Cryptococcosis is a fungal infection caused mainly by the pathogenic yeasts Cryptococcus neoformans and Cryptococcus gattii. The infection initiates with the inhalation of propagules that are then deposited in the lungs. If not properly treated, cryptococci cells can disseminate and reach the central nervous system. The current recommended treatment for cryptococcosis employs a three-stage regimen, with the administration of amphotericin B, flucytosine and fluconazole. Although effective, these drugs are often unavailable worldwide, can lead to resistance development, and may display toxic effects on the patients. Thus, new drugs for cryptococcosis treatment are needed. Recently, an iridoid named plumieridine was found in Allamanda polyantha seed extract; it exhibited antifungal activity against C. neoformans with a MIC of 250 μg/mL. To address the mode of action of plumieridine, several in silico and in vitro experiments were performed. Through a ligand-based a virtual screening approach, chitinases were identified as potential targets. Confirmatory in vitro assays showed that C. neoformans cell-free supernatant incubated with plumieridine displayed reduced chitinase activity, while chitinolytic activity was not inhibited in the insoluble cell fraction. Additionally, confocal microscopy revealed changes in the distribution of chitooligomers in the cryptococcal cell wall, from a polarized to a diffuse cell pattern state. Remarkably, further assays have shown that plumieridine can also inhibit the chitinolytic activity from the supernatant and cell-free extracts of bacteria, insect and mouse-derived macrophage cells (J774.A1). Together, our results suggest that plumieridine can be a broad-spectrum chitinase inhibitor.
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Affiliation(s)
- Eden Silva E Souza
- Bioinformatics Multidisciplinary Environment, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | | | - Nicolau Sbaraini
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | | | - Adriana Corrêa da Silva
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, Brazil
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17
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Andryianau G, Kowalski M, Piotrowicz MC, Rajkiewicz AA, Dymek B, Sklepkiewicz PL, Pluta E, Stefaniak F, Czestkowski W, Olejniczak S, Mazur M, Niedziejko P, Koralewski R, Matyszewski K, Gruza M, Zagozdzon A, Salamon M, Rymaszewska A, Welzer M, Dzwonek K, Golab J, Olczak J, Bartoszewicz A, Golebiowski A. Benzoxazepine-Derived Selective, Orally Bioavailable Inhibitor of Human Acidic Mammalian Chitinase. ACS Med Chem Lett 2020; 11:1228-1235. [PMID: 32551005 DOI: 10.1021/acsmedchemlett.0c00092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/24/2020] [Indexed: 01/06/2023] Open
Abstract
Human acidic mammalian chitinase (hAMCase) is one of two true chitinases in humans, the function of which remains elusive. In addition to the defense against highly antigenic chitin and chitin-containing pathogens in the gastric and intestinal contents, AMCase has been implicated in asthma, allergic inflammation, and ocular pathologies. Potent and selective small-molecule inhibitors of this enzyme have not been identified to date. Here we describe structural modifications of compound OAT-177, a previously developed inhibitor of mouse AMCase, leading to OAT-1441, which displays high activity and selectivity toward hAMCase. Significantly reduced off-target activity toward the human ether-à-go-go-related gene (hERG) and a good pharmacokinetic profile make OAT-1441 a potential candidate for further preclinical development as well as a useful tool compound to study the physiological role of hAMCase.
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Affiliation(s)
- Gleb Andryianau
- OncoArendi Therapeutics S.A., Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Michal Kowalski
- OncoArendi Therapeutics S.A., Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | | | - Adam A. Rajkiewicz
- OncoArendi Therapeutics S.A., Żwirki i Wigury 101, 02-089 Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland
| | - Barbara Dymek
- OncoArendi Therapeutics S.A., Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | | | - Elzbieta Pluta
- OncoArendi Therapeutics S.A., Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Filip Stefaniak
- OncoArendi Therapeutics S.A., Żwirki i Wigury 101, 02-089 Warsaw, Poland
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Ks. Trojdena 4, 02-109 Warsaw, Poland
| | | | - Sylwia Olejniczak
- OncoArendi Therapeutics S.A., Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Marzena Mazur
- OncoArendi Therapeutics S.A., Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Piotr Niedziejko
- OncoArendi Therapeutics S.A., Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Robert Koralewski
- OncoArendi Therapeutics S.A., Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | | | - Mariusz Gruza
- OncoArendi Therapeutics S.A., Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | | | - Magdalena Salamon
- OncoArendi Therapeutics S.A., Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | | | - Mikolaj Welzer
- OncoArendi Therapeutics S.A., Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Karolina Dzwonek
- OncoArendi Therapeutics S.A., Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Jakub Golab
- OncoArendi Therapeutics S.A., Żwirki i Wigury 101, 02-089 Warsaw, Poland
- Department of Immunology, Medical University of Warsaw, Nielubowicza 5, 02-097 Warsaw, Poland
| | - Jacek Olczak
- OncoArendi Therapeutics S.A., Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | | | - Adam Golebiowski
- OncoArendi Therapeutics S.A., Żwirki i Wigury 101, 02-089 Warsaw, Poland
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18
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Whittingham JL, Hanai S, Brannigan JA, Ferreira WT, Dodson EJ, Turkenburg JP, Cartwright J, Cutting SM, Wilkinson AJ. Crystal structures of the GH18 domain of the bifunctional peroxiredoxin-chitinase CotE from Clostridium difficile. Acta Crystallogr F Struct Biol Commun 2020; 76:241-249. [PMID: 32510464 PMCID: PMC7278498 DOI: 10.1107/s2053230x20006147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 05/06/2020] [Indexed: 12/20/2022] Open
Abstract
CotE is a coat protein that is present in the spores of Clostridium difficile, an obligate anaerobic bacterium and a pathogen that is a leading cause of antibiotic-associated diarrhoea in hospital patients. Spores serve as the agents of disease transmission, and CotE has been implicated in their attachment to the gut epithelium and subsequent colonization of the host. CotE consists of an N-terminal peroxiredoxin domain and a C-terminal chitinase domain. Here, a C-terminal fragment of CotE comprising residues 349-712 has been crystallized and its structure has been determined to reveal a core eight-stranded β-barrel fold with a neighbouring subdomain containing a five-stranded β-sheet. A prominent groove running across the top of the barrel is lined by residues that are conserved in family 18 glycosyl hydrolases and which participate in catalysis. Electron density identified in the groove defines the pentapeptide Gly-Pro-Ala-Met-Lys derived from the N-terminus of the protein following proteolytic cleavage to remove an affinity-purification tag. These observations suggest the possibility of designing peptidomimetics to block C. difficile transmission.
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Affiliation(s)
- Jean L. Whittingham
- Structural Biology Laboratory, York Biomedical Research Institute, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Shumpei Hanai
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - James A. Brannigan
- Structural Biology Laboratory, York Biomedical Research Institute, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - William T. Ferreira
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, United Kingdom
| | - Eleanor J. Dodson
- Structural Biology Laboratory, York Biomedical Research Institute, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Johan P. Turkenburg
- Structural Biology Laboratory, York Biomedical Research Institute, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Jared Cartwright
- Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Simon M. Cutting
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, United Kingdom
| | - Anthony J. Wilkinson
- Structural Biology Laboratory, York Biomedical Research Institute, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
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19
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Liu T, Han H, Wang D, Guo X, Zhou Y, Fukamizo T, Yang Q. Potent Fungal Chitinase for the Bioconversion of Mycelial Waste. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:5384-5390. [PMID: 32275147 DOI: 10.1021/acs.jafc.0c01342] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Aspergillus niger mycelial waste is a good raw material for production of N-acetyl-d-glucosamine (GlcNAc). In this study, AnChiB, an A. niger chitinase which is upregulated during autolysis, was found to degrade A. niger mycelial waste with high efficiency. It could produce 1.45 mM (GlcNAc)2 in 8 h from raw mycelial waste, outperforming other chitinases, including bacterial SmChiA, human HsCht, and insect OfChtI and OfChi-h. The crystal structure of AnChiB was determined, and residues Trp106 and Trp118 were found to be important for the activity of AnChiB toward mycelial waste; mutation of either Trp106 or Trp118 into phenylalanine or alanine resulted in dramatically decreased activity. A recombinant strain of Bacillus subtilis was constructed to extracellularly produce AnChiB, and the culture supernatant was used to treat mycelial waste. This eco-friendly strategy could produce 3.7 mM of GlcNAc from 10 g of mycelial waste in 94 h with a yield of 71.3%.
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Affiliation(s)
- Tian Liu
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Hongyu Han
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
- Shandong Food Ferment Industry Research & Design Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250013, China
| | - Di Wang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Xiaoguang Guo
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Yong Zhou
- School of Software, Dalian University of Technology, Dalian 116024, China
| | - Tamo Fukamizo
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Qing Yang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
- 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, China
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20
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Jiang X, Kumar A, Motomura Y, Liu T, Zhou Y, Moro K, Zhang KYJ, Yang Q. A Series of Compounds Bearing a Dipyrido-Pyrimidine Scaffold Acting as Novel Human and Insect Pest Chitinase Inhibitors. J Med Chem 2020; 63:987-1001. [PMID: 31928006 DOI: 10.1021/acs.jmedchem.9b01154] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Chitinases not only play vital roles in the human innate immune system but are also essential for the development of pathogenic fungi and pests. Chitinase inhibitors are efficient tools to investigate the elusive role of human chitinases and to control pathogens and pests. Via hierarchical virtual screening, we have discovered a series of chitinase inhibitors with a novel scaffold that have high inhibitory activities and selectivities against human and insect chitinases. The most potent human chitotriosidase inhibitor, compound 40, exhibited a Ki of 49 nM, and the most potent inhibitor of the insect pest chitinase OfChi-h, compound 53, exhibited a Ki of 9 nM. The binding of these two most potent inhibitors was confirmed by X-ray crystallography. In a murine model of bleomycin-induced pulmonary fibrosis, compound 40 was found to suppress the chitotriosidase activity by 60%, leading to a significant increase in inflammatory cells and suggesting that chitotriosidase played a protective role.
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Affiliation(s)
- Xi Jiang
- School of Bioengineering , Dalian University of Technology , 2 Linggong Road , Dalian 116024 , China
| | - Ashutosh Kumar
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research , RIKEN , 1-7-22 Suehiro , Tsurumi, Yokohama , Kanagawa 230-0045 , Japan
| | - Yasutaka Motomura
- Laboratory for Innate Immune Systems, Center for Integrative Medical Sciences , RIKEN , 1-7-22 Suehiro , Tsurumi, Yokohama , Kanagawa 230-0045 , Japan.,Laboratory for Innate Immune Systems, Department of Microbiology and Immunology, Graduate School of Medicine , Osaka University , 2-2 Yamadaoka , Suita-shi, Osaka 565-0871 , Japan
| | - Tian Liu
- School of Bioengineering , Dalian University of Technology , 2 Linggong Road , Dalian 116024 , China
| | - Yong Zhou
- School of Software , Dalian University of Technology , 2 Linggong Road , Dalian 116024 , China
| | - Kazuyo Moro
- Laboratory for Innate Immune Systems, Center for Integrative Medical Sciences , RIKEN , 1-7-22 Suehiro , Tsurumi, Yokohama , Kanagawa 230-0045 , Japan.,Laboratory for Innate Immune Systems, Department of Microbiology and Immunology, Graduate School of Medicine , Osaka University , 2-2 Yamadaoka , Suita-shi, Osaka 565-0871 , Japan
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research , RIKEN , 1-7-22 Suehiro , Tsurumi, Yokohama , Kanagawa 230-0045 , Japan
| | - Qing Yang
- School of Bioengineering , Dalian University of Technology , 2 Linggong Road , Dalian 116024 , China.,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 , 2 West Yuanmingyuan Road , Beijing 100193 , China
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21
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Merritt HI, Sawyer N, Arora PS. Bent Into Shape: Folded Peptides to Mimic Protein Structure and Modulate Protein Function. Pept Sci (Hoboken) 2020; 112:e24145. [PMID: 33575525 PMCID: PMC7875438 DOI: 10.1002/pep2.24145] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 12/11/2019] [Indexed: 12/16/2022]
Abstract
Protein secondary and tertiary structure mimics have served as model systems to probe biophysical parameters that guide protein folding and as attractive reagents to modulate protein interactions. Here we review contemporary methods to reproduce loop, helix, sheet and coiled-coil conformations in short peptides.
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Affiliation(s)
| | | | - Paramjit S. Arora
- Department of Chemistry New York University, New York, New York 10003, United States
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22
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Deng JJ, Shi D, Mao HH, Li ZW, Liang S, Ke Y, Luo XC. Heterologous expression and characterization of an antifungal chitinase (Chit46) from Trichoderma harzianum GIM 3.442 and its application in colloidal chitin conversion. Int J Biol Macromol 2019; 134:113-121. [DOI: 10.1016/j.ijbiomac.2019.04.177] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/25/2019] [Accepted: 04/25/2019] [Indexed: 01/21/2023]
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23
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Chen W, Zhou Y, Yang Q. Structural dissection reveals a general mechanistic principle for group II chitinase (ChtII) inhibition. J Biol Chem 2019; 294:9358-9364. [PMID: 31053640 DOI: 10.1074/jbc.ra119.007812] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/30/2019] [Indexed: 12/13/2022] Open
Abstract
Small-molecule inhibitors of insect chitinases have potential applications for controlling insect pests. Insect group II chitinase (ChtII) is the most important chitinase in insects and functions throughout all developmental stages. However, the possibility of inhibiting ChtII by small molecules has not been explored yet. Here, we report the structural characteristics of four molecules that exhibited similar levels of inhibitory activity against OfChtII, a group II chitinase from the agricultural pest Asian corn borer Ostrinia furnacalis These inhibitors were chitooctaose ((GlcN)8), dipyrido-pyrimidine derivative (DP), piperidine-thienopyridine derivative (PT), and naphthalimide derivative (NI). The crystal structures of the OfChtII catalytic domain complexed with each of the four inhibitors at 1.4-2.0 Å resolutions suggested they all exhibit similar binding modes within the substrate-binding cleft; specifically, two hydrophobic groups of the inhibitor interact with +1/+2 tryptophan and a -1 hydrophobic pocket. The structure of the (GlcN)8 complex surprisingly revealed that the oligosaccharide chain of the inhibitor is orientated in the opposite direction to that previously observed in complexes with other chitinases. Injection of the inhibitors into 4th instar O. furnacalis larvae led to defects in development and pupation. The results of this study provide insights into a general mechanistic principle that confers inhibitory activity against ChtII, which could facilitate rational design of agrochemicals that target ecdysis of insect pests.
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Affiliation(s)
- Wei Chen
- From the State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 2 West Yuanmingyuan Road, Beijing 100193, China and
| | - Yong Zhou
- School of Biotechnology and School of Software, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China
| | - Qing Yang
- From the State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 2 West Yuanmingyuan Road, Beijing 100193, China and .,School of Biotechnology and School of Software, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China
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24
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Malde AK, Hill TA, Iyer A, Fairlie DP. Crystal Structures of Protein-Bound Cyclic Peptides. Chem Rev 2019; 119:9861-9914. [DOI: 10.1021/acs.chemrev.8b00807] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alpeshkumar K. Malde
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Timothy A. Hill
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Abishek Iyer
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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25
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Kumar A, Zhang KYJ. Human Chitinases: Structure, Function, and Inhibitor Discovery. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1142:221-251. [PMID: 31102249 DOI: 10.1007/978-981-13-7318-3_11] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chitinases are glycosyl hydrolases that hydrolyze the β-(1-4)-linkage of N-acetyl-D-glucosamine units present in chitin polymers. Chitinases are widely distributed enzymes and are present in a wide range of organisms including insects, plants, bacteria, fungi, and mammals. These enzymes play key roles in immunity, nutrition, pathogenicity, and arthropod molting. Humans express two chitinases, chitotriosidase 1 (CHIT1) and acid mammalian chitinase (AMCase) along with several chitinase-like proteins (CLPs). Human chitinases are reported to play a protective role against chitin-containing pathogens through their capability to degrade chitin present in the cell wall of pathogens. Now, human chitinases are gaining attention as the key players in innate immune response. Although the exact mechanism of their role in immune response is not known, studies in recent years begin to relate chitin recognition and degradation with the activation of signaling pathways involved in inflammation. The roles of both CHIT1 and AMCase in the development of various diseases have been revealed and several classes of inhibitors have been developed. However, a clear understanding could not be established due to complexities in the design of the right experiment for studying the role of human chitinase in various diseases. In this chapter, we will first outline the structural features of CHIT1 and AMcase. We will then review the progress in understanding the role of human chitinases in the development of various diseases. Finally, we will summarize the inhibitor discovery efforts targeting both CHIT1 and AMCase.
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Affiliation(s)
- Ashutosh Kumar
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
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26
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Yang J, Zhang KQ. Chitin Synthesis and Degradation in Fungi: Biology and Enzymes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1142:153-167. [PMID: 31102246 DOI: 10.1007/978-981-13-7318-3_8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chitin is one of the most important carbohydrates of the fungal cell wall, and is synthesized by chitin synthases. Chitin can be degraded by chitinases, which are important virulence factors in pathogenic fungi. Knowledge about the biosynthesis and degradation of chitin, and the enzymes responsible, has accumulated in recent years. In this review, we analyze the amino acid sequences of chitin synthases from several typical fungi. These enzymes can be divided into seven groups. While the different chitin synthases from a single fungus share a low degree of similarity, the same type of chitin synthase from different fungi shows high similarity. The number of chitinase genes in fungi display wide variation, from a single gene in Schizosaccharomyces pombe, to 36 genes in Trichoderma virens. Chitinases from different fungi can be divided into four groups. The functions of chitin synthases and chitinases in several typical fungi are summarized, and the crystal structures of chitinases and chitinase modification are also discussed.
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Affiliation(s)
- Jinkui Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, 650091, Kunming, Yunnan, China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, 650091, Kunming, Yunnan, China.
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27
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Giles AR, Sims JJ, Turner KB, Govindasamy L, Alvira MR, Lock M, Wilson JM. Deamidation of Amino Acids on the Surface of Adeno-Associated Virus Capsids Leads to Charge Heterogeneity and Altered Vector Function. Mol Ther 2018; 26:2848-2862. [PMID: 30343890 DOI: 10.1016/j.ymthe.2018.09.013] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 09/10/2018] [Accepted: 09/13/2018] [Indexed: 12/19/2022] Open
Abstract
Post-translational modification of the adeno-associated virus capsids is a poorly understood factor in the development of these viral vectors into pharmaceutical products. Here we report the extensive capsid deamidation of adeno-associated virus serotype 8 and seven other diverse adeno-associated virus serotypes, with supporting evidence from structural, biochemical, and mass spectrometry approaches. The extent of deamidation at each site depended on the vector's age and multiple primary-sequence and three-dimensional structural factors. However, the extent of deamidation was largely independent of the vector recovery and purification conditions. We demonstrate the potential for deamidation to impact transduction activity and, moreover, correlate an early time point loss in vector activity to rapidly progressing spontaneous deamidation at several adeno-associated virus 8 asparagines. We explore mutational strategies that stabilize side-chain amides, improving vector transduction and reducing the lot-to-lot molecular variability that presents a key concern in biologics manufacturing. This study illuminates a previously unknown aspect of adeno-associated virus capsid heterogeneity and highlights its importance in the development of these vectors for gene therapy.
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Affiliation(s)
- April R Giles
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joshua J Sims
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kevin B Turner
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lakshmanan Govindasamy
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mauricio R Alvira
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Martin Lock
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James M Wilson
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Kidibule PE, Santos-Moriano P, Jiménez-Ortega E, Ramírez-Escudero M, Limón MC, Remacha M, Plou FJ, Sanz-Aparicio J, Fernández-Lobato M. Use of chitin and chitosan to produce new chitooligosaccharides by chitinase Chit42: enzymatic activity and structural basis of protein specificity. Microb Cell Fact 2018; 17:47. [PMID: 29566690 PMCID: PMC5863366 DOI: 10.1186/s12934-018-0895-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/17/2018] [Indexed: 11/30/2022] Open
Abstract
Background Chitinases are ubiquitous enzymes that have gained a recent biotechnological attention due to their ability to transform biological waste from chitin into valued chito-oligomers with wide agricultural, industrial or medical applications. The biological activity of these molecules is related to their size and acetylation degree. Chitinase Chit42 from Trichoderma harzianum hydrolyses chitin oligomers with a minimal of three N-acetyl-d-glucosamine (GlcNAc) units. Gene chit42 was previously characterized, and according to its sequence, the encoded protein included in the structural Glycoside Hydrolase family GH18. Results Chit42 was expressed in Pichia pastoris using fed-batch fermentation to about 3 g/L. Protein heterologously expressed showed similar biochemical properties to those expressed by the natural producer (42 kDa, optima pH 5.5–6.5 and 30–40 °C). In addition to hydrolyse colloidal chitin, this enzyme released reducing sugars from commercial chitosan of different sizes and acetylation degrees. Chit42 hydrolysed colloidal chitin at least 10-times more efficiently (defined by the kcat/Km ratio) than any of the assayed chitosan. Production of partially acetylated chitooligosaccharides was confirmed in reaction mixtures using HPAEC-PAD chromatography and mass spectrometry. Masses corresponding to (d-glucosamine)1–8-GlcNAc were identified from the hydrolysis of different substrates. Crystals from Chit42 were grown and the 3D structure determined at 1.8 Å resolution, showing the expected folding described for other GH18 chitinases, and a characteristic groove shaped substrate-binding site, able to accommodate at least six sugar units. Detailed structural analysis allows depicting the features of the Chit42 specificity, and explains the chemical nature of the partially acetylated molecules obtained from analysed substrates. Conclusions Chitinase Chit42 was expressed in a heterologous system to levels never before achieved. The enzyme produced small partially acetylated chitooligosaccharides, which have enormous biotechnological potential in medicine and food. Chit42 3D structure was characterized and analysed. Production and understanding of how the enzymes generating bioactive chito-oligomers work is essential for their biotechnological application, and paves the way for future work to take advantage of chitinolytic activities. Electronic supplementary material The online version of this article (10.1186/s12934-018-0895-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Peter Elias Kidibule
- Department of Molecular Biology, Centre for Molecular Biology Severo Ochoa (CSIC-UAM), University Autonomous from Madrid, C/ Nicolás Cabrera, 1, Cantoblanco, 28049, Madrid, Spain
| | - Paloma Santos-Moriano
- Institute of Catalysis and Petrochemistry, CSIC, C/ Marie Curie, 2, Cantoblanco, 28049, Madrid, Spain
| | - Elena Jiménez-Ortega
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano (CSIC), C/ Serrano, 119, 28006, Madrid, Spain
| | - Mercedes Ramírez-Escudero
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano (CSIC), C/ Serrano, 119, 28006, Madrid, Spain
| | - M Carmen Limón
- Department of Genetic, University of Sevilla, Avenida Reina Mercedes s/n, 41012, Seville, Spain
| | - Miguel Remacha
- Department of Molecular Biology, Centre for Molecular Biology Severo Ochoa (CSIC-UAM), University Autonomous from Madrid, C/ Nicolás Cabrera, 1, Cantoblanco, 28049, Madrid, Spain
| | - Francisco José Plou
- Institute of Catalysis and Petrochemistry, CSIC, C/ Marie Curie, 2, Cantoblanco, 28049, Madrid, Spain
| | - Julia Sanz-Aparicio
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano (CSIC), C/ Serrano, 119, 28006, Madrid, Spain
| | - María Fernández-Lobato
- Department of Molecular Biology, Centre for Molecular Biology Severo Ochoa (CSIC-UAM), University Autonomous from Madrid, C/ Nicolás Cabrera, 1, Cantoblanco, 28049, Madrid, Spain.
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Chitin Deacetylases: Structures, Specificities, and Biotech Applications. Polymers (Basel) 2018; 10:polym10040352. [PMID: 30966387 PMCID: PMC6415152 DOI: 10.3390/polym10040352] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 03/15/2018] [Accepted: 03/19/2018] [Indexed: 12/20/2022] Open
Abstract
Depolymerization and de-N-acetylation of chitin by chitinases and deacetylases generates a series of derivatives including chitosans and chitooligosaccharides (COS), which are involved in molecular recognition events such as modulation of cell signaling and morphogenesis, immune responses, and host-pathogen interactions. Chitosans and COS are also attractive scaffolds for the development of bionanomaterials for drug/gene delivery and tissue engineering applications. Most of the biological activities associated with COS seem to be largely dependent not only on the degree of polymerization but also on the acetylation pattern, which defines the charge density and distribution of GlcNAc and GlcNH₂ moieties in chitosans and COS. Chitin de-N-acetylases (CDAs) catalyze the hydrolysis of the acetamido group in GlcNAc residues of chitin, chitosan, and COS. The deacetylation patterns are diverse, some CDAs being specific for single positions, others showing multiple attack, processivity or random actions. This review summarizes the current knowledge on substrate specificity of bacterial and fungal CDAs, focusing on the structural and molecular aspects of their modes of action. Understanding the structural determinants of specificity will not only contribute to unravelling structure-function relationships, but also to use and engineer CDAs as biocatalysts for the production of tailor-made chitosans and COS for a growing number of applications.
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30
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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: 16] [Impact Index Per Article: 2.7] [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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Wang X, Lin M, Xu D, Lai D, Zhou L. Structural Diversity and Biological Activities of Fungal Cyclic Peptides, Excluding Cyclodipeptides. Molecules 2017; 22:E2069. [PMID: 29186926 PMCID: PMC6150023 DOI: 10.3390/molecules22122069] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 11/20/2017] [Accepted: 11/23/2017] [Indexed: 11/23/2022] Open
Abstract
Cyclic peptides are cyclic compounds formed mainly by the amide bonds between either proteinogenic or non-proteinogenic amino acids. This review highlights the occurrence, structures and biological activities of fungal cyclic peptides (excluding cyclodipeptides, and peptides containing ester bonds in the core ring) reported until August 2017. About 293 cyclic peptides belonging to the groups of cyclic tri-, tetra-, penta-, hexa-, hepta-, octa-, nona-, deca-, undeca-, dodeca-, tetradeca-, and octadecapeptides as well as cyclic peptides containing ether bonds in the core ring have been isolated from fungi. They were mainly isolated from the genera Aspergillus, Penicillium, Fusarium, Acremonium and Amanita. Some of them were screened to have antimicrobial, antiviral, cytotoxic, phytotoxic, insecticidal, nematicidal, immunosuppressive and enzyme-inhibitory activities to show their potential applications. Some fungal cyclic peptides such as the echinocandins, pneumocandins and cyclosporin A have been developed as pharmaceuticals.
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Affiliation(s)
- Xiaohan Wang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China.
| | - Minyi Lin
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China.
| | - Dan Xu
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China.
| | - Daowan Lai
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China.
| | - Ligang Zhou
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China.
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32
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Hong SH, Song YS, Seo DJ, Kim KY, Jung WJ. Antifungal activity and expression patterns of extracellular chitinase and β-1,3-glucanase in Wickerhamomyces anomalus EG2 treated with chitin and glucan. Microb Pathog 2017; 110:159-164. [PMID: 28668604 DOI: 10.1016/j.micpath.2017.06.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 05/23/2017] [Accepted: 06/26/2017] [Indexed: 11/15/2022]
Abstract
In this study, the expression patterns of extracellular chitinase and β-1,3-glucanase from cultured Wickerhamomyces anomalus EG2 treated with chitin, glucan, and chemical chitinase inhibitors (kinetin, caffeine, and acetazolamide) were investigated using SDS-PAGE. Relationship between enzyme expression and antifungal activity from yeast plays a very important role for biocontrol of phytopathoges. To determine antifungal activity against phytopathogens, W. anomalus EG2 was shown to strongly inhibit hyphal growth of Fusarium oxysporum KACC 40032 and Rhizoctonia solani KACC 40111. Slight chitinase activity was observed 12 h after incubation in both PDB and YPD medium without colloidal chitin. The molecular weight of chitinase was approximately 124 kDa β-1,3-Glucanase isoenzyme (GN1 and GN2) was observed distinctly on SDS-PAGE gels when laminarin was used as a substrate. β-1,3-Glucanase isoenzyme was not observed when using glucan-containing high polymer complex (GHPC) as a substrate. Production of chitinase from W. anomalus EG2 was inhibited slightly by acetazolamide. Abnormal and cluster-shaped cells of W. anomalus EG2 were observed in both PDB and YPD medium treated with colloidal chitin. These results indicated that W. anomalus EG2 could be applied commercially as a biological control agent of phytopathogens and as a bioinhibitor of yeast cell growth.
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Affiliation(s)
- Sin-Hyoung Hong
- Department of Agricultural Chemistry, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agricultural and Life Science, Chonnam National University, Gwangju 61186, South Korea
| | - Yong-Su Song
- Department of Agricultural Chemistry, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agricultural and Life Science, Chonnam National University, Gwangju 61186, South Korea
| | - Dong-Jun Seo
- Department of Agricultural Chemistry, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agricultural and Life Science, Chonnam National University, Gwangju 61186, South Korea
| | - Kil-Yong Kim
- Department of Agricultural Chemistry, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agricultural and Life Science, Chonnam National University, Gwangju 61186, South Korea
| | - Woo-Jin Jung
- Department of Agricultural Chemistry, Institute of Environmentally-Friendly Agriculture (IEFA), College of Agricultural and Life Science, Chonnam National University, Gwangju 61186, South Korea.
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Maccari G, Deodato D, Fiorucci D, Orofino F, Truglio GI, Pasero C, Martini R, De Luca F, Docquier JD, Botta M. Design and synthesis of a novel inhibitor of T. Viride chitinase through an in silico target fishing protocol. Bioorg Med Chem Lett 2017; 27:3332-3336. [PMID: 28610983 DOI: 10.1016/j.bmcl.2017.06.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 06/01/2017] [Accepted: 06/03/2017] [Indexed: 12/31/2022]
Abstract
In the last ten years, we identified and developed a new therapeutic class of antifungal agents, the macrocyclic amidinoureas. These compounds are active against several Candida species, including clinical isolates resistant to currently available antifungal drugs. The mode of action of these molecules is still unknown. In this work, we developed an in-silico target fishing procedure to identify a possible target for this class of compounds based on shape similarity, inverse docking procedure and consensus score rank-by-rank. Chitinase enzyme emerged as possible target. To confirm this hypothesis a novel macrocyclic derivative has been produced, specifically designed to increase the inhibition of the chitinase. Biological evaluation highlights a stronger enzymatic inhibition for the new derivative, while its antifungal activity drops probably because of pharmacokinetic issues. Collectively, our data suggest that chitinase represent at least one of the main target of macrocyclic amidinoureas.
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Affiliation(s)
- Giorgio Maccari
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy
| | - Davide Deodato
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy
| | - Diego Fiorucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy
| | - Francesco Orofino
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy
| | - Giuseppina I Truglio
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy
| | - Carolina Pasero
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy
| | - Riccardo Martini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy
| | - Filomena De Luca
- Department of Medical Biotechnology, University of Siena, I-53100 Siena, Italy
| | - Jean-Denis Docquier
- Department of Medical Biotechnology, University of Siena, I-53100 Siena, Italy; Lead Discovery Siena s.r.l, Via Vittorio Alfieri 31, I-53019 Castelnuovo Berardenga, Italy
| | - Maurizio Botta
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy; Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, BioLife Science Building, Suite 333, 1900 N 12th Street, Philadelphia, PA 19122, USA; Lead Discovery Siena s.r.l, Via Vittorio Alfieri 31, I-53019 Castelnuovo Berardenga, Italy.
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Chen L, Liu T, Duan Y, Lu X, Yang Q. Microbial Secondary Metabolite, Phlegmacin B 1, as a Novel Inhibitor of Insect Chitinolytic Enzymes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:3851-3857. [PMID: 28457127 DOI: 10.1021/acs.jafc.7b01710] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Periodic chitin remodeling during insect growth and development requires a synergistic action of two glycosyl hydrolase (GH) family enzymes, GH18 chitinase and GH20 β-N-acetylhexosaminidase (Hex). Inhibiting either or both of these enzymes is a promising strategy for pest control and management. In this study, OfChi-h (a GH18 chitinase) and OfHex1 (a GH20 Hex) from Ostrinia furnacalis were used to screen a library of microbial secondary metabolites. Phlegmacin B1 was found to be the inhibitor of both OfChi-h and OfHex1 with Ki values of 5.5 μM and 26 μM, respectively. Injection and feeding experiments demonstrated that phlegmacin B1 has insecticidal effect on O. furnacalis's larvae. Phlegmacin B1 was predicted to bind to the active pockets of both OfChi-h and OfHex1. Phlegmacin B1 also showed moderate inhibitory activities against other bacterial and insect GH18 enzymes. This work provides an example of exploiting microbial secondary metabolites as potential pest control and management agents.
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Affiliation(s)
- Lei Chen
- State Key Laboratory of Fine Chemical Engineering and School of Life Science and Biotechnology, Dalian University of Technology , Dalian 116024, China
| | - Tian Liu
- State Key Laboratory of Fine Chemical Engineering and School of Life Science and Biotechnology, Dalian University of Technology , Dalian 116024, China
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences , Beijing 100193, China
| | - Yanwei Duan
- State Key Laboratory of Fine Chemical Engineering and School of Life Science and Biotechnology, Dalian University of Technology , Dalian 116024, China
| | - Xinhua Lu
- New Drug Research & Development Center, North China Pharmaceutical Group Corporation , Shijiazhuang 050015, China
| | - Qing Yang
- State Key Laboratory of Fine Chemical Engineering and School of Life Science and Biotechnology, Dalian University of Technology , Dalian 116024, China
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences , Beijing 100193, China
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Liu T, Chen L, Zhou Y, Jiang X, Duan Y, Yang Q. Structure, Catalysis, and Inhibition of OfChi-h, the Lepidoptera-exclusive Insect Chitinase. J Biol Chem 2017; 292:2080-2088. [PMID: 28053084 DOI: 10.1074/jbc.m116.755330] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 11/28/2016] [Indexed: 12/31/2022] Open
Abstract
Chitinase-h (Chi-h) is of special interest among insect chitinases due to its exclusive distribution in lepidopteran insects and high sequence identity with bacterial and baculovirus homologs. Here OfChi-h, a Chi-h from Ostrinia furnacalis, was investigated. Crystal structures of both OfChi-h and its complex with chitoheptaose ((GlcN)7) reveal that OfChi-h possesses a long and asymmetric substrate binding cleft, which is a typical characteristics of a processive exo-chitinase. The structural comparison between OfChi-h and its bacterial homolog SmChiA uncovered two phenylalanine-to-tryptophan site variants in OfChi-h at subsites +2 and possibly -7. The F232W/F396W double mutant endowed SmChiA with higher hydrolytic activities toward insoluble substrates, such as insect cuticle, α-chitin, and chitin nanowhisker. An enzymatic assay demonstrated that OfChi-h outperformed OfChtI, an insect endo-chitinase, toward the insoluble substrates, but showed lower activity toward the soluble substrate ethylene glycol chitin. Furthermore, OfChi-h was found to be inhibited by N,N',N″-trimethylglucosamine-N,N',N″,N″'-tetraacetylchitotetraose (TMG-(GlcNAc)4), a substrate analog which can be degraded into TMG-(GlcNAc)1-2 Injection of TMG-(GlcNAc)4 into 5th-instar O. furnacalis larvae led to severe defects in pupation. This work provides insights into a molting-indispensable insect chitinase that is phylogenetically closer to bacterial chitinases than insect chitinases.
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Affiliation(s)
- Tian Liu
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China and
| | - Lei Chen
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China and
| | - Yong Zhou
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China and
| | - Xi Jiang
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China and
| | - Yanwei Duan
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China and
| | - Qing Yang
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, 2 Linggong Road, Dalian 116024, China and .,Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 2 West Yuanmingyuan Road, Beijing 100193, China
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Sharma V, Salwan R, Sharma P, Kanwar S. Molecular cloning and characterization of ech 46 endochitinase from Trichoderma harzianum. Int J Biol Macromol 2016; 92:615-624. [DOI: 10.1016/j.ijbiomac.2016.07.067] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 07/17/2016] [Accepted: 07/21/2016] [Indexed: 01/24/2023]
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Molecular, Structural and Immunological Characterization of Der p 18, a Chitinase-Like House Dust Mite Allergen. PLoS One 2016; 11:e0160641. [PMID: 27548813 PMCID: PMC4993390 DOI: 10.1371/journal.pone.0160641] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 07/24/2016] [Indexed: 12/27/2022] Open
Abstract
Background The house dust mite (HDM) allergen Der p 18 belongs to the glycoside hydrolase family 18 chitinases. The relevance of Der p 18 for house dust mite allergic patients has only been partly investigated. Objective To perform a detailed characterization of Der p 18 on a molecular, structural and immunological level. Methods Der p 18 was expressed in E. coli, purified to homogeneity, tested for chitin-binding activity and its secondary structure was analyzed by circular dichroism. Der p 18-specific IgG antibodies were produced in rabbits to localize the allergen in mites using immunogold electron microscopy and to search for cross-reactive allergens in other allergen sources (i.e. mites, crustacea, mollusca and insects). IgE reactivity of rDer p 18 was tested with sera from clinically well characterized HDM-allergic patients (n = 98) and its allergenic activity was analyzed in basophil activation experiments. Results Recombinant Der p 18 was expressed and purified as a folded, biologically active protein. It shows weak chitin-binding activity and partial cross-reactivity with Der f 18 from D. farinae but not with proteins from the other tested allergen sources. The allergen was mainly localized in the peritrophic matrix of the HDM gut and to a lower extent in fecal pellets. Der p 18 reacted with IgE from 10% of mite allergic patients from Austria and showed allergenic activity when tested for basophil activation in Der p 18-sensitized patients. Conclusion Der p 18 is a rather genus-specific minor allergen with weak chitin-binding activity but exhibits allergenic activity and therefore should be included in diagnostic test panels for HDM allergy.
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Hirose T, Sunazuka T, Ōmura S. Rapid Identification via <i>In Situ</i> Click Chemistry of a Novel Chitinase Inhibitor. J SYN ORG CHEM JPN 2016. [DOI: 10.5059/yukigoseikyokaishi.74.1090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Tomoyasu Hirose
- Kitasato Institute for Life Sciences, Kitasato University
- Graduate School of Infection Control Sciences, Kitasato University
| | - Toshiaki Sunazuka
- Kitasato Institute for Life Sciences, Kitasato University
- Graduate School of Infection Control Sciences, Kitasato University
| | - Satoshi Ōmura
- Kitasato Institute for Life Sciences, Kitasato University
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Ueda M, Shimosaka M, Arai R. Expression, purification, crystallization and X-ray diffraction analysis of ChiL, a chitinase from Chitiniphilus shinanonensis. Acta Crystallogr F Struct Biol Commun 2015; 71:1516-20. [PMID: 26625294 PMCID: PMC4666480 DOI: 10.1107/s2053230x15022001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 11/18/2015] [Indexed: 11/10/2022] Open
Abstract
Chitin, a linear polysaccharide consisting of β-1,4-linked N-acetyl-D-glucosamine (GlcNAc), is widely used because of its biochemical properties. GlcNAc oligomers prepared from chitin have useful biological activities, such as immunostimulation and the induction of plant defence responses. Microbial chitinolytic enzymes have been investigated extensively for their potential use in the eco-friendly enzymatic production of GlcNAc and its oligomers. Chitiniphilus shinanonensis SAY3(T) is a recently found bacterium with a strong chitinolytic activity. The chitinolytic enzymes from this strain are potentially useful for the efficient production of GlcNAc and its oligomers from chitin. ChiL from C. shinanonensis is an endo-type chitinase belonging to the family 18 glycoside hydrolases (GH18). To understand the enzymatic reaction mechanism of ChiL and utilize it for further enzyme engineering, the catalytic domain (41-406) of ChiL, the construct for which was carefully designed, was expressed, purified and crystallized by the vapour-diffusion method. The crystal belonged to the orthorhombic space group P212121, with unit-cell parameters a = 69.19, b = 81.55, c = 130.01 Å, and diffracted to 1.25 Å resolution. The Matthews coefficient (VM = 2.2 Å(3) Da(-1)) suggested the presence of two monomers per asymmetric unit with a solvent content of 45%.
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Affiliation(s)
- Miruku Ueda
- Division of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, 3-15-1 Tokida, Ueda, Nagano 386-8567, Japan
| | - Makoto Shimosaka
- Division of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, 3-15-1 Tokida, Ueda, Nagano 386-8567, Japan
| | - Ryoichi Arai
- Division of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, 3-15-1 Tokida, Ueda, Nagano 386-8567, Japan
- Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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Fadel F, Zhao Y, Cachau R, Cousido-Siah A, Ruiz FX, Harlos K, Howard E, Mitschler A, Podjarny A. New insights into the enzymatic mechanism of human chitotriosidase (CHIT1) catalytic domain by atomic resolution X-ray diffraction and hybrid QM/MM. ACTA ACUST UNITED AC 2015; 71:1455-70. [PMID: 26143917 DOI: 10.1107/s139900471500783x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 04/21/2015] [Indexed: 11/10/2022]
Abstract
Chitotriosidase (CHIT1) is a human chitinase belonging to the highly conserved glycosyl hydrolase family 18 (GH18). GH18 enzymes hydrolyze chitin, an N-acetylglucosamine polymer synthesized by lower organisms for structural purposes. Recently, CHIT1 has attracted attention owing to its upregulation in immune-system disorders and as a marker of Gaucher disease. The 39 kDa catalytic domain shows a conserved cluster of three acidic residues, Glu140, Asp138 and Asp136, involved in the hydrolysis reaction. Under an excess concentration of substrate, CHIT1 and other homologues perform an additional activity, transglycosylation. To understand the catalytic mechanism of GH18 chitinases and the dual enzymatic activity, the structure and mechanism of CHIT1 were analyzed in detail. The resolution of the crystals of the catalytic domain was improved from 1.65 Å (PDB entry 1waw) to 0.95-1.10 Å for the apo and pseudo-apo forms and the complex with chitobiose, allowing the determination of the protonation states within the active site. This information was extended by hybrid quantum mechanics/molecular mechanics (QM/MM) calculations. The results suggest a new mechanism involving changes in the conformation and protonation state of the catalytic triad, as well as a new role for Tyr27, providing new insights into the hydrolysis and transglycosylation activities.
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Affiliation(s)
- Firas Fadel
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Yuguang Zhao
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford University, Roosevelt Drive, Headington, Oxford, England
| | - Raul Cachau
- Leidos Biomedical Research Inc. Advanced Biomedical Computer Center, Information Systems Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Alexandra Cousido-Siah
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Francesc X Ruiz
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Karl Harlos
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford University, Roosevelt Drive, Headington, Oxford, England
| | - Eduardo Howard
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Andre Mitschler
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
| | - Alberto Podjarny
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UdS, 1 Rue Laurent Fries, 67404 Illkirch CEDEX, France
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Sugawara A, Maita N, Gouda H, Yamamoto T, Hirose T, Kimura S, Saito Y, Nakano H, Kasai T, Nakano H, Shiomi K, Hirono S, Watanabe T, Taniguchi H, O̅mura S, Sunazuka T. Creation of Customized Bioactivity within a 14-Membered Macrolide Scaffold: Design, Synthesis, and Biological Evaluation Using a Family-18 Chitinase. J Med Chem 2015; 58:4984-97. [DOI: 10.1021/acs.jmedchem.5b00175] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Akihiro Sugawara
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Nobuo Maita
- Institute
for Enzyme Research, University of Tokushima, 3-18-15 Kuramotocho, Tokushima City, Tokushima, 770-8503, Japan
| | - Hiroaki Gouda
- School
of Pharmacy, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Tsuyoshi Yamamoto
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Tomoyasu Hirose
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Saori Kimura
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Yoshifumi Saito
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Hayato Nakano
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Takako Kasai
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Hirofumi Nakano
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Kazuro Shiomi
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Shuichi Hirono
- School
of Pharmacy, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Takeshi Watanabe
- Department
of Applied Biological Chemistry, Faculty of Agriculture, Niigata University, 8050 Ikarashi-2, Niigata 950-2181, Japan
| | - Hisaaki Taniguchi
- Institute
for Enzyme Research, University of Tokushima, 3-18-15 Kuramotocho, Tokushima City, Tokushima, 770-8503, Japan
| | - Satoshi O̅mura
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Toshiaki Sunazuka
- The
Kitasato Institute, Kitasato Institute for Life Sciences and Graduate
School of Infection Control Sciences, Kitasato University, 5-9-1, Shirokane, Minato-ku, Tokyo 108-8641, Japan
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Gao X, Ren Q, Choi S, Xu Z, Ye T. Total synthesis of the putative structure of the proposed Banyasin A. Front Chem 2015; 3:19. [PMID: 25853121 PMCID: PMC4362330 DOI: 10.3389/fchem.2015.00019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/02/2015] [Indexed: 11/13/2022] Open
Abstract
The first total synthesis of four possible isomers of a molecule possessing the configuration proposed for Banyasin A is described. The structure synthesized appears to be different from that of the natural product.
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Affiliation(s)
- Xuguang Gao
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School Shenzhen, China
| | - Qi Ren
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School Shenzhen, China
| | - Sun Choi
- National Leading Research Laboratory of Molecular Modeling and Drug Design, College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University Seoul, South Korea
| | - Zhengshuang Xu
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School Shenzhen, China
| | - Tao Ye
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School Shenzhen, China ; Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University Hong Kong, China
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Kinetic characterization of Aspergillus niger chitinase CfcI using a HPAEC-PAD method for native chitin oligosaccharides. Carbohydr Res 2015; 407:73-8. [DOI: 10.1016/j.carres.2015.01.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 01/23/2015] [Indexed: 01/14/2023]
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Recombinant CBM-fusion technology - Applications overview. Biotechnol Adv 2015; 33:358-69. [PMID: 25689072 DOI: 10.1016/j.biotechadv.2015.02.006] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 02/06/2015] [Accepted: 02/09/2015] [Indexed: 02/04/2023]
Abstract
Carbohydrate-binding modules (CBMs) are small components of several enzymes, which present an independent fold and function, and specific carbohydrate-binding activity. Their major function is to bind the enzyme to the substrate enhancing its catalytic activity, especially in the case of insoluble substrates. The immense diversity of CBMs, together with their unique properties, has long raised their attention for many biotechnological applications. Recombinant DNA technology has been used for cloning and characterizing new CBMs. In addition, it has been employed to improve the purity and availability of many CBMs, but mainly, to construct bi-functional CBM-fused proteins for specific applications. This review presents a comprehensive summary of the uses of CBMs recombinantly produced from heterologous organisms, or by the original host, along with the latest advances. Emphasis is given particularly to the applications of recombinant CBM-fusions in: (a) modification of fibers, (b) production, purification and immobilization of recombinant proteins, (c) functionalization of biomaterials and (d) development of microarrays and probes.
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Screening-based discovery of Aspergillus fumigatus plant-type chitinase inhibitors. FEBS Lett 2014; 588:3282-90. [PMID: 25063338 PMCID: PMC4158421 DOI: 10.1016/j.febslet.2014.07.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 07/10/2014] [Accepted: 07/11/2014] [Indexed: 11/20/2022]
Abstract
We performed a high-throughput screen of 60,000 compounds against A. fumigatus chitinase A1. Novel low micromolar competitive inhibitors were identified. These represent the most potent selective plant-type A. fumigatus chitinase inhibitors to date. We provide new tools for probing chitinase inhibition in A. fumigatus and other fungi.
A limited therapeutic arsenal against increasing clinical disease due to Aspergillus spp. necessitates urgent characterisation of new antifungal targets. Here we describe the discovery of novel, low micromolar chemical inhibitors of Aspergillus fumigatus family 18 plant-type chitinase A1 (AfChiA1) by high-throughput screening (HTS). Analysis of the binding mode by X-ray crystallography confirmed competitive inhibition and kinetic studies revealed two compounds with selectivity towards fungal plant-type chitinases. These inhibitors provide new chemical tools to probe the effects of chitinase inhibition on A. fumigatus growth and virulence, presenting attractive starting points for the development of further potent drug-like molecules.
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Dorfmueller HC, Ferenbach AT, Borodkin VS, van Aalten DMF. A structural and biochemical model of processive chitin synthesis. J Biol Chem 2014; 289:23020-23028. [PMID: 24942743 PMCID: PMC4132801 DOI: 10.1074/jbc.m114.563353] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Chitin synthases (CHS) produce chitin, an essential component of the fungal cell wall. The molecular mechanism of processive chitin synthesis is not understood, limiting the discovery of new inhibitors of this enzyme class. We identified the bacterial glycosyltransferase NodC as an appropriate model system to study the general structure and reaction mechanism of CHS. A high throughput screening-compatible novel assay demonstrates that a known inhibitor of fungal CHS also inhibit NodC. A structural model of NodC, on the basis of the recently published BcsA cellulose synthase structure, enabled probing of the catalytic mechanism by mutagenesis, demonstrating the essential roles of the DD and QXXRW catalytic motifs. The NodC membrane topology was mapped, validating the structural model. Together, these approaches give insight into the CHS structure and mechanism and provide a platform for the discovery of inhibitors for this antifungal target.
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Affiliation(s)
- Helge C Dorfmueller
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom.
| | - Andrew T Ferenbach
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Vladimir S Borodkin
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Daan M F van Aalten
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom; MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom.
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Chitinase fromAutographa californicaMultiple Nucleopolyhedrovirus: Rapid Purification from Sf-9 Medium and Mode of Action. Biosci Biotechnol Biochem 2014; 75:1763-9. [DOI: 10.1271/bbb.110300] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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48
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Chen L, Zhou Y, Qu M, Zhao Y, Yang Q. Fully deacetylated chitooligosaccharides act as efficient glycoside hydrolase family 18 chitinase inhibitors. J Biol Chem 2014; 289:17932-40. [PMID: 24828498 DOI: 10.1074/jbc.m114.564534] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Small molecule inhibitors against chitinases have potential applications as pesticides, fungicides, and antiasthmatics. Here, we report that a series of fully deacetylated chitooligosaccharides (GlcN)2-7 can act as inhibitors against the insect chitinase OfChtI, the human chitinase HsCht, and the bacterial chitinases SmChiA and SmChiB with IC50 values at micromolar to millimolar levels. The injection of mixed (GlcN)2-7 into the fifth instar larvae of the insect Ostrinia furnacalis resulted in 85% of the larvae being arrested at the larval stage and death after 10 days, also suggesting that (GlcN)2-7 might inhibit OfChtI in vivo. Crystal structures of the catalytic domain of OfChtI (OfChtI-CAD) complexed with (GlcN)5,6 were obtained at resolutions of 2.0 Å. These structures, together with mutagenesis and thermodynamic analysis, suggested that the inhibition was strongly related to the interaction between the -1 GlcN residue of the inhibitor and the catalytic Glu(148) of the enzyme. Structure-based comparison showed that the fully deacetylated chitooligosaccharides mimic the substrate chitooligosaccharides by binding to the active cleft. This work first reports the inhibitory activity and proposed inhibitory mechanism of fully deacetylated chitooligosaccharides. Because the fully deacetylated chitooligosaccharides can be easily derived from chitin, one of the most abundant materials in nature, this work also provides a platform for developing eco-friendly inhibitors against chitinases.
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Affiliation(s)
- Lei Chen
- From the School of Life Science and Biotechnology, Dalian University of Technology, 2 Linggong Road, Dalian, Liaoning 116024, China
| | - Yong Zhou
- the School of Software, Dalian University of Technology, Dalian 116620, China, and
| | - Mingbo Qu
- From the School of Life Science and Biotechnology, Dalian University of Technology, 2 Linggong Road, Dalian, Liaoning 116024, China
| | - Yong Zhao
- the Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Qing Yang
- From the School of Life Science and Biotechnology, Dalian University of Technology, 2 Linggong Road, Dalian, Liaoning 116024, China,
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49
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Chen L, Liu T, Zhou Y, Chen Q, Shen X, Yang Q. Structural characteristics of an insect group I chitinase, an enzyme indispensable to moulting. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:932-42. [PMID: 24699639 PMCID: PMC3975886 DOI: 10.1107/s1399004713033841] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 12/13/2013] [Indexed: 11/23/2022]
Abstract
Insects possess a greater number of chitinases than any other organisms. This work is the first report of unliganded and oligosaccharide-complexed crystal structures of the insect chitinase OfChtI from Ostrinia furnacalis, which is essential to moulting. The obtained crystal structures were solved at resolutions between 1.7 and 2.2 Å. A structural comparison with other chitinases revealed that OfChtI contains a long substrate-binding cleft similar to the bacterial chitinase SmChiB from Serratia marcescens. However, unlike the exo-acting SmChiB, which has a blocked and tunnel-like cleft, OfChtI possesses an open and groove-like cleft. The complexed structure of the catalytic domain of OfChtI (OfChtI-CAD) with (GlcNAc)2/3 indicates that the reducing sugar at subsite -1 is in an energetically unfavoured `boat' conformation, a state that possibly exists just before the completion of catalysis. Because OfChtI is known to act from nonreducing ends, (GlcNAc)3 would be a hydrolysis product of (GlcNAc)6, suggesting that OfChtI possesses an endo enzymatic activity. Furthermore, a hydrophobic plane composed of four surface-exposed aromatic residues is adjacent to the entrance to the substrate-binding cleft. Mutations of these residues greatly impair the chitin-binding activity, indicating that this hydrophobic plane endows OfChtI-CAD with the ability to anchor chitin. This work reveals the unique structural characteristics of an insect chitinase.
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Affiliation(s)
- Lei Chen
- School of Life Science and Biotechnology, Dalian University of Technology, 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
| | - Tian Liu
- School of Life Science and Biotechnology, Dalian University of Technology, 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
- State Key Laboratory for Biocontrol, Sun Yat-Sen University, Higher Education Mega Center, Guangzhou, Guangdong 510006, People’s Republic of China
| | - Yong Zhou
- School of Software, Dalian University of Technology, 321 Tuqiang Street, Dalian, Liaoning 116620, People’s Republic of China
| | - Qi Chen
- School of Life Science and Biotechnology, Dalian University of Technology, 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
| | - Xu Shen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, People’s Republic of China
| | - Qing Yang
- School of Life Science and Biotechnology, Dalian University of Technology, 2 Linggong Road, Dalian, Liaoning 116024, People’s Republic of China
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50
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Hirose T. [Study on the discovery of novel chitinase inhibitors based on natural products]. YAKUGAKU ZASSHI 2014; 132:1001-10. [PMID: 23023416 DOI: 10.1248/yakushi.132.1001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chitin, the second most abundant polysaccharide in nature, is a constituent of fungal cell walls, the exoskeletons of crustaceans and insects and the microfilarial sheaths of parasitic nematodes. Chitin has, so far, not been found in mammals. Accumulation of chitin by organisms is modulated by chitin synthase-mediated biosynthesis and by chitinase-mediated hydrolytic degradation. Thus, chitinases are expected to be specific targets for antifungal, insecticidal and antiparasitic agents. Paradoxically, while chitin does not exist in mammals, human chitinase family members, such as acidic mammalian chitinase, have recently been described, and offer significant potential for the treatment of asthma and other related diseases in humans. This review covers the development of two chitinase inhibitors of natural origin, Argifin and Argadin, isolated from the cultured broth of microorganisms in our laboratory. In particular, the practical total synthesis of these natural products and discovery methods that generate only highly-active compounds using a kinetic target (chitinase)-guided synthesis approach (termed in situ click chemistry) are described.
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Affiliation(s)
- Tomoyasu Hirose
- Kitasato Institute for Life Sciences, Kitasato University, Tokyo, Japan.
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