1
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Wang H, Wang C, Wang Z, Niu X. Active Discovery of the Allosteric Inhibitor Targeting Botrytis cinerea Chitinase Based on Neural Relational Inference for Food Preservation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:16128-16139. [PMID: 39003764 DOI: 10.1021/acs.jafc.4c03023] [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: 07/16/2024]
Abstract
Currently, allosteric inhibitors have emerged as an effective strategy in the development of preservatives against the drug-resistant Botrytis cinerea (B. cinerea). However, their passively driven development efficiency has proven challenging to meet the practical demands. Here, leveraging the deep learning Neural Relational Inference (NRI) framework, we actively identified an allosteric inhibitor targeting B. cinerea Chitinase, namely, 2-acetonaphthone. 2-Acetonaphthone binds to the crucial domain of Chitinase, forming the strong interaction with the allosteric sites. Throughout the interaction process, 2-acetonaphthone diminished the overall connectivity of the protein, inducing conformational changes. These findings align with the results obtained from Chitinase activity experiments, revealing an IC50 value of 67.6 μg/mL. Moreover, 2-acetonaphthone exhibited outstanding anti-B. cinerea activity by inhibiting Chitinase. In the gray mold infection model, 2-acetonaphthone significantly extended the preservation time of cherry tomatoes, positioning it as a promising preservative for fruit storage.
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Affiliation(s)
- Hongsu 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
| | - Ziyou Wang
- College of Food Science and Engineering, Jilin University, Changchun 130062, P.R. China
| | - Xiaodi Niu
- College of Food Science and Engineering, Jilin University, Changchun 130062, P.R. China
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2
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de Oliveira Viana J, Silva E Souza E, Sbaraini N, Vainstein MH, Gomes JNS, de Moura RO, Barbosa EG. Scaffold repositioning of spiro-acridine derivatives as fungi chitinase inhibitor by target fishing and in vitro studies. Sci Rep 2023; 13:7320. [PMID: 37147323 PMCID: PMC10163251 DOI: 10.1038/s41598-023-33279-9] [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: 11/24/2022] [Accepted: 04/11/2023] [Indexed: 05/07/2023] Open
Abstract
The concept of "one target, one drug, one disease" is not always true, as compounds with previously described therapeutic applications can be useful to treat other maladies. For example, acridine derivatives have several potential therapeutic applications. In this way, identifying new potential targets for available drugs is crucial for the rational management of diseases. Computational methodologies are interesting tools in this field, as they use rational and direct methods. Thus, this study focused on identifying other rational targets for acridine derivatives by employing inverse virtual screening (IVS). This analysis revealed that chitinase enzymes can be potential targets for these compounds. Subsequently, we coupled molecular docking consensus analysis to screen the best chitinase inhibitor among acridine derivatives. We observed that 3 compounds displayed potential enhanced activity as fungal chitinase inhibitors, showing that compound 5 is the most active molecule, with an IC50 of 0.6 ng/µL. In addition, this compound demonstrated a good interaction with the active site of chitinases from Aspergillus fumigatus and Trichoderma harzianum. Additionally, molecular dynamics and free energy demonstrated complex stability for compound 5. Therefore, this study recommends IVS as a powerful tool for drug development. The potential applications are highlighted as this is the first report of spiro-acridine derivatives acting as chitinase inhibitors that can be potentially used as antifungal and antibacterial candidates.
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Affiliation(s)
- Jéssika de Oliveira Viana
- Post-Graduate Program in Bioinformatics, Bioinformatics Multidisciplinary Environment, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Eden Silva E Souza
- School of Biomolecular and Biomedical Science & BiOrbic-Bioeconomy Research Center, University College Dublin, Dublin, Ireland
| | - Nicolau Sbaraini
- Biotechnology Center, Postgraduate Program in Cellular and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Marilene Henning Vainstein
- Biotechnology Center, Postgraduate Program in Cellular and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | | | | | - Euzébio Guimarães Barbosa
- Post-Graduate Program in Bioinformatics, Bioinformatics Multidisciplinary Environment, Federal University of Rio Grande do Norte, Natal, Brazil.
- Post-Graduate Program in Pharmaceutical Sciences, Faculty of Pharmacy, Federal University of Rio Grande do Norte, Natal, Brazil.
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3
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Balestri LI, Trivisani CI, Orofino F, Fiorucci D, Truglio GI, D’Agostino I, Poggialini F, Botta L, Docquier JD, Dreassi E. Discovery and Optimization of a Novel Macrocyclic Amidinourea Series Active as Acidic Mammalian Chitinase Inhibitors. ACS Med Chem Lett 2023; 14:417-424. [PMID: 37077400 PMCID: PMC10107916 DOI: 10.1021/acsmedchemlett.2c00472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 03/14/2023] [Indexed: 04/21/2023] Open
Abstract
Our research group has been involved for a long time in the development of macrocyclic amidinoureas (MCAs) as antifungal agents. The mechanistic investigation drove us to perform an in silico target fishing study, which allowed the identification of chitinases as one of their putative targets, with 1a showing a submicromolar inhibition of Trichoderma viride chitinase. In this work, we investigated the possibility to further inhibit the corresponding human enzymes, acidic mammalian chitinase (AMCase) and chitotriosidase (CHIT1), involved in several chronic inflammatory lung diseases. Thus, we first validated the inhibitory activity of 1a against AMCase and CHIT1 and then designed and synthesized new derivatives aimed at improving the potency and selectivity against AMCase. Among them, compound 3f emerged for its activity profile along with its promising in vitro ADME properties. We also gained a good understanding of the key interactions with the target enzyme through in silico studies.
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Affiliation(s)
| | | | - Francesco Orofino
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Diego Fiorucci
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Giuseppina Ivana Truglio
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Ilaria D’Agostino
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Federica Poggialini
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Lorenzo Botta
- Lead
Discovery Siena s.r.l., Via Vittorio Alfieri 31, I-53019 Castelnuovo Berardenga, Italy
- Department
of Ecological and Biological Sciences, University
of Tuscia, Largo Università s.n.c., I-01100 Viterbo, Italy
| | - Jean-Denis Docquier
- Dipartimento
di Biotecnologie Mediche, University of
Siena, Viale Bracci 16, I-53100, Siena, Italy
- Laboratoire
de Bactériologie Moléculaire, Centre d’Ingénierie
des Protéines, UR-InBioS, University
of Liège, Allée
du 6 Août, 4000 Liège, Belgium
| | - Elena Dreassi
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
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4
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He B, Yang L, Yang D, Jiang M, Ling C, Chen H, Ji F, Pan L. Biochemical purification and characterization of a truncated acidic, thermostable chitinase from marine fungus for N-acetylglucosamine production. Front Bioeng Biotechnol 2022; 10:1013313. [PMID: 36267443 PMCID: PMC9578694 DOI: 10.3389/fbioe.2022.1013313] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 08/22/2022] [Indexed: 12/05/2022] Open
Abstract
N-acetylglucosamine (GlcNAc) is widely used in nutritional supplement and is generally produced from chitin using chitinases. While most GlcNAc is produced from colloidal chitin, it is essential that chitinases be acidic enzymes. Herein, we characterized an acidic, highly salinity tolerance and thermostable chitinase AfChiJ, identified from the marine fungus Aspergillus fumigatus df673. Using AlphaFold2 structural prediction, a truncated Δ30AfChiJ was heterologously expressed in E. coli and successfully purified. It was also found that it is active in colloidal chitin, with an optimal temperature of 45°C, an optimal pH of 4.0, and an optimal salt concentration of 3% NaCl. Below 45°C, it was sound over a wide pH range of 2.0–6.0 and maintained high activity (≥97.96%) in 1–7% NaCl. A notable increase in chitinase activity was observed of Δ30AfChiJ by the addition of Mg2+, Ba2+, urea, and chloroform. AfChiJ first decomposed colloidal chitin to generate mainly N-acetyl chitobioase, which was successively converted to its monomer GlcNAc. This indicated that AfChiJ is a bifunctional enzyme, composed of chitobiosidase and β-N-acetylglucosaminidase. Our result suggested that AfChiJ likely has the potential to convert chitin-containing biomass into high-value added GlcNAc.
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Affiliation(s)
- Bin He
- School of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning, Guangxi, China
| | - Liyan Yang
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning, Guangxi, China
| | - Dengfeng Yang
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning, Guangxi, China
| | - Minguo Jiang
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning, China
| | - Chengjin Ling
- Nanning Dabeinong Feed Technology Co., Ltd., Nanning, Guangxi, China
| | - Hailan Chen
- School of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
- *Correspondence: Hailan Chen, ; Feng Ji, ; Lixia Pan,
| | - Feng Ji
- Guangxi Huaren Medical Technolgoy Group, Nanning, Guangxi, China
- *Correspondence: Hailan Chen, ; Feng Ji, ; Lixia Pan,
| | - Lixia Pan
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Academy of Sciences, Nanning, Guangxi, China
- *Correspondence: Hailan Chen, ; Feng Ji, ; Lixia Pan,
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5
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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: 10] [Impact Index Per Article: 5.0] [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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6
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Goughenour KD, Whalin J, Slot JC, Rappleye CA. Diversification of Fungal Chitinases and Their Functional Differentiation in Histoplasma capsulatum. Mol Biol Evol 2021; 38:1339-1355. [PMID: 33185664 PMCID: PMC8042737 DOI: 10.1093/molbev/msaa293] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Chitinases enzymatically hydrolyze chitin, a highly abundant and utilized polymer of N-acetyl-glucosamine. Fungi are a rich source of chitinases; however, the phylogenetic and functional diversity of fungal chitinases are not well understood. We surveyed fungal chitinases from 373 publicly available genomes, characterized domain architecture, and conducted phylogenetic analyses of the glycoside hydrolase (GH18) domain. This large-scale analysis does not support the previous division of fungal chitinases into three major clades (A, B, C) as chitinases previously assigned to the “C” clade are not resolved as distinct from the “A” clade. Fungal chitinase diversity was partly shaped by horizontal gene transfer, and at least one clade of bacterial origin occurs among chitinases previously assigned to the “B” clade. Furthermore, chitin-binding domains (including the LysM domain) do not define specific clades, but instead are found more broadly across clades of chitinases. To gain insight into biological function diversity, we characterized all eight chitinases (Cts) from the thermally dimorphic fungus, Histoplasma capsulatum: six A clade, one B clade, and one formerly classified C clade chitinases. Expression analyses showed variable induction of chitinase genes in the presence of chitin but preferential expression of CTS3 in the mycelial stage. Activity assays demonstrated that Cts1 (B-I), Cts2 (A-V), Cts3 (A-V), Cts4 (A-V) have endochitinase activities with varying degrees of chitobiosidase function. Cts6 (C-I) has activity consistent with N-acetyl-glucosaminidase exochitinase function and Cts8 (A-II) has chitobiase activity. These results suggest chitinase activity is variable even within subclades and that predictions of functionality require more sophisticated models.
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Affiliation(s)
| | - Janice Whalin
- Department of Microbiology, Ohio State University, Columbus, OH
| | - Jason C Slot
- Department of Plant Pathology, Ohio State University, Columbus, OH
| | - Chad A Rappleye
- Department of Microbiology, Ohio State University, Columbus, OH
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7
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Yuan P, Jiang X, Wang S, Shao X, Yang Q, Qian X. X-ray Structure and Molecular Docking Guided Discovery of Novel Chitinase Inhibitors with a Scaffold of Dipyridopyrimidine-3-carboxamide. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:13584-13593. [PMID: 33151676 DOI: 10.1021/acs.jafc.0c03742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Chitinases are the glycosyl hydrolase for catalyzing the degradation of chitin and play an indispensable role in bacterial pathogenesis, fungal cell wall remodeling, and insect molting. Thus, chitinases are attractive targets for therapeutic drugs and pesticides. Here, we present a strategy of developing a novel chemotype of chitinase inhibitors by the construction of planar heterocycles that can stack with conserved aromatic residues. The rational design, guided by crystallographic analysis and docking results, leads to a series of dipyridopyrimidine-3-carboxamide derivatives as chitinase inhibitors. Among them, compound 6t showed the most potent activity against bacterial chitinase SmChiB and insect chitinase OfChi-h, with a Ki value of 0.14 and 0.0056 μM, respectively. The strong stacking interaction of compound 6p with Trp99 and Trp220 found in the SmChiB-6p co-crystal structure verifies the feasibility of our design. Our results provide novel insights into developing potent chitinase inhibitors for pathogen and pest control.
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Affiliation(s)
- Pengtao Yuan
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, People's Republic of China
| | - Xi Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfei Road, Shenzhen 518120, People's Republic of China
| | - Siyu Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfei Road, Shenzhen 518120, People's Republic of China
| | - Xusheng Shao
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, People's Republic of China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Qing Yang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfei Road, Shenzhen 518120, People's Republic of China
| | - Xuhong Qian
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, People's Republic of China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, People's Republic of China
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8
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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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9
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Mathew GM, Madhavan A, Arun KB, Sindhu R, Binod P, Singhania RR, Sukumaran RK, Pandey A. Thermophilic Chitinases: Structural, Functional and Engineering Attributes for Industrial Applications. Appl Biochem Biotechnol 2020; 193:142-164. [PMID: 32827066 DOI: 10.1007/s12010-020-03416-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 08/12/2020] [Indexed: 02/07/2023]
Abstract
Chitin is the second most widely found natural polymer next to cellulose. Chitinases degrade the insoluble chitin to bioactive chitooligomers and monomers for various industrial applications. Based on their function, these enzymes act as biocontrol agents against pathogenic fungi and invasive pests compared with conventional chemical fungicides and insecticides. They have other functional roles in shellfish waste management, fungal protoplast generation, and Single-Cell Protein production. Among the chitinases, thermophilic and thermostable chitinases are gaining popularity in recent years, as they can withstand high temperatures and maintain the enzyme stability for longer periods. Not all chitinases are thermostable; hence, tailor-made thermophilic chitinases are designed to enhance their thermostability by direct evolution, genetic engineering involving mutagenesis, and proteomics approach. Although research has been done extensively on cloning and expression of thermophilic chitinase genes, there are only few papers discussing on the mechanism of chitin degradation using thermophiles. The current review discusses the sources of thermophilic chitinases, improvement of protein stability by gene manipulation, metagenomics approaches, chitin degradation mechanism in thermophiles, and their prospective applications for industrial, agricultural, and pharmaceutical purposes.
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Affiliation(s)
- Gincy M Mathew
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | - Aravind Madhavan
- Rajiv Gandhi Center for Biotechnology, Jagathy, Thiruvananthapuram, 695 014, India
| | - K B Arun
- Rajiv Gandhi Center for Biotechnology, Jagathy, Thiruvananthapuram, 695 014, India
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | | | - Rajeev K Sukumaran
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | - Ashok Pandey
- Center for Innovation and Translational Research, CSIR - Indian Institute of Toxicology Research, Lucknow, 226 001, India.
- Frontier Research Lab, Yonsei University, Seoul, South Korea.
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10
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Liu W, Yuan L, Wang S. Recent Progress in the Discovery of Antifungal Agents Targeting the Cell Wall. J Med Chem 2020; 63:12429-12459. [PMID: 32692166 DOI: 10.1021/acs.jmedchem.0c00748] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Due to the limit of available treatments and the emergence of drug resistance in the clinic, invasive fungal infections are an intractable problem with high morbidity and mortality. The cell wall, as a fungi-specific structure, is an appealing target for the discovery and development of novel and low-toxic antifungal agents. In an attempt to accelerate the discovery of novel cell wall targeted drugs, this Perspective will provide a comprehensive review of the progress made to date on the development of fungal cell wall inhibitors. Specifically, this review will focus on the targets, discovery process, chemical structures, antifungal activities, and structure-activity relationships. Although two types of cell wall antifungal agents are clinically available or in clinical trials, it is still a long way for the other cell wall targeted inhibitors to be translated into clinical applications. Future efforts should be focused on the identification of inhibitors against novel conserved cell wall targets.
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Affiliation(s)
- Wei Liu
- Faculty of Pharmacy, School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xuefu Middle Road, Xi'an 710021, People's Republic of China
| | - Lin Yuan
- Faculty of Pharmacy, School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xuefu Middle Road, Xi'an 710021, People's Republic of China
| | - Shengzheng Wang
- Department of Medicinal Chemistry and Pharmaceutical Analysis, School of Pharmacy, Fourth Military Medical University, 169 Changle West Road, Xi'an 710032, People's Republic of China
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11
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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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12
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He X, Yu M, Wu Y, Ran L, Liu W, Zhang XH. Two Highly Similar Chitinases from Marine Vibrio Species have Different Enzymatic Properties. Mar Drugs 2020; 18:E139. [PMID: 32120805 PMCID: PMC7143101 DOI: 10.3390/md18030139] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/21/2020] [Accepted: 02/25/2020] [Indexed: 12/16/2022] Open
Abstract
Chitinase, as one of the most important extracellular enzymes in the marine environment, has great ecological and applied values. In this study, two chitinases (Chi1557 and Chi4668) with 97.33% amino acid sequences identity were individually found in Vibrio rotiferianus and Vibrio harveyi. They both were encoding by 561 amino acids, but differed in 15 amino acids and showed different enzymatic properties. The optimal temperature and pH ranges were 45-50 °C and pH 5.0-7.0 for Chi1557, while ~50 °C and pH 3.0-6.0 for Chi4668. K+, Mg2+, and EDTA increased the enzymatic activity of Chi4668 significantly, yet these factors were inhibitory to Chi1557. Moreover, Chi1557 degraded colloidal chitin to produce (GlcNAc)2 and minor GlcNAc, whereas Chi4668 produce (GlcNAc)2 with minor (GlcNAc)3 and (GlcNAc)4. The Kcat/Km of Chi4668 was ~4.7 times higher than that of Chi1557, indicating that Chi4668 had stronger catalytic activity than Chi1557. Furthermore, site-directed mutagenesis was performed on Chi1557 focusing on seven conserved amino acid residues of family GH18 chitinases. Chi1557 was almost completely inactive after Glu154, Gln219, Tyr221, or Trp312 was individually mutated, retained ~50% activity after Tyr37 was mutated, and increased two times activity after Asp152 was mutated, indicating that these six amino acids were key sites for Chi1557.
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Affiliation(s)
- Xinxin He
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (X.H.); (M.Y.); (Y.W.); (L.R.); (W.L.)
| | - Min Yu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (X.H.); (M.Y.); (Y.W.); (L.R.); (W.L.)
| | - Yanhong Wu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (X.H.); (M.Y.); (Y.W.); (L.R.); (W.L.)
| | - Lingman Ran
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (X.H.); (M.Y.); (Y.W.); (L.R.); (W.L.)
| | - Weizhi Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (X.H.); (M.Y.); (Y.W.); (L.R.); (W.L.)
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (X.H.); (M.Y.); (Y.W.); (L.R.); (W.L.)
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
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13
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Martins MP, Silva LG, Rossi A, Sanches PR, Souza LDR, Martinez-Rossi NM. Global Analysis of Cell Wall Genes Revealed Putative Virulence Factors in the Dermatophyte Trichophyton rubrum. Front Microbiol 2019; 10:2168. [PMID: 31608026 PMCID: PMC6761320 DOI: 10.3389/fmicb.2019.02168] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 09/04/2019] [Indexed: 12/25/2022] Open
Abstract
The fungal cell wall is a structure in constant contact with the external environment. It confers shape to the cell and protects it from external threats. During host adaptation, the cell wall structure of fungal pathogens is continuously reshaped by the orchestrated action of numerous genes. These genes respond to environmental stresses and challenging growth conditions, influencing the infective potential of the fungus. Here, we aimed to identify cell wall biosynthesis-related genes that putatively encode virulence factors in Trichophyton rubrum. We used RNA-seq to examine the impact of two drugs, namely undecanoic acid, and acriflavine as well as the effects of the carbon source switching from glucose to keratin on T. rubrum cell wall metabolism. By using functional annotation based on Gene Ontology terms, we identified significantly differentially expressed cell wall-related genes in all stress conditions. We also exposed T. rubrum to osmotic and other cell wall stressors and evaluated the susceptibility and gene modulation in response to stress. The changes in the ambient environment caused continuous cell wall remodeling, forcing the fungus to undergo modulatory restructuring. The influence of the external challenges indicated a highly complex response pattern. The genes that were modulated simultaneously in the three stress conditions highlight potential targets for antifungal development.
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Affiliation(s)
- Maíra P Martins
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Larissa G Silva
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Antonio Rossi
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Pablo R Sanches
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Larissa D R Souza
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Nilce M Martinez-Rossi
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
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14
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Synthesis, homology modeling, molecular docking, dynamics, and antifungal screening of new 4-hydroxycoumarin derivatives as potential chitinase inhibitors. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.11.099] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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15
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Marine chitinolytic enzymes, a biotechnological treasure hidden in the ocean? Appl Microbiol Biotechnol 2018; 102:9937-9948. [PMID: 30276711 DOI: 10.1007/s00253-018-9385-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/04/2018] [Accepted: 09/06/2018] [Indexed: 12/11/2022]
Abstract
Chitinolytic enzymes are capable to catalyze the chitin hydrolysis. Due to their biomedical and biotechnological applications, nowadays chitinolytic enzymes have attracted worldwide attention. Chitinolytic enzymes have provided numerous useful materials in many different industries, such as food, pharmaceutical, cosmetic, or biomedical industry. Marine enzymes are commonly employed in industry because they display better operational properties than animal, plant, or bacterial homologs. In this mini-review, we want to describe marine chitinolytic enzymes as versatile enzymes in different biotechnological fields. In this regard, interesting comments about their biological role, reaction mechanism, production, functional characterization, immobilization, and biotechnological application are shown in this work.
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16
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Vaikuntapu PR, Mallakuntla MK, Das SN, Bhuvanachandra B, Ramakrishna B, Nadendla SR, Podile AR. Applicability of endochitinase of Flavobacterium johnsoniae with transglycosylation activity in generating long-chain chitooligosaccharides. Int J Biol Macromol 2018; 117:62-71. [DOI: 10.1016/j.ijbiomac.2018.05.129] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 05/17/2018] [Accepted: 05/18/2018] [Indexed: 01/08/2023]
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17
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Brandt SC, Ellinger B, van Nguyen T, Thi QD, van Nguyen G, Baschien C, Yurkov A, Hahnke RL, Schäfer W, Gand M. A unique fungal strain collection from Vietnam characterized for high performance degraders of bioecological important biopolymers and lipids. PLoS One 2018; 13:e0202695. [PMID: 30161149 PMCID: PMC6117010 DOI: 10.1371/journal.pone.0202695] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 08/07/2018] [Indexed: 11/18/2022] Open
Abstract
Fungal strains are abundantly used throughout all areas of biotechnology and many of them are adapted to degrade complex biopolymers like chitin or lignocellulose. We therefore assembled a collection of 295 fungi from nine different habitats in Vietnam, known for its rich biodiversity, and investigated their cellulase, chitinase, xylanase and lipase activity. The collection consists of 70 isolates from wood, 55 from soil, 44 from rice straw, 3 found on fruits, 24 from oil environments (butchery), 12 from hot springs, 47 from insects as well as 27 from shrimp shells and 13 strains from crab shells. These strains were cultivated and selected by growth differences to enrich phenotypes, resulting in 211 visually different fungi. DNA isolation of 183 isolates and phylogenetic analysis was performed and 164 species were identified. All were subjected to enzyme activity assays, yielding high activities for every investigated enzyme set. In general, enzyme activity corresponded with the environment of which the strain was isolated from. Therefore, highest cellulase activity strains were isolated from wood substrates, rice straw and soil and similar substrate effects were observed for chitinase and lipase activity. Xylanase activity was similarly distributed as cellulase activity, but substantial activity was also found from fungi isolated from insects and shrimp shells. Seven strains displayed significant activities against three of the four tested substrates, while three degraded all four investigated carbon sources. The collection will be an important source for further studies. Therefore representative strains were made available to the scientific community and deposited in the public collection of the Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig.
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Affiliation(s)
- Sophie C. Brandt
- Department of Molecular Phytopathology, University Hamburg, Hamburg, Germany
| | - Bernhard Ellinger
- Department ScreeningPort, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Hamburg, Germany
| | - Thuat van Nguyen
- Department of Molecular Phytopathology, University Hamburg, Hamburg, Germany
| | - Quyen Dinh Thi
- Institue of Biotechnology, Vietnam Academy of Science and Technology, Cau Giay, Hanoi, Vietnam
| | - Giang van Nguyen
- Faculty of Biotechnology, Vietnam National University of Agriculture, Trâu Quỳ, Gia Lâm, Hanoi, Vietnam
| | - Christiane Baschien
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Andrey Yurkov
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Richard L. Hahnke
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Wilhelm Schäfer
- Department of Molecular Phytopathology, University Hamburg, Hamburg, Germany
| | - Martin Gand
- Department of Molecular Phytopathology, University Hamburg, Hamburg, Germany
- * E-mail:
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18
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Ashok D, Devulapally MG, Gundu S, Aamate VK, Chintalapally S. Synthesis and Antimicrobial Evaluation of Novel Pyrazole-Annulated Oxygen-Containing Macrocycles. Chem Heterocycl Compd (N Y) 2016. [DOI: 10.1007/s10593-016-1939-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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19
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Niu XD, Lv Z, Zhou XR, Wang HS. Insight into the key active sites of afChiA1 based on molecular dynamics simulations and free energy calculations. MOLECULAR SIMULATION 2016. [DOI: 10.1080/08927022.2016.1148265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Xiao D. Niu
- Department of Food Quality and Safety, Jilin University, Changchun, P.R. China
| | - Zhuo Lv
- Department of Food Quality and Safety, Jilin University, Changchun, P.R. China
| | - Xin R. Zhou
- Department of Food Quality and Safety, Jilin University, Changchun, P.R. China
| | - Hong S. Wang
- Department of Food Quality and Safety, Jilin University, Changchun, P.R. China
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20
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Arnhold FS, Linden A, Heimgartner H. Synthesis of Aib- and Phe(2Me)-Containing Cyclopentapeptides. Helv Chim Acta 2015. [DOI: 10.1002/hlca.201400323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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21
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Masuda T, Zhao G, Mikami B. Crystal structure of class III chitinase from pomegranate provides the insight into its metal storage capacity. Biosci Biotechnol Biochem 2015; 79:45-50. [DOI: 10.1080/09168451.2014.962475] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Abstract
Chitinase hydrolyzes the β-1,4-glycosidic bond in chitin. In higher plants, this enzyme has been regarded as a pathogenesis-related protein. Recently, we identified a class III chitinase, which functions as a calcium storage protein in pomegranate (Punica granatum) seed (PSC, pomegranate seed chitinase). Here, we solved a crystal structure of PSC at 1.6 Å resolution. Although its overall structure, including the structure of catalytic site and non-proline cis-peptides, was closely similar to those of other class III chitinases, PSC had some unique structural characteristics. First, there were some metal-binding sites with coordinated water molecules on the surface of PSC. Second, many unconserved aspartate residues were present in the PSC sequence which rendered the surface of PSC negatively charged. This acidic electrostatic property is in contrast to that of hevamine, well-characterized plant class III chitinase, which has rather a positively charged surface. Thus, the crystal structure provides a clue for metal association property of PSC.
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Affiliation(s)
- Taro Masuda
- Laboratory of Food Quality Design and Development, Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto, Japan
| | - Guanghua Zhao
- CAU & ACC Joint-Laboratory of Space Food, College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Food from Plant Resources, Beijing, China
| | - Bunzo Mikami
- Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto, Japan
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22
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Jaszek M, Kos K, Matuszewska A, Grąz M, Stefaniuk D, Osińska-Jaroszuk M, Prendecka M, Jóźwik E, Grzywnowicz K. Effective stimulation of the biotechnological potential of the medicinal white rot fungus: Phellinus pini by menadione-mediated oxidative stress. Appl Biochem Biotechnol 2014; 174:644-56. [PMID: 25086919 PMCID: PMC4149882 DOI: 10.1007/s12010-014-1064-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 07/22/2014] [Indexed: 01/24/2023]
Abstract
The effect of menadione (MQ; 2-methyl-1,4-naphtoquinone), a superoxide-generating agent, on the natural biodegradation system in the medicinal white rot fungus Phellinus pini was determined. While measuring the activities of extracellular manganese-dependent peroxidase (MnP) and intracellular chitinase, it was found that the application of MQ (0.75 mM) distinctly stimulated the activities of these enzymes in comparison to the control values (without MQ). Using the capillary electrophoresis (CE) method, an increase in the extracellular oxalic acid (OXA) concentration was detected during the first days after the addition of MQ. It was observed that the rate of intracellular proteolysis at pH 3.5 evidently decreased under oxidative stress conditions. Contrary to these results, the activities of serine proteases at pH 9.5 measured against fluorogenic peptide substrates distinctly increased in stressed cultures. The MQ treatment also caused an evident increase in the catalase (CAT) activity, as well as the levels of superoxide anion radicals (SORs), formaldehyde (FA), and phenolic compounds (PHC) in the experimental cultures. The results obtained confirm that prooxidants may find application as an effective way to stimulate biotechnological production of MnP and chitinase by white rot fungi.
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Affiliation(s)
- Magdalena Jaszek
- Department of Biochemistry, Maria Curie-Skłodowska University, 19 Akademicka Street, 20-033 Lublin, Poland
| | - Katarzyna Kos
- Department of Biochemistry, Maria Curie-Skłodowska University, 19 Akademicka Street, 20-033 Lublin, Poland
| | - Anna Matuszewska
- Department of Biochemistry, Maria Curie-Skłodowska University, 19 Akademicka Street, 20-033 Lublin, Poland
| | - Marcin Grąz
- Department of Biochemistry, Maria Curie-Skłodowska University, 19 Akademicka Street, 20-033 Lublin, Poland
| | - Dawid Stefaniuk
- Department of Biochemistry, Maria Curie-Skłodowska University, 19 Akademicka Street, 20-033 Lublin, Poland
| | - Monika Osińska-Jaroszuk
- Department of Biochemistry, Maria Curie-Skłodowska University, 19 Akademicka Street, 20-033 Lublin, Poland
| | - Monika Prendecka
- Chair and Department of Human Physiology, Medical University, 11 Radziwiłłowska Street, 20-080 Lublin, Poland
| | - Ewa Jóźwik
- Department of Biochemistry, Maria Curie-Skłodowska University, 19 Akademicka Street, 20-033 Lublin, Poland
| | - Krzysztof Grzywnowicz
- Department of Biochemistry, Maria Curie-Skłodowska University, 19 Akademicka Street, 20-033 Lublin, Poland
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23
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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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24
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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: 47] [Impact Index Per Article: 4.7] [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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25
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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: 44] [Impact Index Per Article: 4.4] [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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26
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Malecki PH, Raczynska JE, Vorgias CE, Rypniewski W. Structure of a complete four-domain chitinase from Moritella marina, a marine psychrophilic bacterium. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:821-9. [PMID: 23633591 DOI: 10.1107/s0907444913002011] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 01/21/2013] [Indexed: 11/10/2022]
Abstract
X-ray crystallography reveals chitinase from the psychrophilic bacterium Moritella marina to be an elongated molecule which in addition to the catalytic β/α-barrel domain contains two Ig-like domains and a chitin-binding domain, all linked in a chain. A ligand-binding study using NAG oligomers showed the enzyme to be active in the crystal lattice and resulted in complexes of the protein with oxazolinium ion (the reaction intermediate) and with NAG2, a reaction product. The characteristic motif DXDXE, containing three acidic amino-acid residues, which is a signature of type 18 chitinases, is conserved in the enzyme. Further analysis of the unliganded enzyme with the two protein-ligand complexes and a comparison with other known chitinases elucidated the roles of other conserved residues near the active site. Several features have been identified that are probably important for the reaction mechanism, substrate binding and the efficiency of the enzyme at low temperatures. The chitin-binding domain and the tryptophan patch on the catalytic domain provide general affinity for chitin, in addition to the affinity of the binding site; the two Ig-like domains give the protein a long reach over the chitin surface, and the flexible region between the chitin-binding domain and the adjacent Ig-like domain suggests an ability of the enzyme to probe the surface of the substrate, while the open shallow substrate-binding groove allows easy access to the active site.
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Affiliation(s)
- Piotr H Malecki
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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Insect-Derived Chitinases. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 136:19-50. [DOI: 10.1007/10_2013_207] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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28
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van Munster JM, van der Kaaij RM, Dijkhuizen L, van der Maarel MJEC. Biochemical characterization of Aspergillus niger CfcI, a glycoside hydrolase family 18 chitinase that releases monomers during substrate hydrolysis. MICROBIOLOGY-SGM 2012; 158:2168-2179. [PMID: 22575895 DOI: 10.1099/mic.0.054650-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The genome of the industrially important fungus Aspergillus niger encodes a large number of glycoside hydrolase family 18 members annotated as chitinases. We identified one of these putative chitinases, CfcI, as a representative of a distinct phylogenetic clade of homologous enzymes conserved in all sequenced Aspergillus species. Where the catalytic domain of more distantly related chitinases consists of a triosephosphate isomerase barrel in which a small additional (α+β) domain is inserted, CfcI-like proteins were found to have, in addition, a carbohydrate-binding module (CBM18) that is inserted in the (α+β) domain next to the substrate-binding cleft. This unusual domain structure and sequence dissimilarity to previously characterized chitinases suggest that CfcI has a novel activity or function different from chitinases investigated so far. Following its heterologous expression and purification, its biochemical characterization showed that CfcI displays optimal activity at pH 4 and 55-65 °C and degrades chitin oligosaccharides by releasing N-acetylglucosamine from the reducing end, possibly via a processive mechanism. This is the first fungal family 18 exochitinase described, to our knowledge, that exclusively releases monomers. The cfcI expression profile suggests that its physiological function is important in processes that take place during the late stages of the aspergillus life cycle, such as autolysis or sporulation.
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Affiliation(s)
- Jolanda M van Munster
- Microbial Physiology Research Group, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands
| | - Rachel M van der Kaaij
- Microbial Physiology Research Group, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands
| | - Lubbert Dijkhuizen
- Microbial Physiology Research Group, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands
| | - Marc J E C van der Maarel
- Microbial Physiology Research Group, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands
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29
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Iminoheterocycle as a druggable motif: BACE1 inhibitors and beyond. Trends Pharmacol Sci 2012; 33:233-40. [DOI: 10.1016/j.tips.2012.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 02/01/2012] [Accepted: 02/21/2012] [Indexed: 11/20/2022]
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30
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Santana LADP, Vainstein MH, Tomazett PK, Santos-Silva LK, Góes AM, Schrank A, Soares CMDA, Pereira M. Distinct chitinases are expressed during various growth phases of the human pathogen Paracoccidioides brasiliensis. Mem Inst Oswaldo Cruz 2012; 107:310-6. [DOI: 10.1590/s0074-02762012000300004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2011] [Accepted: 02/01/2012] [Indexed: 11/22/2022] Open
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31
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Fungal chitinases: diversity, mechanistic properties and biotechnological potential. Appl Microbiol Biotechnol 2011; 93:533-43. [PMID: 22134638 PMCID: PMC3257436 DOI: 10.1007/s00253-011-3723-3] [Citation(s) in RCA: 179] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 10/27/2011] [Accepted: 11/08/2011] [Indexed: 12/15/2022]
Abstract
Chitin derivatives, chitosan and substituted chito-oligosaccharides have a wide spectrum of applications ranging from medicine to cosmetics and dietary supplements. With advancing knowledge about the substrate-binding properties of chitinases, enzyme-based production of these biotechnologically relevant sugars from biological resources is becoming increasingly interesting. Fungi have high numbers of glycoside hydrolase family 18 chitinases with different substrate-binding site architectures. As presented in this review, the large diversity of fungal chitinases is an interesting starting point for protein engineering. In this review, recent data about the architecture of the substrate-binding clefts of fungal chitinases, in connection with their hydrolytic and transglycolytic abilities, and the development of chitinase inhibitors are summarized. Furthermore, the biological functions of chitinases, chitin and chitosan utilization by fungi, and the effects of these aspects on biotechnological applications, including protein overexpression and autolysis during industrial processes, are discussed in this review.
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Schüttelkopf AW, Andersen OA, Rao FV, Allwood M, Rush CL, Eggleston IM, van Aalten DMF. Bisdionin C-a rationally designed, submicromolar inhibitor of family 18 chitinases. ACS Med Chem Lett 2011; 2:428-32. [PMID: 24900325 DOI: 10.1021/ml200008b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Accepted: 03/11/2011] [Indexed: 11/29/2022] Open
Abstract
Chitinases of the GH18 family play important roles in a variety of pathogenic organisms and have also been shown to be involved in human asthma progression, making these enzymes potential drug targets. While a number of potent GH18 chitinase inhibitors have been described, in general, these compounds suffer from limited synthetic accessibility or unfavorable medicinal-chemical properties, making them poor starting points for the development of chitinase-targeted drugs. Exploiting available structural data, we have rationally designed bisdionin C, a submicromolar inhibitor of GH18 enzymes, that possesses desirable druglike properties and tractable chemical synthesis. A crystallographic structure of a chitinase-bisdionin C complex shows the two aromatic systems of the ligand interacting with two conserved tryptophan residues exposed in the active site cleft of the enzyme, while at the same time forming extensive hydrogen-bonding interactions with the catalytic machinery. The observed mode of binding, together with inhibition data, suggests that bisdionin C presents an attractive starting point for the development of specific inhibitors of bacterial-type, but not plant-type, GH 18 chitinases.
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Affiliation(s)
- Alexander W. Schüttelkopf
- Division of Molecular Microbiology and ‡Division of Biological Chemistry and Molecular Microbiology, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland
| | - Ole A. Andersen
- Division of Molecular Microbiology and ‡Division of Biological Chemistry and Molecular Microbiology, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland
| | - Francesco V. Rao
- Division of Molecular Microbiology and ‡Division of Biological Chemistry and Molecular Microbiology, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland
| | - Matthew Allwood
- Division of Molecular Microbiology and ‡Division of Biological Chemistry and Molecular Microbiology, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland
| | - Christina L. Rush
- Division of Molecular Microbiology and ‡Division of Biological Chemistry and Molecular Microbiology, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland
| | - Ian M. Eggleston
- Division of Molecular Microbiology and ‡Division of Biological Chemistry and Molecular Microbiology, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland
| | - Daan M. F. van Aalten
- Division of Molecular Microbiology and ‡Division of Biological Chemistry and Molecular Microbiology, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland
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