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Wang J, Liu Z, Pan X, Wang N, Li L, Du Y, Li J, Li M. Structural and Biochemical Analysis Reveals Catalytic Mechanism of Fucoidan Lyase from Flavobacterium sp. SA-0082. Mar Drugs 2022; 20:md20080533. [PMID: 36005536 PMCID: PMC9410043 DOI: 10.3390/md20080533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/24/2022] Open
Abstract
Fucoidans represent a type of polyanionic fucose-containing sulfated polysaccharides (FCSPs) that are cleaved by fucoidan-degrading enzymes, producing low-molecular-weight fucoidans with multiple biological activities suitable for pharmacological use. Most of the reported fucoidan-degrading enzymes are glycoside hydrolases, which have been well studied for their structures and catalytic mechanisms. Little is known, however, about the rarer fucoidan lyases, primarily due to the lack of structural information. FdlA from Flavobacterium sp. SA-0082 is an endo-type fucoidan-degrading enzyme that cleaves the sulfated fuco-glucuronomannan (SFGM) through a lytic mechanism. Here, we report nine crystal structures of the catalytic N-terminal domain of FdlA (FdlA-NTD), in both its wild type (WT) and mutant forms, at resolutions ranging from 1.30 to 2.25 Å. We show that the FdlA-NTD adopts a right-handed parallel β-helix fold, and possesses a substrate binding site composed of a long groove and a unique alkaline pocket. Our structural, biochemical, and enzymological analyses strongly suggest that FdlA-NTD utilizes catalytic residues different from other β-helix polysaccharide lyases, potentially representing a novel polysaccharide lyase family.
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Affiliation(s)
- Juanjuan Wang
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zebin Liu
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- College of Life Science, Capital Normal University, Beijing 100101, China
| | - Xiaowei Pan
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, Capital Normal University, Beijing 100101, China
| | - Ning Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Legong Li
- College of Life Science, Capital Normal University, Beijing 100101, China
| | - Yuguang Du
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Jianjun Li
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- Correspondence: (J.L.); (M.L.)
| | - Mei Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Correspondence: (J.L.); (M.L.)
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Bakherad Z, Bakherad H, Sepehri S, Faramarzi MA, Mahnam K, Mojtabavi S, Mahdavi M. In silico and in vitro studies of thiosemicarbazone-indole hybrid compounds as potent α-glycosidase inhibitors. Comput Biol Chem 2022; 97:107642. [PMID: 35183819 DOI: 10.1016/j.compbiolchem.2022.107642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 12/28/2021] [Accepted: 02/07/2022] [Indexed: 11/03/2022]
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Zhao B, Zhang X, Yu T, Liu Y, Zhang X, Yao Y, Feng X, Liu H, Yu D, Ma L, Qin S. Discovery of thiosemicarbazone derivatives as effective New Delhi metallo- β-lactamase-1 (NDM-1) inhibitors against NDM-1 producing clinical isolates. Acta Pharm Sin B 2021; 11:203-221. [PMID: 33532189 PMCID: PMC7838035 DOI: 10.1016/j.apsb.2020.07.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 06/02/2020] [Accepted: 06/28/2020] [Indexed: 12/23/2022] Open
Abstract
New Delhi metallo-β-lactamase-1 (NDM-1) is capable of hydrolyzing nearly all β-lactam antibiotics, posing an emerging threat to public health. There are currently less effective treatment options for treating NDM-1 positive “superbug”, and no promising NDM-1 inhibitors were used in clinical practice. In this study, structure–activity relationship based on thiosemicarbazone derivatives was systematically characterized and their potential activities combined with meropenem (MEM) were evaluated. Compounds 19bg and 19bh exhibited excellent activity against 10 NDM-positive isolate clinical isolates in reversing MEM resistance. Further studies demonstrated compounds 19bg and 19bh were uncompetitive NDM-1 inhibitors with Ki = 0.63 and 0.44 μmol/L, respectively. Molecular docking speculated that compounds 19bg and 19bh were most likely to bind in the allosteric pocket which would affect the catalytic effect of NDM-1 on the substrate meropenem. Toxicity evaluation experiment showed that no hemolysis activities even at concentrations of 1000 mg/mL against red blood cells. In vivo experimental results showed combination of MEM and compound 19bh was markedly effective in treating infections caused by NDM-1 positive strain and prolonging the survival time of sepsis mice. Our finding showed that compound 19bh might be a promising lead in developing new inhibitor to treat NDM-1 producing superbug.
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Key Words
- (Boc)2O, di-tert-butyl decarbonate
- 3-AP, 3-aminopyridine carboxaldehyde thiosemicarbazone
- AcOH, acetic acid
- Antibiotic resistance
- Boc, tert-butoxycarbonyl
- CLSI, Clinical and Laboratory Standards Institute
- DMAP, 4-dimethylaminopyridine
- DpC, di-2-pyridylketone-4-cyclohexyl-4-methyl-3-thiosemicarbazone
- E. coli, Escherichia coli
- EDTA, ethylene diamine tetraacetic acid
- ESI, electrospray ionization
- HR-MS, high-resolution mass spectra
- IC50, half-maximal inhibitory concentrations
- Inhibitor
- K. pneumoniae, Klebsiella pneumoniae
- LQTS, long QT syndrome
- MBLs, metallo-β-lactamases class B
- MEM, meropenem
- MHA, Mueller-Hinton Agar
- MHB, Mueller-Hinton Broth
- MIC, minimum inhibitory concentration
- NDM-1, New Delhi metallo-β-lactamase-1
- New Delhi metallo-β-lactamase-1
- PBS, phosphate-buffered saline
- PK, pharmacokinetic
- RBCs, red blood cells
- SAR, structure–activity relationship
- THF, tetrahydrofuran
- TLC, thin layer chromatography
- TMS, tetramethylsilane
- Thiosemicarbazone derivatives
- UPLC, ultra-performance liquid chromatography
- conc. HCl, concentrated hydrochloric acid
- r.t., room temperature
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Patil S, Bhadane B, Shirsath L, Patil R, Chaudhari B. Steroidal fraction ofCarissa carandasL. inhibits microbial hyaluronidase activity by mixed inhibition mechanism. Prep Biochem Biotechnol 2019; 49:298-306. [DOI: 10.1080/10826068.2018.1541811] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Sandip Patil
- Department of Microbiology and Biotechnology, R. C. Patel Arts, Commerce and Science College, Shirpur, India
| | - Bhushan Bhadane
- Department of Microbiology and Biotechnology, R. C. Patel Arts, Commerce and Science College, Shirpur, India
| | - Leena Shirsath
- Department of Microbiology and Biotechnology, R. C. Patel Arts, Commerce and Science College, Shirpur, India
| | - Ravindra Patil
- Department of Microbiology and Biotechnology, R. C. Patel Arts, Commerce and Science College, Shirpur, India
| | - Bhushan Chaudhari
- Department of Microbiology, School of Life Sciences, Kavayitri Bahinabai Chaudhari North Maharashtra University, Jalgaon, India
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WANG MANYUAN, MOTAFAKKERAZAD ROUHOLLAH, MATSUGO SEIICHI, WADA NAOKI, KONISHI TETSUYA. Activity assay of Lipoamidase, an expected modulator of metabolic fate of externally administered lipoic acid. Inflamm Regen 2011. [DOI: 10.2492/inflammregen.31.88] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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Hayakawa K, Katsumata N, Abe K, Hirano M, Yoshikawa K, Ogata T, Horikawa R, Nagamine T. Wide Range of Biotin (Vitamin H) Content in Foodstuffs and Powdered Milks as Assessed by High-performance Affinity Chromatography. Clin Pediatr Endocrinol 2009; 18:41-9. [PMID: 24790379 PMCID: PMC4004883 DOI: 10.1297/cpe.18.41] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2008] [Accepted: 11/20/2008] [Indexed: 11/04/2022] Open
Abstract
The biotin (vitamin H) contents of various foodstuffs were determined by using
a newly developed high-performance affinity chromatography with a trypsin-treated
avidin-bound column. Biotin was derivatized with 9-anthryldiazomethane (ADAM) to
fluorescent biotin-ADAM ester. A wide range of biotin contents were found in various
foodstuffs depending upon the species (strain), season, organ (of plants and animals),
geography, freshness, preparation method and storage method. Among the foodstuffs and
fermented foods tested, it was found that wide distributions of biotin content were
observed in powdered milk, natto, sake (rice wine), beer, edible oil and sea weed. Since
powdered milk is important for child health and development, 14 kinds of powdered and
special milks for use in children’s diseases were intensively measured. We found that
several special milk powders for children with allergies contained low levels of free
biotin. Use of these powdered milks caused skin diseases and alopecia in some patients
possessing thermolabile serum biotinidase, and administration of free biotin improved
their symptoms dramatically. Therefore, it is essential to estimate the total and free
biotin contents on each foodstuff in order to improve effective biotin intake and support
better health and quality of life for people.
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Affiliation(s)
- Kou Hayakawa
- Department of Endocrinology and Metabolism, National Research Institute for Child Health and Development
| | - Noriyuki Katsumata
- Department of Endocrinology and Metabolism, National Research Institute for Child Health and Development
| | - Kiyomi Abe
- Department of Endocrinology and Metabolism, National Research Institute for Child Health and Development
| | - Masahiko Hirano
- Department of Endocrinology and Metabolism, National Research Institute for Child Health and Development
| | - Kazuyuki Yoshikawa
- Department of Endocrinology and Metabolism, National Research Institute for Child Health and Development
| | - Tsutomu Ogata
- Department of Endocrinology and Metabolism, National Research Institute for Child Health and Development
| | - Reiko Horikawa
- Department of Endocrinology and Metabolism, National Research Institute for Child Health and Development
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