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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] [What about the content of this article? (0)] [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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Minami A, Ishibashi S, Ikeda K, Ishitsubo E, Hori T, Tokiwa H, Taguchi R, Ieno D, Otsubo T, Matsuda Y, Sai S, Inada M, Suzuki T. Catalytic preference of Salmonella typhimurium LT2 sialidase for N-acetylneuraminic acid residues over N-glycolylneuraminic acid residues. FEBS Open Bio 2013; 3:231-6. [PMID: 23772399 PMCID: PMC3678298 DOI: 10.1016/j.fob.2013.05.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 05/17/2013] [Accepted: 05/17/2013] [Indexed: 01/21/2023] Open
Abstract
In a comparison of sialidase activities toward N-acetylneuraminic acid (Neu5Ac) and N-glycolylneuraminic acid (Neu5Gc), we found that Salmonella typhimurium LT2 sialidase (STSA) hardly cleaved 4-methylumbelliferyl Neu5Gc (4MU-Neu5Gc). The k cat/K m value of STSA for 4MU-Neu5Gc was found to be 110 times lower than that for 4-methylumbelliferyl Neu5Ac (4MU-Neu5Ac). Additionally, STSA had remarkably weak ability to cleave α2-3-linked-Neu5Gc contained in gangliosides and equine erythrocytes. In silico analysis based on first-principle calculations with transition-state analogues suggested that the binding affinity of Neu5Gc2en is 14.3 kcal/mol more unstable than that of Neu5Ac2en. The results indicated that STSA preferentially cleaves Neu5Ac residues rather than Neu5Gc residues, which is important for anyone using this enzyme to cleave α2-3-linked sialic acids.
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Key Words
- 4MU, 4-methylumbelliferone
- 4MU-Neu5Ac, 4-methylumbelliferyl N-acetylneuraminic acid
- 4MU-Neu5Gc
- 4MU-Neu5Gc, 4-methylumbelliferyl N-glycolylneuraminic acid
- AUSA, Arthrobacter ureafaciens sialidase
- Boc, tert-butoxycarbonyl
- CPSA, Clostridium perfingens sialidase
- DANA, 2,3-dehydro-2-deoxy-N-acetylneuraminic acid
- DMAP, 4-dimethylaminopyridine
- DMB, 1,2-diamino-4,5-methylenedioxybenzene
- Docking simulations
- E. coli, Escherichia coli
- HPLC, high-performance liquid chromatography
- MDSA, Macrobdella decora sialidase
- N-glycolylneuraminic acid
- N.D., not detected
- Neu5Ac, N-acetylneuraminic acid
- Neu5Gc, N-glycolylneuraminic acid
- PBS, phosphate buffered saline
- STSA, Salmonella typhimurium LT2 sialidase
- Salmonella typhimurium LT2 sialidase
- Sia, sialic acid
- Sialic acid
- Substrate specificity
- THF, tetrahydrofuran
- VCSA, Vibrio cholerae sialidase
- rt, room temperature
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Affiliation(s)
- Akira Minami
- Department of Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Sayaka Ishibashi
- Department of Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Kiyoshi Ikeda
- Department of Organic Chemistry, School of Pharmaceutical Sciences, Hiroshima International University, 5-1-1, Hirokoshingai, Kure-shi, Hiroshima 737-0112, Japan
| | - Erika Ishitsubo
- Department of Chemistry, Faculty of Science, Rikkyo University, Tokyo 171-8501, Japan
| | - Takanori Hori
- Department of Chemistry, Faculty of Science, Rikkyo University, Tokyo 171-8501, Japan
| | - Hiroaki Tokiwa
- Department of Chemistry, Faculty of Science, Rikkyo University, Tokyo 171-8501, Japan
| | - Risa Taguchi
- Department of Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Daisuke Ieno
- Department of Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Tadamune Otsubo
- Department of Organic Chemistry, School of Pharmaceutical Sciences, Hiroshima International University, 5-1-1, Hirokoshingai, Kure-shi, Hiroshima 737-0112, Japan
| | - Yukino Matsuda
- Department of Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Saki Sai
- Department of Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Mari Inada
- Department of Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Takashi Suzuki
- Department of Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
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