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Meelua W, Thinkumrob N, Saparpakorn P, Pengthaisong S, Hannongbua S, Ketudat Cairns JR, Jitonnom J. Structural basis for inhibition of a GH116 β-glucosidase and its missense mutants by GBA2 inhibitors: Crystallographic and quantum chemical study. Chem Biol Interact 2023; 384:110717. [PMID: 37726065 DOI: 10.1016/j.cbi.2023.110717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/24/2023] [Accepted: 09/15/2023] [Indexed: 09/21/2023]
Abstract
The crystal structure of the Thermoanaerobacterium xylanolyticum in glycoside hydrolase family 116 (TxGH116) β-glucosidase provides a structural model for human GBA2 glucosylceramidase, an enzyme defective in hereditary spastic paraplegia and a potential therapeutic target for treating Gaucher disease. To assess the therapeutic potential of known inhibitors, the X-ray structure of TxGH116 in complex with isofagomine (IFG) was determined at 2.0 Å resolution and showed the IFG bound in a relaxed chair conformation. The binding of IFG and 7 other iminosugar inhibitors to wild-type and mutant enzymes (Asp508His and Arg786His) mimicking GBA2 pathogenic variants was then evaluated computationally by two-layered ONIOM calculations (at the B3LYP:PM7 level). Calculations showed that six charged residues, Glu441, Asp452, His507, Asp593, Glu777, and Arg786 influence inhibitor binding most. His507, Glu777 and Arg786, form strong hydrogen bonds with the inhibitors (∼1.4-1.6 Å). Thus, the missense mutation of one of these residues in Arg786His has a greater effect on the interaction energies for all inhibitors compared to Asp508His. In line with the experimental data for the inhibitors that have been tested, the favorable interaction energy between the inhibitors and the TxGH116 protein followed the trend: isofagomine > 1-deoxynojirimycin > glucoimidazole > N-butyl-deoxynojirimycin ≈ N-nonyl-deoxynojirimycin > conduritol B epoxide ≈ azepane 1 > azepane 2. The obtained structural and energetic properties and comparison to the GBA2 model can lead to understanding of structural requirement for inhibitor binding in GH116 to aid the design of high potency GBA2 inhibitors.
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Affiliation(s)
- Wijitra Meelua
- Demonstration School, University of Phayao, Phayao, 56000, Thailand; Unit of Excellence in Computational Molecular Science and Catalysis, and Division of Chemistry, School of Science, University of Phayao, Phayao, 56000, Thailand
| | - Natechanok Thinkumrob
- Unit of Excellence in Computational Molecular Science and Catalysis, and Division of Chemistry, School of Science, University of Phayao, Phayao, 56000, Thailand
| | | | - Salila Pengthaisong
- Center for Biomolecular Structure, Function and Application, and School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - James R Ketudat Cairns
- Center for Biomolecular Structure, Function and Application, and School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand.
| | - Jitrayut Jitonnom
- Unit of Excellence in Computational Molecular Science and Catalysis, and Division of Chemistry, School of Science, University of Phayao, Phayao, 56000, Thailand.
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Jiménez-Pérez C, Guzmán-Rodríguez F, Cruz-Guerrero AE, Alatorre-Santamaría S. The dual role of fucosidases: tool or target. Biologia (Bratisl) 2023; 78:1-16. [PMID: 37363646 PMCID: PMC9972328 DOI: 10.1007/s11756-023-01351-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 02/07/2023] [Indexed: 03/06/2023]
Abstract
Regular intake of fucosylated oligosaccharides has been associated with several benefits for human health, particularly for new-borns. Since these biologically active molecules can be found naturally in human milk, research efforts have been focused on the alternative synthetic routes leading to their production. In particular, utilization of fucosidases to perform stereoselective transglycosylation reactions has been widely investigated. Other reasons that bring these enzymes to the spotlight are their role in viral infections and cancer proliferation. Since their involvement in the pathogenesis of these diseases have been widely described, fucosidases have become a target in newly developed therapies. Finally, activity disorders of biologically important fucosidases can lead to health problems such as fucosidosis. What is common for both mechanisms is the interaction between the enzyme and substrates in and around the active site. Therefore, this review will analyse different substrate structures that have been tested in terms of their interaction with fucosidases active sites, either in synthesis or inhibition reactions. The published results will be compared from this perspective.
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Affiliation(s)
- Carlos Jiménez-Pérez
- Dpto. de Biotecnología, Universidad Autónoma Metropolitana Unidad Iztapalapa, C.P. 09340 Mexico City, Mexico
| | - Francisco Guzmán-Rodríguez
- Dpto. de Biotecnología, Universidad Autónoma Metropolitana Unidad Iztapalapa, C.P. 09340 Mexico City, Mexico
| | - Alma E. Cruz-Guerrero
- Dpto. de Biotecnología, Universidad Autónoma Metropolitana Unidad Iztapalapa, C.P. 09340 Mexico City, Mexico
| | - Sergio Alatorre-Santamaría
- Dpto. de Biotecnología, Universidad Autónoma Metropolitana Unidad Iztapalapa, C.P. 09340 Mexico City, Mexico
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Zamoner LOB, Aragão-Leoneti V, Carvalho I. Iminosugars: Effects of Stereochemistry, Ring Size, and N-Substituents on Glucosidase Activities. Pharmaceuticals (Basel) 2019; 12:E108. [PMID: 31336868 PMCID: PMC6789487 DOI: 10.3390/ph12030108] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 07/08/2019] [Accepted: 07/10/2019] [Indexed: 01/18/2023] Open
Abstract
N-substituted iminosugar analogues are potent inhibitors of glucosidases and glycosyltransferases with broad therapeutic applications, such as treatment of diabetes and Gaucher disease, immunosuppressive activities, and antibacterial and antiviral effects against HIV, HPV, hepatitis C, bovine diarrhea (BVDV), Ebola (EBOV) and Marburg viruses (MARV), influenza, Zika, and dengue virus. Based on our previous work on functionalized isomeric 1,5-dideoxy-1,5-imino-D-gulitol (L-gulo-piperidines, with inverted configuration at C-2 and C-5 in respect to glucose or deoxynojirimycin (DNJ)) and 1,6-dideoxy-1,6-imino-D-mannitol (D-manno-azepane derivatives) cores N-linked to different sites of glucopyranose units, we continue our studies on these alternative iminosugars bearing simple N-alkyl chains instead of glucose to understand if these easily accessed scaffolds could preserve the inhibition profile of the corresponding glucose-based N-alkyl derivatives as DNJ cores found in miglustat and miglitol drugs. Thus, a small library of iminosugars (14 compounds) displaying different stereochemistry, ring size, and N-substitutions was successfully synthesized from a common precursor, D-mannitol, by utilizing an SN2 aminocyclization reaction via two isomeric bis-epoxides. The evaluation of the prospective inhibitors on glucosidases revealed that merely D-gluco-piperidine (miglitol, 41a) and L-ido-azepane (41b) DNJ-derivatives bearing the N-hydroxylethyl group showed inhibition towards α-glucosidase with IC50 41 µM and 138 µM, respectively, using DNJ as reference (IC50 134 µM). On the other hand, β-glucosidase inhibition was achieved for glucose-inverted configuration (C-2 and C-5) derivatives, as novel L-gulo-piperidine (27a) and D-manno-azepane (27b), preserving the N-butyl chain, with IC50 109 and 184 µM, respectively, comparable to miglustat with the same N-butyl substituent (40a, IC50 172 µM). Interestingly, the seven-membered ring L-ido-azepane (40b) displayed near twice the activity (IC50 80 µM) of the corresponding D-gluco-piperidine miglustat drug (40a). Furthermore, besides α-glucosidase inhibition, both miglitol (41a) and L-ido-azepane (41b) proved to be the strongest β-glucosidase inhibitors of the series with IC50 of 4 µM.
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Affiliation(s)
- Luís O B Zamoner
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café s/n, Monte Alegre, CEP14040-903 Ribeirão Preto, Brazil
| | - Valquiria Aragão-Leoneti
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café s/n, Monte Alegre, CEP14040-903 Ribeirão Preto, Brazil
| | - Ivone Carvalho
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café s/n, Monte Alegre, CEP14040-903 Ribeirão Preto, Brazil.
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Zhu S, Tran AT, Hirokami Y, Gontard G, Khaled O, Zhang Y, Kato A, Blériot Y, Sollogoub M. Bi(OTf)3-mediated intramolecular epoxide opening for bicyclic azepane synthesis. J Carbohydr Chem 2019. [DOI: 10.1080/07328303.2019.1581887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Sha Zhu
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, Paris, France
| | - Anh Tuan Tran
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, Paris, France
| | - Yuki Hirokami
- Department of Hospital Pharmacy, University of Toyama, Toyama, Japan
| | - Geoffrey Gontard
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, Paris, France
| | - Omar Khaled
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, Paris, France
| | - Yongmin Zhang
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, Paris, France
| | - Atsushi Kato
- Department of Hospital Pharmacy, University of Toyama, Toyama, Japan
| | - Yves Blériot
- IC2MP-UMR CNRS 7285, Université de Poitiers, Equipe “Synthèse Organique”, Groupe Glycochimie, Poitiers cedex 9, France
| | - Matthieu Sollogoub
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, Paris, France
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Miranda Pedroso TFD, Bonamigo TR, da Silva J, Vasconcelos P, Félix JM, Cardoso CAL, Souza RIC, dos Santos AC, Volobuff CRF, Formagio ASN, Trichez VDK. Chemical constituents of Cochlospermum regium (Schrank) Pilg. root and its antioxidant, antidiabetic, antiglycation, and anticholinesterase effects in Wistar rats. Biomed Pharmacother 2019; 111:1383-1392. [DOI: 10.1016/j.biopha.2019.01.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 01/02/2019] [Accepted: 01/03/2019] [Indexed: 12/17/2022] Open
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Zha GF, Rakesh K, Manukumar H, Shantharam C, Long S. Pharmaceutical significance of azepane based motifs for drug discovery: A critical review. Eur J Med Chem 2019; 162:465-494. [DOI: 10.1016/j.ejmech.2018.11.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/13/2018] [Accepted: 11/09/2018] [Indexed: 12/11/2022]
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Pino-Gonzalez MS, Romero-Carrasco A, Calvo-Losada S, Oña-Bernal N, Quirante JJ, Sarabia F. Synthesis of tetrazole fused azepanes and quantum chemical topology study on the mechanism of the intramolecular cycloaddition reaction. RSC Adv 2017. [DOI: 10.1039/c7ra10899k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Syntheses of novel tetrazolo azepanes by intramolecular 1,3-dipolar cycloaddition are described. Cyclization mechanistic topology study showed a pseudo concerted mechanism.
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Affiliation(s)
| | - A. Romero-Carrasco
- Department of Organic Chemistry
- Faculty of Sciences
- University of Málaga
- Spain
| | - S. Calvo-Losada
- Department of Physical Chemistry
- Faculty of Sciences
- University of Málaga
- Spain
| | - N. Oña-Bernal
- Department of Organic Chemistry
- Faculty of Sciences
- University of Málaga
- Spain
| | - J. J. Quirante
- Department of Physical Chemistry
- Faculty of Sciences
- University of Málaga
- Spain
| | - F. Sarabia
- Department of Organic Chemistry
- Faculty of Sciences
- University of Málaga
- Spain
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Jagadeesh Y, Tran AT, Luo B, Auberger N, Désiré J, Nakagawa S, Kato A, Zhang Y, Sollogoub M, Blériot Y. γ-Aminoalcohol rearrangement applied to pentahydroxylated azepanes provides pyrrolidines epimeric to homoDMDP. Org Biomol Chem 2015; 13:3446-56. [PMID: 25666467 DOI: 10.1039/c5ob00050e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of pentahydroxylated pyrrolidines, displaying five contiguous stereogenic centres and epimeric to α-glucosidase inhibitor homoDMDP, have been synthesized. The key step involves a γ-aminoalcohol rearrangement applied to polyhydroxylated azepanes. These five-membered iminosugars demonstrate micromolar inhibition of glycosidases.
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Affiliation(s)
- Y Jagadeesh
- Glycochemistry Group of "Organic Synthesis" Team, Université de Poitiers, UMR-CNRS 7285 IC2MP, 4 rue Michel Brunet, 86073 Poitiers Cedex 9, France.
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