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Maccarana M, Li B, Li H, Fang J, Yu M, Li JP. Inhibitors of dermatan sulfate epimerase 1 decreased accumulation of glycosaminoglycans in mucopolysaccharidosis type I fibroblasts. Glycobiology 2024; 34:cwae025. [PMID: 38760939 PMCID: PMC11101759 DOI: 10.1093/glycob/cwae025] [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: 12/12/2023] [Revised: 03/12/2024] [Accepted: 03/12/2024] [Indexed: 05/20/2024] Open
Abstract
Genetic deficiency of alpha-L-iduronidase causes mucopolysaccharidosis type I (MPS-I) disease, due to accumulation of glycosaminoglycans (GAGs) including chondroitin/dermatan sulfate (CS/DS) and heparan sulfate (HS) in cells. Currently, patients are treated by infusion of recombinant iduronidase or by hematopoietic stem cell transplantation. An alternative approach is to reduce the L-iduronidase substrate, through limiting the biosynthesis of iduronic acid. Our earlier study demonstrated that ebselen attenuated GAGs accumulation in MPS-I cells, through inhibiting iduronic acid producing enzymes. However, ebselen has multiple pharmacological effects, which prevents its application for MPS-I. Thus, we continued the study by looking for novel inhibitors of dermatan sulfate epimerase 1 (DS-epi1), the main responsible enzyme for production of iduronic acid in CS/DS chains. Based on virtual screening of chemicals towards chondroitinase AC, we constructed a library with 1,064 compounds that were tested for DS-epi1 inhibition. Seventeen compounds were identified to be able to inhibit 27%-86% of DS-epi1 activity at 10 μM. Two compounds were selected for further investigation based on the structure properties. The results show that both inhibitors had a comparable level in inhibition of DS-epi1while they had negligible effect on HS epimerase. The two inhibitors were able to reduce iduronic acid biosynthesis in CS/DS and GAG accumulation in WT and MPS-I fibroblasts. Docking of the inhibitors into DS-epi1 structure shows high affinity binding of both compounds to the active site. The collected data indicate that these hit compounds may be further elaborated to a potential lead drug used for attenuation of GAGs accumulation in MPS-I patients.
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Affiliation(s)
- Marco Maccarana
- Department of Medical Biochemistry and Microbiology, University of Uppsala, Husargatan 3, 75123, Uppsala, Sweden
| | - Binjie Li
- Beijing Advanced Innovation Centre for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, No. 15 North Third Ring Road East, Chaoyang District, Beijing, 100029, P. R. China
| | - Honglian Li
- Department of Medical Biochemistry and Microbiology, University of Uppsala, Husargatan 3, 75123, Uppsala, Sweden
| | - Jianping Fang
- GlycoNovo Technologies Co. Ltd., Room 202, Building 83-84, 887 Zuchongzhi Road, Pilot Free Trade Zone, Shanghai 201203, China
| | - Mingjia Yu
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, No 8 and 9 Yards, Liangxiang East Road, Fangshan District, Beijing 102488, China
| | - Jin-ping Li
- Department of Medical Biochemistry and Microbiology, University of Uppsala, Husargatan 3, 75123, Uppsala, Sweden
- SciLifeLab, Uppsala University, Husargatan 3, 75123, Uppsala, Sweden
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Durán-Gutiérrez DP, López-Hidalgo M, Peña-Gomar IM, Zamorano-Carrillo A, Gómez-Esquivel ML, Castrejón-Flores JL, Reyes-López CA. Molecular docking analysis of a dermatan sulfate tetra-saccharide to human alpha-L-iduronidase. Bioinformation 2023; 19:1116-1123. [PMID: 38250526 PMCID: PMC10794756 DOI: 10.6026/973206300191116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/31/2023] [Accepted: 12/31/2023] [Indexed: 01/23/2024] Open
Abstract
Human alpha-L-iduronidase (IDUA) is a 653 amino acid protein involved in the sequential degradation of glycos-amino-glycans (GAG), heparan sulfate (HS), and dermatan sulfate (DS). Some variants in the IDUA gene produce a deficient enzyme that causes un-degraded DS and HS to accumulate in multiple tissues, leading to an organ dysfunction known as muco-poly-saccharidosis type I (MPS I). Molecular and catalytic activity assays of new or rare variants of IDUA do not predict the phenotype that a patient will develop. Therefore, it is of interest to describe the molecular docking analysis, to locate binding regions of DS to IDUA to better understand the effect of a variant on MPS I development. The results presented herein demonstrate the presence of a polar/acidic catalytic site and a basic region in the putative binding site of DS to IDUA. Further, synthetic substrate docking with the enzyme could help in the predictions of the MPS I phenotype.
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Affiliation(s)
- Darinka P Durán-Gutiérrez
- Sección de Estudios de Posgrado e Investigación, ENMyH, Instituto Politécnico Nacional, Guillermo Massieu Helguera, No. 239, Fracc. "La Escalera", Ticomán, C.P. 07320, Mexico City, Mexico
| | - Marisol López-Hidalgo
- Sección de Estudios de Posgrado e Investigación, ENMyH, Instituto Politécnico Nacional, Guillermo Massieu Helguera, No. 239, Fracc. "La Escalera", Ticomán, C.P. 07320, Mexico City, Mexico
| | - Iliana M Peña-Gomar
- Departamento de Genética, Hospital IMSS-Bienestar Cuajimalpa, Cuajimalpa de Morelos, Mexico City, Mexico
| | - Absalom Zamorano-Carrillo
- Sección de Estudios de Posgrado e Investigación, ENMyH, Instituto Politécnico Nacional, Guillermo Massieu Helguera, No. 239, Fracc. "La Escalera", Ticomán, C.P. 07320, Mexico City, Mexico
| | - Mónica L Gómez-Esquivel
- Sección de Estudios de Posgrado e Investigación, ENMyH, Instituto Politécnico Nacional, Guillermo Massieu Helguera, No. 239, Fracc. "La Escalera", Ticomán, C.P. 07320, Mexico City, Mexico
| | - José L Castrejón-Flores
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología, Gustavo A. Madero, Mexico City, Mexico
| | - César A Reyes-López
- Sección de Estudios de Posgrado e Investigación, ENMyH, Instituto Politécnico Nacional, Guillermo Massieu Helguera, No. 239, Fracc. "La Escalera", Ticomán, C.P. 07320, Mexico City, Mexico
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Gaardløsa M, Lervikb A, Samsonova SA. Computational modeling of the molecular basis for the calcium-dependence of the mannuronan C-5 epimerase AvAlgE6 from Azotobacter vinelandii. Comput Struct Biotechnol J 2023; 21:2188-2196. [PMID: 37013001 PMCID: PMC10066508 DOI: 10.1016/j.csbj.2023.03.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 03/13/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
The mannuronan C-5 epimerases catalyze epimerization of β-d-mannuronic acid to α-l-guluronic acid in alginate polymers. The seven extracellular Azotobacter vinelandii epimerases (AvAlgE1-7) are calcium-dependent, and calcium is essential for the structural integrity of their carbohydrate binding R-modules. Ca2+ is also found in the crystal structures of the A-modules, where it is suggested to play a structural role. In this study, the structure of the catalytic A-module of the A. vinelandii mannuronan C-5 epimerase AvAlgE6 is used to investigate the role of this Ca2+. Molecular dynamics (MD) simulations with and without calcium reveal the possible importance of the bound Ca2+ in the hydrophobic packing of β-sheets. In addition, a putative calcium binding site is found in the active site, indicating a potential direct role of this calcium in the catalysis. According to the literature, two of the residues coordinating calcium in this site are essential for the activity. MD simulations of the interaction with bound substrate indicate that the presence of a calcium ion in this binding site increases the binding strength. Further, explicit calculations of the substrate dissociation pathways with umbrella sampling simulations show and energetically higher dissociation barrier when calcium is present. The present study eludes to a putative catalytic role of calcium in the charge neutralizing first step of the enzymatic reaction. In addition to the importance for understanding these enzymes' molecular mechanisms, this could have implications for engineering strategies of the epimerases in industrial alginate processing.
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Maccarana M, Tykesson E, Pera EM, Gouignard N, Fang J, Malmström A, Ghiselli G, Li JP. Inhibition of iduronic acid biosynthesis by ebselen reduces glycosaminoglycan accumulation in mucopolysaccharidosis type I fibroblasts. Glycobiology 2021; 31:1319-1329. [PMID: 34192316 PMCID: PMC8600295 DOI: 10.1093/glycob/cwab066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 06/08/2021] [Accepted: 06/21/2021] [Indexed: 11/13/2022] Open
Abstract
Mucopolysaccharidosis type I (MPS-I) is a rare lysosomal storage disorder caused by deficiency of the enzyme alpha-L-iduronidase, which removes iduronic acid in both chondroitin/dermatan sulfate (CS/DS) and heparan sulfate (HS) and thereby contributes to the catabolism of glycosaminoglycans (GAGs). To ameliorate this genetic defect, the patients are currently treated by enzyme replacement and bone marrow transplantation, which have a number of drawbacks. This study was designed to develop an alternative treatment by inhibition of iduronic acid formation. By screening the Prestwick drug library, we identified ebselen as a potent inhibitor of enzymes that produce iduronic acid in CS/DS and HS. Ebselen efficiently inhibited iduronic acid formation during CS/DS synthesis in cultured fibroblasts. Treatment of MPS-I fibroblasts with ebselen not only reduced accumulation of CS/DS but also promoted GAG degradation. In early Xenopus embryos, this drug phenocopied the effect of downregulation of DS-epimerase 1, the main enzyme responsible for iduronic production in CS/DS, suggesting that ebselen inhibits iduronic acid production in vivo. However, ebselen failed to ameliorate the CS/DS and GAG burden in MPS-I mice. Nevertheless, the results propose a potential of iduronic acid substrate reduction therapy for MPS-I patients.
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Affiliation(s)
- Marco Maccarana
- Department of Medical Biochemistry and Microbiology, BMC B11, Uppsala University, Husargatan 3 Box 582 751 23 Uppsala, Sweden
- Department of Experimental Medical Science, BMC C12, Lund University, BMC H11, 221 84 Lund, Sweden
| | - Emil Tykesson
- Department of Experimental Medical Science, BMC C12, Lund University, BMC H11, 221 84 Lund, Sweden
| | - Edgar M Pera
- Department of Laboratory Medicine, Lund Stem Cell Center, Lund University, BMC H11, 221 84 Lund, Sweden
| | - Nadège Gouignard
- Department of Laboratory Medicine, Lund Stem Cell Center, Lund University, BMC H11, 221 84 Lund, Sweden
| | - Jianping Fang
- GlycoNovo Technologies Co., Ltd., Shanghai 201203, China
| | - Anders Malmström
- Department of Experimental Medical Science, BMC C12, Lund University, BMC H11, 221 84 Lund, Sweden
| | - Giancarlo Ghiselli
- Glyconova Srl, Parco Scientifico Silvano Fumero, Bioindustry Park Silvano Fumero S.p.A Via Ribes, 5 - 10010 - Colleretto Giacosa (TO), Italy
| | - Jin-ping Li
- Department of Medical Biochemistry and Microbiology, BMC B11, Uppsala University, Husargatan 3 Box 582 751 23 Uppsala, Sweden
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Khakzad H, Happonen L, Malmström J, Malmström L. Cheetah-MS: a web server to model protein complexes using tandem cross-linking mass spectrometry data. Bioinformatics 2021; 37:4871-4872. [PMID: 34128979 PMCID: PMC8665757 DOI: 10.1093/bioinformatics/btab449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/07/2021] [Accepted: 06/14/2021] [Indexed: 11/13/2022] Open
Abstract
Summary Protein–protein interactions (PPIs) are central in many biological processes but difficult to characterize, especially in complex, unfractionated samples. Chemical cross-linking combined with mass spectrometry (MS) and computational modeling is gaining recognition as a viable tool in protein interaction studies. Here, we introduce Cheetah-MS, a web server for predicting the PPIs in a complex mixture of samples. It combines the capability and sensitivity of MS to analyze complex samples with the power and resolution of protein–protein docking. It produces the quaternary structure of the PPI of interest by analyzing tandem MS/MS data (also called MS2). Combining MS analysis and modeling increases the sensitivity and, importantly, facilitates the interpretation of the results. Availability and implementation Cheetah-MS is freely available as a web server at https://www.txms.org.
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Affiliation(s)
- Hamed Khakzad
- Equipe Signalisation Calcique et Infections Microbiennes, École Normale Supérieure Paris-Saclay, Gif-sur-Yvette, 91190, France.,Institut National de la Santé et de la Recherche Médicale U1282, Gif-sur-Yvette, 91190, France
| | - Lotta Happonen
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Sweden
| | - Johan Malmström
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Sweden
| | - Lars Malmström
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Sweden
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