1
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Nguyen DLB, Okolicsanyi RK, Haupt LM. Heparan sulfate proteoglycans: Mediators of cellular and molecular Alzheimer's disease pathogenic factors via tunnelling nanotubes? Mol Cell Neurosci 2024; 129:103936. [PMID: 38750678 DOI: 10.1016/j.mcn.2024.103936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/14/2024] [Accepted: 05/01/2024] [Indexed: 05/19/2024] Open
Abstract
Neurological disorders impact around one billion individuals globally (15 % approx.), with significant implications for disability and mortality with their impact in Australia currently amounts to 6.8 million deaths annually. Heparan sulfate proteoglycans (HSPGs) are complex extracellular molecules implicated in promoting Tau fibril formation resulting in Tau tangles, a hallmark of Alzheimer's disease (AD). HSPG-Tau protein interactions contribute to various AD stages via aggregation, toxicity, and clearance, largely via interactions with the glypican 1 and syndecan 3 core proteins. The tunnelling nanotubes (TNTs) pathway is emerging as a facilitator of intercellular molecule transport, including Tau and Amyloid β proteins, across extensive distances. While current TNT-associated evidence primarily stems from cancer models, their role in Tau propagation and its effects on recipient cells remain unclear. This review explores the interplay of TNTs, HSPGs, and AD-related factors and proposes that HSPGs influence TNT formation in neurodegenerative conditions such as AD.
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Affiliation(s)
- Duy L B Nguyen
- Stem Cell and Neurogenesis Group, Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology (QUT), 60 Musk Ave., Kelvin Grove, Queensland 4059, Australia
| | - Rachel K Okolicsanyi
- Stem Cell and Neurogenesis Group, Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology (QUT), 60 Musk Ave., Kelvin Grove, Queensland 4059, Australia; ARC Training Centre for Cell and Tissue Engineering Technologies, Queensland University of Technology (QUT), Australia
| | - Larisa M Haupt
- Stem Cell and Neurogenesis Group, Genomics Research Centre, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology (QUT), 60 Musk Ave., Kelvin Grove, Queensland 4059, Australia; Centre for Biomedical Technologies, Queensland University of Technology (QUT), 60 Musk Ave., Kelvin Grove, QLD 4059, Australia; ARC Training Centre for Cell and Tissue Engineering Technologies, Queensland University of Technology (QUT), Australia; Max Planck Queensland Centre for the Materials Sciences of Extracellular Matrices, Queensland University of Technology (QUT), Australia.
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2
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Parafioriti M, Elli S, Muñoz-García JC, Ramírez-Cárdenas J, Yates EA, Angulo J, Guerrini M. Differential Solvent DEEP-STD NMR and MD Simulations Enable the Determinants of the Molecular Recognition of Heparin Oligosaccharides by Antithrombin to Be Disentangled. Int J Mol Sci 2024; 25:4669. [PMID: 38731888 PMCID: PMC11083112 DOI: 10.3390/ijms25094669] [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: 02/28/2024] [Revised: 04/16/2024] [Accepted: 04/20/2024] [Indexed: 05/13/2024] Open
Abstract
The interaction of heparin with antithrombin (AT) involves a specific sequence corresponding to the pentasaccharide GlcNAc/NS6S-GlcA-GlcNS3S6S-IdoA2S-GlcNS6S (AGA*IA). Recent studies have revealed that two AGA*IA-containing hexasaccharides, which differ in the sulfation degree of the iduronic acid unit, exhibit similar binding to AT, albeit with different affinities. However, the lack of experimental data concerning the molecular contacts between these ligands and the amino acids within the protein-binding site prevents a detailed description of the complexes. Differential epitope mapping (DEEP)-STD NMR, in combination with MD simulations, enables the experimental observation and comparison of two heparin pentasaccharides interacting with AT, revealing slightly different bound orientations and distinct affinities of both glycans for AT. We demonstrate the effectiveness of the differential solvent DEEP-STD NMR approach in determining the presence of polar residues in the recognition sites of glycosaminoglycan-binding proteins.
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Affiliation(s)
- Michela Parafioriti
- Istituto di Ricerche Chimiche e Biochimiche “G. Ronzoni”, Via Giuseppe Colombo 81, 20133 Milano, Italy; (M.P.); (S.E.)
| | - Stefano Elli
- Istituto di Ricerche Chimiche e Biochimiche “G. Ronzoni”, Via Giuseppe Colombo 81, 20133 Milano, Italy; (M.P.); (S.E.)
| | - Juan C. Muñoz-García
- Instituto de Investigationes Químicas (IIQ)-Consejo Superior de Investigaciones Científicas (CSIC), Avenida Americo Vespucio 49, 41092 Sevilla, Spain; (J.C.M.-G.); (J.R.-C.)
| | - Jonathan Ramírez-Cárdenas
- Instituto de Investigationes Químicas (IIQ)-Consejo Superior de Investigaciones Científicas (CSIC), Avenida Americo Vespucio 49, 41092 Sevilla, Spain; (J.C.M.-G.); (J.R.-C.)
| | - Edwin A. Yates
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK;
- Centre for Glycoscience, Keele University, Newcastle-Under-Lyme ST5 5BG, UK
| | - Jesús Angulo
- Instituto de Investigationes Químicas (IIQ)-Consejo Superior de Investigaciones Científicas (CSIC), Avenida Americo Vespucio 49, 41092 Sevilla, Spain; (J.C.M.-G.); (J.R.-C.)
| | - Marco Guerrini
- Istituto di Ricerche Chimiche e Biochimiche “G. Ronzoni”, Via Giuseppe Colombo 81, 20133 Milano, Italy; (M.P.); (S.E.)
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3
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Widmalm G. Glycan Shape, Motions, and Interactions Explored by NMR Spectroscopy. JACS AU 2024; 4:20-39. [PMID: 38274261 PMCID: PMC10807006 DOI: 10.1021/jacsau.3c00639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 01/27/2024]
Abstract
Glycans in the form of oligosaccharides, polysaccharides, and glycoconjugates are ubiquitous in nature, and their structures range from linear assemblies to highly branched and decorated constructs. Solution state NMR spectroscopy facilitates elucidation of preferred conformations and shapes of the saccharides, motions, and dynamic aspects related to processes over time as well as the study of transient interactions with proteins. Identification of intermolecular networks at the atomic level of detail in recognition events by carbohydrate-binding proteins known as lectins, unraveling interactions with antibodies, and revealing substrate scope and action of glycosyl transferases employed for synthesis of oligo- and polysaccharides may efficiently be analyzed by NMR spectroscopy. By utilizing NMR active nuclei present in glycans and derivatives thereof, including isotopically enriched compounds, highly detailed information can be obtained by the experiments. Subsequent analysis may be aided by quantum chemical calculations of NMR parameters, machine learning-based methodologies and artificial intelligence. Interpretation of the results from NMR experiments can be complemented by extensive molecular dynamics simulations to obtain three-dimensional dynamic models, thereby clarifying molecular recognition processes involving the glycans.
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Affiliation(s)
- Göran Widmalm
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
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4
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Notaro A, Zaretsky M, Molinaro A, De Castro C, Eichler J. N-glycosylation in Archaea: Unusual sugars and unique modifications. Carbohydr Res 2023; 534:108963. [PMID: 37890267 DOI: 10.1016/j.carres.2023.108963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/26/2023] [Accepted: 10/02/2023] [Indexed: 10/29/2023]
Abstract
Archaea are microorganisms that comprise a distinct branch of the universal tree of life and which are best known as extremophiles, residing in a variety of environments characterized by harsh physical conditions. One seemingly universal trait of Archaea is the ability to perform N-glycosylation. At the same time, archaeal N-linked glycans present variety in terms of both composition and architecture not seen in the parallel eukaryal or bacterial processes. In this mini-review, many of the unique and unusual sugars found in archaeal N-linked glycans as identified by nuclear magnetic resonance spectroscopy are described.
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Affiliation(s)
- Anna Notaro
- Department of Agricultural Sciences, University of Napoli Federico II, Portici, Italy
| | - Marianna Zaretsky
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheva, Israel
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Napoli Federico II, Napoli, Italy
| | - Cristina De Castro
- Department of Chemical Sciences, University of Napoli Federico II, Napoli, Italy
| | - Jerry Eichler
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheva, Israel.
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5
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Bhoge PR, Raigawali R, Mardhekar S, Anand S, Kikkeri R. Synergestic interplay of uronic acid and sulfation composition of heparan sulfate on molecular recognition to activity. Carbohydr Res 2023; 532:108919. [PMID: 37557021 DOI: 10.1016/j.carres.2023.108919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/02/2023] [Accepted: 08/02/2023] [Indexed: 08/11/2023]
Abstract
Heparan sulfate (HS) is ubiquitous polysaccharide on the surface of all mammalian cells and extracellular matrices. The incredible structural complexity of HS arises from its sulfation patterns and disaccharide compositions, which orchestrate a wide range of biological activities. Researchers have developed elegant synthetic methods to obtain well-defined HS oligosaccharides to understand the structure-activity relationship. These studies revealed that specific sulfation codes and uronic acid variants could synergistically modulate HS-protein interactions (HSPI). Additionally, the conformational flexibility of l-Iduronic acid, a uronic acid unit has emerged as a critical factor in fine-tuning the microenvironment to modulate HSPI. This review delineates how uronic acid composition in HS modulates protein binding affinity, selectivity, and biological activity. Finally, the significance of sulfated homo-oligo uronic acid as heparin mimics in drug development is also discussed.
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Affiliation(s)
- Preeti Ravindra Bhoge
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 4110008, India
| | - Rakesh Raigawali
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 4110008, India
| | - Sandhya Mardhekar
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 4110008, India
| | - Saurabh Anand
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 4110008, India
| | - Raghavendra Kikkeri
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 4110008, India.
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6
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Pągielska M, Samsonov SA. Molecular Dynamics-Based Comparative Analysis of Chondroitin and Dermatan Sulfates. Biomolecules 2023; 13:biom13020247. [PMID: 36830616 PMCID: PMC9953526 DOI: 10.3390/biom13020247] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
Glycosaminoglycans (GAGs) are a class of linear anionic periodic polysaccharides containing disaccharide repetitive units. These molecules interact with a variety of proteins in the extracellular matrix and so participate in biochemically crucial processes such as cell signalling affecting tissue regeneration as well as the onset of cancer, Alzheimer's or Parkinson's diseases. Due to their flexibility, periodicity and chemical heterogeneity, often termed "sulfation code", GAGs are challenging molecules both for experiments and computation. One of the key questions in the GAG research is the specificity of their intermolecular interactions. In this study, we make a step forward to deciphering the "sulfation code" of chondroitin sulfates-4,6 (CS4, CS6, where the numbers correspond to the position of sulfation in NAcGal residue) and dermatan sulfate (DS), which is different from CSs by the presence of IdoA acid instead of GlcA. We rigorously investigate two sets of these GAGs in dimeric, tetrameric and hexameric forms with molecular dynamics-based descriptors. Our data clearly suggest that CS4, CS6 and DS are substantially different in terms of their structural, conformational and dynamic properties, which contributes to the understanding of how these molecules can be different when they bind proteins, which could have practical implications for the GAG-based drug design strategies in the regenerative medicine.
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7
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Notaro A, Vershinin Z, Guan Z, Eichler J, De Castro C. An N-linked tetrasaccharide from Halobacterium salinarum presents a novel modification, sulfation of iduronic acid at the O-3 position. Carbohydr Res 2022; 521:108651. [PMID: 36037649 DOI: 10.1016/j.carres.2022.108651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/15/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022]
Abstract
Halobacterium salinarum, a halophilic archaeon that grows at near-saturating salt concentrations, provided the first example of N-glycosylation outside Eukarya. Yet, almost 50 years later, numerous aspects of such post-translational protein processing in this microorganism remain to be determined, including the architecture of glycoprotein-bound glycans. In the present report, nuclear magnetic resonance spectroscopy was used to define a tetrasaccharide N-linked to both archaellins, building blocks of the archaeal swimming device (the archaellum), and the S-layer glycoprotein that comprises the protein shell surrounding the Hbt. salinarum cell as β-GlcA(2S)-(1 → 4)-α-IdoA(3S)-(1 → 4)-β-GlcA-(1 → 4)-β-Glc-Asn. The structure of this tetrasaccharide fills gaps remaining from previous studies, including confirmation of the first known inclusion of iduronic acid in an archaeal N-linked glycan. At the same time, the sulfation of this iduronic acid at the O-3 position has not, to the best of our knowledge, been previously seen. As such, this may represent yet another unique facet of N-glycosylation in Archaea.
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Affiliation(s)
- Anna Notaro
- Department of Agricultural Sciences, University of Napoli Federico II, Portici, Italy
| | - Zlata Vershinin
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheva, Israel
| | - Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Jerry Eichler
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheva, Israel.
| | - Cristina De Castro
- Department of Agricultural Sciences, University of Napoli Federico II, Portici, Italy.
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8
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Meneghetti M, Naughton L, O’Shea C, Koffi Teki DSE, Chagnault V, Nader HB, Rudd TR, Yates EA, Kovensky J, Miller GJ, Lima MA. Using NMR to Dissect the Chemical Space and O-Sulfation Effects within the O- and S-Glycoside Analogues of Heparan Sulfate. ACS OMEGA 2022; 7:24461-24467. [PMID: 35874203 PMCID: PMC9301708 DOI: 10.1021/acsomega.2c02070] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Heparan sulfate (HS), a sulfated linear carbohydrate that decorates the cell surface and extracellular matrix, is ubiquitously distributed throughout the animal kingdom and represents a key regulator of biological processes and a largely untapped reservoir of potential therapeutic targets. The temporal and spatial variations in the HS structure underpin the concept of "heparanome" and a complex network of HS binding proteins. However, despite its widespread biological roles, the determination of direct structure-to-function correlations is impaired by HS chemical heterogeneity. Attempts to correlate substitution patterns (mostly at the level of sulfation) with a given biological activity have been made. Nonetheless, these do not generally consider higher-level conformational effects at the carbohydrate level. Here, the use of NMR chemical shift analysis, NOEs, and spin-spin coupling constants sheds new light on how different sulfation patterns affect the polysaccharide backbone geometry. Furthermore, the substitution of native O-glycosidic linkages to hydrolytically more stable S-glycosidic forms leads to observable conformational changes in model saccharides, suggesting that alternative chemical spaces can be accessed and explored using such mimetics. Employing a series of systematically modified heparin oligosaccharides (as a proxy for HS) and chemically synthesized O- and S-glycoside analogues, the chemical space occupied by such compounds is explored and described.
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Affiliation(s)
- Maria
C.Z. Meneghetti
- Departamento
de Bioquímica, Instituto de Farmacologia e Biologia Molecular,
Escola Paulista de Medicina, Universidade
Federal de São Paulo, Rua Três de Maio, 100, São Paulo 04044-020, São Paulo, Brazil
| | - Lucy Naughton
- School
of Life Sciences, Keele University, Keele ST55BG, Staffordshire, U.K.
- Centre
for Glycosciences, Keele University, Keele ST55BG, Staffordshire, U.K.
| | - Conor O’Shea
- Centre
for Glycosciences, Keele University, Keele ST55BG, Staffordshire, U.K.
- Lennard-Jones
Laboratories, School of Chemical and Physical Sciences, Keele University, Keele ST55BG, Staffordshire, U.K.
| | - Dindet S.-E. Koffi Teki
- Laboratoire
de Glycochimie, des Antimicrobiens et des Agroressources (LG2A), UMR
7378 CNRS, Université de Picardie
Jules Verne, 33 rue Saint Leu, Amiens Cedex F-80039, France
| | - Vincent Chagnault
- Laboratoire
de Glycochimie, des Antimicrobiens et des Agroressources (LG2A), UMR
7378 CNRS, Université de Picardie
Jules Verne, 33 rue Saint Leu, Amiens Cedex F-80039, France
| | - Helena B. Nader
- Departamento
de Bioquímica, Instituto de Farmacologia e Biologia Molecular,
Escola Paulista de Medicina, Universidade
Federal de São Paulo, Rua Três de Maio, 100, São Paulo 04044-020, São Paulo, Brazil
| | - Timothy R. Rudd
- National
Institute for Biological Standards and Control (NIBSC), Blanche Lane, South Mimms, Potters Bar EN6 3QG, Hertfordshire, U.K.
- Department
of Biochemistry and Systems Biology, Institute of Systems, Molecular
and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K.
| | - Edwin A. Yates
- Department
of Biochemistry and Systems Biology, Institute of Systems, Molecular
and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K.
| | - José Kovensky
- Laboratoire
de Glycochimie, des Antimicrobiens et des Agroressources (LG2A), UMR
7378 CNRS, Université de Picardie
Jules Verne, 33 rue Saint Leu, Amiens Cedex F-80039, France
| | - Gavin J. Miller
- Centre
for Glycosciences, Keele University, Keele ST55BG, Staffordshire, U.K.
- Lennard-Jones
Laboratories, School of Chemical and Physical Sciences, Keele University, Keele ST55BG, Staffordshire, U.K.
| | - Marcelo A. Lima
- School
of Life Sciences, Keele University, Keele ST55BG, Staffordshire, U.K.
- Centre
for Glycosciences, Keele University, Keele ST55BG, Staffordshire, U.K.
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9
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Holmes SG, Nagarajan B, Desai UR. 3- O-Sulfation induces sequence-specific compact topologies in heparan sulfate that encode a dynamic sulfation code. Comput Struct Biotechnol J 2022; 20:3884-3898. [PMID: 35891779 PMCID: PMC9309406 DOI: 10.1016/j.csbj.2022.07.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/05/2022] [Accepted: 07/05/2022] [Indexed: 11/17/2022] Open
Abstract
Heparan sulfate (HS) is arguably the most diverse linear biopolymer that is known to modulate hundreds of proteins. Whereas the configurational and conformational diversity of HS is well established in terms of varying sulfation patterns and iduronic acid (IdoA) puckers, a linear helical topology resembling a cylindrical rod is the only topology thought to be occupied by the biopolymer. We reasoned that 3-O-sulfation, a rare modification in natural HS, may induce novel topologies that contribute to selective recognition of proteins. In this work, we studied a library of 24 distinct HS hexasaccharides using molecular dynamics (MD). We discovered novel compact (C) topologies that are populated significantly by a unique group of 3-O-sulfated sequences containing IdoA residues. 3-O-sulfated sequences containing glucuronic acid (GlcA) residue and sequences devoid of 3-O-sulfate groups did not exhibit high levels of the C topology and primarily exhibited only the canonical linear (L) form. The C topology arises under dynamical conditions due to rotation around an IdoA → GlcN glycosidic linkage, especially in psi (Ψ) torsion. At an atomistic level, the L → C transformation is a multi-factorial phenomenon engineered to reduce like-charge repulsion, release one or more HS-bound water molecules, and organize a bi-dentate "IdoA-cation-IdoA" interaction. These forces also drive an L → C transformation in a 3-O-sulfated octasaccharide, which has shown evidence of the unique C topology in the co-crystallized state. The 3-O-sulfate-based generation of unique, sequence-specific, compact topologies indicate that natural HS encodes a dynamic sulfation code that could be exploited for selective recognition of target proteins.
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Affiliation(s)
- Samuel G. Holmes
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Balaji Nagarajan
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Umesh R. Desai
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA
- Corresponding author at: Institute for Structural Biology, Drug Discovery, and Development, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA.
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10
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Liu J, Pedersen LC. Emerging chemical and biochemical tools for studying 3- O-sulfated heparan sulfate. Am J Physiol Cell Physiol 2022; 322:C1166-C1175. [PMID: 35417268 PMCID: PMC9169821 DOI: 10.1152/ajpcell.00110.2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/08/2022] [Accepted: 04/08/2022] [Indexed: 11/22/2022]
Abstract
Heparan sulfate is a widely expressed polysaccharide in the extracellular matrix and on the cell surface. 3-O-sulfated heparan sulfate represents only a small percentage of heparan sulfate from biological sources. However, this subpopulation is closely associated with biological functions of heparan sulfate. The 3-O-sulfated heparan sulfate is biosynthesized by heparan sulfate 3-O-sulfotransferase, which exists in seven different isoforms. This review article summarizes the recent progress in the substrate specificity studies of different 3-O-sulfotransferase isoforms involving the use of homogeneous oligosaccharide substrates and crystal structural analysis. The article also reviews a newly developed liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based method to analyze the level of 3-O-sulfated heparan sulfate with high sensitivity and quantitative capability. This newly emerged technology will provide new tools to study the structure and function relationship of heparan sulfate.
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Affiliation(s)
- Jian Liu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina
| | - Lars C Pedersen
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
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11
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Molecular dynamics simulations to understand glycosaminoglycan interactions in the free- and protein-bound states. Curr Opin Struct Biol 2022; 74:102356. [DOI: 10.1016/j.sbi.2022.102356] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/08/2022] [Accepted: 02/13/2022] [Indexed: 11/18/2022]
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12
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Nagarajan B, Desai U. Aqueous Molecular Dynamics for Understanding Glycosaminoglycan Recognition by Proteins. Methods Mol Biol 2022; 2303:49-62. [PMID: 34626369 DOI: 10.1007/978-1-0716-1398-6_5] [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] [Indexed: 06/13/2023]
Abstract
Glycosaminoglycans (GAGs) are biopolymers that exist in most organisms. GAGs are known to bind to hundreds of proteins and partake in multiple biological processes such as growth, morphogenesis, inflammation, infection, and others. Their intrinsic structural heterogeneity and conformational variability introduce major challenges in experimental studies. On the other hand, recent advances in force field development and computational technology have yielded phenomenal opportunity to study thousands of GAG sequences simultaneously to understand recognition of target protein(s). Here, we describe experimental setup for conventional molecular dynamics simulations of GAGs to position an experimental biologist favorably in performance, analysis and interpretation of stability, specificity, and conformational properties of GAGs, while also elucidating their interactions with amino acid residues of a protein at an atomistic level in presence of water.
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Affiliation(s)
- Balaji Nagarajan
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA.
| | - Umesh Desai
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA
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13
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Wander R, Kaminski AM, Wang Z, Stancanelli E, Xu Y, Pagadala V, Li J, Krahn JM, Pham TQ, Liu J, Pedersen LC. Structural and substrate specificity analysis of 3- O-sulfotransferase isoform 5 to synthesize heparan sulfate. ACS Catal 2021; 11:14956-14966. [PMID: 35223137 PMCID: PMC8865405 DOI: 10.1021/acscatal.1c04520] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Heparan sulfate 3-O-sulfotransferase (3-OST) transfers a sulfo group to the 3-OH position of a glucosamine saccharide unit to form 3-O-sulfated heparan sulfate. 3-O-sulfation is known to be critically important for bestowing anticoagulant activity and other biological functions of heparan sulfate. Here, we report two ternary crystal structures of 3-OST-5 with PAP (3'-phosphoadenosine 5'-phosphate) and two octasaccharide substrates. We also used 3-OST-5 to synthesize six 3-O-sulfated 8-mers. Results from the structural analysis of the six 3-O-sulfated 8-mers revealed the substrate specificity of 3-OST-5. The enzyme prefers to sulfate a 6-O-sulfo glucosamine saccharide that is surrounded by glucuronic acid over a 6-O-sulfo glucosamine saccharide that is surrounded by 2-O-sulfated iduronic acid. 3-OST-5 modified 8-mers display a broad range of anti-factor Xa activity, depending on the structure of the 8-mer. We also discovered that the substrate specificity of 3-OST-5 is not governed solely by the side chains from amino acid residues in the active site. The conformational flexibility of the 2-O-sulfated iduronic acid in the saccharide substrates also contributes to the substrate specificity. These findings advance our understanding for how to control the biosynthesis of 3-O-sulfated heparan sulfate with desired biological activities.
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Affiliation(s)
- Rylee Wander
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Andrea M. Kaminski
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Zhangjie Wang
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Eduardo Stancanelli
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Yongmei Xu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Jine Li
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Juno M. Krahn
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Truong Quang Pham
- Glycan Therapeutics Corp, 617 Hutton Street, Raleigh, North Carolina, USA
| | - Jian Liu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Lars C. Pedersen
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
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14
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Jaeschke SO, Lindhorst TK. Versatile Synthesis of Diaminoxylosides via Iodosulfonamidation of Xylal Derivatives. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Sven Ole Jaeschke
- Otto Diels Institute of Organic Chemistry Christiana Albertina University of Kiel Otto-Hahn-Platz 3–4 24118 Kiel Germany
| | - Thisbe K. Lindhorst
- Otto Diels Institute of Organic Chemistry Christiana Albertina University of Kiel Otto-Hahn-Platz 3–4 24118 Kiel Germany
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15
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Shanthamurthy CD, Gimeno A, Leviatan Ben-Arye S, Kumar NV, Jain P, Padler-Karavani V, Jiménez-Barbero J, Kikkeri R. Sulfation Code and Conformational Plasticity of l-Iduronic Acid Homo-Oligosaccharides Mimic the Biological Functions of Heparan Sulfate. ACS Chem Biol 2021; 16:2481-2489. [PMID: 34586794 DOI: 10.1021/acschembio.1c00582] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Recently, the activity of heparan sulfate (HS) has led to the discovery of many drug candidates that have the potential to impact both medical science and human health. However, structural diversity and synthetic challenges impede the progress of HS research. Here, we report a library of novel l-iduronic acid (IdoA)-based HS mimics that are highly tunable in conformation plasticity and sulfation patterns to produce many of the functions of native HS oligosaccharides. The NMR analysis of HS mimics confirmed that 4-O-sulfation enhances the population of the 1C4 geometry. Interestingly, the 1C4 conformer becomes exclusive upon additional 2-O-sulfation. HS mimic microarray binding studies with different growth factors showed that selectivity and avidity are greatly modulated by the oligosaccharide length, sulfation code, and IdoA conformation. Particularly, we have identified 4-O-sulfated IdoA disaccharide (I-21) as a potential ligand for vascular endothelial growth factor (VEGF165), which in a multivalent display modulated endothelial cell proliferation, migration, and angiogenesis. Overall, these results encourage the consideration of HS mimics for therapeutic applications.
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Affiliation(s)
| | - Ana Gimeno
- CIC bioGUNE, Basque Research Technology Alliance, BRTA, Bizkaia Technology park, 48160 Derio, Spain
| | - Shani Leviatan Ben-Arye
- Department of Cell Research and Immunology, The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Nanjundaswamy Vijendra Kumar
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, India
- Department of Chemistry, JSS College of Arts, Commerce & Science, Mysuru 570025, India
| | - Prashant Jain
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, India
| | - Vered Padler-Karavani
- Department of Cell Research and Immunology, The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Basque Research Technology Alliance, BRTA, Bizkaia Technology park, 48160 Derio, Spain
- Ikerbasque, Basque Foundation for Science, 48009 Bilbao, Spain
- Department Organic Chemistry II, Faculty of Science and Technology, UPV-EHU, 48940 Leioa, Spain
| | - Ragahvendra Kikkeri
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, India
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16
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Li J, Su G, Xu Y, Arnold K, Pagadala V, Wang C, Liu J. Synthesis of 3- O-Sulfated Heparan Sulfate Oligosaccharides Using 3- O-Sulfotransferase Isoform 4. ACS Chem Biol 2021; 16:2026-2035. [PMID: 34351732 DOI: 10.1021/acschembio.1c00474] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Heparan sulfate (HS) 3-O-sulfotransferase isoform 4 (3-OST-4) is a specialized carbohydrate sulfotransferase participating in the biosynthesis of heparan sulfate. Here, we report the expression and purification of the recombinant 3-OST-4 enzyme and use it for the synthesis of a library of 3-O-sulfated hexasaccharides and 3-O-sulfated octasaccharides. The unique structural feature of the library is that each oligosaccharide contains a disaccharide domain with a 2-O-sulfated glucuronic acid (GlcA2S) and 3-O-sulfated glucosamine (GlcNS3S). By rearranging the order of the enzymatic modification steps, we demonstrate the synthesis of oligosaccharides with different saccharide sequences. The structural characterization was completed by electrospray ionization mass spectrometry and NMR. These 3-O-sulfated oligosaccharides show weak to very weak anti-Factor Xa activity, a measurement of anticoagulant activity. We discovered that HSoligo 7 (HS oligosaccharide 7), a 3-O-sulfated octasaccharide, binds to high mobility group box 1 protein (HMGB1) and tau protein, both believed to be involved in the process of inflammation. Access to the recombinant 3-OST-4 expands the capability of the chemoenzymatic method to synthesize novel 3-O-sulfated oligosaccharides. The oligosaccharides will become valuable reagents to probe the biological functions of 3-O-sulfated HS and to develop HS-based therapeutic agents.
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Affiliation(s)
- Jine Li
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Guowei Su
- Glycan Therapeutics Corporation, 617 Hutton Street, Raleigh, North Carolina 27606, United States
| | - Yongmei Xu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Katelyn Arnold
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Vijayakanth Pagadala
- Glycan Therapeutics Corporation, 617 Hutton Street, Raleigh, North Carolina 27606, United States
| | - Chunyu Wang
- Department of Biological Sciences, Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, New York 12180, United States
| | - Jian Liu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
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17
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Lutsyk V, Plazinski W. Conformational Properties of Glycosaminoglycan Disaccharides: A Molecular Dynamics Study. J Phys Chem B 2021; 125:10900-10916. [PMID: 34550710 DOI: 10.1021/acs.jpcb.1c04860] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The structure and conformation of glycosaminoglycans (GAGs) are of central importance to understand the mechanisms behind their functions in biological systems. Due to the inherent chemical and structural heterogeneity of GAGs, focusing on longer, naturally existing GAG chains hinders drawing conclusions on the influence of the chemical functionalization on the basic conformational degree of freedom, that is, the dynamic shape of glycosidic linkage present in the particular disaccharide repeating unit. In the present study, we have considered the complete set of 106 GAG-related disaccharides, being potential building blocks for longer GAG chains (including hyaluronan, chondroitin, keratan, dermatan, and heparan). Both the unfunctionalized units and all possible combinations of either partially or fully sulfated derivatives contribute to this number. The unbiased and enhanced sampling molecular dynamics simulations provide a link to understand the influence of sulfation on the conformational properties of GAG glycosidic linkages. Residue-residue hydrogen bonding is not significant for either the glycosidic linkage conformation or its flexibility. It was found that in the majority of cases, the dominating conformation of the linkage is weakly affected by sulfation and the main role is played by the steric and stereoelectronic effects. However, there exist numerous cases where sulfation increases the contribution of alternative conformations to a nonnegligible extent and, in some rare cases (restricted to disaccharides building heparan), leads to the reorientation of the glycosidic linkage. The identified sulfation sites, being the most important in this context, are C6 and C3 at the GlcNAc residue. Finally, the full set of free energy maps relying on the glycosidic dihedral angle values for diverse GAG disaccharides are provided; they may be used for further studies, focused on longer GAG chains.
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Affiliation(s)
- Valery Lutsyk
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, Krakow 30-239, Poland
| | - Wojciech Plazinski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, Krakow 30-239, Poland
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18
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Gesteira TF, Marforio TD, Mueller JW, Calvaresi M, Coulson-Thomas VJ. Structural Determinants of Substrate Recognition and Catalysis by Heparan Sulfate Sulfotransferases. ACS Catal 2021; 11:10974-10987. [PMID: 37799563 PMCID: PMC10550706 DOI: 10.1021/acscatal.1c03088] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Heparan sulfate (HS) and heparin contain imprinted "sulfation codes", which dictate their diverse physiological and pathological functions. A group of orchestrated biosynthetic enzymes cooperate in polymerizing and modifying HS chains. The biotechnological development of enzymes that can recreate this sulfation pattern on synthetic heparin is challenging, primarily due to the paucity of quantitative data for sulfotransferase enzymes. Herein, we identified critical structural characteristics that determine substrate specificity and shed light on the catalytic mechanism of sugar sulfation of two HS sulfotransferases, 2-O-sulfotransferase (HS2ST) and 6-O-sulfotransferase (HS6ST). Two sets of molecular clamps in HS2ST recognize appropriate substrates; these clamps flank the acceptor binding site on opposite sides. The hexuronic epimers, and not their puckers, have a critical influence on HS2ST selectivity. In contrast, HS6ST recognizes a broader range of substrates. This promiscuity is granted by a conserved tryptophan residue, W210, that positions the acceptor within the active site for catalysis by means of strong electrostatic interactions. Lysines K131 and K132 act in concert with a second tryptophan, W153, shedding water molecules from within the active site, thus providing HS6ST with a binding preference toward 2-O-sulfated substrates. QM/MM calculations provided valuable mechanistic insights into the catalytic process, identifying that the sulfation of both HS2ST and HS6ST follows a SN2-like mechanism. When they are taken together, our findings reveal the molecular basis of how these enzymes recognize different substrates and catalyze sugar sulfation, enabling the generation of enzymes that could create specific heparin epitopes.
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Affiliation(s)
| | - Tainah Dorina Marforio
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Bologna 40126, Italy
| | - Jonathan Wolf Mueller
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham B15 2TT, U.K
| | - Matteo Calvaresi
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Bologna 40126, Italy
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19
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Kidgell JT, Carnachan SM, Magnusson M, Lawton RJ, Sims IM, Hinkley SFR, de Nys R, Glasson CRK. Are all ulvans equal? A comparative assessment of the chemical and gelling properties of ulvan from blade and filamentous Ulva. Carbohydr Polym 2021; 264:118010. [PMID: 33910714 DOI: 10.1016/j.carbpol.2021.118010] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/10/2021] [Accepted: 03/27/2021] [Indexed: 01/31/2023]
Abstract
Green seaweeds of the genus Ulva are rich in the bioactive sulfated polysaccharide ulvan. Herein we characterise ulvan from Ulva species collected from the Bay of Plenty, Aotearoa New Zealand. Using standardised procedures, we quantified, characterised, and compared ulvans from blade (U. australis, U. rigida, U. sp. B, and Ulva sp.) and filamentous (U. flexuosa, U. compressa, U. prolifera, and U. ralfsii) Ulva species. There were distinct differences in composition and structure of ulvans between morphologies. Ulvan isolated from blade species had higher yields (14.0-19.3 %) and iduronic acid content (IdoA = 7-18 mol%), and lower molecular weight (Mw = 190-254 kDa) and storage moduli (G' = 0.1-6.6 Pa) than filamentous species (yield = 7.2-14.6 %; IdoA = 4-7 mol%; Mw = 260-406 kDa; G' = 22.7-74.2 Pa). These results highlight the variability of the physicochemical properties of ulvan from different Ulva sources, and identifies a morphology-based division within the genus Ulva.
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Affiliation(s)
- Joel T Kidgell
- MACRO - The Centre for Macroalgal Resources and Biotechnology, College of Science and Engineering, James Cook University, Townsville, 4811, Australia.
| | - Susan M Carnachan
- The Ferrier Research Institute, Victoria University of Wellington, Wellington, 6012, New Zealand.
| | - Marie Magnusson
- Environmental Research Institute, School of Science, University of Waikato, Tauranga, 3110, New Zealand.
| | - Rebecca J Lawton
- Environmental Research Institute, School of Science, University of Waikato, Tauranga, 3110, New Zealand.
| | - Ian M Sims
- The Ferrier Research Institute, Victoria University of Wellington, Wellington, 6012, New Zealand.
| | - Simon F R Hinkley
- The Ferrier Research Institute, Victoria University of Wellington, Wellington, 6012, New Zealand.
| | - Rocky de Nys
- MACRO - The Centre for Macroalgal Resources and Biotechnology, College of Science and Engineering, James Cook University, Townsville, 4811, Australia.
| | - Christopher R K Glasson
- Environmental Research Institute, School of Science, University of Waikato, Tauranga, 3110, New Zealand.
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20
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Chhabra M, Doherty GG, See NW, Gandhi NS, Ferro V. From Cancer to COVID-19: A Perspective on Targeting Heparan Sulfate-Protein Interactions. CHEM REC 2021; 21:3087-3101. [PMID: 34145723 PMCID: PMC8441866 DOI: 10.1002/tcr.202100125] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/01/2021] [Indexed: 12/16/2022]
Abstract
Heparan sulfate (HS) is a complex, polyanionic polysaccharide ubiquitously expressed on cell surfaces and in the extracellular matrix. HS interacts with numerous proteins to mediate a vast array of biological and pathological processes. Inhibition of HS‐protein interactions is thus an attractive approach for new therapeutic development for cancer and infectious diseases, including COVID‐19; however, synthesis of well‐defined native HS oligosaccharides remains challenging. This has aroused significant interest in the development of HS mimetics which are more synthetically tractable and have fewer side effects, such as undesired anticoagulant activity. This account provides a perspective on the design and synthesis of different classes of HS mimetics with useful properties, and the development of various assays and molecular modelling tools to progress our understanding of their interactions with HS‐binding proteins.
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Affiliation(s)
- Mohit Chhabra
- School of Chemistry and Molecular Biosciences, The University of Queensland, 4072, Brisbane, QLD, Australia
| | - Gareth G Doherty
- School of Chemistry and Molecular Biosciences, The University of Queensland, 4072, Brisbane, QLD, Australia
| | - Nicholas W See
- School of Chemistry and Molecular Biosciences, The University of Queensland, 4072, Brisbane, QLD, Australia
| | - Neha S Gandhi
- School of Chemistry and Physics, Queensland University of Technology, 4000, Brisbane, QLD, Australia
| | - Vito Ferro
- School of Chemistry and Molecular Biosciences, The University of Queensland, 4072, Brisbane, QLD, Australia
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21
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Vo Y, Schwartz BD, Onagi H, Ward JS, Gardiner MG, Banwell MG, Nelms K, Malins LR. A Rapid and Mild Sulfation Strategy Reveals Conformational Preferences in Therapeutically Relevant Sulfated Xylooligosaccharides. Chemistry 2021; 27:9830-9838. [PMID: 33880824 DOI: 10.1002/chem.202100527] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Indexed: 01/31/2023]
Abstract
Although sulfated xylooligosaccharides are promising therapeutic leads for a multitude of afflictions, the structural complexity and heterogeneity of commercially deployed forms (e. g. Pentosan polysulfate 1) complicates their path to further clinical development. We describe herein the synthesis of the largest homogeneous persulfated xylooligomers prepared to date, comprising up to eight xylose residues, as standards for biological studies. Near quantitative sulfation was accomplished using a remarkably mild and operationally simple protocol which avoids the need for high temperatures and a large excess of the sulfating reagent. Moreover, the sulfated xylooligomer standards so obtained enabled definitive identification of a pyridinium contaminant in a sample of a commercially prepared Pentosan drug and provided significant insights into the conformational preferences of the constituent persulfated monosaccharide residues. As the spatial distribution of sulfates is a key determinant of the binding of sulfated oligosaccharides to endogenous targets, these findings have broad implications for the advancement of Pentosan-based treatments.
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Affiliation(s)
- Yen Vo
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Brett D Schwartz
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Hideki Onagi
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Jas S Ward
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Michael G Gardiner
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Martin G Banwell
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Keats Nelms
- Beta Therapeutics Pty. Ltd. Level 6, 121 Marcus Clarke Street, Canberra, ACT 2601, Australia
| | - Lara R Malins
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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22
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Balogh G, Gyöngyösi T, Timári I, Herczeg M, Borbás A, Sadiq SK, Fehér K, Kövér KE. Conformational Analysis of Heparin-Analogue Pentasaccharides by Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulations. J Chem Inf Model 2021; 61:2926-2936. [PMID: 34029080 DOI: 10.1021/acs.jcim.1c00200] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Elucidation and improvement of the blood coagulant properties of heparin are the focus of intense research. In this study, we performed conformational analysis using nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations on the heparin pentasaccharide analogue idraparinux, its disulfonatomethyl analogue, which features a slightly improved blood coagulation property, and a trisulfonatomethyl analogue, in which the activity has been totally abolished. As the ring conformation of the G subunit has been suggested as a major determinant of the biological properties, we analyzed the sugar ring conformations and dynamics of the interglycosidic linkages. We found that the conformation of the G ring is dominated by the 2SO skewed boat next to the 1C4 chair in all three derivatives. Both the thermodynamics and the kinetics of the conformational states were found to be highly similar in the three derivatives. Molecular kinetic analysis showed that the 2SO skewed boat state of the G ring is equally favorable in the three analogues, resulting in similar 2SO populations. Also, the transition kinetics from the 1C4 chair to the 2SO skewed boat was found to be comparable in the derivatives, which indicates a similar energy barrier between the two states of the G subunit. We also identified a slower conformational transition between the dominant 4C1 chair and the boat conformations on the E subunit. Both G and E ring flips are also accompanied by changes along the interglycosidic linkages, which take place highly synchronously with the ring flips. These findings indicate that conformational plasticity of the G ring and the dominance of the 2SO skewed boat populations do not necessarily warrant the biological activity of the derivatives and hence the impact of other factors also needs to be considered.
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Affiliation(s)
- Gábor Balogh
- Division of Clinical Laboratory Science, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98, H-4032 Debrecen, Hungary
| | - Tamás Gyöngyösi
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary.,MTA-DE Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - István Timári
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Mihály Herczeg
- Department of Pharmaceutical Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary.,Research Group for Oligosaccharide Chemistry of Hungarian Academy of Sciences, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Anikó Borbás
- Department of Pharmaceutical Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - S Kashif Sadiq
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Krisztina Fehér
- MTA-DE Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Katalin E Kövér
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary.,MTA-DE Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
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23
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Wang Z, Arnold K, Dhurandhare VM, Xu Y, Liu J. Investigation of the biological functions of heparan sulfate using a chemoenzymatic synthetic approach. RSC Chem Biol 2021; 2:702-712. [PMID: 34179782 PMCID: PMC8190904 DOI: 10.1039/d0cb00199f] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 02/19/2021] [Indexed: 01/31/2023] Open
Abstract
Heparan sulfate (HS) is a highly sulfated polysaccharide playing essential physiological and pathophysiological roles in the animal kingdom. Heparin, a highly sulfated form of HS, is a widely used anticoagulant drug. Isolated from biological sources, both heparin and HS are polysaccharide mixtures with different sugar chain lengths and sulfation patterns. Structural heterogeneity of HS complicates the investigation of HS-related biological activities. The availability of structurally defined HS oligosaccharides is critical in understanding the contribution of saccharide structures to the functions. The chemoenzymatic synthetic approach is emerging as a cost-effective method to synthesize HS oligosaccharides. Structurally defined oligosaccharides are now widely available for biologists. This review summarizes our efforts in using this new synthetic method to develop new anticoagulant therapeutics and discover the role of HS to protect liver damage under pathological conditions. The synthetic method also allows us to prepare reference saccharide standards to improve structural analysis of HS.
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Affiliation(s)
- Zhangjie Wang
- Division of Medicinal Chemistry and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina Chapel Hill North Carolina USA
| | - Katelyn Arnold
- Division of Medicinal Chemistry and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina Chapel Hill North Carolina USA
| | - Vijay Manohar Dhurandhare
- Division of Medicinal Chemistry and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina Chapel Hill North Carolina USA
| | - Yongmei Xu
- Division of Medicinal Chemistry and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina Chapel Hill North Carolina USA
| | - Jian Liu
- Division of Medicinal Chemistry and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina Chapel Hill North Carolina USA
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24
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Gorle AK, Haselhorst T, Katner SJ, Everest-Dass AV, Hampton JD, Peterson EJ, Koblinski JE, Katsuta E, Takabe K, von Itzstein M, Berners-Price SJ, Farrell NP. Conformational Modulation of Iduronic Acid-Containing Sulfated Glycosaminoglycans by a Polynuclear Platinum Compound and Implications for Development of Antimetastatic Platinum Drugs. Angew Chem Int Ed Engl 2021; 60:3283-3289. [PMID: 33174390 PMCID: PMC7902481 DOI: 10.1002/anie.202013749] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Indexed: 12/19/2022]
Abstract
1 H NMR spectroscopic studies on the 1:1 adduct of the pentasaccharide Fondaparinux (FPX) and the substitution-inert polynuclear platinum complex TriplatinNC show significant modulation of geometry around the glycosidic linkages of the FPX constituent monosaccharides. FPX is a valid model for the highly sulfated cell signalling molecule heparan sulfate (HS). The conformational ratio of the 1 C4 :2 S0 forms of the FPX residue IdoA(2S) is altered from ca. 35:65 (free FPX) to ca. 75:25 in the adduct; the first demonstration of a small molecule affecting conformational changes on a HS oligosaccharide. Functional consequences of such binding are suggested to be inhibition of HS cleavage in MDA-MB-231 triple-negative breast cancer (TNBC) cells. We further describe inhibition of metastasis by TriplatinNC in the TNBC 4T1 syngeneic tumour model. Our work provides insight into a novel approach for design of platinum drugs (and coordination compounds in general) with intrinsic anti-metastatic potential.
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Affiliation(s)
- Anil K. Gorle
- Institute for Glycomics, Griffith University, Gold Coast Campus, Southport, Queensland, 4222, Australia
| | - Thomas Haselhorst
- Institute for Glycomics, Griffith University, Gold Coast Campus, Southport, Queensland, 4222, Australia
| | - Samantha J. Katner
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, USA
- Department of Biochemistry, Chemistry and Geology, Minnesota State University, Mankato, Mankato, Minnesota 56001, USA
| | - Arun V. Everest-Dass
- Institute for Glycomics, Griffith University, Gold Coast Campus, Southport, Queensland, 4222, Australia
| | - James D. Hampton
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, USA
| | - Erica J. Peterson
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, USA
| | - Jennifer E. Koblinski
- Department of Pathology, Division of Cellular and Molecular Pathogenesis, Virginia Commonwealth University, Richmond, Virginia 23284-2006, USA
| | - Eriko Katsuta
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, University at Buffalo, Buffalo, New York, 14203, USA
| | - Kazuaki Takabe
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, University at Buffalo, Buffalo, New York, 14203, USA
| | - Mark von Itzstein
- Institute for Glycomics, Griffith University, Gold Coast Campus, Southport, Queensland, 4222, Australia
| | - Susan J. Berners-Price
- Institute for Glycomics, Griffith University, Gold Coast Campus, Southport, Queensland, 4222, Australia
| | - Nicholas P. Farrell
- Institute for Glycomics, Griffith University, Gold Coast Campus, Southport, Queensland, 4222, Australia
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, USA
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Gorle AK, Haselhorst T, Katner SJ, Everest‐Dass AV, Hampton JD, Peterson EJ, Koblinski JE, Katsuta E, Takabe K, Itzstein M, Berners‐Price SJ, Farrell NP. Conformational Modulation of Iduronic Acid‐Containing Sulfated Glycosaminoglycans by a Polynuclear Platinum Compound and Implications for Development of Antimetastatic Platinum Drugs. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202013749] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Anil K. Gorle
- Institute for Glycomics Griffith University Gold Coast Campus Southport Queensland 4222 Australia
| | - Thomas Haselhorst
- Institute for Glycomics Griffith University Gold Coast Campus Southport Queensland 4222 Australia
| | - Samantha J. Katner
- Department of Chemistry Virginia Commonwealth University Richmond VA 23284-2006 USA
- Department of Biochemistry, Chemistry and Geology Minnesota State University Mankato, Mankato MN 56001 USA
| | - Arun V. Everest‐Dass
- Institute for Glycomics Griffith University Gold Coast Campus Southport Queensland 4222 Australia
| | - James D. Hampton
- Department of Chemistry Virginia Commonwealth University Richmond VA 23284-2006 USA
- Massey Cancer Center Virginia Commonwealth University Richmond VA 23298-0037 USA
| | - Erica J. Peterson
- Department of Chemistry Virginia Commonwealth University Richmond VA 23284-2006 USA
- Massey Cancer Center Virginia Commonwealth University Richmond VA 23298-0037 USA
| | - Jennifer E. Koblinski
- Massey Cancer Center Virginia Commonwealth University Richmond VA 23298-0037 USA
- Department of Pathology Division of Cellular and Molecular Pathogenesis Virginia Commonwealth University Richmond VA 23284-2006 USA
| | - Eriko Katsuta
- Department of Surgical Oncology Roswell Park Comprehensive Cancer Center University at Buffalo Buffalo NY 14203 USA
| | - Kazuaki Takabe
- Department of Surgical Oncology Roswell Park Comprehensive Cancer Center University at Buffalo Buffalo NY 14203 USA
| | - Mark Itzstein
- Institute for Glycomics Griffith University Gold Coast Campus Southport Queensland 4222 Australia
| | - Susan J. Berners‐Price
- Institute for Glycomics Griffith University Gold Coast Campus Southport Queensland 4222 Australia
| | - Nicholas P. Farrell
- Institute for Glycomics Griffith University Gold Coast Campus Southport Queensland 4222 Australia
- Department of Chemistry Virginia Commonwealth University Richmond VA 23284-2006 USA
- Massey Cancer Center Virginia Commonwealth University Richmond VA 23298-0037 USA
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26
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Denardo A, Elli S, Federici S, Asperti M, Gryzik M, Ruzzenenti P, Carmona F, Bergese P, Naggi A, Arosio P, Poli M. BMP6 binding to heparin and heparan sulfate is mediated by N-terminal and C-terminal clustered basic residues. Biochim Biophys Acta Gen Subj 2020; 1865:129799. [PMID: 33232799 DOI: 10.1016/j.bbagen.2020.129799] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/16/2020] [Accepted: 11/18/2020] [Indexed: 12/31/2022]
Abstract
BACKGROUND The bone morphogenetic protein 6 (BMP6) is a crucial inducer of hepcidin, the peptide hormone that regulates the iron availability in our body. Hepcidin expression is influenced by hepatic heparan sulfate (HS) and by heparin administration, suggesting BMP6 interaction with heparin/HS. The BMP2/4 subfamily has been deeply characterized to have a N-terminal heparin/HS binding domain (HBD), whose basic residues contact the sulfate groups on heparin and HS. Such detailed characterization is still required for other, structurally different BMPs, including BMP6. METHODS BMP6 peptides encompassing potential HBDs were analysed on heparin-functionalized plates and microcantilevers, and on membrane HS expressing CHO-K1 cells. Monomeric wild-type BMP6 and mutants were produced, substituting the basic residues with non-charged ones, and their affinity to the heparin-column was measured. The BMP6-heparin interaction was also predicted at atomic level by in silico molecular dynamics. RESULTS N-terminal and C-terminal BMP6 peptides showed high heparin affinity in solid-phase assays. The mutation of the two sites (R5L, R6S, R7L and K126N, K127N, R129S) abolished the heparin-binding activity of the recombinant monomeric BMP6. Monomeric BMP6 and peptides specifically bound to membrane HS of CHO-K1 cells through the same domains. Molecular dynamic studies supported the role of the two HBDs, suggesting a cooperative behaviour. CONCLUSIONS In BMP6, N-terminal (R5, R6, R7) and C-terminal (K126, K127, R129) domains mediate the interaction with heparin and HS. GENERAL SIGNIFICANCE This study provides the molecular mechanism supporting the use of heparin to sequester BMP6 and inhibit hepcidin expression, a novel clinical approach for high-hepcidin iron disorders.
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Affiliation(s)
- Andrea Denardo
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Stefano Elli
- G. Ronzoni Institute for Chemical and Biochemical Research, Via Giuseppe Colombo 81, 20133 Milan, Italy
| | - Stefania Federici
- Department of Mechanical and Industrial Engineering and INSTM, University of Brescia, Via Branze 38, 25123 Brescia, Italy
| | - Michela Asperti
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Magdalena Gryzik
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Paola Ruzzenenti
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Fernando Carmona
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Paolo Bergese
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Annamaria Naggi
- G. Ronzoni Institute for Chemical and Biochemical Research, Via Giuseppe Colombo 81, 20133 Milan, Italy
| | - Paolo Arosio
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Maura Poli
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy.
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27
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Whitmore EK, Martin D, Guvench O. Constructing 3-Dimensional Atomic-Resolution Models of Nonsulfated Glycosaminoglycans with Arbitrary Lengths Using Conformations from Molecular Dynamics. Int J Mol Sci 2020; 21:ijms21207699. [PMID: 33080973 PMCID: PMC7589010 DOI: 10.3390/ijms21207699] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/15/2020] [Accepted: 10/15/2020] [Indexed: 12/24/2022] Open
Abstract
Glycosaminoglycans (GAGs) are the linear carbohydrate components of proteoglycans (PGs) and are key mediators in the bioactivity of PGs in animal tissue. GAGs are heterogeneous, conformationally complex, and polydisperse, containing up to 200 monosaccharide units. These complexities make studying GAG conformation a challenge for existing experimental and computational methods. We previously described an algorithm we developed that applies conformational parameters (i.e., all bond lengths, bond angles, and dihedral angles) from molecular dynamics (MD) simulations of nonsulfated chondroitin GAG 20-mers to construct 3-D atomic-resolution models of nonsulfated chondroitin GAGs of arbitrary length. In the current study, we applied our algorithm to other GAGs, including hyaluronan and nonsulfated forms of dermatan, keratan, and heparan and expanded our database of MD-generated GAG conformations. Here, we show that individual glycosidic linkages and monosaccharide rings in 10- and 20-mers of hyaluronan and nonsulfated dermatan, keratan, and heparan behave randomly and independently in MD simulation and, therefore, using a database of MD-generated 20-mer conformations, that our algorithm can construct conformational ensembles of 10- and 20-mers of various GAG types that accurately represent the backbone flexibility seen in MD simulations. Furthermore, our algorithm efficiently constructs conformational ensembles of GAG 200-mers that we would reasonably expect from MD simulations.
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Affiliation(s)
- Elizabeth K. Whitmore
- Department of Pharmaceutical Sciences and Administration, University of New England School of Pharmacy, 716 Stevens Avenue, Portland, ME 04103, USA; (E.K.W.); (D.M.)
- Graduate School of Biomedical Science and Engineering, University of Maine, 5775 Stodder Hall, Orono, ME 04469, USA
| | - Devon Martin
- Department of Pharmaceutical Sciences and Administration, University of New England School of Pharmacy, 716 Stevens Avenue, Portland, ME 04103, USA; (E.K.W.); (D.M.)
- Graduate School of Biomedical Science and Engineering, University of Maine, 5775 Stodder Hall, Orono, ME 04469, USA
| | - Olgun Guvench
- Department of Pharmaceutical Sciences and Administration, University of New England School of Pharmacy, 716 Stevens Avenue, Portland, ME 04103, USA; (E.K.W.); (D.M.)
- Graduate School of Biomedical Science and Engineering, University of Maine, 5775 Stodder Hall, Orono, ME 04469, USA
- Correspondence: ; Tel.: +1-207-221-4171
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28
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Dong C, Choi YK, Lee J, Zhang XF, Honerkamp-Smith A, Widmalm G, Lowe-Krentz LJ, Im W. Structure, Dynamics, and Interactions of GPI-Anchored Human Glypican-1 with Heparan Sulfates in a Membrane. Glycobiology 2020; 31:593-602. [PMID: 33021626 DOI: 10.1093/glycob/cwaa092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/24/2020] [Accepted: 09/24/2020] [Indexed: 12/12/2022] Open
Abstract
Glypican-1 and its heparan sulfate (HS) chains play important roles in modulating many biological processes including growth factor signaling. Glypican-1 is bound to a membrane surface via a glycosylphosphatidylinositol (GPI)-anchor. In this study, we used all-atom molecular modeling and simulation to explore the structure, dynamics, and interactions of GPI-anchored glypican-1, three HS chains, membranes, and ions. The folded glypican-1 core structure is stable, but has substantial degrees of freedom in terms of movement and orientation with respect to the membrane due to the long unstructured C-terminal region linking the core to the GPI-anchor. With unique structural features depending on the extent of sulfation, high flexibility of HS chains can promote multi-site interactions with surrounding molecules near and above the membrane. This study is a first step toward all-atom molecular modeling and simulation of the glycocalyx, as well as its modulation of interactions between growth factors and their receptors.
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Affiliation(s)
- Chuqiao Dong
- Department of Mechanical Engineering and Mechanicss, Lehigh University, Bethlehem, PA, 18015, United States
| | - Yeol Kyo Choi
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, 18015, United States
| | - Jumin Lee
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, 18015, United States
| | - X Frank Zhang
- Department of Mechanical Engineering and Mechanicss, Lehigh University, Bethlehem, PA, 18015, United States.,Department of Bioengineering, Lehigh University, Bethlehem, PA, 18015, United States
| | | | - Göran Widmalm
- Department of Organic Chemistry, Stockholm University, S-106 91 Stockholm, Sweden
| | - Linda J Lowe-Krentz
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, 18015, United States
| | - Wonpil Im
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, 18015, United States.,Department of Bioengineering, Lehigh University, Bethlehem, PA, 18015, United States.,Department of Chemistry, Lehigh University, Bethlehem, PA, 18015, United States
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29
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The conformation of the idopyranose ring revisited: How subtle O-substituent induced changes can be deduced from vicinal 1H-NMR coupling constants. Carbohydr Res 2020; 496:108052. [PMID: 32738719 DOI: 10.1016/j.carres.2020.108052] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/17/2020] [Accepted: 05/27/2020] [Indexed: 01/18/2023]
Abstract
The idopyranose ring plays a pivotal role in the conformational, dynamical, and intermolecular binding aspects of glycosaminoglycans like heparin and dermatan sulfate and it was early on assigned a role in the Sugar Code governing biological recognition processes. There is consensus that next to the two canonical 1C4 and 4C1 chair conformations, the conformational space accessible to the idopyranose ring entails a 2SO skew-boat conformation, but the equilibrium between these three ring puckers has evaded satisfactory quantification. In this study a meta-analysis of X-ray solid-state data and vicinal NMR coupling constants is presented, based on the Truncated Fourier Puckering (TFP) formalism and the generalized Karplus (CAGPLUS) equation. This approach yields a model-free, granular and consistent reckoning of 159 idopyranose solution puckering equilibria studied by NMR and allows us to reproduce the involved 636 NMR vicinal couplings with an overall residual RMS(Jobs-Jcalc) of 0.184 Hz. Our analyses show that for all ring systems examined, the idopyranosyl chair conformations take up the same ring pucker irrespective of the ring substituent pattern or a vast variety in experimental conditions. Instead, it is the (skew-)boat conformation that adapts to the substitution pattern of the idopyranose ring or a specific sulfation pattern of neighboring saccharides. All idopyranose rings are involved in conformational equilibria that subsume the aforementioned conformers which turn out to differ only a few kJ/mole in conformational energy. Thus, the plasticity and flexibility of idopyranose remains intact under practically all circumstances and, as the glycosidic linkages in heparin are considered to be relatively stiff, the iduronic moiety functions as the linchpin of heparin flexibility thereby being rather a "space(r)" than a "letter" in the alleged Sugar Code alphabet.
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30
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Nagarajan B, Sankaranarayanan NV, Desai UR. Rigorous analysis of free solution glycosaminoglycan dynamics using simple, new tools. Glycobiology 2020; 30:516-527. [PMID: 32080710 PMCID: PMC8179626 DOI: 10.1093/glycob/cwaa015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 02/03/2020] [Accepted: 02/09/2020] [Indexed: 11/15/2022] Open
Abstract
Heparin/heparan sulfates (H/HS) are ubiquitous biopolymers that interact with many proteins to induce a range of biological functions. Unfortunately, how these biopolymers recognize their preferred protein targets remain poorly understood. It is suggested that computational simulations offer attractive avenues but a number of challenges, e.g., difficulty of selecting a comprehensive force field, few simple tools to interpret data, among others, remain. This work addresses several such challenges so as to help ease the implementation and analysis of computational experiments. First, this work presents a rigorous comparison of two different recent force fields, CHARMM36 and GLYCAM06, for H/HS studies. Second, it introduces two new straightforward parameters, i.e., end-to-end distance and minimum volume enclosing ellipsoid, to understand the myriad conformational forms of oligosaccharides that evolve over time in water. Third, it presents an application to elucidate the number and nature of inter and intramolecular, nondirect bridging water molecules, which help stabilize unique forms of H/HS. The results show that nonspecialists can use either CHARMM36 or GLYCAM06 force fields because both gave comparable results, albeit with small differences. The comparative study shows that the HS hexasaccharide samples a range of conformations with nearly equivalent energies, which could be the reason for its recognition by different proteins. Finally, analysis of the nondirect water bridges across the dynamics trajectory shows their importance in stabilization of certain conformational forms, which may become important for protein recognition. Overall, the work aids nonspecialists employ computational studies for understanding the solution behavior of H/HS.
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Affiliation(s)
- Balaji Nagarajan
- Institute for Structural Biology, Drug Discovery and Development, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA
- Department of Medicinal Chemistry, 800 E. Leigh Street, Suite 205, Richmond, VA 23298, USA
| | - Nehru Viji Sankaranarayanan
- Institute for Structural Biology, Drug Discovery and Development, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA
- Department of Medicinal Chemistry, 800 E. Leigh Street, Suite 205, Richmond, VA 23298, USA
| | - Umesh R Desai
- Institute for Structural Biology, Drug Discovery and Development, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA
- Department of Medicinal Chemistry, 800 E. Leigh Street, Suite 205, Richmond, VA 23298, USA
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31
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Nguyen TH, Xu Y, Brandt S, Mandelkow M, Raschke R, Strobel U, Delcea M, Zhou W, Liu J, Greinacher A. Characterization of the interaction between platelet factor 4 and homogeneous synthetic low molecular weight heparins. J Thromb Haemost 2020; 18:390-398. [PMID: 31573759 PMCID: PMC7236814 DOI: 10.1111/jth.14657] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 09/25/2019] [Indexed: 01/03/2023]
Abstract
BACKGROUND Heparins are usually produced from animal tissues. It is now possible to synthesize heparins. This provides the abilities to overcome shortages of heparin, to optimize biological effects, and to reduce adverse drug effects. Heparins interact with platelet factor 4 (PF4), which can induce an immune response causing thrombocytopenia. This side effect is called heparin-induced thrombocytopenia (HIT). We characterized the interaction of PF4 and HIT antibodies with oligosaccharides of 6-, 8-, 10-, and 12-mer size and a hypersulfated 12-mer (S12-mer). METHODS We utilized multiple methodologies including isothermal calorimetry, circular dichroism spectroscopy, single molecule force spectroscopy (SMFS), enzyme immunosorbent assay (EIA), and platelet aggregation test to characterize the interaction of synthetic heparin analogs with PF4 and anti-PF4/heparin antibodies. RESULTS The synthetic heparin-like compounds display stronger binding characteristics to PF4 than animal-derived heparins of corresponding lengths. Upon complexation with PF4, 6-mer and S12-mer heparins showed much lower enthalpy, induced less conformational changes in PF4, and interacted with weaker forces than 8-, 10-, and 12-mer heparins. Anti-PF4/heparin antibodies bind more weakly to complexes formed between PF4 and heparins ≤ 8-mer than with complexes formed between PF4 and heparins ≥ 10-mer. Addition of one sulfate group to the 12-mer resulted in a S12-mer, which showed substantial changes in its binding characteristics to PF4. CONCLUSIONS We provide a template for characterizing interactions of newly developed heparin-based anticoagulant drugs with proteins, especially PF4 and the resulting potential antigenicity.
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Affiliation(s)
- Thi-Huong Nguyen
- institut für Immunologie und Transfusionsmedizin, Universitätsmedizin Greifswald, Greifswald, Germany
- Institute for Bioprocessing and Analytical Measurement Techniques, Heiligenstadt, Germany
- ZIK HIKE—Center for Innovation Competence, Humoral Immune Reactions in Cardiovascular Diseases, University Greifswald, Greifswald, Germany
| | - Yongmei Xu
- Division of Chemical Biology and Medicinal Chemistry, School of Pharmacy, University of North Carolina, Eshelman, Chapel Hill, NC, USA
| | - Sven Brandt
- ZIK HIKE—Center for Innovation Competence, Humoral Immune Reactions in Cardiovascular Diseases, University Greifswald, Greifswald, Germany
| | - Martin Mandelkow
- ZIK HIKE—Center for Innovation Competence, Humoral Immune Reactions in Cardiovascular Diseases, University Greifswald, Greifswald, Germany
| | - Ricarda Raschke
- institut für Immunologie und Transfusionsmedizin, Universitätsmedizin Greifswald, Greifswald, Germany
| | - Ulrike Strobel
- institut für Immunologie und Transfusionsmedizin, Universitätsmedizin Greifswald, Greifswald, Germany
| | - Mihaela Delcea
- ZIK HIKE—Center for Innovation Competence, Humoral Immune Reactions in Cardiovascular Diseases, University Greifswald, Greifswald, Germany
- Division of Chemical Biology and Medicinal Chemistry, School of Pharmacy, University of North Carolina, Eshelman, Chapel Hill, NC, USA
| | - Wen Zhou
- Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Jian Liu
- Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Andreas Greinacher
- institut für Immunologie und Transfusionsmedizin, Universitätsmedizin Greifswald, Greifswald, Germany
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32
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Zhang C, Tang F, Zhang J, Cao J, Li H, Liu C. Uncovering the detailed mode of cleavage of heparinase I toward structurally defined heparin oligosaccharides. Int J Biol Macromol 2019; 141:756-764. [PMID: 31479666 DOI: 10.1016/j.ijbiomac.2019.08.260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/30/2019] [Accepted: 08/30/2019] [Indexed: 10/26/2022]
Abstract
For a more insightful investigation into the specificity of bacterial heparinase I, a series of structurally well-defined heparin oligosaccharides was synthesized using a highly efficient chemoenzymatic strategy. Apart from the primary cleavage site, five glycosidic linkages of oligosaccharides with varying modifications to obtain secondary cleavage sites were degraded by a high concentration of heparinase I. The reactivity of linkages toward heparinase I was not entirely dependent on the 2-O-sulfated iduronic acid being cleaved or the neighboring 6-O-sulfated glucosamine residues, but it was dependent on higher degrees of sulfation of oligosaccharides and indispensable N-substituted glucosamine adjacent to the cleavable linkage. Moreover, the enzyme demonstrated less preferential cleavage toward glycosidic linkages containing glucuronic acid than those containing iduronic acid of the counterpart oligosaccharides. Biolayer interferometry revealed differences in reactivity that are not completely consistent with different affinities of substrates to enzyme. Our study presented accurate information on the cleavage promiscuity of heparinase I that is crucial for heparin depolymerization.
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Affiliation(s)
- Chengying Zhang
- Key Laboratory of Chemical Biology (Ministry of Education), Institute of Biochemical and Biotechnological Drugs, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, Shandong, PR China
| | - Fengyan Tang
- Key Laboratory of Chemical Biology (Ministry of Education), Institute of Biochemical and Biotechnological Drugs, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, Shandong, PR China
| | - Jingjing Zhang
- Key Laboratory of Chemical Biology (Ministry of Education), Institute of Biochemical and Biotechnological Drugs, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, Shandong, PR China
| | - Jichao Cao
- Key Laboratory of Chemical Biology (Ministry of Education), Institute of Biochemical and Biotechnological Drugs, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, Shandong, PR China
| | - Huijuan Li
- Department of Bioengineering, College of Chemical and Environmental Engineering, Shandong University of Science and Technology, Qingdao 266590, Shandong, PR China
| | - Chunhui Liu
- Key Laboratory of Chemical Biology (Ministry of Education), Institute of Biochemical and Biotechnological Drugs, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, Shandong, PR China; National Glycoengineering Research Center, Shandong University, Jinan 250012, Shandong, PR China.
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33
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Alibay I, Bryce RA. Ring Puckering Landscapes of Glycosaminoglycan-Related Monosaccharides from Molecular Dynamics Simulations. J Chem Inf Model 2019; 59:4729-4741. [PMID: 31609614 DOI: 10.1021/acs.jcim.9b00529] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The conformational flexibility of the glycosaminoglycans (GAGs) is known to be key in their binding and biological function, for example in regulating coagulation and cell growth. In this work, we employ enhanced sampling molecular dynamics simulations to probe the ring conformations of GAG-related monosaccharides, including a range of acetylated and sulfated GAG residues. We first perform unbiased MD simulations of glucose anomers and the epimers glucuronate and iduronate. These calculations indicate that in some cases, an excess of 15 μs is required for adequate sampling of ring pucker due to the high energy barriers between states. However, by applying our recently developed msesMD simulation method (multidimensional swarm-enhanced sampling molecular dynamics), we were able to quantitatively and rapidly reproduce these ring pucker landscapes. From msesMD simulations, the puckering free energy profiles were then compared for 15 further monosaccharides related to GAGs; this includes to our knowledge the first simulation study of sulfation effects on β-GalNAc ring puckering. For the force field employed, we find that in general the calculated pucker free energy profiles for sulfated sugars were similar to the corresponding unsulfated profiles. This accords with recent experimental studies suggesting that variation in ring pucker of sulfated GAG residues is primarily dictated by interactions with surrounding residues rather than by intrinsic conformational preference. As an exception to this, however, we predict that 4-O-sulfation of β-GalNAc leads to reduced ring rigidity, with a significant lowering in energy of the 1C4 ring conformation; this observation may have implications for understanding the structural basis of the biological function of β-GalNAc-containing glycosaminoglycans such as dermatan sulfate.
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Affiliation(s)
- Irfan Alibay
- Division of Pharmacy and Optometry, School of Health Sciences , University of Manchester , Oxford Road , Manchester M13 9PT , U.K.,Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K
| | - Richard A Bryce
- Division of Pharmacy and Optometry, School of Health Sciences , University of Manchester , Oxford Road , Manchester M13 9PT , U.K
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34
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Balogh G, Gyöngyösi T, Timári I, Herczeg M, Borbás A, Fehér K, Kövér KE. Comparison of Carbohydrate Force Fields Using Gaussian Accelerated Molecular Dynamics Simulations and Development of Force Field Parameters for Heparin-Analogue Pentasaccharides. J Chem Inf Model 2019; 59:4855-4867. [DOI: 10.1021/acs.jcim.9b00666] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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35
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Pandey P, Aytenfisu AH, MacKerell AD, Mallajosyula SS. Drude Polarizable Force Field Parametrization of Carboxylate and N-Acetyl Amine Carbohydrate Derivatives. J Chem Theory Comput 2019; 15:4982-5000. [PMID: 31411469 PMCID: PMC6852669 DOI: 10.1021/acs.jctc.9b00327] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In this work, we report the development of Drude polarizable force field parameters for the carboxylate and N-acetyl amine derivatives, extending the functionality of the existing Drude polarizable carbohydrate force field. The force field parameters have been developed in a hierarchical manner, reproducing the quantum mechanical gas-phase properties of small model compounds representing the key functional group in the carbohydrate derivatives, including optimization of the electrostatic and bonded parameters. The optimized parameters were then used to generate the models for carboxylate and N-acetyl amine carbohydrate derivatives. The transferred parameters were further tested and optimized to reproduce crystal geometries and J-coupling data from nuclear magnetic resonance experiments. The parameter development resulted in the incorporation of d-glucuronate, l-iduronate, N-acetyl-d-glucosamine (GlcNAc), and N-acetyl-d-galactosamine (GalNAc) sugars into the Drude polarizable force field. The parameters developed in this study were then applied to study the conformational properties of glycosaminoglycan polymer hyaluronan, composed of d-glucuronate and N-acetyl-d-glucosamine, in aqueous solution. Upon comparing the results from the additive and polarizable simulations, it was found that the inclusion of polarization improved the description of the electrostatic interactions observed in hyaluronan, resulting in enhanced conformational flexibility. The developed Drude polarizable force field parameters in conjunction with the remainder of the Drude polarizable force field parameters can be used for future studies involving carbohydrates and their conjugates in complex, heterogeneous systems.
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Affiliation(s)
| | - Asaminew H Aytenfisu
- Department of Pharmaceutical Sciences , University of Maryland School of Pharmacy , 20 Penn Street , Baltimore , Maryland 21201 , United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences , University of Maryland School of Pharmacy , 20 Penn Street , Baltimore , Maryland 21201 , United States
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36
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Gerbst AG, Krylov VB, Nifantiev NE. Conformational changes in common monosaccharides caused by per-O-sulfation. PURE APPL CHEM 2019. [DOI: 10.1515/pac-2018-1212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Abstract
Polysulfated carbohydrates play an important role in many biological processes because of their ability to bind to various protein receptors such as different growth factors, blood coagulation factors, adhesion lectins etc. Precise information about spatial organization of sulfated derivatives is of high demand for molecular modelling of such interactions as well as for understanding of the mechanism of pyranoside-into-furanoside rearrangement. In this review we summarize the changes recently revealed for the conformations of common pyranosides and furanosides upon total O-sulfation which were studied by means of NMR spectroscopy as well as molecular modelling. It was found that pentoses, being more flexible, undergo complete conformational chair inversion. Meanwhile, for hexoses the situation strongly depends on the monosaccharide configuration. Conformational changes are most pronounced in gluco-compounds though quantum chemical calculations helped to establish that no complete chair inversion occurred. In furanosides distortions of two types were observed: either the ring conformation or the conformation of the side chain changed. The presented data may be used for the analysis of chemical, physical and biological properties of sulfated carbohydrates.
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Affiliation(s)
- Alexey G. Gerbst
- Laboratory of Glycoconjugate Chemistry , N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences , Leninsky Prospect 47 , 119991 Moscow , Russia
| | - Vadim B. Krylov
- Laboratory of Glycoconjugate Chemistry , N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences , Leninsky Prospect 47 , 119991 Moscow , Russia
| | - Nikolay E. Nifantiev
- Laboratory of Glycoconjugate Chemistry , N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences , Leninsky Prospect 47 , 119991 Moscow , Russia
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37
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Affiliation(s)
| | - Raghavendra Kikkeri
- Indian Institute of Science Education and Research; Dr. Homi Bhabha Road 411008 Pune India
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38
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Nagarajan B, Sankaranarayanan NV, Desai UR. Perspective on computational simulations of glycosaminoglycans. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2019; 9:e1388. [PMID: 31080520 PMCID: PMC6504973 DOI: 10.1002/wcms.1388] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/07/2018] [Indexed: 01/06/2023]
Abstract
Glycosaminoglycans (GAGs) represent a formidable frontier for chemists, biochemists, biologists, medicinal chemists and drug delivery specialists because of massive structural complexity. GAGs are arguably the most complex, natural linear biopolymers with theoretical diversity orders of magnitude higher than proteins and nucleic acids. Yet, this diversity remains generally untapped. Computational approaches offer major routes to understand GAG structure and dynamics so as to enable novel applications of these biopolymers. In fact, computational algorithms, softwares, online tools and techniques have reached a level of sophistication that help understand atomistic details of conformational variation and protein recognition of individual GAG sequences. This review describes current approaches and challenges in computational study of GAGs. It presents a history of major findings since the earliest mention of GAGs (the 1960s), the development of parameters and force fields specific for GAGs, and the application of these tools in understanding GAG structure-function relationship. This review also presents a section on how to perform simulation of GAGs, which is directed toward researchers interested in entering this promising field with potential to impact therapy.
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Affiliation(s)
- Balaji Nagarajan
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond,
VA 23298, USA
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Nehru Viji Sankaranarayanan
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond,
VA 23298, USA
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Umesh R. Desai
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond,
VA 23298, USA
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
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39
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Demeter F, Gyöngyösi T, Bereczky Z, Kövér KE, Herczeg M, Borbás A. Replacement of the L-iduronic acid unit of the anticoagulant pentasaccharide idraparinux by a 6-deoxy-L-talopyranose - Synthesis and conformational analysis. Sci Rep 2018; 8:13736. [PMID: 30213971 PMCID: PMC6137110 DOI: 10.1038/s41598-018-31854-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 08/23/2018] [Indexed: 01/05/2023] Open
Abstract
One critical part of the synthesis of heparinoid anticoagulants is the creation of the L-iduronic acid building block featured with unique conformational plasticity which is crucial for the anticoagulant activity. Herein, we studied whether a much more easily synthesizable sugar, the 6-deoxy-L-talose, built in a heparinoid oligosaccharide, could show a similar conformational plasticity, thereby can be a potential substituent of the L-idose. Three pentasaccharides related to the synthetic anticoagulant pentasaccharide idraparinux were prepared, in which the L-iduronate was replaced by a 6-deoxy-L-talopyranoside unit. The talo-configured building block was formed by C4 epimerisation of the commercially available L-rhamnose with high efficacy at both the monosaccharide and the disaccharide level. The detailed conformational analysis of these new derivatives, differing only in their methylation pattern, was performed and the conformationally relevant NMR parameters, such as proton-proton coupling constants and interproton distances were compared to the corresponding ones measured in idraparinux. The lack of anticoagulant activity of these novel heparin analogues could be explained by the biologically not favorable 1C4 chair conformation of their 6-deoxy-L-talopyranoside residues.
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Affiliation(s)
- Fruzsina Demeter
- Department of Pharmaceutical Chemistry, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary
| | - Tamás Gyöngyösi
- Department of Inorganic and Analytical Chemistry, University of Debrecen, P.O. Box 400, Debrecen, 4002, Hungary
| | - Zsuzsanna Bereczky
- Division of Clinical Laboratory Sciences, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 98 Nagyerdei krt., Debrecen, 4032, Hungary
| | - Katalin E Kövér
- Department of Inorganic and Analytical Chemistry, University of Debrecen, P.O. Box 400, Debrecen, 4002, Hungary.
| | - Mihály Herczeg
- Department of Pharmaceutical Chemistry, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary.
| | - Anikó Borbás
- Department of Pharmaceutical Chemistry, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary.
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40
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Abstract
Complex carbohydrates are ubiquitous in nature, and together with proteins and nucleic acids they comprise the building blocks of life. But unlike proteins and nucleic acids, carbohydrates form nonlinear polymers, and they are not characterized by robust secondary or tertiary structures but rather by distributions of well-defined conformational states. Their molecular flexibility means that oligosaccharides are often refractory to crystallization, and nuclear magnetic resonance (NMR) spectroscopy augmented by molecular dynamics (MD) simulation is the leading method for their characterization in solution. The biological importance of carbohydrate-protein interactions, in organismal development as well as in disease, places urgency on the creation of innovative experimental and theoretical methods that can predict the specificity of such interactions and quantify their strengths. Additionally, the emerging realization that protein glycosylation impacts protein function and immunogenicity places the ability to define the mechanisms by which glycosylation impacts these features at the forefront of carbohydrate modeling. This review will discuss the relevant theoretical approaches to studying the three-dimensional structures of this fascinating class of molecules and interactions, with reference to the relevant experimental data and techniques that are key for validation of the theoretical predictions.
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Affiliation(s)
- Robert J Woods
- Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology , University of Georgia , 315 Riverbend Road , Athens , Georgia 30602 , United States
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41
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Thieker DF, Xu Y, Chapla D, Nora C, Qiu H, Felix T, Wang L, Moremen KW, Liu J, Esko JD, Woods RJ. Downstream Products are Potent Inhibitors of the Heparan Sulfate 2-O-Sulfotransferase. Sci Rep 2018; 8:11832. [PMID: 30087361 PMCID: PMC6081452 DOI: 10.1038/s41598-018-29602-4] [Citation(s) in RCA: 9] [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: 05/03/2018] [Accepted: 07/09/2018] [Indexed: 12/31/2022] Open
Abstract
Heparan Sulfate (HS) is a cell signaling molecule linked to pathological processes ranging from cancer to viral entry, yet fundamental aspects of its biosynthesis remain incompletely understood. Here, the binding preferences of the uronyl 2-O-sulfotransferase (HS2ST) are examined with variably-sulfated hexasaccharides. Surprisingly, heavily sulfated oligosaccharides formed by later-acting sulfotransferases bind more tightly to HS2ST than those corresponding to its natural substrate or product. Inhibition assays also indicate that the IC50 values correlate simply with degree of oligosaccharide sulfation. Structural analysis predicts a mode of inhibition in which 6-O-sulfate groups located on glucosamine residues present in highly-sulfated oligosaccharides occupy the canonical binding site of the nucleotide cofactor. The unexpected finding that oligosaccharides associated with later stages in HS biosynthesis inhibit HS2ST indicates that the enzyme must be separated temporally and/or spatially from downstream products during biosynthesis in vivo, and highlights a challenge for the enzymatic synthesis of lengthy HS chains in vitro.
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Affiliation(s)
- David F Thieker
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Yongmei Xu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Rm 1044, Genetic Medicine Building, Chapel Hill, USA
| | - Digantkumar Chapla
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Chelsea Nora
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Hong Qiu
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Thomas Felix
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Lianchun Wang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Kelley W Moremen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Jian Liu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Rm 1044, Genetic Medicine Building, Chapel Hill, USA
| | - Jeffrey D Esko
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Robert J Woods
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA.
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA.
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Stopschinski BE, Holmes BB, Miller GM, Manon VA, Vaquer-Alicea J, Prueitt WL, Hsieh-Wilson LC, Diamond MI. Specific glycosaminoglycan chain length and sulfation patterns are required for cell uptake of tau versus α-synuclein and β-amyloid aggregates. J Biol Chem 2018; 293:10826-10840. [PMID: 29752409 DOI: 10.1074/jbc.ra117.000378] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 05/07/2018] [Indexed: 12/21/2022] Open
Abstract
Transcellular propagation of protein aggregate "seeds" has been proposed to mediate the progression of neurodegenerative diseases in tauopathies and α-synucleinopathies. We previously reported that tau and α-synuclein aggregates bind heparan sulfate proteoglycans (HSPGs) on the cell surface, promoting cellular uptake and intracellular seeding. However, the specificity and binding mode of these protein aggregates to HSPGs remain unknown. Here, we measured direct interaction with modified heparins to determine the size and sulfation requirements for tau, α-synuclein, and β-amyloid (Aβ) aggregate binding to glycosaminoglycans (GAGs). Varying the GAG length and sulfation patterns, we next conducted competition studies with heparin derivatives in cell-based assays. Tau aggregates required a precise GAG architecture with defined sulfate moieties in the N- and 6-O-positions, whereas the binding of α-synuclein and Aβ aggregates was less stringent. To determine the genes required for aggregate uptake, we used CRISPR/Cas9 to individually knock out the major genes of the HSPG synthesis pathway in HEK293T cells. Knockouts of the extension enzymes exostosin 1 (EXT1), exostosin 2 (EXT2), and exostosin-like 3 (EXTL3), as well as N-sulfotransferase (NDST1) or 6-O-sulfotransferase (HS6ST2) significantly reduced tau uptake, consistent with our biochemical findings, and knockouts of EXT1, EXT2, EXTL3, or NDST1, but not HS6ST2 reduced α-synuclein uptake. In summary, tau aggregates display specific interactions with HSPGs that depend on GAG length and sulfate moiety position, whereas α-synuclein and Aβ aggregates exhibit more flexible interactions with HSPGs. These principles may inform the development of mechanism-based therapies to block transcellular propagation of amyloid protein-based pathologies.
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Affiliation(s)
- Barbara E Stopschinski
- From the Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, Texas 75390.,the Department of Neurology, RWTH University Aachen, D-52074 Aachen, Germany
| | - Brandon B Holmes
- From the Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, Texas 75390.,the Medical Scientist Training Program, Washington University School of Medicine, St. Louis, Missouri 63110, and
| | - Gregory M Miller
- the Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Victor A Manon
- From the Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Jaime Vaquer-Alicea
- From the Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - William L Prueitt
- From the Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Linda C Hsieh-Wilson
- the Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125
| | - Marc I Diamond
- From the Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, Texas 75390,
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43
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Xu D, Arnold K, Liu J. Using structurally defined oligosaccharides to understand the interactions between proteins and heparan sulfate. Curr Opin Struct Biol 2018; 50:155-161. [PMID: 29684759 DOI: 10.1016/j.sbi.2018.04.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 04/09/2018] [Accepted: 04/09/2018] [Indexed: 01/02/2023]
Abstract
Heparan sulfate (HS) is widely present on the animal cell surface and in the extracellular matrix. HS achieves its biological functions by interacting with proteins to change proteins' conformation, oligomerization state and cellular location. The challenging question to study HS is how to dissect the relationship between the structures of HS and the biological activities. In the past several years, crucial techniques have been developed to overcome this challenge. A novel chemoenzymatic method to synthesize structurally defined HS oligosaccharides has offered a key access to this class of sulfated carbohydrate molecules. Recent rapid progress of HS microarray technology allows screening of the interaction of a target protein with a large number of HS oligosaccharides. The improved availability of HS oligosaccharides and HS microarray analysis will undoubtedly accelerate the investigation of the contribution of the specific sulfated carbohydrate structures of HS in a wide range of biological contexts.
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Affiliation(s)
- Ding Xu
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, SUNY, Buffalo, NY 14214, USA.
| | - Katelyn Arnold
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jian Liu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA.
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44
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Gao Q, Yang JY, Moremen KW, Flanagan JG, Prestegard JH. Structural Characterization of a Heparan Sulfate Pentamer Interacting with LAR-Ig1-2. Biochemistry 2018; 57:2189-2199. [PMID: 29570275 DOI: 10.1021/acs.biochem.8b00241] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Leukocyte common antigen-related (LAR) protein is one of the type IIa receptor protein tyrosine phosphatases (RPTPs) that are important for signal transduction in biological processes, including axon growth and regeneration. Glycosaminoglycan chains, including heparan sulfate (HS) and chondroitin sulfate (CS), act as ligands that regulate LAR signaling. Here, we report the structural characterization of the first two immunoglobulin domains (Ig1-2) of LAR interacting with an HS pentasaccharide (GlcNS6S-GlcA-GlcNS3,6S-IdoA2S-GlcNS6S-OME, fondaparinux) using multiple solution-based NMR methods. In the course of the study, we extended an assignment strategy useful for sparsely labeled proteins expressed in mammalian cell culture supplemented with a single type of isotopically enriched amino acid ([15N]-Lys in this case) by including paramagnetic perturbations to NMR resonances. The folded two-domain structure for LAR-Ig1-2 seen in previous crystal structures has been validated in solution using residual dipolar coupling data, and a combination of chemical shift perturbation on titration of LAR-Ig1-2 with fondaparinux, saturation transfer difference (STD) spectra, and transferred nuclear Overhauser effects (trNOEs) have been employed in the docking program HADDOCK to generate models for the LAR-fondaparinux complex. These models are further analyzed by postprocessing energetic analysis to identify key binding interactions. In addition to providing insight into the ligand interaction mechanisms of type IIa RPTPs and the origin of opposing effects of CS and HS ligands, these results may assist in future design of therapeutic compounds for nervous system repair.
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Affiliation(s)
- Qi Gao
- Complex Carbohydrate Research Center , University of Georgia , Athens , Georgia 30602 , United States
| | - Jeong-Yeh Yang
- Complex Carbohydrate Research Center , University of Georgia , Athens , Georgia 30602 , United States
| | - Kelley W Moremen
- Complex Carbohydrate Research Center , University of Georgia , Athens , Georgia 30602 , United States
| | - John G Flanagan
- Department of Cell Biology and Program in Neuroscience , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - James H Prestegard
- Complex Carbohydrate Research Center , University of Georgia , Athens , Georgia 30602 , United States
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45
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Stancanelli E, Elli S, Hsieh PH, Liu J, Guerrini M. Recognition and Conformational Properties of an Alternative Antithrombin Binding Sequence Obtained by Chemoenzymatic Synthesis. Chembiochem 2018; 19:10.1002/cbic.201800095. [PMID: 29573524 PMCID: PMC6517080 DOI: 10.1002/cbic.201800095] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Indexed: 12/24/2022]
Abstract
Heparin is a highly sulfated glycosaminoglycan (GAG) of natural origin used as an anticoagulant and antithrombotic drug. These properties are principally based on the binding and activation of antithrombin (AT) through the pentasaccharide sequence GlcNAc/NS,6S-GlcA-GlcNS,3,6S-IdoA2S-GlcNS,6S (AGA*IA). Literature data show that the population of the 2 S0 ring conformation of the 2-O-sulfo-α-l-iduronic acid (IdoA2S) motif correlates with the affinity and activation of AT. It was recently demonstrated that two synthetic AGA*IA-containing hexasaccharides (one G unit added at the reducing end), differing in the degree of sulfation of the IdoA unit, show comparable affinity and ability to activate AT, despite a different conformation of the IdoA residue. In this paper, the binding of these two glycans to AT was studied by isothermal titration microcalorimetry (ITC), transferred (tr-) NOESY, saturation transfer difference (STD) NMR spectroscopy and molecular dynamics (MD) simulations. Results indicated that both the IdoA2S and the IdoA units assume a 2 S0 conformation when bound with AT, and so present a common binding epitope for the two glycans, centred on the AGA*IA sequence.
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Affiliation(s)
- Eduardo Stancanelli
- Department NMR and Carbohydrates, Istituto di Ricerche Chimiche e Biochimiche "G. Ronzoni", via G. Colombo 81, 20133, Milan, Italy
| | - Stefano Elli
- Department NMR and Carbohydrates, Istituto di Ricerche Chimiche e Biochimiche "G. Ronzoni", via G. Colombo 81, 20133, Milan, Italy
| | - Po-Hung Hsieh
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jian Liu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Marco Guerrini
- Department NMR and Carbohydrates, Istituto di Ricerche Chimiche e Biochimiche "G. Ronzoni", via G. Colombo 81, 20133, Milan, Italy
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Hu G, Shao M, Gao X, Wang F, Liu C. Probing cleavage promiscuity of heparinase III towards chemoenzymatically synthetic heparan sulfate oligosaccharides. Carbohydr Polym 2017; 173:276-285. [DOI: 10.1016/j.carbpol.2017.05.071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/10/2017] [Accepted: 05/23/2017] [Indexed: 01/07/2023]
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47
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Zhang X, Pagadala V, Jester HM, Lim AM, Pham TQ, Goulas AMP, Liu J, Linhardt RJ. Chemoenzymatic synthesis of heparan sulfate and heparin oligosaccharides and NMR analysis: paving the way to a diverse library for glycobiologists. Chem Sci 2017; 8:7932-7940. [PMID: 29568440 PMCID: PMC5849142 DOI: 10.1039/c7sc03541a] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 09/20/2017] [Indexed: 12/14/2022] Open
Abstract
A library of diverse heparan sulfate (HS) oligosaccharides was chemoenzymatically synthesized and systematically studied using NMR.
Heparan sulfate (HS) is a member of the glycosaminoglycans (GAG) family that plays essential roles in biological processes from animal sources. Heparin, a highly sulfated form of HS, is widely used as anticoagulant drug worldwide. The high diversity and complexity of HS and heparin represent a roadblock for structural characterization and biological activity studies. Access to structurally defined oligosaccharides is critical for the successful development of HS and heparin structure–activity relationships. In this study, a library of 66 HS and heparin oligosaccharides covering different sulfation patterns and sizes was prepared through an efficient method of chemoenzymatic synthesis. A systematic nuclear magnetic resonance spectroscopy study was firstly undertaken for every oligosaccharide in the library. In addition to the availability of different oligosaccharides, this work also provides spectroscopic data helpful for characterizing more complicated polysaccharide structures providing a safeguard to ensure the quality of the drug heparin. This HS/heparin library will be useful for activity screening and facilitate future structure–activity relationship studies.
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Affiliation(s)
- Xing Zhang
- Department of Chemistry and Chemical Biology , Rensselaer Polytechnic Institute , Troy , New York 12180 , USA .
| | | | - Hannah M Jester
- Glycan Therapeutics , LLC , Chapel Hill , North Carolina 27599 , USA
| | - Andrew M Lim
- Glycan Therapeutics , LLC , Chapel Hill , North Carolina 27599 , USA
| | - Truong Quang Pham
- Division of Chemical Biology and Medicinal Chemistry , Eshelman School of Pharmacy , University of North Carolina , Chapel Hill , North Carolina 27599 , USA .
| | | | - Jian Liu
- Division of Chemical Biology and Medicinal Chemistry , Eshelman School of Pharmacy , University of North Carolina , Chapel Hill , North Carolina 27599 , USA .
| | - Robert J Linhardt
- Department of Chemistry and Chemical Biology , Rensselaer Polytechnic Institute , Troy , New York 12180 , USA .
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48
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Wang Z, Hsieh PH, Xu Y, Thieker D, Chai EJE, Xie S, Cooley B, Woods RJ, Chi L, Liu J. Synthesis of 3-O-Sulfated Oligosaccharides to Understand the Relationship between Structures and Functions of Heparan Sulfate. J Am Chem Soc 2017; 139:5249-5256. [PMID: 28340300 PMCID: PMC5624809 DOI: 10.1021/jacs.7b01923] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The sulfation at the 3-OH position of glucosamine is an important modification in forming structural domains for heparan sulfate to enable its biological functions. Seven 3-O-sulfotransferase isoforms in the human genome are involved in the biosynthesis of 3-O-sulfated heparan sulfate. As a rare modification present in heparan sulfate, the availability of 3-O-sulfated oligosaccharides is very limited. Here, we report the use of a chemoenzymatic synthetic approach to synthesize six 3-O-sulfated oligosaccharides, including three hexasaccharides and three octasaccharides. The synthesis was achieved by rearranging the enzymatic modification sequence to accommodate the substrate specificity of 3-O-sulfotransferase 3. We studied the impact of 3-O-sulfation on the conformation of the pyranose ring of 2-O-sulfated iduronic acid using NMR, and on the correlation between ring conformation and anticoagulant activity. We identified a novel octasaccharide that interacts with antithrombin and displays anti factor Xa activity. Interestingly, the octasaccharide displays a faster clearance rate than fondaparinux, an FDA-approved pentasaccharide drug, in a rat model, making this octasaccharide a potential short-acting anticoagulant drug candidate that could reduce bleeding risk. Having access to a set of critically important 3-O-sulfated oligosaccharides offers the potential to develop new heparan sulfate-based therapeutics.
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Affiliation(s)
- Zhangjie Wang
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina , Chapel Hill, North Carolina 27599, United States
- National Glycoengineering Research Center, Shandong University , Jinan 250100, China
| | - Po-Hung Hsieh
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina , Chapel Hill, North Carolina 27599, United States
| | - Yongmei Xu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina , Chapel Hill, North Carolina 27599, United States
| | - David Thieker
- Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
| | - Evangeline Juan En Chai
- School of Pharmacy, University College London , 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Shaoshuai Xie
- National Glycoengineering Research Center, Shandong University , Jinan 250100, China
| | - Brian Cooley
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina , Chapel Hill, North Carolina 27599, United States
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
| | - Lianli Chi
- National Glycoengineering Research Center, Shandong University , Jinan 250100, China
| | - Jian Liu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina , Chapel Hill, North Carolina 27599, United States
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49
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Huang TY, Irene D, Zulueta MML, Tai TJ, Lain SH, Cheng CP, Tsai PX, Lin SY, Chen ZG, Ku CC, Hsiao CD, Chyan CL, Hung SC. Structure of the Complex between a Heparan Sulfate Octasaccharide and Mycobacterial Heparin-Binding Hemagglutinin. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201612518] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Teng-Yi Huang
- Genomics Research Center; Academia Sinica; No. 128, Section 2, Academia Road Taipei 115 Taiwan
| | - Deli Irene
- Department of Chemistry; National Dong Hwa University; No. 1, Section 2, Da Hsueh Road, Shoufeng Hualien 974 Taiwan
| | - Medel Manuel L. Zulueta
- Genomics Research Center; Academia Sinica; No. 128, Section 2, Academia Road Taipei 115 Taiwan
| | - Tzu-Jui Tai
- Department of Chemistry; National Dong Hwa University; No. 1, Section 2, Da Hsueh Road, Shoufeng Hualien 974 Taiwan
| | - Shih-Han Lain
- Department of Chemistry; National Dong Hwa University; No. 1, Section 2, Da Hsueh Road, Shoufeng Hualien 974 Taiwan
| | - Cheng-Po Cheng
- Genomics Research Center; Academia Sinica; No. 128, Section 2, Academia Road Taipei 115 Taiwan
| | - Ping-Xi Tsai
- Genomics Research Center; Academia Sinica; No. 128, Section 2, Academia Road Taipei 115 Taiwan
| | - Shu-Yi Lin
- Genomics Research Center; Academia Sinica; No. 128, Section 2, Academia Road Taipei 115 Taiwan
| | - Zhi-Geng Chen
- Genomics Research Center; Academia Sinica; No. 128, Section 2, Academia Road Taipei 115 Taiwan
| | - Chiao-Chu Ku
- Institute of Molecular Biology; Academia Sinica; No. 128, Section 2, Academia Road Taipei 115 Taiwan
| | - Chwan-Deng Hsiao
- Institute of Molecular Biology; Academia Sinica; No. 128, Section 2, Academia Road Taipei 115 Taiwan
| | - Chia-Lin Chyan
- Department of Chemistry; National Dong Hwa University; No. 1, Section 2, Da Hsueh Road, Shoufeng Hualien 974 Taiwan
| | - Shang-Cheng Hung
- Genomics Research Center; Academia Sinica; No. 128, Section 2, Academia Road Taipei 115 Taiwan
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Huang TY, Irene D, Zulueta MML, Tai TJ, Lain SH, Cheng CP, Tsai PX, Lin SY, Chen ZG, Ku CC, Hsiao CD, Chyan CL, Hung SC. Structure of the Complex between a Heparan Sulfate Octasaccharide and Mycobacterial Heparin-Binding Hemagglutinin. Angew Chem Int Ed Engl 2017; 56:4192-4196. [PMID: 28294485 DOI: 10.1002/anie.201612518] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Revised: 02/11/2016] [Indexed: 11/06/2022]
Abstract
Heparin-binding hemagglutinin (HBHA) is a 199 amino acid virulence factor at the envelope of Mycobacterium tuberculosis that contributes to latent tuberculosis. The binding of HBHA to respiratory epithelial cells, which leads to extrapulmonary dissemination of the pathogen, is mediated by cell-surface heparan sulfate (HS). We report the structural characterization of the HBHA/HS complex by NMR spectroscopy. To develop a model for the molecular recognition, the first chemically synthesized uniformly 13 C- and 15 N-labeled HS octasaccharide and a uniformly 13 C- and 15 N-labeled form of HBHA were prepared. Residues 180-195 at the C-terminal region of HBHA show large chemical shift perturbation upon association with the octasaccharide. Molecular dynamics simulations conforming to the multidimensional NMR data revealed key electrostatic and even hydrophobic interactions between the binding partners that may aid in the development of agents targeting the binding event.
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Affiliation(s)
- Teng-Yi Huang
- Genomics Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan
| | - Deli Irene
- Department of Chemistry, National Dong Hwa University, No. 1, Section 2, Da Hsueh Road, Shoufeng, Hualien, 974, Taiwan
| | - Medel Manuel L Zulueta
- Genomics Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan
| | - Tzu-Jui Tai
- Department of Chemistry, National Dong Hwa University, No. 1, Section 2, Da Hsueh Road, Shoufeng, Hualien, 974, Taiwan
| | - Shih-Han Lain
- Department of Chemistry, National Dong Hwa University, No. 1, Section 2, Da Hsueh Road, Shoufeng, Hualien, 974, Taiwan
| | - Cheng-Po Cheng
- Genomics Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan
| | - Ping-Xi Tsai
- Genomics Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan
| | - Shu-Yi Lin
- Genomics Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan
| | - Zhi-Geng Chen
- Genomics Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan
| | - Chiao-Chu Ku
- Institute of Molecular Biology, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan
| | - Chwan-Deng Hsiao
- Institute of Molecular Biology, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan
| | - Chia-Lin Chyan
- Department of Chemistry, National Dong Hwa University, No. 1, Section 2, Da Hsueh Road, Shoufeng, Hualien, 974, Taiwan
| | - Shang-Cheng Hung
- Genomics Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan
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