1
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Painter C, Sankaranarayanan NV, Nagarajan B, Mandel Clausen T, West AM, Setiawan NJ, Park J, Porell RN, Bartels PL, Sandoval DR, Vasquez GJ, Chute JP, Godula K, Vander Kooi CW, Gordts PL, Corbett KD, Termini CM, Desai UR, Esko JD. Alteration of Neuropilin-1 and Heparan Sulfate Interaction Impairs Murine B16 Tumor Growth. ACS Chem Biol 2024; 19:1820-1835. [PMID: 39099090 PMCID: PMC11334110 DOI: 10.1021/acschembio.4c00389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/18/2024] [Accepted: 07/22/2024] [Indexed: 08/06/2024]
Abstract
Neuropilin-1 acts as a coreceptor with vascular endothelial growth factor receptors to facilitate binding of its ligand, vascular endothelial growth factor. Neuropilin-1 also binds to heparan sulfate, but the functional significance of this interaction has not been established. A combinatorial library screening using heparin oligosaccharides followed by molecular dynamics simulations of a heparin tetradecasaccharide suggested a highly conserved binding site composed of amino acid residues extending across the b1 and b2 domains of murine neuropilin-1. Mutagenesis studies established the importance of arginine513 and lysine514 for binding of heparin to a recombinant form of Nrp1 composed of the a1, a2, b1, and b2 domains. Recombinant Nrp1 protein bearing R513A,K514A mutations showed a significant loss of heparin-binding, heparin-induced dimerization, and heparin-dependent thermal stabilization. Isothermal calorimetry experiments suggested a 1:2 complex of heparin tetradecasaccharide:Nrp1. To study the impact of altered heparin binding in vivo, a mutant allele of Nrp1 bearing the R513A,K514A mutations was created in mice (Nrp1D) and crossbred to Nrp1+/- mice to examine the impact of altered heparan sulfate binding. Analysis of tumor formation showed variable effects on tumor growth in Nrp1D/D mice, resulting in a frank reduction in tumor growth in Nrp1D/- mice. Expression of mutant Nrp1D protein was normal in tissues, suggesting that the reduction in tumor growth was due to the altered binding of heparin/heparan sulfate to neuropilin-1. These findings suggest that the interaction of neuropilin-1 with heparan sulfate modulates its stability and its role in tumor formation and growth.
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Affiliation(s)
- Chelsea
D. Painter
- Department
of Cellular and Molecular Medicine, University
of California, San Diego, La Jolla, California 92093, United States
- Glycobiology
Research and Training Center, University
of California, San Diego, La Jolla, California 92093, United States
| | - Nehru Viji Sankaranarayanan
- Department
of Medicinal Chemistry, Virginia Commonwealth
University, Richmond, Virginia 23298, United States
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Balaji Nagarajan
- Department
of Medicinal Chemistry, Virginia Commonwealth
University, Richmond, Virginia 23298, United States
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Thomas Mandel Clausen
- Department
of Cellular and Molecular Medicine, University
of California, San Diego, La Jolla, California 92093, United States
- Glycobiology
Research and Training Center, University
of California, San Diego, La Jolla, California 92093, United States
| | - Alan M.V. West
- Department
of Cellular and Molecular Medicine, University
of California, San Diego, La Jolla, California 92093, United States
| | - Nicollette J. Setiawan
- Translational
Science and Therapeutics Division, Fred
Hutchinson Cancer Center, Seattle, Washington 98109, United States
| | - Jeeyoung Park
- Department
of Cellular and Molecular Medicine, University
of California, San Diego, La Jolla, California 92093, United States
| | - Ryan N. Porell
- Glycobiology
Research and Training Center, University
of California, San Diego, La Jolla, California 92093, United States
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - Phillip L. Bartels
- Glycobiology
Research and Training Center, University
of California, San Diego, La Jolla, California 92093, United States
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - Daniel R. Sandoval
- Department
of Cellular and Molecular Medicine, University
of California, San Diego, La Jolla, California 92093, United States
- Glycobiology
Research and Training Center, University
of California, San Diego, La Jolla, California 92093, United States
| | - Gabriel J. Vasquez
- Department
of Cellular and Molecular Medicine, University
of California, San Diego, La Jolla, California 92093, United States
| | - John P. Chute
- Samuel
Oschin Cancer Center, Cedars Sinai Medical
Center, Los Angeles, California 90048, United States
- Division
of Hematology & Cellular Therapy, Cedars
Sinai Medical Center, Los Angeles, California 90048, United States
- Regenerative
Medicine Institute, Cedars Sinai Medical
Center, Los Angeles, California 90048, United States
| | - Kamil Godula
- Glycobiology
Research and Training Center, University
of California, San Diego, La Jolla, California 92093, United States
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - Craig W. Vander Kooi
- Department
of Biochemistry and Molecular Biology, University
of Florida, Gainesville, Florida 32610, United
States
| | - Philip L.S.M. Gordts
- Glycobiology
Research and Training Center, University
of California, San Diego, La Jolla, California 92093, United States
- Department
of Medicine, University of California, San
Diego, La Jolla, California 92093, United States
| | - Kevin D. Corbett
- Department
of Cellular and Molecular Medicine, University
of California, San Diego, La Jolla, California 92093, United States
- Department
of Molecular Biology, University of California,
San Diego, La Jolla, California 92093, United States
| | - Christina M. Termini
- Translational
Science and Therapeutics Division, Fred
Hutchinson Cancer Center, Seattle, Washington 98109, United States
| | - Umesh R. Desai
- Department
of Medicinal Chemistry, Virginia Commonwealth
University, Richmond, Virginia 23298, United States
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Jeffrey D. Esko
- Department
of Cellular and Molecular Medicine, University
of California, San Diego, La Jolla, California 92093, United States
- Glycobiology
Research and Training Center, University
of California, San Diego, La Jolla, California 92093, United States
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2
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Shivgan AT, Marzinek JK, Krah A, Matsudaira P, Verma CS, Bond PJ. Coarse-Grained Model of Glycosaminoglycans for Biomolecular Simulations. J Chem Theory Comput 2024; 20:3308-3321. [PMID: 38358378 DOI: 10.1021/acs.jctc.3c01088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Proteoglycans contain glycosaminoglycans (GAGs) which are negatively charged linear polymers made of repeating disaccharide units of uronic acid and hexosamine units. They play vital roles in numerous physiological and pathological processes, particularly in governing cellular communication and attachment. Depending on their sulfonation state, acetylation, and glycosidic linkages, GAGs belong to different families. The high molecular weight, heterogeneity, and flexibility of GAGs hamper their characterization at atomic resolution, but this may be circumvented via coarse-grained (CG) approaches. In this work, we report a CG model for a library of common GAG types in their isolated or proteoglycan-linked states compatible with version 2.2 (v2.2) of the widely popular CG Martini force field. The model reproduces conformational and thermodynamic properties for a wide variety of GAGs, as well as matching structural and binding data for selected proteoglycan test systems. The parameters developed here may thus be employed to study a range of GAG-containing biomolecular systems, thereby benefiting from the efficiency and broad applicability of the Martini framework.
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Affiliation(s)
- Aishwary T Shivgan
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543, Singapore
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Jan K Marzinek
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Alexander Krah
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Paul Matsudaira
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543, Singapore
| | - Chandra S Verma
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543, Singapore
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
- School of Biological sciences, Nanyang Technological University, 50 Nanyang Drive, Singapore 637551, Singapore
| | - Peter J Bond
- National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, Singapore 117543, Singapore
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
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3
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Holmes SG, Desai UR. Assessing Genetic Algorithm-Based Docking Protocols for Prediction of Heparin Oligosaccharide Binding Geometries onto Proteins. Biomolecules 2023; 13:1633. [PMID: 38002315 PMCID: PMC10669598 DOI: 10.3390/biom13111633] [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: 10/12/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Although molecular docking has evolved dramatically over the years, its application to glycosaminoglycans (GAGs) has remained challenging because of their intrinsic flexibility, highly anionic character and rather ill-defined site of binding on proteins. GAGs have been treated as either fully "rigid" or fully "flexible" in molecular docking. We reasoned that an intermediate semi-rigid docking (SRD) protocol may be better for the recapitulation of native heparin/heparan sulfate (Hp/HS) topologies. Herein, we study 18 Hp/HS-protein co-complexes containing chains from disaccharide to decasaccharide using genetic algorithm-based docking with rigid, semi-rigid, and flexible docking protocols. Our work reveals that rigid and semi-rigid protocols recapitulate native poses for longer chains (5→10 mers) significantly better than the flexible protocol, while 2→4-mer poses are better predicted using the semi-rigid approach. More importantly, the semi-rigid docking protocol is likely to perform better when no crystal structure information is available. We also present a new parameter for parsing selective versus non-selective GAG-protein systems, which relies on two computational parameters including consistency of binding (i.e., RMSD) and docking score (i.e., GOLD Score). The new semi-rigid protocol in combination with the new computational parameter is expected to be particularly useful in high-throughput screening of GAG sequences for identifying promising druggable targets as well as drug-like Hp/HS sequences.
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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, 800 E. Leigh Street, Suite 212, 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, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA
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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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5
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Kogut MM, Danielsson A, Ricard-Blum S, Samsonov SA. Impact of calcium ions on the structural and dynamic properties of heparin oligosaccharides by computational analysis. Comput Biol Chem 2022; 99:107727. [PMID: 35841830 DOI: 10.1016/j.compbiolchem.2022.107727] [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: 05/12/2022] [Revised: 06/24/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022]
Abstract
Heparin (HP) belongs to glycosaminoglycans (GAGs), anionic linear polysaccharides composed of repetitive disaccharide units. They are key players in many biological processes occurring in the extracellular matrix and at the cell surface. GAGs are challenging molecules for computational research due to their high chemical heterogeneity, flexibility, periodicity, pseudosymmetry, predominantly electrostatics-driven nature of interactions with their protein partners and potential multipose binding. The molecular mechanisms underlying GAG interactions mediated by divalent ions, which are important for GAG binding to several proteins, are not well understood. The goal of this study was to characterize the binding of Ca2+ to two HP oligosaccharides of different lengths (dp10 and dp18, dp: degree of polymerization) and their impact on HP conformational space and their dynamic behavior with the use of molecular dynamics (MD)-based approaches with two Ca2+ parameter sets. MD data suggested that the flexibility of the monosaccharides, the glycosidic linkages and ring puckering were not affected by the presence of Ca2+, in contrast to H-bond propensities and the calculated Rg for a fraction of the oligosaccharide populations in both dp10 and dp18. Moreover, the essential differences in the data obtained by using two Ca2+ parameter sets were reported.
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Affiliation(s)
- Małgorzata M Kogut
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Annemarie Danielsson
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Sylvie Ricard-Blum
- Univ Lyon, University Claude Bernard Lyon 1, CNRS, Institute of Molecular and Supramolecular Chemistry and Biochemistry, UMR 5246, Villeurbanne CEDEX F-69622, France
| | - Sergey A Samsonov
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, Gdańsk 80-308, Poland.
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6
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Abstract
Glycoscience assembles all the scientific disciplines involved in studying various molecules and macromolecules containing carbohydrates and complex glycans. Such an ensemble involves one of the most extensive sets of molecules in quantity and occurrence since they occur in all microorganisms and higher organisms. Once the compositions and sequences of these molecules are established, the determination of their three-dimensional structural and dynamical features is a step toward understanding the molecular basis underlying their properties and functions. The range of the relevant computational methods capable of addressing such issues is anchored by the specificity of stereoelectronic effects from quantum chemistry to mesoscale modeling throughout molecular dynamics and mechanics and coarse-grained and docking calculations. The Review leads the reader through the detailed presentations of the applications of computational modeling. The illustrations cover carbohydrate-carbohydrate interactions, glycolipids, and N- and O-linked glycans, emphasizing their role in SARS-CoV-2. The presentation continues with the structure of polysaccharides in solution and solid-state and lipopolysaccharides in membranes. The full range of protein-carbohydrate interactions is presented, as exemplified by carbohydrate-active enzymes, transporters, lectins, antibodies, and glycosaminoglycan binding proteins. A final section features a list of 150 tools and databases to help address the many issues of structural glycobioinformatics.
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Affiliation(s)
- Serge Perez
- Centre de Recherche sur les Macromolecules Vegetales, University of Grenoble-Alpes, Centre National de la Recherche Scientifique, Grenoble F-38041, France
| | - Olga Makshakova
- FRC Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, Kazan 420111, Russia
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7
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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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8
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Molecular dynamics simulation: A new way to understand the functionality of the endothelial glycocalyx. Curr Opin Struct Biol 2022; 73:102330. [DOI: 10.1016/j.sbi.2022.102330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/02/2021] [Accepted: 12/30/2021] [Indexed: 11/22/2022]
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9
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Wang X, Bie L, Gao J. Structural Insights into the Cofactor Role of Heparin/Heparan Sulfate in Binding between the SARS-CoV-2 Spike Protein and Host Angiotensin-Converting Enzyme II. J Chem Inf Model 2022; 62:656-667. [PMID: 35060381 PMCID: PMC8791032 DOI: 10.1021/acs.jcim.1c01484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Indexed: 02/07/2023]
Abstract
The viral entry process of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires heparin and heparan sulfates from the cell surface, functioning as a cofactor for human angiotensin-converting enzyme 2 (ACE2) for recognizing the receptor-binding domain (RBD) of the spike (S) protein on the surface of the virion. In the present study, the binding poses of an oligosaccharide with four repeating units of GlcNS6S-IdoA2S (octa) predicted by Vina-Carb in the RBD binding site were employed in molecular dynamics (MD) simulations to provide atomic details for studying the cofactor mechanism. The molecular model in the MD simulations reproduced the length- and sequence-dependent behavior observed from the microarray experiments and revealed an important planar U-turn shape for HP/HS binding to RBD. The model for octa with this shape in the ACE2-RBD complex enhanced the interactions in the binding interface. The comparisons with the ACE2-RBD complex suggested that the presence of octa in the RBD binding site blocked the movements in a loop region at the distal end of the RBD binding interface and promoted the contacts of this loop region with the ACE2 N-terminus helix. This study shed light on the atomic and dynamic details for HP/HS interacting with RBD and provided insights into their cofactor role in the ACE2-RBD interactions.
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Affiliation(s)
- Xiaocong Wang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics,
Huazhong Agricultural University, Wuhan 430070, Hubei,
China
| | - Lihua Bie
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics,
Huazhong Agricultural University, Wuhan 430070, Hubei,
China
| | - Jun Gao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics,
Huazhong Agricultural University, Wuhan 430070, Hubei,
China
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10
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Yamazaki M, Yabe M, Iijima K. Analysis of the formation mechanism of polyion complexes of polysaccharides by molecular dynamics simulation with oligosaccharides. Polym J 2022. [DOI: 10.1038/s41428-021-00602-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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11
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In-Depth Molecular Dynamics Study of All Possible Chondroitin Sulfate Disaccharides Reveals Key Insight into Structural Heterogeneity and Dynamism. Biomolecules 2022; 12:biom12010077. [PMID: 35053225 PMCID: PMC8773825 DOI: 10.3390/biom12010077] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/23/2021] [Accepted: 12/29/2021] [Indexed: 12/18/2022] Open
Abstract
GAGs exhibit a high level of conformational and configurational diversity, which remains untapped in terms of the recognition and modulation of proteins. Although GAGs are suggested to bind to more than 800 biologically important proteins, very few therapeutics have been designed or discovered so far. A key challenge is the inability to identify, understand and predict distinct topologies accessed by GAGs, which may help design novel protein-binding GAG sequences. Recent studies on chondroitin sulfate (CS), a key member of the GAG family, pinpointing its role in multiple biological functions led us to study the conformational dynamism of CS building blocks using molecular dynamics (MD). In the present study, we used the all-atom GLYCAM06 force field for the first time to explore the conformational space of all possible CS building blocks. Each of the 16 disaccharides was solvated in a TIP3P water box with an appropriate number of counter ions followed by equilibration and a production run. We analyzed the MD trajectories for torsional space, inter- and intra-molecular H-bonding, bridging water, conformational spread and energy landscapes. An in-house phi and psi probability density analysis showed that 1→3-linked sequences were more flexible than 1→4-linked sequences. More specifically, phi and psi regions for 1→4-linked sequences were held within a narrower range because of intra-molecular H-bonding between the GalNAc O5 atom and GlcA O3 atom, irrespective of sulfation pattern. In contrast, no such intra-molecular interaction arose for 1→3-linked sequences. Further, the stability of 1→4-linked sequences also arose from inter-molecular interactions involving bridged water molecules. The energy landscape for both classes of CS disaccharides demonstrated increased ruggedness as the level of sulfation increased. The results show that CS building blocks present distinct conformational dynamism that offers the high possibility of unique electrostatic surfaces for protein recognition. The fundamental results presented here will support the development of algorithms that help to design longer CS chains for protein recognition.
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12
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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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13
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A Bittersweet Computational Journey among Glycosaminoglycans. Biomolecules 2021; 11:biom11050739. [PMID: 34063530 PMCID: PMC8156566 DOI: 10.3390/biom11050739] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/10/2021] [Accepted: 05/12/2021] [Indexed: 01/22/2023] Open
Abstract
Glycosaminoglycans (GAGs) are linear polysaccharides. In proteoglycans (PGs), they are attached to a core protein. GAGs and PGs can be found as free molecules, associated with the extracellular matrix or expressed on the cell membrane. They play a role in the regulation of a wide array of physiological and pathological processes by binding to different proteins, thus modulating their structure and function, and their concentration and availability in the microenvironment. Unfortunately, the enormous structural diversity of GAGs/PGs has hampered the development of dedicated analytical technologies and experimental models. Similarly, computational approaches (in particular, molecular modeling, docking and dynamics simulations) have not been fully exploited in glycobiology, despite their potential to demystify the complexity of GAGs/PGs at a structural and functional level. Here, we review the state-of-the art of computational approaches to studying GAGs/PGs with the aim of pointing out the “bitter” and “sweet” aspects of this field of research. Furthermore, we attempt to bridge the gap between bioinformatics and glycobiology, which have so far been kept apart by conceptual and technical differences. For this purpose, we provide computational scientists and glycobiologists with the fundamentals of these two fields of research, with the aim of creating opportunities for their combined exploitation, and thereby contributing to a substantial improvement in scientific knowledge.
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14
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Souza PR, de Oliveira AC, Vilsinski BH, Kipper MJ, Martins AF. Polysaccharide-Based Materials Created by Physical Processes: From Preparation to Biomedical Applications. Pharmaceutics 2021; 13:621. [PMID: 33925380 PMCID: PMC8146878 DOI: 10.3390/pharmaceutics13050621] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 02/07/2023] Open
Abstract
Polysaccharide-based materials created by physical processes have received considerable attention for biomedical applications. These structures are often made by associating charged polyelectrolytes in aqueous solutions, avoiding toxic chemistries (crosslinking agents). We review the principal polysaccharides (glycosaminoglycans, marine polysaccharides, and derivatives) containing ionizable groups in their structures and cellulose (neutral polysaccharide). Physical materials with high stability in aqueous media can be developed depending on the selected strategy. We review strategies, including coacervation, ionotropic gelation, electrospinning, layer-by-layer coating, gelation of polymer blends, solvent evaporation, and freezing-thawing methods, that create polysaccharide-based assemblies via in situ (one-step) methods for biomedical applications. We focus on materials used for growth factor (GFs) delivery, scaffolds, antimicrobial coatings, and wound dressings.
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Affiliation(s)
- Paulo R. Souza
- Group of Polymeric Materials and Composites, Department of Chemistry, State University of Maringá (UEM), Maringá 87020-900, PR, Brazil; (P.R.S.); (A.C.d.O.); (B.H.V.)
| | - Ariel C. de Oliveira
- Group of Polymeric Materials and Composites, Department of Chemistry, State University of Maringá (UEM), Maringá 87020-900, PR, Brazil; (P.R.S.); (A.C.d.O.); (B.H.V.)
- Laboratory of Materials, Macromolecules and Composites, Federal University of Technology—Paraná (UTFPR), Apucarana 86812-460, PR, Brazil
| | - Bruno H. Vilsinski
- Group of Polymeric Materials and Composites, Department of Chemistry, State University of Maringá (UEM), Maringá 87020-900, PR, Brazil; (P.R.S.); (A.C.d.O.); (B.H.V.)
| | - Matt J. Kipper
- Department of Chemical and Biological Engineering, Colorado State University (CSU), Fort Collins, CO 80523, USA
- School of Advanced Materials Discovery, Colorado State University (CSU), Fort Collins, CO 80523, USA
- School of Biomedical Engineering, Colorado State University (CSU), Fort Collins, CO 80523, USA
| | - Alessandro F. Martins
- Group of Polymeric Materials and Composites, Department of Chemistry, State University of Maringá (UEM), Maringá 87020-900, PR, Brazil; (P.R.S.); (A.C.d.O.); (B.H.V.)
- Laboratory of Materials, Macromolecules and Composites, Federal University of Technology—Paraná (UTFPR), Apucarana 86812-460, PR, Brazil
- Department of Chemical and Biological Engineering, Colorado State University (CSU), Fort Collins, CO 80523, USA
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15
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Hayes AJ, Melrose J. Electro‐Stimulation, a Promising Therapeutic Treatment Modality for Tissue Repair: Emerging Roles of Sulfated Glycosaminoglycans as Electro‐Regulatory Mediators of Intrinsic Repair Processes. ADVANCED THERAPEUTICS 2020. [DOI: 10.1002/adtp.202000151] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Anthony J. Hayes
- Bioimaging Research Hub Cardiff School of Biosciences Cardiff University Cardiff Wales CF10 3AX UK
| | - James Melrose
- Raymond Purves Bone and Joint Research Laboratory Kolling Institute Northern Sydney Local Health District Faculty of Medicine and Health University of Sydney Royal North Shore Hospital St. Leonards NSW 2065 Australia
- Graduate School of Biomedical Engineering University of New South Wales Sydney NSW 2052 Australia
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16
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Ho CH, Chu PY, Peng SL, Huang SC, Lin YH. The Development of Hyaluronan/Fucoidan-Based Nanoparticles as Macrophages Targeting an Epigallocatechin-3-Gallate Delivery System. Int J Mol Sci 2020; 21:E6327. [PMID: 32878305 PMCID: PMC7504059 DOI: 10.3390/ijms21176327] [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: 07/20/2020] [Revised: 08/11/2020] [Accepted: 08/28/2020] [Indexed: 12/12/2022] Open
Abstract
The aim of this study was to develop a macrophage-targeted nanoparticle composed of hyaluronan/fucoidan complexes with polyethylene glycol-gelatin to encapsulate and deliver epigallocatechin-3-gallate (EGCG), a compound that can regulate macrophage activation and pro-inflammatory mediator production. We show that our nanoparticles can successfully bond to macrophages and deliver more EGCG than an EGCG solution treatment, confirming the anti-inflammatory effects of these nanoparticles in lipopolysaccharide-stimulated macrophages. The prepared nanoparticles were established with a small mean particle size (217.00 ± 14.00 nm), an acceptable polydispersity index (0.28 ± 0.07), an acceptable zeta potential value (-33.60 ± 1.30 mV), and a high EGCG loading efficiency (52.08% ± 5.37%). The targeting abilities of CD44 binding were increased as the hyaluronan concentration increased and decreased by adding a competitor CD44 antibody. Moreover, we found that fucoidan treatment significantly reduced macrophage migration after lipopolysaccharide treatment in a dose-responsive manner. In summary, we successfully created macrophage-targeted nanoparticles for effective targeted delivery of EGCG, which should aid in the development of future anti-inflammatory drugs against macrophage-related diseases.
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Affiliation(s)
- Chang-Hsun Ho
- Department of Anesthesiology, Show Chwan Memorial Hospital, Changhua 50008, Taiwan;
| | - Pei-Yi Chu
- Faculty of Pharmacy, National Yang-Ming University, Taipei 11221, Taiwan; (P.-Y.C.); (S.-C.H.)
| | - Shin-Lei Peng
- Department of Biomedical Imaging and Radiological Science, China Medical University, Taichung 40402, Taiwan;
| | - Shun-Chih Huang
- Faculty of Pharmacy, National Yang-Ming University, Taipei 11221, Taiwan; (P.-Y.C.); (S.-C.H.)
| | - Yu-Hsin Lin
- Faculty of Pharmacy, National Yang-Ming University, Taipei 11221, Taiwan; (P.-Y.C.); (S.-C.H.)
- Department of Medical Research, China Medical University, Taichung 404332, Taiwan
- Department and Institute of Pharmacology, Center for Advanced Pharmaceutics and Drug Delivery Research, Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taipei 11221, Taiwan
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17
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Rajarathnam K, Desai UR. Structural Insights Into How Proteoglycans Determine Chemokine-CXCR1/CXCR2 Interactions: Progress and Challenges. Front Immunol 2020; 11:660. [PMID: 32391006 PMCID: PMC7193095 DOI: 10.3389/fimmu.2020.00660] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/23/2020] [Indexed: 01/01/2023] Open
Abstract
Proteoglycans (PGs), present in diverse environments, such as the cell membrane surface, extracellular milieu, and intracellular granules, are fundamental to life. Sulfated glycosaminoglycans (GAGs) are covalently attached to the core protein of proteoglycans. PGs are complex structures, and are diverse in terms of amino acid sequence, size, shape, and in the nature and number of attached GAG chains, and this diversity is further compounded by the phenomenal diversity in GAG structures. Chemokines play vital roles in human pathophysiology, from combating infection and cancer to leukocyte trafficking, immune surveillance, and neurobiology. Chemokines mediate their function by activating receptors that belong to the GPCR class, and receptor interactions are regulated by how, when, and where chemokines bind GAGs. GAGs fine-tune chemokine function by regulating monomer/dimer levels and chemotactic/haptotactic gradients, which are also coupled to how they are presented to their receptors. Despite their small size and similar structures, chemokines show a range of GAG-binding geometries, affinities, and specificities, indicating that chemokines have evolved to exploit the repertoire of chemical and structural features of GAGs. In this review, we summarize the current status of research on how GAG interactions regulate ELR-chemokine activation of CXCR1 and CXCR2 receptors, and discuss knowledge gaps that must be overcome to establish causal relationships governing the impact of GAG interactions on chemokine function in human health and disease.
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Affiliation(s)
- Krishna Rajarathnam
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX, United States.,Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch at Galveston, Galveston, TX, United States.,Department of Microbiology and Immunology, The University of Texas Medical Branch at Galveston, Galveston, TX, United States
| | - Umesh R Desai
- Department of Medicinal Chemistry, Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
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18
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Kutálková E, Hrnčiřík J, Witasek R, Ingr M. Effect of solvent and ions on the structure and dynamics of a hyaluronan molecule. Carbohydr Polym 2020; 234:115919. [PMID: 32070538 DOI: 10.1016/j.carbpol.2020.115919] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 01/18/2020] [Accepted: 01/25/2020] [Indexed: 12/13/2022]
Abstract
Hyaluronic acid (hyaluronan, HA) is a negatively charged polysaccharide forming highly swollen random coils in aqueous solutions. Their size decreases along with growing salt concentration, but the mechanism of this phenomenon remains unclear. We carry out molecular-dynamics simulations of a 48-monosaccharide HA oligomer in varying salt concentration and temperature. They identify the interaction points of Na+ ions with the HA chain and reveal their influence on the HA solvation-shell structure. The salt-dependent variation of the molecular size does not consist in the distribution of the dihedral angles of the glycosidic connections but is driven by the random flips of individual dihedral angles, which cause the formation of temporary hairpin-like structures effectively shortening the chain. They are induced by the frequency of cation-chain interactions that grow with the salt concentration, but is reduced by the simultaneous decrease of ions' activities. This leads to an anomalous random-coil shrinkage at 0.6 M salt concentration.
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Affiliation(s)
- Eva Kutálková
- Tomas Bata University in Zlín, Faculty of Technology, Department of Physics and Materials Engineering, Nám. T.G. Masaryka 5555, 76001 Zlín, Czech Republic.
| | - Josef Hrnčiřík
- Tomas Bata University in Zlín, Faculty of Technology, Department of Physics and Materials Engineering, Nám. T.G. Masaryka 5555, 76001 Zlín, Czech Republic.
| | - Roman Witasek
- Tomas Bata University in Zlín, Faculty of Technology, Department of Physics and Materials Engineering, Nám. T.G. Masaryka 5555, 76001 Zlín, Czech Republic.
| | - Marek Ingr
- Tomas Bata University in Zlín, Faculty of Technology, Department of Physics and Materials Engineering, Nám. T.G. Masaryka 5555, 76001 Zlín, Czech Republic; Charles University, Faculty of Science, Department of Biochemistry, Hlavova 8/2030, 12843 Praha 2, Czech Republic.
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19
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Gray CJ, Migas LG, Barran PE, Pagel K, Seeberger PH, Eyers CE, Boons GJ, Pohl NLB, Compagnon I, Widmalm G, Flitsch SL. Advancing Solutions to the Carbohydrate Sequencing Challenge. J Am Chem Soc 2019; 141:14463-14479. [PMID: 31403778 DOI: 10.1021/jacs.9b06406] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Carbohydrates possess a variety of distinct features with stereochemistry playing a particularly important role in distinguishing their structure and function. Monosaccharide building blocks are defined by a high density of chiral centers. Additionally, the anomericity and regiochemistry of the glycosidic linkages carry important biological information. Any carbohydrate-sequencing method needs to be precise in determining all aspects of this stereodiversity. Recently, several advances have been made in developing fast and precise analytical techniques that have the potential to address the stereochemical complexity of carbohydrates. This perspective seeks to provide an overview of some of these emerging techniques, focusing on those that are based on NMR and MS-hybridized technologies including ion mobility spectrometry and IR spectroscopy.
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Affiliation(s)
- Christopher J Gray
- School of Chemistry & Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
| | - Lukasz G Migas
- School of Chemistry & Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
| | - Perdita E Barran
- School of Chemistry & Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
| | - Kevin Pagel
- Institute for Chemistry and Biochemistry , Freie Universität Berlin , Takustraße 3 , 14195 Berlin , Germany
| | - Peter H Seeberger
- Biomolecular Systems Department , Max Planck Institute for Colloids and Interfaces , Am Muehlenberg 1 , 14476 Potsdam , Germany
| | - Claire E Eyers
- Department of Biochemistry, Institute of Integrative Biology , University of Liverpool , Crown Street , Liverpool L69 7ZB , U.K
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center , University of Georgia , Athens , Georgia 30602 , United States
| | - Nicola L B Pohl
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Isabelle Compagnon
- Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS , Université de Lyon , 69622 Villeurbanne Cedex , France.,Institut Universitaire de France IUF , 103 Blvd St Michel , 75005 Paris , France
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory , Stockholm University , S-106 91 Stockholm , Sweden
| | - Sabine L Flitsch
- School of Chemistry & Manchester Institute of Biotechnology , The University of Manchester , 131 Princess Street , Manchester M1 7DN , U.K
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20
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Caputo HE, Straub JE, Grinstaff MW. Design, synthesis, and biomedical applications of synthetic sulphated polysaccharides. Chem Soc Rev 2019; 48:2338-2365. [DOI: 10.1039/c7cs00593h] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review summarizes the synthetic methods to sulphated polysaccharides, describes their compositional and structural diversity in regards to activity, and showcases their biomedical applications.
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Affiliation(s)
| | | | - Mark W. Grinstaff
- Department of Chemistry
- Boston University
- Boston
- USA
- Department of Biomedical Engineering
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