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Abstract

Siglecs are the major homologous subfamily of I-type lectins with an ability to recognize sialylated glycans. Siglecs are attractive therapeutic targets because of their endocytic properties, ability to modulate receptor signaling and cell-type specific expression pattern. Sialoadhesin (Sn/Siglec-1/CD169), a member of the Siglec family expressed on subsets of resident and inflammatory macrophages and involves in modulation of inflammation and immunity. In this work, 3-D structure of human Siglec-1 (hSiglec-1) was predicted based on X-ray crystallo-graphically determined structure of mouse Siglec-1[mSiglec-1(PDB ID: 1QFP)] using molecular modeling techniques. The structure of complexes in solution of hSiglec-1 with ligands, glycopeptide and 3′-sialyllactose were predicted using a novel docking technique comprising of repeated cycles of molecular dynamics and energy minimization. Calculation of the free energies of binding of complexes suggested that glycopeptide can form stable complex with dissociation constant value of 3.31 μM whereas complex formation of 3′-sialyllactose with the protein in aqueous medium is thermodynamically unfavorable. The structural analysis of theses complexes represent the functional recognition interactions of this protein with the bound sugar molecule and as such provide detailed information about functional roles of such sugar binding protein.

Keywords

Glycopeptide Docking Sialic acid Sialoadhesin 3′-Sialyllactose

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Dandopath Patra, M. (2020). Structural Studies on Different Ligand Binding Ability of Sialoadhesin Using Molecular Modeling Techniques. Asian Journal of Organic & Medicinal Chemistry, 5(4), 277–282. https://doi.org/10.14233/ajomc.2020.AJOMC-P279
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References

  1. P.R. Crocker, E.A. Clark, M. Filbin, S. Gordon, Y. Jones, J.H. Kehrl, S. Kelm, N. Le Douarin, L. Powell, J. Roder, R.L. Schnaar, D.C. Sgroi, K. Stamenkovic, R. Schauer, M. Schachner, T.K. van den Berg, P.A. van der Merwe, S.M. Watt and A. Varki, Siglecs: A Family of Sialic-Acid Binding Lectins, Glycobiology, 8, v (1998); https://doi.org/10.1093/oxfordjournals.glycob.a018832
  2. O. Blixt, B.E. Collins, I.M. van den Nieuwenhof, P.R. Crocker and J.C. Paulson, Sialoside Specificity of the Siglec Family Assessed using Novel Multivalent Probes-Identification of Potent Inhibitors of Myelin-Associated Glycoprotein, J. Biol. Chem., 278, 31007 (2003); https://doi.org/10.1074/jbc.M304331200
  3. S. Kelm, R. Schauer, J.C. Manuguerra, H.J. Gross and P.R. Crocker, Modifications of Cell Surface Sialic Acids Modulate Cell Adhesion Mediated by Sialoadhesin and CD22, Glycoconj. J., 11, 576 (1994); https://doi.org/10.1007/BF00731309
  4. L.D. Powell and A. Varki, The Oligosaccharide Binding Specificities of CD22 beta, A Sialic Acid-Specific Lectin of B Cells, J. Biol. Chem., 269, 10628 (1994).
  5. E.C. Brinkman-Van der Linden and A. Varki, New Aspects of Siglec Binding Specificities, Including the Significance of Fucosylation and of the Sialyl-Tn Epitope, J. Biol. Chem., 275, 8625 (2000); https://doi.org/10.1074/jbc.275.12.8625
  6. A.L. Cornish, S. Freeman, G. Forbes, J. Ni, M. Zhang, M. Cepeda, R. Gentz, M. Augustus, K.C. Carter and P.R. Crocker, Characterization of Siglec-5, A Novel Glycoprotein Expressed on Myeloid Cells Related to CD33, Blood, 92, 2123 (1998); https://doi.org/10.1182/blood.V92.6.2123
  7. G. Nicoll, J. Ni, D. Liu, P. Klenerman, J. Munday, S. Dubock, M.-G. Mattei and P.R. Crocker, Identification and Characterization of a Novel Siglec, Siglec-7, Expressed by Human Natural Killer Cells and Monocytes, J. Biol. Chem., 274, 34089 (1999); https://doi.org/10.1074/jbc.274.48.34089
  8. A. Varki, Sialic acids as Ligands in Recognition Phenomena, FASEB J., 11, 248 (1997); https://doi.org/10.1096/fasebj.11.4.9068613
  9. K.A. Karlsson, Meaning and Therapeutic Potential of Microbial Recognition of Host Glycoconjugates, Mol. Microbiol., 29, 1 (1998); https://doi.org/10.1046/j.1365-2958.1998.00854.x
  10. P.R. Crocker and A. Varki, Siglecs, Sialic Acids and Innate Immunity, Trends Immunol., 22, 337 (2001); https://doi.org/10.1016/S1471-4906(01)01930-5
  11. K. Drickamer, Increasing Diversity of Animal Lectin Structures, Curr. Opin. Struct. Biol., 5, 612 (1995); https://doi.org/10.1016/0959-440X(95)80052-2
  12. K.F. Bornhöfft, T. Goldammer, A. Rebl and S.P. Galuska, Siglecs: A Journey through the Evolution of Sialic Acid-Binding Immunoglobulin-Type Lectins, Dev. Comp. Immunol., 86, 219 (2018); https://doi.org/10.1016/j.dci.2018.05.008
  13. T. Angata, R. Hingorani, N.M. Varki and A. Varki, Cloning and Characterization of a Novel Mouse Siglec, mSiglec-F-Differential Evolution of the Mouse and Human (Cd33) Siglec-3-Related Gene Clusters, J. Biol. Chem., 276, 45128 (2001); https://doi.org/10.1074/jbc.M108573200
  14. P.R. Crocker, Siglecs: Sialic-Acid-Binding Immunoglobulin-like Lectins in Cell-Cell Interactions and Signalling, Curr. Opin. Struct. Biol., 12, 609 (2002); https://doi.org/10.1016/S0959-440X(02)00375-5
  15. P.R. Crocker, A. Hartnell, J. Munday and D. Nath, The Potential Role of Sialoadhesin as a Macrophage Recognition Molecule in Health and Disease, Glycoconj. J., 14, 601 (1997); https://doi.org/10.1023/A:1018588526788
  16. S.D. Freeman, S. Kelm, E.K. Barber and P.R. Crocker, Characterization of CD33 as a New Member of the Sialoadhesin Family of Cellular Interaction Molecules, Blood, 85, 2005 (1995); https://doi.org/10.1182/blood.V85.8.2005.bloodjournal8582005
  17. J.G. Cyster and C.C. Goodnow, Tuning Antigen Receptor Signaling by CD22: Integrating Cues from Antigens and the Microenvironment, Immunity, 6, 509 (1997); https://doi.org/10.1016/S1074-7613(00)80339-8
  18. C. Li, M.B. Tropak, R. Gerlai, S. Clapoff, W. Abramow-Newerly, B. Trapp, A. Peterson and J. Roder, Myelination in the Absence of Myelin-Associated Glycoprotein, Nature, 369, 747 (1994); https://doi.org/10.1038/369747a0
  19. D. Montag, K.P. Giese, U. Bartsch, R. Martini, Y. Lang, H. Blüthmann, J. Karthigasan, D.A. Kirschner, E.S. Wintergerst, K.-A. Nave, J. Zielasek, K.V. Toyka, H.-P. Lipp and M. Schachner, Mice Deficient for the Glycoprotein Show Subtle Abnormalities in Myelin, Neuron, 13, 229 (1994); https://doi.org/10.1016/0896-6273(94)90472-3
  20. T. Angata, Siglec-15: A Potential Regulator of Osteoporosis, Cancer, and Infectious Diseases, J. Biomed. Sci., 27, 10 (2020); https://doi.org/10.1186/s12929-019-0610-1
  21. Y.-C. Liu, M.-M. Yu, Y.-F. Chai and S.-T. Shou, Sialic Acids in the Immune Response during Sepsis, Front. Immunol., 8, 1601 (2017); https://doi.org/10.3389/fimmu.2017.01601
  22. S. Duan and J.C. Paulson, Siglecs as Immune Cell Checkpoints in Disease, Annu. Rev. Immunol., 38, 365 (2020); https://doi.org/10.1146/annurev-immunol-102419-035900
  23. T. Angata, C.M. Nycholat and M.S. Macauley, Therapeutic Targeting of Siglecs using Antibody- and Glycan-Based Approaches, Trends Pharmacol. Sci., 36, 645 (2015); https://doi.org/10.1016/j.tips.2015.06.008
  24. C. Mandal, MODELYN – A Molecular Modelling Program Version PC-1 0 Indian Copyright No 9/98 (1998).
  25. J. Aqvist, C. Medina and J.-E. Samuelsson, A new Method for Predicting Binding Affinity in Computer-aided Drug Design, Protein Eng., 7, 385 (1994); https://doi.org/10.1093/protein/7.3.385
  26. Johan and S.L. Mowbray, Sugar Recognition by a Glucose/Galactose Receptor-Evaluation of Binding Energetics from Molecular Dynamics Simulations, J. Biol. Chem., 270, 9978 (1995); https://doi.org/10.1074/jbc.270.17.9978
  27. J. Hulte’n, N.M. Bonham, U. Nillroth, T. Hansson, G. Zuccarello, J. Åqvist, A. Bouzide, B. Classon, U.H. Danielson, A. Karlen, I. Kvarnstrom, B. Samuelsson and A. Hallberg, Cyclic HIV-1 Protease Inhibitors Derived from Mannitol: Synthesis, Inhibitory Potencies and Computational Predictions of Binding Affinities, J. Med. Chem., 40, 885 (1997); https://doi.org/10.1021/jm960728j
  28. R. Koradi, M. Billeter and K. Wuthrich, MOLMOL: A Program for Display and Analysis of Macromolecular Structures, J. Mol. Graph., 14, 51 (1996); https://doi.org/10.1016/0263-7855(96)00009-4
  29. R.A. Laskowski, M.W. MacArthur, D.S. Moss and J.M. Thornton, PROCHECK: A Program to Check the Stereochemical Quality of Protein Structures, J. Appl. Cryst., 26, 283 (1993); https://doi.org/10.1107/S0021889892009944
  30. I.W. Davis, L.W. Murray, J.S. Richardson and D.C. Richardson, MOLPROBITY: Structure Validation and All-Atom Contact Analysis for Nucleic Acids and their Complexes, Nucleic Acids Res., 32(Web Server), W615 (2004); https://doi.org/10.1093/nar/gkh398
  31. S.F. Altschul, T.L. Madden, A.A. Schäffer, J. Zhang, Z. Zhang, W. Miller and D.J. Lipman, Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs, Nucleic Acids Res., 25, 3389 (1997); https://doi.org/10.1093/nar/25.17.3389
  32. P.R. Crocker, S. Freeman, S. Gordon and S. Kelm, Sialoadhesin Binds Preferentially to Cells of the Granulocytic Lineage, J. Clin. Invest., 95, 635 (1995); https://doi.org/10.1172/JCI117708
  33. P.R. Crocker, S. Kelm, C. Dubois, B. Martin, A.S. McWilliam, D.M. Shotton, J.C. Paulson and S. Gordon, Sialoadhesin Binds Preferentially to Cells of the Granulocytic Lineage, Purification and Properties of Sialoadhesin, A Sialic Acid-Binding Receptor of Murine Tissue Macrophages, EMBO J., 10, 1661 (1991); https://doi.org/10.1002/j.1460-2075.1991.tb07689.x
  34. T.K. van den Berg, J.J. Brevé, J.G. Damoiseaux, E.A. Döpp, S. Kelm, P.R. Crocker, C.D. Dijkstra and G. Kraal, Sialoadhesin on Macrophages: its Identification as a Lymphocyte Adhesion Molecule, J. Exp. Med., 176, 647 (1992); https://doi.org/10.1084/jem.176.3.647
  35. B. Steiniger, P. Barth, B. Herbst, A. Hartnell and P.R. Crocker, The Species-Specific Structure of Microanatomical Compartments in the Human Spleen: Strongly Sialoadhesin-positive Macrophages Occur in the Perifollicular Zone, But Not in the Marginal Zone, Immunology, 92, 307 (1997); https://doi.org/10.1046/j.1365-2567.1997.00328.x
  36. J. Munday, H. Floyd and P.R. Crocker, Sialic Acid Binding Receptors (Siglecs) Expressed by Macrophages, J. Leukoc. Biol., 66, 705 (1999); https://doi.org/10.1002/jlb.66.5.705
  37. N.R. Zaccai, K. Maenaka, T. Maenaka, P.R. Crocker, R. Brossmer, S. Kelm and E.Y. Jones, Structure-Guided Design of Sialic Acid-Based Siglec Inhibitors and Crystallographic Analysis in Complex with Sialoadhesin, Structure, 11, 557 (2003); https://doi.org/10.1016/S0969-2126(03)00073-X
  38. A.P. May, R.C. Robinson, M. Vinson, P.R. Crocker and E.Y. Jones, Crystal Structure of the N-Terminal Domain of Sialoadhesin in Complex with 3¢-Sialyllactose at 1.85 Å Resolution, Mol. Cell, 1, 719 (1998); https://doi.org/10.1016/S1097-2765(00)80071-4
  39. A. Varki and T. Angata, Siglecs-The Major Subfamily of I-Type Lectins, Glycobiology, 16, 1R (2006); https://doi.org/10.1093/glycob/cwj008
  40. J.T. Bukrinsky, P.M. St. Hilaire, M. Meldal, P.R. Crocker and A. Henriksen, Complex of Sialoadhesin with a Glycopeptide Ligand, Biochim. Biophys. Acta, 1702, 173 (2004); https://doi.org/10.1016/j.bbapap.2004.08.015