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Shastry DG, Irudayanathan FJ, Williams A, Koffas M, Linhardt RJ, Nangia S, Karande P. Rational identification and characterisation of peptide ligands for targeting polysialic acid. Sci Rep 2020; 10:7697. [PMID: 32376914 PMCID: PMC7203153 DOI: 10.1038/s41598-020-64088-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 04/08/2020] [Indexed: 11/09/2022] Open
Abstract
The alpha-2,8-linked form of the polysaccharide polysialic acid (PSA) has widespread implications in physiological and pathological processes, ranging from neurological development to disease progression. Though the high electronegativity and excluded volume of PSA often promotes interference of biomolecular interactions, PSA-binding ligands have important implications for both biological processes and biotechnological applications. As such, the design, identification, and characterisation of novel ligands towards PSA is critical for expanding knowledge of PSA interactions and achieving selective glycan targeting. Here, we report on a rational approach for the identification of alpha-2,8-PSA-binding peptides, involving design from the endogenous ligand Siglec-11 and multi-platform characterisation of peptide binding. Microarray-based examination of peptides revealed charge and sequence characteristics influencing peptide affinity to PSA, and carbohydrate-peptide binding was further quantified with a novel fluorescence anisotropy assay. PSA-binding peptides exhibited specific binding to polymeric SA, as well as different degrees of selective binding in various conditions, including competition with PSA of alternating 2,8/9-linkages and screening with PSA-expressing cells. A computational study of Siglec-11 and Siglec-11-derived peptides offered synergistic insight into ligand binding. These results demonstrate the potential of PSA-binding peptides for selective targeting and highlight the importance of the approaches described herein for the study of carbohydrate interactions.
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Affiliation(s)
- Divya G Shastry
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA. .,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
| | | | - Asher Williams
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Mattheos Koffas
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.,Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Robert J Linhardt
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.,Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.,Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.,Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Shikha Nangia
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY, 13244, USA
| | - Pankaj Karande
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA. .,Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
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Shastry DG, Karande P. Microarrays for the screening and identification of carbohydrate-binding peptides. Analyst 2019; 144:7378-7389. [PMID: 31670365 DOI: 10.1039/c9an01465a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The development of carbohydrate-binding ligands is crucial for expanding knowledge on the glycocode and for achieving systematic carbohydrate targeting. Amongst such ligands, carbohydrate-binding peptides (CBPs) are attractive for use in bioanalytical and biomedical systems due to their biochemical and physicochemical properties; moreover, given the biological significance of lectin-carbohydrate interactions, these ligands offer an opportunity to study peptide sequence and binding characteristics to inform on natural target/ligand interactions. Here, a high-throughput microarray screening technique is described for the identification and study of CBPs, with a focus on polysialic acid (PSA), a polysaccharide found on neural stem cells. The chemical and biological uniqueness of PSA suggests that an ability to exclusively target this glycan may promote a number of diagnostic and therapeutic applications. PSA-binding peptides from phage display screening and from epitope mapping of an scFv for oligosialic acid were screened in an optimized microarray format with three ligand density conditions. Hypothesis-driven mutations were additionally applied to select peptides to modulate peptide affinity and selectivity to PSA. Peptide compositional and positional analyses revealed the significance of various residues for PSA binding and suggested the importance of basic residue positioning for PSA recognition. Furthermore, selectivity studies performed directly on microarrays with chondroitin sulfate A (CS-A) demonstrated the value of screening for both affinity and selectivity in the development of CBPs. Thus, the integrated approach described, with attention to design strategy, screening, and peptide characterization, successfully identified novel PSA-binding ligands and offers a platform for the identification and study of additional polysaccharide-binding peptides.
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Affiliation(s)
- Divya G Shastry
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
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Ramaker K, Henkel M, Krause T, Röckendorf N, Frey A. Cell penetrating peptides: a comparative transport analysis for 474 sequence motifs. Drug Deliv 2018; 25:928-937. [PMID: 29656676 PMCID: PMC6058608 DOI: 10.1080/10717544.2018.1458921] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Delivering reagents into cells is a key demand in molecular medicine. The vehicle of choice is often cell penetrating peptides (CPPs), which can ferry conjugated cargo across membranes. Although numerous peptides have been shown to promote such uptake events, there has been no comprehensive comparison of individual performance under standardized conditions. We have devised a method to rapidly analyze the ability of a multitude of CPP conjugates to carry a model cargo into HeLa cells. Sequence information for 474 CPPs was collected from literature sources, and the respective peptides were synthesized and modified with carboxyfluorescein (FAM) as model cargo. All candidates were evaluated in an identical uptake test, and transport was quantified using cellular fluorescence intensities. Substantial differences in the ability to carry the fluorophore into the cells were observed, with transport performance differing by a factor of 70 between the best CPP investigated and cargo alone. Strong correlations were observed between uptake efficiency and both sequence length and the presence of positive net charge. A compilation of the 20 top performers with regard to cargo delivery performance and cell compatibility is provided.
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Affiliation(s)
- Katrin Ramaker
- a Division of Mucosal Immunology and Diagnostics, Priority Area Asthma & Allergy , Research Center Borstel , Borstel , Germany
| | - Maik Henkel
- a Division of Mucosal Immunology and Diagnostics, Priority Area Asthma & Allergy , Research Center Borstel , Borstel , Germany
| | - Thorsten Krause
- a Division of Mucosal Immunology and Diagnostics, Priority Area Asthma & Allergy , Research Center Borstel , Borstel , Germany
| | - Niels Röckendorf
- a Division of Mucosal Immunology and Diagnostics, Priority Area Asthma & Allergy , Research Center Borstel , Borstel , Germany
| | - Andreas Frey
- a Division of Mucosal Immunology and Diagnostics, Priority Area Asthma & Allergy , Research Center Borstel , Borstel , Germany
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Meyer NH, Mayerhofer H, Tripsianes K, Blindow S, Barths D, Mewes A, Weimar T, Köhli T, Bade S, Madl T, Frey A, Haas H, Mueller-Dieckmann J, Sattler M, Schramm G. A Crystallin Fold in the Interleukin-4-inducing Principle of Schistosoma mansoni Eggs (IPSE/α-1) Mediates IgE Binding for Antigen-independent Basophil Activation. J Biol Chem 2015; 290:22111-26. [PMID: 26163514 DOI: 10.1074/jbc.m115.675066] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Indexed: 11/06/2022] Open
Abstract
The IL-4-inducing principle from Schistosoma mansoni eggs (IPSE/α-1), the major secretory product of eggs from the parasitic worm S. mansoni, efficiently triggers basophils to release the immunomodulatory key cytokine interleukin-4. Activation by IPSE/α-1 requires the presence of IgE on the basophils, but the detailed molecular mechanism underlying activation is unknown. NMR and crystallographic analysis of IPSEΔNLS, a monomeric IPSE/α-1 mutant, revealed that IPSE/α-1 is a new member of the βγ-crystallin superfamily. We demonstrate that this molecule is a general immunoglobulin-binding factor with highest affinity for IgE. NMR binding studies of IPSEΔNLS with the 180-kDa molecule IgE identified a large positively charged binding surface that includes a flexible loop, which is unique to the IPSE/α-1 crystallin fold. Mutational analysis of amino acids in the binding interface showed that residues contributing to IgE binding are important for IgE-dependent activation of basophils. As IPSE/α-1 is unable to cross-link IgE, we propose that this molecule, by taking advantage of its unique IgE-binding crystallin fold, activates basophils by a novel, cross-linking-independent mechanism.
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Affiliation(s)
- N Helge Meyer
- From the Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, the Munich Center for Integrated Protein Science and Biomolecular NMR, Department of Chemie, Technische Universität München, 85747 Garching
| | | | - Konstantinos Tripsianes
- From the Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, the Munich Center for Integrated Protein Science and Biomolecular NMR, Department of Chemie, Technische Universität München, 85747 Garching
| | | | | | | | - Thomas Weimar
- the Institute of Chemistry, University of Lübeck, 23562 Lübeck, Germany
| | - Thies Köhli
- the Institute of Chemistry, University of Lübeck, 23562 Lübeck, Germany
| | - Steffen Bade
- Mucosal Immunology and Diagnostic Section, Research Center Borstel, 23845 Borstel, and
| | - Tobias Madl
- From the Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, the Munich Center for Integrated Protein Science and Biomolecular NMR, Department of Chemie, Technische Universität München, 85747 Garching
| | - Andreas Frey
- Mucosal Immunology and Diagnostic Section, Research Center Borstel, 23845 Borstel, and
| | | | | | - Michael Sattler
- From the Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, the Munich Center for Integrated Protein Science and Biomolecular NMR, Department of Chemie, Technische Universität München, 85747 Garching,
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Stocker BL, Timmer MSM. Chemical Tools for Studying the Biological Function of Glycolipids. Chembiochem 2013; 14:1164-84. [DOI: 10.1002/cbic.201300064] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Indexed: 01/04/2023]
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Röckendorf N, Borschbach M, Frey A. Molecular evolution of peptide ligands with custom-tailored characteristics for targeting of glycostructures. PLoS Comput Biol 2012; 8:e1002800. [PMID: 23271960 PMCID: PMC3521706 DOI: 10.1371/journal.pcbi.1002800] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 10/09/2012] [Indexed: 11/19/2022] Open
Abstract
As an advanced approach to identify suitable targeting molecules required for various diagnostic and therapeutic interventions, we developed a procedure to devise peptides with customizable features by an iterative computer-assisted optimization strategy. An evolutionary algorithm was utilized to breed peptides in silico and the “fitness” of peptides was determined in an appropriate laboratory in vitro assay. The influence of different evolutional parameters and mechanisms such as mutation rate, crossover probability, gaussian variation and fitness value scaling on the course of this artificial evolutional process was investigated. As a proof of concept peptidic ligands for a model target molecule, the cell surface glycolipid ganglioside GM1, were identified. Consensus sequences describing local fitness optima were reached from diverse sets of L- and proteolytically stable D lead peptides. Ten rounds of evolutional optimization encompassing a total of just 4400 peptides lead to an increase in affinity of the peptides towards fluorescently labeled ganglioside GM1 by a factor of 100 for L- and 400 for D-peptides. A clever identification procedure is crucial when peptidic ligands for diagnostic and therapeutic techniques such as in vivo imaging or drug targeting are to be developed. Here, we present a propitious and versatile approach for the discovery of peptide sequences with custom features that is based on an iterative computer-assisted optimization process. The methodology smartly combines in silico evolution with in vitro testing to quickly obtain promising peptide ligand candidates with desired properties. To validate our method in a proof of concept we tried to identify peptide sequences that can bind to a glycosidic cell membrane component. We applied the evolution process by starting out with a small population of peptide lead sequences and achieved a constant increase in affinity between the peptide candidates and their target molecule with each generation. After 10 rounds and a total number of only 4400 peptides synthesized and tested, a more than 100fold improvement in target recognition could be achieved. Since all kinds of building blocks useable in chemical solid phase peptide synthesis can in principle be employed in this evolutionary optimization process, our method should prove a most versatile approach for the optimization of peptides, peptoids and peptomers towards a preset functionality.
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Affiliation(s)
- Niels Röckendorf
- Division of Mucosal Immunology & Diagnostics, Priority Program Asthma & Allergy, Research Center Borstel, Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Borstel, Germany
| | | | - Andreas Frey
- Division of Mucosal Immunology & Diagnostics, Priority Program Asthma & Allergy, Research Center Borstel, Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Borstel, Germany
- * E-mail:
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Polyakova SM, Belov VN, Yan SF, Eggeling C, Ringemann C, Schwarzmann G, de Meijere A, Hell SW. New GM1 Ganglioside Derivatives for Selective Single and Double Labelling of the Natural Glycosphingolipid Skeleton. European J Org Chem 2009. [DOI: 10.1002/ejoc.200900645] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Matsubara T, Iida M, Tsumuraya T, Fujii I, Sato T. Selection of a carbohydrate-binding domain with a helix-loop-helix structure. Biochemistry 2008; 47:6745-51. [PMID: 18540680 DOI: 10.1021/bi8000837] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We obtained a novel carbohydrate-binding peptide having a helix-loop-helix scaffold from a random peptide library. The helix-loop-helix peptide library randomized at five amino acid residues was displayed on the major coat protein of a filamentous phage. Affinity selection with a ganglioside, Galbeta1-3GalNAcbeta1-4(Neu5Acalpha2-3)Galbeta1-4Glcbeta1-1'Cer (GM1), gave positive phage clones. Surface plasmon resonance spectroscopy showed that a corresponding 35-mer synthetic peptide had high affinity for GM1 with a dissociation constant of 0.24 microM. This peptide preferentially binds to GM1 rather than asialo GM1 and GM2, suggesting that a terminal galactose and sialic acid are required for the binding as for cholera toxin. Circular dichroism spectroscopic studies indicated that a helical structure is important for the affinity and specificity. Furthermore, alanine scanning at randomized positions showed that arginine and phenylalanine play an especially important role in the recognition of carbohydrates. Such a de novo helix-loop-helix peptide would be available for the design of carbohydrate-binding proteins.
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