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Lefèbre J, Falk T, Ning Y, Rademacher C. Secondary Sites of the C-type Lectin-Like Fold. Chemistry 2024; 30:e202400660. [PMID: 38527187 DOI: 10.1002/chem.202400660] [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: 02/18/2024] [Revised: 03/23/2024] [Accepted: 03/25/2024] [Indexed: 03/27/2024]
Abstract
C-type lectins are a large superfamily of proteins involved in a multitude of biological processes. In particular, their involvement in immunity and homeostasis has rendered them attractive targets for diverse therapeutic interventions. They share a characteristic C-type lectin-like domain whose adaptability enables them to bind a broad spectrum of ligands beyond the originally defined canonical Ca2+-dependent carbohydrate binding. Together with variable domain architecture and high-level conformational plasticity, this enables C-type lectins to meet diverse functional demands. Secondary sites provide another layer of regulation and are often intricately linked to functional diversity. Located remote from the canonical primary binding site, secondary sites can accommodate ligands with other physicochemical properties and alter protein dynamics, thus enhancing selectivity and enabling fine-tuning of the biological response. In this review, we outline the structural determinants allowing C-type lectins to perform a large variety of tasks and to accommodate the ligands associated with it. Using the six well-characterized Ca2+-dependent and Ca2+-independent C-type lectin receptors DC-SIGN, langerin, MGL, dectin-1, CLEC-2 and NKG2D as examples, we focus on the characteristics of non-canonical interactions and secondary sites and their potential use in drug discovery endeavors.
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Affiliation(s)
- Jonathan Lefèbre
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
- Vienna Doctoral School of Pharmaceutical, Nutritional and Sport, Sciences, University of Vienna, Vienna, Austria
- Department of Microbiology, Immunology and Genetics, University of Vienna, Max F. Perutz Labs, Vienna, Austria
| | - Torben Falk
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
- Vienna Doctoral School of Pharmaceutical, Nutritional and Sport, Sciences, University of Vienna, Vienna, Austria
- Department of Microbiology, Immunology and Genetics, University of Vienna, Max F. Perutz Labs, Vienna, Austria
| | - Yunzhan Ning
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
- Vienna Doctoral School of Pharmaceutical, Nutritional and Sport, Sciences, University of Vienna, Vienna, Austria
- Department of Microbiology, Immunology and Genetics, University of Vienna, Max F. Perutz Labs, Vienna, Austria
| | - Christoph Rademacher
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
- Department of Microbiology, Immunology and Genetics, University of Vienna, Max F. Perutz Labs, Vienna, Austria
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2
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Belouin A, Simard RD, Joyal M, Maharsy W, Lau A, Prévost M, Nemer M, Guindon Y. Sialyl Lewis X glycomimetics bearing an extended anionic chain targeting E- and P- selectin binding sites. Bioorg Med Chem 2024; 98:117553. [PMID: 38128297 DOI: 10.1016/j.bmc.2023.117553] [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: 10/30/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023]
Abstract
Neutrophil binding to vascular P- and E-selectin is the rate-limiting step in the recruitment of immune cells to sites of inflammation. Many diseases, including sickle cell anemia, post-myocardial infarction reperfusion injury, and acute respiratory distress syndrome are characterized by dysregulated inflammation. We have recently reported sialyl Lewisx analogues as potent antagonists of P- and E-selectin and demonstrated their in vivo immunosuppressive activity. A key component of these molecules is a tartrate diester that serves as an acyclic tether to orient the fucoside and the galactoside moiety in the required gauche conformation for optimal binding. The next stage of our study involved attaching an extended carbon chain onto one of the esters. This chain could be utilized to tether other pharmacophores, lipids, and contrast agents in the context of enhancing pharmacological applications through the sialyl Lewisx / receptor-mediated mechanism. Herein, we report our preliminary studies to generate a small library of tartrate based sialyl Lewisx analogues bearing extended carbon chains. Anionic charged chemical entities are attached to take advantage of proximal charged amino acids in the carbohydrate recognition domain of the selectin receptors. Starting with a common azido intermediate, synthesized using copper-catalyzed Huisgen 1,3-dipolar cycloadditions, these molecules demonstrate E- and P-selectin binding properties.
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Affiliation(s)
- Audrey Belouin
- Bioorganic Chemistry Laboratory, Institut de recherches cliniques de Montréal (IRCM), Montréal, Québec H2W 1R7, Canada; Department of Chemistry, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Ryan D Simard
- Bioorganic Chemistry Laboratory, Institut de recherches cliniques de Montréal (IRCM), Montréal, Québec H2W 1R7, Canada; Department of Chemistry, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Mathieu Joyal
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Wael Maharsy
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Alice Lau
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Michel Prévost
- Bioorganic Chemistry Laboratory, Institut de recherches cliniques de Montréal (IRCM), Montréal, Québec H2W 1R7, Canada
| | - Mona Nemer
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada.
| | - Yvan Guindon
- Bioorganic Chemistry Laboratory, Institut de recherches cliniques de Montréal (IRCM), Montréal, Québec H2W 1R7, Canada; Department of Chemistry, Université de Montréal, Montréal, Québec H3C 3J7, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada.
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3
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Sladek V, Šmak P, Tvaroška I. How E-, L-, and P-Selectins Bind to sLe x and PSGL-1: A Quantification of Critical Residue Interactions. J Chem Inf Model 2023; 63:5604-5618. [PMID: 37486087 DOI: 10.1021/acs.jcim.3c00704] [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: 07/25/2023]
Abstract
Selectins and their ability to interact with specific ligands are a cornerstone in cell communication. Over the last three decades, a considerable wealth of experimental and molecular modeling insights into their structure and modus operandi were gathered. Nonetheless, explaining the role of individual selectin residues on a quantitative level remained elusive, despite its importance in understanding the structure-function relationship in these molecules and designing their inhibitors. This work explores essential interactions of selectin-ligand binding, employing a multiscale approach that combines molecular dynamics, quantum-chemical calculations, and residue interaction network models. Such an approach successfully reproduces most of the experimental findings. It proves to be helpful, with the potential for becoming an established tool for quantitative predictions of residue contribution to the binding of biomolecular complexes. The results empower us to quantify the importance of particular residues and functional groups in the protein-ligand interface and to pinpoint differences in molecular recognition by the three selectins. We show that mutations in the E-, L-, and P-selectins, e.g., different residues in positions 46, 85, 97, and 107, present a crucial difference in how the ligand is engaged. We assess the role of sulfation of tyrosine residues in PSGL-1 and suggest that TyrSO3- in position 51 interacting with Arg85 in P-selectin is a significant factor in the increased affinity of P-selectin to PSGL-1 compared to E- and L-selectins. We propose an original pharmacophore targeting five essential PSGL-binding sites based on the analysis of the selectin···PSGL-1 interactions.
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Affiliation(s)
- Vladimir Sladek
- Institute of Chemistry, SAS, Dubravska cesta 9, 84538 Bratislava, Slovakia
| | - Pavel Šmak
- Department of Biochemistry, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Igor Tvaroška
- Institute of Chemistry, SAS, Dubravska cesta 9, 84538 Bratislava, Slovakia
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4
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Leusmann S, Ménová P, Shanin E, Titz A, Rademacher C. Glycomimetics for the inhibition and modulation of lectins. Chem Soc Rev 2023; 52:3663-3740. [PMID: 37232696 PMCID: PMC10243309 DOI: 10.1039/d2cs00954d] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Indexed: 05/27/2023]
Abstract
Carbohydrates are essential mediators of many processes in health and disease. They regulate self-/non-self- discrimination, are key elements of cellular communication, cancer, infection and inflammation, and determine protein folding, function and life-times. Moreover, they are integral to the cellular envelope for microorganisms and participate in biofilm formation. These diverse functions of carbohydrates are mediated by carbohydrate-binding proteins, lectins, and the more the knowledge about the biology of these proteins is advancing, the more interfering with carbohydrate recognition becomes a viable option for the development of novel therapeutics. In this respect, small molecules mimicking this recognition process become more and more available either as tools for fostering our basic understanding of glycobiology or as therapeutics. In this review, we outline the general design principles of glycomimetic inhibitors (Section 2). This section is then followed by highlighting three approaches to interfere with lectin function, i.e. with carbohydrate-derived glycomimetics (Section 3.1), novel glycomimetic scaffolds (Section 3.2) and allosteric modulators (Section 3.3). We summarize recent advances in design and application of glycomimetics for various classes of lectins of mammalian, viral and bacterial origin. Besides highlighting design principles in general, we showcase defined cases in which glycomimetics have been advanced to clinical trials or marketed. Additionally, emerging applications of glycomimetics for targeted protein degradation and targeted delivery purposes are reviewed in Section 4.
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Affiliation(s)
- Steffen Leusmann
- Chemical Biology of Carbohydrates (CBCH), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, 66123 Saarbrücken, Germany.
- Department of Chemistry, Saarland University, 66123 Saarbrücken, Germany
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig, Germany
| | - Petra Ménová
- University of Chemistry and Technology, Prague, Technická 5, 16628 Prague 6, Czech Republic
| | - Elena Shanin
- Department of Pharmaceutical Sciences, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria.
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Biocenter 5, 1030 Vienna, Austria
| | - Alexander Titz
- Chemical Biology of Carbohydrates (CBCH), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, 66123 Saarbrücken, Germany.
- Department of Chemistry, Saarland University, 66123 Saarbrücken, Germany
- Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig, Germany
| | - Christoph Rademacher
- Department of Pharmaceutical Sciences, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria.
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Biocenter 5, 1030 Vienna, Austria
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5
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LeBlanc RM, Mesleh MF. A drug discovery toolbox for Nuclear Magnetic Resonance (NMR) characterization of ligands and their targets. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 37:51-60. [PMID: 34895655 DOI: 10.1016/j.ddtec.2020.11.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 11/22/2020] [Accepted: 11/27/2020] [Indexed: 10/22/2022]
Abstract
Information about the structure, dynamics, and ligand-binding properties of biomolecules can be derived from Nuclear Magnetic Resonance (NMR) spectroscopy and provides valuable information for drug discovery. A multitude of experimental approaches provides a wealth of information that can be tailored to the system of interest. Methods to study the behavior of ligands upon target binding enable the identification of weak binders in a robust manner that is critical for the identification of truly novel binding interactions. This is particularly important for challenging targets. Observing the solution behavior of biomolecules yields information about their structure, dynamics, and interactions. This review describes the breadth of approaches that are available, many of which are under-utilized in a drug-discovery environment, and focuses on recent advances that continue to emerge.
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Affiliation(s)
- Regan M LeBlanc
- Structural Biology and Biophysics, Vertex Pharmaceuticals Inc., Boston, MA, 02210, United States
| | - Michael F Mesleh
- Structural Biology and Biophysics, Vertex Pharmaceuticals Inc., Boston, MA, 02210, United States.
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6
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Wawrzinek R, Wamhoff EC, Lefebre J, Rentzsch M, Bachem G, Domeniconi G, Schulze J, Fuchsberger FF, Zhang H, Modenutti C, Schnirch L, Marti MA, Schwardt O, Bräutigam M, Guberman M, Hauck D, Seeberger PH, Seitz O, Titz A, Ernst B, Rademacher C. A Remote Secondary Binding Pocket Promotes Heteromultivalent Targeting of DC-SIGN. J Am Chem Soc 2021; 143:18977-18988. [PMID: 34748320 PMCID: PMC8603350 DOI: 10.1021/jacs.1c07235] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
Dendritic cells (DC)
are antigen-presenting cells coordinating
the interplay of the innate and the adaptive immune response. The
endocytic C-type lectin receptors DC-SIGN and Langerin display expression
profiles restricted to distinct DC subtypes and have emerged as prime
targets for next-generation immunotherapies and anti-infectives. Using
heteromultivalent liposomes copresenting mannosides bearing aromatic
aglycones with natural glycan ligands, we serendipitously discovered
striking cooperativity effects for DC-SIGN+ but not for
Langerin+ cell lines. Mechanistic investigations combining
NMR spectroscopy with molecular docking and molecular dynamics simulations
led to the identification of a secondary binding pocket for the glycomimetics.
This pocket, located remotely of DC-SIGN’s carbohydrate bindings
site, can be leveraged by heteromultivalent avidity enhancement. We
further present preliminary evidence that the aglycone allosterically
activates glycan recognition and thereby contributes to DC-SIGN-specific
cell targeting. Our findings have important implications for both
translational and basic glycoscience, showcasing heteromultivalent
targeting of DCs to improve specificity and supporting potential allosteric
regulation of DC-SIGN and CLRs in general.
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Affiliation(s)
- Robert Wawrzinek
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Eike-Christian Wamhoff
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie University of Berlin, 14195 Berlin, Germany
| | - Jonathan Lefebre
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie University of Berlin, 14195 Berlin, Germany
| | - Mareike Rentzsch
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie University of Berlin, 14195 Berlin, Germany
| | - Gunnar Bachem
- Department of Chemistry, Humboldt University of Berlin, 12489 Berlin, Germany
| | - Gary Domeniconi
- Department of Chemistry, Humboldt University of Berlin, 12489 Berlin, Germany
| | - Jessica Schulze
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie University of Berlin, 14195 Berlin, Germany
| | - Felix F Fuchsberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie University of Berlin, 14195 Berlin, Germany
| | - Hengxi Zhang
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie University of Berlin, 14195 Berlin, Germany
| | - Carlos Modenutti
- Departamento de Química Biológica e IQUIBICEN-CONICET, Universidad de Buenos Aires, C1428EHA Ciudad de Buenos Aires, Argentina
| | - Lennart Schnirch
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie University of Berlin, 14195 Berlin, Germany
| | - Marcelo A Marti
- Departamento de Química Biológica e IQUIBICEN-CONICET, Universidad de Buenos Aires, C1428EHA Ciudad de Buenos Aires, Argentina
| | - Oliver Schwardt
- Department of Pharmaceutical Sciences, University of Basel, 4056 Basel, Switzerland
| | - Maria Bräutigam
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Mónica Guberman
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Dirk Hauck
- Chemical Biology of Carbohydrates, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, 66123 Saarbrücken, Germany.,German Centre for Infection Research, Campus Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie University of Berlin, 14195 Berlin, Germany
| | - Oliver Seitz
- Department of Chemistry, Humboldt University of Berlin, 12489 Berlin, Germany
| | - Alexander Titz
- Chemical Biology of Carbohydrates, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, 66123 Saarbrücken, Germany.,German Centre for Infection Research, Campus Hannover-Braunschweig, 38124 Braunschweig, Germany.,Department of Chemistry, Saarland University, 66123 Saarbrücken, Germany
| | - Beat Ernst
- Department of Pharmaceutical Sciences, University of Basel, 4056 Basel, Switzerland
| | - Christoph Rademacher
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie University of Berlin, 14195 Berlin, Germany.,University of Vienna, Department of Pharmaceutical Sciences, Althanstrasse 14, 1090 Vienna, Austria.,University of Vienna, Department of Microbiology, Immunology and Genetics, Max F. Perutz Laboratories, Biocenter 5, 1030 Vienna, Austria
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7
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Šmak P, Chandrabose S, Tvaroška I, Koča J. Pan-selectin inhibitors as potential therapeutics for COVID-19 treatment: in silico screening study. Glycobiology 2021; 31:975-987. [PMID: 33822042 PMCID: PMC8083503 DOI: 10.1093/glycob/cwab021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 03/06/2021] [Accepted: 03/06/2021] [Indexed: 12/15/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) has spread rapidly throughout the globe. The spectrum of disease is broad but among hospitalized patients with COVID-19, respiratory failure from acute respiratory distress syndrome is the leading cause of mortality. There is an urgent need for an effective treatment. The current focus has been developing novel therapeutics, including antivirals, protease inhibitors, vaccines and targeting the overactive cytokine response with anti-cytokine therapy. The overproduction of early response proinflammatory cytokines results in what has been described as a "cytokine storm" is leading eventually to death when the cells fail to terminate the inflammatory response. Accumulating evidence shows that inflammatory cytokines induce selectin ligands that play a crucial role in the pathogenesis of inflammatory diseases by mediating leukocyte migration from the blood into the tissue. Thus, the selectins and selectin ligands represent a promising therapeutic target for the treatment of COVID-19. In this paper, potential pan-selectin inhibitors were identified employing a virtual screening using a docking procedure. For this purpose, the Asinex and ZINC databases of ligands, including approved drugs, biogenic compounds and glycomimetics, altogether 923,602 compounds, were screened against the P-, L- and E-selectin. At first, the experimentally confirmed inhibitors were docked into all three selectins' carbohydrate recognition domains to assess the suitability of the screening procedure. Finally, based on the evaluation of ligands binding, we propose 10 purchasable pan-selectin inhibitors to develop COVID-19 therapeutics.
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Affiliation(s)
- Pavel Šmak
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Selvaraj Chandrabose
- Central European Institute of Technology (CEITEC), Masaryk University, 625 00 Brno, Czech Republic
| | - Igor Tvaroška
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- Institute of Chemistry, Slovak Academy of Sciences, 845 38 Bratislava, Slovak Republic
| | - Jaroslav Koča
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- Central European Institute of Technology (CEITEC), Masaryk University, 625 00 Brno, Czech Republic
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8
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Non-carbohydrate strategies to inhibit lectin proteins with special emphasis on galectins. Eur J Med Chem 2021; 222:113561. [PMID: 34146913 DOI: 10.1016/j.ejmech.2021.113561] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 05/16/2021] [Accepted: 05/17/2021] [Indexed: 12/29/2022]
Abstract
Lectins are a family of glycan-binding proteins, many of which have been established as key targets for therapeutic intervention. They play a central role in many physiological and cellular processes. With the advances in protein crystallography, NMR spectroscopy and computational power over the past couple of decades, the carbohydrate-receptor interactions are now well understood and characterized. Nevertheless, designing efficient carbohydrate inhibitors is a laborious endeavour. They are known to have weak affinities, unsuitable pharmacokinetic properties and highly cumbersome/complex synthetic routes. To circumvent these issues many non-carbohydrate strategies have been reported. Galectins are a sub-family of lectin proteins which have been recognized as crucial targets for a wide variety of diseases. Many candidates targeting galectins are currently in advanced stages of clinical trials. There have been a few reports of non-carbohydrate inhibitors targeting galectins which comprise of peptide-based inhibitors and a recent flourish of heterocyclic inhibitors. In this review, we have briefly highlighted the strategies like fragment-based drug-design and high-throughput screens utilized to identify non-carbohydrate based antagonists for proteins wherein the presence of a sugar was believed to be essential. Additionally, we have described the literature pertaining to non-carbohydrate inhibitors of galectins and how previous reports on rational substitution of a sugar motif could aid in design of heterocyclics that inhibit lectins/galectins. We have concluded with remarks on challenges, gap in our understanding and future perspectives concerned with rational design of non-carbohydrate molecules targeting lectins/galectins.
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9
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Nimbarte VD, Wirmer‐Bartoschek J, Gande SL, Alshamleh I, Seibert M, Nasiri HR, Schnütgen F, Serve H, Schwalbe H. Synthesis and in Vitro Evaluation of Novel 5-Nitroindole Derivatives as c-Myc G-Quadruplex Binders with Anticancer Activity. ChemMedChem 2021; 16:1667-1679. [PMID: 33508167 PMCID: PMC8252724 DOI: 10.1002/cmdc.202000835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 01/26/2021] [Indexed: 01/05/2023]
Abstract
Lead-optimization strategies for compounds targeting c-Myc G-quadruplex (G4) DNA are being pursued to develop anticancer drugs. Here, we investigate the structure-activity- relationship (SAR) of a newly synthesized series of molecules based on the pyrrolidine-substituted 5-nitro indole scaffold to target G4 DNA. Our synthesized series allows modulation of flexible elements with a structurally preserved scaffold. Biological and biophysical analyses illustrate that substituted 5-nitroindole scaffolds bind to the c-Myc promoter G-quadruplex. These compounds downregulate c-Myc expression and induce cell-cycle arrest in the sub-G1/G1 phase in cancer cells. They further increase the concentration of intracellular reactive oxygen species. NMR spectra show that three of the newly synthesized compounds interact with the terminal G-quartets (5'- and 3'-ends) in a 2 : 1 stoichiometry.
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Affiliation(s)
- Vijaykumar D. Nimbarte
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Goethe University FrankfurtMax-von-Laue-Straße 760438Frankfurt am MainGermany
| | - Julia Wirmer‐Bartoschek
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Goethe University FrankfurtMax-von-Laue-Straße 760438Frankfurt am MainGermany
| | - Santosh L. Gande
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Goethe University FrankfurtMax-von-Laue-Straße 760438Frankfurt am MainGermany
- German Cancer Research Center and German Cancer ConsortiumIm Neuenheimer Feld 28069120HeidelbergGermany
| | - Islam Alshamleh
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Goethe University FrankfurtMax-von-Laue-Straße 760438Frankfurt am MainGermany
| | - Marcel Seibert
- Department of Medicine 2Hematology/OncologyUniversity Hospital FrankfurtGoethe UniversityTheodor-Stern-Kai 760596Frankfurt am MainGermany
| | - Hamid Reza Nasiri
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Goethe University FrankfurtMax-von-Laue-Straße 760438Frankfurt am MainGermany
| | - Frank Schnütgen
- German Cancer Research Center and German Cancer ConsortiumIm Neuenheimer Feld 28069120HeidelbergGermany
- Department of Medicine 2Hematology/OncologyUniversity Hospital FrankfurtGoethe UniversityTheodor-Stern-Kai 760596Frankfurt am MainGermany
- Frankfurt Cancer Institute (FCI)Theodor-Stern-Kai 760596Frankfurt am MainGermany
| | - Hubert Serve
- German Cancer Research Center and German Cancer ConsortiumIm Neuenheimer Feld 28069120HeidelbergGermany
- Department of Medicine 2Hematology/OncologyUniversity Hospital FrankfurtGoethe UniversityTheodor-Stern-Kai 760596Frankfurt am MainGermany
- Frankfurt Cancer Institute (FCI)Theodor-Stern-Kai 760596Frankfurt am MainGermany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Goethe University FrankfurtMax-von-Laue-Straße 760438Frankfurt am MainGermany
- German Cancer Research Center and German Cancer ConsortiumIm Neuenheimer Feld 28069120HeidelbergGermany
- Frankfurt Cancer Institute (FCI)Theodor-Stern-Kai 760596Frankfurt am MainGermany
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10
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Damalanka VC, Maddirala AR, Janetka JW. Novel approaches to glycomimetic design: development of small molecular weight lectin antagonists. Expert Opin Drug Discov 2021; 16:513-536. [PMID: 33337918 DOI: 10.1080/17460441.2021.1857721] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Introduction: The direct binding of carbohydrates or those presented on glycoproteins or glycolipids to proteins is the primary effector of many biological responses. One class of carbohydrate-binding proteins, lectins are important in all forms of life. Their functions in animals include regulating cell adhesion, glycoprotein synthesis, metabolism, and mediating immune system response while in bacteria and viruses a lectin-mediated carbohydrate-protein interaction between host cells and the pathogen initiates pathogenesis of the infection.Areas covered: In this review, the authors outline the structural and functional pathogenesis of lectins from bacteria, amoeba, and humans. Mimics of a carbohydrate are referred to as glycomimetics, which are much smaller in molecular weight and are devised to mimic the key binding interactions of the carbohydrate while also allowing additional contacts with the lectin. This article emphasizes the various approaches used over the past 10-15 years in the rational design of glycomimetic ligands.Expert opinion: Medicinal chemistry efforts enabled by X-ray structural biology have identified small-molecule glycomimetic lectin antagonists that have entered or are nearing clinical trials. A common theme in these strategies is the use of biaryl ring systems to emulate the carbohydrate interactions with the lectin.
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Affiliation(s)
- Vishnu C Damalanka
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis USA
| | - Amarendar Reddy Maddirala
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis USA
| | - James W Janetka
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis USA
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11
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Hribernik N, Tamburrini A, Falletta E, Bernardi A. One pot synthesis of thio-glycosides via aziridine opening reactions. Org Biomol Chem 2021; 19:233-247. [DOI: 10.1039/d0ob01956a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
thio-Glycosides with a pseudo-disaccharide structure are synthesized via aziridine opening reactions starting from glycosyl thioacetates with a one-pot protocol, which affords glycomimetics equipped for easy and stable conjugation to aglycones.
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Affiliation(s)
- Nives Hribernik
- Università degli Studi di Milano
- Dipartimento di Chimica
- 20133 Milano
- Italy
| | - Alice Tamburrini
- Università degli Studi di Milano
- Dipartimento di Chimica
- 20133 Milano
- Italy
| | - Ermelinda Falletta
- Università degli Studi di Milano
- Dipartimento di Chimica
- 20133 Milano
- Italy
| | - Anna Bernardi
- Università degli Studi di Milano
- Dipartimento di Chimica
- 20133 Milano
- Italy
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12
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The Interaction of Fluorinated Glycomimetics with DC-SIGN: Multiple Binding Modes Disentangled by the Combination of NMR Methods and MD Simulations. Pharmaceuticals (Basel) 2020; 13:ph13080179. [PMID: 32759765 PMCID: PMC7463913 DOI: 10.3390/ph13080179] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/29/2020] [Accepted: 08/01/2020] [Indexed: 12/22/2022] Open
Abstract
Fluorinated glycomimetics are frequently employed to study and eventually modulate protein–glycan interactions. However, complex glycans and their glycomimetics may display multiple binding epitopes that enormously complicate the access to a complete picture of the protein–ligand complexes. We herein present a new methodology based on the synergic combination of experimental 19F-based saturation transfer difference (STD) NMR data with computational protocols, applied to analyze the interaction between DC-SIGN, a key lectin involved in inflammation and infection events with the trifluorinated glycomimetic of the trimannoside core, ubiquitous in human glycoproteins. A novel 2D-STD-TOCSYreF NMR experiment was employed to obtain the experimental STD NMR intensities, while the Complete Relaxation Matrix Analysis (CORCEMA-ST) was used to predict that expected for an ensemble of geometries extracted from extensive MD simulations. Then, an in-house built computer program was devised to find the ensemble of structures that provide the best fit between the theoretical and the observed STD data. Remarkably, the experimental STD profiles obtained for the ligand/DC-SIGN complex could not be satisfactorily explained by a single binding mode, but rather with a combination of different modes coexisting in solution. Therefore, the method provides a precise view of those ligand–receptor complexes present in solution.
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13
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Tvaroška I, Selvaraj C, Koča J. Selectins-The Two Dr. Jekyll and Mr. Hyde Faces of Adhesion Molecules-A Review. Molecules 2020; 25:molecules25122835. [PMID: 32575485 PMCID: PMC7355470 DOI: 10.3390/molecules25122835] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/27/2020] [Accepted: 06/17/2020] [Indexed: 02/06/2023] Open
Abstract
Selectins belong to a group of adhesion molecules that fulfill an essential role in immune and inflammatory responses and tissue healing. Selectins are glycoproteins that decode the information carried by glycan structures, and non-covalent interactions of selectins with these glycan structures mediate biological processes. The sialylated and fucosylated tetrasaccharide sLex is an essential glycan recognized by selectins. Several glycosyltransferases are responsible for the biosynthesis of the sLex tetrasaccharide. Selectins are involved in a sequence of interactions of circulated leukocytes with endothelial cells in the blood called the adhesion cascade. Recently, it has become evident that cancer cells utilize a similar adhesion cascade to promote metastases. However, like Dr. Jekyll and Mr. Hyde’s two faces, selectins also contribute to tissue destruction during some infections and inflammatory diseases. The most prominent function of selectins is associated with the initial stage of the leukocyte adhesion cascade, in which selectin binding enables tethering and rolling. The first adhesive event occurs through specific non-covalent interactions between selectins and their ligands, with glycans functioning as an interface between leukocytes or cancer cells and the endothelium. Targeting these interactions remains a principal strategy aimed at developing new therapies for the treatment of immune and inflammatory disorders and cancer. In this review, we will survey the significant contributions to and the current status of the understanding of the structure of selectins and the role of selectins in various biological processes. The potential of selectins and their ligands as therapeutic targets in chronic and acute inflammatory diseases and cancer will also be discussed. We will emphasize the structural characteristic of selectins and the catalytic mechanisms of glycosyltransferases involved in the biosynthesis of glycan recognition determinants. Furthermore, recent achievements in the synthesis of selectin inhibitors will be reviewed with a focus on the various strategies used for the development of glycosyltransferase inhibitors, including substrate analog inhibitors and transition state analog inhibitors, which are based on knowledge of the catalytic mechanism.
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Affiliation(s)
- Igor Tvaroška
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
- Institute of Chemistry, Slovak Academy of Sciences, 84538 Bratislava, Slovak Republic
- Correspondence: (I.T.); (J.K.); Tel.: +421-948-535-601 (I.T.); +420-731-682-606 (J.K.)
| | - Chandrabose Selvaraj
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
| | - Jaroslav Koča
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
- Correspondence: (I.T.); (J.K.); Tel.: +421-948-535-601 (I.T.); +420-731-682-606 (J.K.)
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14
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Bancet A, Raingeval C, Lomberget T, Le Borgne M, Guichou JF, Krimm I. Fragment Linking Strategies for Structure-Based Drug Design. J Med Chem 2020; 63:11420-11435. [DOI: 10.1021/acs.jmedchem.0c00242] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Alexandre Bancet
- EA 4446 Bioactive Molecules and Medicinal Chemistry, Faculté de Pharmacie, ISPB, SFR Santé Lyon-Est CNRS UMS3453, INSERM US7, Université de Lyon, Université Claude Bernard Lyon 1, 69373 Lyon Cedex 8, France
- Centre de RMN à Très Hauts Champs, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS, 5 Rue de la Doua, F-69100 Villeurbanne, France
| | - Claire Raingeval
- Centre de RMN à Très Hauts Champs, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS, 5 Rue de la Doua, F-69100 Villeurbanne, France
| | - Thierry Lomberget
- EA 4446 Bioactive Molecules and Medicinal Chemistry, Faculté de Pharmacie, ISPB, SFR Santé Lyon-Est CNRS UMS3453, INSERM US7, Université de Lyon, Université Claude Bernard Lyon 1, 69373 Lyon Cedex 8, France
| | - Marc Le Borgne
- EA 4446 Bioactive Molecules and Medicinal Chemistry, Faculté de Pharmacie, ISPB, SFR Santé Lyon-Est CNRS UMS3453, INSERM US7, Université de Lyon, Université Claude Bernard Lyon 1, 69373 Lyon Cedex 8, France
| | | | - Isabelle Krimm
- Centre de RMN à Très Hauts Champs, Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS, 5 Rue de la Doua, F-69100 Villeurbanne, France
- Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, 69008 Lyon, France
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15
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Keller BG, Rademacher C. Allostery in C-type lectins. Curr Opin Struct Biol 2019; 62:31-38. [PMID: 31838280 DOI: 10.1016/j.sbi.2019.11.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/30/2019] [Accepted: 11/04/2019] [Indexed: 10/25/2022]
Abstract
C-type lectins are the largest and most diverse family of mammalian carbohydrate-binding proteins. They share a common protein fold, which provides the unifying basis for calcium-mediated carbohydrate recognition. Their involvement in a multitude of biological functions is remarkable. Here, we review the variety of tasks these lectins are involved in alongside with the structural demands on the overall protein architecture. Subtle changes of the protein structure are implemented to cope with such diverse functional requirements. The presence of a high level of structural dynamics over a broad palette of time scales is paired with the presence of secondary binding sites and allosteric coordination of remote sites and renders this lectin fold a highly adaptable scaffold.
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Affiliation(s)
- Bettina G Keller
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
| | - Christoph Rademacher
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany; Max Planck Institute of Colloids and Interfaces, Department of Biomolecular Systems, 14424 Potsdam, Germany.
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16
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Lectin antagonists in infection, immunity, and inflammation. Curr Opin Chem Biol 2019; 53:51-67. [DOI: 10.1016/j.cbpa.2019.07.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/12/2019] [Accepted: 07/18/2019] [Indexed: 12/12/2022]
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17
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Valverde P, Ardá A, Reichardt NC, Jiménez-Barbero J, Gimeno A. Glycans in drug discovery. MEDCHEMCOMM 2019; 10:1678-1691. [PMID: 31814952 PMCID: PMC6839814 DOI: 10.1039/c9md00292h] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/10/2019] [Indexed: 02/06/2023]
Abstract
Glycans are key players in many biological processes. They are essential for protein folding and stability and act as recognition elements in cell-cell and cell-matrix interactions. Thus, being at the heart of medically relevant biological processes, glycans have come onto the scene and are considered hot spots for biomedical intervention. The progress in biophysical techniques allowing access to an increasing molecular and structural understanding of these processes has led to the development of effective therapeutics. Indeed, strategies aimed at designing glycomimetics able to block specific lectin-carbohydrate interactions, carbohydrate-based vaccines mimicking self- and non-self-antigens as well as the exploitation of the therapeutic potential of glycosylated antibodies are being pursued. In this mini-review the most prominent contributions concerning recurrent diseases are highlighted, including bacterial and viral infections, cancer or immune-related pathologies, which certainly show the great promise of carbohydrates in drug discovery.
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Affiliation(s)
- Pablo Valverde
- CIC bioGUNE , Bizkaia Technology Park, Building 800 , 48162 Derio , Bizkaia , Spain .
| | - Ana Ardá
- CIC bioGUNE , Bizkaia Technology Park, Building 800 , 48162 Derio , Bizkaia , Spain .
| | | | - Jesús Jiménez-Barbero
- CIC bioGUNE , Bizkaia Technology Park, Building 800 , 48162 Derio , Bizkaia , Spain .
- Ikerbasque , Basque Foundation for Science , 48013 Bilbao , Bizkaia , Spain
- Department of Organic Chemistry II , University of the Basque Country , UPV/EHU , 48940 Leioa , Bizkaia , Spain
| | - Ana Gimeno
- CIC bioGUNE , Bizkaia Technology Park, Building 800 , 48162 Derio , Bizkaia , Spain .
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18
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Brinkø A, Risinger C, Lambert A, Blixt O, Grandjean C, Jensen HH. Combining Click Reactions for the One-Pot Synthesis of Modular Biomolecule Mimetics. Org Lett 2019; 21:7544-7548. [PMID: 31502847 DOI: 10.1021/acs.orglett.9b02811] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here, we report on the first combined one-pot use of the two so-called "click reactions": the thiol-ene coupling and the copper-catalyzed alkyne-azide cycloaddition. These reactions were employed in an alternating and one-pot fashion to combine appropriately functionalized monomeric carbohydrate building blocks to create mimics of trisaccharides and tetrasaccharides as single anomers, with only minimal purification necessary. The deprotected oligosaccharide mimics were found to bind both plant lectins and human galectin-3.
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Affiliation(s)
- Anne Brinkø
- Department of Chemistry , Aarhus University , Langelandsgade 140 , 8000 Aarhus C, Denmark
| | - Christian Risinger
- Department of Chemistry, Chemical Biology , University of Copenhagen , Thorvaldsensvej 40 , 1871 Frederiksberg C, Denmark
| | - Annie Lambert
- Faculté des Sciences et des Techniques, Unité Fonctionnalité et Ingénierie des Protéines (UFIP) , Université de Nantes , UMR CNRS 6286, 2, rue de la Houssinière , BP92208, 44322 Nantes Cedex 3, France
| | - Ola Blixt
- Department of Chemistry, Chemical Biology , University of Copenhagen , Thorvaldsensvej 40 , 1871 Frederiksberg C, Denmark
| | - Cyrille Grandjean
- Faculté des Sciences et des Techniques, Unité Fonctionnalité et Ingénierie des Protéines (UFIP) , Université de Nantes , UMR CNRS 6286, 2, rue de la Houssinière , BP92208, 44322 Nantes Cedex 3, France
| | - Henrik H Jensen
- Department of Chemistry , Aarhus University , Langelandsgade 140 , 8000 Aarhus C, Denmark
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19
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Wamhoff EC, Schulze J, Bellmann L, Rentzsch M, Bachem G, Fuchsberger FF, Rademacher J, Hermann M, Del Frari B, van Dalen R, Hartmann D, van Sorge NM, Seitz O, Stoitzner P, Rademacher C. A Specific, Glycomimetic Langerin Ligand for Human Langerhans Cell Targeting. ACS CENTRAL SCIENCE 2019; 5:808-820. [PMID: 31139717 PMCID: PMC6535779 DOI: 10.1021/acscentsci.9b00093] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Indexed: 05/30/2023]
Abstract
Langerhans cells are a subset of dendritic cells residing in the epidermis of the human skin. As such, they are key mediators of immune regulation and have emerged as prime targets for novel transcutaneous cancer vaccines. Importantly, the induction of protective T cell immunity by these vaccines requires the efficient and specific delivery of both tumor-associated antigens and adjuvants. Langerhans cells uniquely express Langerin (CD207), an endocytic C-type lectin receptor. Here, we report the discovery of a specific, glycomimetic Langerin ligand employing a heparin-inspired design strategy and structural characterization by NMR spectroscopy and molecular docking. The conjugation of this glycomimetic to liposomes enabled the specific and efficient targeting of Langerhans cells in the human skin. We further demonstrate the doxorubicin-mediated killing of a Langerin+ monocyte cell line, highlighting its therapeutic and diagnostic potential in Langerhans cell histiocytosis, caused by the abnormal proliferation of Langerin+ myeloid progenitor cells. Overall, our delivery platform provides superior versatility over antibody-based approaches and novel modalities to overcome current limitations of dendritic cell-targeted immuno- and chemotherapy.
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Affiliation(s)
- Eike-Christian Wamhoff
- Department
of Biomolecular Systems, Max Planck Institute
of Colloids and Interfaces, 14424 Potsdam, Germany
- Department
of Biology, Chemistry and Pharmacy, Freie
Universität Berlin, 14195 Berlin, Germany
| | - Jessica Schulze
- Department
of Biomolecular Systems, Max Planck Institute
of Colloids and Interfaces, 14424 Potsdam, Germany
- Department
of Biology, Chemistry and Pharmacy, Freie
Universität Berlin, 14195 Berlin, Germany
| | - Lydia Bellmann
- Department of Dermatology, Venereology and Allergology, Department of Anesthesiology
and Intensive Care Medicine, and Department of Plastic, Reconstructive and
Aesthetic Surgery, Medical University of
Innsbruck, 6020 Innsbruck, Austria
| | - Mareike Rentzsch
- Department
of Biomolecular Systems, Max Planck Institute
of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Gunnar Bachem
- Department
of Chemistry, Humboldt-Universität
zu Berlin, 12489 Berlin, Germany
| | - Felix F. Fuchsberger
- Department
of Biomolecular Systems, Max Planck Institute
of Colloids and Interfaces, 14424 Potsdam, Germany
- Medical
Microbiology, University Medical Center
Utrecht, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Juliane Rademacher
- Department
of Biomolecular Systems, Max Planck Institute
of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Martin Hermann
- Department of Dermatology, Venereology and Allergology, Department of Anesthesiology
and Intensive Care Medicine, and Department of Plastic, Reconstructive and
Aesthetic Surgery, Medical University of
Innsbruck, 6020 Innsbruck, Austria
| | - Barbara Del Frari
- Department of Dermatology, Venereology and Allergology, Department of Anesthesiology
and Intensive Care Medicine, and Department of Plastic, Reconstructive and
Aesthetic Surgery, Medical University of
Innsbruck, 6020 Innsbruck, Austria
| | - Rob van Dalen
- Medical
Microbiology, University Medical Center
Utrecht, Utrecht University, 3584 CX Utrecht, Netherlands
| | - David Hartmann
- Department
of Biomolecular Systems, Max Planck Institute
of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Nina M. van Sorge
- Medical
Microbiology, University Medical Center
Utrecht, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Oliver Seitz
- Department
of Chemistry, Humboldt-Universität
zu Berlin, 12489 Berlin, Germany
| | - Patrizia Stoitzner
- Department of Dermatology, Venereology and Allergology, Department of Anesthesiology
and Intensive Care Medicine, and Department of Plastic, Reconstructive and
Aesthetic Surgery, Medical University of
Innsbruck, 6020 Innsbruck, Austria
| | - Christoph Rademacher
- Department
of Biomolecular Systems, Max Planck Institute
of Colloids and Interfaces, 14424 Potsdam, Germany
- Department
of Biology, Chemistry and Pharmacy, Freie
Universität Berlin, 14195 Berlin, Germany
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20
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Zhang S, Song Q, Wang X, Wei Z, Yu R, Wang X, Jiang T. Virtual Screening Guided Design, Synthesis and Bioactivity Study of Benzisoselenazolones (BISAs) on Inhibition of c-Met and Its Downstream Signalling Pathways. Int J Mol Sci 2019; 20:E2489. [PMID: 31137515 PMCID: PMC6566228 DOI: 10.3390/ijms20102489] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 05/14/2019] [Accepted: 05/15/2019] [Indexed: 12/12/2022] Open
Abstract
c-Met is a transmembrane receptor tyrosine kinase and an important therapeutic target for anticancer drugs. In this study, we designed a small library containing 300 BISAs molecules that consisted of carbohydrates, amino acids, isothiourea, tetramethylthiourea, guanidine and heterocyclic groups and screened c-Met targeting compounds using docking and MM/GBSA. Guided by virtual screening, we synthesised a series of novel compounds and their activity on inhibition of the autophosphorylation of c-Met and its downstream signalling pathway proteins were evaluated. We found a panel of benzisoselenazolones (BISAs) obtained by introducing isothiourea, tetramethylthiourea and heterocyclic groups into the C-ring of Ebselen, including 7a, 7b, 8a, 8b and 12c (with IC50 values of less than 20 μM in MET gene amplified lung cancer cell line EBC-1), exhibited more potent antitumour activity than Ebselen by cell growth assay combined with in vitro biochemical assays. In addition, we also tested the antitumour activity of three cancer cell lines without MET gene amplification/activation, including DLD1, MDA-MB-231 and A549. The neuroblastoma SK-N-SH cells with HGF overexpression which activates MET signalling are sensitive to MET inhibitors. The results reveal that our compounds may be nonspecific multitarget kinase inhibitors, just like type-II small molecule inhibitors. Western blot analysis showed that these inhibitors inhibited autophosphorylation of c-MET, and its downstream signalling pathways, such as PI3K/AKT and MARK/ERK. Results suggest that bensoisoselenones can be used as a scaffold for the design of c-Met inhibiting drug leads, and this study opens up new possibilities for future antitumour drug design.
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Affiliation(s)
- Siqi Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
| | - Qiaoling Song
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
- Center for Innovative Marine Drug Screening & Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266100, China.
| | - Xueting Wang
- Center for High Performance Computing & System simulation, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266100, China.
| | - Zhiqiang Wei
- Center for High Performance Computing & System simulation, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266100, China.
| | - Rilei Yu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
- Center for Innovative Marine Drug Screening & Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266100, China.
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China.
| | - Xin Wang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
- Center for Innovative Marine Drug Screening & Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266100, China.
| | - Tao Jiang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
- Center for Innovative Marine Drug Screening & Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266100, China.
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China.
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21
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Frei P, Hevey R, Ernst B. Dynamic Combinatorial Chemistry: A New Methodology Comes of Age. Chemistry 2018; 25:60-73. [DOI: 10.1002/chem.201803365] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Priska Frei
- Institute of Molecular Pharmacy, PharmacenterUniversity of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Rachel Hevey
- Institute of Molecular Pharmacy, PharmacenterUniversity of Basel Klingelbergstrasse 50 4056 Basel Switzerland
| | - Beat Ernst
- Institute of Molecular Pharmacy, PharmacenterUniversity of Basel Klingelbergstrasse 50 4056 Basel Switzerland
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22
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Romagnoli R, Prencipe F, Lopez-Cara LC, Oliva P, Baraldi S, Baraldi PG, Estévez-Sarmiento F, Quintana J, Estévez F. Synthesis and biological evaluation of alpha-bromoacryloylamido indolyl pyridinyl propenones as potent apoptotic inducers in human leukaemia cells. J Enzyme Inhib Med Chem 2018; 33:727-742. [PMID: 29620429 PMCID: PMC6009983 DOI: 10.1080/14756366.2018.1450749] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 03/07/2018] [Indexed: 02/06/2023] Open
Abstract
The combination of two pharmacophores into a single molecule represents one of the methods that can be adopted for the synthesis of new anticancer molecules. To investigate the influence of the position of the pyridine nitrogen on biological activity, two different series of α-bromoacryloylamido indolyl pyridinyl propenones 3a-h and 4a-d were designed and synthesized by a pharmacophore hybridization approach and evaluated for their antiproliferative activity against a panel of six human cancer cell lines. These hybrid molecules were prepared to combine the α-bromoacryloyl moiety with two series of indole-inspired chalcone analogues, possessing an indole derivative and a 3- or 4-pyridine ring, respectively, linked on either side of 2-propen-1-one system. The structure-activity relationship was also investigated by the insertion of alkyl or benzyl moieties at the N-1 position of the indole nucleus. We found that most of the newly synthesized displayed high antiproliferative activity against U-937, MOLT-3, K-562, and NALM-6 leukaemia cell lines, with one-digit to double-digit nanomolar IC50 values. The antiproliferative activities of 3-pyridinyl derivatives 3f-h revealed that N-benzyl indole analogues generally exhibited lower activity compared to N-H or N-alkyl derivatives 3a-b and 3c-e, respectively. Moreover, cellular mechanism studies elucidated that compound 4a induced apoptosis along with a decrease of mitochondrial membrane potential and activated caspase-3 in a concentration-dependent manner.
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Affiliation(s)
- Romeo Romagnoli
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Ferrara, Ferrara, Italy
| | - Filippo Prencipe
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Ferrara, Ferrara, Italy
| | - Luisa Carlota Lopez-Cara
- Departamento de Química Farmaceútica y Orgánica Facultad de Farmacia, Campus de Cartuja s/n, Granada, Spain
| | - Paola Oliva
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Ferrara, Ferrara, Italy
| | - Stefania Baraldi
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Ferrara, Ferrara, Italy
| | - Pier Giovanni Baraldi
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Ferrara, Ferrara, Italy
| | - Francisco Estévez-Sarmiento
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Investigaciones Biomédicas y Sanitarias, Universidad de las Palmas de Gran Canaria, Spain
| | - José Quintana
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Investigaciones Biomédicas y Sanitarias, Universidad de las Palmas de Gran Canaria, Spain
| | - Francisco Estévez
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Investigaciones Biomédicas y Sanitarias, Universidad de las Palmas de Gran Canaria, Spain
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23
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Aretz J, Anumala UR, Fuchsberger FF, Molavi N, Ziebart N, Zhang H, Nazaré M, Rademacher C. Allosteric Inhibition of a Mammalian Lectin. J Am Chem Soc 2018; 140:14915-14925. [DOI: 10.1021/jacs.8b08644] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Jonas Aretz
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam, Germany
- Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Upendra R. Anumala
- Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Strasse 10, 13125 Berlin, Germany
| | - Felix F. Fuchsberger
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam, Germany
| | - Narges Molavi
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam, Germany
- Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Strasse 10, 13125 Berlin, Germany
| | - Nandor Ziebart
- Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Strasse 10, 13125 Berlin, Germany
| | - Hengxi Zhang
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam, Germany
| | - Marc Nazaré
- Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Strasse 10, 13125 Berlin, Germany
- Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Strasse 2, 10178 Berlin, Germany
| | - Christoph Rademacher
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam, Germany
- Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
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25
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Zetterberg FR, Peterson K, Johnsson RE, Brimert T, Håkansson M, Logan DT, Leffler H, Nilsson UJ. Monosaccharide Derivatives with Low-Nanomolar Lectin Affinity and High Selectivity Based on Combined Fluorine-Amide, Phenyl-Arginine, Sulfur-π, and Halogen Bond Interactions. ChemMedChem 2018; 13:133-137. [PMID: 29194992 DOI: 10.1002/cmdc.201700744] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Indexed: 12/20/2022]
Abstract
The design of small and high-affinity lectin inhibitors remains a major challenge because the natural ligand binding sites of lectin are often shallow and have polar character. Herein we report that derivatizing galactose with un-natural structural elements that form multiple non-natural lectin-ligand interactions (orthogonal multipolar fluorine-amide, phenyl-arginine, sulfur-π, and halogen bond) can provide inhibitors with extraordinary affinity (low nanomolar) for the model lectin, galectin-3, which is more than five orders of magnitude higher than the parent galactose; moreover, is selective over other galectins.
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Affiliation(s)
- Fredrik R Zetterberg
- Galecto Biotech AB, Sahlgrenska Science Park, Medicinaregatan 8A, 413 46, Gothenburg, Sweden
| | - Kristoffer Peterson
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, Box 124, 221 00, Lund, Sweden
| | | | - Thomas Brimert
- Red Glead Discovery AB, Medicon Village, 223 63, Lund, Sweden
| | - Maria Håkansson
- SARomics Biostructures AB, Medicon Village, 223 63, Lund, Sweden
| | - Derek T Logan
- SARomics Biostructures AB, Medicon Village, 223 63, Lund, Sweden.,Biochemistry and Structural Biology, Center for Molecular Protein Science, Department of Chemistry, Lund University, Box 124, 221 00, Lund, Sweden
| | - Hakon Leffler
- Department of Laboratory Medicine, Section MIG, Lund University BMC-C1228b, Klinikgatan 28, 221 84, Lund, Sweden
| | - Ulf J Nilsson
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, Box 124, 221 00, Lund, Sweden
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Heparin Mimetics: Their Therapeutic Potential. Pharmaceuticals (Basel) 2017; 10:ph10040078. [PMID: 28974047 PMCID: PMC5748635 DOI: 10.3390/ph10040078] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 09/21/2017] [Accepted: 09/22/2017] [Indexed: 01/04/2023] Open
Abstract
Heparin mimetics are synthetic and semi-synthetic compounds that are highly sulfated, structurally distinct analogues of glycosaminoglycans. These mimetics are often rationally designed to increase potency and binding selectivity towards specific proteins involved in disease manifestations. Some of the major therapeutic arenas towards which heparin mimetics are targeted include: coagulation and thrombosis, cancers, and inflammatory diseases. Although Fondaparinux, a rationally designed heparin mimetic, is now approved for prophylaxis and treatment of venous thromboembolism, the search for novel anticoagulant heparin mimetics with increased affinity and fewer side effects remains a subject of research. However, increasingly, research is focusing on the non-anticoagulant activities of these molecules. Heparin mimetics have potential as anti-cancer agents due to their ability to: (1) inhibit heparanase, an endoglycosidase which facilitates the spread of tumor cells; and (2) inhibit angiogenesis by binding to growth factors. The heparin mimetic, PI-88 is in clinical trials for post-surgical hepatocellular carcinoma and advanced melanoma. The anti-inflammatory properties of heparin mimetics have primarily been attributed to their ability to interact with: complement system proteins, selectins and chemokines; each of which function differently to facilitate inflammation. The efficacy of low/non-anticoagulant heparin mimetics in animal models of different inflammatory diseases has been demonstrated. These findings, plus clinical data that indicates heparin has anti-inflammatory activity, will raise the momentum for developing heparin mimetics as a new class of therapeutic agent for inflammatory diseases.
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Kulp JL, Cloudsdale IS, Kulp JL, Guarnieri F. Hot-spot identification on a broad class of proteins and RNA suggest unifying principles of molecular recognition. PLoS One 2017; 12:e0183327. [PMID: 28837642 PMCID: PMC5570288 DOI: 10.1371/journal.pone.0183327] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 08/02/2017] [Indexed: 01/03/2023] Open
Abstract
Chemically diverse fragments tend to collectively bind at localized sites on proteins, which is a cornerstone of fragment-based techniques. A central question is how general are these strategies for predicting a wide variety of molecular interactions such as small molecule-protein, protein-protein and protein-nucleic acid for both experimental and computational methods. To address this issue, we recently proposed three governing principles, (1) accurate prediction of fragment-macromolecule binding free energy, (2) accurate prediction of water-macromolecule binding free energy, and (3) locating sites on a macromolecule that have high affinity for a diversity of fragments and low affinity for water. To test the generality of these concepts we used the computational technique of Simulated Annealing of Chemical Potential to design one small fragment to break the RecA-RecA protein-protein interaction and three fragments that inhibit peptide-deformylase via water-mediated multi-body interactions. Experiments confirm the predictions that 6-hydroxydopamine potently inhibits RecA and that PDF inhibition quantitatively tracks the water-mediated binding predictions. Additionally, the principles correctly predict the essential bound waters in HIV Protease, the surprisingly extensive binding site of elastase, the pinpoint location of electron transfer in dihydrofolate reductase, the HIV TAT-TAR protein-RNA interactions, and the MDM2-MDM4 differential binding to p53. The experimental confirmations of highly non-obvious predictions combined with the precise characterization of a broad range of known phenomena lend strong support to the generality of fragment-based methods for characterizing molecular recognition.
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Affiliation(s)
- John L. Kulp
- Conifer Point Pharmaceuticals, Doylestown, Pennsylvania, United States of America
- Department of Chemistry, Baruch S. Blumberg Institute, Doylestown, Pennsylvania, United States of America
| | - Ian S. Cloudsdale
- Conifer Point Pharmaceuticals, Doylestown, Pennsylvania, United States of America
| | - John L. Kulp
- Conifer Point Pharmaceuticals, Doylestown, Pennsylvania, United States of America
| | - Frank Guarnieri
- PAKA Pulmonary Pharmaceuticals, Acton, Massachusetts, United States of America
- * E-mail:
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Aretz J, Baukmann H, Shanina E, Hanske J, Wawrzinek R, Zapol'skii VA, Seeberger PH, Kaufmann DE, Rademacher C. Identifikation sekundärer Bindestellen auf DC-SIGN mithilfe eines Fragment-Screenings. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701943] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jonas Aretz
- Abteilung für Biomolekulare Systeme; Max-Planck-Institut für Kolloid- und Grenzflächenforschung; Am Mühlenberg 1 14476 Potsdam Deutschland
- Fachbereich für Biologie, Chemie und Pharmazie; Freie Universität Berlin; Takustraße 3 14195 Berlin Deutschland
| | - Hannes Baukmann
- Abteilung für Biomolekulare Systeme; Max-Planck-Institut für Kolloid- und Grenzflächenforschung; Am Mühlenberg 1 14476 Potsdam Deutschland
- Fachbereich für Biologie, Chemie und Pharmazie; Freie Universität Berlin; Takustraße 3 14195 Berlin Deutschland
| | - Elena Shanina
- Abteilung für Biomolekulare Systeme; Max-Planck-Institut für Kolloid- und Grenzflächenforschung; Am Mühlenberg 1 14476 Potsdam Deutschland
- Fachbereich für Biologie, Chemie und Pharmazie; Freie Universität Berlin; Takustraße 3 14195 Berlin Deutschland
| | - Jonas Hanske
- Abteilung für Biomolekulare Systeme; Max-Planck-Institut für Kolloid- und Grenzflächenforschung; Am Mühlenberg 1 14476 Potsdam Deutschland
- Fachbereich für Biologie, Chemie und Pharmazie; Freie Universität Berlin; Takustraße 3 14195 Berlin Deutschland
| | - Robert Wawrzinek
- Abteilung für Biomolekulare Systeme; Max-Planck-Institut für Kolloid- und Grenzflächenforschung; Am Mühlenberg 1 14476 Potsdam Deutschland
| | - Viktor A. Zapol'skii
- Institut für Organische Chemie; Technische Universität Clausthal; Leibnizstraße 6 38678 Clausthal-Zellerfeld Deutschland
| | - Peter H. Seeberger
- Abteilung für Biomolekulare Systeme; Max-Planck-Institut für Kolloid- und Grenzflächenforschung; Am Mühlenberg 1 14476 Potsdam Deutschland
- Fachbereich für Biologie, Chemie und Pharmazie; Freie Universität Berlin; Takustraße 3 14195 Berlin Deutschland
| | - Dieter E. Kaufmann
- Institut für Organische Chemie; Technische Universität Clausthal; Leibnizstraße 6 38678 Clausthal-Zellerfeld Deutschland
| | - Christoph Rademacher
- Abteilung für Biomolekulare Systeme; Max-Planck-Institut für Kolloid- und Grenzflächenforschung; Am Mühlenberg 1 14476 Potsdam Deutschland
- Fachbereich für Biologie, Chemie und Pharmazie; Freie Universität Berlin; Takustraße 3 14195 Berlin Deutschland
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Aretz J, Baukmann H, Shanina E, Hanske J, Wawrzinek R, Zapol'skii VA, Seeberger PH, Kaufmann DE, Rademacher C. Identification of Multiple Druggable Secondary Sites by Fragment Screening against DC-SIGN. Angew Chem Int Ed Engl 2017; 56:7292-7296. [PMID: 28523851 DOI: 10.1002/anie.201701943] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 03/28/2017] [Indexed: 01/08/2023]
Abstract
DC-SIGN is a cell-surface receptor for several pathogenic threats, such as HIV, Ebola virus, or Mycobacterium tuberculosis. Multiple attempts to develop inhibitors of the underlying carbohydrate-protein interactions have been undertaken in the past fifteen years. Still, drug-like DC-SIGN ligands are sparse, which is most likely due to its hydrophilic, solvent-exposed carbohydrate-binding site. Herein, we report on a parallel fragment screening against DC-SIGN applying SPR and a reporter displacement assay, which complements previous screenings using 19 F NMR spectroscopy and chemical fragment microarrays. Hit validation by SPR and 1 H-15 N HSQC NMR spectroscopy revealed that although no fragment bound in the primary carbohydrate site, five secondary sites are available to harbor drug-like molecules. Building on key interactions of the reported fragment hits, these pockets will be targeted in future approaches to accelerate the development of DC-SIGN inhibitors.
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Affiliation(s)
- Jonas Aretz
- Abteilung für Biomolekulare Systeme, Max-Planck-Institut für Kolloid- und Grenzflächenforschung, Am Mühlenberg 1, 14476, Potsdam, Germany.,Fachbereich für Biologie, Chemie und Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195, Berlin, Germany
| | - Hannes Baukmann
- Abteilung für Biomolekulare Systeme, Max-Planck-Institut für Kolloid- und Grenzflächenforschung, Am Mühlenberg 1, 14476, Potsdam, Germany.,Fachbereich für Biologie, Chemie und Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195, Berlin, Germany
| | - Elena Shanina
- Abteilung für Biomolekulare Systeme, Max-Planck-Institut für Kolloid- und Grenzflächenforschung, Am Mühlenberg 1, 14476, Potsdam, Germany.,Fachbereich für Biologie, Chemie und Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195, Berlin, Germany
| | - Jonas Hanske
- Abteilung für Biomolekulare Systeme, Max-Planck-Institut für Kolloid- und Grenzflächenforschung, Am Mühlenberg 1, 14476, Potsdam, Germany.,Fachbereich für Biologie, Chemie und Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195, Berlin, Germany
| | - Robert Wawrzinek
- Abteilung für Biomolekulare Systeme, Max-Planck-Institut für Kolloid- und Grenzflächenforschung, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Viktor A Zapol'skii
- Institut für Organische Chemie, Technische Universität Clausthal, Leibnizstrasse 6, 38678, Clausthal-Zellerfeld, Germany
| | - Peter H Seeberger
- Abteilung für Biomolekulare Systeme, Max-Planck-Institut für Kolloid- und Grenzflächenforschung, Am Mühlenberg 1, 14476, Potsdam, Germany.,Fachbereich für Biologie, Chemie und Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195, Berlin, Germany
| | - Dieter E Kaufmann
- Institut für Organische Chemie, Technische Universität Clausthal, Leibnizstrasse 6, 38678, Clausthal-Zellerfeld, Germany
| | - Christoph Rademacher
- Abteilung für Biomolekulare Systeme, Max-Planck-Institut für Kolloid- und Grenzflächenforschung, Am Mühlenberg 1, 14476, Potsdam, Germany.,Fachbereich für Biologie, Chemie und Pharmazie, Freie Universität Berlin, Takustrasse 3, 14195, Berlin, Germany
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Abstract
Since 2004, when the first synthetic glycoconjugate vaccine against the pneumonia and meningitis causing bacterium Haemophilus influenza type b (Hib) approved for human use in Cuba was reported, 34 million doses of the synthetic vaccine have been already distributed in several countries under the commercial name of Quimi-Hib. However, despite the success of this product, no other synthetic glycoconjugate vaccine has been licensed in the following 13 years. As well as avoiding the need to handle pathogens, synthetic glycoconjugates offer clear advantages in terms of product characterization and the possibility to understand the parameters influencing immunogenicity. Nevertheless, large scale application of synthetic sugars has been perceived as challenging because of manufacturing costs and process complexity compared to natural polysaccharides. Chemoenzymatic approaches, one-pot protocols, and automated solid-phase synthesis are rendering carbohydrate production considerably more attractive for industrialization. Here we identify three areas where chemical approaches can advance this progress: (i) chemical or enzymatic methods enabling the delivery of the minimal polysaccharide portion responsible for an effective immune response; (ii) site-selective chemical or enzymatic conjugation strategies for the exploration of the conjugation point in immune responses against carbohydrate-based vaccines, and the consistent preparation of more homogeneous products; (iii) multicomponent constructs targeting receptors responsible for immune response modulation in order to control its quality and magnitude. We discuss how synthesis of bacterial oligosaccharides is useful toward understanding the polysaccharide portion responsible for immunogenicity, and for developing robust and consistent alternatives to natural heterogeneous polysaccharides. The synthesis of sugar analogues can lead to the identification of hydrolytically more stable versions of oligosaccharide antigens. The study of bacterial polysaccharide biosynthesis aids the development of in vitro hazard-free oligosaccharide production. Novel site-selective conjugation methods contribute toward deciphering the role of conjugation sites in the immunogenicity of glycoconjugates and prove to be particularly useful when glycans are conjugated to protein serving as carrier and antigen. The orthogonal incorporation of two different carbohydrate haptens enables the reduction of vaccine components. Finally, coordinated conjugation of glycans and small molecule immunopotentiators supports simplification of vaccine formulation and localization of adjuvant. Synergistic advancement of these areas, combined with competitive manufacturing processes, will contribute to a better understanding of the features guiding the immunological activity of glycoconjugates and, ultimately, to the design of improved, safer vaccines.
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Doak BC, Norton RS, Scanlon MJ. The ways and means of fragment-based drug design. Pharmacol Ther 2016; 167:28-37. [DOI: 10.1016/j.pharmthera.2016.07.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 07/08/2016] [Indexed: 12/21/2022]
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Kanabar V, Tedaldi L, Jiang J, Nie X, Panina I, Descroix K, Man F, Pitchford SC, Page CP, Wagner GK. Base-modified UDP-sugars reduce cell surface levels of P-selectin glycoprotein 1 (PSGL-1) on IL-1β-stimulated human monocytes. Glycobiology 2016; 26:1059-1071. [PMID: 27233805 PMCID: PMC5072147 DOI: 10.1093/glycob/cww053] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Revised: 04/07/2016] [Accepted: 04/22/2016] [Indexed: 12/26/2022] Open
Abstract
P-selectin glycoprotein ligand-1 (PSGL-1, CD162) is a cell-surface glycoprotein that is expressed, either constitutively or inducibly, on all myeloid and lymphoid cell lineages. PSGL-1 is implicated in cell-cell interactions between platelets, leukocytes and endothelial cells, and a key mediator of inflammatory cell recruitment and transmigration into tissues. Here, we have investigated the effects of the β-1,4-galactosyltransferase inhibitor 5-(5-formylthien-2-yl) UDP-Gal (5-FT UDP-Gal, compound 1: ) and two close derivatives on the cell surface levels of PSGL-1 on human peripheral blood mononuclear cells (hPBMCs). PSGL-1 levels were studied both under basal conditions, and upon stimulation of hPBMCs with interleukin-1β (IL-1β). Between 1 and 24 hours after IL-1β stimulation, we observed initial PSGL-1 shedding, followed by an increase in PSGL-1 levels on the cell surface, with a maximal window between IL-1β-induced and basal levels after 72 h. All three inhibitors reduce PSGL-1 levels on IL-1β-stimulated cells in a concentration-dependent manner, but show no such effect in resting cells. Compound 1: also affects the cell surface levels of adhesion molecule CD11b in IL-1β-stimulated hPBMCs, but not of glycoproteins CD14 and CCR2. This activity profile may be linked to the inhibition of global Sialyl Lewis presentation on hPBMCs by compound 1: , which we have also observed. Although this mechanistic explanation remains hypothetical at present, our results show, for the first time, that small molecules can discriminate between IL-1β-induced and basal levels of cell surface PSGL-1. These findings open new avenues for intervention with PSGL-1 presentation on the cell surface of primed hPBMCs and may have implications for anti-inflammatory drug development.
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Affiliation(s)
- Varsha Kanabar
- Sackler Institute of Pulmonary Pharmacology
- Institute of Pharmaceutical Science, King's College London, Franklin Wilkins Building, London SE1 9NH, UK
| | - Lauren Tedaldi
- Institute of Pharmaceutical Science, King's College London, Franklin Wilkins Building, London SE1 9NH, UK
- Department of Chemistry, Faculty of Natural & Mathematical Sciences, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Jingqian Jiang
- Department of Chemistry, Faculty of Natural & Mathematical Sciences, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Xiaodan Nie
- Sackler Institute of Pulmonary Pharmacology
- Institute of Pharmaceutical Science, King's College London, Franklin Wilkins Building, London SE1 9NH, UK
| | - Irina Panina
- Institute of Pharmaceutical Science, King's College London, Franklin Wilkins Building, London SE1 9NH, UK
| | - Karine Descroix
- School of Pharmacy, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Francis Man
- Sackler Institute of Pulmonary Pharmacology
- Institute of Pharmaceutical Science, King's College London, Franklin Wilkins Building, London SE1 9NH, UK
| | - Simon C Pitchford
- Sackler Institute of Pulmonary Pharmacology
- Institute of Pharmaceutical Science, King's College London, Franklin Wilkins Building, London SE1 9NH, UK
| | - Clive P Page
- Sackler Institute of Pulmonary Pharmacology
- Institute of Pharmaceutical Science, King's College London, Franklin Wilkins Building, London SE1 9NH, UK
| | - Gerd K Wagner
- Department of Chemistry, Faculty of Natural & Mathematical Sciences, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
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34
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He XP, Zeng YL, Zang Y, Li J, Field RA, Chen GR. Carbohydrate CuAAC click chemistry for therapy and diagnosis. Carbohydr Res 2016; 429:1-22. [DOI: 10.1016/j.carres.2016.03.022] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/22/2016] [Accepted: 03/23/2016] [Indexed: 12/12/2022]
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35
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Sommer R, Wagner S, Varrot A, Nycholat CM, Khaledi A, Häussler S, Paulson JC, Imberty A, Titz A. The virulence factor LecB varies in clinical isolates: consequences for ligand binding and drug discovery. Chem Sci 2016; 7:4990-5001. [PMID: 30155149 PMCID: PMC6018602 DOI: 10.1039/c6sc00696e] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/05/2016] [Indexed: 01/18/2023] Open
Abstract
P. aeruginosa causes a substantial number of nosocomial infections and is the leading cause of death of cystic fibrosis patients. This Gram-negative bacterium is highly resistant against antibiotics and further protects itself by forming a biofilm. Moreover, a high genomic variability among clinical isolates complicates therapy. Its lectin LecB is a virulence factor and necessary for adhesion and biofilm formation. We analyzed the sequence of LecB variants in a library of clinical isolates and demonstrate that it can serve as a marker for strain family classification. LecB from the highly virulent model strain PA14 presents 13% sequence divergence with LecB from the well characterized PAO1 strain. These differences might result in differing ligand binding specificities and ultimately in reduced efficacy of drugs directed towards LecB. Despite several amino acid variations at the carbohydrate binding site, glycan array analysis showed a comparable binding pattern for both variants. A common high affinity ligand could be identified and after its chemoenzymatic synthesis verified in a competitive binding assay: an N-glycan presenting two blood group O epitopes (H-type 2 antigen). Molecular modeling of the complex suggests a bivalent interaction of the ligand with the LecB tetramer by bridging two separate binding sites. This binding rationalizes the strong avidity (35 nM) of LecBPA14 to this human fucosylated N-glycan. Biochemical evaluation of a panel of glycan ligands revealed that LecBPA14 demonstrated higher glycan affinity compared to LecBPAO1 including the extraordinarily potent affinity of 70 nM towards the monovalent human antigen Lewisa. The structural basis of this unusual high affinity ligand binding for lectins was rationalized by solving the protein crystal structures of LecBPA14 with several glycans.
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Affiliation(s)
- Roman Sommer
- Chemical Biology of Carbohydrates , Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , D-66123 Saarbrücken , Germany . ; http://www.helmholtz-hzi.de/cbch.,Deutsches Zentrum für Infektionsforschung (DZIF) , Standort Hannover , Braunschweig , Germany
| | - Stefanie Wagner
- Chemical Biology of Carbohydrates , Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , D-66123 Saarbrücken , Germany . ; http://www.helmholtz-hzi.de/cbch.,Deutsches Zentrum für Infektionsforschung (DZIF) , Standort Hannover , Braunschweig , Germany
| | - Annabelle Varrot
- Centre de Recherche sur les Macromolécules Végétales (CERMAV-UPR5301) , CNRS and Université Grenoble Alpes , BP53 , F-38041 Grenoble cedex 9 , France
| | - Corwin M Nycholat
- Department of Cell and Molecular Biology and Department of Chemical Physiology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , CA 92037 , USA
| | - Ariane Khaledi
- Molecular Bacteriology , Helmholtz Centre for Infection Research , D-38124 Braunschweig , Germany
| | - Susanne Häussler
- Molecular Bacteriology , Helmholtz Centre for Infection Research , D-38124 Braunschweig , Germany
| | - James C Paulson
- Department of Cell and Molecular Biology and Department of Chemical Physiology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , CA 92037 , USA
| | - Anne Imberty
- Centre de Recherche sur les Macromolécules Végétales (CERMAV-UPR5301) , CNRS and Université Grenoble Alpes , BP53 , F-38041 Grenoble cedex 9 , France
| | - Alexander Titz
- Chemical Biology of Carbohydrates , Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , D-66123 Saarbrücken , Germany . ; http://www.helmholtz-hzi.de/cbch.,Deutsches Zentrum für Infektionsforschung (DZIF) , Standort Hannover , Braunschweig , Germany
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36
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Barra PA, Jiménez VA, Gavin JA, Daranas AH, Alderete JB. Discovery of New E-Selectin Inhibitors by Virtual Screening, Fluorescence Binding Assays, and STD NMR Experiments. ChemMedChem 2016; 11:1008-14. [DOI: 10.1002/cmdc.201600058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 03/07/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Pabla A. Barra
- Department of Organic Chemistry; Universidad de Concepción; Casilla 160-C Concepción Chile
| | - Verónica A. Jiménez
- Department of Chemical Sciences; Faculty of Exact Sciences; Universidad Andres Bello; Autopista Concepción-Talcahuano 7100 Talcahuano Chile
| | - José A. Gavin
- Instituto Universitario de Bioorgánica “A. González”; Universidad de La Laguna; Avenida Astrofísico Francisco Sánchez 38206 La Laguna Tenerife Spain
| | - Antonio H. Daranas
- Instituto Universitario de Bioorgánica “A. González”; Universidad de La Laguna; Avenida Astrofísico Francisco Sánchez 38206 La Laguna Tenerife Spain
| | - Joel B. Alderete
- Department of Organic Chemistry; Universidad de Concepción; Casilla 160-C Concepción Chile
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37
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Solé D, Bennasar ML, Roca T, Valldosera M. Exploration of Ring-Closing Enyne Metathesis for the Synthesis of Azonino[5,4-b]indoles. European J Org Chem 2016. [DOI: 10.1002/ejoc.201501517] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Drickamer K, Taylor ME. Recent insights into structures and functions of C-type lectins in the immune system. Curr Opin Struct Biol 2015; 34:26-34. [PMID: 26163333 PMCID: PMC4681411 DOI: 10.1016/j.sbi.2015.06.003] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 05/22/2015] [Accepted: 06/19/2015] [Indexed: 12/05/2022]
Abstract
Sugar-binding C-type carbohydrate-recognition domains fall in five structural groups. Structures for many of these domains, covering all of the groups, have been obtained. Not all human C-type lectins have clear orthologues in other mammals such as mice. Different mechanisms by which C-type lectins initiate signalling remain to be defined. Hetero-oligomeric receptors add to the complexity of overlapping specificities.
The majority of the C-type lectin-like domains in the human genome likely to bind sugars have been investigated structurally, although novel mechanisms of sugar binding are still being discovered. In the immune system, adhesion and endocytic receptors that bind endogenous mammalian glycans are often conserved, while pathogen-binding C-type lectins on cells of the innate immune system are more divergent. Lack of orthology between some human and mouse receptors, as well as overlapping specificities of many receptors and formation of receptor hetero-oligomers, can make it difficult to define the roles of individual receptors. There is good evidence that C-type lectins initiate signalling pathways in several different ways, but this function remains the least well understood from a mechanistic perspective.
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Affiliation(s)
- Kurt Drickamer
- Department of Life Sciences, Imperial College, London SW7 2AZ, United Kingdom
| | - Maureen E Taylor
- Department of Life Sciences, Imperial College, London SW7 2AZ, United Kingdom.
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39
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Fernández-Tejada A, Cañada FJ, Jiménez-Barbero J. Recent Developments in Synthetic Carbohydrate-Based Diagnostics, Vaccines, and Therapeutics. Chemistry 2015; 21:10616-28. [PMID: 26095198 DOI: 10.1002/chem.201500831] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Glycans are everywhere in biological systems, being involved in many cellular events with important implications for medical purposes. Building upon a detailed understanding of the functional roles of carbohydrates in molecular recognition processes and disease states, glycans are increasingly being considered as key players in pharmacological research. On the basis of the important progress recently made in glycochemistry, glycobiology, and glycomedicine, we provide a complete overview of successful applications and future perspectives of carbohydrates in the biopharmaceutical and medical fields. This review highlights the development of carbohydrate-based diagnostics, exemplified by glycan imaging techniques and microarray platforms, synthetic oligosaccharide vaccines against infectious diseases (e.g., HIV) and cancer, and finally carbohydrate-derived therapeutics, including glycomimetic drugs and glycoproteins.
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Affiliation(s)
| | - F Javier Cañada
- Chemical and Physical Biology, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid (Spain)
| | - Jesús Jiménez-Barbero
- Infectious Disease Programme, Center for Cooperative Research in Biosciences, CIC-bioGUNE, Bizkaia Technology Park, 48160 Derio (Spain). .,Ikerbasque, Basque Foundation for Science, María López de Haro 13, 48009 Bilbao (Spain).
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40
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Washington AZ, Tapadar S, George A, Oyelere AK. Exploiting translational stalling peptides in an effort to extend azithromycin interaction within the prokaryotic ribosome nascent peptide exit tunnel. Bioorg Med Chem 2015; 23:5198-209. [PMID: 26037612 DOI: 10.1016/j.bmc.2015.04.078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 04/18/2015] [Accepted: 04/29/2015] [Indexed: 10/23/2022]
Abstract
The ribosome is the primary protein synthesis machine in the cell and is a target for treatment of a variety of diseases including bacterial infection and cancer. The ribosomal peptide exit tunnel, the route of egress for the nascent peptide, is an inviting site for drug design. Toward a rational engagement of the nascent peptide components for the design of small molecule inhibitors of ribosome function, we designed and disclosed herein a set of N-10 indole functionalized azithromycin analogs. The indole moiety of these compounds is designed to mimic the translation stalling interaction of SecM W155 side-chain with the prokaryotic (Escherichia coli) ribosome A751 residue. Many of these N-10 functionalized compounds have enhanced translation inhibition activities against E. coli ribosome relative to azithromycin while a subset inhibited the growth of representative susceptible bacteria strains to about the same extent as azithromycin. Moreover, the inclusion of bovine serum in the bacterial growth media enhanced the anti-bacterial potency of the N-10 functionalized azithromycin analogs by as high as 10-fold.
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Affiliation(s)
- Arren Z Washington
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA
| | - Subhasish Tapadar
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA
| | - Alex George
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA
| | - Adegboyega K Oyelere
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA; Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.
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41
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Ng S, Lin E, Kitov PI, Tjhung KF, Gerlits OO, Deng L, Kasper B, Sood A, Paschal BM, Zhang P, Ling CC, Klassen JS, Noren CJ, Mahal LK, Woods RJ, Coates L, Derda R. Genetically encoded fragment-based discovery of glycopeptide ligands for carbohydrate-binding proteins. J Am Chem Soc 2015; 137:5248-51. [PMID: 25860443 PMCID: PMC5553193 DOI: 10.1021/ja511237n] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We describe an approach to accelerate the search for competitive inhibitors for carbohydrate-recognition domains (CRDs). Genetically encoded fragment-based discovery (GE-FBD) uses selection of phage-displayed glycopeptides to dock a glycan fragment at the CRD and guide selection of synergistic peptide motifs adjacent to the CRD. Starting from concanavalin A (ConA), a mannose (Man)-binding protein, as a bait, we narrowed a library of 10(8) glycopeptides to 86 leads that share a consensus motif, Man-WYD. Validation of synthetic leads yielded Man-WYDLF that exhibited 40-50-fold enhancement in affinity over methyl α-d-mannopyranoside (MeMan). Lectin array suggested specificity: Man-WYD derivative bound only to 3 out of 17 proteins—ConA, LcH, and PSA—that bind to Man. An X-ray structure of ConA:Man-WYD proved that the trimannoside core and Man-WYD exhibit identical CRD docking, but their extra-CRD binding modes are significantly different. Still, they have comparable affinity and selectivity for various Man-binding proteins. The intriguing observation provides new insight into functional mimicry of carbohydrates by peptide ligands. GE-FBD may provide an alternative to rapidly search for competitive inhibitors for lectins.
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Affiliation(s)
- Simon Ng
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Edith Lin
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Pavel I. Kitov
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Katrina F. Tjhung
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Oksana O. Gerlits
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6475, United States
| | - Lu Deng
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Brian Kasper
- Biomedical Chemistry Institute, Department of Chemistry, New York University, New York, New York 10003, United States
| | - Amika Sood
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Beth M. Paschal
- New England Biolabs, Ipswich, Massachusetts 01938, United States
| | - Ping Zhang
- Alberta Glycomics Centre, Department of Chemistry, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Chang-Chun Ling
- Alberta Glycomics Centre, Department of Chemistry, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - John S. Klassen
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | | | - Lara K. Mahal
- Biomedical Chemistry Institute, Department of Chemistry, New York University, New York, New York 10003, United States
| | - Robert J. Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
- School of Chemistry, National University of Ireland, Galway, University Road, Galway, Ireland
| | - Leighton Coates
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6475, United States
| | - Ratmir Derda
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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42
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Biophysical characterization of lectin–glycan interactions for therapeutics, vaccines and targeted drug-delivery. Future Med Chem 2014; 6:2113-29. [DOI: 10.4155/fmc.14.130] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Lectin–glycan interactions play a role in biological processes, host–pathogen interactions and in disease. A more detailed understanding of these interactions is not only useful for the elucidation of their biological function but can also be applied in immunology, drug development and delivery and diagnostics. We review some commonly used biophysical techniques for studying lectin–glycan interactions; namely: frontal affinity chromatography, glycan/lectin microarray, surface plasmon resonance, electrochemical impedance spectroscopy, isothermal titration calorimetry, fluorescent assays, enzyme linked lectin sorbent assay and saturation transfer difference nuclear magnetic resonance spectroscopy. Each method is evaluated on efficiency, cost and throughput. We also consider the advantages and limitations of each technique and provide examples of their application in biology, drug discovery and delivery, immunology, glycoprofiling and biosensing.
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43
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Calosso M, Tambutet G, Charpentier D, St-Pierre G, Vaillancourt M, Bencheqroun M, Gratton JP, Prévost M, Guindon Y. Acyclic tethers mimicking subunits of polysaccharide ligands: selectin antagonists. ACS Med Chem Lett 2014; 5:1054-9. [PMID: 25221666 DOI: 10.1021/ml500266x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 07/16/2014] [Indexed: 11/28/2022] Open
Abstract
We report on the design and synthesis of molecules having E- and P-selectins blocking activity both in vitro and in vivo. The GlcNAc component of the selectin ligand sialyl Lewis(X) was replaced by an acyclic tether that links two saccharide units. The minimization of intramolecular dipole-dipole interactions and the gauche effect would be at the origin of the conformational bias imposed by this acyclic tether. The stereoselective synthesis of these molecules, their biochemical and biological evaluations using surface plasmon resonance spectroscopy (SPR), and in vivo assays are described. Because the structure of our analogues differs from the most potent E-selectin antagonists reported, our acyclic analogues offer new opportunities for chemical diversity.
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Affiliation(s)
- Mickael Calosso
- Bio-Organic
Chemistry Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec H2W 1R7, Canada
| | - Guillaume Tambutet
- Bio-Organic
Chemistry Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec H2W 1R7, Canada
| | - Daniel Charpentier
- Bio-Organic
Chemistry Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec H2W 1R7, Canada
| | - Gabrielle St-Pierre
- Bio-Organic
Chemistry Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec H2W 1R7, Canada
| | - Marc Vaillancourt
- Bio-Organic
Chemistry Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec H2W 1R7, Canada
| | - Mohammed Bencheqroun
- Bio-Organic
Chemistry Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec H2W 1R7, Canada
| | - Jean-Philippe Gratton
- Département
de Pharmacologie, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Michel Prévost
- Bio-Organic
Chemistry Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec H2W 1R7, Canada
| | - Yvan Guindon
- Bio-Organic
Chemistry Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec H2W 1R7, Canada
- Département
de Chimie, Université de Montréal, Montréal, Québec H3C 3J7, Canada
- Department
of Chemistry, McGill University, Montréal, Québec H3A 2K6, Canada
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44
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Barelier S, Cummings J, Rauwerdink AM, Hitchcock DS, Farelli JD, Almo SC, Raushel FM, Allen KN, Shoichet BK. Substrate deconstruction and the nonadditivity of enzyme recognition. J Am Chem Soc 2014; 136:7374-82. [PMID: 24791931 PMCID: PMC4046767 DOI: 10.1021/ja501354q] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Indexed: 12/15/2022]
Abstract
Predicting substrates for enzymes of unknown function is a major postgenomic challenge. Substrate discovery, like inhibitor discovery, is constrained by our ability to explore chemotypes; it would be expanded by orders of magnitude if reactive sites could be probed with fragments rather than fully elaborated substrates, as is done for inhibitor discovery. To explore the feasibility of this approach, substrates of six enzymes from three different superfamilies were deconstructed into 41 overlapping fragments that were tested for activity or binding. Surprisingly, even those fragments containing the key reactive group had little activity, and most fragments did not bind measurably, until they captured most of the substrate features. Removing a single atom from a recognized substrate could often reduce catalytic recognition by 6 log-orders. To explore recognition at atomic resolution, the structures of three fragment complexes of the β-lactamase substrate cephalothin were determined by X-ray crystallography. Substrate discovery may be difficult to reduce to the fragment level, with implications for function discovery and for the tolerance of enzymes to metabolite promiscuity. Pragmatically, this study supports the development of libraries of fully elaborated metabolites as probes for enzyme function, which currently do not exist.
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Affiliation(s)
- Sarah Barelier
- Department
of Pharmaceutical Chemistry, University
of California - San Francisco, 1700 Fourth Street, Byers Hall, San Francisco, California 94158, United States
| | - Jennifer
A. Cummings
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Alissa M. Rauwerdink
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Daniel S. Hitchcock
- Department
of Biochemistry and Biophysics, Texas A&M
University, College Station, Texas, United States
| | - Jeremiah D. Farelli
- Department
of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215-2521, United States
| | - Steven C. Almo
- Department
of Biochemistry, Albert Einstein College
of Medicine, New York, New York 10461, United
States
| | - Frank M. Raushel
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
- Department
of Biochemistry and Biophysics, Texas A&M
University, College Station, Texas, United States
| | - Karen N. Allen
- Department
of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215-2521, United States
| | - Brian K. Shoichet
- Department
of Pharmaceutical Chemistry, University
of California - San Francisco, 1700 Fourth Street, Byers Hall, San Francisco, California 94158, United States
- Faculty of
Pharmacy, University of Toronto, Donnelly Centre Suite 604, 160 College
Street, Toronto, Ontario, Canada, M5S 3E1
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45
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Hudak JE, Bertozzi CR. Glycotherapy: new advances inspire a reemergence of glycans in medicine. CHEMISTRY & BIOLOGY 2014; 21:16-37. [PMID: 24269151 PMCID: PMC4111574 DOI: 10.1016/j.chembiol.2013.09.010] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Revised: 09/16/2013] [Accepted: 09/30/2013] [Indexed: 12/21/2022]
Abstract
The beginning of the 20(th) century marked the dawn of modern medicine with glycan-based therapies at the forefront. However, glycans quickly became overshadowed as DNA- and protein-focused treatments became readily accessible. The recent development of new tools and techniques to study and produce structurally defined carbohydrates has spurred renewed interest in the therapeutic applications of glycans. This review focuses on advances within the past decade that are bringing glycan-based treatments back to the forefront of medicine and the technologies that are driving these efforts. These include the use of glycans themselves as therapeutic molecules as well as engineering protein and cell surface glycans to suit clinical applications. Glycan therapeutics offer a rich and promising frontier for developments in the academic, biopharmaceutical, and medical fields.
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Affiliation(s)
- Jason E Hudak
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Carolyn R Bertozzi
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
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46
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Titz A. Carbohydrate-Based Anti-Virulence Compounds Against Chronic Pseudomonas aeruginosa Infections with a Focus on Small Molecules. TOPICS IN MEDICINAL CHEMISTRY 2014. [DOI: 10.1007/7355_2014_44] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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