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Chittum JE, Thompson A, Desai UR. Glycosaminoglycan microarrays for studying glycosaminoglycan-protein systems. Carbohydr Polym 2024; 335:122106. [PMID: 38616080 PMCID: PMC11032185 DOI: 10.1016/j.carbpol.2024.122106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/16/2024]
Abstract
More than 3000 proteins are now known to bind to glycosaminoglycans (GAGs). Yet, GAG-protein systems are rather poorly understood in terms of selectivity of recognition, molecular mechanism of action, and translational promise. High-throughput screening (HTS) technologies are critically needed for studying GAG biology and developing GAG-based therapeutics. Microarrays, developed within the past two decades, have now improved to the point of being the preferred tool in the HTS of biomolecules. GAG microarrays, in which GAG sequences are immobilized on slides, while similar to other microarrays, have their own sets of challenges and considerations. GAG microarrays are rapidly becoming the first choice in studying GAG-protein systems. Here, we review different modalities and applications of GAG microarrays presented to date. We discuss advantages and disadvantages of this technology, explain covalent and non-covalent immobilization strategies using different chemically reactive groups, and present various assay formats for qualitative and quantitative interpretations, including selectivity screening, binding affinity studies, competitive binding studies etc. We also highlight recent advances in implementing this technology, cataloging of data, and project its future promise. Overall, the technology of GAG microarray exhibits enormous potential of evolving into more than a mere screening tool for studying GAG - protein systems.
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Affiliation(s)
- John E Chittum
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, United States of America; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, United States of America
| | - Ally Thompson
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, United States of America; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, United States of America
| | - Umesh R Desai
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, United States of America; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, United States of America.
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2
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Che S, Yang Y, Li Z, Su Z, Zhang S. Integration of Zn 2+, ATP, and bFGF to Nanodressing with Core-Shell Structure Fabricated by Emulsion Electrospinning for Wound Healing. ACS APPLIED BIO MATERIALS 2024; 7:3316-3329. [PMID: 38691017 DOI: 10.1021/acsabm.4c00258] [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] [Indexed: 05/03/2024]
Abstract
Basic fibroblast growth factor (bFGF) plays an important role in active wound repair. However, the existing dosage forms in clinical applications are mainly sprays and freeze-dried powders, which are prone to inactivation and cannot achieve a controlled release. In this study, a bioactive wound dressing named bFGF-ATP-Zn/polycaprolactone (PCL) nanodressing with a "core-shell" structure was fabricated by emulsion electrospinning, enabling the sustained release of bFGF. Based on the coordination and electrostatic interactions among bFGF, ATP, and Zn2+, as well as their synergistic effect on promoting wound healing, a bFGF-ATP-Zn ternary combination system was prepared with higher cell proliferation activity and used as the water phase for emulsion electrospinning. The bFGF-ATP-Zn/PCL nanodressing demonstrated improved mechanical properties, sustained release of bFGF, cytocompatibility, and hemocompatibility. It increased the proliferation activity of human dermal fibroblasts (HDFs) and enhanced collagen secretion by 1.39 and 3.45 times, respectively, while reducing the hemolysis rate to 3.13%. The application of the bFGF-ATP-Zn/PCL nanodressing in mouse full-thickness skin defect repair showed its ability to accelerate wound healing and reduce wound scarring within 14 days. These results provide a research basis for the development and application of this bioactive wound dressing product.
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Affiliation(s)
- Shiyi Che
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, No. 19 Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yanli Yang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Zhengjun Li
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, Beijing 100190, China
| | - Zhiguo Su
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, Beijing 100190, China
| | - Songping Zhang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, Beijing 100190, China
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3
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Alotaibi FS, Alsadun MMR, Alsaiari SA, Ramakrishnan K, Yates EA, Fernig DG. Interactions of proteins with heparan sulfate. Essays Biochem 2024:EBC20230093. [PMID: 38646914 DOI: 10.1042/ebc20230093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/22/2024] [Accepted: 04/02/2024] [Indexed: 04/23/2024]
Abstract
Heparan sulfate (HS) is a glycosaminoglycan, polysaccharides that are considered to have arisen in the last common unicellular ancestor of multicellular animals. In this light, the large interactome of HS and its myriad functions in relation to the regulation of cell communication are not surprising. The binding of proteins to HS determines their localisation and diffusion, essential for embryonic development and homeostasis. Following the biosynthesis of the initial heparosan polymer, the subsequent modifications comprise an established canonical pathway and a minor pathway. The more frequent former starts with N-deacetylation and N-sulfation of GlcNAc residues, the latter with C-5 epimerisation of a GlcA residue adjacent to a GlcNAc. The binding of proteins to HS is driven by ionic interactions. The multivalent effect arising from the many individual ionic bonds between a single protein and a polysaccharide chain results in a far stronger interaction than would be expected from an ion-exchange process. In many instances, upon binding, both parties undergo substantial conformational change, the resulting hydrogen and van der Waal bonds contributing significant free energy to the binding reaction. Nevertheless, ionic bonds dominate the protein-polysaccharide interaction kinetically. Together with the multivalent effect, this provides an explanation for the observed trapping of HS-binding proteins in extracellular matrix. Importantly, individual ionic bonds have been observed to be dynamic; breaking and reforming, while the protein remains bound to the polysaccharide. These considerations lead to a model for 1D diffusion of proteins in extracellular matrix on HS, involving mechanisms such as sliding, chain switching and rolling.
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Affiliation(s)
- Faizah S Alotaibi
- Department of Biochemistry, Systems and Cell Biology, Institute of Molecular, Integrative and Systems Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Marim M R Alsadun
- Department of Biochemistry, Systems and Cell Biology, Institute of Molecular, Integrative and Systems Biology, University of Liverpool, Liverpool L69 7ZB, U.K
- Department of Biology, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Sarah A Alsaiari
- Department of Biochemistry, Systems and Cell Biology, Institute of Molecular, Integrative and Systems Biology, University of Liverpool, Liverpool L69 7ZB, U.K
- Department of Biological Sciences, College of Science, University of Jeddah, Jeddah 21589, Saudi Arabia
| | - Krithika Ramakrishnan
- Department of Biochemistry, Systems and Cell Biology, Institute of Molecular, Integrative and Systems Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Edwin A Yates
- Department of Biochemistry, Systems and Cell Biology, Institute of Molecular, Integrative and Systems Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - David G Fernig
- Department of Biochemistry, Systems and Cell Biology, Institute of Molecular, Integrative and Systems Biology, University of Liverpool, Liverpool L69 7ZB, U.K
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4
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Guimond S, Mycroft-West CJ, Gandhi NS, Tree JA, Le TT, Spalluto CM, Humbert MV, Buttigieg KR, Coombes N, Elmore MJ, Wand M, Nyström K, Said J, Setoh YX, Amarilla AA, Modhiran N, Sng JDJ, Chhabra M, Young PR, Rawle DJ, Lima MA, Yates EA, Karlsson R, Miller RL, Chen YH, Bagdonaite I, Yang Z, Stewart J, Nguyen D, Laidlaw S, Hammond E, Dredge K, Wilkinson TMA, Watterson D, Khromykh AA, Suhrbier A, Carroll MW, Trybala E, Bergström T, Ferro V, Skidmore MA, Turnbull JE. Synthetic Heparan Sulfate Mimetic Pixatimod (PG545) Potently Inhibits SARS-CoV-2 by Disrupting the Spike-ACE2 Interaction. ACS CENTRAL SCIENCE 2022; 8:527-545. [PMID: 35647275 PMCID: PMC9136977 DOI: 10.1021/acscentsci.1c01293] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Indexed: 05/03/2023]
Abstract
Heparan sulfate (HS) is a cell surface polysaccharide recently identified as a coreceptor with the ACE2 protein for the S1 spike protein on SARS-CoV-2 virus, providing a tractable new therapeutic target. Clinically used heparins demonstrate an inhibitory activity but have an anticoagulant activity and are supply-limited, necessitating alternative solutions. Here, we show that synthetic HS mimetic pixatimod (PG545), a cancer drug candidate, binds and destabilizes the SARS-CoV-2 spike protein receptor binding domain and directly inhibits its binding to ACE2, consistent with molecular modeling identification of multiple molecular contacts and overlapping pixatimod and ACE2 binding sites. Assays with multiple clinical isolates of SARS-CoV-2 virus show that pixatimod potently inhibits the infection of monkey Vero E6 cells and physiologically relevant human bronchial epithelial cells at safe therapeutic concentrations. Pixatimod also retained broad potency against variants of concern (VOC) including B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617.2 (Delta), and B.1.1.529 (Omicron). Furthermore, in a K18-hACE2 mouse model, pixatimod significantly reduced SARS-CoV-2 viral titers in the upper respiratory tract and virus-induced weight loss. This demonstration of potent anti-SARS-CoV-2 activity tolerant to emerging mutations establishes proof-of-concept for targeting the HS-Spike protein-ACE2 axis with synthetic HS mimetics and provides a strong rationale for clinical investigation of pixatimod as a potential multimodal therapeutic for COVID-19.
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Affiliation(s)
- Scott
E. Guimond
- Centre
for Glycoscience, School of Life Sciences, Keele University, Newcastle-Under-Lyme, Staffordshire ST5 5BG, United Kingdom
| | - Courtney J. Mycroft-West
- Centre
for Glycoscience, School of Life Sciences, Keele University, Newcastle-Under-Lyme, Staffordshire ST5 5BG, United Kingdom
| | - Neha S. Gandhi
- School
of Chemistry and Physics, Centre for Genomics and Personalized Health, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4000, Australia
| | - Julia A. Tree
- National
Infection Service, UK Health Security Agency, Porton Down, Salisbury, Wiltshire SP4
0JG, United Kingdom
| | - Thuy T. Le
- QIMR
Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - C. Mirella Spalluto
- School
of Clinical and Experimental Sciences, University
of Southampton Faculty of Medicine, Southampton SO17 1BJ, United Kingdom
| | - Maria V. Humbert
- School
of Clinical and Experimental Sciences, University
of Southampton Faculty of Medicine, Southampton SO17 1BJ, United Kingdom
| | - Karen R. Buttigieg
- National
Infection Service, UK Health Security Agency, Porton Down, Salisbury, Wiltshire SP4
0JG, United Kingdom
| | - Naomi Coombes
- National
Infection Service, UK Health Security Agency, Porton Down, Salisbury, Wiltshire SP4
0JG, United Kingdom
| | - Michael J. Elmore
- National
Infection Service, UK Health Security Agency, Porton Down, Salisbury, Wiltshire SP4
0JG, United Kingdom
| | - Matthew Wand
- National
Infection Service, UK Health Security Agency, Porton Down, Salisbury, Wiltshire SP4
0JG, United Kingdom
| | - Kristina Nyström
- Department
of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10B, S-413 46 Goteborg, Sweden
| | - Joanna Said
- Department
of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10B, S-413 46 Goteborg, Sweden
| | - Yin Xiang Setoh
- School
of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
- Australian
Infectious Diseases Research Centre, GVN
Center of Excellence, Brisbane, Queensland 4072/4079, Australia
| | - Alberto A. Amarilla
- School
of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
- Australian
Infectious Diseases Research Centre, GVN
Center of Excellence, Brisbane, Queensland 4072/4079, Australia
| | - Naphak Modhiran
- School
of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
- Australian
Infectious Diseases Research Centre, GVN
Center of Excellence, Brisbane, Queensland 4072/4079, Australia
| | - Julian D. J. Sng
- School
of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
- Australian
Infectious Diseases Research Centre, GVN
Center of Excellence, Brisbane, Queensland 4072/4079, Australia
| | - Mohit Chhabra
- School
of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
- Australian
Infectious Diseases Research Centre, GVN
Center of Excellence, Brisbane, Queensland 4072/4079, Australia
| | - Paul R. Young
- School
of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
- Australian
Infectious Diseases Research Centre, GVN
Center of Excellence, Brisbane, Queensland 4072/4079, Australia
| | - Daniel J. Rawle
- QIMR
Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Marcelo A. Lima
- Centre
for Glycoscience, School of Life Sciences, Keele University, Newcastle-Under-Lyme, Staffordshire ST5 5BG, United Kingdom
| | - Edwin A. Yates
- Department
of Biochemistry and Systems Biology, Institute of Systems, Molecular
and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Richard Karlsson
- Copenhagen
Center for Glycomics, Department of Cellular & Molecular Medicine, University of Copenhagen, Copenhagen N 2200, Denmark
| | - Rebecca L. Miller
- Copenhagen
Center for Glycomics, Department of Cellular & Molecular Medicine, University of Copenhagen, Copenhagen N 2200, Denmark
| | - Yen-Hsi Chen
- Copenhagen
Center for Glycomics, Department of Cellular & Molecular Medicine, University of Copenhagen, Copenhagen N 2200, Denmark
| | - Ieva Bagdonaite
- Copenhagen
Center for Glycomics, Department of Cellular & Molecular Medicine, University of Copenhagen, Copenhagen N 2200, Denmark
| | - Zhang Yang
- Copenhagen
Center for Glycomics, Department of Cellular & Molecular Medicine, University of Copenhagen, Copenhagen N 2200, Denmark
| | - James Stewart
- Department
of Infection Biology & Microbiomes, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Dung Nguyen
- Wellcome
Centre for Human Genetics, Nuffield Department of Medicine, Oxford University, Roosevelt Drive, Headington, Oxford OX3 7BN, United
Kingdom
| | - Stephen Laidlaw
- Wellcome
Centre for Human Genetics, Nuffield Department of Medicine, Oxford University, Roosevelt Drive, Headington, Oxford OX3 7BN, United
Kingdom
| | - Edward Hammond
- Zucero Therapeutics Ltd, 1 Westlink Court, Brisbane, Queensland 4076, Australia
| | - Keith Dredge
- Zucero Therapeutics Ltd, 1 Westlink Court, Brisbane, Queensland 4076, Australia
| | - Tom M. A. Wilkinson
- School
of Clinical and Experimental Sciences, University
of Southampton Faculty of Medicine, Southampton SO17 1BJ, United Kingdom
- NIHR
Southampton Biomedical Research Centre, University Hospital Southampton, Southampton SO16 6YD, United Kingdom
| | - Daniel Watterson
- School
of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
- Australian
Infectious Diseases Research Centre, GVN
Center of Excellence, Brisbane, Queensland 4072/4079, Australia
| | - Alexander A. Khromykh
- School
of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
- Australian
Infectious Diseases Research Centre, GVN
Center of Excellence, Brisbane, Queensland 4072/4079, Australia
| | - Andreas Suhrbier
- QIMR
Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Miles W. Carroll
- National
Infection Service, UK Health Security Agency, Porton Down, Salisbury, Wiltshire SP4
0JG, United Kingdom
- Wellcome
Centre for Human Genetics, Nuffield Department of Medicine, Oxford University, Roosevelt Drive, Headington, Oxford OX3 7BN, United
Kingdom
| | - Edward Trybala
- Department
of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10B, S-413 46 Goteborg, Sweden
| | - Tomas Bergström
- Department
of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10B, S-413 46 Goteborg, Sweden
| | - Vito Ferro
- School
of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
- Australian
Infectious Diseases Research Centre, GVN
Center of Excellence, Brisbane, Queensland 4072/4079, Australia
| | - Mark A. Skidmore
- Centre
for Glycoscience, School of Life Sciences, Keele University, Newcastle-Under-Lyme, Staffordshire ST5 5BG, United Kingdom
| | - Jeremy E. Turnbull
- Centre
for Glycoscience, School of Life Sciences, Keele University, Newcastle-Under-Lyme, Staffordshire ST5 5BG, United Kingdom
- Department
of Biochemistry and Systems Biology, Institute of Systems, Molecular
and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
- Copenhagen
Center for Glycomics, Department of Cellular & Molecular Medicine, University of Copenhagen, Copenhagen N 2200, Denmark
- ;
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5
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Bertini S, Alekseeva A, Elli S, Pagani I, Zanzoni S, Eisele G, Krishnan R, Maag KP, Reiter C, Lenhart D, Gruber R, Yates E, Vicenzi E, Naggi A, Bisio A, Guerrini M. Pentosan polysulfate inhibits attachment and infection by SARS-CoV-2 in vitro: insights into structural requirements for binding. Thromb Haemost 2022; 122:984-997. [PMID: 35322395 PMCID: PMC9252607 DOI: 10.1055/a-1807-0168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Two years since the outbreak of the novel coronavirus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic, there remain few clinically effective drugs to complement vaccines. One is the anticoagulant, heparin, which in 2004 was found able to inhibit invasion of SARS-CoV (CoV-1) and which has been employed during the current pandemic to prevent thromboembolic complications and moderate potentially damaging inflammation. Heparin has also been shown experimentally to inhibit SARS-CoV-2 attachment and infection in susceptible cells. At high therapeutic doses however, heparin increases the risk of bleeding and prolonged use can cause heparin-induced thrombocytopenia, a serious side effect. One alternative, with structural similarities to heparin, is the plant-derived, semi-synthetic polysaccharide, pentosan polysulfate (PPS). PPS is an established drug for the oral treatment of interstitial cystitis, is well-tolerated, and exhibits weaker anticoagulant effects than heparin. In an established Vero cell model, PPS and its fractions of varying molecular weights inhibited invasion by SARS-CoV-2. Intact PPS and its size-defined fractions were characterized by molecular weight distribution and chemical structure using nuclear magnetic resonance spectroscopy and liquid chromatography–mass spectrometry, then employed to explore the structural basis of interactions with SARS-CoV-2 spike protein receptor-binding domain (S1 RBD) and the inhibition of Vero cell invasion. PPS was as effective as unfractionated heparin, but more effective in inhibiting cell infection than low-molecular-weight heparin (on a weight/volume basis). Isothermal titration calorimetry and viral plaque-forming assays demonstrated size-dependent binding to S1 RBD and inhibition of Vero cell invasion, suggesting the potential application of PPS as a novel inhibitor of SARS-CoV-2 infection.
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Affiliation(s)
- Sabrina Bertini
- Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni, Milan, Italy
| | - Anna Alekseeva
- Centro Alta Tecnologia Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni, Milan, Italy
| | - Stefano Elli
- Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni, Milan, Italy
| | - Isabel Pagani
- IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Serena Zanzoni
- Centro Piattaforme Tecnologiche, University of Verona, Verona, Italy
| | - Giorgio Eisele
- Centro Alta Tecnologia Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni, Milan, Italy
| | - Ravi Krishnan
- Paradigm Biopharmaceuticals Ltd, Melbourne, Australia
| | - Klaus P Maag
- bene pharmaChem GmbH & Co.KG, Geretsried, Germany
| | | | | | | | - Edwin Yates
- Structural and Chemical Biology, University of Liverpool, Liverpool, United Kingdom of Great Britain and Northern Ireland
| | - Elisa Vicenzi
- IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Annamaria Naggi
- Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni, Milan, Italy
| | - Antonella Bisio
- Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni, Milan, Italy
| | - Marco Guerrini
- Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni, Milan, Italy
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6
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Mycroft-West CJ, Devlin AJ, Cooper LC, Guimond SE, Procter P, Guerrini M, Miller GJ, Fernig DG, Yates EA, Lima MA, Skidmore MA. Glycosaminoglycans from Litopenaeus vannamei Inhibit the Alzheimer's Disease β Secretase, BACE1. Mar Drugs 2021; 19:203. [PMID: 33916819 PMCID: PMC8067017 DOI: 10.3390/md19040203] [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: 02/28/2021] [Revised: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 11/16/2022] Open
Abstract
Only palliative therapeutic options exist for the treatment of Alzheimer's Disease; no new successful drug candidates have been developed in over 15 years. The widely used clinical anticoagulant heparin has been reported to exert beneficial effects through multiple pathophysiological pathways involved in the aetiology of Alzheimer's Disease, for example, amyloid peptide production and clearance, tau phosphorylation, inflammation and oxidative stress. Despite the therapeutic potential of heparin as a multi-target drug for Alzheimer's disease, the repurposing of pharmaceutical heparin is proscribed owing to the potent anticoagulant activity of this drug. Here, a heterogenous non-anticoagulant glycosaminoglycan extract, obtained from the shrimp Litopenaeus vannamei, was found to inhibit the key neuronal β-secretase, BACE1, displaying a more favorable therapeutic ratio compared to pharmaceutical heparin when anticoagulant activity is considered.
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Affiliation(s)
- Courtney J. Mycroft-West
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire ST5 5BG, UK; (C.J.M.-W.); (A.J.D.); (L.C.C.); (P.P.); (M.A.L.)
| | - Anthony J. Devlin
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire ST5 5BG, UK; (C.J.M.-W.); (A.J.D.); (L.C.C.); (P.P.); (M.A.L.)
| | - Lynsay C. Cooper
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire ST5 5BG, UK; (C.J.M.-W.); (A.J.D.); (L.C.C.); (P.P.); (M.A.L.)
| | - Scott E. Guimond
- School of Medicine, Keele University, Huxley Building, Keele, Staffordshire ST5 5BG, UK;
| | - Patricia Procter
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire ST5 5BG, UK; (C.J.M.-W.); (A.J.D.); (L.C.C.); (P.P.); (M.A.L.)
| | - Marco Guerrini
- Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni, via G. Colombo 81, 20133 Milan, Italy;
| | - Gavin J. Miller
- School of Chemistry, Keele University, Huxley Building, Keele, Staffordshire ST5 5BG, UK;
| | - David G. Fernig
- Department of Biochemistry and Systems Biology, ISMIB, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK; (D.G.F.); (E.A.Y.)
| | - Edwin A. Yates
- Department of Biochemistry and Systems Biology, ISMIB, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK; (D.G.F.); (E.A.Y.)
| | - Marcelo A. Lima
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire ST5 5BG, UK; (C.J.M.-W.); (A.J.D.); (L.C.C.); (P.P.); (M.A.L.)
| | - Mark A. Skidmore
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire ST5 5BG, UK; (C.J.M.-W.); (A.J.D.); (L.C.C.); (P.P.); (M.A.L.)
- Department of Biochemistry and Systems Biology, ISMIB, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK; (D.G.F.); (E.A.Y.)
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7
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Tree JA, Turnbull JE, Buttigieg KR, Elmore MJ, Coombes N, Hogwood J, Mycroft-West CJ, Lima MA, Skidmore MA, Karlsson R, Chen YH, Yang Z, Spalluto CM, Staples KJ, Yates EA, Gray E, Singh D, Wilkinson T, Page CP, Carroll MW. Unfractionated heparin inhibits live wild type SARS-CoV-2 cell infectivity at therapeutically relevant concentrations. Br J Pharmacol 2021. [PMID: 33125711 DOI: 10.1111/bph.v178.310.1111/bph.15304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023] Open
Abstract
BACKGROUND AND PURPOSE Currently, there are no licensed vaccines and limited antivirals for the treatment of COVID-19. Heparin (delivered systemically) is currently used to treat anticoagulant anomalies in COVID-19 patients. Additionally, in the United Kingdom, Brazil and Australia, nebulised unfractionated heparin (UFH) is being trialled in COVID-19 patients as a potential treatment. A systematic comparison of the potential antiviral effect of various heparin preparations on live wild type SARS-CoV-2, in vitro, is needed. EXPERIMENTAL APPROACH Seven different heparin preparations including UFH and low MW heparins (LMWH) of porcine or bovine origin were screened for antiviral activity against live SARS-CoV-2 (Australia/VIC01/2020) using a plaque inhibition assay with Vero E6 cells. Interaction of heparin with spike protein RBD was studied using differential scanning fluorimetry and the inhibition of RBD binding to human ACE2 protein using elisa assays was examined. KEY RESULTS All the UFH preparations had potent antiviral effects, with IC50 values ranging between 25 and 41 μg·ml-1 , whereas LMWHs were less inhibitory by ~150-fold (IC50 range 3.4-7.8 mg·ml-1 ). Mechanistically, we observed that heparin binds and destabilizes the RBD protein and furthermore, we show heparin directly inhibits the binding of RBD to the human ACE2 protein receptor. CONCLUSION AND IMPLICATIONS This comparison of clinically relevant heparins shows that UFH has significantly stronger SARS-CoV-2 antiviral activity compared to LMWHs. UFH acts to directly inhibit binding of spike protein to the human ACE2 protein receptor. Overall, the data strongly support further clinical investigation of UFH as a potential treatment for patients with COVID-19.
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Affiliation(s)
- Julia A Tree
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Jeremy E Turnbull
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool, UK
- Copenhagen Center for Glycomics, Department of Cellular & Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Karen R Buttigieg
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Michael J Elmore
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Naomi Coombes
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - John Hogwood
- Haemostasis Section, Biotherapeutics, National Institute for Biological Standards and Control (NIBSC), Potters Bar, UK
| | - Courtney J Mycroft-West
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Newcastle-Under-Lyme, UK
| | - Marcelo A Lima
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Newcastle-Under-Lyme, UK
| | - Mark A Skidmore
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Newcastle-Under-Lyme, UK
| | - Richard Karlsson
- Copenhagen Center for Glycomics, Department of Cellular & Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Yen-Hsi Chen
- Copenhagen Center for Glycomics, Department of Cellular & Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Zhang Yang
- Copenhagen Center for Glycomics, Department of Cellular & Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | - Karl J Staples
- Department of Respiratory Medicine, University of Southampton, Southampton, UK
| | - Edwin A Yates
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool, UK
| | - Elaine Gray
- Haemostasis Section, Biotherapeutics, National Institute for Biological Standards and Control (NIBSC), Potters Bar, UK
- Sackler Institute of Pulmonary Pharmacology, King's College London, London, UK
| | - Dave Singh
- Medicines Evaluation Unit, University of Manchester, Manchester University Hospital NHS Foundation Trust, Manchester, UK
| | - Tom Wilkinson
- Department of Respiratory Medicine, University of Southampton, Southampton, UK
| | - Clive P Page
- Sackler Institute of Pulmonary Pharmacology, King's College London, London, UK
| | - Miles W Carroll
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
- Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, UK
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8
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Tree JA, Turnbull JE, Buttigieg KR, Elmore MJ, Coombes N, Hogwood J, Mycroft-West CJ, Lima MA, Skidmore MA, Karlsson R, Chen YH, Yang Z, Spalluto CM, Staples KJ, Yates EA, Gray E, Singh D, Wilkinson T, Page CP, Carroll MW. Unfractionated heparin inhibits live wild type SARS-CoV-2 cell infectivity at therapeutically relevant concentrations. Br J Pharmacol 2020; 178:626-635. [PMID: 33125711 PMCID: PMC9328389 DOI: 10.1111/bph.15304] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/08/2020] [Accepted: 10/18/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND AND PURPOSE Currently, there are no licensed vaccines and limited antivirals for the treatment of COVID-19. Heparin (delivered systemically) is currently used to treat anticoagulant anomalies in COVID-19 patients. Additionally, in the United Kingdom, Brazil and Australia, nebulised unfractionated heparin (UFH) is being trialled in COVID-19 patients as a potential treatment. A systematic comparison of the potential antiviral effect of various heparin preparations on live wild type SARS-CoV-2, in vitro, is needed. EXPERIMENTAL APPROACH Seven different heparin preparations including UFH and low MW heparins (LMWH) of porcine or bovine origin were screened for antiviral activity against live SARS-CoV-2 (Australia/VIC01/2020) using a plaque inhibition assay with Vero E6 cells. Interaction of heparin with spike protein RBD was studied using differential scanning fluorimetry and the inhibition of RBD binding to human ACE2 protein using elisa assays was examined. KEY RESULTS All the UFH preparations had potent antiviral effects, with IC50 values ranging between 25 and 41 μg·ml-1 , whereas LMWHs were less inhibitory by ~150-fold (IC50 range 3.4-7.8 mg·ml-1 ). Mechanistically, we observed that heparin binds and destabilizes the RBD protein and furthermore, we show heparin directly inhibits the binding of RBD to the human ACE2 protein receptor. CONCLUSION AND IMPLICATIONS This comparison of clinically relevant heparins shows that UFH has significantly stronger SARS-CoV-2 antiviral activity compared to LMWHs. UFH acts to directly inhibit binding of spike protein to the human ACE2 protein receptor. Overall, the data strongly support further clinical investigation of UFH as a potential treatment for patients with COVID-19.
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Affiliation(s)
- Julia A Tree
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Jeremy E Turnbull
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool, UK.,Copenhagen Center for Glycomics, Department of Cellular & Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Karen R Buttigieg
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Michael J Elmore
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - Naomi Coombes
- National Infection Service, Public Health England, Porton Down, Salisbury, UK
| | - John Hogwood
- Haemostasis Section, Biotherapeutics, National Institute for Biological Standards and Control (NIBSC), Potters Bar, UK
| | - Courtney J Mycroft-West
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Newcastle-Under-Lyme, UK
| | - Marcelo A Lima
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Newcastle-Under-Lyme, UK
| | - Mark A Skidmore
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Newcastle-Under-Lyme, UK
| | - Richard Karlsson
- Copenhagen Center for Glycomics, Department of Cellular & Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Yen-Hsi Chen
- Copenhagen Center for Glycomics, Department of Cellular & Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Zhang Yang
- Copenhagen Center for Glycomics, Department of Cellular & Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | - Karl J Staples
- Department of Respiratory Medicine, University of Southampton, Southampton, UK
| | - Edwin A Yates
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool, UK
| | - Elaine Gray
- Haemostasis Section, Biotherapeutics, National Institute for Biological Standards and Control (NIBSC), Potters Bar, UK.,Sackler Institute of Pulmonary Pharmacology, King's College London, London, UK
| | - Dave Singh
- Medicines Evaluation Unit, University of Manchester, Manchester University Hospital NHS Foundation Trust, Manchester, UK
| | - Tom Wilkinson
- Department of Respiratory Medicine, University of Southampton, Southampton, UK
| | - Clive P Page
- Sackler Institute of Pulmonary Pharmacology, King's College London, London, UK
| | - Miles W Carroll
- National Infection Service, Public Health England, Porton Down, Salisbury, UK.,Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, UK
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9
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Mycroft-West CJ, Devlin AJ, Cooper LC, Procter P, Miller GJ, Fernig DG, Guerrini M, Guimond SE, Lima MA, Yates EA, Skidmore MA. Inhibition of BACE1, the β-secretase implicated in Alzheimer's disease, by a chondroitin sulfate extract from Sardina pilchardus. Neural Regen Res 2020; 15:1546-1553. [PMID: 31997821 PMCID: PMC7059579 DOI: 10.4103/1673-5374.274341] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 08/23/2019] [Accepted: 10/26/2019] [Indexed: 12/24/2022] Open
Abstract
The pharmaceutical and anticoagulant agent heparin, a member of the glycosaminoglycan family of carbohydrates, has previously been identified as a potent inhibitor of a key Alzheimer's disease drug target, the primary neuronal β-secretase, β-site amyloid precursor protein cleaving enzyme 1 (BACE1). The anticoagulant activity of heparin has, however, precluded the repurposing of this widely used pharmaceutical as an Alzheimer's disease therapeutic. Here, a glycosaminoglycan extract, composed predominantly of 4-sulfated chondroitin sulfate, has been isolated from Sardina pilchardus, which possess the ability to inhibit BACE1 (IC50 [half maximal inhibitory concentration] = 4.8 μg/mL), while displaying highly attenuated anticoagulant activities (activated partial thromboplastin time EC50 [median effective concentration] = 403.8 μg/mL, prothrombin time EC50 = 1.3 mg/mL). The marine-derived, chondroitin sulfate extract destabilizes BACE1, determined via differential scanning fluorimetry (ΔTm -5°C), to a similar extent as heparin, suggesting that BACE1 inhibition by glycosaminoglycans may occur through a common mode of action, which may assist in the screening of glycan-based BACE1 inhibitors for Alzheimer's disease.
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Affiliation(s)
- Courtney J. Mycroft-West
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire, ST5 5BG, UK
| | - Anthony J. Devlin
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire, ST5 5BG, UK
| | - Lynsay C. Cooper
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire, ST5 5BG, UK
| | - Patricia Procter
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire, ST5 5BG, UK
| | - Gavin J. Miller
- Lennard-Jones Laboratory, School of Chemical and Physical Sciences, Keele University, Keele, Staffordshire, ST5 5BG, UK
| | - David G. Fernig
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Marco Guerrini
- Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni, Via G. Colombo 81, 20133 Milan, Italy
| | - Scott E. Guimond
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire, ST5 5BG, UK
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
- School of Medicine, Keele, Staffordshire, ST5 5BG, UK
| | - Marcelo A. Lima
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire, ST5 5BG, UK
| | - Edwin A. Yates
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire, ST5 5BG, UK
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Mark Andrew Skidmore
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire, ST5 5BG, UK
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
- School of Medicine, Keele, Staffordshire, ST5 5BG, UK
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10
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Tang H, Shi K, Shi C, Aihara H, Zhang J, Du G. Enhancing subtilisin thermostability through a modified normalized B-factor analysis and loop-grafting strategy. J Biol Chem 2019; 294:18398-18407. [PMID: 31615894 PMCID: PMC6885650 DOI: 10.1074/jbc.ra119.010658] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/09/2019] [Indexed: 01/07/2023] Open
Abstract
Rational design-guided improvement of protein thermostability typically requires identification of residues or regions contributing to instability and introduction of mutations into these residues or regions. One popular method, B-FIT, utilizes B-factors to identify unstable residues or regions and combines them with other strategies, such as directed evolution. Here, we performed structure-based engineering to improve the thermostability of the subtilisin E-S7 (SES7) peptidase. The B-value of each residue was redefined in a normalized B-factor calculation, which was implemented with a refined bioinformatics analysis strategy to identify the critical area (loop 158-162) related to flexibility and to screen for suitable thermostable motif sequences in the Protein Data Bank that can act as transplant loops. In total, we analyzed 445 structures and identified 29 thermostable motifs as candidates. Using these motifs as a starting point, we performed iterative homologous modeling to obtain a desirable chimera loop and introduced five different mutations into this loop to construct thermostable SES7 proteins. Differential scanning fluorimetry revealed increases of 7.3 °C in the melting temperature of an SES7 variant designated M5 compared with the WT. The X-ray crystallographic structure of this variant was resolved at 1.96 Å resolution. The crystal structure disclosed that M5 forms more hydrogen bonds than the WT protein, consistent with design and molecular dynamics simulation results. In summary, the modified B-FIT strategy reported here has yielded a subtilisin variant with improved thermostability and promising industrial applications, supporting the notion that this modified method is a powerful tool for protein engineering.
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Affiliation(s)
- Heng Tang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China; School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Ke Shi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, Minnesota 55455
| | - Cheng Shi
- School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, Minnesota 55455.
| | - Juan Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China; School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China.
| | - Guocheng Du
- School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China.
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11
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Sun C, Liu M, Sun P, Yang M, Yates EA, Guo Z, Fernig DG. Sulfated polysaccharides interact with fibroblast growth factors and protect from denaturation. FEBS Open Bio 2019; 9:1477-1487. [PMID: 31271519 PMCID: PMC6668377 DOI: 10.1002/2211-5463.12696] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 06/26/2019] [Accepted: 07/03/2019] [Indexed: 01/08/2023] Open
Abstract
Fibroblast growth factors (FGFs) regulate embryonic development and homeostasis, including tissue and organ repair and specific aspects of metabolism. The basic FGF and acidic FGF, now known as FGF2 and FGF1, are widely used protein drugs for tissue repair. However, they are susceptible to denaturation at ambient temperatures and during long-time storage, which will reduce their biological activity. The interaction of FGFs with the sulfated domains of heparan sulfate and heparin is essential for their cellular signaling and stability. Therefore, we analyzed the interactions of FGF1 and FGF2 with four sulfated polysaccharides: heparin, dextran sulfate (DXS), λ-carrageenan, and chondroitin sulfate. The results of thermal stability and cell proliferation assays demonstrate that heparin, DXS, and λ-carrageenan bound to both FGFs and protected them from denaturation. Our results suggest heparin, DXS, and λ-carrageenan are potential formulation materials that bind and stabilize FGFs, and which may also potentiate their activity and control their delivery.
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Affiliation(s)
- Changye Sun
- Henan Key Laboratory of Medical Tissue RegenerationXinxiang Medical UniversityChina
| | - Mengxin Liu
- Henan Key Laboratory of Medical Tissue RegenerationXinxiang Medical UniversityChina
| | - Panwen Sun
- Henan Key Laboratory of Medical Tissue RegenerationXinxiang Medical UniversityChina
| | - Mingming Yang
- Department of CardiologySchool of MedicineAffiliated Zhongda HospitalSoutheast UniversityNanjingChina
| | - Edwin A. Yates
- Department of BiochemistryInstitute of Integrative BiologyUniversity of LiverpoolUK
| | - Zhikun Guo
- Henan Key Laboratory of Medical Tissue RegenerationXinxiang Medical UniversityChina
| | - David G. Fernig
- Department of BiochemistryInstitute of Integrative BiologyUniversity of LiverpoolUK
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12
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A Glycosaminoglycan Extract from Portunus pelagicus Inhibits BACE1, the β Secretase Implicated in Alzheimer's Disease. Mar Drugs 2019; 17:md17050293. [PMID: 31100859 PMCID: PMC6562973 DOI: 10.3390/md17050293] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 12/23/2022] Open
Abstract
Therapeutic options for Alzheimer’s disease, the most common form of dementia, are currently restricted to palliative treatments. The glycosaminoglycan heparin, widely used as a clinical anticoagulant, has previously been shown to inhibit the Alzheimer’s disease-relevant β-secretase 1 (BACE1). Despite this, the deployment of pharmaceutical heparin for the treatment of Alzheimer’s disease is largely precluded by its potent anticoagulant activity. Furthermore, ongoing concerns regarding the use of mammalian-sourced heparins, primarily due to prion diseases and religious beliefs hinder the deployment of alternative heparin-based therapeutics. A marine-derived, heparan sulphate-containing glycosaminoglycan extract, isolated from the crab Portunus pelagicus, was identified to inhibit human BACE1 with comparable bioactivity to that of mammalian heparin (IC50 = 1.85 μg mL−1 (R2 = 0.94) and 2.43 μg mL−1 (R2 = 0.93), respectively), while possessing highly attenuated anticoagulant activities. The results from several structural techniques suggest that the interactions between BACE1 and the extract from P. pelagicus are complex and distinct from those of heparin.
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13
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Differential Scanning Fluorimetry and Hydrogen Deuterium Exchange Mass Spectrometry to Monitor the Conformational Dynamics of NBD1 in Cystic Fibrosis. Methods Mol Biol 2019; 1873:53-67. [PMID: 30341603 DOI: 10.1007/978-1-4939-8820-4_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cystic fibrosis (CF) is one of the most common, lethal autosomal recessive diseases in Caucasians with a life expectancy of 37-47 years. The CF transmembrane conductance regulator (CFTR) is a plasma membrane ion channel, confined to apical membrane of epithelia, and ensures transepithelial water and solute movement across secretory epithelia in several organs. Numerous CF mutations, including the most prevalent deletion of F508 (ΔF508) in the nucleotide binding domain 1 (NBD1) leads to CFTR global misfolding and premature intracellular degradation at the endoplasmic reticulum (ER). To better understand the misfolding mechanism caused by CF-causing point mutations in the NBD1, which is poorly understood, differential scanning fluorimetry (DSF) and hydrogen deuterium exchange coupled with mass spectrometry (HDX-MS) are the choice of techniques. These established methods can measure the conformational dynamics of the NBD1 globally and at peptide resolution level by monitoring backbone amide HDX, respectively, and will be instrumental to evaluate the mechanism of action of CF mutations and folding correctors that rescue CFTR folding defects via stabilizing the mutant NBD1.
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14
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Smith RAA, Murali S, Rai B, Lu X, Lim ZXH, Lee JJL, Nurcombe V, Cool SM. Minimum structural requirements for BMP-2-binding of heparin oligosaccharides. Biomaterials 2018; 184:41-55. [PMID: 30205243 DOI: 10.1016/j.biomaterials.2018.08.056] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/24/2018] [Accepted: 08/27/2018] [Indexed: 12/27/2022]
Abstract
Bone morphogenetic proteins (BMPs) are essential during tissue repair and remodeling after injury. Glycosaminoglycan (GAG) sugars are known to enhance BMP activity in vitro and in vivo; here the interactions of BMP-2 with various glycosaminoglycan classes were compared and shown to be selective for heparin over other comparable saccharides. The minimal chain lengths and specific sulfate moieties required for heparin-derived oligosaccharide binding to BMP-2, and the ability of such oligosaccharides to promote BMP-2-induced osteogenic differentiation in vitro were then determined. BMP-2 could bind to heparin hexasaccharides (dp6) and octasaccharides (dp8), but decasaccharides (dp10) were the minimum chain length required for both efficient binding of BMP-2 and consequent heparin-dependent cell responses. N-sulfation is the most important, and 6-O-sulfation moderately important for BMP-2 binding and activity, whereas 2-O-sulfation was much less critical. Bone formation assays in vivo further confirmed that dp10, N-sulfated heparin oligosaccharides were the minimal requirement for effective enhancement of BMP-2-induced bone formation. Such information is necessary for the rational design of the next generations of heparan-based devices for bone tissue repair.
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Affiliation(s)
- Raymond A A Smith
- Glycotherapeutics Group, Institute of Medical Biology, 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
| | - Sadasivam Murali
- Glycotherapeutics Group, Institute of Medical Biology, 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
| | - Bina Rai
- Glycotherapeutics Group, Institute of Medical Biology, 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
| | - Xiaohua Lu
- Glycotherapeutics Group, Institute of Medical Biology, 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
| | - Zophia Xue Hui Lim
- Glycotherapeutics Group, Institute of Medical Biology, 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
| | - Jaslyn J L Lee
- Glycotherapeutics Group, Institute of Medical Biology, 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore
| | - Victor Nurcombe
- Glycotherapeutics Group, Institute of Medical Biology, 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University-Imperial College London, Singapore
| | - Simon M Cool
- Glycotherapeutics Group, Institute of Medical Biology, 8A Biomedical Grove, #06-06 Immunos, 138648, Singapore; Dept. of Orthopaedic Surgery, Yong Loo Lin School of Medicine, National University of Singapore, 119074, Singapore.
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15
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Smith RA, Chua R, Carnachan SM, Tan CL, Sims IM, Hinkley SF, Nurcombe V, Cool SM. Retention of the Structure and Function of Heparan Sulfate Biomaterials After Gamma Irradiation. Tissue Eng Part A 2018; 24:729-739. [DOI: 10.1089/ten.tea.2017.0263] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Raymond A.A. Smith
- Glycotherapeutics Group, Institute of Medical Biology, Agency for Science, Technology and Research, Singapore
| | - R.J.E. Chua
- Glycotherapeutics Group, Institute of Medical Biology, Agency for Science, Technology and Research, Singapore
| | - Susan M. Carnachan
- The Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand
| | - Clarissa L.L. Tan
- Glycotherapeutics Group, Institute of Medical Biology, Agency for Science, Technology and Research, Singapore
| | - Ian M. Sims
- The Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand
| | - Simon F.R. Hinkley
- The Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand
| | - Victor Nurcombe
- Glycotherapeutics Group, Institute of Medical Biology, Agency for Science, Technology and Research, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University-Imperial College London, Singapore
| | - Simon M. Cool
- Glycotherapeutics Group, Institute of Medical Biology, Agency for Science, Technology and Research, Singapore
- Department of Orthopaedic Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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16
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Tsuboi R, Sasaki JI, Kitagawa H, Yoshimoto I, Takeshige F, Imazato S. Development of a novel dental resin cement incorporating FGF-2-loaded polymer particles with the ability to promote tissue regeneration. Dent Mater 2018; 34:641-648. [DOI: 10.1016/j.dental.2018.01.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 01/10/2018] [Accepted: 01/10/2018] [Indexed: 11/16/2022]
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17
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2,3-Di-O-sulfo glucuronic acid: An unmodified and unusual residue in a highly sulfated chondroitin sulfate from Litopenaeus vannamei. Carbohydr Polym 2018; 183:192-200. [DOI: 10.1016/j.carbpol.2017.12.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 12/07/2017] [Accepted: 12/09/2017] [Indexed: 12/26/2022]
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18
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Kitagawa H, Takeda K, Tsuboi R, Hayashi M, Sasaki JI, Imazato S. Influence of polymerization properties of 4-META/MMA-based resin on the activity of fibroblast growth factor-2. Dent Mater J 2017. [PMID: 28626207 DOI: 10.4012/dmj.2016-372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Dental adhesive resins based on 4-methacryloxyethyl trimellitate anhydride (4-META)/methyl methacrylate (MMA) have been utilized for root-end filling and the bonding of fractured roots. To increase the success rate of these treatments, it would be beneficial to promote the healing of surrounding tissue by applying growth factors. In this study, the influences of the polymerization properties of 4-META/MMA-based resins on the activity of fibroblast growth factor-2 (FGF-2) were evaluated in vitro. The temperature increase caused by the heat generation during polymerization of the 4-META/MMA-based resin was insufficient to change the structure and function of FGF-2. Unpolymerized monomers released from the cured 4-META/MMA-based resin had no negative influences on the ability of FGF-2 to promote the proliferation of osteoblast-like cells. These findings suggest that it is possible to use FGF-2 in combination with 4-META/MMA-based resins.
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Affiliation(s)
- Haruaki Kitagawa
- Department of Biomaterials Science, Osaka University Graduate School of Dentistry
| | - Kahoru Takeda
- Department of Restorative Dentistry and Endodontology, Osaka University Graduate School of Dentistry
| | - Ririko Tsuboi
- Department of Biomaterials Science, Osaka University Graduate School of Dentistry.,Division for Interdisciplinary Dentistry, Osaka University Dental Hospital
| | - Mikako Hayashi
- Department of Restorative Dentistry and Endodontology, Osaka University Graduate School of Dentistry
| | - Jun-Ichi Sasaki
- Department of Biomaterials Science, Osaka University Graduate School of Dentistry
| | - Satoshi Imazato
- Department of Biomaterials Science, Osaka University Graduate School of Dentistry
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19
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Endogenous regeneration: Engineering growth factors for stroke. Neurochem Int 2017; 107:57-65. [PMID: 28411103 DOI: 10.1016/j.neuint.2017.03.024] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 03/30/2017] [Accepted: 03/31/2017] [Indexed: 12/31/2022]
Abstract
Despite the efforts in developing therapeutics for stroke, recombinant tissue plasminogen activator (rtPA) remains the only FDA approved drug for ischemic stroke. Regenerative medicine targeting endogenous growth factors has drawn much interest in the clinical field as it provides potential restoration for the damaged brain tissue without being limited by a narrow therapeutic window. To date, most of the translational studies using regenerative medicines have encountered problems and failures. In this review, we discuss the effects of some trophic factors which include of erythropoietin (EPO), brain derived neurotrophic factor (BDNF), granulocyte-colony stimulating factor (G-CSF), vascular endothelial growth factor (VEGF), fibroblast growth factor (FGF), epidermal growth factor (EGF) and heparin binding epidermal growth factor (HB-EGF) in experimental ischemic stroke models and elaborate the lost in translation of the candidate growth factors from bench to bedside. Several new methodologies have been developed to overcome the caveats in translational studies. This review highlights the latest bioengineering approaches including the controlled release and delivery of growth factors by hydrogel-based scaffolds and the enhancement of half-life and selectivity of growth factors by a novel approach facilitated by glycosaminoglycans.
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20
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Li Y, Sun C, Yates EA, Jiang C, Wilkinson MC, Fernig DG. Heparin binding preference and structures in the fibroblast growth factor family parallel their evolutionary diversification. Open Biol 2016; 6:rsob.150275. [PMID: 27030175 PMCID: PMC4821243 DOI: 10.1098/rsob.150275] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The interaction of a large number of extracellular proteins with heparan sulfate (HS) regulates their transport and effector functions, but the degree of molecular specificity underlying protein–polysaccharide binding is still debated. The 15 paracrine fibroblast growth factors (FGFs) are one of the paradigms for this interaction. Here, we measure the binding preferences of six FGFs (FGF3, FGF4, FGF6, FGF10, FGF17, FGF20) for a library of modified heparins, representing structures in HS, and model glycosaminoglycans, using differential scanning fluorimetry. This is complemented by the identification of the lysine residues in the primary and secondary binding sites of the FGFs by a selective labelling approach. Pooling these data with previous sets provides good coverage of the FGF phylogenetic tree, deduced from amino acid sequence alignment. This demonstrates that the selectivity of the FGFs for binding structures in sulfated polysaccharides and the pattern of secondary binding sites on the surface of FGFs follow the phylogenetic relationship of the FGFs, and so are likely to be the result of the natural selection pressures that led to the expansion of the FGF family in the course of the evolution of more complex animal body plans.
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Affiliation(s)
- Yong Li
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK
| | - Changye Sun
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK
| | - Edwin A Yates
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK
| | - Chao Jiang
- School of Pharmaceutical Science, Wenzhou Medical University, Chashan University Park, Wenzhou 325035, China
| | - Mark C Wilkinson
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK
| | - David G Fernig
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK
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21
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The Extracellular Matrix, Basement Membrane, and Glycocalyx. Protein Sci 2016. [DOI: 10.1201/9781315374307-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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22
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Wijesinghe SJ, Ling L, Murali S, Qing YH, Hinkley SFR, Carnachan SM, Bell TJ, Swaminathan K, Hui JH, van Wijnen AJ, Nurcombe V, Cool SM. Affinity Selection of FGF2-Binding Heparan Sulfates for Ex Vivo Expansion of Human Mesenchymal Stem Cells. J Cell Physiol 2016; 232:566-575. [PMID: 27291835 DOI: 10.1002/jcp.25454] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 06/10/2016] [Indexed: 12/25/2022]
Abstract
The future of human mesenchymal stem cells (hMSCs) as a successful cell therapy relies on bioprocessing strategies to improve the scalability of these cells without compromising their therapeutic ability. The culture-expansion of hMSCs can be enhanced by supplementation with growth factors, particularly fibroblast growth factor 2 (FGF2). The biological activity of FGF2 is controlled through interactions with heparan sulfate (HS) that facilitates ligand-receptor complex formation. We previously reported on an FGF2-interacting HS variant (termed HS2) isolated from embryonic tissue by anionic exchange chromatography that increased the proliferation and potency of hMSCs. Here, we detail the isolation of an FGF2 affinity-purified HS variant (HS8) using a scalable platform technology previously employed to generate HS variants with increased affinity for BMP-2 or VEGF165 . This process used a peptide sequence derived from the heparin-binding domain of FGF2 as a substrate to affinity-isolate HS8 from a commercially available source of porcine mucosal HS. Our data show that HS8 binds to FGF2 with higher affinity than to FGF1, FGF7, BMP2, PDGF-BB, or VEGF165 . Also, HS8 protects FGF2 from thermal destabilization and increases FGF signaling and hMSC proliferation through FGF receptor 1. Long-term supplementation of cultures with HS8 increased both hMSC numbers and their colony-forming efficiency without adversely affecting the expression of hMSC-related cell surface antigens. This strategy further exemplifies the utility of affinity-purifying HS variants against particular ligands important to the stem cell microenvironment and advocates for their addition as adjuvants for the culture-expansion of hMSCs destined for cellular therapy. J. Cell. Physiol. 232: 566-575, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
| | - Ling Ling
- Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Sadasivam Murali
- Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Yeong Hui Qing
- Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Simon F R Hinkley
- The Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand
| | - Susan M Carnachan
- The Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand
| | - Tracey J Bell
- The Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand
| | | | - James H Hui
- Department of Orthopaedic Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Andre J van Wijnen
- Department of Orthopedic Surgery and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Victor Nurcombe
- Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Simon M Cool
- Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Singapore.,Department of Orthopaedic Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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23
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Putative histidine kinase inhibitors with antibacterial effect against multi-drug resistant clinical isolates identified by in vitro and in silico screens. Sci Rep 2016; 6:26085. [PMID: 27173778 PMCID: PMC4865847 DOI: 10.1038/srep26085] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 03/15/2016] [Indexed: 01/21/2023] Open
Abstract
Novel antibacterials are urgently needed to address the growing problem of bacterial resistance to conventional antibiotics. Two-component systems (TCS) are widely used by bacteria to regulate gene expression in response to various environmental stimuli and physiological stress and have been previously proposed as promising antibacterial targets. TCS consist of a sensor histidine kinase (HK) and an effector response regulator. The HK component contains a highly conserved ATP-binding site that is considered to be a promising target for broad-spectrum antibacterial drugs. Here, we describe the identification of putative HK autophosphorylation inhibitors following two independent experimental approaches: in vitro fragment-based screen via differential scanning fluorimetry and in silico structure-based screening, each followed up by the exploration of analogue compounds as identified by ligand-based similarity searches. Nine of the tested compounds showed antibacterial effect against multi-drug resistant clinical isolates of bacterial pathogens and include three novel scaffolds, which have not been explored so far in other antibacterial compounds. Overall, putative HK autophosphorylation inhibitors were found that together provide a promising starting point for further optimization as antibacterials.
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24
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Sun C, Marcello M, Li Y, Mason D, Lévy R, Fernig DG. Selectivity in glycosaminoglycan binding dictates the distribution and diffusion of fibroblast growth factors in the pericellular matrix. Open Biol 2016; 6:150277. [PMID: 27009190 PMCID: PMC4821244 DOI: 10.1098/rsob.150277] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/02/2016] [Indexed: 12/13/2022] Open
Abstract
The range of biological outcomes generated by many signalling proteins in development and homeostasis is increased by their interactions with glycosaminoglycans, particularly heparan sulfate (HS). This interaction controls the localization and movement of these signalling proteins, but whether such control depends on the specificity of the interactions is not known. We used five fibroblast growth factors with an N-terminal HaloTag (Halo-FGFs) for fluorescent labelling, with well-characterized and distinct HS-binding properties, and measured their binding and diffusion in pericellular matrix of fixed rat mammary 27 fibroblasts. Halo-FGF1, Halo-FGF2 and Halo-FGF6 bound to HS, whereas Halo-FGF10 also interacted with chondroitin sulfate/dermatan sulfate, and FGF20 did not bind detectably. The distribution of bound FGFs in the pericellular matrix was not homogeneous, and for FGF10 exhibited striking clusters. Fluorescence recovery after photobleaching showed that FGF2 and FGF6 diffused faster, whereas FGF1 diffused more slowly, and FGF10 was immobile. The results demonstrate that the specificity of the interactions of proteins with glycosaminoglycans controls their binding and diffusion. Moreover, cells regulate the spatial distribution of different protein-binding sites in glycosaminoglycans independently of each other, implying that the extracellular matrix has long-range structure.
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Affiliation(s)
- Changye Sun
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Marco Marcello
- Centre for Cell Imaging, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Yong Li
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - David Mason
- Centre for Cell Imaging, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Raphaël Lévy
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - David G Fernig
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
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25
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Gallagher J. Fell-Muir Lecture: Heparan sulphate and the art of cell regulation: a polymer chain conducts the protein orchestra. Int J Exp Pathol 2015; 96:203-31. [PMID: 26173450 PMCID: PMC4561558 DOI: 10.1111/iep.12135] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 05/22/2015] [Indexed: 12/12/2022] Open
Abstract
Heparan sulphate (HS) sits at the interface of the cell and the extracellular matrix. It is a member of the glycosaminoglycan family of anionic polysaccharides with unique structural features designed for protein interaction and regulation. Its client proteins include soluble effectors (e.g. growth factors, morphogens, chemokines), membrane receptors and cell adhesion proteins such as fibronectin, fibrillin and various types of collagen. The protein-binding properties of HS, together with its strategic positioning in the pericellular domain, are indicative of key roles in mediating the flow of regulatory signals between cells and their microenvironment. The control of transmembrane signalling is a fundamental element in the complex biology of HS. It seems likely that, in some way, HS orchestrates diverse signalling pathways to facilitate information processing inside the cell. A dictionary definition of an orchestra is 'a large group of musicians who play together on various instruments …' to paraphrase, the HS orchestra is 'a large group of proteins that play together on various receptors'. HS conducts this orchestra to ensure that proteins hit the right notes on their receptors but, in the manner of a true conductor, does it also set 'the musical pulse' and create rhythm and harmony attractive to the cell? This is too big a question to answer but fun to think about as you read this review.
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Affiliation(s)
- John Gallagher
- Cancer Research UK Manchester Institute, Institute of Cancer Sciences, Paterson Building, University of Manchester, Manchester, UK
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26
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Structural insights into alginate binding by bacterial cell-surface protein. Carbohydr Res 2015; 404:39-45. [DOI: 10.1016/j.carres.2014.11.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 11/05/2014] [Accepted: 11/17/2014] [Indexed: 11/21/2022]
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27
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Vivoli M, Novak HR, Littlechild JA, Harmer NJ. Determination of protein-ligand interactions using differential scanning fluorimetry. J Vis Exp 2014:51809. [PMID: 25285605 PMCID: PMC4692391 DOI: 10.3791/51809] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A wide range of methods are currently available for determining the dissociation constant between a protein and interacting small molecules. However, most of these require access to specialist equipment, and often require a degree of expertise to effectively establish reliable experiments and analyze data. Differential scanning fluorimetry (DSF) is being increasingly used as a robust method for initial screening of proteins for interacting small molecules, either for identifying physiological partners or for hit discovery. This technique has the advantage that it requires only a PCR machine suitable for quantitative PCR, and so suitable instrumentation is available in most institutions; an excellent range of protocols are already available; and there are strong precedents in the literature for multiple uses of the method. Past work has proposed several means of calculating dissociation constants from DSF data, but these are mathematically demanding. Here, we demonstrate a method for estimating dissociation constants from a moderate amount of DSF experimental data. These data can typically be collected and analyzed within a single day. We demonstrate how different models can be used to fit data collected from simple binding events, and where cooperative binding or independent binding sites are present. Finally, we present an example of data analysis in a case where standard models do not apply. These methods are illustrated with data collected on commercially available control proteins, and two proteins from our research program. Overall, our method provides a straightforward way for researchers to rapidly gain further insight into protein-ligand interactions using DSF.
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Uniewicz KA, Ori A, Ahmed YA, Yates EA, Fernig DG. Characterisation of the interaction of neuropilin-1 with heparin and a heparan sulfate mimetic library of heparin-derived sugars. PeerJ 2014; 2:e461. [PMID: 25024924 PMCID: PMC4089425 DOI: 10.7717/peerj.461] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 06/09/2014] [Indexed: 12/22/2022] Open
Abstract
Background. Neuropilin-1 (NRP-1) is a multidomain membrane protein with soluble isoforms interacting with a complex network of other membrane receptors, their respective ligands and heparan sulfate (HS). It is involved in the development of vasculature, neural patterning, immunological responses and pathological angiogenesis. Methods. We have characterised the binding of a Fc fusion of rat NRP-1 (Fc rNRP-1) and of a soluble isoform, corresponding to the first four extracellular domains of human NRP-1, shNRP-1, using optical biosensor-based binding assays with a library of heparin derivatives. Selective labelling of lysines protected upon heparin binding allowed their identification by mass spectrometry. Results. Fc rNRP-1 bound to heparin with high affinity (2.5 nM) and fast ka (9.8 × 10(6) M(-1)s(-1)). Unusually, NRP-1 bound both highly sulfated and completely desulfated stretches of heparin and exhibited a complex pattern of preferences for chemically modified heparins possessing one or two sulfate groups, e.g., it bound heparin with just a 6-O sulfate group better than heparin with any two of N-sulfate, 6-O sulfate and 2-O sulfate. Mass-spectrometry based mapping identified that, in addition to the expected the b1 domain, the a1, and c domains and the L2 linker were also involved in the interaction. In contrast, shNRP-1 bound heparin far more weakly. This could only be shown by affinity chromatography and by differential scanning fluorimetry. Discussion. The results suggest that the interaction of NRP-1 with HS is more complex than anticipated and involving a far greater extent of the protein than just the b1-b2 domains. NRP-1's preference for binding long saccharide structures suggests it has the potential to bind large segments of HS chains and so organise their local structure. In contrast, the four domain soluble isoform, shNRP-1 binds heparin weakly and so would be expected to diffuse away rapidly from the source cell.
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Affiliation(s)
- Katarzyna A Uniewicz
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool , Liverpool , United Kingdom
| | - Alessandro Ori
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool , Liverpool , United Kingdom
| | - Yassir A Ahmed
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool , Liverpool , United Kingdom
| | - Edwin A Yates
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool , Liverpool , United Kingdom
| | - David G Fernig
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool , Liverpool , United Kingdom
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29
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In silico docking of forchlorfenuron (FCF) to septins suggests that FCF interferes with GTP binding. PLoS One 2014; 9:e96390. [PMID: 24787956 PMCID: PMC4008567 DOI: 10.1371/journal.pone.0096390] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 04/07/2014] [Indexed: 11/19/2022] Open
Abstract
Septins are GTP-binding proteins that form cytoskeleton-like filaments, which are essential for many functions in eukaryotic organisms. Small molecule compounds that disrupt septin filament assembly are valuable tools for dissecting septin functions with high temporal control. To date, forchlorfenuron (FCF) is the only compound known to affect septin assembly and functions. FCF dampens the dynamics of septin assembly inducing the formation of enlarged stable polymers, but the underlying mechanism of action is unknown. To investigate how FCF binds and affects septins, we performed in silico simulations of FCF docking to all available crystal structures of septins. Docking of FCF with SEPT2 and SEPT3 indicated that FCF interacts preferentially with the nucleotide-binding pockets of septins. Strikingly, FCF is predicted to form hydrogen bonds with residues involved in GDP-binding, mimicking nucleotide binding. FCF docking with the structure of SEPT2-GppNHp, a nonhydrolyzable GTP analog, and SEPT7 showed that FCF may assume two alternative non-overlapping conformations deeply into and on the outer side of the nucleotide-binding pocket. Surprisingly, FCF was predicted to interact with the P-loop Walker A motif GxxxxGKS/T, which binds the phosphates of GTP, and the GTP specificity motif AKAD, which interacts with the guanine base of GTP, and highly conserved amino acids including a threonine, which is critical for GTP hydrolysis. Thus, in silico FCF exhibits a conserved mechanism of binding, interacting with septin signature motifs and residues involved in GTP binding and hydrolysis. Taken together, our results suggest that FCF stabilizes septins by locking them into a conformation that mimics a nucleotide-bound state, preventing further GTP binding and hydrolysis. Overall, this study provides the first insight into how FCF may bind and stabilize septins, and offers a blueprint for the rational design of FCF derivatives that could target septins with higher affinity and specificity.
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30
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A heparin-like glycosaminoglycan from shrimp containing high levels of 3-O-sulfated d-glucosamine groups in an unusual trisaccharide sequence. Carbohydr Res 2014; 390:59-66. [DOI: 10.1016/j.carres.2014.03.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 03/02/2014] [Accepted: 03/03/2014] [Indexed: 11/22/2022]
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31
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Southard JN. Protein analysis using real-time PCR instrumentation: incorporation in an integrated, inquiry-based project. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2014; 42:142-151. [PMID: 24375992 DOI: 10.1002/bmb.20747] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 10/05/2013] [Indexed: 06/03/2023]
Abstract
Instrumentation for real-time PCR is used primarily for amplification and quantitation of nucleic acids. The capability to measure fluorescence while controlling temperature in multiple samples can also be applied to the analysis of proteins. Conformational stability and changes in stability due to ligand binding are easily assessed. Protein structure studies possible with a real-time PCR instrument address core topics in biochemistry and have valuable high-throughput applications in the fields of drug discovery and protein engineering. Protein analysis using real-time PCR instrumentation has been incorporated in an undergraduate laboratory project based on previously described projects. Students express, purify, and characterize a protein. Based on literature research and analysis using bioinformatics tools, they select a specific mutation to investigate. They then attempt to express, purify, and characterize their mutated protein. Thermal denaturation using a real-time PCR instrument is the primary tool used to compare the wild-type and mutated proteins. Alternative means for incorporation of protein analysis by real-time PCR instrumentation into laboratory experiences and additional modes of analysis are also described.
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Affiliation(s)
- Jonathan N Southard
- Department of Chemistry, Indiana University of Pennsylvania, Indiana, Pennsylvania, 15705
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32
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A non-hemorrhagic hybrid heparin/heparan sulfate with anticoagulant potential. Carbohydr Polym 2014; 99:372-8. [DOI: 10.1016/j.carbpol.2013.08.063] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 08/20/2013] [Accepted: 08/23/2013] [Indexed: 11/19/2022]
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33
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Daudé D, Topham CM, Remaud-Siméon M, André I. Probing impact of active site residue mutations on stability and activity of Neisseria polysaccharea amylosucrase. Protein Sci 2013; 22:1754-65. [PMID: 24115119 DOI: 10.1002/pro.2375] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 09/10/2013] [Indexed: 11/06/2022]
Abstract
The amylosucrase from Neisseria polysaccharea is a transglucosidase from the GH13 family of glycoside-hydrolases that naturally catalyzes the synthesis of α-glucans from the widely available donor sucrose. Interestingly, natural molecular evolution has modeled a dense hydrogen bond network at subsite -1 responsible for the specific recognition of sucrose and conversely, it has loosened interactions at the subsite +1 creating a highly promiscuous subsite +1. The residues forming these subsites are considered to be likely involved in the activity as well as the overall stability of the enzyme. To assess their role, a structure-based approach was followed to reshape the subsite -1. A strategy based on stability change predictions, using the FoldX algorithm, was considered to identify the best candidates for site-directed mutagenesis and guide the construction of a small targeted library. A miniaturized purification protocol was developed and both mutant stability and substrate promiscuity were explored. A range of 8 °C between extreme melting temperature values was observed and some variants were able to synthesize series of oligosaccharides with distributions differing from that of the parental enzyme. The crucial role of subsite -1 was thus highlighted and the biocatalysts generated can now be considered as starting points for further engineering purposes.
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Affiliation(s)
- David Daudé
- Université de Toulouse; INSA, UPS,INP, LISBP, 135 Avenue de Rangueil, F-31077, Toulouse, France; CNRS, UMR5504, F-31400, Toulouse, France; INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400, Toulouse, France
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Jedrusik-Bode M, Studencka M, Smolka C, Baumann T, Schmidt H, Kampf J, Paap F, Martin S, Tazi J, Müller KM, Krüger M, Braun T, Bober E. The sirtuin SIRT6 regulates stress granule formation in C. elegans and mammals. J Cell Sci 2013; 126:5166-77. [PMID: 24013546 DOI: 10.1242/jcs.130708] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
SIRT6 is a NAD(+)-dependent deacetylase that modulates chromatin structure and safeguards genomic stability. Until now, SIRT6 has been assigned to the nucleus and only nuclear targets of SIRT6 are known. Here, we demonstrate that in response to stress, C. elegans SIR-2.4 and its mammalian orthologue SIRT6 localize to cytoplasmic stress granules, interact with various stress granule components and induce their assembly. Loss of SIRT6 or inhibition of its catalytic activity in mouse embryonic fibroblasts impairs stress granule formation and delays disassembly during recovery, whereas deficiency of SIR-2.4 diminishes maintenance of P granules and decreases survival of C. elegans under stress conditions. Our findings uncover a novel, evolutionary conserved function of SIRT6 in the maintenance of stress granules in response to stress.
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Affiliation(s)
- Monika Jedrusik-Bode
- Max Planck Institute for Biophysical Chemistry, Epigenetics in C. elegans group, Am Faßberg 11, 37077 Göttingen, Germany
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35
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Seabrook SA, Newman J. High-throughput thermal scanning for protein stability: making a good technique more robust. ACS COMBINATORIAL SCIENCE 2013; 15:387-92. [PMID: 23710551 DOI: 10.1021/co400013v] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a high-throughput approach to help define experimental formulations that enhance protein stability, which is based on differential scanning fluorimetry (DSF). The method involves defining the thermal stability of a protein against a screen of 13 buffer systems, systematically sampling pH from 5.0 to 9.0 at high and low salt concentrations, using both redundancy and extensive controls to make the method robust. The screen allows rapid determination of a suitable base formulation for protein samples, and is particularly useful for difficult samples: those that are rapidly degraded or cannot be sufficiently concentrated for downstream analyses. Data obtained from three samples in this assay illustrate the vastly different values for thermal stability that can be obtained from different formulations. This approach is simple to interpret and reliable enough that it has been implemented as a service through the Collaborative Crystallisation Centre (C3).
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Affiliation(s)
- Shane A. Seabrook
- Collaborative Crystallisation Centre
(C3), Division
of Materials Science and Engineering, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville,
Victoria, Australia
| | - Janet Newman
- Collaborative Crystallisation Centre
(C3), Division
of Materials Science and Engineering, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville,
Victoria, Australia
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36
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Differential scanning fluorimetry: Rapid screening of formulations that promote the stability of reference preparations. J Pharm Biomed Anal 2013; 77:163-6. [DOI: 10.1016/j.jpba.2013.01.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 12/20/2012] [Accepted: 01/01/2013] [Indexed: 11/22/2022]
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37
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Xu R, Rudd TR, Hughes AJ, Siligardi G, Fernig DG, Yates EA. Analysis of the fibroblast growth factor receptor (FGFR) signalling network with heparin as coreceptor: evidence for the expansion of the core FGFR signalling network. FEBS J 2013; 280:2260-70. [DOI: 10.1111/febs.12201] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 02/06/2013] [Accepted: 02/18/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Ruoyan Xu
- Department of Structural and Chemical Biology, Institute of Integrative Biology; University of Liverpool; UK
| | | | | | | | - David G. Fernig
- Department of Structural and Chemical Biology, Institute of Integrative Biology; University of Liverpool; UK
| | - Edwin A. Yates
- Department of Structural and Chemical Biology, Institute of Integrative Biology; University of Liverpool; UK
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38
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Lima MA, Hughes AJ, Veraldi N, Rudd TR, Hussain R, Brito AS, Chavante SF, Tersariol II, Siligardi G, Nader HB, Yates EA. Antithrombin stabilisation by sulfated carbohydrates correlates with anticoagulant activity. MEDCHEMCOMM 2013. [DOI: 10.1039/c3md00048f] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Menzen T, Friess W. High-throughput melting-temperature analysis of a monoclonal antibody by differential scanning fluorimetry in the presence of surfactants. J Pharm Sci 2012; 102:415-28. [PMID: 23212746 DOI: 10.1002/jps.23405] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 10/31/2012] [Accepted: 11/09/2012] [Indexed: 01/07/2023]
Abstract
Differential scanning fluorimetry (DSF) is successfully used as a high-throughput screening method for the analysis of the protein melting temperature (T(m)) in the development of therapeutic monoclonal antibody (MAb) formulations. Typically, surfactants are utilized in MAb formulations as a stabilizer, but the commonly applied polarity-sensitive dye SYPRO® Orange shows bright fluorescence in the presence of micelles, concealing the signal of protein unfolding. Studying various MAb formulations containing polysorbate 20, polysorbate 80, or poloxamer 188 (PX 188), the molecular rotor probe 4-(dicyanovinyl)julolidine (DCVJ) was investigated. Although limited to higher MAb concentrations, DCVJ enabled the determination of T(m) in many formulations where SYPRO® Orange failed. It is important to note that careful background correction of placebo formulations is essential for the precise determination of T(m) and especially T(m onset). Thermal shifts of T(m1) (lowest observed thermal transition) indicating stabilizing or destabilizing effects of pH or excipient were in good agreement across all tested formulations and correlated well with differential scanning calorimetry measurements. Additionally, the micellization temperature of PX 188 was confirmed, which leads to a nonproteinous transition. With this new method, it is possible to apply DSF during the development of therapeutic proteins in surfactant-containing formulations.
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Affiliation(s)
- Tim Menzen
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics, Ludwig-Maximilians-Universität München, Munich 81377, Germany.
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40
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Xu R, Ori A, Rudd TR, Uniewicz KA, Ahmed YA, Guimond SE, Skidmore MA, Siligardi G, Yates EA, Fernig DG. Diversification of the structural determinants of fibroblast growth factor-heparin interactions: implications for binding specificity. J Biol Chem 2012; 287:40061-73. [PMID: 23019343 DOI: 10.1074/jbc.m112.398826] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The functions of a large number (>435) of extracellular regulatory proteins are controlled by their interactions with heparan sulfate (HS). In the case of fibroblast growth factors (FGFs), HS binding determines their transport between cells and is required for the assembly of high affinity signaling complexes with their cognate FGF receptor. However, the specificity of the interaction of FGFs with HS is still debated. Here, we use a panel of FGFs (FGF-1, FGF-2, FGF-7, FGF-9, FGF-18, and FGF-21) spanning five FGF subfamilies to probe their specificities for HS at different levels as follows: binding parameters, identification of heparin-binding sites (HBSs) in the FGFs, changes in their secondary structure caused by heparin binding and structures in the sugar required for binding. For interaction with heparin, the FGFs exhibit K(D) values varying between 38 nM (FGF-18) and 620 nM (FGF-9) and association rate constants spanning over 20-fold (FGF-1, 2,900,000 M(-1) s(-1) and FGF-9, 130,000 M(-1) s(-1)). The canonical HBS in FGF-1, FGF-2, FGF-7, FGF-9, and FGF-18 differs in its size, and these FGFs have a different complement of secondary HBS, ranging from none (FGF-9) to two (FGF-1). Differential scanning fluorimetry identified clear preferences in these FGFs for distinct structural features in the polysaccharide. These data suggest that the differences in heparin-binding sites in both the protein and the sugar are greatest between subfamilies and may be more restricted within a FGF subfamily in accord with the known conservation of function within FGF subfamilies.
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Affiliation(s)
- Ruoyan Xu
- Institute of Integrative Biology, Department of Chemical and Structural Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
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A zinc complex of heparan sulfate destabilises lysozyme and alters its conformation. Biochem Biophys Res Commun 2012; 425:794-9. [PMID: 22884801 DOI: 10.1016/j.bbrc.2012.07.154] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 07/27/2012] [Indexed: 11/22/2022]
Abstract
The naturally occurring anionic cell surface polysaccharide heparan sulfate is involved in key biological activities and is implicated in amyloid formation. Following addition of Zn-heparan sulfate, hen lysozyme, a model amyloid forming protein, resembled β-rich amyloid by far UV circular dichroism (increased β-sheet: +25%), with a significantly reduced melting temperature (from 68 to 58 °C) by fluorescence shift assay. Secondary structure stability of the Zn-heparan sulfate complex with lysozyme was also distinct from that with heparan sulfate, under stronger denaturation conditions using synchrotron radiation circular dichroism. Changing the cation associated with heparan sulfate is sufficient to alter the conformation and stability of complexes formed between heparan sulfate and lysozyme, substantially reducing the stability of the protein. Complexes of heparan sulfate and cations, such as Zn, which are abundant in the brain, may provide alternative folding routes for proteins.
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Rudd TR, Hughes A, Holman J, Solari V, Ferreira EDO, Domingues RMCP, Yates EA. Heparan sulphate, its derivatives and analogues share structural characteristics that can be exploited, particularly in inhibiting microbial attachment. Braz J Med Biol Res 2012; 45:386-91. [PMID: 22473323 PMCID: PMC3854285 DOI: 10.1590/s0100-879x2012007500048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 03/20/2012] [Indexed: 12/13/2022] Open
Abstract
Heparan sulphate (HS) and the related polysaccharide, heparin, exhibit conformational and charge arrangement properties, which provide a degree of redundancy allowing several seemingly distinct sequences to exhibit the same activity. This can also be mimicked by other sulphated polysaccharides, both in overall effect and in the details of interactions and structural consequences of interactions with proteins. Together, these provide a source of active compounds suitable for further development as potential drugs. These polysaccharides also possess considerable size, which bestows upon them an additional useful property: the capability of disrupting processes comprising many individual interactions, such as those characterising the attachment of microbial pathogens to host cells. The range of involvement of HS in microbial attachment is reviewed and examples, which include viral, bacterial and parasitic infections and which, in many cases, are now being investigated as potential targets for intervention, are identified.
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Affiliation(s)
- T R Rudd
- Istituto di Chimica e Biochimica, Milano, Italy
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Soderholm JF, Bird SL, Kalab P, Sampathkumar Y, Hasegawa K, Uehara-Bingen M, Weis K, Heald R. Importazole, a small molecule inhibitor of the transport receptor importin-β. ACS Chem Biol 2011; 6:700-8. [PMID: 21469738 PMCID: PMC3137676 DOI: 10.1021/cb2000296] [Citation(s) in RCA: 180] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
During interphase, the transport receptor importin-β carries cargoes into the nucleus, where RanGTP releases them. A similar mechanism operates in mitosis to generate a gradient of active spindle assembly factors around mitotic chromosomes. Importin-β and RanGTP have been implicated in additional cellular processes, but the precise roles of the Ran/importin-β pathway throughout the cell cycle remain poorly understood. We implemented a FRET-based, high-throughput small molecule screen for compounds that interfere with the interaction between RanGTP and importin-β and identified importazole, a 2,4-diaminoquinazoline. Importazole specifically blocks importin-β-mediated nuclear import both in Xenopus egg extracts and cultured cells, without disrupting transportin-mediated nuclear import or CRM1-mediated nuclear export. When added during mitosis, importazole impairs the release of an importin-β cargo FRET probe and causes both predicted and novel defects in spindle assembly. Together, these results indicate that importazole specifically inhibits the function of importin-β, likely by altering its interaction with RanGTP. Importazole is a valuable tool to evaluate the function of the importin-β/RanGTP pathway at specific stages during the cell cycle.
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Affiliation(s)
- Jonathan F Soderholm
- The Department of Molecular and Cell Biology, University of California, Berkeley, MC 3200 LSA, Berkeley, California 94720-3200, United States
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Hokanson CA, Cappuccilli G, Odineca T, Bozic M, Behnke CA, Mendez M, Coleman WJ, Crea R. Engineering highly thermostable xylanase variants using an enhanced combinatorial library method. Protein Eng Des Sel 2011; 24:597-605. [DOI: 10.1093/protein/gzr028] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Horn M, Jílková A, Vondrášek J, Marešová L, Caffrey CR, Mareš M. Mapping the pro-peptide of the Schistosoma mansoni cathepsin B1 drug target: modulation of inhibition by heparin and design of mimetic inhibitors. ACS Chem Biol 2011; 6:609-17. [PMID: 21375333 DOI: 10.1021/cb100411v] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Blood flukes of the genus Schistosoma cause the disease schistosomiasis that infects over 200 million people worldwide. Treatment relies on just one drug, and new therapies are needed should drug resistance emerge. Schistosoma mansoni cathepsin B1 (SmCB1) is a gut-associated protease that digests host blood proteins as source of nutrients. It is under evaluation as a therapeutic target. Enzymatic activity of the SmCB1 zymogen is prevented by the pro-peptide that sterically blocks the active site until activation of the zymogen to the mature enzyme. We investigated the structure-inhibition relationships of how the SmCB1 pro-peptide interacts with the enzyme core using a SmCB1 zymogen model and pro-peptide-derived synthetic fragments. Two regions were identified within the pro-peptide that govern its inhibitory interaction with the enzyme core: an "active site region" and a unique "heparin-binding region" that requires heparin. The latter region is apparently only found in the pro-peptides of cathepsins B associated with the gut of trematode parasites. Finally, using the active site region as a template and a docking model of SmCB1, we designed a series of inhibitors mimicking the pro-peptide structure, the best of which yielded low micromolar inhibition constants. Overall, we identify a novel glycosaminoglycan-mediated mechanism of inhibition by the pro-peptide that potentially regulates zymogen activation and describe a promising design strategy to develop antischistosomal drugs.
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Affiliation(s)
- Martin Horn
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 16610 Prague, Czech Republic
| | - Adéla Jílková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 16610 Prague, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12843 Prague, Czech Republic
| | - Jiří Vondrášek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 16610 Prague, Czech Republic
| | - Lucie Marešová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 16610 Prague, Czech Republic
| | - Conor R. Caffrey
- Sandler Center for Drug Discovery, California Institute for Quantitative Biosciences (QB3), University of California San Francisco, 1700 Fourth Street, San Francisco, California 94158, United States
| | - Michael Mareš
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 16610 Prague, Czech Republic
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Killelea T, Connolly BA. Role of disulfide bridges in archaeal family-B DNA polymerases. Chembiochem 2011; 12:1330-6. [PMID: 21598372 DOI: 10.1002/cbic.201100145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Indexed: 11/09/2022]
Abstract
The family-B DNA polymerases obtained from the order Thermococcales, for example, Pyrococcus furiosus (Pfu-Pol) are commonly used in the polymerase chain reaction (PCR) because of their high thermostability and low error rates. Most of these polymerases contain four cysteines, arranged as two disulfide bridges. With Pfu-Pol C429-C443 forms one of the disulfides (DB1) and C507-C510 (DB2) the other. Although the disulfides are well conserved in the enzymes from the hyperthermophilic Thermococcales, they are less prevalent in euryarchaeal polymerases from other orders, and tend to be only found in other hyperthermophiles. Here, we report on the effects of deleting the disulfide bridges by mutating the relevant cysteines to serines. A variety of techniques, including differential scanning calorimetry and differential scanning fluorimetry, have shown that both disulfides make a contribution to thermostability, with DB1 being more important than DB2. However, even when both disulfides are removed, sufficient thermostability remains for normal (identical to the wild type) performance in PCR and quantitative (real-time) PCR. Therefore, polymerases totally lacking cysteine are fully compatible with most PCR-based applications. This observation opens the way to further engineering of polymerases by introduction of a single cysteine followed by appropriate chemical modification.
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Affiliation(s)
- Tom Killelea
- Institute of Cell and Molecular Biosciences (ICaMB), University of Newcastle, Newcastle upon Tyne, UK
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47
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Ross A, Zhang D, Deng X, Chang SL, Lahann J. Chemical-vapor-deposition-based polymer substrates for spatially resolved analysis of protein binding by imaging ellipsometry. Anal Chem 2011; 83:874-80. [PMID: 21226461 PMCID: PMC3061569 DOI: 10.1021/ac102535j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Biomolecular interactions between proteins and synthetic surfaces impact diverse biomedical fields. Simple, quantitative, label-free technologies for the analysis of protein adsorption and binding of biomolecules are thus needed. Here, we report the use of a novel type of substrate, poly-p-xylylene coatings prepared by chemical vapor deposition (CVD) polymerization, for surface plasmon resonance enhanced ellipsometry (SPREE) studies and assess the reactive coatings as spatially resolved biomolecular sensing arrays. Prior to use in binding studies, reactive coatings were fully characterized by Fourier transform infrared spectroscopy, electrochemical impedance spectroscopy, and ellipsometry. As a result, the chemical structure, thickness, and homogeneous coverage of the substrate surface were confirmed for a series of CVD-coated samples. Subsequent SPREE imaging and fluorescence microscopy indicated that the synthetic substrates supported detectable binding of a cascade of biomolecules. Moreover, analysis revealed a useful thickness range for CVD films in the assessment of protein and/or antigen-antibody binding via SPREE imaging. With a variety of functionalized end groups available for biomolecule immobilization and ease of patterning, CVD thin films are useful substrates for spatially resolved, quantitative binding arrays.
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Affiliation(s)
- Aftin Ross
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Di Zhang
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Xiaopei Deng
- Department of Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Seiwon Laura Chang
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Joerg Lahann
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
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48
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Rudd TR, Uniewicz KA, Ori A, Guimond SE, Skidmore MA, Gaudesi D, Xu R, Turnbull JE, Guerrini M, Torri G, Siligardi G, Wilkinson MC, Fernig DG, Yates EA. Comparable stabilisation, structural changes and activities can be induced in FGF by a variety of HS and non-GAG analogues: implications for sequence-activity relationships. Org Biomol Chem 2010; 8:5390-7. [DOI: 10.1039/c0ob00246a] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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