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Sultana R, Kamihira M. Bioengineered heparin: Advances in production technology. Biotechnol Adv 2024; 77:108456. [PMID: 39326809 DOI: 10.1016/j.biotechadv.2024.108456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 09/16/2024] [Accepted: 09/18/2024] [Indexed: 09/28/2024]
Abstract
Heparin, a highly sulfated glycosaminoglycan, is considered an indispensable anticoagulant with diverse therapeutic applications and has been a mainstay in medical practice for nearly a century. Its potential extends beyond anticoagulation, showing promise in treating inflammation, cancer, and infectious diseases such as COVID-19. However, its current sourcing from animal tissues poses challenges due to variable structures and adulterations, impacting treatment efficacy and safety. Recent advancements in metabolic engineering and synthetic biology offer alternatives through bioengineered heparin production, albeit with challenges such as controlling molecular weight and sulfonation patterns. This review offers comprehensive insight into recent advancements, encompassing: (i) the metabolic engineering strategies in prokaryotic systems for heparin production; (ii) strides made in the development of bioengineered heparin; and (iii) groundbreaking approaches driving production enhancements in eukaryotic systems. Additionally, it explores the potential of recombinant Chinese hamster ovary cells in heparin synthesis, discussing recent progress, challenges, and future prospects, thereby opening up new avenues in biomedical research.
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Affiliation(s)
- Razia Sultana
- Department of Chemical Engineering, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan; Department of Biotechnology and Genetic Engineering, Faculty of Science, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Masamichi Kamihira
- Department of Chemical Engineering, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
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2
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Böhm EW, Buonfiglio F, Korb CA, Dauth A, Pfeiffer N, Bręborowicz A, Gericke A. Potential of Sulodexide in the Treatment of Diabetic Retinopathy and Retinal Vein Occlusion. Thromb Haemost 2024. [PMID: 39293483 DOI: 10.1055/s-0044-1791232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2024]
Abstract
Retinal vascular diseases, such as diabetic retinopathy or retinal vein occlusion, are common causes of severe vision loss. Central to the pathophysiology of these conditions are endothelial dysfunction, inflammation, capillary leakage, ischemia, and pathological neoangiogenesis. Capillary damage leads to leakage and the development of macular edema, which is associated with vision loss and requires complex treatment. Sulodexide, a glycosaminoglycan composed of heparan sulfate and dermatan sulfate with high oral bioavailability, exhibits several favorable pharmacologic properties, including antithrombotic, anti-inflammatory, and endothelium-protective effects. Additionally, treatment with sulodexide has been associated with the reduction of oxidative stress and decreased expression of angiogenic growth factors, such as vascular endothelial growth factor. This review aims to provide an overview of the pharmacological properties, mechanisms of action, and therapeutic effects of sulodexide. Furthermore, its potential for clinical application in venous and diabetic diseases, such as venous thromboembolism, chronic venous insufficiency, peripheral artery disease, or diabetic nephropathy, is summarized. We also present experimental and clinical studies evaluating the potential of sulodexide in ocular conditions and discuss its therapeutic implications for the treatment of retinal vascular diseases.
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Affiliation(s)
- Elsa Wilma Böhm
- Department of Ophthalmology, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Francesco Buonfiglio
- Department of Ophthalmology, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Christina A Korb
- Department of Ophthalmology, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Alice Dauth
- Department of Neurosurgery, University Medical Center Mainz, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Norbert Pfeiffer
- Department of Ophthalmology, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Andrzej Bręborowicz
- Department of Pathophysiology, Poznan University of Medical Sciences, Poznan, Poland
- Collegium Medicum, Zielona Góra University, Zielona Góra, Poland
| | - Adrian Gericke
- Department of Ophthalmology, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
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3
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Kumar Villuri B, Desai UR. Synthesis and Reactivity of Masked Organic Sulfates. Chemistry 2024; 30:e202402268. [PMID: 39024030 DOI: 10.1002/chem.202402268] [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: 06/12/2024] [Revised: 07/17/2024] [Accepted: 07/18/2024] [Indexed: 07/20/2024]
Abstract
Nature offers a variety of structurally unique, sulfated endobiotics including sulfated glycosaminoglycans, sulfated tyrosine peptides, sulfated steroids/bile acids/catecholamines. Sulfated molecules display a large number of biological activities including antithrombotic, antimicrobial, anticancer, anti-inflammatory, and others, which arise from modulation of intracellular signaling and enhanced in vivo retention of certain hormones. These characteristics position sulfated molecules very favorably as drug-like agents. However, few have reached the clinic. Major hurdles exist in realizing sulfated molecules as drugs. This state-of-the-art has been transformed through recent works on the development of sulfate masking technologies for both alkyl (sulfated carbohydrates, sulfated steroids) and aryl (sTyr-bearing peptides/proteins, sulfated flavonoids) sulfates. This review compiles the literature on different strategies implemented for different types of sulfate groups. Starting from early efforts in protection of sulfate groups to the design of newer SuFEx, trichloroethyl, and gem-dimethyl-based protection technologies, this review presents the evolution and application of concepts in realizing highly diverse, sulfated molecules as candidate drugs and/or prodrugs. Overall, the newer strategies for sulfate masking and demasking are likely to greatly enhance the design and development of sulfated molecules as non-toxic drugs of the future.
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Affiliation(s)
- Bharath Kumar Villuri
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298, United States
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia, 23219, United States
| | - Umesh R Desai
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298, United States
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia, 23219, United States
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4
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Parafioriti M, Elli S, Muñoz-García JC, Ramírez-Cárdenas J, Yates EA, Angulo J, Guerrini M. Differential Solvent DEEP-STD NMR and MD Simulations Enable the Determinants of the Molecular Recognition of Heparin Oligosaccharides by Antithrombin to Be Disentangled. Int J Mol Sci 2024; 25:4669. [PMID: 38731888 PMCID: PMC11083112 DOI: 10.3390/ijms25094669] [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: 02/28/2024] [Revised: 04/16/2024] [Accepted: 04/20/2024] [Indexed: 05/13/2024] Open
Abstract
The interaction of heparin with antithrombin (AT) involves a specific sequence corresponding to the pentasaccharide GlcNAc/NS6S-GlcA-GlcNS3S6S-IdoA2S-GlcNS6S (AGA*IA). Recent studies have revealed that two AGA*IA-containing hexasaccharides, which differ in the sulfation degree of the iduronic acid unit, exhibit similar binding to AT, albeit with different affinities. However, the lack of experimental data concerning the molecular contacts between these ligands and the amino acids within the protein-binding site prevents a detailed description of the complexes. Differential epitope mapping (DEEP)-STD NMR, in combination with MD simulations, enables the experimental observation and comparison of two heparin pentasaccharides interacting with AT, revealing slightly different bound orientations and distinct affinities of both glycans for AT. We demonstrate the effectiveness of the differential solvent DEEP-STD NMR approach in determining the presence of polar residues in the recognition sites of glycosaminoglycan-binding proteins.
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Affiliation(s)
- Michela Parafioriti
- Istituto di Ricerche Chimiche e Biochimiche “G. Ronzoni”, Via Giuseppe Colombo 81, 20133 Milano, Italy; (M.P.); (S.E.)
| | - Stefano Elli
- Istituto di Ricerche Chimiche e Biochimiche “G. Ronzoni”, Via Giuseppe Colombo 81, 20133 Milano, Italy; (M.P.); (S.E.)
| | - Juan C. Muñoz-García
- Instituto de Investigationes Químicas (IIQ)-Consejo Superior de Investigaciones Científicas (CSIC), Avenida Americo Vespucio 49, 41092 Sevilla, Spain; (J.C.M.-G.); (J.R.-C.)
| | - Jonathan Ramírez-Cárdenas
- Instituto de Investigationes Químicas (IIQ)-Consejo Superior de Investigaciones Científicas (CSIC), Avenida Americo Vespucio 49, 41092 Sevilla, Spain; (J.C.M.-G.); (J.R.-C.)
| | - Edwin A. Yates
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK;
- Centre for Glycoscience, Keele University, Newcastle-Under-Lyme ST5 5BG, UK
| | - Jesús Angulo
- Instituto de Investigationes Químicas (IIQ)-Consejo Superior de Investigaciones Científicas (CSIC), Avenida Americo Vespucio 49, 41092 Sevilla, Spain; (J.C.M.-G.); (J.R.-C.)
| | - Marco Guerrini
- Istituto di Ricerche Chimiche e Biochimiche “G. Ronzoni”, Via Giuseppe Colombo 81, 20133 Milano, Italy; (M.P.); (S.E.)
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5
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Pagani I, Ottoboni L, Panina-Bordignon P, Martino G, Poli G, Taylor S, Turnbull JE, Yates E, Vicenzi E. Heparin Precursors with Reduced Anticoagulant Properties Retain Antiviral and Protective Effects That Potentiate the Efficacy of Sofosbuvir against Zika Virus Infection in Human Neural Progenitor Cells. Pharmaceuticals (Basel) 2023; 16:1385. [PMID: 37895856 PMCID: PMC10609960 DOI: 10.3390/ph16101385] [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: 07/27/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 10/29/2023] Open
Abstract
Zika virus (ZIKV) infection during pregnancy can result in severe birth defects, such as microcephaly, as well as a range of other related health complications. Heparin, a clinical-grade anticoagulant, is shown to protect neural progenitor cells from death following ZIKV infection. Although heparin can be safely used during pregnancy, it retains off-target anticoagulant effects if directly employed against ZIKV infection. In this study, we investigated the effects of chemically modified heparin derivatives with reduced anticoagulant activities. These derivatives were used as experimental probes to explore the structure-activity relationships. Precursor fractions of porcine heparin, obtained during the manufacture of conventional pharmaceutical heparin with decreased anticoagulant activities, were also explored. Interestingly, these modified heparin derivatives and precursor fractions not only prevented cell death but also inhibited the ZIKV replication of infected neural progenitor cells grown as neurospheres. These effects were observed regardless of the specific sulfation position or overall charge. Furthermore, the combination of heparin with Sofosbuvir, an antiviral licensed for the treatment of hepatitis C (HCV) that also belongs to the same Flaviviridae family as ZIKV, showed a synergistic effect. This suggested that a combination therapy approach involving heparin precursors and Sofosbuvir could be a potential strategy for the prevention or treatment of ZIKV infections.
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Affiliation(s)
- Isabel Pagani
- Viral Pathogenesis and Biosafety Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Linda Ottoboni
- Neuroimmunology Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Paola Panina-Bordignon
- Neuroimmunology Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, Via Olgettina 58, 20132 Milan, Italy
| | - Gianvito Martino
- Neuroimmunology Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, Via Olgettina 58, 20132 Milan, Italy
| | - Guido Poli
- School of Medicine, Vita-Salute San Raffaele University, Via Olgettina 58, 20132 Milan, Italy
- Human Immuno-Virology Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Sarah Taylor
- Department of Biochemistry & Systems Biology, ISMIB, University of Liverpool, Liverpool L69 7ZB, UK
| | - Jeremy E Turnbull
- Department of Biochemistry & Systems Biology, ISMIB, University of Liverpool, Liverpool L69 7ZB, UK
- Department of Life Sciences, Keele University, Keele, Staffs ST5 5BG, UK
| | - Edwin Yates
- Department of Biochemistry & Systems Biology, ISMIB, University of Liverpool, Liverpool L69 7ZB, UK
- Department of Life Sciences, Keele University, Keele, Staffs ST5 5BG, UK
| | - Elisa Vicenzi
- Viral Pathogenesis and Biosafety Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
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Abdelfadiel E, Gunta R, Villuri BK, Afosah DK, Sankaranarayanan NV, Desai UR. Designing Smaller, Synthetic, Functional Mimetics of Sulfated Glycosaminoglycans as Allosteric Modulators of Coagulation Factors. J Med Chem 2023; 66:4503-4531. [PMID: 37001055 PMCID: PMC10108365 DOI: 10.1021/acs.jmedchem.3c00132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Indexed: 04/03/2023]
Abstract
Natural glycosaminoglycans (GAGs) are arguably the most diverse collection of natural products. Unfortunately, this bounty of structures remains untapped. Decades of research has realized only one GAG-like synthetic, small-molecule drug, fondaparinux. This represents an abysmal output because GAGs present a frontier that few medicinal chemists, and even fewer pharmaceutical companies, dare to undertake. GAGs are heterogeneous, polymeric, polydisperse, highly water soluble, synthetically challenging, too rapidly cleared, and difficult to analyze. Additionally, GAG binding to proteins is not very selective and GAG-binding sites are shallow. This Perspective attempts to transform this negative view into a much more promising one by highlighting recent advances in GAG mimetics. The Perspective focuses on the principles used in the design/discovery of drug-like, synthetic, sulfated small molecules as allosteric modulators of coagulation factors, such as antithrombin, thrombin, and factor XIa. These principles will also aid the design/discovery of sulfated agents against cancer, inflammation, and microbial infection.
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Affiliation(s)
- Elsamani
I. Abdelfadiel
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Rama Gunta
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Bharath Kumar Villuri
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Daniel K. Afosah
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Nehru Viji Sankaranarayanan
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Umesh R. Desai
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
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7
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Hogwood J, Mulloy B, Lever R, Gray E, Page CP. Pharmacology of Heparin and Related Drugs: An Update. Pharmacol Rev 2023; 75:328-379. [PMID: 36792365 DOI: 10.1124/pharmrev.122.000684] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 02/17/2023] Open
Abstract
Heparin has been used extensively as an antithrombotic and anticoagulant for close to 100 years. This anticoagulant activity is attributed mainly to the pentasaccharide sequence, which potentiates the inhibitory action of antithrombin, a major inhibitor of the coagulation cascade. More recently it has been elucidated that heparin exhibits anti-inflammatory effect via interference of the formation of neutrophil extracellular traps and this may also contribute to heparin's antithrombotic activity. This illustrates that heparin interacts with a broad range of biomolecules, exerting both anticoagulant and nonanticoagulant actions. Since our previous review, there has been an increased interest in these nonanticoagulant effects of heparin, with the beneficial role in patients infected with SARS2-coronavirus a highly topical example. This article provides an update on our previous review with more recent developments and observations made for these novel uses of heparin and an overview of the development status of heparin-based drugs. SIGNIFICANCE STATEMENT: This state-of-the-art review covers recent developments in the use of heparin and heparin-like materials as anticoagulant, now including immunothrombosis observations, and as nonanticoagulant including a role in the treatment of SARS-coronavirus and inflammatory conditions.
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Affiliation(s)
- John Hogwood
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., E.G., C.P.P.); National Institute for Biological Standards and Control, South Mimms, Hertfordshire, United Kingdom (J.H., E.G.) and School of Pharmacy, University College London, London, United Kingdom (R.L.)
| | - Barbara Mulloy
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., E.G., C.P.P.); National Institute for Biological Standards and Control, South Mimms, Hertfordshire, United Kingdom (J.H., E.G.) and School of Pharmacy, University College London, London, United Kingdom (R.L.)
| | - Rebeca Lever
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., E.G., C.P.P.); National Institute for Biological Standards and Control, South Mimms, Hertfordshire, United Kingdom (J.H., E.G.) and School of Pharmacy, University College London, London, United Kingdom (R.L.)
| | - Elaine Gray
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., E.G., C.P.P.); National Institute for Biological Standards and Control, South Mimms, Hertfordshire, United Kingdom (J.H., E.G.) and School of Pharmacy, University College London, London, United Kingdom (R.L.)
| | - Clive P Page
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., E.G., C.P.P.); National Institute for Biological Standards and Control, South Mimms, Hertfordshire, United Kingdom (J.H., E.G.) and School of Pharmacy, University College London, London, United Kingdom (R.L.)
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8
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Hedgehog is relayed through dynamic heparan sulfate interactions to shape its gradient. Nat Commun 2023; 14:758. [PMID: 36765094 PMCID: PMC9918555 DOI: 10.1038/s41467-023-36450-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 01/27/2023] [Indexed: 02/12/2023] Open
Abstract
Cellular differentiation is directly determined by concentration gradients of morphogens. As a central model for gradient formation during development, Hedgehog (Hh) morphogens spread away from their source to direct growth and pattern formation in Drosophila wing and eye discs. What is not known is how extracellular Hh spread is achieved and how it translates into precise gradients. Here we show that two separate binding areas located on opposite sides of the Hh molecule can interact directly and simultaneously with two heparan sulfate (HS) chains to temporarily cross-link the chains. Mutated Hh lacking one fully functional binding site still binds HS but shows reduced HS cross-linking. This, in turn, impairs Hhs ability to switch between both chains in vitro and results in striking Hh gradient hypomorphs in vivo. The speed and propensity of direct Hh switching between HS therefore shapes the Hh gradient, revealing a scalable design principle in morphogen-patterned tissues.
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Al-Horani RA, Afosah DK, Kar S, Aliter KF, Mottamal M. Sulphated penta-galloyl glucopyranoside (SPGG) is glycosaminoglycan mimetic allosteric inhibitor of cathepsin G. RPS PHARMACY AND PHARMACOLOGY REPORTS 2023; 2:rqad001. [PMID: 36844783 PMCID: PMC9942669 DOI: 10.1093/rpsppr/rqad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023]
Abstract
Objective Cathepsin G (CatG) is a cationic serine protease with wide substrate specificity. CatG is reported to play a role in several inflammatory pathologies. Thus, we aimed at identifying a potent and allosteric inhibitor of CatG to be used as a platform in further drug development opportunities. Methods Chromogenic substrate hydrolysis assays were used to evaluate the inhibition potency and selectivity of SPGG towards CatG. Salt-dependent studies, Michaelis-Menten kinetics and SDS-PAGE were exploited to decipher the mechanism of CatG inhibition by SPGG. Molecular modelling was also used to identify a plausible binding site. Key findings SPGG displayed an inhibition potency of 57 nM against CatG, which was substantially selective over other proteases. SPGG protected fibronectin and laminin against CatG-mediated degradation. SPGG reduced VMAX of CatG hydrolysis of a chromogenic substrate without affecting KM, suggesting an allosteric mechanism. Resolution of energy contributions indicated that non-ionic interactions contribute ~91% of binding energy, suggesting a substantial possibility of specific recognition. Molecular modelling indicated that SPGG plausibly binds to an anion-binding sequence of 109SRRVRRNRN117. Conclusion We present the discovery of SPGG as the first small molecule, potent, allosteric glycosaminoglycan mimetic inhibitor of CatG. SPGG is expected to open a major route to clinically relevant allosteric CatG anti-inflammatory agents.
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Affiliation(s)
- Rami A Al-Horani
- Division of Basic Pharmaceutical Sciences, College of Pharmacy, Xavier University of Louisiana, New Orleans, LA, USA
| | - Daniel K Afosah
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA
| | - Srabani Kar
- Division of Basic Pharmaceutical Sciences, College of Pharmacy, Xavier University of Louisiana, New Orleans, LA, USA
| | - Kholoud F Aliter
- Department of Chemistry, School of STEM, Dillard University, New Orleans, LA, USA
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10
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Wulftange WJ, Kucukal E, Man Y, An R, Monchamp K, Sevrain CD, Dashora HR, Owusu-Ansah AT, Bode A, Ilich A, Little JA, Key NS, Gurkan UA. Antithrombin-III mitigates thrombin-mediated endothelial cell contraction and sickle red blood cell adhesion in microscale flow. Br J Haematol 2022; 198:893-902. [PMID: 35822297 PMCID: PMC9542057 DOI: 10.1111/bjh.18328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/10/2022] [Accepted: 06/11/2022] [Indexed: 11/27/2022]
Abstract
Individuals with sickle cell disease (SCD) have persistently elevated thrombin generation that results in a state of systemic hypercoagulability. Antithrombin‐III (ATIII), an endogenous serine protease inhibitor, inhibits several enzymes in the coagulation cascade, including thrombin. Here, we utilize a biomimetic microfluidic device to model the morphology and adhesive properties of endothelial cells (ECs) activated by thrombin and examine the efficacy of ATIII in mitigating the adhesion of SCD patient‐derived red blood cells (RBCs) and EC retraction. Microfluidic devices were fabricated, seeded with ECs, and incubated under physiological shear stress. Cells were then activated with thrombin with or without an ATIII pretreatment. Blood samples from subjects with normal haemoglobin (HbAA) and subjects with homozygous SCD (HbSS) were used to examine RBC adhesion to ECs. Endothelial cell surface adhesion molecule expression and confluency in response to thrombin and ATIII treatments were also evaluated. We found that ATIII pretreatment of ECs reduced HbSS RBC adhesion to thrombin‐activated endothelium. Furthermore, ATIII mitigated cellular contraction and reduced surface expression of von Willebrand factor and vascular cell adhesion molecule‐1 (VCAM‐1) mediated by thrombin. Our findings suggest that, by attenuating thrombin‐mediated EC damage and RBC adhesion to endothelium, ATIII may alleviate the thromboinflammatory manifestations of SCD.
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Affiliation(s)
- William J Wulftange
- Department of Mechanical and Aerospace Engineering, Case Western Reserve University, Cleveland, Ohio, USA
| | - Erdem Kucukal
- Department of Mechanical and Aerospace Engineering, Case Western Reserve University, Cleveland, Ohio, USA
| | - Yuncheng Man
- Department of Mechanical and Aerospace Engineering, Case Western Reserve University, Cleveland, Ohio, USA
| | - Ran An
- Department of Mechanical and Aerospace Engineering, Case Western Reserve University, Cleveland, Ohio, USA
| | - Karamoja Monchamp
- Department of Mechanical and Aerospace Engineering, Case Western Reserve University, Cleveland, Ohio, USA
| | - Charlotte D Sevrain
- Department of Mechanical and Aerospace Engineering, Case Western Reserve University, Cleveland, Ohio, USA
| | - Himanshu R Dashora
- Department of Mechanical and Aerospace Engineering, Case Western Reserve University, Cleveland, Ohio, USA
| | - Amma T Owusu-Ansah
- Department of Pediatrics, Division of Hematology Oncology, University Hospitals Rainbow Babies and Children's Hospital, Cleveland, Ohio, USA
| | - Allison Bode
- Department of Mechanical and Aerospace Engineering, Case Western Reserve University, Cleveland, Ohio, USA
| | - Anton Ilich
- Division of Hematology and UNC Blood Research Center, Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jane A Little
- Division of Hematology and UNC Blood Research Center, Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Nigel S Key
- Division of Hematology and UNC Blood Research Center, Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Umut A Gurkan
- Department of Mechanical and Aerospace Engineering, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, USA
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11
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Danielsson A, Kogut MM, Maszota-Zieleniak M, Chopra P, Boons GJ, Samsonov SA. Molecular Dynamics-based descriptors of 3-O-Sulfated Heparan Sulfate as Contributors of Protein Binding Specificity. Comput Biol Chem 2022; 99:107716. [DOI: 10.1016/j.compbiolchem.2022.107716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/03/2022] [Accepted: 06/20/2022] [Indexed: 11/03/2022]
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12
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Onodera W, Asahi T, Sawamura N. Rapid evolution of mammalian APLP1 as a synaptic adhesion molecule. Sci Rep 2021; 11:11305. [PMID: 34050225 PMCID: PMC8163877 DOI: 10.1038/s41598-021-90737-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/17/2021] [Indexed: 01/10/2023] Open
Abstract
Amyloid precursor protein (APP) family members are involved in essential neuronal development including neurite outgrowth, neuronal migration and maturation of synapse and neuromuscular junction. Among the APP gene family members, amyloid precursor-like protein 1 (APLP1) is selectively expressed in neurons and has specialized functions during synaptogenesis. Although a potential role for APLP1 in neuronal evolution has been indicated, its precise evolutionary and functional contributions are unknown. This study shows the molecular evolution of the vertebrate APP family based on phylogenetic analysis, while contrasting the evolutionary differences within the APP family. Phylogenetic analysis showed 15 times higher substitution rate that is driven by positive selection at the stem branch of the mammalian APLP1, resulting in dissimilar protein sequences compared to APP/APLP2. Docking simulation identified one positively selected site in APLP1 that alters the heparin-binding site, which could affect its function, and dimerization rate. Furthermore, the evolutionary rate covariation between the mammalian APP family and synaptic adhesion molecules (SAMs) was confirmed, indicating that only APLP1 has evolved to gain synaptic adhesion property. Overall, our results suggest that the enhanced synaptogenesis property of APLP1 as one of the SAMs may have played a role in mammalian brain evolution.
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Affiliation(s)
- Wataru Onodera
- Faculty of Science and Engineering, Waseda University, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo, 162-8480, Japan
| | - Toru Asahi
- Faculty of Science and Engineering, Waseda University, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo, 162-8480, Japan.,Research Organization for Nano & Life Innovation, Waseda University, #03C309, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo, 162-8480, Japan
| | - Naoya Sawamura
- Research Organization for Nano & Life Innovation, Waseda University, #03C309, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo, 162-8480, Japan. .,Green Computing Systems Research Organization, Waseda University, Shinjuku, Japan.
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13
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Insights into Interactions between Interleukin-6 and Dendritic Polyglycerols. Int J Mol Sci 2021; 22:ijms22052415. [PMID: 33670858 PMCID: PMC7957513 DOI: 10.3390/ijms22052415] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 11/23/2022] Open
Abstract
Interleukin-6 (IL-6) is involved in physiological and pathological processes. Different pharmacological agents have been developed to block IL-6 deleterious effects and to recover homeostatic IL-6 signaling. One of the proposed nanostructures in pre-clinical investigations which reduced IL-6 concentrations is polyglycerol dendrimer, a nano-structure with multiple sulfate groups. The aim of the present study was to uncover the type of binding between critical positions in the human IL-6 structure available for binding dPGS and compare it with heparin sulfate binding. We studied these interactions by performing docking simulations of dPGS and heparins with human IL-6 using AutoDock Vina. These molecular docking analyses indicate that the two ligands have comparable affinities for the positively charged positions on the surface of IL-6. All-atom molecular dynamics simulations (MD) employing Gromacs were used to explore the binding sites and binding strengths. Results suggest two major binding sites and show that the strengths of binding are similar for heparin and dPGS (−5.5–6.4 kcal/ mol). dPGS or its analogs could be used in the therapeutic intervention in sepsis and inflammatory disorders to reduce unbound IL-6 in the plasma or tissues and its binding to the receptors. We propose that analogs of dPGS could specifically block IL-6 binding in the desired signaling mode and would be valuable new probes to establish optimized therapeutic intervention in inflammation.
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14
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Wolpe AG, Ruddiman CA, Hall PJ, Isakson BE. Polarized Proteins in Endothelium and Their Contribution to Function. J Vasc Res 2021; 58:65-91. [PMID: 33503620 DOI: 10.1159/000512618] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 10/27/2020] [Indexed: 12/11/2022] Open
Abstract
Protein localization in endothelial cells is tightly regulated to create distinct signaling domains within their tight spatial restrictions including luminal membranes, abluminal membranes, and interendothelial junctions, as well as caveolae and calcium signaling domains. Protein localization in endothelial cells is also determined in part by the vascular bed, with differences between arteries and veins and between large and small arteries. Specific protein polarity and localization is essential for endothelial cells in responding to various extracellular stimuli. In this review, we examine protein localization in the endothelium of resistance arteries, with occasional references to other vessels for contrast, and how that polarization contributes to endothelial function and ultimately whole organism physiology. We highlight the protein localization on the luminal surface, discussing important physiological receptors and the glycocalyx. The protein polarization to the abluminal membrane is especially unique in small resistance arteries with the presence of the myoendothelial junction, a signaling microdomain that regulates vasodilation, feedback to smooth muscle cells, and ultimately total peripheral resistance. We also discuss the interendothelial junction, where tight junctions, adherens junctions, and gap junctions all convene and regulate endothelial function. Finally, we address planar cell polarity, or axial polarity, and how this is regulated by mechanosensory signals like blood flow.
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Affiliation(s)
- Abigail G Wolpe
- Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA.,Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Claire A Ruddiman
- Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA.,Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Phillip J Hall
- Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Brant E Isakson
- Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA, .,Department of Molecular Physiology and Biophysics, University of Virginia School of Medicine, Charlottesville, Virginia, USA,
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15
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Nagarajan B, Sankaranarayanan NV, Desai UR. Rigorous analysis of free solution glycosaminoglycan dynamics using simple, new tools. Glycobiology 2020; 30:516-527. [PMID: 32080710 PMCID: PMC8179626 DOI: 10.1093/glycob/cwaa015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 02/03/2020] [Accepted: 02/09/2020] [Indexed: 11/15/2022] Open
Abstract
Heparin/heparan sulfates (H/HS) are ubiquitous biopolymers that interact with many proteins to induce a range of biological functions. Unfortunately, how these biopolymers recognize their preferred protein targets remain poorly understood. It is suggested that computational simulations offer attractive avenues but a number of challenges, e.g., difficulty of selecting a comprehensive force field, few simple tools to interpret data, among others, remain. This work addresses several such challenges so as to help ease the implementation and analysis of computational experiments. First, this work presents a rigorous comparison of two different recent force fields, CHARMM36 and GLYCAM06, for H/HS studies. Second, it introduces two new straightforward parameters, i.e., end-to-end distance and minimum volume enclosing ellipsoid, to understand the myriad conformational forms of oligosaccharides that evolve over time in water. Third, it presents an application to elucidate the number and nature of inter and intramolecular, nondirect bridging water molecules, which help stabilize unique forms of H/HS. The results show that nonspecialists can use either CHARMM36 or GLYCAM06 force fields because both gave comparable results, albeit with small differences. The comparative study shows that the HS hexasaccharide samples a range of conformations with nearly equivalent energies, which could be the reason for its recognition by different proteins. Finally, analysis of the nondirect water bridges across the dynamics trajectory shows their importance in stabilization of certain conformational forms, which may become important for protein recognition. Overall, the work aids nonspecialists employ computational studies for understanding the solution behavior of H/HS.
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Affiliation(s)
- Balaji Nagarajan
- Institute for Structural Biology, Drug Discovery and Development, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA
- Department of Medicinal Chemistry, 800 E. Leigh Street, Suite 205, Richmond, VA 23298, USA
| | - Nehru Viji Sankaranarayanan
- Institute for Structural Biology, Drug Discovery and Development, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA
- Department of Medicinal Chemistry, 800 E. Leigh Street, Suite 205, Richmond, VA 23298, USA
| | - Umesh R Desai
- Institute for Structural Biology, Drug Discovery and Development, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA
- Department of Medicinal Chemistry, 800 E. Leigh Street, Suite 205, Richmond, VA 23298, USA
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16
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Sankaranarayanan NV, Bi Y, Kuberan B, Desai UR. Combinatorial virtual library screening analysis of antithrombin binding oligosaccharide motif generation by heparan sulfate 3- O-Sulfotransferase 1. Comput Struct Biotechnol J 2020; 18:933-941. [PMID: 32346466 PMCID: PMC7183009 DOI: 10.1016/j.csbj.2020.03.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 03/07/2020] [Accepted: 03/08/2020] [Indexed: 12/31/2022] Open
Abstract
Pharmaceutical heparin's activity arises from a key high affinity and high selectivity antithrombin binding motif, which forms the basis for its use as an anticoagulant. The current problems with the supply of pig heparin raises the emphasis of understanding heparin biosynthesis so as to control and advance recombinantly expressed agent that could bypass the need for animals. Unfortunately, much remains to be understood about the generation of the antithrombin-binding motif by the key enzyme involved in its biosynthesis, 3-O-sulfotransferase-1 (3OST-1). In this work, we present a novel computational approach to understand recognition of oligosaccharide sequences by 3OST-1. Application of combinatorial virtual library screening (CVLS) algorithm on hundreds of tetrasaccharide and hexasaccharide sequences shows that 3OST-1 belongs to the growing number of proteins that recognize glycosaminoglycans with very high selectivity. It prefers very well defined pentasaccharide sequences carrying distinct groups in each of the five residues to generate the antithrombin binding motif. CVLS also identifies key residues including His271, Arg72, Arg197 and Lys173, which interact with 6-sulfate, 5-COO¯, 2-/6-sulfates and 2-sulfate at the -2, -1, +2, and +1 positions of the precursor pentasaccharide, respectively. Additionally, uncharged residues, especially Gln163 and Asn167, were also identified as playing important roles in recognition. Overall, the success of CVLS in predicting 3OST-1 recognition characteristics that help engineer selectivity lead to the expectation that recombinant enzymes could be designed to help resolve the current problems in the supply of anticoagulant heparin.
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Affiliation(s)
- Nehru Viji Sankaranarayanan
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
| | - Yiling Bi
- Departments of Biology, Bioengineering & Medicinal Chemistry and Interdepartmental Program in Neurosciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Balagurunathan Kuberan
- Departments of Biology, Bioengineering & Medicinal Chemistry and Interdepartmental Program in Neurosciences, University of Utah, Salt Lake City, UT 84112, USA
- Interdepartmental Program in Neurosciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Umesh R. Desai
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
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17
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Neves MI, Araújo M, Moroni L, da Silva RM, Barrias CC. Glycosaminoglycan-Inspired Biomaterials for the Development of Bioactive Hydrogel Networks. Molecules 2020; 25:E978. [PMID: 32098281 PMCID: PMC7070556 DOI: 10.3390/molecules25040978] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/14/2020] [Accepted: 02/20/2020] [Indexed: 02/07/2023] Open
Abstract
Glycosaminoglycans (GAG) are long, linear polysaccharides that display a wide range of relevant biological roles. Particularly, in the extracellular matrix (ECM) GAG specifically interact with other biological molecules, such as growth factors, protecting them from proteolysis or inhibiting factors. Additionally, ECM GAG are partially responsible for the mechanical stability of tissues due to their capacity to retain high amounts of water, enabling hydration of the ECM and rendering it resistant to compressive forces. In this review, the use of GAG for developing hydrogel networks with improved biological activity and/or mechanical properties is discussed. Greater focus is given to strategies involving the production of hydrogels that are composed of GAG alone or in combination with other materials. Additionally, approaches used to introduce GAG-inspired features in biomaterials of different sources will also be presented.
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Affiliation(s)
- Mariana I. Neves
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (M.I.N.); (M.A.)
- INEB-Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- FEUP-Faculdade de Engenharia da Universidade do Porto, Departamento de Engenharia Metalúrgica e de Materiais, Rua Dr Roberto Frias s/n, 4200-465 Porto, Portugal
| | - Marco Araújo
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (M.I.N.); (M.A.)
- INEB-Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Lorenzo Moroni
- MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, 6229 ET Maastricht, The Netherlands;
| | - Ricardo M.P. da Silva
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (M.I.N.); (M.A.)
- INEB-Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Cristina C. Barrias
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (M.I.N.); (M.A.)
- INEB-Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- ICBAS-Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
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18
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Hu X, Maffucci I, Contini A. Advances in the Treatment of Explicit Water Molecules in Docking and Binding Free Energy Calculations. Curr Med Chem 2020; 26:7598-7622. [DOI: 10.2174/0929867325666180514110824] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 02/26/2018] [Accepted: 04/18/2018] [Indexed: 12/30/2022]
Abstract
Background:
The inclusion of direct effects mediated by water during the ligandreceptor
recognition is a hot-topic of modern computational chemistry applied to drug discovery
and development. Docking or virtual screening with explicit hydration is still debatable,
despite the successful cases that have been presented in the last years. Indeed, how to select
the water molecules that will be included in the docking process or how the included waters
should be treated remain open questions.
Objective:
In this review, we will discuss some of the most recent methods that can be used in
computational drug discovery and drug development when the effect of a single water, or of a
small network of interacting waters, needs to be explicitly considered.
Results:
Here, we analyse the software to aid the selection, or to predict the position, of water
molecules that are going to be explicitly considered in later docking studies. We also present
software and protocols able to efficiently treat flexible water molecules during docking, including
examples of applications. Finally, we discuss methods based on molecular dynamics
simulations that can be used to integrate docking studies or to reliably and efficiently compute
binding energies of ligands in presence of interfacial or bridging water molecules.
Conclusions:
Software applications aiding the design of new drugs that exploit water molecules,
either as displaceable residues or as bridges to the receptor, are constantly being developed.
Although further validation is needed, workflows that explicitly consider water will
probably become a standard for computational drug discovery soon.
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Affiliation(s)
- Xiao Hu
- Università degli Studi di Milano, Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica “A. Marchesini”, Via Venezian, 21 20133 Milano, Italy
| | - Irene Maffucci
- Pasteur, Département de Chimie, École Normale Supérieure, PSL Research University, Sorbonne Universités, UPMC Univ. Paris 06, CNRS, 75005 Paris, France
| | - Alessandro Contini
- Università degli Studi di Milano, Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica “A. Marchesini”, Via Venezian, 21 20133 Milano, Italy
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19
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Siddiqui F, Hoppensteadt D, Bontekoe E, Farooqui A, Jeske W, Fareed J. Comparative Anticoagulant and Thrombin Generation Inhibitory Profile of Heparin, Sulodexide and Its Components. Clin Appl Thromb Hemost 2020; 26:1076029620954913. [PMID: 33030036 PMCID: PMC7549168 DOI: 10.1177/1076029620954913] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/20/2020] [Accepted: 08/13/2020] [Indexed: 12/11/2022] Open
Abstract
INTRODUCTION Sulodexide represents a mixture of fast-moving heparin (FMH) and dermatan sulfate (DS) and has been used for the management of venous diseases such as DVT and related disorders. The purpose of this study is to compare sulodexide and its components with unfractionated heparin (UFH) to determine its suitability for the indications in which UFH is used. MATERIALS AND METHOD Active pharmaceutical ingredients (API) versions of sulodexide, FMH and DS were obtained from Alfasigma. API versions of UFH were obtained from Medefil Inc. Normal human citrated plasma was obtained from blood bank of the Loyola University Medical Center. Each of the individual agents were supplemented in plasma at a graded concentration of 0.0-10 µg/mL. Clotting assays (PiCT, aPTT, PT and TT), anti-Xa and anti-IIa and thrombin generation studies were carried out. Results were compiled as mean ± SD of 3 individual determination. RESULT In the clot based (PiCT, aPTT and TT), anti-Xa and IIa assays, both the UFH and FMH produced stronger activities in these assays followed by sulodexide. DS did not show any anticoagulant activity. In the thrombin generation assay, FMH and UFH produced comparable inhibition of thrombin generation as measured by various parameters. Sulodexide was slightly weaker in this assay, whereas DS produced relatively weaker effects. CONCLUSION In comparison to sulodexide, both UFH and FMH exhibit comparable anticoagulant activity despite differences in their molecular weight. These results suggest that sulodexide can be developed as a parenteral anticoagulant for indications in which UFH is used.
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Affiliation(s)
- Fakiha Siddiqui
- Department of Pathology and Laboratory Medicine, Cardiovascular
Research Institute, Loyola University Chicago, Health Sciences Division, Maywood,
IL, USA
| | - Debra Hoppensteadt
- Department of Pathology and Laboratory Medicine, Cardiovascular
Research Institute, Loyola University Chicago, Health Sciences Division, Maywood,
IL, USA
- Department of Pharmacology and Neuroscience, Cardiovascular Research
Institute, Loyola University Chicago, Health Sciences Division, Maywood, IL,
USA
| | - Emily Bontekoe
- Department of Pathology and Laboratory Medicine, Cardiovascular
Research Institute, Loyola University Chicago, Health Sciences Division, Maywood,
IL, USA
| | - Ambar Farooqui
- Department of Pathology and Laboratory Medicine, Cardiovascular
Research Institute, Loyola University Chicago, Health Sciences Division, Maywood,
IL, USA
| | - Walter Jeske
- Department of Pathology and Laboratory Medicine, Cardiovascular
Research Institute, Loyola University Chicago, Health Sciences Division, Maywood,
IL, USA
- Department of Thoracic and Cardiovascular Surgery, Cardiovascular
Research Institute, Loyola University Chicago, Health Sciences Division, Maywood,
IL, USA
| | - Jawed Fareed
- Department of Pharmacology and Neuroscience, Cardiovascular Research
Institute, Loyola University Chicago, Health Sciences Division, Maywood, IL,
USA
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20
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In-Vitro Hemocompatibility of Polyaniline Functionalized by Bioactive Molecules. Polymers (Basel) 2019; 11:polym11111861. [PMID: 31718055 PMCID: PMC6918175 DOI: 10.3390/polym11111861] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/22/2019] [Accepted: 11/01/2019] [Indexed: 11/17/2022] Open
Abstract
Hemocompatibility is an essential prerequisite for the application of materials in the field of biomedicine and biosensing. In addition, mixed ionic and electronic conductivity of conducting polymers is an advantageous property for these applications. Heparin-like materials containing sulfate, sulfamic, and carboxylic groups may have an anticoagulation effect. Therefore, sodium dodecylbenzenesulfonate, 2-aminoethane-1-sulfonic acid and N-(2-acetamido)-2-aminoethanesulfonic acid were used for modification of the representative of conducting polymers, polyaniline, and the resulting products were studied in the context of interactions with human blood. The anticoagulation activity was then correlated to surface energy and conductivity of the materials. Results show that anticoagulation activity is highly affected by the presence of suitable functional groups originating from the used heparin-like substances, and by the properties of polyaniline polymer itself.
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Abstract
Sulodexide is a glycosaminoglycan extracted from porcine intestinal mucosa. The purpose of this review is to discuss sulodexide's complex pharmacological profile and its clinical applications for venous disease. Sulodexide has wide-ranging biological effects on the vascular system, including antithrombotic, profibrinolytic, anti-inflammatory, endothelial protective and vasoregulatory effects. Sulodexide has emerged as a potential therapeutic option for the management of chronic venous insufficiency, including venous ulceration, and the prevention of recurrent venous thromboembolism, with a low rate of major bleeding complications. Sulodexide's pleiotropic vascular effects may facilitate the management of common venous disorders.
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Affiliation(s)
- B J Carroll
- Division of Cardiovascular Medicine, Department of Medicine, Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - G Piazza
- Division of Cardiovascular Medicine, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - S Z Goldhaber
- Division of Cardiovascular Medicine, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
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22
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Approaches to prevent bleeding associated with anticoagulants: current status and recent developments. Drug Deliv Transl Res 2018; 8:928-944. [PMID: 28741113 DOI: 10.1007/s13346-017-0413-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Anticoagulants are widely used for the prophylaxis and treatment of cardiovascular disorders and to prevent blood clotting during surgeries. However, the major limitation associated with anticoagulant therapy is bleeding; all the current anticoagulants do have a bleeding risk. The propensity to bleed is much higher among the elderly population and patients with renal insufficiency. Therefore, there is an utmost and urgent clinical need for a highly efficient, nontoxic antidote with excellent anticoagulant reversal activity. This will significantly improve the safety of anticoagulation therapy. This review summarizes the current options and approaches to reverse anticoagulation activity of clinically used anticoagulants. We start with an introduction to thrombosis and then summarize the details of current clinically available anticoagulants and their mechanisms of action and limitations. This is followed by current practices in anticoagulant neutralization including the details of the only clinically approved unfractionated heparin antidote, protamine; recent advances in the development of antidotes against heparin-based drugs; and direct oral anticoagulants (DOACs).
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23
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Lim TC, Cai S, Huber RG, Bond PJ, Siew Chia PX, Khou SL, Gao S, Lee SS, Lee SG. Facile saccharide-free mimetics that recapitulate key features of glycosaminoglycan sulfation patterns. Chem Sci 2018; 9:7940-7947. [PMID: 30429999 PMCID: PMC6201788 DOI: 10.1039/c8sc02303d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/21/2018] [Indexed: 12/16/2022] Open
Abstract
We report a new class of saccharide-free glycosaminoglycan (GAG) mimetics where polyproline imparts facilely-made sulfation patterns with GAG-like structure, function and tunability.
Controlling glycosaminoglycan (GAG) activity to exploit its immense potential in biology ultimately requires facile manipulation of sulfation patterns associated with GAGs. However, satisfying this requirement in full remains challenging, given that synthesis of GAGs is technically arduous while convenient GAG mimetics often produce sulfation patterns that are uncharacteristic of GAGs. To overcome this, we develop saccharide-free polyproline-based GAG mimetics (PGMs) that can be facilely assembled via amide coupling chemistry. Molecular dynamics simulations show that PGMs recapitulate key GAG structural features (i.e. ∼9 Å-sized repeating units, periodicity and helicity) and as with GAGs, can be tuned to introduce systematic variations in sulfate clustering and spacing. Functionally, a variety of PGMs control various GAG activities (concerning P-selectin, neurotrophic factors and heparinase) and exhibit GAG-like characteristics such as progressive modulation, comparable effectiveness with heparins, need for different sequences to suit different activities and the presence of a “minimal bioactive length”. Furthermore, PGMs produce consistent effects in vivo and successfully provide therapeutic benefits over cancer metastasis. Taken together with their high level of biosafety, PGMs answer the long-standing need for an effective and practicable strategy to manipulate GAG-appropriate sulfation patterns and exploit GAG activity in medicine and biotechnology.
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Affiliation(s)
- Teck Chuan Lim
- Institute of Bioengineering and Nanotechnology , 31 Biopolis Way, The Nanos , Singapore 138669 , Singapore .
| | - Shuting Cai
- Institute of Bioengineering and Nanotechnology , 31 Biopolis Way, The Nanos , Singapore 138669 , Singapore .
| | - Roland G Huber
- Bioinformatics Institute , 30 Biopolis Street, #07-01 Matrix , Singapore 138671 , Singapore
| | - Peter J Bond
- Bioinformatics Institute , 30 Biopolis Street, #07-01 Matrix , Singapore 138671 , Singapore.,Department of Biological Sciences , National University of Singapore , 14 Science Drive 4 , Singapore 117543 , Singapore
| | - Priscilla Xian Siew Chia
- Institute of Bioengineering and Nanotechnology , 31 Biopolis Way, The Nanos , Singapore 138669 , Singapore .
| | - Siv Ly Khou
- Institute of Bioengineering and Nanotechnology , 31 Biopolis Way, The Nanos , Singapore 138669 , Singapore .
| | - Shujun Gao
- Institute of Bioengineering and Nanotechnology , 31 Biopolis Way, The Nanos , Singapore 138669 , Singapore .
| | - Su Seong Lee
- Institute of Bioengineering and Nanotechnology , 31 Biopolis Way, The Nanos , Singapore 138669 , Singapore .
| | - Song-Gil Lee
- Institute of Bioengineering and Nanotechnology , 31 Biopolis Way, The Nanos , Singapore 138669 , Singapore .
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24
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Bolten SN, Rinas U, Scheper T. Heparin: role in protein purification and substitution with animal-component free material. Appl Microbiol Biotechnol 2018; 102:8647-8660. [PMID: 30094590 PMCID: PMC6153649 DOI: 10.1007/s00253-018-9263-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/20/2018] [Accepted: 07/21/2018] [Indexed: 01/27/2023]
Abstract
Heparin is a highly sulfated polysaccharide which belongs to the family of glycosaminoglycans. It is involved in various important biological activities. The major biological purpose is the inhibition of the coagulation cascade to maintain the blood flow in the vasculature. These properties are employed in several therapeutic drugs. Heparin’s activities are associated with its interaction to various proteins. To date, the structural heparin-protein interactions are not completely understood. This review gives a general overview of specific patterns and functional groups which are involved in the heparin-protein binding. An understanding of the heparin-protein interactions at the molecular level is not only advantageous in the therapeutic application but also in biotechnological application of heparin for downstreaming. This review focuses on the heparin affinity chromatography. Diverse recombinant proteins can be successfully purified by this method. While effective, it is disadvantageous that heparin is an animal-derived material. Animal-based components carry the risk of contamination. Therefore, they are liable to strict quality controls and the validation of effective good manufacturing practice (GMP) implementation. Hence, adequate alternatives to animal-derived components are needed. This review examines strategies to avoid these disadvantages. Thereby, alternatives for the provision of heparin such as chemical synthesized heparin, chemoenzymatic heparin, and bioengineered heparin are discussed. Moreover, the usage of other chromatographic systems mimetic the heparin effect is reviewed.
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Affiliation(s)
- Svenja Nicolin Bolten
- Institute of Technical Chemistry, Leibniz University of Hannover, Callinstraße 5, 30167, Hannover, Germany
| | - Ursula Rinas
- Institute of Technical Chemistry, Leibniz University of Hannover, Callinstraße 5, 30167, Hannover, Germany
- Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Thomas Scheper
- Institute of Technical Chemistry, Leibniz University of Hannover, Callinstraße 5, 30167, Hannover, Germany.
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Sankaranarayanan NV, Nagarajan B, Desai UR. So you think computational approaches to understanding glycosaminoglycan-protein interactions are too dry and too rigid? Think again! Curr Opin Struct Biol 2018; 50:91-100. [PMID: 29328962 PMCID: PMC6037615 DOI: 10.1016/j.sbi.2017.12.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 11/17/2017] [Accepted: 12/15/2017] [Indexed: 12/20/2022]
Abstract
Glycosaminoglycans (GAGs) play key roles in virtually all biologic responses through their interaction with proteins. A major challenge in understanding these roles is their massive structural complexity. Computational approaches are extremely useful in navigating this bottleneck and, in some cases, the only avenue to gain comprehensive insight. We discuss the state-of-the-art on computational approaches and present a flowchart to help answer most basic, and some advanced, questions on GAG-protein interactions. For example, firstly, does my protein bind to GAGs?; secondly, where does the GAG bind?; thirdly, does my protein preferentially recognize a particular GAG type?; fourthly, what is the most optimal GAG chain length?; fifthly, what is the structure of the most favored GAG sequence?; and finally, is my GAG-protein system 'specific', 'non-specific', or a combination of both? Recent advances show the field is now poised to enable a non-computational researcher perform advanced experiments through the availability of various tools and online servers.
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Affiliation(s)
- Nehru Viji Sankaranarayanan
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA
| | - Balaji Nagarajan
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA
| | - Umesh R Desai
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA.
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26
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Smith DK. From fundamental supramolecular chemistry to self-assembled nanomaterials and medicines and back again – how Sam inspired SAMul. Chem Commun (Camb) 2018; 54:4743-4760. [DOI: 10.1039/c8cc01753k] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Personal inspiration led to the development of a programme of research targeting the use of self-assembled systems in nanomedicine, which in the process of approaching a range of applications has uncovered new fundamental concepts in supramolecular science.
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27
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Ayerst BI, Merry CLR, Day AJ. The Good the Bad and the Ugly of Glycosaminoglycans in Tissue Engineering Applications. Pharmaceuticals (Basel) 2017; 10:E54. [PMID: 28608822 PMCID: PMC5490411 DOI: 10.3390/ph10020054] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 06/05/2017] [Accepted: 06/05/2017] [Indexed: 12/14/2022] Open
Abstract
High sulfation, low cost, and the status of heparin as an already FDA- and EMA- approved product, mean that its inclusion in tissue engineering (TE) strategies is becoming increasingly popular. However, the use of heparin may represent a naïve approach. This is because tissue formation is a highly orchestrated process, involving the temporal expression of numerous growth factors and complex signaling networks. While heparin may enhance the retention and activity of certain growth factors under particular conditions, its binding 'promiscuity' means that it may also inhibit other factors that, for example, play an important role in tissue maintenance and repair. Within this review we focus on articular cartilage, highlighting the complexities and highly regulated processes that are involved in its formation, and the challenges that exist in trying to effectively engineer this tissue. Here we discuss the opportunities that glycosaminoglycans (GAGs) may provide in advancing this important area of regenerative medicine, placing emphasis on the need to move away from the common use of heparin, and instead focus research towards the utility of specific GAG preparations that are able to modulate the activity of growth factors in a more controlled and defined manner, with less off-target effects.
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Affiliation(s)
- Bethanie I Ayerst
- Wellcome Trust Centre for Cell-Matrix Research, Division of Cell-Matrix Biology & Regenerative Medicine, School of Biology, Faculty of Biology, Medicine & Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PL, UK.
| | - Catherine L R Merry
- Stem Cell Glycobiology Group, Wolfson Centre for Stem Cells, Tissue Engineering & Modelling (STEM), Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
| | - Anthony J Day
- Wellcome Trust Centre for Cell-Matrix Research, Division of Cell-Matrix Biology & Regenerative Medicine, School of Biology, Faculty of Biology, Medicine & Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PL, UK.
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28
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Grigorov B, Reungoat E, Gentil Dit Maurin A, Varbanov M, Blaising J, Michelet M, Manuel R, Parent R, Bartosch B, Zoulim F, Ruggiero F, Pécheur EI. Hepatitis C virus infection propagates through interactions between Syndecan-1 and CD81 and impacts the hepatocyte glycocalyx. Cell Microbiol 2017; 19:e12711. [PMID: 27930836 DOI: 10.1111/cmi.12711] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 11/23/2016] [Accepted: 11/30/2016] [Indexed: 12/17/2022]
Abstract
The hepatitis C virus (HCV) infects hepatocytes after binding to heparan sulfate proteoglycans, in particular Syndecan-1, followed by recognition of the tetraspanin CD81 and other receptors. Heparan sulfate proteoglycans are found in a specific microenvironment coating the hepatocyte surface called the glycocalyx and are receptors for extracellular matrix proteins, cytokines, growth factors, lipoproteins, and infectious agents. We investigated the mutual influence of HCV infection on the glycocalyx and revealed new links between Syndecan-1 and CD81. Hepatocyte infection by HCV was inhibited after knocking down Syndecan-1 or Xylosyltransferase 2, a key enzyme of Syndecan-1 biosynthesis. Simultaneous knockdown of Syndecan-1 and CD81 strongly inhibited infection, suggesting their cooperative action. At early infection stages, Syndecan-1 and virions colocalized at the plasma membrane and were internalized in endosomes. Direct interactions between Syndecan-1 and CD81 were revealed in primary and transformed hepatocytes by immunoprecipitation and proximity ligation assays. Expression of Syndecan-1 and Xylosyltransferase 2 was altered within days post-infection, and the remaining Syndecan-1 pool colocalized poorly with CD81. The data indicate a profound reshuffling of the hepatocyte glycocalyx during HCV infection, possibly required for establishing optimal conditions of viral propagation.
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Affiliation(s)
- Boyan Grigorov
- CRCL, Inserm U1052, CNRS 5286, Université Lyon 1, France
| | - Emma Reungoat
- CRCL, Inserm U1052, CNRS 5286, Université Lyon 1, France
| | | | | | - Julie Blaising
- CRCL, Inserm U1052, CNRS 5286, Université Lyon 1, France
| | - Maud Michelet
- CRCL, Inserm U1052, CNRS 5286, Université Lyon 1, France
| | - Rachel Manuel
- IGFL, ENS Lyon, CNRS UMR 5242, Université Lyon 1, France
| | - Romain Parent
- CRCL, Inserm U1052, CNRS 5286, Université Lyon 1, France
| | - Birke Bartosch
- CRCL, Inserm U1052, CNRS 5286, Université Lyon 1, France
| | - Fabien Zoulim
- CRCL, Inserm U1052, CNRS 5286, Université Lyon 1, France
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29
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Mulloy B, Hogwood J, Gray E, Lever R, Page CP. Pharmacology of Heparin and Related Drugs. Pharmacol Rev 2016; 68:76-141. [PMID: 26672027 DOI: 10.1124/pr.115.011247] [Citation(s) in RCA: 225] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Heparin has been recognized as a valuable anticoagulant and antithrombotic for several decades and is still widely used in clinical practice for a variety of indications. The anticoagulant activity of heparin is mainly attributable to the action of a specific pentasaccharide sequence that acts in concert with antithrombin, a plasma coagulation factor inhibitor. This observation has led to the development of synthetic heparin mimetics for clinical use. However, it is increasingly recognized that heparin has many other pharmacological properties, including but not limited to antiviral, anti-inflammatory, and antimetastatic actions. Many of these activities are independent of its anticoagulant activity, although the mechanisms of these other activities are currently less well defined. Nonetheless, heparin is being exploited for clinical uses beyond anticoagulation and developed for a wide range of clinical disorders. This article provides a "state of the art" review of our current understanding of the pharmacology of heparin and related drugs and an overview of the status of development of such drugs.
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Affiliation(s)
- Barbara Mulloy
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., C.P.P.); National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, United Kingdom (J.H., E.G.); and University College London School of Pharmacy, London, United Kingdom (R.L.)
| | - John Hogwood
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., C.P.P.); National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, United Kingdom (J.H., E.G.); and University College London School of Pharmacy, London, United Kingdom (R.L.)
| | - Elaine Gray
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., C.P.P.); National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, United Kingdom (J.H., E.G.); and University College London School of Pharmacy, London, United Kingdom (R.L.)
| | - Rebecca Lever
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., C.P.P.); National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, United Kingdom (J.H., E.G.); and University College London School of Pharmacy, London, United Kingdom (R.L.)
| | - Clive P Page
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., C.P.P.); National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, United Kingdom (J.H., E.G.); and University College London School of Pharmacy, London, United Kingdom (R.L.)
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30
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Sarkar A, Yu W, Desai UR, MacKerell AD, Mosier PD. Estimating glycosaminoglycan-protein interaction affinity: water dominates the specific antithrombin-heparin interaction. Glycobiology 2016; 26:1041-1047. [PMID: 27496757 DOI: 10.1093/glycob/cww073] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/01/2016] [Accepted: 07/12/2016] [Indexed: 11/13/2022] Open
Abstract
Glycosaminoglycan (GAG)-protein interactions modulate many important biological processes. Structure-function studies on GAGs may reveal probes and drugs, but their structural complexity and highly acidic nature confound such work. Productivity will increase if we are able to identify tight-binding oligosaccharides in silico. An extension of the CHARMM force field is presented to enable modeling of polysaccharides containing sulfamate functionality, and is used to develop a reliable alchemical free-energy perturbation protocol that estimates changes in affinity for the prototypical heparin-antithrombin system to within 2.3 kcal/mol using modest simulation times. Inclusion of water is crucial during simulation as solvation energy was equal in magnitude to the sum of all other thermodynamic factors. In summary, we have identified and optimized a reliable method for estimation of GAG-protein binding affinity, and shown that solvation is a crucial component in GAG-protein interactions.
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Affiliation(s)
- Aurijit Sarkar
- Department of Basic Pharmaceutical Sciences, Fred Wilson School of Pharmacy, High Point University, One University Parkway, High Point, NC 27268, USA .,Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University, PO Box 980133, Richmond, VA 23298, USA
| | - Wenbo Yu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
| | - Umesh R Desai
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University, PO Box 980133, Richmond, VA 23298, USA
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
| | - Philip D Mosier
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, School of Pharmacy, Virginia Commonwealth University, PO Box 980133, Richmond, VA 23298, USA
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31
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Meneghetti MCZ, Hughes AJ, Rudd TR, Nader HB, Powell AK, Yates EA, Lima MA. Heparan sulfate and heparin interactions with proteins. J R Soc Interface 2016; 12:0589. [PMID: 26289657 DOI: 10.1098/rsif.2015.0589] [Citation(s) in RCA: 198] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Heparan sulfate (HS) polysaccharides are ubiquitous components of the cell surface and extracellular matrix of all multicellular animals, whereas heparin is present within mast cells and can be viewed as a more sulfated, tissue-specific, HS variant. HS and heparin regulate biological processes through interactions with a large repertoire of proteins. Owing to these interactions and diverse effects observed during in vitro, ex vivo and in vivo experiments, manifold biological/pharmacological activities have been attributed to them. The properties that have been thought to bestow protein binding and biological activity upon HS and heparin vary from high levels of sequence specificity to a dependence on charge. In contrast to these opposing opinions, we will argue that the evidence supports both a level of redundancy and a degree of selectivity in the structure-activity relationship. The relationship between this apparent redundancy, the multi-dentate nature of heparin and HS polysaccharide chains, their involvement in protein networks and the multiple binding sites on proteins, each possessing different properties, will also be considered. Finally, the role of cations in modulating HS/heparin activity will be reviewed and some of the implications for structure-activity relationships and regulation will be discussed.
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Affiliation(s)
- Maria C Z Meneghetti
- Departamento de Bioquímica, Universidade Federal de São Paulo (UNIFESP), Rua Três de Maio, São Paulo 40440-020, Brazil
| | - Ashley J Hughes
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 40530, Sweden Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Timothy R Rudd
- The National Institute for Biological Standards and Control (NIBSC), South Mimms, Potters Bar, Hertfordshire EN6 3QC, UK Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Helena B Nader
- Departamento de Bioquímica, Universidade Federal de São Paulo (UNIFESP), Rua Três de Maio, São Paulo 40440-020, Brazil
| | - Andrew K Powell
- School of Pharmacy and Biomolecular Science, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Edwin A Yates
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK Departamento de Bioquímica, Universidade Federal de São Paulo (UNIFESP), Rua Três de Maio, São Paulo 40440-020, Brazil
| | - Marcelo A Lima
- Departamento de Bioquímica, Universidade Federal de São Paulo (UNIFESP), Rua Três de Maio, São Paulo 40440-020, Brazil Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
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32
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Wang Y, Zhao W, Bie F, Wu L, Li X, Jiang H. Ruthenium(II) Complexes of Aryl Triazole Foldamers as Receptors for Anions. Chemistry 2016; 22:5233-42. [PMID: 26918407 DOI: 10.1002/chem.201504910] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Indexed: 12/15/2022]
Abstract
Ruthenium(II) complexes of oligo(bipyridine-phenyl triazole)s were synthesized as receptors for anions. The receptors, which are partially preorganized through metal-ligand interactions, can fold into a helical conformation to bind chloride, bromide, iodide, or nitrate anions in their inner cavities in acetone or competitive H-bonding media such as 5% water in acetone and DMSO. The short oligomer 1 can sandwich the studied anions with high affinity in acetone. Addition of 5% water to acetone results in overall decreases in the binding strength due to the binding competition from water, but does not change the basic binding mode. The highly competitive H-bonding solvent DMSO causes the receptor-anion interactions to become even weaker. However, in DMSO, the short receptor 1 is still able to bind the halide anions with moderate affinities in a 1:1 stoichiometry, whereas the longer oligomer 2 forms double-strand helices with an anion wrapped inside for all anions investigated so far.
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Affiliation(s)
- Ying Wang
- Key Laboratory of Theoretical and Computational Photochemistry and Key Laboratory of Radiopharmaceuticals of Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, P.R. China.
| | - Wei Zhao
- Key Laboratory of Theoretical and Computational Photochemistry and Key Laboratory of Radiopharmaceuticals of Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, P.R. China.,Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P.R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
| | - Fusheng Bie
- Key Laboratory of Theoretical and Computational Photochemistry and Key Laboratory of Radiopharmaceuticals of Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, P.R. China.,Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P.R. China
| | - Le Wu
- Key Laboratory of Theoretical and Computational Photochemistry and Key Laboratory of Radiopharmaceuticals of Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, P.R. China
| | - Xichen Li
- Key Laboratory of Theoretical and Computational Photochemistry and Key Laboratory of Radiopharmaceuticals of Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, P.R. China
| | - Hua Jiang
- Key Laboratory of Theoretical and Computational Photochemistry and Key Laboratory of Radiopharmaceuticals of Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, P.R. China. .,Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P.R. China.
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33
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Sarkar A, Desai UR. A Simple Method for Discovering Druggable, Specific Glycosaminoglycan-Protein Systems. Elucidation of Key Principles from Heparin/Heparan Sulfate-Binding Proteins. PLoS One 2015; 10:e0141127. [PMID: 26488293 PMCID: PMC4619353 DOI: 10.1371/journal.pone.0141127] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 10/05/2015] [Indexed: 01/25/2023] Open
Abstract
Glycosaminoglycans (GAGs) affect human physiology and pathology by modulating more than 500 proteins. GAG-protein interactions are generally assumed to be ionic and nonspecific, but specific interactions do exist. Here, we present a simple method to identify the GAG-binding site (GBS) on proteins that in turn helps predict high specific GAG-protein systems. Contrary to contemporary thinking, we found that the electrostatic potential at basic arginine and lysine residues neither identifies the GBS consistently, nor its specificity. GBSs are better identified by considering the potential at neutral hydrogen bond donors such as asparagine or glutamine sidechains. Our studies also reveal that an unusual constellation of ionic and non-ionic residues in the binding site leads to specificity. Nature engineers the local environment of Asn45 of antithrombin, Gln255 of 3-O-sulfotransferase 3, Gln163 and Asn167 of 3-O-sulfotransferase 1 and Asn27 of basic fibroblast growth factor in the respective GBSs to induce specificity. Such residues are distinct from other uncharged residues on the same protein structure in possessing a significantly higher electrostatic potential, resultant from the local topology. In contrast, uncharged residues on nonspecific GBSs such as thrombin and serum albumin possess a diffuse spread of electrostatic potential. Our findings also contradict the paradigm that GAG-binding sites are simply a collection of contiguous Arg/Lys residues. Our work demonstrates the basis for discovering specifically interacting and druggable GAG-protein systems based on the structure of protein alone, without requiring access to any structure-function relationship data.
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Affiliation(s)
- Aurijit Sarkar
- Institute for Structural Biology, Drug Discovery & Development and Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Umesh R. Desai
- Institute for Structural Biology, Drug Discovery & Development and Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia, United States of America
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34
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Boothello RS, Sarkar A, Tran VM, Nguyen TKN, Sankaranarayanan NV, Mehta AY, Alabbas A, Brown S, Rossi A, Joice AC, Mencio CP, Quintero MV, Kuberan B, Desai UR. Chemoenzymatically prepared heparan sulfate containing rare 2-O-sulfonated glucuronic acid residues. ACS Chem Biol 2015; 10:1485-94. [PMID: 25742429 DOI: 10.1021/acschembio.5b00071] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The structural diversity of natural sulfated glycosaminoglycans (GAGs) presents major promise for discovery of chemical biology tools or therapeutic agents. Yet, few GAGs have been identified so far to exhibit this promise. We reasoned that a simple approach to identify such GAGs is to explore sequences containing rare residues, for example, 2-O-sulfonated glucuronic acid (GlcAp2S). Genetic algorithm-based computational docking and filtering suggested that GlcAp2S containing heparan sulfate (HS) may exhibit highly selective recognition of antithrombin, a key plasma clot regulator. HS containing only GlcAp2S and 2-N-sulfonated glucosamine residues, labeled as HS2S2S, was chemoenzymatically synthesized in just two steps and was found to preferentially bind antithrombin over heparin cofactor II, a closely related serpin. Likewise, HS2S2S directly inhibited thrombin but not factor Xa, a closely related protease. The results show that a HS containing rare GlcAp2S residues exhibits the unusual property of selective antithrombin activation and direct thrombin inhibition. More importantly, HS2S2S is also the first molecule to activate antithrombin nearly as well as the heparin pentasaccharide although being completely devoid of the critical 3-O-sulfonate group. Thus, this work shows that novel functions and mechanisms may be uncovered by studying rare GAG residues/sequences.
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Affiliation(s)
- Rio S. Boothello
- Institute for Structural Biology & Drug Discovery and Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Aurijit Sarkar
- Institute for Structural Biology & Drug Discovery and Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | | | | | - Nehru Viji Sankaranarayanan
- Institute for Structural Biology & Drug Discovery and Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Akul Y. Mehta
- Institute for Structural Biology & Drug Discovery and Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - AlHumaidi Alabbas
- Institute for Structural Biology & Drug Discovery and Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | | | | | | | | | | | | | - Umesh R. Desai
- Institute for Structural Biology & Drug Discovery and Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298, United States
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Heparin/Heparan sulfate proteoglycans glycomic interactome in angiogenesis: biological implications and therapeutical use. Molecules 2015; 20:6342-88. [PMID: 25867824 PMCID: PMC6272510 DOI: 10.3390/molecules20046342] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 03/31/2015] [Accepted: 04/01/2015] [Indexed: 12/20/2022] Open
Abstract
Angiogenesis, the process of formation of new blood vessel from pre-existing ones, is involved in various intertwined pathological processes including virus infection, inflammation and oncogenesis, making it a promising target for the development of novel strategies for various interventions. To induce angiogenesis, angiogenic growth factors (AGFs) must interact with pro-angiogenic receptors to induce proliferation, protease production and migration of endothelial cells (ECs). The action of AGFs is counteracted by antiangiogenic modulators whose main mechanism of action is to bind (thus sequestering or masking) AGFs or their receptors. Many sugars, either free or associated to proteins, are involved in these interactions, thus exerting a tight regulation of the neovascularization process. Heparin and heparan sulfate proteoglycans undoubtedly play a pivotal role in this context since they bind to almost all the known AGFs, to several pro-angiogenic receptors and even to angiogenic inhibitors, originating an intricate network of interaction, the so called "angiogenesis glycomic interactome". The decoding of the angiogenesis glycomic interactome, achievable by a systematic study of the interactions occurring among angiogenic modulators and sugars, may help to design novel antiangiogenic therapies with implications in the cure of angiogenesis-dependent diseases.
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36
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Wu M, Algar WR. Acceleration of proteolytic activity associated with selection of thiol ligand coatings on quantum dots. ACS APPLIED MATERIALS & INTERFACES 2015; 7:2535-2545. [PMID: 25607728 DOI: 10.1021/am507466b] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Nanoparticle bioconjugates are attractive probes for measuring the activity of hydrolytic enzymes. In these configurations, the localization of multiple copies of a hydrolase substrate to a nanoparticle scaffold has been reported to enhance apparent activity by factors of 2 to 3 compared to that for equivalent amounts of substrate in bulk solution. Here, we studied the effect of surface chemistry on protease activity using multivalent QD-peptide substrate conjugates as a model system. QDs were coated with cysteine (CYS), glutathione (GSH), dihydrolipoic acid (DHLA), or 3-mercaptopropionic acid (MPA) ligands, and thrombin and trypsin were used as model proteases. Proteolytic activity was measured for different combinations of ligand and protease using Förster resonance energy transfer (FRET)-based assays. The highest levels of activity were observed with CYS and GSH coatings, and the lowest levels of activity were observed with DHLA and MPA coatings. In all cases, proteolytic activity was accelerated compared to that for an equivalent amount of substrate in bulk solution, with up to 80- and 65-fold increases in the apparent specificity constants for thrombin and trypsin, respectively. Thrombin was more strongly affected by the QD surface chemistry, with up to a 50-fold variation in its apparent specificity constant between ligand coatings, whereas only a 5-fold variation was observed with trypsin. These trends were correlated to adsorption of the proteases on the QDs and are discussed in the context of the physicochemical properties of both components. This work clearly indicates a critical role for the nanoparticle interface in mediating substrate turnover and provides some of the strongest support to date for a so-called hopping model of activity.
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Affiliation(s)
- Miao Wu
- Department of Chemistry, University of British Columbia , 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
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Wang C, Jin Y, Desai UR, Yadavalli VK. Investigation of the heparin-thrombin interaction by dynamic force spectroscopy. Biochim Biophys Acta Gen Subj 2015; 1850:1099-106. [PMID: 25647100 DOI: 10.1016/j.bbagen.2015.01.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 01/08/2015] [Accepted: 01/25/2015] [Indexed: 11/28/2022]
Abstract
BACKGROUND The interaction between heparin and thrombin is a vital step in the blood (anti)coagulation process. Unraveling the molecular basis of the interactions is therefore extremely important in understanding the mechanisms of this complex biological process. METHODS In this study, we use a combination of an efficient thiolation chemistry of heparin, a self-assembled monolayer-based single molecule platform, and a dynamic force spectroscopy to provide new insights into the heparin-thrombin interaction from an energy viewpoint at the molecular scale. RESULTS Well-separated single molecules of heparin covalently attached to mixed self-assembled monolayers are demonstrated, whereby interaction forces with thrombin can be measured via atomic force microscopy-based spectroscopy. Further these interactions are studied at different loading rates and salt concentrations to directly obtain kinetic parameters. CONCLUSIONS An increase in the loading rate shows a higher interaction force between the heparin and thrombin, which can be directly linked to the kinetic dissociation rate constant (koff). The stability of the heparin/thrombin complex decreased with increasing NaCl concentration such that the off-rate was found to be driven primarily by non-ionic forces. GENERAL SIGNIFICANCE These results contribute to understanding the role of specific and nonspecific forces that drive heparin-thrombin interactions under applied force or flow conditions.
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Affiliation(s)
- Congzhou Wang
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond VA 23284, United States
| | - Yingzi Jin
- Department of Medicinal Chemistry, Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23298, United States
| | - Umesh R Desai
- Department of Medicinal Chemistry, Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23298, United States
| | - Vamsi K Yadavalli
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond VA 23284, United States.
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Sankaranarayanan NV, Desai UR. Toward a robust computational screening strategy for identifying glycosaminoglycan sequences that display high specificity for target proteins. Glycobiology 2014; 24:1323-33. [PMID: 25049239 DOI: 10.1093/glycob/cwu077] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Glycosaminoglycans (GAGs) interact with many proteins to regulate processes such as hemostasis, cell adhesion, growth and differentiation and viral infection. Yet, majority of these interactions remain poorly understood at a molecular level. A major reason for this state is the phenomenal structural diversity of GAGs, which has precluded analysis of specificity of their interactions. We had earlier presented a computational protocol for predicting "high-specificity" GAG sequences based on combinatorial virtual library screening (CVLS) technology. In this work, we expand the robustness of this technology through rigorous studies of parameters affecting GAG recognition of proteins, especially antithrombin and thrombin. The CVLS approach involves automated construction of a virtual library of all possible oligosaccharide sequences (di- to octasaccharide) followed by a two-step selection strategy consisting of "affinity" (GOLD score) and "specificity" (consistency of binding) filters. We find that "specificity" features are optimally evaluated using 100 genetic algorithm experiments, 100,000 evolutions and variable docking radius from 10 Å (disaccharide) to 14 Å (hexasaccharide). The results highlight critical interactions in H/HS oligosaccharides that govern specificity. Application of CVLS technology to the antithrombin-heparin system indicates that the minimal "specificity" element is the GlcAp(1 → 4)GlcNp2S3S disaccharide of heparin. The CVLS technology affords a simple, intuitive framework for the design of longer GAG sequences that can exhibit high "specificity" without resorting to exhaustive screening of millions of theoretical sequences.
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Affiliation(s)
- Nehru Viji Sankaranarayanan
- Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA
| | - Umesh R Desai
- Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA
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Al-Horani RA, Desai UR. Designing allosteric inhibitors of factor XIa. Lessons from the interactions of sulfated pentagalloylglucopyranosides. J Med Chem 2014; 57:4805-18. [PMID: 24844380 PMCID: PMC4216218 DOI: 10.1021/jm500311e] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
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We recently introduced sulfated pentagalloylglucopyranoside
(SPGG)
as an allosteric inhibitor of factor XIa (FXIa) (Al-Horani et al.,2013, 56, 867–87823316863). To better understand the SPGG–FXIa interaction,
we utilized eight SPGG variants and a range of biochemical techniques.
The results reveal that SPGG’s sulfation level moderately affected
FXIa inhibition potency and selectivity over thrombin and factor Xa.
Variation in the anomeric configuration did not affect potency. Interestingly,
zymogen factor XI bound SPGG with high affinity, suggesting its possible
use as an antidote. Acrylamide quenching experiments suggested that
SPGG induced significant conformational changes in the active site
of FXIa. Inhibition studies in the presence of heparin showed marginal
competition with highly sulfated SPGG variants but robust competition
with less sulfated variants. Resolution of energetic contributions
revealed that nonionic forces contribute nearly 87% of binding energy
suggesting a strong possibility of specific interaction. Overall,
the results indicate that SPGG may recognize more than one anion-binding,
allosteric site on FXIa. An SPGG molecule containing approximately
10 sulfate groups on positions 2 through 6 of the pentagalloylglucopyranosyl
scaffold may be the optimal FXIa inhibitor for further preclinical
studies.
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Affiliation(s)
- Rami A Al-Horani
- Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University , 800 E. Leigh Street, Suite 212, Richmond, Virginia 23219, United States
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Mehta AY, Thakkar JN, Mohammed BM, Martin EJ, Brophy DF, Kishimoto T, Desai UR. Targeting the GPIbα binding site of thrombin to simultaneously induce dual anticoagulant and antiplatelet effects. J Med Chem 2014; 57:3030-9. [PMID: 24635452 PMCID: PMC4203406 DOI: 10.1021/jm4020026] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
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Exosite 2 of human thrombin contributes
to two opposing pathways, the anticoagulant pathway and the platelet
aggregation pathway. We reasoned that an exosite 2 directed allosteric
thrombin inhibitor should simultaneously induce anticoagulant and
antiplatelet effects. To assess this, we synthesized SbO4L based on
the sulfated tyrosine-containing sequence of GPIbα. SbO4L was
synthesized in three simple steps in high yield and found to be a
highly selective, direct inhibitor of thrombin. Michelis–Menten
kinetic studies indicated a noncompetitive mechanism of inhibition.
Competitive inhibition studies suggested ideal competition with heparin
and glycoprotein Ibα, as predicted. Studies with site-directed
mutants of thrombin indicated that SbO4L binds to Arg233, Lys235,
and Lys236 of exosite 2. SbO4L prevented thrombin-mediated platelet
activation and aggregation as expected on the basis of competition
with GPIbα. SbO4L presents a novel paradigm of simultaneous
dual anticoagulant and antiplatelet effects achieved through the GPIbα
binding site of thrombin.
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Affiliation(s)
- Akul Y Mehta
- Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University , Richmond, Virginia 23219, United States
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The promise of sulfated synthetic small molecules as modulators of glycosaminoglycan function. Future Med Chem 2014; 5:1363-6. [PMID: 23919545 DOI: 10.4155/fmc.13.117] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Molecular docking of heparin oligosaccharides with Hep-II heparin-binding domain of fibronectin reveals an interplay between the different positions of sulfate groups. Glycoconj J 2013; 31:161-9. [DOI: 10.1007/s10719-013-9512-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 11/04/2013] [Accepted: 11/05/2013] [Indexed: 12/20/2022]
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Natural variation in the heparan sulfate binding domain of the eastern equine encephalitis virus E2 glycoprotein alters interactions with cell surfaces and virulence in mice. J Virol 2013; 87:8582-90. [PMID: 23720725 DOI: 10.1128/jvi.00937-13] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recently, we compared amino acid sequences of the E2 glycoprotein of natural North American eastern equine encephalitis virus (NA-EEEV) isolates and demonstrated that naturally circulating viruses interact with heparan sulfate (HS) and that this interaction contributes to the extreme neurovirulence of EEEV (C. L. Gardner, G. D. Ebel, K. D. Ryman, and W. B. Klimstra, Proc. Natl. Acad. Sci. U. S. A., 108:16026-16031, 2011). In the current study, we have examined the contribution to HS binding of each of three lysine residues in the E2 71-to-77 region that comprise the primary HS binding site of wild-type (WT) NA-EEEV viruses. We also report that the original sequence comparison identified five virus isolates, each with one of three amino acid differences in the E2 71-to-77 region, including mutations in residues critical for HS binding by the WT virus. The natural variant viruses, which possessed either a mutation from lysine to glutamine at E2 71, a mutation from lysine to threonine at E2 71, or a mutation from threonine to lysine at E2 72, exhibited altered interactions with heparan sulfate and cell surfaces and altered virulence in a mouse model of EEEV disease. An electrostatic map of the EEEV E1/E2 heterotrimer based upon the recent Chikungunya virus crystal structure (J. E. Voss, M. C. Vaney, S. Duquerroy, C. Vonrhein, C. Girard-Blanc, E. Crublet, A. Thompson, G. Bricogne, and F. A. Rey, Nature, 468:709-712, 2010) showed the HS binding site to be at the apical surface of E2, with variants affecting the electrochemical nature of the binding site. Together, these results suggest that natural variation in the EEEV HS binding domain may arise during EEEV sylvatic cycles and that this variation may influence receptor interaction and the severity of EEEV disease.
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Correia-da-Silva M, Sousa E, Pinto MMM. Emerging sulfated flavonoids and other polyphenols as drugs: nature as an inspiration. Med Res Rev 2013; 34:223-79. [PMID: 23553315 DOI: 10.1002/med.21282] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Nature uses sulfation of endogenous and exogenous molecules mainly to avoid potential toxicity. The growing importance of natural sulfated molecules, as modulators of a number of physiological and pathological processes, has inspired the synthesis of non-natural sulfated scaffolds. Until the 1990s, the synthesis of sulfated small molecules was almost restricted to derivatives of flavonoids and aimed mainly at structure elucidation and plant biosynthesis studies. Currently, the synthesis of this type of compounds concerns structurally diverse scaffolds and is aimed at the development of potential drugs and/or exploitation of the biological effects of sulfated metabolites. Some important hit compounds are emerging from sulfated flavonoids and other polyphenols mainly as anticoagulant and antiviral agents. When compared with polymeric macromolecules such as heparins, sulfated small molecules could be of value in therapeutics due to their hydrophobic nature that can contribute to improve the bioavailability. This review highlights the synthetic approaches that were applied to obtain monosulfated or polysulfated phenolic small molecules and compiles the diverse biological activities already reported for this type of derivatives. Toxicity and pharmacokinetic parameters of this emerging class of derivatives will also be considered, emphasizing their value for therapeutic applications.
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Affiliation(s)
- Marta Correia-da-Silva
- Centro de Química Medicinal da Universidade do Porto (CEQUIMED-UP), Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
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Karuturi R, Al-Horani RA, Mehta SC, Gailani D, Desai UR. Discovery of allosteric modulators of factor XIa by targeting hydrophobic domains adjacent to its heparin-binding site. J Med Chem 2013; 56:2415-28. [PMID: 23451707 DOI: 10.1021/jm301757v] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
To discover promising sulfated allosteric modulators (SAMs) of glycosaminoglycan-binding proteins (GBPs), such as human factor XIa (FXIa), we screened a library of 26 synthetic, sulfated quinazolin-4(3H)-ones (QAOs) resulting in the identification of six molecules that reduced the Vmax of substrate hydrolysis without influencing the KM. Mutagenesis of residues of the heparin-binding site (HBS) of FXIa introduced a nearly 5-fold loss in inhibition potency supporting recognition of an allosteric site. Fluorescence studies showed a sigmoidal binding profile indicating highly cooperative binding. Competition with a positively charged, heparin-binding polymer did not fully nullify inhibition suggesting importance of hydrophobic forces to binding. This discovery suggests the operation of a dual-element recognition process, which relies on an initial Coulombic attraction of anionic SAMs to the cationic HBS of FXIa that forms a locked complex through tight interaction with an adjacent hydrophobic patch. The dual-element strategy may be widely applicable for discovering SAMs of other GBPs.
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Affiliation(s)
- Rajesh Karuturi
- Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia 23298, USA
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