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Melo-Filho CC, Su G, Liu K, Muratov EN, Tropsha A, Liu J. Modeling interactions between Heparan sulfate and proteins based on the Heparan sulfate microarray analysis. Glycobiology 2024; 34:cwae039. [PMID: 38836441 PMCID: PMC11180703 DOI: 10.1093/glycob/cwae039] [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: 03/17/2024] [Revised: 04/30/2024] [Accepted: 05/29/2024] [Indexed: 06/06/2024] Open
Abstract
Heparan sulfate (HS), a sulfated polysaccharide abundant in the extracellular matrix, plays pivotal roles in various physiological and pathological processes by interacting with proteins. Investigating the binding selectivity of HS oligosaccharides to target proteins is essential, but the exhaustive inclusion of all possible oligosaccharides in microarray experiments is impractical. To address this challenge, we present a hybrid pipeline that integrates microarray and in silico techniques to design oligosaccharides with desired protein affinity. Using fibroblast growth factor 2 (FGF2) as a model protein, we assembled an in-house dataset of HS oligosaccharides on microarrays and developed two structural representations: a standard representation with all atoms explicit and a simplified representation with disaccharide units as "quasi-atoms." Predictive Quantitative Structure-Activity Relationship (QSAR) models for FGF2 affinity were developed using the Random Forest (RF) algorithm. The resulting models, considering the applicability domain, demonstrated high predictivity, with a correct classification rate of 0.81-0.80 and improved positive predictive values (PPV) up to 0.95. Virtual screening of 40 new oligosaccharides using the simplified model identified 15 computational hits, 11 of which were experimentally validated for high FGF2 affinity. This hybrid approach marks a significant step toward the targeted design of oligosaccharides with desired protein interactions, providing a foundation for broader applications in glycobiology.
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Affiliation(s)
- Cleber C Melo-Filho
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, 301 Beard Hall, University of North Carolina, Chapel Hill, NC 27599, United States
| | - Guowei Su
- Glycan Therapeutics, 617 Hutton Street, Raleigh, NC 27606, United States
| | - Kevin Liu
- Glycan Therapeutics, 617 Hutton Street, Raleigh, NC 27606, United States
| | - Eugene N Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, 301 Beard Hall, University of North Carolina, Chapel Hill, NC 27599, United States
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, 301 Beard Hall, University of North Carolina, Chapel Hill, NC 27599, United States
| | - Jian Liu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, 1044 Genetic Medicine Bldg., University of North Carolina, Chapel Hill, NC 27599, United States
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Chiarantin GMD, Delgado-Garcia LM, Zamproni LN, Lima MA, Nader HB, Tersariol ILS, Porcionatto M. Neuroprotective effect of heparin Trisulfated disaccharide on ischemic stroke. Glycoconj J 2021; 38:35-43. [PMID: 33411076 DOI: 10.1007/s10719-020-09966-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/15/2020] [Accepted: 11/26/2020] [Indexed: 10/22/2022]
Abstract
Cells undergoing hypoxia experience intense cytoplasmic calcium (Ca2+) overload. High concentrations of intracellular calcium ([Ca2+]i) can trigger cell death in the neural tissue, a hallmark of stroke. Neural Ca2+ homeostasis involves regulation by the Na+/Ca2+ exchanger (NCX). Previous data published by our group showed that a product of the enzymatic depolymerization of heparin by heparinase, the unsaturated trisulfated disaccharide (TD; ΔU, 2S-GlcNS, 6S), can accelerate Na+/Ca2+ exchange via NCX, in hepatocytes and aorta vascular smooth muscle cells. Thus, the objective of this work was to verify whether TD could act as a neuroprotective agent able to prevent neuronal cell death by reducing [Ca2+]i. Pretreatment of N2a cells with TD reduced [Ca2+]i rise induced by thapsigargin and increased cell viability under [Ca2+]I overload conditions and in hypoxia. Using a murine model of stroke, we observed that pretreatment with TD decreased cerebral infarct volume and cell death. However, when mice received KB-R7943, an NCX blocker, the neuroprotective effect of TD was abolished, strongly suggesting that this neuroprotection requires a functional NCX to happen. Thus, we propose TD-NCX as a new therapeutic axis for the prevention of neuronal death induced by [Ca2+]i overload.
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Affiliation(s)
- Gabrielly M D Chiarantin
- Laboratory of Molecular Neurobiology, Universidade Federal de São Paulo, São Paulo, SP, Brazil
- Department of Biochemistry, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Lina M Delgado-Garcia
- Laboratory of Molecular Neurobiology, Universidade Federal de São Paulo, São Paulo, SP, Brazil
- Department of Biochemistry, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Laura N Zamproni
- Laboratory of Molecular Neurobiology, Universidade Federal de São Paulo, São Paulo, SP, Brazil
- Department of Biochemistry, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Marcelo A Lima
- Department of Biochemistry, Universidade Federal de São Paulo, São Paulo, SP, Brazil
- Molecular & Structural Biosciences, School of Life Sciences, Keele University, Newcastle-Under-Lyme, Staffordshire, ST5 5BG, UK
| | - Helena B Nader
- Department of Biochemistry, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Ivarne L S Tersariol
- Department of Biochemistry, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
| | - Marimélia Porcionatto
- Laboratory of Molecular Neurobiology, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
- Department of Biochemistry, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
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Chemoenzymatic synthesis of ultralow and low-molecular weight heparins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140301. [DOI: 10.1016/j.bbapap.2019.140301] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 12/17/2022]
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Miller CM, Xu Y, Kudrna KM, Hass BE, Kellar BM, Egger AW, Liu J, Harris EN. 3-O sulfation of heparin leads to hepatotropism and longer circulatory half-life. Thromb Res 2018; 167:80-87. [PMID: 29793137 DOI: 10.1016/j.thromres.2018.05.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 04/20/2018] [Accepted: 05/15/2018] [Indexed: 01/13/2023]
Abstract
INTRODUCTION Heparins are common blood anticoagulants that are critical for many surgical and biomedical procedures used in modern medicine. In contrast to natural heparin derived from porcine gut mucosa, synthetic heparins are homogenous by mass, polymer length, and chemistry. MATERIALS & METHODS Stable cell lines expressing the human and mouse Stabilin receptors were used to evaluate endocytosis of natural and synthetic heparin. We chemoenzymatically produced synthetic heparin consisting of 12 sugars (dodecamers) containing 14 sulfate groups resulting in a non-3-O sulfated structure (n12mer). Half of the n12mer was modified with a 3-O sulfate on a single GlcNS sugar producing the 3-O sulfated heparin (12mer). Wildtype (WT), Stabilin-1 knock-out (KO), and Stabilin-2 KO C57BL/6 mice were developed and used for metabolic studies and provided as a source for primary liver sinusoidal endothelial cells. RESULTS & CONCLUSIONS Human and mouse Stabilin-2 receptors had very similar endocytosis rates of both the 12mer and n12mer, suggesting that they are functionally similar in primary cells. Subcutaneous injections of the n12mer and 12mer revealed that the 12mer had a much longer half-life in circulation and a higher accumulation in liver. The n12mer never accumulated in circulation and was readily excreted by the kidneys before liver accumulation could occur. Liver sinusoidal endothelial cells from the Stabilin-2 KO mice had lower uptake rates for both dodecamers, whereas, the Stabilin-1 KO mice had lower endocytosis rates for the 12mer than the n12mer. 3-O sulfation of heparin is correlated to both a longer circulatory half-life and hepatotropism which is largely performed by the Stabilin receptors.
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Affiliation(s)
- Colton M Miller
- Dept. of Biochemistry, University of Nebraska, Lincoln, NE 68588, United States
| | - Yongmei Xu
- Dept. of Pharmacy and Natural Products, University of North Carolina, Chapel Hill, NC 27099, United States
| | - Katrina M Kudrna
- Dept. of Biochemistry, University of Nebraska, Lincoln, NE 68588, United States
| | - Blake E Hass
- Dept. of Biochemistry, University of Nebraska, Lincoln, NE 68588, United States
| | - Brianna M Kellar
- Dept. of Biochemistry, University of Nebraska, Lincoln, NE 68588, United States
| | - Andrew W Egger
- Dept. of Biochemistry, University of Nebraska, Lincoln, NE 68588, United States
| | - Jian Liu
- Dept. of Pharmacy and Natural Products, University of North Carolina, Chapel Hill, NC 27099, United States
| | - Edward N Harris
- Dept. of Biochemistry, University of Nebraska, Lincoln, NE 68588, United States.
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Sommers CD, Ye H, Liu J, Linhardt RJ, Keire DA. Heparin and homogeneous model heparin oligosaccharides form distinct complexes with protamine: Light scattering and zeta potential analysis. J Pharm Biomed Anal 2017; 140:113-121. [DOI: 10.1016/j.jpba.2017.03.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 02/06/2017] [Accepted: 03/09/2017] [Indexed: 12/17/2022]
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Laroche JP, Schved JF. [Vitamin K antagonist, direct oral anticoagulants: Where is the truth?]. ACTA ACUST UNITED AC 2016; 41:383-388. [PMID: 27817997 DOI: 10.1016/j.jmv.2016.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 09/26/2016] [Indexed: 10/20/2022]
Abstract
Vitamin K antagonists (VKA) and direct oral anticoagulants (DOACs) are now in competition. The companies are trying to replace VKA by DOACs, totally or at least greatly VKA should VKA disappear in favor of DOACs? There are still many questions about DOACs. The purpose of this article is to make a well-considered decision in this area. The aim is not to denigrate one or the other but to share things between these two families of anticoagulants. Physicians using these drugs must have a full knowledge about compared efficacy and safety. We feel necessary to increase distance between effective results of the clinical trials and industrial communication around DOACs.
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Affiliation(s)
- J-P Laroche
- Service de médecine vasculaire, hôpital Saint-Éloi, CHU de Montpellier, 80, avenue Augustin-Fliche, 34295 Montpellier cedex 5, France.
| | - J-F Schved
- Département d'hématologie biologique, hôpital Saint-Éloi, CHU de Montpellier, 80, avenue Augustin-Fliche, 34295 Montpellier cedex 5, France.
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