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, 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 Search for other works by this author on: Oxford Academic Guowei Su Glycan Therapeutics , 617 Hutton Street, Raleigh, NC 27606 , United States Search for other works by this author on: Oxford Academic Kevin Liu Glycan Therapeutics , 617 Hutton Street, Raleigh, NC 27606 , United States Search for other works by this author on: Oxford Academic 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 Search for other works by this author on: Oxford Academic 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 Corresponding author: Alexander Tropsha, 100K Beard Hall, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, United States. Email: alex_tropsha@unc.edu; Jian Liu, 1044 Genetic Medicine Bldg, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, United States. Email: liuj@email.unc.edu Search for other works by this author on: Oxford Academic 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 Corresponding author: Alexander Tropsha, 100K Beard Hall, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, United States. Email: alex_tropsha@unc.edu; Jian Liu, 1044 Genetic Medicine Bldg, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, United States. Email: liuj@email.unc.edu Search for other works by this author on: Oxford Academic
https://orcid.org/0000-0001-8552-1400 Glycobiology, Volume 34, Issue 7, July 2024, cwae039, https://doi.org/10.1093/glycob/cwae039
Published:
05 June 2024
Article history
Received:
17 March 2024
Revision received:
30 April 2024
Accepted:
29 May 2024
Published:
05 June 2024
Corrected and typeset:
15 June 2024
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Cleber C Melo-Filho, Guowei Su, Kevin Liu, Eugene N Muratov, Alexander Tropsha, Jian Liu, Modeling interactions between Heparan sulfate and proteins based on the Heparan sulfate microarray analysis, Glycobiology, Volume 34, Issue 7, July 2024, cwae039, https://doi.org/10.1093/glycob/cwae039
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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.
chemoenzymatic synthesis, Glycan microarray, heparin, oligosaccharides
© The Author(s) 2024. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com
This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/pages/standard-publication-reuse-rights)
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