GlycCompSoft: Software for Automated Comparison of Low Molecular Weight Heparins Using Top-Down LC/MS Data

Wang, Xiaohua; Liu, Xinyue; Li, Lingyun; Zhang, Fuming; Hu, Min; Ren, Fuji; Linhardt, Robert J.

doi:10.1371/journal.pone.0167727

Cited by 11 publications

(5 citation statements)

References 13 publications

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“…Charge deconvolution was autoprocessed by DeconTools software. NACHs structural assignment was done by automatic processing using GlycReSoft 2.0 software, which established NACHs’ structural features, which involved 2,5-anhydromannitol affording the oxidative cleavage by nitrous acid, glycol-split uronic acid obtained by sodium periodate oxidation used in the preparation of D-NACH (see Figure ), and odd saccharides affording the preparation of NACH. ,,− (). For automatic processing, GlycReSoft 2.0 parameters were set as follows: Minimum Number of Scans, 1; Molecular Weight Lower Boundary, 150 Da; Molecular Weight Upper Boundary, 6000 Da; Mass Shift, ammonium; Match Error (E_M), 5.0 ppm; Grouping Error (E_G), 80 ppm; Adduct Tolerance (E_A), 5.0 ppm.…”

Section: Methodsmentioning

confidence: 99%

Non-Anticoagulant Low Molecular Weight Heparins for Pharmaceutical Applications

Ouyang

Zhang

et al. 2019

J. Med. Chem.

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Heparin is a polypharmacological agent with anticoagulant activity. Periodate oxidation of the nonsulfated glucuronic acid residue results in non-anticoagulant heparin derivative (NACH) of reduced molecular weight. Similar treatment of a low molecular weight heparin, dalteparin, also removes its anticoagulant activity, affording a second heparin derivative (D-NACH). A full structural characterization of these two derivatives reveals their structural differences. SPR studies display their ability to bind to several important heparin-binding proteins, suggesting potential new therapeutic applications.

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Section: Methodsmentioning

confidence: 99%

Non-Anticoagulant Low Molecular Weight Heparins for Pharmaceutical Applications

Ouyang

Zhang

et al. 2019

J. Med. Chem.

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“…Starting from early developed software package HOST for heparin/HS oligosaccharide sequencing [ 68 ], today, researchers and pharmaceutical industry have variety of choices for undertaking identification of GAG oligosaccharides different structures and elemental composition analysis. Amongst these, bioinformatics tools include the following: (i) GlycoWorkbench [ 69 ] for analyzing carbohydrate mass spectra through matching an artificially generated library of possible glycan structures, fragments, and compositions using all known and modified disaccharide building blocks against the dataset of peaks derived from the MS sequencing (the system aims to fully facilitate the everyday manual interpretation of MS data); (ii) Manatee for rapid extracting, assigning, and contrasting glycan compositions from LC–MS datasets [ 70 ]; (iii) GlycReSoft [ 71 ] for processing bottom-up and top-down data auto-processed by open source software Decon2LS/DeconTools to generate the identity and quantitative information for LMWHs; (iv) GlyTouCan by Kinoshita et al to unify databases for extensive glycan analysis [ 72 ]; (v) GlycCompSoft for automated comparison of LMWHs using top-down LC/MS data [ 73 ]; (vi) GlycoDeNovo — an efficient algorithm for accurate de novo glycan topology reconstruction from tandem mass spectra [ 74 ]; (vii) GAGfinder — the first software package for MS/MS spectrum peak ending and elemental composition analysis of GAG [ 75 ] (GAGfinder is a targeted approach to spectrum analysis and annotating peak isotopes composition that exploits precursor product information for generating hypothetical library of fragments for experimental result matching); and (viii) GAG-ID — a multivariate mixture model to estimate the automate assignment of LC–MS/MS-fragmented derivatized heparins [ 76 ].…”

Section: Bioinformatics Tools For Lmwh Oligosaccharide Mass Spectra A...mentioning

confidence: 99%

Commercial Low Molecular Weight Heparins — Patent Ecosystem and Technology Paradigm for Quality Characterization

Iqbal¹,

Sadaf

2022

J Pharm Innov

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Heparin is a subject of ever-growing interest for laboratory researchers and pharmaceutical industry. One of the driving factors is its critical life-saving drug status, which during the COVID-19 pandemic has assumed a central role in disease treatment and/or prevention. Apart, heparin is one amongst few drugs enjoying a “demand constant” status. In 2020, heparin market size was valued to US$6.5 bn., and given the ongoing stability in the COVID-19 health crisis, it is expected to reach US$11.43 bn. by 2027 with yearly growth rate momentum (CAGR) of 3.9% during the forecast period (Pepi et al., Mol Cell Proteomics 20:100,025, 2021). As patent is a limited monopoly, every year, many patents on low molecular weight heparin (LMWH; a chemically or enzymatically degraded product of unfractionated heparin) are losing market exclusivity worldwide, inviting the generic/biosimilar drug manufacturers to capture market share with cheaper drug products. By tracking patent expiration, drugs in patent litigation, regulatory setbacks for innovator companies (such as those seeking data exclusivity or patent term extension), or other unexpected events affecting market demand and competition, generics can make investment decisions in manufacturing off-patent LMWH drug products of commercial significance. However, given the US Food and Drug Administration (FDA), European Medicine Agency (EMA), Drug Regulatory Authority of Pakistan (DRAP), and other regulatory authorities scientifically rigorous standards for generic/biosimilar LMWH drug products marketing approval, the market is secured and momentous for drug makers that could demonstrate through scientific and clinical dataset that the generic/biosimilar LMWH drug product is of the same quality and purity as the innovator drug product. This study presents an overview of the patent landscape of commercially available LMWHs and advanced analytical techniques for their structural and biochemical characterization for quality control and quality assurance during manufacturing and post-marketing. The study also covers FDA, EMA, Health Canada, and DRAP’s current approaches to evaluating the generic/biosimilar LMWH drug products for quality, safety including immunogenicity, and efficacy.

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“…The Zaia group then developed GlycReSoft, which added noise reduction and confidence measurements to the efficient data analysis of Manatee ( 135 ). Recently developed programs GlycCompSoft and GRITS Toolbox have made composition assignment software more user-friendly with features that automatically assign peaks, allow postprocessing, and facilitate more specific experimental analysis ( 136 , 137 ).…”

Section: Glycosaminoglycan Software Developmentsmentioning

confidence: 99%

“…The Zaia group then developed GlycReSoft, which added noise reduction and confidence measurements to the efficient data analysis of Manatee(137). Recently developed programs GlycCompSoft and GRITS Toolbox have made composition assignment software more user friendly with features that automatically assign peaks, allow post-processing, and facilitate more specific experimental analysis(138,139).The next step after composition is automated characterization of GAG structures from MS/MS data. Ion activation allows researchers to pinpoint modifications to specific residues or sites within a residue.…”

mentioning

confidence: 99%

Developments in Mass Spectrometry for Glycosaminoglycan Analysis: A Review

Pepi

Sanderson

Stickney

et al. 2021

Molecular & Cellular Proteomics

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This review covers recent developments in glycosaminoglycan (GAG) analysis via mass spectrometry (MS). GAGs participate in a variety of biological functions, including cellular communication, wound healing, and anticoagulation, and are important targets for structural characterization. GAGs exhibit a diverse range of structural features due to the variety of O- and N-sulfation modifications and uronic acid C-5 epimerization that can occur, making their analysis a challenging target. Mass spectrometry approaches to the structure assignment of GAGs have been widely investigated, and new methodologies remain the subject of development. Advances in sample preparation, tandem MS techniques (MS/MS), on-line separations and automated analysis software have advanced the field of GAG analysis. These recent developments have led to remarkable improvements in the precision and time efficiency for the structural characterization of GAGs.

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GlycCompSoft: Software for Automated Comparison of Low Molecular Weight Heparins Using Top-Down LC/MS Data

Cited by 11 publications

References 13 publications

Non-Anticoagulant Low Molecular Weight Heparins for Pharmaceutical Applications

Non-Anticoagulant Low Molecular Weight Heparins for Pharmaceutical Applications

Commercial Low Molecular Weight Heparins — Patent Ecosystem and Technology Paradigm for Quality Characterization

Developments in Mass Spectrometry for Glycosaminoglycan Analysis: A Review

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