1
|
Klünemann M, Romero LF, Acman M, Milfort MC, Fuller AL, Rekaya R, Aggrey SE, Payling LM, Lemme A. Multitissue transcriptomics demonstrates the systemic physiology of methionine deficiency in broiler chickens. Animal 2024; 18:101143. [PMID: 38640782 DOI: 10.1016/j.animal.2024.101143] [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: 10/04/2023] [Revised: 03/15/2024] [Accepted: 03/19/2024] [Indexed: 04/21/2024] Open
Abstract
Methionine (Met) supplementation is common practice in broilers to support nutrition, yet there are gaps in the understanding of its role in systemic physiology. Furthermore, several different Met sources are available that may have different physiological effects. This study evaluated the mode of action of Met deficiency (no Met-supplementation) and supplementation (0.25% DL- or L-Met, 0.41% liquid methionine hydroxy analog-free acid (MHA-FA)), and of Met source (DL-, L- or MHA-FA) in broiler chickens, via host transcriptomics. Biological pathway activation modeling was performed to predict the likely phenotypic effects of differentially expressed genes (DEGs) in tissue samples from the jejunum, liver and breast obtained at 10, 21 and 34/35 d of age from three experiments in a combined analysis. Animal performance data showed that Met deficiency reduced BW, daily BW gain, daily feed intake, and breast yield, and increased feed conversion ratio in all experiments (P < 0.05). Effects of Met deficiency on gene expression were least evident in the jejunum and most evident in the liver and breast, as evidenced by the number of DEG and activated pathways. Activated pathways suggested Met deficiency was associated with inhibited protein turnover, gut barrier integrity, and adaptive immunity functions in the jejunum, that predicted reduced breast yield. There was an interaction with age; in Met-deficient birds, there were 333 DEGs in the jejunum of starter vs finisher birds suggesting young birds were more sensitive to Met deficiency than older birds. In the liver, Met deficiency activated pathways associated with lipid turnover, amino acid metabolism, oxidative stress, and the immune system, whereas in breast, it activated pathways involved in metabolic regulation, hemostasis, the neuronal system, and oxidative stress, again predicting a negative impact on breast yield. In the starter phase, supplementation with DL-Met compared to MHA-FA inhibited gamma-aminobutyric acid activity and oxidative stress in breast tissue. When data from all tissues were integrated, increased expression of a liver gene (ENSGALG00000042797) was found to be correlated with the expression of several genes that best explained variation due to the Met deficiency in jejunum and breast muscle. Some of these genes were involved in anti-oxidant systems. Overall, the findings indicate that impaired growth performance due to Met deficiency results from an array of tissue-specific molecular mechanisms in which oxidative stress plays a key systemic role. Young birds are more sensitive to Met-deficiency and DL-Met was a preferential source of Met than L- or MHA-FA during the starter phase.
Collapse
Affiliation(s)
- M Klünemann
- Animal Nutrition Research, Evonik Operations GmbH, Hanau Germany
| | | | | | - M C Milfort
- Department of Poultry Science, University of Georgia, Athens, GA 30602, United States
| | - A L Fuller
- Department of Poultry Science, University of Georgia, Athens, GA 30602, United States
| | - R Rekaya
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, United States
| | - S E Aggrey
- Department of Poultry Science, University of Georgia, Athens, GA 30602, United States
| | | | - A Lemme
- Animal Nutrition Research, Evonik Operations GmbH, Hanau Germany.
| |
Collapse
|
2
|
Olteanu G, Neacșu SM, Joița FA, Musuc AM, Lupu EC, Ioniță-Mîndrican CB, Lupuliasa D, Mititelu M. Advancements in Regenerative Hydrogels in Skin Wound Treatment: A Comprehensive Review. Int J Mol Sci 2024; 25:3849. [PMID: 38612660 PMCID: PMC11012090 DOI: 10.3390/ijms25073849] [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: 01/30/2024] [Revised: 03/19/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
This state-of-the-art review explores the emerging field of regenerative hydrogels and their profound impact on the treatment of skin wounds. Regenerative hydrogels, composed mainly of water-absorbing polymers, have garnered attention in wound healing, particularly for skin wounds. Their unique properties make them well suited for tissue regeneration. Notable benefits include excellent water retention, creating a crucially moist wound environment for optimal healing, and facilitating cell migration, and proliferation. Biocompatibility is a key feature, minimizing adverse reactions and promoting the natural healing process. Acting as a supportive scaffold for cell growth, hydrogels mimic the extracellular matrix, aiding the attachment and proliferation of cells like fibroblasts and keratinocytes. Engineered for controlled drug release, hydrogels enhance wound healing by promoting angiogenesis, reducing inflammation, and preventing infection. The demonstrated acceleration of the wound healing process, particularly beneficial for chronic or impaired healing wounds, adds to their appeal. Easy application and conformity to various wound shapes make hydrogels practical, including in irregular or challenging areas. Scar minimization through tissue regeneration is crucial, especially in cosmetic and functional regions. Hydrogels contribute to pain management by creating a protective barrier, reducing friction, and fostering a soothing environment. Some hydrogels, with inherent antimicrobial properties, aid in infection prevention, which is a crucial aspect of successful wound healing. Their flexibility and ability to conform to wound contours ensure optimal tissue contact, enhancing overall treatment effectiveness. In summary, regenerative hydrogels present a promising approach for improving skin wound healing outcomes across diverse clinical scenarios. This review provides a comprehensive analysis of the benefits, mechanisms, and challenges associated with the use of regenerative hydrogels in the treatment of skin wounds. In this review, the authors likely delve into the application of rational design principles to enhance the efficacy and performance of hydrogels in promoting wound healing. Through an exploration of various methodologies and approaches, this paper is poised to highlight how these principles have been instrumental in refining the design of hydrogels, potentially revolutionizing their therapeutic potential in addressing skin wounds. By synthesizing current knowledge and highlighting potential avenues for future research, this review aims to contribute to the advancement of regenerative medicine and ultimately improve clinical outcomes for patients with skin wounds.
Collapse
Affiliation(s)
- Gabriel Olteanu
- Department of Clinical Laboratory and Food Safety, Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020956 Bucharest, Romania; (G.O.); (M.M.)
| | - Sorinel Marius Neacșu
- Department of Pharmaceutical Technology and Bio-Pharmacy, Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020945 Bucharest, Romania; (S.M.N.); (D.L.)
| | - Florin Alexandru Joița
- Department of Pharmaceutical Technology and Bio-Pharmacy, Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020945 Bucharest, Romania; (S.M.N.); (D.L.)
| | | | - Elena Carmen Lupu
- Department of Mathematics and Informatics, Faculty of Pharmacy, “Ovidius” University of Constanta, 900001 Constanta, Romania;
| | - Corina-Bianca Ioniță-Mîndrican
- Department of Toxicology, Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020945 Bucharest, Romania;
| | - Dumitru Lupuliasa
- Department of Pharmaceutical Technology and Bio-Pharmacy, Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020945 Bucharest, Romania; (S.M.N.); (D.L.)
| | - Magdalena Mititelu
- Department of Clinical Laboratory and Food Safety, Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020956 Bucharest, Romania; (G.O.); (M.M.)
| |
Collapse
|
3
|
Petersen SI, Okolicsanyi RK, Haupt LM. Exploring Heparan Sulfate Proteoglycans as Mediators of Human Mesenchymal Stem Cell Neurogenesis. Cell Mol Neurobiol 2024; 44:30. [PMID: 38546765 PMCID: PMC10978659 DOI: 10.1007/s10571-024-01463-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/19/2024] [Indexed: 04/01/2024]
Abstract
Alzheimer's disease (AD) and traumatic brain injury (TBI) are major public health issues worldwide, with over 38 million people living with AD and approximately 48 million people (27-69 million) experiencing TBI annually. Neurodegenerative conditions are characterised by the accumulation of neurotoxic amyloid beta (Aβ) and microtubule-associated protein Tau (Tau) with current treatments focused on managing symptoms rather than addressing the underlying cause. Heparan sulfate proteoglycans (HSPGs) are a diverse family of macromolecules that interact with various proteins and ligands and promote neurogenesis, a process where new neural cells are formed from stem cells. The syndecan (SDC) and glypican (GPC) HSPGs have been implicated in AD pathogenesis, acting as drivers of disease, as well as potential therapeutic targets. Human mesenchymal stem cells (hMSCs) provide an attractive therapeutic option for studying and potentially treating neurodegenerative diseases due to their relative ease of isolation and subsequent extensive in vitro expansive potential. Understanding how HSPGs regulate protein aggregation, a key feature of neurodegenerative disorders, is essential to unravelling the underlying disease processes of AD and TBI, as well as any link between these two neurological disorders. Further research may validate HSPG, specifically SDCs or GPCs, use as neurodegenerative disease targets, either via driving hMSC stem cell therapy or direct targeting.
Collapse
Affiliation(s)
- Sofia I Petersen
- Stem Cell and Neurogenesis Group, School of Biomedical Sciences, Genomics Research Centre, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), 60 Musk Ave, Kelvin Grove, QLD, 4059, Australia
| | - Rachel K Okolicsanyi
- Stem Cell and Neurogenesis Group, School of Biomedical Sciences, Genomics Research Centre, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), 60 Musk Ave, Kelvin Grove, QLD, 4059, Australia
- Max Planck Queensland Centre for the Materials Sciences of Extracellular Matrices, Kelvin Grove, Australia
| | - Larisa M Haupt
- Stem Cell and Neurogenesis Group, School of Biomedical Sciences, Genomics Research Centre, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), 60 Musk Ave, Kelvin Grove, QLD, 4059, Australia.
- ARC Training Centre for Cell and Tissue Engineering Technologies, Queensland University of Technology (QUT), Kelvin Grove, Australia.
- Max Planck Queensland Centre for the Materials Sciences of Extracellular Matrices, Kelvin Grove, Australia.
| |
Collapse
|
4
|
Xie Y, Butler M. N-glycomic profiling of capsid proteins from Adeno-Associated Virus serotypes. Glycobiology 2024; 34:cwad074. [PMID: 37774344 PMCID: PMC10950483 DOI: 10.1093/glycob/cwad074] [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: 05/01/2023] [Revised: 09/14/2023] [Accepted: 09/23/2023] [Indexed: 10/01/2023] Open
Abstract
Adeno-associated virus (AAV) vector has become the leading platform for gene delivery. Each serotype exhibits a different tissue tropism, immunogenicity, and in vivo transduction performance. Therefore, selecting the most suitable AAV serotype is critical for efficient gene delivery to target cells or tissues. Genome divergence among different serotypes is due mainly to the hypervariable regions of the AAV capsid proteins. However, the heterogeneity of capsid glycosylation is largely unexplored. In the present study, the N-glycosylation profiles of capsid proteins of AAV serotypes 1 to 9 have been systemically characterized and compared using a previously developed high-throughput and high-sensitivity N-glycan profiling platform. The results showed that all 9 investigated AAV serotypes were glycosylated, with comparable profiles. The most conspicuous feature was the high abundance mannosylated N-glycans, including FM3, M5, M6, M7, M8, and M9, that dominated the chromatograms within a range of 74 to 83%. Another feature was the relatively lower abundance of fucosylated and sialylated N-glycan structures, in the range of 23%-40% and 10%-17%, respectively. However, the exact N-glycan composition differed. These differences may be utilized to identify potential structural relationships between the 9 AAV serotypes. The current research lays the foundation for gaining better understanding of the importance of N-glycans on the AAV capsid surface that may play a significant role in tissue tropism, interaction with cell surface receptors, cellular uptake, and intracellular processing.
Collapse
Affiliation(s)
- Yongjing Xie
- National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, A94 X099, Ireland
| | - Michael Butler
- National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, A94 X099, Ireland
- School of Chemical and Bioprocess Engineering, University College Dublin (UCD), Belfield, Dublin 4, D04 V1W8, Ireland
| |
Collapse
|
5
|
Ricard-Blum S, Vivès RR, Schaefer L, Götte M, Merline R, Passi A, Heldin P, Magalhães A, Reis CA, Skandalis SS, Karamanos NK, Perez S, Nikitovic D. A biological guide to glycosaminoglycans: current perspectives and pending questions. FEBS J 2024. [PMID: 38500384 DOI: 10.1111/febs.17107] [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: 10/10/2023] [Revised: 01/08/2024] [Accepted: 02/20/2024] [Indexed: 03/20/2024]
Abstract
Mammalian glycosaminoglycans (GAGs), except hyaluronan (HA), are sulfated polysaccharides that are covalently attached to core proteins to form proteoglycans (PGs). This article summarizes key biological findings for the most widespread GAGs, namely HA, chondroitin sulfate/dermatan sulfate (CS/DS), keratan sulfate (KS), and heparan sulfate (HS). It focuses on the major processes that remain to be deciphered to get a comprehensive view of the mechanisms mediating GAG biological functions. They include the regulation of GAG biosynthesis and postsynthetic modifications in heparin (HP) and HS, the composition, heterogeneity, and function of the tetrasaccharide linkage region and its role in disease, the functional characterization of the new PGs recently identified by glycoproteomics, the selectivity of interactions mediated by GAG chains, the display of GAG chains and PGs at the cell surface and their impact on the availability and activity of soluble ligands, and on their move through the glycocalyx layer to reach their receptors, the human GAG profile in health and disease, the roles of GAGs and particular PGs (syndecans, decorin, and biglycan) involved in cancer, inflammation, and fibrosis, the possible use of GAGs and PGs as disease biomarkers, and the design of inhibitors targeting GAG biosynthetic enzymes and GAG-protein interactions to develop novel therapeutic approaches.
Collapse
Affiliation(s)
- Sylvie Ricard-Blum
- Univ Lyon 1, ICBMS, UMR 5246 University Lyon 1 - CNRS, Villeurbanne cedex, France
| | | | - Liliana Schaefer
- Institute of Pharmacology and Toxicology, Goethe University, Frankfurt, Germany
| | - Martin Götte
- Department of Gynecology and Obstetrics, Münster University Hospital, Germany
| | - Rosetta Merline
- Institute of Pharmacology and Toxicology, Goethe University, Frankfurt, Germany
| | | | - Paraskevi Heldin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Sweden
| | - Ana Magalhães
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
- ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal
| | - Celso A Reis
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
- ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal
| | - Spyros S Skandalis
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Res. Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, Greece
| | - Nikos K Karamanos
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Res. Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, Greece
| | - Serge Perez
- Centre de Recherche sur les Macromolécules Végétales, University of Grenoble-Alpes, CNRS, France
| | - Dragana Nikitovic
- Laboratory of Histology-Embryology, School of Medicine, University of Crete, Heraklion, Greece
| |
Collapse
|
6
|
Denes A, Hansen CE, Oezorhan U, Figuerola S, de Vries HE, Sorokin L, Planas AM, Engelhardt B, Schwaninger M. Endothelial cells and macrophages as allies in the healthy and diseased brain. Acta Neuropathol 2024; 147:38. [PMID: 38347307 PMCID: PMC10861611 DOI: 10.1007/s00401-024-02695-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/19/2024] [Accepted: 01/20/2024] [Indexed: 02/15/2024]
Abstract
Diseases of the central nervous system (CNS) are often associated with vascular disturbances or inflammation and frequently both. Consequently, endothelial cells and macrophages are key cellular players that mediate pathology in many CNS diseases. Macrophages in the brain consist of the CNS-associated macrophages (CAMs) [also referred to as border-associated macrophages (BAMs)] and microglia, both of which are close neighbours or even form direct contacts with endothelial cells in microvessels. Recent progress has revealed that different macrophage populations in the CNS and a subset of brain endothelial cells are derived from the same erythromyeloid progenitor cells. Macrophages and endothelial cells share several common features in their life cycle-from invasion into the CNS early during embryonic development and proliferation in the CNS, to their demise. In adults, microglia and CAMs have been implicated in regulating the patency and diameter of vessels, blood flow, the tightness of the blood-brain barrier, the removal of vascular calcification, and the life-time of brain endothelial cells. Conversely, CNS endothelial cells may affect the polarization and activation state of myeloid populations. The molecular mechanisms governing the pas de deux of brain macrophages and endothelial cells are beginning to be deciphered and will be reviewed here.
Collapse
Affiliation(s)
- Adam Denes
- "Momentum" Laboratory of Neuroimmunology, Institute of Experimental Medicine, Budapest, Hungary
| | - Cathrin E Hansen
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, The Netherlands
- MS Center Amsterdam, Amsterdam UMC Location VU Medical Center, Amsterdam, The Netherlands
| | - Uemit Oezorhan
- Institute of Experimental and Clinical Pharmacology and Toxicology, Center of Brain, Behavior and Metabolism, University of Lübeck, Lübeck, Germany
| | - Sara Figuerola
- Department of Neuroscience and Experimental Therapeutics, Instituto de Investigaciones Biomedicas de Barcelona (IIBB), Consejo Superior de Investigaciones Cientificas (CSIC), 08036, Barcelona, Spain
- Cerebrovascular Research Group, Institut d'Investigacions Biomediques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Helga E de Vries
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, The Netherlands
- MS Center Amsterdam, Amsterdam UMC Location VU Medical Center, Amsterdam, The Netherlands
| | - Lydia Sorokin
- Institute of Physiological Chemistry and Pathobiochemistry, University of Muenster, Munster, Germany
- Cells-in-Motion Interfaculty Centre (CIMIC), University of Münster, Münster, Germany
| | - Anna M Planas
- Department of Neuroscience and Experimental Therapeutics, Instituto de Investigaciones Biomedicas de Barcelona (IIBB), Consejo Superior de Investigaciones Cientificas (CSIC), 08036, Barcelona, Spain
- Cerebrovascular Research Group, Institut d'Investigacions Biomediques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | | | - Markus Schwaninger
- Institute of Experimental and Clinical Pharmacology and Toxicology, Center of Brain, Behavior and Metabolism, University of Lübeck, Lübeck, Germany.
- German Research Centre for Cardiovascular Research (DZHK), Partner Site Hamburg, Lübeck, Kiel, Germany.
| |
Collapse
|
7
|
An Z, Bu C, Shi D, Chen Q, Zhang B, Wang Q, Jin L, Chi L. Structurally defined heparin octasaccharide domain for binding to SARS-CoV-2 Omicron BA.4/BA.5/BA.5.2 spike protein RBD. Int J Biol Macromol 2024; 259:129032. [PMID: 38159696 DOI: 10.1016/j.ijbiomac.2023.129032] [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: 06/26/2023] [Revised: 11/15/2023] [Accepted: 11/30/2023] [Indexed: 01/03/2024]
Abstract
Heparin, a bio-molecule with the highest negative charge density, is pharmaceutically important to prevent SARS-CoV-2 infection due to its strong competitive binding to spike protein compared with cellular heparan sulfate, which was confirmed as a co-receptor for virus-host cell interaction. Hence, the refined structural characterization of heparin targeting viral protein-HS interaction was significant for developing antiviral pharmaceuticals. In our study, heparin oligomers (dp ≥ 4) were prepared using heparinase I. The affinity oligosaccharides binding to Omicron spike protein RBD were separated by affinity chromatography and size exclusion chromatography. HILIC-ESI-FTMS was used for chain mapping analysis. The basic building blocks were analyzed and the binding domain sequence was produced by Seq-GAG software and further measured by SAX chromatography. As results, heparin octasaccharide was found with significantly higher binding ability than hexasaccharide and tetrasaccharide, and the octasaccharide [ΔUA-GlcNS6S-GlcA-GlcNS6S-IdoA2S-GlcNS6S-IdoA2S-GlcNS6S] with 12 sulfate groups showed high binding to RBD. The mechanism of this structurally well-defined octasaccharide binding to RBD was further investigated by molecular docking. The affinity energy of optimal pose was -6.8 kcal/mol and the basic amino acid residues in RBD sequence (Arg403, Arg452, Arg493 and His505) were identified as the major contribution factor to interacting with sulfate/carboxyl groups on saccharide chain. Our study demonstrated that heparin oligosaccharide with well-defined structure could be potentially developed as anti-SARS-CoV-2 drugs.
Collapse
Affiliation(s)
- Zizhe An
- National Glycoengineering Research Center, Shandong University, No. 72, Binhai Road, Qingdao, Shandong Province 266237, China
| | - Changkai Bu
- National Glycoengineering Research Center, Shandong University, No. 72, Binhai Road, Qingdao, Shandong Province 266237, China
| | - Deling Shi
- National Glycoengineering Research Center, Shandong University, No. 72, Binhai Road, Qingdao, Shandong Province 266237, China
| | - Qingqing Chen
- National Glycoengineering Research Center, Shandong University, No. 72, Binhai Road, Qingdao, Shandong Province 266237, China
| | - Bin Zhang
- National Glycoengineering Research Center, Shandong University, No. 72, Binhai Road, Qingdao, Shandong Province 266237, China
| | - Qingchi Wang
- National Glycoengineering Research Center, Shandong University, No. 72, Binhai Road, Qingdao, Shandong Province 266237, China
| | - Lan Jin
- National Glycoengineering Research Center, Shandong University, No. 72, Binhai Road, Qingdao, Shandong Province 266237, China.
| | - Lianli Chi
- National Glycoengineering Research Center, Shandong University, No. 72, Binhai Road, Qingdao, Shandong Province 266237, China.
| |
Collapse
|
8
|
Cingolani M, Lugli F, Zaffagnini M, Genovese D. Fluorogenic Hyaluronan Nanogels Track Individual Early Protein Aggregates Originated under Oxidative Stress. ACS APPLIED MATERIALS & INTERFACES 2024; 16:3056-3063. [PMID: 38194274 PMCID: PMC10811615 DOI: 10.1021/acsami.3c13202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/27/2023] [Accepted: 12/13/2023] [Indexed: 01/10/2024]
Abstract
Proteins are broadly versatile biochemical materials, whose functionality is tightly related to their folding state. Native folding can be lost to yield misfolded conformations, often leading to formation of protein oligomers, aggregates, and biomolecular phase condensates. The fluorogenic hyaluronan HA-RB, a nonsulfonated glycosaminoglycan with a combination of polyanionic character and of hydrophobic spots due to rhodamine B dyes, binds to early aggregates of the model protein cytoplasmic glyceraldehyde-3-phosphate dehydrogenase 1 from Arabidopsis thaliana (AtGAPC1) since the very onset of the oligomeric phase, making them brightly fluorescent. This initial step of aggregation has, until now, remained elusive with other fluorescence- or scattering-based techniques. The information gathered from nanotracking (via light-sheet fluorescence microscopy) and from FCS in a confocal microscope converges to highlight the ability of HA-RB to bind protein aggregates from the very early steps of aggregation and with high affinity. Altogether, this fluorescence-based approach allows one to monitor and track individual early AtGAPC1 aggregates in the size range from 10 to 100 nm with high time (∼10-2 s) and space (∼250 nm) resolution.
Collapse
Affiliation(s)
- Matteo Cingolani
- Dipartimento
di Chimica “Giacomo Ciamician”, Università di Bologna, 40126 Bologna, Italy
| | - Francesca Lugli
- Dipartimento
di Chimica “Giacomo Ciamician”, Università di Bologna, 40126 Bologna, Italy
| | - Mirko Zaffagnini
- Dipartimento
di Farmacia e Biotecnologie, Università
di Bologna, 40126 Bologna, Italy
| | - Damiano Genovese
- Dipartimento
di Chimica “Giacomo Ciamician”, Università di Bologna, 40126 Bologna, Italy
| |
Collapse
|
9
|
Sanjanwala D, Londhe V, Trivedi R, Bonde S, Sawarkar S, Kale V, Patravale V. Polysaccharide-based hydrogels for medical devices, implants and tissue engineering: A review. Int J Biol Macromol 2024; 256:128488. [PMID: 38043653 DOI: 10.1016/j.ijbiomac.2023.128488] [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: 06/20/2023] [Revised: 11/10/2023] [Accepted: 11/27/2023] [Indexed: 12/05/2023]
Abstract
Hydrogels are highly biocompatible biomaterials composed of crosslinked three-dimensional networks of hydrophilic polymers. Owing to their natural origin, polysaccharide-based hydrogels (PBHs) possess low toxicity, high biocompatibility and demonstrate in vivo biodegradability, making them great candidates for use in various biomedical devices, implants, and tissue engineering. In addition, many polysaccharides also show additional biological activities such as antimicrobial, anticoagulant, antioxidant, immunomodulatory, hemostatic, and anti-inflammatory, which can provide additional therapeutic benefits. The porous nature of PBHs allows for the immobilization of antibodies, aptamers, enzymes and other molecules on their surface, or within their matrix, potentiating their use in biosensor devices. Specific polysaccharides can be used to produce transparent hydrogels, which have been used widely to fabricate ocular implants. The ability of PBHs to encapsulate drugs and other actives has been utilized for making neural implants and coatings for cardiovascular devices (stents, pacemakers and venous catheters) and urinary catheters. Their high water-absorption capacity has been exploited to make superabsorbent diapers and sanitary napkins. The barrier property and mechanical strength of PBHs has been used to develop gels and films as anti-adhesive formulations for the prevention of post-operative adhesion. Finally, by virtue of their ability to mimic various body tissues, they have been explored as scaffolds and bio-inks for tissue engineering of a wide variety of organs. These applications have been described in detail, in this review.
Collapse
Affiliation(s)
- Dhruv Sanjanwala
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga (E), Mumbai 400019, Maharashtra, India; Department of Pharmaceutical Sciences, College of Pharmacy, 428 Church Street, University of Michigan, Ann Arbor, MI 48109, United States.
| | - Vaishali Londhe
- SVKM's NMIMS, Shobhaben Pratapbhai College of Pharmacy and Technology Management, V.L. Mehta Road, Vile Parle (W), Mumbai 400056, Maharashtra, India
| | - Rashmi Trivedi
- Smt. Kishoritai Bhoyar College of Pharmacy, Kamptee, Nagpur 441002, Maharashtra, India
| | - Smita Bonde
- SVKM's NMIMS, School of Pharmacy and Technology Management, Shirpur Campus, Maharashtra, India
| | - Sujata Sawarkar
- Department of Pharmaceutics, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, University of Mumbai, Mumbai 400056, Maharashtra, India
| | - Vinita Kale
- Department of Pharmaceutics, Gurunanak College of Pharmacy, Kamptee Road, Nagpur 440026, Maharashtra, India
| | - Vandana Patravale
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga (E), Mumbai 400019, Maharashtra, India.
| |
Collapse
|
10
|
Makshakova ON, Bogdanova LR, Faizullin DA, Ermakova EA, Zuev YF. Sulfated Polysaccharides as a Fighter with Protein Non-Physiological Aggregation: The Role of Polysaccharide Flexibility and Charge Density. Int J Mol Sci 2023; 24:16223. [PMID: 38003413 PMCID: PMC10671430 DOI: 10.3390/ijms242216223] [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: 09/23/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Proteins can lose native functionality due to non-physiological aggregation. In this work, we have shown the power of sulfated polysaccharides as a natural assistant to restore damaged protein structures. Protein aggregates enriched by cross-β structures are a characteristic of amyloid fibrils related to different health disorders. Our recent studies demonstrated that model fibrils of hen egg white lysozyme (HEWL) can be disaggregated and renatured by some negatively charged polysaccharides. In the current work, using the same model protein system and FTIR spectroscopy, we studied the role of conformation and charge distribution along the polysaccharide chain in the protein secondary structure conversion. The effects of three carrageenans (κ, ι, and λ) possessing from one to three sulfate groups per disaccharide unit were shown to be different. κ-Carrageenan was able to fully eliminate cross-β structures and complete the renaturation process. ι-Carrageenan only initiated the formation of native-like β-structures in HEWL, retaining most of the cross-β structures. In contrast, λ-carrageenan even increased the content of amyloid cross-β structures. Furthermore, κ-carrageenan in rigid helical conformation loses its capability to restore protein native structures, largely increasing the amount of amyloid cross-β structures. Our findings create a platform for the design of novel natural chaperons to counteract protein unfolding.
Collapse
Affiliation(s)
- Olga N. Makshakova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 2/31 Lobachevsky Street, 420111 Kazan, Russia
| | | | | | | | | |
Collapse
|
11
|
Zhou HL, Jiang XZ, Ventikos Y. Role of blood flow in endothelial functionality: a review. Front Cell Dev Biol 2023; 11:1259280. [PMID: 37905167 PMCID: PMC10613523 DOI: 10.3389/fcell.2023.1259280] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 10/04/2023] [Indexed: 11/02/2023] Open
Abstract
Endothelial cells, located on the surface of blood vessel walls, are constantly stimulated by mechanical forces from the blood flow. The mechanical forces, i.e., fluid shear stress, induced by the blood flow play a pivotal role in controlling multiple physiological processes at the endothelium and in regulating various pathways that maintain homeostasis and vascular function. In this review, research looking at different blood fluid patterns and fluid shear stress in the circulation system is summarized, together with the interactions between the blood flow and the endothelial cells. This review also highlights the flow profile as a response to the configurational changes of the endothelial glycocalyx, which is less revisited in previous reviews. The role of endothelial glycocalyx in maintaining endothelium health and the strategies for the restoration of damaged endothelial glycocalyx are discussed from the perspective of the fluid shear stress. This review provides a new perspective regarding our understanding of the role that blood flow plays in regulating endothelial functionality.
Collapse
Affiliation(s)
- Hui Lin Zhou
- School of Mechanical Engineering and Automation, Northeastern University, Shenyang, China
| | - Xi Zhuo Jiang
- School of Mechanical Engineering and Automation, Northeastern University, Shenyang, China
| | - Yiannis Ventikos
- Department of Mechanical Engineering, Monash University, Melbourne, VIC, Australia
| |
Collapse
|
12
|
Schulze C, Danielsson A, Liwo A, Huster D, Samsonov SA, Penk A. Ligand binding of interleukin-8: a comparison of glycosaminoglycans and acidic peptides. Phys Chem Chem Phys 2023; 25:24930-24947. [PMID: 37694394 DOI: 10.1039/d3cp02457a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Recognition and binding of regulatory proteins to glycosaminoglycans (GAGs) from the extracellular matrix is a process of high biological importance. The interaction between negatively charged sulfate or carboxyl groups of the GAGs and clusters of basic amino acids on the protein is crucial in this binding process and it is believed that electrostatics represent the key factor for this interaction. However, given the rather undirected nature of electrostatics, it is important to achieve a clear understanding of its role in protein-GAG interactions and how specificity and selectivity in these systems can be achieved, when the classical key-lock binding motif is not applicable. Here, we compare protein binding of a highly charged heparin (HP) hexasaccharide with four de novo designed decapeptides of varying negative net charge. The charge density of these peptides was comparable to typical GAGs of the extracellular matrix. We used the regulatory protein interleukin-8 (IL-8) because its interactions with GAGs are well described. All four peptide ligands bind to the same epitope of IL-8 but show much weaker binding affinity as revealed in 1H-15N HSQC NMR titration experiments. Complementary molecular docking and molecular dynamics simulations revealed further atomistic details of the interaction mode of GAG versus peptide ligands. Overall, similar contributions to the binding energy and hydrogen bond formation are determined for HP and the highly charged peptides, suggesting that the entropic loss of the peptides upon binding likely account for the remarkably different affinity of GAG versus peptide ligands to IL-8.
Collapse
Affiliation(s)
- Christian Schulze
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, 04107 Leipzig, Germany.
| | - Annemarie Danielsson
- Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland.
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland.
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, 04107 Leipzig, Germany.
| | - Sergey A Samsonov
- Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland.
| | - Anja Penk
- Institute for Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, 04107 Leipzig, Germany.
| |
Collapse
|
13
|
Weaver DF. Druggable targets for the immunopathy of Alzheimer's disease. RSC Med Chem 2023; 14:1645-1661. [PMID: 37731705 PMCID: PMC10507808 DOI: 10.1039/d3md00096f] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 06/21/2023] [Indexed: 09/22/2023] Open
Abstract
Alzheimer's disease (AD) is one of the leading threats to the health and socioeconomic well-being of humankind. Though research to develop disease modifying therapies for AD has traditionally focussed on the misfolding and aggregation of proteins, this approach has failed to yield a definitively curative agent. Accordingly, the search for additional or alternative approaches is a medicinal chemistry priority. Dysfunction of the brain's neuroimmune-neuroinflammation axis has emerged as a leading contender. Neuroimmunity however is mechanistically complex, rendering the recognition of candidate receptors a challenging task. Herein, a review of the role of neuroimmunity in the biomolecular pathogenesis of AD is presented with the identification of a 'druggable dozen' targets; in turn, each identified target represents one or more discrete receptors centred on a common biochemical mechanism. The druggable dozen is composed of both cellular and molecular messenger targets, with a 'targetable ten' microglial targets as well as two cytokine-based targets. For each target, the underlying molecular basis, with a consideration of strengths and weaknesses, is considered.
Collapse
Affiliation(s)
- Donald F Weaver
- Krembil Research Institute, University Health Network, Department of Chemistry, University of Toronto 60 Leonard Avenue Toronto ON M5T 0S8 Canada
| |
Collapse
|
14
|
Dhurua S, Jana M. Sulfation Effects of Chondroitin Sulfate to Bind a Chemokine in Aqueous Medium: Conformational Heterogeneity and Dynamics from Molecular Simulation. J Chem Inf Model 2023; 63:5660-5675. [PMID: 37611186 DOI: 10.1021/acs.jcim.3c00668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
The sulfation patterns and degree of sulfation of chondroitin sulfate (CS), an important class of glycosaminoglycans (GAG), and their interactions with chemokines are accountable for various diseases. To realize the underlying mechanism of such complex biological phenomena at a molecular level and their application in rational drug design, a study on conformations and dynamics of CSs is necessary. To explore this, in this study, we performed a series of atomistic molecular dynamics (MD) simulations with different sulfated variants of octadecasaccharide CS, like CS-C, CS-E, and CS-T, in their free forms and when bound to the protein chemokine CXCL8 dimer in an aqueous medium. The calculated binding free energy of CSs with the CXCL8 dimer is favorable, and the degree of sulfation favors the complexation process further with prominent hydrophobic and hydrogen-bonded interactions. We find that the recognition is associated with the configurational entropy loss of the CS molecules as calculated from the Gaussian mixture approach, which supports that the degree of sulfation regulates the process. Cluster analysis through the k-means algorithm and end-to-end distance measurement revealed that although the free CS molecules adopted linear conformations, the nonlinear conformations during binding with protein were noted. Adaptation of nonlinear forms in the bound forms is noteworthy for the less-sulfated CS-C and CS-E. Apart from favorable 4C1 conformations, the occasional appearance of skew-boat forms from the free-energy map of ring pucker for the GlcUA unit was observed, which remains unaffected by the sulfation. We find that during recognition, the average relaxation time of intra-CS and inter-CS-CXCL8 hydrogen bonds (HBs) is about a magnitude lesser than that of CS-water HBs, most prominent on the involvement of higher sulfated CS-T analogues. The translational motion of surrounded water molecules in CSs exhibited sublinear diffusion, and the degree of sublinearity increases around the heavily sulfated molecules due to the hindrance created by them as well as the presence of the chemokine and exhibited markedly slow heterogeneous diffusion.
Collapse
Affiliation(s)
- Shakuntala Dhurua
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela 769008, India
| | - Madhurima Jana
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela 769008, India
| |
Collapse
|
15
|
Waseem T, Ahmed M, Rajput TA, Babar MM. Molecular implications of glycosaminoglycans in diabetes pharmacotherapy. Int J Biol Macromol 2023; 247:125821. [PMID: 37467830 DOI: 10.1016/j.ijbiomac.2023.125821] [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: 02/05/2023] [Revised: 06/26/2023] [Accepted: 07/11/2023] [Indexed: 07/21/2023]
Abstract
Diabetes mellitus causes a wide range of metabolic derangements with multiple organ damage. The microvascular and macrovascular complications of diabetes result partly from the damage to the glycosaminoglycans (GAG) in the basement membrane. GAGs are negatively charged polysaccharides with repeating disaccharide units. They play a significant role in cellular proliferation and signal transduction. Destruction of extracellular matrix results in diseases in various organs including myocardial fibrosis, retinal damage and nephropathy. To substitute the natural GAGs pharmacotherapeutically, they have been synthesized by using basic disaccharide units. Among the four classes of GAGs, heparin is the most widely studied. Recent studies have revealed multiple significant GAG-protein interactions suggesting their use for the management of diabetic complications. Moreover, they can act as biomarkers for assessing the disease progression. A number of GAG-based therapeutic agents are being evaluated for managing diabetic complications. The current review provides an outline of the role of GAGs in diabetes while covering their interaction with different molecular players that can serve as targets for the diagnosis, management and prevention of diabetes and its complications. The medicinal chemistry and clinical pharmacotherapeutics aspects have are covered to aid in the establishment of GAG-based therapies as a possible avenue for diabetes.
Collapse
Affiliation(s)
- Tanya Waseem
- Department of Pharmaceutical Chemistry, Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad 44000, Pakistan
| | - Madiha Ahmed
- Department of Pharmaceutical Chemistry, Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad 44000, Pakistan
| | - Tausif Ahmed Rajput
- Department of Pharmaceutical Chemistry, Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad 44000, Pakistan
| | - Mustafeez Mujtaba Babar
- Department of Basic Medical Sciences, Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad 44000, Pakistan.
| |
Collapse
|
16
|
Muraleedharan A, Vanderperre B. The endo-lysosomal system in Parkinson's disease: expanding the horizon. J Mol Biol 2023:168140. [PMID: 37148997 DOI: 10.1016/j.jmb.2023.168140] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 04/22/2023] [Accepted: 04/27/2023] [Indexed: 05/08/2023]
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disorder after Alzheimer's disease, and its prevalence is increasing with age. A wealth of genetic evidence indicates that the endo-lysosomal system is a major pathway driving PD pathogenesis with a growing number of genes encoding endo-lysosomal proteins identified as risk factors for PD, making it a promising target for therapeutic intervention. However, detailed knowledge and understanding of the molecular mechanisms linking these genes to the disease are available for only a handful of them (e.g. LRRK2, GBA1, VPS35). Taking on the challenge of studying poorly characterized genes and proteins can be daunting, due to the limited availability of tools and knowledge from previous literature. This review aims at providing a valuable source of molecular and cellular insights into the biology of lesser-studied PD-linked endo-lysosomal genes, to help and encourage researchers in filling the knowledge gap around these less popular genetic players. Specific endo-lysosomal pathways discussed range from endocytosis, sorting, and vesicular trafficking to the regulation of membrane lipids of these membrane-bound organelles and the specific enzymatic activities they contain. We also provide perspectives on future challenges that the community needs to tackle and propose approaches to move forward in our understanding of these poorly studied endo-lysosomal genes. This will help harness their potential in designing innovative and efficient treatments to ultimately re-establish neuronal homeostasis in PD but also other diseases involving endo-lysosomal dysfunction.
Collapse
Affiliation(s)
- Amitha Muraleedharan
- Centre d'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois and Biological Sciences Department, Université du Québec à Montréal
| | - Benoît Vanderperre
- Centre d'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois and Biological Sciences Department, Université du Québec à Montréal
| |
Collapse
|
17
|
Cell–scaffold interactions in tissue engineering for oral and craniofacial reconstruction. Bioact Mater 2023; 23:16-44. [DOI: 10.1016/j.bioactmat.2022.10.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/22/2022] [Accepted: 10/30/2022] [Indexed: 11/09/2022] Open
|
18
|
Gilliland HN, Beckman OK, Olive AJ. A Genome-Wide Screen in Macrophages Defines Host Genes Regulating the Uptake of Mycobacterium abscessus. mSphere 2023; 8:e0066322. [PMID: 36794958 PMCID: PMC10117111 DOI: 10.1128/msphere.00663-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 01/26/2023] [Indexed: 02/17/2023] Open
Abstract
The interactions between a host cell and a pathogen can dictate disease outcomes and are important targets for host-directed therapies. Mycobacterium abscessus (Mab) is a highly antibiotic resistant, rapidly growing nontuberculous mycobacterium that infects patients with chronic lung diseases. Mab can infect host immune cells, such as macrophages, which contribute to its pathogenesis. However, our understanding of initial host-Mab interactions remains unclear. Here, we developed a functional genetic approach to define these host-Mab interactions by coupling a Mab fluorescent reporter with a genome-wide knockout library in murine macrophages. We used this approach to conduct a forward genetic screen to define host genes that contribute to the uptake of Mab by macrophages. We identified known regulators of phagocytosis, such as the integrin ITGB2, and uncovered a key requirement for glycosaminoglycan (sGAG) synthesis for macrophages to efficiently take up Mab. CRISPR-Cas9 targeting of three key sGAG biosynthesis regulators, Ugdh, B3gat3, and B4galt7 resulted in reduced uptake of both smooth and rough Mab variants by macrophages. Mechanistic studies suggest that sGAGs function upstream of pathogen engulfment and are required for the uptake of Mab, but not Escherichia coli or latex beads. Further investigation found that the loss of sGAGs reduced the surface expression, but not the mRNA expression, of key integrins, suggesting an important role for sGAGs in modulating surface receptor availability. Together, these studies globally define and characterize important regulators of macrophage-Mab interactions and are a first step to understanding host genes that contribute to Mab pathogenesis and disease. IMPORTANCE Pathogen interactions with immune cells like macrophages contribute to pathogenesis, yet the mechanisms underlying these interactions remain largely undefined. For emerging respiratory pathogens, like Mycobacterium abscessus, understanding these host-pathogen interactions is important to fully understand disease progression. Given that M. abscessus is broadly recalcitrant to antibiotic treatments, new therapeutic approaches are needed. Here, we leveraged a genome-wide knockout library in murine macrophages to globally define host genes required for M. abscessus uptake. We identified new macrophage uptake regulators during M. abscessus infection, including a subset of integrins and the glycosaminoglycan synthesis (sGAG) pathway. While ionic characteristics of sGAGs are known to drive pathogen-cell interactions, we discovered a previously unrecognized requirement for sGAGs to maintain robust surface expression of key uptake receptors. Thus, we developed a flexible forward-genetic pipeline to define important interactions during M. abscessus infection and more broadly identified a new mechanism by which sGAGs control pathogen uptake.
Collapse
Affiliation(s)
- Haleigh N. Gilliland
- Department of Microbiology and Molecular Genetics, College of Osteopathic Medicine, Michigan State University, East Lansing, Michigan, USA
| | - Olivia K. Beckman
- Department of Microbiology and Molecular Genetics, College of Osteopathic Medicine, Michigan State University, East Lansing, Michigan, USA
| | - Andrew J. Olive
- Department of Microbiology and Molecular Genetics, College of Osteopathic Medicine, Michigan State University, East Lansing, Michigan, USA
| |
Collapse
|
19
|
Marcisz M, Samsonov SA. Solvent Model Benchmark for Molecular Dynamics of Glycosaminoglycans. J Chem Inf Model 2023; 63:2147-2157. [PMID: 36989082 PMCID: PMC10091405 DOI: 10.1021/acs.jcim.2c01472] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
In computational studies of glycosaminoglycans (GAGs), a group of anionic, periodic linear polysaccharides, so far there has been very little discussion about the role of solvent models in the molecular dynamics simulations of these molecules. Predominantly, the TIP3P water model is commonly used as one of the most popular explicit water models in general. However, there are numerous alternative explicit and implicit water models that are neglected in the computational research of GAGs. Since solvent-mediated interactions are particularly important for GAG dynamic and structural properties, it would be of great interest for the GAG community to establish the solvent model that is suited the best in terms of the quality of theoretically obtained GAG parameters and, at the same time, would be reasonably demanding in terms of computational resources required. In this study, heparin (HP) was simulated using five implicit and six explicit solvent models with the aim to find out how different solvent models influence HP's molecular descriptors in the molecular dynamics simulations. Here, we initiate the search for the most appropriate solvent representation for GAG systems and we hope to encourage other groups to contribute to this highly relevant subject.
Collapse
Affiliation(s)
- Mateusz Marcisz
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
- Intercollegiate Faculty of Biotechnology of UG and MUG, ul. Abrahama 58, 80-307 Gdańsk, Poland
| | - Sergey A Samsonov
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| |
Collapse
|
20
|
Richards TL, Burron S, Ma DWL, Pearson W, Trevizan L, Minikhiem D, Grant C, Patterson K, Shoveller AK. Effects of dietary camelina, flaxseed, and canola oil supplementation on inflammatory and oxidative markers, transepidermal water loss, and coat quality in healthy adult dogs. Front Vet Sci 2023; 10:1085890. [PMID: 36968475 PMCID: PMC10034026 DOI: 10.3389/fvets.2023.1085890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 02/10/2023] [Indexed: 03/11/2023] Open
Abstract
IntroductionCamelina oil contains a greater concentration of omega-3 (n-3) a-linolenic acid (C18:3n-3; ALA) than omega-6 (n-6) linoleic acid (C18:2n-6; LA), in comparison to alternative fat sources commonly used to formulate canine diets. Omega-3 FAs are frequently used to support canine skin and coat health claims and reduce inflammation and oxidative stress; however, there is a lack of research investigating camelina oil supplementation and its effects on these applications in dogs. The objective of this study was to evaluate the effects of camelina oil supplementation on coat quality, skin barrier function, and circulating inflammatory and oxidative marker concentrations.MethodsThirty healthy [17 females; 13 males; 7.2 ± 3.1 years old; 27.4 ± 14.0 kg body weight (BW)] privately-owned dogs of various breeds were used. After a 4-week wash-in period consuming sunflower oil (n6:n3 = 1:0) and a commercial kibble, dogs were blocked by age, breed, and size, and randomly assigned to one of three treatment oils: camelina (n6:n3 = 1:1.18), canola (n6:n3 = 1:0.59), flaxseed (n6:n3 = 1:4.19) (inclusion level: 8.2 g oil/100 g of total food intake) in a randomized complete block design. Transepidermal water loss (TEWL) was measured using a VapoMeter on the pinna, paw pad, and inner leg. Fasted blood samples were collected to measure serum inflammatory and oxidative marker concentrations using enzyme-linked immunosorbent assay (ELISA) kits and spectrophotometric assays. A 5-point-Likert scale was used to assess coat characteristics. All data were collected on weeks 0, 2, 4, 10, and 16 and analyzed using PROC GLIMMIX in SAS.ResultsNo significant changes occurred in TEWL, or inflammatory and oxidative marker concentrations among treatments, across weeks, or for treatment by week interactions. Softness, shine, softness uniformity, color intensity, and follicle density of the coat increased from baseline in all treatment groups (P < 0.05).DiscussionOutcomes did not differ (P > 0.05) among treatment groups over 16-weeks, indicating that camelina oil is comparable to existing plant-based canine oil supplements, flaxseed, and canola, at supporting skin and coat health and inflammation in dogs. Future research employing an immune or exercise challenge is warranted, as the dogs in this study were not subjected to either.
Collapse
Affiliation(s)
- Taylor L. Richards
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Scarlett Burron
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - David W. L. Ma
- Department of Human Health and Nutritional Sciences, University of Guelph, Guelph, ON, Canada
| | - Wendy Pearson
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Luciano Trevizan
- Department of Animal Science, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Caitlin Grant
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Keely Patterson
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Anna K. Shoveller
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
- *Correspondence: Anna K. Shoveller
| |
Collapse
|
21
|
Laniel A, Marouseau É, Nguyen DT, Froehlich U, McCartney C, Boudreault PL, Lavoie C. Characterization of PGua 4, a Guanidinium-Rich Peptoid that Delivers IgGs to the Cytosol via Macropinocytosis. Mol Pharm 2023; 20:1577-1590. [PMID: 36781165 PMCID: PMC9997486 DOI: 10.1021/acs.molpharmaceut.2c00783] [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: 09/15/2022] [Revised: 01/19/2023] [Accepted: 01/19/2023] [Indexed: 02/15/2023]
Abstract
To investigate the structure-cellular penetration relationship of guanidinium-rich transporters (GRTs), we previously designed PGua4, a five-amino acid peptoid containing a conformationally restricted pattern of eight guanidines, which showed high cell-penetrating abilities and low cell toxicity. Herein, we characterized the cellular uptake selectivity, internalization pathway, and intracellular distribution of PGua4, as well as its capacity to deliver cargo. PGua4 exhibits higher penetration efficiency in HeLa cells than in six other cell lines (A549, Caco-2, fibroblast, HEK293, Mia-PaCa2, and MCF7) and is mainly internalized by clathrin-mediated endocytosis and macropinocytosis. Confocal microscopy showed that it remained trapped in endosomes at low concentrations but induced pH-dependent endosomal membrane destabilization at concentrations ≥10 μM, allowing its diffusion into the cytoplasm. Importantly, PGua4 significantly enhanced macropinocytosis and the cellular uptake and cytosolic delivery of large IgGs following noncovalent complexation. Therefore, in addition to its peptoid nature conferring high resistance to proteolysis, PGua4 presents characteristics of a promising tool for IgG delivery and therapeutic applications.
Collapse
Affiliation(s)
- Andréanne Laniel
- Institut de Pharmacologie
de Sherbrooke, Department of Pharmacology and Physiology, Faculty
of Medicine and Health Sciences, Université
de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
| | - Étienne Marouseau
- Institut de Pharmacologie
de Sherbrooke, Department of Pharmacology and Physiology, Faculty
of Medicine and Health Sciences, Université
de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
| | - Duc Tai Nguyen
- Institut de Pharmacologie
de Sherbrooke, Department of Pharmacology and Physiology, Faculty
of Medicine and Health Sciences, Université
de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
| | - Ulrike Froehlich
- Institut de Pharmacologie
de Sherbrooke, Department of Pharmacology and Physiology, Faculty
of Medicine and Health Sciences, Université
de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
| | - Claire McCartney
- Institut de Pharmacologie
de Sherbrooke, Department of Pharmacology and Physiology, Faculty
of Medicine and Health Sciences, Université
de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
| | - Pierre-Luc Boudreault
- Institut de Pharmacologie
de Sherbrooke, Department of Pharmacology and Physiology, Faculty
of Medicine and Health Sciences, Université
de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
| | - Christine Lavoie
- Institut de Pharmacologie
de Sherbrooke, Department of Pharmacology and Physiology, Faculty
of Medicine and Health Sciences, Université
de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
| |
Collapse
|
22
|
Solis-Cordova J, Edwards JH, Fermor HL, Riches P, Brockett CL, Herbert A. Characterisation of native and decellularised porcine tendon under tension and compression: A closer look at glycosaminoglycan contribution to tendon mechanics. J Mech Behav Biomed Mater 2023; 139:105671. [PMID: 36682172 DOI: 10.1016/j.jmbbm.2023.105671] [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: 09/29/2022] [Revised: 11/17/2022] [Accepted: 01/07/2023] [Indexed: 01/13/2023]
Abstract
Decellularised porcine superflexor tendon (pSFT) has been characterised as a suitable scaffold for anterior cruciate ligament replacement, with dimensions similar to hamstring tendon autograft. However, decellularisation of tissues may reduce or damage extracellular matrix components, leading to undesirable biomechanical changes at a whole tissue scale. Although the role of collagen in tendons is well established, the mechanical contribution of glycosaminoglycans (GAGs) is less evident and could be altered by the decellularisation process. In this study, the contribution of GAGs to the tensile and compressive mechanical properties of pSFT was determined and whether decellularisation affected these properties by reducing GAG content or functionality. PSFTs were either enzymatically treated using chondroitinase ABC to remove GAGs or decellularised using previously established methods. Native, GAG-depleted and decellularised pSFT groups were then subjected to quantitative assays and biomechanical characterisation. In tension, specimens underwent stress relaxation and strength testing. In compression, specimens underwent confined compression testing. The GAG-depleted group was found to have circa 86% reduction of GAG content compared to native and decellularised groups. There was no significant difference in GAG content between native (3.75 ± 0.58 μg/mg) and decellularised (3.40 ± 0.37 μg/mg) groups. Stress relaxation testing discovered the time-independent and time-dependent relaxation moduli of the decellularised group were reduced ≥50% compared to native and GAG-depleted groups. However, viscoelastic behaviour of native and GAG-depleted groups resulted similar. Strength testing discovered no differences between native and GAG-depleted group's properties, albeit a reduction ∼20% for decellularised specimens' linear modulus and tensile strength compared to native tissue. In compression testing, the aggregate modulus was found to be circa 74% lower in the GAG-depleted group than the native and decellularised groups, while the zero-strain permeability was significantly higher in the GAG-depleted group (0.86 ± 0.65 mm4/N) than the decellularised group (0.03 ± 0.04 mm4/N). The results indicate that GAGs may significantly contribute to the mechanical properties of pSFT in compression, but not in tension. Furthermore, the content and function of GAGs in pSFTs are unaffected by decellularisation and the mechanical properties of the tissue remain comparable to native tissue.
Collapse
Affiliation(s)
- Jacqueline Solis-Cordova
- Institute of Medical and Biological Engineering, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom; Institute of Medical and Biological Engineering, School of Mechanical Engineering, Faculty of Engineering and Physical Sciences, University of Leeds, Leeds, United Kingdom.
| | - Jennifer H Edwards
- Institute of Medical and Biological Engineering, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Hazel L Fermor
- Institute of Medical and Biological Engineering, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Philip Riches
- Department of Biomedical Engineering, Faculty of Engineering, University of Strathclyde, Wolfson Centre, Glasgow, United Kingdom
| | - Claire L Brockett
- Institute of Medical and Biological Engineering, School of Mechanical Engineering, Faculty of Engineering and Physical Sciences, University of Leeds, Leeds, United Kingdom
| | - Anthony Herbert
- Institute of Medical and Biological Engineering, School of Mechanical Engineering, Faculty of Engineering and Physical Sciences, University of Leeds, Leeds, United Kingdom
| |
Collapse
|
23
|
McQuaid C, Solorzano A, Dickerson I, Deane R. Uptake of severe acute respiratory syndrome coronavirus 2 spike protein mediated by angiotensin converting enzyme 2 and ganglioside in human cerebrovascular cells. Front Neurosci 2023; 17:1117845. [PMID: 36875642 PMCID: PMC9980911 DOI: 10.3389/fnins.2023.1117845] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/30/2023] [Indexed: 02/18/2023] Open
Abstract
Introduction There is clinical evidence of neurological manifestations in coronavirus disease-19 (COVID-19). However, it is unclear whether differences in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)/spike protein (SP) uptake by cells of the cerebrovasculature contribute to significant viral uptake to cause these symptoms. Methods Since the initial step in viral invasion is binding/uptake, we used fluorescently labeled wild type and mutant SARS-CoV-2/SP to study this process. Three cerebrovascular cell types were used (endothelial cells, pericytes, and vascular smooth muscle cells), in vitro. Results There was differential SARS-CoV-2/SP uptake by these cell types. Endothelial cells had the least uptake, which may limit SARS-CoV-2 uptake into brain from blood. Uptake was time and concentration dependent, and mediated by angiotensin converting enzyme 2 receptor (ACE2), and ganglioside (mono-sialotetrahexasylganglioside, GM1) that is predominantly expressed in the central nervous system and the cerebrovasculature. SARS-CoV-2/SPs with mutation sites, N501Y, E484K, and D614G, as seen in variants of interest, were also differentially taken up by these cell types. There was greater uptake compared to that of the wild type SARS-CoV-2/SP, but neutralization with anti-ACE2 or anti-GM1 antibodies was less effective. Conclusion The data suggested that in addition to ACE2, gangliosides are also an important entry point of SARS-CoV-2/SP into these cells. Since SARS-CoV-2/SP binding/uptake is the initial step in the viral penetration into cells, a longer exposure and higher titer are required for significant uptake into the normal brain. Gangliosides, including GM1, could be an additional potential SARS-CoV-2 and therapeutic target at the cerebrovasculature.
Collapse
Affiliation(s)
| | | | | | - Rashid Deane
- Department of Neuroscience, Del Monte Institute Neuroscience, University of Rochester, University of Rochester Medical Center (URMC), Rochester, NY, United States
| |
Collapse
|
24
|
Basu A, Weiss RJ. Glycosaminoglycan Analysis: Purification, Structural Profiling, and GAG-Protein Interactions. Methods Mol Biol 2023; 2597:159-176. [PMID: 36374421 DOI: 10.1007/978-1-0716-2835-5_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Glycosaminoglycans (GAGs) are long, linear polysaccharides that are ubiquitously expressed on the cell surface and in the extracellular matrix of all animal cells. These complex carbohydrates are composed of alternating glucosamine and uronic acids that can be heterogeneously N- and O-sulfated. The arrangement and orientation of the sulfated sugar residues specify the location of distinct ligand binding sites on the cell surface, and their capacity to bind ligands impacts cell growth and development, the ability to form tissues and organs, and normal physiology. The heterogeneous nature of GAGs and their inherent structural diversity across different tissues, cell types, and disease states creates challenges to characterizing their structure and function. Here, we describe detailed methods to investigate GAG-protein interactions in vitro and evaluate the structural composition of two classes of sulfated GAGs, heparan sulfate and chondroitin/dermatan sulfate, using liquid chromatography, mass spectrometry, and radiolabeling techniques. Overall, these methods facilitate the evaluation of GAG structure and function to uncover the unique roles these molecules play in cell biology and human disease.
Collapse
Affiliation(s)
- Amrita Basu
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Ryan J Weiss
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA.
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.
| |
Collapse
|
25
|
Eilts F, Bauer S, Fraser K, Dordick JS, Wolff MW, Linhardt RJ, Zhang F. The diverse role of heparan sulfate and other GAGs in SARS-CoV-2 infections and therapeutics. Carbohydr Polym 2023; 299:120167. [PMID: 36876764 PMCID: PMC9516881 DOI: 10.1016/j.carbpol.2022.120167] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 11/25/2022]
Abstract
In December 2019, the global coronavirus disease 2019 (COVID-19) pandemic began in Wuhan, China. COVID-19 is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which infects host cells primarily through the angiotensin-converting enzyme 2 (ACE2) receptor. In addition to ACE2, several studies have shown the importance of heparan sulfate (HS) on the host cell surface as a co-receptor for SARS-CoV-2-binding. This insight has driven research into antiviral therapies, aimed at inhibiting the HS co-receptor-binding, e.g., by glycosaminoglycans (GAGs), a family of sulfated polysaccharides that includes HS. Several GAGs, such as heparin (a highly sulfated analog of HS), are used to treat various health indications, including COVID-19. This review is focused on current research on the involvement of HS in SARS-CoV-2 infection, implications of viral mutations, as well as the use of GAGs and other sulfated polysaccharides as antiviral agents.
Collapse
Affiliation(s)
- Friederike Eilts
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA; Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen (THM), Giessen, Germany
| | - Sarah Bauer
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Keith Fraser
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Jonathan S Dordick
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA; Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA; Department of Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Michael W Wolff
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen (THM), Giessen, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
| | - Robert J Linhardt
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA; Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA; Department of Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA; Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA.
| | - Fuming Zhang
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA.
| |
Collapse
|
26
|
Marcisz M, Maszota-Zieleniak M, Samsonov SA. Repulsive Scaling Replica Exchange Molecular Dynamics in Modeling Protein-Glycosaminoglycan Complexes. Methods Mol Biol 2023; 2619:153-167. [PMID: 36662469 DOI: 10.1007/978-1-0716-2946-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Glycosaminoglycans are long linear periodic anionic polysaccharides consisting of disaccharide units exhibiting different sulfation patterns forming a highly heterogeneous group of molecules. Due to their flexibility, length, high charge, and periodicity, they are challenging for computational approaches. Despite their biological significance in terms of the important role in various diseases (e.g., Alzheimer, cancer, SARS-CoV-2) and proper cell functioning (e.g., proliferation, maturation), there is a lack of effective molecular docking tools designed specifically for glycosaminoglycans due to their challenging physical-chemical nature. In this chapter we present protocols for the Repulsive Scaling Replica Exchange Molecular Dynamics (RS-REMD) methods to dock glycosaminoglycans with both implicit and explicit solvent models implemented. This novel molecular dynamics-based replica exchange technique should help to elevate our current knowledge on the complexes and interactions between glycosaminoglycans and their protein receptors.
Collapse
Affiliation(s)
- Mateusz Marcisz
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
- Intercollegiate Faculty of Biotechnology of UG and MUG, Gdańsk, Poland
| | | | | |
Collapse
|
27
|
Sahu B, Shrama DD, Jayakumar GC, Madhan B, Zameer F. A review on an imperative by-product: Glycosaminoglycans- A Holistic approach. CARBOHYDRATE POLYMER TECHNOLOGIES AND APPLICATIONS 2022. [DOI: 10.1016/j.carpta.2022.100275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
|
28
|
Wang Q, Chi L. The Alterations and Roles of Glycosaminoglycans in Human Diseases. Polymers (Basel) 2022; 14:polym14225014. [PMID: 36433141 PMCID: PMC9694910 DOI: 10.3390/polym14225014] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/22/2022] Open
Abstract
Glycosaminoglycans (GAGs) are a heterogeneous family of linear polysaccharides which are composed of a repeating disaccharide unit. They are also linked to core proteins to form proteoglycans (PGs). GAGs/PGs are major components of the cell surface and the extracellular matrix (ECM), and they display critical roles in development, normal function, and damage response in the body. Some properties (such as expression quantity, molecular weight, and sulfation pattern) of GAGs may be altered under pathological conditions. Due to the close connection between these properties and the function of GAGs/PGs, the alterations are often associated with enormous changes in the physiological/pathological status of cells and organs. Therefore, these GAGs/PGs may serve as marker molecules of disease. This review aimed to investigate the structural alterations and roles of GAGs/PGs in a range of diseases, such as atherosclerosis, cancer, diabetes, neurodegenerative disease, and virus infection. It is hoped to provide a reference for disease diagnosis, monitoring, prognosis, and drug development.
Collapse
|
29
|
Huang C, Dong L, Zhao B, Lu Y, Huang S, Yuan Z, Luo G, Xu Y, Qian W. Anti-inflammatory hydrogel dressings and skin wound healing. Clin Transl Med 2022; 12:e1094. [PMID: 36354147 PMCID: PMC9647861 DOI: 10.1002/ctm2.1094] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 10/04/2022] [Accepted: 10/11/2022] [Indexed: 11/11/2022] Open
Abstract
Hydrogels are promising and widely utilized in the biomedical field. In recent years, the anti-inflammatory function of hydrogel dressings has been significantly improved, addressing many clinical challenges presented in ongoing endeavours to promote wound healing. Wound healing is a cascaded and highly complex process, especially in chronic wounds, such as diabetic and severe burn wounds, in which adverse endogenous or exogenous factors can interfere with inflammatory regulation, leading to the disruption of the healing process. Although insufficient wound inflammation is uncommon, excessive inflammatory infiltration is an almost universal feature of chronic wounds, which impedes a histological repair of the wound in a predictable biological step and chronological order. Therefore, resolving excessive inflammation in wound healing is essential. In the past 5 years, extensive research has been conducted on hydrogel dressings to address excessive inflammation in wound healing, specifically by efficiently scavenging excessive free radicals, sequestering chemokines and promoting M1 -to-M2 polarization of macrophages, thereby regulating inflammation and promoting wound healing. In this study, we introduced novel anti-inflammatory hydrogel dressings and demonstrated innovative methods for their preparation and application to achieve enhanced healing. In addition, we summarize the most important properties required for wound healing and discuss our analysis of potential challenges yet to be addressed.
Collapse
Affiliation(s)
- Can Huang
- Institute of Burn ResearchSouthwest HospitalState Key Laboratory of TraumaBurn and Combined InjuryChongqing Key Laboratory for Disease ProteomicsArmy Medical UniversityChongqingChina
| | - Lanlan Dong
- Institute of Burn ResearchSouthwest HospitalState Key Laboratory of TraumaBurn and Combined InjuryChongqing Key Laboratory for Disease ProteomicsArmy Medical UniversityChongqingChina
| | - Baohua Zhao
- Institute of Burn ResearchSouthwest HospitalState Key Laboratory of TraumaBurn and Combined InjuryChongqing Key Laboratory for Disease ProteomicsArmy Medical UniversityChongqingChina
| | - Yifei Lu
- Institute of Burn ResearchSouthwest HospitalState Key Laboratory of TraumaBurn and Combined InjuryChongqing Key Laboratory for Disease ProteomicsArmy Medical UniversityChongqingChina
| | - Shurun Huang
- Department of Burns and Plastic Surgerythe 910th Hospital of Joint Logistic Force of Chinese People's Liberation ArmyQuanzhouFujianChina
| | - Zhiqiang Yuan
- Institute of Burn ResearchSouthwest HospitalState Key Laboratory of TraumaBurn and Combined InjuryChongqing Key Laboratory for Disease ProteomicsArmy Medical UniversityChongqingChina
| | - Gaoxing Luo
- Institute of Burn ResearchSouthwest HospitalState Key Laboratory of TraumaBurn and Combined InjuryChongqing Key Laboratory for Disease ProteomicsArmy Medical UniversityChongqingChina
| | - Yong Xu
- Orthopedic InstituteSuzhou Medical CollegeSoochow UniversitySuzhouChina,B CUBE Center for Molecular BioengineeringTechnische Universität DresdenDresdenGermany
| | - Wei Qian
- Institute of Burn ResearchSouthwest HospitalState Key Laboratory of TraumaBurn and Combined InjuryChongqing Key Laboratory for Disease ProteomicsArmy Medical UniversityChongqingChina
| |
Collapse
|
30
|
Jiang M, Chattopadhyay AN, Li CH, Geng Y, Luther DC, Huang R, Rotello VM. Direct discrimination of cell surface glycosylation signatures using a single pH-responsive boronic acid-functionalized polymer. Chem Sci 2022; 13:12899-12905. [PMID: 36519060 PMCID: PMC9645398 DOI: 10.1039/d2sc02116a] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 10/05/2022] [Indexed: 08/05/2023] Open
Abstract
Cell surface glycans serve fundamental roles in many biological processes, including cell-cell interaction, pathogen infection, and cancer metastasis. Cancer cell surface have alternative glycosylation to healthy cells, making these changes useful hallmarks of cancer. However, the diversity of glycan structures makes glycosylation profiling very challenging, with glycan 'fingerprints' providing an important tool for assessing cell state. In this work, we utilized the pH-responsive differential binding of boronic acid (BA) moieties with cell surface glycans to generate a high-content six-channel BA-based sensor array that uses a single polymer to distinguish mammalian cell types. This sensing platform provided efficient discrimination of cancer cells and readily discriminated between Chinese hamster ovary (CHO) glycomutants, providing evidence that discrimination is glycan-driven. The BA-functionalized polymer sensor array is readily scalable, providing access to new diagnostic and therapeutic strategies for cell surface glycosylation-associated diseases.
Collapse
Affiliation(s)
- Mingdi Jiang
- Department of Chemistry, University of Massachusetts Amherst 710 N. Pleasant St. Amherst MA 01003 USA
| | - Aritra Nath Chattopadhyay
- Department of Chemistry, University of Massachusetts Amherst 710 N. Pleasant St. Amherst MA 01003 USA
| | - Cheng Hsuan Li
- Department of Chemistry, University of Massachusetts Amherst 710 N. Pleasant St. Amherst MA 01003 USA
| | - Yingying Geng
- Department of Chemistry, University of Massachusetts Amherst 710 N. Pleasant St. Amherst MA 01003 USA
| | - David C Luther
- Department of Chemistry, University of Massachusetts Amherst 710 N. Pleasant St. Amherst MA 01003 USA
| | - Rui Huang
- Department of Chemistry, University of Massachusetts Amherst 710 N. Pleasant St. Amherst MA 01003 USA
| | - Vincent M Rotello
- Department of Chemistry, University of Massachusetts Amherst 710 N. Pleasant St. Amherst MA 01003 USA
| |
Collapse
|
31
|
Shikina E, Kovalevsky R, Shirkovskaya A, Toukach P. Prospective bacterial and fungal sources of hyaluronic acid: A review. Comput Struct Biotechnol J 2022; 20:6214-6236. [PMID: 36420162 PMCID: PMC9676211 DOI: 10.1016/j.csbj.2022.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/05/2022] [Accepted: 11/05/2022] [Indexed: 11/11/2022] Open
Abstract
The unique biological and rheological properties make hyaluronic acid a sought-after material for medicine and cosmetology. Due to very high purity requirements for hyaluronic acid in medical applications, the profitability of streptococcal fermentation is reduced. Production of hyaluronic acid by recombinant systems is considered a promising alternative. Variations in combinations of expressed genes and fermentation conditions alter the yield and molecular weight of produced hyaluronic acid. This review is devoted to the current state of hyaluronic acid production by recombinant bacterial and fungal organisms.
Collapse
|
32
|
Kruszewska N, Mazurkiewicz A, Szala G, Słomion M. Characterization of Synovial Fluid Components: Albumin-Chondroitin Sulfate Interactions Seen through Molecular Dynamics. MATERIALS (BASEL, SWITZERLAND) 2022; 15:6935. [PMID: 36234275 PMCID: PMC9572199 DOI: 10.3390/ma15196935] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/28/2022] [Accepted: 10/01/2022] [Indexed: 06/16/2023]
Abstract
The friction coefficient of articular cartilage (AC) is very low. A method of producing tailor-made materials with even similar lubrication properties is still a challenge. The physicochemical reasons for such excellent lubrication properties of AC are still not fully explained; however, a crucial factor seems to be synergy between synovial fluid (SF) components. As a stepping stone to being able to produce innovative materials characterized by a very low friction coefficient, we studied the interactions between two important components of SF: human serum albumin (HSA) and chondroitin sulfate (CS). The molecular dynamics method, preceded by docking, is used in the study. Interactions of HSA with two types of CS (IV and VI), with the addition of three types of ions often found in physiological solutions: Ca2+, Na+, and Mg2+, are compared. It was found that there were differences in the energy of binding values and interaction maps between CS-4 and CS-6 complexes. HSA:CS-4 complexes were bound stronger than in the case of HSA:CS-6 because more interactions were formed across all types of interactions except one-the only difference was for ionic bridges, which were more often found in HSA:CS-6 complexes. RMSD and RMSF indicated that complexes HSA:CS-4 behave much more stably than HSA:CS-6. The type of ions added to the solution was also very important and changed the interaction map. However, the biggest difference was caused by the addition of Ca2+ ions which were prone to form ionic bridges.
Collapse
Affiliation(s)
- Natalia Kruszewska
- Institute of Mathematics and Physics, Bydgoszcz University of Science and Technology, Kaliskiego 7 Street, 85-796 Bydgoszcz, Poland
| | - Adam Mazurkiewicz
- Faculty of Mechanical Engineering, Bydgoszcz University of Science and Technology, Kaliskiego 7 Street, 85-796 Bydgoszcz, Poland
| | - Grzegorz Szala
- Faculty of Mechanical Engineering, Bydgoszcz University of Science and Technology, Kaliskiego 7 Street, 85-796 Bydgoszcz, Poland
| | - Małgorzata Słomion
- Faculty of Management, Bydgoszcz University of Science and Technology, Kaliskiego 7 Street, 85-796 Bydgoszcz, Poland
| |
Collapse
|
33
|
Denamur S, Chazeirat T, Maszota-Zieleniak M, Vivès RR, Saidi A, Zhang F, Linhardt RJ, Labarthe F, Samsonov SA, Lalmanach G, Lecaille F. Binding of heparan sulfate to human cystatin C modulates inhibition of cathepsin L: Putative consequences in mucopolysaccharidosis. Carbohydr Polym 2022; 293:119734. [DOI: 10.1016/j.carbpol.2022.119734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/30/2022] [Accepted: 06/11/2022] [Indexed: 11/02/2022]
|
34
|
Menezes R, Vincent R, Osorno L, Hu P, Arinzeh TL. Biomaterials and Tissue Engineering Approaches using Glycosaminoglycans for Tissue Repair: Lessons Learned from the Native Extracellular Matrix. Acta Biomater 2022; 163:210-227. [PMID: 36182056 PMCID: PMC10043054 DOI: 10.1016/j.actbio.2022.09.064] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 09/13/2022] [Accepted: 09/23/2022] [Indexed: 01/30/2023]
Abstract
Glycosaminoglycans (GAGs) are an important component of the extracellular matrix as they influence cell behavior and have been sought for tissue regeneration, biomaterials, and drug delivery applications. GAGs are known to interact with growth factors and other bioactive molecules and impact tissue mechanics. This review will provide an overview of native GAGs, their structure, and properties, specifically their interaction with proteins, their effect on cell behavior, and their mechanical role in the ECM. GAGs' function in the extracellular environment is still being understood however, promising studies have led to the development of medical devices and therapies. Native GAGs, including hyaluronic acid, chondroitin sulfate, and heparin, have been widely explored in tissue engineering and biomaterial approaches for tissue repair or replacement. This review will focus on orthopaedic and wound healing applications. The use of GAGs in these applications have had significant advances leading to clinical use. Promising studies using GAG mimetics and future directions will also be discussed. STATEMENT OF SIGNIFICANCE: Glycosaminoglycans (GAGs) are an important component of the native extracellular matrix and have shown promise in medical devices and therapies. This review emphasizes the structure and properties of native GAGs, their role in the ECM providing biochemical and mechanical cues that influence cell behavior, and their use in tissue regeneration and biomaterial approaches for orthopaedic and wound healing applications.
Collapse
Affiliation(s)
- Roseline Menezes
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ 07102
| | - Richard Vincent
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ 07102
| | - Laura Osorno
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ 07102
| | - Phillip Hu
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ 07102
| | - Treena Livingston Arinzeh
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ 07102; Department of Biomedical Engineering, Columbia University, New York, NY 10027.
| |
Collapse
|
35
|
Shi D, He P, Song Y, Cheng S, Linhardt RJ, Dordick JS, Chi L, Zhang F. Kinetic and Structural Aspects of Glycosaminoglycan-Monkeypox Virus Protein A29 Interactions Using Surface Plasmon Resonance. Molecules 2022; 27:5898. [PMID: 36144634 PMCID: PMC9503980 DOI: 10.3390/molecules27185898] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/05/2022] [Accepted: 09/08/2022] [Indexed: 12/02/2022] Open
Abstract
Monkeypox virus (MPXV), a member of the Orthopoxvirus genus, has begun to spread into many countries worldwide. While the prevalence of monkeypox in Central and Western Africa is well-known, the recent rise in the number of cases spread through intimate personal contact, particularly in the United States, poses a grave international threat. Previous studies have shown that cell-surface heparan sulfate (HS) is important for vaccinia virus (VACV) infection, particularly the binding of VACV A27, which appears to mediate the binding of virus to cellular HS. Some other glycosaminoglycans (GAGs) also bind to proteins on Orthopoxviruses. In this study, by using surface plasmon resonance, we demonstrated that MPXV A29 protein (a homolog of VACV A27) binds to GAGs including heparin and chondroitin sulfate/dermatan sulfate. The negative charges on GAGs are important for GAG-MPXV A29 interaction. GAG analogs, pentosan polysulfate and mucopolysaccharide polysulfate, show strong inhibition of MPXV A29-heparin interaction. A detailed understanding on the molecular interactions involved in this disease should accelerate the development of therapeutics and drugs for the treatment of MPXV.
Collapse
Affiliation(s)
- Deling Shi
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, China
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Peng He
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Yuefan Song
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Shuihong Cheng
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Robert J. Linhardt
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Jonathan S. Dordick
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Lianli Chi
- National Glycoengineering Research Center, Shandong University, Qingdao 266237, China
| | - Fuming Zhang
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| |
Collapse
|
36
|
Hoffmann M, Snyder NL, Hartmann L. Polymers Inspired by Heparin and Heparan Sulfate for Viral Targeting. Macromolecules 2022; 55:7957-7973. [PMID: 36186574 PMCID: PMC9520969 DOI: 10.1021/acs.macromol.2c00675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 08/12/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Miriam Hoffmann
- Department of Organic Chemistry and Macromolecular Chemistry, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Nicole L. Snyder
- Department of Chemistry, Davidson College, Davidson, North Carolina 28035, United States
| | - Laura Hartmann
- Department of Organic Chemistry and Macromolecular Chemistry, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| |
Collapse
|
37
|
The Key Role of Lysosomal Protease Cathepsins in Viral Infections. Int J Mol Sci 2022; 23:ijms23169089. [PMID: 36012353 PMCID: PMC9409221 DOI: 10.3390/ijms23169089] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 11/17/2022] Open
Abstract
Cathepsins encompass a family of lysosomal proteases that mediate protein degradation and turnover. Although mainly localized in the endolysosomal compartment, cathepsins are also found in the cytoplasm, nucleus, and extracellular space, where they are involved in cell signaling, extracellular matrix assembly/disassembly, and protein processing and trafficking through the plasma and nuclear membrane and between intracellular organelles. Ubiquitously expressed in the body, cathepsins play regulatory roles in a wide range of physiological processes including coagulation, hormone secretion, immune responses, and others. A dysregulation of cathepsin expression and/or activity has been associated with many human diseases, including cancer, diabetes, obesity, cardiovascular and inflammatory diseases, kidney dysfunctions, and neurodegenerative disorders, as well as infectious diseases. In viral infections, cathepsins may promote (1) activation of the viral attachment glycoproteins and entry of the virus into target cells; (2) antigen processing and presentation, enabling the virus to replicate in infected cells; (3) up-regulation and processing of heparanase that facilitates the release of viral progeny and the spread of infection; and (4) activation of cell death that may either favor viral clearance or assist viral propagation. In this review, we report the most relevant findings on the molecular mechanisms underlying cathepsin involvement in viral infection physiopathology, and we discuss the potential of cathepsin inhibitors for therapeutical applications in viral infectious diseases.
Collapse
|
38
|
Marcisz M, Gaardløs M, Bojarski KK, Siebenmorgen T, Zacharias M, Samsonov SA. Explicit solvent repulsive scaling replica exchange molecular dynamics (RS-REMD) in molecular modeling of protein-glycosaminoglycan complexes. J Comput Chem 2022; 43:1633-1640. [PMID: 35796487 DOI: 10.1002/jcc.26965] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 11/10/2022]
Abstract
Glycosaminoglcyans (GAGs), linear anionic periodic polysaccharides, are crucial for many biologically relevant functions in the extracellular matrix. By interacting with proteins GAGs mediate processes such as cancer development, cell proliferation and the onset of neurodegenerative diseases. Despite this eminent importance of GAGs, they still represent a limited focus for the computational community in comparison to other classes of biomolecules. Therefore, there is a lack of modeling tools designed specifically for docking GAGs. One has to rely on existing docking software developed mostly for small drug molecules substantially differing from GAGs in their basic physico-chemical properties. In this study, we present an updated protocol for docking GAGs based on the Repulsive Scaling Replica Exchange Molecular Dynamics (RS-REMD) that includes explicit solvent description. The use of this water model improved docking performance both in terms of its accuracy and speed. This method represents a significant computational progress in GAG-related research.
Collapse
Affiliation(s)
- Mateusz Marcisz
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland.,Intercollegiate Faculty of Biotechnology, Universuty of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | | | - Krzysztof K Bojarski
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland.,Department of Physical Chemistry, Gdańsk University of Technology, Gdańsk, Poland
| | - Till Siebenmorgen
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Martin Zacharias
- Physics Department, Technical University of Munich, Garching, Germany
| | | |
Collapse
|
39
|
Application of biomolecules modification strategies on PEEK and its composites for osteogenesis and antibacterial properties. Colloids Surf B Biointerfaces 2022; 215:112492. [PMID: 35430485 DOI: 10.1016/j.colsurfb.2022.112492] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/24/2022] [Accepted: 04/04/2022] [Indexed: 12/24/2022]
Abstract
As orthopedic and dental implants, polyetheretherketone (PEEK) is expected to be a common substitute material of titanium (Ti) and its alloys due to its good biocompatibility, chemical stability, and elastic modulus close to that of bone tissue. It could avoid metal allergy and bone resorption caused by the stress shielding effect of Ti implants, widely studied in the medical field. However, the lack of biological activity is not conducive to the clinical application of PEEK implants. Therefore, the surface modification of PEEK has increasingly become one of the research hotspots. Researchers have explored various biomolecules modification methods to effectively enhance the osteogenic and antibacterial activities of PEEK and its composites. Therefore, this review mainly summarizes the recent research of PEEK modified by biomolecules and discusses the further research directions to promote the clinical transformation of PEEK implants.
Collapse
|
40
|
Pedersen LC, Yi M, Pedersen LG, Kaminski AM. From Steroid and Drug Metabolism to Glycobiology, Using Sulfotransferase Structures to Understand and Tailor Function. Drug Metab Dispos 2022; 50:1027-1041. [PMID: 35197313 PMCID: PMC10753775 DOI: 10.1124/dmd.121.000478] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 12/06/2021] [Indexed: 11/22/2022] Open
Abstract
Sulfotransferases are ubiquitous enzymes that transfer a sulfo group from the universal cofactor donor 3'-phosphoadenosine 5'-phosphosulfate to a broad range of acceptor substrates. In humans, the cytosolic sulfotransferases are involved in the sulfation of endogenous compounds such as steroids, neurotransmitters, hormones, and bile acids as well as xenobiotics including drugs, toxins, and environmental chemicals. The Golgi associated membrane-bound sulfotransferases are involved in post-translational modification of macromolecules from glycosaminoglycans to proteins. The sulfation of small molecules can have profound biologic effects on the functionality of the acceptor, including activation, deactivation, or enhanced metabolism and elimination. Sulfation of macromolecules has been shown to regulate a number of physiologic and pathophysiological pathways by enhancing binding affinity to regulatory proteins or binding partners. Over the last 25 years, crystal structures of these enzymes have provided a wealth of information on the mechanisms of this process and the specificity of these enzymes. This review will focus on the general commonalities of the sulfotransferases, from enzyme structure to catalytic mechanism as well as providing examples into how structural information is being used to either design drugs that inhibit sulfotransferases or to modify the enzymes to improve drug synthesis. SIGNIFICANCE STATEMENT: This manuscript honors Dr. Masahiko Negishi's contribution to the understanding of sulfotransferase mechanism, specificity, and roles in biology by analyzing the crystal structures that have been solved over the last 25 years.
Collapse
Affiliation(s)
- Lars C Pedersen
- Genome Integrity and Structural Biology Laboratory (L.C.P., L.G.P., A.M.K.) and Reproductive and Developmental Biology Laboratory (M.Y.), National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina; and Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (L.G.P.)
| | - MyeongJin Yi
- Genome Integrity and Structural Biology Laboratory (L.C.P., L.G.P., A.M.K.) and Reproductive and Developmental Biology Laboratory (M.Y.), National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina; and Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (L.G.P.)
| | - Lee G Pedersen
- Genome Integrity and Structural Biology Laboratory (L.C.P., L.G.P., A.M.K.) and Reproductive and Developmental Biology Laboratory (M.Y.), National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina; and Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (L.G.P.)
| | - Andrea M Kaminski
- Genome Integrity and Structural Biology Laboratory (L.C.P., L.G.P., A.M.K.) and Reproductive and Developmental Biology Laboratory (M.Y.), National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina; and Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (L.G.P.)
| |
Collapse
|
41
|
De Masi R, Orlando S. GANAB and N-Glycans Substrates Are Relevant in Human Physiology, Polycystic Pathology and Multiple Sclerosis: A Review. Int J Mol Sci 2022; 23:7373. [PMID: 35806376 PMCID: PMC9266668 DOI: 10.3390/ijms23137373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/22/2022] [Accepted: 06/28/2022] [Indexed: 11/29/2022] Open
Abstract
Glycans are one of the four fundamental macromolecular components of living matter, and they are highly regulated in the cell. Their functions are metabolic, structural and modulatory. In particular, ER resident N-glycans participate with the Glc3Man9GlcNAc2 highly conserved sequence, in protein folding process, where the physiological balance between glycosylation/deglycosylation on the innermost glucose residue takes place, according GANAB/UGGT concentration ratio. However, under abnormal conditions, the cell adapts to the glucose availability by adopting an aerobic or anaerobic regimen of glycolysis, or to external stimuli through internal or external recognition patterns, so it responds to pathogenic noxa with unfolded protein response (UPR). UPR can affect Multiple Sclerosis (MS) and several neurological and metabolic diseases via the BiP stress sensor, resulting in ATF6, PERK and IRE1 activation. Furthermore, the abnormal GANAB expression has been observed in MS, systemic lupus erythematous, male germinal epithelium and predisposed highly replicating cells of the kidney tubules and bile ducts. The latter is the case of Polycystic Liver Disease (PCLD) and Polycystic Kidney Disease (PCKD), where genetically induced GANAB loss affects polycystin-1 (PC1) and polycystin-2 (PC2), resulting in altered protein quality control and cyst formation phenomenon. Our topics resume the role of glycans in cell physiology, highlighting the N-glycans one, as a substrate of GANAB, which is an emerging key molecule in MS and other human pathologies.
Collapse
Affiliation(s)
- Roberto De Masi
- Complex Operative Unit of Neurology, “F. Ferrari” Hospital, Casarano, 73042 Lecce, Italy;
- Laboratory of Neuroproteomics, Multiple Sclerosis Centre, “F. Ferrari” Hospital, Casarano, 73042 Lecce, Italy
| | - Stefania Orlando
- Laboratory of Neuroproteomics, Multiple Sclerosis Centre, “F. Ferrari” Hospital, Casarano, 73042 Lecce, Italy
| |
Collapse
|
42
|
Heparin: An old drug for new clinical applications. Carbohydr Polym 2022; 295:119818. [DOI: 10.1016/j.carbpol.2022.119818] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/26/2022] [Accepted: 06/28/2022] [Indexed: 12/23/2022]
|
43
|
Sagulkoo P, Chuntakaruk H, Rungrotmongkol T, Suratanee A, Plaimas K. Multi-Level Biological Network Analysis and Drug Repurposing Based on Leukocyte Transcriptomics in Severe COVID-19: In Silico Systems Biology to Precision Medicine. J Pers Med 2022; 12:jpm12071030. [PMID: 35887528 PMCID: PMC9319133 DOI: 10.3390/jpm12071030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/16/2022] [Accepted: 06/20/2022] [Indexed: 01/08/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic causes many morbidity and mortality cases. Despite several developed vaccines and antiviral therapies, some patients experience severe conditions that need intensive care units (ICU); therefore, precision medicine is necessary to predict and treat these patients using novel biomarkers and targeted drugs. In this study, we proposed a multi-level biological network analysis framework to identify key genes via protein–protein interaction (PPI) network analysis as well as survival analysis based on differentially expressed genes (DEGs) in leukocyte transcriptomic profiles, discover novel biomarkers using microRNAs (miRNA) from regulatory network analysis, and provide candidate drugs targeting the key genes using drug–gene interaction network and structural analysis. The results show that upregulated DEGs were mainly enriched in cell division, cell cycle, and innate immune signaling pathways. Downregulated DEGs were primarily concentrated in the cellular response to stress, lysosome, glycosaminoglycan catabolic process, and mature B cell differentiation. Regulatory network analysis revealed that hsa-miR-6792-5p, hsa-let-7b-5p, hsa-miR-34a-5p, hsa-miR-92a-3p, and hsa-miR-146a-5p were predicted biomarkers. CDC25A, GUSB, MYBL2, and SDAD1 were identified as key genes in severe COVID-19. In addition, drug repurposing from drug–gene and drug–protein database searching and molecular docking showed that camptothecin and doxorubicin were candidate drugs interacting with the key genes. In conclusion, multi-level systems biology analysis plays an important role in precision medicine by finding novel biomarkers and targeted drugs based on key gene identification.
Collapse
Affiliation(s)
- Pakorn Sagulkoo
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand; (P.S.); (H.C.); (T.R.)
- Center of Biomedical Informatics, Department of Family Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Hathaichanok Chuntakaruk
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand; (P.S.); (H.C.); (T.R.)
- Center of Excellence in Biocatalyst and Sustainable Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Thanyada Rungrotmongkol
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand; (P.S.); (H.C.); (T.R.)
- Center of Excellence in Biocatalyst and Sustainable Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Apichat Suratanee
- Department of Mathematics, Faculty of Applied Science, King Mongkut’s University of Technology North Bangkok, Bangkok 10800, Thailand;
- Intelligent and Nonlinear Dynamics Innovations Research Center, Science and Technology Research Institute, King Mongkut’s University of Technology North Bangkok, Bangkok 10800, Thailand
| | - Kitiporn Plaimas
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand; (P.S.); (H.C.); (T.R.)
- Advance Virtual and Intelligent Computing (AVIC) Center, Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Omics Science and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Correspondence:
| |
Collapse
|
44
|
Effect of Ion and Binding Site on the Conformation of Chosen Glycosaminoglycans at the Albumin Surface. ENTROPY 2022; 24:e24060811. [PMID: 35741532 PMCID: PMC9222412 DOI: 10.3390/e24060811] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 12/24/2022]
Abstract
Albumin is one of the major components of synovial fluid. Due to its negative surface charge, it plays an essential role in many physiological processes, including the ability to form molecular complexes. In addition, glycosaminoglycans such as hyaluronic acid and chondroitin sulfate are crucial components of synovial fluid involved in the boundary lubrication regime. This study presents the influence of Na+, Mg2+ and Ca2+ ions on human serum albumin–hyaluronan/chondroitin-6-sulfate interactions examined using molecular docking followed by molecular dynamics simulations. We analyze chosen glycosaminoglycans binding by employing a conformational entropy approach. In addition, several protein–polymer complexes have been studied to check how the binding site and presence of ions influence affinity. The presence of divalent cations contributes to the decrease of conformational entropy near carboxyl and sulfate groups. This observation can indicate the higher affinity between glycosaminoglycans and albumin. Moreover, domains IIIA and IIIB of albumin have the highest affinity as those are two domains that show a positive net charge that allows for binding with negatively charged glycosaminoglycans. Finally, in discussion, we suggest some research path to find particular features that would carry information about the dynamics of the particular type of polymers or ions.
Collapse
|
45
|
Glycosaminoglycan interaction networks and databases. Curr Opin Struct Biol 2022; 74:102355. [DOI: 10.1016/j.sbi.2022.102355] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 02/02/2022] [Accepted: 02/04/2022] [Indexed: 12/14/2022]
|
46
|
Molecular dynamics simulations to understand glycosaminoglycan interactions in the free- and protein-bound states. Curr Opin Struct Biol 2022; 74:102356. [DOI: 10.1016/j.sbi.2022.102356] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/08/2022] [Accepted: 02/13/2022] [Indexed: 11/18/2022]
|
47
|
Roy R, Jonniya NA, Kar P. Effect of Sulfation on the Conformational Dynamics of Dermatan Sulfate Glycosaminoglycan: A Gaussian Accelerated Molecular Dynamics Study. J Phys Chem B 2022; 126:3852-3866. [PMID: 35594147 DOI: 10.1021/acs.jpcb.2c01807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Glycosaminoglycans (GAGs) are anionic biopolymers present on cell surfaces as a part of proteoglycans. The biological activities of GAGs depend on the sulfation pattern. In our study, we have considered three octadecasaccharide dermatan sulfate (DS) chains with increasing order of sulfation (dp6s, dp7s, and dp12s) to illuminate the role of sulfation on the GAG units and its chain conformation through 10 μs-long Gaussian accelerated molecular dynamics simulations. DS is composed of repeating disaccharide units of iduronic acid (IdoA) and N-acetylgalactosamine (N-GalNAc). Here, N-GalNAc is linked to IdoA via β(1-4), while IdoA is linked to N-GalNAc through α(1-3). With the increase in sulfation, the DS structure becomes more rigid and linear, as is evident from the distribution of root-mean-square deviations (RMSDs) and end-to-end distances. The tetrasaccharide linker region of the main chain shows a rigid conformation in terms of the glycosidic linkage. We have observed that upon sulfation (i.e., dp12s), the ring flip between two chair forms vanished for IdoA. The dynamic cross-correlation analysis reveals that the anticorrelation motions in dp12s are reduced significantly compared to dp6s or dp7s. An increase in sulfation generates relatively more stable hydrogen-bond networks, including water bridging with the neighboring monosaccharides. Despite the favorable linear structures of the GAG chains, our study also predicts few significant bendings related to the different puckering states, which may play a notable role in the function of the DS. The relation between the global conformation with the micro-level parameters such as puckering and water-mediated hydrogen bonds shapes the overall conformational space of GAGs. Overall, atomistic details of the DS chain provided in this study will help understand their functional and mechanical roles, besides developing new biomaterials.
Collapse
Affiliation(s)
- Rajarshi Roy
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Indore 453552, Madhya Pradesh, India
| | - Nisha Amarnath Jonniya
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Indore 453552, Madhya Pradesh, India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Indore 453552, Madhya Pradesh, India
| |
Collapse
|
48
|
Vallet SD, Berthollier C, Ricard-Blum S. The glycosaminoglycan interactome 2.0. Am J Physiol Cell Physiol 2022; 322:C1271-C1278. [PMID: 35544698 DOI: 10.1152/ajpcell.00095.2022] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Glycosaminoglycans (GAGs) are complex linear polysaccharides, which are covalently attached to core proteins (except for hyaluronan) to form proteoglycans. They play key roles in the organization of the extracellular matrix, and at the cell surface where they contribute to the regulation of cell signaling and of cell adhesion. To explore the mechanisms and pathways underlying their functions, we have generated an expanded dataset of 4290 interactions corresponding to 3464 unique GAG-binding proteins, four times more than the first version of the GAG interactome (Vallet and Ricard-Blum, 2021 J Histochem Cytochem 69:93-104). The increased size of the GAG network is mostly due to the addition of GAG-binding proteins captured from cell lysates and biological fluids by affinity chromatography and identified by mass spectrometry. We review here the interaction repertoire of natural GAGs and of synthetic sulfated hyaluronan, the specificity and molecular functions of GAG-binding proteins, and the biological processes and pathways they are involved in. This dataset is also used to investigate the differences between proteins binding to iduronic acid-containing GAGs (dermatan sulfate and heparin/heparan sulfate) and those interacting with GAGs lacking iduronic acid (chondroitin sulfate, hyaluronan, and keratan sulfate).
Collapse
|
49
|
Basu A, Patel NG, Nicholson ED, Weiss RJ. Spatiotemporal diversity and regulation of glycosaminoglycans in cell homeostasis and human disease. Am J Physiol Cell Physiol 2022; 322:C849-C864. [PMID: 35294848 PMCID: PMC9037703 DOI: 10.1152/ajpcell.00085.2022] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Glycosaminoglycans (GAGs) are long, linear polysaccharides that are ubiquitously expressed on the cell surface and in the extracellular matrix of all animal cells. These complex carbohydrates play important roles in many cellular processes and have been implicated in many disease states, including cancer, inflammation, and genetic disorders. GAGs are among the most complex molecules in biology with enormous information content and extensive structural and functional heterogeneity. GAG biosynthesis is a nontemplate-driven process facilitated by a large group of biosynthetic enzymes that have been extensively characterized over the past few decades. Interestingly, the expression of the enzymes and the consequent structure and function of the polysaccharide chains can vary temporally and spatially during development and under certain pathophysiological conditions, suggesting their assembly is tightly regulated in cells. Due to their many key roles in cell homeostasis and disease, there is much interest in targeting the assembly and function of GAGs as a therapeutic approach. Recent advances in genomics and GAG analytical techniques have pushed the field and generated new perspectives on the regulation of mammalian glycosylation. This review highlights the spatiotemporal diversity of GAGs and the mechanisms guiding their assembly and function in human biology and disease.
Collapse
Affiliation(s)
- Amrita Basu
- 1Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia
| | - Neil G. Patel
- 1Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia,2Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia
| | - Elijah D. Nicholson
- 2Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia
| | - Ryan J. Weiss
- 1Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia,2Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia
| |
Collapse
|
50
|
Homayonia S, Ling CC. Highly Efficient and Stereoselective Synthesis of 6,7‐Dideoxy‐β‐D‐ido‐octopyranuronates. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Saba Homayonia
- University of Calgary Department of Chemistry 2500 University Drive NW T2N 1N4 Calgary CANADA
| | - Chang-Chun Ling
- University of Calgary Department of Chemistry 2500 University Drive NW T2N 1N4 Calgary CANADA
| |
Collapse
|