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Bains RK, Nasseri SA, Wardman JF, Withers SG. Advances in the understanding and exploitation of carbohydrate-active enzymes. Curr Opin Chem Biol 2024; 80:102457. [PMID: 38657391 DOI: 10.1016/j.cbpa.2024.102457] [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: 02/06/2024] [Revised: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 04/26/2024]
Abstract
Carbohydrate-active enzymes (CAZymes) are responsible for the biosynthesis, modification and degradation of all glycans in Nature. Advances in genomic and metagenomic methodologies, in conjunction with lower cost gene synthesis, have provided access to a steady stream of new CAZymes with both well-established and novel mechanisms. At the same time, increasing access to cryo-EM has resulted in exciting new structures, particularly of transmembrane glycosyltransferases of various sorts. This improved understanding has resulted in widespread progress in applications of CAZymes across diverse fields, including therapeutics, organ transplantation, foods, and biofuels. Herein, we highlight a few of the many important advances that have recently been made in the understanding and applications of CAZymes.
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Affiliation(s)
- Rajneesh K Bains
- Department of Chemistry, University of British Columbia, Vancouver, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Seyed Amirhossein Nasseri
- Department of Chemistry, University of British Columbia, Vancouver, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Jacob F Wardman
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada; Department of Biochemistry, University of British Columbia, Vancouver, Canada
| | - Stephen G Withers
- Department of Chemistry, University of British Columbia, Vancouver, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, Canada; Department of Biochemistry, University of British Columbia, Vancouver, Canada.
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2
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Fujita K, Urano Y. Activity-Based Fluorescence Diagnostics for Cancer. Chem Rev 2024; 124:4021-4078. [PMID: 38518254 DOI: 10.1021/acs.chemrev.3c00612] [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: 03/24/2024]
Abstract
Fluorescence imaging is one of the most promising approaches to achieve intraoperative assessment of the tumor/normal tissue margins during cancer surgery. This is critical to improve the patients' prognosis, and therefore various molecular fluorescence imaging probes have been developed for the identification of cancer lesions during surgery. Among them, "activatable" fluorescence probes that react with cancer-specific biomarker enzymes to generate fluorescence signals have great potential for high-contrast cancer imaging due to their low background fluorescence and high signal amplification by enzymatic turnover. Over the past two decades, activatable fluorescence probes employing various fluorescence control mechanisms have been developed worldwide for this purpose. Furthermore, new biomarker enzymatic activities for specific types of cancers have been identified, enabling visualization of various types of cancers with high sensitivity and specificity. This Review focuses on recent advances in the design, function and characteristics of activatable fluorescence probes that target cancer-specific enzymatic activities for cancer imaging and also discusses future prospects in the field of activity-based diagnostics for cancer.
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Furderer ML, Berhe B, Chen TC, Wincovitch S, Jiang X, Tayebi N, Sidransky E, Han TU. A Comparative Biochemical and Pathological Evaluation of Brain Samples from Knock-In Murine Models of Gaucher Disease. Int J Mol Sci 2024; 25:1827. [PMID: 38339105 PMCID: PMC10855869 DOI: 10.3390/ijms25031827] [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: 01/04/2024] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Gaucher disease (GD) is a lysosomal storage disorder stemming from biallelic mutations in GBA1, characterized by glucocerebrosidase dysfunction and glucocerebroside and glucosylsphingosine accumulation. Since phenotypes of murine models of GD often differ from those in patients, the careful characterization of Gba1 mutant mice is necessary to establish their ability to model GD. We performed side-by-side comparative biochemical and pathologic analyses of four murine Gba1 models with genotypes L444P/L444P (p.L483P/p.L483P), L444P/null, D409H/D409H (p.D448H/p.D448H) and D409H/null, along with matched wildtype mice, all with the same genetic background and cage conditions. All mutant mice exhibited significantly lower glucocerebrosidase activity (p < 0.0001) and higher glucosylsphingosine levels than wildtype, with the lowest glucocerebrosidase and the highest glucosylsphingosine levels in mice carrying a null allele. Although glucocerebrosidase activity in L444P and D409H mice was similar, D409H mice showed more lipid accumulation. No Gaucher or storage-like cells were detected in any of the Gba1 mutant mice. Quantification of neuroinflammation, dopaminergic neuronal loss, alpha-synuclein levels and motor behavior revealed no significant findings, even in aged animals. Thus, while the models may have utility for testing the effect of different therapies on enzymatic activity, they did not recapitulate the pathological phenotype of patients with GD, and better models are needed.
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Affiliation(s)
- Makaila L. Furderer
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; (M.L.F.); (B.B.); (T.C.C.); (N.T.)
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Bahafta Berhe
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; (M.L.F.); (B.B.); (T.C.C.); (N.T.)
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Tiffany C. Chen
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; (M.L.F.); (B.B.); (T.C.C.); (N.T.)
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Stephen Wincovitch
- Advanced Imaging & Analysis Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Xuntian Jiang
- Washington University Metabolomics Facility, Washington University School of Medicine, St. Louis, MO 63110, USA;
| | - Nahid Tayebi
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; (M.L.F.); (B.B.); (T.C.C.); (N.T.)
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Ellen Sidransky
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; (M.L.F.); (B.B.); (T.C.C.); (N.T.)
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Tae-Un Han
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; (M.L.F.); (B.B.); (T.C.C.); (N.T.)
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
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Deen MC, Gilormini PA, Vocadlo DJ. Strategies for quantifying the enzymatic activities of glycoside hydrolases within cells and in vivo. Curr Opin Chem Biol 2023; 77:102403. [PMID: 37856901 DOI: 10.1016/j.cbpa.2023.102403] [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: 03/11/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 10/21/2023]
Abstract
Within their native milieu of the cell, the activities of enzymes are controlled by a range of factors including protein interactions and post-translational modifications. The involvement of these factors in fundamental cell biology and the etiology of diseases is stimulating interest in monitoring enzyme activities within tissues. The creation of synthetic substrates, and their use with different imaging modalities, to detect and quantify enzyme activities has great potential to propel these areas of research. Here we describe the latest developments relating to the creation of substrates for imaging and quantifying the activities of glycoside hydrolases, focusing on mammalian systems. The limitations of current tools and the difficulties within the field are summarised, as are prospects for overcoming these challenges.
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Affiliation(s)
- Matthew C Deen
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Pierre-André Gilormini
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - David J Vocadlo
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.
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Abstract
The structural complexity of glycans poses a serious challenge in the chemical synthesis of glycosides, oligosaccharides and glycoconjugates. Glycan complexity, determined by composition, connectivity, and configuration far exceeds what nature achieves with nucleic acids and proteins. Consequently, glycoside synthesis ranks among the most complex tasks in organic synthesis, despite involving only a simple type of bond-forming reaction. Here, we introduce the fundamental principles of glycoside bond formation and summarize recent advances in glycoside bond formation and oligosaccharide synthesis.
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Affiliation(s)
- Conor J Crawford
- Department of Biomolecular Systems, Max Planck Institute for Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max Planck Institute for Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany.
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
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Kim Y, Li H, Choi J, Boo J, Jo H, Hyun JY, Shin I. Glycosidase-targeting small molecules for biological and therapeutic applications. Chem Soc Rev 2023; 52:7036-7070. [PMID: 37671645 DOI: 10.1039/d3cs00032j] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Glycosidases are ubiquitous enzymes that catalyze the hydrolysis of glycosidic linkages in oligosaccharides and glycoconjugates. These enzymes play a vital role in a wide variety of biological events, such as digestion of nutritional carbohydrates, lysosomal catabolism of glycoconjugates, and posttranslational modifications of glycoproteins. Abnormal glycosidase activities are associated with a variety of diseases, particularly cancer and lysosomal storage disorders. Owing to the physiological and pathological significance of glycosidases, the development of small molecules that target these enzymes is an active area in glycoscience and medicinal chemistry. Research efforts carried out thus far have led to the discovery of numerous glycosidase-targeting small molecules that have been utilized to elucidate biological processes as well as to develop effective chemotherapeutic agents. In this review, we describe the results of research studies reported since 2018, giving particular emphasis to the use of fluorescent probes for detection and imaging of glycosidases, activity-based probes for covalent labelling of these enzymes, glycosidase inhibitors, and glycosidase-activatable prodrugs.
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Affiliation(s)
- Yujun Kim
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
| | - Hui Li
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
| | - Joohee Choi
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
| | - Jihyeon Boo
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
| | - Hyemi Jo
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
- Department of Drug Discovery, Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea.
| | - Ji Young Hyun
- Department of Drug Discovery, Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea.
| | - Injae Shin
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
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7
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Zhu S, Deen MC, Zhu Y, Gilormini PA, Chen X, Davis OB, Chin MY, Henry AG, Vocadlo DJ. A Fixable Fluorescence-Quenched Substrate for Quantitation of Lysosomal Glucocerebrosidase Activity in Both Live and Fixed Cells. Angew Chem Int Ed Engl 2023; 62:e202309306. [PMID: 37582679 DOI: 10.1002/anie.202309306] [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: 06/30/2023] [Revised: 08/10/2023] [Accepted: 08/15/2023] [Indexed: 08/17/2023]
Abstract
Fluorogenic substrates are emerging tools that enable studying enzymatic processes within their native cellular environments. However, fluorogenic substrates that function within live cells are generally incompatible with cellular fixation, preventing their tandem application with fundamental cell biology methods such as immunocytochemistry. Here we report a simple approach to enable the chemical fixation of a dark-to-light substrate, LysoFix-GBA, which enables quantification of glucocerebrosidase (GCase) activity in both live and fixed cells. LysoFix-GBA enables measuring responses to both chemical and genetic perturbations to lysosomal GCase activity. Further, LysoFix-GBA permits simple multiplexed co-localization studies of GCase activity with subcellular protein markers. This tool will aid studying the role of GCase activity in Parkinson's Disease, creating new therapeutic approaches targeting the GCase pathway. This approach also lays the foundation for an approach to create fixable substrates for other lysosomal enzymes.
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Affiliation(s)
- Sha Zhu
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Matthew C Deen
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Yanping Zhu
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Pierre-André Gilormini
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Xi Chen
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Oliver B Davis
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA, 94080, USA
| | - Marcus Y Chin
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA, 94080, USA
| | - Anastasia G Henry
- Denali Therapeutics Inc., 161 Oyster Point Blvd., South San Francisco, CA, 94080, USA
| | - David J Vocadlo
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
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8
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Chen XX, Gomila RM, García-Arcos JM, Vonesch M, Gonzalez-Sanchis N, Roux A, Frontera A, Sakai N, Matile S. Fluorogenic In Situ Thioacetalization: Expanding the Chemical Space of Fluorescent Probes, Including Unorthodox, Bifurcated, and Mechanosensitive Chalcogen Bonds. JACS AU 2023; 3:2557-2565. [PMID: 37772186 PMCID: PMC10523495 DOI: 10.1021/jacsau.3c00364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/09/2023] [Accepted: 08/09/2023] [Indexed: 09/30/2023]
Abstract
Progress with fluorescent flippers, small-molecule probes to image membrane tension in living systems, has been limited by the effort needed to synthesize the twisted push-pull mechanophore. Here, we move to a higher oxidation level to introduce a new design paradigm that allows the screening of flipper probes rapidly, at best in situ. Late-stage clicking of thioacetals and acetals allows simultaneous attachment of targeting units and interfacers and exploration of the critical chalcogen-bonding donor at the same time. Initial studies focus on plasma membrane targeting and develop the chemical space of acetals and thioacetals, from acyclic amino acids to cyclic 1,3-heterocycles covering dioxanes as well as dithiolanes, dithianes, and dithiepanes, derived also from classics in biology like cysteine, lipoic acid, asparagusic acid, DTT, and epidithiodiketopiperazines. From the functional point of view, the sensitivity of membrane tension imaging in living cells could be doubled, with lifetime differences in FLIM images increasing from 0.55 to 1.11 ns. From a theoretical point of view, the complexity of mechanically coupled chalcogen bonding is explored, revealing, among others, intriguing bifurcated chalcogen bonds.
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Affiliation(s)
- Xiao-Xiao Chen
- Department
of Organic Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Rosa M. Gomila
- Departament
de Química, Universitat de les Illes
Balears, SP-07122 Palma de Mallorca, Spain
| | | | - Maxime Vonesch
- Department
of Organic Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | | | - Aurelien Roux
- Department
of Biochemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Antonio Frontera
- Departament
de Química, Universitat de les Illes
Balears, SP-07122 Palma de Mallorca, Spain
| | - Naomi Sakai
- Department
of Organic Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Stefan Matile
- Department
of Organic Chemistry, University of Geneva, 1211 Geneva, Switzerland
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Blochouse E, Eid R, Araji N, Tuo W, Châtre R, Papot S, Lévêque N, Thuillier R, Poinot P. VOC-Based Probes, a New Set of Analytical Tools to Monitor Patient Health from Blood Sample. Proof of Concept on Tracking COVID-19 Infection. Anal Chem 2023; 95:11572-11577. [PMID: 37405898 DOI: 10.1021/acs.analchem.3c01732] [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: 07/07/2023]
Abstract
Induced volatolomics is an emerging field that holds promise for many biomedical applications including disease detection and prognosis. In this pilot study, we report the first use of a cocktail of volatile organic compounds (VOCs)-based probes to highlight new metabolic markers allowing disease prognosis. In this pilot study, we specifically targeted a set of circulating glycosidases whose activities could be associated with critical COVID-19 illness. Starting from blood sample collection, our approach relies on the incubation of VOC-based probes in plasma samples. Once activated, the probes released a set of VOCs in the sample headspace. The dynamic monitoring of the signals of VOC tracers enabled the identification of three dysregulated glycosidases in the initial phase after infection, for which preliminary machine learning analyses suggested an ability to anticipate critical disease development. This study demonstrates that our VOC-based probes are a new set of analytical tools that can provide access to biological signals until now unavailable to biologists and clinicians and which could be included in biomedical research to properly construct multifactorial therapy algorithms, necessary for personalized medicine.
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Affiliation(s)
- Estelle Blochouse
- University of Poitiers, UMR CNRS 7285, Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), 4 rue Michel-Brunet, TSA 51106, 86073 Poitiers cedex 9, France
| | - Rony Eid
- University of Poitiers, UMR CNRS 7285, Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), 4 rue Michel-Brunet, TSA 51106, 86073 Poitiers cedex 9, France
| | - Nahla Araji
- University of Poitiers, UMR CNRS 7285, Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), 4 rue Michel-Brunet, TSA 51106, 86073 Poitiers cedex 9, France
| | - Wei Tuo
- University of Poitiers, UMR CNRS 7285, Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), 4 rue Michel-Brunet, TSA 51106, 86073 Poitiers cedex 9, France
| | - Rémi Châtre
- University of Poitiers, UMR CNRS 7285, Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), 4 rue Michel-Brunet, TSA 51106, 86073 Poitiers cedex 9, France
| | - Sébastien Papot
- University of Poitiers, UMR CNRS 7285, Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), 4 rue Michel-Brunet, TSA 51106, 86073 Poitiers cedex 9, France
| | - Nicolas Lévêque
- University of Poitiers, Laboratoire de Virologie et Mycobactériologie, CHU de Poitiers, UR 15560/LITEC, 2 rue Milétrie, 86000 Poitiers, France
| | - Raphaël Thuillier
- Faculty of Medicine and Pharmacy, University of Poitiers, F-86021 Poitiers, France
- Inserm UMR U1313, Ischémie Reperfusion, Métabolisme et Inflammation Stérile en Transplantation (IRMETIST), F-86021 Poitiers, France
- Biochemistry Department, CHU Poitiers, F-86021 Poitiers, France
| | - Pauline Poinot
- University of Poitiers, UMR CNRS 7285, Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), 4 rue Michel-Brunet, TSA 51106, 86073 Poitiers cedex 9, France
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