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Sokratous K, Cooper-Shepherd DA, Ujma J, Qu F, Giles K, Ben-Younis A, Hensen M, Langridge JI, Gault J, Jazayeri A, Liko I, Hopper JTS. Enhanced Declustering Enables Native Top-Down Analysis of Membrane Protein Complexes using Ion-Mobility Time-Aligned Fragmentation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 39007842 DOI: 10.1021/jasms.4c00190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Native mass spectrometry (MS) is proving to be a disruptive technique for studying the interactions of proteins, necessary for understanding the functional roles of these biomolecules. Recent research is expanding the application of native MS towards membrane proteins directly from isolated membrane preparations or from purified detergent micelles. The former results in complex spectra comprising several heterogeneous protein complexes; the latter enables therapeutic protein targets to be screened against multiplexed preparations of compound libraries. In both cases, the resulting spectra are increasingly complex to assign/interpret, and the key to these new directions of native MS research is the ability to perform native top-down analysis, which allows unambiguous peak assignment. To achieve this, detergent removal is necessary prior to MS analyzers, which allow selection of specific m/z values, representing the parent ion for downstream activation. Here, we describe a novel, enhanced declustering (ED) device installed into the first pumping region of a cyclic IMS-enabled mass spectrometry platform. The device enables declustering of ions prior to the quadrupole by imparting collisional activation through an oscillating electric field applied between two parallel plates. The positioning of the device enables liberation of membrane protein ions from detergent micelles. Quadrupole selection can now be utilized to isolate protein-ligand complexes, and downstream collision cells enable the dissociation and identification of binding partners. We demonstrate that ion mobility (IM) significantly aids in the assignment of top-down spectra, aligning fragments to their corresponding parent ions by means of IM drift time. Using this approach, we were able to confidently assign and identify a novel hit compound against PfMATE, obtained from multiplexed ligand libraries.
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Affiliation(s)
- Kleitos Sokratous
- OMass Therapeutics, Chancellor Court, John Smith Drive, ARC Oxford OX4 2GX, United Kingdom
| | | | - Jakub Ujma
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United Kingdom
| | - Feng Qu
- OMass Therapeutics, Chancellor Court, John Smith Drive, ARC Oxford OX4 2GX, United Kingdom
| | - Kevin Giles
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United Kingdom
| | - Aisha Ben-Younis
- OMass Therapeutics, Chancellor Court, John Smith Drive, ARC Oxford OX4 2GX, United Kingdom
| | - Mario Hensen
- OMass Therapeutics, Chancellor Court, John Smith Drive, ARC Oxford OX4 2GX, United Kingdom
| | - James I Langridge
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, United Kingdom
| | - Joseph Gault
- OMass Therapeutics, Chancellor Court, John Smith Drive, ARC Oxford OX4 2GX, United Kingdom
| | - Ali Jazayeri
- OMass Therapeutics, Chancellor Court, John Smith Drive, ARC Oxford OX4 2GX, United Kingdom
| | - Idlir Liko
- OMass Therapeutics, Chancellor Court, John Smith Drive, ARC Oxford OX4 2GX, United Kingdom
| | - Jonathan T S Hopper
- OMass Therapeutics, Chancellor Court, John Smith Drive, ARC Oxford OX4 2GX, United Kingdom
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2
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Stincone P, Naimi A, Saviola AJ, Reher R, Petras D. Decoding the molecular interplay in the central dogma: An overview of mass spectrometry-based methods to investigate protein-metabolite interactions. Proteomics 2024; 24:e2200533. [PMID: 37929699 DOI: 10.1002/pmic.202200533] [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: 07/07/2023] [Revised: 10/15/2023] [Accepted: 10/23/2023] [Indexed: 11/07/2023]
Abstract
With the emergence of next-generation nucleotide sequencing and mass spectrometry-based proteomics and metabolomics tools, we have comprehensive and scalable methods to analyze the genes, transcripts, proteins, and metabolites of a multitude of biological systems. Despite the fascinating new molecular insights at the genome, transcriptome, proteome and metabolome scale, we are still far from fully understanding cellular organization, cell cycles and biology at the molecular level. Significant advances in sensitivity and depth for both sequencing as well as mass spectrometry-based methods allow the analysis at the single cell and single molecule level. At the same time, new tools are emerging that enable the investigation of molecular interactions throughout the central dogma of molecular biology. In this review, we provide an overview of established and recently developed mass spectrometry-based tools to probe metabolite-protein interactions-from individual interaction pairs to interactions at the proteome-metabolome scale.
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Affiliation(s)
- Paolo Stincone
- University of Tuebingen, CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Infection Medicine, Tuebingen, Germany
- University of Tuebingen, Center for Plant Molecular Biology, Tuebingen, Germany
| | - Amira Naimi
- University of Marburg, Institute of Pharmaceutical Biology and Biotechnology, Marburg, Germany
| | | | - Raphael Reher
- University of Marburg, Institute of Pharmaceutical Biology and Biotechnology, Marburg, Germany
| | - Daniel Petras
- University of Tuebingen, CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Infection Medicine, Tuebingen, Germany
- University of California Riverside, Department of Biochemistry, Riverside, USA
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3
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Fiorentino F, Rotili D, Mai A. Native mass spectrometry-directed drug discovery: Recent advances in investigating protein function and modulation. Drug Discov Today 2023; 28:103548. [PMID: 36871843 DOI: 10.1016/j.drudis.2023.103548] [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: 12/18/2022] [Revised: 02/15/2023] [Accepted: 02/28/2023] [Indexed: 03/07/2023]
Abstract
Native mass spectrometry (nMS) is a biophysical method for studying protein complexes and can provide insights into subunit stoichiometry and composition, protein-ligand, and protein-protein interactions (PPIs). These analyses are made possible by preserving non-covalent interactions in the gas phase, thereby allowing the analysis of proteins in their native state. Consequently, nMS has been increasingly applied in early drug discovery campaigns for the characterization of protein-drug interactions and the evaluation of PPI modulators. Here, we discuss recent developments in nMS-directed drug discovery and provide a timely perspective on the possible applications of this technology in drug discovery.
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Affiliation(s)
- Francesco Fiorentino
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; Pasteur Institute, Cenci-Bolognetti Foundation, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
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4
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Scherf M, Koy C, Röwer C, Neamtu A, Glocker MO. Characterization of Phosphorylation-Dependent Antibody Binding to Cancer-Mutated Linkers of C 2H 2 Zinc Finger Proteins by Intact Transition Epitope Mapping-Thermodynamic Weak-Force Order Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:171-181. [PMID: 36656134 DOI: 10.1021/jasms.2c00244] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
With Intact Transition Epitope Mapping-Thermodynamic Weak-force Order (ITEM-TWO) analysis in combination with molecular modeling, the phosphorylation-dependent molecular recognition motif of the anti-HpTGEKP antibody has been investigated with binary and ternary component mixtures consisting of antibody and (phospho-) peptides. Amino acid sequences have been selected to match either the antibody's recognition motif or the cancer-related zinc finger protein mutations and phosphorylations of the respective amino acid residues. Upon electrospraying of all the components of the mixtures, that is, hexapeptides, antibody, and intact immune complexes, the produced ions were subjected to mass spectrometric mass filtering. The antibody ions as well as the immune complex ions traversed into the mass spectrometer's collision chamber, whereas paths of unbound peptide ions were blocked prior to entering the collision cell. After dissociation of the multiply charged immune complexes in the gas phase, the complex-released peptide ions were recorded after having traversed the second mass filter. Complex-released peptides were unambiguously identified by their masses using mass analysis with isotope resolution. From the results of our studies with seven (phospho-) peptides with distinct amino acid sequences, which resembled either the antibody's binding motif or mutations, we conclude the following: (i) A negatively charged phospho group, located near the peptide's N-terminus is mandatory for antibody binding when placed on the peptide surface at a precise distance to the C-terminally located positively charged ε-amino group of a lysinyl residue. (ii) A bulky amino acid residue, such as the tyrosinyl residue at the N-terminal position of the (phospho-) threoninyl residue, abolishes antibody binding. (iii) Two closely spaced phospho groups negatively interfere with the surface polarity pattern and abolish antibody binding as well. (iv) Non-phosphorylated peptides are not binding partners of the anti-HpTGEKP antibody.
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Affiliation(s)
- Maximilian Scherf
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Schillingallee 69, 18059 Rostock, Germany
| | - Cornelia Koy
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Schillingallee 69, 18059 Rostock, Germany
| | - Claudia Röwer
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Schillingallee 69, 18059 Rostock, Germany
| | - Andrei Neamtu
- TRANSCEND Centre, Regional Institute of Oncology (IRO) Iasi, Str. General Henri Mathias Berthelot Nr. 2-4, 700483 Iasi, Romania
- Department of Physiology, Grigore T. Popa University of Medicine and Pharmacy of Iasi, Str. Universitatii Nr. 16, 700115 Iasi, Romania
| | - Michael O Glocker
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Schillingallee 69, 18059 Rostock, Germany
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5
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Bui DT, Kitova EN, Mahal LK, Klassen JS. Mass spectrometry-based shotgun glycomics for discovery of natural ligands of glycan-binding proteins. Curr Opin Struct Biol 2022; 77:102448. [PMID: 36088799 DOI: 10.1016/j.sbi.2022.102448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/15/2022] [Accepted: 07/26/2022] [Indexed: 12/14/2022]
Abstract
The non-covalent associations of complex carbohydrates (glycans) with glycan-binding proteins mediate many important physiological and pathophysiological processes. Identifying these interactions is essential to understanding their diverse biological functions and enables the development of new disease treatments and diagnostics. Knowledge of the repertoire of glycans recognized by most glycan-binding proteins and their affinities is incomplete. Mass spectrometry-based screening of natural glycan libraries has emerged as a promising approach to defining the glycan interactome of glycan-binding proteins. Here, we review recent advances in mass spectrometry-based natural library screening that have led to the discovery of glycan ligands of endogenous and exogenous proteins and illuminated their binding specificities.
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Affiliation(s)
- Duong T Bui
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada. https://twitter.com/@Duong_T_Bui
| | - Elena N Kitova
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Lara K Mahal
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - John S Klassen
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.
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6
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Gavriilidou AFM, Sokratous K, Yen HY, De Colibus L. High-Throughput Native Mass Spectrometry Screening in Drug Discovery. Front Mol Biosci 2022; 9:837901. [PMID: 35495635 PMCID: PMC9047894 DOI: 10.3389/fmolb.2022.837901] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/15/2022] [Indexed: 12/15/2022] Open
Abstract
The design of new therapeutic molecules can be significantly informed by studying protein-ligand interactions using biophysical approaches directly after purification of the protein-ligand complex. Well-established techniques utilized in drug discovery include isothermal titration calorimetry, surface plasmon resonance, nuclear magnetic resonance spectroscopy, and structure-based drug discovery which mainly rely on protein crystallography and, more recently, cryo-electron microscopy. Protein-ligand complexes are dynamic, heterogeneous, and challenging systems that are best studied with several complementary techniques. Native mass spectrometry (MS) is a versatile method used to study proteins and their non-covalently driven assemblies in a native-like folded state, providing information on binding thermodynamics and stoichiometry as well as insights on ternary and quaternary protein structure. Here, we discuss the basic principles of native mass spectrometry, the field’s recent progress, how native MS is integrated into a drug discovery pipeline, and its future developments in drug discovery.
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7
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Nguyen L, McCord KA, Bui DT, Bouwman KM, Kitova EN, Elaish M, Kumawat D, Daskhan GC, Tomris I, Han L, Chopra P, Yang TJ, Willows SD, Mason AL, Mahal LK, Lowary TL, West LJ, Hsu STD, Hobman T, Tompkins SM, Boons GJ, de Vries RP, Macauley MS, Klassen JS. Sialic acid-containing glycolipids mediate binding and viral entry of SARS-CoV-2. Nat Chem Biol 2022; 18:81-90. [PMID: 34754101 DOI: 10.1038/s41589-021-00924-1] [Citation(s) in RCA: 117] [Impact Index Per Article: 58.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 10/15/2021] [Indexed: 11/09/2022]
Abstract
Emerging evidence suggests that host glycans influence severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Here, we reveal that the receptor-binding domain (RBD) of the spike (S) protein on SARS-CoV-2 recognizes oligosaccharides containing sialic acid (Sia), with preference for monosialylated gangliosides. Gangliosides embedded within an artificial membrane also bind to the RBD. The monomeric affinities (Kd = 100-200 μM) of gangliosides for the RBD are similar to another negatively charged glycan ligand of the RBD proposed as a viral co-receptor, heparan sulfate (HS) dp2-dp6 oligosaccharides. RBD binding and infection of SARS-CoV-2 pseudotyped lentivirus to angiotensin-converting enzyme 2 (ACE2)-expressing cells is decreased following depletion of cell surface Sia levels using three approaches: sialyltransferase (ST) inhibition, genetic knockout of Sia biosynthesis, or neuraminidase treatment. These effects on RBD binding and both pseudotyped and authentic SARS-CoV-2 viral entry are recapitulated with pharmacological or genetic disruption of glycolipid biosynthesis. Together, these results suggest that sialylated glycans, specifically glycolipids, facilitate viral entry of SARS-CoV-2.
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Affiliation(s)
- Linh Nguyen
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Kelli A McCord
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Duong T Bui
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Kim M Bouwman
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
| | - Elena N Kitova
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Mohamed Elaish
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada.,Poultry Disease Department, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Dhanraj Kumawat
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Gour C Daskhan
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Ilhan Tomris
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
| | - Ling Han
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Pradeep Chopra
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Tzu-Jing Yang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Steven D Willows
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Andrew L Mason
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Lara K Mahal
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Todd L Lowary
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada.,Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Lori J West
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada.,Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Tom Hobman
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada.,Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Stephen M Tompkins
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA.,Emory-UGA Centers of Excellence for Influenza Research and Surveillance (CEIRS), Athens, GA, USA
| | - Geert-Jan Boons
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands.,Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA.,Department of Chemistry, University of Georgia, Athens, GA, USA.,Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Robert P de Vries
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
| | - Matthew S Macauley
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada. .,Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada.
| | - John S Klassen
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada.
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8
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Nguyen GTH, Bennett JL, Liu S, Hancock SE, Winter DL, Glover DJ, Donald WA. Multiplexed Screening of Thousands of Natural Products for Protein-Ligand Binding in Native Mass Spectrometry. J Am Chem Soc 2021; 143:21379-21387. [PMID: 34886668 DOI: 10.1021/jacs.1c10408] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The structural diversity of natural products offers unique opportunities for drug discovery, but challenges associated with their isolation and screening can hinder the identification of drug-like molecules from complex natural product extracts. Here we introduce a mass spectrometry-based approach that integrates untargeted metabolomics with multistage, high-resolution native mass spectrometry to rapidly identify natural products that bind to therapeutically relevant protein targets. By directly screening crude natural product extracts containing thousands of drug-like small molecules using a single, rapid measurement, we could identify novel natural product ligands of human drug targets without fractionation. This method should significantly increase the efficiency of target-based natural product drug discovery workflows.
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Affiliation(s)
- Giang T H Nguyen
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Jack L Bennett
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Sherrie Liu
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Sarah E Hancock
- School of Medical Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Daniel L Winter
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Dominic J Glover
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - William A Donald
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
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9
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Shao S, Wang Y, Xie Z, Xu R, Wan X, Wang E, Wang Z, Liu S, Chen C, Yang H. 96-well plate format in conjunction with ultra-high-performance liquid chromatography coupled to orbitrap mass spectrometry for high-throughput screening protein binders from ginseng. J Pharm Biomed Anal 2021; 209:114498. [PMID: 34952293 DOI: 10.1016/j.jpba.2021.114498] [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: 06/09/2021] [Revised: 11/02/2021] [Accepted: 11/24/2021] [Indexed: 10/19/2022]
Abstract
Conventional strategies for screening of protein binders cannot be used for complicated samples such as ligand libraries created by combinatorial chemistry or from natural product extracts. In the current study, we developed a novel method in a competitive binding configuration for screening protein binders from complicated samples by a combination of streptavidin-coated 96-well plate format in conjunction with ultra-high-performance liquid chromatography coupled with Orbitrap mass spectrometry (UHPLC-Orbitrap-MS). The concanavalin A (Con A) modified 96-well plate and lysozyme modified 96-well plate (as control) were incubated with oligosaccharide standards respectively, and the compounds with the decreased peak areas in experimental group compared to those in the control group were detected as binders by UHPLC-ESI-MS. The factors such as incubation time, incubation temperature, and buffer, which might affect the binding affinity and reproducibility were optimized. The potential of the approach is examined using the extracts of Radix ginseng cruda and American ginseng. The relative binding degrees (RBDs) of the detected disaccharides were relatively high in the extracts of Radix ginseng cruda, and those of the trisaccharides were similar in the extracts of the two kinds of ginseng. To our knowledge, it's the first time to reveal the differences and analogies in lectin peanut agglutinin (PNA)-binding capabilities of oligosaccharides between the extracts of radix ginseng cruda and American ginseng, indicating the efficiency of the method for analysis of complicated samples.
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Affiliation(s)
- Simeng Shao
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China
| | - Yihan Wang
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China
| | - Zhaoyang Xie
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China
| | - Ruiyang Xu
- Jilin Shenshi Biological Technology Co., Ltd., Changchun 130028, China
| | - Xilin Wan
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China
| | - Enpeng Wang
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China
| | - Zhongxi Wang
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China
| | - Shuying Liu
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China
| | - Changbao Chen
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Hongmei Yang
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun 130117, China.
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10
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Fucosylated human milk oligosaccharide foraging within the species Bifidobacterium pseudocatenulatum is driven by glycosyl hydrolase content and specificity. Appl Environ Microbiol 2021; 88:e0170721. [PMID: 34757822 DOI: 10.1128/aem.01707-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Human milk enriches members of the genus Bifidobacterium in the infant gut. One species, Bifidobacterium pseudocatenulatum, is found in the gastrointestinal tracts of adults and breastfed infants. In this study, B. pseudocatenulatum strains were isolated and characterized to identify genetic adaptations to the breastfed infant gut. During growth on pooled human milk oligosaccharides (HMOs) we observed two distinct groups of B. pseudocatenulatum, isolates that readily consumed HMOs and those that did not, a difference driven by variable catabolism of fucosylated HMOs. A conserved gene cluster for fucosylated HMO utilization was identified in several sequenced B. pseudocatenulatum strains. One isolate, B. pseudocatenulatum MP80, which uniquely possessed GH95 and GH29 α-fucosidases consumed the majority of fucosylated HMOs tested. Furthermore, B. pseudocatenulatum SC585, which possesses only a single GH95 α-fucosidase, lacked the ability to consume the complete repertoire of linkages within the fucosylated HMO pool. Analysis of the purified GH29 and GH95 fucosidase activities directly on HMOs revealed complementing enzyme specificities with the GH95 enzyme preferring 1-2 fucosyl linkages and the GH29 enzyme favoring 1-3 and 1-4 linkages. The HMO binding specificity of the Family 1 solute binding protein component linked to the fucosylated HMO gene cluster in both SC585 and MP80 are similar, suggesting differential transport of fucosylated HMO is not a driving factor in each strain's distinct HMO consumption pattern. Taken together, this data indicates the presence or absence of specific α-fucosidases directs the strain-specific fucosylated HMO utilization pattern among bifidobacteria and likely influences competitive behavior for HMO foraging in situ. IMPORTANCE Often isolated from the human gut, microbes from the bacterial family Bifidobacteriaceae commonly possess genes enabling carbohydrate utilization. Isolates from breast fed infants often grow on and possess genes for the catabolism of human milk oligosaccharides (HMOs), glycans found in human breast milk. However, catabolism of structurally diverse HMOs differs between bifidobacterial strains. This study identifies gene differences between Bifidobacterium pseudocatenulatum isolates that may impact whether a microbe successfully colonizes an infant gut. In this case, the presence of complementary α-fucosidases may provide an advantage to microbes seeking residence in the infant gut. Such knowledge furthers our understanding of how diet drives bacterial colonization of the infant gut.
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11
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Bennett JL, Nguyen GTH, Donald WA. Protein-Small Molecule Interactions in Native Mass Spectrometry. Chem Rev 2021; 122:7327-7385. [PMID: 34449207 DOI: 10.1021/acs.chemrev.1c00293] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Small molecule drug discovery has been propelled by the continual development of novel scientific methodologies to occasion therapeutic advances. Although established biophysical methods can be used to obtain information regarding the molecular mechanisms underlying drug action, these approaches are often inefficient, low throughput, and ineffective in the analysis of heterogeneous systems including dynamic oligomeric assemblies and proteins that have undergone extensive post-translational modification. Native mass spectrometry can be used to probe protein-small molecule interactions with unprecedented speed and sensitivity, providing unique insights into polydisperse biomolecular systems that are commonly encountered during the drug discovery process. In this review, we describe potential and proven applications of native MS in the study of interactions between small, drug-like molecules and proteins, including large multiprotein complexes and membrane proteins. Approaches to quantify the thermodynamic and kinetic properties of ligand binding are discussed, alongside a summary of gas-phase ion activation techniques that have been used to interrogate the structure of protein-small molecule complexes. We additionally highlight some of the key areas in modern drug design for which native mass spectrometry has elicited significant advances. Future developments and applications of native mass spectrometry in drug discovery workflows are identified, including potential pathways toward studying protein-small molecule interactions on a whole-proteome scale.
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Affiliation(s)
- Jack L Bennett
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Giang T H Nguyen
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - William A Donald
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
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12
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Kostelic MM, Zak CK, Jayasekera HS, Marty MT. Assembly of Model Membrane Nanodiscs for Native Mass Spectrometry. Anal Chem 2021; 93:5972-5979. [PMID: 33797873 DOI: 10.1021/acs.analchem.1c00735] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Native mass spectrometry (MS) with nanodiscs is a promising technique for characterizing membrane protein and peptide interactions in lipid bilayers. However, prior studies have used nanodiscs made of only one or two lipids, which lack the complexity of a natural lipid bilayer. To better model specific biological membranes, we developed model mammalian, bacterial, and mitochondrial nanodiscs with up to four different phospholipids. Careful selection of lipids with similar masses that balance the fluidity and curvature enabled these complex nanodiscs to be assembled and resolved with native MS. We then applied this approach to characterize the specificity and incorporation of LL-37, a human antimicrobial peptide, in single-lipid nanodiscs versus model bacterial nanodiscs. Overall, development of these model membrane nanodiscs reveals new insights into the assembly of complex nanodiscs and provides a useful toolkit for studying membrane protein, peptide, and lipid interactions in model biological membranes.
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Affiliation(s)
- Marius M Kostelic
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Ciara K Zak
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Hiruni S Jayasekera
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Michael T Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States.,Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
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13
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Tao Y, Yan J, Cai B. LABEL-FREE BIO-AFFINITY MASS SPECTROMETRY FOR SCREENING AND LOCATING BIOACTIVE MOLECULES. MASS SPECTROMETRY REVIEWS 2021; 40:53-71. [PMID: 31755145 DOI: 10.1002/mas.21613] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 11/04/2019] [Indexed: 06/10/2023]
Abstract
Despite the recent increase in the development of bioactive molecules in the drug industry, the enormous chemical space and lack of productivity are still important issues. Additional alternative approaches to screen and locate bioactive molecules are urgently needed. Label-free bio-affinity mass spectrometry (BA-MS) provides opportunities for the discovery and development of innovative drugs. This review provides a comprehensive portrayal of BA-MS techniques and of their applications in screening and locating bioactive molecules. After introducing the basic principles, alongside some application notes, the current state-of-the-art of BA-MS-assisted drug discovery is discussed, including native MS, size-exclusion chromatography-MS, ultrafiltration-MS, solid-phase micro-extraction-MS, and cell membrane chromatography-MS. Finally, several challenges and limitations of the current methods are summarized, with a view to potential future directions for BA-MS-assisted drug discovery. © 2019 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Yi Tao
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Jizhong Yan
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Baochang Cai
- Jiangsu Key Laboratory of Chinese Medicine Processing, Nanjing University of Chinese Medicine, Nanjing, 210023, PR China
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14
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Paraskevopoulou V, Schimpl M, Overman RC, Stolnik S, Chen Y, Nguyen L, Winkler GS, Gellert P, Klassen JS, Falcone FH. Structural and binding characterization of the LacdiNAc-specific adhesin (LabA; HopD) exodomain from Helicobacter pylori. Curr Res Struct Biol 2020; 3:19-29. [PMID: 34235483 PMCID: PMC8244420 DOI: 10.1016/j.crstbi.2020.12.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/31/2020] [Accepted: 12/10/2020] [Indexed: 01/02/2023] Open
Abstract
Helicobacter pylori (H. pylori) uses several outer membrane proteins for adhering to its host's gastric mucosa, an important step in establishing and preserving colonization. Several adhesins (SabA, BabA, HopQ) have been characterized in terms of their three-dimensional structure. A recent addition to the growing list of outer membrane porins is LabA (LacdiNAc-binding adhesin), which is thought to bind specifically to GalNAcβ1-4GlcNAc, occurring in the gastric mucosa. LabA47-496 protein expressed as His-tagged protein in the periplasm of E. coli and purified via subtractive IMAC after TEV cleavage and subsequent size exclusion chromatography, resulted in bipyramidal crystals with good diffraction properties. Here, we describe the 2.06 Å resolution structure of the exodomain of LabA from H. pylori strain J99 (PDB ID: 6GMM). Strikingly, despite the relatively low levels of sequence identity with the other three structurally characterized adhesins (20-49%), LabA shares an L-shaped fold with SabA and BabA. The 'head' region contains a 4 + 3 α-helix bundle, with a small insertion domain consisting of a short antiparallel beta sheet and an unstructured region, not resolved in the crystal structure. Sequence alignment of LabA from different strains shows a high level of conservation in the N- and C-termini, and identifies two main types based on the length of the insertion domain ('crown' region), the 'J99-type' (insertion ~31 amino acids), and the H. pylori '26695 type' (insertion ~46 amino acids). Analysis of ligand binding using Native Electrospray Ionization Mass Spectrometry (ESI-MS) together with solid phase-bound, ELISA-type assays could not confirm the originally described binding of GalNAcβ1-4GlcNAc-containing oligosaccharides, in line with other recent reports, which also failed to confirm LacdiNAc binding.
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Affiliation(s)
| | - Marianne Schimpl
- Structure, Biophysics and Fragment-based Lead Generation, Discovery Sciences, R&D, AstraZeneca, Cambridge, United Kingdom
| | - Ross C. Overman
- Protein Science, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
| | - Snow Stolnik
- School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Yajie Chen
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, Canada
| | - Linh Nguyen
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, Canada
| | | | - Paul Gellert
- Innovation Strategy & External Liaison, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, United Kingdom
| | - John S. Klassen
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, T6G 2G2, Canada
| | - Franco H. Falcone
- School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
- Institute for Parasitology, Justus-Liebig-University Gießen, Schubertstr. 81, D-35392, Gießen, Germany
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15
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Park H, Jung J, Rodrigues E, Kitova EN, Macauley MS, Klassen JS. Mass Spectrometry-Based Shotgun Glycomics for Discovery of Natural Ligands of Glycan-Binding Proteins. Anal Chem 2020; 92:14012-14020. [PMID: 32936606 DOI: 10.1021/acs.analchem.0c02931] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Glycans attached to lipids and membrane-bound and secreted proteins and peptides mediate many important physiological and pathophysiological processes through interactions with glycan-binding proteins (GBPs). However, uncovering functional glycan ligands is challenging due to the large number of naturally occurring glycan structures, the limited availability of glycans in their purified form, the low affinities of GBP-glycan interactions, and limitations in existing binding assays. This work explores the application of catch-and-release electrospray ionization mass spectrometry (CaR-ESI-MS) for screening libraries of N-glycans derived from natural sources. The assay was tested by screening a small-defined library of complex N-glycans at equimolar concentrations against plant and human GBPs with known specificities for either α2-3- or α2-6-linked sialosides, with affinities in the millimolar to micromolar range. Validation experiments, performed in negative ion mode, revealed that bound N-glycan ligands are readily released, as intact deprotonated ions, from GBPs in the gas phase using collision-induced dissociation. Moreover, the relative abundances of the released ligands closely match their solution affinities. The results obtained for a natural N-glycan library produced from cultured immune cells serve to highlight the ease with which CaR-ESI-MS can screen complex mixtures of N-glycans for interactions. Additionally, scaling the relative abundances of released glycan ligands according to their relative abundances in solution, as determined by hydrophilic interaction-ultrahigh-performance liquid chromatography of the fluorescently labeled library, allows the relative affinities of glycan ligands to be ranked.
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Affiliation(s)
- Heajin Park
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Jaesoo Jung
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Emily Rodrigues
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Elena N Kitova
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Matthew S Macauley
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.,Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - John S Klassen
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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16
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Haab BB, Klamer Z. Advances in Tools to Determine the Glycan-Binding Specificities of Lectins and Antibodies. Mol Cell Proteomics 2020; 19:224-232. [PMID: 31848260 PMCID: PMC7000120 DOI: 10.1074/mcp.r119.001836] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/13/2019] [Indexed: 01/17/2023] Open
Abstract
Proteins that bind carbohydrate structures can serve as tools to quantify or localize specific glycans in biological specimens. Such proteins, including lectins and glycan-binding antibodies, are particularly valuable if accurate information is available about the glycans that a protein binds. Glycan arrays have been transformational for uncovering rich information about the nuances and complexities of glycan-binding specificity. A challenge, however, has been the analysis of the data. Because protein-glycan interactions are so complex, simplistic modes of analyzing the data and describing glycan-binding specificities have proven inadequate in many cases. This review surveys the methods for handling high-content data on protein-glycan interactions. We contrast the approaches that have been demonstrated and provide an overview of the resources that are available. We also give an outlook on the promising experimental technologies for generating new insights into protein-glycan interactions, as well as a perspective on the limitations that currently face the field.
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17
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Wang Y, Park H, Lin H, Kitova EN, Klassen JS. Multipronged ESI–MS Approach for Studying Glycan-Binding Protein Interactions with Glycoproteins. Anal Chem 2019; 91:2140-2147. [DOI: 10.1021/acs.analchem.8b04673] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Yilin Wang
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Heajin Park
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Hong Lin
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Elena N. Kitova
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - John S. Klassen
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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18
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El-Hawiet A, Chen Y, Shams-Ud-Doha K, Kitova EN, Kitov PI, Bode L, Hage N, Falcone FH, Klassen JS. Screening natural libraries of human milk oligosaccharides against lectins using CaR-ESI-MS. Analyst 2018; 143:536-548. [PMID: 29239412 DOI: 10.1039/c7an01397c] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Human milk oligosaccharides (HMOs) afford many health benefits to breast-fed infants, such as protection against infection and regulation of the immune system, through the formation of non-covalent interactions with protein receptors. However, the molecular details of these interactions are poorly understood. Here, we describe the application of catch-and-release electrospray ionization mass spectrometry (CaR-ESI-MS) for screening natural libraries of HMOs against lectins. The HMOs in the libraries were first identified based on molecular weights (MWs), ion mobility separation arrival times (IMS-ATs) and collision-induced dissociation (CID) fingerprints of their deprotonated anions. The libraries were then screened against lectins and the ligands identified from the MWs, IMS-ATs and CID fingerprints of HMOs released from the lectin in the gas phase. To demonstrate the assay, four fractions, extracted from pooled human milk and containing ≥35 different HMOs, were screened against a C-terminal fragment of human galectin-3 (hGal-3C), for which the HMOs specificities have been previously investigated, and a fragment of the blood group antigen-binding adhesin (BabA) from Helicobacter pylori, for which the HMO specificities have not been previously established. The structures of twenty-one ligands, corresponding to both neutral and acidic HMOs, of hGal-3C were identified; all twenty-one were previously shown to be ligands for this lectin. The presence of HMO ligands at six other MWs was also ascertained. Application of the assay to BabA revealed nineteen specific HMO structures that are recognized by the protein and HMO ligands at two other MWs. Notably, it was found that BabA exhibits broad specificity for HMOs, and recognizes both neutral HMOs, including non-fucosylated ones, and acidic HMOs. The results of competitive binding experiments indicate that HMOs can interact with BabA at previously unknown binding sites. The affinities of eight purified HMOs for BabA were measured by ESI-MS and found to be in the 103 M-1 to 104 M-1 range.
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Affiliation(s)
- Amr El-Hawiet
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2.
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19
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Ghosh S, Malik YS, Kobayashi N. Therapeutics and Immunoprophylaxis Against Noroviruses and Rotaviruses: The Past, Present, and Future. Curr Drug Metab 2018; 19:170-191. [PMID: 28901254 PMCID: PMC5971199 DOI: 10.2174/1389200218666170912161449] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 09/25/2016] [Accepted: 03/19/2017] [Indexed: 12/20/2022]
Abstract
Background: Noroviruses and rotaviruses are important viral etiologies of severe gastroenteritis. Noroviruses are the primary cause of nonbacterial diarrheal outbreaks in humans, whilst rotaviruses are a major cause of childhood diarrhea. Although both enteric pathogens substantially impact human health and economies, there are no approved drugs against noroviruses and rotaviruses so far. On the other hand, whilst the currently licensed rotavirus vaccines have been successfully implemented in over 100 countries, the most advanced norovirus vaccine has recently completed phase-I and II trials. Methods: We performed a structured search of bibliographic databases for peer-reviewed research litera-ture on advances in the fields of norovirus and rotavirus therapeutics and immunoprophylaxis. Results: Technological advances coupled with a proper understanding of viral morphology and replication over the past decade has facilitated pioneering research on therapeutics and immunoprophylaxis against noroviruses and rotaviruses, with promising outcomes in human clinical trials of some of the drugs and vaccines. This review focuses on the various developments in the fields of norovirus and rotavirus thera-peutics and immunoprophylaxis, such as potential antiviral drug molecules, passive immunotherapies (oral human immunoglobulins, egg yolk and bovine colostral antibodies, llama-derived nanobodies, and anti-bodies expressed in probiotics, plants, rice grains and insect larvae), immune system modulators, probiot-ics, phytochemicals and other biological substances such as bovine milk proteins, therapeutic nanoparti-cles, hydrogels and viscogens, conventional viral vaccines (live and inactivated whole virus vaccines), and genetically engineered viral vaccines (reassortant viral particles, virus-like particles (VLPs) and other sub-unit recombinant vaccines including multi-valent viral vaccines, edible plant vaccines, and encapsulated viral particles). Conclusions: This review provides important insights into the various approaches to therapeutics and im-munoprophylaxis against noroviruses and rotaviruses..
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Affiliation(s)
- Souvik Ghosh
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, St. Kitts and Nevis, West Indies.,Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
| | - Yashpal Singh Malik
- Indian Veterinary Research Institute, Izatnagar 243 122, Uttar Pradesh, India
| | - Nobumichi Kobayashi
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
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20
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Haramija M, Peter-Katalinić J. Quantitative characterization of galectin-3-C affinity mass spectrometry measurements: Comprehensive data analysis, obstacles, shortcuts and robustness. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:1709-1719. [PMID: 28805274 DOI: 10.1002/rcm.7956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 07/14/2017] [Accepted: 08/06/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE Affinity mass spectrometry (AMS) is an emerging tool in the field of the study of protein•carbohydrate complexes. However, experimental obstacles and data analysis are preventing faster integration of AMS methods into the glycoscience field. Here we show how analysis of direct electrospray ionization mass spectrometry (ESI-MS) AMS data can be simplified for screening purposes, even for complex AMS spectra. METHODS A direct ESI-MS assay was tested in this study and binding data for the galectin-3C•lactose complex were analyzed using a comprehensive and simplified data analysis approach. In the comprehensive data analysis approach, noise, all protein charge states, alkali ion adducts and signal overlap were taken into account. In a simplified approach, only the intensities of the fully protonated free protein and the protein•carbohydrate complex for the main protein charge state were taken into account. RESULTS In our study, for high intensity signals, noise was negligible, sodiated protein and sodiated complex signals cancelled each other out when calculating the Kd value, and signal overlap influenced the Kd value only to a minor extent. Influence of these parameters on low intensity signals was much higher. However, low intensity protein charge states should be avoided in quantitative AMS analyses due to poor ion statistics. CONCLUSIONS The results indicate that noise, alkali ion adducts, signal overlap, as well as low intensity protein charge states, can be neglected for preliminary experiments, as well as in screening assays. One comprehensive data analysis performed as a control should be sufficient to validate this hypothesis for other binding systems as well.
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Affiliation(s)
- Marko Haramija
- Institute of Medical Physics and Biophysics, University of Münster, Robert-Koch-Strasse 31, D-48149, Münster, Germany
| | - Jasna Peter-Katalinić
- Institute of Medical Physics and Biophysics, University of Münster, Robert-Koch-Strasse 31, D-48149, Münster, Germany
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21
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El-Hawiet A, Chen Y, Shams-Ud-Doha K, Kitova EN, St-Pierre Y, Klassen JS. High-Throughput Label- and Immobilization-Free Screening of Human Milk Oligosaccharides Against Lectins. Anal Chem 2017; 89:8713-8722. [PMID: 28749685 DOI: 10.1021/acs.analchem.7b00542] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The intense interest in the mechanisms responsible for the beneficial effects of breast-feeding on infant health has created a significant need for analytical methods capable of rapidly identifying interactions between human milk oligosaccharides (HMOs) and their protein receptors. Currently, there are no established, high-throughput assays for the screening libraries of free (unmodified) HMOs against lectins. The present work describes a rapid and label- and immobilization-free assay, based on catch-and-release electrospray ionization mass spectrometry (CaR-ESI-MS), capable of simultaneously screening mixtures of free HMOs of known concentration for binding to lectins in vitro. Ligand identification relies on the molecular weights (MWs), ion mobility separation arrival times, and collision-induced dissociation fingerprints of HMO anions released from the target protein in the gas phase. To establish the reliability of the assay, a library of 31 free HMOs, ranging in size from tri- to octasaccharide, was screened against three human galectin (hGal) proteins (a stable mutant of hGal1 (hGal-1), a C-terminal fragment of hGal-3 (hGal-3C) and hGal-7), with known HMO affinities. When implemented using an equimolar concentration library, the CaR-ESI-MS assay identified 100% of ligands with affinities >500 M-1 and ≥93% of all HMO ligands (hGal-1-31 of 31 ligands; hGal-3C-25 of 25; hGal-7-28 of 30); no false positives were detected. The assay also successfully identified the majority of the highest affinity HMO ligands (or isomer sets that contain the highest affinity ligands) in the library for each of the three hGal. Notably, for each lectin, CaR-ESI-MS screening required <1 h to complete and consumed <5 ng of each HMO and <0.5 μg of protein.
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Affiliation(s)
- Amr El-Hawiet
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta , Edmonton, Alberta Canada T6G 2G2.,Department of Pharmacognosy, Faculty of Pharmacy, Alexandria University , Alexandria, Egypt
| | - Yajie Chen
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta , Edmonton, Alberta Canada T6G 2G2
| | - Km Shams-Ud-Doha
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta , Edmonton, Alberta Canada T6G 2G2
| | - Elena N Kitova
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta , Edmonton, Alberta Canada T6G 2G2
| | - Yves St-Pierre
- INRS-Institut Armand-Frappier , Laval, Québec H7V 1B7, Canada
| | - John S Klassen
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta , Edmonton, Alberta Canada T6G 2G2
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22
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Göth M, Pagel K. Ion mobility–mass spectrometry as a tool to investigate protein–ligand interactions. Anal Bioanal Chem 2017; 409:4305-4310. [DOI: 10.1007/s00216-017-0384-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 04/13/2017] [Accepted: 04/26/2017] [Indexed: 02/07/2023]
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Lössl P, van de Waterbeemd M, Heck AJ. The diverse and expanding role of mass spectrometry in structural and molecular biology. EMBO J 2016; 35:2634-2657. [PMID: 27797822 PMCID: PMC5167345 DOI: 10.15252/embj.201694818] [Citation(s) in RCA: 171] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 07/25/2016] [Accepted: 10/07/2016] [Indexed: 12/20/2022] Open
Abstract
The emergence of proteomics has led to major technological advances in mass spectrometry (MS). These advancements not only benefitted MS-based high-throughput proteomics but also increased the impact of mass spectrometry on the field of structural and molecular biology. Here, we review how state-of-the-art MS methods, including native MS, top-down protein sequencing, cross-linking-MS, and hydrogen-deuterium exchange-MS, nowadays enable the characterization of biomolecular structures, functions, and interactions. In particular, we focus on the role of mass spectrometry in integrated structural and molecular biology investigations of biological macromolecular complexes and cellular machineries, highlighting work on CRISPR-Cas systems and eukaryotic transcription complexes.
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Affiliation(s)
- Philip Lössl
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands
- Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Michiel van de Waterbeemd
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands
- Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Albert Jr Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands
- Netherlands Proteomics Center, Utrecht, The Netherlands
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24
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Han L, Shams-Ud-Doha K, Kitova EN, Klassen JS. Screening Oligosaccharide Libraries against Lectins Using the Proxy Protein Electrospray Ionization Mass Spectrometry Assay. Anal Chem 2016; 88:8224-31. [DOI: 10.1021/acs.analchem.6b02044] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Ling Han
- Alberta Glycomics Centre
and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G
2G2
| | - Km Shams-Ud-Doha
- Alberta Glycomics Centre
and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G
2G2
| | - Elena N. Kitova
- Alberta Glycomics Centre
and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G
2G2
| | - John S. Klassen
- Alberta Glycomics Centre
and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G
2G2
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25
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Rezaei Darestani R, Winter P, Kitova EN, Tuszynski JA, Klassen JS. Screening Anti-Cancer Drugs against Tubulin using Catch-and-Release Electrospray Ionization Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:876-885. [PMID: 26944280 DOI: 10.1007/s13361-016-1360-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 01/22/2016] [Accepted: 02/01/2016] [Indexed: 06/05/2023]
Abstract
Tubulin, which is the building block of microtubules, plays an important role in cell division. This critical role makes tubulin an attractive target for the development of chemotherapeutic drugs to treat cancer. Currently, there is no general binding assay for tubulin-drug interactions. The present work describes the application of the catch-and-release electrospray ionization mass spectrometry (CaR-ESI-MS) assay to investigate the binding of colchicinoid drugs to αβ-tubulin dimers extracted from porcine brain. Proof-of-concept experiments using positive (ligands with known affinities) and negative (non-binders) controls were performed to establish the reliability of the assay. The assay was then used to screen a library of seven colchicinoid analogues to test their binding to tubulin and to rank their affinities.
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Affiliation(s)
- Reza Rezaei Darestani
- Department of Chemistry and Alberta Glycomics Center, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - Philip Winter
- Department of Oncology, University of Alberta, Edmonton, AB, T6G 1Z2, Canada
| | - Elena N Kitova
- Department of Chemistry and Alberta Glycomics Center, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - Jack A Tuszynski
- Department of Oncology, University of Alberta, Edmonton, AB, T6G 1Z2, Canada
| | - John S Klassen
- Department of Chemistry and Alberta Glycomics Center, University of Alberta, Edmonton, AB, T6G 2G2, Canada.
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26
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Yao Y, Richards MR, Kitova EN, Klassen JS. Influence of Sulfolane on ESI-MS Measurements of Protein-Ligand Affinities. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:498-506. [PMID: 26667179 DOI: 10.1007/s13361-015-1312-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 11/22/2015] [Accepted: 11/24/2015] [Indexed: 06/05/2023]
Abstract
The results of an investigation into the influence of sulfolane, a commonly used supercharging agent, on electrospray ionization mass spectrometry (ESI-MS) measurements of protein-ligand affinities are described. Binding measurements carried out on four protein-carbohydrate complexes, lysozyme with β-D-GlcNAc-(1→4)-β-D-GlcNAc-(1→4)-β-D-GlcNAc-(1→4)-D-GlcNAc, a single chain variable fragment and α-D-Gal-(1→2)-[α-D-Abe-(1→3)]-α-D-Man-OCH3, cholera toxin B subunit homopentamer with β-D-Gal-(1→3)-β-D-GalNAc-(1→4)[α-D-Neu5Ac-(2→3)]-β-D-Gal-(1→4)-β-D-Glc, and a fragment of galectin 3 and α-L-Fuc-(1→2)-β-D-Gal-(1→3)-β-D-GlcNAc-(1→3)-β-D-Gal-(1→4)-β-D-Glc, revealed that sulfolane generally reduces the apparent (as measured by ESI-MS) protein-ligand affinities. To establish the origin of this effect, a detailed study was undertaken using the lysozyme-tetrasaccharide interaction as a model system. Measurements carried out using isothermal titration calorimetry (ITC), circular dichroism, and nuclear magnetic resonance spectroscopies reveal that sulfolane reduces the binding affinity in solution but does not cause any significant change in the higher order structure of lysozyme or to the intermolecular interactions. These observations confirm that changes to the structure of lysozyme in bulk solution are not responsible for the supercharging effect induced by sulfolane. Moreover, the agreement between the ESI-MS and ITC-derived affinities indicates that there is no dissociation of the complex during ESI or in the gas phase (i.e., in-source dissociation). This finding suggests that supercharging of lysozyme by sulfolane is not related to protein unfolding during the ESI process. Binding measurements performed using liquid sample desorption ESI-MS revealed that protein supercharging with sulfolane can be achieved without a reduction in affinity.
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Affiliation(s)
- Yuyu Yao
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Michele R Richards
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Elena N Kitova
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - John S Klassen
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada.
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27
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Galasiti Kankanamalage AC, Weerawarna PM, Kim Y, Chang KO, Groutas WC. Anti-norovirus therapeutics: a patent review (2010-2015). Expert Opin Ther Pat 2016; 26:297-308. [PMID: 26881878 PMCID: PMC4948123 DOI: 10.1517/13543776.2016.1153065] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Human noroviruses are the primary causative agents of acute gastroenteritis and are a pressing public health burden worldwide. There are currently no vaccines or small molecule therapeutics available for the treatment or prophylaxis of norovirus infections. An improved understanding of norovirus biology, as well as the pathogenic mechanisms underlying the disease, has provided the impetus for a range of intense exploratory drug discovery efforts targeting viral and host factors. AREAS COVERED An overview of norovirus inhibitors disclosed in the patent literature (2010-present) and Clinicaltrials.gov is presented. The review is further enriched and supplemented by recent literature reports. EXPERT OPINION Seminal discoveries made in recent years, including a better understanding of the pathobiology and life cycle of norovirus, the identification and targeting of multiple viral and host factors, the advent of a replicon system and a small animal model for the preclinical evaluation of lead compounds, and the availability of high resolution X-ray crystal structures that can be utilized in structure-based drug design and lead optimization campaigns, collectively suggest that a small molecule therapeutic and prophylactic for norovirus infection is likely to emerge in the not too distant future.
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Affiliation(s)
| | | | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, Manhattan, Kansas 66506, USA
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, Manhattan, Kansas 66506, USA
| | - William C. Groutas
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
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28
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Kim Y, Galasiti Kankanamalage AC, Chang KO, Groutas WC. Recent Advances in the Discovery of Norovirus Therapeutics. J Med Chem 2015; 58:9438-50. [PMID: 26258852 DOI: 10.1021/acs.jmedchem.5b00762] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Noroviruses are members of the family Caliciviridae. Norovirus infections are a global health burden that impacts >20 million individuals annually in the U.S. alone. Noroviruses are associated with high morbidity among vulnerable populations, particularly immunocompromised patients. This perspective highlights recent developments related to the discovery and development of norovirus-specific small-molecule therapeutics as well as recent advances in our understanding of norovirus biology and pathogenesis. Most of the work in this area is at the early discovery stage and has been primarily focused on inhibitors of norovirus 3C-like protease and RNA dependent RNA polymerase. However, recent discoveries emanating from basic studies in norovirus research have resulted in the identification of new host-related drug targets that can be exploited. A repurposed compound has been advanced to human clinical studies.
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Affiliation(s)
- Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University , Manhattan, Kansas 66506, United States
| | | | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University , Manhattan, Kansas 66506, United States
| | - William C Groutas
- Department of Chemistry, Wichita State University , 1845 North Fairmount Avenue, Wichita, Kansas 67260, United States
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29
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Yao Y, Shams-Ud-Doha K, Daneshfar R, Kitova EN, Klassen JS. Quantifying protein-carbohydrate interactions using liquid sample desorption electrospray ionization mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:98-106. [PMID: 25315460 DOI: 10.1007/s13361-014-1008-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 09/03/2014] [Accepted: 09/05/2014] [Indexed: 06/04/2023]
Abstract
The application of liquid sample desorption electrospray ionization mass spectrometry (liquid sample DESI-MS) for quantifying protein-carbohydrate interactions in vitro is described. Association constants for the interactions between lysozyme and β-D-GlcNAc-(1 → 4)-β-D-GlcNAc-(1 → 4)-D-GlcNAc and β-D-GlcNAc-(1 → 4)-β-D-GlcNAc-(1 → 4)-β-D-GlcNAc-(1 → 4)-D-GlcNAc, and between a single chain antibody and α-D-Galp-(1 → 2)-[α-D-Abep-(1 → 3)]-α-D-Manp-OCH3 and β-D-Glcp-(1 → 2)-[α-D-Abep-(1 → 3)]-α-D-Manp-OCH3 measured using liquid sample DESI-MS were found to be in good agreement with values measured by isothermal titration calorimetry and the direct ESI-MS assay. The reference protein method, which was originally developed to correct ESI mass spectra for the occurrence of nonspecific ligand-protein binding, was shown to reliably correct liquid sample DESI mass spectra for nonspecific binding. The suitability of liquid sample DESI-MS for quantitative binding measurements carried out using solutions containing high concentrations of the nonvolatile biological buffer phosphate buffered saline (PBS) was also explored. Binding of lysozyme to β-D-GlcNAc-(1 → 4)-β-D-GlcNAc-(1 → 4)-D-GlcNAc in aqueous solutions containing up to 1× PBS was successfully monitored using liquid sample DESI-MS; with ESI-MS the binding measurements were limited to concentrations less than 0.02 X PBS.
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Affiliation(s)
- Yuyu Yao
- Alberta Glycomics Center and Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
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30
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Hopper JTS, Robinson CV. Mass spectrometry quantifies protein interactions--from molecular chaperones to membrane porins. Angew Chem Int Ed Engl 2014; 53:14002-15. [PMID: 25354304 DOI: 10.1002/anie.201403741] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Indexed: 12/16/2022]
Abstract
Proteins possess an intimate relationship between their structure and function, with folded protein structures generating recognition motifs for the binding of ligands and other proteins. Mass spectrometry (MS) can provide information on a number of levels of protein structure, from the primary amino acid sequence to its three-dimensional fold and quaternary interactions. Given that MS is a gas-phase technique, with its foundations in analytical chemistry, it is perhaps counter-intuitive to use it to study the structure and non-covalent interactions of proteins that form in solution. Herein we show, however, that MS can go beyond simply preserving protein interactions in the gas phase by providing new insight into dynamic interaction networks, dissociation mechanisms, and the cooperativity of ligand binding. We consider potential pitfalls in data interpretation and place particular emphasis on recent studies that revealed quantitative information about dynamic protein interactions, in both soluble and membrane-embedded assemblies.
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Affiliation(s)
- Jonathan T S Hopper
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ (UK)
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31
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Kitova EN, El-Hawiet A, Klassen JS. Screening carbohydrate libraries for protein interactions using the direct ESI-MS assay. Applications to libraries of unknown concentration. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1908-16. [PMID: 25135608 DOI: 10.1007/s13361-014-0964-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 07/02/2014] [Accepted: 07/04/2014] [Indexed: 05/22/2023]
Abstract
A semiquantitative electrospray ionization mass spectrometry (ESI-MS) binding assay suitable for analyzing mixtures of oligosaccharides, at unknown concentrations, for interactions with target proteins is described. The assay relies on the differences in the ratio of the relative abundances of the ligand-bound and free protein ions measured by ESI-MS at two or more initial protein concentrations to distinguish low affinity (≤10(3) M(-1)) ligands from moderate and high affinity (>10(5) M(-1)) ligands present in the library and to rank their affinities. Control experiments were performed on solutions of a single chain antibody and a mixture of synthetic oligosaccharides, with known affinities, in the absence and presence of a 40-component carbohydrate library to demonstrate the implementation and reliability of the assay. The application of the assay for screening natural libraries of carbohydrates against proteins is also demonstrated using mixtures of human milk oligosaccharides, isolated from breast milk, and fragments of a bacterial toxin and human galectin 3.
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Affiliation(s)
- Elena N Kitova
- Alberta Glycomics Center and Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
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32
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Hopper JTS, Robinson CV. Massenspektrometrie zur Quantifizierung von Wechselwirkungen zwischen Proteinen - von molekularen Chaperonen zu Membranporinen. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403741] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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33
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Han L, Tan M, Xia M, Kitova EN, Jiang X, Klassen JS. Gangliosides are ligands for human noroviruses. J Am Chem Soc 2014; 136:12631-7. [PMID: 25105447 PMCID: PMC4160279 DOI: 10.1021/ja505272n] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
![]()
Human
noroviruses (NoVs) are known to recognize histo-blood group
antigens (HBGAs) as attachment factors. We report the first experimental
evidence that sialic acid-containing glycosphingolipids (gangliosides)
are also ligands for human NoVs. Electrospray ionization mass spectrometry-based
carbohydrate binding measurements performed on assemblies (P dimer,
P particle, and virus-like particle) of recombinant viral capsid proteins
of two NoV strains, VA387 (GII.4) and VA115 (GI.3), identified binding
to the oligosaccharides of mono-, di-, and trisialylated gangliosides.
The intrinsic (per binding site) affinities measured for these ligands
are similar in magnitude (102–103 M–1) to those of human HBGAs. Binding of NoV VLPs, P
particles, and glutathione S-transferase (GST)-P domain fusion proteins
to sialic acid-containing glycoconjugates, observed in enzyme-linked
immunosorbent assays, provided additional confirmation of the NoV–ganglioside
interactions.
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Affiliation(s)
- Ling Han
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta , Edmonton, Alberta T6G 2G2, Canada
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34
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Newburg DS, Grave G. Recent advances in human milk glycobiology. Pediatr Res 2014; 75:675-9. [PMID: 24522101 PMCID: PMC4125201 DOI: 10.1038/pr.2014.24] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 10/23/2013] [Indexed: 01/03/2023]
Affiliation(s)
| | - Gilman Grave
- Pediatric Growth and Nutrition Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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35
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Han L, Kitova EN, Tan M, Jiang X, Klassen JS. Identifying carbohydrate ligands of a norovirus P particle using a catch and release electrospray ionization mass spectrometry assay. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:111-119. [PMID: 24096878 DOI: 10.1007/s13361-013-0752-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 08/12/2013] [Accepted: 08/15/2013] [Indexed: 06/02/2023]
Abstract
Noroviruses (NoVs), the major cause of epidemic acute gastroenteritis, recognize human histo-blood group antigens (HBGAs), which are present as free oligosaccharides in bodily fluid or glycolipids and glycoproteins on the surfaces of cells. The subviral P particle formed by the protruding (P) domain of the NoV capsid protein serves as a useful model for the study NoV-HBGA interactions. Here, we demonstrate the application of a catch-and-release electrospray ionization mass spectrometry (CaR-ESI-MS) assay for screening carbohydrate libraries against the P particle to rapidly identify NoV ligands and potential inhibitors. Carbohydrate libraries of 50 and 146 compounds, which included 18 and 24 analogs of HBGA receptors, respectively, were screened against the P particle of VA387, a member of the predominant GII.4 NoVs. Deprotonated ions corresponding to the P particle bound to carbohydrates were isolated and subjected to collision-induced dissociation to release the ligands in their deprotonated forms. The released ligands were identified by ion mobility separation followed by mass analysis. All 13 and 16 HBGA ligands with intrinsic affinities >500 M(-1) were identified in the 50 and the 146 compound libraries, respectively. Furthermore, screening revealed interactions with a series of oligosaccharides with structures found in the cell wall of mycobacteria and human milk. The affinities of these newly discovered ligands are comparable to those of the HBGA receptors, as estimated from the relative abundance of released ligand ions.
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Affiliation(s)
- Ling Han
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
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36
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Zhang H, Cui W, Gross ML. Mass spectrometry for the biophysical characterization of therapeutic monoclonal antibodies. FEBS Lett 2013; 588:308-17. [PMID: 24291257 DOI: 10.1016/j.febslet.2013.11.027] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 11/16/2013] [Accepted: 11/18/2013] [Indexed: 10/26/2022]
Abstract
Monoclonal antibodies (mAbs) are powerful therapeutics, and their characterization has drawn considerable attention and urgency. Unlike small-molecule drugs (150-600 Da) that have rigid structures, mAbs (∼150 kDa) are engineered proteins that undergo complicated folding and can exist in a number of low-energy structures, posing a challenge for traditional methods in structural biology. Mass spectrometry (MS)-based biophysical characterization approaches can provide structural information, bringing high sensitivity, fast turnaround, and small sample consumption. This review outlines various MS-based strategies for protein biophysical characterization and then reviews how these strategies provide structural information of mAbs at the protein level (intact or top-down approaches), peptide, and residue level (bottom-up approaches), affording information on higher order structure, aggregation, and the nature of antibody complexes.
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Affiliation(s)
- Hao Zhang
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Weidong Cui
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA.
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37
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El-Hawiet A, Kitova EN, Klassen JS. Quantifying Protein Interactions with Isomeric Carbohydrate Ligands Using a Catch and Release Electrospray Ionization-Mass Spectrometry Assay. Anal Chem 2013; 85:7637-44. [DOI: 10.1021/ac401627t] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amr El-Hawiet
- Alberta Glycomics Centre and Department
of Chemistry, University of Alberta, Edmonton,
Alberta, Canada T6G 2G2
| | - Elena N. Kitova
- Alberta Glycomics Centre and Department
of Chemistry, University of Alberta, Edmonton,
Alberta, Canada T6G 2G2
| | - John S. Klassen
- Alberta Glycomics Centre and Department
of Chemistry, University of Alberta, Edmonton,
Alberta, Canada T6G 2G2
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38
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Chen X, Li L, Chen S, Xu Y, Xia Q, Guo Y, Liu X, Tang Y, Zhang T, Chen Y, Yang C, Shui W. Identification of inhibitors of the antibiotic-resistance target New Delhi metallo-β-lactamase 1 by both nanoelectrospray ionization mass spectrometry and ultrafiltration liquid chromatography/mass spectrometry approaches. Anal Chem 2013; 85:7957-65. [PMID: 23863032 DOI: 10.1021/ac401732d] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mass spectrometry-based platforms have gained increasing success in discovery of ligands bound to therapeutic targets as drug candidates. We established both a nanoelectrospray ionization mass spectrometry (nanoESI-MS) assay and an ultrafiltration liquid chromatography/mass spectrometry (LC/MS) assay to identify new ligands for New Delhi metallo-β-lactamase 1 (NDM-1), responsible for worldwide antibiotic resistance. To alleviate nonspecific binding of hydrophobic compounds and eliminate false positives typically encountered in the indirect LC/MS-based assay, we introduced a blocking protein in the control, which remarkably enhances the selectivity and accuracy of the indirect approach. Side-by-side comparison of the two MS-based approaches for the first time further reveals unique advantages of the indirect approach, including better reproducibility and tolerance of interference. Moreover, the success of fishing out a potent ligand from a mixture of small-molecule fragments demonstrates great potential of the indirect LC/MS-based approach for constructing a robust screening platform against combinatorial libraries or natural product extracts. More importantly, by combining the results of MS-based analyses, enzymatic activity assay, competition experiments, and structural simulation, we discovered a new compound as a promising drug candidate targeting NDM-1.
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Affiliation(s)
- Xin Chen
- College of Life Sciences and Tianjin State Laboratory of Protein Science, Nankai University, Tianjin, China
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39
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Duffell KM, Hudson SA, McLean KJ, Munro AW, Abell C, Matak-Vinković D. Nanoelectrospray Ionization Mass Spectrometric Study of Mycobacterium tuberculosis CYP121–Ligand Interactions. Anal Chem 2013; 85:5707-14. [DOI: 10.1021/ac400236z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Katie M. Duffell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge
CB2 1EW, United Kingdom
| | - Sean A. Hudson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge
CB2 1EW, United Kingdom
| | - Kirsty J. McLean
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester
M1 7DN, United Kingdom
| | - Andrew W. Munro
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester
M1 7DN, United Kingdom
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge
CB2 1EW, United Kingdom
| | - Dijana Matak-Vinković
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge
CB2 1EW, United Kingdom
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40
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Beck A, Wagner-Rousset E, Ayoub D, Van Dorsselaer A, Sanglier-Cianférani S. Characterization of Therapeutic Antibodies and Related Products. Anal Chem 2012; 85:715-36. [DOI: 10.1021/ac3032355] [Citation(s) in RCA: 445] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Alain Beck
- Centre d’Immunologie Pierre Fabre (CIPF), 5 Av. Napoléon III, BP 60497, 74164 Saint-Julien-en-Genevois,
France
| | - Elsa Wagner-Rousset
- Centre d’Immunologie Pierre Fabre (CIPF), 5 Av. Napoléon III, BP 60497, 74164 Saint-Julien-en-Genevois,
France
| | - Daniel Ayoub
- Centre d’Immunologie Pierre Fabre (CIPF), 5 Av. Napoléon III, BP 60497, 74164 Saint-Julien-en-Genevois,
France
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie
de Masse BioOrganique (LSMBO), Université de Strasbourg, IPHC, 25 rue Becquerel 67087, Strasbourg, France and CNRS, UMR7178, 67037 Strasbourg, France
| | - Sarah Sanglier-Cianférani
- Laboratoire de Spectrométrie
de Masse BioOrganique (LSMBO), Université de Strasbourg, IPHC, 25 rue Becquerel 67087, Strasbourg, France and CNRS, UMR7178, 67037 Strasbourg, France
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41
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Zhang Y, Liu L, Daneshfar R, Kitova EN, Li C, Jia F, Cairo CW, Klassen JS. Protein–Glycosphingolipid Interactions Revealed Using Catch-and-Release Mass Spectrometry. Anal Chem 2012; 84:7618-21. [DOI: 10.1021/ac3023857] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yixuan Zhang
- Alberta Glycomics
Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G
2G2
| | - Lan Liu
- Alberta Glycomics
Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G
2G2
| | - Rambod Daneshfar
- Alberta Glycomics
Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G
2G2
| | - Elena N. Kitova
- Alberta Glycomics
Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G
2G2
| | - Caishun Li
- Alberta Glycomics
Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G
2G2
| | - Feng Jia
- Alberta Glycomics
Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G
2G2
| | - Christopher W. Cairo
- Alberta Glycomics
Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G
2G2
| | - John S. Klassen
- Alberta Glycomics
Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G
2G2
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42
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El-Hawiet A, Kitova EN, Klassen JS. Quantifying Carbohydrate–Protein Interactions by Electrospray Ionization Mass Spectrometry Analysis. Biochemistry 2012; 51:4244-53. [DOI: 10.1021/bi300436x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Amr El-Hawiet
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G
2G2
| | - Elena N. Kitova
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G
2G2
| | - John S. Klassen
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G
2G2
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