1
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Sinsinbar G, Gudlur S, Liedberg B. Rapid Detection of Escherichia coli: Optimized Peptide-Polythiophene Interactions Help Reduce Assay Time and Improve Naked-Eye Detection. ACS APPLIED MATERIALS & INTERFACES 2022; 14:31541-31550. [PMID: 35797225 DOI: 10.1021/acsami.2c03294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Recent improvements in methods for rapid detection of microbial contamination in food and water samples have aided in the development of on-site and point-of-care testing. Early detection, made possible via on-site testing, can help limit the spread of food and waterborne illnesses. Recently, we reported a novel fluorescence-based Omptin-Polythiophene assay (the assay) to detect Escherichia coli in contaminated water samples. The assay targets OmpT─an E. coli outer membrane protease─and exploits the protease's ability to cleave at dibasic sites within a peptide. By combining a peptide substrate optimized for OmpT with a conjugated polythiophene reporter molecule whose optical properties vary upon interaction with the intact or cleaved peptide, we demonstrated the detection of 1-10 CFU/mL and 105 CFU/mL E. coli in 5.5 and 1 h, respectively. In comparison, most microbial detection methods that rely on culturing and plating techniques take anywhere between 8 and 24 h to report their results. Herein we report significant improvements in the assay which include reducing the assay time from an already short 1 h to a mere 10 min for detecting E. coli in highly contaminated samples and augmenting the assay with colorimetric sensing capability for naked eye discernment under normal visible light or under UV-A light. These improvements were made possible by characterizing the optical changes resulting from the interaction of the peptide with five carboxylate-functionalized polythiophene variants carrying different 3- side chain carboxylic acids and by identifying preferential peptide substrates via the screening of ten peptide sequence variants for OmpT activity.
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Affiliation(s)
- Gaurav Sinsinbar
- Center for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Drive, Singapore 637553, Singapore
| | - Sushanth Gudlur
- Center for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Drive, Singapore 637553, Singapore
| | - Bo Liedberg
- Center for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Drive, Singapore 637553, Singapore
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2
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Hayat H, Nukala A, Nyamira A, Fan J, Wang P. A concise review: the synergy between artificial intelligence and biomedical nanomaterials that empowers nanomedicine. Biomed Mater 2021; 16. [PMID: 34280907 DOI: 10.1088/1748-605x/ac15b2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 07/19/2021] [Indexed: 12/17/2022]
Abstract
Nanomedicine has recently experienced unprecedented growth and development. However, the complexity of operations at the nanoscale introduces a layer of difficulty in the clinical translation of nanodrugs and biomedical nanotechnology. This problem is further exacerbated when engineering and optimizing nanomaterials for biomedical purposes. To navigate this issue, artificial intelligence (AI) algorithms have been applied for data analysis and inference, allowing for a more applicable understanding of the complex interaction amongst the abundant variables in a system involving the synthesis or use of nanomedicine. Here, we report on the current relationship and implications of nanomedicine and AI. Particularly, we explore AI as a tool for enabling nanomedicine in the context of nanodrug screening and development, brain-machine interfaces and nanotoxicology. We also report on the current state and future direction of nanomedicine and AI in cancer, diabetes, and neurological disorder therapy.
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Affiliation(s)
- Hasaan Hayat
- Precision Health Program,, Michigan State University, East Lansing, MI, United States of America.,Lyman Briggs College, Michigan State University, East Lansing, MI, United States of America
| | - Arijit Nukala
- Precision Health Program,, Michigan State University, East Lansing, MI, United States of America.,Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, United States of America
| | - Anthony Nyamira
- Lyman Briggs College, Michigan State University, East Lansing, MI, United States of America
| | - Jinda Fan
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, United States of America
| | - Ping Wang
- Precision Health Program,, Michigan State University, East Lansing, MI, United States of America.,Department of Radiology, College of Human Medicine, Michigan State University, East Lansing, MI, United States of America
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3
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McLaren DG, Shah V, Wisniewski T, Ghislain L, Liu C, Zhang H, Saldanha SA. High-Throughput Mass Spectrometry for Hit Identification: Current Landscape and Future Perspectives. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:168-191. [PMID: 33482074 DOI: 10.1177/2472555220980696] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
For nearly two decades mass spectrometry has been used as a label-free, direct-detection method for both functional and affinity-based screening of a wide range of therapeutically relevant target classes. Here, we present an overview of several established and emerging mass spectrometry platforms and summarize the unique strengths and performance characteristics of each as they apply to high-throughput screening. Multiple examples from the recent literature are highlighted in order to illustrate the power of each individual technique, with special emphasis given to cases where the use of mass spectrometry was found to be differentiating when compared with other detection formats. Indeed, as many of these examples will demonstrate, the inherent strengths of mass spectrometry-sensitivity, specificity, wide dynamic range, and amenability to complex matrices-can be leveraged to enhance the discriminating power and physiological relevance of assays included in screening cascades. It is our hope that this review will serve as a useful guide to readers of all backgrounds and experience levels on the applicability and benefits of mass spectrometry in the search for hits, leads, and, ultimately, drugs.
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4
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Abstract
The importance of post-translational glycosylation in protein structure and function has gained significant clinical relevance recently. The latest developments in glycobiology, glycochemistry, and glycoproteomics have made the field more manageable and relevant to disease progression and immune-response signaling. Here, we summarize the current progress in glycoscience, including the new methodologies that have led to the introduction of programmable and automatic as well as large-scale enzymatic synthesis, and the development of glycan array, glycosylation probes, and inhibitors of carbohydrate-associated enzymes or receptors. These novel methodologies and tools have facilitated our understanding of the significance of glycosylation and development of carbohydrate-derived medicines that bring the field to the next level of scientific and medical significance.
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Affiliation(s)
- Sachin S Shivatare
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, USA
| | - Chi-Huey Wong
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, USA
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
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5
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Mukherjee P, Berns EJ, Patino CA, Hakim Moully E, Chang L, Nathamgari SSP, Kessler JA, Mrksich M, Espinosa HD. Temporal Sampling of Enzymes from Live Cells by Localized Electroporation and Quantification of Activity by SAMDI Mass Spectrometry. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2000584. [PMID: 32452612 PMCID: PMC7401324 DOI: 10.1002/smll.202000584] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 04/07/2020] [Accepted: 04/16/2020] [Indexed: 05/07/2023]
Abstract
Measuring changes in enzymatic activity over time from small numbers of cells remains a significant technical challenge. In this work, a method for sampling the cytoplasm of cells is introduced to extract enzymes and measure their activity at multiple time points. A microfluidic device, termed the live cell analysis device (LCAD), is designed, where cells are cultured in microwell arrays fabricated on polymer membranes containing nanochannels. Localized electroporation of the cells opens transient pores in the cell membrane at the interface with the nanochannels, enabling extraction of enzymes into nanoliter-volume chambers. In the extraction chambers, the enzymes modify immobilized substrates, and their activity is quantified by self-assembled monolayers for matrix-assisted laser desorption/ionization (SAMDI) mass spectrometry. By employing the LCAD-SAMDI platform, protein delivery into cells is demonstrated. Next, it is shown that enzymes can be extracted, and their activity measured without a loss in viability. Lastly, cells are sampled at multiple time points to study changes in phosphatase activity in response to oxidation by hydrogen peroxide. With this unique sampling device and label-free assay format, the LCAD with SAMDI enables a powerful new method for monitoring the dynamics of cellular activity from small populations of cells.
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Affiliation(s)
- Prithvijit Mukherjee
- Department of Mechanical Engineering, Northwestern University, Evanston, IL, 60208, USA
- Theoretical and Applied Mechanics Program, Northwestern University, Evanston, IL, 60208, USA
| | - Eric J Berns
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Cesar A Patino
- Department of Mechanical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | | | - Lingqian Chang
- Department of Mechanical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - S Shiva P Nathamgari
- Department of Mechanical Engineering, Northwestern University, Evanston, IL, 60208, USA
- Theoretical and Applied Mechanics Program, Northwestern University, Evanston, IL, 60208, USA
| | - John A Kessler
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Milan Mrksich
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
- Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA
- Department of Cell and Development Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Horacio D Espinosa
- Department of Mechanical Engineering, Northwestern University, Evanston, IL, 60208, USA
- Theoretical and Applied Mechanics Program, Northwestern University, Evanston, IL, 60208, USA
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6
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Self-assembly TiO2 nanosheets as a SALDI-TOF-MS matrix for high-throughput identification of polyfluorinated compounds in water samples. Microchem J 2020. [DOI: 10.1016/j.microc.2019.104294] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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7
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Simon RP, Winter M, Kleiner C, Ries R, Schnapp G, Heimann A, Li J, Zuvela-Jelaska L, Bretschneider T, Luippold AH, Reindl W, Bischoff D, Büttner FH. MALDI-TOF Mass Spectrometry-Based High-Throughput Screening for Inhibitors of the Cytosolic DNA Sensor cGAS. SLAS DISCOVERY 2019; 25:372-383. [DOI: 10.1177/2472555219880185] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Comprehensive and unbiased detection methods are a prerequisite for high-throughput screening (HTS) campaigns within drug discovery research. Label-free matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) has been introduced as an HTS-compatible readout for biochemical test systems to support the drug discovery process. So far, reported HTS applications were based on surface-modified systems or proof-of-concept studies. We present the utilization of a MALDI-TOF-based screening platform to identify inhibitors of human cyclic GMP-AMP synthase (cGAS), a mediator of innate immune response whose aberration has been causally correlated to a number of inflammatory disorders. In this context, the development and validation of a MALDI-TOF-based activity assay is reported to demonstrate fast, robust, and accurate detection of chemical cGAS inhibition by direct quantification of the physiological reaction product cyclic GMP-ATP (cGAMP). Results from a screen of a diverse library of more than 1 million small molecules in 1536-well format against the catalytic cGAS activity are presented with excellent assay performance and data quality. Identified hits were qualified in dose–response experiments and confirmed by RapidFire-MS measurements. Conclusively, the presented data provide the first proof of applicability of direct automated MALDI-TOF MS as a readout strategy for large-scale drug discovery HTS campaigns.
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Affiliation(s)
- Roman P. Simon
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Martin Winter
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Carola Kleiner
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Robert Ries
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Gisela Schnapp
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Annekatrin Heimann
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Jun Li
- Immunology & Respiratory Disease Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, USA
| | - Ljiljana Zuvela-Jelaska
- Immunology & Respiratory Disease Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, USA
| | - Tom Bretschneider
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Andreas H. Luippold
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Wolfgang Reindl
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Daniel Bischoff
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Frank H. Büttner
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
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8
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Dai R, Ten AS, Mrksich M. Profiling Protease Activity in Laundry Detergents with Peptide Arrays and SAMDI Mass Spectrometry. Ind Eng Chem Res 2019. [DOI: 10.1021/acs.iecr.9b00057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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9
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Mattes DS, Jung N, Weber LK, Bräse S, Breitling F. Miniaturized and Automated Synthesis of Biomolecules-Overview and Perspectives. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1806656. [PMID: 31033052 DOI: 10.1002/adma.201806656] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 02/02/2019] [Indexed: 06/09/2023]
Abstract
Chemical synthesis is performed by reacting different chemical building blocks with defined stoichiometry, while meeting additional conditions, such as temperature and reaction time. Such a procedure is especially suited for automation and miniaturization. Life sciences lead the way to synthesizing millions of different oligonucleotides in extremely miniaturized reaction sites, e.g., pinpointing active genes in whole genomes, while chemistry advances different types of automation. Recent progress in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) imaging could match miniaturized chemical synthesis with a powerful analytical tool to validate the outcome of many different synthesis pathways beyond applications in the life sciences. Thereby, due to the radical miniaturization of chemical synthesis, thousands of molecules can be synthesized. This in turn should allow ambitious research, e.g., finding novel synthesis routes or directly screening for photocatalysts. Herein, different technologies are discussed that might be involved in this endeavor. A special emphasis is given to the obstacles that need to be tackled when depositing tiny amounts of materials to many different extremely miniaturized reaction sites.
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Affiliation(s)
- Daniela S Mattes
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Nicole Jung
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Laura K Weber
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Stefan Bräse
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Frank Breitling
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
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10
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Bugga P, Mrksich M. Sequential Photoactivation of Self-Assembled Monolayers to Direct Cell Adhesion and Migration. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:5937-5943. [PMID: 30943037 PMCID: PMC8262134 DOI: 10.1021/acs.langmuir.8b04203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Dynamic substrates for cell culture control the spatial and temporal presentation of extracellular matrix ligands that interact with adherent cells. This paper reports a photoactive surface chemistry that can repeatedly activate regions of the substrate for cell adhesion, spreading, and migration. The approach uses self-assembled monolayers presenting the integrin ligand RGD that is caged with a nitrophenyl-based photoprotecting group. The group is also modified with a maltoheptaose oligosaccharide to prevent nonspecific protein adsorption and cell attachment. The peptide is uncaged when irradiated with a laser source at 405 nm on a microscope to reveal micron-size regions for single cell attachment. This method is applied to studies of gap junction-mediated communication between two neighboring cells and requires the patterning of an initial receiver cell population and then the patterning of a second sender population to give a culture wherein each pair of cells are separated by 30 μm. Finally, activation of the region between the cells permits cell-cell contact and gap junction assembly between the sender and receiver cells. This example demonstrates the broad relevance of this method to studying complex phenotypes in cell culture.
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Affiliation(s)
- Pradeep Bugga
- Department of Chemistry, Department of Biomedical Engineering, and Department of Cell and Molecular Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Milan Mrksich
- Department of Chemistry, Department of Biomedical Engineering, and Department of Cell and Molecular Biology, Northwestern University, Evanston, Illinois 60208, United States
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11
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Exploration of the nanomedicine-design space with high-throughput screening and machine learning. Nat Biomed Eng 2019; 3:318-327. [PMID: 30952978 DOI: 10.1038/s41551-019-0351-1] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 01/14/2019] [Indexed: 01/13/2023]
Abstract
Only a tiny fraction of the nanomedicine-design space has been explored, owing to the structural complexity of nanomedicines and the lack of relevant high-throughput synthesis and analysis methods. Here, we report a methodology for determining structure-activity relationships and design rules for spherical nucleic acids (SNAs) functioning as cancer-vaccine candidates. First, we identified ~1,000 candidate SNAs on the basis of reasonable ranges for 11 design parameters that can be systematically and independently varied to optimize SNA performance. Second, we developed a high-throughput method for making SNAs at the picomolar scale in a 384-well format, and used a mass spectrometry assay to rapidly measure SNA immune activation. Third, we used machine learning to quantitatively model SNA immune activation and identify the minimum number of SNAs needed to capture optimum structure-activity relationships for a given SNA library. Our methodology is general, can reduce the number of nanoparticles that need to be tested by an order of magnitude, and could serve as a screening tool for the development of nanoparticle therapeutics.
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12
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Li F, Hopwood JP, Galey MM, Sanchez LM, Ciszek JW. Chemically transformed monolayers on acene thin films for improved metal/organic interfaces. Chem Commun (Camb) 2019; 55:13975-13978. [DOI: 10.1039/c9cc07234a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chemically installed functional groups on top of organic semiconductors allow for improved adhesion with metal top contacts.
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Affiliation(s)
- Feifei Li
- Department of Chemistry and Biochemistry
- Loyola University Chicago
- Chicago
- USA
| | | | - Melissa M. Galey
- Department of Pharmaceutical Sciences
- University of Illinois at Chicago
- Chicago
- USA
| | - Laura M. Sanchez
- Department of Pharmaceutical Sciences
- University of Illinois at Chicago
- Chicago
- USA
| | - Jacob W. Ciszek
- Department of Chemistry and Biochemistry
- Loyola University Chicago
- Chicago
- USA
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13
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Gao C, Zhen D, He N, An Z, Zhou Q, Li C, Grimes CA, Cai Q. Two-dimensional TiO 2 nanoflakes enable rapid SALDI-TOF-MS detection of toxic small molecules (dyes and their metabolites) in complex environments. Talanta 2018; 196:1-8. [PMID: 30683337 DOI: 10.1016/j.talanta.2018.11.104] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/26/2018] [Accepted: 11/29/2018] [Indexed: 12/25/2022]
Abstract
High surface area (136 m2 g-1) nanoporous two-dimensional TiO2 nanoflakes are applied as an adsorbent and meanwhile a matrix for toxic small molecule analysis using positive-ion surface-assisted laser desorption/ionization time-of-flight mass spectrometry (SALDI-TOF MS). The TiO2 nanoflakes enable one-step enrichment and analysis, greatly simplifying the analysis technique. Due to the high enrichment efficiency and low background noise, small molecule organic contaminants at ppt or even sub-ppt concentrations such as malachite green (10 pg/mL), leucomalachite green (10 pg/mL), cetyltrimethylammonium bromide (0.001 pg/mL), rhodamine B (0.001 pg/mL), and crystal violet (0.1 pg/mL) were detected. In addition, malachite green and its metabolite leucomalachite green at ng/mL concentrations were successfully detected from fish blood and fish extracts, and crystal violet and its homologues at ng/cm2 concentrations were detected from inks on thermal receipt papers obtained from local supermarket.
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Affiliation(s)
- Chan Gao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Deshuai Zhen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China; College of Chemistry and Chemical Engineering, Qiannan Normal University for Nationalities, Duyun, Guizhou 558000, China
| | - Ni He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Zhengbin An
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Qiulan Zhou
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Chenyi Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Craig A Grimes
- Flux Photon Corporation,5950 Shiloh Road East, Alpharetta, GA 30005 United States
| | - Qingyun Cai
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China.
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14
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Serna S, Ercibengoa M, Marimón JM, Reichardt NC. Measuring Bacterial Glycosyl Hydrolase Activity with a Soluble Capture Probe by Mass Spectrometry. Anal Chem 2018; 90:12536-12543. [DOI: 10.1021/acs.analchem.8b02434] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Sonia Serna
- Glycotechnology Laboratory, CIC biomaGUNE, Paseo Miramón 182, San Sebastian 20014, Spain
| | - María Ercibengoa
- Hospital Universitario Donostia-Instituto de Investigación Sanitaria Biodonostia, Begiristain Doktorea Pasealekua 109, San Sebastián 20014, Spain
- Biomedical Research Center Network for Respiratory Diseases (CIBERES), ISCIII, Madrid 28029, Spain
| | - Jose María Marimón
- Hospital Universitario Donostia-Instituto de Investigación Sanitaria Biodonostia, Begiristain Doktorea Pasealekua 109, San Sebastián 20014, Spain
- Biomedical Research Center Network for Respiratory Diseases (CIBERES), ISCIII, Madrid 28029, Spain
| | - Niels-Christian Reichardt
- Glycotechnology Laboratory, CIC biomaGUNE, Paseo Miramón 182, San Sebastian 20014, Spain
- CIBER-BBN, Paseo Miramón 182, San Sebastian 20014, Spain
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15
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Helal KY, Alamgir A, Berns EJ, Mrksich M. Traceless Immobilization of Analytes for High-Throughput Experiments with SAMDI Mass Spectrometry. J Am Chem Soc 2018; 140:8060-8063. [PMID: 29901996 PMCID: PMC6578359 DOI: 10.1021/jacs.8b02918] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Label-free assays, and particularly
those based on the combination
of mass spectroscopy with surface chemistries, enable high-throughput
experiments of a broad range of reactions. However, these methods
can still require the incorporation of functional groups that allow
immobilization of reactants and products to surfaces prior to analysis.
In this paper, we report a traceless method for attaching molecules
to a self-assembled monolayer for matrix-assisted laser desorption
and ionization (SAMDI) mass spectrometry. This method uses monolayers
that are functionalized with a 3-trifluoromethyl-3-phenyl-diazirine
group that liberates nitrogen when irradiated and gives a carbene
that inserts into a wide range of bonds to covalently immobilize molecules.
Analysis of the monolayer with SAMDI then reveals peaks for each of
the adducts formed from molecules in the sample. This method is applied
to characterize a P450 drug metabolizing enzyme and to monitor a Suzuki–Miyaura
coupling chemical reaction and is important because modification of
the substrates with a functional group would alter their activities.
This method will be important for high-throughput experiments in many
areas, including reaction discovery and optimization.
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Affiliation(s)
| | | | | | - Milan Mrksich
- Department of Cell and Molecular Biology , Northwestern University Feinberg School of Medicine , Chicago , Illinois 60611 , United States
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16
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Szymczak LC, Huang CF, Berns EJ, Mrksich M. Combining SAMDI Mass Spectrometry and Peptide Arrays to Profile Phosphatase Activities. Methods Enzymol 2018; 607:389-403. [PMID: 30149867 PMCID: PMC6457119 DOI: 10.1016/bs.mie.2018.04.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Phosphatases, the enzymes responsible for dephosphorylating proteins, play critical roles in many cellular processes. While their importance is widely recognized, phosphatase activity and regulation remain poorly understood. Currently, there are few assays available that are capable of directly measuring phosphatase activity and specificity. We have previously introduced SAMDI (self-assembled monolayers on gold for matrix-assisted laser desorption/ionization) mass spectrometry as a technique to profile the substrate specificities of enzymes. SAMDI mass spectrometry assays are well suited to examine phosphatase activities and offer many advantages over current methods. This technique uses monolayers that terminate with a peptide or molecular enzyme substrate and allows for enzyme reactions to be performed on a surface that can easily be rinsed and analyzed by mass spectrometry without the need for analyte labeling. In this chapter, we describe the process of combining SAMDI mass spectrometry with peptide arrays to study the substrate specificities of two protein tyrosine phosphatases.
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Affiliation(s)
- Lindsey C Szymczak
- Department of Chemistry, Northwestern University, Evanston, IL, United States
| | - Che-Fan Huang
- Department of Chemistry, Northwestern University, Evanston, IL, United States
| | - Eric J Berns
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, United States
| | - Milan Mrksich
- Department of Chemistry, Northwestern University, Evanston, IL, United States; Department of Biomedical Engineering, Northwestern University, Evanston, IL, United States.
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17
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Affiliation(s)
- Lindsey C. Szymczak
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Hsin-Yu Kuo
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Milan Mrksich
- Institute of Chemical Biology and Nanomedicine, Hunan University, Changsha 410082, China
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
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18
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Wood SE, Sinsinbar G, Gudlur S, Nallani M, Huang CF, Liedberg B, Mrksich M. A Bottom-Up Proteomic Approach to Identify Substrate Specificity of Outer-Membrane Protease OmpT. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707535] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sarah E. Wood
- Departments of Chemistry and Biomedical Engineering; Northwestern University; 2145 Sheridan Road Evanston IL 60208 USA
| | - Gaurav Sinsinbar
- Center for Biomimetic Sensor Science; School of Materials Science & Engineering; Nanyang Technological University; 50 Nanyang Drive 637553 Singapore
| | - Sushanth Gudlur
- Center for Biomimetic Sensor Science; School of Materials Science & Engineering; Nanyang Technological University; 50 Nanyang Drive 637553 Singapore
| | - Madhavan Nallani
- Center for Biomimetic Sensor Science; School of Materials Science & Engineering; Nanyang Technological University; 50 Nanyang Drive 637553 Singapore
| | - Che-Fan Huang
- Departments of Chemistry and Biomedical Engineering; Northwestern University; 2145 Sheridan Road Evanston IL 60208 USA
| | - Bo Liedberg
- Center for Biomimetic Sensor Science; School of Materials Science & Engineering; Nanyang Technological University; 50 Nanyang Drive 637553 Singapore
| | - Milan Mrksich
- Departments of Chemistry and Biomedical Engineering; Northwestern University; 2145 Sheridan Road Evanston IL 60208 USA
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19
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Wood SE, Sinsinbar G, Gudlur S, Nallani M, Huang CF, Liedberg B, Mrksich M. A Bottom-Up Proteomic Approach to Identify Substrate Specificity of Outer-Membrane Protease OmpT. Angew Chem Int Ed Engl 2017; 56:16531-16535. [DOI: 10.1002/anie.201707535] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/06/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Sarah E. Wood
- Departments of Chemistry and Biomedical Engineering; Northwestern University; 2145 Sheridan Road Evanston IL 60208 USA
| | - Gaurav Sinsinbar
- Center for Biomimetic Sensor Science; School of Materials Science & Engineering; Nanyang Technological University; 50 Nanyang Drive 637553 Singapore
| | - Sushanth Gudlur
- Center for Biomimetic Sensor Science; School of Materials Science & Engineering; Nanyang Technological University; 50 Nanyang Drive 637553 Singapore
| | - Madhavan Nallani
- Center for Biomimetic Sensor Science; School of Materials Science & Engineering; Nanyang Technological University; 50 Nanyang Drive 637553 Singapore
| | - Che-Fan Huang
- Departments of Chemistry and Biomedical Engineering; Northwestern University; 2145 Sheridan Road Evanston IL 60208 USA
| | - Bo Liedberg
- Center for Biomimetic Sensor Science; School of Materials Science & Engineering; Nanyang Technological University; 50 Nanyang Drive 637553 Singapore
| | - Milan Mrksich
- Departments of Chemistry and Biomedical Engineering; Northwestern University; 2145 Sheridan Road Evanston IL 60208 USA
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20
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O'Kane PT, Mrksich M. An Assay Based on SAMDI Mass Spectrometry for Profiling Protein Interaction Domains. J Am Chem Soc 2017; 139:10320-10327. [PMID: 28689418 DOI: 10.1021/jacs.7b03805] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This paper describes an assay that can profile the binding of a protein to ligands and can rank the affinities of a library of ligands. The method is based on the enhanced rate of an enzyme-mediated reaction that follows from colocalization of the enzyme and substrate by a protein-ligand interaction. This assay uses a self-assembled monolayer that presents a candidate peptide ligand for a receptor and a peptide substrate for an enzyme. The receptor is prepared as a fusion to the relevant enzyme so that binding of the receptor to the immobilized ligand brings the enzyme to the surface, where it can more rapidly modify its substrate. The extent of conversion of the substrate to product is therefore a measure of the average time the ligand-receptor complex is present and is quantified using the SAMDI mass spectrometry technique. The approach is used to profile the binding of chromodomain proteins to methylated lysine peptides derived from the histone 3 protein. The relative affinities for the peptide ligands found in this work agreed with results from prior studies. Additionally, this work revealed cross-talk interactions whereby phosphorylation of certain residues impaired binding of chromodomains to the peptide ligands. The method presented here, which we term protein interaction by SAMDI (PI-SAMDI), has the advantages that it is applicable to low-affinity interactions because the complexes are not observed directly, but rather leave a "covalent record" of the interaction that is measured with mass spectrometry and because it is compatible with laboratory automation for high-throughput analysis.
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Affiliation(s)
- Patrick T O'Kane
- Department of Chemistry, Department of Biomedical Engineering, and Department of Cell & Molecular Biology, Northwestern University , Evanston, Illinois 60208, United States
| | - Milan Mrksich
- Department of Chemistry, Department of Biomedical Engineering, and Department of Cell & Molecular Biology, Northwestern University , Evanston, Illinois 60208, United States
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21
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Structural insights into lipoprotein N-acylation by Escherichia coli apolipoprotein N-acyltransferase. Proc Natl Acad Sci U S A 2017; 114:E6044-E6053. [PMID: 28698362 DOI: 10.1073/pnas.1707813114] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gram-negative bacteria express a diverse array of lipoproteins that are essential for various aspects of cell growth and virulence, including nutrient uptake, signal transduction, adhesion, conjugation, sporulation, and outer membrane protein folding. Lipoprotein maturation requires the sequential activity of three enzymes that are embedded in the cytoplasmic membrane. First, phosphatidylglycerol:prolipoprotein diacylglyceryl transferase (Lgt) recognizes a conserved lipobox motif within the prolipoprotein signal sequence and catalyzes the addition of diacylglycerol to an invariant cysteine. The signal sequence is then cleaved by signal peptidase II (LspA) to give an N-terminal S-diacylglyceryl cysteine. Finally, apolipoprotein N-acyltransferase (Lnt) catalyzes the transfer of the sn-1-acyl chain of phosphatidylethanolamine to this N-terminal cysteine, generating a mature, triacylated lipoprotein. Although structural studies of Lgt and LspA have yielded significant mechanistic insights into this essential biosynthetic pathway, the structure of Lnt has remained elusive. Here, we present crystal structures of wild-type and an active-site mutant of Escherichia coli Lnt. The structures reveal a monomeric eight-transmembrane helix fold that supports a periplasmic carbon-nitrogen hydrolase domain containing a Cys-Glu-Lys catalytic triad. Two lipids are bound at the active site in the structures, and we propose a putative phosphate recognition site where a chloride ion is coordinated near the active site. Based on these structures and complementary cell-based, biochemical, and molecular dynamics approaches, we propose a mechanism for substrate engagement and catalysis by E. coli Lnt.
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22
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Dosekova E, Filip J, Bertok T, Both P, Kasak P, Tkac J. Nanotechnology in Glycomics: Applications in Diagnostics, Therapy, Imaging, and Separation Processes. Med Res Rev 2017; 37:514-626. [PMID: 27859448 PMCID: PMC5659385 DOI: 10.1002/med.21420] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 09/08/2016] [Accepted: 09/21/2016] [Indexed: 12/14/2022]
Abstract
This review comprehensively covers the most recent achievements (from 2013) in the successful integration of nanomaterials in the field of glycomics. The first part of the paper addresses the beneficial properties of nanomaterials for the construction of biosensors, bioanalytical devices, and protocols for the detection of various analytes, including viruses and whole cells, together with their key characteristics. The second part of the review focuses on the application of nanomaterials integrated with glycans for various biomedical applications, that is, vaccines against viral and bacterial infections and cancer cells, as therapeutic agents, for in vivo imaging and nuclear magnetic resonance imaging, and for selective drug delivery. The final part of the review describes various ways in which glycan enrichment can be effectively done using nanomaterials, molecularly imprinted polymers with polymer thickness controlled at the nanoscale, with a subsequent analysis of glycans by mass spectrometry. A short section describing an active glycoprofiling by microengines (microrockets) is covered as well.
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Affiliation(s)
- Erika Dosekova
- Department of Glycobiotechnology, Institute of ChemistrySlovak Academy of SciencesDubravska cesta 9845 38BratislavaSlovakia
| | - Jaroslav Filip
- Center for Advanced MaterialsQatar UniversityP.O. Box 2713DohaQatar
| | - Tomas Bertok
- Department of Glycobiotechnology, Institute of ChemistrySlovak Academy of SciencesDubravska cesta 9845 38BratislavaSlovakia
| | - Peter Both
- School of Chemistry, Manchester Institute of BiotechnologyThe University of Manchester131 Princess StreetManchesterM1 7DNUK
| | - Peter Kasak
- Center for Advanced MaterialsQatar UniversityP.O. Box 2713DohaQatar
| | - Jan Tkac
- Department of Glycobiotechnology, Institute of ChemistrySlovak Academy of SciencesDubravska cesta 9845 38BratislavaSlovakia
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23
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He J, Fang C, Shelp RA, Zimmt MB. Tracking Invisible Transformations of Physisorbed Monolayers: LDI-TOF and MALDI-TOF Mass Spectrometry as Complements to STM Imaging. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:459-467. [PMID: 27989120 DOI: 10.1021/acs.langmuir.6b03252] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Triphenyleneethynylene (TPEE) derivatives bearing one long aliphatic chain on each terminal aryl ring and two short aliphatic chains on the central aryl ring (core chains) self-assemble single component and 1-D patterned, two-component, crystalline monolayers at the solution-graphite interface. The monolayer morphology directs the core chains off the graphite, making them accessible for chemical reactions but invisible to imaging by scanning tunneling microscopy (STM). This precludes using STM to monitor transformations of the core chains, either by reaction or solution-monolayer exchange of TPEE molecules. Laser desorption/ionization time-of-flight mass spectrometry (LDI-TOF MS) successfully identifies TPEE compounds within physisorbed monolayers. The LDI-TOF spectra of TPEE monolayer-graphite samples exhibit strong molecular ion peaks and minimal fragmentation or background. LDI-TOF and STM techniques are combined to evaluate monolayer composition and morphology, track solution-monolayer exchange, to identify reaction products and to measure kinetics of chemical reactions at the solution-monolayer interface. LDI-TOF MS provides rapid qualitative evaluation of monolayer composition across a graphite substrate. Challenges to quantitative composition evaluation by LDI-TOF include compound-specific light absorption, surface desorption/ionization and fragmentation characteristics. For some, but not all, compounds, applying matrix onto a self-assembled monolayer increases molecular ion intensities and affords more accurate assessment of monolayer composition via matrix assisted laser desorption/ionization (MALDI) MS. Matrix addition precludes subsequent chemical or STM studies of the monolayer, whereas reactions and STM may be performed at nonirradiated regions following LDI-TOF measurements. LDI- and MALDI-TOF MS are useful complements to STM and are easily implemented tools for study of physisorbed monolayers.
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Affiliation(s)
- Jian He
- Department of Chemistry, Brown University , Providence, Rhode Island 02912, United States
| | - Chen Fang
- Department of Chemistry, Brown University , Providence, Rhode Island 02912, United States
| | - Russell A Shelp
- Department of Chemistry, Brown University , Providence, Rhode Island 02912, United States
| | - Matthew B Zimmt
- Department of Chemistry, Brown University , Providence, Rhode Island 02912, United States
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24
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Anderson LL, Berns EJ, Bugga P, George AL, Mrksich M. Measuring Drug Metabolism Kinetics and Drug-Drug Interactions Using Self-Assembled Monolayers for Matrix-Assisted Laser Desorption-Ionization Mass Spectrometry. Anal Chem 2016; 88:8604-9. [PMID: 27467208 DOI: 10.1021/acs.analchem.6b01750] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The competition of two drugs for the same metabolizing enzyme is a common mechanism for drug-drug interactions that can lead to altered kinetics in drug metabolism and altered elimination rates in vivo. With the prevalence of multidrug therapy, there is great potential for serious drug-drug interactions and adverse drug reactions. In an effort to prevent adverse drug reactions, the FDA mandates the evaluation of the potential for metabolic inhibition by every new chemical entity. Conventional methods for assaying drug metabolism (e.g., those based on HPLC) have been established for measuring drug-drug interactions; however, they are low-throughput. Here we describe an approach to measure the catalytic activity of CYP2C9 using the high-throughput technique self-assembled monolayers for matrix-assisted laser desorption-ionization (SAMDI) mass spectrometry. We measured the kinetics of CYP450 metabolism of the substrate, screened a set of drugs for inhibition of CYP2C9 and determined the Ki values for inhibitors. The throughput of this platform may enable drug metabolism and drug-drug interactions to be interrogated at a scale that cannot be achieved with current methods.
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Affiliation(s)
- Lyndsey L Anderson
- Department of Pharmacology, Northwestern University Feinberg School of Medicine , Chicago, Illinois 60611, United States
| | | | | | - Alfred L George
- Department of Pharmacology, Northwestern University Feinberg School of Medicine , Chicago, Illinois 60611, United States
| | - Milan Mrksich
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine , Chicago, Illinois 60611, United States
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25
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Berns EJ, Cabezas MD, Mrksich M. Cellular Assays with a Molecular Endpoint Measured by SAMDI Mass Spectrometry. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:3811-8. [PMID: 27240220 PMCID: PMC4981186 DOI: 10.1002/smll.201502940] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 01/12/2016] [Indexed: 05/07/2023]
Abstract
Cell-based, high-throughput screening (HTS) assays are increasingly important tools used in drug discovery, but frequently rely on readouts of gene expression or phenotypic changes and require development of specialized, labeled reporters. Here a cell-based, label-free assay compatible with HTS is introduced that can report quantitatively on enzyme activities by measuring mass changes of substrates with matrix-assisted laser desorption/ionization mass spectrometry. The assay uses self-assembled monolayers to culture cells on arrays presenting substrates, which serve as reporters for a desired enzyme activity. Each spot of cells is treated with a compound, cultured and lysed, enabling endogenous enzymes to act on the immobilized peptide substrate. It is demonstrated that the assay can measure protein tyrosine phosphatase (PTP) activity from as few as five cells and a screen is described that identifies a compound that reduces PTP activity in cell lysates. This approach offers a valuable addition to the methods available for cell-based screening.
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Affiliation(s)
- Eric J. Berns
- Department of Biomedical Engineering, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, 60611, USA
| | - Maria D. Cabezas
- Department of Biomedical Engineering, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, 60611, USA
| | - Milan Mrksich
- Department of Biomedical Engineering, Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, 60611, USA
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26
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Li X, Martin SJH, Chinoy ZS, Liu L, Rittgers B, Dluhy RA, Boons GJ. Label-Free Detection of Glycan-Protein Interactions for Array Development by Surface-Enhanced Raman Spectroscopy (SERS). Chemistry 2016; 22:11180-11185. [PMID: 27304194 DOI: 10.1002/chem.201602706] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Indexed: 12/20/2022]
Abstract
A glyco-array platform has been developed, in which glycans are attached to plasmonic nanoparticles through strain-promoted azide-alkyne cycloaddition. Glycan-protein binding events can then be detected in a label-free manner employing surface-enhanced Raman spectroscopy (SERS). As proof of concept, we have analyzed the binding of Gal1, Gal3, and influenza hemagglutinins (HAs) to various glycans and demonstrated that binding partners can be identified with high confidence. The attraction of SERS for optical sensing is that it can provide unique spectral signatures for glycan-protein complexes, confirm identity through statistical validation, and minimizes false positive results common to indirect methods. Furthermore, SERS is very sensitive and has multiplexing capabilities thereby allowing the simultaneous detection of multiple analytes.
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Affiliation(s)
- Xiuru Li
- Complex Carbohydrate Research Center and Department of Chemistry The University of Georgia, 315 Riverbend Road, Athens, GA 30602 (USA)
| | - Sharon J H Martin
- Department of Chemistry, The University of Georgia Athens, GA 30602 (USA)
| | - Zoeisha S Chinoy
- Complex Carbohydrate Research Center and Department of Chemistry The University of Georgia, 315 Riverbend Road, Athens, GA 30602 (USA).,Department of Chemistry, The University of Georgia Athens, GA 30602 (USA)
| | - Lin Liu
- Complex Carbohydrate Research Center and Department of Chemistry The University of Georgia, 315 Riverbend Road, Athens, GA 30602 (USA)
| | - Brandon Rittgers
- Department of Chemistry, The University of Georgia Athens, GA 30602 (USA)
| | - Richard A Dluhy
- Department of Chemistry, The University of Georgia Athens, GA 30602 (USA).,Department of Chemistry, The University of Alabama at Birmingham Birmingham, AL 35294 (USA)
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center and Department of Chemistry The University of Georgia, 315 Riverbend Road, Athens, GA 30602 (USA).,Department of Chemistry, The University of Georgia Athens, GA 30602 (USA).,Department of Chemical Biology and Drug Discovery Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University Universiteitsweg 99, 3584 CG Utrecht (The Netherlands)
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27
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Ambrose EA. Botulinum Neurotoxin, Tetanus Toxin, and Anthrax Lethal Factor Countermeasures. TOPICS IN MEDICINAL CHEMISTRY 2016. [DOI: 10.1007/7355_2016_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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28
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Diagne AB, Li S, Perkowski GA, Mrksich M, Thomson RJ. SAMDI Mass Spectrometry-Enabled High-Throughput Optimization of a Traceless Petasis Reaction. ACS COMBINATORIAL SCIENCE 2015; 17:658-62. [PMID: 26521847 DOI: 10.1021/acscombsci.5b00131] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Development of the self-assembled monolayer/MALDI mass spectrometry (SAMDI) platform to enable a high-throughput optimization of a traceless Petasis reaction is described. More than 1800 unique reactions were conducted simultaneously on an array of self-assembled monolayers of alkanethiolates on gold to arrive at optimized conditions, which were then successfully transferred to the solution phase. The utility of this reaction was validated by the efficient synthesis of a variety of di- and trisubstituted allenes.
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Affiliation(s)
- Abdallah B. Diagne
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Shuheng Li
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Gregory A. Perkowski
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Milan Mrksich
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Regan J. Thomson
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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29
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Kurbanov EK, Chiu TL, Solberg J, Francis S, Maize KM, Fernandez J, Johnson RL, Hawkinson JE, Walters MA, Finzel BC, Amin EA. Probing the S2′ Subsite of the Anthrax Toxin Lethal Factor Using Novel N-Alkylated Hydroxamates. J Med Chem 2015; 58:8723-33. [DOI: 10.1021/acs.jmedchem.5b01446] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elbek K. Kurbanov
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Ting-Lan Chiu
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Jonathan Solberg
- Institute
for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Subhashree Francis
- Institute
for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Kimberly M. Maize
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Jenna Fernandez
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Rodney L. Johnson
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Jon E. Hawkinson
- Institute
for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Michael A. Walters
- Institute
for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Barry C. Finzel
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Elizabeth Ambrose Amin
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55414, United States
- Minnesota
Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota 55455, United States
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30
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Kwon SR, Jeon CS, Hong NY, Kim KP, Hwang I, Chung TD. Gold-plated magnetic polymers for highly specific enrichment and label-free detection of blood biomarkers under physiological conditions. Chem Commun (Camb) 2015; 50:10066-9. [PMID: 25036285 DOI: 10.1039/c4cc04281f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A mass-based label-free detection of blood biomarkers under physiological conditions is realised using gold-plated magnetic polymer microspheres covered with self-assembled monolayers of polyethylene glycol alkanethiolates that effectively prevent heavy nonspecific binding of serum proteins.
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Affiliation(s)
- Seung-Ryong Kwon
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea.
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31
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Kim S, Oh H, Yeo WS. Analysis of alkanethiolates on gold with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/s13765-015-0018-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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32
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Kang H, Kim Y, Choi I, Chang R, Yeo WS. Determination of self-exchange rate of alkanethiolates in self-assembled monolayers on gold using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal Chim Acta 2014; 843:38-45. [PMID: 25150695 DOI: 10.1016/j.aca.2014.07.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/18/2014] [Accepted: 07/20/2014] [Indexed: 10/25/2022]
Abstract
In this paper, we describe a new method for determining the exchange rates of alkanethiolates in self-assembled monolayers (SAMs) on gold using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze the compositions of the alkanethiolate in SAMs rapidly and directly. In particular, to investigate the self-exchange of alkanethiols, we prepared a deuterated alkanethiol that has the same molecular properties as the non-deuterated alkanethiol but a different molecular weight. SAMs consisting of deuterated alkanethiolates were immersed in a solution of the non-deuterated alkanethiol, and the influences of the immersion time, temperature, concentration, and solvent on the self-exchange rates were investigated. Furthermore, we assessed the exchange rates among alkanethiols with different carbon chain lengths and different size of ethylene glycol units. In addition, we performed molecular dynamics simulations using a model SAM system in order to understand the molecular mechanism of the exchange process.
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Affiliation(s)
- Hyunook Kang
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Seoul 143-701, Republic of Korea
| | - Yongbin Kim
- Department of Chemistry, Kwangwoon University, Seoul 139-701, Republic of Korea
| | - Inseong Choi
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Seoul 143-701, Republic of Korea
| | - Rakwoo Chang
- Department of Chemistry, Kwangwoon University, Seoul 139-701, Republic of Korea
| | - Woon-Seok Yeo
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Seoul 143-701, Republic of Korea.
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33
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de Rond T, Danielewicz M, Northen T. High throughput screening of enzyme activity with mass spectrometry imaging. Curr Opin Biotechnol 2014; 31:1-9. [PMID: 25129648 DOI: 10.1016/j.copbio.2014.07.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 07/29/2014] [Accepted: 07/29/2014] [Indexed: 10/24/2022]
Abstract
Mass spectrometry imaging (MSI) has found a diversity of applications ranging from localizing metabolites and proteins in tissues to investigating microbial interactions, and as a result is perhaps the fastest growing subfield of mass spectrometry. Advances in surface mass spectrometry technologies are equally applicable to the analysis of arrayed samples. One promising field in which this capacity has been leveraged is the high-throughput analysis of enzyme activity, an important step in the development of a wide range of biotechnologies. This review article describes several emerging approaches that seek to improve the quality and scope of this application of MSI.
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Affiliation(s)
- Tristan de Rond
- Dept. of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Megan Danielewicz
- Lawrence Berkeley National Lab, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Trent Northen
- Lawrence Berkeley National Lab, One Cyclotron Road, Berkeley, CA 94720, USA; Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA.
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34
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Gray CJ, Weissenborn MJ, Eyers CE, Flitsch SL. Enzymatic reactions on immobilised substrates. Chem Soc Rev 2014; 42:6378-405. [PMID: 23579870 DOI: 10.1039/c3cs60018a] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This review gives an overview of enzymatic reactions that have been conducted on substrates attached to solid surfaces. Such biochemical reactions have become more important with the drive to miniaturisation and automation in chemistry, biology and medicine. Technical aspects such as choice of solid surface and analytical methods are discussed and examples of enzyme reactions that have been successful on these surfaces are provided.
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Affiliation(s)
- Christopher J Gray
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Road, Manchester, M1 7DN, UK
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35
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HA MS, SEO H, BAE DH, YEO WS. Detection of Enrofloxacin and Its Metabolite Ciprofloxacin Using Gold Nanoparticles and Laser Desorption/Ionization Time-of-Flight Mass Spectrometry. ANAL SCI 2014; 30:451-5. [DOI: 10.2116/analsci.30.451] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Mi-Sun HA
- Department of Bioscience and Biotechnology, Konkuk University
| | - Hyunjung SEO
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University
| | - Dong-Ho BAE
- Department of Bioscience and Biotechnology, Konkuk University
| | - Woon-Seok YEO
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University
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36
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Both P, Green AP, Gray CJ, Sardzík R, Voglmeir J, Fontana C, Austeri M, Rejzek M, Richardson D, Field RA, Widmalm G, Flitsch SL, Eyers CE. Discrimination of epimeric glycans and glycopeptides using IM-MS and its potential for carbohydrate sequencing. Nat Chem 2013; 6:65-74. [PMID: 24345949 DOI: 10.1038/nchem.1817] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 11/05/2013] [Indexed: 12/14/2022]
Abstract
Mass spectrometry is the primary analytical technique used to characterize the complex oligosaccharides that decorate cell surfaces. Monosaccharide building blocks are often simple epimers, which when combined produce diastereomeric glycoconjugates indistinguishable by mass spectrometry. Structure elucidation frequently relies on assumptions that biosynthetic pathways are highly conserved. Here, we show that biosynthetic enzymes can display unexpected promiscuity, with human glycosyltransferase pp-α-GanT2 able to utilize both uridine diphosphate N-acetylglucosamine and uridine diphosphate N-acetylgalactosamine, leading to the synthesis of epimeric glycopeptides in vitro. Ion-mobility mass spectrometry (IM-MS) was used to separate these structures and, significantly, enabled characterization of the attached glycan based on the drift times of the monosaccharide product ions generated following collision-induced dissociation. Finally, ion-mobility mass spectrometry following fragmentation was used to determine the nature of both the reducing and non-reducing glycans of a series of epimeric disaccharides and the branched pentasaccharide Man3 glycan, demonstrating that this technique may prove useful for the sequencing of complex oligosaccharides.
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Affiliation(s)
- P Both
- 1] School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK [2]
| | - A P Green
- 1] School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK [2]
| | - C J Gray
- 1] School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK [2]
| | - R Sardzík
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - J Voglmeir
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - C Fontana
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - M Austeri
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - M Rejzek
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - D Richardson
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - R A Field
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - G Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - S L Flitsch
- 1] School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK [2]
| | - C E Eyers
- 1] School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK [2]
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37
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Cheng X, Hiras J, Deng K, Bowen B, Simmons BA, Adams PD, Singer SW, Northen TR. High throughput nanostructure-initiator mass spectrometry screening of microbial growth conditions for maximal β-glucosidase production. Front Microbiol 2013; 4:365. [PMID: 24367356 PMCID: PMC3854461 DOI: 10.3389/fmicb.2013.00365] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 11/17/2013] [Indexed: 11/13/2022] Open
Abstract
Production of biofuels via enzymatic hydrolysis of complex plant polysaccharides is a subject of intense global interest. Microbial communities are known to express a wide range of enzymes necessary for the saccharification of lignocellulosic feedstocks and serve as a powerful reservoir for enzyme discovery. However, the growth temperature and conditions that yield high cellulase activity vary widely, and the throughput to identify optimal conditions has been limited by the slow handling and conventional analysis. A rapid method that uses small volumes of isolate culture to resolve specific enzyme activity is needed. In this work, a high throughput nanostructure-initiator mass spectrometry (NIMS)-based approach was developed for screening a thermophilic cellulolytic actinomycete, Thermobispora bispora, for β-glucosidase production under various growth conditions. Media that produced high β-glucosidase activity were found to be I/S + glucose or microcrystalline cellulose (MCC), Medium 84 + rolled oats, and M9TE + MCC at 45°C. Supernatants of cell cultures grown in M9TE + 1% MCC cleaved 2.5 times more substrate at 45°C than at all other temperatures. While T. bispora is reported to grow optimally at 60°C in Medium 84 + rolled oats and M9TE + 1% MCC, approximately 40% more conversion was observed at 45°C. This high throughput NIMS approach may provide an important tool in discovery and characterization of enzymes from environmental microbes for industrial and biofuel applications.
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Affiliation(s)
- Xiaoliang Cheng
- 1Technology Division, Joint BioEnergy Institute Emeryville, CA, USA ; 2Department of Bioenergy/GTL & Structural Biology, Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Jennifer Hiras
- 3Deconstruction Division, Joint BioEnergy Institute Emeryville, CA, USA ; 4Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Kai Deng
- 1Technology Division, Joint BioEnergy Institute Emeryville, CA, USA ; 5Biological and Materials Science Center, Sandia National Laboratories Livermore, CA, USA
| | - Benjamin Bowen
- 2Department of Bioenergy/GTL & Structural Biology, Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Blake A Simmons
- 3Deconstruction Division, Joint BioEnergy Institute Emeryville, CA, USA ; 5Biological and Materials Science Center, Sandia National Laboratories Livermore, CA, USA
| | - Paul D Adams
- 1Technology Division, Joint BioEnergy Institute Emeryville, CA, USA ; 4Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Steven W Singer
- 3Deconstruction Division, Joint BioEnergy Institute Emeryville, CA, USA ; 6Department of Geochemistry, Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA ; 7Department of Ecology, Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Trent R Northen
- 1Technology Division, Joint BioEnergy Institute Emeryville, CA, USA ; 2Department of Bioenergy/GTL & Structural Biology, Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
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38
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Li J, Lipson RH. Assays Using a NIMS Chip: Loosely Bound but Highly Selective. Anal Chem 2013; 85:6860-5. [DOI: 10.1021/ac401101j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- J. Li
- Department of Chemistry, University of Victoria, P.O. Box 3065,
Stn CSC, Victoria BC V8W 3V6, Canada
| | - R. H. Lipson
- Department of Chemistry, University of Victoria, P.O. Box 3065,
Stn CSC, Victoria BC V8W 3V6, Canada
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39
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Beloqui A, Calvo J, Serna S, Yan S, Wilson IBH, Martin-Lomas M, Reichardt NC. Analysis of Microarrays by MALDI-TOF MS. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302455] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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40
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Beloqui A, Calvo J, Serna S, Yan S, Wilson IBH, Martin-Lomas M, Reichardt NC. Analysis of microarrays by MALDI-TOF MS. Angew Chem Int Ed Engl 2013; 52:7477-81. [PMID: 23757366 DOI: 10.1002/anie.201302455] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Indexed: 01/21/2023]
Abstract
Ligand libraries can be printed onto a sandwich composed of activated lipids embedded in a hydrophobic layer conjugated to an indium-tin oxide (ITO) surface. Arrays produced this way can be analyzed by fluorescence spectroscopy and mass spectrometry. Applications include the assignment of enzyme specificity, the profiling of glycoforms and the identification of lectins.
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Affiliation(s)
- Ana Beloqui
- CICbiomaGUNE, Biofunctional Nanomaterials Unit, Paseo Miramon 182, 20009 San Sebastian, Spain
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Li J, Hu XK, Lipson RH. On-chip Enrichment and Analysis of Peptide Subsets Using a Maleimide-functionalized Fluorous Affinity Biochip and Nanostructure Initiator Mass Spectrometry. Anal Chem 2013; 85:5499-505. [DOI: 10.1021/ac4006233] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- J. Li
- Department
of Chemistry, University of Victoria, P.O.
Box 3065, Stn CSC, Victoria, British Columbia V8W 3V6, Canada
| | - X. K. Hu
- Department
of Chemistry, University of Victoria, P.O.
Box 3065, Stn CSC, Victoria, British Columbia V8W 3V6, Canada
| | - R. H. Lipson
- Department
of Chemistry, University of Victoria, P.O.
Box 3065, Stn CSC, Victoria, British Columbia V8W 3V6, Canada
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Enhanced cell adhesion and mature intracellular structure promoted by squaramide-based RGD mimics on bioinert surfaces. Bioorg Med Chem 2013; 21:2210-2216. [DOI: 10.1016/j.bmc.2013.02.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 02/05/2013] [Accepted: 02/13/2013] [Indexed: 01/21/2023]
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Chiu TL, Amin EA. Development of a comprehensive, validated pharmacophore hypothesis for anthrax toxin lethal factor (LF) inhibitors using genetic algorithms, Pareto scoring, and structural biology. J Chem Inf Model 2012; 52:1886-97. [PMID: 22697455 PMCID: PMC3477282 DOI: 10.1021/ci300121p] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Anthrax is an acute infectious disease caused by the spore-forming bacterium Bacillus anthracis. The anthrax toxin lethal factor (LF), an 89-kDa zinc hydrolase secreted by the bacilli, is the toxin component chiefly responsible for pathogenesis and has been a popular target for rational and structure-based drug design. Although hundreds of small-molecule compounds have been designed to target the LF active site, relatively few reported inhibitors have exhibited activity in cell-based assays, and no LF inhibitor is currently available to treat or prevent anthrax. This study presents a new pharmacophore map assembly, validated by experiment, designed to rapidly identify and prioritize promising LF inhibitor scaffolds from virtual compound libraries. The new hypothesis incorporates structural information from all five available LF enzyme-inhibitor complexes deposited in the Protein Data Bank (PDB) and is the first LF pharmacophore map reported to date that includes features representing interactions involving all three key subsites of the LF catalytic binding region. In a wide-ranging validation study on all 546 compounds for which published LF biological activity data exist, this model displayed strong selectivity toward nanomolar-level LF inhibitors, successfully identifying 72.1% of existing nanomolar-level compounds in an unbiased test set, while rejecting 100% of weakly active (>100 μM) compounds. In addition to its capabilities as a database searching tool, this comprehensive model points to a number of key design principles and previously unidentified ligand-receptor interactions that are likely to influence compound potency.
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Affiliation(s)
- Ting-Lan Chiu
- Department of Medicinal Chemistry and Minnesota Supercomputing Institute for Advanced Computational Research, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959
| | - Elizabeth A. Amin
- Department of Medicinal Chemistry and Minnesota Supercomputing Institute for Advanced Computational Research, University of Minnesota, 717 Delaware St. SE, Minneapolis, Minnesota 55414-2959
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45
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Ban L, Pettit N, Li L, Stuparu AD, Cai L, Chen W, Guan W, Han W, Wang PG, Mrksich M. Discovery of glycosyltransferases using carbohydrate arrays and mass spectrometry. Nat Chem Biol 2012; 8:769-73. [PMID: 22820418 PMCID: PMC3471075 DOI: 10.1038/nchembio.1022] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Accepted: 06/08/2012] [Indexed: 01/23/2023]
Abstract
Glycosyltransferases (GTs) catalyze the reaction between an activated sugar donor and an acceptor to form a new glycosidic linkage. GTs are responsible for the assembly of oligosaccharides in vivo and are also important for the in vitro synthesis of these biomolecules. However, the functional identification and characterization of new GTs are both difficult and tedious. This paper describes an approach that combines arrays of reactions on an immobilized array of acceptors with analysis by mass spectrometry to screen putative GTs. A total of 14,280 combinations of GT, acceptor and donor in four buffer conditions were screened and led to the identification and characterization of four new GTs. This work is significant because it provides a label-free method for the rapid functional annotation of putative enzymes.
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Affiliation(s)
- Lan Ban
- Howard Hughes Medical Institute, Northwestern University, Evanston, IL, USA
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46
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Choi I, Yeo WS. Self-Assembled Monolayers with Dynamicity Stemming from (Bio)Chemical Conversions: From Construction to Application. Chemphyschem 2012; 14:55-69. [DOI: 10.1002/cphc.201200293] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Indexed: 11/11/2022]
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Šardzík R, Green AP, Laurent N, Both P, Fontana C, Voglmeir J, Weissenborn MJ, Haddoub R, Grassi P, Haslam SM, Widmalm G, Flitsch SL. Chemoenzymatic Synthesis of O-Mannosylpeptides in Solution and on Solid Phase. J Am Chem Soc 2012; 134:4521-4. [DOI: 10.1021/ja211861m] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Robert Šardzík
- School of Chemistry, Manchester
Interdisciplinary Biocentre, The University of Manchester, Manchester M1 7DN, U.K
| | - Anthony P. Green
- School of Chemistry, Manchester
Interdisciplinary Biocentre, The University of Manchester, Manchester M1 7DN, U.K
| | - Nicolas Laurent
- School of Chemistry, Manchester
Interdisciplinary Biocentre, The University of Manchester, Manchester M1 7DN, U.K
| | - Peter Both
- School of Chemistry, Manchester
Interdisciplinary Biocentre, The University of Manchester, Manchester M1 7DN, U.K
| | - Carolina Fontana
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Josef Voglmeir
- School of Chemistry, Manchester
Interdisciplinary Biocentre, The University of Manchester, Manchester M1 7DN, U.K
| | - Martin J. Weissenborn
- School of Chemistry, Manchester
Interdisciplinary Biocentre, The University of Manchester, Manchester M1 7DN, U.K
| | - Rose Haddoub
- School of Chemistry, Manchester
Interdisciplinary Biocentre, The University of Manchester, Manchester M1 7DN, U.K
| | - Paola Grassi
- Division of Molecular Biosciences,
Faculty of Natural Sciences, Imperial College London, London, SW7 2AZ, U.K
| | - Stuart M. Haslam
- Division of Molecular Biosciences,
Faculty of Natural Sciences, Imperial College London, London, SW7 2AZ, U.K
| | - Göran Widmalm
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Sabine L. Flitsch
- School of Chemistry, Manchester
Interdisciplinary Biocentre, The University of Manchester, Manchester M1 7DN, U.K
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Laurent N, Haddoub R, Voglmeir J, Flitsch SL. MALDI-ToF MS analysis of glycosyltransferase activities on gold surface arrays. Methods Mol Biol 2012; 808:269-284. [PMID: 22057532 DOI: 10.1007/978-1-61779-373-8_19] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Glycan-processing enzymes such as glycosyltransferases and glycosidases are responsible for the makeup of the glycome. The definition of their substrate specificities is, therefore, a central task in glycomics. In addition, these enzymes are themselves useful synthetic tools for the generation of complex carbohydrate structures as an alternative to tedious chemical synthesis. There has been great interest in using microarrays for studying these glycoenzymes because it allows the specificity of the enzyme to be probed against a panel of immobilized potential substrates, and also expands the repertoire of sugar arrays available for further carbohydrate-protein interaction studies. In particular, self-assembled monolayers (SAMs) of alkanethiols on gold surfaces have proven to be a valuable platform for such studies due to their robustness and their biocompatible, well-defined structure. Furthermore, a direct observation of the change in mass of immobilized substrates due to enzymatic processing is possible through label-free MALDI-ToF MS (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry) technique. In this chapter, we describe the preparation of SAMs-coated gold surface arrays presenting carbohydrate or (glyco)peptide substrates, either pre-formed or directly synthesized on-chip, and MALDI-ToF MS analysis of glycosyltransferase activities on these immobilized substrates.
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Affiliation(s)
- Nicolas Laurent
- Manchester Interdisciplinary Biocentre & School of Chemistry, The University of Manchester, Manchester, UK
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Abstract
Glycan microarrays, carrying hundreds of different sugars on chip surfaces, have become a standard tool for the study of interactions of biomolecules with carbohydrates. The chip-based format offers important advantages, including the ability to screen in parallel several thousand binding events on a single slide, the minimal amount of sample required for one experiment, and the multivalent display of sugars on the chip that mimics the presentation of carbohydrates in nature. This chapter presents recent advances and future challenges in glycan microarray technology. We describe different immobilization and detection methods as well as applications in glycomics, drug discovery, and biomedicine.
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Affiliation(s)
- José L de Paz
- Instituto de Investigaciones Químicas, Centro de Investigaciones Científicas Isla de la Cartuja, CSIC and US, Sevilla, Spain.
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50
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Beloqui A, Sanchez-Ruiz A, Martin-Lomas M, Reichardt NC. A surface-based mass spectrometry method for screening glycosidase specificity in environmental samples. Chem Commun (Camb) 2011; 48:1701-3. [PMID: 22189916 DOI: 10.1039/c2cc16537f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A new surface-based MALDI-Tof-MS glycosyl hydrolase assay has been developed in which lipid-tagged oligosaccharides, representing defined fragments of major plant cell wall polysaccharides, are immobilized via hydrophobic interactions on an alkylthiol functionalised gold sample plate and employed in the functional screening of several purified enzymes, environmental samples and saliva.
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Affiliation(s)
- Ana Beloqui
- Biofunctional Nanomaterials Department, CICbiomaGUNE, Paseo Miramon 182, 20009 San Sebastian, Spain
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