1
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Sternicki LM, Poulsen SA. Native Mass Spectrometry: Insights and Opportunities for Targeted Protein Degradation. Anal Chem 2023; 95:18655-18666. [PMID: 38090751 DOI: 10.1021/acs.analchem.3c03853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Native mass spectrometry (nMS) is one of the most powerful biophysical methods for the direct observation of noncovalent protein interactions with both small molecules and other proteins. With the advent of targeted protein degradation (TPD), nMS is now emerging as a compelling approach to characterize the multiple fundamental interactions that underpin the TPD mechanism. Specifically, nMS enables the simultaneous observation of the multiple binary and ternary complexes [i.e., all combinations of E3 ligase, target protein of interest, and small molecule proximity-inducing reagents (such as PROteolysis TArgeting Chimeras (PROTACs) and molecular glues)], formed as part of the TPD equilibrium; this is not possible with any other biophysical method. In this paper we overview the proof-of-concept applications of nMS within the field of TPD and demonstrate how it is providing researchers with critical insight into the systems under study. We also provide an outlook on the scope and future opportunities offered by nMS as a core and agnostic biophysical tool for advancing research developments in TPD.
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Affiliation(s)
- Louise M Sternicki
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, Queensland 4111, Australia
| | - Sally-Ann Poulsen
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, Queensland 4111, Australia
- School of Environment and Science, Griffith University, Nathan, Brisbane, Queensland 4111, Australia
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2
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Westphall MS, Lee KW, Salome AZ, Coon JJ, Grant T. Mass spectrometers as cryoEM grid preparation instruments. Curr Opin Struct Biol 2023; 83:102699. [PMID: 37703606 PMCID: PMC11019453 DOI: 10.1016/j.sbi.2023.102699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 07/18/2023] [Accepted: 08/15/2023] [Indexed: 09/15/2023]
Abstract
Structure determination by single-particle cryoEM has matured into a core structural biology technique. Despite many methodological advancements, most cryoEM grids are still prepared using the plunge-freezing method developed ∼40 years ago. Embedding samples in thin films and exposing them to the air-water interface often leads to sample damage and preferential orientation of the particles. Using native mass spectrometry to create cryoEM samples, potentially avoids these problems and allows the use of mass spectrometry sample isolation techniques during EM grid creation. We review the recent publications that have demonstrated protein complexes can be ionized, flown through the mass spectrometer, gently landed onto EM grids, imaged, and reconstructed in 3D. Although many uncertainties and challenges remain, the combination of cryoEM and MS has great potential.
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Affiliation(s)
- Michael S Westphall
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Kenneth W Lee
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Austin Z Salome
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Joshua J Coon
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States; Morgridge Institute for Research, 330 N Orchard Street, Madison, WI 53706, United States.
| | - Timothy Grant
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, United States; Morgridge Institute for Research, 330 N Orchard Street, Madison, WI 53706, United States.
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3
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Villa R, Nieto S, Donaire A, Lozano P. Direct Biocatalytic Processes for CO 2 Capture as a Green Tool to Produce Value-Added Chemicals. Molecules 2023; 28:5520. [PMID: 37513391 PMCID: PMC10383722 DOI: 10.3390/molecules28145520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/14/2023] [Accepted: 07/16/2023] [Indexed: 07/30/2023] Open
Abstract
Direct biocatalytic processes for CO2 capture and transformation in value-added chemicals may be considered a useful tool for reducing the concentration of this greenhouse gas in the atmosphere. Among the other enzymes, carbonic anhydrase (CA) and formate dehydrogenase (FDH) are two key biocatalysts suitable for this challenge, facilitating the uptake of carbon dioxide from the atmosphere in complementary ways. Carbonic anhydrases accelerate CO2 uptake by promoting its solubility in water in the form of hydrogen carbonate as the first step in converting the gas into a species widely used in carbon capture storage and its utilization processes (CCSU), particularly in carbonation and mineralization methods. On the other hand, formate dehydrogenases represent the biocatalytic machinery evolved by certain organisms to convert CO2 into enriched, reduced, and easily transportable hydrogen species, such as formic acid, via enzymatic cascade systems that obtain energy from chemical species, electrochemical sources, or light. Formic acid is the basis for fixing C1-carbon species to other, more reduced molecules. In this review, the state-of-the-art of both methods of CO2 uptake is assessed, highlighting the biotechnological approaches that have been developed using both enzymes.
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Affiliation(s)
- Rocio Villa
- Departamento de Bioquímica y Biología Molecular B e Inmunología, Facultad de Química, Universidad de Murcia, 30100 Murcia, Spain
- Department of Biotechnology, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Susana Nieto
- Departamento de Bioquímica y Biología Molecular B e Inmunología, Facultad de Química, Universidad de Murcia, 30100 Murcia, Spain
| | - Antonio Donaire
- Departamento de Química Inorgánica, Facultad de Química, Universidad de Murcia, 30100 Murcia, Spain
| | - Pedro Lozano
- Departamento de Bioquímica y Biología Molecular B e Inmunología, Facultad de Química, Universidad de Murcia, 30100 Murcia, Spain
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4
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Vaaltyn MC, Mateos‐Jimenez M, Müller R, Mackay CL, Edkins AL, Clarke DJ, Veale CGL. Native Mass Spectrometry-Guided Screening Identifies Hit Fragments for HOP-HSP90 PPI Inhibition. Chembiochem 2022; 23:e202200322. [PMID: 36017658 PMCID: PMC9826382 DOI: 10.1002/cbic.202200322] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/25/2022] [Indexed: 01/11/2023]
Abstract
Contemporary medicinal chemistry considers fragment-based drug discovery (FBDD) and inhibition of protein-protein interactions (PPI) as important means of expanding the volume of druggable chemical space. However, the ability to robustly identify valid fragments and PPI inhibitors is an enormous challenge, requiring the application of sensitive biophysical methodology. Accordingly, in this study, we exploited the speed and sensitivity of nanoelectrospray (nano-ESI) native mass spectrometry to identify a small collection of fragments which bind to the TPR2AB domain of HOP. Follow-up biophysical assessment of a small selection of binding fragments confirmed binding to the single TPR2A domain, and that this binding translated into PPI inhibitory activity between TPR2A and the HSP90 C-terminal domain. An in-silico assessment of binding fragments at the PPI interfacial region, provided valuable structural insight for future fragment elaboration strategies, including the identification of losartan as a weak, albeit dose-dependent inhibitor of the target PPI.
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Affiliation(s)
- Michaelone C. Vaaltyn
- The Biomedical Biotechnology Research Unit (BioBRU) Department of Biochemistry and Microbiology DepartmentRhodes UniversityMakhanda6139South Africa
| | - Maria Mateos‐Jimenez
- EaStCHEM School of ChemistryJoseph Black Building, David Brewster RoadEdinburghEH93FJUK
| | - Ronel Müller
- School of Chemistry and PhysicsUniversity of KwaZulu-NatalScottsville3209South Africa
| | - C. Logan Mackay
- EaStCHEM School of ChemistryJoseph Black Building, David Brewster RoadEdinburghEH93FJUK
| | - Adrienne L. Edkins
- The Biomedical Biotechnology Research Unit (BioBRU) Department of Biochemistry and Microbiology DepartmentRhodes UniversityMakhanda6139South Africa
| | - David J. Clarke
- EaStCHEM School of ChemistryJoseph Black Building, David Brewster RoadEdinburghEH93FJUK
| | - Clinton G. L. Veale
- Department of ChemistryUniversity of Cape Town RondeboschCape Town7700South Africa
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5
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Combs J, Andring J, McKenna R. Ibuprofen: a weak inhibitor of carbonic anhydrase II. Acta Crystallogr F Struct Biol Commun 2022; 78:395-402. [PMID: 36322425 PMCID: PMC9629514 DOI: 10.1107/s2053230x22009761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/05/2022] [Indexed: 11/22/2022] Open
Abstract
Carbonic anhydrases (CAs) are drug targets for a variety of diseases. While many clinically relevant CA inhibitors are sulfonamide-based, novel CA inhibitors are being developed that incorporate alternative zinc-binding groups, such as carboxylic acid moieties, to develop CA isoform-specific inhibitors. Here, the X-ray crystal structure of human CA II (hCA II) in complex with the carboxylic acid ibuprofen [2-(4-isobutylphenyl)propanoic acid, a common over-the-counter nonsteroidal anti-inflammatory drug] is reported to 1.54 Å resolution. The binding of ibuprofen is overlaid with the structures of other carboxylic acids in complex with hCA II to compare their inhibition mechanisms by direct or indirect (via a water) binding to the active-site zinc. Additionally, enzyme-inhibition assays using ibuprofen, nicotinic acid and ferulic acid were performed with hCA II to determine their IC50 values and were compared with those of other carboxylic acid binders. This study discusses the potential development of CA inhibitors utilizing the carboxylic acid moiety.
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Affiliation(s)
- Jacob Combs
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Jacob Andring
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
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6
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Togre NS, Vargas AM, Bhargavi G, Mallakuntla MK, Tiwari S. Fragment-Based Drug Discovery against Mycobacteria: The Success and Challenges. Int J Mol Sci 2022; 23:ijms231810669. [PMID: 36142582 PMCID: PMC9500838 DOI: 10.3390/ijms231810669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/10/2022] [Accepted: 09/10/2022] [Indexed: 11/29/2022] Open
Abstract
The emergence of drug-resistant mycobacteria, including Mycobacterium tuberculosis (Mtb) and non-tuberculous mycobacteria (NTM), poses an increasing global threat that urgently demands the development of new potent anti-mycobacterial drugs. One of the approaches toward the identification of new drugs is fragment-based drug discovery (FBDD), which is the most ingenious among other drug discovery models, such as structure-based drug design (SBDD) and high-throughput screening. Specialized techniques, such as X-ray crystallography, nuclear magnetic resonance spectroscopy, and many others, are part of the drug discovery approach to combat the Mtb and NTM global menaces. Moreover, the primary drawbacks of traditional methods, such as the limited measurement of biomolecular toxicity and uncertain bioavailability evaluation, are successfully overcome by the FBDD approach. The current review focuses on the recognition of fragment-based drug discovery as a popular approach using virtual, computational, and biophysical methods to identify potent fragment molecules. FBDD focuses on designing optimal inhibitors against potential therapeutic targets of NTM and Mtb (PurC, ArgB, MmpL3, and TrmD). Additionally, we have elaborated on the challenges associated with the FBDD approach in the identification and development of novel compounds. Insights into the applications and overcoming the challenges of FBDD approaches will aid in the identification of potential therapeutic compounds to treat drug-sensitive and drug-resistant NTMs and Mtb infections.
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7
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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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8
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Petit GA, Mohanty B, McMahon RM, Nebl S, Hilko DH, Wilde KL, Scanlon MJ, Martin JL, Halili MA. Identification and characterization of two drug-like fragments that bind to the same cryptic binding pocket of Burkholderia pseudomallei DsbA. Acta Crystallogr D Struct Biol 2022; 78:75-90. [PMID: 34981764 PMCID: PMC8725163 DOI: 10.1107/s2059798321011475] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/29/2021] [Indexed: 01/10/2023] Open
Abstract
Disulfide-bond-forming proteins (Dsbs) play a crucial role in the pathogenicity of many Gram-negative bacteria. Disulfide-bond-forming protein A (DsbA) catalyzes the formation of the disulfide bonds necessary for the activity and stability of multiple substrate proteins, including many virulence factors. Hence, DsbA is an attractive target for the development of new drugs to combat bacterial infections. Here, two fragments, bromophenoxy propanamide (1) and 4-methoxy-N-phenylbenzenesulfonamide (2), were identified that bind to DsbA from the pathogenic bacterium Burkholderia pseudomallei, the causative agent of melioidosis. The crystal structures of oxidized B. pseudomallei DsbA (termed BpsDsbA) co-crystallized with 1 or 2 show that both fragments bind to a hydrophobic pocket that is formed by a change in the side-chain orientation of Tyr110. This conformational change opens a `cryptic' pocket that is not evident in the apoprotein structure. This binding location was supported by 2D-NMR studies, which identified a chemical shift perturbation of the Tyr110 backbone amide resonance of more than 0.05 p.p.m. upon the addition of 2 mM fragment 1 and of more than 0.04 p.p.m. upon the addition of 1 mM fragment 2. Although binding was detected by both X-ray crystallography and NMR, the binding affinity (Kd) for both fragments was low (above 2 mM), suggesting weak interactions with BpsDsbA. This conclusion is also supported by the crystal structure models, which ascribe partial occupancy to the ligands in the cryptic binding pocket. Small fragments such as 1 and 2 are not expected to have a high energetic binding affinity due to their relatively small surface area and the few functional groups that are available for intermolecular interactions. However, their simplicity makes them ideal for functionalization and optimization. The identification of the binding sites of 1 and 2 to BpsDsbA could provide a starting point for the development of more potent novel antimicrobial compounds that target DsbA and bacterial virulence.
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Affiliation(s)
- Guillaume A. Petit
- Griffith Institute for Drug Discovery, Griffith University, Building N75, 46 Don Young Road, Nathan, QLD 4111, Australia
| | - Biswaranjan Mohanty
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- ARC Centre for Fragment-Based Design, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Sydney Analytical Core Research Facility, The University of Sydney, Sydney, NSW 2006, Australia
| | - Róisín M. McMahon
- Griffith Institute for Drug Discovery, Griffith University, Building N75, 46 Don Young Road, Nathan, QLD 4111, Australia
| | - Stefan Nebl
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - David H. Hilko
- Griffith Institute for Drug Discovery, Griffith University, Building N75, 46 Don Young Road, Nathan, QLD 4111, Australia
| | - Karyn L. Wilde
- National Deuteration Facility, Australian Nuclear Science and Technology Organization (ANSTO), New Illawarra Road, Lucas Heights, NSW 2234, Australia
| | - Martin J. Scanlon
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- ARC Centre for Fragment-Based Design, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Jennifer L. Martin
- Griffith Institute for Drug Discovery, Griffith University, Building N75, 46 Don Young Road, Nathan, QLD 4111, Australia
- Vice-Chancellor’s Unit, University of Wollongong, Building 36, Wollongong, NSW 2522, Australia
| | - Maria A. Halili
- Griffith Institute for Drug Discovery, Griffith University, Building N75, 46 Don Young Road, Nathan, QLD 4111, Australia
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9
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Veale CGL, Mateos-Jiménez M, Vaaltyn MC, Müller R, Makhubu MP, Alhassan M, de la Torre BG, Albericio F, Mackay CL, Edkins AL, Clarke DJ. A native mass spectrometry platform identifies HOP inhibitors that modulate the HSP90-HOP protein-protein interaction. Chem Commun (Camb) 2021; 57:10919-10922. [PMID: 34591048 DOI: 10.1039/d1cc04257b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Herein we describe a native mass spectromery protein-peptide model as a competent surrogate for the HOP-HSP90 protein-protein interaction (PPI), application of which led to the qualititive identification of two new peptides capable of in vitro PPI disruption. This proof of concept study offers a viable alternative for PPI inhibitor screening.
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Affiliation(s)
- Clinton G L Veale
- FLAIR Research Fellow, School of Chemistry and Physics, Pietermaritzburg Campus, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, South Africa.
| | - Maria Mateos-Jiménez
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH93FJ, UK.
| | - Michaelone C Vaaltyn
- The Biomedical Biotechnology Research Unit (BioBRU), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Ronel Müller
- FLAIR Research Fellow, School of Chemistry and Physics, Pietermaritzburg Campus, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, South Africa.
| | - Matodzi P Makhubu
- The Biomedical Biotechnology Research Unit (BioBRU), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Mahama Alhassan
- FLAIR Research Fellow, School of Chemistry and Physics, Pietermaritzburg Campus, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, South Africa.
| | - Beatriz G de la Torre
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, South Africa
| | - Fernando Albericio
- FLAIR Research Fellow, School of Chemistry and Physics, Pietermaritzburg Campus, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, South Africa.
| | - C Logan Mackay
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH93FJ, UK.
| | - Adrienne L Edkins
- The Biomedical Biotechnology Research Unit (BioBRU), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - David J Clarke
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH93FJ, UK.
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10
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Kaeslin J, Brunner C, Ghiasikhou S, Schneider G, Zenobi R. Bioaffinity Screening with a Rapid and Sample-Efficient Autosampler for Native Electrospray Ionization Mass Spectrometry. Anal Chem 2021; 93:13342-13350. [PMID: 34546705 DOI: 10.1021/acs.analchem.1c03130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fast and efficient handling of ligands and biological targets are required in bioaffinity screening based on native electrospray ionization mass spectrometry (ESI-MS). We use a prototype microfluidic autosampler, called the "gap sampler", to sequentially mix and electrospray individual small molecule ligands together with a target protein and compare the screening results with data from thermal shift assay and surface plasmon resonance. In a first round, all three techniques were used for a screening of 110 ligands against bovine carbonic anhydrase II, which resulted in five mutual hits and some false positives with ESI-MS presumably due to the high ligand concentration or interferences from dimethyl sulfoxide. In a second round, 33 compounds were screened in lower concentrations and in a less complex matrix, resulting in only true positives with ESI-MS. Within a cycle time of 30 s, dissociation constants were determined within an order of magnitude accuracy consuming only 5 pmol of ligand and less than 15 pmol of protein per screened compound. In a third round, dissociation constants of five compounds were accurately determined in a titration experiment. Thus, the gap sampler can rapidly and efficiently be used for high-throughput screening.
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Affiliation(s)
- Jérôme Kaeslin
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
| | - Cyrill Brunner
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
| | - Sahar Ghiasikhou
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
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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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Abstract
![]()
Native mass spectrometry
(MS) involves the analysis and characterization
of macromolecules, predominantly intact proteins and protein complexes,
whereby as much as possible the native structural features of the
analytes are retained. As such, native MS enables the study of secondary,
tertiary, and even quaternary structure of proteins and other biomolecules.
Native MS represents a relatively recent addition to the analytical
toolbox of mass spectrometry and has over the past decade experienced
immense growth, especially in enhancing sensitivity and resolving
power but also in ease of use. With the advent of dedicated mass analyzers,
sample preparation and separation approaches, targeted fragmentation
techniques, and software solutions, the number of practitioners and
novel applications has risen in both academia and industry. This review
focuses on recent developments, particularly in high-resolution native
MS, describing applications in the structural analysis of protein
assemblies, proteoform profiling of—among others—biopharmaceuticals
and plasma proteins, and quantitative and qualitative analysis of
protein–ligand interactions, with the latter covering lipid,
drug, and carbohydrate molecules, to name a few.
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Affiliation(s)
- Sem Tamara
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Maurits A den Boer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
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13
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Mueller SL, Chrysanthopoulos PK, Halili MA, Hepburn C, Nebl T, Supuran CT, Nocentini A, Peat TS, Poulsen SA. The Glitazone Class of Drugs as Carbonic Anhydrase Inhibitors-A Spin-Off Discovery from Fragment Screening. Molecules 2021; 26:3010. [PMID: 34070212 PMCID: PMC8158703 DOI: 10.3390/molecules26103010] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/11/2021] [Accepted: 05/14/2021] [Indexed: 12/22/2022] Open
Abstract
The approved drugs that target carbonic anhydrases (CA, EC 4.2.1.1), a family of zinc metalloenzymes, comprise almost exclusively of primary sulfonamides (R-SO2NH2) as the zinc binding chemotype. New clinical applications for CA inhibitors, particularly for hard-to-treat cancers, has driven a growing interest in the development of novel CA inhibitors. We recently discovered that the thiazolidinedione heterocycle, where the ring nitrogen carries no substituent, is a new zinc binding group and an alternate CA inhibitor chemotype. This heterocycle is curiously also a substructure of the glitazone class of drugs used in the treatment options for type 2 diabetes. Herein, we investigate and characterise three glitazone drugs (troglitazone 11, rosiglitazone 12 and pioglitazone 13) for binding to CA using native mass spectrometry, protein X-ray crystallography and hydrogen-deuterium exchange (HDX) mass spectrometry, followed by CA enzyme inhibition studies. The glitazone drugs all displayed appreciable binding to and inhibition of CA isozymes. Given that thiazolidinediones are not credited as a zinc binding group nor known as CA inhibitors, our findings indicate that CA may be an off-target of these compounds when used clinically. Furthermore, thiazolidinediones may represent a new opportunity for the development of novel CA inhibitors as future drugs.
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Affiliation(s)
- Sarah L. Mueller
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, QLD 4111, Australia; (S.L.M.); (P.K.C.); (M.A.H.)
- ARC Centre for Fragment-Based Design, Griffith University, Nathan, Brisbane, QLD 4111, Australia
- CSIRO, Biomedical Manufacturing Program, Parkville, Melbourne, VIC 3052, Australia; (T.N.); (T.S.P.)
| | - Panagiotis K. Chrysanthopoulos
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, QLD 4111, Australia; (S.L.M.); (P.K.C.); (M.A.H.)
| | - Maria A. Halili
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, QLD 4111, Australia; (S.L.M.); (P.K.C.); (M.A.H.)
- ARC Centre for Fragment-Based Design, Griffith University, Nathan, Brisbane, QLD 4111, Australia
| | - Caryn Hepburn
- Waters Australia Pty Ltd., Rydalmere, NSW 2116, Australia;
| | - Tom Nebl
- CSIRO, Biomedical Manufacturing Program, Parkville, Melbourne, VIC 3052, Australia; (T.N.); (T.S.P.)
| | - Claudiu T. Supuran
- Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche Nutraceutiche, Università Degli Studi di Firenze, Sesto Fiorentino, 50019 Florence, Italy; (C.T.S.); (A.N.)
| | - Alessio Nocentini
- Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche Nutraceutiche, Università Degli Studi di Firenze, Sesto Fiorentino, 50019 Florence, Italy; (C.T.S.); (A.N.)
| | - Thomas S. Peat
- CSIRO, Biomedical Manufacturing Program, Parkville, Melbourne, VIC 3052, Australia; (T.N.); (T.S.P.)
| | - Sally-Ann Poulsen
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, QLD 4111, Australia; (S.L.M.); (P.K.C.); (M.A.H.)
- ARC Centre for Fragment-Based Design, Griffith University, Nathan, Brisbane, QLD 4111, Australia
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14
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De Simone G, Bua S, Supuran CT, Alterio V. Benzyl alcohol inhibits carbonic anhydrases by anchoring to the zinc coordinated water molecule. Biochem Biophys Res Commun 2021; 548:217-221. [PMID: 33647799 DOI: 10.1016/j.bbrc.2021.02.067] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 12/14/2022]
Abstract
Up to date alcohols have been scarcely investigated as carbonic anhydrase (CA) inhibitors. To get more insights into the CA inhibition properties of this class of molecules, in this paper, by means of inhibition assays and X-ray crystallographic studies we report a detailed characterization of the CA inhibition properties and the binding mode to human CA II of benzyl alcohol. Results show that, although possessing a very simple scaffold, this molecule acts as a micromolar CA II inhibitor, which anchors to the enzyme active site by means of an H-bond interaction with the zinc bound solvent molecule. Taken together our results clearly indicate primary alcohols as a class of CA inhibitors that deserve to be more investigated.
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Affiliation(s)
| | - Silvia Bua
- Neurofarba Department, Section of Pharmaceutical and Nutriceutical Sciences, Università degli Studi di Firenze, Sesto Fiorentino, Florence, Italy
| | - Claudiu T Supuran
- Neurofarba Department, Section of Pharmaceutical and Nutriceutical Sciences, Università degli Studi di Firenze, Sesto Fiorentino, Florence, Italy
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15
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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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16
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Diethelm-Varela B. Using NMR Spectroscopy in the Fragment-Based Drug Discovery of Small-Molecule Anticancer Targeted Therapies. ChemMedChem 2020; 16:725-742. [PMID: 33236493 DOI: 10.1002/cmdc.202000756] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/21/2020] [Indexed: 12/19/2022]
Abstract
Against the challenge of providing personalized cancer care, the development of targeted therapies stands as a promising approach. The discovery of these agents can benefit from fragment-based drug discovery (FBDD) methods that help guide ligand design and provide key structural information on the targets of interest. In particular, nuclear magnetic resonance spectroscopy is a promising biophysical tool in fragment discovery due to its detection capabilities and versatility. This review provides an overview of FBDD, describes the basis of NMR-based fragment screening, summarizes some exciting technical advances reported over the past decades, and closes with a discussion of selected case studies where this technique has been used as part of drug discovery campaigns to produce lead compounds towards the design of anti-cancer targeted therapies.
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Affiliation(s)
- Benjamin Diethelm-Varela
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., Baltimore, MD 21201, USA
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17
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Lv X, Fu H, Xie J, Liu Z, Tuo X. Integrated multi-techniques to probe the binding mechanism between amlodipine and lactate dehydrogenase. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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18
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D'Ambrosio K, Carradori S, Cesa S, Angeli A, Monti SM, Supuran CT, De Simone G. Catechols: a new class of carbonic anhydrase inhibitors. Chem Commun (Camb) 2020; 56:13033-13036. [PMID: 33000794 DOI: 10.1039/d0cc05172a] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
To date, catechols have been only poorly investigated as carbonic anhydrase (CA) inhibitors. Here we report the first structural information on the CA inhibition mechanism of these molecules, showing that they adopt a peculiar binding mode to the enzyme active site which involves the zinc-bound water molecule and the "deep water".
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Affiliation(s)
| | - Simone Carradori
- Department of Pharmacy, "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
| | - Stefania Cesa
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza University of Rome, 00185 Rome, Italy
| | - Andrea Angeli
- Neurofarba Department, Università degli Studi di Firenze, Sesto Fiorentino, Florence, Italy
| | - Simona M Monti
- Istituto di Biostrutture e Bioimmagini-CNR, Naples, Italy.
| | - Claudiu T Supuran
- Neurofarba Department, Università degli Studi di Firenze, Sesto Fiorentino, Florence, Italy
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19
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Zoppi C, Nocentini A, Supuran CT, Pratesi A, Messori L. Native mass spectrometry of human carbonic anhydrase I and its inhibitor complexes. J Biol Inorg Chem 2020; 25:979-993. [PMID: 32926233 PMCID: PMC7584553 DOI: 10.1007/s00775-020-01818-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/30/2020] [Indexed: 02/03/2023]
Abstract
Abstract Native mass spectrometry is a potent technique to study and characterize biomacromolecules in their native state. Here, we have applied this method to explore the solution chemistry of human carbonic anhydrase I (hCA I) and its interactions with four different inhibitors, namely three sulfonamide inhibitors (AAZ, MZA, SLC-0111) and the dithiocarbamate derivative of morpholine (DTC). Through high-resolution ESI-Q-TOF measurements, the native state of hCA I and the binding of the above inhibitors were characterized in the molecular detail. Native mass spectrometry was also exploited to assess the direct competition in solution among the various inhibitors in relation to their affinity constants. Additional studies were conducted on the interaction of hCA I with the metallodrug auranofin, under various solution and instrumental conditions. Auranofin is a selective reagent for solvent-accessible free cysteine residues, and its reactivity was analyzed also in the presence of CA inhibitors. Overall, our investigation reveals that native mass spectrometry represents an excellent tool to characterize the solution behavior of carbonic anhydrase. Graphic abstract ![]()
Electronic supplementary material The online version of this article (10.1007/s00775-020-01818-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Carlotta Zoppi
- Laboratory of Metals in Medicine (MetMed), Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy
| | - Alessio Nocentini
- Department of Neurofarba, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Via U. Schiff 6, 50019, Sesto Fiorentino, Italy
| | - Claudiu T Supuran
- Department of Neurofarba, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Via U. Schiff 6, 50019, Sesto Fiorentino, Italy
| | - Alessandro Pratesi
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124, Pisa, Italy.
| | - Luigi Messori
- Laboratory of Metals in Medicine (MetMed), Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy.
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20
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Anti-SARS-CoV-2 activities in vitro of Shuanghuanglian preparations and bioactive ingredients. Acta Pharmacol Sin 2020; 41:1167-1177. [PMID: 32737471 PMCID: PMC7393338 DOI: 10.1038/s41401-020-0483-6] [Citation(s) in RCA: 278] [Impact Index Per Article: 69.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 07/14/2020] [Indexed: 12/24/2022] Open
Abstract
Human infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19) and there is no cure currently. The 3CL protease (3CLpro) is a highly conserved protease which is indispensable for CoVs replication, and is a promising target for development of broad-spectrum antiviral drugs. In this study we investigated the anti-SARS-CoV-2 potential of Shuanghuanglian preparation, a Chinese traditional patent medicine with a long history for treating respiratory tract infection in China. We showed that either the oral liquid of Shuanghuanglian, the lyophilized powder of Shuanghuanglian for injection or their bioactive components dose-dependently inhibited SARS-CoV-2 3CLpro as well as the replication of SARS-CoV-2 in Vero E6 cells. Baicalin and baicalein, two ingredients of Shuanghuanglian, were characterized as the first noncovalent, nonpeptidomimetic inhibitors of SARS-CoV-2 3CLpro and exhibited potent antiviral activities in a cell-based system. Remarkably, the binding mode of baicalein with SARS-CoV-2 3CLpro determined by X-ray protein crystallography was distinctly different from those of known 3CLpro inhibitors. Baicalein was productively ensconced in the core of the substrate-binding pocket by interacting with two catalytic residues, the crucial S1/S2 subsites and the oxyanion loop, acting as a “shield” in front of the catalytic dyad to effectively prevent substrate access to the catalytic dyad within the active site. Overall, this study provides an example for exploring the in vitro potency of Chinese traditional patent medicines and effectively identifying bioactive ingredients toward a specific target, and gains evidence supporting the in vivo studies of Shuanghuanglian oral liquid as well as two natural products for COVID-19 treatment.
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21
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Veale CGL, Mateos Jimenez M, Mackay CL, Clarke DJ. Native ion mobility mass spectrometry reveals that small organic acid fragments impart gas-phase stability to carbonic anhydrase II. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8570. [PMID: 31479545 DOI: 10.1002/rcm.8570] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/25/2019] [Accepted: 08/28/2019] [Indexed: 06/10/2023]
Abstract
RATIONALE A key element of studies that utilise ion mobility mass spectrometry (IM-MS) under native electrospray conditions for the analysis of protein-ligand binding is the maintenance of the native conformation of a protein during the removal of bulk solvent. Ruotolo and co-workers have demonstrated that the binding and subsequent dissociation of the anionic component of inorganic salts stabilise native protein conformations in the gas phase. In this study, we investigated the effect that organic acid fragments identified from a fragment-based drug discovery (FBDD) campaign might have on the gas-phase stability of carbonic anhydrase II (CA II). METHODS We utilised native IM-MS to monitor changes in the conformation of CA II in the absence and presence of four acidic fragments. By performing a series of collision-induced unfolding (CIU) experiments we determined the effect of fragment binding on the gas-phase stability of CA II. RESULTS Binding and dissociation of acidic fragments result in increased gas-phase stability of CA II. CFU experiments revealed that the native-like compact gas-phase conformation of the protein is stable with higher degree of pre-activation when bound to a series of acidic fragments. Importantly, although acetate was present in high concentrations, the stabilising effect was not observed without the addition of the acidic fragments. CONCLUSIONS Binding and subsequent dissociation of acidic fragments from CA II significantly delayed CIU in a manner which is probably analogous to the effect of inorganic anions. Furthermore, we saw a slightly altered stabilising effect between the different fragments investigated in this study. This suggests that the prevention of CIU by organic acids may be tuneable to specific properties of a bound ligand. These observations may open avenues to exploit IM-MS as a screening platform in FBDD.
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Affiliation(s)
- Clinton G L Veale
- School of Chemistry and Physics, Pietermaritzburg Campus, University of KwaZulu-Natal, Private Bag X01, Scottsville, 3209, South Africa
| | - Maria Mateos Jimenez
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - C Logan Mackay
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - David J Clarke
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK
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22
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Mayerthaler F, Finley MF, Pfeifer TA, Antolin AA. Meeting Proceedings from ICBS 2018- Toward Translational Impact. ACS Chem Biol 2019; 14:567-578. [PMID: 30860357 DOI: 10.1021/acschembio.9b00169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Florian Mayerthaler
- Institute of Biochemistry, Department of Chemistry and Pharmacy, University of Münster, Münster, Germany
| | - Michael F. Finley
- Janssen Research & Development, Spring House, Pennsylvania 19477, United States
| | - Tom A. Pfeifer
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada V6T 1Z3
| | - Albert A. Antolin
- The Department of Data Science, The Institute of Cancer Research, London, SM2 5NG, United Kingdom
- The Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SM2 5NG, United Kingdom
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23
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Lomelino CL, McKenna R. Carbonic anhydrase II in complex with carboxylic acid-based inhibitors. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2019; 75:166-170. [PMID: 30839290 DOI: 10.1107/s2053230x18018344] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 12/26/2018] [Indexed: 12/29/2022]
Abstract
Carbonic anhydrases (CAs) are molecular targets in various diseases. While many sulfonamide-based drugs are in clinical use, CA inhibitor design is moving towards the incorporation of alternative zinc-binding groups, such as carboxylic acids, to promote CA isoform-specific inhibition. Here, X-ray crystal structures of CA II in complex with nicotinic acid and ferulic acid determined to 1.70 and 1.50 Å resolution, respectively, are reported. Furthermore, the structures of these two compounds are superimposed with previously determined structures to compare the mechanisms of inhibition and the properties of carboxylic acid-based CA inhibitors. This study examines an important class of alternative, non-sulfonamide-based CA inhibitors and provides insight to facilitate the structure-guided design of CA isoform-specific inhibitors.
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Affiliation(s)
- Carrie L Lomelino
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
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24
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MS methods to study macromolecule-ligand interaction: Applications in drug discovery. Methods 2018; 144:152-174. [PMID: 29890284 DOI: 10.1016/j.ymeth.2018.06.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/01/2018] [Accepted: 06/03/2018] [Indexed: 12/12/2022] Open
Abstract
The interaction of small compounds (i.e. ligands) with macromolecules or macromolecule assemblies (i.e. targets) is the mechanism of action of most of the drugs available today. Mass spectrometry is a popular technique for the interrogation of macromolecule-ligand interactions and therefore is also widely used in drug discovery and development. Thanks to its versatility, mass spectrometry is used for multiple purposes such as biomarker screening, identification of the mechanism of action, ligand structure optimization or toxicity assessment. The evolution and automation of the instruments now allows the development of high throughput methods with high sensitivity and a minimized false discovery rate. Herein, all these approaches are described with a focus on the methods for studying macromolecule-ligand interaction aimed at defining the structure-activity relationships of drug candidates, along with their mechanism of action, metabolism and toxicity.
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25
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Nazarshodeh E, Sheikhpour R, Gharaghani S, Sarram MA. A novel proteochemometrics model for predicting the inhibition of nine carbonic anhydrase isoforms based on supervised Laplacian score and k-nearest neighbour regression. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2018; 29:419-437. [PMID: 29882433 DOI: 10.1080/1062936x.2018.1447995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 02/28/2018] [Indexed: 06/08/2023]
Abstract
Carbonic anhydrases (CAs) are essential enzymes in biological processes. Prediction of the activity of compounds towards CA isoforms could be evaluated by computational techniques to discover a novel therapeutic inhibitor. Studies such as quantitative structure-activity relationships (QSARs), molecular docking and pharmacophore modelling have been carried out to design potent inhibitors. Unfortunately, QSAR does not consider the information of target space in the model. We successfully developed an in silico proteochemometrics model that simultaneously uses target and ligand descriptors to predict the activities of CA inhibitors. Herein, a strong predictive model was built for the prediction of protein-ligand binding affinity between nine human CA isoforms and 549 ligands. We applied descriptors obtained from the PROFEAT webserver for the proteins. Ligands were encoded by descriptors from PaDEL-Descriptor software. Supervised Laplacian score (SLS) and particle swarm optimization were used for feature selection. Models were derived using k-nearest neighbour (KNN) regression and a kernel smoother model. The predictive ability of the models was evaluated by an external validation test. Statistical results (Q2ext = 0.7806, r2test = 0.7811 and RMSEtest = 0.5549) showed that the model generated using SLS and KNN regression outperformed the other models. Consequently, the selectivity of compounds towards these enzymes will be predicted prior to synthesis.
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Affiliation(s)
- E Nazarshodeh
- a Laboratory of Bioinformatics and Drug Design (LBD), Institute of Biochemistry and Biophysics , University of Tehran , Tehran , Iran
| | - R Sheikhpour
- b Department of Computer Engineering , Yazd University , Yazd , Iran
| | - S Gharaghani
- a Laboratory of Bioinformatics and Drug Design (LBD), Institute of Biochemistry and Biophysics , University of Tehran , Tehran , Iran
| | - M A Sarram
- b Department of Computer Engineering , Yazd University , Yazd , Iran
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26
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Gavriilidou AFM, Holding FP, Coyle JE, Zenobi R. Application of Native ESI-MS to Characterize Interactions between Compounds Derived from Fragment-Based Discovery Campaigns and Two Pharmaceutically Relevant Proteins. SLAS DISCOVERY 2018; 23:951-959. [PMID: 29852073 DOI: 10.1177/2472555218775921] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Native electrospray ionization mass spectrometry (ESI-MS) was applied to analyze the binding of compounds generated during fragment-based drug discovery (FBDD) campaigns against two functionally distinct proteins, the X-linked inhibitor of apoptosis protein (XIAP) and cyclin-dependent kinase 2 (CDK2). Compounds of different molecular weights and a wide range of binding affinities obtained from the hits to leads and lead optimization stages of FBDD campaigns were studied, and their dissociation constants (Kd) were measured by native ESI-MS. We demonstrate that native ESI-MS has the potential to be applied to the stages of an FBDD campaign downstream of primary screening for the detection and quantification of protein-ligand binding. Native ESI-MS was used to derive Kd values for compounds binding to XIAP, and the dissociation of the complex between XIAP and a peptide derived from the second mitochondria-derived activator of caspases (SMAC) protein induced by one of the test compounds was also investigated. Affinities of compounds binding to CDK2 gave Kd values in the low nanomolar to low millimolar range, and Kd values generated by MS and isothermal titration calorimetry (ITC) followed the same trend for both proteins. Practical considerations for the application of native ESI-MS are discussed in detail.
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Affiliation(s)
- Agni F M Gavriilidou
- 1 Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | | | | | - Renato Zenobi
- 1 Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
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27
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Chingin K, Barylyuk K. Charge-State-Dependent Variation of Signal Intensity Ratio between Unbound Protein and Protein-Ligand Complex in Electrospray Ionization Mass Spectrometry: The Role of Solvent-Accessible Surface Area. Anal Chem 2018; 90:5521-5528. [PMID: 29653057 DOI: 10.1021/acs.analchem.7b05349] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Native electrospray ionization mass spectrometry (ESI-MS) is nowadays widely used for the direct and sensitive determination of protein complex stoichiometry and binding affinity constants ( Ka). A common yet poorly understood phenomenon in native ESI-MS is the difference between the charge-state distributions (CSDs) of the bound protein-ligand complex (PL) and unbound protein (P) signals. This phenomenon is typically attributed to experimental artifacts such as nonspecific binding or in-source dissociation and is considered highly undesirable, because the determined Ka values display strong variation with charge state. This situation raises serious concerns regarding the reliability of ESI-MS for the analysis of protein complexes. Here we demonstrate that, contrary to the common belief, the CSD difference between P and PL ions can occur without any loss of complex integrity, simply due to a change in the solvent-accessible surface area (ΔSASA) of the protein upon ligand binding in solution. The experimental CSD shifts for PL and P ions in ESI-MS are explained in relation to the magnitude of ΔSASA for diverse protein-ligand systems using a simple model based on the charged residue mechanism. Our analysis shows that the revealed ΔSASA factor should be considered rather general and be given attention for the correct spectral interpretation of protein complexes.
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Affiliation(s)
- Konstantin Chingin
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation , East China University of Technology , Guanglan Road 418 , Nanchang , Jiangxi , China 330013
| | - Konstantin Barylyuk
- Department of Biochemistry , University of Cambridge , Hopkins Building, Tennis Court Road , Cambridge CB2 1QW , United Kingdom
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28
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Hinman SS, McKeating KS, Cheng Q. Surface Plasmon Resonance: Material and Interface Design for Universal Accessibility. Anal Chem 2018; 90:19-39. [PMID: 29053253 PMCID: PMC6041476 DOI: 10.1021/acs.analchem.7b04251] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Samuel S. Hinman
- Environmental Toxicology, University of California–Riverside, Riverside, California 92521, United States
| | - Kristy S. McKeating
- Department of Chemistry, University of California–Riverside, Riverside, California 92521, United States
| | - Quan Cheng
- Environmental Toxicology, University of California–Riverside, Riverside, California 92521, United States
- Department of Chemistry, University of California–Riverside, Riverside, California 92521, United States
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29
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Mass spectrometry for fragment screening. Essays Biochem 2017; 61:465-473. [PMID: 28986384 DOI: 10.1042/ebc20170071] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 09/12/2017] [Accepted: 09/14/2017] [Indexed: 12/31/2022]
Abstract
Fragment-based approaches in chemical biology and drug discovery have been widely adopted worldwide in both academia and industry. Fragment hits tend to interact weakly with their targets, necessitating the use of sensitive biophysical techniques to detect their binding. Common fragment screening techniques include differential scanning fluorimetry (DSF) and ligand-observed NMR. Validation and characterization of hits is usually performed using a combination of protein-observed NMR, isothermal titration calorimetry (ITC) and X-ray crystallography. In this context, MS is a relatively underutilized technique in fragment screening for drug discovery. MS-based techniques have the advantage of high sensitivity, low sample consumption and being label-free. This review highlights recent examples of the emerging use of MS-based techniques in fragment screening.
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30
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Chrysanthopoulos PK, Mujumdar P, Woods LA, Dolezal O, Ren B, Peat TS, Poulsen SA. Identification of a New Zinc Binding Chemotype by Fragment Screening. J Med Chem 2017; 60:7333-7349. [PMID: 28817930 DOI: 10.1021/acs.jmedchem.7b00606] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The discovery of a new zinc binding chemotype from screening a nonbiased fragment library is reported. Using the orthogonal fragment screening methods of native state mass spectrometry and surface plasmon resonance a 3-unsubstituted 2,4-oxazolidinedione fragment was found to have low micromolar binding affinity to the zinc metalloenzyme carbonic anhydrase II (CA II). This affinity approached that of fragment sized primary benzenesulfonamides, the classical zinc binding group found in most CA II inhibitors. Protein X-ray crystallography established that 3-unsubstituted 2,4-oxazolidinediones bound to CA II via an interaction of the acidic ring nitrogen with the CA II active site zinc, as well as two hydrogen bonds between the oxazolidinedione ring oxygen and the CA II protein backbone. Furthermore, 3-unsubstituted 2,4-oxazolidinediones appear to be a viable starting point for the development of an alternative class of CA inhibitor, wherein the medicinal chemistry pedigree of primary sulfonamides has dominated for several decades.
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Affiliation(s)
| | - Prashant Mujumdar
- Griffith University , Griffith Institute for Drug Discovery, Nathan, Brisbane, Queensland 4111, Australia
| | - Lucy A Woods
- Griffith University , Griffith Institute for Drug Discovery, Nathan, Brisbane, Queensland 4111, Australia
| | - Olan Dolezal
- CSIRO , Biomedical Manufacturing Program, 343 Royal Parade, Parkville, Melbourne, Victoria 3052, Australia
| | - Bin Ren
- CSIRO , Biomedical Manufacturing Program, 343 Royal Parade, Parkville, Melbourne, Victoria 3052, Australia
| | - Thomas S Peat
- CSIRO , Biomedical Manufacturing Program, 343 Royal Parade, Parkville, Melbourne, Victoria 3052, Australia
| | - Sally-Ann Poulsen
- Griffith University , Griffith Institute for Drug Discovery, Nathan, Brisbane, Queensland 4111, Australia
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Göth M, Badock V, Weiske J, Pagel K, Kuropka B. Critical Evaluation of Native Electrospray Ionization Mass Spectrometry for Fragment-Based Screening. ChemMedChem 2017; 12:1201-1211. [PMID: 28618179 DOI: 10.1002/cmdc.201700177] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/19/2017] [Indexed: 12/24/2022]
Abstract
Fragment-based screening presents a promising alternative to high-throughput screening and has gained great attention in recent years. So far, only a few studies have discussed mass spectrometry as a screening technology for fragments. Herein, we report the application of native electrospray ionization mass spectrometry (MS) for screening defined sets of fragments against four different target proteins. Fragments were selected from a primary screening conducted with a thermal shift assay (TSA) and represented different binding categories. Our data indicated that, beside specific complex formation, many fragments show extensive multiple binding and also charge-state shifts. Both of these factors complicate automated data analysis and decrease the attractiveness of native MS as a primary screening tool for fragments. A comparison of the hits identified by native MS and TSA showed good agreement for two of the proteins. Furthermore, we discuss general challenges, including the determination of an optimal fragment concentration and the question of how to rank fragment hits according to their affinity. In conclusion, we consider native MS to be a highly valuable tool for the validation and deeper investigation of promising fragment hits rather than a method for primary screening.
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Affiliation(s)
- Melanie Göth
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195, Berlin, Germany.,Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany
| | - Volker Badock
- Protein Technologies, Lead Discovery Berlin, Bayer AG, Müllerstraße 178, 13353, Berlin, Germany
| | - Jörg Weiske
- Protein Technologies, Lead Discovery Berlin, Bayer AG, Müllerstraße 178, 13353, Berlin, Germany
| | - Kevin Pagel
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195, Berlin, Germany.,Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany
| | - Benno Kuropka
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany.,Protein Technologies, Lead Discovery Berlin, Bayer AG, Müllerstraße 178, 13353, Berlin, Germany
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Eschweiler JD, Kerr R, Rabuck-Gibbons J, Ruotolo BT. Sizing Up Protein-Ligand Complexes: The Rise of Structural Mass Spectrometry Approaches in the Pharmaceutical Sciences. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2017; 10:25-44. [PMID: 28301749 DOI: 10.1146/annurev-anchem-061516-045414] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Capturing the dynamic interplay between proteins and their myriad interaction partners is critically important for advancing our understanding of almost every biochemical process and human disease. The importance of this general area has spawned many measurement methods capable of assaying such protein complexes, and the mass spectrometry-based structural biology methods described in this review form an important part of that analytical arsenal. Here, we survey the basic principles of such measurements, cover recent applications of the technology that have focused on protein-small-molecule complexes, and discuss the bright future awaiting this group of technologies.
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Affiliation(s)
| | - Richard Kerr
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109;
| | | | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109;
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Chan DSH, Mendes V, Thomas SE, McConnell BN, Matak-Vinković D, Coyne AG, Blundell TL, Abell C. Fragment Screening against the EthR-DNA Interaction by Native Mass Spectrometry. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702888] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Daniel Shiu-Hin Chan
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Vitor Mendes
- Department of Biochemistry; University of Cambridge; 80 Tennis Court Road CB2 1GA Cambridge UK
| | - Sherine E. Thomas
- Department of Biochemistry; University of Cambridge; 80 Tennis Court Road CB2 1GA Cambridge UK
| | - Brendan N. McConnell
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Dijana Matak-Vinković
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Anthony G. Coyne
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Tom L. Blundell
- Department of Biochemistry; University of Cambridge; 80 Tennis Court Road CB2 1GA Cambridge UK
| | - Chris Abell
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
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Chan DSH, Mendes V, Thomas SE, McConnell BN, Matak-Vinković D, Coyne AG, Blundell TL, Abell C. Fragment Screening against the EthR-DNA Interaction by Native Mass Spectrometry. Angew Chem Int Ed Engl 2017; 56:7488-7491. [DOI: 10.1002/anie.201702888] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Daniel Shiu-Hin Chan
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Vitor Mendes
- Department of Biochemistry; University of Cambridge; 80 Tennis Court Road CB2 1GA Cambridge UK
| | - Sherine E. Thomas
- Department of Biochemistry; University of Cambridge; 80 Tennis Court Road CB2 1GA Cambridge UK
| | - Brendan N. McConnell
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Dijana Matak-Vinković
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Anthony G. Coyne
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Tom L. Blundell
- Department of Biochemistry; University of Cambridge; 80 Tennis Court Road CB2 1GA Cambridge UK
| | - Chris Abell
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
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35
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Finn MG. Technical Advances in Medicinal Chemistry. ACS COMBINATORIAL SCIENCE 2017; 19:277-278. [PMID: 28374995 DOI: 10.1021/acscombsci.7b00053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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36
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Teruya K, Rankin GM, Chrysanthopoulos PK, Tonissen KF, Poulsen S. Characterisation of Photoaffinity‐Based Chemical Probes by Fluorescence Imaging and Native‐State Mass Spectrometry. Chembiochem 2017; 18:739-754. [DOI: 10.1002/cbic.201600598] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Indexed: 12/28/2022]
Affiliation(s)
- Kanae Teruya
- Griffith Institute for Drug Discovery Griffith University Don Young Road Nathan Queensland 4111 Australia
- School of Natural Sciences Griffith University Nathan Queensland 4111 Australia
| | - Gregory M. Rankin
- Griffith Institute for Drug Discovery Griffith University Don Young Road Nathan Queensland 4111 Australia
| | | | - Kathryn F. Tonissen
- Griffith Institute for Drug Discovery Griffith University Don Young Road Nathan Queensland 4111 Australia
- School of Natural Sciences Griffith University Nathan Queensland 4111 Australia
| | - Sally‐Ann Poulsen
- Griffith Institute for Drug Discovery Griffith University Don Young Road Nathan Queensland 4111 Australia
- School of Natural Sciences Griffith University Nathan Queensland 4111 Australia
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Abstract
INTRODUCTION The enzyme carbonic anhydrase (CA, EC 4.2.1.1) is found in numerous organisms across the tree of life, with seven distinct classes known to date. CA inhibition can be exploited for the treatment of edema, glaucoma, seizures, obesity, cancer and infectious diseases. A myriad of CA inhibitor (CAI) classes and inhibition mechanisms have been identified over the past decade, mainly through structure-based drug design approaches. Five different CA inhibition mechanisms are presently known. Areas covered: Recent advances in structure-based CAI design are reviewed, with periodic table-based organization of inhibitor classes. Expert opinion: Various structure-based drug design studies have led to deep understanding of factors governing tight binding and selectivity for the various isoforms. Carboxylic acids, phenols, polyamines, diols, borols, boronic acids, coumarins and sulfonamides represent successful stories which led to an anti-tumor sulfonamide in Phase I clinical trials (SLC-0111). For many inhibitor classes, no detailed crystallographic data are available. Detailed structural characterization of all CAI classes may lead to further advances in the field with potential therapeutic implications in the management of indications including neuropathic pain, cerebral ischemia, arthritis and tumor imaging.
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Affiliation(s)
- Claudiu T Supuran
- a Neurofarba Department, Sezione di Scienze Farmaceutiche e Nutraceutiche , Università degli Studi di Firenze , Sesto Fiorentino (Florence) , Italy
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Djuric SW, Meanwell NA. Journal of Medicinal Chemistry, Technological Advances: Highlights 2015–2016. J Med Chem 2016; 60:1-3. [DOI: 10.1021/acs.jmedchem.6b01600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stevan W. Djuric
- AbbVie, R467, AP10-2, 1 North Waukegan Road, North
Chicago, Illinois 60064, United States
| | - Nicholas A. Meanwell
- Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
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Native Mass Spectrometry in Fragment-Based Drug Discovery. Molecules 2016; 21:molecules21080984. [PMID: 27483215 PMCID: PMC6274484 DOI: 10.3390/molecules21080984] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 07/14/2016] [Accepted: 07/23/2016] [Indexed: 11/17/2022] Open
Abstract
The advent of native mass spectrometry (MS) in 1990 led to the development of new mass spectrometry instrumentation and methodologies for the analysis of noncovalent protein-ligand complexes. Native MS has matured to become a fast, simple, highly sensitive and automatable technique with well-established utility for fragment-based drug discovery (FBDD). Native MS has the capability to directly detect weak ligand binding to proteins, to determine stoichiometry, relative or absolute binding affinities and specificities. Native MS can be used to delineate ligand-binding sites, to elucidate mechanisms of cooperativity and to study the thermodynamics of binding. This review highlights key attributes of native MS for FBDD campaigns.
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Lomelino CL, Supuran CT, McKenna R. Non-Classical Inhibition of Carbonic Anhydrase. Int J Mol Sci 2016; 17:ijms17071150. [PMID: 27438828 PMCID: PMC4964523 DOI: 10.3390/ijms17071150] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/02/2016] [Accepted: 07/07/2016] [Indexed: 11/16/2022] Open
Abstract
Specific isoforms from the carbonic anhydrase (CA) family of zinc metalloenzymes have been associated with a variety of diseases. Isoform-specific carbonic anhydrase inhibitors (CAIs) are therefore a major focus of attention for specific disease treatments. Classical CAIs, primarily sulfonamide-based compounds and their bioisosteres, are examined as antiglaucoma, antiepileptic, antiobesity, antineuropathic pain and anticancer compounds. However, many sulfonamide compounds inhibit all CA isoforms nonspecifically, diluting drug effectiveness and causing undesired side effects due to off-target inhibition. In addition, a small but significant percentage of the general population cannot be treated with sulfonamide-based compounds due to a sulfa allergy. Therefore, CAIs must be developed that are not only isoform specific, but also non-classical, i.e. not based on sulfonamides, sulfamates, or sulfamides. This review covers the classes of non-classical CAIs and the recent advances in the development of isoform-specific inhibitors based on phenols, polyamines, coumarins and their derivatives.
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Affiliation(s)
- Carrie L Lomelino
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32611, USA.
| | - Claudiu T Supuran
- Neurofarba Department, University of Florence, Piazza di San Marco, Firenze 50019, Italy.
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32611, USA.
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