1
|
Heel SV, Breuker K. Investigating the Intramolecular Competition of Different RNA Binding Motifs for Neomycin B by Native Top-Down Mass Spectrometry. Chempluschem 2024:e202400178. [PMID: 38758051 DOI: 10.1002/cplu.202400178] [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: 03/06/2024] [Revised: 04/13/2024] [Indexed: 05/18/2024]
Abstract
The ongoing search for small molecule drugs that target ribonucleic acids (RNA) is complicated by a limited understanding of the principles that govern RNA-small molecule interactions. Here we have used stoichiometry-resolved native top-down mass spectrometry (MS) to study the binding of neomycin B to small model hairpin RNAs, an unstructured RNA, and a viral RNA construct. For 15-22 nt model RNAs with hairpin structure, we found that neomycin B binding to hairpin loops relies on interactions with both the nucleobases and the 2'-OH groups, and that a simple 5' or 3' overhang can introduce an additional binding motif. For a 47 nt RNA construct derived from stem IA of the human immunodeficiency virus 1 (HIV-1) rev response element (RRE) RNA, native top-down MS identified four different binding motifs, of which the purine-rich internal loop showed the highest affinity for neomycin B. Stoichiometry-resolved binding site mapping by native top-down MS allows for a new perspective on binding specificity, and has the potential to reveal unexpected principles of small molecule binding to RNA.
Collapse
Affiliation(s)
- Sarah Viola Heel
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Kathrin Breuker
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| |
Collapse
|
2
|
Nguyen GTH, Nocentini A, Angeli A, Gratteri P, Supuran CT, Donald WA. Perfluoroalkyl Substances of Significant Environmental Concern Can Strongly Inhibit Human Carbonic Anhydrase Isozymes. Anal Chem 2020; 92:4614-4622. [PMID: 32096628 DOI: 10.1021/acs.analchem.0c00163] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Perfluoroalkyl substances (PFASs) persist and are ubiquitous in the environment. The origins of PFAS toxicity and how they specifically affect the functions of proteins remain unclear. Herein, we report that PFASs can strongly inhibit the activity of human carbonic anhydrases (hCAs), which are ubiquitous enzymes that catalyze the hydration of CO2, are abundant in the blood and organs of mammals, and involved in pH regulation, ion homeostasis, and biosynthesis. The interactions between PFASs and hCAs were investigated using stopped-flow kinetic enzyme-inhibition measurements, native mass spectrometry (MS), and ligand-docking simulations. Narrow-bore emitters in native MS with inner diameters of ∼300 nm were used to directly and simultaneously measure the dissociation constants of 11 PFASs to an enzyme, which was not possible using conventional emitters. The data from native MS and stopped-flow measurements were in excellent agreement. Of 15 PFASs investigated, eight can inhibit at least one of four hCA isozymes (I, II, IX, and XII) with submicromolar inhibition constants, including perfluorooctanoic acid, perfluorooctanesulfonamide, and perfluorooctanesulfonic acid. Some PFASs, including those with both short and long perfluoromethylene chains, can effectively inhibit at least one hCA isozyme with low nanomolar inhibition constants.
Collapse
Affiliation(s)
- Giang T H Nguyen
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Alessio Nocentini
- Department NEUROFARBA-Pharmaceutical and Nutraceutical Section, University of Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Firenze, Italy.,Department NEUROFARBA-Pharmaceutical and Nutraceutical Section, Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Firenze, Italy
| | - Andrea Angeli
- Department NEUROFARBA-Pharmaceutical and Nutraceutical Section, University of Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Firenze, Italy
| | - Paola Gratteri
- Department NEUROFARBA-Pharmaceutical and Nutraceutical Section, Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Firenze, Italy
| | - Claudiu T Supuran
- Department NEUROFARBA-Pharmaceutical and Nutraceutical Section, University of Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Firenze, Italy
| | - William A Donald
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| |
Collapse
|
3
|
Wolff P, Ennifar E. Native Electrospray Ionization Mass Spectrometry of RNA-Ligand Complexes. Methods Mol Biol 2020; 2113:111-118. [PMID: 32006311 DOI: 10.1007/978-1-0716-0278-2_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Native electrospray ionization mass spectrometry (native ESI-MS) is a powerful tool to investigate non-covalent biomolecular interactions. It has been widely used to study protein complexes, but only few examples are described for the analysis of complexes involving RNA-RNA interactions. Here, we provide a detailed protocol for native ESI-MS analysis of RNA complexes. As an example, we present the analysis of the HIV-1 genomic RNA dimerization initiation site (DIS) extended duplex dimer bound to the aminoglycoside antibiotic lividomycin.
Collapse
Affiliation(s)
- Philippe Wolff
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France. .,Plateforme protéomique Strasbourg Esplanade, FRC1589 du CNRS, Université de Strasbourg, Strasbourg, France.
| | - Eric Ennifar
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| |
Collapse
|
4
|
Root K, Barylyuk K, Schwab A, Thelemann J, Illarionov B, Geist JG, Gräwert T, Bacher A, Fischer M, Diederich F, Zenobi R. Aryl bis-sulfonamides bind to the active site of a homotrimeric isoprenoid biosynthesis enzyme IspF and extract the essential divalent metal cation cofactor. Chem Sci 2018; 9:5976-5986. [PMID: 30079212 PMCID: PMC6050538 DOI: 10.1039/c8sc00814k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 06/17/2018] [Indexed: 12/22/2022] Open
Abstract
Characterizing the mode of action of non-covalent inhibitors in multisubunit enzymes often presents a great challenge. Most of the conventionally used methods are based on ensemble measurements of protein-ligand binding in bulk solution. They often fail to accurately describe multiple binding processes occurring in such systems. Native electrospray ionization mass spectrometry (ESI-MS) of intact protein complexes is a direct, label-free approach that can render the entire distribution of ligand-bound states in multimeric protein complexes. Here we apply native ESI-MS to comprehensively characterize the isoprenoid biosynthesis enzyme IspF from Arabidopsis thaliana, an example of a homomeric protein complex with multiple binding sites for several types of ligands, including a metal cofactor and a synthetic inhibitor. While standard biophysical techniques failed to reveal the mode of action of recently discovered aryl-sulfonamide-based inhibitors of AtIspF, direct native ESI-MS titrations of the protein with the ligands and ligand competition assays allowed us to accurately capture the solution-phase protein-ligand binding equilibria in full complexity and detail. Based on these combined with computational modeling, we propose a mechanism of AtIspF inhibition by aryl bis-sulfonamides that involves both the competition with the substrate for the ligand-binding pocket and the extraction of Zn2+ from the enzyme active site. This inhibition mode is therefore mixed competitive and non-competitive, the latter exerting a key inhibitory effect on the enzyme activity. The results of our study deliver a profound insight into the mechanisms of AtIspF action and inhibition, open new perspectives for designing inhibitors of this important drug target, and demonstrate the applicability and value of the native ESI-MS approach for deep analysis of complex biomolecular binding equilibria.
Collapse
Affiliation(s)
- Katharina Root
- Department of Chemistry and Applied Biosciences , ETH Zurich , Zurich , Switzerland .
| | - Konstantin Barylyuk
- Department of Chemistry and Applied Biosciences , ETH Zurich , Zurich , Switzerland .
| | - Anatol Schwab
- Department of Chemistry and Applied Biosciences , ETH Zurich , Zurich , Switzerland .
| | - Jonas Thelemann
- Department of Chemistry and Applied Biosciences , ETH Zurich , Zurich , Switzerland .
| | - Boris Illarionov
- Hamburg School of Food Science , University of Hamburg , Hamburg , Germany
| | - Julie G Geist
- Department of Chemistry and Applied Biosciences , ETH Zurich , Zurich , Switzerland .
| | - Tobias Gräwert
- Hamburg School of Food Science , University of Hamburg , Hamburg , Germany
| | - Adelbert Bacher
- Department of Chemistry , Technical University of Munich , Garching , Germany
| | - Markus Fischer
- Hamburg School of Food Science , University of Hamburg , Hamburg , Germany
| | - François Diederich
- Department of Chemistry and Applied Biosciences , ETH Zurich , Zurich , Switzerland .
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences , ETH Zurich , Zurich , Switzerland .
| |
Collapse
|
5
|
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.
Collapse
|
6
|
Gülbakan B, Barylyuk K, Schneider P, Pillong M, Schneider G, Zenobi R. Native Electrospray Ionization Mass Spectrometry Reveals Multiple Facets of Aptamer–Ligand Interactions: From Mechanism to Binding Constants. J Am Chem Soc 2018; 140:7486-7497. [DOI: 10.1021/jacs.7b13044] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Basri Gülbakan
- Department of Chemistry and Applied Bioscience, ETH Zürich, CH-8093 Zürich, Switzerland
- Hacettepe University Institute of Child Health, Ihsan Dogramaci Children’s Hospital, Sıhhiye Square, 06100 Ankara, Turkey
| | - Konstantin Barylyuk
- Department of Chemistry and Applied Bioscience, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Petra Schneider
- Department of Chemistry and Applied Bioscience, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Max Pillong
- Department of Chemistry and Applied Bioscience, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Gisbert Schneider
- Department of Chemistry and Applied Bioscience, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Bioscience, ETH Zürich, CH-8093 Zürich, Switzerland
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|