1
|
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
|
2
|
Bertoletti L, Regazzoni L, Altomare A, Colombo R, Colzani M, Vistoli G, Marchese L, Carini M, De Lorenzi E, Aldini G. Advanced glycation end products of beta2-microglobulin in uremic patients as determined by high resolution mass spectrometry. J Pharm Biomed Anal 2013; 91:193-201. [PMID: 24469019 DOI: 10.1016/j.jpba.2013.12.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Revised: 12/16/2013] [Accepted: 12/19/2013] [Indexed: 11/25/2022]
Abstract
By using a high resolution top-down and bottom-up approach we identified and characterized the AGEs of beta2-microglobulin (β2-m) formed by incubating the protein in the presence of glucose and of the main reactive carbonyl species. Glucose induced glycation on the N-terminal residue, while glyoxal (GO) and methylglyoxal (MGO) covalently reacted with Arg3. Carboxymethyl (CM-R) and imidazolinone (R-GO) derivatives were identified in the case of GO and carboxyethyl arginine (CE-R) and methyl-imidazolinone (R-MGO) for MGO. Interestingly, α,β-unsaturated aldehydes [4-hydroxy-2-nonenal (HNE); 4-oxo-2-nonenal (ONE); acrolein (ACR)] did not induce any covalent modifications up to 100μM. The different reactivity of β2-m towards the different RCS was then rationalized by molecular modeling studies. The MS method was then applied to fully characterize the AGEs of β2-m isolated from the urine of uremic subjects. CM-R, CE-R and R-MGO were easily identified on Arg3 and their relative abundance in respect to the native protein determined by a semi-quantitative approach. Overall, the AGEs content of urinary β2-m ranged from 0.2 to 1% in uremic subjects. The results here reported offer novel insights and technical achievements for a potential biological role of AGEs-β2-m in pathological conditions.
Collapse
Affiliation(s)
- Laura Bertoletti
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy.
| | - Luca Regazzoni
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milan, Italy.
| | - Alessandra Altomare
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milan, Italy.
| | - Raffaella Colombo
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy.
| | - Mara Colzani
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milan, Italy.
| | - Giulio Vistoli
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milan, Italy.
| | - Loredana Marchese
- Department of Molecular Medicine, University of Pavia, Via Forlanini 6, 27100 Pavia, Italy.
| | - Marina Carini
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milan, Italy.
| | - Ersilia De Lorenzi
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy.
| | - Giancarlo Aldini
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milan, Italy.
| |
Collapse
|
3
|
Bertoletti L, Regazzoni L, Aldini G, Colombo R, Abballe F, Caccialanza G, De Lorenzi E. Separation and characterisation of beta2-microglobulin folding conformers by ion-exchange liquid chromatography and ion-exchange liquid chromatography–mass spectrometry. Anal Chim Acta 2013; 771:108-14. [DOI: 10.1016/j.aca.2013.01.058] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 01/29/2013] [Accepted: 01/31/2013] [Indexed: 01/07/2023]
|
4
|
Sterling HJ, Cassou CA, Susa AC, Williams ER. Electrothermal supercharging of proteins in native electrospray ionization. Anal Chem 2012; 84:3795-801. [PMID: 22409200 DOI: 10.1021/ac300468a] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The formation of high charge-state protein ions with nanoelectrospray ionization (nESI) from purely aqueous ammonium bicarbonate solutions at neutral pH, where the proteins have native or native-like conformations prior to ESI droplet formation, is demonstrated. This "electrothermal" supercharging method depends on the temperature of the instrument entrance capillary, the nESI spray potential, and the solution ionic strength and buffer, although other factors almost certainly contribute. Mass spectra obtained with electrothermal supercharging appear similar to those obtained from denaturing solutions where charging beyond the total number of basic sites can be achieved. For example, a 17+ ion of bovine ubiquitin was formed by nESI of a 100 mM ammonium bicarbonate, pH 7.0, solution, which is three more charges than the total number of basic amino acids plus the N-terminus. Heating of the ESI droplets in the vacuum/atmosphere interface and the concomitant denaturation of the protein in the ESI droplets prior to ion formation appears to be the primary origin of the very high charge-state ions formed from these purely aqueous, buffered solutions. nESI mass spectra resembling those obtained under traditional native or denaturing conditions can be reversibly obtained simply by toggling the spray voltage between low and high values.
Collapse
Affiliation(s)
- Harry J Sterling
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | | | | | | |
Collapse
|
5
|
Sterling HJ, Kintzer AF, Feld GK, Cassou CA, Krantz BA, Williams ER. Supercharging protein complexes from aqueous solution disrupts their native conformations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:191-200. [PMID: 22161509 PMCID: PMC3265691 DOI: 10.1007/s13361-011-0301-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Revised: 11/11/2011] [Accepted: 11/15/2011] [Indexed: 05/25/2023]
Abstract
The effects of aqueous solution supercharging on the solution- and gas-phase structures of two protein complexes were investigated using traveling-wave ion mobility-mass spectrometry (TWIMS-MS). Low initial concentrations of m-nitrobenzyl alcohol (m-NBA) in the electrospray ionization (ESI) solution can effectively increase the charge of concanavalin A dimers and tetramers, but at higher m-NBA concentrations, the increases in charge are accompanied by solution-phase dissociation of the dimers and up to a ~22% increase in the collision cross section (CCS) of the tetramers. With just 0.8% m-NBA added to the ESI solution of a ~630 kDa anthrax toxin octamer complex, the average charge is increased by only ~4% compared with the "native" complex, but it is sufficiently destabilized so that extensive gas-phase fragmentation occurs in the relatively high pressure regions of the TWIMS device. Anthrax toxin complexes exist in either a prechannel or a transmembrane channel state. With m-NBA, the prechannel state of the complex has the same CCS/charge ratio in the gas phase as the transmembrane channel state of the same complex formed without m-NBA, yet undergoes extensive dissociation, indicating that destabilization from supercharging occurs in the ESI droplet prior to ion formation and is not a result of Coulombic destabilization in the gas phase as a result of higher charging. These results demonstrate that the supercharging of large protein complexes is the result of conformational changes induced by the reagents in the ESI droplets, where enrichment of the supercharging reagent during droplet evaporation occurs.
Collapse
Affiliation(s)
- Harry J. Sterling
- Department of Chemistry, University of California, Berkeley, California 94720-1460
| | - Alexander F. Kintzer
- Department of Chemistry, University of California, Berkeley, California 94720-1460
| | - Geoffrey K. Feld
- Department of Chemistry, University of California, Berkeley, California 94720-1460
| | - Catherine A. Cassou
- Department of Chemistry, University of California, Berkeley, California 94720-1460
| | - Bryan A. Krantz
- Department of Chemistry, University of California, Berkeley, California 94720-1460
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-1460
| | - Evan R. Williams
- Department of Chemistry, University of California, Berkeley, California 94720-1460
| |
Collapse
|
6
|
Woods LA, Platt GW, Hellewell AL, Hewitt EW, Homans SW, Ashcroft AE, Radford SE. Ligand binding to distinct states diverts aggregation of an amyloid-forming protein. Nat Chem Biol 2011; 7:730-9. [PMID: 21873994 PMCID: PMC3182555 DOI: 10.1038/nchembio.635] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 06/30/2011] [Indexed: 11/21/2022]
Abstract
Although small molecules that modulate amyloid formation in vitro have been identified, significant challenges remain in determining precisely how these species act. Here we describe the identification of rifamycin SV as a potent inhibitor of β(2) microglobulin (β(2)m) fibrillogenesis when added during the lag time of assembly or early during fibril elongation. Biochemical experiments demonstrate that the small molecule does not act by a colloidal mechanism. Exploiting the ability of electrospray ionization-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS) to resolve intermediates of amyloid assembly, we show instead that rifamycin SV inhibits β(2)m fibrillation by binding distinct monomeric conformers, disfavoring oligomer formation and diverting the course of assembly to the formation of spherical aggregates. The results demonstrate the power of ESI-IMS-MS to identify specific protein conformers as targets for intervention in fibrillogenesis using small molecules and reveal a mechanism of action in which ligand binding diverts unfolded protein monomers toward alternative assembly pathways.
Collapse
Affiliation(s)
| | | | - Andrew L. Hellewell
- Astbury Centre for Structural Molecular Biology and Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Eric W. Hewitt
- Astbury Centre for Structural Molecular Biology and Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Steve W. Homans
- Astbury Centre for Structural Molecular Biology and Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Alison E. Ashcroft
- Astbury Centre for Structural Molecular Biology and Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Sheena E. Radford
- Astbury Centre for Structural Molecular Biology and Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
| |
Collapse
|
7
|
Screening of fibrillogenesis inhibitors of β2-microglobulin: Integrated strategies by mass spectrometry capillary electrophoresis and in silico simulations. Anal Chim Acta 2011; 685:153-61. [DOI: 10.1016/j.aca.2010.11.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Revised: 11/10/2010] [Accepted: 11/11/2010] [Indexed: 11/18/2022]
|