1
|
Fan Y, Si H, Zhang Z, Zhong L, Sun H, Zhu C, Yin Z, Li H, Tang G, Yao SQ, Sun P, Zhang ZM, Ding K, Li Z. Novel Electrophilic Warhead Targeting a Triple-Negative Breast Cancer Driver in Live Cells Revealed by "Inverse Drug Discovery". J Med Chem 2021; 64:15582-15592. [PMID: 34623802 DOI: 10.1021/acs.jmedchem.0c02024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The "inverse drug discovery" strategy is a potent means of exploring the cellular targets of latent electrophiles not typically used in medicinal chemistry. Cyclopropenone, a powerful electrophile, is generally used in bio-orthogonal reactions mediated by triarylphosphine or in photo-triggered cycloaddition reactions. Here, we have studied, for the first time, the proteome reactivity of cyclopropenones in live cells and discovered that the cyclopropenone warhead can specifically and efficiently modify a triple-negative breast cancer driver, glutathione S-transferase pi-1 (GSTP1), by covalently binding at the catalytic active site. Further structure optimization and signaling pathway validation have led to the discovery of potent inhibitors of GSTP1.
Collapse
Affiliation(s)
- Youlong Fan
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Hongfei Si
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhang Zhang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Liang Zhong
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Hongyan Sun
- Department of Chemistry, City University of Hong Kong, Hong Kong 999077, China
| | - Chengjun Zhu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhibin Yin
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Huilin Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Guanghui Tang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Pinghua Sun
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhi-Min Zhang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Ke Ding
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhengqiu Li
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| |
Collapse
|
2
|
Direct Measurement of S-Nitrosothiols with an Orbitrap Fusion Mass Spectrometer: S-Nitrosoglutathione Reductase as a Model Protein. Methods Mol Biol 2018. [PMID: 29600457 DOI: 10.1007/978-1-4939-7695-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Recent studies suggest cysteine S-nitrosation of S-nitrosoglutathione reductase (GSNOR) could regulate protein redox homeostasis. "Switch" assays enable discovery of putatively S-nitrosated proteins. However, with few exceptions, researchers have not examined the kinetics and biophysical consequences of S-nitrosation. Methods to quantify protein S-nitrosothiol (SNO) abundance and formation kinetics would bridge this mechanistic gap and allow interpretation of the consequences of specific modifications, as well as facilitate development of specific S-nitrosation inhibitors. Here, we describe a rapid assay to estimate protein SNO abundance with intact protein electrospray ionization mass spectrometry. Originally designed using recombinant GSNOR, these methods are applicable to any purified protein to test for or further study nitrosatable cysteines.
Collapse
|
3
|
Baez NOD, Reisz JA, Furdui CM. Mass spectrometry in studies of protein thiol chemistry and signaling: opportunities and caveats. Free Radic Biol Med 2015; 80:191-211. [PMID: 25261734 PMCID: PMC4355329 DOI: 10.1016/j.freeradbiomed.2014.09.016] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 09/08/2014] [Accepted: 09/11/2014] [Indexed: 12/13/2022]
Abstract
Mass spectrometry (MS) has become a powerful and widely utilized tool in the investigation of protein thiol chemistry, biochemistry, and biology. Very early biochemical studies of metabolic enzymes have brought to light the broad spectrum of reactivity profiles that distinguish cysteine thiols with functions in catalysis and protein stability from other cysteine residues in proteins. The development of MS methods for the analysis of proteins using electrospray ionization (ESI) or matrix-assisted laser desorption/ionization (MALDI) coupled with the emergence of high-resolution mass analyzers has been instrumental in advancing studies of thiol modifications, both in single proteins and within the cellular context. This article reviews MS instrumentation and methods of analysis employed in investigations of thiols and their reactivity toward a range of small biomolecules. A selected number of studies are detailed to highlight the advantages brought about by the MS technologies along with the caveats associated with these analyses.
Collapse
Affiliation(s)
- Nelmi O Devarie Baez
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Julie A Reisz
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Cristina M Furdui
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA.
| |
Collapse
|
4
|
Affiliation(s)
- Gregory
F. Pirrone
- Department of Chemistry and
Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115 United States
| | - Roxana E. Iacob
- Department of Chemistry and
Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115 United States
| | - John R. Engen
- Department of Chemistry and
Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115 United States
| |
Collapse
|
5
|
Salisbury JP, Liu Q, Agar JN. QUDeX-MS: hydrogen/deuterium exchange calculation for mass spectra with resolved isotopic fine structure. BMC Bioinformatics 2014; 15:403. [PMID: 25495703 PMCID: PMC4274694 DOI: 10.1186/s12859-014-0403-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 12/01/2014] [Indexed: 12/25/2022] Open
Abstract
Background Hydrogen/deuterium exchange (HDX) coupled to mass spectrometry permits analysis of structure, dynamics, and molecular interactions of proteins. HDX mass spectrometry is confounded by deuterium exchange-associated peaks overlapping with peaks of heavy, natural abundance isotopes, such as carbon-13. Recent studies demonstrated that high-performance mass spectrometers could resolve isotopic fine structure and eliminate this peak overlap, allowing direct detection and quantification of deuterium incorporation. Results Here, we present a graphical tool that allows for a rapid and automated estimation of deuterium incorporation from a spectrum with isotopic fine structure. Given a peptide sequence (or elemental formula) and charge state, the mass-to-charge ratios of deuterium-associated peaks of the specified ion is determined. Intensities of peaks in an experimental mass spectrum within bins corresponding to these values are used to determine the distribution of deuterium incorporated. A theoretical spectrum can then be calculated based on the estimated distribution of deuterium exchange to confirm interpretation of the spectrum. Deuterium incorporation can also be detected for ion signals without a priori specification of an elemental formula, permitting detection of exchange in complex samples of unidentified material such as natural organic matter. A tool is also incorporated into QUDeX-MS to help in assigning ion signals from peptides arising from enzymatic digestion of proteins. MATLAB-deployable and standalone versions are available for academic use at qudex-ms.sourceforge.net and agarlabs.com. Conclusion Isotopic fine structure HDX-MS offers the potential to increase sequence coverage of proteins being analyzed through mass accuracy and deconvolution of overlapping ion signals. As previously demonstrated, however, the data analysis workflow for HDX-MS data with resolved isotopic fine structure is distinct. QUDeX-MS we hope will aid in the adoption of isotopic fine structure HDX-MS by providing an intuitive workflow and interface for data analysis.
Collapse
Affiliation(s)
- Joseph P Salisbury
- Departments of Chemistry and Chemical Biology and Pharmaceutical Sciences and Barnett Institute of Chemical and Biological Analysis, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, USA.
| | - Qian Liu
- Departments of Chemistry and Chemical Biology and Pharmaceutical Sciences and Barnett Institute of Chemical and Biological Analysis, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, USA.
| | - Jeffrey N Agar
- Departments of Chemistry and Chemical Biology and Pharmaceutical Sciences and Barnett Institute of Chemical and Biological Analysis, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, USA.
| |
Collapse
|
6
|
Naicker P, Stoychev S, Dirr HW, Sayed Y. Amide hydrogen exchange in HIV-1 subtype B and C proteases - insights into reduced drug susceptibility and dimer stability. FEBS J 2014; 281:5395-410. [DOI: 10.1111/febs.13084] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 08/29/2014] [Accepted: 09/29/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Previn Naicker
- Protein Structure-Function Research Unit; School of Molecular and Cell Biology; University of the Witwatersrand; Johannesburg South Africa
| | - Stoyan Stoychev
- Council for Scientific and Industrial Research; Biosciences; Pretoria South Africa
| | - Heini W. Dirr
- Protein Structure-Function Research Unit; School of Molecular and Cell Biology; University of the Witwatersrand; Johannesburg South Africa
| | - Yasien Sayed
- Protein Structure-Function Research Unit; School of Molecular and Cell Biology; University of the Witwatersrand; Johannesburg South Africa
| |
Collapse
|