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Ruwolt M, Piazza I, Liu F. The potential of cross-linking mass spectrometry in the development of protein-protein interaction modulators. Curr Opin Struct Biol 2023; 82:102648. [PMID: 37423038 DOI: 10.1016/j.sbi.2023.102648] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/03/2023] [Accepted: 06/08/2023] [Indexed: 07/11/2023]
Abstract
Cross-linking mass spectrometry (XL-MS) can provide a wealth of information on endogenous protein-protein interaction (PPI) networks and protein binding interfaces. These features make XL-MS an attractive tool to support the development of PPI-targeting drugs. Though not yet widely used, applications of XL-MS to drug characterization are beginning to emerge. Here, we compare XL-MS to established structural proteomics methods in drug research, discuss the current state and remaining challenges of XL-MS technology, and provide a perspective on the future role XL-MS can play in drug development, with a particular emphasis on PPI modulators.
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Affiliation(s)
- Max Ruwolt
- Department of Structural Biology, Leibniz, Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, 13125 Berlin, Germany. https://twitter.com/@MRuwolt
| | - Ilaria Piazza
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC Berlin), Berlin, Germany.
| | - Fan Liu
- Department of Structural Biology, Leibniz, Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, 13125 Berlin, Germany; Charité - Universitätsmedizin Berlin, Charitépl. 1, 10117 Berlin, Germany.
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2
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Nisar N, Mir SA, Kareem O, Pottoo FH. Proteomics approaches in the identification of cancer biomarkers and drug discovery. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00001-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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3
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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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4
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Engen JR, Botzanowski T, Peterle D, Georgescauld F, Wales TE. Developments in Hydrogen/Deuterium Exchange Mass Spectrometry. Anal Chem 2020; 93:567-582. [DOI: 10.1021/acs.analchem.0c04281] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- John R. Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Thomas Botzanowski
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Daniele Peterle
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Florian Georgescauld
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Thomas E. Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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5
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Lin X, Ammosova T, Choy MS, Pietzsch CA, Ivanov A, Ahmad A, Saygideğer Y, Kumari N, Kovalskyy D, Üren A, Peti W, Bukreyev A, Nekhai S. Targeting the Non-catalytic RVxF Site of Protein Phosphatase-1 With Small Molecules for Ebola Virus Inhibition. Front Microbiol 2019; 10:2145. [PMID: 31572348 PMCID: PMC6753193 DOI: 10.3389/fmicb.2019.02145] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 08/30/2019] [Indexed: 12/17/2022] Open
Abstract
Ebola virus (EBOV) is a non-segmented negative-sense RNA virus that causes a severe human disease. The ongoing EBOV outbreak in the Eastern part of Democratic Republic of the Congo has resulted to date in over 2500 confirmed cases including over 1500 deaths. Difficulties with vaccine administration indicate the necessity for development of new general drugs and therapeutic strategies against EBOV. Host Ser/Thr protein phosphatases, particularly PP1 and PP2A, facilitate EBOV transcription by dephosphorylating the EBOV VP30 protein and switching activity of the polymerase complex toward replication. Previously, we developed small molecule 1E7-03 that targeted host protein phosphatase-1 (PP1) and induces phosphorylation of EBOV VP30 protein thus shifting transcription-replication balance and inhibiting EBOV replication. Here, we developed a new EBOV inhibitor, 1E7-07, that potently inhibits EBOV replication and displays significantly improved metabolic stability when compared to previously described 1E7-03. Proteome analysis of VP30 shows that 1E7-07 increases its phosphorylation on Thr-119 and Ser-124 over 3-fold with p < 0.001, which likely contributes to EBOV inhibition. We analyzed 1E7-07 binding to PP1 using a mass spectrometry-based protein painting approach. Combined with computational docking, protein painting shows that 1E7-07 binds to several PP1 sites including the RVxF site, C-terminal groove and NIPP1-helix binding pocket. Further analysis using surface plasmon resonance and a split NanoBiT system demonstrates that 1E7-07 binds primarily to the RVxF site. Together, detailed analysis of 1E7-07 binding to PP1 and identification of the RVxF site as the main binding site opens up an opportunity for future development of PP1-targeting EBOV inhibitors.
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Affiliation(s)
- Xionghao Lin
- Center for Sickle Cell Disease, College of Medicine, Howard University, Washington, DC, United States
- College of Dentistry, Howard University, Washington, DC, United States
| | - Tatiana Ammosova
- Center for Sickle Cell Disease, College of Medicine, Howard University, Washington, DC, United States
- Department of Medicine, College of Medicine, Howard University, Washington, DC, United States
- Yakut Science Centre of Complex Medical Problems, Yakutsk, Russia
| | - Meng S. Choy
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, United States
| | - Colette A. Pietzsch
- Department of Pathology, Department of Microbiology and Immunology, and Galveston National Laboratory, University of Texas Medical Branch at Galveston, Galveston, TX, United States
| | - Andrey Ivanov
- Center for Sickle Cell Disease, College of Medicine, Howard University, Washington, DC, United States
| | - Asrar Ahmad
- Center for Sickle Cell Disease, College of Medicine, Howard University, Washington, DC, United States
| | - Yasemin Saygideğer
- Georgetown Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
| | - Namita Kumari
- Center for Sickle Cell Disease, College of Medicine, Howard University, Washington, DC, United States
| | - Dmytro Kovalskyy
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX, United States
| | - Aykut Üren
- Georgetown Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
| | - Wolfgang Peti
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, United States
| | - Alexander Bukreyev
- Department of Pathology, Department of Microbiology and Immunology, and Galveston National Laboratory, University of Texas Medical Branch at Galveston, Galveston, TX, United States
| | - Sergei Nekhai
- Center for Sickle Cell Disease, College of Medicine, Howard University, Washington, DC, United States
- Department of Medicine, College of Medicine, Howard University, Washington, DC, United States
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Haymond A, Davis JB, Espina V. Proteomics for cancer drug design. Expert Rev Proteomics 2019; 16:647-664. [PMID: 31353977 PMCID: PMC6736641 DOI: 10.1080/14789450.2019.1650025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 07/26/2019] [Indexed: 12/29/2022]
Abstract
Introduction: Signal transduction cascades drive cellular proliferation, apoptosis, immune, and survival pathways. Proteins have emerged as actionable drug targets because they are often dysregulated in cancer, due to underlying genetic mutations, or dysregulated signaling pathways. Cancer drug development relies on proteomic technologies to identify potential biomarkers, mechanisms-of-action, and to identify protein binding hot spots. Areas covered: Brief summaries of proteomic technologies for drug discovery include mass spectrometry, reverse phase protein arrays, chemoproteomics, and fragment based screening. Protein-protein interface mapping is presented as a promising method for peptide therapeutic development. The topic of biosimilar therapeutics is presented as an opportunity to apply proteomic technologies to this new class of cancer drug. Expert opinion: Proteomic technologies are indispensable for drug discovery. A suite of technologies including mass spectrometry, reverse phase protein arrays, and protein-protein interaction mapping provide complimentary information for drug development. These assays have matured into well controlled, robust technologies. Recent regulatory approval of biosimilar therapeutics provides another opportunity to decipher the molecular nuances of their unique mechanisms of action. The ability to identify previously hidden protein hot spots is expanding the gamut of potential drug targets. Proteomic profiling permits lead compound evaluation beyond the one drug, one target paradigm.
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Affiliation(s)
- Amanda Haymond
- Center for Applied Proteomics and Molecular Medicine, George Mason University , Manassas , VA , USA
| | - Justin B Davis
- Center for Applied Proteomics and Molecular Medicine, George Mason University , Manassas , VA , USA
| | - Virginia Espina
- Center for Applied Proteomics and Molecular Medicine, George Mason University , Manassas , VA , USA
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7
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Haymond A, Dey D, Carter R, Dailing A, Nara V, Nara P, Venkatayogi S, Paige M, Liotta L, Luchini A. Protein painting, an optimized MS-based technique, reveals functionally relevant interfaces of the PD-1/PD-L1 complex and the YAP2/ZO-1 complex. J Biol Chem 2019; 294:11180-11198. [PMID: 31167787 DOI: 10.1074/jbc.ra118.007310] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 05/31/2019] [Indexed: 12/26/2022] Open
Abstract
Protein-protein interactions lie at the heart of many biological processes and therefore represent promising drug targets. Despite this opportunity, identification of protein-protein interfaces remains challenging. We have previously developed a method that relies on coating protein surfaces with small-molecule dyes to discriminate between solvent-accessible protein surfaces and hidden interface regions. Dye-bound, solvent-accessible protein regions resist trypsin digestion, whereas hidden interface regions are revealed by denaturation and sequenced by MS. The small-molecule dyes bind promiscuously and with high affinity, but their binding mechanism is unknown. Here, we report on the optimization of a novel dye probe used in protein painting, Fast Blue B + naphthionic acid, and show that its affinity for proteins strongly depends on hydrophobic moieties that we call here "hydrophobic clamps." We demonstrate the utility of this probe by sequencing the protein-protein interaction regions between the Hippo pathway protein Yes-associated protein 2 (YAP2) and tight junction protein 1 (TJP1 or ZO-1), uncovering interactions via the known binding domain as well as ZO-1's MAGUK domain and YAP's N-terminal proline-rich domain. Additionally, we demonstrate how residues predicted by protein painting are present exclusively in the complex interface and how these residues may guide the development of peptide inhibitors using a case study of programmed cell death protein 1 (PD-1) and programmed cell death 1 ligand 1 (PD-L1). Inhibitors designed around the PD-1/PD-L1 interface regions identified via protein painting effectively disrupted complex formation, with the most potent inhibitor having an IC50 of 5 μm.
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Affiliation(s)
- Amanda Haymond
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia 20110
| | - Douglass Dey
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia 20110
| | - Rachel Carter
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia 20110
| | - Angela Dailing
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia 20110
| | - Vaishnavi Nara
- Thomas Jefferson High School for Science and Technology, Alexandria, Virginia 22312
| | - Pranavi Nara
- University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Sravani Venkatayogi
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia 20110
| | - Mikell Paige
- Department of Chemistry and Biochemistry, George Mason University, Fairfax, Virginia 20110
| | - Lance Liotta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia 20110
| | - Alessandra Luchini
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia 20110
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8
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Minic Z, Dahms TES, Babu M. Chromatographic separation strategies for precision mass spectrometry to study protein-protein interactions and protein phosphorylation. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1102-1103:96-108. [PMID: 30380468 DOI: 10.1016/j.jchromb.2018.10.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 11/30/2022]
Abstract
Investigating protein-protein interactions and protein phosphorylation can be of great significance when studying biological processes and human diseases at the molecular level. However, sample complexity, presence of low abundance proteins, and dynamic nature of the proteins often impede in achieving sufficient analytical depth in proteomics research. In this regard, chromatographic separation methodologies have played a vital role in the identification and quantification of proteins in complex sample mixtures. The combination of peptide and protein fractionation techniques with advanced high-performance mass spectrometry has allowed the researchers to successfully study the protein-protein interactions and protein phosphorylation. Several new fractionation strategies for large scale analysis of proteins and peptides have been developed to study protein-protein interactions and protein phosphorylation. These emerging chromatography methodologies have enabled the identification of several hundred protein complexes and even thousands of phosphorylation sites in a single study. In this review, we focus on current workflow strategies and chromatographic tools, highlighting their advantages and disadvantages, and examining their associated challenges and future potential.
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Affiliation(s)
- Zoran Minic
- Department of Chemistry and Biomolecular Science, University of Ottawa, John L. Holmes, Mass Spectrometry Facility, 10 Marie-Curie, Marion Hall, Room 02, Ottawa, ON K1N 1A2, Canada.
| | - Tanya E S Dahms
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
| | - Mohan Babu
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
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Yu C, Huang L. Cross-Linking Mass Spectrometry: An Emerging Technology for Interactomics and Structural Biology. Anal Chem 2018; 90:144-165. [PMID: 29160693 PMCID: PMC6022837 DOI: 10.1021/acs.analchem.7b04431] [Citation(s) in RCA: 222] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Clinton Yu
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA 92697
| | - Lan Huang
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA 92697
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10
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The proteome of baker's yeast mitochondria. Mitochondrion 2017; 33:15-21. [DOI: 10.1016/j.mito.2016.08.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 08/12/2016] [Accepted: 08/13/2016] [Indexed: 01/29/2023]
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11
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Liu G, Wang P, Li C, Wang J, Sun Z, Zhao X, Zheng X. Confirming therapeutic target of protopine using immobilized β 2 -adrenoceptor coupled with site-directed molecular docking and the target-drug interaction by frontal analysis and injection amount-dependent method. J Mol Recognit 2017; 30. [PMID: 28124461 DOI: 10.1002/jmr.2613] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Revised: 12/17/2016] [Accepted: 01/03/2017] [Indexed: 11/09/2022]
Abstract
Drug-protein interaction analysis is pregnant in designing new leads during drug discovery. We prepared the stationary phase containing immobilized β2 -adrenoceptor (β2 -AR) by linkage of the receptor on macroporous silica gel surface through N,N'-carbonyldiimidazole method. The stationary phase was applied in identifying antiasthmatic target of protopine guided by the prediction of site-directed molecular docking. Subsequent application of immobilized β2 -AR in exploring the binding of protopine to the receptor was realized by frontal analysis and injection amount-dependent method. The association constants of protopine to β2 -AR by the 2 methods were (1.00 ± 0.06) × 105 M-1 and (1.52 ± 0.14) × 104 M-1 . The numbers of binding sites were (1.23 ± 0.07) × 10-7 M and (9.09 ± 0.06) × 10-7 M, respectively. These results indicated that β2 -AR is the specific target for therapeutic action of protopine in vivo. The target-drug binding occurred on Ser169 in crystal structure of the receptor. Compared with frontal analysis, injection amount-dependent method is advantageous to drug saving, improvement of sampling efficiency, and performing speed. It has grave potential in high-throughput drug-receptor interaction analysis.
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Affiliation(s)
- Guangxin Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Pei Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Chan Li
- Drug Certificate Center, Shaanxi Food and Drug Administration, Xi'an, China
| | - Jing Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Zhenyu Sun
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Xinfeng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Xiaohui Zheng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
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Two-Dimensional Electrophoresis Protocols to Analyze the Microtubule-Associated Tau Proteins from Several Biological Sources. Methods Mol Biol 2017; 1523:251-261. [PMID: 27975254 DOI: 10.1007/978-1-4939-6598-4_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Technology breakthrough in proteomics enables to gather qualitative and quantitative information about a protein or a complex mixture of proteins. Two-dimensional gel electrophoresis remains an interesting technique, which provides an overview of the complexity of isovariants from a single protein when coupled to western blotting. Here, we describe a detailed protocol for the two-dimensional analysis of microtubule-associated Tau isovariants from cell to human or mouse brain tissue. We provide protocol enabling to separate native and Tau proteins that are aggregated in neurodegenerative disorders such as Alzheimer's disease.
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13
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Hydrogen deuterium exchange mass spectrometry in biopharmaceutical discovery and development – A review. Anal Chim Acta 2016; 940:8-20. [DOI: 10.1016/j.aca.2016.08.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/25/2016] [Accepted: 08/07/2016] [Indexed: 01/14/2023]
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