1
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Bailey MA, Martyr JG, Hargrove AE, Fitzgerald MC. Stability-Based Proteomics for Investigation of Structured RNA-Protein Interactions. Anal Chem 2024:10.1021/acs.analchem.3c04978. [PMID: 38341805 PMCID: PMC11316846 DOI: 10.1021/acs.analchem.3c04978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2024]
Abstract
RNA-protein interactions are essential to RNA function throughout biology. Identifying the protein interactions associated with a specific RNA, however, is currently hindered by the need for RNA labeling or costly tiling-based approaches. Conventional strategies, which commonly rely on affinity pull-down approaches, are also skewed to the detection of high affinity interactions and frequently miss weaker interactions that may be biologically important. Reported here is the first adaptation of stability-based mass spectrometry methods for the global analysis of RNA-protein interactions. The stability of proteins from rates of oxidation (SPROX) and thermal protein profiling (TPP) methods are used to identify the protein targets of three RNA ligands, the MALAT1 triple helix (TH), a viral stem loop (SL), and an unstructured RNA (PolyU), in LNCaP nuclear lysate. The 315 protein hits with RNA-induced conformational and stability changes detected by TPP and/or SPROX were enriched in previously annotated RNA-binding proteins and included new proteins for hypothesis generation. Also demonstrated are the orthogonality of the SPROX and TPP approaches and the utility of the domain-specific information available with SPROX. This work establishes a novel platform for the global discovery and interrogation of RNA-protein interactions that is generalizable to numerous biological contexts and RNA targets.
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Affiliation(s)
- Morgan A Bailey
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Justin G Martyr
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Amanda E Hargrove
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Michael C Fitzgerald
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
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2
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Li Y, Lyu J, Wang Y, Ye M, Wang H. Ligand Modification-Free Methods for the Profiling of Protein-Environmental Chemical Interactions. Chem Res Toxicol 2024; 37:1-15. [PMID: 38146056 DOI: 10.1021/acs.chemrestox.3c00282] [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
Adverse health outcomes caused by environmental chemicals are often initiated via their interactions with proteins. Essentially, one environmental chemical may interact with a number of proteins and/or a protein may interact with a multitude of environmental chemicals, forming an intricate interaction network. Omics-wide protein-environmental chemical interaction profiling (PECI) is of prominent importance for comprehensive understanding of these interaction networks, including the toxicity mechanisms of action (MoA), and for providing systematic chemical safety assessment. However, such information remains unknown for most environmental chemicals, partly due to their vast chemical diversity. In recent years, with the continuous efforts afforded, especially in mass spectrometry (MS) based omics technologies, several ligand modification-free methods have been developed, and new attention for systematic PECI profiling was gained. In this Review, we provide a comprehensive overview on these methodologies for the identification of ligand-protein interactions, including affinity interaction-based methods of affinity-driven purification, covalent modification profiling, and activity-based protein profiling (ABPP) in a competitive mode, physicochemical property changes assessment methods of ligand-directed nuclear magnetic resonance (ligand-directed NMR), MS integrated with equilibrium dialysis for the discovery of allostery systematically (MIDAS), thermal proteome profiling (TPP), limited proteolysis-coupled mass spectrometry (LiP-MS), stability of proteins from rates of oxidation (SPROX), and several intracellular downstream response characterization methods. We expect that the applications of these ligand modification-free technologies will drive a considerable increase in the number of PECI identified, facilitate unveiling the toxicological mechanisms, and ultimately contribute to systematic health risk assessment of environmental chemicals.
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Affiliation(s)
- Yanan Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jiawen Lyu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Yan Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
- State Key Laboratory of Medical Proteomics, Beijing, 102206, China
| | - Hailin Wang
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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3
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Tabana Y, Babu D, Fahlman R, Siraki AG, Barakat K. Target identification of small molecules: an overview of the current applications in drug discovery. BMC Biotechnol 2023; 23:44. [PMID: 37817108 PMCID: PMC10566111 DOI: 10.1186/s12896-023-00815-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 09/22/2023] [Indexed: 10/12/2023] Open
Abstract
Target identification is an essential part of the drug discovery and development process, and its efficacy plays a crucial role in the success of any given therapy. Although protein target identification research can be challenging, two main approaches can help researchers make significant discoveries: affinity-based pull-down and label-free methods. Affinity-based pull-down methods use small molecules conjugated with tags to selectively isolate target proteins, while label-free methods utilize small molecules in their natural state to identify targets. Target identification strategy selection is essential to the success of any drug discovery process and must be carefully considered when determining how to best pursue a specific project. This paper provides an overview of the current target identification approaches in drug discovery related to experimental biological assays, focusing primarily on affinity-based pull-down and label-free approaches, and discusses their main limitations and advantages.
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Affiliation(s)
- Yasser Tabana
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Dinesh Babu
- Li Ka Shing Applied Virology Institute, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Richard Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Arno G Siraki
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Khaled Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada.
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4
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Kang J, Seshadri M, Cupp-Sutton KA, Wu S. Toward the analysis of functional proteoforms using mass spectrometry-based stability proteomics. FRONTIERS IN ANALYTICAL SCIENCE 2023; 3:1186623. [PMID: 39072225 PMCID: PMC11281393 DOI: 10.3389/frans.2023.1186623] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Functional proteomics aims to elucidate biological functions, mechanisms, and pathways of proteins and proteoforms at the molecular level to examine complex cellular systems and disease states. A series of stability proteomics methods have been developed to examine protein functionality by measuring the resistance of a protein to chemical or thermal denaturation or proteolysis. These methods can be applied to measure the thermal stability of thousands of proteins in complex biological samples such as cell lysate, intact cells, tissues, and other biological fluids to measure proteome stability. Stability proteomics methods have been popularly applied to observe stability shifts upon ligand binding for drug target identification. More recently, these methods have been applied to characterize the effect of structural changes in proteins such as those caused by post-translational modifications (PTMs) and mutations, which can affect protein structures or interactions and diversify protein functions. Here, we discussed the current application of a suite of stability proteomics methods, including thermal proteome profiling (TPP), stability of proteomics from rates of oxidation (SPROX), and limited proteolysis (LiP) methods, to observe PTM-induced structural changes on protein stability. We also discuss future perspectives highlighting the integration of top-down mass spectrometry and stability proteomics methods to characterize intact proteoform stability and understand the function of variable protein modifications.
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Affiliation(s)
- Ji Kang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, United States
| | - Meena Seshadri
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, United States
| | - Kellye A. Cupp-Sutton
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, United States
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, United States
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5
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Quan B, Bailey MA, Mantyh J, Hsu DS, Fitzgerald MC. Protein Folding Stability Profiling of Colorectal Cancer Chemoresistance Identifies Functionally Relevant Biomarkers. J Proteome Res 2023; 22:1923-1935. [PMID: 37126456 PMCID: PMC10441206 DOI: 10.1021/acs.jproteome.3c00045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Reported here is the application of three protein folding stability profiling techniques (including the stability of proteins from rates of oxidation, thermal protein profiling, and limited proteolysis approaches) to identify differentially stabilized proteins in six patient-derived colorectal cancer (CRC) cell lines with different oxaliplatin sensitivities and eight CRC patient-derived xenografts (PDXs) derived from two of the patient derived cell lines with different oxaliplatin sensitivities. Compared to conventional protein expression level analyses, which were also performed here, the stability profiling techniques identified both unique and novel proteins and cellular components that differentiated the sensitive and resistant samples including 36 proteins that were differentially stabilized in at least two techniques in both the cell line and PDX studies of oxaliplatin resistance. These 36 differentially stabilized proteins included 10 proteins previously connected to cancer chemoresistance. Two differentially stabilized proteins, fatty acid synthase and elongation factor 2, were functionally validated in vitro and found to be druggable protein targets with biological functions that can be modulated to improve the efficacy of CRC chemotherapy. These results add to our understanding of CRC oxaliplatin resistance, suggest biomarker candidates for predicting oxaliplatin sensitivity in CRC, and inform new strategies for overcoming chemoresistance in CRC.
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Affiliation(s)
- Baiyi Quan
- Department of Chemistry, Duke University, Durham, NC 27708-0346
| | | | - John Mantyh
- Deparment of Medicine, Duke University Medical Center, Durham, NC
| | - David S. Hsu
- Deparment of Medicine, Duke University Medical Center, Durham, NC
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6
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Bailey MA, Tang Y, Park HJ, Fitzgerald MC. Comparative Analysis of Protein Folding Stability-Based Profiling Methods for Characterization of Biological Phenotypes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:383-393. [PMID: 36802530 PMCID: PMC10164353 DOI: 10.1021/jasms.2c00248] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Recently, a new suite of mass spectrometry-based proteomic methods has been developed that enables evaluation of protein folding stability on the proteomic scale. These methods utilize chemical and thermal denaturation approaches (SPROX and TPP, respectively) as well as proteolysis strategies (DARTS, LiP, and PP) to assess protein folding stability. The analytical capabilities of these technique have been well-established for protein target discovery applications. However, less is known about the relative advantages and disadvantages of using these different strategies to characterize biological phenotypes. Reported here is a comparative study of SPROX, TPP, LiP, and conventional protein expression level measurements using both a mouse model of aging and a mammalian cell culture model of breast cancer. Analyses on proteins in brain tissue cell lysates derived from 1- and 18-month-old mice (n = 4-5 at each time point) and on proteins in cell lysates derived from the MCF-7 and MCF-10A cell lines revealed a majority of the differentially stabilized protein hits in each phenotype analysis had unchanged expression levels. In both phenotype analyses, TPP generated the largest number and fraction of differentially stabilized protein hits. Only a quarter of all the protein hits identified in each phenotype analysis had a differential stability that was detected using multiple techniques. This work also reports the first peptide-level analysis of TPP data, which was required for the correct interpretation of the phenotype analyses performed here. Studies on selected protein stability hits also uncovered phenotype-related functional changes.
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Affiliation(s)
- Morgan A. Bailey
- Department of Chemistry, Duke University, Durham, North Carolina 27708
- These authors contributed equally
| | - Yun Tang
- Department of Chemistry, Duke University, Durham, North Carolina 27708
- These authors contributed equally
| | - Hye-Jin Park
- Department of Chemistry, Duke University, Durham, North Carolina 27708
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7
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Abstract
Environmental agents of exposure can damage proteins, affecting protein function and cellular protein homeostasis. Specific residues are inherently chemically susceptible to damage from individual types of exposure. Amino acid content is not completely predictive of protein susceptibility, as secondary, tertiary, and quaternary structures of proteins strongly influence the reactivity of the proteome to individual exposures. Because we cannot readily predict which proteins will be affected by which chemical exposures, mass spectrometry-based proteomic strategies are necessary to determine the protein targets of environmental toxins and toxicants. This review describes the mechanisms by which environmental exposure to toxins and toxicants can damage proteins and affect their function, and emerging omic methodologies that can be used to identify the protein targets of a given agent. These methods include target identification strategies that have recently revolutionized the drug discovery field, such as activity-based protein profiling, protein footprinting, and protein stability profiling technologies. In particular, we highlight the necessity of multiple, complementary approaches to fully interrogate how protein integrity is challenged by individual exposures.
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Affiliation(s)
- Joseph C Genereux
- Department of Chemistry, University of California, Riverside, CA 92521, USA.
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8
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Melder FTI, Lindemann P, Welle A, Trouillet V, Heißler S, Nazaré M, Selbach M. Compound Interaction Screen on a Photoactivatable Cellulose Membrane (CISCM) Identifies Drug Targets. ChemMedChem 2022; 17:e202200346. [PMID: 35867055 PMCID: PMC9826412 DOI: 10.1002/cmdc.202200346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Indexed: 01/11/2023]
Abstract
Identifying the protein targets of drugs is an important but tedious process. Existing proteomic approaches enable unbiased target identification but lack the throughput needed to screen larger compound libraries. Here, we present a compound interaction screen on a photoactivatable cellulose membrane (CISCM) that enables target identification of several drugs in parallel. To this end, we use diazirine-based undirected photoaffinity labeling (PAL) to immobilize compounds on cellulose membranes. Functionalized membranes are then incubated with protein extract and specific targets are identified via quantitative affinity purification and mass spectrometry. CISCM reliably identifies known targets of natural products in less than three hours of analysis time per compound. In summary, we show that combining undirected photoimmobilization of compounds on cellulose with quantitative interaction proteomics provides an efficient means to identify the targets of natural products.
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Affiliation(s)
- F. Teresa I. Melder
- Proteome Dynamics LabMax Delbruck Center for Molecular Medicine in the Helmholtz AssociationRobert-Roessle-Str. 1013125BerlinGermany
| | - Peter Lindemann
- Medicinal ChemistryLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)13125BerlinGermany
| | - Alexander Welle
- Institute of Functional Interfaces and Karlsruhe Nano Micro Facility (KNMFi)Karlsruhe Institute of Technology (KIT)Hermann-von-Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
| | - Vanessa Trouillet
- Institute for Applied Materials (IAM-ESS) and Karlsruhe Nano Micro Facility (KNMFi)Karlsruhe Institute of Technology (KIT)Hermann-von-Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
| | - Stefan Heißler
- Institute of Functional Interfaces and Karlsruhe Nano Micro Facility (KNMFi)Karlsruhe Institute of Technology (KIT)Hermann-von-Helmholtz-Platz 176344Eggenstein-LeopoldshafenGermany
| | - Marc Nazaré
- Medicinal ChemistryLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)13125BerlinGermany
| | - Matthias Selbach
- Proteome Dynamics LabMax Delbruck Center for Molecular Medicine in the Helmholtz AssociationRobert-Roessle-Str. 1013125BerlinGermany
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9
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Blackburn MR, Minkoff BB, Sussman MR. Mass spectrometry-based technologies for probing the 3D world of plant proteins. PLANT PHYSIOLOGY 2022; 189:12-22. [PMID: 35139210 PMCID: PMC9070838 DOI: 10.1093/plphys/kiac039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 12/30/2021] [Indexed: 05/03/2023]
Abstract
Over the past two decades, mass spectrometric (MS)-based proteomics technologies have facilitated the study of signaling pathways throughout biology. Nowhere is this needed more than in plants, where an evolutionary history of genome duplications has resulted in large gene families involved in posttranslational modifications and regulatory pathways. For example, at least 5% of the Arabidopsis thaliana genome (ca. 1,200 genes) encodes protein kinases and protein phosphatases that regulate nearly all aspects of plant growth and development. MS-based technologies that quantify covalent changes in the side-chain of amino acids are critically important, but they only address one piece of the puzzle. A more crucially important mechanistic question is how noncovalent interactions-which are more difficult to study-dynamically regulate the proteome's 3D structure. The advent of improvements in protein 3D technologies such as cryo-electron microscopy, nuclear magnetic resonance, and X-ray crystallography has allowed considerable progress to be made at this level, but these methods are typically limited to analyzing proteins, which can be expressed and purified in milligram quantities. Newly emerging MS-based technologies have recently been developed for studying the 3D structure of proteins. Importantly, these methods do not require protein samples to be purified and require smaller amounts of sample, opening the wider proteome for structural analysis in complex mixtures, crude lysates, and even in intact cells. These MS-based methods include covalent labeling, crosslinking, thermal proteome profiling, and limited proteolysis, all of which can be leveraged by established MS workflows, as well as newly emerging methods capable of analyzing intact macromolecules and the complexes they form. In this review, we discuss these recent innovations in MS-based "structural" proteomics to provide readers with an understanding of the opportunities they offer and the remaining challenges for understanding the molecular underpinnings of plant structure and function.
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Affiliation(s)
- Matthew R Blackburn
- Department of Biochemistry and Center for Genomic Science Innovation, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Benjamin B Minkoff
- Department of Biochemistry and Center for Genomic Science Innovation, University of Wisconsin, Madison, Wisconsin 53706, USA
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10
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Unmodified methodologies in target discovery for small molecule drugs: A rising star. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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11
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Wiebelhaus N, Singh N, Zhang P, Craig SL, Beratan DN, Fitzgerald MC. Discovery of the Xenon-Protein Interactome Using Large-Scale Measurements of Protein Folding and Stability. J Am Chem Soc 2022; 144:3925-3938. [PMID: 35213151 PMCID: PMC10166008 DOI: 10.1021/jacs.1c11900] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The intermolecular interactions of noble gases in biological systems are associated with numerous biochemical responses, including apoptosis, inflammation, anesthesia, analgesia, and neuroprotection. The molecular modes of action underlying these responses are largely unknown. This is in large part due to the limited experimental techniques to study protein-gas interactions. The few techniques that are amenable to such studies are relatively low-throughput and require large amounts of purified proteins. Thus, they do not enable the large-scale analyses that are useful for protein target discovery. Here, we report the application of stability of proteins from rates of oxidation (SPROX) and limited proteolysis (LiP) methodologies to detect protein-xenon interactions on the proteomic scale using protein folding stability measurements. Over 5000 methionine-containing peptides and over 5000 semi-tryptic peptides, mapping to ∼1500 and ∼950 proteins, respectively, in the yeast proteome, were assayed for Xe-interacting activity using the SPROX and LiP techniques. The SPROX and LiP analyses identified 31 and 60 Xe-interacting proteins, respectively, none of which were previously known to bind Xe. A bioinformatics analysis of the proteomic results revealed that these Xe-interacting proteins were enriched in those involved in ATP-driven processes. A fraction of the protein targets that were identified are tied to previously established modes of action related to xenon's anesthetic and organoprotective properties. These results enrich our knowledge and understanding of biologically relevant xenon interactions. The sample preparation protocols and analytical methodologies developed here for xenon are also generally applicable to the discovery of a wide range of other protein-gas interactions in complex biological mixtures, such as cell lysates.
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Affiliation(s)
- Nancy Wiebelhaus
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Niven Singh
- Program in Computational Biology and Bioinformatics, Center for Genomics and Computational Biology, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Peng Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Stephen L. Craig
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - David N. Beratan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Program in Computational Biology and Bioinformatics, Center for Genomics and Computational Biology, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Michael C. Fitzgerald
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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12
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Hatstat AK, Quan B, Bailey MA, Fitzgerald MC, Reinhart MC, McCafferty DG. Chemoproteomic-enabled characterization of small GTPase Rab1a as a target of an N-arylbenzimidazole ligand's rescue of Parkinson's-associated cell toxicity. RSC Chem Biol 2022; 3:96-111. [PMID: 35128413 PMCID: PMC8729260 DOI: 10.1039/d1cb00103e] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 11/08/2021] [Indexed: 11/21/2022] Open
Abstract
The development of phenotypic models of Parkinson's disease (PD) has enabled screening and identification of phenotypically active small molecules that restore complex biological pathways affected by PD toxicity.
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Affiliation(s)
| | - Baiyi Quan
- Department of Chemistry, Duke University, Durham, NC 27708, USA
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13
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Lizano-Fallas V, Carrasco Del Amor A, Cristobal S. Systematic analysis of chemical-protein interactions from zebrafish embryo by proteome-wide thermal shift assay, bridging the gap between molecular interactions and toxicity pathways. J Proteomics 2021; 249:104382. [PMID: 34555547 DOI: 10.1016/j.jprot.2021.104382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 09/15/2021] [Indexed: 02/06/2023]
Abstract
The molecular interaction between chemicals and proteins often promotes alteration of cellular function. One of the challenges of the toxicology is to predict the impact of exposure to chemicals. Assessing the impact of exposure implies to understand their mechanism of actions starting from identification of specific protein targets of the interaction. Current methods can mainly predict effects of characterized chemicals with knowledge of its targets, and mechanism of actions. Here, we show that proteome-wide thermal shift methods can identify chemical-protein interactions and the protein targets from bioactive chemicals. We analyzed the identified targets from a soluble proteome extracted from zebrafish embryo, that is a model system for toxicology. To evaluate the utility to predict mechanism of actions, we discussed the applicability in four cases: single chemicals, chemical mixtures, novel chemicals, and novel drugs. Our results showed that this methodology could identify the protein targets, discriminate between protein increasing and decreasing in solubility, and offering additional data to complement the map of intertwined mechanism of actions. We anticipate that the proteome integral solubility alteration (PISA) assay, as it is defined here for the unbiased identification of protein targets of chemicals could bridge the gap between molecular interactions and toxicity pathways. SIGNIFICANCE: One of the challenges of the environmental toxicology is to predict the impact of exposure to chemicals on environment and human health. Our phenotype should be explained by our genotype and the environmental exposure. Genomic methodologies can offer a deep analysis of human genome that alone cannot explain our risks of disease. We are starting to understand the key role of exposure to chemicals on our health and risks of disease. Here, we present a proteomic-based method for the identification of soluble proteins interacting with chemicals in zebrafish embryo and discuss the opportunities to complement the map of toxicity pathway perturbations. We anticipate that this PISA assay could bridge the gap between molecular interactions and toxicity pathways.
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Affiliation(s)
- Veronica Lizano-Fallas
- Department of Biomedical and Clinical Sciences, Cell Biology, Medical Faculty, Linköping University, Linköping 581 85, Sweden
| | - Ana Carrasco Del Amor
- Department of Biomedical and Clinical Sciences, Cell Biology, Medical Faculty, Linköping University, Linköping 581 85, Sweden
| | - Susana Cristobal
- Department of Biomedical and Clinical Sciences, Cell Biology, Medical Faculty, Linköping University, Linköping 581 85, Sweden.; Ikerbasque, Basque Foundation for Science, Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Barrio Sarriena, s/n, Leioa 48940, Spain..
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14
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Xu Y, West GM, Abdelmessih M, Troutman MD, Everley RA. A Comparison of Two Stability Proteomics Methods for Drug Target Identification in OnePot 2D Format. ACS Chem Biol 2021; 16:1445-1455. [PMID: 34374519 DOI: 10.1021/acschembio.1c00317] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Stability proteomics techniques that do not require drug modifications have emerged as an attractive alternative to affinity purification methods in drug target engagement studies. Two representative techniques include the chemical-denaturation-based SPROX (Stability of Proteins from Rates of Oxidation), which utilizes peptide-level quantification and thermal-denaturation-based TPP (Thermal Proteome Profiling), which utilizes protein-level quantification. Recently, the "OnePot" strategy was adapted for both SPROX and TPP to increase the throughput. When combined with the 2D setup which measures both the denaturation and the drug dose dimensions, the OnePot 2D format offers improved analysis specificity with higher resource efficiency. However, a systematic evaluation of the OnePot 2D format and a comparison between SPROX and TPP are still lacking. Here, we performed SPROX and TPP to identify protein targets of a well-studied pan-kinase inhibitor staurosporine with K562 lysate, in curve-fitting and OnePot 2D formats. We found that the OnePot 2D format provided ∼10× throughput, achieved ∼1.6× protein coverage and involves more straightforward data analysis. We also compared SPROX with the current "gold-standard" stability proteomics technique TPP in the OnePot 2D format. The protein coverage of TPP is ∼1.5 fold of SPROX; however, SPROX offers protein domain-level information, identifies comparable numbers of kinase hits, has higher signal (R value), and requires ∼3× less MS time. Unique SPROX hits encompass higher-molecular-weight proteins, compared to the unique TPP hits, and include atypical kinases. We also discuss hit stratification and prioritization strategies to promote the efficiency of hit followup.
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Affiliation(s)
- Yingrong Xu
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Graham M. West
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Mario Abdelmessih
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Matthew D. Troutman
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Robert A. Everley
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
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15
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Sun J, Prabhu N, Tang J, Yang F, Jia L, Guo J, Xiao K, Tam WL, Nordlund P, Dai L. Recent advances in proteome-wide label-free target deconvolution for bioactive small molecules. Med Res Rev 2021; 41:2893-2926. [PMID: 33533067 DOI: 10.1002/med.21788] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/04/2021] [Accepted: 01/20/2021] [Indexed: 01/01/2023]
Abstract
Small-molecule drugs modulate biological processes and disease states through engagement of target proteins in cells. Assessing drug-target engagement on a proteome-wide scale is of utmost importance in better understanding the molecular mechanisms of action of observed beneficial and adverse effects, as well as in developing next generation tool compounds and drugs with better efficacies and specificities. However, systematic assessment of drug-target engagement has been an arduous task. With the continuous development of mass spectrometry-based proteomics instruments and techniques, various chemical proteomics approaches for drug target deconvolution (i.e., the identification of molecular target for drugs) have emerged. Among these, the label-free target deconvolution approaches that do not involve the chemical modification of compounds of interest, have gained increased attention in the community. Here we provide an overview of the basic principles and recent biological applications of the most important label-free methods including the cellular thermal shift assay, pulse proteolysis, chemical denaturant and protein precipitation, stability of proteins from rates of oxidation, drug affinity responsive target stability, limited proteolysis, and solvent-induced protein precipitation. The state-of-the-art technical implications and future outlook for the label-free approaches are also discussed.
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Affiliation(s)
- Jichao Sun
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Urology Minimally Invasive Engineering Center, Shenzhen, Guangdong, China.,Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Nayana Prabhu
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jun Tang
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Urology Minimally Invasive Engineering Center, Shenzhen, Guangdong, China.,Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, Guangdong, China
| | - Fan Yang
- Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China.,Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, Guangdong, China
| | - Lin Jia
- College of Pharmacy, Shenzhen Technology University, Shenzhen, Guangdong, China
| | - Jinan Guo
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Urology Minimally Invasive Engineering Center, Shenzhen, Guangdong, China
| | - Kefeng Xiao
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Urology Minimally Invasive Engineering Center, Shenzhen, Guangdong, China
| | - Wai Leong Tam
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Pär Nordlund
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Lingyun Dai
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Urology Minimally Invasive Engineering Center, Shenzhen, Guangdong, China.,Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
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Wiebelhaus N, Zaengle-Barone JM, Hwang KK, Franz KJ, Fitzgerald MC. Protein Folding Stability Changes Across the Proteome Reveal Targets of Cu Toxicity in E. coli. ACS Chem Biol 2021; 16:214-224. [PMID: 33305953 DOI: 10.1021/acschembio.0c00900] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The ability of metal ionophores to induce cellular metal hyperaccumulation endows them with potent antimicrobial activity; however, the targets and mechanisms behind these outcomes are not well understood. This work describes the first utilization of proteome-wide measurements of protein folding stability in combination with protein expression level analysis to identify protein targets of copper, thereby providing new insight into ionophore-induced copper toxicity in E. coli. The protein folding stability analysis employed a one-pot protocol for pulse proteolysis (PP) in combination with a semi-tryptic peptide enrichment strategy for proteolysis procedures (STEPP) to generate stability profiles for proteins in cell lysates derived from E. coli exposed to copper with and without two ionophores, the antimicrobial agent pyrithione and its β-lactamase-activated prodrug, PcephPT. As part of this work, the above cell lysates were also subject to protein expression level analysis using conventional quantitative bottom-up proteomic methods. The protein folding stability and expression level profiles generated here enabled the effects of ionophore vs copper to be distinguished and revealed copper-driven stability changes in proteins involved in processes spanning metabolism, translation, and cell redox homeostasis. The 159 differentially stabilized proteins identified in this analysis were significantly more numerous (∼3×) than the 53 proteins identified with differential expression levels. These results illustrate the unique information that protein stability measurements can provide to decipher metal-dependent processes in drug mode of action studies.
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Affiliation(s)
- Nancy Wiebelhaus
- Department of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
| | | | - Kevin K. Hwang
- Department of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
| | - Katherine J. Franz
- Department of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
| | - Michael C. Fitzgerald
- Department of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
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17
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Ha J, Park H, Park J, Park SB. Recent advances in identifying protein targets in drug discovery. Cell Chem Biol 2020; 28:394-423. [PMID: 33357463 DOI: 10.1016/j.chembiol.2020.12.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/11/2020] [Accepted: 11/30/2020] [Indexed: 02/06/2023]
Abstract
Phenotype-based screening has emerged as an alternative route for discovering new chemical entities toward first-in-class therapeutics. However, clarifying their mode of action has been a significant bottleneck for drug discovery. For target protein identification, conventionally bioactive small molecules are conjugated onto solid supports and then applied to isolate target proteins from whole proteome. This approach requires a high binding affinity between bioactive small molecules and their target proteins. Besides, the binding affinity can be significantly hampered after structural modifications of bioactive molecules with linkers. To overcome these limitations, two major strategies have recently been pursued: (1) the covalent conjugation between small molecules and target proteins using photoactivatable moieties or electrophiles, and (2) label-free target identification through monitoring target engagement by tracking the thermal, proteolytic, or chemical stability of target proteins. This review focuses on recent advancements in target identification from covalent capturing to label-free strategies.
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Affiliation(s)
- Jaeyoung Ha
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul 08826, Korea
| | - Hankum Park
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Jongmin Park
- Department of Chemistry, Kangwon National University, Chuncheon 24341, Korea.
| | - Seung Bum Park
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul 08826, Korea; CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul 08826, Korea.
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18
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Dai L, Li Z, Chen D, Jia L, Guo J, Zhao T, Nordlund P. Target identification and validation of natural products with label-free methodology: A critical review from 2005 to 2020. Pharmacol Ther 2020; 216:107690. [PMID: 32980441 DOI: 10.1016/j.pharmthera.2020.107690] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 02/08/2023]
Abstract
Natural products (NPs) have been an important source of therapeutic drugs in clinic use and contributed many chemical probes for research. The usefulness of NPs is however often marred by the incomplete understanding of their direct cellular targets. A number of experimental methods for drug target identification have been developed over the years. One class of methods, termed "label-free" methodology, exploits the energetic and biophysical features accompanying the association of macromolecules with drugs and other compounds in their native forms. Herein we review the working principles, assay implementations, and key applications of the most important approaches, and also give examples where they have been applied to NPs. We also assess the key advantages and limitations of each method. Furthermore, we address when and how the label-free methodology can be particularly useful considering some of the unique features of NP chemistry and bioactivation.
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Affiliation(s)
- Lingyun Dai
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Urology Minimally Invasive Engineering Center, Shenzhen 518020, Guangdong, China; Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, Guangdong, China; Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore.
| | - Zhijie Li
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Urology Minimally Invasive Engineering Center, Shenzhen 518020, Guangdong, China; Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, Guangdong, China
| | - Dan Chen
- Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore
| | - Lin Jia
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China
| | - Jinan Guo
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Urology Minimally Invasive Engineering Center, Shenzhen 518020, Guangdong, China
| | - Tianyun Zhao
- Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore
| | - Pär Nordlund
- Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore; Department of Oncology and Pathology, Karolinska Institutet, 171 77 Stockholm, Sweden.
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