1
|
George AL, Dueñas ME, Marín-Rubio JL, Trost M. Stability-based approaches in chemoproteomics. Expert Rev Mol Med 2024; 26:e6. [PMID: 38604802 PMCID: PMC11062140 DOI: 10.1017/erm.2024.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/17/2024] [Accepted: 02/22/2024] [Indexed: 04/13/2024]
Abstract
Target deconvolution can help understand how compounds exert therapeutic effects and can accelerate drug discovery by helping optimise safety and efficacy, revealing mechanisms of action, anticipate off-target effects and identifying opportunities for therapeutic expansion. Chemoproteomics, a combination of chemical biology with mass spectrometry has transformed target deconvolution. This review discusses modification-free chemoproteomic approaches that leverage the change in protein thermodynamics induced by small molecule ligand binding. Unlike modification-based methods relying on enriching specific protein targets, these approaches offer proteome-wide evaluations, driven by advancements in mass spectrometry sensitivity, increasing proteome coverage and quantitation methods. Advances in methods based on denaturation/precipitation by thermal or chemical denaturation, or by protease degradation are evaluated, emphasising the evolving landscape of chemoproteomics and its potential impact on future drug-development strategies.
Collapse
Affiliation(s)
- Amy L. George
- Laboratory for Biomedical Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Maria Emilia Dueñas
- Laboratory for Biomedical Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - José Luis Marín-Rubio
- Laboratory for Biomedical Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Matthias Trost
- Laboratory for Biomedical Mass Spectrometry, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| |
Collapse
|
2
|
Burtscher ML, Gade S, Garrido-Rodriguez M, Rutkowska A, Werner T, Eberl HC, Petretich M, Knopf N, Zirngibl K, Grandi P, Bergamini G, Bantscheff M, Fälth-Savitski M, Saez-Rodriguez J. Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition. Mol Syst Biol 2024; 20:458-474. [PMID: 38454145 PMCID: PMC10987601 DOI: 10.1038/s44320-024-00025-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 03/09/2024] Open
Abstract
Complex disease phenotypes often span multiple molecular processes. Functional characterization of these processes can shed light on disease mechanisms and drug effects. Thermal Proteome Profiling (TPP) is a mass-spectrometry (MS) based technique assessing changes in thermal protein stability that can serve as proxies of functional protein changes. These unique insights of TPP can complement those obtained by other omics technologies. Here, we show how TPP can be integrated with phosphoproteomics and transcriptomics in a network-based approach using COSMOS, a multi-omics integration framework, to provide an integrated view of transcription factors, kinases and proteins with altered thermal stability. This allowed us to recover consequences of Poly (ADP-ribose) polymerase (PARP) inhibition in ovarian cancer cells on cell cycle and DNA damage response as well as interferon and hippo signaling. We found that TPP offers a complementary perspective to other omics data modalities, and that its integration allowed us to obtain a more complete molecular overview of PARP inhibition. We anticipate that this strategy can be used to integrate functional proteomics with other omics to study molecular processes.
Collapse
Affiliation(s)
- Mira L Burtscher
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
- Cellzome, a GSK company, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | | | - Martin Garrido-Rodriguez
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | | | | | | | | | - Katharina Zirngibl
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
- Cellzome, a GSK company, Heidelberg, Germany
| | | | | | | | | | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany.
| |
Collapse
|
3
|
Gerault MA, Granjeaud S, Camoin L, Nordlund P, Dai L. IMPRINTS.CETSA and IMPRINTS.CETSA.app: an R package and a Shiny application for the analysis and interpretation of IMPRINTS-CETSA data. Brief Bioinform 2024; 25:bbae128. [PMID: 38557673 PMCID: PMC10982947 DOI: 10.1093/bib/bbae128] [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] [Received: 10/15/2023] [Revised: 02/10/2024] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
IMPRINTS-CETSA (Integrated Modulation of Protein Interaction States-Cellular Thermal Shift Assay) provides a highly resolved means to systematically study the interactions of proteins with other cellular components, including metabolites, nucleic acids and other proteins, at the proteome level, but no freely available and user-friendly data analysis software has been reported. Here, we report IMPRINTS.CETSA, an R package that provides the basic data processing framework for robust analysis of the IMPRINTS-CETSA data format, from preprocessing and normalization to visualization. We also report an accompanying R package, IMPRINTS.CETSA.app, which offers a user-friendly Shiny interface for analysis and interpretation of IMPRINTS-CETSA results, with seamless features such as functional enrichment and mapping to other databases at a single site. For the hit generation part, the diverse behaviors of protein modulations have been typically segregated with a two-measure scoring method, i.e. the abundance and thermal stability changes. We present a new algorithm to classify modulated proteins in IMPRINTS-CETSA experiments by a robust single-measure scoring. In this way, both the numerical changes and the statistical significances of the IMPRINTS information can be visualized on a single plot. The IMPRINTS.CETSA and IMPRINTS.CETSA.app R packages are freely available on GitHub at https://github.com/nkdailingyun/IMPRINTS.CETSA and https://github.com/mgerault/IMPRINTS.CETSA.app, respectively. IMPRINTS.CETSA.app is also available as an executable program at https://zenodo.org/records/10636134.
Collapse
Affiliation(s)
- Marc-Antoine Gerault
- Department of Oncology and Pathology, Karolinska Institutet, 171 77 Stockholm, Sweden
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, F-13009 Marseille, France
| | - Samuel Granjeaud
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, F-13009 Marseille, France
| | - Luc Camoin
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, F-13009 Marseille, France
| | - Pär Nordlund
- Department of Oncology and Pathology, Karolinska Institutet, 171 77 Stockholm, Sweden
- Institute of Molecular and Cell Biology, A*STAR, 138673, Singapore
| | - Lingyun Dai
- Institute of Molecular and Cell Biology, A*STAR, 138673, Singapore
- Department of Geriatrics, and Shenzhen Clinical Research Centre for Geriatrics, The First Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen 518020, China
| |
Collapse
|
4
|
Figueroa-Navedo AM, Ivanov AR. Experimental and data analysis advances in thermal proteome profiling. CELL REPORTS METHODS 2024; 4:100717. [PMID: 38412830 PMCID: PMC10921035 DOI: 10.1016/j.crmeth.2024.100717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/17/2023] [Accepted: 02/05/2024] [Indexed: 02/29/2024]
Abstract
Method development for mass spectrometry (MS)-based thermal shift proteomic assays have advanced to probe small molecules with known and unknown protein-ligand interaction mechanisms and specificity, which is predominantly used in characterization of drug-protein interactions. In the discovery of target and off-target protein-ligand interactions, a thorough investigation of method development and their impact on the sensitivity and accuracy of protein-small molecule and protein-protein interactions is warranted. In this review, we discuss areas of improvement at each stage of thermal proteome profiling data analysis that includes processing of MS-based data, method development, and their effect on the overall quality of thermal proteome profiles. We also overview the optimization of experimental strategies and prioritization of an increased number of independent biological replicates over the number of evaluated temperatures.
Collapse
Affiliation(s)
- Amanda M Figueroa-Navedo
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Alexander R Ivanov
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA.
| |
Collapse
|
5
|
Noberini R, Bonaldi T. Proteomics contributions to epigenetic drug discovery. Proteomics 2023; 23:e2200435. [PMID: 37727062 DOI: 10.1002/pmic.202200435] [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] [Received: 06/09/2023] [Revised: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 09/21/2023]
Abstract
The combined activity of epigenetic features, which include histone post-translational modifications, DNA methylation, and nucleosome positioning, regulates gene expression independently from changes in the DNA sequence, defining how the shared genetic information of an organism is used to generate different cell phenotypes. Alterations in epigenetic processes have been linked with a multitude of diseases, including cancer, fueling interest in the discovery of drugs targeting the proteins responsible for writing, erasing, or reading histone and DNA modifications. Mass spectrometry (MS)-based proteomics has emerged as a versatile tool that can assist drug discovery pipelines from target validation, through target deconvolution, to monitoring drug efficacy in vivo. Here, we provide an overview of the contributions of MS-based proteomics to epigenetic drug discovery, describing the main approaches that can be used to support different drug discovery pipelines and highlighting how they contributed to the development and characterization of epigenetic drugs.
Collapse
Affiliation(s)
- Roberta Noberini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
| |
Collapse
|
6
|
Bayer FP, Gander M, Kuster B, The M. CurveCurator: a recalibrated F-statistic to assess, classify, and explore significance of dose-response curves. Nat Commun 2023; 14:7902. [PMID: 38036588 PMCID: PMC10689459 DOI: 10.1038/s41467-023-43696-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/16/2023] [Indexed: 12/02/2023] Open
Abstract
Dose-response curves are key metrics in pharmacology and biology to assess phenotypic or molecular actions of bioactive compounds in a quantitative fashion. Yet, it is often unclear whether or not a measured response significantly differs from a curve without regulation, particularly in high-throughput applications or unstable assays. Treating potency and effect size estimates from random and true curves with the same level of confidence can lead to incorrect hypotheses and issues in training machine learning models. Here, we present CurveCurator, an open-source software that provides reliable dose-response characteristics by computing p-values and false discovery rates based on a recalibrated F-statistic and a target-decoy procedure that considers dataset-specific effect size distributions. The application of CurveCurator to three large-scale datasets enables a systematic drug mode of action analysis and demonstrates its scalable utility across several application areas, facilitated by a performant, interactive dashboard for fast data exploration.
Collapse
Affiliation(s)
- Florian P Bayer
- Proteomics and Bioanalytics, School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Manuel Gander
- Proteomics and Bioanalytics, School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Bernhard Kuster
- Proteomics and Bioanalytics, School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, 80336, Munich, Germany
| | - Matthew The
- Proteomics and Bioanalytics, School of Life Sciences, Technical University of Munich, 85354, Freising, Germany.
| |
Collapse
|
7
|
Ji H, Lu X, Zhao S, Wang Q, Liao B, Bauer LG, Huber KVM, Luo R, Tian R, Tan CSH. Target deconvolution with matrix-augmented pooling strategy reveals cell-specific drug-protein interactions. Cell Chem Biol 2023; 30:1478-1487.e7. [PMID: 37652024 PMCID: PMC10840709 DOI: 10.1016/j.chembiol.2023.08.002] [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] [Received: 11/11/2022] [Revised: 05/18/2023] [Accepted: 08/09/2023] [Indexed: 09/02/2023]
Abstract
Target deconvolution is a crucial but costly and time-consuming task that hinders large-scale profiling for drug discovery. We present a matrix-augmented pooling strategy (MAPS) which mixes multiple drugs into samples with optimized permutation and delineates targets of each drug simultaneously with mathematical processing. We validated this strategy with thermal proteome profiling (TPP) testing of 15 drugs concurrently, increasing experimental throughput by 60x while maintaining high sensitivity and specificity. Benefiting from the lower cost and higher throughput of MAPS, we performed target deconvolution of the 15 drugs across 5 cell lines. Our profiling revealed that drug-target interactions can differ vastly in targets and binding affinity across cell lines. We further validated BRAF and CSNK2A2 as potential off-targets of bafetinib and abemaciclib, respectively. This work represents the largest thermal profiling of structurally diverse drugs across multiple cell lines to date.
Collapse
Affiliation(s)
- Hongchao Ji
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China PR; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xue Lu
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China PR
| | - Shiji Zhao
- Department of Molecular Biology and Biochemistry, Department of Chemical and Biomolecular Engineering, Department of Materials Science and Engineering, Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Qiqi Wang
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China PR
| | - Bin Liao
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China PR
| | - Ludwig G Bauer
- Centre for Medicines Discovery, Nuffield Department of Medicine, OX3 7FZ Oxford, UK; Target Discovery Institute, Nuffield Department of Medicine, OX3 7FZ Oxford, UK
| | - Kilian V M Huber
- Centre for Medicines Discovery, Nuffield Department of Medicine, OX3 7FZ Oxford, UK; Target Discovery Institute, Nuffield Department of Medicine, OX3 7FZ Oxford, UK
| | - Ray Luo
- Department of Molecular Biology and Biochemistry, Department of Chemical and Biomolecular Engineering, Department of Materials Science and Engineering, Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Ruijun Tian
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China PR
| | - Chris Soon Heng Tan
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China PR.
| |
Collapse
|
8
|
Cacace E, Kim V, Varik V, Knopp M, Tietgen M, Brauer-Nikonow A, Inecik K, Mateus A, Milanese A, Mårli MT, Mitosch K, Selkrig J, Brochado AR, Kuipers OP, Kjos M, Zeller G, Savitski MM, Göttig S, Huber W, Typas A. Systematic analysis of drug combinations against Gram-positive bacteria. Nat Microbiol 2023; 8:2196-2212. [PMID: 37770760 PMCID: PMC10627819 DOI: 10.1038/s41564-023-01486-9] [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] [Received: 12/23/2022] [Accepted: 08/30/2023] [Indexed: 09/30/2023]
Abstract
Drug combinations can expand options for antibacterial therapies but have not been systematically tested in Gram-positive species. We profiled ~8,000 combinations of 65 antibacterial drugs against the model species Bacillus subtilis and two prominent pathogens, Staphylococcus aureus and Streptococcus pneumoniae. Thereby, we recapitulated previously known drug interactions, but also identified ten times more novel interactions in the pathogen S. aureus, including 150 synergies. We showed that two synergies were equally effective against multidrug-resistant S. aureus clinical isolates in vitro and in vivo. Interactions were largely species-specific and synergies were distinct from those of Gram-negative species, owing to cell surface and drug uptake differences. We also tested 2,728 combinations of 44 commonly prescribed non-antibiotic drugs with 62 drugs with antibacterial activity against S. aureus and identified numerous antagonisms that might compromise the efficacy of antimicrobial therapies. We identified even more synergies and showed that the anti-aggregant ticagrelor synergized with cationic antibiotics by modifying the surface charge of S. aureus. All data can be browsed in an interactive interface ( https://apps.embl.de/combact/ ).
Collapse
Affiliation(s)
- Elisabetta Cacace
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Vladislav Kim
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Vallo Varik
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Michael Knopp
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Manuela Tietgen
- Goethe University Frankfurt, University Hospital, Institute for Medical Microbiology and Infection Control, Frankfurt am Main, Germany
| | | | - Kemal Inecik
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - André Mateus
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Alessio Milanese
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
- Department of Biology, Institute of Microbiology, and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Marita Torrissen Mårli
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Karin Mitosch
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Joel Selkrig
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Institute of Medical Microbiology, University Hospital of RWTH, Aachen, Germany
| | - Ana Rita Brochado
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Molecular Biology and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Morten Kjos
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Georg Zeller
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Mikhail M Savitski
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Stephan Göttig
- Goethe University Frankfurt, University Hospital, Institute for Medical Microbiology and Infection Control, Frankfurt am Main, Germany
| | - Wolfgang Huber
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Athanasios Typas
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.
| |
Collapse
|
9
|
Irazoki O, Ter Beek J, Alvarez L, Mateus A, Colin R, Typas A, Savitski MM, Sourjik V, Berntsson RPA, Cava F. D-amino acids signal a stress-dependent run-away response in Vibrio cholerae. Nat Microbiol 2023; 8:1549-1560. [PMID: 37365341 PMCID: PMC10390336 DOI: 10.1038/s41564-023-01419-6] [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] [Received: 01/03/2023] [Accepted: 05/31/2023] [Indexed: 06/28/2023]
Abstract
To explore favourable niches while avoiding threats, many bacteria use a chemotaxis navigation system. Despite decades of studies on chemotaxis, most signals and sensory proteins are still unknown. Many bacterial species release D-amino acids to the environment; however, their function remains largely unrecognized. Here we reveal that D-arginine and D-lysine are chemotactic repellent signals for the cholera pathogen Vibrio cholerae. These D-amino acids are sensed by a single chemoreceptor MCPDRK co-transcribed with the racemase enzyme that synthesizes them under the control of the stress-response sigma factor RpoS. Structural characterization of this chemoreceptor bound to either D-arginine or D-lysine allowed us to pinpoint the residues defining its specificity. Interestingly, the specificity for these D-amino acids appears to be restricted to those MCPDRK orthologues transcriptionally linked to the racemase. Our results suggest that D-amino acids can shape the biodiversity and structure of complex microbial communities under adverse conditions.
Collapse
Affiliation(s)
- Oihane Irazoki
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Science for Life Laboratory (SciLifeLab), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Josy Ter Beek
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Laura Alvarez
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Science for Life Laboratory (SciLifeLab), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - André Mateus
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Remy Colin
- Max Planck Institute for Terrestrial Microbiology, and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Athanasios Typas
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mikhail M Savitski
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology, and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Ronnie P-A Berntsson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Felipe Cava
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Science for Life Laboratory (SciLifeLab), Department of Molecular Biology, Umeå University, Umeå, Sweden.
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Tu Y, Tan L, Tao H, Li Y, Liu H. CETSA and thermal proteome profiling strategies for target identification and drug discovery of natural products. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 116:154862. [PMID: 37216761 DOI: 10.1016/j.phymed.2023.154862] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/21/2023] [Accepted: 05/04/2023] [Indexed: 05/24/2023]
Abstract
BACKGROUND Monitoring target engagement at various stages of drug development is essential for natural product (NP)-based drug discovery and development. The cellular thermal shift assay (CETSA) developed in 2013 is a novel, broadly applicable, label-free biophysical assay based on the principle of ligand-induced thermal stabilization of target proteins, which enables direct assessment of drug-target engagement in physiologically relevant contexts, including intact cells, cell lysates and tissues. This review aims to provide an overview of the work principles of CETSA and its derivative strategies and their recent progress in protein target validation, target identification and drug lead discovery of NPs. METHODS A literature-based survey was conducted using the Web of Science and PubMed databases. The required information was reviewed and discussed to highlight the important role of CETSA-derived strategies in NP studies. RESULTS After nearly ten years of upgrading and evolution, CETSA has been mainly developed into three formats: classic Western blotting (WB)-CETSA for target validation, thermal proteome profiling (TPP, also known as MS-CETSA) for unbiased proteome-wide target identification, and high-throughput (HT)-CETSA for drug hit discovery and lead optimization. Importantly, the application possibilities of a variety of TPP approaches for the target discovery of bioactive NPs are highlighted and discussed, including TPP-temperature range (TPP-TR), TPP-compound concentration range (TPP-CCR), two-dimensional TPP (2D-TPP), cell surface-TPP (CS-TPP), simplified TPP (STPP), thermal stability shift-based fluorescence difference in 2D gel electrophoresis (TS-FITGE) and precipitate supported TPP (PSTPP). In addition, the key advantages, limitations and future outlook of CETSA strategies for NP studies are discussed. CONCLUSION The accumulation of CETSA-based data can significantly accelerate the elucidation of the mechanism of action and drug lead discovery of NPs, and provide strong evidence for NP treatment against certain diseases. The CETSA strategy will certainly bring a great return far beyond the initial investment and open up more possibilities for future NP-based drug research and development.
Collapse
Affiliation(s)
- Yanbei Tu
- School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Lihua Tan
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao SAR 999078, China
| | - Hongxun Tao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Yanfang Li
- School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, China.
| | - Hanqing Liu
- School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu 212013, China.
| |
Collapse
|
12
|
Phaneuf CG, Aizikov K, Grinfeld D, Kreutzmann A, Mourad D, Lange O, Dai D, Zhang B, Belenky A, Makarov AA, Ivanov AR. Experimental strategies to improve drug-target identification in mass spectrometry-based thermal stability assays. Commun Chem 2023; 6:64. [PMID: 37024568 PMCID: PMC10079678 DOI: 10.1038/s42004-023-00861-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 03/23/2023] [Indexed: 04/08/2023] Open
Abstract
Mass spectrometry (MS)-based thermal stability assays have recently emerged as one of the most promising solutions for the identification of protein-ligand interactions. Here, we have investigated eight combinations of several recently introduced MS-based advancements, including the Phase-Constrained Spectral Deconvolution Method, Field Asymmetric Ion Mobility Spectrometry, and the implementation of a carrier sample as improved MS-based acquisition approaches for thermal stability assays (iMAATSA). We used intact Jurkat cells treated with a commercially available MEK inhibitor, followed by heat treatment, to prepare a set of unfractionated isobarically-labeled proof-of-concept samples to compare the performance of eight different iMAATSAs. Finally, the best-performing iMAATSA was compared to a conventional approach and evaluated in a fractionation experiment. Improvements of up to 82% and 86% were demonstrated in protein identifications and high-quality melting curves, respectively, over the conventional approach in the proof-of-concept study, while an approximately 12% improvement in melting curve comparisons was achieved in the fractionation experiment.
Collapse
Affiliation(s)
- Clifford G Phaneuf
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
- Sanofi, Disease Profiling and Functional Genomics, Cambridge, MA, USA
| | | | | | | | | | | | - Daniel Dai
- Sanofi, Disease Profiling and Functional Genomics, Cambridge, MA, USA
| | - Bailin Zhang
- Sanofi, Disease Profiling and Functional Genomics, Cambridge, MA, USA
| | | | | | - Alexander R Ivanov
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA.
| |
Collapse
|
13
|
Duran-Frigola M, Cigler M, Winter GE. Advancing Targeted Protein Degradation via Multiomics Profiling and Artificial Intelligence. J Am Chem Soc 2023; 145:2711-2732. [PMID: 36706315 PMCID: PMC9912273 DOI: 10.1021/jacs.2c11098] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Only around 20% of the human proteome is considered to be druggable with small-molecule antagonists. This leaves some of the most compelling therapeutic targets outside the reach of ligand discovery. The concept of targeted protein degradation (TPD) promises to overcome some of these limitations. In brief, TPD is dependent on small molecules that induce the proximity between a protein of interest (POI) and an E3 ubiquitin ligase, causing ubiquitination and degradation of the POI. In this perspective, we want to reflect on current challenges in the field, and discuss how advances in multiomics profiling, artificial intelligence, and machine learning (AI/ML) will be vital in overcoming them. The presented roadmap is discussed in the context of small-molecule degraders but is equally applicable for other emerging proximity-inducing modalities.
Collapse
Affiliation(s)
- Miquel Duran-Frigola
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria,Ersilia
Open Source Initiative, 28 Belgrave Road, CB1 3DE, Cambridge, United Kingdom,
| | - Marko Cigler
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Georg E. Winter
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria,
| |
Collapse
|
14
|
Sauer P, Bantscheff M. Thermal Proteome Profiling for Drug Target Identification and Probing of Protein States. Methods Mol Biol 2023; 2718:73-98. [PMID: 37665455 DOI: 10.1007/978-1-0716-3457-8_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Proteins are central drivers of physiological and pathological processes in the cell. Methods evaluating protein functional states are therefore vital to fundamental research as well as drug discovery. Thermal proteome profiling (TPP) to this date constitutes the only approach that permits examining protein states in live cells, under native conditions and at a proteome-wide scale. TPP harnesses ligand/perturbation-induced changes in protein thermal stability, which are monitored by multiplexed quantitative mass spectrometry. In this chapter, we describe a modular experimental workflow for TPP experiments using live cells or crude cell extracts. We provide the tools to perform different TPP formats, i.e., temperature range experiments, TPP-TR; isothermal compound titrations, TPP-CCR; and a combination thereof, 2D-TPP.
Collapse
Affiliation(s)
- Patricia Sauer
- Cellzome GmbH, GlaxoSmithKline (GSK), Heidelberg, Germany
| | | |
Collapse
|
15
|
Sivanich MK, Gu T, Tabang DN, Li L. Recent advances in isobaric labeling and applications in quantitative proteomics. Proteomics 2022; 22:e2100256. [PMID: 35687565 PMCID: PMC9787039 DOI: 10.1002/pmic.202100256] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 05/21/2022] [Accepted: 06/07/2022] [Indexed: 12/30/2022]
Abstract
Mass spectrometry (MS) has emerged at the forefront of quantitative proteomic techniques. Liquid chromatography-mass spectrometry (LC-MS) can be used to determine abundances of proteins and peptides in complex biological samples. Several methods have been developed and adapted for accurate quantification based on chemical isotopic labeling. Among various chemical isotopic labeling techniques, isobaric tagging approaches rely on the analysis of peptides from MS2-based quantification rather than MS1-based quantification. In this review, we will provide an overview of several isobaric tags along with some recent developments including complementary ion tags, improvements in sensitive quantitation of analytes with lower abundance, strategies to increase multiplexing capabilities, and targeted analysis strategies. We will also discuss limitations of isobaric tags and approaches to alleviate these restrictions through bioinformatic tools and data acquisition methods. This review will highlight several applications of isobaric tags, including biomarker discovery and validation, thermal proteome profiling, cross-linking for structural investigations, single-cell analysis, top-down proteomics, along with applications to different molecules including neuropeptides, glycans, metabolites, and lipids, while providing considerations and evaluations to each application.
Collapse
Affiliation(s)
| | - Ting‐Jia Gu
- School of PharmacyUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | | | - Lingjun Li
- Department of ChemistryUniversity of Wisconsin‐MadisonMadisonWisconsinUSA,School of PharmacyUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| |
Collapse
|
16
|
Trowbridge AD, Seath CP, Rodriguez-Rivera FP, Li BX, Dul BE, Schwaid AG, Buksh BF, Geri JB, Oakley JV, Fadeyi OO, Oslund RC, Ryu KA, White C, Reyes-Robles T, Tawa P, Parker DL, MacMillan DWC. Small molecule photocatalysis enables drug target identification via energy transfer. Proc Natl Acad Sci U S A 2022; 119:e2208077119. [PMID: 35969791 PMCID: PMC9407219 DOI: 10.1073/pnas.2208077119] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/14/2022] [Indexed: 12/24/2022] Open
Abstract
Over half of new therapeutic approaches fail in clinical trials due to a lack of target validation. As such, the development of new methods to improve and accelerate the identification of cellular targets, broadly known as target ID, remains a fundamental goal in drug discovery. While advances in sequencing and mass spectrometry technologies have revolutionized drug target ID in recent decades, the corresponding chemical-based approaches have not changed in over 50 y. Consigned to outdated stoichiometric activation modes, modern target ID campaigns are regularly confounded by poor signal-to-noise resulting from limited receptor occupancy and low crosslinking yields, especially when targeting low abundance membrane proteins or multiple protein target engagement. Here, we describe a broadly general platform for photocatalytic small molecule target ID, which is founded upon the catalytic amplification of target-tag crosslinking through the continuous generation of high-energy carbene intermediates via visible light-mediated Dexter energy transfer. By decoupling the reactive warhead tag from the small molecule ligand, catalytic signal amplification results in unprecedented levels of target enrichment, enabling the quantitative target and off target ID of several drugs including (+)-JQ1, paclitaxel (Taxol), dasatinib (Sprycel), as well as two G-protein-coupled receptors-ADORA2A and GPR40.
Collapse
Affiliation(s)
| | - Ciaran P. Seath
- Merck Center for Catalysis, Princeton University, Princeton, NJ 08544
| | | | - Beryl X. Li
- Merck Center for Catalysis, Princeton University, Princeton, NJ 08544
| | - Barbara E. Dul
- Department of Chemistry, Princeton University, Princeton, NJ 08544
| | | | - Benito F. Buksh
- Merck Center for Catalysis, Princeton University, Princeton, NJ 08544
| | - Jacob B. Geri
- Merck Center for Catalysis, Princeton University, Princeton, NJ 08544
| | - James V. Oakley
- Merck Center for Catalysis, Princeton University, Princeton, NJ 08544
| | | | - Rob C. Oslund
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141
| | - Keun Ah Ryu
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141
| | - Cory White
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141
| | | | - Paul Tawa
- Pharmacology, Merck & Co., Inc., Kenilworth, NJ 07033
| | - Dann L. Parker
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ 07033
| | | |
Collapse
|
17
|
Li GX, Zhao T, Wang LC, Choi H, Lim YT, Sobota RM. KOPI: Kinase inhibitOr Proteome Impact analysis. Sci Rep 2022; 12:13015. [PMID: 35906361 PMCID: PMC9338059 DOI: 10.1038/s41598-022-16557-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 07/12/2022] [Indexed: 11/10/2022] Open
Abstract
Kinase inhibitors often exert on/off-target effects, and efficient data analysis is essential for assessing these effects on the proteome. We developed a workflow for rapidly performing such a proteomic assessment, termed as kinase inhibitor proteome impact analysis (KOPI). We demonstrate KOPI’s utility with staurosporine (STS) on the leukemic K562 cell proteome. We identified systematically staurosporine’s non-kinome interactors, and showed for the first time that it caused paradoxical hyper- and biphasic phosphorylation.
Collapse
Affiliation(s)
- Ginny Xiaohe Li
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Tianyun Zhao
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Loo Chien Wang
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
| | - Hyungwon Choi
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yan Ting Lim
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore.
| | - Radoslaw M Sobota
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore.
| |
Collapse
|
18
|
Cox D, Ang CS, Nillegoda NB, Reid GE, Hatters DM. Hidden information on protein function in censuses of proteome foldedness. Nat Commun 2022; 13:1992. [PMID: 35422070 PMCID: PMC9010426 DOI: 10.1038/s41467-022-29661-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 03/25/2022] [Indexed: 12/12/2022] Open
Abstract
Methods that assay protein foldedness with proteomics have generated censuses of apparent protein folding stabilities in biological milieu. However, different censuses poorly correlate with each other. Here, we show that the reason for this is that methods targeting foldedness through monitoring amino acid sidechain reactivity also detect changes in conformation and ligand binding, which can be a substantial fraction of the data. We show that the reactivity of only one quarter of cysteine or methionine sidechains in proteins in a urea denaturation curve of mammalian cell lysate can be confidently explained by a two-state unfolding isotherm. Contrary to that expected from unfolding, up to one third of the cysteines decreased reactivity. These cysteines were enriched in proteins with functions relating to unfolded protein stress. One protein, chaperone HSPA8, displayed changes arising from ligand and cofactor binding. Unmasking this hidden information using the approaches outlined here should improve efforts to understand both folding and the remodeling of protein function directly in complex biological settings. Proteomics can define features of proteome foldedness by assessing the reactivity of surface exposed amino acids. Here, the authors show that such exposure patterns yield insight to structural changes in chaperones as they bind to unfolded proteins in urea-denatured mammalian cell lysate.
Collapse
|
19
|
Abstract
In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.
Collapse
Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| |
Collapse
|
20
|
Hu J, Gong X, Strömblad S. Local temporal Rac1-GTP nadirs and peaks restrict cell protrusions and retractions. SCIENCE ADVANCES 2022; 8:eabl3667. [PMID: 35319996 PMCID: PMC8942371 DOI: 10.1126/sciadv.abl3667] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Cells probe their microenvironment using membrane protrusion-retraction cycles. Spatiotemporal coordination of Rac1 and RhoA GTP-binding activities initiates and reinforces protrusions and retractions, but the control of their finite lifetime remains unclear. We examined the relations of Rac1 and RhoA GTP-binding levels to key protrusion and retraction events, as well as to cell-ECM traction forces at physiologically relevant ECM stiffness. High RhoA-GTP preceded retractions and Rac1-GTP elevation before protrusions. Notable temporal Rac1-GTP nadirs and peaks occurred at the maximal edge velocity of local membrane protrusions and retractions, respectively, followed by declined edge velocity. Moreover, altered local Rac1-GTP consistently preceded similarly altered traction force. Local optogenetic Rac1-GTP perturbations defined a function of Rac1 in restricting protrusions and retractions and in promoting local traction force. Together, we show that Rac1 plays a fundamental role in restricting the size and durability of protrusions and retractions, plausibly in part through controlling traction forces.
Collapse
|
21
|
Ji H, Lu X, Zheng Z, Sun S, Tan CSH. ProSAP: a GUI software tool for statistical analysis and assessment of thermal stability data. Brief Bioinform 2022; 23:6542221. [PMID: 35246677 DOI: 10.1093/bib/bbac057] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 01/18/2022] [Accepted: 02/04/2022] [Indexed: 11/14/2022] Open
Abstract
The Cellular Thermal Shift Assay (CETSA) plays an important role in drug-target identification, and statistical analysis is a crucial step significantly affecting conclusion. We put forward ProSAP (Protein Stability Analysis Pod), an open-source, cross-platform and user-friendly software tool, which provides multiple methods for thermal proteome profiling (TPP) analysis, nonparametric analysis (NPA), proteome integral solubility alteration and isothermal shift assay (iTSA). For testing the performance of ProSAP, we processed several datasets and compare the performance of different algorithms. Overall, TPP analysis is more accurate with fewer false positive targets, but NPA methods are flexible and free from parameters. For iTSA, edgeR and DESeq2 identify more true targets than t-test and Limma, but when it comes to ranking, the four methods show not much difference. ProSAP software is available at https://github.com/hcji/ProSAP and https://zenodo.org/record/5763315.
Collapse
Affiliation(s)
- Hongchao Ji
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xue Lu
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zhenxiang Zheng
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Siyuan Sun
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Chris Soon Heng Tan
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| |
Collapse
|
22
|
Herneisen AL, Lourido S. Thermal Proteome Profiling to Identify Protein-ligand Interactions in the Apicomplexan Parasite Toxoplasma gondii. Bio Protoc 2021; 11:e4207. [PMID: 34859122 DOI: 10.21769/bioprotoc.4207] [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: 04/04/2021] [Revised: 07/08/2021] [Accepted: 08/13/2021] [Indexed: 01/23/2023] Open
Abstract
Toxoplasma gondii is a single-celled eukaryotic parasite that chronically infects a quarter of the global population. In recent years, phenotypic screens have identified compounds that block parasite replication. Unraveling the pathways and molecular mechanisms perturbed by such compounds requires target deconvolution. In parasites, such deconvolution has been achieved via chemogenomic approaches-for example, directed evolution followed by whole-genome sequencing or genome-wide knockout screens. As a proteomic alternative that directly probes the physical interaction between compound and protein, thermal proteome profiling (TPP), also known as the cellular thermal shift assay (CETSA), recently emerged as a method to identify small molecule-target interactions in living cells and cell extracts in a variety of organisms, including unicellular eukaryotic pathogens. Ligand binding induces a thermal stability shift-stabilizing or destabilizing proteins that change conformationally in response to the ligand-that can be measured by mass spectrometry (MS). Cells are incubated with different concentrations of ligand and heated, causing thermal denaturation of proteins. The soluble protein is extracted and quantified with multiplexed, quantitative MS, resulting in thousands of thermal denaturation profiles. Proteins engaging the ligand can be identified by their compound-dependent thermal shift. The protocol provided here can be used to identify ligand-target interactions and assess the impact of environmental or genetic perturbations on the thermal stability of the proteome in T. gondii and other eukaryotic pathogens. Graphic abstract: Thermal proteome profiling for target identification in the apicomplexan parasite T. gondii.
Collapse
Affiliation(s)
- Alice L Herneisen
- Whitehead Institute for Biomedical Research, Cambridge, MA, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Sebastian Lourido
- Whitehead Institute for Biomedical Research, Cambridge, MA, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States
| |
Collapse
|
23
|
Mateus A, Kurzawa N, Perrin J, Bergamini G, Savitski MM. Drug Target Identification in Tissues by Thermal Proteome Profiling. Annu Rev Pharmacol Toxicol 2021; 62:465-482. [PMID: 34499524 DOI: 10.1146/annurev-pharmtox-052120-013205] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Drug target deconvolution can accelerate the drug discovery process by identifying a drug's targets (facilitating medicinal chemistry efforts) and off-targets (anticipating toxicity effects or adverse drug reactions). Multiple mass spectrometry-based approaches have been developed for this purpose, but thermal proteome profiling (TPP) remains to date the only one that does not require compound modification and can be used to identify intracellular targets in living cells. TPP is based on the principle that the thermal stability of a protein can be affected by its interactions. Recent developments of this approach have expanded its applications beyond drugs and cell cultures to studying protein-drug interactions and biological phenomena in tissues. These developments open up the possibility of studying drug treatment or mechanisms of disease in a holistic fashion, which can result in the design of better drugs and lead to a better understanding of fundamental biology. Expected final online publication date for the Annual Review of Pharmacology and Toxicology, Volume 62 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- André Mateus
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany;
| | - Nils Kurzawa
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; .,Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Jessica Perrin
- Cellzome GmbH, GlaxoSmithKline, 69117 Heidelberg, Germany
| | | | - Mikhail M Savitski
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany;
| |
Collapse
|
24
|
Mateus A, Savitski MM, Piazza I. The rise of proteome-wide biophysics. Mol Syst Biol 2021; 17:e10442. [PMID: 34293219 PMCID: PMC8297615 DOI: 10.15252/msb.202110442] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/26/2021] [Accepted: 06/04/2021] [Indexed: 11/23/2022] Open
Affiliation(s)
- Andre Mateus
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mikhail M Savitski
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Ilaria Piazza
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC Berlin), Berlin, Germany
| |
Collapse
|
25
|
Tampere M, Pettke A, Salata C, Wallner O, Koolmeister T, Cazares-Körner A, Visnes T, Hesselman MC, Kunold E, Wiita E, Kalderén C, Lightowler M, Jemth AS, Lehtiö J, Rosenquist Å, Warpman-Berglund U, Helleday T, Mirazimi A, Jafari R, Puumalainen MR. Novel Broad-Spectrum Antiviral Inhibitors Targeting Host Factors Essential for Replication of Pathogenic RNA Viruses. Viruses 2020; 12:E1423. [PMID: 33322045 PMCID: PMC7762994 DOI: 10.3390/v12121423] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/26/2020] [Accepted: 12/07/2020] [Indexed: 12/14/2022] Open
Abstract
Recent RNA virus outbreaks such as Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Ebola virus (EBOV) have caused worldwide health emergencies highlighting the urgent need for new antiviral strategies. Targeting host cell pathways supporting viral replication is an attractive approach for development of antiviral compounds, especially with new, unexplored viruses where knowledge of virus biology is limited. Here, we present a strategy to identify host-targeted small molecule inhibitors using an image-based phenotypic antiviral screening assay followed by extensive target identification efforts revealing altered cellular pathways upon antiviral compound treatment. The newly discovered antiviral compounds showed broad-range antiviral activity against pathogenic RNA viruses such as SARS-CoV-2, EBOV and Crimean-Congo hemorrhagic fever virus (CCHFV). Target identification of the antiviral compounds by thermal protein profiling revealed major effects on proteostasis pathways and disturbance in interactions between cellular HSP70 complex and viral proteins, illustrating the supportive role of HSP70 on many RNA viruses across virus families. Collectively, this strategy identifies new small molecule inhibitors with broad antiviral activity against pathogenic RNA viruses, but also uncovers novel virus biology urgently needed for design of new antiviral therapies.
Collapse
Affiliation(s)
- Marianna Tampere
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
- National Veterinary Institute, SE-756 51 Uppsala, Sweden;
| | - Aleksandra Pettke
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Cristiano Salata
- Department of Microbiology, Public Health Agency of Sweden, 171 65 Stockholm, Sweden;
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy
| | - Olov Wallner
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Tobias Koolmeister
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Armando Cazares-Körner
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Torkild Visnes
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Maria Carmen Hesselman
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Elena Kunold
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Elisee Wiita
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Christina Kalderén
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Molly Lightowler
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Ann-Sofie Jemth
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Janne Lehtiö
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Åsa Rosenquist
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Ulrika Warpman-Berglund
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Ali Mirazimi
- National Veterinary Institute, SE-756 51 Uppsala, Sweden;
- Unit of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute and Karolinska University Hospital, 17177 Stockholm, Sweden
| | - Rozbeh Jafari
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Marjo-Riitta Puumalainen
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| |
Collapse
|