1
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LIU T, QIN W, YANG H. [Recent advances in protein precipitation-based methods for drug-target screening]. Se Pu 2024; 42:613-622. [PMID: 38966970 PMCID: PMC11224935 DOI: 10.3724/sp.j.1123.2023.11019] [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: 11/23/2023] [Indexed: 07/06/2024] Open
Abstract
Drug targets are biological macromolecules that bind drug molecules in vivo. Therefore, the system-wide identification of drug targets plays a vital role in fully understanding the mechanism of drug action, efficacy, and side effects. The unbiased screening of drug targets may accelerate the process of drug discovery and candidate screening. Mass spectrometry is a key tool for large-scale protein identification and accurate quantification owing to its high acquisition speed, resolution, and sensitivity. Mass spectrometry-based proteomics has been widely used for drug-target screening. It can systematically identify the protein-target landscape of a drug and elucidate drug-protein interactions. Commonly used drug-target characterization methods, such as labeling-based affinity enrichment, require the chemical derivatization of drug molecules, which is not only time-consuming but may also affect the affinity of the drug towards its targets. Furthermore, the spatial effects of the derivatization groups may block interactions between the drug and its targets. Considering the disadvantages of affinity-enrichment methods, strategies that do not require chemical derivatization have received widespread attention. Proteins may undergo denaturation, unfolding, and precipitation under different conditions such as high temperatures, extreme pH, denaturants, and mechanical stress. Binding to small-molecule drugs may alter the folding balance of target proteins. The conformational stability of target proteins can be stabilized by binding with drugs, and protein-drug complexes are more resistant than free proteins to the precipitation induced by different conditions. Based on this mechanism, various large-scale drug-target identification methods using protein precipitation have been developed by combining proteomics and mass spectrometry analysis, including thermal proteome profiling and solvent-, mechanical stress-, and pH-induced protein precipitation. These methods have been successfully applied to the characterization of small-molecule drug targets. In this review, we describe the protein precipitation-based methods used for the high-throughput discovery of drug targets and elucidation of the interactions between drugs and proteins in the past decade. We also summarize the characteristics of each method and discuss their application potential in drug-efficacy evaluation and drug discovery.
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2
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Yu X, Lin H, Li F, Wang J, Lu D. Development of Biochemical and Cellular Probes to Study RIPK1 Target Engagement. ACS Med Chem Lett 2024; 15:906-916. [PMID: 38894934 PMCID: PMC11181498 DOI: 10.1021/acsmedchemlett.4c00104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 06/21/2024] Open
Abstract
RIPK1 inhibitors have emerged as promising candidates for treating diverse diseases, including inflammatory diseases, autoimmune disorders, Alzheimer's disease, and cancer. However, the previously reported binding assays have limited sensitivity and stability, impeding high-throughput screening and robust characterization of the RIPK1 inhibitors. To address this challenge, we introduced two probes, T2-BDP-FL and T3-BDP-FL, derived from distinct RIPK1 inhibitors with different binding modes to establish time-resolved fluorescence resonance energy transfer (TR-FRET) displacement assays. Employing our TR-FRET displacement assays, we quantified the biochemical binding affinities of a series of RIPK1 inhibitors with diverse structural and binding modes for human RIPK1. Consistent results were obtained with these two probes in the TR-FRET displacement assay. Furthermore, we developed a RIPK1 fluorescent probe, T2-BDP589, for the NanoBRET assay. This assay enabled the characterization of RIPK1 target engagement by various RIPK1 inhibitors for both human and mouse RIPK1 in live cells. Our developed fluorescent probe displacement assays offer a sensitive and high-throughput approach to identify RIPK1 inhibitors based on both biochemical and cellular activities.
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Affiliation(s)
- Xin Yu
- Department
of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Hanfeng Lin
- Department
of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Feng Li
- Center
for Drug Discovery, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Jin Wang
- Department
of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
- Department
of Molecular and Cellular Biology, Baylor
College of Medicine, Houston, Texas 77030, United States
| | - Dong Lu
- Department
of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
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3
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Veth TS, Kannegieter NM, de Graaf EL, Ruijtenbeek R, Joore J, Ressa A, Altelaar M. Innovative strategies for measuring kinase activity to accelerate the next wave of novel kinase inhibitors. Drug Discov Today 2024; 29:103907. [PMID: 38301799 DOI: 10.1016/j.drudis.2024.103907] [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: 06/23/2023] [Revised: 01/18/2024] [Accepted: 01/25/2024] [Indexed: 02/03/2024]
Abstract
The development of protein kinase inhibitors (PKIs) has gained significance owing to their therapeutic potential for diseases like cancer. In addition, there has been a rise in refining kinase activity assays, each possessing unique biological and analytical characteristics crucial for PKI development. However, the PKI development pipeline experiences high attrition rates and approved PKIs exhibit unexploited potential because of variable patient responses. Enhancing PKI development efficiency involves addressing challenges related to understanding the PKI mechanism of action and employing biomarkers for precision medicine. Selecting appropriate kinase activity assays for these challenges can overcome these attrition rate issues. This review delves into the current obstacles in kinase inhibitor development and elucidates kinase activity assays that can provide solutions.
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Affiliation(s)
- Tim S Veth
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands; Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | | | - Erik L de Graaf
- Pepscope, Nieuwe Kanaal 7, 6709 PA Wageningen, The Netherlands
| | | | - Jos Joore
- Pepscope, Nieuwe Kanaal 7, 6709 PA Wageningen, The Netherlands
| | - Anna Ressa
- Pepscope, Nieuwe Kanaal 7, 6709 PA Wageningen, The Netherlands
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands; Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands.
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4
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Patel S, Karlsson M, Klahn JT, Gambino F, Costa H, McGuire KA, Baumgartner CK, Williams J, Sandoz S, Kath JE. Quantitative target engagement of RIPK1 in human whole blood via the cellular thermal shift assay for potential pre-clinical and clinical applications. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100135. [PMID: 38101572 DOI: 10.1016/j.slasd.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/29/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023]
Abstract
The cellular thermal shift assay (CETSA®) is a target engagement method widely used for preclinical characterization of small molecule compounds. CETSA® has been used for semi-quantitative readouts in whole blood with PBMC isolation, and quantitative, plate-based readouts using cell lines. However, there has been no quantitative evaluation of CETSA® in unprocessed human whole blood, which is preferred for clinical applications. Here we report two separate assay formats - Alpha CETSA® and MSD CETSA® - that require less than 100 μL of whole blood per sample without PBMC isolation. We chose RIPK1 as a proof-of-concept target and, by measuring engagement of seven different inhibitors, demonstrate high assay sensitivity and robustness. These quantitative CETSA® platforms enable possible applications in preclinical pharmacokinetic-pharmacodynamic studies, and direct target engagement with small molecules in clinical trials.
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5
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Marchesan E, Nardin A, Mauri S, Bernardo G, Chander V, Di Paola S, Chinellato M, von Stockum S, Chakraborty J, Herkenne S, Basso V, Schrepfer E, Marin O, Cendron L, Medina DL, Scorrano L, Ziviani E. Activation of Ca 2+ phosphatase Calcineurin regulates Parkin translocation to mitochondria and mitophagy in flies. Cell Death Differ 2024; 31:217-238. [PMID: 38238520 PMCID: PMC10850161 DOI: 10.1038/s41418-023-01251-9] [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: 12/05/2022] [Revised: 11/23/2023] [Accepted: 12/05/2023] [Indexed: 02/09/2024] Open
Abstract
Selective removal of dysfunctional mitochondria via autophagy is crucial for the maintenance of cellular homeostasis. This event is initiated by the translocation of the E3 ubiquitin ligase Parkin to damaged mitochondria, and it requires the Serine/Threonine-protein kinase PINK1. In a coordinated set of events, PINK1 operates upstream of Parkin in a linear pathway that leads to the phosphorylation of Parkin, Ubiquitin, and Parkin mitochondrial substrates, to promote ubiquitination of outer mitochondrial membrane proteins. Ubiquitin-decorated mitochondria are selectively recruiting autophagy receptors, which are required to terminate the organelle via autophagy. In this work, we show a previously uncharacterized molecular pathway that correlates the activation of the Ca2+-dependent phosphatase Calcineurin to Parkin translocation and Parkin-dependent mitophagy. Calcineurin downregulation or genetic inhibition prevents Parkin translocation to CCCP-treated mitochondria and impairs stress-induced mitophagy, whereas Calcineurin activation promotes Parkin mitochondrial recruitment and basal mitophagy. Calcineurin interacts with Parkin, and promotes Parkin translocation in the absence of PINK1, but requires PINK1 expression to execute mitophagy in MEF cells. Genetic activation of Calcineurin in vivo boosts basal mitophagy in neurons and corrects locomotor dysfunction and mitochondrial respiratory defects of a Drosophila model of impaired mitochondrial functions. Our study identifies Calcineurin as a novel key player in the regulation of Parkin translocation and mitophagy.
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Affiliation(s)
| | - Alice Nardin
- Department of Biology, University of Padova, Padova, Italy
| | - Sofia Mauri
- Department of Biology, University of Padova, Padova, Italy
| | - Greta Bernardo
- Department of Biology, University of Padova, Padova, Italy
| | - Vivek Chander
- Department of Biology, University of Padova, Padova, Italy
| | - Simone Di Paola
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
- Institute for Experimental Endocrinology and Oncology (IEOS), National Research Council (CNR), Napoli, Italy
| | | | | | | | | | | | - Emilie Schrepfer
- Department of Biology, University of Padova, Padova, Italy
- Dulbecco-Telethon Institute, Venetian Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Oriano Marin
- Department of Biomedical Sciences (DSB), University of Padova, Padova, Italy
| | - Laura Cendron
- Department of Biology, University of Padova, Padova, Italy
| | - Diego L Medina
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
- Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Naples, Italy
| | - Luca Scorrano
- Department of Biology, University of Padova, Padova, Italy
- Dulbecco-Telethon Institute, Venetian Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Elena Ziviani
- Department of Biology, University of Padova, Padova, Italy.
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6
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Monticelli M, Wright DM, Cubellis MV, Andreotti G. ReBaTSA: A simplified CeTSA protocol for studying recombinant mutant proteins in bacterial extracts. Biochim Biophys Acta Gen Subj 2024; 1868:130526. [PMID: 38049040 DOI: 10.1016/j.bbagen.2023.130526] [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: 10/09/2023] [Revised: 11/15/2023] [Accepted: 11/27/2023] [Indexed: 12/06/2023]
Abstract
INTRODUCTION The study of protein stability is crucial to biochemistry and relies on different methodologies. Recently, the Cellular Thermal Shift Assay has been introduced to study protein stability in whole cells. METHODS We report a novel application of CeTSA named ReBaTSA. This Recombinant Bacterial TSA was performed using clear extracts from bacteria expressing a recombinant protein, incubated at different temperatures, centrifuged and analyzed via SDS-PAGE. RESULTS AND CONCLUSIONS We demonstrated the feasibility and reliability of this simplified approach. We validated the method using the protein phosphomannomutase-2 and its common mutants, which were compared in the presence or the absence of a known ligand.
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Affiliation(s)
- Maria Monticelli
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy; Department of Biology, University of Napoli "Federico II", Complesso Universitario Monte Sant'Angelo, Via Cinthia, 80126 Napoli, Italy
| | - Demi Marie Wright
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy; Institute of Chemistry and Biochemistry, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Maria Vittoria Cubellis
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy; Department of Biology, University of Napoli "Federico II", Complesso Universitario Monte Sant'Angelo, Via Cinthia, 80126 Napoli, Italy; Stazione Zoologica "Anton Dohrn", Villa Comunale, Naples, Italy.
| | - Giuseppina Andreotti
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy.
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7
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Bingham M, Pesnot T, Scott AD. Biophysical screening and characterisation in medicinal chemistry. PROGRESS IN MEDICINAL CHEMISTRY 2023; 62:61-104. [PMID: 37981351 DOI: 10.1016/bs.pmch.2023.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
In the last two decades the use of biophysical assays and methods in medicinal chemistry has increased significantly, to meet the demands of the novel targets and modalities that drug discoverers are looking to tackle. The desire to obtain accurate affinities, kinetics, thermodynamics and structural data as early as possible in the drug discovery process has fuelled this innovation. This review introduces the principles underlying the techniques in common use and provides a perspective on the weaknesses and strengths of different methods. Case studies are used to further illustrate some of the applications in medicinal chemistry and a discussion of the emerging biophysical methods on the horizon is presented.
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8
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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: 3] [Impact Index Per Article: 3.0] [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.
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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.
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9
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Li M, Zhang A, Qi X, Yu R, Li J. A novel inhibitor of PGK1 suppresses the aerobic glycolysis and proliferation of hepatocellular carcinoma. Biomed Pharmacother 2023; 158:114115. [PMID: 36516697 DOI: 10.1016/j.biopha.2022.114115] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/24/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Phosphoglycerate kinase 1(PGK1) is an important enzyme in the metabolic glycolysis pathway. Nowadays, PGK1 is an appealing therapeutic target for multiple cancers. However, no effective inhibitor of PGK1 has been reported. In this study, we demonstrate that Ilicicolin H a 5-(4-hydroxyphenyl)-pyridone with a decalin ring system and a non-ATP-competitive inhibitor of PGK1, inhibits the proliferation and promotes apoptosis of Hepatocellular carcinoma (HCC). Many cancer cells display enhanced glycolysis which is critical for tumor development. Here we identified that Ilicicolin H can target PGK1 in vitro to inhibit the lactate production and glucose uptake of HCC cells. These findings suggest that the PGK1 inhibitor- Ilicicolin H is a promising anticancer agent and may provide a better therapeutic strategy for HCC treatment in the future.
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Affiliation(s)
- Mingfeng Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Aotong Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Xin Qi
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Rilei Yu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, People's Republic of China
| | - Jing Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, People's Republic of China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, 266237, People's Republic of China.
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10
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Feng F, Zhang W, Chai Y, Guo D, Chen X. Label-free target protein characterization for small molecule drugs: recent advances in methods and applications. J Pharm Biomed Anal 2023; 223:115107. [DOI: 10.1016/j.jpba.2022.115107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/08/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022]
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11
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Qian S, Han Y, Zhang Y, Du Y, Li J, Yang X, Kang J. Discovery of AHCY as an Off-Target of Doxorubicin by Integrative Analysis of Photoaffinity Labeling Chemoproteomics and Untargeted Metabolomics. Anal Chem 2022; 94:17121-17130. [PMID: 36445716 DOI: 10.1021/acs.analchem.2c03377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Target identification is critically important for understanding the mechanism of action of drugs. Here, we reported a new strategy for deconvolution of drug targets (or off-targets) with photoaffinity labeling chemoproteomics in combination with untargeted metabolomics by using doxorubicin (DOX) as a model. The DOX-derived photoaffinity probes were prepared and applied to capture DOX-interacting proteins in living cells. The captured DOX-interacting proteins were then identified by label-free quantitative proteomics. Totally, 151 significant proteins were identified with high confidence (fold change >4, p-value < 0.005). The gene ontology enrichment analysis suggested that the proteins were mainly involved in carbon metabolism, citrate cycle, fatty acid metabolism, and metabolic pathways. Therefore, untargeted metabolomics was applied to quantify the significantly altered metabolites in cells upon drug treatment. The pathway enrichment analysis suggested that DOX mainly interrupted with the processes of pyrimidine and purine metabolism, carbon metabolism, methionine metabolism, and phosphatidylcholine biosynthesis. Integrative analysis of chemoproteomics and metabolomics indicated that adenosylhomocysteinase (AHCY) is a new target (off-target) of DOX leading to the accumulation of S-adenosyl homocysteine. This deduced DOX target was confirmed by the cellular thermal shift assay, affinity competitive pull-down assay, biochemical assay, and siRNA knock down experiments. Our result suggested that AHCY is the uncovered off-target of DOX.
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Affiliation(s)
- Shanshan Qian
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai200032, China.,University of Chinese Academy of Sciences, Yuquan Road 19, Beijing100049, China
| | - Ying Han
- School of Life Science and Technology, ShanghaiTech University, Haike Road 100, Shanghai200120, China
| | - Yue Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai200032, China.,University of Chinese Academy of Sciences, Yuquan Road 19, Beijing100049, China
| | - Yanan Du
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai200032, China.,School of Physical Science and Technology, ShanghaiTech University, Haike Road 100, Shanghai200120, China
| | - Jing Li
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai200032, China.,School of Physical Science and Technology, ShanghaiTech University, Haike Road 100, Shanghai200120, China
| | - Xin Yang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai200032, China.,School of Physical Science and Technology, ShanghaiTech University, Haike Road 100, Shanghai200120, China
| | - Jingwu Kang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai200032, China.,School of Physical Science and Technology, ShanghaiTech University, Haike Road 100, Shanghai200120, China
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12
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Shi K, Zhang J, Zhou E, Wang J, Wang Y. Small-Molecule Receptor-Interacting Protein 1 (RIP1) Inhibitors as Therapeutic Agents for Multifaceted Diseases: Current Medicinal Chemistry Insights and Emerging Opportunities. J Med Chem 2022; 65:14971-14999. [DOI: 10.1021/acs.jmedchem.2c01518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Kunyu Shi
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
| | - Jifa Zhang
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
- Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
- Tianfu Jincheng Laboratory, Chengdu, 610041 Sichuan, China
| | - Enda Zhou
- West China School of Pharmacy, Sichuan University, Chengdu, 610041 Sichuan, China
| | - Jiaxing Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Yuxi Wang
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
- Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041 Sichuan, China
- Tianfu Jincheng Laboratory, Chengdu, 610041 Sichuan, China
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13
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Chana CK, Maisonneuve P, Posternak G, Grinberg NGA, Poirson J, Ona SM, Ceccarelli DF, Mader P, St-Cyr DJ, Pau V, Kurinov I, Tang X, Deng D, Cui W, Su W, Kuai L, Soll R, Tyers M, Röst HL, Batey RA, Taipale M, Gingras AC, Sicheri F. Discovery and Structural Characterization of Small Molecule Binders of the Human CTLH E3 Ligase Subunit GID4. J Med Chem 2022; 65:12725-12746. [PMID: 36117290 PMCID: PMC9574856 DOI: 10.1021/acs.jmedchem.2c00509] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Targeted protein
degradation (TPD) strategies exploit bivalent
small molecules to bridge substrate proteins to an E3 ubiquitin ligase
to induce substrate degradation. Few E3s have been explored as degradation
effectors due to a dearth of E3-binding small molecules. We show that
genetically induced recruitment to the GID4 subunit of the CTLH E3
complex induces protein degradation. An NMR-based fragment screen
followed by structure-guided analog elaboration identified two binders
of GID4, 16 and 67, with Kd values of 110 and 17 μM in vitro. A parallel DNA-encoded library (DEL) screen identified five binders
of GID4, the best of which, 88, had a Kd of 5.6 μM in vitro and an EC50 of 558 nM in cells with strong selectivity for GID4. X-ray
co-structure determination revealed the basis for GID4–small
molecule interactions. These results position GID4-CTLH as an E3 for
TPD and provide candidate scaffolds for high-affinity moieties that
bind GID4.
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Affiliation(s)
- Chetan K Chana
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario M5G 1X5, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Pierre Maisonneuve
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario M5G 1X5, Canada
| | - Ganna Posternak
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario M5G 1X5, Canada
| | - Nicolas G A Grinberg
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Juline Poirson
- Donnelly Centre for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Samara M Ona
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Derek F Ceccarelli
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario M5G 1X5, Canada
| | - Pavel Mader
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario M5G 1X5, Canada
| | | | - Victor Pau
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario M5G 1X5, Canada
| | - Igor Kurinov
- Department of Chemistry and Chemical Biology, Cornell University, NE-CAT, Argonne, Illinois 60439, United States
| | - Xiaojing Tang
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario M5G 1X5, Canada
| | - Dongjing Deng
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Weiren Cui
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Wenji Su
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Letian Kuai
- WuXi AppTec, 55 Cambridge Parkway, 8th Floor, Cambridge, Massachusetts 02142, United States
| | - Richard Soll
- WuXi AppTec, 55 Cambridge Parkway, 8th Floor, Cambridge, Massachusetts 02142, United States
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, University of Montréal, Québec H3C 3J7, Canada
| | - Hannes L Röst
- Donnelly Centre for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario M5S 2E4, Canada
| | - Robert A Batey
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Mikko Taipale
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario M5G 1X5, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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14
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Yang X, Da Q, Qian P, Veeravalli B, Leong TW, Dai L, Nordlund P, Prabhu N, Zhao Z, Zeng Z. CETSA Feature Based Clustering for Protein Outlier Discovery by Protein-to-Protein Interaction Prediction. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2022; 2022:1659-1662. [PMID: 36085889 DOI: 10.1109/embc48229.2022.9871558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The Cellular Thermal Shift Assay (CETSA) is a biophysical assay based on the principle of ligand-induced thermal stabilization of target proteins. This technology has revolutionized cell-based target engagement studies and has been used as guidance for drug design. Although many ap-plications of CETSA data have been explored, the correlations between CETSA data and protein-protein interactions (PPI) have barely been touched. In this study, we conduct the first exploration study applying CETSA data for PPI prediction. We use a machine learning method, Decision Tree, to predict PPI scores using proteins' CETSA features. It shows promising results that the predicted PPI scores closely match the ground-truth PPI scores. Furthermore, for a small number of protein pairs, whose PPI score predictions mismatch the ground truth, we use iterative clustering strategy to gradually reduce the number of these pairs. At the end of iterative clustering, the remaining protein pairs may have some unusual properties and are of scientific value for further biological investigation. Our study has demonstrated that PPI is a brand-new application of CETSA data. At the same time, it also manifests that CETSA data can be used as a new data source for PPI exploration study.
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15
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Novel quinoline-based derivatives: A new class of PDE4B inhibitors for adjuvant-induced arthritis. Eur J Med Chem 2022; 238:114497. [PMID: 35660249 DOI: 10.1016/j.ejmech.2022.114497] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/22/2022] [Accepted: 05/25/2022] [Indexed: 11/24/2022]
Abstract
A total of 31 quinoline-based derivatives were designed and synthesized to develop novel anti-inflammatory drugs. After the toxicity of synthetic compounds to RAW264.7 cells were evaluated in vitro, their anti-inflammatory activity was assessed by inhibiting lipopolysaccharide (LPS)-induced NO production levels in the RAW264.7 cells. Among the derivatives, compound f4 had the best anti-inflammatory activity, which could reduce the production of pro-inflammatory cytokines NO, IL-1β, and TNF-α with corresponding IC50 values of 20.40 ± 0.94, 18.98 ± 0.21 and 23.48 ± 0.46 μM. Western blot showed that f4 could inhibit the expression of LPS-induced inflammatory mediators iNOS and COX-2. Molecular docking showed that f4 could also enter the PDE4B receptor binding pocket, and the cellular thermal shift assay method indicated that the PDE4B protein bound to f4 had increased stability. Meanwhile, the inhibitory effect of this compound on the PDE4B enzyme (IC50 = 0.94 ± 0.36 μM) was comparable to that of the positive drug rolipram (IC50 = 1.04 ± 0.28 μM). Finally, in vivo studies showed that f4 could improve the degree of foot swelling and knee joint pathology in adjuvant-induced arthritic rats and decrease the levels of serum inflammatory factors TNF-α and IL-1β in a dose-dependent manner. Therefore, the development and design of quinoline-based derivatives for anti-inflammatory applications could be considered opportunities and challenges.
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16
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Karvonen H, Raivola J, Ungureanu D. Cellular thermal shift assay (CETSA) for determining the drug binding affinity using Ba/F3 clones stably expressing receptor pseudokinases. Methods Enzymol 2022; 667:339-363. [PMID: 35525546 DOI: 10.1016/bs.mie.2022.03.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The majority of drug screening approaches are performed using recombinant proteins, however, drug binding to its target(s) in cells should be also assessed, especially for drugs aimed at modulating intracellular signaling pathways. As a result, the development of a cellular thermal shift assay (CETSA) has become an important tool for determining the binding affinity of drugs to their intracellular targets. Cell lines, such as Ba/F3, are an excellent model system to stably express and study a target protein when this protein is not endogenously expressed or only present at low levels. Together with CETSA, Ba/F3 clones allow study of the transforming properties of the protein in question, its downstream intracellular signaling activation pathways, as well as its drug binding kinetics. This chapter describes in detail the establishment of Ba/F3 clones stably expressing receptor pseudokinases, such as receptor tyrosine kinase-like orphan receptors (ROR1, ROR2) and protein tyrosine kinase 7 (PTK7), and the use thereof to evaluate binding of small molecule inhibitors to their intracellular (pseudo)kinase domain by CETSA.
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Affiliation(s)
- Hanna Karvonen
- Cancer Signaling, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Juuli Raivola
- Applied Tumor Genomics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Daniela Ungureanu
- Cancer Signaling, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Applied Tumor Genomics, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.
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17
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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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18
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Osman S, Bendtsen C, Peel S, Yrlid L, Muthas D, Simpson J, Willison KR, Klug DR. Evaluation of FOXO1 Target Engagement Using a Single-Cell Microfluidic Platform. Anal Chem 2021; 93:14659-14666. [PMID: 34694778 DOI: 10.1021/acs.analchem.1c02808] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The cellular thermal shift assay (CETSA) has been used extensively since its introduction to study drug-target engagement within both live cells and cellular lysate. This has proven to be a useful tool in early stage drug discovery and is used to study a wide range of protein classes. We describe the application of a single-cell CETSA workflow within a microfluidic affinity capture (MAC) chip. This has enabled us to quantitatively determine the active FOXO1 single-molecule count and observe FOXO1 stabilization and destabilization in the presence of three small molecule inhibitors, including demonstrating the determination of EC50. The successful use of the MAC chip for single-cell CETSA paves the way for the study of precious clinical samples owing to the low number of cells needed by the chip. It also provides a useful tool for studying any underlying population heterogeneity that exists within a cellular system, a feature that is usually masked when conducting ensemble measurements.
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Affiliation(s)
- Suhuur Osman
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 80 Wood Lane, London, W12 0BZ, United Kingdom
| | - Claus Bendtsen
- Discovery Sciences, R&D, AstraZeneca, 310 Milton Road, Cambridge, CB4 0WG, United Kingdom
| | - Samantha Peel
- Discovery Sciences, R&D, AstraZeneca, 310 Milton Road, Cambridge, CB4 0WG, United Kingdom
| | - Linda Yrlid
- Early Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43150 Gothenburg, Sweden
| | - Daniel Muthas
- Early Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43150 Gothenburg, Sweden
| | - John Simpson
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 80 Wood Lane, London, W12 0BZ, United Kingdom
| | - Keith R Willison
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 80 Wood Lane, London, W12 0BZ, United Kingdom
| | - David R Klug
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 80 Wood Lane, London, W12 0BZ, United Kingdom
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19
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Very long chain fatty acid metabolism is required in acute myeloid leukemia. Blood 2021; 137:3518-3532. [PMID: 33720355 DOI: 10.1182/blood.2020008551] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 02/21/2021] [Indexed: 12/28/2022] Open
Abstract
Acute myeloid leukemia (AML) cells have an atypical metabolic phenotype characterized by increased mitochondrial mass, as well as a greater reliance on oxidative phosphorylation and fatty acid oxidation (FAO) for survival. To exploit this altered metabolism, we assessed publicly available databases to identify FAO enzyme overexpression. Very long chain acyl-CoA dehydrogenase (VLCAD; ACADVL) was found to be overexpressed and critical to leukemia cell mitochondrial metabolism. Genetic attenuation or pharmacological inhibition of VLCAD hindered mitochondrial respiration and FAO contribution to the tricarboxylic acid cycle, resulting in decreased viability, proliferation, clonogenic growth, and AML cell engraftment. Suppression of FAO at VLCAD triggered an increase in pyruvate dehydrogenase activity that was insufficient to increase glycolysis but resulted in adenosine triphosphate depletion and AML cell death, with no effect on normal hematopoietic cells. Together, these results demonstrate the importance of VLCAD in AML cell biology and highlight a novel metabolic vulnerability for this devastating disease.
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20
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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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21
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Wang Y, Sun L, Yu G, Qi X, Zhang A, Lu Z, Li D, Li J. Identification of a novel non-ATP-competitive protein kinase inhibitor of PGK1 from marine nature products. Biochem Pharmacol 2020; 183:114343. [PMID: 33212041 DOI: 10.1016/j.bcp.2020.114343] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 10/26/2020] [Accepted: 11/13/2020] [Indexed: 11/28/2022]
Abstract
Phosphoglycerate kinase 1 (PGK1) acts as both a glycolytic enzyme and a protein kinase playing critical roles in cancer progression, thereby being regarded as an attractive therapeutic target for cancer treatment. However, no effective inhibitor of PGK1 has been reported. Here, we demonstrate that GQQ-792, a thiodiketopiperazine derivative from marine nature products, is a non-ATP-competitive inhibitor of PGK1 with the disulfide group within the structure of GQQ-792 as a key pharmacophore. The disulfide group of GQQ-792 binds to Cys379 and Cys380 of PGK1, resulting in occlusion of ATP from binding to PGK1. GQQ-792 treatment blocks hypoxic condition- and EGF stimulation-enhanced protein kinase activity of PGK1 that phosphorylates PDHK1 at T338 in glioblastoma cells; this treatment leads to decreased lactate production and glucose uptake, and subsequent apoptosis of glioblastoma cells. Animal studies reveal that GQQ-792 significantly inhibits the growth of tumor derived from glioblastoma cells. These findings underscore the potential of GQQ-792 as a promising anticancer agent and pave an avenue to further optimize the structure of GQQ-792 basing on its target molecule and pharmacophore in future.
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Affiliation(s)
- Yuying Wang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Lulu Sun
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Guihong Yu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Xin Qi
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Aotong Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Zhimin Lu
- Zhejiang Provincial Key Laboratory of Pancreatic Disease of The First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310029, China
| | - Dehai Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Open Studio for Druggability Research of Marine Natural Products, Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| | - Jing Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Open Studio for Druggability Research of Marine Natural Products, Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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22
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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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23
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Akakpo JY, Ramachandran A, Duan L, Schaich MA, Jaeschke MW, Freudenthal BD, Ding WX, Rumack BH, Jaeschke H. Delayed Treatment With 4-Methylpyrazole Protects Against Acetaminophen Hepatotoxicity in Mice by Inhibition of c-Jun n-Terminal Kinase. Toxicol Sci 2020; 170:57-68. [PMID: 30903181 DOI: 10.1093/toxsci/kfz077] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Acetaminophen (APAP) overdose is the most common cause of hepatotoxicity and acute liver failure in the United States and many western countries. However, the only clinically approved antidote, N-acetylcysteine, has a limited therapeutic window. 4-Methylpyrazole (4MP) is an antidote for methanol and ethylene glycol poisoning, and we have recently shown that cotreatment of 4MP with APAP effectively prevents toxicity by inhibiting Cyp2E1. To evaluate if 4MP can be used therapeutically, C57BL/6J mice were treated with 300 mg/kg APAP followed by 50 mg/kg 4MP 90 min later (after the metabolism phase). In these experiments, 4MP significantly attenuated liver injury at 3, 6, and 24 h after APAP as shown by 80%-90% reduction in plasma alanine aminotransferase activities and reduced areas of necrosis. 4MP prevented c-Jun c-Jun N-terminal kinase (JNK) activation and its mitochondrial translocation, and reduced mitochondrial oxidant stress and nuclear DNA fragmentation. 4MP also prevented JNK activation in other liver injury models. Molecular docking experiments showed that 4MP can bind to the ATP binding site of JNK. These data suggest that treatment with 4MP after the metabolism phase effectively prevents APAP-induced liver injury in the clinically relevant mouse model in vivo mainly through the inhibition of JNK activation. 4MP, a drug approved for human use, is as effective as N-acetylcysteine or can be even more effective in cases of severe overdoses with prolonged metabolism (600 mg/kg). 4MP acts on alternative therapeutic targets and thus may be a novel approach to treatment of APAP overdose in patients that complements N-acetylcysteine.
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Affiliation(s)
| | | | - Luqi Duan
- Department of Pharmacology Toxicology & Therapeutics
| | - Matthew A Schaich
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas 66160
| | | | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas 66160
| | - Wen-Xing Ding
- Department of Pharmacology Toxicology & Therapeutics
| | - Barry H Rumack
- Department of Emergency Medicine and Pediatrics, University of Colorado School of Medicine, Aurora, Colorado 80045
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24
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Liu XQ, Jin J, Li Z, Jiang L, Dong YH, Cai YT, Wu MF, Wang JN, Ma TT, Wen JG, Liu MM, Li J, Wu YG, Meng XM. Rutaecarpine derivative Cpd-6c alleviates acute kidney injury by targeting PDE4B, a key enzyme mediating inflammation in cisplatin nephropathy. Biochem Pharmacol 2020; 180:114132. [PMID: 32622666 DOI: 10.1016/j.bcp.2020.114132] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/27/2020] [Accepted: 06/30/2020] [Indexed: 12/18/2022]
Abstract
Acute kidney injury (AKI), characterized by a rapid decline in renal function, is triggered by an acute inflammatory response that leads to kidney damage. An effective treatment for AKI is lacking. Using in vitro and in vivo AKI models, our laboratory has identified a series of anti-inflammatory molecules and their derivatives. In the current study, we identified the protective role of rutaecarpine (Ru) on renal tubules. We obtained a series of 3-aromatic sulphonamide-substituted Ru derivatives exhibiting enhanced renoprotective and anti-inflammatory function. We identified Compound-6c(Cpd-6c) as having the best activity and examined its protective effect against cisplatin nephropathy both in vivo and in vitro in cisplatin-stimulated tubular epithelial cells (TECs). Our results showed that Cpd-6c restored renal function more effectively than Ru, as evidenced by reduced blood urea nitrogen and serum creatinine levels in mice. Cpd-6c alleviated tubular injury, as shown by PAS staining and molecular analysis of kidney injury molecule-1 (KIM-1), with both prevention and treatment protocols in cisplatin-treated mice. Moreover, Cpd-6c decreased kidney inflammation, oxidative stress and programmed cell death. These results have also been confirmed in cisplatin-treated TECs. Using web-prediction algorithms, molecular docking, and cellular thermal shift assay (CETSA), we identified phosphodiesterase 4B (PDE4B) as a Cpd-6c target. In addition, we firstly found that PDE4B was up-regulated significantly in the serum of AKI patients. After identifying the function of PDE4B in cisplatin-treated tubular epithelial cells by siRNA transfection or PDE4 inhibitor rolipram, we showed that Cpd-6c treatment did not protect against cisplatin-induced injury in PDE4B knockdown TECs, thus indicating that Cpd-6c exerts its renoprotective and anti-oxidative effects via the PDE4B-dependent pathway. Collectively, Cpd-6c might serve as a potential therapeutic agent for AKI and PDE4B may be highly involved in the initiation and progression of AKI.
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Affiliation(s)
- Xue-Qi Liu
- Department of Nephropathy, The First Affiliated Hospital of Anhui Medical University, Hefei, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei 230032, China
| | - Juan Jin
- School of Basic Medical Sciences, Anhui Medical University, Anhui, China
| | - Zeng Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei 230032, China
| | - Ling Jiang
- Department of Nephropathy, The First Affiliated Hospital of Anhui Medical University, Hefei, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei 230032, China
| | - Yu-Hang Dong
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei 230032, China
| | - Yu-Ting Cai
- Department of Nephropathy, The First Affiliated Hospital of Anhui Medical University, Hefei, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei 230032, China
| | - Ming-Fei Wu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei 230032, China
| | - Jia-Nan Wang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei 230032, China
| | - Tao-Tao Ma
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei 230032, China
| | - Jia-Gen Wen
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei 230032, China
| | - Ming-Ming Liu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei 230032, China
| | - Jun Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei 230032, China
| | - Yong-Gui Wu
- Department of Nephropathy, The First Affiliated Hospital of Anhui Medical University, Hefei, China; The Center for Scientific Research of Anhui Medical University, Hefei, China.
| | - Xiao-Ming Meng
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Hefei 230032, China.
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25
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Dziekan JM, Wirjanata G, Dai L, Go KD, Yu H, Lim YT, Chen L, Wang LC, Puspita B, Prabhu N, Sobota RM, Nordlund P, Bozdech Z. Cellular thermal shift assay for the identification of drug-target interactions in the Plasmodium falciparum proteome. Nat Protoc 2020; 15:1881-1921. [PMID: 32341577 DOI: 10.1038/s41596-020-0310-z] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 01/13/2020] [Indexed: 02/06/2023]
Abstract
Despite decades of research, little is known about the cellular targets and the mode of action of the vast majority of antimalarial drugs. We recently demonstrated that the cellular thermal shift assay (CETSA) protocol in its two variants: the melt curve and the isothermal dose-response, represents a comprehensive strategy for the identification of antimalarial drug targets. CETSA enables proteome-wide target screening for unmodified antimalarial compounds with undetermined mechanisms of action, providing quantitative evidence about direct drug-protein interactions. The experimental workflow involves treatment of P. falciparum-infected erythrocytes with a compound of interest, heat exposure to denature proteins, soluble protein isolation, enzymatic digestion, peptide labeling with tandem mass tags, offline fractionation, and liquid chromatography-tandem mass spectrometry analysis. Methodological optimizations necessary for the analysis of this intracellular parasite are discussed, including enrichment of parasitized cells and hemoglobin depletion strategies to overcome high hemoglobin abundance in the host red blood cells. We outline an effective data processing workflow using the mineCETSA R package, which enables prioritization of drug-target candidates for follow-up studies. The entire protocol can be completed within 2 weeks.
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Affiliation(s)
- Jerzy Michal Dziekan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Grennady Wirjanata
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Lingyun Dai
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,The Second Clinical Medical College of Jinan University, First Affiliated Hospital of Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, China
| | - Ka Diam Go
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Han Yu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yan Ting Lim
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Liyan Chen
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Loo Chien Wang
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Brenda Puspita
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Nayana Prabhu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Radoslaw M Sobota
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore. .,Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
| | - Pär Nordlund
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore. .,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.
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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26
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Brown JI, Page BDG, Frankel A. The application of differential scanning fluorimetry in exploring bisubstrate binding to protein arginine N-methyltransferase 1. Methods 2020; 175:10-23. [PMID: 31726226 DOI: 10.1016/j.ymeth.2019.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 10/25/2022] Open
Abstract
Protein arginine N-methyltransferases (PRMTs) are a family of 9 enzymes that catalyze mono- or di-methylation of arginine residues using S-adenosyl-l-methionine (SAM). Arginine methylation is an important post-translational modification that can regulate the activity and structure of target proteins. Altered PRMT activity can lead to a variety of health issues including neurodevelopmental disease, autoimmune disorders, cancer, and cardiovascular disease. Thus, developing a robust mechanistic understanding of PRMT function may provide insight into these various disease states and enable the development of potential therapeutic agents. Although PRMTs have been studied for nearly two decades, a consensus regarding the mechanism of action for this class of enzymes has remained noticeably elusive. To address this shortcoming, differential scanning fluorimetry (DSF) was used to gain mechanistic insight into the order of PRMT substrate and cofactor binding. This methodology confirms that PRMT cofactor binding precedes target substrate binding and supports the use of DSF to study bisubstrate enzymatic reaction mechanisms.
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Affiliation(s)
- Jennifer I Brown
- Faculty of Pharmaceutical Sciences, University of British Columbia, 2405 Wesbrook Mall, Vancouver, Canada
| | - Brent D G Page
- Faculty of Pharmaceutical Sciences, University of British Columbia, 2405 Wesbrook Mall, Vancouver, Canada; Department of Oncology and Pathology, Karolinska Institutet, Tomtebodavagen 23A, Stockholm, Sweden.
| | - Adam Frankel
- Faculty of Pharmaceutical Sciences, University of British Columbia, 2405 Wesbrook Mall, Vancouver, Canada.
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27
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Lyu J, Wang K, Ye M. Modification-free approaches to screen drug targets at proteome level. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.06.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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28
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Mateus A, Kurzawa N, Becher I, Sridharan S, Helm D, Stein F, Typas A, Savitski MM. Thermal proteome profiling for interrogating protein interactions. Mol Syst Biol 2020; 16:e9232. [PMID: 32133759 PMCID: PMC7057112 DOI: 10.15252/msb.20199232] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/15/2020] [Accepted: 01/27/2020] [Indexed: 12/11/2022] Open
Abstract
Thermal proteome profiling (TPP) is based on the principle that, when subjected to heat, proteins denature and become insoluble. Proteins can change their thermal stability upon interactions with small molecules (such as drugs or metabolites), nucleic acids or other proteins, or upon post-translational modifications. TPP uses multiplexed quantitative mass spectrometry-based proteomics to monitor the melting profile of thousands of expressed proteins. Importantly, this approach can be performed in vitro, in situ, or in vivo. It has been successfully applied to identify targets and off-targets of drugs, or to study protein-metabolite and protein-protein interactions. Therefore, TPP provides a unique insight into protein state and interactions in their native context and at a proteome-wide level, allowing to study basic biological processes and their underlying mechanisms.
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Affiliation(s)
- André Mateus
- Genome Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Nils Kurzawa
- Genome Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Faculty of BiosciencesEMBL and Heidelberg UniversityHeidelbergGermany
| | - Isabelle Becher
- Genome Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Sindhuja Sridharan
- Genome Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Dominic Helm
- Proteomics Core FacilityEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Frank Stein
- Proteomics Core FacilityEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Athanasios Typas
- Genome Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Mikhail M Savitski
- Genome Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
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29
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Inhibitors Targeting RIPK1/RIPK3: Old and New Drugs. Trends Pharmacol Sci 2020; 41:209-224. [PMID: 32035657 DOI: 10.1016/j.tips.2020.01.002] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/13/2019] [Accepted: 01/02/2020] [Indexed: 12/26/2022]
Abstract
The scaffolding function of receptor-interacting protein kinase 1 (RIPK1) regulates prosurvival signaling and inflammatory gene expression, while its kinase activity mediates both apoptosis and necroptosis; the latter involving RIPK3 kinase activity. The mutual transition between the scaffold and kinase functions of RIPK1 is regulated by (de)ubiquitylation and (de)phosphorylation. RIPK1-mediated cell death leads to disruption of epithelial barriers and/or release of damage-associated molecular patterns (DAMPs), cytokines, and chemokines, propagating inflammatory and degenerative diseases. Many drug development programs have pursued targeting RIPK1, and to a lesser extent RIPK3 kinase activity. In this review, we classify existing and novel small-molecule drugs based on their pharmacodynamic (PD) type I, II, and III binding mode. Finally, we discuss their applicability and therapeutic potential in inflammatory and degenerative experimental disease models.
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30
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Identifying drug targets in tissues and whole blood with thermal-shift profiling. Nat Biotechnol 2020; 38:303-308. [PMID: 31959954 DOI: 10.1038/s41587-019-0388-4] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 12/04/2019] [Accepted: 12/06/2019] [Indexed: 12/31/2022]
Abstract
Monitoring drug-target interactions with methods such as the cellular thermal-shift assay (CETSA) is well established for simple cell systems but remains challenging in vivo. Here we introduce tissue thermal proteome profiling (tissue-TPP), which measures binding of small-molecule drugs to proteins in tissue samples from drug-treated animals by detecting changes in protein thermal stability using quantitative mass spectrometry. We report organ-specific, proteome-wide thermal stability maps and derive target profiles of the non-covalent histone deacetylase inhibitor panobinostat in rat liver, lung, kidney and spleen and of the B-Raf inhibitor vemurafenib in mouse testis. In addition, we devised blood-CETSA and blood-TPP and applied it to measure target and off-target engagement of panobinostat and the BET family inhibitor JQ1 directly in whole blood. Blood-TPP analysis of panobinostat confirmed its binding to known targets and also revealed thermal stabilization of the zinc-finger transcription factor ZNF512. These methods will help to elucidate the mechanisms of drug action in vivo.
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31
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Langebäck A, Bacanu S, Laursen H, Mout L, Seki T, Erkens-Schulze S, Ramos AD, Berggren A, Cao Y, Hartman J, van Weerden W, Bergh J, Nordlund P, Lööf S. CETSA-based target engagement of taxanes as biomarkers for efficacy and resistance. Sci Rep 2019; 9:19384. [PMID: 31852908 PMCID: PMC6920357 DOI: 10.1038/s41598-019-55526-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 11/27/2019] [Indexed: 12/22/2022] Open
Abstract
The use of taxanes has for decades been crucial for treatment of several cancers. A major limitation of these therapies is inherent or acquired drug resistance. A key to improved outcome of taxane-based therapies is to develop tools to predict and monitor drug efficacy and resistance in the clinical setting allowing for treatment and dose stratification for individual patients. To assess treatment efficacy up to the level of drug target engagement, we have established several formats of tubulin-specific Cellular Thermal Shift Assays (CETSAs). This technique was evaluated in breast and prostate cancer models and in a cohort of breast cancer patients. Here we show that taxanes induce significant CETSA shifts in cell lines as well as in animal models including patient-derived xenograft (PDX) models. Furthermore, isothermal dose response CETSA measurements allowed for drugs to be rapidly ranked according to their reported potency. Using multidrug resistant cancer cell lines and taxane-resistant PDX models we demonstrate that CETSA can identify taxane resistance up to the level of target engagement. An imaging-based CETSA format was also established, which in principle allows for taxane target engagement to be accessed in specific cell types in complex cell mixtures. Using a highly sensitive implementation of CETSA, we measured target engagement in fine needle aspirates from breast cancer patients, revealing a range of different sensitivities. Together, our data support that CETSA is a robust tool for assessing taxane target engagement in preclinical models and clinical material and therefore should be evaluated as a prognostic tool during taxane-based therapies.
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Affiliation(s)
- Anette Langebäck
- Department of Oncology-Pathology, Karolinska Institutet, BioClinicum, Solna, 171 64, Sweden
| | - Smaranda Bacanu
- Department of Oncology-Pathology, Karolinska Institutet, BioClinicum, Solna, 171 64, Sweden
| | - Henriette Laursen
- Department of Oncology-Pathology, Karolinska Institutet, BioClinicum, Solna, 171 64, Sweden
| | - Lisanne Mout
- Department of Urology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Takahiro Seki
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, 171 65, Sweden
| | | | - Anderson Daniel Ramos
- Department of Oncology-Pathology, Karolinska Institutet, BioClinicum, Solna, 171 64, Sweden
| | - Anna Berggren
- Department of Oncology-Pathology, Karolinska Institutet, BioClinicum, Solna, 171 64, Sweden
| | - Yihai Cao
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, 171 65, Sweden
| | - Johan Hartman
- Department of Oncology-Pathology, Karolinska Institutet, BioClinicum, Solna, 171 64, Sweden
| | - Wytske van Weerden
- Department of Urology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Jonas Bergh
- Department of Oncology-Pathology, Karolinska Institutet, BioClinicum, Solna, 171 64, Sweden
| | - Pär Nordlund
- Department of Oncology-Pathology, Karolinska Institutet, BioClinicum, Solna, 171 64, Sweden. .,School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore. .,Institute of Molecular and Cell Biology, A*STAR, Singapore, 138673, Singapore.
| | - Sara Lööf
- Department of Oncology-Pathology, Karolinska Institutet, BioClinicum, Solna, 171 64, Sweden
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32
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Seashore-Ludlow B, Axelsson H, Lundbäck T. Perspective on CETSA Literature: Toward More Quantitative Data Interpretation. SLAS DISCOVERY 2019; 25:118-126. [PMID: 31665966 DOI: 10.1177/2472555219884524] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The cellular thermal shift assay (CETSA) was introduced in 2013 to investigate drug-target engagement inside live cells and tissues. As with all thermal shift assays, the response measured by CETSA is not simply governed by ligand affinity to the investigated target protein, but the thermodynamics and kinetics of ligand binding and protein unfolding also contribute to the observed protein stabilization. This limitation is commonly neglected in current applications of the method to validate the target of small-molecule probes. Instead, there is an eagerness to make direct comparisons of CETSA measurements with functional and phenotypic readouts from cells at 37 °C. Here, we present a perspective of the early CETSA literature and put the accumulated data into a quantitative context. The analysis includes annotation of ~270 peer-reviewed papers, the majority of which do not consider the underlying biophysical basis of CETSA. We also detail what future technology developments are needed to enable CETSA-based optimization of structure-activity relationships and more appropriate comparisons of these data with functional or phenotypic responses. Finally, we describe ongoing developments in assay formats that allow for CETSA measurements at single-cell resolution, with the aspiration to allow differentiation in cellular target engagement between cells in co-cultures and more complex models, such as organoids and potentially even tissue.
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Affiliation(s)
- Brinton Seashore-Ludlow
- Department of Oncology and Pathology, Science for Life Laboratories, Karolinska Institutet, Solna, Sweden
| | - Hanna Axelsson
- Chemical Biology Consortium Sweden, Science for Life Laboratories, Karolinska Institutet, Solna, Sweden
| | - Thomas Lundbäck
- Chemical Biology Consortium Sweden, Science for Life Laboratories, Karolinska Institutet, Solna, Sweden.,Mechanistic Biology & Profiling, Discovery Sciences, R&D, AstraZeneca, Mölndal, Sweden
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33
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Rodriguez-Furlan C, Domozych D, Qian W, Enquist PA, Li X, Zhang C, Schenk R, Winbigler HS, Jackson W, Raikhel NV, Hicks GR. Interaction between VPS35 and RABG3f is necessary as a checkpoint to control fusion of late compartments with the vacuole. Proc Natl Acad Sci U S A 2019; 116:21291-21301. [PMID: 31570580 PMCID: PMC6800349 DOI: 10.1073/pnas.1905321116] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Vacuoles are essential organelles in plants, playing crucial roles, such as cellular material degradation, ion and metabolite storage, and turgor maintenance. Vacuoles receive material via the endocytic, secretory, and autophagic pathways. Membrane fusion is the last step during which prevacuolar compartments (PVCs) and autophagosomes fuse with the vacuole membrane (tonoplast) to deliver cargoes. Protein components of the canonical intracellular fusion machinery that are conserved across organisms, including Arabidopsis thaliana, include complexes, such as soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs), that catalyze membrane fusion, and homotypic fusion and vacuole protein sorting (HOPS), that serve as adaptors which tether cargo vesicles to target membranes for fusion under the regulation of RAB-GTPases. The mechanisms regulating the recruitment and assembly of tethering complexes are not well-understood, especially the role of RABs in this dynamic regulation. Here, we report the identification of the small synthetic molecule Endosidin17 (ES17), which interferes with synthetic, endocytic, and autophagic traffic by impairing the fusion of late endosome compartments with the tonoplast. Multiple independent target identification techniques revealed that ES17 targets the VPS35 subunit of the retromer tethering complex, preventing its normal interaction with the Arabidopsis RAB7 homolog RABG3f. ES17 interference with VPS35-RABG3f interaction prevents the retromer complex to endosome anchoring, resulting in retention of RABG3f. Using multiple approaches, we show that VPS35-RABG3f-GTP interaction is necessary to trigger downstream events like HOPS complex assembly and fusion of late compartments with the tonoplast. Overall, our results support a role for the interaction of RABG3f-VPS35 as a checkpoint in the control of traffic toward the vacuole.
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Affiliation(s)
- Cecilia Rodriguez-Furlan
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92506
- Institute of Integrative Genome Biology, University of California, Riverside, CA 92506
| | - David Domozych
- Biology Department, Skidmore College, Saratoga Springs, NY 12866
| | - Weixing Qian
- Department of Chemistry, Umea University, SE-901 87 Umea, Sweden
- Department of Chemistry, Chemical Biology Consortium Sweden, SE-901 87 Umea, Sweden
| | - Per-Anders Enquist
- Department of Chemistry, Umea University, SE-901 87 Umea, Sweden
- Department of Chemistry, Chemical Biology Consortium Sweden, SE-901 87 Umea, Sweden
| | - Xiaohui Li
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47906
- Center for Plant Biology, Purdue University, West Lafayette, IN 47906
| | - Chunhua Zhang
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47906
- Center for Plant Biology, Purdue University, West Lafayette, IN 47906
| | - Rolf Schenk
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92506
- Institute of Integrative Genome Biology, University of California, Riverside, CA 92506
| | - Holly Saulsbery Winbigler
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 20201
| | - William Jackson
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 20201
| | - Natasha V Raikhel
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92506
- Institute of Integrative Genome Biology, University of California, Riverside, CA 92506
| | - Glenn R Hicks
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92506;
- Institute of Integrative Genome Biology, University of California, Riverside, CA 92506
- Uppsala BioCenter, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
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34
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Kath JE, Baranczak A. Target engagement approaches for pharmacological evaluation in animal models. Chem Commun (Camb) 2019; 55:9241-9250. [PMID: 31328738 DOI: 10.1039/c9cc02824b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The field of chemical biology has introduced several approaches, typically using chemical probes, to measure the direct binding interaction of a small molecule with its biological target in cells. The use of these direct target engagement assays in pharmaceutical development can support mechanism of action hypothesis testing, rank ordering of compounds, and iterative improvements of chemical matter. This Feature Article highlights a newer application of these approaches: the quantification of target engagement in animal models to support late stage preclinical development and the nomination of a drug candidate to clinical trials. Broadly speaking, these efforts can be divided between compounds that covalently and reversibly interact with protein targets; recent examples for both categories are discussed for a range of targets, along with their limitations. New, promising technologies are also highlighted, in addition to the application of target engagement determination to new therapeutic modalities.
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Affiliation(s)
- James E Kath
- Drug Discovery Science and Technology, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064-6101, USA.
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35
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RIPK1 inhibitor Cpd-71 attenuates renal dysfunction in cisplatin-treated mice via attenuating necroptosis, inflammation and oxidative stress. Clin Sci (Lond) 2019; 133:1609-1627. [DOI: 10.1042/cs20190599] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 07/12/2019] [Accepted: 07/17/2019] [Indexed: 12/13/2022]
Abstract
Abstract
Acute kidney injury (AKI) is a destructive clinical condition induced by multiple insults including ischemic reperfusion, nephrotoxic drugs and sepsis. It is characterized by a sudden decline in renal function, in addition to excessive inflammation, oxidative stress and programmed cell death of renal tubular epithelial cells. RIPK1-mediated necroptosis plays an important role in AKI. In the present study, we evaluated the treatment effects of Compound-71 (Cpd-71), a novel RIPK1 inhibitor, by comparing with Necrostatin-1 (Nec-1), a classic RIPK1 inhibitor, which has several drawbacks like the narrow structure–activity relationship (SAR) profile, moderate potency and non-ideal pharmacokinetic properties, in vivo and in vitro. Our results showed that pretreatment of Cpd-71 attenuated cisplatin-induced renal injury, restored renal function and suppressed renal inflammation, oxidative stress and cell necroptosis. In addition, Cpd-71 inhibited renal damage while reducing the up-regulated serum creatinine (Cr) and blood urea nitrogen (BUN) levels in established AKI mice model. Consistently, we confirmed that Cpd-71 exhibited more effectively suppressive effect on cisplatin-induced renal tubular cell necroptosis than Nec-1, by physically binding to the allosteric type III ligand binding site of RIPK1, thereby reduced RIPK1 kinase activity, RIPK1/RIPK3 complex formation and phosphor-MLKL membrane translocation by molecular docking, Western blot, co-immunoprecipitation and cellular thermal shift assay (CETSA). Taken together, we currently showed that targeting RIPK1 with Cpd-71 may serve as a promising clinical candidate for AKI treatment.
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36
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Lundgren S. Focusing on Relevance: CETSA-Guided Medicinal Chemistry and Lead Generation. ACS Med Chem Lett 2019; 10:690-693. [PMID: 31097981 DOI: 10.1021/acsmedchemlett.9b00112] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Confirmation of target engagement in relevant physiological environment ensures successful drug discovery and the right project prioritization. The Cellular Thermal Shift Assay (CETSA) offers a robust label-free method for studying protein-compound interactions in a cellular environment. This Viewpoint covers the broad applicability of CETSA in lead generation. The method can be used for deconvolution studies, target validation, screening of compound libraries, and hit confirmation. Moreover, the method is well suited for generation of relevant structure-activity relationship (SAR) data, enabling optimal compound design.
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37
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Affiliation(s)
- Oliver Plettenburg
- Institute of Medicinal ChemistryHelmholtz Zentrum München Ingolstädter Landstr. 1 D-85764 Neuherberg Germany
- Institute of Organic Chemistry and Centre of Biomolecular Drug Research (BMWZ)Leibniz Universität Hannover Schneiderberg 1b D-30167 Hannover Germany
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38
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Aziz N, Son YJ, Cho JY. Thymoquinone Suppresses IRF-3-Mediated Expression of Type I Interferons via Suppression of TBK1. Int J Mol Sci 2018; 19:E1355. [PMID: 29751576 PMCID: PMC5983753 DOI: 10.3390/ijms19051355] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 04/30/2018] [Accepted: 05/02/2018] [Indexed: 12/13/2022] Open
Abstract
Interferon regulatory factor (IRF)-3 is known to have a critical role in viral and bacterial innate immune responses by regulating the production of type I interferon (IFN). Thymoquinone (TQ) is a compound derived from black cumin (Nigella sativa L.) and is known to regulate immune responses by affecting transcription factors associated with inflammation, including nuclear factor-κB (NF-κB) and activator protein-1 (AP-1). However, the role of TQ in the IRF-3 signaling pathway has not been elucidated. In this study, we explored the molecular mechanism of TQ-dependent regulation of enzymes in IRF-3 signaling pathways using the lipopolysaccharide (LPS)-stimulated murine macrophage-like RAW264.7 cell line. TQ decreased mRNA expression of the interferon genes IFN-α and IFN-β in these cells. This inhibition was due to its suppression of the transcriptional activation of IRF-3, as shown by inhibition of IRF-3 PRD (III-I) luciferase activity as well as the phosphorylation pattern of IRF-3 in the immunoblotting experiment. Moreover, TQ targeted the autophosphorylation of TANK-binding kinase 1 (TBK1), an upstream key enzyme responsible for IRF-3 activation. Taken together, these findings suggest that TQ can downregulate IRF-3 activation via inhibition of TBK1, which would subsequently decrease the production of type I IFN. TQ also regulated IRF-3, one of the inflammatory transcription factors, providing a novel insight into its anti-inflammatory activities.
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Affiliation(s)
- Nur Aziz
- Department of Integrative Biotechnology and Biomedical Institute for Convergence (BICS), Sungkyunkwan University, Suwon 16419, Korea.
| | - Young-Jin Son
- Department of Pharmacy, Sunchon National University, Suncheon 57922, Korea.
| | - Jae Youl Cho
- Department of Integrative Biotechnology and Biomedical Institute for Convergence (BICS), Sungkyunkwan University, Suwon 16419, Korea.
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39
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Comess KM, McLoughlin SM, Oyer JA, Richardson PL, Stöckmann H, Vasudevan A, Warder SE. Emerging Approaches for the Identification of Protein Targets of Small Molecules - A Practitioners’ Perspective. J Med Chem 2018; 61:8504-8535. [DOI: 10.1021/acs.jmedchem.7b01921] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Kenneth M. Comess
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Shaun M. McLoughlin
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Jon A. Oyer
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Paul L. Richardson
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Henning Stöckmann
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Anil Vasudevan
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Scott E. Warder
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
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40
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Yoshikawa M, Saitoh M, Katoh T, Seki T, Bigi SV, Shimizu Y, Ishii T, Okai T, Kuno M, Hattori H, Watanabe E, Saikatendu KS, Zou H, Nakakariya M, Tatamiya T, Nakada Y, Yogo T. Discovery of 7-Oxo-2,4,5,7-tetrahydro-6 H-pyrazolo[3,4- c]pyridine Derivatives as Potent, Orally Available, and Brain-Penetrating Receptor Interacting Protein 1 (RIP1) Kinase Inhibitors: Analysis of Structure-Kinetic Relationships. J Med Chem 2018; 61:2384-2409. [PMID: 29485864 DOI: 10.1021/acs.jmedchem.7b01647] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We report the discovery of 7-oxo-2,4,5,7-tetrahydro-6 H-pyrazolo[3,4- c]pyridine derivatives as a novel class of receptor interacting protein 1 (RIP1) kinase inhibitors. On the basis of the overlay study between HTS hit 10 and GSK2982772 (6) in RIP1 kinase, we designed and synthesized a novel class of RIP1 kinase inhibitor 11 possessing moderate RIP1 kinase inhibitory activity and P-gp mediated efflux. The optimization of the core structure and the exploration of appropriate substituents utilizing SBDD approach led to the discovery of 22, a highly potent, orally available, and brain-penetrating RIP1 kinase inhibitor with excellent PK profiles. Compound 22 significantly suppressed necroptotic cell death both in mouse and human cells. Oral administration of 22 (10 mg/kg, bid) attenuated disease progression in the mouse experimental autoimmune encephalomyelitis (EAE) model of multiple sclerosis (MS). Moreover, analysis of structure-kinetic relationship (SKR) for our novel chemical series was also discussed.
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Affiliation(s)
- Masato Yoshikawa
- Research , Takeda Pharmaceutical Company Limited , 26-1 Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Morihisa Saitoh
- Research , Takeda Pharmaceutical Company Limited , 26-1 Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Taisuke Katoh
- Research , Takeda Pharmaceutical Company Limited , 26-1 Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Tomohiro Seki
- Research , Takeda Pharmaceutical Company Limited , 26-1 Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Simone V Bigi
- Takeda Pharmaceuticals , 10410 Science Center Drive , San Diego , California 92121 , United States
| | - Yuji Shimizu
- Research , Takeda Pharmaceutical Company Limited , 26-1 Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Tsuyoshi Ishii
- Research , Takeda Pharmaceutical Company Limited , 26-1 Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Takuro Okai
- Research , Takeda Pharmaceutical Company Limited , 26-1 Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Masako Kuno
- Research , Takeda Pharmaceutical Company Limited , 26-1 Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Harumi Hattori
- Research , Takeda Pharmaceutical Company Limited , 26-1 Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Etsuro Watanabe
- Research , Takeda Pharmaceutical Company Limited , 26-1 Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Kumar S Saikatendu
- Takeda Pharmaceuticals , 10410 Science Center Drive , San Diego , California 92121 , United States
| | - Hua Zou
- Takeda Pharmaceuticals , 10410 Science Center Drive , San Diego , California 92121 , United States
| | - Masanori Nakakariya
- Research , Takeda Pharmaceutical Company Limited , 26-1 Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Takayuki Tatamiya
- Research , Takeda Pharmaceutical Company Limited , 26-1 Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Yoshihisa Nakada
- Research , Takeda Pharmaceutical Company Limited , 26-1 Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
| | - Takatoshi Yogo
- Research , Takeda Pharmaceutical Company Limited , 26-1 Muraoka-Higashi 2-chome , Fujisawa , Kanagawa 251-8555 , Japan
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