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Li M, Bei ZC, Yuan Y, Wang B, Zhang D, Xu L, Zhao L, Xu Q, Song Y. In-cell bioluminescence resonance energy transfer (BRET)-based assay uncovers ceritinib and CA-074 as SARS-CoV-2 papain-like protease inhibitors. J Enzyme Inhib Med Chem 2024; 39:2387417. [PMID: 39163165 PMCID: PMC11338211 DOI: 10.1080/14756366.2024.2387417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2024] Open
Abstract
Papain-like protease (PLpro) is an attractive anti-coronavirus target. The development of PLpro inhibitors, however, is hampered by the limitations of the existing PLpro assay and the scarcity of validated active compounds. We developed a novel in-cell PLpro assay based on BRET and used it to evaluate and discover SARS-CoV-2 PLpro inhibitors. The developed assay demonstrated remarkable sensitivity for detecting the reduction of intracellular PLpro activity while presenting high reliability and performance for inhibitor evaluation and high-throughput screening. Using this assay, three protease inhibitors were identified as novel PLpro inhibitors that are structurally disparate from those previously known. Subsequent enzymatic assays and ligand-protein interaction analysis based on molecular docking revealed that ceritinib directly inhibited PLpro, showing high geometric complementarity with the substrate-binding pocket in PLpro, whereas CA-074 methyl ester underwent intracellular hydrolysis, exposing a free carboxyhydroxyl group essential for hydrogen bonding with G266 in the BL2 groove, resulting in PLpro inhibition.
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Affiliation(s)
- Mei Li
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing, China
| | - Zhu-Chun Bei
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing, China
| | - Yongtian Yuan
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing, China
| | - Baogang Wang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing, China
| | - Dongna Zhang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing, China
| | - Likun Xu
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing, China
| | - Liangliang Zhao
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing, China
| | - Qin Xu
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yabin Song
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing, China
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2
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Espinosa-Bustos C, Bertrand J, Villegas-Menares A, Guerrero S, Di Marcotullio L, Navacci S, Schulte G, Kozielewicz P, Bloch N, Villela V, Paulino M, Kogan MJ, Cantero J, Salas CO. New Smoothened ligands based on the purine scaffold as potential agents for treating pancreatic cancer. Bioorg Chem 2024; 151:107681. [PMID: 39106711 DOI: 10.1016/j.bioorg.2024.107681] [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: 03/28/2024] [Revised: 06/27/2024] [Accepted: 07/27/2024] [Indexed: 08/09/2024]
Abstract
Aberrant activation of the Hedgehog (Hh) signalling pathway has been associated with the development and progression of pancreatic cancer. For this reason, blockade of Hh pathway by inhibitors targeting the G protein-coupled receptor Smoothened (SMO) has been considered as a therapeutic target for the treatment of this cancer. In our previous work, we obtained a new SMO ligand based on a purine scaffold (compound I), which showed interesting antitumor activity in several cancer cell lines. In this work, we report the design and synthesis of 17 new purine derivatives, some of which showed high cytotoxic effect on Mia-PaCa-2 (Hh-dependent pancreatic cancer cell lines) and low toxicity on non-neoplastic HEK-293 cells compared with gemcitabine, such as 8f, 8g and 8h (IC50 = 4.56, 4.11 and 3.08 μM, respectively). Two of these purines also showed their ability to bind to SMO through NanoBRET assays (pKi = 5.17 for 8f and 5.01 for 8h), with higher affinities to compound I (pKi = 1.51). In addition, docking studies provided insight the purine substitution pattern is related to the affinity on SMO. Finally, studies of Hh inhibition for selected purines, using a transcriptional functional assay based on luciferase activity in NIH3T3 Shh-Light II cells, demonstrated that 8g reduced GLI activity with a IC50 = 6.4 μM as well as diminished the expression of Hh target genes in two specific Hh-dependent cell models, Med1 cells and Ptch1-/- mouse embryonic fibroblasts. Therefore, our results provide a platform for the design of SMO ligands that could be potential selective cytotoxic agents for the treatment of pancreatic cancer.
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Affiliation(s)
- Christian Espinosa-Bustos
- Departamento de Farmacia, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, 702843 Santiago, Chile
| | - Jeanluc Bertrand
- Departamento de Química Orgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, 702843 Santiago, Chile
| | - Alondra Villegas-Menares
- Departamento de Química Orgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, 702843 Santiago, Chile
| | - Simón Guerrero
- Facultad de Medicina, Universidad de Atacama, 153601 Copiapó, Chile
| | - Lucia Di Marcotullio
- Department of Molecular Medicine, Faculty Pharmacy and Medicine, Sapienza University, 00161 Rome, Italy; Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University, 00161 Rome, Italy
| | - Shirin Navacci
- Department of Molecular Medicine, Faculty Pharmacy and Medicine, Sapienza University, 00161 Rome, Italy
| | - Gunnar Schulte
- Department of Physiology and Pharmacology, Karolinska Institute, 17165 Solna, Stockholm, Sweden
| | - Pawel Kozielewicz
- Department of Physiology and Pharmacology, Karolinska Institute, 17165 Solna, Stockholm, Sweden
| | - Nicolas Bloch
- Departamento de Química Orgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, 702843 Santiago, Chile
| | - Valentina Villela
- Departamento de Química Orgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, 702843 Santiago, Chile
| | - Margot Paulino
- Departamento DETEMA, Facultad de Química, Universidad de la República, 11800 Montevideo, Uruguay
| | - Marcelo J Kogan
- Departamento de Química Farmacológica y Toxicológica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, 8380492 Santiago, Chile; Advanced Center of Chronic Diseases (ACCDiS), Universidad de Chile, 8380492 Santiago, Chile
| | - Jorge Cantero
- Departamento DETEMA, Facultad de Química, Universidad de la República, 11800 Montevideo, Uruguay
| | - Cristian O Salas
- Departamento de Química Orgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, 702843 Santiago, Chile.
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3
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Hoang HTM, George K, Ahmad M. Application of bioluminescence resonance energy transfer assays in primary mouse neuronal cultures. STAR Protoc 2024; 5:103228. [PMID: 39068655 PMCID: PMC11339249 DOI: 10.1016/j.xpro.2024.103228] [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: 04/25/2024] [Revised: 05/28/2024] [Accepted: 07/08/2024] [Indexed: 07/30/2024] Open
Abstract
Bioluminescence resonance energy transfer (BRET) is widely employed for real-time monitoring of G protein-coupled receptor activity, interactions, and trafficking in heterologous cell lines, yet its use in neuronal systems remains limited. Here, we present a protocol to apply BRET assays to primary neuronal cultures from mouse embryos. We describe steps and key concepts for generating plasmid constructs and lentivirus preparations, plating and lentiviral transduction of primary cultured neurons in 96-well plates, and BRET data collection and analysis. For complete details on the use and execution of this protocol, please refer to George et al.1.
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Affiliation(s)
- Hanh T M Hoang
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Kiran George
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Mohiuddin Ahmad
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.
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4
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Vickery HR, Virta JM, Konstantinidou M, Arkin MR. Development of a NanoBRET assay for evaluation of 14-3-3σ molecular glues. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100165. [PMID: 38797286 DOI: 10.1016/j.slasd.2024.100165] [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: 12/30/2023] [Revised: 05/08/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024]
Abstract
We report the development of a 384-well formatted NanoBRET assay to characterize molecular glues of 14-3-3/client interactions in living cells. The seven isoforms of 14-3-3 are dimeric hub proteins with diverse roles including transcription factor regulation and signal transduction. 14-3-3 interacts with hundreds of client proteins to regulate their function and is therefore an ideal therapeutic target when client selectivity can be achieved. We have developed the NanoBRET system for three 14-3-3σ client proteins CRAF, TAZ, and estrogen receptor α (ERα), which represent three specific binding modes. We have measured stabilization of 14-3-3σ/client complexes by molecular glues with EC50 values between 100 nM and 1 μM in cells, which align with the EC50 values calculated by fluorescence anisotropy in vitro. Developing this NanoBRET system for the hub protein 14-3-3σ allows for a streamlined approach, bypassing multiple optimization steps in the assay development process for other 14-3-3σ clients. The NanoBRET system allows for an assessment of PPI stabilization in a more physiologically relevant, cell-based environment using full-length proteins. The method is applicable to diverse protein-protein interactions (PPIs) and offers a robust platform to explore libraries of compounds for both PPI stabilizers and inhibitors.
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Affiliation(s)
- Holly R Vickery
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco 94158, USA
| | - Johanna M Virta
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco 94158, USA
| | - Markella Konstantinidou
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco 94158, USA
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco 94158, USA.
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5
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Sultana A, Geethakumari AM, Islam Z, Kolatkar PR, Biswas KH. BRET-based biosensors for SARS-CoV-2 oligonucleotide detection. Front Bioeng Biotechnol 2024; 12:1353479. [PMID: 38887615 PMCID: PMC11181354 DOI: 10.3389/fbioe.2024.1353479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 05/09/2024] [Indexed: 06/20/2024] Open
Abstract
The need for the early detection of emerging pathogenic viruses and their newer variants has driven the urgent demand for developing point-of-care diagnostic tools. Although nucleic acid-based methods such as reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and loop-mediated isothermal amplification (LAMP) have been developed, a more facile and robust platform is still required. To address this need, as a proof-of-principle study, we engineered a prototype-the versatile, sensitive, rapid, and cost-effective bioluminescence resonance energy transfer (BRET)-based biosensor for oligonucleotide detection (BioOD). Specifically, we designed BioODs against the SARS-CoV-2 parental (Wuhan strain) and B.1.617.2 Delta variant through the conjugation of specific, fluorescently modified molecular beacons (sensor module) through a complementary oligonucleotide handle DNA functionalized with the NanoLuc (NLuc) luciferase protein such that the dissolution of the molecular beacon loop upon the binding of the viral oligonucleotide will result in a decrease in BRET efficiency and, thus, a change in the bioluminescence spectra. Following the assembly of the BioODs, we determined their kinetics response, affinity for variant-specific oligonucleotides, and specificity, and found them to be rapid and highly specific. Furthermore, the decrease in BRET efficiency of the BioODs in the presence of viral oligonucleotides can be detected as a change in color in cell phone camera images. We envisage that the BioODs developed here will find application in detecting viral infections with variant specificity in a point-of-care-testing format, thus aiding in large-scale viral infection surveillance.
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Affiliation(s)
- Asfia Sultana
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Anupriya M. Geethakumari
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Zeyaul Islam
- Diabetes Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Prasanna R. Kolatkar
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
- Diabetes Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Kabir H. Biswas
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
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6
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Ahmed WS, Geethakumari AM, Sultana A, Fatima A, Philip AM, Uddin SMN, Biswas KH. A slow but steady nanoLuc: R162A mutation results in a decreased, but stable, nanoLuc activity. Int J Biol Macromol 2024; 269:131864. [PMID: 38692549 DOI: 10.1016/j.ijbiomac.2024.131864] [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: 11/04/2023] [Revised: 04/21/2024] [Accepted: 04/23/2024] [Indexed: 05/03/2024]
Abstract
NanoLuc (NLuc) luciferase has found extensive application in designing a range of biological assays, including gene expression analysis, protein-protein interaction, and protein conformational changes due to its enhanced brightness and small size. However, questions related to its mechanism of interaction with the substrate, furimazine, as well as bioluminescence activity remain elusive. Here, we combined molecular dynamics (MD) simulation and mutational analysis to show that the R162A mutation results in a decreased but stable bioluminescence activity of NLuc in living cells and in vitro. Specifically, we performed multiple, all-atom, explicit solvent MD simulations of the apo and furimazine-docked (holo) NLuc structures revealing differential dynamics of the protein in the absence and presence of the ligand. Further, analysis of trajectories for hydrogen bonds (H-bonds) formed between NLuc and furimazine revealed substantial H-bond interaction between R162 and Q32 residues. Mutation of the two residues in NLuc revealed a decreased but stable activity of the R162A, but not Q32A, mutant NLuc in live cell and in vitro assays performed using lysates prepared from cells expressing the proteins and with the furimazine substrate. In addition to highlighting the role of the R162 residue in NLuc activity, we believe that the mutant NLuc will find wide application in designing in vitro assays requiring extended monitoring of NLuc bioluminescence activity. SIGNIFICANCE: Bioluminescence has been extensively utilized in developing a variety of biological and biomedical assays. In this regard, engineering of brighter bioluminescent proteins, i.e. luciferases, has played a significant role. This is acutely exemplified by the engineering of the NLuc luciferase, which is small in size and displays much enhanced bioluminescence and thermal stability compared to previously available luciferases. While enhanced bioluminescent activity is desirable in a multitude of biological and biomedical assays, it would also be useful to develop variants of the protein that display a prolonged bioluminescence activity. This is specifically relevant in designing assays that require bioluminescence for extended periods, such as in the case of biosensors designed for monitoring slow enzymatic or cellular signaling reactions, without necessitating multiple rounds of luciferase substrate addition or any specialized reagents that result in increased assay costs. In the current manuscript, we report a mutant NLuc that possesses a stable and prolonged bioluminescence activity, albeit lower than the wild-type NLuc, and envisage a wider application of the mutant NLuc in designing biosensors for monitoring slower biological and biomedical events.
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Affiliation(s)
- Wesam S Ahmed
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
| | - Anupriya M Geethakumari
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
| | - Asfia Sultana
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
| | - Asma Fatima
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
| | - Angelin M Philip
- Division of Genomics and Translational Biomedicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
| | - S M Nasir Uddin
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
| | - Kabir H Biswas
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar.
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7
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Balıkçı E, Marques ASMC, Bauer LG, Seupel R, Bennett J, Raux B, Buchan K, Simelis K, Singh U, Rogers C, Ward J, Cheng C, Szommer T, Schützenhofer K, Elkins JM, Sloman DL, Ahel I, Fedorov O, Brennan PE, Huber KVM. Unexpected Noncovalent Off-Target Activity of Clinical BTK Inhibitors Leads to Discovery of a Dual NUDT5/14 Antagonist. J Med Chem 2024; 67:7245-7259. [PMID: 38635563 PMCID: PMC11089510 DOI: 10.1021/acs.jmedchem.4c00072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/20/2024]
Abstract
Cofactor mimicry represents an attractive strategy for the development of enzyme inhibitors but can lead to off-target effects due to the evolutionary conservation of binding sites across the proteome. Here, we uncover the ADP-ribose (ADPr) hydrolase NUDT5 as an unexpected, noncovalent, off-target of clinical BTK inhibitors. Using a combination of biochemical, biophysical, and intact cell NanoBRET assays as well as X-ray crystallography, we confirm catalytic inhibition and cellular target engagement of NUDT5 and reveal an unusual binding mode that is independent of the reactive acrylamide warhead. Further investigation of the prototypical BTK inhibitor ibrutinib also revealed potent inhibition of the largely unstudied NUDIX hydrolase family member NUDT14. By exploring structure-activity relationships (SARs) around the core scaffold, we identify a potent, noncovalent, and cell-active dual NUDT5/14 inhibitor. Cocrystallization experiments yielded new insights into the NUDT14 hydrolase active site architecture and inhibitor binding, thus providing a basis for future chemical probe design.
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Affiliation(s)
- Esra Balıkçı
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Anne-Sophie M. C. Marques
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Ludwig G. Bauer
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Raina Seupel
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - James Bennett
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Brigitt Raux
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Karly Buchan
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Klemensas Simelis
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Usha Singh
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Catherine Rogers
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Jennifer Ward
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Carol Cheng
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Tamas Szommer
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Kira Schützenhofer
- Sir
William Dunn School of Pathology, University
of Oxford, South Parks
Road, Oxford OX1 3RE, U.K.
| | - Jonathan M. Elkins
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - David L. Sloman
- Departments
of Discovery Chemistry, Merck & Co.
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Ivan Ahel
- Sir
William Dunn School of Pathology, University
of Oxford, South Parks
Road, Oxford OX1 3RE, U.K.
| | - Oleg Fedorov
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Paul E. Brennan
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Alzheimer’s
Research UK Oxford Drug Discovery Institute, Nuffield Department of
Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Kilian V. M. Huber
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
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8
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Garbagnoli M, Linciano P, Listro R, Rossino G, Vasile F, Collina S. Biophysical Assays for Investigating Modulators of Macromolecular Complexes: An Overview. ACS OMEGA 2024; 9:17691-17705. [PMID: 38680367 PMCID: PMC11044174 DOI: 10.1021/acsomega.4c01309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/26/2024] [Accepted: 03/29/2024] [Indexed: 05/01/2024]
Abstract
Drug discovery is a lengthy and intricate process, and in its early stage, crucial steps are the selection of the therapeutic target and the identification of novel ligands. Most targets are dysregulated in pathogenic cells; typically, their activation or deactivation leads to the desired effect, while in other cases, interfering with the target-natural binder complex achieves the therapeutic results. Biophysical assays are a suitable strategy for finding new ligands or interferent agents, being able to evaluate ligand-protein interactions and assessing the effect of small molecules (SMols) on macromolecular complexes. This mini-review provides a detailed analysis of widely used biophysical methods, including fluorescence-based approaches, circular dichroism, isothermal titration calorimetry, microscale thermophoresis, and NMR spectroscopy. After a brief description of the methodologies, examples of interaction and competition experiments are described, together with an analysis of the advantages and disadvantages of each technique. This mini-review provides an overview of the most relevant biophysical technologies that can help in identifying SMols able not only to bind proteins but also to interfere with macromolecular complexes.
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Affiliation(s)
- Martina Garbagnoli
- Department
of Drug Sciences, University of Pavia, viale Taramelli 12, Pavia 27100, Italy
| | - Pasquale Linciano
- Department
of Drug Sciences, University of Pavia, viale Taramelli 12, Pavia 27100, Italy
| | - Roberta Listro
- Department
of Drug Sciences, University of Pavia, viale Taramelli 12, Pavia 27100, Italy
| | - Giacomo Rossino
- Department
of Drug Sciences, University of Pavia, viale Taramelli 12, Pavia 27100, Italy
| | - Francesca Vasile
- Department
of Chemistry, University of Milan, Via Golgi 19, Milano 20133, Italy
| | - Simona Collina
- Department
of Drug Sciences, University of Pavia, viale Taramelli 12, Pavia 27100, Italy
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9
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Dolberg TB, Gunnels TF, Ling T, Sarnese KA, Crispino JD, Leonard JN. Building Synthetic Biosensors Using Red Blood Cell Proteins. ACS Synth Biol 2024; 13:1273-1289. [PMID: 38536408 DOI: 10.1021/acssynbio.3c00754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
As the use of engineered cell therapies expands from pioneering efforts in cancer immunotherapy to other applications, an attractive but less explored approach is the use of engineered red blood cells (RBCs). Compared to other cells, RBCs have a very long circulation time and reside in the blood compartment, so they could be ideally suited for applications as sentinel cells that enable in situ sensing and diagnostics. However, we largely lack tools for converting RBCs into biosensors. A unique challenge is that RBCs remodel their membranes during maturation, shedding many membrane components, suggesting that an RBC-specific approach may be needed. Toward addressing this need, here we develop a biosensing architecture built on RBC membrane proteins that are retained through erythropoiesis. This biosensor employs a mechanism in which extracellular ligand binding is transduced into intracellular reconstitution of a split output protein (including either a fluorophore or an enzyme). By comparatively evaluating a range of biosensor architectures, linker types, scaffold choices, and output signals, we identify biosensor designs and design features that confer substantial ligand-induced signal in vitro. Finally, we demonstrate that erythroid precursor cells engineered with our RBC-protein biosensors function in vivo. This study establishes a foundation for developing RBC-based biosensors that could ultimately address unmet needs including noninvasive monitoring of physiological signals for a range of diagnostic applications.
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Affiliation(s)
- Taylor B Dolberg
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Taylor F Gunnels
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Te Ling
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, United States
| | - Kelly A Sarnese
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - John D Crispino
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, United States
| | - Joshua N Leonard
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Interdisciplinary Biological Sciences Training Program, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Member, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, Illinois 60208, United States
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10
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Mattson NM, Chan AKN, Miyashita K, Mukhaleva E, Chang WH, Yang L, Ma N, Wang Y, Pokharel SP, Li M, Liu Q, Xu X, Chen R, Singh P, Zhang L, Elsayed Z, Chen B, Keen D, Pirrotte P, Rosen ST, Chen J, LaBarge MA, Shively JE, Vaidehi N, Rockne RC, Feng M, Chen CW. A novel class of inhibitors that disrupts the stability of integrin heterodimers identified by CRISPR-tiling-instructed genetic screens. Nat Struct Mol Biol 2024; 31:465-475. [PMID: 38316881 PMCID: PMC10948361 DOI: 10.1038/s41594-024-01211-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 01/02/2024] [Indexed: 02/07/2024]
Abstract
The plasma membrane is enriched for receptors and signaling proteins that are accessible from the extracellular space for pharmacological intervention. Here we conducted a series of CRISPR screens using human cell surface proteome and integrin family libraries in multiple cancer models. Our results identified ITGAV (integrin αV) and its heterodimer partner ITGB5 (integrin β5) as the essential integrin α/β pair for cancer cell expansion. High-density CRISPR gene tiling further pinpointed the integral pocket within the β-propeller domain of ITGAV for integrin αVβ5 dimerization. Combined with in silico compound docking, we developed a CRISPR-Tiling-Instructed Computer-Aided (CRISPR-TICA) pipeline for drug discovery and identified Cpd_AV2 as a lead inhibitor targeting the β-propeller central pocket of ITGAV. Cpd_AV2 treatment led to rapid uncoupling of integrin αVβ5 and cellular apoptosis, providing a unique class of therapeutic action that eliminates the integrin signaling via heterodimer dissociation. We also foresee the CRISPR-TICA approach to be an accessible method for future drug discovery studies.
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Affiliation(s)
- Nicole M Mattson
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Anthony K N Chan
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
- Division of Epigenetic and Transcriptional Engineering, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Kazuya Miyashita
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Elizaveta Mukhaleva
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Wen-Han Chang
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Lu Yang
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
- Division of Epigenetic and Transcriptional Engineering, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Ning Ma
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Yingyu Wang
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Sheela Pangeni Pokharel
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
- Division of Epigenetic and Transcriptional Engineering, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Mingli Li
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Qiao Liu
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Xiaobao Xu
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Renee Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Priyanka Singh
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Leisi Zhang
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Zeinab Elsayed
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Bryan Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Denise Keen
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Patrick Pirrotte
- Integrated Mass Spectrometry Shared Resource, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Steven T Rosen
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Mark A LaBarge
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - John E Shively
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Department of Immunology and Theranostics, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Russell C Rockne
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Mingye Feng
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Chun-Wei Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA.
- Division of Epigenetic and Transcriptional Engineering, Beckman Research Institute, City of Hope, Duarte, CA, USA.
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA.
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11
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Holdgate GA, Bardelle C, Berry SK, Lanne A, Cuomo ME. Screening for molecular glues - Challenges and opportunities. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100136. [PMID: 38104659 DOI: 10.1016/j.slasd.2023.12.008] [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: 09/01/2023] [Revised: 11/03/2023] [Accepted: 12/14/2023] [Indexed: 12/19/2023]
Abstract
Molecular glues are small molecules, typically smaller than PROTACs, and usually with improved physicochemical properties that aim to stabilise the interaction between two proteins. Most often this approach is used to improve or induce an interaction between the target and an E3 ligase, but other interactions which stabilise interactions to increase activity or to inhibit binding to a natural effector have also been demonstrated. This review will describe the effects of induced proximity, discuss current methods used to identify molecular glues and introduce approaches that could be adapted for molecular glue screening.
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Affiliation(s)
| | - Catherine Bardelle
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Sophia K Berry
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Alice Lanne
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
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12
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Rad-Faraji M, Mousazadeh M, Nikkhah M, Rezaei A, Moradi S, Hosseinkhani S. A comparative study of structural and catalytic activity alterations in firefly luciferase induced by carbon quantum dots containing amine and carboxyl functional groups. Int J Biol Macromol 2024; 260:129503. [PMID: 38244744 DOI: 10.1016/j.ijbiomac.2024.129503] [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: 10/25/2023] [Revised: 01/02/2024] [Accepted: 01/12/2024] [Indexed: 01/22/2024]
Abstract
Despite of growing interest in use of carbon-based nanomaterials as carriers of functional proteins, less attention has been paid to the effects of these nanomaterials on the structure and function of the proteins. In this study, with the aim of shedding light on the mechanisms of interaction between carbon-based nanomaterials and proteins, the interactions of carbon quantum dots (CQDs) containing amine (CQD-NH2) or carboxyl groups (CQD-COOH) with Photinus pyralis firefly luciferase enzyme were investigated by experimental and computational approaches. The structural changes and reduction in activity of the luciferase upon treatment with CQDs were experimentally proved. CQD-NH2 induced more reduction in enzyme activity (15 %) compared to CQD-COOH (7.4 %). The interactions CQD-NH2 with luciferase led to higher affinity of the enzyme for its substrate. It was found by molecular dynamic simulations that CQD-NH2 binds to multiple regions on the surface of luciferase. Secondary structure analysis showed that CQD-NH2 had more profound effects on the active site amino acids, the adjacent amino acids to the active site and the residues involved in ATP binding site. In addition, CQD-NH2 interactions with luciferase were suggested to be stronger than CQD-COOH based on the number of hydrogen bonds and the binding energies.
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Affiliation(s)
- Mehrnaz Rad-Faraji
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, P. O. Box: 14115-154, Tehran, Iran
| | - Marziyeh Mousazadeh
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, P. O. Box: 14115-154, Tehran, Iran
| | - Maryam Nikkhah
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, P. O. Box: 14115-154, Tehran, Iran.
| | - Aram Rezaei
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Sajad Moradi
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Saman Hosseinkhani
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, P. O. Box: 14115-154, Tehran, Iran
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13
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Gomez SM, Axtman AD, Willson TM, Major MB, Townsend RR, Sorger PK, Johnson GL. Illuminating function of the understudied druggable kinome. Drug Discov Today 2024; 29:103881. [PMID: 38218213 PMCID: PMC11262466 DOI: 10.1016/j.drudis.2024.103881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 12/21/2023] [Accepted: 01/09/2024] [Indexed: 01/15/2024]
Abstract
The human kinome, with more than 500 proteins, is crucial for cell signaling and disease. Yet, about one-third of kinases lack in-depth study. The Data and Resource Generating Center for Understudied Kinases has developed multiple resources to address this challenge including creation of a heavy amino acid peptide library for parallel reaction monitoring and quantitation of protein kinase expression, use of understudied kinases tagged with a miniTurbo-biotin ligase to determine interaction networks by proximity-dependent protein biotinylation, NanoBRET probe development for screening chemical tool target specificity in live cells, characterization of small molecule chemical tools inhibiting understudied kinases, and computational tools for defining kinome architecture. These resources are available through the Dark Kinase Knowledgebase, supporting further research into these understudied protein kinases.
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Affiliation(s)
- Shawn M Gomez
- University of North Carolina School of Medicine, Chapel Hill, NC, USA.
| | - Alison D Axtman
- University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Timothy M Willson
- University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Michael B Major
- Washington University School of Medicine in St. Louis, MO, USA
| | - Reid R Townsend
- Washington University School of Medicine in St. Louis, MO, USA
| | | | - Gary L Johnson
- University of North Carolina School of Medicine, Chapel Hill, NC, USA.
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14
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Kinsolving J, Bous J, Kozielewicz P, Košenina S, Shekhani R, Grätz L, Masuyer G, Wang Y, Stenmark P, Dong M, Schulte G. Structural and functional insight into the interaction of Clostridioides difficile toxin B and FZD 7. Cell Rep 2024; 43:113727. [PMID: 38308843 DOI: 10.1016/j.celrep.2024.113727] [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: 09/25/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 02/05/2024] Open
Abstract
The G protein-coupled receptors of the Frizzled (FZD) family, in particular FZD1,2,7, are receptors that are exploited by Clostridioides difficile toxin B (TcdB), the major virulence factor responsible for pathogenesis associated with Clostridioides difficile infection. We employ a live-cell assay examining the affinity between full-length FZDs and TcdB. Moreover, we present cryoelectron microscopy structures of TcdB alone and in complex with full-length FZD7, which reveal that large structural rearrangements of the combined repetitive polypeptide domain are required for interaction with FZDs and other TcdB receptors, constituting a first step for receptor recognition. Furthermore, we show that bezlotoxumab, an FDA-approved monoclonal antibody to treat Clostridioides difficile infection, favors the apo-TcdB structure and thus disrupts binding with FZD7. The dynamic transition between the two conformations of TcdB also governs the stability of the pore-forming region. Thus, our work provides structural and functional insight into how conformational dynamics of TcdB determine receptor binding.
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Affiliation(s)
- Julia Kinsolving
- Karolinska Institutet, Department Physiology & Pharmacology, Sec. Receptor Biology & Signaling, Biomedicum, 17165 Stockholm, Sweden
| | - Julien Bous
- Karolinska Institutet, Department Physiology & Pharmacology, Sec. Receptor Biology & Signaling, Biomedicum, 17165 Stockholm, Sweden
| | - Pawel Kozielewicz
- Karolinska Institutet, Department Physiology & Pharmacology, Sec. Receptor Biology & Signaling, Biomedicum, 17165 Stockholm, Sweden
| | - Sara Košenina
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Rawan Shekhani
- Karolinska Institutet, Department Physiology & Pharmacology, Sec. Receptor Biology & Signaling, Biomedicum, 17165 Stockholm, Sweden
| | - Lukas Grätz
- Karolinska Institutet, Department Physiology & Pharmacology, Sec. Receptor Biology & Signaling, Biomedicum, 17165 Stockholm, Sweden
| | - Geoffrey Masuyer
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Yuankai Wang
- Department of Urology, Boston Children's Hospital, Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Min Dong
- Department of Urology, Boston Children's Hospital, Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Gunnar Schulte
- Karolinska Institutet, Department Physiology & Pharmacology, Sec. Receptor Biology & Signaling, Biomedicum, 17165 Stockholm, Sweden.
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15
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Markovinovic A, Martín-Guerrero SM, Mórotz GM, Salam S, Gomez-Suaga P, Paillusson S, Greig J, Lee Y, Mitchell JC, Noble W, Miller CCJ. Stimulating VAPB-PTPIP51 ER-mitochondria tethering corrects FTD/ALS mutant TDP43 linked Ca 2+ and synaptic defects. Acta Neuropathol Commun 2024; 12:32. [PMID: 38395965 PMCID: PMC10885568 DOI: 10.1186/s40478-024-01742-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) are clinically linked major neurodegenerative diseases. Notably, TAR DNA-binding protein-43 (TDP43) accumulations are hallmark pathologies of FTD/ALS and mutations in the gene encoding TDP43 cause familial FTD/ALS. There are no cures for FTD/ALS. FTD/ALS display damage to a broad range of physiological functions, many of which are regulated by signaling between the endoplasmic reticulum (ER) and mitochondria. This signaling is mediated by the VAPB-PTPIP51 tethering proteins that serve to recruit regions of ER to the mitochondrial surface so as to facilitate inter-organelle communications. Several studies have now shown that disrupted ER-mitochondria signaling including breaking of the VAPB-PTPIP51 tethers are features of FTD/ALS and that for TDP43 and other familial genetic FTD/ALS insults, this involves activation of glycogen kinase-3β (GSK3β). Such findings have prompted suggestions that correcting damage to ER-mitochondria signaling and the VAPB-PTPIP51 interaction may be broadly therapeutic. Here we provide evidence to support this notion. We show that overexpression of VAPB or PTPIP51 to enhance ER-mitochondria signaling corrects mutant TDP43 induced damage to inositol 1,4,5-trisphosphate (IP3) receptor delivery of Ca2+ to mitochondria which is a primary function of the VAPB-PTPIP51 tethers, and to synaptic function. Moreover, we show that ursodeoxycholic acid (UDCA), an FDA approved drug linked to FTD/ALS and other neurodegenerative diseases therapy and whose precise therapeutic target is unclear, corrects TDP43 linked damage to the VAPB-PTPIP51 interaction. We also show that this effect involves inhibition of TDP43 mediated activation of GSK3β. Thus, correcting damage to the VAPB-PTPIP51 tethers may have therapeutic value for FTD/ALS and other age-related neurodegenerative diseases.
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Affiliation(s)
- Andrea Markovinovic
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, SE5 9RX, London, UK.
| | - Sandra M Martín-Guerrero
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, SE5 9RX, London, UK
| | - Gábor M Mórotz
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, SE5 9RX, London, UK
| | - Shaakir Salam
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, SE5 9RX, London, UK
| | - Patricia Gomez-Suaga
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, SE5 9RX, London, UK
| | - Sebastien Paillusson
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, SE5 9RX, London, UK
| | - Jenny Greig
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, SE5 9RX, London, UK
| | - Younbok Lee
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, SE5 9RX, London, UK
| | - Jacqueline C Mitchell
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, SE5 9RX, London, UK
| | - Wendy Noble
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, SE5 9RX, London, UK
| | - Christopher C J Miller
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, SE5 9RX, London, UK.
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16
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Maw JJ, Coker JA, Arya T, Goins CM, Sonawane D, Han SH, Rees MG, Ronan MM, Roth JA, Wang NS, Heemers HV, Macdonald JD, Stauffer SR. Discovery and Characterization of Selective, First-in-Class Inhibitors of Citron Kinase. J Med Chem 2024; 67:2631-2666. [PMID: 38330278 DOI: 10.1021/acs.jmedchem.3c01807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Citron kinase (CITK) is an AGC-family serine/threonine kinase that regulates cytokinesis. Despite knockdown experiments implicating CITK as an anticancer target, no selective CITK inhibitors exist. We transformed a previously reported kinase inhibitor with weak off-target CITK activity into a first-in-class CITK chemical probe, C3TD879. C3TD879 is a Type I kinase inhibitor which potently inhibits CITK catalytic activity (biochemical IC50 = 12 nM), binds directly to full-length human CITK in cells (NanoBRET Kd < 10 nM), and demonstrates favorable DMPK properties for in vivo evaluation. We engineered exquisite selectivity for CITK (>17-fold versus 373 other human kinases), making C3TD879 the first chemical probe suitable for interrogating the complex biology of CITK. Our small-molecule CITK inhibitors could not phenocopy the effects of CITK knockdown in cell proliferation, cell cycle progression, or cytokinesis assays, providing preliminary evidence that the structural roles of CITK may be more important than its kinase activity.
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Affiliation(s)
- Joshua J Maw
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, United States
| | - Jesse A Coker
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, United States
| | - Tarun Arya
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, United States
| | - Christopher M Goins
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, United States
| | - Dhiraj Sonawane
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, United States
| | - Sang Hoon Han
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, United States
| | - Matthew G Rees
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge Massachusetts 02142, United States
| | - Melissa M Ronan
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge Massachusetts 02142, United States
| | - Jennifer A Roth
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge Massachusetts 02142, United States
| | - Nancy S Wang
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, United States
| | - Hannelore V Heemers
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, United States
| | - Jonathan D Macdonald
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, United States
| | - Shaun R Stauffer
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, United States
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17
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Yu J, Zhao K, Zhang Z, Zhang Y, Zhang X, Ren H. Development of a bioluminescence resonance energy transfer Quenchbody sensor for the detection of organophosphorus pesticides in water bodies. WATER RESEARCH 2024; 250:121051. [PMID: 38157605 DOI: 10.1016/j.watres.2023.121051] [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: 08/16/2023] [Revised: 12/01/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
Rapid and precise quantification of organophosphorus pesticides (OPPs) in environmental water bodies is crucial for evaluating ecological risks and safeguarding human health. Traditional instrumental methods are complex, time-consuming, and expensive, while enzyme-based biosensors suffer from instability and require a constant supply of substrates. Hence, there is an urgent need for a fast, simple, and sensitive biosensor for OPPs. In this study, we developed a novel non-enzymatic biosensor for the detection of methyl parathion (MP) by employing the bioluminescence resonance energy transfer (BRET) Q-body strategy. Optimizing the spacer arm and screening fluorescent dyes identified the R6G BRET MP Q-body sensor with the best performance. Key parameters affecting the sensor's detection performance were optimized by using single-factor experiments. Under optimal conditions, the detection exhibited a detection limit of 5.09 ng·mL-1 and a linear range of 16.21-848.81 ng·mL-1. The sensor's accuracy was validated using standard recovery experiments, yielding a recovery rate of 84.47 %-102.08 % with a standard deviation of 1.93 %-9.25 %. The detection results of actual water samples demonstrate that this fast, simple, and highly sensitive BRET Q-body sensor holds great promise for practical water quality monitoring.
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Affiliation(s)
- Jie Yu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Kanglin Zhao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Zhanao Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yan Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China.
| | - Xuxiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
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18
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Zhuang J, Shang Q, Rastinejad F, Wu D. Decoding Allosteric Control in Hypoxia-Inducible Factors. J Mol Biol 2024; 436:168352. [PMID: 37935255 DOI: 10.1016/j.jmb.2023.168352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/10/2023] [Accepted: 11/01/2023] [Indexed: 11/09/2023]
Abstract
The mammalian family of basic helix-loop-helix-PER-ARNT-SIM (bHLH-PAS) transcription factors possess the ability to sense and respond to diverse environmental and physiological cues. These proteins all share a common structural framework, comprising a bHLH domain, two PAS domains, and transcriptional activation or repression domain. To function effectively as transcription factors, members of the family must form dimers, bringing together bHLH segments to create a functional unit that allows for DNA response element binding. The significance of bHLH-PAS family is underscored by their involvement in many major human diseases, offering potential avenues for therapeutic intervention. Notably, the clear identification of ligand-binding cavities within their PAS domains enables the development of targeted small molecules. Two examples are Belzutifan, targeting hypoxia-inducible factor (HIF)-2α, and Tapinarof, targeting the aryl hydrocarbon receptor (AHR), both of which have gained regulatory approval recently. Here, we focus on the HIF subfamily. The crystal structures of all three HIF-α proteins have been elucidated, revealing their bHLH and tandem PAS domains are used to engage their dimerization partner aryl hydrocarbon receptor nuclear translocator (ARNT, also called HIF-1β). A broad range of recent findings point to a shared allosteric modulation mechanism among these proteins, whereby small-molecules at the PAS-B domains exert direct influence over the HIF-α transcriptional functions. As our understanding of the architectural and allosteric mechanisms of bHLH-PAS proteins continues to advance, the possibility of discovering new therapeutic drugs becomes increasingly promising.
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Affiliation(s)
- Jingjing Zhuang
- Marine College, Shandong University, Weihai 264209, China; Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Qinghong Shang
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Fraydoon Rastinejad
- Target Discovery Institute, Nuffield Department of Medicine Research Building, University of Oxford, Old Road Campus, Oxford OX3 7FZ, UK.
| | - Dalei Wu
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
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19
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Nagl M, Mönnich D, Rosier N, Schihada H, Sirbu A, Konar N, Reyes-Resina I, Navarro G, Franco R, Kolb P, Annibale P, Pockes S. Fluorescent Tools for the Imaging of Dopamine D 2 -Like Receptors. Chembiochem 2024; 25:e202300659. [PMID: 37942961 DOI: 10.1002/cbic.202300659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/10/2023]
Abstract
The family of dopamine D2 -like receptors represents an interesting target for a variety of neurological diseases, e. g. Parkinson's disease (PD), addiction, or schizophrenia. In this study we describe the synthesis of a new set of fluorescent ligands as tools for visualization of dopamine D2 -like receptors. Pharmacological characterization in radioligand binding studies identified UR-MN212 (20) as a high-affinity ligand for D2 -like receptors (pKi (D2long R)=8.24, pKi (D3 R)=8.58, pKi (D4 R)=7.78) with decent selectivity towards D1 -like receptors. Compound 20 is a neutral antagonist in a Go1 activation assay at the D2long R, D3 R, and D4 R, which is an important feature for studies using whole cells. The neutral antagonist 20, equipped with a 5-TAMRA dye, displayed rapid association to the D2long R in binding studies using confocal microscopy demonstrating its suitability for fluorescence microscopy. Furthermore, in molecular brightness studies, the ligand's binding affinity could be determined in a single-digit nanomolar range that was in good agreement with radioligand binding data. Therefore, the fluorescent compound can be used for quantitative characterization of native D2 -like receptors in a broad variety of experimental setups.
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Affiliation(s)
- Martin Nagl
- Institute of Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053, Regensburg, Germany
| | - Denise Mönnich
- Institute of Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053, Regensburg, Germany
| | - Niklas Rosier
- Institute of Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053, Regensburg, Germany
| | - Hannes Schihada
- Department of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35037, Marburg, Germany
| | - Alexei Sirbu
- Max Delbrück Center for Molecular Medicine, Berlin, 13125, Germany
| | - Nergis Konar
- Max Delbrück Center for Molecular Medicine, Berlin, 13125, Germany
| | - Irene Reyes-Resina
- CiberNed, Network Center for Neurodegenerative diseases, National Spanish Health Institute Carlos III, Madrid, Spain
- Department Biochemistry and Physiology, School of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Spain
| | - Gemma Navarro
- CiberNed, Network Center for Neurodegenerative diseases, National Spanish Health Institute Carlos III, Madrid, Spain
- Department Biochemistry and Physiology, School of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Spain
| | - Rafael Franco
- CiberNed, Network Center for Neurodegenerative diseases, National Spanish Health Institute Carlos III, Madrid, Spain
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain
| | - Peter Kolb
- Department of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35037, Marburg, Germany
| | - Paolo Annibale
- Max Delbrück Center for Molecular Medicine, Berlin, 13125, Germany
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, Scotland
| | - Steffen Pockes
- Institute of Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053, Regensburg, Germany
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN, 55414, USA
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20
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Rosier N, Mönnich D, Nagl M, Schihada H, Sirbu A, Konar N, Reyes-Resina I, Navarro G, Franco R, Kolb P, Annibale P, Pockes S. Shedding Light on the D 1 -Like Receptors: A Fluorescence-Based Toolbox for Visualization of the D 1 and D 5 Receptors. Chembiochem 2024; 25:e202300658. [PMID: 37983731 DOI: 10.1002/cbic.202300658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/08/2023] [Indexed: 11/22/2023]
Abstract
Dopamine D1 -like receptors are the most abundant type of dopamine receptors in the central nervous system and, even after decades of discovery, still highly interesting for the study of neurological diseases. We herein describe the synthesis of a new set of fluorescent ligands, structurally derived from D1 R antagonist SCH-23390 and labeled with two different fluorescent dyes, as tool compounds for the visualization of D1 -like receptors. Pharmacological characterization in radioligand binding studies identified UR-NR435 (25) as a high-affinity ligand for D1 -like receptors (pKi (D1 R)=8.34, pKi (D5 R)=7.62) with excellent selectivity towards D2 -like receptors. Compound 25 proved to be a neutral antagonist at the D1 R and D5 R in a Gs heterotrimer dissociation assay, an important feature to avoid receptor internalization and degradation when working with whole cells. The neutral antagonist 25 displayed rapid association and complete dissociation to the D1 R in kinetic binding studies using confocal microscopy verifying its applicability for fluorescence microscopy. Moreover, molecular brightness studies determined a single-digit nanomolar binding affinity of the ligand, which was in good agreement with radioligand binding data. For this reason, this fluorescent ligand is a useful tool for a sophisticated characterization of native D1 receptors in a variety of experimental setups.
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Affiliation(s)
- Niklas Rosier
- Institute of Pharmacy, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany
| | - Denise Mönnich
- Institute of Pharmacy, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany
| | - Martin Nagl
- Institute of Pharmacy, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany
| | - Hannes Schihada
- Department of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35037, Marburg, Germany
| | - Alexei Sirbu
- Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
| | - Nergis Konar
- Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
| | - Irene Reyes-Resina
- CiberNed, Network Center for Neurodegenerative Diseases, National Spanish Health Institute Carlos III, Madrid, Spain
- Department Biochemistry and Physiology, School of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Spain
| | - Gemma Navarro
- CiberNed, Network Center for Neurodegenerative Diseases, National Spanish Health Institute Carlos III, Madrid, Spain
- Department Biochemistry and Physiology, School of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Spain
| | - Rafael Franco
- CiberNed, Network Center for Neurodegenerative Diseases, National Spanish Health Institute Carlos III, Madrid, Spain
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain
| | - Peter Kolb
- Department of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35037, Marburg, Germany
| | - Paolo Annibale
- Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
- School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews, Scotland, UK
| | - Steffen Pockes
- Institute of Pharmacy, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN 55414, USA
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21
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Campbell E, Luxton T, Kohl D, Goodchild SA, Walti C, Jeuken LJC. Chimeric Protein Switch Biosensors. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2024; 187:1-35. [PMID: 38273207 DOI: 10.1007/10_2023_241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Rapid detection of protein and small-molecule analytes is a valuable technique across multiple disciplines, but most in vitro testing of biological or environmental samples requires long, laborious processes and trained personnel in laboratory settings, leading to long wait times for results and high expenses. Fusion of recognition with reporter elements has been introduced to detection methods such as enzyme-linked immunoassays (ELISA), with enzyme-conjugated secondary antibodies removing one of the many incubation and wash steps. Chimeric protein switch biosensors go further and provide a platform for homogenous mix-and-read assays where long wash and incubation steps are eradicated from the process. Chimeric protein switch biosensors consist of an enzyme switch (the reporter) coupled to a recognition element, where binding of the analyte results in switching the activity of the reporter enzyme on or off. Several chimeric protein switch biosensors have successfully been developed for analytes ranging from small molecule drugs to large protein biomarkers. There are two main formats of chimeric protein switch biosensor developed, one-component and multi-component, and these formats exhibit unique advantages and disadvantages. Genetically fusing a recognition protein to the enzyme switch has many advantages in the production and performance of the biosensor. A range of immune and synthetic binding proteins have been developed as alternatives to antibodies, including antibody mimetics or antibody fragments. These are mainly small, easily manipulated proteins and can be genetically fused to a reporter for recombinant expression or manipulated to allow chemical fusion. Here, aspects of chimeric protein switch biosensors will be reviewed with a comparison of different classes of recognition elements and switching mechanisms.
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Affiliation(s)
- Emma Campbell
- School of Biomedical Sciences, University of Leeds, Leeds, UK
| | - Timothy Luxton
- School of Biomedical Sciences, University of Leeds, Leeds, UK
| | - Declan Kohl
- School of Biomedical Sciences, University of Leeds, Leeds, UK
| | | | - Christoph Walti
- School of Electronic and Electrical Engineering, University of Leeds, Leeds, UK
| | - Lars J C Jeuken
- School of Biomedical Sciences, University of Leeds, Leeds, UK.
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.
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22
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Calabretta MM, Michelini E. Current advances in the use of bioluminescence assays for drug discovery: an update of the last ten years. Expert Opin Drug Discov 2024; 19:85-95. [PMID: 37814480 DOI: 10.1080/17460441.2023.2266989] [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: 05/24/2023] [Accepted: 10/02/2023] [Indexed: 10/11/2023]
Abstract
INTRODUCTION Bioluminescence is a well-established optical detection technique widely used in several bioanalytical applications, including high-throughput and high-content screenings. Thanks to advances in synthetic biology techniques and deep learning, a wide portfolio of luciferases is now available with tuned emission wavelengths, kinetics, and high stability. These luciferases can be implemented in the drug discovery and development pipeline, allowing high sensitivity and multiplexing capability. AREAS COVERED This review summarizes the latest advancements of bioluminescent systems as toolsets in drug discovery programs for in vitro applications. Particular attention is paid to the most advanced bioluminescence-based technologies for drug screening over the past 10 years (from 2013 to 2023) such as cell-free assays, cell-based assays based on genetically modified cells, bioluminescence resonance energy transfer, and protein complementation assays in 2D and 3D cell models. EXPERT OPINION The availability of tuned bioluminescent proteins with improved emission and stability properties is vital for the development of bioluminescence assays for drug discovery, spanning from reporter gene technology to protein-protein techniques. Further studies, combining machine learning with synthetic biology, will be necessary to obtain new tools for sustainable and highly predictive bioluminescent drug discovery platforms.
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Affiliation(s)
- Maria Maddalena Calabretta
- Department of Chemistry "Giacomo Ciamician", Alma Mater Studiorum-University of Bologna, Bologna, Italy
- Center for Applied Biomedical Research (CRBA), IRCCS St. Orsola Hospital, Bologna, Italy
| | - Elisa Michelini
- Department of Chemistry "Giacomo Ciamician", Alma Mater Studiorum-University of Bologna, Bologna, Italy
- Center for Applied Biomedical Research (CRBA), IRCCS St. Orsola Hospital, Bologna, Italy
- Health Sciences and Technologies Interdepartmental Center for Industrial Research (HSTICIR), University of Bologna, Bologna, Italy
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23
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Dolberg TB, Gunnels TF, Ling T, Sarnese KA, Crispino JD, Leonard JN. Building synthetic biosensors using red blood cell proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.16.571988. [PMID: 38168174 PMCID: PMC10760168 DOI: 10.1101/2023.12.16.571988] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
As the use of engineered cell therapies expands from pioneering efforts in cancer immunotherapy to other applications, an attractive but less explored approach is the use of engineered red blood cells (RBCs). Compared to other cells, RBCs have a very long circulation time and reside in the blood compartment, so they could be ideally suited for applications as sentinel cells that enable in situ sensing and diagnostics. However, we largely lack tools for converting RBCs into biosensors. A unique challenge is that RBCs remodel their membranes during maturation, shedding many membrane components, suggesting that an RBC-specific approach may be needed. Towards addressing this need, here we develop a biosensing architecture built on RBC membrane proteins that are retained through erythropoiesis. This biosensor employs a mechanism in which extracellular ligand binding is transduced into intracellular reconstitution of a split output protein (including either a fluorophore or an enzyme). By comparatively evaluating a range of biosensor architectures, linker types, scaffold choices, and output signals, we identify biosensor designs and design features that confer substantial ligand-induced signal in vitro. Finally, we demonstrate that erythroid precursor cells engineered with our RBC protein biosensors function in vivo. This study establishes a foundation for developing RBC-based biosensors that could ultimately address unmet needs including non-invasive monitoring of physiological signals for a range of diagnostic applications.
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Affiliation(s)
- Taylor B. Dolberg
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Taylor F. Gunnels
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Te Ling
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Kelly A. Sarnese
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - John D. Crispino
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Joshua N. Leonard
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Interdisciplinary Biological Sciences Training Program, Northwestern University, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
- Member, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL, 60208, USA
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24
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Mersal KI, Abdel-Maksoud MS, Ali EMH, Ammar UM, Zaraei SO, Haque MM, Das T, Hassan NF, Kim EE, Lee JS, Park H, Lee KH, El-Gamal MI, Kim HK, Ibrahim TM, Oh CH. Evaluation of novel pyrazol-4-yl pyridine derivatives possessing arylsulfonamide tethers as c-Jun N-terminal kinase (JNK) inhibitors in leukemia cells. Eur J Med Chem 2023; 261:115779. [PMID: 37776574 DOI: 10.1016/j.ejmech.2023.115779] [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: 05/18/2023] [Revised: 08/14/2023] [Accepted: 08/29/2023] [Indexed: 10/02/2023]
Abstract
A series of 36 pyrazol-4-yl pyridine derivatives (8a-i, 9a-i, 10a-i, and 11a-i) was designed, synthesized, and evaluated for its antiproliferative activity over NCI-60 cancer cell line panel and inhibitory effect against JNK isoforms (JNK1, JNK2, and JNK3). All the synthesized compounds were tested against the NCI-60 cancer cell line panel. Compounds 11b, 11c, 11g, and 11i were selected to determine their GI50s and exerted a superior potency over the reference standard SP600125 against the tested cell lines. 11c showed a GI50 of 1.28 μM against K562 leukemic cells. Vero cells were used to assess 11c cytotoxicity compared to the tested cancer cells. The target compounds were tested against hJNK isoforms in which compound 11e exhibited the highest potency against JNK isoforms with IC50 values of 1.81, 12.7, and 10.5 nM against JNK1, JNK2, and JNK3, respectively. Kinase profiling of 11e showed higher JNK selectivity in 50 kinase panels. Compounds 11c and 11e showed cell population arrest at the G2/M phase, induced early apoptosis, and slightly inhibited beclin-1 production at higher concentrations in K562 leukemia cells relative to SP600125. NanoBRET assay of 11e showed intracellular JNK1 inhibition with an IC50 of 2.81 μM. Also, it inhibited CYP2D6 and 3A4 with different extent and its hERG activity showed little cardiac toxicity with an IC50 of 4.82 μM. hJNK3 was used as a template to generate the hJNK1 crystal structure to explore the binding mode of 11e (PDB ID: 8ENJ) with a resolution of 2.8 °A and showed a typical type I kinase inhibition against hJNK1. Binding energy scores showed that selectivity of 11e towards JNK1 could be attributed to additional hydrophobic interactions relative to JNK3.
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Affiliation(s)
- Karim I Mersal
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Modern University for Technology and Information (MTI), Cairo, 12055, Egypt; University of Science & Technology (UST), Daejeon, Yuseong-gu, 34113, Republic of Korea; Center of Biomaterials, Korea Institute of Science & Technology (KIST School), Seoul, Seongbuk-gu, 02792, Republic of Korea
| | - Mohammed S Abdel-Maksoud
- Medicinal & Pharmaceutical Chemistry Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre NRC (ID: 60014618), Dokki, Giza, 12622, Egypt
| | - Eslam M H Ali
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Modern University for Technology and Information (MTI), Cairo, 12055, Egypt; Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 West Stadium Avenue, West Lafayette, IN, 47907, USA
| | - Usama M Ammar
- School of Applied Sciences, Edinburgh Napier University, Sighthill Campus, 9 Sighthill Court, Edinburgh, EH11 4BN, United Kingdom
| | - Seyed-Omar Zaraei
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Md Mamunul Haque
- Department of Neural and Pain Sciences, School of Dentistry, University of Maryland, Baltimore, MD, 21201, USA
| | - Tanuza Das
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Noha F Hassan
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Modern University for Technology and Information (MTI), Cairo, 12055, Egypt
| | - Eunice EunKyeong Kim
- Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, 02792, South Korea
| | - Jun-Seok Lee
- Department of Pharmacology, College of Medicine, Korea University, Seoul, 02841, South Korea
| | - HaJeung Park
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, USA
| | - Kwan Hyi Lee
- Center for Advanced Biomolecular Recognition, Korea Institute of Science & Technology (KIST School), Seoul, Seongbuk-gu, 02792, Republic of Korea; KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02841, Republic of Korea
| | - Mohammed I El-Gamal
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates; Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates; Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Hee-Kwon Kim
- Department of Nuclear Medicine, Molecular Imaging & Therapeutic Medicine Research Center, Jeonbuk National University Medical School and Hospital, 20 Geonji-ro, Deokjin-gu, Jeonju, 54907, Republic of Korea; Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, 20 Geonji-ro, Deokjin-gu, Jeonju, 54907, Republic of Korea.
| | - Tamer M Ibrahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, P.O. Box 33516, Egypt
| | - Chang-Hyun Oh
- University of Science & Technology (UST), Daejeon, Yuseong-gu, 34113, Republic of Korea; Center of Biomaterials, Korea Institute of Science & Technology (KIST School), Seoul, Seongbuk-gu, 02792, Republic of Korea.
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25
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Szulc NA, Piechota M, Biriczová L, Thapa P, Pokrzywa W. Lysine deserts and cullin-RING ligase receptors: Navigating untrodden paths in proteostasis. iScience 2023; 26:108344. [PMID: 38026164 PMCID: PMC10665810 DOI: 10.1016/j.isci.2023.108344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 09/15/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
The ubiquitin-proteasome system (UPS) governs the degradation of proteins by ubiquitinating their lysine residues. Our study focuses on lysine deserts - regions in proteins conspicuously low in lysine residues - in averting ubiquitin-dependent proteolysis. We spotlight the prevalence of lysine deserts among bacteria leveraging the pupylation-dependent proteasomal degradation, and in the UPS of eukaryotes. To further scrutinize this phenomenon, we focused on human receptors VHL and SOCS1 to ascertain if lysine deserts could limit their ubiquitination within the cullin-RING ligase (CRL) complex. Our data indicate that the wild-type and lysine-free variants of VHL and SOCS1 maintain consistent turnover rates, unaltered by CRL-mediated ubiquitination, hinting at a protective mechanism facilitated by lysine deserts. Nonetheless, we noted their ubiquitination at non-lysine sites, alluding to alternative regulation by the UPS. Our research underscores the role of lysine deserts in limiting CRL-mediated ubiquitin tagging while promoting non-lysine ubiquitination, thereby advancing our understanding of proteostasis.
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Affiliation(s)
- Natalia A. Szulc
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Str., 02-109 Warsaw, Poland
| | - Małgorzata Piechota
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Str., 02-109 Warsaw, Poland
| | - Lilla Biriczová
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Str., 02-109 Warsaw, Poland
| | - Pankaj Thapa
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Str., 02-109 Warsaw, Poland
| | - Wojciech Pokrzywa
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Str., 02-109 Warsaw, Poland
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26
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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: 0] [Impact Index Per Article: 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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27
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Benabdallah NS, Dalal V, Scott RW, Marcous F, Sotiriou A, Kommoss FKF, Pejkovska A, Gaspar L, Wagner L, Sánchez-Rivera FJ, Ta M, Thornton S, Nielsen TO, Underhill TM, Banito A. Aberrant gene activation in synovial sarcoma relies on SSX specificity and increased PRC1.1 stability. Nat Struct Mol Biol 2023; 30:1640-1652. [PMID: 37735617 PMCID: PMC10643139 DOI: 10.1038/s41594-023-01096-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 08/15/2023] [Indexed: 09/23/2023]
Abstract
The SS18-SSX fusion drives oncogenic transformation in synovial sarcoma by bridging SS18, a member of the mSWI/SNF (BAF) complex, to Polycomb repressive complex 1 (PRC1) target genes. Here we show that the ability of SS18-SSX to occupy H2AK119ub1-rich regions is an intrinsic property of its SSX C terminus, which can be exploited by fusion to transcriptional regulators beyond SS18. Accordingly, SS18-SSX recruitment occurs in a manner that is independent of the core components and catalytic activity of BAF. Alternative SSX fusions are also recruited to H2AK119ub1-rich chromatin and reproduce the expression signatures of SS18-SSX by engaging with transcriptional activators. Variant Polycomb repressive complex 1.1 (PRC1.1) acts as the main depositor of H2AK119ub1 and is therefore required for SS18-SSX occupancy. Importantly, the SSX C terminus not only depends on H2AK119ub1 for localization, but also further increases it by promoting PRC1.1 complex stability. Consequently, high H2AK119ub1 levels are a feature of murine and human synovial sarcomas. These results uncover a critical role for SSX-C in mediating gene deregulation in synovial sarcoma by providing specificity to chromatin and further enabling oncofusion binding by enhancing PRC1.1 stability and H2AK119ub1 deposition.
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Affiliation(s)
- Nezha S Benabdallah
- Soft Tissue Sarcoma Research Group, Hopp Children's Cancer Center, Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Vineet Dalal
- Soft Tissue Sarcoma Research Group, Hopp Children's Cancer Center, Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - R Wilder Scott
- Department of Cellular and Physiological Sciences, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Fady Marcous
- Soft Tissue Sarcoma Research Group, Hopp Children's Cancer Center, Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Afroditi Sotiriou
- Soft Tissue Sarcoma Research Group, Hopp Children's Cancer Center, Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix K F Kommoss
- Soft Tissue Sarcoma Research Group, Hopp Children's Cancer Center, Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - Anastasija Pejkovska
- Soft Tissue Sarcoma Research Group, Hopp Children's Cancer Center, Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ludmila Gaspar
- Soft Tissue Sarcoma Research Group, Hopp Children's Cancer Center, Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lena Wagner
- Soft Tissue Sarcoma Research Group, Hopp Children's Cancer Center, Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Francisco J Sánchez-Rivera
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute, New York, NY, USA
| | - Monica Ta
- Department of Pathology and Laboratory Medicine, Vancouver Coastal Health Research Institute and Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Shelby Thornton
- Department of Pathology and Laboratory Medicine, Vancouver Coastal Health Research Institute and Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Torsten O Nielsen
- Department of Pathology and Laboratory Medicine, Vancouver Coastal Health Research Institute and Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - T Michael Underhill
- Department of Cellular and Physiological Sciences, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Ana Banito
- Soft Tissue Sarcoma Research Group, Hopp Children's Cancer Center, Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Heidelberg, Germany.
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28
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Ganguly A, Quon T, Jenkins L, Joseph B, Al-Awar R, Chevigne A, Tobin AB, Uehling DE, Hoffmann C, Drube J, Milligan G. G protein-receptor kinases 5/6 are the key regulators of G protein-coupled receptor 35-arrestin interactions. J Biol Chem 2023; 299:105218. [PMID: 37660910 PMCID: PMC10520886 DOI: 10.1016/j.jbc.2023.105218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/07/2023] [Accepted: 08/17/2023] [Indexed: 09/05/2023] Open
Abstract
Human G protein-coupled receptor 35 is regulated by agonist-mediated phosphorylation of a set of five phospho-acceptor amino acids within its C-terminal tail. Alteration of both Ser300 and Ser303 to alanine in the GPR35a isoform greatly reduces the ability of receptor agonists to promote interactions with arrestin adapter proteins. Here, we have integrated the use of cell lines genome edited to lack expression of combinations of G protein receptor kinases (GRKs), selective small molecule inhibitors of subsets of these kinases, and antisera able to specifically identify either human GPR35a or mouse GPR35 only when Ser300 and Ser303 (orce; the equivalent residues in mouse GPR35) have become phosphorylated to demonstrate that GRK5 and GRK6 cause agonist-dependent phosphorylation of these residues. Extensions of these studies demonstrated the importance of the GRK5/6-mediated phosphorylation of these amino acids for agonist-induced internalization of the receptor. Homology and predictive modeling of the interaction of human GPR35 with GRKs showed that the N terminus of GRK5 is likely to dock in the same methionine pocket on the intracellular face of GPR35 as the C terminus of the α5 helix of Gα13 and, that while this is also the case for GRK6, GRK2 and GRK3 are unable to do so effectively. These studies provide unique and wide-ranging insights into modes of regulation of GPR35, a receptor that is currently attracting considerable interest as a novel therapeutic target in diseases including ulcerative colitis.
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Affiliation(s)
- Amlan Ganguly
- Centre for Translational Pharmacology, School of Molecular Biosciences, Advanced Research Centre (ARC), College of Medical, Veterinary and Life Sciences University of Glasgow, Glasgow, UK
| | - Tezz Quon
- Centre for Translational Pharmacology, School of Molecular Biosciences, Advanced Research Centre (ARC), College of Medical, Veterinary and Life Sciences University of Glasgow, Glasgow, UK
| | - Laura Jenkins
- Centre for Translational Pharmacology, School of Molecular Biosciences, Advanced Research Centre (ARC), College of Medical, Veterinary and Life Sciences University of Glasgow, Glasgow, UK
| | - Babu Joseph
- Drug Discovery Program, Ontario Institute for Cancer Research, MaRS Centre, Toronto, Ontario, Canada
| | - Rima Al-Awar
- Drug Discovery Program, Ontario Institute for Cancer Research, MaRS Centre, Toronto, Ontario, Canada
| | - Andy Chevigne
- Division of Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Andrew B Tobin
- Centre for Translational Pharmacology, School of Molecular Biosciences, Advanced Research Centre (ARC), College of Medical, Veterinary and Life Sciences University of Glasgow, Glasgow, UK
| | - David E Uehling
- Drug Discovery Program, Ontario Institute for Cancer Research, MaRS Centre, Toronto, Ontario, Canada
| | - Carsten Hoffmann
- Institute for Molecular Cell Biology, CMB-Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany
| | - Julia Drube
- Institute for Molecular Cell Biology, CMB-Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany
| | - Graeme Milligan
- Centre for Translational Pharmacology, School of Molecular Biosciences, Advanced Research Centre (ARC), College of Medical, Veterinary and Life Sciences University of Glasgow, Glasgow, UK.
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29
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Casella B, Farmer JP, Nesheva DN, Williams HEL, Charlton SJ, Holliday ND, Laughton CA, Mistry SN. Design, Synthesis, and Application of Fluorescent Ligands Targeting the Intracellular Allosteric Binding Site of the CXC Chemokine Receptor 2. J Med Chem 2023; 66:12911-12930. [PMID: 37523859 PMCID: PMC10544029 DOI: 10.1021/acs.jmedchem.3c00849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Indexed: 08/02/2023]
Abstract
The inhibition of CXC chemokine receptor 2 (CXCR2), a key inflammatory mediator, is a potential strategy in the treatment of several pulmonary diseases and cancers. The complexity of endogenous chemokine interaction with the orthosteric binding site has led to the development of CXCR2 negative allosteric modulators (NAMs) targeting an intracellular pocket near the G protein binding site. Our understanding of NAM binding and mode of action has been limited by the availability of suitable tracer ligands for competition studies, allowing direct ligand binding measurements. Here, we report the rational design, synthesis, and pharmacological evaluation of a series of fluorescent NAMs, based on navarixin (2), which display high affinity and preferential binding for CXCR2 over CXCR1. We demonstrate their application in fluorescence imaging and NanoBRET binding assays, in whole cells or membranes, capable of kinetic and equilibrium analysis of NAM binding, providing a platform to screen for alternative chemophores targeting these receptors.
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Affiliation(s)
- Bianca
Maria Casella
- Division
of Biomolecular Sciences and Medicinal Chemistry, School of Pharmacy, University of Nottingham Biodiscovery Institute, Nottingham NG7 2RD, UK
| | - James P. Farmer
- Division
of Physiology, Pharmacology & Neuroscience, Medical School, School
of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
| | - Desislava N. Nesheva
- Division
of Physiology, Pharmacology & Neuroscience, Medical School, School
of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
| | - Huw E. L. Williams
- School
of Chemistry, University of Nottingham Biodiscovery
Institute, Nottingham NG7 2RD, UK
| | - Steven J. Charlton
- Division
of Physiology, Pharmacology & Neuroscience, Medical School, School
of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
- OMass
Therapeutics Ltd., Oxford OX4 2GX, UK
| | - Nicholas D. Holliday
- Division
of Physiology, Pharmacology & Neuroscience, Medical School, School
of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
- Excellerate
Bioscience Ltd., Biocity, University of
Nottingham, Nottingham NG1 1GF, UK
| | - Charles A. Laughton
- Division
of Biomolecular Sciences and Medicinal Chemistry, School of Pharmacy, University of Nottingham Biodiscovery Institute, Nottingham NG7 2RD, UK
| | - Shailesh N. Mistry
- Division
of Biomolecular Sciences and Medicinal Chemistry, School of Pharmacy, University of Nottingham Biodiscovery Institute, Nottingham NG7 2RD, UK
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30
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Boon K, Vanalken N, Meyen E, Schols D, Van Loy T. REGA-SIGN: Development of a Novel Set of NanoBRET-Based G Protein Biosensors. BIOSENSORS 2023; 13:767. [PMID: 37622853 PMCID: PMC10452170 DOI: 10.3390/bios13080767] [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] [Received: 04/12/2023] [Revised: 07/07/2023] [Accepted: 07/25/2023] [Indexed: 08/26/2023]
Abstract
Despite G protein-coupled receptors (GPCRs) being important theapeutic targets, the signaling properties of many GPCRs remain poorly characterized. GPCR activation primarily initiates heterotrimeric G protein signaling. To detect ligand-induced G protein activation, Bioluminescence Resonance Energy Transfer (BRET)-based biosensors were previously developed. Here, we designed a novel set of Nanoluciferase (NLuc) BRET-based biosensors (REGA-SIGN) that covers all Gα protein families (i.e., Gαi/o, GαSs/L, Gα12/13 and Gαq/15). REGA-SIGN uses NLuc as a bioluminescent donor and LSS-mKATE2, a red-shifted fluorophore, as an acceptor. Due to the enhanced spectral separation between donor and acceptor emission and the availability of a stable substrate for NLuc, this donor-acceptor pair enables sensitive kinetic assessment of G protein activity. After optimization, the NLuc integration sites into the Gα subunit largely corresponded with previously reported integration sites, except for GαSs/L for which we describe an alternative NLuc insertion site. G protein rescue experiments validated the biological activity of these Gα donor proteins. Direct comparison between EGFP and LSS-mKATE2 as acceptor fluorophores revealed improved sensitivity for nearly all G protein subtypes when using the latter one. Hence, REGA-SIGN can be used as a panel of kinetic G protein biosensors with high sensitivity.
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Affiliation(s)
| | | | | | | | - Tom Van Loy
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, P.O. Box 1030, 3000 Leuven, Belgium; (K.B.); (N.V.); (E.M.); (D.S.)
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31
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Wang Y, Li W, Ye B, Bi X. Chemical and Biological Strategies for Profiling Protein-Protein Interactions in Living Cells. Chem Asian J 2023; 18:e202300226. [PMID: 37089007 PMCID: PMC10946512 DOI: 10.1002/asia.202300226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 04/25/2023]
Abstract
Protein-protein interactions (PPIs) play critical roles in almost all cellular signal transduction events. Characterization of PPIs without interfering with the functions of intact cells is very important for basic biology study and drug developments. However, the ability to profile PPIs especially those weak/transient interactions in their native states remains quite challenging. To this end, many endeavors are being made in developing new methods with high efficiency and strong operability. By coupling with advanced fluorescent microscopy and mass spectroscopy techniques, these strategies not only allow us to visualize the subcellular locations and monitor the functions of protein of interest (POI) in real time, but also enable the profiling and identification of potential unknown interacting partners in high-throughput manner, which greatly facilitates the elucidation of molecular mechanisms underlying numerous pathophysiological processes. In this review, we will summarize the typical methods for PPIs identification in living cells and their principles, advantages and limitations will also be discussed in detail.
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Affiliation(s)
- You‐Yu Wang
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals & College of Pharmaceutical SciencesZhejiang University of TechnologyHangzhou310014, Zhejiang ProvinceP. R. China
| | - Wenyi Li
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityVictoria3086Australia
| | - Bang‐Ce Ye
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals & College of Pharmaceutical SciencesZhejiang University of TechnologyHangzhou310014, Zhejiang ProvinceP. R. China
| | - Xiao‐Bao Bi
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals & College of Pharmaceutical SciencesZhejiang University of TechnologyHangzhou310014, Zhejiang ProvinceP. R. China
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32
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Lay CS, Kilpatrick LE, Craggs PD, Hill SJ. Use of NanoBiT and NanoBRET to characterise interleukin-23 receptor dimer formation in living cells. Br J Pharmacol 2023; 180:1444-1459. [PMID: 36560872 PMCID: PMC10953408 DOI: 10.1111/bph.16018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 12/02/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND AND PURPOSE Interleukin-23 (IL-23) and its receptor are important drug targets for the treatment of auto-inflammatory diseases. IL-23 binds to a receptor complex composed of two single transmembrane spanning proteins IL23R and IL12Rβ1. In this study, we aimed to gain further understanding of how ligand binding induces signalling of IL-23 receptor complexes using the proximity-based techniques of NanoLuc Binary Technology (NanoBiT) and Bioluminescence Resonance Energy Transfer (BRET). EXPERIMENTAL APPROACH To monitor the formation of IL-23 receptor complexes, we developed a split luciferase (NanoBiT) assay whereby heteromerisation of receptor subunits can be measured through luminescence. The affinity of NanoBiT complemented complexes for IL-23 was measured using NanoBRET, and cytokine-induced signal transduction was measured using a phospho-STAT3 AlphaLISA assay. KEY RESULTS NanoBiT measurements demonstrated that IL-23 receptor complexes formed to an equal degree in the presence and absence of ligand. NanoBRET measurements confirmed that these complexes bound IL-23 with a picomolar binding affinity. Measurement of STAT3 phosphorylation demonstrated that pre-formed IL-23 receptor complexes induced signalling following ligand binding. It was also demonstrated that synthetic ligand-independent signalling could be induced by high affinity (HiBit) but not low affinity (SmBit) NanoBiT crosslinking of the receptor N-terminal domains. CONCLUSIONS AND IMPLICATIONS These results indicate that receptor complexes form prior to ligand binding and are not sufficient to induce signalling alone. Our findings indicate that IL-23 induces a conformational change in heteromeric receptor complexes, to enable signal transduction. These observations have direct implications for drug discovery efforts to target the IL-23 receptor.
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Affiliation(s)
- Charles S. Lay
- Division of Physiology, Pharmacology and Neuroscience, School of Life SciencesUniversity of NottinghamNottinghamUK
- Centre of Membrane Proteins and ReceptorsUniversity of Birmingham and NottinghamThe MidlandsUK
- Medicine Design, Medicinal Science and TechnologyGlaxoSmithKlineStevenageUK
| | - Laura E. Kilpatrick
- Centre of Membrane Proteins and ReceptorsUniversity of Birmingham and NottinghamThe MidlandsUK
- Division of Bimolecular Science and Medicinal Chemistry, School of Pharmacy, Biodiscovery InstituteUniversity of NottinghamNottinghamUK
| | - Peter D. Craggs
- Medicine Design, Medicinal Science and TechnologyGlaxoSmithKlineStevenageUK
- Crick‐GSK Biomedical LinklabsGlaxoSmithKlineStevenageUK
| | - Stephen J. Hill
- Division of Physiology, Pharmacology and Neuroscience, School of Life SciencesUniversity of NottinghamNottinghamUK
- Centre of Membrane Proteins and ReceptorsUniversity of Birmingham and NottinghamThe MidlandsUK
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33
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Saecker L, Häberlein H, Franken S. Investigation of adenosine A1 receptor-mediated β-arrestin 2 recruitment using a split-luciferase assay. Front Pharmacol 2023; 14:1172551. [PMID: 37324481 PMCID: PMC10268005 DOI: 10.3389/fphar.2023.1172551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/15/2023] [Indexed: 06/17/2023] Open
Abstract
Background: Adenosine A1 receptor (A1AR) plays a prominent role in neurological and cardiac diseases and inflammatory processes. Its endogenous ligand adenosine is known to be one of the key players in the sleep-wake cycle. Like other G protein-coupled receptors (GPCRs), stimulation of A1AR leads to the recruitment of arrestins in addition to the activation of G proteins. So far, little is known about the role of these proteins in signal transduction and regulation of A1AR compared to the activation of G proteins. In this work, we characterized a live cell assay for A1AR-mediated β-arrestin 2 recruitment. We have applied this assay to a set of different compounds that interact with this receptor. Methods: Based on NanoBit® technology, a protein complementation assay was developed in which the A1AR is coupled to the large part of the nanoluciferase (LgBiT), whereas its small part (SmBiT) is fused to the N-terminus of β-arrestin 2. Stimulation of A1AR results in the recruitment of β-arrestin 2 and subsequent complementation of a functional nanoluciferase. For comparison, corresponding data on the effect of receptor stimulation on intracellular cAMP levels were collected for some data sets using the GloSensor™ assay. Results: The assay gives highly reproducible results with a very good signal-to-noise ratio. Capadenoson, in contrast to adenosine, CPA, or NECA, shows only partial agonism in this assay with respect to the recruitment of β-arrestin 2, whereas it shows full agonism in the case of the inhibitory effect of A1AR on cAMP production. By using a GRK2 inhibitor, it becomes clear that the recruitment is at least partially dependent on the phosphorylation of the receptor by this kinase. Interestingly, this was also the first time that we demonstrate the A1AR-mediated recruitment of β-arrestin 2 by stimulation with a valerian extract. Conclusion: The presented assay is a useful tool for the quantitative study of A1AR-mediated β-arrestin 2 recruitment. It allows data collection for stimulatory, inhibitory, and modulatory substances and is also suitable for more complex substance mixtures such as valerian extract.
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34
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Zhang Y, Chen M, Liu T, Qin K, Fernie AR. Investigating the dynamics of protein-protein interactions in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:965-983. [PMID: 36919339 DOI: 10.1111/tpj.16182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 02/22/2023] [Accepted: 03/01/2023] [Indexed: 05/27/2023]
Abstract
Both stable and transient protein interactions play an important role in the complex assemblies required for the proper functioning of living cells. Several methods have been developed to monitor protein-protein interactions in plants. However, the detection of dynamic protein complexes is very challenging, with few technologies available for this purpose. Here, we developed a new platform using the plant UBIQUITIN promoter to drive transgene expression and thereby to detect protein interactions in planta. Typically, to decide which side of the protein to link the tags, the subcellular localization of the protein fused either N-terminal or C-terminal mCitrine was firstly confirmed by using eight different specific mCherry markers. Following stable or transient protein expression in plants, the protein interaction network was detected by affinity purification mass spectrometry. These interactions were subsequently confirmed by bimolecular fluorescence complementation (BiFC), bioluminescence resonance energy transfer and co-immunoprecipitation assays. The dynamics of these interactions were monitored by Förster resonance energy transfer (FRET) and split-nano luciferase, whilst the ternary protein complex association was monitored by BiFC-FRET. Using the canonical glycolytic metabolon as an example, the interaction between these enzymes was characterized under conditions that mimic physiologically relevant energy statuses.
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Affiliation(s)
- Youjun Zhang
- Center of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Moxian Chen
- Co-Innovation Center for Sustainable Forestry in Southern China & Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Tieyuan Liu
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, China
| | - Kezhen Qin
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Center of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
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35
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Li J, Wang N, Xiong M, Dai M, Xie C, Wang Q, Quan K, Zhou Y, Qing Z. A Reaction-Based Ratiometric Bioluminescent Platform for Point-of-Care and Quantitative Detection Using a Smartphone. Anal Chem 2023; 95:7142-7149. [PMID: 37122064 DOI: 10.1021/acs.analchem.2c05422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Fluorescent probes have emerged as powerful tools for the detection of different analytes by virtue of structural tenability. However, the requirement of an excitation source largely hinders their applicability in point-of-care detection, as well as causing autofluorescence interference in complex samples. Herein, based on bioluminescence resonance energy transfer (BRET), we developed a reaction-based ratiometric bioluminescent platform, which allows the excitation-free detection of analytes. The platform has a modular design consisting of a NanoLuc-HaloTag fusion as an energy donor, to which a synthetic fluorescent probe is bioorthogonally labeled as recognition moiety and energy acceptor. Once activated by the target, the fluorescent probe can be excited by NanoLuc to generate a remarkable BRET signal, resulting in obvious color changes of luminescence, which can be easily recorded and quantitatively analyzed by a smartphone. As a proof of concept, a fluorescent probe for HOCl was synthesized to construct the bioluminescent system. Results demonstrated the system showed a constant blue/red emission ratio which is independent to the signal intensity, allowing the quantification of HOCl concentration with high sensitivity (limit of detection (LOD) = 13 nM) and accuracy. Given the universality, this reaction-based bioluminescent platform holds great potential for point-of-care and quantitative detection of reactive species.
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Affiliation(s)
- Junbin Li
- Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, School of Food Science and Bioengineering, Changsha University of Science and Technology, Changsha 410114, People's Republic of China
| | - Na Wang
- Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, School of Food Science and Bioengineering, Changsha University of Science and Technology, Changsha 410114, People's Republic of China
| | - Mengyi Xiong
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People's Republic of China
| | - Min Dai
- Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, School of Food Science and Bioengineering, Changsha University of Science and Technology, Changsha 410114, People's Republic of China
| | - Cheng Xie
- Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, School of Food Science and Bioengineering, Changsha University of Science and Technology, Changsha 410114, People's Republic of China
| | - Qianqian Wang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People's Republic of China
| | - Ke Quan
- Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, School of Food Science and Bioengineering, Changsha University of Science and Technology, Changsha 410114, People's Republic of China
| | - Yibo Zhou
- Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, School of Food Science and Bioengineering, Changsha University of Science and Technology, Changsha 410114, People's Republic of China
| | - Zhihe Qing
- Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, School of Food Science and Bioengineering, Changsha University of Science and Technology, Changsha 410114, People's Republic of China
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36
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Shi X, Zhang J. Using NanoB 2 to gain insights into ligand pharmacology. CELL REPORTS METHODS 2023; 3:100438. [PMID: 37056367 PMCID: PMC10088232 DOI: 10.1016/j.crmeth.2023.100438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
In this issue of Cell Reports Methods, van den Bor et al.1 report a novel assay called NanoB2, which harnesses the use of nanobodies to broaden the applications of NanoBRET approaches for investigating ligand pharmacology. They demonstrate the generalizability of NanoB2 on a range of membrane proteins.
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Affiliation(s)
- Xinchao Shi
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jian Zhang
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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37
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van den Bor J, Bergkamp ND, Anbuhl SM, Dekker F, Comez D, Perez Almeria CV, Bosma R, White CW, Kilpatrick LE, Hill SJ, Siderius M, Smit MJ, Heukers R. NanoB 2 to monitor interactions of ligands with membrane proteins by combining nanobodies and NanoBRET. CELL REPORTS METHODS 2023; 3:100422. [PMID: 37056381 PMCID: PMC10088090 DOI: 10.1016/j.crmeth.2023.100422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/31/2023] [Accepted: 02/17/2023] [Indexed: 03/14/2023]
Abstract
The therapeutic potential of ligands targeting disease-associated membrane proteins is predicted by ligand-receptor binding constants, which can be determined using NanoLuciferase (NanoLuc)-based bioluminescence resonance energy transfer (NanoBRET) methods. However, the broad applicability of these methods is hampered by the restricted availability of fluorescent probes. We describe the use of antibody fragments, like nanobodies, as universal building blocks for fluorescent probes for use in NanoBRET. Our nanobody-NanoBRET (NanoB2) workflow starts with the generation of NanoLuc-tagged receptors and fluorescent nanobodies, enabling homogeneous, real-time monitoring of nanobody-receptor binding. Moreover, NanoB2 facilitates the assessment of receptor binding of unlabeled ligands in competition binding experiments. The broad significance is illustrated by the successful application of NanoB2 to different drug targets (e.g., multiple G protein-coupled receptors [GPCRs] and a receptor tyrosine kinase [RTK]) at distinct therapeutically relevant binding sites (i.e., extracellular and intracellular).
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Affiliation(s)
- Jelle van den Bor
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Nick D. Bergkamp
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Stephanie M. Anbuhl
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- QVQ Holding B.V., Utrecht, the Netherlands
| | - Françoise Dekker
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Dehan Comez
- Cell Signalling Research Group, Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, the Midlands, UK
| | - Claudia V. Perez Almeria
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Reggie Bosma
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Carl W. White
- Cell Signalling Research Group, Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, the Midlands, UK
| | - Laura E. Kilpatrick
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, the Midlands, UK
- Division of Bimolecular Science and Medicinal Chemistry, School of Pharmacy, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Stephen J. Hill
- Cell Signalling Research Group, Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, the Midlands, UK
| | - Marco Siderius
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Martine J. Smit
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Raimond Heukers
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- QVQ Holding B.V., Utrecht, the Netherlands
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38
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Yu J, Zhang Y, Zhao Y, Zhang X, Ren H. Highly Sensitive and Selective Detection of Inorganic Phosphates in the Water Environment by Biosensors Based on Bioluminescence Resonance Energy Transfer. Anal Chem 2023; 95:4904-4913. [PMID: 36942460 DOI: 10.1021/acs.analchem.2c04748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
The accurate detection of phosphate in water is very important to prevent water eutrophication and ensure the health of water quality. However, traditional phosphomolybdenum blue spectrophotometry is not sensitive, is time-consuming, and demands large amounts of chemical reagents. Therefore, highly sensitive, rapid, and environmentally friendly Pi detection methods are urgently needed. Here, we developed a bioluminescence resonance energy transfer (BRET)-based biosensor, which can detect Pi in water quickly, highly sensitively, and highly selectively. The NanoLuc and the Venus fluorescent protein were selected as the bioluminescence donor and energy acceptor, respectively. The best-performing BRET sensor variant, VenusΔC10-PΔC12-ΔN4Nluc, was identified by Pi-specific binding protein (PiBP) screening and systematic truncation. Single-factor experiments optimized the key parameters affecting the detection performance of the sensor. Under the optimal detection conditions, the detection limit of this method was 1.3 μg·L-1, the detection range was 3.3-434 μg·L-1, and it had excellent selectivity, repeatability, and stability. This low-cost and environment-friendly BRET sensor showed a good application prospect in real water quality detection.
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Affiliation(s)
- Jie Yu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yan Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yanping Zhao
- School of Environment, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Xuxiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
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Mi L, Yu Q, Mudiyanselage APK, Wu R, Sun Z, Zheng R, Ren K, You M. Genetically Encoded RNA-Based Bioluminescence Resonance Energy Transfer (BRET) Sensors. ACS Sens 2023; 8:308-316. [PMID: 36608281 PMCID: PMC10630924 DOI: 10.1021/acssensors.2c02213] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
RNA-based nanostructures and molecular devices have become popular for developing biosensors and genetic regulators. These programmable RNA nanodevices can be genetically encoded and modularly engineered to detect various cellular targets and then induce output signals, most often a fluorescence readout. Although powerful, the high reliance of fluorescence on the external excitation light raises concerns about its high background, photobleaching, and phototoxicity. Bioluminescence signals can be an ideal complementary readout for these genetically encoded RNA nanodevices. However, RNA-based real-time bioluminescent reporters have been rarely developed. In this study, we reported the first type of genetically encoded RNA-based bioluminescence resonance energy transfer (BRET) sensors that can be used for real-time target detection in living cells. By coupling a luciferase bioluminescence donor with a fluorogenic RNA-based acceptor, our BRET system can be modularly designed to image and detect various cellular analytes. We expect that this novel RNA-based bioluminescent system can be potentially used broadly in bioanalysis and nanomedicine for engineering biosensors, characterizing cellular RNA-protein interactions, and high-throughput screening or in vivo imaging.
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Affiliation(s)
- Lan Mi
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Qikun Yu
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | | | - Rigumula Wu
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Zhining Sun
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Ru Zheng
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Kewei Ren
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
- Molecular and Cellular Biology Program, University of Massachusetts, Amherst, MA 01003, USA
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40
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Baljinnyam B, Ronzetti M, Simeonov A. Advances in luminescence-based technologies for drug discovery. Expert Opin Drug Discov 2023; 18:25-35. [PMID: 36562206 PMCID: PMC9892298 DOI: 10.1080/17460441.2023.2160441] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Luminescence-based technologies, specifically bioluminescence and chemiluminescence, are powerful tools with extensive use in drug discovery. Production of light during chemiluminescence and bioluminescence, unlike fluorescence, doesn't require an excitation light source, resulting in high signal-to-noise ratio, less background interference, and no issues from phototoxicity and photobleaching. These characteristics of luminescence technologies offer unique advantages for experimental designs, allowing for greater flexibility to target a wide range of proteins and biological processes for drug discovery at different stages. AREAS COVERED This review provides a basic overview of luciferase-based technologies and details recent advances and use cases of luciferase and luciferin variations and their applicability in the drug discovery toolset. The authors expand upon specific applications of luciferase technologies, including chemiluminescent and bioluminescent-based microscopy. Finally, the authors lay out forward-looking statements on the field of luminescence and how it may shape the translational scientists' work moving forward. EXPERT OPINION The demand for improved luciferase and luciferin pairs correlates strongly with efforts to improve the sensitivity and robustness of high-throughput assays. As luminescent reporter systems improve, so will the expansion of use cases for luminescence-based technologies in early-stage drug discovery. With the synthesis of novel, non-enzymatic chemiluminescence-based probes, which previously were restrained to only basic research applications, they may now be readily implemented in drug discovery campaigns.
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Affiliation(s)
- Bolormaa Baljinnyam
- Staff Scientist, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Michael Ronzetti
- Predoctoral IRTA Fellow, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Anton Simeonov
- Group Leader, Scientific Director, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
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Szewczyk MM, Owens DDG, Barsyte-Lovejoy D. Measuring Protein-Protein Interactions in Cells using Nanoluciferase Bioluminescence Resonance Energy Transfer (NanoBRET) Assay. Methods Mol Biol 2023; 2706:137-148. [PMID: 37558946 DOI: 10.1007/978-1-0716-3397-7_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Protein-protein interactions (PPIs) are increasingly recognized for their roles in functional cellular networks and their importance in disease-targeting contexts. Assessing PPI in the native cellular environment is challenging and requires specific and quantitative methods. Bioluminescence resonance energy transfer (BRET) is a biophysical process that can be used to quantify PPI. With Nanoluciferase bioluminescent protein as a donor and a fluorescent chloroalkane ligand covalently bound to HaloTag protein as an acceptor, NanoBRET provides a versatile and robust system to quantitatively measure PPI in living cells. BRET efficiency is proportional to the distance between the donor and acceptor, allowing for the measurement of PPI in real time. In this paper, we describe the use of NanoBRET to study specific interactions between proteins of interest in living cells that can be perturbed by using small-molecule antagonists and genetic mutations. Here, we provide a detailed protocol for expressing NanoLuc and HaloTag fusion proteins in cell culture and the necessary optimization of NanoBRET assay conditions. Our example results demonstrate the reliability and sensitivity of NanoBRET for measuring interactions between proteins, protein domains, and short peptides and quantitating the PPI antagonist compound activity in living cells.
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Affiliation(s)
| | - Dominic D G Owens
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada.
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada.
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42
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Kotliar IB, Lorenzen E, Schwenk JM, Hay DL, Sakmar TP. Elucidating the Interactome of G Protein-Coupled Receptors and Receptor Activity-Modifying Proteins. Pharmacol Rev 2023; 75:1-34. [PMID: 36757898 PMCID: PMC9832379 DOI: 10.1124/pharmrev.120.000180] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 09/27/2022] [Indexed: 12/13/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are known to interact with several other classes of integral membrane proteins that modulate their biology and pharmacology. However, the extent of these interactions and the mechanisms of their effects are not well understood. For example, one class of GPCR-interacting proteins, receptor activity-modifying proteins (RAMPs), comprise three related and ubiquitously expressed single-transmembrane span proteins. The RAMP family was discovered more than two decades ago, and since then GPCR-RAMP interactions and their functional consequences on receptor trafficking and ligand selectivity have been documented for several secretin (class B) GPCRs, most notably the calcitonin receptor-like receptor. Recent bioinformatics and multiplexed experimental studies suggest that GPCR-RAMP interactions might be much more widespread than previously anticipated. Recently, cryo-electron microscopy has provided high-resolution structures of GPCR-RAMP-ligand complexes, and drugs have been developed that target GPCR-RAMP complexes. In this review, we provide a summary of recent advances in techniques that allow the discovery of GPCR-RAMP interactions and their functional consequences and highlight prospects for future advances. We also provide an up-to-date list of reported GPCR-RAMP interactions based on a review of the current literature. SIGNIFICANCE STATEMENT: Receptor activity-modifying proteins (RAMPs) have emerged as modulators of many aspects of G protein-coupled receptor (GPCR)biology and pharmacology. The application of new methodologies to study membrane protein-protein interactions suggests that RAMPs interact with many more GPCRs than had been previously known. These findings, especially when combined with structural studies of membrane protein complexes, have significant implications for advancing GPCR-targeted drug discovery and the understanding of GPCR pharmacology, biology, and regulation.
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Affiliation(s)
- Ilana B Kotliar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York (I.B.K., E.L., T.P.S.); Tri-Institutional PhD Program in Chemical Biology, New York, New York (I.B.K.); Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Solna, Sweden (J.M.S.); Department of Pharmacology and Toxicology, School of Biomedical Sciences, Division of Health Sciences, University of Otago, Dunedin, New Zealand (D.L.H.); and Department of Neurobiology, Care Sciences and Society (NVS), Division for Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden (T.P.S.)
| | - Emily Lorenzen
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York (I.B.K., E.L., T.P.S.); Tri-Institutional PhD Program in Chemical Biology, New York, New York (I.B.K.); Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Solna, Sweden (J.M.S.); Department of Pharmacology and Toxicology, School of Biomedical Sciences, Division of Health Sciences, University of Otago, Dunedin, New Zealand (D.L.H.); and Department of Neurobiology, Care Sciences and Society (NVS), Division for Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden (T.P.S.)
| | - Jochen M Schwenk
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York (I.B.K., E.L., T.P.S.); Tri-Institutional PhD Program in Chemical Biology, New York, New York (I.B.K.); Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Solna, Sweden (J.M.S.); Department of Pharmacology and Toxicology, School of Biomedical Sciences, Division of Health Sciences, University of Otago, Dunedin, New Zealand (D.L.H.); and Department of Neurobiology, Care Sciences and Society (NVS), Division for Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden (T.P.S.)
| | - Debbie L Hay
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York (I.B.K., E.L., T.P.S.); Tri-Institutional PhD Program in Chemical Biology, New York, New York (I.B.K.); Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Solna, Sweden (J.M.S.); Department of Pharmacology and Toxicology, School of Biomedical Sciences, Division of Health Sciences, University of Otago, Dunedin, New Zealand (D.L.H.); and Department of Neurobiology, Care Sciences and Society (NVS), Division for Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden (T.P.S.)
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York (I.B.K., E.L., T.P.S.); Tri-Institutional PhD Program in Chemical Biology, New York, New York (I.B.K.); Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Solna, Sweden (J.M.S.); Department of Pharmacology and Toxicology, School of Biomedical Sciences, Division of Health Sciences, University of Otago, Dunedin, New Zealand (D.L.H.); and Department of Neurobiology, Care Sciences and Society (NVS), Division for Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden (T.P.S.)
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43
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Fuchs O. Targeting cereblon in hematologic malignancies. Blood Rev 2023; 57:100994. [PMID: 35933246 DOI: 10.1016/j.blre.2022.100994] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 01/28/2023]
Abstract
The protein cereblon (CRBN) is a substrate receptor of the cullin 4-really interesting new gene (RING) E3 ubiquitin ligase complex CRL4CRBN. Targeting CRBN mediates selective protein ubiquitination and subsequent degradation via the proteasome. This review describes novel thalidomide analogs, immunomodulatory drugs, also known as CRBN E3 ubiquitin ligase modulators or molecular glues (avadomide, iberdomide, CC-885, CC-90009, BTX-1188, CC-92480, CC-99282, CFT7455, and CC-91633), and CRBN-based proteolysis targeting chimeras (PROTACs) with increased efficacy and potent activity for application in hematologic malignancies. Both types of CRBN-binding drugs, molecular glues, and PROTACs stimulate the interaction between CRBN and its neosubstrates, recruiting target disease-promoting proteins and the E3 ubiquitin ligase CRL4CRBN. Proteins that are traditionally difficult to target (transcription factors and oncoproteins) can be polyubiquitinated and degraded in this way. The competition of CRBN neosubstrates with endogenous CRBN-interacting proteins and the pharmacology and rational combination therapies of and mechanisms of resistance to CRL4CRBN modulators or CRBN-based PROTACs are described.
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Affiliation(s)
- Ota Fuchs
- Institute of Hematology and Blood Transfusion, U Nemocnice 1, 12800 Praha 2, Czech Republic.
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44
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Apostolidou D, Zhang P, Yang W, Marszalek PE. Mechanical Unfolding and Refolding of NanoLuc via Single-Molecule Force Spectroscopy and Computer Simulations. Biomacromolecules 2022; 23:5164-5178. [PMID: 36350253 DOI: 10.1021/acs.biomac.2c00997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A highly bioluminescent protein, NanoLuc (Nluc), has seen numerous applications in biological assays since its creation. We recently engineered a NanoLuc polyprotein that showed high bioluminescence but displayed a strong misfolding propensity after mechanical unfolding. Here, we present our single-molecule force spectroscopy (SMFS) studies by atomic force microscopy (AFM) and steered molecular dynamics (SMD) simulations on two new hybrid protein constructs comprised of Nluc and I91 titin domains, I91-I91-Nluc-I91-I91-I91-I91 (I912-Nluc-I914) and I91-Nluc-I91-Nluc-I91-Nluc-I91, to characterize the unfolding behavior of Nluc in detail and to further investigate its misfolding properties that we observed earlier for the I912-Nluc3-I912 construct. Our SMFS results confirm that Nluc's unfolding proceeds similarly in all constructs; however, Nluc's refolding differs in these constructs, and its misfolding is minimized when Nluc is monomeric or separated by I91 domains. Our simulations on monomeric Nluc, Nluc dyads, and Nluc triads pinpointed the origin of its mechanical stability and captured interesting unfolding intermediates, which we also observed experimentally.
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Affiliation(s)
- Dimitra Apostolidou
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina27708, United States
| | - Pan Zhang
- Department of Chemistry, Duke University, Durham, North Carolina27708, United States
| | - Weitao Yang
- Department of Chemistry, Duke University, Durham, North Carolina27708, United States
| | - Piotr E Marszalek
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina27708, United States
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Brennan CK, Yao Z, Ionkina AA, Rathbun CM, Sathishkumar B, Prescher JA. Multiplexed bioluminescence imaging with a substrate unmixing platform. Cell Chem Biol 2022; 29:1649-1660.e4. [PMID: 36283402 PMCID: PMC9675729 DOI: 10.1016/j.chembiol.2022.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 08/31/2022] [Accepted: 09/30/2022] [Indexed: 01/31/2023]
Abstract
Bioluminescent tools can illuminate cellular features in whole organisms. Multi-component tracking remains challenging, though, owing to a lack of well-resolved probes and long imaging times. To address the need for more rapid, quantitative, and multiplexed bioluminescent readouts, we developed an analysis pipeline featuring sequential substrate administration and serial image acquisition. Light output from each luciferin is layered on top of the previous image, with minimal delay between substrate delivery. A MATLAB algorithm was written to analyze bioluminescent images generated from the rapid imaging protocol and deconvolute (i.e., unmix) signals from luciferase-luciferin pairs. Mixtures comprising three to five luciferase reporters were readily distinguished in under 50 min; this same experiment would require days using conventional workflows. We further showed that the algorithm can be used to accurately quantify luciferase levels in heterogeneous mixtures. Based on its speed and versatility, the multiplexed imaging platform will expand the scope of bioluminescence technology.
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Affiliation(s)
- Caroline K Brennan
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Zi Yao
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Anastasia A Ionkina
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Colin M Rathbun
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | | | - Jennifer A Prescher
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA.
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46
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Kurose H. [Biased Signaling through G Protein-coupled Receptors]. YAKUGAKU ZASSHI 2022; 142:1091-1101. [PMID: 36184444 DOI: 10.1248/yakushi.22-00087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
It is well-established that G protein-coupled receptors (GPCRs) transduce signals into cells using G proteins as intermediary molecules. β-Arrestins are molecules involved in regulating GPCRs; however, it has recently been reported that β-arrestins can also mediate signaling through GPCRs. Signaling through G proteins or β-arrestins can be activated selectively using specific agonists; of the latter, those that can selectively activate either G proteins or β-arrestins are called biased agonists. The clinical use of biased agonists could potentially induce fewer side effects. However, partial agonists can also explain the mechanism of G protein-biased agonists; thus, appropriate assay systems must be considered. Endogenous agonists are known to bind to orthosteric and allosteric sites in the agonist binding site, and the allosteric site is associated with the activity of biased agonists. This current review presents a detailed discussion of biased agonists.
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Affiliation(s)
- Hitoshi Kurose
- Department of Pharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Kyushu University
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47
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Theillet FX, Luchinat E. In-cell NMR: Why and how? PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:1-112. [PMID: 36496255 DOI: 10.1016/j.pnmrs.2022.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/17/2023]
Abstract
NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy; CERM - Magnetic Resonance Center, and Neurofarba Department, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
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48
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Geethakumari AM, Ahmed WS, Rasool S, Fatima A, Nasir Uddin SM, Aouida M, Biswas KH. A genetically encoded BRET-based SARS-CoV-2 M pro protease activity sensor. Commun Chem 2022; 5:117. [PMID: 36187754 PMCID: PMC9516532 DOI: 10.1038/s42004-022-00731-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 09/07/2022] [Indexed: 01/27/2023] Open
Abstract
The main protease, Mpro, is critical for SARS-CoV-2 replication and an appealing target for designing anti-SARS-CoV-2 agents. Therefore, there is a demand for the development of improved sensors to monitor its activity. Here, we report a pair of genetically encoded, bioluminescence resonance energy transfer (BRET)-based sensors for detecting Mpro proteolytic activity in live cells as well as in vitro. The sensors were generated by sandwiching peptides containing the Mpro N-terminal autocleavage sites, either AVLQSGFR (short) or KTSAVLQSGFRKME (long), in between the mNeonGreen and NanoLuc proteins. Co-expression of the sensors with Mpro in live cells resulted in their cleavage while mutation of the critical C145 residue (C145A) in Mpro completely abrogated their cleavage. Additionally, the sensors recapitulated the inhibition of Mpro by the well-characterized pharmacological agent GC376. Further, in vitro assays with the BRET-based Mpro sensors revealed a molecular crowding-mediated increase in the rate of Mpro activity and a decrease in the inhibitory potential of GC376. The sensors developed here will find direct utility in studies related to drug discovery targeting the SARS-CoV-2 Mpro and functional genomics application to determine the effect of sequence variation in Mpro.
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Affiliation(s)
- Anupriya M. Geethakumari
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
| | - Wesam S. Ahmed
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
| | - Saad Rasool
- Division of Genomics and Precision Medicine, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
| | - Asma Fatima
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
| | - S. M. Nasir Uddin
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
| | - Mustapha Aouida
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
| | - Kabir H. Biswas
- Division of Biological and Biomedical Sciences, College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, 34110 Qatar
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A Luciferase Mutant with Improved Brightness and Stability for Whole-Cell Bioluminescent Biosensors and In Vitro Biosensing. BIOSENSORS 2022; 12:bios12090742. [PMID: 36140127 PMCID: PMC9496056 DOI: 10.3390/bios12090742] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 08/30/2022] [Accepted: 09/05/2022] [Indexed: 11/17/2022]
Abstract
The availability of new bioluminescent proteins with tuned properties, both in terms of emission wavelength, kinetics and protein stability, is highly valuable in the bioanalytical field, with the potential to improve the sensitivity and analytical performance of the currently used methods for ATP detection, whole-cell biosensors, and viability assays among others. We present a new luciferase mutant, called BgLuc, suitable for developing whole-cell biosensors and in vitro biosensors characterized by a bioluminescence maximum of 548 nm, narrow emission bandwidth, favorable kinetic properties, and excellent pH- and thermo-stabilities at 37 and 45 °C and pH from 5.0 to 8.0. We assessed the suitability of this new luciferase for whole-cell biosensing with a cell-based bioreporter assay for Nuclear Factor-kappa B (NF-kB) signal transduction pathway using 2D and 3D human embryonic kidney (HEK293T) cells, and for ATP detection with the purified enzyme. In both cases the luciferase showed suitable for sensitive detection of the target analytes, with better or similar performance than the commercial counterparts.
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Abu Rabah RR, Sebastian A, Vunnam S, Sultan S, Tarazi H, Anbar HS, Shehata MK, Zaraei SO, Elgendy SM, Al Shamma SA, Omar HA, Al-Tel TH, El-Gamal MI. Design, synthesis, and biological evaluation of a new series of pyrazole derivatives: Discovery of potent and selective JNK3 kinase inhibitors. Bioorg Med Chem 2022; 69:116894. [DOI: 10.1016/j.bmc.2022.116894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/16/2022] [Accepted: 06/16/2022] [Indexed: 11/02/2022]
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