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Peach CJ, Tonello R, Gomez K, Calderon-Rivera A, Bruni R, Bansia H, Maile L, Manu AM, Hahn H, Thomsen ARB, Schmidt BL, Davidson S, des Georges A, Khanna R, Bunnett NW. Neuropilin-1 is a co-receptor for NGF and TrkA-evoked pain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.06.570398. [PMID: 38106002 PMCID: PMC10723411 DOI: 10.1101/2023.12.06.570398] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Nerve growth factor (NGF) monoclonal antibodies (mAb) are one of the few patient-validated non-opioid treatments for chronic pain, despite failing to gain FDA approval due to worsened joint damage in some osteoarthritis patients. Herein, we demonstrate that neuropilin-1 (NRP1) is a nociceptor-enriched co-receptor for NGF that is necessary for tropomyosin-related kinase A (TrkA) signaling of pain. NGF binds NRP1 with nanomolar affinity. NRP1 and G Alpha Interacting Protein C-terminus 1 (GIPC1), a NRP1/TrkA adaptor, are coexpressed with TrkA in human and mouse nociceptors. NRP1 small molecule inhibitors and blocking mAb prevent NGF-stimulated action potential firing and activation of Na+ and Ca2+ channels in human and mouse nociceptors and abrogate NGF-evoked and inflammatory nociception in mice. NRP1 knockdown blunts NGF-stimulated TrkA phosphorylation, kinase signaling and transcription, whereas NRP1 overexpression enhances NGF and TrkA signaling. As well as interacting with NGF, NRP1 forms a heteromeric complex with TrkA. NRP1 thereby chaperones TrkA from the biosynthetic pathway to the plasma membrane and then to signaling endosomes, which enhances NGF-induced TrkA dimerization, endocytosis and signaling. Knockdown of GIPC1, a PDZ-binding protein that scaffolds NRP1 and TrkA to myosin VI, abrogates NGF-evoked excitation of nociceptors and pain-like behavior in mice. We identify NRP1 as a previously unrecognized co-receptor necessary for NGF/TrkA pain signaling by direct NGF binding and by chaperoning TrkA to the plasma membrane and signaling endosomes via the adaptor protein GIPC1. Antagonism of NRP1 and GIPC1 in nociceptors offers a long-awaited alternative to systemic sequestration of NGF with mAbs for the treatment of pain.
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Tamura T, Yamamoto H, Ogino S, Morioka Y, Tsujino S, Suzuki R, Hiono T, Suzuki S, Isoda N, Sakoda Y, Fukuhara T. A rapid and versatile reverse genetics approach for generating recombinant positive-strand RNA viruses that use IRES-mediated translation. J Virol 2024; 98:e0163823. [PMID: 38353536 PMCID: PMC10949505 DOI: 10.1128/jvi.01638-23] [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: 10/19/2023] [Accepted: 01/24/2024] [Indexed: 03/20/2024] Open
Abstract
Reverse genetics systems have played a central role in developing recombinant viruses for a wide spectrum of virus research. The circular polymerase extension reaction (CPER) method has been applied to studying positive-strand RNA viruses, allowing researchers to bypass molecular cloning of viral cDNA clones and thus leading to the rapid generation of recombinant viruses. However, thus far, the CPER protocol has only been established using cap-dependent RNA viruses. Here, we demonstrate that a modified version of the CPER method can be successfully applied to positive-strand RNA viruses that use cap-independent, internal ribosomal entry site (IRES)-mediated translation. As a proof-of-concept, we employed mammalian viruses with different types (classes I, II, and III) of IRES to optimize the CPER method. Using the hepatitis C virus (HCV, class III), we found that inclusion in the CPER assembly of an RNA polymerase I promoter and terminator, instead of those from polymerase II, allowed greater viral production. This approach was also successful in generating recombinant bovine viral diarrhea virus (class III) following transfection of MDBK/293T co-cultures to overcome low transfection efficiency. In addition, we successfully generated the recombinant viruses from clinical specimens. Our modified CPER could be used for producing hepatitis A virus (HAV, type I) as well as de novo generation of encephalomyocarditis virus (type II). Finally, we generated recombinant HCV and HAV reporter viruses that exhibited replication comparable to that of the wild-type parental viruses. The recombinant HAV reporter virus helped evaluate antivirals. Taking the findings together, this study offers methodological advances in virology. IMPORTANCE The lack of versatility of reverse genetics systems remains a bottleneck in viral research. Especially when (re-)emerging viruses reach pandemic levels, rapid characterization and establishment of effective countermeasures using recombinant viruses are beneficial in disease control. Indeed, numerous studies have attempted to establish and improve the methods. The circular polymerase extension reaction (CPER) method has overcome major obstacles in generating recombinant viruses. However, this method has not yet been examined for positive-strand RNA viruses that use cap-independent, internal ribosome entry site-mediated translation. Here, we engineered a suitable gene cassette to expand the CPER method for all positive-strand RNA viruses. Furthermore, we overcame the difficulty of generating recombinant viruses because of low transfection efficiency. Using this modified method, we also successfully generated reporter viruses and recombinant viruses from a field sample without virus isolation. Taking these findings together, our adapted methodology is an innovative technology that could help advance virologic research.
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Affiliation(s)
- Tomokazu Tamura
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Hirotaka Yamamoto
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Saho Ogino
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Yuhei Morioka
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Shuhei Tsujino
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
| | - Takahiro Hiono
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Saori Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
| | - Norikazu Isoda
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yoshihiro Sakoda
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
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103
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Guzman J, Weigelt K, Neumann A, Tripal P, Schmid B, Winter Z, Palmisano R, Culig Z, Cronauer MV, Muschler P, Wullich B, Taubert H, Wach S. NanoLuc Binary Technology as a methodological approach: an important new tool for studying the localization of androgen receptor and androgen receptor splice variant V7 homo and heterodimers. BMC Cancer 2024; 24:346. [PMID: 38500100 PMCID: PMC10949640 DOI: 10.1186/s12885-024-12110-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/12/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND The androgen/androgen receptor (AR)-signaling axis plays a central role in prostate cancer (PCa). Upon androgen-binding the AR dimerizes with another AR, and translocates into the nucleus where the AR-dimer activates/inactivates androgen-dependent genes. Consequently, treatments for PCa are commonly based on androgen deprivation therapy (ADT). The clinical benefits of ADT are only transitory and most tumors develop mechanisms allowing the AR to bypass its need for physiological levels of circulating androgens. Clinical failure of ADT is often characterized by the synthesis of a constitutively active AR splice variant, termed AR-V7. AR-V7 mRNA expression is considered as a resistance mechanism following ADT. AR-V7 no longer needs androgenic stimuli for nuclear entry and/or dimerization. METHODS Our goal was to mechanistically decipher the interaction between full-length AR (AR-FL) and AR-V7 in AR-null HEK-293 cells using the NanoLuc Binary Technology under androgen stimulation and deprivation conditions. RESULTS Our data point toward a hypothesis that AR-FL/AR-FL homodimers form in the cytoplasm, whereas AR-V7/AR-V7 homodimers localize in the nucleus. However, after androgen stimulation, all the AR-FL/AR-FL, AR-FL/AR-V7 and AR-V7/AR-V7 dimers were localized in the nucleus. CONCLUSIONS We showed that AR-FL and AR-V7 form heterodimers that localize to the nucleus, whereas AR-V7/AR-V7 dimers were found to localize in the absence of androgens in the nucleus.
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Affiliation(s)
- Juan Guzman
- Department of Urology and Pediatric Urology, Uniklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, 91054, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, 91054, Germany
| | - Katrin Weigelt
- Department of Urology and Pediatric Urology, Uniklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, 91054, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, 91054, Germany
| | - Angela Neumann
- Department of Urology and Pediatric Urology, Uniklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, 91054, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, 91054, Germany
| | - Philipp Tripal
- Optical Imaging Centre Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, 91054, Germany
| | - Benjamin Schmid
- Optical Imaging Centre Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, 91054, Germany
| | - Zoltán Winter
- Optical Imaging Centre Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, 91054, Germany
| | - Ralph Palmisano
- Optical Imaging Centre Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, 91054, Germany
| | - Zoran Culig
- Department of Urology, Division of Experimental Urology, Medical University of Innsbruck, Innsbruck, 6020, Austria
| | - Marcus V Cronauer
- Institute of Pathology, Universitätsklinikum Bonn, Universität Bonn, Bonn, 53127, Germany
| | | | - Bernd Wullich
- Department of Urology and Pediatric Urology, Uniklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, 91054, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, 91054, Germany
| | - Helge Taubert
- Department of Urology and Pediatric Urology, Uniklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, 91054, Germany.
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, 91054, Germany.
| | - Sven Wach
- Department of Urology and Pediatric Urology, Uniklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, 91054, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, 91054, Germany
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104
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Li M, Zhang C, Xu Y, Li S, Huang C, Wu J, Lei M. Structural insights into human EMC and its interaction with VDAC. Aging (Albany NY) 2024; 16:5501-5525. [PMID: 38517390 PMCID: PMC11006472 DOI: 10.18632/aging.205660] [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: 11/06/2023] [Accepted: 02/08/2024] [Indexed: 03/23/2024]
Abstract
The endoplasmic reticulum (ER) membrane protein complex (EMC) is a conserved, multi-subunit complex acting as an insertase at the ER membrane. Growing evidence shows that the EMC is also involved in stabilizing and trafficking membrane proteins. However, the structural basis and regulation of its multifunctionality remain elusive. Here, we report cryo-electron microscopy structures of human EMC in apo- and voltage-dependent anion channel (VDAC)-bound states at resolutions of 3.47 Å and 3.32 Å, respectively. We discovered a specific interaction between VDAC proteins and the EMC at mitochondria-ER contact sites, which is conserved from yeast to humans. Moreover, we identified a gating plug located inside the EMC hydrophilic vestibule, the substrate-binding pocket for client insertion. Conformation changes of this gating plug during the apo-to-VDAC-bound transition reveal that the EMC unlikely acts as an insertase in the VDAC1-bound state. Based on the data analysis, the gating plug may regulate EMC functions by modifying the hydrophilic vestibule in different states. Our discovery offers valuable insights into the structural basis of EMC's multifunctionality.
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Affiliation(s)
- Mingyue Li
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Chunli Zhang
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Yuntao Xu
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Shaobai Li
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Chenhui Huang
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Jian Wu
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Ming Lei
- Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
- Shanghai Institute of Precision Medicine, Shanghai 200125, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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105
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Zeng R, Fang M, Shen A, Chai X, Zhao Y, Liu M, Zhu L, Rui W, Feng B, Hong L, Ding C, Song Z, Lu W, Zhang A. Discovery of a Highly Potent Oxysterol Receptor GPR183 Antagonist Bearing the Benzo[ d]thiazole Structural Motif for the Treatment of Inflammatory Bowel Disease (IBD). J Med Chem 2024; 67:3520-3541. [PMID: 38417036 DOI: 10.1021/acs.jmedchem.3c01905] [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: 03/01/2024]
Abstract
Accumulating evidence has demonstrated a critical pathological role of oxysterol receptor GPR183 in various inflammatory and autoimmune diseases, including inflammatory bowel disease (IBD). However, the currently reported GPR183 antagonists are very limited and not qualified for in vivo studies due to their inferior druglike properties. Herein, we conducted a structural elaboration focusing on improving its PK and safety profile based on a reference antagonist NIBR189. Of note, compound 33, bearing an aminobenzothiazole motif, exhibited reduced hERG inhibition, improved PK properties, and robust antagonistic activity (IC50 = 0.82 nM) with high selectivity against GPR183. Moreover, compound 33 displayed strong in vitro antimigration and anti-inflammatory activity in monocytes. Oral administration of compound 33 effectively improved the pathological symptoms of DSS-induced experimental colitis. All of these findings demonstrate that compound 33 is a novel and promising GPR183 antagonist suitable for further investigation to treat IBD.
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Affiliation(s)
- Ruoqing Zeng
- Shanghai Frontiers Science Center for Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Innovative Immunotherapy, Shanghai 200240, China
| | - Meimiao Fang
- Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Ancheng Shen
- Shanghai Frontiers Science Center for Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- Lingang Laboratory, Shanghai 200210, China
- National Key Laboratory of Innovative Immunotherapy, Shanghai 200240, China
| | - Xiaolei Chai
- Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yumiao Zhao
- Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Mingyao Liu
- Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Lingfeng Zhu
- Chemical Biology Research Center at School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Weiwei Rui
- Department of General Surgery and Department of Pathology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Bo Feng
- Department of General Surgery and Department of Pathology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Liang Hong
- Shanghai Frontiers Science Center for Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Innovative Immunotherapy, Shanghai 200240, China
| | - Chunyong Ding
- Shanghai Frontiers Science Center for Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Innovative Immunotherapy, Shanghai 200240, China
| | - Zilan Song
- Shanghai Frontiers Science Center for Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Innovative Immunotherapy, Shanghai 200240, China
| | - Weiqiang Lu
- Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Ao Zhang
- Shanghai Frontiers Science Center for Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- Lingang Laboratory, Shanghai 200210, China
- National Key Laboratory of Innovative Immunotherapy, Shanghai 200240, China
- Chemical Biology Research Center at School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035, China
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106
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Malmsheimer S, Grin I, Bohn E, Franz-Wachtel M, Macek B, Sahr T, Smollich F, Chetrit D, Meir A, Roy C, Buchrieser C, Wagner S. The T4bSS of Legionella features a two-step secretion pathway with an inner membrane intermediate for secretion of transmembrane effectors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.14.584949. [PMID: 38559167 PMCID: PMC10980071 DOI: 10.1101/2024.03.14.584949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
To promote intracellular survival and infection, Legionella spp. translocate hundreds of effector proteins into eukaryotic host cells using a type IV b protein secretion system (T4bSS). T4bSS are well known to translocate soluble as well as transmembrane domain-containing effector proteins (TMD-effectors) but the mechanisms of secretion are still poorly understood. Herein we investigated the secretion of hydrophobic TMD-effectors, of which about 80 were previously reported to be encoded by L. pneumophila. A proteomic analysis of fractionated membranes revealed that TMD-effectors are targeted to and inserted into the bacterial inner membranes of L. pneumophila independent of the presence of a functional T4bSS. While the T4bSS chaperones IcmS and IcmW were critical for secretion of all tested TMD-effectors, they did not influence inner membrane targeting of these proteins. As for soluble effector proteins, translocation of TMD-effectors into host cells depended on a C-terminal secretion signal and this signal needed to be presented towards the cytoplasmic side of the inner membrane. A different secretion behavior of TMD- and soluble effectors and the need for small periplasmic loops within TMD-effectors provided strong evidence that TMD-effectors are secreted in a two-step secretion process: Initially, an inner membrane intermediate is formed, that is extracted towards the cytoplasmic side, possibly by the help of the type IV coupling protein complex and subsequently secreted into eukaryotic host cells by the T4bSS core complex. Overall, our study highlights the amazing versatility of T4bSS to secrete soluble and TMD-effectors from different subcellular locations of the bacterial cell.
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Affiliation(s)
- Silke Malmsheimer
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Section of Cellular and Molecular Microbiology, Elfriede-Aulhorn-Str. 6, 72076 Tübingen, Germany
- Current address: Institut de Recherche en Infectiologie de Montpellier, Equipe Kremer, UMR 9004 - CNRS / UM, 1919 route de Mende, 34293 Montpellier cedex 5, France
| | - Iwan Grin
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Section of Cellular and Molecular Microbiology, Elfriede-Aulhorn-Str. 6, 72076 Tübingen, Germany
| | - Erwin Bohn
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Institute of Medical Microbiology and Hygiene, Elfriede-Aulhorn-Str. 6, 72076 Tübingen, Germany
| | - Mirita Franz-Wachtel
- University of Tübingen, Proteome Center Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Boris Macek
- University of Tübingen, Proteome Center Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Tobias Sahr
- Institute Pasteur, Université Paris Cité, Biologie des Bactéries Intracellulaires, 75015 Paris, France
| | - Fabian Smollich
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Section of Cellular and Molecular Microbiology, Elfriede-Aulhorn-Str. 6, 72076 Tübingen, Germany
| | - David Chetrit
- Yale University, Department of Microbial Pathogenesis, 295 Congress Avenue, New Haven, CT 06536-0812, USA
| | - Amit Meir
- Yale University, Department of Microbial Pathogenesis, 295 Congress Avenue, New Haven, CT 06536-0812, USA
- Birkbeck Institute of Structural and Molecular Biology, Birkbeck and UCL, Malet Street, London WC1E 7HX, UK
- Current address: University of Glasgow, MRC Centre for Virus Research, School of Infection and Immunity, Glasgow, UK
| | - Craig Roy
- Yale University, Department of Microbial Pathogenesis, 295 Congress Avenue, New Haven, CT 06536-0812, USA
| | - Carmen Buchrieser
- Institute Pasteur, Université Paris Cité, Biologie des Bactéries Intracellulaires, 75015 Paris, France
| | - Samuel Wagner
- University of Tübingen, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Section of Cellular and Molecular Microbiology, Elfriede-Aulhorn-Str. 6, 72076 Tübingen, Germany
- Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), Elfriede-Aulhorn-Str. 6, 72076 Tébingen, Germany
- German Center for Infection Research (DZIF), partner-site Tübingen, Elfriede-Aulhorn-Str. 6, 72076 Tübingen, Germany
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107
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Zarca AM, Adlere I, Viciano CP, Arimont-Segura M, Meyrath M, Simon IA, Bebelman JP, Laan D, Custers HGJ, Janssen E, Versteegh KL, Buzink MCML, Nesheva DN, Bosma R, de Esch IJP, Vischer HF, Wijtmans M, Szpakowska M, Chevigné A, Hoffmann C, de Graaf C, Zarzycka BA, Windhorst AD, Smit MJ, Leurs R. Pharmacological Characterization and Radiolabeling of VUF15485, a High-Affinity Small-Molecule Agonist for the Atypical Chemokine Receptor ACKR3. Mol Pharmacol 2024; 105:301-312. [PMID: 38346795 DOI: 10.1124/molpharm.123.000835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/16/2024] [Indexed: 03/16/2024] Open
Abstract
Atypical chemokine receptor 3 (ACKR3), formerly referred to as CXCR7, is considered to be an interesting drug target. In this study, we report on the synthesis, pharmacological characterization and radiolabeling of VUF15485, a new ACKR3 small-molecule agonist, that will serve as an important new tool to study this β-arrestin-biased chemokine receptor. VUF15485 binds with nanomolar affinity (pIC50 = 8.3) to human ACKR3, as measured in [125I]CXCL12 competition binding experiments. Moreover, in a bioluminescence resonance energy transfer-based β-arrestin2 recruitment assay VUF15485 acts as a potent ACKR3 agonist (pEC50 = 7.6) and shows a similar extent of receptor activation compared with CXCL12 when using a newly developed, fluorescence resonance energy transfer-based ACKR3 conformational sensor. Moreover, the ACKR3 agonist VUF15485, tested against a (atypical) chemokine receptor panel (agonist and antagonist mode), proves to be selective for ACKR3. VUF15485 labeled with tritium at one of its methoxy groups ([3H]VUF15485), binds ACKR3 saturably and with high affinity (K d = 8.2 nM). Additionally, [3H]VUF15485 shows rapid binding kinetics and consequently a short residence time (<2 minutes) for binding to ACKR3. The selectivity of [3H]VUF15485 for ACKR3, was confirmed by binding studies, whereupon CXCR3, CXCR4, and ACKR3 small-molecule ligands were competed for binding against the radiolabeled agonist. Interestingly, the chemokine ligands CXCL11 and CXCL12 are not able to displace the binding of [3H]VUF15485 to ACKR3. The radiolabeled VUF15485 was subsequently used to evaluate its binding pocket. Site-directed mutagenesis and docking studies using a recently solved cryo-EM structure propose that VUF15485 binds in the major and the minor binding pocket of ACKR3. SIGNIFICANCE STATEMENT: The atypical chemokine receptor atypical chemokine receptor 3 (ACKR3) is considered an interesting drug target in relation to cancer and multiple sclerosis. The study reports on new chemical biology tools for ACKR3, i.e., a new agonist that can also be radiolabeled and a new ACKR3 conformational sensor, that both can be used to directly study the interaction of ACKR3 ligands with the G protein-coupled receptor.
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Affiliation(s)
- Aurelien M Zarca
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Ilze Adlere
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Cristina P Viciano
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Marta Arimont-Segura
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Max Meyrath
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Icaro A Simon
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Jan Paul Bebelman
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Dennis Laan
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Hans G J Custers
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Elwin Janssen
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Kobus L Versteegh
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Maurice C M L Buzink
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Desislava N Nesheva
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Reggie Bosma
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Iwan J P de Esch
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Henry F Vischer
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Maikel Wijtmans
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Martyna Szpakowska
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Andy Chevigné
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Carsten Hoffmann
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Chris de Graaf
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Barbara A Zarzycka
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Albert D Windhorst
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Martine J Smit
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
| | - Rob Leurs
- Department of Medicinal Chemistry (A.M.Z., M.A.-S., I.A.S., J.P.B., H.G.J.C., K.L.V., M.C.M.L.B., D.N.N., R.B., I.J.P.dE., H.F.V., M.W., C.dG., B.A.Z., M.J.S., R.L.) and Department of Chemistry & Pharmaceutical Sciences (E.J.), Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV Amsterdam, Netherlands; Griffin Discoveries BV, Amsterdam, Netherlands (I.A., I.J.P.dE., R.L.); Bio-Imaging-Center/Rudolf-Virchow-Zentrum, Institut für Pharmakologie, Versbacher Strasse 9, 97078 Würzburg, Germany (C.P.V., C.H.); Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg (M.M., M.S., A.C.); and Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands (D.L., A.D.W.)
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108
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Bogaert B, Debisschop A, Ehouarne T, Van Eeckhoutte HP, De Volder J, Jacobs A, Pottie E, De Rycke R, Crabbé A, Mestdagh P, Lentacker I, Brusselle GG, Stove C, Verstraelen S, Maes T, Bracke KR, De Smedt SC, Raemdonck K. Selective Replacement of Cholesterol with Cationic Amphiphilic Drugs Enables the Design of Lipid Nanoparticles with Improved RNA Delivery. NANO LETTERS 2024; 24:2961-2971. [PMID: 38477058 DOI: 10.1021/acs.nanolett.3c03345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
The delivery of RNA across biological barriers can be achieved by encapsulation in lipid nanoparticles (LNPs). Cationic amphiphilic drugs (CADs) are pharmacologically diverse compounds with ionizable lipid-like features. In this work, we applied CADs as a fifth component of state-of-the-art LNPs via microfluidic mixing. Improved cytosolic delivery of both siRNA and mRNA was achieved by partly replacing the cholesterol fraction of LNPs with CADs. The LNPs could cross the mucus layer in a mucus-producing air-liquid interface model of human primary bronchial epithelial cells following nebulization. Moreover, CAD-LNPs demonstrated improved epithelial and endothelial targeting following intranasal administration in mice, without a marked pro-inflammatory signature. Importantly, quantification of the CAD-LNP molar composition, as demonstrated for nortriptyline, revealed a gradual leakage of the CAD from the formulation during LNP dialysis. Altogether, these data suggest that the addition of a CAD prior to the rapid mixing process might have an impact on the composition, structure, and performance of LNPs.
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Affiliation(s)
- Bram Bogaert
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Aliona Debisschop
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Thomas Ehouarne
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Hannelore P Van Eeckhoutte
- Laboratory for Translational Research in Obstructive Pulmonary Diseases, Department of Respiratory Medicine, Ghent University Hospital, Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium
| | - Joyceline De Volder
- Laboratory for Translational Research in Obstructive Pulmonary Diseases, Department of Respiratory Medicine, Ghent University Hospital, Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium
| | - An Jacobs
- Health Unit, Flemish Institute for Technological Research (VITO), Boeretang 200, 2400 Mol, Belgium
| | - Eline Pottie
- Laboratory of Toxicology, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Riet De Rycke
- Ghent University Expertise Center for Transmission Electron Microscopy and VIB BioImaging Core, 9000 Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, VIB Center for Inflammation Research, 9052 Ghent, Belgium
| | - Aurélie Crabbé
- Laboratory of Pharmaceutical Microbiology, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Pieter Mestdagh
- Department of Biomolecular Medicine, OncoRNAlab, Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium
| | - Ine Lentacker
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Guy G Brusselle
- Laboratory for Translational Research in Obstructive Pulmonary Diseases, Department of Respiratory Medicine, Ghent University Hospital, Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium
| | - Christophe Stove
- Laboratory of Toxicology, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Sandra Verstraelen
- Health Unit, Flemish Institute for Technological Research (VITO), Boeretang 200, 2400 Mol, Belgium
| | - Tania Maes
- Laboratory for Translational Research in Obstructive Pulmonary Diseases, Department of Respiratory Medicine, Ghent University Hospital, Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium
| | - Ken R Bracke
- Laboratory for Translational Research in Obstructive Pulmonary Diseases, Department of Respiratory Medicine, Ghent University Hospital, Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium
| | - Stefaan C De Smedt
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Koen Raemdonck
- Ghent Research Group on Nanomedicines, Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
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109
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Imamura K, Akagi KI, Miyanoiri Y, Tsujimoto H, Hirokawa T, Ashida H, Murakami K, Inoue A, Suno R, Ikegami T, Sekiyama N, Iwata S, Kobayashi T, Tochio H. Interaction modes of human orexin 2 receptor with selective and nonselective antagonists studied by NMR spectroscopy. Structure 2024; 32:352-361.e5. [PMID: 38194963 DOI: 10.1016/j.str.2023.12.008] [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: 02/24/2023] [Revised: 08/17/2023] [Accepted: 12/13/2023] [Indexed: 01/11/2024]
Abstract
Orexin neuropeptides have many physiological roles in the sleep-wake cycle, feeding behavior, reward demands, and stress responses by activating cognitive receptors, the orexin receptors (OX1R and OX2R), distributed in the brain. There are only subtle differences between OX1R and OX2R in the orthosteric site, which has hindered the rational development of subtype-selective antagonists. In this study, we utilized solution-state NMR to capture the structural plasticity of OX2R labeled with 13CH3-ε-methionine in complex with antagonists. Mutations in the orthosteric site allosterically affected the intracellular tip of TM6. Ligand exchange experiments with the subtype-selective EMPA and the nonselective suvorexant identified three methionine residues that were substantially perturbed. The NMR spectra suggested that the suvorexant-bound state exhibited more structural plasticity than the EMPA-bound state, which has not been foreseen from the close similarity of their crystal structures, providing insights into dynamic features to be considered in understanding the ligand recognition mode.
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Affiliation(s)
- Kayo Imamura
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Ken-Ichi Akagi
- Section of Laboratory Equipment, National Institute of Biomedical Innovation, Health, and Nutrition, Osaka 567-0085, Japan
| | - Yohei Miyanoiri
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hirokazu Tsujimoto
- Department of Cell Biology and Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Takatsugu Hirokawa
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575, Japan; Transborder Medical Research Center, University of Tsukuba, Tsukuba 305-8575, Japan
| | - Hideo Ashida
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kaori Murakami
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Ryoji Suno
- Department of Medical Chemistry, Kansai Medical University, Hirakata 573-1010, Japan
| | - Takahisa Ikegami
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa 230-0045, Japan
| | - Naotaka Sekiyama
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - So Iwata
- Department of Cell Biology and Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Takuya Kobayashi
- Department of Medical Chemistry, Kansai Medical University, Hirakata 573-1010, Japan
| | - Hidehito Tochio
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
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110
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Iamshanova O, Hämmerli AF, Ramaye E, Seljmani A, Ross-Kaschitza D, Schärz N, Essers M, Guichard S, Rougier JS, Abriel H. The dispensability of 14-3-3 proteins for the regulation of human cardiac sodium channel Nav1.5. PLoS One 2024; 19:e0298820. [PMID: 38452156 PMCID: PMC10919853 DOI: 10.1371/journal.pone.0298820] [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: 07/11/2023] [Accepted: 01/30/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND 14-3-3 proteins are ubiquitous proteins that play a role in cardiac physiology (e.g., metabolism, development, and cell cycle). Furthermore, 14-3-3 proteins were proposed to regulate the electrical function of the heart by interacting with several cardiac ion channels, including the voltage-gated sodium channel Nav1.5. Given the many cardiac arrhythmias associated with Nav1.5 dysfunction, understanding its regulation by the protein partners is crucial. AIMS In this study, we aimed to investigate the role of 14-3-3 proteins in the regulation of the human cardiac sodium channel Nav1.5. METHODS AND RESULTS Amongst the seven 14-3-3 isoforms, only 14-3-3η (encoded by YWHAH gene) weakly co-immunoprecipitated with Nav1.5 when heterologously co-expressed in tsA201 cells. Total and cell surface expression of Nav1.5 was however not modified by 14-3-3η overexpression or inhibition with difopein, and 14-3-3η did not affect physical interaction between Nav1.5 α-α subunits. The current-voltage relationship and the amplitude of Nav1.5-mediated sodium peak current density were also not changed. CONCLUSIONS Our findings illustrate that the direct implication of 14-3-3 proteins in regulating Nav1.5 is not evident in a transformed human kidney cell line tsA201.
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Affiliation(s)
- Oksana Iamshanova
- Faculty of Medicine, Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Anne-Flore Hämmerli
- Faculty of Medicine, Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Elise Ramaye
- Faculty of Medicine, Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Arbresh Seljmani
- Faculty of Medicine, Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
- medi—Center for Medical Education, Bern, Switzerland
| | - Daniela Ross-Kaschitza
- Faculty of Medicine, Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Noëlia Schärz
- Faculty of Medicine, Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
- medi—Center for Medical Education, Bern, Switzerland
| | - Maria Essers
- Faculty of Medicine, Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Sabrina Guichard
- Faculty of Medicine, Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Jean-Sébastien Rougier
- Faculty of Medicine, Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Hugues Abriel
- Faculty of Medicine, Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
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111
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Tang Y, Liao X, Cao Y. A Proximity-Dependent Biosensor System for Visualizing Cell-Cell Interactions Induced by Therapeutic Antibodies. J Pharm Sci 2024; 113:579-586. [PMID: 38103691 PMCID: PMC10922735 DOI: 10.1016/j.xphs.2023.12.008] [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: 09/03/2023] [Revised: 12/08/2023] [Accepted: 12/09/2023] [Indexed: 12/19/2023]
Abstract
Despite the promise of therapeutic antibodies in engaging the immune system to eliminate malignant cells, many aspects of the complex interplay between immune cells and cancer cells induced by antibody therapy remain incompletely understood. This study aimed to develop a biosensor system that can evaluate direct cell-cell physical contact and interactions between immune effector and target cells induced by therapeutic antibodies in physiologically relevant environments. The system uses two structural complementary luciferase units (SmBit and LgBit) expressed on the respective membranes of effector and target cells. Upon cell-cell contact, the two subunits form active NanoLuc, generating a luminescent signal, allowing for real-time monitoring of cell-cell interactions and quantitatively assessing the pharmacological effects of therapeutic antibodies. We optimized the system to ensure selectivity by adjusting the spacer lengths between two luciferase units to minimize interference from nonspecific intercellular contact. The system was applied to quantitatively monitor cell-cell interactions between NK and target cells induced by rituximab and between T and target cells induced by blinatumomab in a 3D cell culture system. The biosensor system has the potential to characterize antibody pharmacology through a deeper understanding of antibody-mediated cell-cell interactions.
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Affiliation(s)
- Yu Tang
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC. 27599, United States
| | - XiaoZhi Liao
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC. 27599, United States
| | - Yanguang Cao
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC. 27599, United States; Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.
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112
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Lin S, Schneider C, Su AH, Alexe G, Root DE, Stegmaier K. The UBE2J2/UBE2K-MARCH5 ubiquitination machinery regulates apoptosis in response to venetoclax in acute myeloid leukemia. Leukemia 2024; 38:652-656. [PMID: 38366087 PMCID: PMC10912020 DOI: 10.1038/s41375-024-02178-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/30/2024] [Accepted: 02/07/2024] [Indexed: 02/18/2024]
Affiliation(s)
- Shan Lin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Constanze Schneider
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Angela H Su
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gabriela Alexe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
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113
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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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114
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Shakhova ES, Karataeva TA, Markina NM, Mitiouchkina T, Palkina KA, Perfilov MM, Wood MG, Hoang TT, Hall MP, Fakhranurova LI, Alekberova AE, Malyshevskaia AK, Gorbachev DA, Bugaeva EN, Pletneva LK, Babenko VV, Boldyreva DI, Gorokhovatsky AY, Balakireva AV, Gao F, Choob VV, Encell LP, Wood KV, Yampolsky IV, Sarkisyan KS, Mishin AS. An improved pathway for autonomous bioluminescence imaging in eukaryotes. Nat Methods 2024; 21:406-410. [PMID: 38253843 PMCID: PMC10927554 DOI: 10.1038/s41592-023-02152-y] [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: 03/17/2023] [Accepted: 12/13/2023] [Indexed: 01/24/2024]
Abstract
The discovery of the bioluminescence pathway in the fungus Neonothopanus nambi enabled engineering of eukaryotes with self-sustained luminescence. However, the brightness of luminescence in heterologous hosts was limited by performance of the native fungal enzymes. Here we report optimized versions of the pathway that enhance bioluminescence by one to two orders of magnitude in plant, fungal and mammalian hosts, and enable longitudinal video-rate imaging.
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Affiliation(s)
- Ekaterina S Shakhova
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana A Karataeva
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Nadezhda M Markina
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana Mitiouchkina
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Kseniia A Palkina
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Maxim M Perfilov
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | | | | | | | - Anna E Alekberova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alena K Malyshevskaia
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry A Gorbachev
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Vladislav V Babenko
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Daria I Boldyreva
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Andrey Y Gorokhovatsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anastasia V Balakireva
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Feng Gao
- Synthetic Biology Group, MRC Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Vladimir V Choob
- Planta LLC, Moscow, Russia
- Botanical Garden of Lomonosov Moscow State University, Moscow, Russia
| | | | | | - Ilia V Yampolsky
- Planta LLC, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Light Bio Inc, Ketchum, ID, USA
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Karen S Sarkisyan
- Planta LLC, Moscow, Russia.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
- Synthetic Biology Group, MRC Laboratory of Medical Sciences, London, UK.
- Institute of Clinical Sciences, Faculty of Medicine and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.
- Light Bio Inc, Ketchum, ID, USA.
| | - Alexander S Mishin
- Planta LLC, Moscow, Russia.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
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115
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Deng M, Zhang C, Yan W, Chen L, He B, Li Y. Development of Fluorescence-Based Assays for Key Viral Proteins in the SARS-CoV-2 Infection Process and Lifecycle. Int J Mol Sci 2024; 25:2850. [PMID: 38474097 DOI: 10.3390/ijms25052850] [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: 01/09/2024] [Revised: 02/09/2024] [Accepted: 02/25/2024] [Indexed: 03/14/2024] Open
Abstract
Since the appearance of SARS-CoV-2 in 2019, the ensuing COVID-19 (Corona Virus Disease 2019) pandemic has posed a significant threat to the global public health system, human health, life, and economic well-being. Researchers worldwide have devoted considerable efforts to curb its spread and development. The latest studies have identified five viral proteins, spike protein (Spike), viral main protease (3CLpro), papain-like protease (PLpro), RNA-dependent RNA polymerase (RdRp), and viral helicase (Helicase), which play crucial roles in the invasion of SARS-CoV-2 into the human body and its lifecycle. The development of novel anti-SARS-CoV-2 drugs targeting these five viral proteins holds immense promise. Therefore, the development of efficient, high-throughput screening methodologies specifically designed for these viral proteins is of utmost importance. Currently, a plethora of screening techniques exists, with fluorescence-based assays emerging as predominant contenders. In this review, we elucidate the foundational principles and methodologies underpinning fluorescence-based screening approaches directed at these pivotal viral targets, hoping to guide researchers in the judicious selection and refinement of screening strategies, thereby facilitating the discovery and development of lead compounds for anti-SARS-CoV-2 pharmaceuticals.
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Affiliation(s)
- Mingzhenlong Deng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China
| | - Chuang Zhang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China
| | - Wanli Yan
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China
| | - Lei Chen
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China
| | - Bin He
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China
| | - Yan Li
- School of Basic Medical Science, Guizhou Medical University, Guiyang 550004, China
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116
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Huber AD, Poudel S, Wu J, Miller DJ, Lin W, Yang L, Bwayi MN, Rimmer MA, Gee RRF, Seetharaman J, Chai SC, Chen T. A bromodomain-independent mechanism of gene regulation by the BET inhibitor JQ1: direct activation of nuclear receptor PXR. Nucleic Acids Res 2024; 52:1661-1676. [PMID: 38084912 PMCID: PMC10899790 DOI: 10.1093/nar/gkad1175] [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: 10/03/2023] [Revised: 11/17/2023] [Accepted: 11/23/2023] [Indexed: 02/29/2024] Open
Abstract
Bromodomain and extraterminal (BET) proteins are extensively studied in multiple pathologies, including cancer. BET proteins modulate transcription of various genes, including those synonymous with cancer, such as MYC. Thus, BET inhibitors are a major area of drug development efforts. (+)-JQ1 (JQ1) is the prototype inhibitor and is a common tool to probe BET functions. While showing therapeutic promise, JQ1 is not clinically usable, partly due to metabolic instability. Here, we show that JQ1 and the BET-inactive (-)-JQ1 are agonists of pregnane X receptor (PXR), a nuclear receptor that transcriptionally regulates genes encoding drug-metabolizing enzymes such as CYP3A4, which was previously shown to oxidize JQ1. A PXR-JQ1 co-crystal structure identified JQ1's tert-butyl moiety as a PXR anchor and explains binding by (-)-JQ1. Analogs differing at the tert-butyl lost PXR binding, validating our structural findings. Evaluation in liver cell models revealed both PXR-dependent and PXR-independent modulation of CYP3A4 expression by BET inhibitors. We have characterized a non-BET JQ1 target, a mechanism of physiological JQ1 instability, a biological function of (-)-JQ1, and BET-dependent transcriptional regulation of drug metabolism genes.
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Affiliation(s)
- Andrew D Huber
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Shyaron Poudel
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Jing Wu
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Darcie J Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Wenwei Lin
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Lei Yang
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Monicah N Bwayi
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Mary Ashley Rimmer
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Rebecca R Florke Gee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Jayaraman Seetharaman
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Sergio C Chai
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
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117
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Nair ASR, Samanta A, Hazra S. Understanding the basis of thermostability for enzyme "Nanoluc" towards designing industry-competent engineered variants. J Biomol Struct Dyn 2024:1-14. [PMID: 38419322 DOI: 10.1080/07391102.2024.2319675] [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: 10/26/2023] [Accepted: 02/12/2024] [Indexed: 03/02/2024]
Abstract
As a leading contender in the study of luminescence, nanoluciferase has recently attracted attention and proven effective in a wide variety of research areas. Although numerous attempts have been made to improve activity, there has yet to be a thorough exploration of further possibilities to improve thermostability. In this study, protein engineering in tandem with molecular dynamics simulation at various temperatures (300 K, 400 K, 450 K and 500 K) was used to improve our understanding of nanoluciferase dynamics and identification of factors that could significantly enhance the thermostability. Based on these, three novel mutations have been narrowed down, which were hypothesised to improve thermostability. Root mean square deviation and root mean square fluctuation studies confirmed higher stability of mutant at high temperature. Solvent-accessible surface area and protein unfolding studies revealed a decreased tendency of mutant to unfold at higher temperatures. Further free energy landscape and principal component analysis was adapted to get deeper insights into the thermodynamic and structural behavior of these proteins at elevated temperature. Thus, this study provides a deeper insight into the dynamic factors for thermostability and introduces a novel, enhanced nanoluciferase candidate with potential use in industry.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Adwaita S R Nair
- Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Arup Samanta
- Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
- Department of Physics, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Saugata Hazra
- Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
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118
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Mikheil D, Larsen MA, Hsiao K, Murray NH, Ugo T, Wang H, Goueli SA. A bioluminescent and homogeneous assay for monitoring GPCR-mediated cAMP modulation and PDE activity. Sci Rep 2024; 14:4440. [PMID: 38396287 PMCID: PMC10891162 DOI: 10.1038/s41598-024-55038-0] [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: 10/30/2023] [Accepted: 02/20/2024] [Indexed: 02/25/2024] Open
Abstract
3',5'-Cyclic adenosine monophosphate (cAMP), the first identified second messenger, is implicated in diverse cellular processes involving cellular metabolism, cell proliferation and differentiation, apoptosis, and gene expression. cAMP is synthesized by adenylyl cyclase (AC), which converts ATP to cAMP upon activation of Gαs-protein coupled receptors (GPCRs) in most cases and hydrolyzed by cyclic nucleotide phosphodiesterases (PDEs) to 5'-AMP. Dysregulation of cAMP signaling is implicated in a wide range of pathophysiological conditions such as cardiovascular diseases, neurodegenerative and behavioral disorders, cancers, diabetes, obesity, cataracts, and others. Therefore, cAMP targeted therapies have been and are still undergoing intense investigation for the treatment of these and other diseases. This highlights the need for developing assays to detect and monitor cAMP levels. In this study, we show cAMP Lumit assay as a highly specific homogeneous bioluminescent assay suitable for high throughput screenings with a large assay window and a wide dynamic range for cAMP detection. We believe that this assay will aid and simplify drug discovery screening efforts for cAMP signaling targeted therapies.
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Affiliation(s)
- Dareen Mikheil
- Promega Corporation, 2800 Woods Hollow Road, Madison, WI, 53711, USA
| | - Matthew A Larsen
- Promega Biosciences, 277 Granada Drive, San Luis Obispo, CA, 93401, USA
| | - Kevin Hsiao
- Promega Corporation, 2800 Woods Hollow Road, Madison, WI, 53711, USA
| | - Nathan H Murray
- Promega Corporation, 2800 Woods Hollow Road, Madison, WI, 53711, USA
| | - Tim Ugo
- Promega Biosciences, 277 Granada Drive, San Luis Obispo, CA, 93401, USA
| | - Hui Wang
- Promega Biosciences, 277 Granada Drive, San Luis Obispo, CA, 93401, USA
| | - Said A Goueli
- Promega Corporation, 2800 Woods Hollow Road, Madison, WI, 53711, USA.
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119
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Rakotoarison LM, Tebo AG, Böken D, Board S, El Hajji L, Gautier A. Improving Split Reporters of Protein-Protein Interactions through Orthology-Based Protein Engineering. ACS Chem Biol 2024; 19:428-441. [PMID: 38289242 DOI: 10.1021/acschembio.3c00631] [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] [Indexed: 02/17/2024]
Abstract
Protein-protein interactions (PPIs) can be detected through selective complementation of split fluorescent reporters made of two complementary fragments that reassemble into a functional fluorescent reporter when in close proximity. We previously introduced splitFAST, a chemogenetic PPI reporter with rapid and reversible complementation. Here, we present the engineering of splitFAST2, an improved reporter displaying higher brightness, lower self-complementation, and higher dynamic range for optimal monitoring of PPI using an original protein engineering strategy that exploits proteins with orthology relationships. Our study allowed the identification of a system with improved properties and enabled a better understanding of the molecular features controlling the complementation properties. Because of the rapidity and reversibility of its complementation, its low self-complementation, high dynamic range, and improved brightness, splitFAST2 is well suited to study PPI with high spatial and temporal resolution, opening great prospects to decipher the role of PPI in various biological contexts.
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Affiliation(s)
- Louise-Marie Rakotoarison
- Laboratoire de Biomolécules, UMR 7203, Sorbonne Université - CNRS - École Normale Supérieure, 75005 Paris, France
- PASTEUR, Department of Chemistry, École Normale Supérieure, Université PSL, Sorbonne Université, CNRS, 75005 Paris, France
| | - Alison G Tebo
- Laboratoire de Biomolécules, UMR 7203, Sorbonne Université - CNRS - École Normale Supérieure, 75005 Paris, France
- PASTEUR, Department of Chemistry, École Normale Supérieure, Université PSL, Sorbonne Université, CNRS, 75005 Paris, France
| | - Dorothea Böken
- PASTEUR, Department of Chemistry, École Normale Supérieure, Université PSL, Sorbonne Université, CNRS, 75005 Paris, France
| | - Stephanie Board
- Laboratoire de Biomolécules, UMR 7203, Sorbonne Université - CNRS - École Normale Supérieure, 75005 Paris, France
| | - Lina El Hajji
- Laboratoire de Biomolécules, UMR 7203, Sorbonne Université - CNRS - École Normale Supérieure, 75005 Paris, France
| | - Arnaud Gautier
- Laboratoire de Biomolécules, UMR 7203, Sorbonne Université - CNRS - École Normale Supérieure, 75005 Paris, France
- PASTEUR, Department of Chemistry, École Normale Supérieure, Université PSL, Sorbonne Université, CNRS, 75005 Paris, France
- Institut Universitaire de France, 75231 Paris, France
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120
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Miao P, Zhou JM, Wang W. A self-assembling split Nano luciferase-based assay for investigating Pseudomonas syringae effector secretion. STRESS BIOLOGY 2024; 4:14. [PMID: 38363371 PMCID: PMC10873255 DOI: 10.1007/s44154-024-00152-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 01/28/2024] [Indexed: 02/17/2024]
Abstract
Many Gram-negative pathogens employ the type III secretion system (T3SS) to deliver effector proteins into host cells, thereby modulating host cellular processes and suppressing host immunity to facilitate pathogenesis and colonization. In this study, we developed a straightforward, rapid, and quantitative method for detecting T3SS-mediated translocation of Pseudomonas syringae effectors using a self-assembling split Nano luciferase (Nluc)-based reporter system. It was demonstrated that this system can detect effector secretion in vitro with an exceptionally high signal-to-noise ratio and sensitivity, attributed to the strong affinity between the split domains of Nluc and the intense luminescence generated by functional Nluc. During natural infections, effectors fused to a small C-terminal fragment of Nluc were successfully translocated into plant cells and retained their virulence functions. Furthermore, upon infection of plants expressing the N-terminal fragment of Nluc with these P. syringae strains, functional Nluc proteins were spontaneously assembled and produced bright luminescence, demonstrating that this system enables the straightforward and rapid assessment of P. syringae T3SS-mediated effector translocation during natural infections. In conclusion, the self-assembling split Nluc-based reporting system developed in this study is suitable for efficient in vitro and in planta detection of effectors secreted via T3SS.
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Affiliation(s)
- Pei Miao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Yazhouwan National Laboratory, Sanya, 572024, China
| | - Jian-Min Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
- Yazhouwan National Laboratory, Sanya, 572024, China
| | - Wei Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China.
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121
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Braga Emidio N, Small BM, Keller AR, Cheloha RW, Wingler LM. Nanobody-Mediated Dualsteric Engagement of the Angiotensin Receptor Broadens Biased Ligand Pharmacology. Mol Pharmacol 2024; 105:260-271. [PMID: 38164609 PMCID: PMC10877709 DOI: 10.1124/molpharm.123.000797] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/15/2023] [Accepted: 12/04/2023] [Indexed: 01/03/2024] Open
Abstract
Dualsteric G protein-coupled receptor (GPCR) ligands are a class of bitopic ligands that consist of an orthosteric pharmacophore, which binds to the pocket occupied by the receptor's endogenous agonist, and an allosteric pharmacophore, which binds to a distinct site. These ligands have the potential to display characteristics of both orthosteric and allosteric ligands. To explore the signaling profiles that dualsteric ligands of the angiotensin II type 1 receptor (AT1R) can access, we ligated a 6e epitope tag-specific nanobody (single-domain antibody fragment) to angiotensin II (AngII) and analogs that show preferential allosteric coupling to Gq (TRV055, TRV056) or β-arrestin (TRV027). While the nanobody itself acts as a probe-specific neutral or negative allosteric ligand of N-terminally 6e-tagged AT1R, nanobody conjugation to orthosteric ligands had varying effects on Gq dissociation and β-arrestin plasma membrane recruitment. The potency of certain AngII analogs was enhanced up to 100-fold, and some conjugates behaved as partial agonists, with up to a 5-fold decrease in maximal efficacy. Nanobody conjugation also biased the signaling of TRV055 and TRV056 toward Gq, suggesting that Gq bias at AT1R can be modulated through molecular mechanisms distinct from those previously elucidated. Both competition radioligand binding experiments and functional assays demonstrated that orthosteric antagonists (angiotensin receptor blockers) act as non-competitive inhibitors of all these nanobody-peptide conjugates. This proof-of-principle study illustrates the array of pharmacological patterns that can be achieved by incorporating neutral or negative allosteric pharmacophores into dualsteric ligands. Nanobodies directed toward linear epitopes could provide a rich source of allosteric reagents for this purpose. SIGNIFICANCE STATEMENT: Here we engineer bitopic (dualsteric) ligands for epitope-tagged angiotensin II type 1 receptor by conjugating angiotensin II or its biased analogs to an epitope-specific nanobody (antibody fragment). Our data demonstrate that nanobody-mediated interactions with the receptor N-terminus endow angiotensin analogs with properties of allosteric modulators and provide a novel mechanism to increase the potency, modulate the maximal effect, or alter the bias of ligands.
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Affiliation(s)
- Nayara Braga Emidio
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (N.B.E., R.W.C.) and Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina (B.M.S., A.R.K., L.M.W.)
| | - Brandi M Small
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (N.B.E., R.W.C.) and Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina (B.M.S., A.R.K., L.M.W.)
| | - Amanda R Keller
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (N.B.E., R.W.C.) and Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina (B.M.S., A.R.K., L.M.W.)
| | - Ross W Cheloha
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (N.B.E., R.W.C.) and Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina (B.M.S., A.R.K., L.M.W.)
| | - Laura M Wingler
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, Maryland (N.B.E., R.W.C.) and Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina (B.M.S., A.R.K., L.M.W.)
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122
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Teske KA, Corona C, Wilkinson J, Mamott D, Good DA, Zambrano D, Lazar DF, Cali JJ, Robers MB, O'Brien MA. Interrogating direct NLRP3 engagement and functional inflammasome inhibition using cellular assays. Cell Chem Biol 2024; 31:349-360.e6. [PMID: 37858335 DOI: 10.1016/j.chembiol.2023.09.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/20/2023] [Accepted: 09/25/2023] [Indexed: 10/21/2023]
Abstract
As a key regulator of the innate immune system, the NLRP3 inflammasome responds to a variety of environmental insults through activation of caspase-1 and release of the proinflammatory cytokines IL-1β and IL-18. Aberrant NLRP3 inflammasome function is implicated in numerous inflammatory diseases, spurring drug discovery efforts at NLRP3 as a therapeutic target. A diverse array of small molecules is undergoing preclinical/clinical evaluation with a reported mode of action involving direct modulation of the NLRP3 pathway. However, for a subset of these ligands the functional link between live-cell target engagement and pathway inhibition has yet to be fully established. Herein we present a cohort of mechanistic assays to both query direct NLRP3 engagement in cells, and functionally interrogate different nodes of NLRP3 pathway activity. This system enabled the stratification of potency for five confirmed NLRP3 inhibitors, and identification of two reported NLRP3 inhibitors that failed to demonstrate direct pathway antagonism.
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Affiliation(s)
- Kelly A Teske
- Promega Corporation, Research & Development, Madison, WI 53711, USA
| | - Cesear Corona
- Promega Corporation, Research & Development, San Luis Obispo, CA 93401, USA
| | | | - Daniel Mamott
- Promega Corporation, Research & Development, Madison, WI 53711, USA
| | - David A Good
- Promega Corporation, Research & Development, San Luis Obispo, CA 93401, USA
| | - Delia Zambrano
- Promega Corporation, Research & Development, San Luis Obispo, CA 93401, USA
| | - Dan F Lazar
- Promega Corporation, Research & Development, Madison, WI 53711, USA
| | - James J Cali
- Promega Corporation, Research & Development, Madison, WI 53711, USA
| | - Matthew B Robers
- Promega Corporation, Research & Development, Madison, WI 53711, USA.
| | - Martha A O'Brien
- Promega Corporation, Research & Development, Madison, WI 53711, USA.
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123
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Rana S, Dranchak P, Dahlin JL, Lamy L, Li W, Oliphant E, Shrimp JH, Rajacharya GH, Tharakan R, Holland DO, Whitten AS, Wilson KM, Singh PK, Durum SK, Tao D, Rai G, Inglese J. Methotrexate-based PROTACs as DHFR-specific chemical probes. Cell Chem Biol 2024; 31:221-233.e14. [PMID: 37875111 PMCID: PMC10922102 DOI: 10.1016/j.chembiol.2023.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/31/2023] [Accepted: 09/26/2023] [Indexed: 10/26/2023]
Abstract
Methotrexate (MTX) is a tight-binding dihydrofolate reductase (DHFR) inhibitor, used as both an antineoplastic and immunosuppressant therapeutic. MTX, like folate undergoes folylpolyglutamate synthetase-mediated γ-glutamylation, which affects cellular retention and target specificity. Mechanisms of MTX resistance in cancers include a decrease in MTX poly-γ-glutamylation and an upregulation of DHFR. Here, we report a series of potent MTX-based proteolysis targeting chimeras (PROTACs) to investigate DHFR degradation pharmacology and one-carbon biochemistry. These on-target, cell-active PROTACs show proteasome- and E3 ligase-dependent activity, and selective degradation of DHFR in multiple cancer cell lines. By comparison, treatment with MTX increases cellular DHFR protein expression. Importantly, these PROTACs produced distinct, less-lethal phenotypes compared to MTX. The chemical probe set described here should complement conventional DHFR inhibitors and serve as useful tools for studying one-carbon biochemistry and dissecting complex polypharmacology of MTX and related drugs. Such compounds may also serve as leads for potential autoimmune and antineoplastic therapeutics.
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Affiliation(s)
- Sandeep Rana
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Rockville, MD 20850, USA
| | - Patricia Dranchak
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Rockville, MD 20850, USA
| | - Jayme L Dahlin
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Rockville, MD 20850, USA
| | - Laurence Lamy
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Rockville, MD 20850, USA
| | - Wenqing Li
- Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD, USA
| | - Erin Oliphant
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Rockville, MD 20850, USA
| | - Jonathan H Shrimp
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Rockville, MD 20850, USA
| | - Girish H Rajacharya
- Department of Oncology Science, University of Oklahoma Health Science Center, Oklahoma City, OK 73104, USA
| | - Ravi Tharakan
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Rockville, MD 20850, USA
| | - David O Holland
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Rockville, MD 20850, USA
| | - Apryl S Whitten
- Department of Oncology Science, University of Oklahoma Health Science Center, Oklahoma City, OK 73104, USA
| | - Kelli M Wilson
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Rockville, MD 20850, USA
| | - Pankaj K Singh
- Department of Oncology Science, University of Oklahoma Health Science Center, Oklahoma City, OK 73104, USA; OU Health Stephenson Center, University of Oklahoma Health Science Center, Oklahoma City, OK 73104, USA
| | - Scott K Durum
- Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD, USA
| | - Dingyin Tao
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Rockville, MD 20850, USA
| | - Ganesha Rai
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Rockville, MD 20850, USA.
| | - James Inglese
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Rockville, MD 20850, USA; Metabolic Medicine Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA.
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124
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Jayakody T, Inoue A, Kannan S, Nakamura G, Kawakami K, Mendis K, Nguyen TB, Li J, Herr DR, Verma CS, Dawe GS. Mechanisms of biased agonism by Gα i/o-biased stapled peptide agonists of the relaxin-3 receptor. Sci Signal 2024; 17:eabl5880. [PMID: 38349968 DOI: 10.1126/scisignal.abl5880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 01/26/2024] [Indexed: 02/15/2024]
Abstract
The neuropeptide relaxin-3 is composed of an A chain and a B chain held together by disulfide bonds, and it modulates functions such as anxiety and food intake by binding to and activating its cognate receptor RXFP3, mainly through the B chain. Biased ligands of RXFP3 would help to determine the molecular mechanisms underlying the activation of G proteins and β-arrestins downstream of RXFP3 that lead to such diverse functions. We showed that the i, i+4 stapled relaxin-3 B chains, 14s18 and d(1-7)14s18, were Gαi/o-biased agonists of RXFP3. These peptides did not induce recruitment of β-arrestin1/2 to RXFP3 by GPCR kinases (GRKs), in contrast to relaxin-3, which enabled the GRK2/3-mediated recruitment of β-arrestin1/2 to RXFP3. Relaxin-3 and the previously reported peptide 4 (an i, i+4 stapled relaxin-3 B chain) did not exhibit biased signaling. The staple linker of peptide 4 and parts of both the A chain and B chain of relaxin-3 interacted with extracellular loop 3 (ECL3) of RXFP3, moving it away from the binding pocket, suggesting that unbiased ligands promote a more open conformation of RXFP3. These findings highlight roles for the A chain and the N-terminal residues of the B chain of relaxin-3 in inducing conformational changes in RXFP3, which will help in designing selective biased ligands with improved therapeutic efficacy.
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Affiliation(s)
- Tharindunee Jayakody
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Neurobiology Programme, Life Sciences Institute, National University of Singapore, Singapore
- Department of Chemistry, University of Colombo, P.O. Box 1490, Colombo 00300, Sri Lanka
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | | | - Gaku Nakamura
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Kouki Kawakami
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Krishan Mendis
- Department of Chemistry, University of Colombo, P.O. Box 1490, Colombo 00300, Sri Lanka
| | - Thanh-Binh Nguyen
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Jianguo Li
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Deron R Herr
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Chandra S Verma
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671
- Department of Biological Sciences, National University of Singapore, 6 Science Drive 4, Singapore 117558
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Dr., Singapore 637551
| | - Gavin S Dawe
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Neurobiology Programme, Life Sciences Institute, National University of Singapore, Singapore
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Precision Medicine Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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125
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Gräwe A, Spruit CM, de Vries RP, Merkx M. Bioluminescent detection of viral surface proteins using branched multivalent protein switches. RSC Chem Biol 2024; 5:148-157. [PMID: 38333197 PMCID: PMC10849123 DOI: 10.1039/d3cb00164d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 11/22/2023] [Indexed: 02/10/2024] Open
Abstract
Fast and reliable virus diagnostics is key to prevent the spread of viruses in populations. A hallmark of viruses is the presence of multivalent surface proteins, a property that can be harnessed to control conformational switching in sensor proteins. Here, we introduce a new sensor platform (dark-LUX) for the detection of viral surface proteins consisting of a general bioluminescent framework that can be post-translationally functionalized with separately expressed binding domains. The platform relies on (1) plug-and-play bioconjugation of different binding proteins via SpyTag/SpyCatcher technology to create branched protein structures, (2) an optimized turn-on bioluminescent switch based on complementation of the split-luciferase NanoBiT upon target binding and (3) straightforward exploration of the protein linker space. The influenza A virus (IAV) surface proteins hemagglutinin (HA) and neuraminidase (NA) were used as relevant multivalent targets to establish proof of principle and optimize relevant parameters such as linker properties, choice of target binding domains and the optimal combination of the competing NanoBiT components SmBiT and DarkBiT. The sensor framework allows rapid conjugation and exchange of various binding domains including scFvs, nanobodies and de novo designed binders for a variety of targets, including the construction of a heterobivalent switch that targets the head and stem region of hemagglutinin. The modularity of the platform thus allows straightforward optimization of binding domains and scaffold properties for existing viral targets, and is well suited to quickly adapt bioluminescent sensor proteins to effectively detect newly evolving viral epitopes.
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Affiliation(s)
- Alexander Gräwe
- Laboratory of Protein Engineering, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology Eindhoven The Netherlands
| | - Cindy M Spruit
- Utrecht Institute for Pharmaceutical Sciences, Department of Chemical Biology and Drug Discovery Utrecht The Netherlands
| | - Robert P de Vries
- Utrecht Institute for Pharmaceutical Sciences, Department of Chemical Biology and Drug Discovery Utrecht The Netherlands
| | - Maarten Merkx
- Laboratory of Protein Engineering, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology Eindhoven The Netherlands
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126
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Dunuweera AN, Dunuweera SP, Ranganathan K. A Comprehensive Exploration of Bioluminescence Systems, Mechanisms, and Advanced Assays for Versatile Applications. Biochem Res Int 2024; 2024:8273237. [PMID: 38347947 PMCID: PMC10861286 DOI: 10.1155/2024/8273237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/10/2023] [Accepted: 01/21/2024] [Indexed: 02/15/2024] Open
Abstract
Bioluminescence has been a fascinating natural phenomenon of light emission from living creatures. It happens when the enzyme luciferase facilitates the oxidation of luciferin, resulting in the creation of an excited-state species that emits light. Although there are many bioluminescent systems, few have been identified. D-luciferin-dependent systems, coelenterazine-dependent systems, Cypridina luciferin-based systems, tetrapyrrole-based luciferins, bacterial bioluminescent systems, and fungal bioluminescent systems are natural bioluminescent systems. Since different bioluminescence systems, such as various combinations of luciferin-luciferase pair reactions, have different light emission wavelengths, they benefit industrial applications such as drug discovery, protein-protein interactions, in vivo imaging in small animals, and controlling neurons. Due to the expression of luciferase and easy permeation of luciferin into most cells and tissues, bioluminescence assays are applied nowadays with modern technologies in most cell and tissue types. It is a versatile technique in a variety of biomedical research. Furthermore, there are some investigated blue-sky research projects, such as bioluminescent plants and lamps. This review article is mainly based on the theory of diverse bioluminescence systems and their past, present, and future applications.
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Affiliation(s)
| | | | - K. Ranganathan
- Department of Botany, University of Jaffna, Jaffna 40000, Sri Lanka
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127
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Jiang S, Lin X, Wu L, Wang L, Wu Y, Xu Z, Xu F. Unveiling the structural mechanisms of nonpeptide ligand recognition and activation in human chemokine receptor CCR8. SCIENCE ADVANCES 2024; 10:eadj7500. [PMID: 38306437 PMCID: PMC10836724 DOI: 10.1126/sciadv.adj7500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 01/03/2024] [Indexed: 02/04/2024]
Abstract
The human CC chemokine receptor 8 (CCR8) is an emerging therapeutic target for cancer immunotherapy and autoimmune diseases. Understanding the molecular recognition of CCR8, particularly with nonpeptide ligands, is valuable for drug development. Here, we report three cryo-electron microscopy structures of human CCR8 complexed with Gi trimers in the ligand-free state or activated by nonpeptide agonists LMD-009 and ZK 756326. A conserved Y1.39Y3.32E7.39 motif in the orthosteric binding pocket is shown to play a crucial role in the chemokine and nonpeptide ligand recognition. Structural and functional analyses indicate that the lack of conservation in Y1143.33 and Y1724.64 among the CC chemokine receptors could potentially contribute to the selectivity of the nonpeptide ligand binding to CCR8. These findings present the characterization of the molecular interaction between a nonpeptide agonist and a chemokine receptor, aiding the development of therapeutics targeting related diseases through a structure-based approach.
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Affiliation(s)
- Shan Jiang
- iHuman Institute, ShanghaiTech University, Pudong, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xi Lin
- iHuman Institute, ShanghaiTech University, Pudong, Shanghai 201210, China
| | - Lijie Wu
- iHuman Institute, ShanghaiTech University, Pudong, Shanghai 201210, China
| | - Ling Wang
- iHuman Institute, ShanghaiTech University, Pudong, Shanghai 201210, China
| | - Yiran Wu
- iHuman Institute, ShanghaiTech University, Pudong, Shanghai 201210, China
| | - Ziyi Xu
- iHuman Institute, ShanghaiTech University, Pudong, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Fei Xu
- iHuman Institute, ShanghaiTech University, Pudong, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Clinical Research Center, Shanghai 201210, China
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128
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Na L, Sun L, Yu M, Zhang Y, Zhang Y, Zhang Z, Zhang H, Qi T, Guo W, Guo X, Wang S, Wang J, Lin Y, Wang X. Avian ANP32A incorporated in avian influenza A virions promotes interspecies transmission by priming early viral replication in mammals. SCIENCE ADVANCES 2024; 10:eadj4163. [PMID: 38295177 PMCID: PMC10830118 DOI: 10.1126/sciadv.adj4163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 12/28/2023] [Indexed: 02/02/2024]
Abstract
Species-specific differences in acidic nuclear phosphoprotein 32 family member A (ANP32A) determine the restriction of avian-signature polymerase in mammalian cells. Mutations that evade this restriction, such as PB2-E627K, are frequently acquired when avian influenza A viruses jump from avian hosts to mammalian hosts. However, the mechanism underlying this adaptation process is still unclear. Here, we report that host factor ANP32 proteins can be incorporated into influenza viral particles through combination with the viral RNA polymerase (vPol) and then transferred into targeted cells where they support virus replication. The packaging of the ANP32 proteins into influenza viruses is dependent on their affinity with the vPol. Avian ANP32A (avANP32A) delivered by avian influenza A virions primes early viral replication in mammalian cells, thereby favoring the downstream interspecies transmission event by increasing the total amount of virus carrying adaptive mutations. Our study clarifies one role of avANP32A where it is used by avian influenza virus to help counteract the restriction barrier in mammals.
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Affiliation(s)
- Lei Na
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Liuke Sun
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Mengmeng Yu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Yingzhi Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Yuan Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Zhenyu Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Haili Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Ting Qi
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Wei Guo
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Xing Guo
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Shida Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Jingfei Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Yuezhi Lin
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Xiaojun Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
- Institute of Western Agriculture, The Chinese Academy of Agricultural Sciences, Harbin 150069, China
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129
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Mason JW, Chow YT, Hudson L, Tutter A, Michaud G, Westphal MV, Shu W, Ma X, Tan ZY, Coley CW, Clemons PA, Bonazzi S, Berst F, Briner K, Liu S, Zécri FJ, Schreiber SL. DNA-encoded library-enabled discovery of proximity-inducing small molecules. Nat Chem Biol 2024; 20:170-179. [PMID: 37919549 PMCID: PMC10917151 DOI: 10.1038/s41589-023-01458-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 09/24/2023] [Indexed: 11/04/2023]
Abstract
Small molecules that induce protein-protein associations represent powerful tools to modulate cell circuitry. We sought to develop a platform for the direct discovery of compounds able to induce association of any two preselected proteins, using the E3 ligase von Hippel-Lindau (VHL) and bromodomains as test systems. Leveraging the screening power of DNA-encoded libraries (DELs), we synthesized ~1 million DNA-encoded compounds that possess a VHL-targeting ligand, a variety of connectors and a diversity element generated by split-and-pool combinatorial chemistry. By screening our DEL against bromodomains in the presence and absence of VHL, we could identify VHL-bound molecules that simultaneously bind bromodomains. For highly barcode-enriched library members, ternary complex formation leading to bromodomain degradation was confirmed in cells. Furthermore, a ternary complex crystal structure was obtained for our most enriched library member with BRD4BD1 and a VHL complex. Our work provides a foundation for adapting DEL screening to the discovery of proximity-inducing small molecules.
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Affiliation(s)
- Jeremy W Mason
- Chemical Biology and Therapeutics Science, Broad Institute, Cambridge, MA, USA
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Yuen Ting Chow
- Chemical Biology and Therapeutics Science, Broad Institute, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Liam Hudson
- Chemical Biology and Therapeutics Science, Broad Institute, Cambridge, MA, USA
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Antonin Tutter
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Gregory Michaud
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Matthias V Westphal
- Chemical Biology and Therapeutics Science, Broad Institute, Cambridge, MA, USA
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Wei Shu
- Structural and Biophysical Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Xiaolei Ma
- Structural and Biophysical Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Zher Yin Tan
- Chemical Biology and Therapeutics Science, Broad Institute, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Connor W Coley
- Chemical Biology and Therapeutics Science, Broad Institute, Cambridge, MA, USA
| | - Paul A Clemons
- Chemical Biology and Therapeutics Science, Broad Institute, Cambridge, MA, USA
| | - Simone Bonazzi
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Frédéric Berst
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, Basel, Switzerland
| | - Karin Briner
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Shuang Liu
- Chemical Biology and Therapeutics Science, Broad Institute, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
| | - Frédéric J Zécri
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Cambridge, MA, USA.
| | - Stuart L Schreiber
- Chemical Biology and Therapeutics Science, Broad Institute, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
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130
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Opadele AE, Nishioka S, Wu PH, Le QT, Shirato H, Nam JM, Onodera Y. The lipid-binding D4 domain of perfringolysin O facilitates the active loading of exogenous cargo into extracellular vesicles. FEBS Lett 2024; 598:446-456. [PMID: 38339784 DOI: 10.1002/1873-3468.14807] [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: 08/04/2023] [Revised: 12/07/2023] [Accepted: 12/15/2023] [Indexed: 02/12/2024]
Abstract
Whereas extracellular vesicles (EVs) have been engineered for cargo loading, innovative strategies for it can still be developed. Here, we describe domain 4 (D4), a cholesterol-binding domain derived from perfringolysin O, as a viable candidate for EV cargo loading. D4 and its mutants localized to the plasma membrane and the membranes of different vesicular structures in the cytoplasm, and facilitate the transport of proteins of interest (POIs) into EVs. D4-EVs were internalized by recipient cells analogous to EVs engineered with CD9. Intracellular cargo discharge from D4-EVs was successfully detected with the assistance of vesicular stomatitis virus glycoprotein. This study presents a novel strategy for recruiting POIs into EVs via a lipid-binding domain that ensures content release in recipient cells.
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Affiliation(s)
- Abayomi Emmanuel Opadele
- Laboratory for Molecular and Cellular Dynamics Research, Graduate School of Biomedical Science and Engineering, Hokkaido University, Sapporo, Japan
| | - Soichiro Nishioka
- Global Center for Biomedical Science and Engineering (GCB), Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Ping-Hsiu Wu
- Department of Radiology, School of Medicine, College of Medicine, Taipei Medical University, Taiwan
| | - Quynh-Thu Le
- Department of Radiation Oncology, Stanford University School of Medicine, CA, USA
| | - Hiroki Shirato
- Global Center for Biomedical Science and Engineering (GCB), Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Jin-Min Nam
- Global Center for Biomedical Science and Engineering (GCB), Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Division of Systemic Life Science, Graduate School of Biostudies, Kyoto University, Japan
| | - Yasuhito Onodera
- Global Center for Biomedical Science and Engineering (GCB), Faculty of Medicine, Hokkaido University, Sapporo, Japan
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131
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Chen X, Huang Y, Gao P, Wu F, Han Y, Zhang C, Hu Z, Zhao F, Shcherbakov DN, Pan W, Niu X, Li X, Liu S, Xu W. Engineering of novel hemagglutinin biosensors for rapid detection and drug screening of Influenza A H7N9 virus. Int J Biol Macromol 2024; 258:129126. [PMID: 38163504 DOI: 10.1016/j.ijbiomac.2023.129126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 12/27/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024]
Abstract
New pathogenic influenza virus strains are constantly emerging, posing a serious risk to both human health and economic growth. To effectively control the spread of this virus, there is an urgent need for early, rapid, sensitive, simple, and cost-effective detection technologies, as well as new and effective antiviral drugs. In this study, we have successfully achieved a significant milestone by successfully fusing the H7N9 influenza virus hemagglutinin (HA) protein with the nano-luciferase component, resulting in the development of a novel set of biosensors. This remarkable achievement marks the first instance of utilizing this biosensor technology for influenza antibody detection. Our biosensor technology also has the potential to facilitate the development of antiviral drugs targeting specific epitopes of the HA protein, providing a promising avenue for the treatment of H7N9 influenza virus infections. Furthermore, our biosensors have broad applications beyond H7N9 influenza virus detection, as they can be expanded for the detection of other pathogens and drug screening applications in the future. By providing a novel and effective solution to the detection and treatment of influenza viruses, our biosensors have the potential to revolutionize the field of infectious disease control.
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Affiliation(s)
- Xin Chen
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Yuan Huang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Peixuan Gao
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Fang Wu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Yongyue Han
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Chuwen Zhang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Zhuowen Hu
- The Fifth Affiliated Hospital, Southern Medical University, Guangzhou, Guangdong 510070, China
| | - Fang Zhao
- National Clinical Research Centre for Infectious Diseases, the Third People's Hospital of Shenzhen and the Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518112, Guangdong Province, China
| | - Dmitry N Shcherbakov
- State Research Center of Virology and Biotechnology VECTOR, Koltsovo 630559, Russia; Department of Physical-Chemistry Biology and Biotechnology, Altai State University, Barnaul 656049, Russia
| | - Weiqi Pan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China
| | - Xuefeng Niu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China
| | - Xiaoyan Li
- The Fifth Affiliated Hospital, Southern Medical University, Guangzhou, Guangdong 510070, China.
| | - Shuwen Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China; State Key Laboratory of Organ Failure Research, Guangdong Provincial Institute of Nephrology, Southern Medical University, Guangzhou 510515, China.
| | - Wei Xu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China; Key Laboratory of Infectious Diseases Research in South China, Ministry of Education, Southern Medical University, Guangzhou, Guangdong 510515, China.
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132
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Pipchuk A, Kelly T, Carew M, Nicol C, Yang X. Development of Novel Bioluminescent Biosensors Monitoring the Conformation and Activity of the Merlin Tumour Suppressor. Int J Mol Sci 2024; 25:1527. [PMID: 38338806 PMCID: PMC10855677 DOI: 10.3390/ijms25031527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
Solid tumours can universally evade contact inhibition of proliferation (CIP), a mechanism halting cell proliferation when cell-cell contact occurs. Merlin, an ERM-like protein, crucially regulates CIP and is frequently deactivated in various cancers, indicating its significance as a tumour suppressor in cancer biology. Despite extensive investigations into Merlin's role in cancer, its lack of intrinsic catalytic activity and frequent conformation changes have made it notoriously challenging to study. To address this challenge, we harnessed innovative luciferase technologies to create and validate a NanoBiT split-luciferase biosensor system in which Merlin is cloned between two split components (LgBiT and SmBiT) of NanoLuc luciferase. This system enables precise quantification of Merlin's conformation and activity both in vitro and within living cells. This biosensor significantly enhances the study of Merlin's molecular functions, serving as a potent tool for exploring its contributions to CIP and tumorigenesis.
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Affiliation(s)
| | | | | | | | - Xiaolong Yang
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON K7L 3N6, Canada; (A.P.); (T.K.); (M.C.); (C.N.)
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133
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Alves J, Schwinn M, Machleidt T, Goueli SA, Cali JJ, Zegzouti H. Monitoring phosphorylation and acetylation of CRISPR-mediated HiBiT-tagged endogenous proteins. Sci Rep 2024; 14:2138. [PMID: 38272933 PMCID: PMC10810970 DOI: 10.1038/s41598-024-51887-x] [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: 09/19/2023] [Accepted: 01/10/2024] [Indexed: 01/27/2024] Open
Abstract
Intracellular pathways transduce signals through changes in post-translational modifications (PTMs) of effector proteins. Among the approaches used to monitor PTM changes are immunoassays and overexpression of recombinant reporter genes. Genome editing by CRISPR/Cas9 provides a new means to monitor PTM changes by inserting reporters onto target endogenous genes while preserving native biology. Ideally, the reporter should be small in order not to interfere with the processes mediated by the target while sensitive enough to detect tightly expressed proteins. HiBiT is a 1.3 kDa reporter peptide capable of generating bioluminescence through complementation with LgBiT, an 18 kDa subunit derived from NanoLuc. Using HiBiT CRISPR/Cas9-modified cell lines in combination with fluorescent antibodies, we developed a HiBiT-BRET immunoassay (a.k.a. Immuno-BRET). This is a homogeneous immunoassay capable of monitoring post-translational modifications on diverse protein targets. Its usefulness was demonstrated for the detection of phosphorylation of multiple signaling pathway targets (EGFR, STAT3, MAPK8 and c-MET), as well as chromatin containing histone H3 acetylation on lysine 9 and 27. These results demonstrate the ability to efficiently monitor endogenous biological processes modulated by post-translational modifications using a small bioluminescent peptide tag and fluorescent antibodies, providing sensitive quantitation of the response dynamics to multiple stimuli.
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Affiliation(s)
- Juliano Alves
- R&D Department, Promega Corporation, 2800 Woods Hollow Road, Madison, WI, 53711, USA.
| | - Marie Schwinn
- R&D Department, Promega Corporation, 2800 Woods Hollow Road, Madison, WI, 53711, USA
| | - Thomas Machleidt
- R&D Department, Promega Corporation, 2800 Woods Hollow Road, Madison, WI, 53711, USA
| | - Said A Goueli
- R&D Department, Promega Corporation, 2800 Woods Hollow Road, Madison, WI, 53711, USA
| | - James J Cali
- R&D Department, Promega Corporation, 2800 Woods Hollow Road, Madison, WI, 53711, USA
| | - Hicham Zegzouti
- R&D Department, Promega Corporation, 2800 Woods Hollow Road, Madison, WI, 53711, USA.
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Zhang L, Shao Y, Wang Y, Yang Q, Guo J, Gao GF, Deng T. Twenty natural amino acid substitution screening at the last residue 121 of influenza A virus NS2 protein reveals the critical role of NS2 in promoting virus genome replication by coordinating with viral polymerase. J Virol 2024; 98:e0116623. [PMID: 38054704 PMCID: PMC10804943 DOI: 10.1128/jvi.01166-23] [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: 08/02/2023] [Accepted: 11/20/2023] [Indexed: 12/07/2023] Open
Abstract
Both influenza A virus genome transcription (vRNA→mRNA) and replication (vRNA→cRNA→vRNA), catalyzed by the influenza RNA polymerase (FluPol), are dynamically regulated across the virus life cycle. It has been reported that the last amino acid I121 of the viral NS2 protein plays a critical role in promoting viral genome replication in influenza mini-replicon systems. Here, we performed a 20 natural amino acid substitution screening at residue NS2-I121 in the context of virus infection. We found that the hydrophobicity of the residue 121 is essential for virus survival. Interestingly, through serial passage of the rescued mutant viruses, we further identified adaptive mutations PA-K19E and PB1-S713N on FluPol which could effectively compensate for the replication-promoting defect caused by NS2-I121 mutation in the both mini-replicon and virus infection systems. Structural analysis of different functional states of FluPol indicates that PA-K19E and PB1-S713N could stabilize the replicase conformation of FluPol. By using a cell-based NanoBiT complementary reporter assay, we further demonstrate that both wild-type NS2 and PA-K19E/PB1-S713N could enhance FluPol dimerization, which is necessary for genome replication. These results reveal the critical role NS2 plays in promoting viral genome replication by coordinating with FluPol.IMPORTANCEThe intrinsic mechanisms of influenza RNA polymerase (FluPol) in catalyzing viral genome transcription and replication have been largely resolved. However, the mechanisms of how transcription and replication are dynamically regulated remain elusive. We recently reported that the last amino acid of the viral NS2 protein plays a critical role in promoting viral genome replication in an influenza mini-replicon system. Here, we conducted a 20 amino acid substitution screening at the last residue 121 in virus rescue and serial passage. Our results demonstrate that the replication-promoting function of NS2 is important for virus survival and efficient multiplication. We further show evidence that NS2 and NS2-I121 adaptive mutations PA-K19E/PB1-S713N regulate virus genome replication by promoting FluPol dimerization. This work highlights the coordination between NS2 and FluPol in fulfilling efficient genome replication. It further advances our understanding of the regulation of viral RNA synthesis for influenza A virus.
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Affiliation(s)
- Lei Zhang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- />Institute of Pediatrics, Shenzhen Children’s Hospital, Shenzhen, China
| | - Yuekun Shao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yingying Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Qiuxian Yang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jiamei Guo
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - George F. Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tao Deng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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135
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Lee EJ, Gladkov N, Miller JE, Yeates TO. Design of Ligand-Operable Protein-Cages That Open Upon Specific Protein Binding. ACS Synth Biol 2024; 13:157-167. [PMID: 38133598 DOI: 10.1021/acssynbio.3c00383] [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] [Indexed: 12/23/2023]
Abstract
Protein nanocages have diverse applications in medicine and biotechnology, including molecular delivery. However, although numerous studies have demonstrated the ability of protein nanocages to encapsulate various molecular species, limited methods are available for subsequently opening a nanocage for cargo release under specific conditions. A modular platform with a specific protein-target-based mechanism of nanocage opening is notably lacking. To address this important technology gap, we present a new class of designed protein cages, the Ligand-Operable Cage (LOC). LOCs primarily comprise a protein nanocage core and a fused surface binding adaptor. The geometry of the LOC is designed so that binding of a target protein ligand (or multiple copies thereof) to the surface binder is sterically incompatible with retention of the assembled state of the cage. Therefore, the tight binding of a target ligand drives cage disassembly by mass action, subsequently exposing the encapsulated cargo. LOCs are modular; direct substitution of the surface binder sequence can reprogram the nanocage to open in response to any target protein ligand of interest. We demonstrate these design principles using both a natural and a designed protein cage as the core, with different proteins acting as the triggering ligand and with different reporter readouts─fluorescence unquenching and luminescence─for cage disassembly. These developments advance the critical problem of targeted molecular delivery and detection.
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Affiliation(s)
- Eric J Lee
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Nika Gladkov
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Justin E Miller
- Molecular Biology Institute, UCLA, Los Angeles, California 90095, United States
| | - Todd O Yeates
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
- Molecular Biology Institute, UCLA, Los Angeles, California 90095, United States
- UCLA-DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095, United States
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136
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Unti MJ, Jaffrey SR. Highly efficient cellular expression of circular mRNA enables prolonged protein expression. Cell Chem Biol 2024; 31:163-176.e5. [PMID: 37883972 PMCID: PMC10841545 DOI: 10.1016/j.chembiol.2023.09.015] [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: 04/30/2023] [Revised: 08/25/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023]
Abstract
A major problem with mRNA therapeutics is that mRNA is usually degraded within a few hours after entering the cytosol. New approaches for in vitro synthesis of circular mRNA have allowed increased levels and duration of protein synthesis from mRNA therapeutics due to the long half-life of circular mRNA. However, it remains difficult to genetically encode circular mRNAs in mammalian cells. Here, we describe the adaptation of the Tornado (Twister-optimized RNA for durable overexpression) system to achieve in-cell synthesis of circular mRNAs. We screen different promoters and internal ribosomal entry sites (IRESs) and identify combinations that result in high levels of circular mRNA and protein expression. We show that these circular mRNAs can be packaged into virus-like particles (VLPs), thus enabling prolonged protein expression. Overall, these data describe a platform for synthesis of circular mRNAs and how these circular mRNAs can improve VLP therapeutics.
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Affiliation(s)
- Mildred J Unti
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.
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137
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Karimian P, Trusov Y, Botella JR. Conserved Role of Heterotrimeric G Proteins in Plant Defense and Cell Death Progression. Genes (Basel) 2024; 15:115. [PMID: 38255003 PMCID: PMC10815853 DOI: 10.3390/genes15010115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Programmed cell death (PCD) is a critical process in plant immunity, enabling the targeted elimination of infected cells to prevent the spread of pathogens. The tight regulation of PCD within plant cells is well-documented; however, specific mechanisms remain elusive or controversial. Heterotrimeric G proteins are multifunctional signaling elements consisting of three distinct subunits, Gα, Gβ, and Gγ. In Arabidopsis, the Gβγ dimer serves as a positive regulator of plant defense. Conversely, in species such as rice, maize, cotton, and tomato, mutants deficient in Gβ exhibit constitutively active defense responses, suggesting a contrasting negative role for Gβ in defense mechanisms within these plants. Using a transient overexpression approach in addition to knockout mutants, we observed that Gβγ enhanced cell death progression and elevated the accumulation of reactive oxygen species in a similar manner across Arabidopsis, tomato, and Nicotiana benthamiana, suggesting a conserved G protein role in PCD regulation among diverse plant species. The enhancement of PCD progression was cooperatively regulated by Gβγ and one Gα, XLG2. We hypothesize that G proteins participate in two distinct mechanisms regulating the initiation and progression of PCD in plants. We speculate that G proteins may act as guardees, the absence of which triggers PCD. However, in Arabidopsis, this G protein guarding mechanism appears to have been lost in the course of evolution.
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Affiliation(s)
| | | | - Jose Ramon Botella
- School of Agriculture and Food Sciences, University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; (P.K.); (Y.T.)
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138
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Campbell E, Adamson H, Luxton T, Tiede C, Wälti C, Tomlinson DC, Jeuken LJC. Therapeutic drug monitoring of immunotherapies with novel Affimer-NanoBiT sensor construct. SENSORS & DIAGNOSTICS 2024; 3:104-111. [PMID: 38249540 PMCID: PMC10795742 DOI: 10.1039/d3sd00126a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 10/23/2023] [Indexed: 01/23/2024]
Abstract
Concentration-therapeutic efficacy relationships have been observed for several therapeutic monoclonal antibodies (TmAb), where low circulating levels can result in ineffective treatment and high concentrations can cause adverse reactions. Rapid therapeutic drug monitoring (TDM) of TmAb drugs would provide the opportunity to adjust an individual patient's dosing regimen to improve treatment results. However, TDM for immunotherapies is currently limited to centralised testing methods with long sample-collection to result timeframes. Here, we show four point-of-care (PoC) TmAb biosensors by combining anti-idiotypic Affimer proteins and NanoBiT split luciferase technology at a molecular level to provide a platform for rapid quantification (<10 minutes) for four clinically relevant TmAb (rituximab, adalimumab, ipilimumab and trastuzumab). The rituximab sensor performed best with 4 pM limit of detection (LoD) and a quantifiable range between 8 pM-2 nM with neglectable matrix effects in serum up to 1%. After dilution of serum samples, the resulting quantifiable range for all four sensors falls within the clinically relevant range and compares favourably with the sensitivity and/or time-to-result of current ELISA standards. Further development of these sensors into a PoC test may improve treatment outcome and quality of life for patients receiving immunotherapy.
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Affiliation(s)
- Emma Campbell
- School of Biomedical Science, University of Leeds Leeds LS2 9JT UK
- Astbury Centre for Structural Molecular Biology, University of Leeds LS2 9JT UK
| | - Hope Adamson
- School of Biomedical Science, University of Leeds Leeds LS2 9JT UK
- Astbury Centre for Structural Molecular Biology, University of Leeds LS2 9JT UK
| | - Timothy Luxton
- School of Biomedical Science, University of Leeds Leeds LS2 9JT UK
- Astbury Centre for Structural Molecular Biology, University of Leeds LS2 9JT UK
| | - Christian Tiede
- Astbury Centre for Structural Molecular Biology, University of Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Leeds LS2 9JT UK
| | - Christoph Wälti
- School of Electronic and Electrical Engineering, University of Leeds LS2 9JT UK
| | - Darren C Tomlinson
- Astbury Centre for Structural Molecular Biology, University of Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Leeds LS2 9JT UK
| | - Lars J C Jeuken
- School of Biomedical Science, University of Leeds Leeds LS2 9JT UK
- Astbury Centre for Structural Molecular Biology, University of Leeds LS2 9JT UK
- Leiden Institute of Chemistry, Leiden University PO Box 9502 2300 RA Leiden The Netherlands
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139
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Hoare BL, Tippett DN, Kaur A, Cullum SA, Miljuš T, Koers EJ, Harwood CR, Dijon N, Holliday ND, Sykes DA, Veprintsev DB. ThermoBRET: A Ligand-Engagement Nanoscale Thermostability Assay Applied to GPCRs. Chembiochem 2024; 25:e202300459. [PMID: 37872746 DOI: 10.1002/cbic.202300459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 10/25/2023]
Abstract
Measurements of membrane protein thermostability reflect ligand binding. Current thermostability assays often require protein purification or rely on pre-existing radiolabelled or fluorescent ligands, limiting their application to established targets. Alternative methods, such as fluorescence-detection size exclusion chromatography thermal shift, detect protein aggregation but are not amenable to high-throughput screening. Here, we present a ThermoBRET method to quantify the relative thermostability of G protein coupled receptors (GPCRs), using cannabinoid receptors (CB1 and CB2 ) and the β2 -adrenoceptor (β2 AR) as model systems. ThermoBRET reports receptor unfolding, does not need labelled ligands and can be used with non-purified proteins. It uses Bioluminescence Resonance Energy Transfer (BRET) between Nanoluciferase (Nluc) and a thiol-reactive fluorescent dye that binds cysteines exposed by unfolding. We demonstrate that the melting point (Tm ) of Nluc-fused GPCRs can be determined in non-purified detergent solubilised membrane preparations or solubilised whole cells, revealing differences in thermostability for different solubilising conditions and in the presence of stabilising ligands. We extended the range of the assay by developing the thermostable tsNLuc by incorporating mutations from the fragments of split-Nluc (Tm of 87 °C versus 59 °C). ThermoBRET allows the determination of GPCR thermostability, which is useful for protein purification optimisation and drug discovery screening.
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Affiliation(s)
- Bradley L Hoare
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Current address, Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3052, Australia
| | - David N Tippett
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Current address, Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Amandeep Kaur
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Sean A Cullum
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Tamara Miljuš
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Eline J Koers
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Clare R Harwood
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Nicola Dijon
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Nicholas D Holliday
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - David A Sykes
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Dmitry B Veprintsev
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
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140
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Janssens LK, De Wilde L, Van Eenoo P, Stove CP. Untargeted Detection of HIF Stabilizers in Doping Samples: Activity-Based Screening with a Stable In Vitro Bioassay. Anal Chem 2024; 96:238-247. [PMID: 38117670 DOI: 10.1021/acs.analchem.3c03816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Hypoxia-inducible factor (HIF) stabilizers are listed in the World Anti-Doping Agency's prohibited list as they can increase aerobic exercise capacity. The rapid pace of emergence of highly structurally diverse HIF stabilizers could pose a risk to conventional structure-based methods in doping control to detect new investigational drugs. Therefore, we developed a strategy that is capable of detecting the presence of any HIF stabilizer, irrespective of its structure, by detecting biological activity. Previously developed cell-based HIF1/2 assays were optimized to a stable format and evaluated for their screening potential toward HIF stabilizers. Improved pharmacological characterization was established by the stable cell-based formats, and broad specificity was demonstrated by pharmacologically characterizing a diverse set of HIF stabilizers (including enarodustat, IOX2, IOX4, MK-8617, JNJ-42041935). The methodological (in solvent) limit of detection of the optimal HIF1 stable bioassay toward detecting the reference compound roxadustat was 100 nM, increasing to 50-100 ng/mL (corresponding to 617-1233 nM in-well) in matching urine samples, owing to strong matrix effects. In a practical context, a urinary limit of detection of 1.15 μg/mL (95% detection rate) was determined, confirming the matrix-dependent detectability of roxadustat in urine. Pending optimization of a universal sample preparation strategy and/or a methodology to correct for the matrix effects, this untargeted approach may serve as a complementing method in antidoping control, as theoretically, it would be capable of detecting any unknown substance with HIF stabilizing activity.
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Affiliation(s)
- Liesl K Janssens
- Laboratory of Toxicology, Department of Bioanalysis, Ghent University, 9000 Ghent, Belgium
| | - Laurie De Wilde
- Doping Control Laboratory, Department Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
| | - Peter Van Eenoo
- Doping Control Laboratory, Department Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
| | - Christophe P Stove
- Laboratory of Toxicology, Department of Bioanalysis, Ghent University, 9000 Ghent, Belgium
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141
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Demby A, Zaccolo M. Investigating G-protein coupled receptor signalling with light-emitting biosensors. Front Physiol 2024; 14:1310197. [PMID: 38260094 PMCID: PMC10801095 DOI: 10.3389/fphys.2023.1310197] [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: 10/09/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
G protein-coupled receptors (GPCRs) are the most frequent target of currently approved drugs and play a central role in both physiological and pathophysiological processes. Beyond the canonical understanding of GPCR signal transduction, the importance of receptor conformation, beta-arrestin (β-arr) biased signalling, and signalling from intracellular locations other than the plasma membrane is becoming more apparent, along with the tight spatiotemporal compartmentalisation of downstream signals. Fluorescent and bioluminescent biosensors have played a pivotal role in elucidating GPCR signalling events in live cells. To understand the mechanisms of action of the GPCR-targeted drugs currently available, and to develop new and better GPCR-targeted therapeutics, understanding these novel aspects of GPCR signalling is critical. In this review, we present some of the tools available to interrogate each of these features of GPCR signalling, we illustrate some of the key findings which have been made possible by these tools and we discuss their limitations and possible developments.
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Affiliation(s)
| | - Manuela Zaccolo
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
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142
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Moghimianavval H, Loi KJ, Hwang SW, Bashirzadeh Y, Liu AP. Light-based juxtacrine signaling between synthetic cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.05.574425. [PMID: 38260570 PMCID: PMC10802317 DOI: 10.1101/2024.01.05.574425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Cell signaling through direct physical cell-cell contacts plays vital roles in biology during development, angiogenesis, and immune response. Intercellular communication mechanisms between synthetic cells constructed from the bottom up are majorly reliant on diffusible chemical signals, thus limiting the range of responses in receiver cells. Engineering contact-dependent signaling between synthetic cells promises to unlock more complicated signaling schemes with different types of responses. Here, we design and demonstrate a light-activated contact-dependent communication tool for synthetic cells. We utilize a split bioluminescent protein to limit signal generation exclusively to contact interfaces of synthetic cells, driving the recruitment of a photoswitchable protein in receiver cells, akin to juxtacrine signaling in living cells. Our modular design not only demonstrates contact-dependent communication between synthetic cells but also provides a platform for engineering orthogonal contact-dependent signaling mechanisms.
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Affiliation(s)
| | - Kyle J. Loi
- Neuroscience Program, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
| | - Sung-Won Hwang
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Yashar Bashirzadeh
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Allen P. Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
- Department of Biophysics, University of Michigan, Ann Arbor, MI, USA
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143
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Tian Y, Okamoto K. The nascent polypeptide-associated complex subunit Egd1 is required for efficient selective mitochondrial degradation in budding yeast. Sci Rep 2024; 14:546. [PMID: 38177147 PMCID: PMC10767044 DOI: 10.1038/s41598-023-50245-7] [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: 07/15/2023] [Accepted: 12/17/2023] [Indexed: 01/06/2024] Open
Abstract
Selective degradation of dysfunctional or excess mitochondria is a fundamental process crucial for cell homeostasis in almost all eukaryotes. This process relies on autophagy, an intracellular self-eating system conserved from yeast to humans and is thus called mitophagy. Detailed mechanisms of mitophagy remain to be fully understood. Here we show that mitochondrial degradation in budding yeast, which requires the pro-mitophagic protein Atg32, is strongly reduced in cells lacking Egd1, a beta subunit of the nascent polypeptide-associated complex acting in cytosolic ribosome attachment and protein targeting to mitochondria. By contrast, loss of the sole alpha subunit Egd2 or the beta subunit paralogue Btt1 led to only a partial or slight reduction in mitophagy. We also found that phosphorylation of Atg32, a crucial step for priming mitophagy, is decreased in the absence of Egd1. Forced Atg32 hyperphosphorylation almost completely restored mitophagy in egd1-null cells. Together, we propose that Egd1 acts in Atg32 phosphorylation to facilitate mitophagy.
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Affiliation(s)
- Yuan Tian
- Laboratory of Mitochondrial Dynamics, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Koji Okamoto
- Laboratory of Mitochondrial Dynamics, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan.
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144
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Maier LP, Felix G, Fliegmann J. LuBiA (Luciferase-Based Binding Assay): Glowing Peptides as Sensitive Probes to Study Ligand-Receptor Interactions. Methods Mol Biol 2024; 2731:265-278. [PMID: 38019441 DOI: 10.1007/978-1-0716-3511-7_20] [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] [Indexed: 11/30/2023]
Abstract
The quantitative and qualitative biochemical description of molecular interactions is fundamental to the study of ligand/receptor pairs and their structure/function relationships. Bioactive peptides often are active at (sub-)nanomolar concentrations, indicating they have a high affinity for their sites of action, notably binding sites on receptors. Since such receptor proteins are commonly of low abundance, highly sensitive detection methods are required to study these ligand/receptor interactions. We present a protocol for an inexpensive luminescence-based detection setup in which the peptide ligand of interest is extended with the 11-amino acid HiBiT tag. This tag can be quantified easily down to fmol amounts by its ability to reconstitute the enzymatic activity of LgBiT, a truncated version of the Oplophorus gracilirostris luciferase.
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Affiliation(s)
- Louis-Philippe Maier
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
- Department of Plant Molecular Biology (DBMV), University of Lausanne, Lausanne, Switzerland
| | - Georg Felix
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Judith Fliegmann
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany.
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145
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Einenkel R, Halte M, Erhardt M. Quantifying Substrate Protein Secretion via the Type III Secretion System of the Bacterial Flagellum. Methods Mol Biol 2024; 2715:577-592. [PMID: 37930553 DOI: 10.1007/978-1-0716-3445-5_36] [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: 11/07/2023]
Abstract
Protein transport across the cytoplasmic membrane is coupled to energy derived from ATP hydrolysis or the proton motive force. A sophisticated, multi-component type III secretion system (T3SS) exports substrate proteins of both the bacterial flagellum and virulence-associated injectisome system of many Gram-negative pathogens. The T3SS is primarily a proton motive force-driven protein exporter. Here, we describe a method to investigate the export of substrate proteins of the flagellar T3SS into the culture supernatant under conditions that manipulate the proton motive force. Further, we describe methods to precisely quantify flagellar protein export into the culture supernatant using a split NanoLuc luciferase, and how fluorescence labeling of the extracellular flagellar filament can bring insights into the protein export rate of individual flagellar T3SS.
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Affiliation(s)
| | | | - Marc Erhardt
- Humboldt Universität zu Berlin, Berlin, Germany.
- Max Planck Unit for the Science of Pathogens, Berlin, Germany.
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146
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Heath NG, Segal DJ. CRISPR-Based Split Luciferase as a Biosensor for Unique DNA Sequences In Situ. Methods Mol Biol 2024; 2784:285-299. [PMID: 38502493 DOI: 10.1007/978-1-0716-3766-1_19] [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] [Indexed: 03/21/2024]
Abstract
To date, CRISPR-based DNA targeting approaches have typically used fusion proteins between full fluorescent reporters and catalytically inactive Cas9 (dCas9) for imaging rather than detection of endogenous genomic DNA sequences. A promising alternative strategy for DNA targeting is the direct biosensing of user-defined sequences at single copy with single-cell resolution. Our recently described DNA biosensing approach using a dual fusion protein biosensor comprised of two independently optimized fragments of NanoLuc luciferase (NLuc) directionally fused to dCas9 paired with user-defined single-guide RNAs (sgRNAs) could allow users to sensitively detect unique copies of a target sequence in individual living cells using common laboratory equipment such as a microscope or a luminescence-equipped microplate reader. Here we describe a protocol for using such a DNA biosensor noninvasively in situ.
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Affiliation(s)
- Nicholas G Heath
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, USA
- Integrative Genetics and Genomics, University of California, Davis, Davis, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - David J Segal
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, USA.
- Integrative Genetics and Genomics, University of California, Davis, Davis, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
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147
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Vasta JD, Michaud A, Aaron Crapster J, Robers MB. A Method to Conditionally Measure Target Engagement at Intracellular RAS and RAF Complexes. Methods Mol Biol 2024; 2797:287-297. [PMID: 38570468 DOI: 10.1007/978-1-0716-3822-4_21] [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] [Indexed: 04/05/2024]
Abstract
Dysfunction of the RAS/mitogen-activated protein kinase (MAPK) pathway is a common driver of human cancers. As such, both the master regulator of the pathway, RAS, and its proximal kinase effectors, RAFs, have been of interest as drug targets for decades. Importantly, signaling within the RAS/MAPK pathway is highly coordinated due to the formation of a higher-order complex called the RAS/RAF signalosome, which may minimally contain dimers of both RAS and RAF protomers. In the disease state, RAS and RAF assemble in homo- and/or heterodimeric forms. Traditionally, drug development campaigns for both RAS and RAF have utilized biochemical assays of purified recombinant protein. As these assays do not query the RAS or RAF proteins in their full-length and complexed forms in cells, potency results collected using these assays have often failed to correlate with inhibition of the MAPK pathway. To more accurately quantify engagement at this signaling components, we present a bioluminescence resonance energy transfer (BRET)-based method to conditionally measure target engagement at individual protomers within the RAS/RAF signalosome in live cells.
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148
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Hawley RG, Hawley TS. CRISPR-Cas9-Mediated Bioluminescent Tagging of Endogenous Proteins by Fluorescent Protein-Assisted Cell Sorting. Methods Mol Biol 2024; 2779:273-286. [PMID: 38526790 DOI: 10.1007/978-1-0716-3738-8_12] [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] [Indexed: 03/27/2024]
Abstract
Oncogenic fusion genes are attractive therapeutic targets because of their tumor-specific expression and central "driver" roles in various human cancers. However, oncogenic fusions involving transcription factors such as PAX3-FOXO1 in alveolar fusion gene-positive rhabdomyosarcoma (FP-RMS) have been difficult to inhibit due to the apparent lack of tractable drug-like binding sites comparable to that recognized by Gleevec (imatinib mesylate) on the BCR-ABL1 tyrosine kinase fusion protein. Toward the identification of novel small molecules that selectively target PAX3-FOXO1, we used CRISPR-Cas9-mediated knock-in to append the pro-luminescent HiBiT tag onto the carboxy terminus of the endogenous PAX3-FOXO1 fusion protein in two human FP-RMS cell lines (RH4 and SCMC). HiBiT is an 11-amino acid peptide derived from the NanoLuc luciferase that produces a luminescence signal which is ~100-fold brighter than firefly or Renilla luciferases through high-affinity binding to a complementary NanoLuc peptide fragment called LgBiT. To facilitate single-cell clonal isolation of knock-ins, the homology-directed repair template encoding HiBiT was followed by a P2A self-cleaving peptide for coexpression of an mCherry fluorescent protein as a fluorescence-activated cell sorter (FACS)-selectable marker. HiBiT tagging thus allows highly sensitive luminescence detection of endogenous PAX3-FOXO1 levels permitting quantitative high-throughput screening of large compound libraries for the discovery of PAX3-FOXO1 inhibitors and degraders.
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Affiliation(s)
- Robert G Hawley
- Department of Anatomy and Cell Biology, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA.
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149
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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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150
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Zeke A, Alexa A, Reményi A. Discovery and Characterization of Linear Motif Mediated Protein-Protein Complexes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:59-71. [PMID: 38507200 DOI: 10.1007/978-3-031-52193-5_5] [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: 03/22/2024]
Abstract
There are myriads of protein-protein complexes that form within the cell. In addition to classical binding events between globular domains, many protein-protein interactions involve short disordered protein regions. The latter contain so-called linear motifs binding specifically to ordered protein domain surfaces. Linear binding motifs are classified based on their consensus sequence, where only a few amino acids are conserved. In this chapter we will review experimental and in silico techniques that can be used for the discovery and characterization of linear motif mediated protein-protein complexes involved in cellular signaling, protein level and gene expression regulation.
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Affiliation(s)
- András Zeke
- Institute of Organic Chemistry, HUN-REN Research Center for Natural Sciences, Budapest, Hungary
| | - Anita Alexa
- Institute of Organic Chemistry, HUN-REN Research Center for Natural Sciences, Budapest, Hungary
| | - Attila Reményi
- Institute of Organic Chemistry, HUN-REN Research Center for Natural Sciences, Budapest, Hungary.
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