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Klett T, Schwer M, Ernst LN, Engelhardt MU, Jaag SJ, Masberg B, Knappe C, Lämmerhofer M, Gehringer M, Boeckler FM. Evaluation of a Covalent Library of Diverse Warheads (CovLib) Binding to JNK3, USP7, or p53. Drug Des Devel Ther 2024; 18:2653-2679. [PMID: 38974119 PMCID: PMC11226190 DOI: 10.2147/dddt.s466829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 06/12/2024] [Indexed: 07/09/2024] Open
Abstract
Purpose Over the last few years, covalent fragment-based drug discovery has gained significant importance. Thus, striving for more warhead diversity, we conceived a library consisting of 20 covalently reacting compounds. Our covalent fragment library (CovLib) contains four different warhead classes, including five α-cyanoacacrylamides/acrylates (CA), three epoxides (EO), four vinyl sulfones (VS), and eight electron-deficient heteroarenes with a leaving group (SNAr/SN). Methods After predicting the theoretical solubility of the fragments by LogP and LogS during the selection process, we determined their experimental solubility using a turbidimetric solubility assay. The reactivities of the different compounds were measured in a high-throughput 5,5'-dithiobis-(2-nitrobenzoic acid) DTNB assay, followed by a (glutathione) GSH stability assay. We employed the CovLib in a (differential scanning fluorimetry) DSF-based screening against different targets: c-Jun N-terminal kinase 3 (JNK3), ubiquitin-specific protease 7 (USP7), and the tumor suppressor p53. Finally, the covalent binding was confirmed by intact protein mass spectrometry (MS). Results In general, the purchased fragments turned out to be sufficiently soluble. Additionally, they covered a broad spectrum of reactivity. All investigated α-cyanoacrylamides/acrylates and all structurally confirmed epoxides turned out to be less reactive compounds, possibly due to steric hindrance and reversibility (for α-cyanoacrylamides/acrylates). The SNAr and vinyl sulfone fragments are either highly reactive or stable. DSF measurements with the different targets JNK3, USP7, and p53 identified reactive fragment hits causing a shift in the melting temperatures of the proteins. MS confirmed the covalent binding mode of all these fragments to USP7 and p53, while additionally identifying the SNAr-type electrophile SN002 as a mildly reactive covalent hit for p53. Conclusion The screening and target evaluation of the CovLib revealed first interesting hits. The highly cysteine-reactive fragments VS004, SN001, SN006, and SN007 covalently modify several target proteins and showed distinct shifts in the melting temperatures up to +5.1 °C and -9.1 °C.
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Affiliation(s)
- Theresa Klett
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Martin Schwer
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Larissa N Ernst
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Marc U Engelhardt
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Simon J Jaag
- Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Benedikt Masberg
- Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Cornelius Knappe
- Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Michael Lämmerhofer
- Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Matthias Gehringer
- Pharmaceutical Chemistry, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
- Medicinal Chemistry, Institute for Biomedical Engineering, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Frank M Boeckler
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
- Interfaculty Institute for Biomedical Informatics (IBMI), Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
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Machitani M, Nomura A, Yamashita T, Yasukawa M, Ueki S, Fujita KI, Ueno T, Yamashita A, Tanzawa Y, Watanabe M, Taniguchi T, Saitoh N, Kaneko S, Kato Y, Mano H, Masutomi K. Maintenance of R-loop structures by phosphorylated hTERT preserves genome integrity. Nat Cell Biol 2024; 26:932-945. [PMID: 38806647 DOI: 10.1038/s41556-024-01427-6] [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: 07/18/2023] [Accepted: 04/23/2024] [Indexed: 05/30/2024]
Abstract
As aberrant accumulation of RNA-DNA hybrids (R-loops) causes DNA damage and genome instability, cells express regulators of R-loop structures. Here we report that RNA-dependent RNA polymerase (RdRP) activity of human telomerase reverse transcriptase (hTERT) regulates R-loop formation. We found that the phosphorylated form of hTERT (p-hTERT) exhibits RdRP activity in nuclear speckles both in telomerase-positive cells and telomerase-negative cells with alternative lengthening of telomeres (ALT) activity. The p-hTERT did not associate with telomerase RNA component in nuclear speckles but, instead, with TERRA RNAs to resolve R-loops. Targeting of the TERT gene in ALT cells ablated RdRP activity and impaired tumour growth. Using a genome-scale CRISPR loss-of-function screen, we identified Fanconi anaemia/BRCA genes as synthetic lethal partners of hTERT RdRP. Inactivation of RdRP and Fanconi anaemia/BRCA genes caused accumulation of R-loop structures and DNA damage. These findings indicate that RdRP activity of p-hTERT guards against genome instability by removing R-loop structures.
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Affiliation(s)
- Mitsuhiro Machitani
- Division of Cancer Stem Cell, National Cancer Center Research Institute, Tokyo, Japan
| | - Akira Nomura
- Division of Cancer Stem Cell, National Cancer Center Research Institute, Tokyo, Japan
- Department of Orthopaedic Surgery, Surgical Science, Tokai University School of Medicine, Isehara, Japan
| | - Taro Yamashita
- Department of Gastroenterology, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
| | - Mami Yasukawa
- Division of Cancer Stem Cell, National Cancer Center Research Institute, Tokyo, Japan
| | - Saori Ueki
- Division of Cancer Stem Cell, National Cancer Center Research Institute, Tokyo, Japan
| | - Ken-Ichi Fujita
- Division of Cancer Stem Cell, National Cancer Center Research Institute, Tokyo, Japan
| | - Toshihide Ueno
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Akio Yamashita
- Department of Investigative Medicine, University of the Ryukyus Graduate School of Medicine, Nakagami, Japan
| | - Yoshikazu Tanzawa
- Department of Orthopaedic Surgery, Surgical Science, Tokai University School of Medicine, Isehara, Japan
| | - Masahiko Watanabe
- Department of Orthopaedic Surgery, Surgical Science, Tokai University School of Medicine, Isehara, Japan
| | - Toshiyasu Taniguchi
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Noriko Saitoh
- Division of Cancer Biology, The Cancer Institute of JFCR, Tokyo, Japan
| | - Shuichi Kaneko
- Department of Gastroenterology, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
| | - Yukinari Kato
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Molecular Pharmacology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hiroyuki Mano
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Kenkichi Masutomi
- Division of Cancer Stem Cell, National Cancer Center Research Institute, Tokyo, Japan.
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Dahal S, Clayton K, Cabral T, Cheng R, Jahanshahi S, Ahmed C, Koirala A, Villasmil Ocando A, Malty R, Been T, Hernandez J, Mangos M, Shen D, Babu M, Calarco J, Chabot B, Attisano L, Houry WA, Cochrane A. On a path toward a broad-spectrum anti-viral: inhibition of HIV-1 and coronavirus replication by SR kinase inhibitor harmine. J Virol 2023; 97:e0039623. [PMID: 37706687 PMCID: PMC10617549 DOI: 10.1128/jvi.00396-23] [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: 03/14/2023] [Accepted: 07/14/2023] [Indexed: 09/15/2023] Open
Abstract
IMPORTANCE This study highlights the crucial role RNA processing plays in regulating viral gene expression and replication. By targeting SR kinases, we identified harmine as a potent inhibitor of HIV-1 as well as coronavirus (HCoV-229E and multiple SARS-CoV-2 variants) replication. Harmine inhibits HIV-1 protein expression and reduces accumulation of HIV-1 RNAs in both cell lines and primary CD4+ T cells. Harmine also suppresses coronavirus replication post-viral entry by preferentially reducing coronavirus sub-genomic RNA accumulation. By focusing on host factors rather than viral targets, our study offers a novel approach to combating viral infections that is effective against a range of unrelated viruses. Moreover, at doses required to inhibit virus replication, harmine had limited toxicity and minimal effect on the host transcriptome. These findings support the viability of targeting host cellular processes as a means of developing broad-spectrum anti-virals.
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Affiliation(s)
- Subha Dahal
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Kiera Clayton
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Tyler Cabral
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Ran Cheng
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Shahrzad Jahanshahi
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Choudhary Ahmed
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Amrit Koirala
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
- Dan L. Duncan Cancer Comprehensive Center, Baylor College of Medicine, Houston, Texas, USA
| | | | - Ramy Malty
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Research and Innovation Centre, Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | - Terek Been
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Javier Hernandez
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Maria Mangos
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - David Shen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Mohan Babu
- Research and Innovation Centre, Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | - John Calarco
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Benoit Chabot
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Liliana Attisano
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Walid A. Houry
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Alan Cochrane
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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Gu Q, Wu J, Xu H, Cao H, Zhang J, Jing C, Wang Z, Du M, Ma R, Feng J. CLASRP oncogene as a novel target for colorectal cancer. Funct Integr Genomics 2023; 23:290. [PMID: 37658940 PMCID: PMC10474993 DOI: 10.1007/s10142-023-01208-8] [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] [Received: 05/31/2023] [Revised: 08/04/2023] [Accepted: 08/11/2023] [Indexed: 09/05/2023]
Abstract
Clk4-associated serine/arginine-rich protein (CLASRP), an alternative splicing regulator, may be involved in the development and progression of cancer by regulating the activity of the CDC-like kinase (Clk) family. This study explored the biological function of CLASRP in colorectal cancer (CRC). The expression of CLASRP, which is associated with clinicopathological features, was analysed in CRC tissues and paired noncancer tissues by RT-PCR. The roles of CLASRP were investigated in CRC cells transfected with plasmids or shRNA through proliferation, migration and invasion assays in vitro and a xenograft model in vivo. Apoptosis was analysed using CLASRP-overexpressing CRC cells by western blotting. Clk inhibitors were used to perform functional research on CLASRP in CLASRP-overexpressing CRC cells. CLASRP was significantly upregulated in CRC cell lines, while high CLASRP expression was correlated with metastasis in CRC patients. Functionally, overexpression of CLASRP significantly promoted the proliferation, migration and invasion of CRC cells in vitro and tumour growth in vivo. Mechanistically, the proliferation, migration and invasion of CLASRP-overexpressing CRC cells were inhibited by Clk inhibitors, accompanied by low expression of CLASRP at the gene and protein levels. Clk inhibitors induced apoptosis of CLASRP-overexpressing CRC cells, resulting in direct blockade of cell growth. The expression levels of cleaved caspase 3 and cleaved caspase 8 were increased in CLASRP-overexpressing CRC cells treated with Clk inhibitors. CLASRP might serve as a promotional oncogene in CRC cells and be suppressed by Clk inhibitors through activation of caspase pathways.
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Affiliation(s)
- Quan Gu
- Nanjing Medical University Affiliated Cancer Hospital and Research Center for Clinical Oncology, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, 42 BaiZiTing Road, Nanjing, Jiangsu, 210000, People's Republic of China
| | - Jianzhong Wu
- Nanjing Medical University Affiliated Cancer Hospital and Research Center for Clinical Oncology, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, 42 BaiZiTing Road, Nanjing, Jiangsu, 210000, People's Republic of China
| | - Heng Xu
- Jiangsu Provincial Institute of Materia Medica, Nanjing Tech University, Nanjing, Jiangsu, China
| | - Haixia Cao
- Nanjing Medical University Affiliated Cancer Hospital and Research Center for Clinical Oncology, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, 42 BaiZiTing Road, Nanjing, Jiangsu, 210000, People's Republic of China
| | - Junying Zhang
- Nanjing Medical University Affiliated Cancer Hospital and Research Center for Clinical Oncology, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, 42 BaiZiTing Road, Nanjing, Jiangsu, 210000, People's Republic of China
| | - Changwen Jing
- Nanjing Medical University Affiliated Cancer Hospital and Research Center for Clinical Oncology, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, 42 BaiZiTing Road, Nanjing, Jiangsu, 210000, People's Republic of China
| | - Zhuo Wang
- Nanjing Medical University Affiliated Cancer Hospital and Research Center for Clinical Oncology, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, 42 BaiZiTing Road, Nanjing, Jiangsu, 210000, People's Republic of China
| | - Mengjie Du
- Jiangsu Provincial Institute of Materia Medica, Nanjing Tech University, Nanjing, Jiangsu, China
| | - Rong Ma
- Nanjing Medical University Affiliated Cancer Hospital and Research Center for Clinical Oncology, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, 42 BaiZiTing Road, Nanjing, Jiangsu, 210000, People's Republic of China.
| | - Jifeng Feng
- Nanjing Medical University Affiliated Cancer Hospital and Research Center for Clinical Oncology, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, 42 BaiZiTing Road, Nanjing, Jiangsu, 210000, People's Republic of China.
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5
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Su CF, Das D, Muhammad Aslam M, Xie JQ, Li XY, Chen MX. Eukaryotic splicing machinery in the plant-virus battleground. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1793. [PMID: 37198737 DOI: 10.1002/wrna.1793] [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: 09/29/2022] [Revised: 02/24/2023] [Accepted: 04/19/2023] [Indexed: 05/19/2023]
Abstract
Plant virual infections are mainly caused by plant-virus parasitism which affects ecological communities. Some viruses are highly pathogen specific that can infect only specific plants, while some can cause widespread harm, such as tobacco mosaic virus (TMV) and cucumber mosaic virus (CMV). After a virus infects the host, undergoes a series of harmful effects, including the destruction of host cell membrane receptors, changes in cell membrane components, cell fusion, and the production of neoantigens on the cell surface. Therefore, competition between the host and the virus arises. The virus starts gaining control of critical cellular functions of the host cells and ultimately affects the fate of the targeted host plants. Among these critical cellular processes, alternative splicing (AS) is an essential posttranscriptional regulation process in RNA maturation, which amplify host protein diversity and manipulates transcript abundance in response to plant pathogens. AS is widespread in nearly all human genes and critical in regulating animal-virus interactions. In particular, an animal virus can hijack the host splicing machinery to re-organize its compartments for propagation. Changes in AS are known to cause human disease, and various AS events have been reported to regulate tissue specificity, development, tumour proliferation, and multi-functionality. However, the mechanisms underlying plant-virus interactions are poorly understood. Here, we summarize the current understanding of how viruses interact with their plant hosts compared with humans, analyze currently used and putative candidate agrochemicals to treat plant-viral infections, and finally discussed the potential research hotspots in the future. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Chang-Feng Su
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, Guizhou Province, China
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
| | - Debatosh Das
- College of Agriculture, Food and Natural Resources (CAFNR), Division of Plant Sciences & Technology, University of Missouri, Columbia, Missouri, USA
| | - Mehtab Muhammad Aslam
- College of Agriculture, Food and Natural Resources (CAFNR), Division of Plant Sciences & Technology, University of Missouri, Columbia, Missouri, USA
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ji-Qin Xie
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, Guizhou Province, China
| | - Xiang-Yang Li
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, Guizhou Province, China
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
| | - Mo-Xian Chen
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, Guizhou Province, China
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
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Pramotton FM, Abukar A, Hudson C, Dunbar J, Potterton A, Tonnicchia S, Taddei A, Mazza E, Giampietro C. DYRK1B inhibition exerts senolytic effects on endothelial cells and rescues endothelial dysfunctions. Mech Ageing Dev 2023; 213:111836. [PMID: 37301518 DOI: 10.1016/j.mad.2023.111836] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 05/15/2023] [Accepted: 06/06/2023] [Indexed: 06/12/2023]
Abstract
Aging is the major risk factor for chronic disease development. Cellular senescence is a key mechanism that triggers or contributes to age-related phenotypes and pathologies. The endothelium, a single layer of cells lining the inner surface of a blood vessel, is a critical interface between blood and all tissues. Many studies report a link between endothelial cell senescence, inflammation, and diabetic vascular diseases. Here we identify, using combined advanced AI and machine learning, the Dual Specificity Tyrosine Phosphorylation Regulated Kinase 1B (DYRK1B) protein as a possible senolytic target for senescent endothelial cells. We demonstrate that upon induction of senescence in vitro DYRK1B expression is increased in endothelial cells and localized at adherens junctions where it impairs their proper organization and functions. DYRK1B knock-down or inhibition restores endothelial barrier properties and collective behavior. DYRK1B is therefore a possible target to counteract diabetes-associated vascular diseases linked to endothelial cell senescence.
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Affiliation(s)
- Francesca M Pramotton
- Swiss Federal Laboratories for Materials Science and Technology (EMPA), Dübendorf 8600, Switzerland; Department of Mechanical and Process Engineering, ETH Zurich, Zurich 8092, Switzerland
| | - Asra Abukar
- Department of Mechanical and Process Engineering, ETH Zurich, Zurich 8092, Switzerland; Senecell AG, Zurich 8057, Switzerland
| | | | | | | | - Simone Tonnicchia
- Swiss Federal Laboratories for Materials Science and Technology (EMPA), Dübendorf 8600, Switzerland; Department of Mechanical and Process Engineering, ETH Zurich, Zurich 8092, Switzerland
| | | | - Edoardo Mazza
- Swiss Federal Laboratories for Materials Science and Technology (EMPA), Dübendorf 8600, Switzerland; Department of Mechanical and Process Engineering, ETH Zurich, Zurich 8092, Switzerland
| | - Costanza Giampietro
- Swiss Federal Laboratories for Materials Science and Technology (EMPA), Dübendorf 8600, Switzerland; Department of Mechanical and Process Engineering, ETH Zurich, Zurich 8092, Switzerland; Senecell AG, Zurich 8057, Switzerland.
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7
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Song M, Pang L, Zhang M, Qu Y, Laster KV, Dong Z. Cdc2-like kinases: structure, biological function, and therapeutic targets for diseases. Signal Transduct Target Ther 2023; 8:148. [PMID: 37029108 PMCID: PMC10082069 DOI: 10.1038/s41392-023-01409-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 03/15/2023] [Accepted: 03/20/2023] [Indexed: 04/09/2023] Open
Abstract
The CLKs (Cdc2-like kinases) belong to the dual-specificity protein kinase family and play crucial roles in regulating transcript splicing via the phosphorylation of SR proteins (SRSF1-12), catalyzing spliceosome molecular machinery, and modulating the activities or expression of non-splicing proteins. The dysregulation of these processes is linked with various diseases, including neurodegenerative diseases, Duchenne muscular dystrophy, inflammatory diseases, viral replication, and cancer. Thus, CLKs have been considered as potential therapeutic targets, and significant efforts have been exerted to discover potent CLKs inhibitors. In particular, clinical trials aiming to assess the activities of the small molecules Lorecivivint on knee Osteoarthritis patients, and Cirtuvivint and Silmitasertib in different advanced tumors have been investigated for therapeutic usage. In this review, we comprehensively documented the structure and biological functions of CLKs in various human diseases and summarized the significance of related inhibitors in therapeutics. Our discussion highlights the most recent CLKs research, paving the way for the clinical treatment of various human diseases.
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Affiliation(s)
- Mengqiu Song
- Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
- China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, Zhengzhou, Henan, 450008, China
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan, China
| | - Luping Pang
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
- Research Center of Basic Medicine, Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Mengmeng Zhang
- Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
- Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Yingzi Qu
- Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
- Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Kyle Vaughn Laster
- China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, Zhengzhou, Henan, 450008, China
| | - Zigang Dong
- Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China.
- China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, Zhengzhou, Henan, 450008, China.
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan, China.
- Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China.
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8
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Lindberg MF, Deau E, Arfwedson J, George N, George P, Alfonso P, Corrionero A, Meijer L. Comparative Efficacy and Selectivity of Pharmacological Inhibitors of DYRK and CLK Protein Kinases. J Med Chem 2023; 66:4106-4130. [PMID: 36876904 DOI: 10.1021/acs.jmedchem.2c02068] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Dual-specificity, tyrosine phosphorylation-regulated kinases (DYRKs) and cdc2-like kinases (CLKs) play a large variety of cellular functions and are involved in several diseases (cognitive disorders, diabetes, cancers, etc.). There is, thus, growing interest in pharmacological inhibitors as chemical probes and potential drug candidates. This study presents an unbiased evaluation of the kinase inhibitory activity of a library of 56 reported DYRK/CLK inhibitors on the basis of comparative, side-by-side, catalytic activity assays on a panel of 12 recombinant human kinases, enzyme kinetics (residence time and Kd), in-cell inhibition of Thr-212-Tau phosphorylation, and cytotoxicity. The 26 most active inhibitors were modeled in the crystal structure of DYRK1A. The results show a rather large diversity of potencies and selectivities among the reported inhibitors and emphasize the difficulties to avoid "off-targets" in this area of the kinome. The use of a panel of DYRKs/CLKs inhibitors is suggested to analyze the functions of these kinases in cellular processes.
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Affiliation(s)
| | - Emmanuel Deau
- Perha Pharmaceuticals, Perharidy Peninsula, 29680 Roscoff, France
| | - Jonas Arfwedson
- Perha Pharmaceuticals, Perharidy Peninsula, 29680 Roscoff, France
| | - Nicolas George
- Oncodesign, 25-27 avenue du Québec, 91140 Villebon-sur-Yvette, France
| | - Pascal George
- Perha Pharmaceuticals, Perharidy Peninsula, 29680 Roscoff, France
| | - Patricia Alfonso
- Enzymlogic, Qube Technology Park, C/Santiago Grisolía, 2, 28760 Madrid, Spain
| | - Ana Corrionero
- Enzymlogic, Qube Technology Park, C/Santiago Grisolía, 2, 28760 Madrid, Spain
| | - Laurent Meijer
- Perha Pharmaceuticals, Perharidy Peninsula, 29680 Roscoff, France
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9
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Yang T, Yang Y, Chen Y, Tang M, Shi M, Tian Y, Yuan X, Yang Z, Chen L. Rational design and appraisal of selective Cdc2-Like kinase 1 (Clk1) inhibitors as novel autophagy inducers for the treatment of acute liver injury (ALI). Eur J Med Chem 2023; 250:115168. [PMID: 36780830 DOI: 10.1016/j.ejmech.2023.115168] [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: 12/07/2022] [Revised: 01/27/2023] [Accepted: 01/28/2023] [Indexed: 02/10/2023]
Abstract
Autophagy inducers are promising agents for treating certain medical illnesses, while no safe autophagy inducers are in clinical applications. Cdc2-like kinase 1 (Clk1) inhibitors induce autophagy efficiently; however, most Clk1 inhibitors lack selectivity, especially against Dyrk1A kinase. Herein, we report a series of 1H-pyrrolo[2,3-b]pyridin-5-amine derivatives as novel Clk1 inhibitors. Through detailed structural modification and structure-activity relationship studies, compound 10ad shows potent and selective inhibition for Clk1, with an IC50 value of 5 nM and over 300-fold selectivity for Dyrk1A. Related kinase screening also validates the selectivity of compound 10ad. Furthermore, compound 10ad potently induces autophagy in vitro and exhibits significant hepatoprotective effects in the acute liver injury model induced by acetaminophen (paracetamol). In general, due to the excellent potency and selectivity, compound 10ad was worth further investigation in the treatment of autophagy-related diseases.
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Affiliation(s)
- Tao Yang
- State Key Laboratory of Biotherapy and Cancer Center and Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China.
| | - Yingxue Yang
- State Key Laboratory of Biotherapy and Cancer Center and Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Yong Chen
- State Key Laboratory of Biotherapy and Cancer Center and Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Minghai Tang
- State Key Laboratory of Biotherapy and Cancer Center and Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Mingsong Shi
- State Key Laboratory of Biotherapy and Cancer Center and Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Yang Tian
- Department of Otolaryngology Head and Neck Surgery, The Third People's Hospital of Chengdu, Chengdu, 610014, China
| | - Xue Yuan
- State Key Laboratory of Biotherapy and Cancer Center and Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Zhuang Yang
- State Key Laboratory of Biotherapy and Cancer Center and Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China; Chengdu Zenitar Biomedical Technology Co., Ltd, Chengdu, 610041, China.
| | - Lijuan Chen
- State Key Laboratory of Biotherapy and Cancer Center and Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China; Chengdu Zenitar Biomedical Technology Co., Ltd, Chengdu, 610041, China.
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10
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ElHady AK, El-Gamil DS, Abadi AH, Abdel-Halim M, Engel M. An overview of cdc2-like kinase 1 (Clk1) inhibitors and their therapeutic indications. Med Res Rev 2023; 43:343-398. [PMID: 36262046 DOI: 10.1002/med.21928] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 06/07/2022] [Accepted: 09/11/2022] [Indexed: 02/05/2023]
Abstract
Over the past decade, Clk1 has been identified as a promising target for the treatment of various diseases, in which deregulated alternative splicing plays a role. First small molecules targeting Clk1 are in clinical trials for the treatment of solid cancer, where variants of oncogenic proteins derived from alternative splicing promote tumor progression. Since many infectious pathogens hi-jack the host cell's splicing machinery to ensure efficient replication, further indications in this area are under investigation, such as Influenza A, HIV-1 virus, and Trypanosoma infections, and more will likely be discovered in the future. In addition, Clk1 was found to contribute to the progression of Alzheimer's disease through causing an imbalance of tau splicing products. Interestingly, homozygous Clk1 knockout mice showed a rather mild phenotype, opposed to what might be expected in view of the profound role of Clk1 in alternative splicing. A major drawback of most Clk1 inhibitors is their insufficient selectivity; in particular, Dyrk kinases and haspin were frequently identified as off-targets, besides the other Clk isoforms. Only few inhibitors were shown to be selective over Dyrk1A and haspin, whereas no Clk1 inhibitor so far achieved selectivity over the Clk4 isoform. In this review, we carefully compiled all Clk1 inhibitors from the scientific literature and summarized their structure-activity relationships (SAR). In addition, we critically discuss the available selectivity data and describe the inhibitor's efficacy in cellular models, if reported. Thus, we provide a comprehensive overview on the current state of Clk1 drug discovery and highlight the most promising chemotypes.
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Affiliation(s)
- Ahmed K ElHady
- Department of Organic and Pharmaceutical Chemistry, School of Life and Medical Sciences, University of Hertfordshire Hosted by Global Academic Foundation, New Administrative Capital, Cairo, Egypt.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Dalia S El-Gamil
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt.,Department of Chemistry, Faculty of Pharmacy, Ahram Canadian University, Cairo, Egypt
| | - Ashraf H Abadi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Mohammad Abdel-Halim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Matthias Engel
- Department of Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
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11
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Zhang W, Tang CS, Xiang SQ. Condensation of acrylonitrile and aryl acetonitrile: construction of α-amino-β-cyano cyclohexene skeletons. RSC Adv 2022; 12:29840-29843. [PMID: 36321094 PMCID: PMC9578340 DOI: 10.1039/d2ra04936h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 09/27/2022] [Indexed: 11/07/2022] Open
Abstract
A representative condensation of acrylonitrile and aryl acetonitrile has been reported for the synthesis of α-amino-β-cyano cyclohexene. The reaction was carried out mildly in an open environment at room temperature. The scope and versatility of the method have been demonstrated with 20 examples, containing highly active ethynyl groups. Further applications for 4-aminopyrimidine compounds were performed. A mechanism was proposed, involving Michael additions between acrylonitrile and aryl acetonitriles as well as intramolecular condensation.
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Affiliation(s)
- Wei Zhang
- Chongqing University of Science and TechnologyChongqing401331China
| | | | - Shi-Qun Xiang
- Key Laboratory of Preparation and Application of Environmental Friendly Materials, Jilin Normal University, Ministry of EducationChangchun130103China,College of Chemistry, Jilin Normal UniversitySiping136000China
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12
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A critical update on the strategies towards small molecule inhibitors targeting Serine/arginine-rich (SR) proteins and Serine/arginine-rich proteins related kinases in alternative splicing. Bioorg Med Chem 2022; 70:116921. [PMID: 35863237 DOI: 10.1016/j.bmc.2022.116921] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 11/02/2022]
Abstract
>90% of genes in the human body undergo alternative splicing (AS) after transcription, which enriches protein species and regulates protein levels. However, there is growing evidence that various genetic isoforms resulting from dysregulated alternative splicing are prevalent in various types of cancers. Dysregulated alternative splicing leads to cancer generation and maintenance of cancer properties such as proliferation differentiation, apoptosis inhibition, invasion metastasis, and angiogenesis. Serine/arginine-rich proteins and SR protein-associated kinases mediate splice site recognition and splice complex assembly during variable splicing. Based on the impact of dysregulated alternative splicing on disease onset and progression, the search for small molecule inhibitors targeting alternative splicing is imminent. In this review, we discuss the structure and specific biological functions of SR proteins and describe the regulation of SR protein function by SR protein related kinases meticulously, which are closely related to the occurrence and development of various types of cancers. On this basis, we summarize the reported small molecule inhibitors targeting SR proteins and SR protein related kinases from the perspective of medicinal chemistry. We mainly categorize small molecule inhibitors from four aspects, including targeting SR proteins, targeting Serine/arginine-rich protein-specific kinases (SRPKs), targeting Cdc2-like kinases (CLKs) and targeting dual-specificity tyrosine-regulated kinases (DYRKs), in terms of structure, inhibition target, specific mechanism of action, biological activity, and applicable diseases. With this review, we are expected to provide a timely summary of recent advances in alternative splicing regulated by kinases and a preliminary introduction to relevant small molecule inhibitors.
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13
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Liu L, Vujovic A, Deshpande NP, Sathe S, Anande G, Chen HTT, Xu J, Minden MD, Yeo GW, Unnikrishnan A, Hope KJ, Lu Y. The splicing factor RBM17 drives leukemic stem cell maintenance by evading nonsense-mediated decay of pro-leukemic factors. Nat Commun 2022; 13:3833. [PMID: 35781533 PMCID: PMC9250932 DOI: 10.1038/s41467-022-31155-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 05/30/2022] [Indexed: 12/01/2022] Open
Abstract
Chemo-resistance in acute myeloid leukemia (AML) patients is driven by leukemic stem cells (LSCs) resulting in high rates of relapse and low overall survival. Here, we demonstrate that upregulation of the splicing factor, RBM17 preferentially marks and sustains LSCs and directly correlates with shorten patient survival. RBM17 knockdown in primary AML cells leads to myeloid differentiation and impaired colony formation and in vivo engraftment. Integrative multi-omics analyses show that RBM17 repression leads to inclusion of poison exons and production of nonsense-mediated decay (NMD)-sensitive transcripts for pro-leukemic factors and the translation initiation factor, EIF4A2. We show that EIF4A2 is enriched in LSCs and its inhibition impairs primary AML progenitor activity. Proteomic analysis of EIF4A2-depleted AML cells shows recapitulation of the RBM17 knockdown biological effects, including pronounced suppression of proteins involved in ribosome biogenesis. Overall, these results provide a rationale to target RBM17 and/or its downstream NMD-sensitive splicing substrates for AML treatment.
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Affiliation(s)
- Lina Liu
- Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ana Vujovic
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Nandan P Deshpande
- Adult Cancer Program, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
- Prince of Wales Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Shashank Sathe
- Department of Cellular and Molecular Medicine, Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, San Diego, CA, USA
| | - Govardhan Anande
- Adult Cancer Program, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
- Prince of Wales Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - He Tian Tony Chen
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Joshua Xu
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Mark D Minden
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, San Diego, CA, USA
| | - Ashwin Unnikrishnan
- Adult Cancer Program, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
- Prince of Wales Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Kristin J Hope
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
| | - Yu Lu
- Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada.
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14
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p53 Isoforms as Cancer Biomarkers and Therapeutic Targets. Cancers (Basel) 2022; 14:cancers14133145. [PMID: 35804915 PMCID: PMC9264937 DOI: 10.3390/cancers14133145] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/22/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary The well-known tumor suppressor protein p53 plays important roles in tumor prevention through transcriptional regulation of its target genes. Reactivation of p53 activity has been a potent strategy for cancer treatment. Accumulating evidences indicate that p53 isoforms truncated/modified in the N- or C-terminus can modulate the p53 pathway in a p53-dependent or p53-independent manner. It is thus imperative to characterize the roles of the p53 isoforms in cancer development. This review illustrates how p53 isoforms participate in tumor development and/or suppression. It also summarizes the knowledge about the p53 isoforms as promising cancer biomarkers and therapeutic targets. Abstract This review aims to summarize the implications of the major isoforms of the tumor suppressor protein p53 in aggressive cancer development. The current knowledge of p53 isoforms, their involvement in cell-signaling pathways, and their interactions with other cellular proteins or factors suggests the existence of an intricate molecular network that regulates their oncogenic function. Moreover, existing literature about the involvement of the p53 isoforms in various cancers leads to the proposition of therapeutic solutions by altering the cellular levels of the p53 isoforms. This review thus summarizes how the major p53 isoforms Δ40p53α/β/γ, Δ133p53α/β/γ, and Δ160p53α/β/γ might have clinical relevance in the diagnosis and effective treatments of cancer.
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15
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Remans K, Lebendiker M, Abreu C, Maffei M, Sellathurai S, May MM, Vaněk O, de Marco A. Protein purification strategies must consider downstream applications and individual biological characteristics. Microb Cell Fact 2022; 21:52. [PMID: 35392897 PMCID: PMC8991485 DOI: 10.1186/s12934-022-01778-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Proteins are used as reagents in a broad range of scientific fields. The reliability and reproducibility of experimental data will largely depend on the quality of the (recombinant) proteins and, consequently, these should undergo thorough structural and functional controls. Depending on the downstream application and the biochemical characteristics of the protein, different sets of specific features will need to be checked. RESULTS A number of examples, representative of recurrent issues and previously published strategies, has been reported that illustrate real cases of recombinant protein production in which careful strategy design at the start of the project combined with quality controls throughout the production process was imperative to obtain high-quality samples compatible with the planned downstream applications. Some proteins possess intrinsic properties (e.g., prone to aggregation, rich in cysteines, or a high affinity for nucleic acids) that require certain precautions during the expression and purification process. For other proteins, the downstream application might demand specific conditions, such as for proteins intended for animal use that need to be endotoxin-free. CONCLUSIONS This review has been designed to act as a practical reference list for researchers who wish to produce and evaluate recombinant proteins with certain specific requirements or that need particular care for their preparation and storage.
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Affiliation(s)
- Kim Remans
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Mario Lebendiker
- Protein Purification Facility, The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Celeste Abreu
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840, Prague, Czech Republic
| | - Mariano Maffei
- Evvivax Biotech, Via di Castel Romano 100, 00128, Rome, Italy
| | | | - Marina M May
- AiCuris Anti-Infective Cures AG, Friedrich-Ebert-Str. 475, 42117, Wuppertal, Germany
| | - Ondřej Vaněk
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12840, Prague, Czech Republic
| | - Ario de Marco
- Lab of Environmental and Life Sciences, University of Nova Gorica, Vipavska Cesta 13, 5000, Rožna Dolina-Nova Gorica, Slovenia.
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16
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Lima E, Medeiros J. Marine Organisms as Alkaloid Biosynthesizers of Potential Anti-Alzheimer Agents. Mar Drugs 2022; 20:75. [PMID: 35049930 PMCID: PMC8780771 DOI: 10.3390/md20010075] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 01/11/2022] [Accepted: 01/11/2022] [Indexed: 12/12/2022] Open
Abstract
The incidence of neurodegenerative diseases, such as Alzheimer's disease (AD), increases continuously demanding the urgent development of anti-Alzheimer's agents. Marine organisms (MO) have to create their own defenses due to the adverse environment where they live and so synthesize several classes of compounds, such as akaloids, to defend themselves. Therefore, the identification of marine natural products with neuroprotective effects is a necessity. Being that AD is not only a genetic but also an environmental complex disease, a treatment for AD remains to discover. As the major clinical indications (CI) of AD are extracellular plaques formed by β-amyloid (Aβ) protein, intracellular neurofibrillary tangles (NFTs) formed by hyper phosphorylated τ-protein, uncommon inflammatory response and neuron apoptosis and death caused by oxidative stress, alkaloids that may decrease CI, might be used against AD. Most of the alkalolids with those properties are derivatives of the amino acid tryptophan mainly with a planar indole scaffold. Certainly, alkaloids targeting more than one CI, multitarget-directed ligands (MTDL), have the potential to become a lead in AD treatment. Alkaloids to have a maximum of activity against CI, should be planar and contain halogens and amine quaternization.
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Affiliation(s)
- Elisabete Lima
- Faculty of Science and Technology (FCT), Institute of Agricultural and Environmental Research and Technology (IITAA), University of Azores, 9500-321 Ponta Delgada, São Miguel, Açores, Portugal;
| | - Jorge Medeiros
- Faculty of Science and Technology (FCT), Biotechnology Centre of Azores (CBA), University of Azores, 9500-321 Ponta Delgada, São Miguel, Açores, Portugal
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17
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Llorach-Pares L, Nonell-Canals A, Avila C, Sanchez-Martinez M. Computer-Aided Drug Design (CADD) to De-Orphanize Marine Molecules: Finding Potential Therapeutic Agents for Neurodegenerative and Cardiovascular Diseases. Mar Drugs 2022; 20:53. [PMID: 35049908 PMCID: PMC8781171 DOI: 10.3390/md20010053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 12/24/2021] [Accepted: 12/27/2021] [Indexed: 11/30/2022] Open
Abstract
Computer-aided drug design (CADD) techniques allow the identification of compounds capable of modulating protein functions in pathogenesis-related pathways, which is a promising line on drug discovery. Marine natural products (MNPs) are considered a rich source of bioactive compounds, as the oceans are home to much of the planet's biodiversity. Biodiversity is directly related to chemodiversity, which can inspire new drug discoveries. Therefore, natural products (NPs) in general, and MNPs in particular, have been used for decades as a source of inspiration for the design of new drugs. However, NPs present both opportunities and challenges. These difficulties can be technical, such as the need to dive or trawl to collect the organisms possessing the compounds, or biological, due to their particular marine habitats and the fact that they can be uncultivable in the laboratory. For all these difficulties, the contributions of CADD can play a very relevant role in simplifying their study, since, for example, no biological sample is needed to carry out an in-silico analysis. Therefore, the amount of natural product that needs to be used in the entire preclinical and clinical study is significantly reduced. Here, we exemplify how this combination between CADD and MNPs can help unlock their therapeutic potential. In this study, using a set of marine invertebrate molecules, we elucidate their possible molecular targets and associated therapeutic potential, establishing a pipeline that can be replicated in future studies.
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Affiliation(s)
- Laura Llorach-Pares
- Mind the Byte S.L., 08028 Barcelona, Catalonia, Spain; (L.L.-P.); (A.N.-C.)
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology and Biodiversity Research Institute (IRBio), University of Barcelona, 08028 Barcelona, Catalonia, Spain;
| | | | - Conxita Avila
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology and Biodiversity Research Institute (IRBio), University of Barcelona, 08028 Barcelona, Catalonia, Spain;
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18
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Astakhov AV, Chernenko AY, Kutyrev VV, Ranny GS, Minyaev ME, Chernyshev VM, Ananikov VP. Selective Buchwald–Hartwig arylation of C-amino-1,2,4-triazoles and other coordinating aminoheterocycles enabled by bulky NHC ligands and TPEDO activator. Inorg Chem Front 2022. [DOI: 10.1039/d2qi01832b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A facile method for selective N-(hetero)arylation of coordinating 3(5)-amino-1,2,4-triazoles under Pd/NHC catalysis using TPEDO as a new efficient Pd(ii) to Pd(0) reductant has been developed.
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Affiliation(s)
- Alexander V. Astakhov
- Platov South-Russian State Polytechnic University, (NPI), Prosvescheniya st., 132, Novocherkassk, 346428, Russia
| | - Andrey Yu. Chernenko
- Platov South-Russian State Polytechnic University, (NPI), Prosvescheniya st., 132, Novocherkassk, 346428, Russia
| | - Vadim V. Kutyrev
- Platov South-Russian State Polytechnic University, (NPI), Prosvescheniya st., 132, Novocherkassk, 346428, Russia
| | - Gleb S. Ranny
- Platov South-Russian State Polytechnic University, (NPI), Prosvescheniya st., 132, Novocherkassk, 346428, Russia
| | - Mikhail E. Minyaev
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, Moscow, 119991, Russia
| | - Victor M. Chernyshev
- Platov South-Russian State Polytechnic University, (NPI), Prosvescheniya st., 132, Novocherkassk, 346428, Russia
| | - Valentine P. Ananikov
- Platov South-Russian State Polytechnic University, (NPI), Prosvescheniya st., 132, Novocherkassk, 346428, Russia
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, Moscow, 119991, Russia
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19
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Unsal Tan O, Zengin M. Insights into the chemistry and therapeutic potential of acrylonitrile derivatives. Arch Pharm (Weinheim) 2021; 355:e2100383. [PMID: 34763365 DOI: 10.1002/ardp.202100383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 12/20/2022]
Abstract
Acrylonitrile is a fascinating scaffold widely found in many natural products, drugs, and drug candidates with various biological activities. Several drug molecules such as entacapone, rilpivirine, teriflunomide, and so forth, bearing an acrylonitrile moiety have been marketed. In this review, diverse synthetic strategies for constructing desired acrylonitriles are discussed, and the different biological activities and medicinal significance of various acrylonitrile derivatives are critically evaluated. The information gathered is expected to provide rational guidance for the development of clinically useful agents from acrylonitriles.
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Affiliation(s)
- Oya Unsal Tan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
| | - Merve Zengin
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
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20
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Design and Microwave Synthesis of New (5 Z) 5-Arylidene-2-thioxo-1,3-thiazolinidin-4-one and (5 Z) 2-Amino-5-arylidene-1,3-thiazol-4(5 H)-one as New Inhibitors of Protein Kinase DYRK1A. Pharmaceuticals (Basel) 2021; 14:ph14111086. [PMID: 34832868 PMCID: PMC8623179 DOI: 10.3390/ph14111086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 02/03/2023] Open
Abstract
Here, we report on the synthesis of libraries of new 5-arylidene-2-thioxo-1,3-thiazolidin-4-ones 3 (twenty-two compounds) and new 2-amino-5-arylidene-1,3-thiazol-4(5H)-ones 5 (twenty-four compounds) with stereo controlled Z-geometry under microwave irradiation. The 46 designed final compounds were tested in order to determine their activity against four representative protein kinases (DYR1A, CK1, CDK5/p25, and GSK3α/β). Among these 1,3-thiazolidin-4-ones, the molecules (5Z) 5-(4-hydroxybenzylidene)-2-thioxo-1,3-thiazolidin-4-one 3e (IC50 0.028 μM) and (5Z)-5-benzo[1,3]dioxol-5-ylmethylene-2-(pyridin-2-yl)amino-1,3-thiazol-4(5H)-one 5s (IC50 0.033 μM) were identified as lead compounds and as new nanomolar DYRK1A inhibitors. Some of these compounds in the two libraries have been also evaluated for their in vitro inhibition of cell proliferation (Huh7 D12, Caco2, MDA-MB 231, HCT 116, PC3, and NCI-H2 tumor cell lines). These results will enable us to use the 1,3-thiazolidin-4-one core as pharmacophores to develop potent treatment for neurological or oncological disorders in which DYRK1A is fully involved.
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21
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Qin Z, Qin L, Feng X, Li Z, Bian J. Development of Cdc2-like Kinase 2 Inhibitors: Achievements and Future Directions. J Med Chem 2021; 64:13191-13211. [PMID: 34519506 DOI: 10.1021/acs.jmedchem.1c00985] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cdc2-like kinases (CLKs; CLK1-4) are associated with various neurodegenerative disorders, metabolic regulation, and viral infection and have been recognized as potential drug targets. Human CLK2 has received increasing attention as a regulator that phosphorylates serine- and arginine-rich (SR) proteins and subsequently modulates the alternative splicing of precursor mRNA (pre-mRNA), which is an attractive target for degenerative disease and cancer. Numerous CLK2 inhibitors have been identified, with several molecules currently in clinical development. The first CLK2 inhibitor Lorecivivint (compound 1) has recently entered phase 3 clinical trials. However, highly selective CLK2 inhibitors are rarely reported. This Perspective summarizes the biological roles and therapeutic potential of CLK2 along with progress on the development of CLK2 inhibitors and discusses the achievements and future prospects of CLK2 inhibitors for therapeutic applications.
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Affiliation(s)
- Zhen Qin
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211100, P. R. China
| | - Lian Qin
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211100, P. R. China
| | - Xi Feng
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211100, P. R. China
| | - Zhiyu Li
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211100, P. R. China
| | - Jinlei Bian
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211100, P. R. China
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22
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Liu H, Sun Q, Chen S, Chen L, Jia W, Zhao J, Sun X. DYRK1A activates NFATC1 to increase glioblastoma migration. Cancer Med 2021; 10:6416-6427. [PMID: 34309232 PMCID: PMC8446559 DOI: 10.1002/cam4.4159] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 07/02/2021] [Accepted: 07/09/2021] [Indexed: 12/27/2022] Open
Abstract
Glioblastoma (GBM) is the most aggressive glioma, and is prone to develop resistance to chemotherapy and radiotherapy; hence, patients with glioblastoma have a high recurrence rate and a low 1-year survival rate. In addition, the pathogenesis of glioblastoma is complex and largely unknown, and the available treatments are limited. Here, we uncovered a fundamental role of DYRK1A in regulating NFATC1 in GBMs. We found that DYRK1A was highly expressed in glioma and glioblastoma cells, and its expression was positively correlated with that of NFATC1. Moreover, inhibition of DYRK1A promoted NFATC1 degradation in GBM cells and sharply reduced the transactivation of NFATC1, not only by decreasing the expression of NFATC1-targeted genes, but also by reducing the luciferase activity, and vice versa. However, DYRK1A had the opposite effect on NFATC2. Most importantly, our data suggest that DYRK1A inhibition reduces glioblastoma migration. Polypeptides derived from the DYRK1A-targeted motif of NFATC1, by competitively blocking DYRK1A kinase activity on NFATC1, clearly destabilized NFATC1 protein and impaired glioblastoma migration. We propose that the recovery of NFATC1 stability is a key oncogenic event in a large proportion of gliomas, and pharmacological inhibition of DYRK1A by polypeptides could represent a promising therapeutic intervention for GBM.
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Affiliation(s)
- Heng Liu
- NHC Key Laboratory of OtorhinolaryngologyQilu Hospital of Shandong UniversityJinanShandongChina
- Department of OtorhinolaryngologyQilu Hospital of Shandong UniversityJinanShandongChina
| | - Qian Sun
- NHC Key Laboratory of OtorhinolaryngologyQilu Hospital of Shandong UniversityJinanShandongChina
- Department of OtorhinolaryngologyQilu Hospital of Shandong UniversityJinanShandongChina
- Immunology InstituteSchool of Basic Medical SciencesCheeloo College of MedicineShandong UniversityJinanShandongChina
| | - Shuai Chen
- NHC Key Laboratory of OtorhinolaryngologyQilu Hospital of Shandong UniversityJinanShandongChina
- Department of OtorhinolaryngologyQilu Hospital of Shandong UniversityJinanShandongChina
- Immunology InstituteSchool of Basic Medical SciencesCheeloo College of MedicineShandong UniversityJinanShandongChina
| | - Long Chen
- NHC Key Laboratory of OtorhinolaryngologyQilu Hospital of Shandong UniversityJinanShandongChina
- Department of OtorhinolaryngologyQilu Hospital of Shandong UniversityJinanShandongChina
| | - Wenming Jia
- NHC Key Laboratory of OtorhinolaryngologyQilu Hospital of Shandong UniversityJinanShandongChina
- Department of OtorhinolaryngologyQilu Hospital of Shandong UniversityJinanShandongChina
| | - Juan Zhao
- NHC Key Laboratory of OtorhinolaryngologyQilu Hospital of Shandong UniversityJinanShandongChina
- Department of OtorhinolaryngologyQilu Hospital of Shandong UniversityJinanShandongChina
| | - Xiulian Sun
- Brain Research InstituteQilu Hospital of Shandong UniversityJinanShandongChina
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23
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Ottesen EW, Luo D, Singh NN, Singh RN. High Concentration of an ISS-N1-Targeting Antisense Oligonucleotide Causes Massive Perturbation of the Transcriptome. Int J Mol Sci 2021; 22:ijms22168378. [PMID: 34445083 PMCID: PMC8395096 DOI: 10.3390/ijms22168378] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/14/2021] [Accepted: 07/31/2021] [Indexed: 12/17/2022] Open
Abstract
Intronic splicing silencer N1 (ISS-N1) located within Survival Motor Neuron 2 (SMN2) intron 7 is the target of a therapeutic antisense oligonucleotide (ASO), nusinersen (Spinraza), which is currently being used for the treatment of spinal muscular atrophy (SMA), a leading genetic disease associated with infant mortality. The discovery of ISS-N1 as a promising therapeutic target was enabled in part by Anti-N1, a 20-mer ASO that restored SMN2 exon 7 inclusion by annealing to ISS-N1. Here, we analyzed the transcriptome of SMA patient cells treated with 100 nM of Anti-N1 for 30 h. Such concentrations are routinely used to demonstrate the efficacy of an ASO. While 100 nM of Anti-N1 substantially stimulated SMN2 exon 7 inclusion, it also caused massive perturbations in the transcriptome and triggered widespread aberrant splicing, affecting expression of essential genes associated with multiple cellular processes such as transcription, splicing, translation, cell signaling, cell cycle, macromolecular trafficking, cytoskeletal dynamics, and innate immunity. We validated our findings with quantitative and semiquantitative PCR of 39 candidate genes associated with diverse pathways. We also showed a substantial reduction in off-target effects with shorter ISS-N1-targeting ASOs. Our findings are significant for implementing better ASO design and dosing regimens of ASO-based drugs.
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24
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Lindberg MF, Meijer L. Dual-Specificity, Tyrosine Phosphorylation-Regulated Kinases (DYRKs) and cdc2-Like Kinases (CLKs) in Human Disease, an Overview. Int J Mol Sci 2021; 22:6047. [PMID: 34205123 PMCID: PMC8199962 DOI: 10.3390/ijms22116047] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 01/09/2023] Open
Abstract
Dual-specificity tyrosine phosphorylation-regulated kinases (DYRK1A, 1B, 2-4) and cdc2-like kinases (CLK1-4) belong to the CMGC group of serine/threonine kinases. These protein kinases are involved in multiple cellular functions, including intracellular signaling, mRNA splicing, chromatin transcription, DNA damage repair, cell survival, cell cycle control, differentiation, homocysteine/methionine/folate regulation, body temperature regulation, endocytosis, neuronal development, synaptic plasticity, etc. Abnormal expression and/or activity of some of these kinases, DYRK1A in particular, is seen in many human nervous system diseases, such as cognitive deficits associated with Down syndrome, Alzheimer's disease and related diseases, tauopathies, dementia, Pick's disease, Parkinson's disease and other neurodegenerative diseases, Phelan-McDermid syndrome, autism, and CDKL5 deficiency disorder. DYRKs and CLKs are also involved in diabetes, abnormal folate/methionine metabolism, osteoarthritis, several solid cancers (glioblastoma, breast, and pancreatic cancers) and leukemias (acute lymphoblastic leukemia, acute megakaryoblastic leukemia), viral infections (influenza, HIV-1, HCMV, HCV, CMV, HPV), as well as infections caused by unicellular parasites (Leishmania, Trypanosoma, Plasmodium). This variety of pathological implications calls for (1) a better understanding of the regulations and substrates of DYRKs and CLKs and (2) the development of potent and selective inhibitors of these kinases and their evaluation as therapeutic drugs. This article briefly reviews the current knowledge about DYRK/CLK kinases and their implications in human disease.
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Affiliation(s)
| | - Laurent Meijer
- Perha Pharmaceuticals, Perharidy Peninsula, 29680 Roscoff, France;
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25
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Sohail M, Shkreta L, Toutant J, Rabea S, Babeu JP, Huard C, Coulombe-Huntington J, Delannoy A, Placet M, Geha S, Gendron FP, Boudreau F, Tyers M, Grierson DS, Chabot B. A novel class of inhibitors that target SRSF10 and promote p53-mediated cytotoxicity on human colorectal cancer cells. NAR Cancer 2021; 3:zcab019. [PMID: 34316707 PMCID: PMC8210162 DOI: 10.1093/narcan/zcab019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 04/22/2021] [Accepted: 05/04/2021] [Indexed: 01/07/2023] Open
Abstract
The elevated expression of the splicing regulator SRSF10 in metastatic colorectal cancer (CRC) stimulates the production of the pro-tumorigenic BCLAF1-L splice variant. We discovered a group of small molecules with an aminothiazole carboxamide core (GPS167, GPS192 and others) that decrease production of BCLAF1-L. While additional alternative splicing events regulated by SRSF10 are affected by GPS167/192 in HCT116 cells (e.g. in MDM4, WTAP, SLK1 and CLK1), other events are shifted in a SRSF10-independent manner (e.g. in MDM2, NAB2 and TRA2A). GPS167/192 increased the interaction of SRSF10 with the CLK1 and CLK4 kinases, leading us to show that GPS167/192 can inhibit CLK kinases preferentially impacting the activity of SRSF10. Notably, GPS167 impairs the growth of CRC cell lines and organoids, inhibits anchorage-independent colony formation, cell migration, and promotes cytoxicity in a manner that requires SRSF10 and p53. In contrast, GPS167 only minimally affects normal colonocytes and normal colorectal organoids. Thus, GPS167 reprograms the tumorigenic activity of SRSF10 in CRC cells to elicit p53-dependent apoptosis.
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Affiliation(s)
- Muhammad Sohail
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke. Sherbrooke, Quebec, Canada
| | - Lulzim Shkreta
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke. Sherbrooke, Quebec, Canada
| | - Johanne Toutant
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke. Sherbrooke, Quebec, Canada
| | - Safwat Rabea
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Jean-Philippe Babeu
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke. Sherbrooke, Quebec, Canada
| | - Caroline Huard
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | | | - Aurélie Delannoy
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke. Sherbrooke, Quebec, Canada
| | - Morgane Placet
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke. Sherbrooke, Quebec, Canada
| | - Sameh Geha
- Department of Pathology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
- Centre de Recherche Clinique du CHUS, CIUSSS de l’Estrie, Sherbrooke, QC, Canada
| | - Fernand-Pierre Gendron
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke. Sherbrooke, Quebec, Canada
- Centre de Recherche Clinique du CHUS, CIUSSS de l’Estrie, Sherbrooke, QC, Canada
| | - François Boudreau
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke. Sherbrooke, Quebec, Canada
- Centre de Recherche Clinique du CHUS, CIUSSS de l’Estrie, Sherbrooke, QC, Canada
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - David S Grierson
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Benoit Chabot
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke. Sherbrooke, Quebec, Canada
- Centre de Recherche Clinique du CHUS, CIUSSS de l’Estrie, Sherbrooke, QC, Canada
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26
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Pang YT, Pavlova A, Tajkhorshid E, Gumbart JC. Parameterization of a drug molecule with a halogen σ-hole particle using ffTK: Implementation, testing, and comparison. J Chem Phys 2021; 153:164104. [PMID: 33138412 DOI: 10.1063/5.0022802] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Halogen atoms are widely used in drug molecules to improve their binding affinity for the receptor proteins. Many of the examples involve "halogen bonding" between the molecule and the binding site, which is a directional interaction between a halogen atom and a nucleophilic atom. Such an interaction is induced by an electron cloud shift of the halogen atom toward its covalently bonded neighbor to form the σ-bond, leaving a small electrostatic positive region opposite to the bond called the "σ-hole." To mimic the effect of the σ-hole in the CHARMM non-polarizable force field, recently CGenFF added a positively charged massless particle to halogen atoms, positioned at the opposite side of the carbon-halogen bond. This particle is referred to as a lone pair (LP) particle because it uses the lone pair implementation in the CHARMM force field. Here, we have added support for LP particles to ffTK, an automated force field parameterization toolkit widely distributed as a plugin to the molecular visualization software VMD. We demonstrate the updated optimization process using an example halogenated drug molecule, AT130, which is a capsid assembly modulator targeting the hepatitis B virus. Our results indicate that parameterization with the LP particle significantly improves the accuracy of the electrostatic response of the molecule, especially around the halogen atom. Although the inclusion of the LP particle does not produce a prominent effect on the interactions between the molecule and its target protein, the protein-ligand binding performance is greatly improved by optimization of the parameters.
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Affiliation(s)
- Yui Tik Pang
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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27
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Biology of the mRNA Splicing Machinery and Its Dysregulation in Cancer Providing Therapeutic Opportunities. Int J Mol Sci 2021; 22:ijms22105110. [PMID: 34065983 PMCID: PMC8150589 DOI: 10.3390/ijms22105110] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 12/13/2022] Open
Abstract
Dysregulation of messenger RNA (mRNA) processing—in particular mRNA splicing—is a hallmark of cancer. Compared to normal cells, cancer cells frequently present aberrant mRNA splicing, which promotes cancer progression and treatment resistance. This hallmark provides opportunities for developing new targeted cancer treatments. Splicing of precursor mRNA into mature mRNA is executed by a dynamic complex of proteins and small RNAs called the spliceosome. Spliceosomes are part of the supraspliceosome, a macromolecular structure where all co-transcriptional mRNA processing activities in the cell nucleus are coordinated. Here we review the biology of the mRNA splicing machinery in the context of other mRNA processing activities in the supraspliceosome and present current knowledge of its dysregulation in lung cancer. In addition, we review investigations to discover therapeutic targets in the spliceosome and give an overview of inhibitors and modulators of the mRNA splicing process identified so far. Together, this provides insight into the value of targeting the spliceosome as a possible new treatment for lung cancer.
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28
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Ghosh K, Das S. Recent advances in ring-opening of donor acceptor cyclopropanes using C-nucleophiles. Org Biomol Chem 2021; 19:965-982. [PMID: 33471020 DOI: 10.1039/d0ob02437f] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Ring-opening transformations of donor-acceptor cyclopropanes (DAC) with carbon-centered nucleophiles is a simple, straight-forward approach to 1,3-bifunctional compounds that has witnessed remarkable progress over the past several years. To date, different reactivity patterns of DACs have been successfully exploited in racemic/stereoselective syntheses of various acyclic compounds or carbocycles with an impressive structural diversity. The thriving strategies have been successfully utilized in multistep synthesis of complex target molecules. Herein, the recent advances (2015-present) in the ring-opening of DAC involving electron rich arenes and indoles, active methylene compounds, various dipolarophiles, organoborates/boronates, vinyl ethers etc. following Friedel-Crafts alkylation, annulation/formal cycloaddition reaction, organocatalytic reaction, Nazarov cyclisation etc. are presented.
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Affiliation(s)
- Koena Ghosh
- Department of Chemistry, Presidency University, 86/1 College Street, Kolkata 700 073, India.
| | - Subhomoy Das
- Department of Chemistry, Bar Ilan University, Ramat Gan 5290002, Israel
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29
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ElHady AK, El-Gamil DS, Chen PJ, Hwang TL, Abadi AH, Abdel-Halim M, Engel M. 5-Methoxybenzothiophene-2-Carboxamides as Inhibitors of Clk1/4: Optimization of Selectivity and Cellular Potency. Molecules 2021; 26:molecules26041001. [PMID: 33668683 PMCID: PMC7918793 DOI: 10.3390/molecules26041001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 02/04/2023] Open
Abstract
Clks have been shown by recent studies to be promising targets for cancer therapy, as they are considered key regulators in the process of pre-mRNA splicing, which in turn affects every aspect of tumor biology. In particular, Clk1 and -4 are overexpressed in several human tumors. Most of the potent Clk1 inhibitors reported in the literature are non-selective, mainly showing off-target activity towards Clk2, Dyrk1A and Dyrk1B. Herein, we present new 5-methoxybenzothiophene-2-carboxamide derivatives with unprecedented selectivity. In particular, the introduction of a 3,5-difluoro benzyl extension to the methylated amide led to the discovery of compound 10b (cell-free IC50 = 12.7 nM), which was four times more selective for Clk1 over Clk2 than the previously published flagship compound 1b. Moreover, 10b showed an improved growth inhibitory activity with T24 cells (GI50 = 0.43 µM). Furthermore, a new binding model in the ATP pocket of Clk1 was developed based on the structure-activity relationships derived from new rigidified analogues.
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Affiliation(s)
- Ahmed K. ElHady
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt; (A.K.E.); (D.S.E.-G.); (A.H.A.); (M.A.-H.)
- School of Life and Medical Sciences, University of Hertfordshire Hosted by Global Academic Foundation, New Administrative Capital, Cairo 11865, Egypt
| | - Dalia S. El-Gamil
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt; (A.K.E.); (D.S.E.-G.); (A.H.A.); (M.A.-H.)
| | - Po-Jen Chen
- Graduate Institute of Natural Products, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (P.-J.C.); (T.-L.H.)
- Department of Cosmetic Science, Providence University, Taichung 433, Taiwan
| | - Tsong-Long Hwang
- Graduate Institute of Natural Products, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (P.-J.C.); (T.-L.H.)
- Research Center for Chinese Herbal Medicine, Graduate Institute of Health Industry Technology, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan 333, Taiwan
- Department of Anesthesiology, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
- Department of Chemical Engineering, Ming Chi University of Technology, New Taipei City 243, Taiwan
| | - Ashraf H. Abadi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt; (A.K.E.); (D.S.E.-G.); (A.H.A.); (M.A.-H.)
| | - Mohammad Abdel-Halim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt; (A.K.E.); (D.S.E.-G.); (A.H.A.); (M.A.-H.)
| | - Matthias Engel
- Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2.3, D-66123 Saarbrücken, Germany
- Correspondence: ; Tel.: +49-681-302-70312; Fax: +49-681-302-70308
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30
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Brahmaiah D, Kanaka Durga Bhavani A, Aparna P, Sampath Kumar N, Solhi H, Le Guevel R, Baratte B, Ruchaud S, Bach S, Singh Jadav S, Raji Reddy C, Roisnel T, Mosset P, Levoin N, Grée R. Discovery of DB18, a potent inhibitor of CLK kinases with a high selectivity against DYRK1A kinase. Bioorg Med Chem 2021; 31:115962. [PMID: 33422908 DOI: 10.1016/j.bmc.2020.115962] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/11/2020] [Accepted: 12/16/2020] [Indexed: 10/22/2022]
Abstract
We describe in this paper the synthesis of a novel series of anilino-2-quinazoline derivatives. These compounds have been screened against a panel of eight mammalian kinases and in parallel they were tested for cytotoxicity on a representative panel of seven cancer cell lines. One of them (DB18) has been found to be a very potent inhibitor of human "CDC2-like kinases" CLK1, CLK2 and CLK4, with IC50 values in the 10-30 nM range. Interestingly, this molecule is inactive at 100 μM on the closely related "dual-specificity tyrosine-regulated kinase 1A" (DYRK1A). Extensive molecular simulation studies have been performed on the relevant kinases to explain the strong affinity of this molecule on CLKs, as well as its selectivity against DYRK1A.
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Affiliation(s)
- Dabbugoddu Brahmaiah
- Chemveda Life Sciences India Pvt. Ltd., #B-11/1, IDA Uppal, Hyderabad 500039, Telangana, India; Jawaharlal Nehru Technological University Hyderabad, Kukatpally, Hyderabad 500 085, Telangana, India
| | | | - Pasula Aparna
- Jawaharlal Nehru Technological University Hyderabad, Kukatpally, Hyderabad 500 085, Telangana, India
| | | | - Hélène Solhi
- Univ Rennes, Plateform ImPACcell, BIOSIT, F-35000 Rennes, France
| | - Rémy Le Guevel
- Univ Rennes, Plateform ImPACcell, BIOSIT, F-35000 Rennes, France
| | - Blandine Baratte
- Sorbonne Université, CNRS, FR 2424, Plateforme de criblage KISSf (Kinase Inhibitor Specialized Screening Facility), Station Biologique de Roscoff, CS 90074, 29688 Roscoff Cedex, France; Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine Models Laboratory (LBI2M), Station Biologique de Roscoff, CS 90074, 29688 Roscoff Cedex, France
| | - Sandrine Ruchaud
- Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine Models Laboratory (LBI2M), Station Biologique de Roscoff, CS 90074, 29688 Roscoff Cedex, France
| | - Stéphane Bach
- Sorbonne Université, CNRS, FR 2424, Plateforme de criblage KISSf (Kinase Inhibitor Specialized Screening Facility), Station Biologique de Roscoff, CS 90074, 29688 Roscoff Cedex, France; Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine Models Laboratory (LBI2M), Station Biologique de Roscoff, CS 90074, 29688 Roscoff Cedex, France
| | - Surender Singh Jadav
- CSIR-Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad 500007, TS, India
| | - Chada Raji Reddy
- CSIR-Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad 500007, TS, India
| | - Thierry Roisnel
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes), UMR 6226, F-35000 Rennes, France
| | - Paul Mosset
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes), UMR 6226, F-35000 Rennes, France
| | - Nicolas Levoin
- Bioprojet-Biotech, 4 rue du Chesnay Beauregard, BP 96205, 35762 Saint Grégoire, France
| | - René Grée
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes), UMR 6226, F-35000 Rennes, France.
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31
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Sireesha R, Sreenivasulu R, Chandrasekhar C, Jadav SS, Pavani Y, Rao MVB, Subbarao M. Design, synthesis, anti-cancer evaluation and binding mode studies of benzimidazole/benzoxazole linked β-carboline derivatives. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129351] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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32
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Wurzlbauer A, Rüben K, Gürdal E, Chaikuad A, Knapp S, Sippl W, Becker W, Bracher F. How to Separate Kinase Inhibition from Undesired Monoamine Oxidase A Inhibition-The Development of the DYRK1A Inhibitor AnnH75 from the Alkaloid Harmine. Molecules 2020; 25:E5962. [PMID: 33339338 PMCID: PMC7765920 DOI: 10.3390/molecules25245962] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 01/15/2023] Open
Abstract
The β-carboline alkaloid harmine is a potent DYRK1A inhibitor, but suffers from undesired potent inhibition of MAO-A, which strongly limits its application. We synthesized more than 60 analogues of harmine, either by direct modification of the alkaloid or by de novo synthesis of β-carboline and related scaffolds aimed at learning about structure-activity relationships for inhibition of both DYRK1A and MAO-A, with the ultimate goal of separating desired DYRK1A inhibition from undesired MAO-A inhibition. Based on evidence from published crystal structures of harmine bound to each of these enzymes, we performed systematic structure modifications of harmine yielding DYRK1A-selective inhibitors characterized by small polar substituents at N-9 (which preserve DYRK1A inhibition and eliminate MAO-A inhibition) and beneficial residues at C-1 (methyl or chlorine). The top compound AnnH75 remains a potent DYRK1A inhibitor, and it is devoid of MAO-A inhibition. Its binding mode to DYRK1A was elucidated by crystal structure analysis, and docking experiments provided additional insights for this attractive series of DYRK1A and MAO-A inhibitors.
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Affiliation(s)
- Anne Wurzlbauer
- Department of Pharmacy—Center for Drug Research, Ludwig-Maximilians University, 81377 Munich, Germany;
| | - Katharina Rüben
- Institute of Pharmacology and Toxicology, RWTH Aachen University, 52074 Aachen, Germany; (K.R.); (W.B.)
| | - Ece Gürdal
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany; (E.G.); (W.S.)
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry and Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-University Frankfurt, 60438 Frankfurt, Germany; (A.C.); (S.K.)
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry and Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-University Frankfurt, 60438 Frankfurt, Germany; (A.C.); (S.K.)
| | - Wolfgang Sippl
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany; (E.G.); (W.S.)
| | - Walter Becker
- Institute of Pharmacology and Toxicology, RWTH Aachen University, 52074 Aachen, Germany; (K.R.); (W.B.)
| | - Franz Bracher
- Department of Pharmacy—Center for Drug Research, Ludwig-Maximilians University, 81377 Munich, Germany;
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33
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Shibata S, Ajiro M, Hagiwara M. Mechanism-Based Personalized Medicine for Cystic Fibrosis by Suppressing Pseudo Exon Inclusion. Cell Chem Biol 2020; 27:1472-1482.e6. [DOI: 10.1016/j.chembiol.2020.08.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/29/2020] [Accepted: 08/20/2020] [Indexed: 12/14/2022]
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34
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Martín Moyano P, Němec V, Paruch K. Cdc-Like Kinases (CLKs): Biology, Chemical Probes, and Therapeutic Potential. Int J Mol Sci 2020; 21:E7549. [PMID: 33066143 PMCID: PMC7593917 DOI: 10.3390/ijms21207549] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/06/2020] [Accepted: 10/09/2020] [Indexed: 12/11/2022] Open
Abstract
Protein kinases represent a very pharmacologically attractive class of targets; however, some members of the family still remain rather unexplored. The biology and therapeutic potential of cdc-like kinases (CLKs) have been explored mainly over the last decade and the first CLK inhibitor, compound SM08502, entered clinical trials only recently. This review summarizes the biological roles and therapeutic potential of CLKs and their heretofore published small-molecule inhibitors, with a focus on the compounds' potential to be utilized as quality chemical biology probes.
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Affiliation(s)
- Paula Martín Moyano
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (P.M.M.); (V.N.)
| | - Václav Němec
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (P.M.M.); (V.N.)
- International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne’s University Hospital in Brno, 602 00 Brno, Czech Republic
| | - Kamil Paruch
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (P.M.M.); (V.N.)
- International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne’s University Hospital in Brno, 602 00 Brno, Czech Republic
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35
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Fergany AAM, Tatarskiy VV. RNA Splicing: Basic Aspects Underlie Antitumor Targeting. Recent Pat Anticancer Drug Discov 2020; 15:293-305. [PMID: 32900350 DOI: 10.2174/1574892815666200908122402] [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: 03/31/2020] [Revised: 07/15/2020] [Accepted: 07/29/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND RNA splicing, a fundamental step in gene expression, is aimed at intron removal and ordering of exons to form the protein's reading frame. OBJECTIVE This review is focused on the role of RNA splicing in cancer biology; the splicing abnormalities that lead to tumor progression emerge as targets for therapeutic intervention. METHODS We discuss the role of aberrant mRNA splicing in carcinogenesis and drug response. RESULTS AND CONCLUSION Pharmacological modulation of RNA splicing sets the stage for treatment approaches in situations where mRNA splicing is a clinically meaningful mechanism of the disease.
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Affiliation(s)
- Alzahraa A M Fergany
- Department of Occupational and Environmental Health, Graduate School of Pharmaceutical Science, Tokyo University of Science, Chiba, Japan
| | - Victor V Tatarskiy
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russian Federation
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36
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Babu N, Pinto SM, Biswas M, Subbannayya T, Rajappa M, Mohan SV, Advani J, Rajagopalan P, Sathe G, Syed N, Radhakrishna VD, Muthusamy O, Navani S, Kumar RV, Gopisetty G, Rajkumar T, Radhakrishnan P, Thiyagarajan S, Pandey A, Gowda H, Majumder P, Chatterjee A. Phosphoproteomic analysis identifies CLK1 as a novel therapeutic target in gastric cancer. Gastric Cancer 2020; 23:796-810. [PMID: 32333232 DOI: 10.1007/s10120-020-01062-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 03/12/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Phosphorylation is an important regulatory mechanism of protein activity in cells. Studies in various cancers have reported perturbations in kinases resulting in aberrant phosphorylation of oncoproteins and tumor suppressor proteins. METHODS In this study, we carried out quantitative phosphoproteomic analysis of gastric cancer tissues and corresponding xenograft samples. Using these data, we employed bioinformatics analysis to identify aberrant signaling pathways. We further performed molecular inhibition and silencing of the upstream regulatory kinase in gastric cancer cell lines and validated its effect on cellular phenotype. Through an ex vivo technology utilizing patient tumor and blood sample, we sought to understand the therapeutic potential of the kinase by recreating the tumor microenvironment. RESULTS Using mass spectrometry-based high-throughput analysis, we identified 1,344 phosphosites and 848 phosphoproteins, including differential phosphorylation of 177 proteins (fold change cut-off ≥ 1.5). Our data showed that a subset of differentially phosphorylated proteins belonged to splicing machinery. Pathway analysis highlighted Cdc2-like kinase (CLK1) as upstream kinase. Inhibition of CLK1 using TG003 and CLK1 siRNA resulted in a decreased cell viability, proliferation, invasion and migration as well as modulation in the phosphorylation of SRSF2. Ex vivo experiments which utilizes patient's own tumor and blood to recreate the tumor microenvironment validated the use of CLK1 as a potential target for gastric cancer treatment. CONCLUSIONS Our data indicates that CLK1 plays a crucial role in the regulation of splicing process in gastric cancer and that CLK1 can act as a novel therapeutic target in gastric cancer.
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Affiliation(s)
- Niraj Babu
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Manipal Academy of Higher Education, Manipal, 576104, India
| | - Sneha M Pinto
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed To Be University), Mangalore, 575018, India
| | | | - Tejaswini Subbannayya
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Mitra Biotech, Bangalore, 560100, India
| | | | - Sonali V Mohan
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Manipal Academy of Higher Education, Manipal, 576104, India
| | - Jayshree Advani
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India
| | - Pavithra Rajagopalan
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India
| | - Nazia Syed
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India
| | | | | | | | - Rekha V Kumar
- Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore, 560029, India
| | - Gopal Gopisetty
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600020, India
| | - Thangarajan Rajkumar
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600020, India
| | | | | | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Manipal Academy of Higher Education, Manipal, 576104, India.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore, 560029, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Manipal Academy of Higher Education, Manipal, 576104, India.,Cancer Precision Medicine, QIMR Berghofer, Royal Brisbane Hospital, Brisbane, QLD, 4029, Australia
| | | | - Aditi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India. .,Manipal Academy of Higher Education, Manipal, 576104, India. .,Mitra Biotech, Bangalore, 560100, India.
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37
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Dekel N, Eisenberg-Domovich Y, Karlas A, Meyer TF, Bracher F, Lebendiker M, Danieli T, Livnah O. Expression, purification and crystallization of CLK1 kinase - A potential target for antiviral therapy. Protein Expr Purif 2020; 176:105742. [PMID: 32866611 DOI: 10.1016/j.pep.2020.105742] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/03/2020] [Accepted: 08/26/2020] [Indexed: 12/15/2022]
Abstract
Cdc-like kinase 1 (CLK1) is a dual-specificity kinase capable of autophosphorylation on tyrosine residues and Ser/Thr phosphorylation of its substrates. CLK1 belongs to the CLK kinase family that regulates alternative splicing through phosphorylation of serine-arginine rich (SR) proteins. Recent studies have demonstrated that CLK1 has an important role in the replication of influenza A and chikungunya viruses. Furthermore, CLK1 was found to be relevant for the replication of HIV-1 and the West Nile virus, making CLK1 an interesting cellular candidate for the development of a host-directed antiviral therapy that might be efficient for treatment of newly emerging viruses. We describe here our attempts and detailed procedures to obtain the recombinant kinase domain of CLK1 in suitable amounts for crystallization in complex with specific inhibitors. The key solution for the reproducibility of crystals resides in devising and refining expression and purification protocols leading to homogeneous protein. Co-expression of CLK1 with λ-phosphatase and careful purification has yielded crystals of CLK1 complexed with the KH-CB19 inhibitor that diffracted to 1.65 Å. These results paved the path to the screening of more structures of CLK1 complexed compounds, leading to further optimization of their inhibitory activity. Moreover, since kinases are desired targets in numerous pathologies, the approach we report here, the co-expression of kinases with λ-phosphatase, previously used in other kinases, can be adopted as a general protocol in numerous kinase targets for obtaining reproducible and homogenic non-phosphorylated (inactive) forms suitable for biochemical and structural studies thus facilitating the development of novel inhibitors.
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Affiliation(s)
- Noa Dekel
- The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yael Eisenberg-Domovich
- The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | | | - Thomas F Meyer
- Max Planck Institute for Infection Biology, Department of Molecular Biology, Charitéplatz 1, 10117, Berlin, Germany
| | - Franz Bracher
- Ludwig-Maximilians University, Department of Pharmacy-Center for Drug Research, Butenandstrasse 5-13, 81377, Munich, Germany
| | - Mario Lebendiker
- The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Tsafi Danieli
- The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Oded Livnah
- The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel; Department of Biological Chemistry, Alexander Silverman Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Israel.
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38
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Schröder M, Bullock AN, Fedorov O, Bracher F, Chaikuad A, Knapp S. DFG-1 Residue Controls Inhibitor Binding Mode and Affinity, Providing a Basis for Rational Design of Kinase Inhibitor Selectivity. J Med Chem 2020; 63:10224-10234. [PMID: 32787076 DOI: 10.1021/acs.jmedchem.0c00898] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Selectivity remains a challenge for ATP-mimetic kinase inhibitors, an issue that may be overcome by targeting unique residues or binding pockets. However, to date only few strategies have been developed. Here we identify that bulky residues located N-terminal to the DFG motif (DFG-1) represent an opportunity for designing highly selective inhibitors with unexpected binding modes. We demonstrate that several diverse inhibitors exerted selective, noncanonical binding modes that exclusively target large hydrophobic DFG-1 residues present in many kinases including PIM, CK1, DAPK, and CLK. By use of the CLK family as a model, structural and biochemical data revealed that the DFG-1 valine controlled a noncanonical binding mode in CLK1, providing a rationale for selectivity over the closely related CLK3 which harbors a smaller DFG-1 alanine. Our data suggest that targeting the restricted back pocket in the small fraction of kinases that harbor bulky DFG-1 residues offers a versatile selectivity filter for inhibitor design.
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Affiliation(s)
- Martin Schröder
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max von Lauestraße 9, 60438 Frankfurt, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-University Frankfurt, Max von Lauestraße 15, 60438 Frankfurt, Germany
| | - Alex N Bullock
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, U.K
| | - Oleg Fedorov
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, U.K
| | - Franz Bracher
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians University Munich, 81377 Munich, Germany
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max von Lauestraße 9, 60438 Frankfurt, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-University Frankfurt, Max von Lauestraße 15, 60438 Frankfurt, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max von Lauestraße 9, 60438 Frankfurt, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-University Frankfurt, Max von Lauestraße 15, 60438 Frankfurt, Germany.,German Translational Cancer Network (DKTK), Frankfurt/Mainz Site, 60438 Frankfurt, Germany
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39
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Li X, Yu H, Liang L, Bi Z, Wang Y, Gao S, Wang M, Li H, Miao Y, Deng R, Ma L, Luan J, Li S, Liu M, Lin J, Zhou H, Yang C. Myricetin ameliorates bleomycin-induced pulmonary fibrosis in mice by inhibiting TGF-β signaling via targeting HSP90β. Biochem Pharmacol 2020; 178:114097. [PMID: 32535102 DOI: 10.1016/j.bcp.2020.114097] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 06/05/2020] [Accepted: 06/09/2020] [Indexed: 01/06/2023]
Abstract
Idiopathic pulmonary fibrosis is a progressive-fibrosing lung disease with high mortality and limited therapy, which characterized by myofibroblasts proliferation and extracellular matrix deposition. Myricetin, a natural flavonoid, has been shown to possess a variety of biological characteristics including anti-inflammatory and anti-tumor. In this study we explored the potential effect and mechanisms of myricetin on pulmonary fibrosis in vivo and vitro. The in vivo studies showed that myricetin effectively alleviated bleomycin (BLM)-induced pulmonary fibrosis. KEGG analysis of RNA-seq data indicated that myricetin could regulate the transforming growth factor (TGF)-β signaling pathway. In vitro studies indicated that myricetin could dose-dependently suppress TGF-β1/Smad signaling and attenuate TGF-β1-induced fibroblast activation and epithelial-mesenchymal transition (EMT). Molecular docking indicated that heat shock protein (HSP) 90β may be a potential target of myricetin, and MST assay demonstrated that the dissociation constant (Kd) of myricetin and HSP90β was 331.59 nM. We demonstrated that myricetin interfered with the binding of HSP90β and TGF-β receptor II and impeded fibroblast activation and EMT. In conclusion, myricetin impedes TGF-β1-induced lung fibroblast activation and EMT via targeting HSP90β and attenuates BLM-induced pulmonary fibrosis in mice.
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Affiliation(s)
- Xiaohe Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People's Republic of China; Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, 300457, People's Republic of China
| | - Haiyan Yu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People's Republic of China; Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, 300457, People's Republic of China
| | - Lu Liang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People's Republic of China
| | - Zhun Bi
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People's Republic of China
| | - Yanhua Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People's Republic of China; Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, 300457, People's Republic of China
| | - Shaoyan Gao
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People's Republic of China; Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, 300457, People's Republic of China
| | - Mukuo Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People's Republic of China
| | - Hailong Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People's Republic of China
| | - Yang Miao
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People's Republic of China
| | - Ruxia Deng
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People's Republic of China; Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, 300457, People's Republic of China
| | - Ling Ma
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People's Republic of China; Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, 300457, People's Republic of China
| | - Jiaoyan Luan
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People's Republic of China; Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, 300457, People's Republic of China
| | - Shuangling Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People's Republic of China; Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, 300457, People's Republic of China
| | - Menghan Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People's Republic of China; Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, 300457, People's Republic of China
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People's Republic of China.
| | - Honggang Zhou
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People's Republic of China; Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, 300457, People's Republic of China.
| | - Cheng Yang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People's Republic of China; Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint Academy of Biomedicine, Tianjin, 300457, People's Republic of China.
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40
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Huang HH, Ferguson ID, Thornton AM, Bastola P, Lam C, Lin YHT, Choudhry P, Mariano MC, Marcoulis MD, Teo CF, Malato J, Phojanakong PJ, Martin TG, Wolf JL, Wong SW, Shah N, Hann B, Brooks AN, Wiita AP. Proteasome inhibitor-induced modulation reveals the spliceosome as a specific therapeutic vulnerability in multiple myeloma. Nat Commun 2020; 11:1931. [PMID: 32321912 PMCID: PMC7176739 DOI: 10.1038/s41467-020-15521-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 03/13/2020] [Indexed: 02/06/2023] Open
Abstract
Enhancing the efficacy of proteasome inhibitors (PI) is a central goal in myeloma therapy. We proposed that signaling-level responses after PI may reveal new mechanisms of action that can be therapeutically exploited. Unbiased phosphoproteomics after treatment with the PI carfilzomib surprisingly demonstrates the most prominent phosphorylation changes on splicing related proteins. Spliceosome modulation is invisible to RNA or protein abundance alone. Transcriptome analysis after PI demonstrates broad-scale intron retention, suggestive of spliceosome interference, as well as specific alternative splicing of protein homeostasis machinery components. These findings lead us to evaluate direct spliceosome inhibition in myeloma, which synergizes with carfilzomib and shows potent anti-tumor activity. Functional genomics and exome sequencing further support the spliceosome as a specific vulnerability in myeloma. Our results propose splicing interference as an unrecognized modality of PI mechanism, reveal additional modes of spliceosome modulation, and suggest spliceosome targeting as a promising therapeutic strategy in myeloma.
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Affiliation(s)
- Hector H Huang
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Ian D Ferguson
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Alexis M Thornton
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Prabhakar Bastola
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Christine Lam
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Yu-Hsiu T Lin
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Priya Choudhry
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Margarette C Mariano
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Makeba D Marcoulis
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Chin Fen Teo
- Department of Physiology, University of California, San Francisco, CA, USA
| | - Julia Malato
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Paul J Phojanakong
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Thomas G Martin
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco, CA, USA
| | - Jeffrey L Wolf
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco, CA, USA
| | - Sandy W Wong
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco, CA, USA
| | - Nina Shah
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco, CA, USA
| | - Byron Hann
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Angela N Brooks
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Arun P Wiita
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA. .,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.
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41
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Haltenhof T, Kotte A, De Bortoli F, Schiefer S, Meinke S, Emmerichs AK, Petermann KK, Timmermann B, Imhof P, Franz A, Loll B, Wahl MC, Preußner M, Heyd F. A Conserved Kinase-Based Body-Temperature Sensor Globally Controls Alternative Splicing and Gene Expression. Mol Cell 2020; 78:57-69.e4. [PMID: 32059760 DOI: 10.1016/j.molcel.2020.01.028] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/12/2019] [Accepted: 01/27/2020] [Indexed: 12/24/2022]
Abstract
Homeothermic organisms maintain their core body temperature in a narrow, tightly controlled range. Whether and how subtle circadian oscillations or disease-associated changes in core body temperature are sensed and integrated in gene expression programs remain elusive. Furthermore, a thermo-sensor capable of sensing the small temperature differentials leading to temperature-dependent sex determination (TSD) in poikilothermic reptiles has not been identified. Here, we show that the activity of CDC-like kinases (CLKs) is highly responsive to physiological temperature changes, which is conferred by structural rearrangements within the kinase activation segment. Lower body temperature activates CLKs resulting in strongly increased phosphorylation of SR proteins in vitro and in vivo. This globally controls temperature-dependent alternative splicing and gene expression, with wide implications in circadian, tissue-specific, and disease-associated settings. This temperature sensor is conserved across evolution and adapted to growth temperatures of diverse poikilotherms. The dynamic temperature range of reptilian CLK homologs suggests a role in TSD.
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Affiliation(s)
- Tom Haltenhof
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Takustrasse 6, 14195 Berlin, Germany
| | - Ana Kotte
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Takustrasse 6, 14195 Berlin, Germany
| | - Francesca De Bortoli
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Takustrasse 6, 14195 Berlin, Germany
| | - Samira Schiefer
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Takustrasse 6, 14195 Berlin, Germany
| | - Stefan Meinke
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Takustrasse 6, 14195 Berlin, Germany
| | - Ann-Kathrin Emmerichs
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Takustrasse 6, 14195 Berlin, Germany
| | - Kristina Katrin Petermann
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Takustrasse 6, 14195 Berlin, Germany
| | - Bernd Timmermann
- Sequencing Core Facility, Max-Planck-Institute for Molecular Genetics, Ihnestraße 63-73, Berlin 14195, Germany
| | - Petra Imhof
- Freie Universität Berlin, Institute of Theoretical Physics, Arnimallee 14, 14195 Berlin, Germany
| | - Andreas Franz
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Takustrasse 6, 14195 Berlin, Germany; Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Takustrasse 6, 14195 Berlin, Germany
| | - Bernhard Loll
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Takustrasse 6, 14195 Berlin, Germany
| | - Markus C Wahl
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Takustrasse 6, 14195 Berlin, Germany; Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, 12489 Berlin, Germany
| | - Marco Preußner
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Takustrasse 6, 14195 Berlin, Germany
| | - Florian Heyd
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Takustrasse 6, 14195 Berlin, Germany.
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42
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Ninomiya K, Adachi S, Natsume T, Iwakiri J, Terai G, Asai K, Hirose T. LncRNA-dependent nuclear stress bodies promote intron retention through SR protein phosphorylation. EMBO J 2020; 39:e102729. [PMID: 31782550 PMCID: PMC6996502 DOI: 10.15252/embj.2019102729] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 10/17/2019] [Accepted: 10/29/2019] [Indexed: 12/19/2022] Open
Abstract
A number of long noncoding RNAs (lncRNAs) are induced in response to specific stresses to construct membrane-less nuclear bodies; however, their function remains poorly understood. Here, we report the role of nuclear stress bodies (nSBs) formed on highly repetitive satellite III (HSATIII) lncRNAs derived from primate-specific satellite III repeats upon thermal stress exposure. A transcriptomic analysis revealed that depletion of HSATIII lncRNAs, resulting in elimination of nSBs, promoted splicing of 533 retained introns during thermal stress recovery. A HSATIII-Comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS) analysis identified multiple splicing factors in nSBs, including serine and arginine-rich pre-mRNA splicing factors (SRSFs), the phosphorylation states of which affect splicing patterns. SRSFs are rapidly de-phosphorylated upon thermal stress exposure. During stress recovery, CDC like kinase 1 (CLK1) was recruited to nSBs and accelerated the re-phosphorylation of SRSF9, thereby promoting target intron retention. Our findings suggest that HSATIII-dependent nSBs serve as a conditional platform for phosphorylation of SRSFs by CLK1 to promote the rapid adaptation of gene expression through intron retention following thermal stress exposure.
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Grants
- JP26113002 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP16H06279 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP17H03630 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP17K19335 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP19K06478 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- Tokyo Biochemical Research Foundation (TBRF)
- Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- Tokyo Biochemical Research Foundation (TBRF)
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Affiliation(s)
| | - Shungo Adachi
- Molecular Profiling Research CenterNational Institute for Advanced Industrial Science and Technology (AIST)TokyoJapan
| | - Tohru Natsume
- Molecular Profiling Research CenterNational Institute for Advanced Industrial Science and Technology (AIST)TokyoJapan
| | - Junichi Iwakiri
- Graduate School of Frontier SciencesUniversity of TokyoKashiwaJapan
| | - Goro Terai
- Graduate School of Frontier SciencesUniversity of TokyoKashiwaJapan
| | - Kiyoshi Asai
- Graduate School of Frontier SciencesUniversity of TokyoKashiwaJapan
| | - Tetsuro Hirose
- Institute for Genetic MedicineHokkaido UniversitySapporoJapan
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43
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Bracher F. Dimethylformamide Acetals and Bredereck’s Reagent as Building Blocks in Natural Products Total Synthesis. MINI-REV ORG CHEM 2020. [DOI: 10.2174/1570193x16666181204122143] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Dimethylformamide acetals and Bredereck’s reagent (tert-butoxy-bis(dimethylamino)
methane) are versatile C1 building blocks due to their ability to undergo condensation reactions with
CH-acidic methyl and methylene moieties. Subsequent modulation of the resulting condensation
products enables the preparation of open-chain products like aldehydes, ketones, enones, enol ethers,
methyl groups, and, most important in alkaloid total synthesis, the annulation of heterocyclic rings
like pyridines, pyridine-N-oxides, bromopyridines, aminopyridines, aminopyrimidines, pyrroles and
chromenones. In certain cases, these reagents can act as alkylating agents. The applications of these
building blocks in natural products total synthesis are reviewed here.
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Affiliation(s)
- Franz Bracher
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians University, Munich, Germany
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44
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Li M, Sun Y, Xie Y, Yu Y, Huang F, Huang H. Copper-catalyzed carbene insertion and ester migration for the synthesis of polysubstituted pyrroles. Chem Commun (Camb) 2020; 56:11050-11053. [DOI: 10.1039/d0cc04157b] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A mild synthetic protocol to access 2-ester pyrroles through Cu(OTf)2-catalysed carbene insertion/ester migration/cyclization of enaminones and α-diazo compounds is reported.
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Affiliation(s)
- Mingrui Li
- School of Pharmaceutical Sciences
- Nanjing Tech University
- Nanjing 211816
- P. R. China
| | - Yiming Sun
- School of Pharmaceutical Sciences
- Nanjing Tech University
- Nanjing 211816
- P. R. China
| | - Yuxing Xie
- School of Food Science and Pharmaceutical Engineering
- Nanjing Normal University
- Nanjing 210023
- P. R. China
| | - Yang Yu
- School of Environmental Science and Engineering
- Nanjing Tech University
- Nanjing 211816
- P. R. China
| | - Fei Huang
- School of Pharmaceutical Sciences
- Nanjing Tech University
- Nanjing 211816
- P. R. China
- School of Food Science and Pharmaceutical Engineering
| | - He Huang
- School of Pharmaceutical Sciences
- Nanjing Tech University
- Nanjing 211816
- P. R. China
- School of Food Science and Pharmaceutical Engineering
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45
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Li Y, Zhu Y, Xiang S, Fan W, Jin J, Huang D. Temperature controlled condensation of nitriles: efficient and convenient synthesis of β-enaminonitriles, 4-aminopyrimidines and 4-amidinopyrimidines in one system. RSC Adv 2020; 10:6576-6583. [PMID: 35496002 PMCID: PMC9049712 DOI: 10.1039/c9ra10866a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 01/21/2020] [Indexed: 11/21/2022] Open
Abstract
A wide variety of β-enaminonitriles, 4-aminopyrimidines and 4-amidinopyrimidines were simply synthesized from organonitriles by controlling the reaction temperature.
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Affiliation(s)
- Yinghua Li
- State Key Laboratory of Structural Chemistry
- Fujian Institute of Research on the Structure of Matter
- Chinese Academy of Sciences Fuzhou
- Fujian 350002
- China
| | - Yingzu Zhu
- State Key Laboratory of Structural Chemistry
- Fujian Institute of Research on the Structure of Matter
- Chinese Academy of Sciences Fuzhou
- Fujian 350002
- China
| | - Shiqun Xiang
- State Key Laboratory of Structural Chemistry
- Fujian Institute of Research on the Structure of Matter
- Chinese Academy of Sciences Fuzhou
- Fujian 350002
- China
| | - Weibin Fan
- State Key Laboratory of Structural Chemistry
- Fujian Institute of Research on the Structure of Matter
- Chinese Academy of Sciences Fuzhou
- Fujian 350002
- China
| | - Jiang Jin
- State Key Laboratory of Structural Chemistry
- Fujian Institute of Research on the Structure of Matter
- Chinese Academy of Sciences Fuzhou
- Fujian 350002
- China
| | - Deguang Huang
- State Key Laboratory of Structural Chemistry
- Fujian Institute of Research on the Structure of Matter
- Chinese Academy of Sciences Fuzhou
- Fujian 350002
- China
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46
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Lechner C, Flaßhoff M, Falke H, Preu L, Loaëc N, Meijer L, Knapp S, Chaikuad A, Kunick C. [ b]-Annulated Halogen-Substituted Indoles as Potential DYRK1A Inhibitors. Molecules 2019; 24:E4090. [PMID: 31766108 PMCID: PMC6891749 DOI: 10.3390/molecules24224090] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/05/2019] [Accepted: 11/07/2019] [Indexed: 12/21/2022] Open
Abstract
Since hyperactivity of the protein kinase DYRK1A is linked to several neurodegenerative disorders, DYRK1A inhibitors have been suggested as potential therapeutics for Down syndrome and Alzheimer's disease. Most published inhibitors to date suffer from low selectivity against related kinases or from unfavorable physicochemical properties. In order to identify DYRK1A inhibitors with improved properties, a series of new chemicals based on [b]-annulated halogenated indoles were designed, synthesized, and evaluated for biological activity. Analysis of crystal structures revealed a typical type-I binding mode of the new inhibitor 4-chlorocyclohepta[b]indol-10(5H)-one in DYRK1A, exploiting mainly shape complementarity for tight binding. Conversion of the DYRK1A inhibitor 8-chloro-1,2,3,9-tetrahydro-4H-carbazol-4-one into a corresponding Mannich base hydrochloride improved the aqueous solubility but abrogated kinase inhibitory activity.
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Affiliation(s)
- Christian Lechner
- Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Beethovenstraße 55, 38106 Braunschweig, Germany
- Zentrum für Pharmaverfahrenstechnik (PVZ), Technische Universität Braunschweig, Franz-Liszt-Straße 35A, 38106 Braunschweig, Germany
| | - Maren Flaßhoff
- Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Beethovenstraße 55, 38106 Braunschweig, Germany
| | - Hannes Falke
- Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Beethovenstraße 55, 38106 Braunschweig, Germany
| | - Lutz Preu
- Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Beethovenstraße 55, 38106 Braunschweig, Germany
| | - Nadége Loaëc
- Faculté de Médecine et des Sciences de la Santé UBO, 22 avenue Camille Desmoulins, 29200-Brest, France
- ManRos Therapeutics & Perha Pharmaceuticals, Perharidy Research Center, 29680 Roscoff, France
| | - Laurent Meijer
- ManRos Therapeutics & Perha Pharmaceuticals, Perharidy Research Center, 29680 Roscoff, France
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry and Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Apirat Chaikuad
- Institute for Pharmaceutical Chemistry and Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Conrad Kunick
- Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Beethovenstraße 55, 38106 Braunschweig, Germany
- Zentrum für Pharmaverfahrenstechnik (PVZ), Technische Universität Braunschweig, Franz-Liszt-Straße 35A, 38106 Braunschweig, Germany
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47
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Bazzi S, Santra R. Ultrafast Charge Transfer and Structural Dynamics Following Outer-Valence Ionization of a Halogen-Bonded Dimer. J Phys Chem A 2019; 123:7351-7360. [DOI: 10.1021/acs.jpca.9b00646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sophia Bazzi
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Chemistry, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Robin Santra
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Chemistry, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
- Department of Physics, Universität Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chausee 149, 22761 Hamburg, Germany
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48
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Structural Basis for the Selective Inhibition of Cdc2-Like Kinases by CX-4945. BIOMED RESEARCH INTERNATIONAL 2019; 2019:6125068. [PMID: 31531359 PMCID: PMC6720368 DOI: 10.1155/2019/6125068] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 07/15/2019] [Indexed: 11/17/2022]
Abstract
Cdc2-like kinases (CLKs) play a crucial role in the alternative splicing of eukaryotic pre-mRNAs through the phosphorylation of serine/arginine-rich proteins (SR proteins). Dysregulation of this processes is linked with various diseases including cancers, neurodegenerative diseases, and many genetic diseases. Thus, CLKs have been regarded to have a potential as a therapeutic target and significant efforts have been exerted to discover an effective inhibitor. In particular, the small molecule CX-4945, originally identified as an inhibitor of casein kinase 2 (CK2), was further revealed to have a strong CLK-inhibitory activity. Four isoforms of CLKs (CLK1, CLK2, CLK3, and CLK4) can be inhibited by CX-4945, with the highest inhibitory effect on CLK2. This study aimed to elucidate the structural basis of the selective inhibitory effect of CX-4945 on different isoforms of CLKs. We determined the crystal structures of CLK1, CLK2, and CLK3 in complex with CX-4945 at resolutions of 2.4 Å, 2.8 Å, and 2.6 Å, respectively. Comparative analysis revealed that CX-4945 was bound in the same active site pocket of the CLKs with similar interacting networks. Intriguingly, the active sites of CLK/CX-4945 complex structures had different sizes and electrostatic surface charge distributions. The active site of CLK1 was somewhat narrow and contained a negatively charged patch. CLK3 had a protruded Lys248 residue in the entrance of the active site pocket. In addition, Ala319, equivalent to Val324 (CLK1) and Val326 (CLK2), contributed to the weak hydrophobic interactions with the benzonaphthyridine ring of CX-4945. In contrast, the charge distribution pattern of CLK2 was the weakest, favoring its interactions with benzonaphthyridine ring. Thus, the relatively strong binding affinities of CX-4945 with CLK2 are consistent with its strong inhibitory effect defined in the previous study. These results may provide insights into structure-based drug discovery processes.
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49
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More than a messenger: Alternative splicing as a therapeutic target. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194395. [PMID: 31271898 DOI: 10.1016/j.bbagrm.2019.06.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/18/2019] [Accepted: 06/19/2019] [Indexed: 12/30/2022]
Abstract
Alternative splicing of pre-mRNA is an essential post- and co-transcriptional mechanism of gene expression regulation that produces multiple mature mRNA transcripts from a single gene. Genetic mutations that affect splicing underlie numerous devastating diseases. The complexity of splicing regulation allows for multiple therapeutic approaches to correct disease-associated mis-splicing events. In this review, we first highlight recent findings from therapeutic strategies that have used splice switching antisense oligonucleotides and small molecules that bind directly to RNA. Second, we summarize different genetic and chemical approaches to target components of the spliceosome to correct splicing defects in pathological conditions. Finally, we present an overview of compounds that target kinases and accessory pathways that intersect with the splicing machinery. Advancements in the understanding of disease-specific defects caused by mis-regulation of alternative splicing will certainly increase the development of therapeutic options for the clinic. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
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50
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Artarini A, Meyer M, Shin YJ, Huber K, Hilz N, Bracher F, Eros D, Orfi L, Keri G, Goedert S, Neuenschwander M, von Kries J, Domovich-Eisenberg Y, Dekel N, Szabadkai I, Lebendiker M, Horváth Z, Danieli T, Livnah O, Moncorgé O, Frise R, Barclay W, Meyer TF, Karlas A. Regulation of influenza A virus mRNA splicing by CLK1. Antiviral Res 2019; 168:187-196. [PMID: 31176694 DOI: 10.1016/j.antiviral.2019.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 06/04/2019] [Accepted: 06/06/2019] [Indexed: 10/26/2022]
Abstract
Influenza A virus carries eight negative single-stranded RNAs and uses spliced mRNAs to increase the number of proteins produced from them. Several genome-wide screens for essential host factors for influenza A virus replication revealed a necessity for splicing and splicing-related factors, including Cdc-like kinase 1 (CLK1). This CLK family kinase plays a role in alternative splicing regulation through phosphorylation of serine-arginine rich (SR) proteins. To examine the influence that modulation of splicing regulation has on influenza infection, we analyzed the effect of CLK1 knockdown and inhibition. CLK1 knockdown in A549 cells reduced influenza A/WSN/33 virus replication and increased the level of splicing of segment 7, which encodes the viral M1 and M2 proteins. CLK1-/- mice infected with influenza A/England/195/2009 (H1N1pdm09) virus supported lower levels of virus replication than wild-type mice. Screening of newly developed CLK inhibitors revealed several compounds that have an effect on the level of splicing of influenza A gene segment M in different models and decrease influenza A/WSN/33 virus replication in A549 cells. The promising inhibitor KH-CB19, an indole-based enaminonitrile with unique binding mode for CLK1, and its even more selective analogue NIH39 showed high specificity towards CLK1 and had a similar effect on influenza mRNA splicing regulation. Taken together, our findings indicate that targeting host factors that regulate splicing of influenza mRNAs may represent a novel therapeutic approach.
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Affiliation(s)
- Anita Artarini
- Max Planck Institute for Infection Biology, Department of Molecular Biology, Charitéplatz 1, 10117, Berlin, Germany
| | - Michael Meyer
- Steinbeis Innovation, Center for Systems Biomedicine, 14612, Falkensee, Germany
| | - Yu Jin Shin
- Max Planck Institute for Infection Biology, Department of Molecular Biology, Charitéplatz 1, 10117, Berlin, Germany
| | - Kilian Huber
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-University, Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Nikolaus Hilz
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-University, Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Franz Bracher
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-University, Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Daniel Eros
- Vichem Chemie Research Ltd., Herman Ottó 15, H-1022, Budapest, Hungary
| | - Laszlo Orfi
- Vichem Chemie Research Ltd., Herman Ottó 15, H-1022, Budapest, Hungary; Department of Pharmaceutical Chemistry, Semmelweis University, Budapest, 1092, Hungary
| | - Gyorgy Keri
- Vichem Chemie Research Ltd., Herman Ottó 15, H-1022, Budapest, Hungary
| | - Sigrid Goedert
- Max Planck Institute for Infection Biology, Department of Molecular Biology, Charitéplatz 1, 10117, Berlin, Germany
| | - Martin Neuenschwander
- Leibniz Institute for Molecular Pharmacology, Robert-Roessle Str. 10, D-13125, Berlin, Germany
| | - Jens von Kries
- Leibniz Institute for Molecular Pharmacology, Robert-Roessle Str. 10, D-13125, Berlin, Germany
| | - Yael Domovich-Eisenberg
- The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, 91904, Jerusalem, Israel
| | - Noa Dekel
- The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, 91904, Jerusalem, Israel
| | - István Szabadkai
- Vichem Chemie Research Ltd., Herman Ottó 15, H-1022, Budapest, Hungary
| | - Mario Lebendiker
- The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, 91904, Jerusalem, Israel
| | - Zoltán Horváth
- Vichem Chemie Research Ltd., Herman Ottó 15, H-1022, Budapest, Hungary
| | - Tsafi Danieli
- The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, 91904, Jerusalem, Israel
| | - Oded Livnah
- The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, 91904, Jerusalem, Israel
| | - Olivier Moncorgé
- Imperial College London, Section of Virology, Faculty of Medicine, St. Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - Rebecca Frise
- Imperial College London, Section of Virology, Faculty of Medicine, St. Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - Wendy Barclay
- Imperial College London, Section of Virology, Faculty of Medicine, St. Mary's Campus, Norfolk Place, London, W2 1PG, UK
| | - Thomas F Meyer
- Max Planck Institute for Infection Biology, Department of Molecular Biology, Charitéplatz 1, 10117, Berlin, Germany.
| | - Alexander Karlas
- Max Planck Institute for Infection Biology, Department of Molecular Biology, Charitéplatz 1, 10117, Berlin, Germany.
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