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Dewey JA, Delalande C, Azizi SA, Lu V, Antonopoulos D, Babnigg G. Molecular Glue Discovery: Current and Future Approaches. J Med Chem 2023; 66:9278-9296. [PMID: 37437222 PMCID: PMC10805529 DOI: 10.1021/acs.jmedchem.3c00449] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
The intracellular interactions of biomolecules can be maneuvered to redirect signaling, reprogram the cell cycle, or decrease infectivity using only a few dozen atoms. Such "molecular glues," which can drive both novel and known interactions between protein partners, represent an enticing therapeutic strategy. Here, we review the methods and approaches that have led to the identification of small-molecule molecular glues. We first classify current FDA-approved molecular glues to facilitate the selection of discovery methods. We then survey two broad discovery method strategies, where we highlight the importance of factors such as experimental conditions, software packages, and genetic tools for success. We hope that this curation of methodologies for directed discovery will inspire diverse research efforts targeting a multitude of human diseases.
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Affiliation(s)
- Jeffrey A Dewey
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Clémence Delalande
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Saara-Anne Azizi
- Pritzker School of Medicine, University of Chicago, Chicago, Illinois 60637, United States
| | - Vivian Lu
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Dionysios Antonopoulos
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Gyorgy Babnigg
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
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2
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Sardina F, Valente D, Fattorini G, Cioffi E, Zanna GD, Tessa A, Trisciuoglio D, Soddu S, Santorelli FM, Casali C, Rinaldo C. New cellular imaging-based method to distinguish the SPG4 subtype of hereditary spastic paraplegia. Eur J Neurol 2023; 30:1734-1744. [PMID: 36815539 DOI: 10.1111/ene.15756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/07/2023] [Accepted: 02/16/2023] [Indexed: 02/24/2023]
Abstract
BACKGROUND AND PURPOSE Microtubule defects are a common feature in several neurodegenerative disorders, including hereditary spastic paraplegia. The most frequent form of hereditary spastic paraplegia is caused by mutations in the SPG4/SPAST gene, encoding the microtubule severing enzyme spastin. To date, there is no effective therapy available but spastin-enhancing therapeutic approaches are emerging; thus prognostic and predictive biomarkers are urgently required. METHODS An automated, simple, fast and non-invasive cell imaging-based method was developed to quantify microtubule cytoskeleton organization changes in lymphoblastoid cells and peripheral blood mononuclear cells. RESULTS It was observed that lymphoblastoid cells and peripheral blood mononuclear cells from individuals affected by SPG4-hereditary spastic paraplegia show a polarized microtubule cytoskeleton organization. In a pilot study on freshly isolated peripheral blood mononuclear cells, our method discriminates SPG4-hereditary spastic paraplegia from healthy donors and other hereditary spastic paraplegia subtypes. In addition, it is shown that our method can detect the effects of spastin protein level changes. CONCLUSIONS These findings open the possibility of a rapid, non-invasive, inexpensive test useful to recognize SPG4-hereditary spastic paraplegia subtype and evaluate the effects of spastin-enhancing drug in non-neuronal cells.
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Affiliation(s)
- Francesca Sardina
- Institute of Molecular Biology and Pathology (IBPM), Consiglio Nazionale delle Ricerche (CNR), c/o Sapienza University of Rome, Rome, Italy
| | - Davide Valente
- Institute of Molecular Biology and Pathology (IBPM), Consiglio Nazionale delle Ricerche (CNR), c/o Sapienza University of Rome, Rome, Italy
- Unit of Cellular Networks and Molecular Therapeutic Targets, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Gaia Fattorini
- Institute of Molecular Biology and Pathology (IBPM), Consiglio Nazionale delle Ricerche (CNR), c/o Sapienza University of Rome, Rome, Italy
- Department of Biology and Biotechnology, "Charles Darwin" Sapienza University of Rome, Rome, Italy
| | - Ettore Cioffi
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Latina, Italy
| | - Gianmarco Dalla Zanna
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Latina, Italy
| | | | - Daniela Trisciuoglio
- Institute of Molecular Biology and Pathology (IBPM), Consiglio Nazionale delle Ricerche (CNR), c/o Sapienza University of Rome, Rome, Italy
| | - Silvia Soddu
- Unit of Cellular Networks and Molecular Therapeutic Targets, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | | | - Carlo Casali
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Latina, Italy
| | - Cinzia Rinaldo
- Institute of Molecular Biology and Pathology (IBPM), Consiglio Nazionale delle Ricerche (CNR), c/o Sapienza University of Rome, Rome, Italy
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3
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Pellegrini FR, De Martino S, Fianco G, Ventura I, Valente D, Fiore M, Trisciuoglio D, Degrassi F. Blockage of autophagosome-lysosome fusion through SNAP29 O-GlcNAcylation promotes apoptosis via ROS production. Autophagy 2023:1-16. [PMID: 36704963 DOI: 10.1080/15548627.2023.2170962] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Macroautophagy/autophagy has been shown to exert a dual role in cancer i.e., promoting cell survival or cell death depending on the cellular context and the cancer stage. Therefore, development of potent autophagy modulators, with a clear mechanistic understanding of their target action, has paramount importance in both mechanistic and clinical studies. In the process of exploring the mechanism of action of a previously identified cytotoxic small molecule (SM15) designed to target microtubules and the interaction domain of microtubules and the kinetochore component NDC80/HEC1, we discovered that the molecule acts as a potent autophagy inhibitor. By using several biochemical and cell biology assays we demonstrated that SM15 blocks basal autophagic flux by inhibiting the fusion of correctly formed autophagosomes with lysosomes. SM15-induced autophagic flux blockage promoted apoptosis-mediated cell death associated with ROS production. Interestingly, autophagic flux blockage, apoptosis induction and ROS production were rescued by genetic or pharmacological inhibition of OGT (O-linked N-acetylglucosamine (GlcNAc) transferase) or by expressing an O-GlcNAcylation-defective mutant of the SNARE fusion complex component SNAP29, pointing to SNAP29 as the molecular target of SM15 in autophagy. Accordingly, SM15 was found to enhance SNAP29 O-GlcNAcylation and, thereby, inhibit the formation of the SNARE fusion complex. In conclusion, these findings identify a new pathway in autophagy connecting O-GlcNAcylated SNAP29 to autophagic flux blockage and autophagosome accumulation, that, in turn, drives ROS production and apoptotic cell death. Consequently, modulation of SNAP29 activity may represent a new opportunity for therapeutic intervention in cancer and other autophagy-associated diseases.
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Affiliation(s)
- Francesca Romana Pellegrini
- IBPM Institute of Molecular Biology and Pathology, CNR National Research Council, c/o Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Sara De Martino
- IBPM Institute of Molecular Biology and Pathology, CNR National Research Council, c/o Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Giulia Fianco
- IBPM Institute of Molecular Biology and Pathology, CNR National Research Council, c/o Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Irene Ventura
- IBPM Institute of Molecular Biology and Pathology, CNR National Research Council, c/o Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Davide Valente
- IBPM Institute of Molecular Biology and Pathology, CNR National Research Council, c/o Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Mario Fiore
- IBPM Institute of Molecular Biology and Pathology, CNR National Research Council, c/o Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Daniela Trisciuoglio
- IBPM Institute of Molecular Biology and Pathology, CNR National Research Council, c/o Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Francesca Degrassi
- IBPM Institute of Molecular Biology and Pathology, CNR National Research Council, c/o Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
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4
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Firdous F, Ibrahim R, Furqan M, Khan H, Raza H, Singh U, Emwas A, Jaremko M, Chotana GA, Faisal A, Saleem RSZ. Synthesis and Characterization of Griseofulvin Derivatives as Microtubule‐Stabilizing Agents. ChemistrySelect 2022. [DOI: 10.1002/slct.202202832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Farhat Firdous
- Department of Chemistry and Chemical Engineering Syed Babar Ali School of Science and Engineering Lahore University of Management Sciences Lahore 54792 Pakistan
| | - Rida Ibrahim
- Department of Chemistry and Chemical Engineering Syed Babar Ali School of Science and Engineering Lahore University of Management Sciences Lahore 54792 Pakistan
| | - Muhammad Furqan
- Department of Life Sciences Syed Babar Ali School of Science and Engineering Lahore University of Management Sciences Lahore 54792 Pakistan
| | - Hina Khan
- Department of Chemistry and Chemical Engineering Syed Babar Ali School of Science and Engineering Lahore University of Management Sciences Lahore 54792 Pakistan
| | - Hadeeqa Raza
- Department of Life Sciences Syed Babar Ali School of Science and Engineering Lahore University of Management Sciences Lahore 54792 Pakistan
| | - Upendra Singh
- Division of Biological and Environmental Sciences and Engineering King Abdullah University of Science and Technology Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Abdul‐Hamid Emwas
- KAUST Core Labs King Abdullah University of Science and Technology Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Mariusz Jaremko
- Division of Biological and Environmental Sciences and Engineering King Abdullah University of Science and Technology Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Ghayoor Abbas Chotana
- Department of Chemistry and Chemical Engineering Syed Babar Ali School of Science and Engineering Lahore University of Management Sciences Lahore 54792 Pakistan
| | - Amir Faisal
- Department of Life Sciences Syed Babar Ali School of Science and Engineering Lahore University of Management Sciences Lahore 54792 Pakistan
| | - Rahman Shah Zaib Saleem
- Department of Chemistry and Chemical Engineering Syed Babar Ali School of Science and Engineering Lahore University of Management Sciences Lahore 54792 Pakistan
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5
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Adak A, Das G, Gupta V, Khan J, Mukherjee N, Mondal P, Roy R, Barman S, Gharai PK, Ghosh S. Evolution of Potential Antimitotic Stapled Peptides from Multiple Helical Peptide Stretches of the Tubulin Heterodimer Interface: Helix-Mimicking Stapled Peptide Tubulin Inhibitors. J Med Chem 2022; 65:13866-13878. [PMID: 36240440 DOI: 10.1021/acs.jmedchem.2c01116] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein-protein interactions play a crucial role in microtubule dynamics. Microtubules are considered as a key target for the design and development of anticancer therapeutics, where inhibition of tubulin-tubulin interactions plays a crucial role. Here, we focused on a few key helical stretches at the interface of α,β-tubulin heterodimers and developed a structural mimic of these helical peptides, which can serve as potent inhibitors of microtubule polymerization. To induce helicity, we have made stapled analogues of these sequences. Thereafter, we modified the lead sequences of the antimitotic stapled peptides with halo derivatives. It is observed that halo-substituted stapled peptides follow an interesting trend for the electronegativity of halogen atoms in interaction patterns with tubulin and a correlation in the toxicity profile. Remarkably, we found that para-fluorophenylalanine-modified stapled peptide is the most potent inhibitors, which perturbs microtubule dynamics, induces apoptotic death, and inhibits the growth of melanoma.
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Affiliation(s)
- Anindyasundar Adak
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India
| | - Gaurav Das
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India
| | - Varsha Gupta
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India
| | - Juhee Khan
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India
| | - Nabanita Mukherjee
- Smart Healthcare Department, Interdisciplinary Research Platform, Indian Institute of Technology Jodhpur, NH 62, Surpura Bypass Road, Karwar, Jodhpur, Rajasthan 342037, India
| | - Prasenjit Mondal
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India
| | - Rajsekhar Roy
- Department of Bioscience & Bioengineering, Indian Institute of Technology Jodhpur, NH 62, Surpura Bypass Road, Karwar, Jodhpur, Rajasthan 342037, India
| | - Surajit Barman
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India
| | - Prabir Kumar Gharai
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India
| | - Surajit Ghosh
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India.,Department of Bioscience & Bioengineering, Indian Institute of Technology Jodhpur, NH 62, Surpura Bypass Road, Karwar, Jodhpur, Rajasthan 342037, India.,Smart Healthcare Department, Interdisciplinary Research Platform, Indian Institute of Technology Jodhpur, NH 62, Surpura Bypass Road, Karwar, Jodhpur, Rajasthan 342037, India
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6
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Diclofenac: A Nonsteroidal Anti-Inflammatory Drug Inducing Cancer Cell Death by Inhibiting Microtubule Polymerization and Autophagy Flux. Antioxidants (Basel) 2022; 11:antiox11051009. [PMID: 35624874 PMCID: PMC9138099 DOI: 10.3390/antiox11051009] [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: 05/02/2022] [Revised: 05/15/2022] [Accepted: 05/19/2022] [Indexed: 12/12/2022] Open
Abstract
Diclofenac, a nonsteroidal anti-inflammatory drug (NSAID) used to treat inflammatory diseases induces cellular toxicity by increasing the production of reactive oxygen species (ROS) and impairing autophagic flux. In this study, we investigated whether diclofenac induces cancer cell death and the mechanism by which diclofenac causes cell death. We observed that diclofenac induces mitotic arrest with a half-maximal effective concentration of 170 μM and cell death with a half-maximal lethal dose of 200 µM during 18-h incubation in HeLa cells. Cellular microtubule imaging and in vitro tubulin polymerization assays demonstrated that treatment with diclofenac elicits microtubule destabilization. Autophagy relies on microtubule-mediated transport and the fusion of autophagic vesicles. We observed that diclofenac inhibits both phagophore movement, an early step of autophagy, and the fusion of autophagosomes and lysosomes, a late step of autophagy. Diclofenac also induces the fragmentation of mitochondria and the Golgi during cell death. We found that diclofenac induces cell death further in combination with 5-fuorouracil, a DNA replication inhibitor than in single treatment in cancer cells. Pancreatic cancer cells, which have high basal autophagy, are particularly sensitive to cell death by diclofenac. Our study suggests that microtubule destabilization by diclofenac induces cancer cell death via compromised spindle assembly checkpoints and increased ROS through impaired autophagy flux. Diclofenac may be a candidate therapeutic drug in certain type of cancers by inhibiting microtubule-mediated cellular events in combination with clinically utilized nucleoside metabolic inhibitors, including 5-fluorouracil, to block cancer cell proliferation.
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7
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Laine LJ, Mäki-Jouppila JHE, Kutvonen E, Tiikkainen P, Nyholm TKM, Tien JF, Umbreit NT, Härmä V, Kallio L, Davis TN, Asbury CL, Poso A, Gorbsky GJ, Kallio MJ. VTT-006, an anti-mitotic compound, binds to the Ndc80 complex and suppresses cancer cell growth in vitro. Oncoscience 2021; 8:134-153. [PMID: 34926718 PMCID: PMC8667816 DOI: 10.18632/oncoscience.549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 12/01/2021] [Indexed: 11/25/2022] Open
Abstract
Hec1 (Highly expressed in cancer 1) resides in the outer kinetochore where it works to facilitate proper kinetochore-microtubule interactions during mitosis. Hec1 is overexpressed in various cancers and its expression shows correlation with high tumour grade and poor patient prognosis. Chemical perturbation of Hec1 is anticipated to impair kinetochore-microtubule binding, activate the spindle assembly checkpoint (spindle checkpoint) and thereby suppress cell proliferation. In this study, we performed high-throughput screen to identify novel small molecules that target the Hec1 calponin homology domain (CHD), which is needed for normal microtubule attachments. 4 million compounds were first virtually fitted against the CHD, and the best hit molecules were evaluated in vitro. These approaches led to the identification of VTT-006, a 1,2-disubstituted-tetrahydro-beta-carboline derivative, which showed binding to recombinant Ndc80 complex and modulated Hec1 association with microtubules in vitro. VTT-006 treatment resulted in chromosome congression defects, reduced chromosome oscillations and induced loss of inter-kinetochore tension. Cells remained arrested in mitosis with an active spindle checkpoint for several hours before undergoing cell death. VTT-006 suppressed the growth of several cancer cell lines and enhanced the sensitivity of HeLa cells to Taxol. Our findings propose that VTT-006 is a potential anti-mitotic compound that disrupts M phase, impairs kinetochore-microtubule interactions, and activates the spindle checkpoint.
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Affiliation(s)
- Leena J Laine
- VTT Health, VTT Technical Research Centre of Finland Ltd., Otaniemi, Finland.,Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland.,These authors contributed equally to this work
| | - Jenni H E Mäki-Jouppila
- VTT Health, VTT Technical Research Centre of Finland Ltd., Otaniemi, Finland.,Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland.,Drug Research Doctoral Programme, University of Turku, Finland.,Department of Pharmacology, Drug Development and Therapeutics, University of Turku, Turku, Finland.,These authors contributed equally to this work
| | - Emma Kutvonen
- VTT Health, VTT Technical Research Centre of Finland Ltd., Otaniemi, Finland.,Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Pekka Tiikkainen
- VTT Health, VTT Technical Research Centre of Finland Ltd., Otaniemi, Finland
| | | | - Jerry F Tien
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Neil T Umbreit
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Ville Härmä
- VTT Health, VTT Technical Research Centre of Finland Ltd., Otaniemi, Finland
| | - Lila Kallio
- VTT Health, VTT Technical Research Centre of Finland Ltd., Otaniemi, Finland
| | - Trisha N Davis
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Charles L Asbury
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Antti Poso
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Gary J Gorbsky
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Marko J Kallio
- VTT Health, VTT Technical Research Centre of Finland Ltd., Otaniemi, Finland.,Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
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8
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PHA-680626 Is an Effective Inhibitor of the Interaction between Aurora-A and N-Myc. Int J Mol Sci 2021; 22:ijms222313122. [PMID: 34884931 PMCID: PMC8658095 DOI: 10.3390/ijms222313122] [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: 10/20/2021] [Revised: 11/26/2021] [Accepted: 12/01/2021] [Indexed: 11/17/2022] Open
Abstract
Neuroblastoma is a severe childhood disease, accounting for ~10% of all infant cancers. The amplification of the MYCN gene, coding for the N-Myc transcription factor, is an essential marker correlated with tumor progression and poor prognosis. In neuroblastoma cells, the mitotic kinase Aurora-A (AURKA), also frequently overexpressed in cancer, prevents N-Myc degradation by directly binding to a highly conserved N-Myc region. As a result, elevated levels of N-Myc are observed. During recent years, it has been demonstrated that some ATP competitive inhibitors of AURKA also cause essential conformational changes in the structure of the activation loop of the kinase that prevents N-Myc binding, thus impairing the formation of the AURKA/N-Myc complex. In this study, starting from a screening of crystal structures of AURKA in complexes with known inhibitors, we identified additional compounds affecting the conformation of the kinase activation loop. We assessed the ability of such compounds to disrupt the interaction between AURKA and N-Myc in vitro, using Surface Plasmon Resonance competition assays, and in tumor cell lines overexpressing MYCN, by performing Proximity Ligation Assays. Finally, their effects on N-Myc cellular levels and cell viability were investigated. Our results identify PHA-680626 as an amphosteric inhibitor both in vitro and in MYCN overexpressing cell lines, thus expanding the repertoire of known conformational disrupting inhibitors of the AURKA/N-Myc complex and confirming that altering the conformation of the activation loop of AURKA with a small molecule is an effective strategy to destabilize the AURKA/N-Myc interaction in neuroblastoma cancer cells.
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9
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Dewey JA, Azizi SA, Lu V, Dickinson BC. A System for the Evolution of Protein-Protein Interaction Inducers. ACS Synth Biol 2021; 10:2096-2110. [PMID: 34319091 DOI: 10.1021/acssynbio.1c00276] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Molecules that induce interactions between proteins, often referred to as "molecular glues", are increasingly recognized as important therapeutic modalities and as entry points for rewiring cellular signaling networks. Here, we report a new PACE-based method to rapidly select and evolve molecules that mediate interactions between otherwise noninteracting proteins: rapid evolution of protein-protein interaction glues (rePPI-G). By leveraging proximity-dependent split RNA polymerase-based biosensors, we developed E. coli-based detection and selection systems that drive gene expression outputs only when interactions between target proteins are induced. We then validated the system using engineered bivalent molecular glues, showing that rePPI-G robustly selects for molecules that induce the target interaction. Proof-of-concept evolutions demonstrated that rePPI-G reduces the "hook effect" of the engineered molecular glues, due at least in part to tuning the interaction affinities of each individual component of the bifunctional molecule. Altogether, this work validates rePPI-G as a continuous, phage-based evolutionary technology for optimizing molecular glues, providing a strategy for developing molecules that reprogram protein-protein interactions.
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Affiliation(s)
- Jeffrey A. Dewey
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60615, United States
| | - Saara-Anne Azizi
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60615, United States
| | - Vivian Lu
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60615, United States
| | - Bryan C. Dickinson
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60615, United States
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10
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Rea J, Carissimo A, Trisciuoglio D, Illi B, Picard D, Remke M, Laneve P, Caffarelli E. Identification and Functional Characterization of Novel MYC-Regulated Long Noncoding RNAs in Group 3 Medulloblastoma. Cancers (Basel) 2021; 13:cancers13153853. [PMID: 34359754 PMCID: PMC8345409 DOI: 10.3390/cancers13153853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Medulloblastoma is the most common malignant pediatric brain tumor, which accounts for approximately 20% of all childhood brain tumors. To date, no pharmacological approaches are decisive in the treatment of this cancer, while the secondary effects of conventional therapies as chemotherapy, radiotherapy or surgical interventions heavily affect the quality of life of patients. This requires the rapid development of alternative molecular therapies, which are the future challenge of personalized medicine. In this context, we addressed our research towards the most aggressive form of Medulloblastoma to identify novel genes responsible for its onset and/or progression. We discovered three newly implicated genes, for which we highlighted a contribution in the control of cancer cell features. Deepening into the Medulloblastoma biology, this study represents a further step forward for the development of molecular therapies in the era of precision oncology. Abstract The impact of protein-coding genes on cancer onset and progression is a well-established paradigm in molecular oncology. Nevertheless, unveiling the contribution of the noncoding genes—including long noncoding RNAs (lncRNAs)—to tumorigenesis represents a great challenge for personalized medicine, since they (i) constitute the majority of the human genome, (ii) are essential and flexible regulators of gene expression and (iii) present all types of genomic alterations described for protein-coding genes. LncRNAs have been increasingly associated with cancer, their highly tissue- and cancer type-specific expression making them attractive candidates as both biomarkers and therapeutic targets. Medulloblastoma is one of the most common malignant pediatric brain tumors. Group 3 is the most aggressive subgroup, showing the highest rate of metastasis at diagnosis. Transcriptomics and reverse genetics approaches were combined to identify lncRNAs implicated in Group 3 Medulloblastoma biology. Here we present the first collection of lncRNAs dependent on the activity of the MYC oncogene, the major driver gene of Group 3 Medulloblastoma. We assessed the expression profile of selected lncRNAs in Group 3 primary tumors and functionally characterized these species. Overall, our data demonstrate the direct involvement of three lncRNAs in Medulloblastoma cancer cell phenotypes.
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Affiliation(s)
- Jessica Rea
- Department of Biology and Biotechnologies “C. Darwin”, Sapienza University of Rome, 00185 Rome, Italy;
| | | | - Daniela Trisciuoglio
- Institute of Molecular Biology and Pathology, CNR, 00185 Rome, Italy; (D.T.); (B.I.)
| | - Barbara Illi
- Institute of Molecular Biology and Pathology, CNR, 00185 Rome, Italy; (D.T.); (B.I.)
| | - Daniel Picard
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, 40225 Düsseldorf, Germany; (D.P.); (M.R.)
- Department of Neuropathology, Faculty of Medicine, University Hospital Düsseldorf, 40225 Düsseldorf, Germany
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Consortium Neuro-Oncogenomics Cancer Research (DKTK), Partner Site Essen/Düsseldorf, 40225 Düsseldorf, Germany
| | - Marc Remke
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, 40225 Düsseldorf, Germany; (D.P.); (M.R.)
- Department of Neuropathology, Faculty of Medicine, University Hospital Düsseldorf, 40225 Düsseldorf, Germany
- Division of Pediatric Neuro-Oncogenomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Consortium Neuro-Oncogenomics Cancer Research (DKTK), Partner Site Essen/Düsseldorf, 40225 Düsseldorf, Germany
| | - Pietro Laneve
- Institute of Molecular Biology and Pathology, CNR, 00185 Rome, Italy; (D.T.); (B.I.)
- Correspondence: (P.L.); (E.C.); Tel.: +39-06-49912205 (P.L.); +39-06-49912201 (E.C.)
| | - Elisa Caffarelli
- Institute of Molecular Biology and Pathology, CNR, 00185 Rome, Italy; (D.T.); (B.I.)
- Correspondence: (P.L.); (E.C.); Tel.: +39-06-49912205 (P.L.); +39-06-49912201 (E.C.)
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11
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Colón-Marrero S, Jusino S, Rivera-Rivera Y, Saavedra HI. Mitotic kinases as drivers of the epithelial-to-mesenchymal transition and as therapeutic targets against breast cancers. Exp Biol Med (Maywood) 2021; 246:1036-1044. [PMID: 33601912 DOI: 10.1177/1535370221991094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Biological therapies against breast cancer patients with tumors positive for the estrogen and progesterone hormone receptors and Her2 amplification have greatly improved their survival. However, to date, there are no effective biological therapies against breast cancers that lack these three receptors or triple-negative breast cancers (TNBC). TNBC correlates with poor survival, in part because they relapse following chemo- and radio-therapies. TNBC is intrinsically aggressive since they have high mitotic indexes and tend to metastasize to the central nervous system. TNBCs are more likely to display centrosome amplification, an abnormal phenotype that results in defective mitotic spindles and abnormal cytokinesis, which culminate in aneuploidy and chromosome instability (known causes of tumor initiation and chemo-resistance). Besides their known role in cell cycle control, mitotic kinases have been also studied in different types of cancer including breast, especially in the context of epithelial-to-mesenchymal transition (EMT). EMT is a cellular process characterized by the loss of cell polarity, reorganization of the cytoskeleton, and signaling reprogramming (upregulation of mesenchymal genes and downregulation of epithelial genes). Previously, we and others have shown the effects of mitotic kinases like Nek2 and Mps1 (TTK) on EMT. In this review, we focus on Aurora A, Aurora B, Bub1, and highly expressed in cancer (Hec1) as novel targets for therapeutic interventions in breast cancer and their effects on EMT. We highlight the established relationships and interactions of these and other mitotic kinases, clinical trial studies involving mitotic kinases, and the importance that represents to develop drugs against these proteins as potential targets in the primary care therapy for TNBC.
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Affiliation(s)
- Stephanie Colón-Marrero
- Department of Basic Sciences, Division of Pharmacology and Cancer Biology, 6650Ponce Health Sciences University/Ponce Research Institute, Ponce, PR 00732, USA
| | - Shirley Jusino
- Department of Basic Sciences, Division of Pharmacology and Cancer Biology, 6650Ponce Health Sciences University/Ponce Research Institute, Ponce, PR 00732, USA
| | - Yainyrette Rivera-Rivera
- Department of Basic Sciences, Division of Pharmacology and Cancer Biology, 6650Ponce Health Sciences University/Ponce Research Institute, Ponce, PR 00732, USA
| | - Harold I Saavedra
- Department of Basic Sciences, Division of Pharmacology and Cancer Biology, 6650Ponce Health Sciences University/Ponce Research Institute, Ponce, PR 00732, USA
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12
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Shwetha B, Sudhanva MS, Jagadeesha GS, Thimmegowda NR, Hamse VK, Sridhar BT, Thimmaiah KN, Ananda Kumar CS, Shobith R, Rangappa KS. Furan-2-carboxamide derivative, a novel microtubule stabilizing agent induces mitotic arrest and potentiates apoptosis in cancer cells. Bioorg Chem 2021; 108:104586. [PMID: 33607574 DOI: 10.1016/j.bioorg.2020.104586] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/12/2020] [Accepted: 12/21/2020] [Indexed: 12/20/2022]
Abstract
The vital role played by microtubules in the cell division process, marks them as a potential druggable target to decimate cancer. A novel furan-2-carboxamide based small molecule, is a selective microtubule stabilizing agent (MSA) with IC50 ranging from 4 µM to 8 µM in different cancer cell lines. Inhibition of tubulin polymerization or stabilization of tubulin polymers abrogates chromosomal segregation during cell division, results in cell cycle arrest and leads to cell death due to the delayed repair mechanism. A novel furan-2-carboxamide based small molecule exhibited potent anti-proliferative and anti-metastatic property In-Vitro against the panel of cancer cells. Annexin V-FITC/PI, double staining reveals potent cytotoxic effect of SH09 against HeLa cells. FACS analysis displays induction of G2/M arrest and accumulation of subG1 population of cells upon treatment with SH09. Molecular docking study unveils SH09 binding affinity to the Taxol binding pocket of tubulin proteins and MM-GBSA also confirms strong binding energies of SH09 with tubulin proteins.
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Affiliation(s)
- B Shwetha
- Department of Nanotechnology, CPGS, Visvesvaraya Technological University, Muddenahalli, Karnataka 562101, India
| | - M Srinivasa Sudhanva
- Adichunchanagiri Institute for Molecular Medicine, AIMS, Adichunchanagiri University, BG Nagara 571448, Karnataka 02, India; Faculty of Natural Sciences, Adichunchanagiri University, BG Nagara 571448, Karnataka, India
| | - G S Jagadeesha
- Department of Chemistry, Govt. S. K. S. J. Technological Institute (Affiliated to Visvesvaraya Technological University), K R Circle, Bangalore, Karnataka 560001, India
| | - N R Thimmegowda
- Department of Chemistry, Govt. S. K. S. J. Technological Institute (Affiliated to Visvesvaraya Technological University), K R Circle, Bangalore, Karnataka 560001, India
| | - Vivek K Hamse
- Faculty of Natural Sciences, Adichunchanagiri University, BG Nagara 571448, Karnataka, India
| | - B T Sridhar
- Department of Chemistry, Maharani's Science College for Women, Palace Road, Bangalore, Karnataka 560001, India
| | - K N Thimmaiah
- Division of Natural Science Northwest Mississippi Community College, University of Mississippi Campus, Desoto Centre, Southaven, MS 38671, USA
| | - C S Ananda Kumar
- Department of Nanotechnology, CPGS, Visvesvaraya Technological University, Muddenahalli, Karnataka 562101, India; Centre for Material Science, University of Mysore, Mysore, Karnataka 570006, India.
| | - Rangappa Shobith
- Adichunchanagiri Institute for Molecular Medicine, AIMS, Adichunchanagiri University, BG Nagara 571448, Karnataka 02, India.
| | - K S Rangappa
- Institution of Excellence, University of Mysore, Manasagangotri, Mysore, Karnataka 570006, India
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13
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Yang L, Han N, Zhang X, Zhou Y, Chen R, Zhang M. ZWINT: A potential therapeutic biomarker in patients with glioblastoma correlates with cell proliferation and invasion. Oncol Rep 2020; 43:1831-1844. [PMID: 32323832 PMCID: PMC7160549 DOI: 10.3892/or.2020.7573] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 02/26/2020] [Indexed: 12/13/2022] Open
Abstract
Glioblastoma (GBM) is the most aggressive primary intracranial tumor in adults. Chemoradiotherapy resistance and recurrence after surgery are the main malignant progression factors, leading to a high mortality rate. Therefore, the exploration of novel biomarkers and molecular mechanisms of GBM is urgent. Differentially expressed genes (DEGs) of GBM were screened in a TCGA dataset. Homo sapiens ZW10 interacting kinetochore protein (ZWINT) was found to be upregulated in GBM, which was confirmed by immunohistochemical staining of a tissue microarray. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) database. A protein-protein interaction (PPI) network was established by the STRING database, and hub genes were visualized by Cytoscape. The correlation results were verified with the GSE15824 dataset. Bioinformatic analysis confirmed that ZWINT was significantly positively correlated with kinetochore protein NDC80 homolog (NDC80), serine/threonine-protein kinase PLK1 (PLK1) and spindle and kinetochore associated complex subunit 1 (SKA1) and together are involved in regulating mitosis and the cell cycle of GBM. ZWINT expression was knocked down in U251 and U87 MG GBM cells by lentiviral vectors carrying a small hairpin RNA (shRNA) targeting ZWINT. The effect of ZWINT silencing on cell proliferation, invasion and apoptosis was determined by the Celigo assay, MTT assay, Transwell assay, flow cytometry and caspase-3/7 assay in vitro. A subcutaneous xenograft tumor model was established to explore the influence of ZWINT knockdown on GBM growth in vivo. Our preliminary study demonstrated that ZWINT knockdown effectively inhibited proliferation and invasion and induced apoptosis of GBM cells and notably suppressed GBM growth in vivo. Therefore, we speculate that ZWINT may be a potential therapeutic biomarker for GBM, with NDC80 and PLK1 conjointly involved in regulating cell division and the mitotic cell cycle.
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Affiliation(s)
- Li Yang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Na Han
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Xiaoxi Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Yangmei Zhou
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Rui Chen
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Mengxian Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
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14
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Chuang SH, Lee YSE, Huang LYL, Chen CK, Lai CL, Lin YH, Yang JY, Yang SC, Chang LH, Chen CH, Liu CW, Lin HS, Lee YR, Huang KP, Fu KC, Jen HM, Lai JY, Jian PS, Wang YC, Hsueh WY, Tsai PY, Hong WH, Chang CC, Wu DZ, Wu J, Chen MH, Yu KM, Chern CY, Chang JM, Lau JYN, Huang JJ. Discovery of T-1101 tosylate as a first-in-class clinical candidate for Hec1/Nek2 inhibition in cancer therapy. Eur J Med Chem 2020; 191:112118. [PMID: 32113126 DOI: 10.1016/j.ejmech.2020.112118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 01/18/2020] [Accepted: 02/03/2020] [Indexed: 02/07/2023]
Abstract
Highly expressed in cancer 1 (Hec1) plays an essential role in mitosis and is correlated with cancer formation, progression, and survival. Phosphorylation of Hec1 by Nek2 kinase is essential for its mitotic function, thus any disruption of Hec1/Nek2 protein-protein interaction has potential for cancer therapy. We have developed T-1101 tosylate (9j tosylate, 9j formerly known as TAI-95), optimized from 4-aryl-N-pyridinylcarbonyl-2-aminothiazole of scaffold 9 by introducing various C-4' substituents to enhance potency and water solubility, as a first-in-class oral clinical candidate for Hec1 inhibition with potential for cancer therapy. T-1101 has good oral absorption, along with potent in vitro antiproliferative activity (IC50: 14.8-21.5 nM). It can achieve high concentrations in Huh-7 and MDA-MB-231 tumor tissues, and showed promise in antitumor activity in mice bearing human tumor xenografts of liver cancer (Huh-7), as well as of breast cancer (BT474, MDA-MB-231, and MCF7) with oral administration. Oral co-administration of T-1101 halved the dose of sorafenib (25 mg/kg to 12.5 mg/kg) required to exhibit comparable in vivo activity towards Huh-7 xenografts. Cellular events resulting from Hec1/Nek2 inhibition with T-1101 treatment include Nek2 degradation, chromosomal misalignment, and apoptotic cell death. A combination of T-1101 with either of doxorubicin, paclitaxel, and topotecan in select cancer cells also resulted in synergistic effects. Inactivity of T-1101 on non-cancerous cells, a panel of kinases, and hERG demonstrates cancer specificity, target specificity, and cardiac safety, respectively. Subsequent salt screening showed that T-1101 tosylate has good oral AUC (62.5 μM·h), bioavailability (F = 77.4%), and thermal stability. T-1101 tosylate is currently in phase I clinical trials as an orally administered drug for cancer therapy.
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Affiliation(s)
- Shih-Hsien Chuang
- Development Center for Biotechnology, National Biotechnology Research Park, Taipei City, 11571, Taiwan
| | - Ying-Shuan E Lee
- Development Center for Biotechnology, National Biotechnology Research Park, Taipei City, 11571, Taiwan
| | - Lynn Y L Huang
- Taivex Therapeutics Corporation, 2nd Floor, Dongxing Rd., Songshan Dist., Taipei City, 10511, Taiwan
| | - Chi-Kuan Chen
- Genomics Research Center, Academia Sinica, Taipei City, Taiwan
| | - Chun-Liang Lai
- Development Center for Biotechnology, National Biotechnology Research Park, Taipei City, 11571, Taiwan
| | - Yu-Hsiang Lin
- Development Center for Biotechnology, National Biotechnology Research Park, Taipei City, 11571, Taiwan
| | - Ju-Ying Yang
- Development Center for Biotechnology, National Biotechnology Research Park, Taipei City, 11571, Taiwan
| | - Sheng-Chuan Yang
- Development Center for Biotechnology, National Biotechnology Research Park, Taipei City, 11571, Taiwan
| | - Lien-Hsiang Chang
- Development Center for Biotechnology, National Biotechnology Research Park, Taipei City, 11571, Taiwan
| | - Ching-Hui Chen
- Development Center for Biotechnology, National Biotechnology Research Park, Taipei City, 11571, Taiwan
| | - Chia-Wei Liu
- Development Center for Biotechnology, National Biotechnology Research Park, Taipei City, 11571, Taiwan
| | - Her-Sheng Lin
- Development Center for Biotechnology, National Biotechnology Research Park, Taipei City, 11571, Taiwan
| | - Yi-Ru Lee
- Development Center for Biotechnology, National Biotechnology Research Park, Taipei City, 11571, Taiwan
| | - Kuan Pin Huang
- Development Center for Biotechnology, National Biotechnology Research Park, Taipei City, 11571, Taiwan
| | - Kuo Chu Fu
- Development Center for Biotechnology, National Biotechnology Research Park, Taipei City, 11571, Taiwan
| | - Hsueh-Min Jen
- Development Center for Biotechnology, National Biotechnology Research Park, Taipei City, 11571, Taiwan
| | - Jun-Yu Lai
- Department of Applied Chemistry, National Chiayi University, No. 300, Syuefu Rd., Chiayi City, 60004, Taiwan
| | - Pei-Shiou Jian
- Department of Applied Chemistry, National Chiayi University, No. 300, Syuefu Rd., Chiayi City, 60004, Taiwan
| | - Yu-Chuan Wang
- Department of Applied Chemistry, National Chiayi University, No. 300, Syuefu Rd., Chiayi City, 60004, Taiwan
| | - Wen-Yun Hsueh
- Department of Applied Chemistry, National Chiayi University, No. 300, Syuefu Rd., Chiayi City, 60004, Taiwan
| | - Pei-Yi Tsai
- Development Center for Biotechnology, National Biotechnology Research Park, Taipei City, 11571, Taiwan
| | - Wan-Hua Hong
- Development Center for Biotechnology, National Biotechnology Research Park, Taipei City, 11571, Taiwan
| | - Chia-Chi Chang
- Taivex Therapeutics Corporation, 2nd Floor, Dongxing Rd., Songshan Dist., Taipei City, 10511, Taiwan
| | - Diana Zc Wu
- Xenobiotic Laboratories, Inc., Plainsboro, NJ, USA
| | - Jinn Wu
- Xenobiotic Laboratories, Inc., Plainsboro, NJ, USA
| | - Meng-Hsin Chen
- Development Center for Biotechnology, National Biotechnology Research Park, Taipei City, 11571, Taiwan
| | - Kuo-Ming Yu
- Taivex Therapeutics Corporation, 2nd Floor, Dongxing Rd., Songshan Dist., Taipei City, 10511, Taiwan
| | - Ching Yuh Chern
- Department of Applied Chemistry, National Chiayi University, No. 300, Syuefu Rd., Chiayi City, 60004, Taiwan
| | - Jia-Ming Chang
- Development Center for Biotechnology, National Biotechnology Research Park, Taipei City, 11571, Taiwan
| | - Johnson Y N Lau
- Taivex Therapeutics Corporation, 2nd Floor, Dongxing Rd., Songshan Dist., Taipei City, 10511, Taiwan
| | - Jiann-Jyh Huang
- Development Center for Biotechnology, National Biotechnology Research Park, Taipei City, 11571, Taiwan; Department of Applied Chemistry, National Chiayi University, No. 300, Syuefu Rd., Chiayi City, 60004, Taiwan.
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15
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Liu ZK, Zhang RY, Yong YL, Zhang ZY, Li C, Chen ZN, Bian H. Identification of crucial genes based on expression profiles of hepatocellular carcinomas by bioinformatics analysis. PeerJ 2019; 7:e7436. [PMID: 31410310 PMCID: PMC6689388 DOI: 10.7717/peerj.7436] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 07/08/2019] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most heterogeneous malignant cancers with no effective targets and treatments. However, the molecular pathogenesis of HCC remains largely uncertain. The aims of our study were to find crucial genes involved in HCC through multidimensional methods and revealed potential molecular mechanisms. Here, we reported the gene expression profile GSE121248 findings from 70 HCC and 37 adjacent normal tissues, all of which had chronic hepatitis B virus (HBV) infection, we were seeking to identify the dysregulated pathways, crucial genes and therapeutic targets implicated in HBV-associated HCC. We found 164 differentially expressed genes (DEGs) (92 downregulated genes and 72 upregulated genes). Gene ontology (GO) analysis of DEGs revealed significant functional enrichment of mitotic nuclear division, cell division, and the epoxygenase P450 pathway. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the DEGs were mainly enriched in metabolism, cell cycle regulation and the p53 signaling pathway. The Mcode plugin was calculated to construct a module complex of DEGs, and the module was mainly enriched in cell cycle checkpoints, RHO GTPase effectors and cytochrome P450. Considering a weak contribution of each gene, gene set enrichment analysis (GSEA) was performed, revealing results consistent with those described above. Six crucial proteins were selected based on the degree of centrality, including NDC80, ESR1, ZWINT, NCAPG, ENO3 and CENPF. Real-time quantitative PCR analysis validated the six crucial genes had the same expression trend as predicted. Furthermore, the methylation data of The Cancer Genome Atlas (TCGA) with HCC showed that mRNA expression of crucial genes was negatively correlated with methylation levels of their promoter region. The overall survival reflected that high expression of NDC80, CENPF, ZWINT, and NCAPG significantly predicted poor prognosis, whereas ESR1 high expression exhibited a favorable prognosis. The identification of the crucial genes and pathways would contribute to the development of novel molecular targets and biomarker-driven treatments for HCC.
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Affiliation(s)
- Ze-Kun Liu
- Fourth Military Medical University, Department of Cell Biology, National Translational Science Center for Molecular Medicine, Xi'an, Shaanxi, China
| | - Ren-Yu Zhang
- Fourth Military Medical University, Department of Cell Biology, National Translational Science Center for Molecular Medicine, Xi'an, Shaanxi, China
| | - Yu-Le Yong
- Fourth Military Medical University, Department of Cell Biology, National Translational Science Center for Molecular Medicine, Xi'an, Shaanxi, China
| | - Zhi-Yun Zhang
- Fourth Military Medical University, Department of Cell Biology, National Translational Science Center for Molecular Medicine, Xi'an, Shaanxi, China
| | - Can Li
- Fourth Military Medical University, Department of Cell Biology, National Translational Science Center for Molecular Medicine, Xi'an, Shaanxi, China
| | - Zhi-Nan Chen
- Fourth Military Medical University, Department of Cell Biology, National Translational Science Center for Molecular Medicine, Xi'an, Shaanxi, China
| | - Huijie Bian
- Fourth Military Medical University, Department of Cell Biology, National Translational Science Center for Molecular Medicine, Xi'an, Shaanxi, China
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16
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Chen X, Li W, Xiao L, Liu L. Nuclear division cycle 80 complex is associated with malignancy and predicts poor survival of hepatocellular carcinoma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2019; 12:1233-1247. [PMID: 31933938 PMCID: PMC6947052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 10/26/2018] [Indexed: 06/10/2023]
Abstract
The NDC80 (nuclear division cycle 80) complex takes part in chromosome segregation by forming an outer kinetochore and providing a platform for the interaction between chromosomes and microtubules, thus impacting the progression of mitosis and the cell cycle. The clinical significance of its components, NDC80, nuf2, spc24, and spc25, were widely explored in various malignancies respectively, yet seldom were they studied from the perspective of a complex. This paper explores the clinical importance of the NDC80 kinetochore complex components in terms of their expression level, prognostic value, and therapeutic potential in HCC (hepatocellular carcinoma) patients. With the data from several paired HCC samples from Nanfang Hospital, HCC patients from the TCGA database and other cases from GSE89377, we analyzed the expression levels of the NDC80 complex components, NDC80/nuf2/spc24/spc25, along with the survival data as well as other clinical features using statistical methods and GSEA. The study found that a high expression of NDC80 complex predicts poor survival, and these components have the potential to be used as therapeutic targets.
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Affiliation(s)
- Xiaowei Chen
- Hepatology Unit and Department of Infectious Diseases, Nanfang Hospital, Southern Medical University Guangzhou 510515, Guangdong, P. R. China
| | - Wenwen Li
- Hepatology Unit and Department of Infectious Diseases, Nanfang Hospital, Southern Medical University Guangzhou 510515, Guangdong, P. R. China
| | - Lushan Xiao
- Hepatology Unit and Department of Infectious Diseases, Nanfang Hospital, Southern Medical University Guangzhou 510515, Guangdong, P. R. China
| | - Li Liu
- Hepatology Unit and Department of Infectious Diseases, Nanfang Hospital, Southern Medical University Guangzhou 510515, Guangdong, P. R. China
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17
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Wu X, Li Z, Shen Y. The small molecule CS1 inhibits mitosis and sister chromatid resolution in HeLa cells. Biochim Biophys Acta Gen Subj 2018; 1862:1134-1147. [PMID: 29410075 DOI: 10.1016/j.bbagen.2018.01.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 12/01/2017] [Accepted: 01/18/2018] [Indexed: 01/03/2023]
Abstract
BACKGROUND Mitosis, the most dramatic event in the cell cycle, involves the reorganization of virtually all cellular components. Antimitotic agents are useful for dissecting the mechanism of this reorganization. Previously, we found that the small molecule CS1 accumulates cells in G2/M phase [1], but the mechanism of its action remains unknown. METHODS Cell cycle analysis, live cell imaging and nuclear staining were used. Chromosomal morphology was detected by chromosome spreading. The effects of CS1 on microtubules were confirmed by tubulin polymerization, colchicine tubulin-binding, cellular tubulin polymerization and immunofluorescence assays and by analysis of microtubule dynamics and molecular modeling. Histone phosphoproteomics was performed using mass spectrometry. Cell signaling cascades were analyzed using immunofluorescence, immunoprecipitation, immunoblotting, siRNA knockdown and chemical inhibition of specific proteins. RESULTS The small molecule CS1 was shown to be an antimitotic agent. CS1 potently inhibited microtubule polymerization via interaction with the colchicine-binding pocket of tubulin in vitro and inhibited the formation of the spindle apparatus by reducing the bulk of growing microtubules in HeLa cells, which led to activation of the spindle assembly checkpoint (SAC) and mitotic arrest of HeLa cells. Compared with colchicine, CS1 impaired the progression of sister chromatid resolution independent of cohesin dissociation, and this was reversed by the removal of CS1. Additionally, CS1 induced unique histone phosphorylation patterns distinct from those induced by colchicine. CONCLUSIONS AND SIGNIFICANCE CS1 is a unique antimitotic small molecule and a powerful tool with unprecedented value over colchicine that makes it possible to specifically and conditionally perturb mitotic progression.
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Affiliation(s)
- Xingkang Wu
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan, Shandong 250012, PR China
| | - Zhenyu Li
- Department of Pharmacy, Shandong Provincial Hospital Affiliated to Shandong University, Jinan 250021, PR China
| | - Yuemao Shen
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan, Shandong 250012, PR China; State Key Laboratory of Microbial Technology, Shandong University, No. 27 South Shanda Road, Jinan, Shandong 250100, PR China.
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