1
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Romer B, Travis SM, Mahon BP, McManus CT, Jeffrey PD, Coudray N, Raghu R, Rale MJ, Zhong ED, Bhabha G, Petry S. Conformational states of the microtubule nucleator, the γ-tubulin ring complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.19.572162. [PMID: 38187763 PMCID: PMC10769196 DOI: 10.1101/2023.12.19.572162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Microtubules (MTs) perform essential functions in the cell, and it is critical that they are made at the correct cellular location and cell cycle stage. This nucleation process is catalyzed by the γ-tubulin ring complex (γ-TuRC), a cone-shaped protein complex composed of over 30 subunits. Despite recent insight into the structure of vertebrate γ-TuRC, which shows that its diameter is wider than that of a MT, and that it exhibits little of the symmetry expected for an ideal MT template, the question of how γ-TuRC achieves MT nucleation remains open. Here, we utilized single particle cryo-EM to identify two conformations of γ-TuRC. The helix composed of 14 γ-tubulins at the top of the γ-TuRC cone undergoes substantial deformation, which is predominantly driven by bending of the hinge between the GRIP1 and GRIP2 domains of the γ-tubulin complex proteins. However, surprisingly, this deformation does not remove the inherent asymmetry of γ-TuRC. To further investigate the role of γ-TuRC conformational change, we used cryo electron-tomography (cryo-ET) to obtain a 3D reconstruction of γ-TuRC bound to a nucleated MT, providing insight into the post-nucleation state. Rigid-body fitting of our cryo-EM structures into this reconstruction suggests that the MT lattice is nucleated by spokes 2 through 14 of the γ-tubulin helix, which entails spokes 13 and 14 becoming more structured than what is observed in apo γ-TuRC. Together, our results allow us to propose a model for conformational changes in γ-TuRC and how these may facilitate MT formation in a cell.
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Affiliation(s)
- Brianna Romer
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Sophie M. Travis
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Brian P. Mahon
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Present address: Molecular Structure and Design, Bristol Myers Squibb, Princeton, NJ, USA
| | - Collin T. McManus
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Philip D. Jeffrey
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Nicolas Coudray
- Department of Cell Biology, NYU School of Medicine, New York City, NY, USA
- Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY, USA
| | - Rishwanth Raghu
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Michael J. Rale
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Present address: Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Ellen D. Zhong
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Gira Bhabha
- Department of Cell Biology, NYU School of Medicine, New York City, NY, USA
| | - Sabine Petry
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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2
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Kornicka A, Gzella K, Garbacz K, Jarosiewicz M, Gdaniec M, Fedorowicz J, Balewski Ł, Kokoszka J, Ordyszewska A. Indole-Acrylonitrile Derivatives as Potential Antitumor and Antimicrobial Agents-Synthesis, In Vitro and In Silico Studies. Pharmaceuticals (Basel) 2023; 16:918. [PMID: 37513830 PMCID: PMC10386429 DOI: 10.3390/ph16070918] [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: 05/10/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
A series of 2-(1H-indol-2-yl)-3-acrylonitrile derivatives, 2a-x, 3, 4a-b, 5a-d, 6a-b, and 7, were synthesized as potential antitumor and antimicrobial agents. The structures of the prepared compounds were evaluated based on elemental analysis, IR, 1H- and 13NMR, as well as MS spectra. X-ray crystal analysis of the representative 2-(1H-indol-2-yl)-3-acrylonitrile 2l showed that the acrylonitrile double bond was Z-configured. All compounds were screened at the National Cancer Institute (USA) for their activities against a panel of approximately 60 human tumor cell lines and the relationship between structure and in vitro antitumor activity is discussed. Compounds of interest 2l and 5a-d showed significant growth inhibition potency against various tumor cell lines with the mean midpoint GI50 values of all tests in the range of 0.38-7.91 μM. The prominent compound with remarkable activity (GI50 = 0.0244-5.06 μM) and high potency (TGI = 0.0866-0.938 μM) against some cell lines of leukemia (HL-60(TB)), non-small cell lung cancer (NCI-H522), colon cancer (COLO 205), CNS cancer (SF-539, SNB-75), ovarian cancer ((OVCAR-3), renal cancer (A498, RXF 393), and breast cancer (MDA-MB-468) was 3-[4-(dimethylamino)phenyl]-2-(1-methyl-1H-indol-2-yl)acrylonitrile (5c). Moreover, the selected 2-(1H-indol-2-yl)-3-acrylonitriles 2a-c and 2e-x were evaluated for their antibacterial and antifungal activities against Gram-positive and Gram-negative pathogens as well as Candida albicans. Among them, 2-(1H-indol-2-yl)-3-(1H-pyrrol-2-yl)acrylonitrile (2x) showed the most potent antimicrobial activity and therefore it can be considered as a lead structure for further development of antimicrobial agents. Finally, molecular docking studies as well as drug-likeness and ADME profile prediction were carried out.
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Affiliation(s)
- Anita Kornicka
- Department of Chemical Technology of Drugs, Faculty of Pharmacy, Medical University of Gdansk, 80-416 Gdansk, Poland
| | - Karol Gzella
- Department of Chemical Technology of Drugs, Faculty of Pharmacy, Medical University of Gdansk, 80-416 Gdansk, Poland
| | - Katarzyna Garbacz
- Department of Oral Microbiology, Medical Faculty, Medical University of Gdansk, 80-204 Gdansk, Poland
| | - Małgorzata Jarosiewicz
- Department of Oral Microbiology, Medical Faculty, Medical University of Gdansk, 80-204 Gdansk, Poland
| | - Maria Gdaniec
- Faculty of Chemistry, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Joanna Fedorowicz
- Department of Chemical Technology of Drugs, Faculty of Pharmacy, Medical University of Gdansk, 80-416 Gdansk, Poland
| | - Łukasz Balewski
- Department of Chemical Technology of Drugs, Faculty of Pharmacy, Medical University of Gdansk, 80-416 Gdansk, Poland
| | - Jakub Kokoszka
- Department of Chemical Technology of Drugs, Faculty of Pharmacy, Medical University of Gdansk, 80-416 Gdansk, Poland
| | - Anna Ordyszewska
- Department of Inorganic Chemistry, Faculty of Chemistry and Advanced Materials Centers, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland
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3
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Replacing the tropolonic methoxyl group of colchicine with methylamino increases tubulin binding affinity with improved therapeutic index and overcomes paclitaxel cross-resistance. Drug Resist Updat 2023; 68:100951. [PMID: 36841134 DOI: 10.1016/j.drup.2023.100951] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/12/2023] [Accepted: 02/12/2023] [Indexed: 02/15/2023]
Abstract
AIMS Microtubule inhibitors are widely used in first line cancer therapy, though drug resistance often develops and causes treatment failure. Colchicine binds to tubulins and inhibits tumor growth, but is not approved for cancer therapy due to systemic toxicity. In this study, we aim to improve the therapeutic index of colchicine through structural modification. METHODS The methoxyl group of the tropolonic ring in colchicine was replaced with amino groups. The cross-resistance of the derivatives with paclitaxel and vincristine was tested. Antitumor effects of target compounds were tested in vivo in A549 and paclitaxel-resistant A549/T xenografts. The interaction of target compounds with tubulins was measured using biological and chemical methods. RESULTS Methylamino replacement of the tropolonic methoxyl group of colchicine increases, while demethylation loses, selective tubulin binding affinity, G2/M arrest and antiproliferation activity. Methylaminocolchicine is more potent than paclitaxel and vincristine to inhibit tumor growth in vitro and in vivo without showing cross-resistance to paclitaxel. Methylaminocolchicine binds to tubulins in unique patterns and inhibits P-gp with a stable pharmacokinetic profile. CONCLUSION Methylanimo replacement of the tropolonic methoxyl group of colchicine increases antitumor activity with improved therapeutic index. Methylaminocolchicine represents a new type of mitotic inhibitor with the ability of overcoming paclitaxel and vincristine resistance.
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4
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Taguchi S, Nakano J, Imasaki T, Kita T, Saijo-Hamano Y, Sakai N, Shigematsu H, Okuma H, Shimizu T, Nitta E, Kikkawa S, Mizobuchi S, Niwa S, Nitta R. Structural model of microtubule dynamics inhibition by kinesin-4 from the crystal structure of KLP-12 -tubulin complex. eLife 2022; 11:77877. [PMID: 36065637 PMCID: PMC9451533 DOI: 10.7554/elife.77877] [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: 02/14/2022] [Accepted: 08/01/2022] [Indexed: 12/02/2022] Open
Abstract
Kinesin superfamily proteins are microtubule-based molecular motors driven by the energy of ATP hydrolysis. Among them, the kinesin-4 family is a unique motor that inhibits microtubule dynamics. Although mutations of kinesin-4 cause several diseases, its molecular mechanism is unclear because of the difficulty of visualizing the high-resolution structure of kinesin-4 working at the microtubule plus-end. Here, we report that KLP-12, a C. elegans kinesin-4 ortholog of KIF21A and KIF21B, is essential for proper length control of C. elegans axons, and its motor domain represses microtubule polymerization in vitro. The crystal structure of the KLP-12 motor domain complexed with tubulin, which represents the high-resolution structural snapshot of the inhibition state of microtubule-end dynamics, revealed the bending effect of KLP-12 for tubulin. Comparison with the KIF5B-tubulin and KIF2C-tubulin complexes, which represent the elongation and shrinking forms of microtubule ends, respectively, showed the curvature of tubulin introduced by KLP-12 is in between them. Taken together, KLP-12 controls the proper length of axons by modulating the curvature of the microtubule ends to inhibit the microtubule dynamics. From meter-long structures that allow nerve cells to stretch across a body to miniscule ‘hairs’ required for lung cells to clear mucus, many life processes rely on cells sporting projections which have the right size for their role. Networks of hollow filaments known as microtubules shape these structures and ensure that they have the appropriate dimensions. Controlling the length of microtubules is therefore essential for organisms, yet how this process takes place is still not fully elucidated. Previous research has shown that microtubules continue to grow when their end is straight but stop when it is curved. A family of molecular motors known as kinesin-4 participate in this process, but the exact mechanisms at play remain unclear. To investigate, Tuguchi, Nakano, Imasaki et al. focused on the KLP-12 protein, a kinesin-4 equivalent which helps to controls the length of microtubules in the tiny worm Caenorhabditis elegans. They performed genetic manipulations and imaged the interactions between KLP-12 and the growing end of a microtubule using X-ray crystallography. This revealed that KLP-12 controls the length of neurons by inhibiting microtubule growth. It does so by modulating the curvature of the growing end of the filament to suppress its extension. A ‘snapshot’ of KLP-12 binding to a microtubule at the resolution of the atom revealed exactly how the protein helps to bend the end of the filament to prevent it from growing further. These results will help to understand how nerve cells are shaped. This may also provide insights into the molecular mechanisms for various neurodegenerative disorders caused by problems with the human equivalents of KLP-12, potentially leading to new therapies.
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Affiliation(s)
- Shinya Taguchi
- Division of Structural Medicine and Anatomy, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Japan.,Division of Anesthesiology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Juri Nakano
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Tsuyoshi Imasaki
- Division of Structural Medicine and Anatomy, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tomoki Kita
- Department of Applied Physics, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Yumiko Saijo-Hamano
- Division of Structural Medicine and Anatomy, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Japan
| | | | | | - Hiromichi Okuma
- Division of Structural Medicine and Anatomy, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Takahiro Shimizu
- Division of Structural Medicine and Anatomy, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Eriko Nitta
- Division of Structural Medicine and Anatomy, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Satoshi Kikkawa
- Division of Structural Medicine and Anatomy, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Satoshi Mizobuchi
- Division of Anesthesiology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Shinsuke Niwa
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan.,Department of Applied Physics, Graduate School of Engineering, Tohoku University, Sendai, Japan.,Frontier Research Institute for Interdisciplinary Sciences (FRIS), Tohoku University, Sendai, Japan
| | - Ryo Nitta
- Division of Structural Medicine and Anatomy, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Japan
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5
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Boček I, Hok L, Persoons L, Daelemans D, Vianello R, Hranjec M. Imidazo[4,5-b]pyridine derived tubulin polymerization inhibitors: Design, synthesis, biological activity in vitro and computational analysis. Bioorg Chem 2022; 127:106032. [PMID: 35872398 DOI: 10.1016/j.bioorg.2022.106032] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/05/2022] [Accepted: 07/13/2022] [Indexed: 11/02/2022]
Abstract
Imidazo[4,5-b]pyridine derived acrylonitriles were synthesized and explored for their in vitro antiproliferative effect on a diverse human cancer cell line panel. Three compounds, 20, 21 and 33, showed strong activity in the submicromolar range (IC50 0.2-0.6 μM), and were chosen for further biological experiments. Immunofluorescence staining and tubulin polymerization assays confirmed tubulin as the main target, but excluded its colchicine-binding site as a potential interacting unit. This was supported by the computational analysis, which revealed that the most potent ligands act on the extended colchicine site on the surface between interacting tubulin subunits, where they interfere with their polymerization and reveal pronounced antitumor properties. In addition, lead molecule 21 potently inhibited cancer cell migration, while it did not affect the viability of normal cells even at the highest concentration tested (100 µM).
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Affiliation(s)
- Ida Boček
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Zagreb, Croatia
| | - Lucija Hok
- Laboratory for the Computational Design and Synthesis of Functional Materials, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Leentje Persoons
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven, Belgium
| | - Dirk Daelemans
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven, Belgium
| | - Robert Vianello
- Laboratory for the Computational Design and Synthesis of Functional Materials, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia.
| | - Marijana Hranjec
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Zagreb, Croatia.
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6
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Stein A, Hilken née Thomopoulou P, Frias C, Hopff SM, Varela P, Wilke N, Mariappan A, Neudörfl JM, Fedorov AY, Gopalakrishnan J, Gigant B, Prokop A, Schmalz HG. B-nor-methylene Colchicinoid PT-100 Selectively Induces Apoptosis in Multidrug-Resistant Human Cancer Cells via an Intrinsic Pathway in a Caspase-Independent Manner. ACS OMEGA 2022; 7:2591-2603. [PMID: 35097257 PMCID: PMC8792921 DOI: 10.1021/acsomega.1c04659] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 12/31/2021] [Indexed: 05/14/2023]
Abstract
Colchicine, the main active alkaloid from Colchicum autumnale L., is a potent tubulin binder and represents an interesting lead structure for the development of potential anticancer chemotherapeutics. We report on the synthesis and investigation of potentially reactive colchicinoids and their surprising biological activities. In particular, the previously undescribed colchicinoid PT-100, a B-ring contracted 6-exo-methylene colchicinoid, exhibits extraordinarily high antiproliferative and apoptosis-inducing effects on various types of cancer cell lines like acute lymphoblastic leukemia (Nalm6), acute myeloid leukemia (HL-60), Burkitt-like lymphoma (BJAB), human melanoma (MelHO), and human breast adenocarcinoma (MCF7) cells at low nanomolar concentrations. Apoptosis induction proved to be especially high in multidrug-resistant Nalm6-derived cancer cell lines, while healthy human leukocytes and hepatocytes were not affected by the concentration range studied. Furthermore, caspase-independent initiation of apoptosis via an intrinsic pathway was observed. PT-100 also shows strong synergistic effects in combination with vincristine on BJAB and Nalm6 cells. Cocrystallization of PT-100 with tubulin dimers revealed its (noncovalent) binding to the colchicine-binding site of β-tubulin at the interface to the α-subunit. A pronounced effect of PT-100 on the cytoskeleton morphology was shown by fluorescence microscopy. While the reactivity of PT-100 as a weak Michael acceptor toward thiols was chemically proven, it remains unclear whether this contributes to the remarkable biological properties of this unusual colchicinoid.
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Affiliation(s)
- Andreas Stein
- Department
of Chemistry, University of Cologne, 50939 Cologne, Germany
| | | | - Corazon Frias
- Department
of Paediatric Oncology, Children’s
Hospital Cologne, 50735 Cologne, Germany
| | - Sina M. Hopff
- Department
of Paediatric Oncology, Children’s
Hospital Cologne, 50735 Cologne, Germany
| | - Paloma Varela
- Université
Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the
Cell (I2BC), 91198 Gif-sur-Yvette cedex, France
| | - Nicola Wilke
- Department
of Paediatric Oncology, Children’s
Hospital Cologne, 50735 Cologne, Germany
| | - Arul Mariappan
- Laboratory
for Centrosome and Cytoskeleton Biology, Institute of Human Genetics, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | | | - Alexey Yu Fedorov
- Department
of Organic Chemistry, N.I. Lobachevsky State
University of Nizhny Novgorod, 603950 Nizhny Novgorod, Russian
Federation
| | - Jay Gopalakrishnan
- Laboratory
for Centrosome and Cytoskeleton Biology, Institute of Human Genetics, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Benoît Gigant
- Université
Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the
Cell (I2BC), 91198 Gif-sur-Yvette cedex, France
| | - Aram Prokop
- Department
of Paediatric Oncology, Children’s
Hospital Cologne, 50735 Cologne, Germany
- Department
of Pediatric Hematology/Oncology, Helios
Clinic Schwerin, 19055 Schwerin, Germany
- MSH
Medical School Hamburg, Am Kaiserkai 1, 20457 Hamburg, Germany
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7
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Beč A, Hok L, Persoons L, Vanstreels E, Daelemans D, Vianello R, Hranjec M. Synthesis, Computational Analysis, and Antiproliferative Activity of Novel Benzimidazole Acrylonitriles as Tubulin Polymerization Inhibitors: Part 2. Pharmaceuticals (Basel) 2021; 14:1052. [PMID: 34681276 PMCID: PMC8540608 DOI: 10.3390/ph14101052] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/09/2021] [Accepted: 10/13/2021] [Indexed: 11/23/2022] Open
Abstract
We used classical linear and microwave-assisted synthesis methods to prepare novel N-substituted, benzimidazole-derived acrylonitriles with antiproliferative activity against several cancer cells in vitro. The most potent systems showed pronounced activity against all tested hematological cancer cell lines, with favorable selectivity towards normal cells. The selection of lead compounds was also tested in vitro for tubulin polymerization inhibition as a possible mechanism of biological action. A combination of docking and molecular dynamics simulations confirmed the suitability of the employed organic skeleton for the design of antitumor drugs and demonstrated that their biological activity relies on binding to the colchicine binding site in tubulin. In addition, it also underlined that higher tubulin affinities are linked with (i) bulkier alkyl and aryl moieties on the benzimidazole nitrogen and (ii) electron-donating substituents on the phenyl group that allow deeper entrance into the hydrophobic pocket within the tubulin's β-subunit, consisting of Leu255, Leu248, Met259, Ala354, and Ile378 residues.
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Affiliation(s)
- Anja Beč
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, HR-10000 Zagreb, Croatia;
| | - Lucija Hok
- Laboratory for the Computational Design and Synthesis of Functional Materials, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia;
| | - Leentje Persoons
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, 3000 Leuven, Belgium; (L.P.); (E.V.); (D.D.)
| | - Els Vanstreels
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, 3000 Leuven, Belgium; (L.P.); (E.V.); (D.D.)
| | - Dirk Daelemans
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, 3000 Leuven, Belgium; (L.P.); (E.V.); (D.D.)
| | - Robert Vianello
- Laboratory for the Computational Design and Synthesis of Functional Materials, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia;
| | - Marijana Hranjec
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, HR-10000 Zagreb, Croatia;
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8
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Mühlethaler T, Gioia D, Prota AE, Sharpe ME, Cavalli A, Steinmetz MO. Comprehensive Analysis of Binding Sites in Tubulin. Angew Chem Int Ed Engl 2021; 60:13331-13342. [PMID: 33951246 PMCID: PMC8251789 DOI: 10.1002/anie.202100273] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Indexed: 01/01/2023]
Abstract
Tubulin plays essential roles in vital cellular activities and is the target of a wide range of proteins and ligands. Here, using a combined computational and crystallographic fragment screening approach, we addressed the question of how many binding sites exist in tubulin. We identified 27 distinct sites, of which 11 have not been described previously, and analyzed their relationship to known tubulin-protein and tubulin-ligand interactions. We further observed an intricate pocket communication network and identified 56 chemically diverse fragments that bound to 10 distinct tubulin sites. Our results offer a unique structural basis for the development of novel small molecules for use as tubulin modulators in basic research applications or as drugs. Furthermore, our method lays down a framework that may help to discover new pockets in other pharmaceutically important targets and characterize them in terms of chemical tractability and allosteric modulation.
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Affiliation(s)
- Tobias Mühlethaler
- Laboratory of Biomolecular ResearchDepartment of Biology and ChemistryPaul Scherrer Institut5232Villigen PSISwitzerland
| | - Dario Gioia
- Computational & Chemical BiologyIstituto Italiano di Tecnologiavia Morego, 3016163GenovaItaly
| | - Andrea E. Prota
- Laboratory of Biomolecular ResearchDepartment of Biology and ChemistryPaul Scherrer Institut5232Villigen PSISwitzerland
| | - May E. Sharpe
- Swiss Light SourcePaul Scherrer Institut5232Villigen PSISwitzerland
| | - Andrea Cavalli
- Computational & Chemical BiologyIstituto Italiano di Tecnologiavia Morego, 3016163GenovaItaly
- Department of Pharmacy and BiotechnologyAlma Mater StudiorumUniversity of Bolognavia Belmeloro 640126BolognaItaly
| | - Michel O. Steinmetz
- Laboratory of Biomolecular ResearchDepartment of Biology and ChemistryPaul Scherrer Institut5232Villigen PSISwitzerland
- University of BaselBiozentrum4056BaselSwitzerland
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9
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Mühlethaler T, Gioia D, Prota AE, Sharpe ME, Cavalli A, Steinmetz MO. Comprehensive Analysis of Binding Sites in Tubulin. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100273] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Tobias Mühlethaler
- Laboratory of Biomolecular Research Department of Biology and Chemistry Paul Scherrer Institut 5232 Villigen PSI Switzerland
| | - Dario Gioia
- Computational & Chemical Biology Istituto Italiano di Tecnologia via Morego, 30 16163 Genova Italy
| | - Andrea E. Prota
- Laboratory of Biomolecular Research Department of Biology and Chemistry Paul Scherrer Institut 5232 Villigen PSI Switzerland
| | - May E. Sharpe
- Swiss Light Source Paul Scherrer Institut 5232 Villigen PSI Switzerland
| | - Andrea Cavalli
- Computational & Chemical Biology Istituto Italiano di Tecnologia via Morego, 30 16163 Genova Italy
- Department of Pharmacy and Biotechnology Alma Mater Studiorum University of Bologna via Belmeloro 6 40126 Bologna Italy
| | - Michel O. Steinmetz
- Laboratory of Biomolecular Research Department of Biology and Chemistry Paul Scherrer Institut 5232 Villigen PSI Switzerland
- University of Basel Biozentrum 4056 Basel Switzerland
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10
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Knossow M, Campanacci V, Khodja LA, Gigant B. The Mechanism of Tubulin Assembly into Microtubules: Insights from Structural Studies. iScience 2020; 23:101511. [PMID: 32920486 PMCID: PMC7491153 DOI: 10.1016/j.isci.2020.101511] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/03/2020] [Accepted: 08/25/2020] [Indexed: 11/26/2022] Open
Abstract
Microtubules are cytoskeletal components involved in pivotal eukaryotic functions such as cell division, ciliogenesis, and intracellular trafficking. They assemble from αβ-tubulin heterodimers and disassemble in a process called dynamic instability, which is driven by GTP hydrolysis. Structures of the microtubule and of soluble tubulin have been determined by cryo-EM and by X-ray crystallography, respectively. Altogether, these data define the mechanism of tubulin assembly-disassembly at atomic or near-atomic level. We review here the structural changes that occur during assembly, tubulin switching from a curved conformation in solution to a straight one in the microtubule core. We also present more subtle changes associated with GTP binding, leading to tubulin activation for assembly. Finally, we show how cryo-EM and X-ray crystallography are complementary methods to characterize the interaction of tubulin with proteins involved either in intracellular transport or in microtubule dynamics regulation.
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Affiliation(s)
- Marcel Knossow
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Valérie Campanacci
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Liza Ammar Khodja
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Benoît Gigant
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
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11
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Discovery of dihydrofuranoallocolchicinoids - Highly potent antimitotic agents with low acute toxicity. Eur J Med Chem 2020; 207:112724. [PMID: 32827941 DOI: 10.1016/j.ejmech.2020.112724] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/16/2020] [Accepted: 08/03/2020] [Indexed: 12/13/2022]
Abstract
Two series of heterocyclic colchicinoids bearing β-methylenedihydrofuran or 2H-pyran-2-one fragments were synthesized by the intramolecular Heck reaction. Methylenedihydrofuran compounds 9a and 9h were found to be the most cytotoxic among currently known colchicinoids, exhibiting outstanding antiproliferative activity on tumor cell lines in picomolar (0.01-2.1 nM) range of concentrations. Compound 9a potently and substoichiometrically inhibits microtubule formation in vitro, being an order of magnitude more active in this assay than colchicine. Derivatives 9a and 9h revealed relatively low acute toxicity in mice (LD50 ≥ 10 mg/kg i.v.). The X-Ray structure of colchicinoid 9a bound to tubulin confirmed interaction of this compound with the colchicine binding site of tubulin.
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12
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Hemmat M, Castle BT, Sachs JN, Odde DJ. Multiscale Computational Modeling of Tubulin-Tubulin Lateral Interaction. Biophys J 2019; 117:1234-1249. [PMID: 31493861 DOI: 10.1016/j.bpj.2019.08.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 07/26/2019] [Accepted: 08/13/2019] [Indexed: 10/26/2022] Open
Abstract
Microtubules are multistranded polymers in eukaryotic cells that support key cellular functions such as chromosome segregation, motor-based cargo transport, and maintenance of cell polarity. Microtubules self-assemble via "dynamic instability," in which the dynamic plus ends switch stochastically between alternating phases of polymerization and depolymerization. A key question in the field is what are the atomistic origins of this switching, i.e., what is different between the GTP- and GDP-tubulin states that enables microtubule growth and shortening, respectively? More generally, a major challenge in biology is how to connect theoretical frameworks across length- and timescales, from atoms to cellular behavior. In this study, we describe a multiscale model by linking atomistic molecular dynamics (MD), molecular Brownian dynamics (BD), and cellular-level thermokinetic modeling of microtubules. Here, we investigated the underlying interaction energy when tubulin dimers associate laterally by performing all-atom MD simulations. We found that the lateral potential energy is not significantly different among three nucleotide states of tubulin, GTP, GDP, and GMPCPP and is estimated to be ≅ -11 kBT. Furthermore, using MD potential energy in our BD simulations of tubulin dimers confirms that the lateral bond is weak on its own, with a mean lifetime of ∼0.1 μs, implying that the longitudinal bond is required for microtubule assembly. We conclude that nucleotide-dependent lateral-bond strength is not the key mediator microtubule dynamic instability, implying that GTP acts elsewhere to exert its stabilizing influence on microtubule polymer. Furthermore, the estimated lateral-bond strength (ΔGlat0≅ -5 kBT) is well-aligned with earlier estimates based on thermokinetic modeling and light microscopy measurements. Thus, we have computationally connected atomistic-level structural information, obtained by cryo-electron microscopy, to cellular-scale microtubule assembly dynamics using a combination of MD, BD, and thermokinetic models to bridge from Ångstroms to micrometers and from femtoseconds to minutes.
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Affiliation(s)
- Mahya Hemmat
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, Minnesota
| | - Brian T Castle
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota
| | - Jonathan N Sachs
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota
| | - David J Odde
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota.
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13
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Röth S, Fulcher LJ, Sapkota GP. Advances in targeted degradation of endogenous proteins. Cell Mol Life Sci 2019; 76:2761-2777. [PMID: 31030225 PMCID: PMC6588652 DOI: 10.1007/s00018-019-03112-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/23/2019] [Accepted: 04/16/2019] [Indexed: 01/07/2023]
Abstract
Protein silencing is often employed as a means to aid investigations in protein function and is increasingly desired as a therapeutic approach. Several types of protein silencing methodologies have been developed, including targeting the encoding genes, transcripts, the process of translation or the protein directly. Despite these advances, most silencing systems suffer from limitations. Silencing protein expression through genetic ablation, for example by CRISPR/Cas9 genome editing, is irreversible, time consuming and not always feasible. Similarly, RNA interference approaches warrant prolonged treatments, can lead to incomplete protein depletion and are often associated with off-target effects. Targeted proteolysis has the potential to overcome some of these limitations. The field of targeted proteolysis has witnessed the emergence of many methodologies aimed at targeting specific proteins for degradation in a spatio-temporal manner. In this review, we provide an appraisal of the different targeted proteolytic systems and discuss their applications in understanding protein function, as well as their potential in therapeutics.
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Affiliation(s)
- Sascha Röth
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Luke J Fulcher
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Gopal P Sapkota
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
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14
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Abstract
Nucleation is one of the least understood steps of microtubule dynamics. It is a kinetically unfavorable process that is templated in the cell by the γ-tubulin ring complex or by preexisting microtubules; it also occurs in vitro from pure tubulin. Here we study the nucleation inhibition potency of natural or artificial proteins in connection with their binding mode to the longitudinal surface of α- or β-tubulin. The structure of tubulin-bound CopN, a Chlamydia protein that delays nucleation, suggests that this protein may interfere with two protofilaments at the (+) end of a nucleus. Designed ankyrin repeat proteins that share a binding mode similar to that of CopN also impede nucleation, whereas those that target only one protofilament do not. In addition, an αRep protein predicted to target two protofilaments at the (-) end does not delay nucleation, pointing to different behaviors at both ends of the nucleus. Our results link the interference with protofilaments at the (+) end and the inhibition of nucleation.
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15
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Traversi G, Staid DS, Fiore M, Percario Z, Trisciuoglio D, Antonioletti R, Morea V, Degrassi F, Cozzi R. A novel resveratrol derivative induces mitotic arrest, centrosome fragmentation and cancer cell death by inhibiting γ-tubulin. Cell Div 2019; 14:3. [PMID: 31007707 PMCID: PMC6457039 DOI: 10.1186/s13008-019-0046-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 03/23/2019] [Indexed: 12/31/2022] Open
Abstract
Background Resveratrol and its natural stilbene-containing derivatives have been extensively investigated as potential chemotherapeutic agents. The synthetic manipulation of the stilbene scaffold has led to the generation of new analogues with improved anticancer activity and better bioavailability. In the present study we investigated the anticancer activity of a novel trimethoxystilbene derivative (3,4,4'-trimethoxylstilbene), where two methoxyl groups are adjacent on the benzene ring (ortho configuration), and compared its activity to 3,5,4'-trimethoxylstilbene, whose methoxyl groups are in meta configuration. Results We provide evidence that the presence of the two methoxyl groups in ortho configuration renders 3,4,4'-trimethoxystilbene more efficient than the meta isomer in inhibiting cell proliferation and producing apoptotic death in colorectal cancer cells. Confocal microscopy of α- and γ-tubulin staining shows that the novel compound strongly depolymerizes the mitotic spindle and produces fragmentation of the pericentrosomal material. Computer assisted docking studies indicate that both molecules potentially interact with γ-tubulin, and that 3,4,4'-trimethoxystilbene is likely to establish stronger interactions with the protein. Conclusions These findings demonstrate the ortho configuration confers higher specificity for γ-tubulin with respect to α-tubulin on 3,4,4' trimethoxystilbene, allowing it to be defined as a new γ-tubulin inhibitor. A strong interaction with γ-tubulin might be a defining feature of molecules with high anticancer activity, as shown for the 3,4,4' isomer.
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Affiliation(s)
| | - David Sasah Staid
- 2Department of Biochemical Sciences 'A. Rossi Fanelli', Sapienza University of Rome, Rome, Italy
| | - Mario Fiore
- 3Institute of Molecular Biology and Pathology, National Research Council of Italy (CNR), c/o Sapienza University of Rome, Rome, Italy
| | - Zulema Percario
- 1Department of Science, University of "Roma Tre", Rome, Italy
| | - Daniela Trisciuoglio
- 3Institute of Molecular Biology and Pathology, National Research Council of Italy (CNR), c/o Sapienza University of Rome, Rome, Italy.,4Preclinical Models and New Therapeutic Agents Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Roberto Antonioletti
- 3Institute of Molecular Biology and Pathology, National Research Council of Italy (CNR), c/o Sapienza University of Rome, Rome, Italy
| | - Veronica Morea
- 3Institute of Molecular Biology and Pathology, National Research Council of Italy (CNR), c/o Sapienza University of Rome, Rome, Italy
| | - Francesca Degrassi
- 3Institute of Molecular Biology and Pathology, National Research Council of Italy (CNR), c/o Sapienza University of Rome, Rome, Italy
| | - Renata Cozzi
- 1Department of Science, University of "Roma Tre", Rome, Italy
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16
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Abstract
Ribosome display has proven to be a powerful in vitro selection and evolution method for generating high-affinity binders from libraries of folded proteins. It works entirely in vitro, and this has two important consequences. First, since no transformation of any cells is required, libraries with much greater diversity can be handled than with most other techniques. Second, since a library does not have to be cloned and transformed, it is very convenient to introduce random errors in the library by PCR-based methods and select improved binders. Thus, a true directed evolution, an iteration between randomization and selection over several generations, can be conveniently carried out, e.g., for affinity maturation, either on a given clone or on the whole library. Ribosome display has been successfully applied to antibody single-chain Fv fragments (scFv), which can be selected not only for specificity but also for stability and catalytic activity. High-affinity binders with new target specificity can be obtained from highly diverse libraries in only a few selection rounds. In this protocol, the selection from the library and the process of affinity maturation and off-rate selection are explained in detail.
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17
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Campanacci V, Urvoas A, Consolati T, Cantos-Fernandes S, Aumont-Nicaise M, Valerio-Lepiniec M, Surrey T, Minard P, Gigant B. Selection and Characterization of Artificial Proteins Targeting the Tubulin α Subunit. Structure 2019; 27:497-506.e4. [PMID: 30661854 PMCID: PMC6408325 DOI: 10.1016/j.str.2018.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/24/2018] [Accepted: 12/03/2018] [Indexed: 11/08/2022]
Abstract
Microtubules are cytoskeletal filaments of eukaryotic cells made of αβ-tubulin heterodimers. Structural studies of non-microtubular tubulin rely mainly on molecules that prevent its self-assembly and are used as crystallization chaperones. Here we identified artificial proteins from an αRep library that are specific to α-tubulin. Turbidity experiments indicate that these αReps impede microtubule assembly in a dose-dependent manner and total internal reflection fluorescence microscopy further shows that they specifically block growth at the microtubule (−) end. Structural data indicate that they do so by targeting the α-tubulin longitudinal surface. Interestingly, in one of the complexes studied, the α subunit is in a conformation that is intermediate between the ones most commonly observed in X-ray structures of tubulin and those seen in the microtubule, emphasizing the plasticity of tubulin. These α-tubulin-specific αReps broaden the range of tools available for the mechanistic study of microtubule dynamics and its regulation. Selection of α-tubulin-specific artificial αRep proteins The αReps inhibit microtubule assembly and specifically block growth at the (−) end The αReps target the longitudinal surface of α-tubulin The αReps are useful tools for the mechanistic study of microtubule dynamics
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Affiliation(s)
- Valérie Campanacci
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France
| | - Agathe Urvoas
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France
| | - Tanja Consolati
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Soraya Cantos-Fernandes
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France
| | - Magali Aumont-Nicaise
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France
| | - Marie Valerio-Lepiniec
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France
| | - Thomas Surrey
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Philippe Minard
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France.
| | - Benoît Gigant
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France.
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18
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Naret T, Khelifi I, Provot O, Bignon J, Levaique H, Dubois J, Souce M, Kasselouri A, Deroussent A, Paci A, Varela PF, Gigant B, Alami M, Hamze A. 1,1-Diheterocyclic Ethylenes Derived from Quinaldine and Carbazole as New Tubulin-Polymerization Inhibitors: Synthesis, Metabolism, and Biological Evaluation. J Med Chem 2018; 62:1902-1916. [PMID: 30525602 DOI: 10.1021/acs.jmedchem.8b01386] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We report the synthesis and metabolic and biological evaluation of a series of 17 novel heterocyclic derivatives of isocombretastatin-A4 (iso-CA-4) and their structure-activity relationships. Among these derivatives, the most active compound, 4f, inhibited the growth of a panel of seven cancer cell lines with an IC50 in the low nanomolar range. In addition, 4f showed interesting activity against CA-4-resistant colon-carcinoma cells and multidrug-resistant leukemia cells. It also induced G2/M cell-cycle arrest. Structural data indicated binding of 4f to the colchicine site of tubulin, likely preventing the curved-to-straight tubulin structural changes that occur during microtubule assembly. Also, 4f disrupted the blood-vessel-like assembly formed by human umbilical-vein endothelial cells in vitro, suggesting its function as a vascular-disrupting agent. An in vitro metabolism study of 4f showed its high human-microsomal stability in comparison with that of iso-CA-4. The physicochemical properties of 4f may be conducive to CNS permeability, suggesting that this compound may be a possible candidate for the treatment of glioblastoma.
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Affiliation(s)
- Timothée Naret
- BioCIS, Université Paris-Sud, CNRS, Équipe Labellisée Ligue Contre le Cancer , Université Paris-Saclay , F-92290 Châtenay-Malabry , France
| | - Ilhem Khelifi
- BioCIS, Université Paris-Sud, CNRS, Équipe Labellisée Ligue Contre le Cancer , Université Paris-Saclay , F-92290 Châtenay-Malabry , France
| | - Olivier Provot
- BioCIS, Université Paris-Sud, CNRS, Équipe Labellisée Ligue Contre le Cancer , Université Paris-Saclay , F-92290 Châtenay-Malabry , France
| | - Jérôme Bignon
- CIBI Plateform , Institut de Chimie des Substances Naturelles, UPR 2301, CNRS , F-91198 Gif sur Yvette , France
| | - Hélène Levaique
- CIBI Plateform , Institut de Chimie des Substances Naturelles, UPR 2301, CNRS , F-91198 Gif sur Yvette , France
| | - Joelle Dubois
- Institut de Chimie des Substances Naturelles, UPR 2301, CNRS , F-91198 Gif sur Yvette , France
| | - Martin Souce
- Lip(Sys)2, Chimie Analytique Pharmaceutique (FKA EA4041 Groupe de Chimie Analytique de Paris-Sud), Université Paris-Sud , Université Paris-Saclay , F-92290 Châtenay-Malabry , France
| | - Athena Kasselouri
- Lip(Sys)2, Chimie Analytique Pharmaceutique (FKA EA4041 Groupe de Chimie Analytique de Paris-Sud), Université Paris-Sud , Université Paris-Saclay , F-92290 Châtenay-Malabry , France
| | - Alain Deroussent
- UMR 8203, Laboratoire de Vectorologie et Thérapeutique Anticancéreuses, CNRS, Université Paris-Sud , Université Paris-Saclay, Gustave Roussy , F-94805 Villejuif , France
| | - Angélo Paci
- UMR 8203, Laboratoire de Vectorologie et Thérapeutique Anticancéreuses, CNRS, Université Paris-Sud , Université Paris-Saclay, Gustave Roussy , F-94805 Villejuif , France.,Department of Pharmacology and Drug Analysis, Gustave Roussy Cancer Campus Grand Paris , Université Paris-Sud , F-94805 Villejuif , France
| | - Paloma F Varela
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS , Université Paris-Sud, Université Paris-Saclay , F-91198 Gif-sur-Yvette , France
| | - Benoît Gigant
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS , Université Paris-Sud, Université Paris-Saclay , F-91198 Gif-sur-Yvette , France
| | - Mouad Alami
- BioCIS, Université Paris-Sud, CNRS, Équipe Labellisée Ligue Contre le Cancer , Université Paris-Saclay , F-92290 Châtenay-Malabry , France
| | - Abdallah Hamze
- BioCIS, Université Paris-Sud, CNRS, Équipe Labellisée Ligue Contre le Cancer , Université Paris-Saclay , F-92290 Châtenay-Malabry , France
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Microtubule-Targeting Agents: Strategies To Hijack the Cytoskeleton. Trends Cell Biol 2018; 28:776-792. [PMID: 29871823 DOI: 10.1016/j.tcb.2018.05.001] [Citation(s) in RCA: 294] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/01/2018] [Accepted: 05/08/2018] [Indexed: 11/20/2022]
Abstract
Microtubule-targeting agents (MTAs) such as paclitaxel and the vinca alkaloids are among the most important medical weapons available to combat cancer. MTAs interfere with intracellular transport, inhibit eukaryotic cell proliferation, and promote cell death by suppressing microtubule dynamics. Recent advances in the structural analysis of MTAs have enabled the extensive characterization of their interactions with microtubules and their building block tubulin. We review here our current knowledge on the molecular mechanisms used by MTAs to hijack the microtubule cytoskeleton, and discuss dual inhibitors that target both kinases and microtubules. We further formulate some outstanding questions related to MTA structural biology and present possible routes for future investigations of this fascinating class of antimitotic agents.
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20
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Advances in the Application of Designed Ankyrin Repeat Proteins (DARPins) as Research Tools and Protein Therapeutics. Methods Mol Biol 2018; 1798:307-327. [PMID: 29868969 DOI: 10.1007/978-1-4939-7893-9_23] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Nonimmunoglobulin scaffolds have been developed to overcome the limitations of monoclonal antibodies with regard to stability and size. Of these scaffolds, the class of designed ankyrin repeat proteins (DARPins) has advanced the most in biochemical and biomedical applications. This review focuses on the recent progress in DARPin technology, highlighting the scaffold's potential and possibilities.
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21
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Design and applications of a clamp for Green Fluorescent Protein with picomolar affinity. Sci Rep 2017; 7:16292. [PMID: 29176615 PMCID: PMC5701241 DOI: 10.1038/s41598-017-15711-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 10/31/2017] [Indexed: 01/15/2023] Open
Abstract
Green fluorescent protein (GFP) fusions are pervasively used to study structures and processes. Specific GFP-binders are thus of great utility for detection, immobilization or manipulation of GFP-fused molecules. We determined structures of two designed ankyrin repeat proteins (DARPins), complexed with GFP, which revealed different but overlapping epitopes. Here we show a structure-guided design strategy that, by truncation and computational reengineering, led to a stable construct where both can bind simultaneously: by linkage of the two binders, fusion constructs were obtained that “wrap around” GFP, have very high affinities of about 10–30 pM, and extremely slow off-rates. They can be natively produced in E. coli in very large amounts, and show excellent biophysical properties. Their very high stability and affinity, facile site-directed functionalization at introduced unique lysines or cysteines facilitate many applications. As examples, we present them as tight yet reversible immobilization reagents for surface plasmon resonance, as fluorescently labelled monomeric detection reagents in flow cytometry, as pull-down ligands to selectively enrich GFP fusion proteins from cell extracts, and as affinity column ligands for inexpensive large-scale protein purification. We have thus described a general design strategy to create a “clamp” from two different high-affinity repeat proteins, even if their epitopes overlap.
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Insight into microtubule disassembly by kinesin-13s from the structure of Kif2C bound to tubulin. Nat Commun 2017; 8:70. [PMID: 28694425 PMCID: PMC5503940 DOI: 10.1038/s41467-017-00091-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 05/31/2017] [Indexed: 12/20/2022] Open
Abstract
Kinesin-13s are critical microtubule regulators which induce microtubule disassembly in an ATP dependent manner. To clarify their mechanism, we report here the crystal structure of a functional construct of the kinesin-13 Kif2C/MCAK in an ATP-like state and bound to the αβ-tubulin heterodimer, a complex mimicking the species that dissociates from microtubule ends during catalytic disassembly. Our results picture how Kif2C stabilizes a curved tubulin conformation. The Kif2C α4-L12-α5 region undergoes a remarkable 25° rotation upon tubulin binding to target the αβ-tubulin hinge. This movement leads the β5a–β5b motif to interact with the distal end of β-tubulin, whereas the neck and the KVD motif, two specific elements of kinesin-13s, target the α-tubulin distal end. Taken together with the study of Kif2C mutants, our data suggest that stabilization of a curved tubulin is an important contribution to the Kif2C mechanism. Kinesin-13s are microtubule depolymerizing enzymes. Here the authors present the crystal structure of a DARPin fused construct comprising the short neck region and motor domain of kinesin-13 in complex with an αβ-tubulin heterodimer, which shows that kinesin-13 functions by stabilizing a curved tubulin conformation.
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Anticancer activities, molecular docking and structure–activity relationship of novel synthesized 4H-chromene, and 5H-chromeno[2,3-d]pyrimidine candidates. Med Chem Res 2017. [DOI: 10.1007/s00044-017-1961-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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