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Lee H, Kim E, Hwang N, Yoo J, Nam Y, Hwang I, Park JG, Park SE, Chung KS, Won Chung H, Song C, Ji MJ, Park HM, Lee IK, Lee KT, Joo Roh E, Hur W. Discovery of N-benzylbenzamide-based allosteric inhibitors of Aurora kinase A. Bioorg Med Chem 2024; 102:117658. [PMID: 38460487 DOI: 10.1016/j.bmc.2024.117658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/11/2024]
Abstract
Aurora kinases (AurkA/B/C) regulate the assembly of bipolar mitotic spindles and the fidelity of chromosome segregation during mitosis, and are attractive therapeutic targets for cancers. Numerous ATP-competitive AurkA inhibitors have been developed as potential anti-cancer agents. Recently, a few allosteric inhibitors have been reported that bind to the allosteric Y-pocket within AurkA kinase domain and disrupt the interaction between AurkA and its activator TPX2. Herein we report a novel allosteric AurkA inhibitor (6h) of N-benzylbenzamide backbone. Compound 6h suppressed the both catalytic activity and non-catalytic functions of AurkA. The inhibitory activity of 6h against AurkA (IC50 = 6.50 μM) was comparable to that of the most potent allosteric AurkA inhibitor AurkinA. Docking analysis against the Y-pocket revealed important pharmacophores and interactions that were coherent with structure-activity relationship. In addition, 6h suppressed DNA replication in G1-S phase, which is a feature of allosteric inhibition of AurA. Our current study may provide a useful insight in designing potent allosteric AurkA inhibitors.
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Affiliation(s)
- Hyomin Lee
- Medicinal Materials Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea; Division of Biomedical Science and Technology, UST KIST School, Seoul 02792, Republic of Korea
| | - Euijung Kim
- Medicinal Materials Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea; Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Narae Hwang
- Medicinal Materials Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Jesik Yoo
- Division of Biomedical Science and Technology, UST KIST School, Seoul 02792, Republic of Korea; Chemical & Biological Integrative Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Yunju Nam
- Medicinal Materials Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Injeoung Hwang
- Medicinal Materials Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea; HY-KIST Bioconvergence, Hanyang University, Seoul 04763, Republic of Korea
| | - Jin-Gyeong Park
- Chemical & Biological Integrative Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea; Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Sang-Eun Park
- Department of Pharmaceutical Biochemistry, College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Kyung-Sook Chung
- Department of Pharmaceutical Biochemistry, College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Hwan Won Chung
- Computational Science Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Chiman Song
- Chemical & Biological Integrative Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Mi-Jung Ji
- Advanced Analysis Data Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Hyun-Mee Park
- Advanced Analysis Data Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - In-Kyun Lee
- Chemical & Biological Integrative Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Kyung-Tae Lee
- Department of Pharmaceutical Biochemistry, College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Eun Joo Roh
- Division of Biomedical Science and Technology, UST KIST School, Seoul 02792, Republic of Korea; Chemical & Biological Integrative Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.
| | - Wooyoung Hur
- Medicinal Materials Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea; HY-KIST Bioconvergence, Hanyang University, Seoul 04763, Republic of Korea.
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2
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Bello M, Bandala C. Evaluating the ability of end-point methods to predict the binding affinity tendency of protein kinase inhibitors. RSC Adv 2023; 13:25118-25128. [PMID: 37614784 PMCID: PMC10443623 DOI: 10.1039/d3ra04916g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 08/14/2023] [Indexed: 08/25/2023] Open
Abstract
Because of the high economic cost of exploring the experimental impact of mutations occurring in kinase proteins, computational approaches have been employed as alternative methods for evaluating the structural and energetic aspects of kinase mutations. Among the main computational methods used to explore the affinity linked to kinase mutations are docking procedures and molecular dynamics (MD) simulations combined with end-point methods or alchemical methods. Although it is known that end-point methods are not able to reproduce experimental binding free energy (ΔG) values, it is also true that they are able to discriminate between a better or a worse ligand through the estimation of ΔG. In this contribution, we selected ten wild-type and mutant cocrystallized EGFR-inhibitor complexes containing experimental binding affinities to evaluate whether MMGBSA or MMPBSA approaches can predict the differences in affinity between the wild type and mutants forming a complex with a similar inhibitor. Our results show that a long MD simulation (the last 50 ns of a 100 ns-long MD simulation) using the MMGBSA method without considering the entropic components reproduced the experimental affinity tendency with a Pearson correlation coefficient of 0.779 and an R2 value of 0.606. On the other hand, the correlation between theoretical and experimental ΔΔG values indicates that the MMGBSA and MMPBSA methods are helpful for obtaining a good correlation using a short rather than a long simulation period.
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Affiliation(s)
- Martiniano Bello
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Diaz Mirón s/n, Col. Casco de Santo Tomas Ciudad de México 11340 Mexico
| | - Cindy Bandala
- Escuela Superior de Medicina, Instituto Politécnico Nacional México City 11340 Mexico
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3
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Shariatzadeh M, Karami A, Moghadam A, Lotfi M, Maggi F, Ebrahimie E. The Essential Oil from Oliveria decumbens Vent. (Apiaceae) as Inhibitor of Breast Cancer Cell (MCF-7) Growth. Pharmaceuticals (Basel) 2022; 16:ph16010059. [PMID: 36678556 PMCID: PMC9863695 DOI: 10.3390/ph16010059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/03/2023] Open
Abstract
Oliveria decumbens Vent. is an aromatic and medicinal plant traditionally used in Iran for the treatment of infections, gastrointestinal diseases, cancer, and inflammation. This research was aimed at investigating the pharmacological potential of O. decumbens essential oil (OEO) and its main compounds, focusing on OEO's cytotoxic effects on MCF-7 breast cancer cells. OEO was obtained by hydro-distillation, and the chemical constituents were identified using GC-MS. Thymol, carvacrol, γ-terpinene, and p-cymene were the main OEO constituents. When MCF-7 cells were treated with OEO, the expressions of genes related to apoptosis (BIM and Bcl-2), tumor suppression (PTEN), and cell growth inhibition (AURKA), were evaluated using real-time PCR. Moreover, molecular docking was used for studying in silico the interaction of OEO principal compounds with PTEN and AURKA. The expression of AURKA was significantly reduced since the OEO treatment enhanced the expression of PTEN. Through in silico molecular docking, it was revealed that thymol, carvacrol, p-cymene, and γ-terpinene can activate PTEN and thus inhibit AURKA. Additionally, the DNA fragmentation assay, acridine orange/ethidium bromide (AO/EB) double-staining assay, and real-time PCR highlighted the fact that the OEO treatment could activate apoptosis and inhibit cell proliferation. Therefore, OEO is a viable candidate to be employed in the pharmaceutical industry, specifically as a possible agent for cancer therapy.
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Affiliation(s)
| | - Akbar Karami
- Department of Horticulture Science, School of Agriculture, Shiraz University, Shiraz 71441, Iran
- Correspondence: (A.K.); (F.M.); Tel.: +39-(073)-740-4506 (F.M.)
| | - Ali Moghadam
- Institute of Biotechnology, Shiraz University, Shiraz 71441, Iran
| | - Mahbobeh Lotfi
- Institute of Biotechnology, Shiraz University, Shiraz 71441, Iran
| | - Filippo Maggi
- Chemistry Interdisciplinary Project (ChIP) Research Center, School of Pharmacy, University of Camerino, 62032 Camerino, Italy
- Correspondence: (A.K.); (F.M.); Tel.: +39-(073)-740-4506 (F.M.)
| | - Esmaeil Ebrahimie
- Genomics Research Platform, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC 3000, Australia
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, SA 5371, Australia
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
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4
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Shin SY, Jung E, Yeo H, Ahn S, Lee Y, Park J, Kang H, Yeo WS, Koh D, Lim Y. Design, synthesis, and biological activities of 3-((4,6-diphenylpyrimidin-2-ylamino)methylene)-2,3-dihydrochromen-4-ones. Bioorg Chem 2022; 120:105634. [PMID: 35114524 DOI: 10.1016/j.bioorg.2022.105634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/25/2021] [Accepted: 01/18/2022] [Indexed: 01/03/2023]
Abstract
Novel (Z)-3-((4,6-diphenylpyrimidin-2-ylamino)methylene)-2,3-dihydrochromen-4-one derivatives were designed and synthesized to find chemotherapeutic agents. Derivative 9 was selected based on its clonogenicity against cancer cells and synthetic yield for further biological experiments. It showed decreases in aurora kinase A, B, and C phosphorylation from western blot analysis. Derivative 9 upregulated the expression of G1 cell cycle inhibitory proteins including p21 and p27, and G1 progressive cyclin D1, and downregulated G1-to-S progressive cyclins, resulting in cell cycle arrest at the G1/S boundary. It stimulated the cleavage of caspase-9, -3, -7, and poly (ADP-ribose) polymerase, resulting in triggering apoptosis through a caspase-dependent pathway. In addition, derivative 9 inhibited in vivo tumor growth in a syngeneic tumor implantation mouse model. The findings of this study suggest that derivative 9 can be considered as a lead compound for chemotherapeutic agents.
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Affiliation(s)
- Soon Young Shin
- Department of Biological Sciences, Konkuk University, Seoul 05029, Republic of Korea
| | - Euitaek Jung
- Department of Biological Sciences, Konkuk University, Seoul 05029, Republic of Korea
| | - Hyunjin Yeo
- Department of Biological Sciences, Konkuk University, Seoul 05029, Republic of Korea
| | - Seunghyun Ahn
- Department of Applied Chemistry, Dongduk Women's University, Seoul 02748, Republic of Korea
| | - Youngshim Lee
- Division of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Jihyun Park
- Division of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Hyunook Kang
- Division of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Woon-Seok Yeo
- Division of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Dongsoo Koh
- Department of Applied Chemistry, Dongduk Women's University, Seoul 02748, Republic of Korea
| | - Yoongho Lim
- Division of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea.
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5
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Baltzer S, Bulatov T, Schmied C, Krämer A, Berger BT, Oder A, Walker-Gray R, Kuschke C, Zühlke K, Eichhorst J, Lehmann M, Knapp S, Weston J, von Kries JP, Süssmuth RD, Klussmann E. Aurora Kinase A Is Involved in Controlling the Localization of Aquaporin-2 in Renal Principal Cells. Int J Mol Sci 2022; 23:ijms23020763. [PMID: 35054947 PMCID: PMC8776063 DOI: 10.3390/ijms23020763] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/30/2021] [Accepted: 01/08/2022] [Indexed: 02/01/2023] Open
Abstract
The cAMP-dependent aquaporin-2 (AQP2) redistribution from intracellular vesicles into the plasma membrane of renal collecting duct principal cells induces water reabsorption and fine-tunes body water homeostasis. However, the mechanisms controlling the localization of AQP2 are not understood in detail. Using immortalized mouse medullary collecting duct (MCD4) and primary rat inner medullary collecting duct (IMCD) cells as model systems, we here discovered a key regulatory role of Aurora kinase A (AURKA) in the control of AQP2. The AURKA-selective inhibitor Aurora-A inhibitor I and novel derivatives as well as a structurally different inhibitor, Alisertib, prevented the cAMP-induced redistribution of AQP2. Aurora-A inhibitor I led to a depolymerization of actin stress fibers, which serve as tracks for the translocation of AQP2-bearing vesicles to the plasma membrane. The phosphorylation of cofilin-1 (CFL1) inactivates the actin-depolymerizing function of CFL1. Aurora-A inhibitor I decreased the CFL1 phosphorylation, accounting for the removal of the actin stress fibers and the inhibition of the redistribution of AQP2. Surprisingly, Alisertib caused an increase in actin stress fibers and did not affect CFL1 phosphorylation, indicating that AURKA exerts its control over AQP2 through different mechanisms. An involvement of AURKA and CFL1 in the control of the localization of AQP2 was hitherto unknown.
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Affiliation(s)
- Sandrine Baltzer
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Strasse 10, 13125 Berlin, Germany; (S.B.); (R.W.-G.); (C.K.); (K.Z.)
- Institute of Chemistry, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany; (T.B.); (R.D.S.)
| | - Timur Bulatov
- Institute of Chemistry, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany; (T.B.); (R.D.S.)
| | - Christopher Schmied
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany; (C.S.); (A.O.); (J.E.); (M.L.); (J.P.v.K.)
| | - Andreas Krämer
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany; (A.K.); (B.-T.B.); (S.K.)
- Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany
- DKTK (German Translational Research Network), Partner Site Frankfurt/Mainz, 60590 Frankfurt am Main, Germany
| | - Benedict-Tilman Berger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany; (A.K.); (B.-T.B.); (S.K.)
- Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany
| | - Andreas Oder
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany; (C.S.); (A.O.); (J.E.); (M.L.); (J.P.v.K.)
| | - Ryan Walker-Gray
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Strasse 10, 13125 Berlin, Germany; (S.B.); (R.W.-G.); (C.K.); (K.Z.)
| | - Christin Kuschke
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Strasse 10, 13125 Berlin, Germany; (S.B.); (R.W.-G.); (C.K.); (K.Z.)
| | - Kerstin Zühlke
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Strasse 10, 13125 Berlin, Germany; (S.B.); (R.W.-G.); (C.K.); (K.Z.)
| | - Jenny Eichhorst
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany; (C.S.); (A.O.); (J.E.); (M.L.); (J.P.v.K.)
| | - Martin Lehmann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany; (C.S.); (A.O.); (J.E.); (M.L.); (J.P.v.K.)
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany; (A.K.); (B.-T.B.); (S.K.)
- Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany
- DKTK (German Translational Research Network), Partner Site Frankfurt/Mainz, 60590 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, 60596 Frankfurt am Main, Germany
| | - John Weston
- JQuest Consulting, Carl-Orff-Weg 25, 65779 Kelkheim, Germany;
| | - Jens Peter von Kries
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany; (C.S.); (A.O.); (J.E.); (M.L.); (J.P.v.K.)
| | - Roderich D. Süssmuth
- Institute of Chemistry, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany; (T.B.); (R.D.S.)
| | - Enno Klussmann
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Strasse 10, 13125 Berlin, Germany; (S.B.); (R.W.-G.); (C.K.); (K.Z.)
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 10785 Berlin, Germany
- Correspondence: ; Tel.: +49-30-9406-2596
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6
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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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7
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Spizzichino S, Boi D, Boumis G, Lucchi R, Liberati FR, Capelli D, Montanari R, Pochetti G, Piacentini R, Parisi G, Paone A, Rinaldo S, Contestabile R, Tramonti A, Paiardini A, Giardina G, Cutruzzolà F. Cytosolic localization and in vitro assembly of human de novo thymidylate synthesis complex. FEBS J 2021; 289:1625-1649. [PMID: 34694685 PMCID: PMC9299187 DOI: 10.1111/febs.16248] [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: 08/21/2021] [Accepted: 10/21/2021] [Indexed: 11/27/2022]
Abstract
De novo thymidylate synthesis is a crucial pathway for normal and cancer cells. Deoxythymidine monophosphate (dTMP) is synthesized by the combined action of three enzymes: serine hydroxymethyltransferase (SHMT1), dihydrofolate reductase (DHFR) and thymidylate synthase (TYMS), with the latter two being targets of widely used chemotherapeutics such as antifolates and 5‐fluorouracil. These proteins translocate to the nucleus after SUMOylation and are suggested to assemble in this compartment into the thymidylate synthesis complex. We report the intracellular dynamics of the complex in cancer cells by an in situ proximity ligation assay, showing that it is also detected in the cytoplasm. This result indicates that the role of the thymidylate synthesis complex assembly may go beyond dTMP synthesis. We have successfully assembled the dTMP synthesis complex in vitro, employing tetrameric SHMT1 and a bifunctional chimeric enzyme comprising human thymidylate synthase and dihydrofolate reductase. We show that the SHMT1 tetrameric state is required for efficient complex assembly, indicating that this aggregation state is evolutionarily selected in eukaryotes to optimize protein–protein interactions. Lastly, our results regarding the activity of the complete thymidylate cycle in vitro may provide a useful tool with respect to developing drugs targeting the entire complex instead of the individual components.
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Affiliation(s)
- Sharon Spizzichino
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Dalila Boi
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Giovanna Boumis
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Roberta Lucchi
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | | | - Davide Capelli
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Roberta Montanari
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Giorgio Pochetti
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Roberta Piacentini
- Center for Life Nano & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Giacomo Parisi
- Center for Life Nano & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Alessio Paone
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Serena Rinaldo
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | | | - Angela Tramonti
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy.,Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Rome, Italy
| | | | - Giorgio Giardina
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Francesca Cutruzzolà
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy.,Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Rome, Italy
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8
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Chi YH, Yeh TK, Ke YY, Lin WH, Tsai CH, Wang WP, Chen YT, Su YC, Wang PC, Chen YF, Wu ZW, Yeh JY, Hung MC, Wu MH, Wang JY, Chen CP, Song JS, Shih C, Chen CT, Chang CP. Discovery and Synthesis of a Pyrimidine-Based Aurora Kinase Inhibitor to Reduce Levels of MYC Oncoproteins. J Med Chem 2021; 64:7312-7330. [PMID: 34009981 PMCID: PMC8279414 DOI: 10.1021/acs.jmedchem.0c01806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The A-type Aurora kinase is upregulated in many human cancers, and it stabilizes MYC-family oncoproteins, which have long been considered an undruggable target. Here, we describe the design and synthesis of a series of pyrimidine-based derivatives able to inhibit Aurora A kinase activity and reduce levels of cMYC and MYCN. Through structure-based drug design of a small molecule that induces the DFG-out conformation of Aurora A kinase, lead compound 13 was identified, which potently (IC50 < 200 nM) inhibited the proliferation of high-MYC expressing small-cell lung cancer (SCLC) cell lines. Pharmacokinetic optimization of 13 by prodrug strategies resulted in orally bioavailable 25, which demonstrated an 8-fold higher oral AUC (F = 62.3%). Pharmacodynamic studies of 25 showed it to effectively reduce cMYC protein levels, leading to >80% tumor regression of NCI-H446 SCLC xenograft tumors in mice. These results support the potential of 25 for the treatment of MYC-amplified cancers including SCLC.
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Affiliation(s)
- Ya-Hui Chi
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan 35053, Taiwan.,Graduate Institute of Biomedical Sciences, China Medical University, Taichung 40402, Taiwan
| | - Teng-Kuang Yeh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan 35053, Taiwan
| | - Yi-Yu Ke
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan 35053, Taiwan
| | - Wen-Hsing Lin
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan 35053, Taiwan
| | - Chia-Hua Tsai
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan 35053, Taiwan
| | - Wan-Ping Wang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan 35053, Taiwan
| | - Yen-Ting Chen
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan 35053, Taiwan
| | - Yu-Chieh Su
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan 35053, Taiwan
| | - Pei-Chen Wang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan 35053, Taiwan
| | - Yan-Fu Chen
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan 35053, Taiwan
| | - Zhong-Wei Wu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan 35053, Taiwan
| | - Jen-Yu Yeh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan 35053, Taiwan
| | - Ming-Chun Hung
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan 35053, Taiwan
| | - Mine-Hsine Wu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan 35053, Taiwan
| | - Jing-Ya Wang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan 35053, Taiwan
| | - Ching-Ping Chen
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan 35053, Taiwan
| | - Jen-Shin Song
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan 35053, Taiwan
| | - Chuan Shih
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan 35053, Taiwan
| | - Chiung-Tong Chen
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan 35053, Taiwan
| | - Chun-Ping Chang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan 35053, Taiwan.,Department of Chemistry, Chung Yuan Christian University, Taoyuan 320314, Taiwan
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9
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Wells CI, Drewry DH, Pickett JE, Tjaden A, Krämer A, Müller S, Gyenis L, Menyhart D, Litchfield DW, Knapp S, Axtman AD. Development of a potent and selective chemical probe for the pleiotropic kinase CK2. Cell Chem Biol 2021; 28:546-558.e10. [PMID: 33484635 DOI: 10.1016/j.chembiol.2020.12.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/30/2020] [Accepted: 12/22/2020] [Indexed: 12/18/2022]
Abstract
Building on the pyrazolopyrimidine CK2 (casein kinase 2) inhibitor scaffold, we designed a small targeted library. Through comprehensive evaluation of inhibitor selectivity, we identified inhibitor 24 (SGC-CK2-1) as a highly potent and cell-active CK2 chemical probe with exclusive selectivity for both human CK2 isoforms. Remarkably, despite years of research pointing to CK2 as a key driver in cancer, our chemical probe did not elicit a broad antiproliferative phenotype in >90% of >140 cell lines when tested in dose-response. While many publications have reported CK2 functions, CK2 biology is complex and an available high-quality chemical tool such as SGC-CK2-1 will be indispensable in deciphering the relationships between CK2 function and phenotypes.
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Affiliation(s)
- Carrow I Wells
- Structural Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC-CH), Chapel Hill, NC 27599, USA; Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, UNC-CH, Chapel Hill, NC 27599, USA
| | - David H Drewry
- Structural Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC-CH), Chapel Hill, NC 27599, USA; Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, UNC-CH, Chapel Hill, NC 27599, USA
| | - Julie E Pickett
- Structural Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC-CH), Chapel Hill, NC 27599, USA; Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, UNC-CH, Chapel Hill, NC 27599, USA
| | - Amelie Tjaden
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Buchman Institute for Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Andreas Krämer
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Buchman Institute for Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Susanne Müller
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Buchman Institute for Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Laszlo Gyenis
- Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Daniel Menyhart
- Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - David W Litchfield
- Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada; Department of Oncology, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Buchman Institute for Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Alison D Axtman
- Structural Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC-CH), Chapel Hill, NC 27599, USA; Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, UNC-CH, Chapel Hill, NC 27599, USA.
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10
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Erguven M, Karakulak T, Diril MK, Karaca E. How Far Are We from the Rapid Prediction of Drug Resistance Arising Due to Kinase Mutations? ACS OMEGA 2021; 6:1254-1265. [PMID: 33490784 PMCID: PMC7818309 DOI: 10.1021/acsomega.0c04672] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 12/11/2020] [Indexed: 06/12/2023]
Abstract
In all living organisms, protein kinases regulate various cell signaling events through phosphorylation. The phosphorylation occurs upon transferring an ATP's terminal phosphate to a target residue. Because of the central role of protein kinases in several proliferative pathways, point mutations occurring within the kinase's ATP-binding site can lead to a constitutively active enzyme, and ultimately, to cancer. A select set of these point mutations can also make the enzyme drug resistant toward the available kinase inhibitors. Because of technical and economical limitations, rapid experimental exploration of the impact of these mutations remains to be a challenge. This underscores the importance of kinase-ligand binding affinity prediction tools that are poised to measure the efficacy of inhibitors in the presence of kinase mutations. To this end, here, we compare the performances of six web-based scoring tools (DSX-ONLINE, KDEEP, HADDOCK2.2, PDBePISA, Pose&Rank, and PRODIGY-LIG) in assessing the impact of kinase mutations on their interactions with their inhibitors. This assessment is carried out on a new structure-based BINDKIN benchmark we compiled. BINDKIN contains wild-type and mutant structure pairs of kinase-inhibitor complexes, together with their corresponding experimental binding affinities (in the form of IC50, K d, and K i). The performance of various web servers over BINDKIN shows that they cannot predict the binding affinities (ΔGs) of wild-type and mutant cases directly. Still, they could catch whether a mutation improves or worsens the ligand binding (ΔΔGs) where the highest Pearson's R correlation coefficient is reached by DSX-ONLINE over the K i dataset. When homology models are used instead of K i-associated crystal structures, DSX-ONLINE loses its predictive capacity. These results highlight that there is room to improve the available scoring functions to estimate the impact of protein kinase point mutations on inhibitor binding. The BINDKIN benchmark with all related results is freely accessible online (https://github.com/CSB-KaracaLab/BINDKIN).
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Affiliation(s)
- Mehmet Erguven
- Izmir
Biomedicine and Genome Center, 35330 Izmir, Turkey
- Izmir
International Biomedicine and Genome Institute, Dokuz Eylul University, 35340 Izmir, Turkey
| | - Tülay Karakulak
- Izmir
Biomedicine and Genome Center, 35330 Izmir, Turkey
- Izmir
International Biomedicine and Genome Institute, Dokuz Eylul University, 35340 Izmir, Turkey
| | - M. Kasim Diril
- Izmir
Biomedicine and Genome Center, 35330 Izmir, Turkey
- Izmir
International Biomedicine and Genome Institute, Dokuz Eylul University, 35340 Izmir, Turkey
| | - Ezgi Karaca
- Izmir
Biomedicine and Genome Center, 35330 Izmir, Turkey
- Izmir
International Biomedicine and Genome Institute, Dokuz Eylul University, 35340 Izmir, Turkey
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11
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Multiresolution non-covalent interaction analysis for ligand–protein promolecular electron density distributions. Theor Chem Acc 2021. [DOI: 10.1007/s00214-020-02705-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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12
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Synthesis, Single Crystal X-Ray Structure, Hirshfeld Surface Analysis, DFT Computations, Docking Studies on Aurora Kinases and an Anticancer Property of 3-(2,3-Dihydrobenzo[b][1,4]dioxin-6-yl)-6-methoxy-4H-chromen-4-one. CRYSTALS 2020. [DOI: 10.3390/cryst10050413] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The isoflavone compound 3-(2,3-dihydrobenzo[b][1,4]dioxin-6-yl)-6-methoxy-4H-chromen-4-one (6) was prepared and structurally characterized using NMR, mass spectrum and X-ray crystallography. Compound 6, C18H14O5, was crystallized in the monoclinic space group P21/n with the cell parameters; a = 7.1869(4) Å, b = 10.2764(6) Å, c = 19.6771(10) Å, β = 99.442(2)°, V = 1433.57(14) Å3, Z = 4. In the title compound, the chromenone ring system is slightly twisted from planarity and the dihedral angle formed between the plane of the chromenone ring and benzene ring is 47.75°. Several intermolecular hydrogen bonds make the crystal stabilized in the three-dimensional structure, which was confirmed by Hirshfeld surface analysis. Density functional theory (DFT) calculations at the B3LYP/6-311++G(d,p) level were carried out and the calculated geometric parameters were compared with the experimental results. A frontier molecular orbital calculation was performed to reveal that the energy values of highest occupied molecular orbital (HOMO) and lowest un-occupied molecular orbital (LUMO) were −5.8223 eV and −1.8447 eV, and the HOMO–LUMO energy gap was 3.9783 eV. A clonogenic long-term survival assay of compound 6 against HCT116 human colon cancer cells showed an anti-cancer ability, with GI50 value of 24.9 μM. Docking experiments within the active sites of aurora kinase A and B were carried out to explain the anti-cancer property of compound 6.
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13
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14
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Xue K, Prezioso SM, Christendat D. QuiC2 represents a functionally distinct class of dehydroshikimate dehydratases identified in Listeria species including Listeria monocytogenes. Environ Microbiol 2020; 22:2680-2692. [PMID: 32190965 DOI: 10.1111/1462-2920.14987] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 03/09/2020] [Accepted: 03/16/2020] [Indexed: 11/28/2022]
Abstract
Many Listeria species including L. monocytogenes contain the pathway for the biosynthesis of protocatechuate from shikimate and quinate. The qui1 and qui2 operons within these Listeria spp. encode enzymes for this pathway. The diversion of shikimate pathway intermediates in some Listeria species to produce protocatechuate suggests an important biological role for this compound to these organisms. A total of seven ORFs, including quiC2, were identified within qui1 and qui2, however only three proteins encoded by the operons have been functionally annotated. The final step in Listeria's protocatechuate biosynthesis involves the conversion of dehydroshikimate by a dehydroshikimate dehydratase (DSD). In this study, we demonstrate that QuiC2 functions as a DSD in Listeria spp. through biochemical and structural analyses. Moreover, we show that QuiC2 forms a phylogenetic cluster distinct from other functionally annotated DSDs. The individual phylogenetic clusters of DSD are represented by enzymes that produce protocatechuate for distinct biological processes. Similarly, QuiC2 is expected to produce protocatechuate for a novel biological process. We postulate that protocatechuate produced by DSDs found within the QuiC2 phylogenetic cluster provides an ecological niche for representative organisms.
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Affiliation(s)
- Kevin Xue
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, Canada, M5S 3B2
| | - Stephanie M Prezioso
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, Canada, M5S 3B2
| | - Dinesh Christendat
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, Canada, M5S 3B2.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada, M5S 3B2
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15
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Cho YW, Lim HJ, Han MH, Kim B, Han S. Inhibitors of Aurora Kinases Screened by a Chip‐based Assay System. B KOREAN CHEM SOC 2019. [DOI: 10.1002/bkcs.11901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Yong Wan Cho
- Department of BiochemistryKangwon National University Chuncheon 24341 South Korea
- Proteogen Inc. Seoul South Korea
| | | | | | - Byung‐Chul Kim
- Department of BiochemistryKangwon National University Chuncheon 24341 South Korea
| | - Sanghwa Han
- Department of BiochemistryKangwon National University Chuncheon 24341 South Korea
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16
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Daina A, Zoete V. Application of the SwissDrugDesign Online Resources in Virtual Screening. Int J Mol Sci 2019; 20:ijms20184612. [PMID: 31540350 PMCID: PMC6770839 DOI: 10.3390/ijms20184612] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/13/2019] [Accepted: 09/14/2019] [Indexed: 02/06/2023] Open
Abstract
SwissDrugDesign is an important initiative led by the Molecular Modeling Group of the SIB Swiss Institute of Bioinformatics. This project provides a collection of freely available online tools for computer-aided drug design. Some of these web-based methods, i.e., SwissSimilarity and SwissTargetPrediction, were especially developed to perform virtual screening, while others such as SwissADME, SwissDock, SwissParam and SwissBioisostere can find applications in related activities. The present review aims at providing a short description of these methods together with examples of their application in virtual screening, where SwissDrugDesign tools successfully supported the discovery of bioactive small molecules.
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Affiliation(s)
- Antoine Daina
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, University of Lausanne, Quartier UNIL-Sorge, Bâtiment Amphipôle, CH-1015 Lausanne, Switzerland.
| | - Vincent Zoete
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, University of Lausanne, Quartier UNIL-Sorge, Bâtiment Amphipôle, CH-1015 Lausanne, Switzerland.
- Department of Fundamental Oncology, University of Lausanne, Ludwig Lausanne Branch, Route de la Corniche 9A, CH-1066 Epalinges, Switzerland.
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17
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Sumi NJ, Ctortecka C, Hu Q, Bryant AT, Fang B, Remsing Rix LL, Ayaz M, Kinose F, Welsh EA, Eschrich SA, Lawrence HR, Koomen JM, Haura EB, Rix U. Divergent Polypharmacology-Driven Cellular Activity of Structurally Similar Multi-Kinase Inhibitors through Cumulative Effects on Individual Targets. Cell Chem Biol 2019; 26:1240-1252.e11. [PMID: 31257184 DOI: 10.1016/j.chembiol.2019.06.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/21/2019] [Accepted: 06/13/2019] [Indexed: 12/18/2022]
Abstract
Despite recent successes of precision and immunotherapies there is a persisting need for novel targeted or multi-targeted approaches in complex diseases. Through a systems pharmacology approach, including phenotypic screening, chemical and phosphoproteomics, and RNA-seq, we elucidated the targets and mechanisms underlying the differential anticancer activity of two structurally related multi-kinase inhibitors, foretinib, and cabozantinib, in lung cancer cells. Biochemical and cellular target validation using probe molecules and RNAi revealed a polypharmacology mechanism involving MEK1/2, FER, and AURKB, which were each more potently inhibited by foretinib than cabozantinib. Based on this, we developed a synergistic combination of foretinib with barasertib, a more potent AURKB inhibitor, for MYC-amplified small-cell lung cancer. This systems pharmacology approach showed that small structural changes of drugs can cumulatively, through multiple targets, result in pronounced anticancer activity differences and that detailed mechanistic understanding of polypharmacology can enable repurposing opportunities for cancers with unmet medical need.
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Affiliation(s)
- Natalia J Sumi
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; Cancer Biology PhD Program, University of South Florida, Tampa, FL 33620, USA
| | - Claudia Ctortecka
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Qianqian Hu
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; Cancer Biology PhD Program, University of South Florida, Tampa, FL 33620, USA
| | - Annamarie T Bryant
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Bin Fang
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Lily L Remsing Rix
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Muhammad Ayaz
- Chemical Biology Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Fumi Kinose
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Eric A Welsh
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Steven A Eschrich
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA
| | - Harshani R Lawrence
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; Chemical Biology Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA
| | - John M Koomen
- Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA; Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Eric B Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Uwe Rix
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA.
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18
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Design, synthesis, and biological evaluation of polyphenols with 4,6-diphenylpyrimidin-2-amine derivatives for inhibition of Aurora kinase A. ACTA ACUST UNITED AC 2019; 27:265-281. [PMID: 31154600 DOI: 10.1007/s40199-019-00272-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 05/08/2019] [Indexed: 01/17/2023]
Abstract
BACKGROUND Several 4,6-diarylpyrimidin-2-amine derivatives show anticancer properties. However, their mode of action is not fully characterized. To develop potent anticancer chemotherapeutic agents, we designed and synthesized 25 4,6-diphenylpyrimidin-2-amine derivatives containing a guanidine moiety. METHODS Clonogenic long-term survival assays were performed to screen anticancer compounds. To derive the structural conditions showing good cytotoxicities against cancer cells, quantitative structure-activity relationships (QSAR) were calculated. Biological activities were determined by flow cytometry for cell cycle analysis and by immunoblot analysis for the detection of Aurora kinase A (AURKA) activity. Because 2-(2-Amino-6-(2,4-dimethoxyphenyl)pyrimidin-4-yl) phenol (derivative 12) selectively inhibited AURKA activity from the kinome assay, in silico docking experiments were performed to elucidate the molecular binding mode between derivative 12 and AURKA. RESULTS The pharmacophores were derived based on the QSAR calculations. Derivative 12 inhibited AURKA activity and reduced phosphorylation of AURKA at Thr283 in HCT116 human colon cancer cells. Derivative 12 caused the accumulation of the G2/M phase of the cell cycle and triggered the cleavages of caspase-3, caspase -7, and poly(ADP-ribose) polymerase. The binding energies of 30 apo-AURKA - derivative 12 complexes obtained from in silico docking ranged from -16.72 to -11.63 kcal/mol. CONCLUSIONS Derivative 12 is an AURKA inhibitor, which reduces clonogenicity, arrests the cell cycle at the G2/M phase, and induces caspase-mediated apoptotic cell death in HCT116 human colon cancer cells. In silico docking demonstrated that derivative 12 binds to AURKA well. The structure-activity relationship calculations showed hydrophobic substituents and 1-naphthalenyl group at the R2 position increased the activity. The existence of an H-bond acceptor at C-2 of the R1 position increased the activity, too. Graphical abstract Derivative 12 inhibits Aurora kinase A activity and causes the G2/M phase arrest of the cell cycle.
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19
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Chen J, Pang L, Wang W, Wang L, Zhang JZH, Zhu T. Decoding molecular mechanism of inhibitor bindings to CDK2 using molecular dynamics simulations and binding free energy calculations. J Biomol Struct Dyn 2019; 38:985-996. [PMID: 30843759 DOI: 10.1080/07391102.2019.1591304] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
CDK2 can be used as an attractive target for development of efficient inhibitors curing multiple disease relating with CDK2. In this work, molecular dynamics (MD) simulations and binding free energy calculations were coupled to probe conformational changes of CDK2 due to inhibitor associations and binding mechanisms of inhibitors PM1, FMD and X64 to CDK2. The results suggest that the binding strength of FMD and X64 to CDK2 is stronger than that of PM1. Principal component (PC) analysis and cross-correlation map calculations based on the equilibrated MD trajectories demonstrate that the structural difference in inhibitors exerts important impact on motion modes and dynamics behavior of CDK2. Residue-based free energy decomposition method was adopted to estimate the inhibitor-residue spectrum. The results not only efficiently identify the hot interaction spot of inhibitors with CDK2 but also show that the hydrophobic rings R1, R2 and R3 as well as polar groups of three inhibitors play key roles in favorably binding of inhibitors to CDK2. This work is expected to contribute energetic basis and dynamics information to development of promising inhibitors toward CDK2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan, China
| | - Laixue Pang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - Wei Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - Lifei Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - John Z H Zhang
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China.,Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Tong Zhu
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, China.,Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
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20
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Inhibitory Effect of Synthetic Flavone Derivatives on Pan-Aurora Kinases: Induction of G2/M Cell-Cycle Arrest and Apoptosis in HCT116 Human Colon Cancer Cells. Int J Mol Sci 2018; 19:ijms19124086. [PMID: 30562979 PMCID: PMC6320900 DOI: 10.3390/ijms19124086] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 12/14/2018] [Accepted: 12/14/2018] [Indexed: 01/27/2023] Open
Abstract
Members of the aurora kinase family are Ser/Thr kinases involved in regulating mitosis. Multiple promising clinical trials to target aurora kinases are in development. To discover flavones showing growth inhibitory effects on cancer cells, 36 flavone derivatives were prepared, and their cytotoxicity was measured using a long-term clonogenic survival assay. Their half-maximal growth inhibitory effects against HCT116 human colon cancer cells were observed at the sub-micromolar level. Pharmacophores were derived based on three-dimensional quantitative structure–activity calculations. Because plant-derived flavones inhibit aurora kinase B, we selected 5-methoxy-2-(2-methoxynaphthalen-1-yl)-4H-chromen-4-one (derivative 31), which showed the best half-maximal cell growth inhibitory effect, and tested whether it can inhibit aurora kinases in HCT116 colon cancer cells. We found that derivative 31 inhibited the phosphorylation of aurora kinases A, aurora kinases B and aurora kinases C, suggesting that derivative 31 is a potential pan-aurora kinase inhibitor. The results of our analysis of the binding modes between derivative 31 and aurora A and aurora B kinases using in-silico docking were consistent with the pharmacophores proposed in this study.
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21
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Najjar A, Platzer C, Luft A, Aßmann CA, Elghazawy NH, Erdmann F, Sippl W, Schmidt M. Computer-aided design, synthesis and biological characterization of novel inhibitors for PKMYT1. Eur J Med Chem 2018; 161:479-492. [PMID: 30388464 DOI: 10.1016/j.ejmech.2018.10.050] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/16/2018] [Accepted: 10/19/2018] [Indexed: 12/12/2022]
Abstract
In the current work, we applied computational methods to analyze the membrane-associated inhibitory kinase PKMYT1 and small molecule inhibitors. PKMYT1 regulates the cell cycle at G2/M transition and phosphorylates Thr14 and Tyr15 in the Cdk1-cyclin B complex. A combination of in silico and in vitro screening was applied to identify novel PKMYT1 inhibitors. The computational approach combined structural analysis, molecular docking, binding free energy calculations, and quantitative structure-activity relationship (QSAR) models. In addition, a computational fragment growing approach was applied to a set of previously identified diaminopyrimidines. Based on the derived computational models, several derivatives were synthesized and tested in vitro on PKMYT1. Novel inhibitors active in the sub-micromolar range were identified which provide the basis for further characterization of PKMYT1 as putative target for cancer therapy.
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Affiliation(s)
- Abdulkarim Najjar
- Institute of Pharmacy, Department of Medicinal Chemistry, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany
| | - Charlott Platzer
- Institute of Pharmacy, Department of Medicinal Chemistry, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany
| | - Anton Luft
- Institute of Pharmacy, Department of Medicinal Chemistry, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany
| | - Chris Alexander Aßmann
- Institute of Pharmacy, Department of Medicinal Chemistry, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany
| | - Nehal H Elghazawy
- Institute of Pharmacy, Department of Medicinal Chemistry, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany
| | - Frank Erdmann
- Institute of Pharmacy, Department of Pharmacology, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany
| | - Wolfgang Sippl
- Institute of Pharmacy, Department of Medicinal Chemistry, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany
| | - Matthias Schmidt
- Institute of Pharmacy, Department of Medicinal Chemistry, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany.
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22
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The multifaceted allosteric regulation of Aurora kinase A. Biochem J 2018; 475:2025-2042. [PMID: 29946042 PMCID: PMC6018539 DOI: 10.1042/bcj20170771] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 04/26/2018] [Accepted: 05/01/2018] [Indexed: 12/22/2022]
Abstract
The protein kinase Aurora A (AurA) is essential for the formation of bipolar mitotic spindles in all eukaryotic organisms. During spindle assembly, AurA is activated through two different pathways operating at centrosomes and on spindle microtubules. Recent studies have revealed that these pathways operate quite differently at the molecular level, activating AurA through multifaceted changes to the structure and dynamics of the kinase domain. These advances provide an intimate atomic-level view of the finely tuned regulatory control operating in protein kinases, revealing mechanisms of allosteric cooperativity that provide graded levels of regulatory control, and a previously unanticipated mechanism for kinase activation by phosphorylation on the activation loop. Here, I review these advances in our understanding of AurA function, and discuss their implications for the use of allosteric small molecule inhibitors to address recently discovered roles of AurA in neuroblastoma, prostate cancer and melanoma.
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23
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Pitsawong W, Buosi V, Otten R, Agafonov RV, Zorba A, Kern N, Kutter S, Kern G, Pádua RA, Meniche X, Kern D. Dynamics of human protein kinase Aurora A linked to drug selectivity. eLife 2018; 7:36656. [PMID: 29901437 PMCID: PMC6054532 DOI: 10.7554/elife.36656] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 06/12/2018] [Indexed: 12/24/2022] Open
Abstract
Protein kinases are major drug targets, but the development of highly-selective inhibitors has been challenging due to the similarity of their active sites. The observation of distinct structural states of the fully-conserved Asp-Phe-Gly (DFG) loop has put the concept of conformational selection for the DFG-state at the center of kinase drug discovery. Recently, it was shown that Gleevec selectivity for the Tyr-kinase Abl was instead rooted in conformational changes after drug binding. Here, we investigate whether protein dynamics after binding is a more general paradigm for drug selectivity by characterizing the binding of several approved drugs to the Ser/Thr-kinase Aurora A. Using a combination of biophysical techniques, we propose a universal drug-binding mechanism, that rationalizes selectivity, affinity and long on-target residence time for kinase inhibitors. These new concepts, where protein dynamics in the drug-bound state plays the crucial role, can be applied to inhibitor design of targets outside the kinome. Protein kinases are a family of enzymes found in all living organisms. These enzymes help to control many biological processes, including cell division. When particular protein kinases do not work correctly, cells may start to divide uncontrollably, which can lead to cancer. One example is the kinase Aurora A, which is over-active in many common human cancers. As a result, researchers are currently trying to design drugs that reduce the activity of Aurora A in the hope that these could form new anticancer treatments. In general, drugs are designed to be as specific in their action as possible to reduce the risk of harmful side effects to the patient. Designing a drug that affects a single protein kinase, however, is difficult because there are hundreds of different kinases in the body, all with similar structures. Because drugs often work by binding to specific structural features, a drug that targets one protein kinase can often alter the activity of a large number of others too. Gleevec is a successful anti-leukemia drug that specifically works on one target kinase, producing minimal side effects. It was recently discovered that the drug works through a phenomenon called ‘induced fit’. This means that after the drug binds it causes a change in the enzyme’s overall shape that alters the activity of the enzyme. The shape change is complex, and so even small structural differences can change the effect of a particular drug. Do other drugs that target other protein kinases also produce induced fit effects? To find out, Pitsawong, Buosi, Otten, Agafonov et al. studied how three anti-cancer drugs interact with Aurora A: two drugs specifically designed to switch off Aurora A, and Gleevec (which does not target Aurora A). The two drugs that specifically target Aurora A were thought to work by targeting one structural feature of the enzyme. However, the biochemical and biophysical experiments performed by Pitsawong et al. revealed that these drugs instead work through an induced fit effect. By contrast, Gleevec did not trigger an induced fit on Aurora A and so bound less tightly to it. In light of these results, Pitsawong et al. suggest that future efforts to design drugs that target protein kinases should focus on exploiting the induced fit process. This will require more research into the structure of particular kinases.
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Affiliation(s)
- Warintra Pitsawong
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| | - Vanessa Buosi
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| | - Renee Otten
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| | - Roman V Agafonov
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| | - Adelajda Zorba
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| | - Nadja Kern
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| | - Steffen Kutter
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| | - Gunther Kern
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| | - Ricardo Ap Pádua
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| | - Xavier Meniche
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Dorothee Kern
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
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24
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Meanwell NA. Fluorine and Fluorinated Motifs in the Design and Application of Bioisosteres for Drug Design. J Med Chem 2018; 61:5822-5880. [PMID: 29400967 DOI: 10.1021/acs.jmedchem.7b01788] [Citation(s) in RCA: 1281] [Impact Index Per Article: 213.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The electronic properties and relatively small size of fluorine endow it with considerable versatility as a bioisostere and it has found application as a substitute for lone pairs of electrons, the hydrogen atom, and the methyl group while also acting as a functional mimetic of the carbonyl, carbinol, and nitrile moieties. In this context, fluorine substitution can influence the potency, conformation, metabolism, membrane permeability, and P-gp recognition of a molecule and temper inhibition of the hERG channel by basic amines. However, as a consequence of the unique properties of fluorine, it features prominently in the design of higher order structural metaphors that are more esoteric in their conception and which reflect a more sophisticated molecular construction that broadens biological mimesis. In this Perspective, applications of fluorine in the construction of bioisosteric elements designed to enhance the in vitro and in vivo properties of a molecule are summarized.
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Affiliation(s)
- Nicholas A Meanwell
- Discovery Chemistry and Molecular Technologies Bristol-Myers Squibb Research and Development P.O. Box 4000, Princeton , New Jersey 08543-4000 , United States
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25
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Park H, Jung HY, Mah S, Hong S. Systematic Computational Design and Identification of Low Picomolar Inhibitors of Aurora Kinase A. J Chem Inf Model 2018; 58:700-709. [DOI: 10.1021/acs.jcim.7b00671] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Hwangseo Park
- Department of Bioscience and Biotechnology & Institute of Anticancer Medicine Development, Sejong University, 209 Neungdong-ro, Kwangjin-gu, Seoul 05006, Korea
| | - Hoi-Yun Jung
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141, Korea
| | - Shinmee Mah
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141, Korea
| | - Sungwoo Hong
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141, Korea
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26
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A water-mediated allosteric network governs activation of Aurora kinase A. Nat Chem Biol 2017; 13:402-408. [PMID: 28166210 DOI: 10.1038/nchembio.2296] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 12/01/2016] [Indexed: 12/23/2022]
Abstract
The catalytic activity of many protein kinases is controlled by conformational changes of a conserved Asp-Phe-Gly (DFG) motif. We used an infrared probe to track the DFG motif of the mitotic kinase Aurora A (AurA) and found that allosteric activation by the spindle-associated protein Tpx2 involves an equilibrium shift toward the active DFG-in state. Förster resonance energy transfer experiments show that the activation loop undergoes a nanometer-scale movement that is tightly coupled to the DFG equilibrium. Tpx2 further activates AurA by stabilizing a water-mediated allosteric network that links the C-helix to the active site through an unusual polar residue in the regulatory spine. The polar spine residue and water network of AurA are essential for phosphorylation-driven activation, but an alternative form of the water network found in related kinases can support Tpx2-driven activation, suggesting that variations in the water-mediated hydrogen bond network mediate regulatory diversification in protein kinases.
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27
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Daniele S, Sestito S, Pietrobono D, Giacomelli C, Chiellini G, Di Maio D, Marinelli L, Novellino E, Martini C, Rapposelli S. Dual Inhibition of PDK1 and Aurora Kinase A: An Effective Strategy to Induce Differentiation and Apoptosis of Human Glioblastoma Multiforme Stem Cells. ACS Chem Neurosci 2017; 8:100-114. [PMID: 27797168 DOI: 10.1021/acschemneuro.6b00251] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The poor prognosis of glioblastoma multiforme (GBM) is mainly attributed to drug resistance mechanisms and to the existence of a subpopulation of glioma stem cells (GSCs). Multitarget compounds able to both affect different deregulated pathways and the GSC subpopulation could escape tumor resistance and, most importantly, eradicate the stem cell reservoir. In this respect, the simultaneous inhibition of phosphoinositide-dependent kinase-1 (PDK1) and aurora kinase A (AurA), each one playing a pivotal role in cellular survival/migration/differentiation, could represent an innovative strategy to overcome GBM resistance and recurrence. Herein, the cross-talk between these pathways was investigated, using the single-target reference compounds MP7 (PDK1 inhibitor) and Alisertib (AurA inhibitor). Furthermore, a new ligand, SA16, was identified for its ability to inhibit the PDK1 and the AurA pathways at once, thus proving to be a useful tool for the simultaneous inhibition of the two kinases. SA16 blocked GBM cell proliferation, reduced tumor invasiveness, and triggered cellular apoptosis. Most importantly, the AurA/PDK1 blocker showed an increased efficacy against GSCs, inducing their differentiation and apoptosis. To the best of our knowledge, this is the first report on combined targeting of PDK1 and AurA. This drug represents an attractive multitarget lead scaffold for the development of new potential treatments for GBM and GSCs.
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Affiliation(s)
| | | | | | | | | | - Danilo Di Maio
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
| | - Luciana Marinelli
- Department
of Pharmacy, University of Naples Federico II, Napoli, Italy
| | - Ettore Novellino
- Department
of Pharmacy, University of Naples Federico II, Napoli, Italy
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28
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Phuangsawai O, Beswick P, Ratanabunyong S, Tabtimmai L, Suphakun P, Obounchoey P, Srisook P, Horata N, Chuckowree I, Hannongbua S, Ward SE, Choowongkomon K, Gleeson MP. Evaluation of the anti-malarial activity and cytotoxicity of 2,4-diamino-pyrimidine-based kinase inhibitors. Eur J Med Chem 2016; 124:896-905. [PMID: 27668758 DOI: 10.1016/j.ejmech.2016.08.055] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 08/23/2016] [Accepted: 08/24/2016] [Indexed: 12/27/2022]
Abstract
A series of 2,4 diamino-pyrimidines have been identified from an analysis of open access high throughput anti-malarial screening data reported by GlaxoSmithKline at the 3D7 and resistant Dd2 strains. SAR expansion has been performed using structural knowledge of the most plausible parasite target. Seventeen new analogs have been synthesized and tested against the resistant K1 strain of Plasmodium falciparum (Pf). The cytotoxicity of the compounds was assessed in Vero and A549 cells and their selectivity towards human kinases including JAK2 and EGFR were undertaken. We identified compound 5n and 5m as sub-micromolar inhibitors, with equivalent anti-malarial activity to Chloroquine (CQ). Compounds 5d and 5k, μM inhibitors of Pf, displayed improved cytotoxicity with weak inhibition of the human kinases.
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Affiliation(s)
- Oraphan Phuangsawai
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Paul Beswick
- School of Life Sciences, University of Sussex, Brighton BN1 9QJ, United Kingdom
| | - Siriluk Ratanabunyong
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Lueacha Tabtimmai
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Praphasri Suphakun
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Phongphat Obounchoey
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Interdisciplinary Program in Genetic Engineering, Graduate School, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Pimonwan Srisook
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Natharinee Horata
- Faculty of Medicinal Technology, Huachiew Chalermprakiet University, Samut Prakarn 10540, Thailand
| | - Irina Chuckowree
- School of Life Sciences, University of Sussex, Brighton BN1 9QJ, United Kingdom
| | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Simon E Ward
- School of Life Sciences, University of Sussex, Brighton BN1 9QJ, United Kingdom.
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - M Paul Gleeson
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.
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29
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Song T, Wang Z, Ji F, Feng Y, Fan Y, Chai G, Li X, Li Z, Zhang Z. Deactivation of Mcl-1 by Dual-Function Small-Molecule Inhibitors Targeting the Bcl-2 Homology 3 Domain and Facilitating Mcl-1 Ubiquitination. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606543] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ting Song
- State Key Laboratory of Fine Chemicals; Zhang Dayu School of Chemistry; Dalian University of Technology; Dalian, Liaoning China
| | - Ziqian Wang
- School of Chemistry; Dalian University of Technology; Dalian, Liaoning China
| | - Fangling Ji
- School of Life Science and Technology; Dalian University of Technology; China
| | - Yingang Feng
- Shandong Key Laboratory of Synthetic Biology; CAS Key Laboratory of Biofuels; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Qingdao, Shandong China
| | - Yudan Fan
- School of Life Science and Technology; Dalian University of Technology; China
| | - Gaobo Chai
- School of Chemistry; Dalian University of Technology; Dalian, Liaoning China
| | - Xiangqian Li
- Institute of Oceanology; Chinese Academy of Sciences; Qingdao, Shandong China
| | - Zhiqiang Li
- School of Chemistry; Dalian University of Technology; Dalian, Liaoning China
| | - Zhichao Zhang
- School of Chemistry; Dalian University of Technology; Dalian, Liaoning China
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30
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Song T, Wang Z, Ji F, Feng Y, Fan Y, Chai G, Li X, Li Z, Zhang Z. Deactivation of Mcl-1 by Dual-Function Small-Molecule Inhibitors Targeting the Bcl-2 Homology 3 Domain and Facilitating Mcl-1 Ubiquitination. Angew Chem Int Ed Engl 2016; 55:14250-14256. [DOI: 10.1002/anie.201606543] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 08/26/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Ting Song
- State Key Laboratory of Fine Chemicals; Zhang Dayu School of Chemistry; Dalian University of Technology; Dalian, Liaoning China
| | - Ziqian Wang
- School of Chemistry; Dalian University of Technology; Dalian, Liaoning China
| | - Fangling Ji
- School of Life Science and Technology; Dalian University of Technology; China
| | - Yingang Feng
- Shandong Key Laboratory of Synthetic Biology; CAS Key Laboratory of Biofuels; Qingdao Institute of Bioenergy and Bioprocess Technology; Chinese Academy of Sciences; Qingdao, Shandong China
| | - Yudan Fan
- School of Life Science and Technology; Dalian University of Technology; China
| | - Gaobo Chai
- School of Chemistry; Dalian University of Technology; Dalian, Liaoning China
| | - Xiangqian Li
- Institute of Oceanology; Chinese Academy of Sciences; Qingdao, Shandong China
| | - Zhiqiang Li
- School of Chemistry; Dalian University of Technology; Dalian, Liaoning China
| | - Zhichao Zhang
- School of Chemistry; Dalian University of Technology; Dalian, Liaoning China
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31
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Durlacher CT, Li ZL, Chen XW, He ZX, Zhou SF. An update on the pharmacokinetics and pharmacodynamics of alisertib, a selective Aurora kinase A inhibitor. Clin Exp Pharmacol Physiol 2016; 43:585-601. [DOI: 10.1111/1440-1681.12571] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 03/12/2016] [Accepted: 03/15/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Cameron T Durlacher
- Department of Pharmaceutical Sciences; College of Pharmacy; University of South Florida; Tampa FL USA
| | - Zhi-Ling Li
- Department of Pharmacy; Shanghai Children's Hospital; Shanghai Jiao Tong University; Shanghai China
| | - Xiao-Wu Chen
- Department of General Surgery; The First People's Hospital of Shunde Affiliated to Southern Medical University; Shunde Foshan Guangdong
| | - Zhi-Xu He
- Guizhou Provincial Key Laboratory for Regenerative Medicine; Stem Cell and Tissue Engineering Research Centre & Sino-US Joint Laboratory for Medical Sciences; Guizhou Medical University; Guiyang Guizhou China
| | - Shu-Feng Zhou
- Department of Pharmaceutical Sciences; College of Pharmacy; University of South Florida; Tampa FL USA
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32
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Grigoroudis AI, Kontopidis G. Preparation of CDK/Cyclin Inhibitor Complexes for Structural Determination. Methods Mol Biol 2016; 1336:29-45. [PMID: 26231706 DOI: 10.1007/978-1-4939-2926-9_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The abundance of biochemical and structural knowledge on the Cyclin-Dependent Kinases (CDKs) has provided a comprehensive but not exhaustive insight into the molecular determinants that govern their function mechanisms. The implementation of structural and functional CDK models towards developing novel anticancer strategies that will specifically target individual or multiple CDKs remains a critical need.More than 250 CDKs crystal structures are available to-date, including truncated or whole, modified or not, active or inactive forms, co-crystallized with the cyclins and/or their respective putative inhibitors, though, to our knowledge, there is no NMR solved structure available to date. We hitherto attempt to provide a useful guide from protein production to crystallization for CDK/Inhibitors complexes based on an overview of the already elucidated CDK structures, constructs and the preferable expression vectors in each case, in order to yield the respective crystals.
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Affiliation(s)
- Asterios I Grigoroudis
- Department of Biochemistry, Veterinary School, University of Thessaly, Trikalon 224 Str., Karditsa, 43100, Greece
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33
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Galindo-Murillo R, Aguilar-Suárez LE, Barroso-Flores J. A mixed DFT-MD methodology for the in silico development of drug releasing macrocycles. Calix and thia-calix[N]arenes as carriers for Bosutinib and Sorafenib. J Comput Chem 2015; 37:940-6. [PMID: 26714797 DOI: 10.1002/jcc.24281] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 11/16/2015] [Indexed: 12/12/2022]
Abstract
Interaction energies between a family of 36 calix[n]arenes, their corresponding thia- analogues, and two commercially available second generation tyrosine kinase III inhibitors-Bosutinib and Sorafenib-were calculated through DFT methods at the B97D/6-31G(d,p) level of theory, based on Natural Population Analysis, for the in silico development of suitable drug carriers based on the aforementioned macrocycles which can increase their bioavailability and in turn their pharmaceutical efficiency. Molecular Dynamics simulations (production runs: +500 ns) using the General Amber Force Field were also carried out in order to assess the releasing process of these drugs in an explicit aqueous environment. In total, 144 host-guest complexes are examined. According to our results, five-membered -SO3H and i-Pr functionalized-calixarenes are the best candidates for Sorafenib-carriers while six-membered ones -SO3H and C2H4NH2 functionalized- are the lead candidates for Bosutinib-carriers.
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Affiliation(s)
- Rodrigo Galindo-Murillo
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, Utah, 84112
| | | | - Joaquín Barroso-Flores
- Centro Conjunto De Investigación En Química Sustentable UAEM-UNAM, Toluca, Estado De México, 50200, Mexico
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34
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Alexander LT, Möbitz H, Drueckes P, Savitsky P, Fedorov O, Elkins JM, Deane CM, Cowan-Jacob SW, Knapp S. Type II Inhibitors Targeting CDK2. ACS Chem Biol 2015; 10:2116-25. [PMID: 26158339 DOI: 10.1021/acschembio.5b00398] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Kinases can switch between active and inactive conformations of the ATP/Mg(2+) binding motif DFG, which has been explored for the development of type I or type II inhibitors. However, factors modulating DFG conformations remain poorly understood. We chose CDK2 as a model system to study the DFG in-out transition on a target that was thought to have an inaccessible DFG-out conformation. We used site-directed mutagenesis of key residues identified in structural comparisons in conjunction with biochemical and biophysical characterization of the generated mutants. As a result, we identified key residues that facilitate the DFG-out movement, facilitating binding of type II inhibitors. However, surprisingly, we also found that wild type CDK2 is able to bind type II inhibitors. Using protein crystallography structural analysis of the CDK2 complex with an aminopyrimidine-phenyl urea inhibitor (K03861) revealed a canonical type II binding mode and the first available type II inhibitor CDK2 cocrystal structure. We found that the identified type II inhibitors compete with binding of activating cyclins. In addition, analysis of the binding kinetics of the identified inhibitors revealed slow off-rates. The study highlights the importance of residues that may be distant to the ATP binding pocket in modulating the energetics of the DFG-out transition and hence inhibitor binding. The presented data also provide the foundation for a new class of slow off-rate cyclin-competitive CDK2 inhibitors targeting the inactive DFG-out state of this important kinase target.
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Affiliation(s)
- Leila T. Alexander
- Structural
Genomics Consortium, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
- Department
of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, United Kingdom
| | - Henrik Möbitz
- Novartis Institutes of Biomedical Research, Basel, Switzerland, Novartis Pharma AG, Postfach, CH-4002 Basel, Switzerland
| | - Peter Drueckes
- Novartis Institutes of Biomedical Research, Basel, Switzerland, Novartis Pharma AG, Postfach, CH-4002 Basel, Switzerland
| | - Pavel Savitsky
- Structural
Genomics Consortium, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Oleg Fedorov
- Structural
Genomics Consortium, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
- Target
Discovery Institute, University of Oxford, NDM Research Building, Roosevelt
Drive, Oxford, OX3 7FZ, United Kingdom
| | - Jonathan M. Elkins
- Structural
Genomics Consortium, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
- Target
Discovery Institute, University of Oxford, NDM Research Building, Roosevelt
Drive, Oxford, OX3 7FZ, United Kingdom
| | - Charlotte M. Deane
- Department
of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, United Kingdom
| | - Sandra W. Cowan-Jacob
- Novartis Institutes of Biomedical Research, Basel, Switzerland, Novartis Pharma AG, Postfach, CH-4002 Basel, Switzerland
| | - Stefan Knapp
- Structural
Genomics Consortium, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
- Target
Discovery Institute, University of Oxford, NDM Research Building, Roosevelt
Drive, Oxford, OX3 7FZ, United Kingdom
- Institute
for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str.
9, D-60438 Frankfurt
am Main, Germany
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35
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Anscombe E, Meschini E, Mora-Vidal R, Martin MP, Staunton D, Geitmann M, Danielson UH, Stanley WA, Wang LZ, Reuillon T, Golding BT, Cano C, Newell DR, Noble MEM, Wedge SR, Endicott JA, Griffin RJ. Identification and Characterization of an Irreversible Inhibitor of CDK2. CHEMISTRY & BIOLOGY 2015; 22:1159-64. [PMID: 26320860 PMCID: PMC4579270 DOI: 10.1016/j.chembiol.2015.07.018] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 07/02/2015] [Accepted: 07/24/2015] [Indexed: 01/04/2023]
Abstract
Irreversible inhibitors that modify cysteine or lysine residues within a protein kinase ATP binding site offer, through their distinctive mode of action, an alternative to ATP-competitive agents. 4-((6-(Cyclohexylmethoxy)-9H-purin-2-yl)amino)benzenesulfonamide (NU6102) is a potent and selective ATP-competitive inhibitor of CDK2 in which the sulfonamide moiety is positioned close to a pair of lysine residues. Guided by the CDK2/NU6102 structure, we designed 6-(cyclohexylmethoxy)-N-(4-(vinylsulfonyl)phenyl)-9H-purin-2-amine (NU6300), which binds covalently to CDK2 as shown by a co-complex crystal structure. Acute incubation with NU6300 produced a durable inhibition of Rb phosphorylation in SKUT-1B cells, consistent with it acting as an irreversible CDK2 inhibitor. NU6300 is the first covalent CDK2 inhibitor to be described, and illustrates the potential of vinyl sulfones for the design of more potent and selective compounds.
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Affiliation(s)
- Elizabeth Anscombe
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Elisa Meschini
- Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Regina Mora-Vidal
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Mathew P Martin
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - David Staunton
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | | | - U Helena Danielson
- Beactica AB, Box 567, 751 22 Uppsala, Sweden; Department of Chemistry-BMC, Uppsala University, 751 23 Uppsala, Sweden
| | - Will A Stanley
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Lan Z Wang
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Tristan Reuillon
- Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Bernard T Golding
- Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
| | - Celine Cano
- Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - David R Newell
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Martin E M Noble
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Stephen R Wedge
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Jane A Endicott
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| | - Roger J Griffin
- Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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Galat A. Multidimensional Drift of Sequence Attributes and Functional Profiles in the Superfamily of the Three-Finger Proteins and Their Structural Homologues. J Chem Inf Model 2015; 55:2026-41. [DOI: 10.1021/acs.jcim.5b00322] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Andrzej Galat
- Commissariat à
l’Energie
Atomique, Direction des Sciences du Vivant, Institut de Biologie et
de Technologies de Saclay, Service d’Ingénierie Moléculaire
des Protéines, F-91191 Gif sur Yvette, France
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Yokoyama T, Kosaka Y, Mizuguchi M. Structural Insight into the Interactions between Death-Associated Protein Kinase 1 and Natural Flavonoids. J Med Chem 2015; 58:7400-8. [PMID: 26322379 DOI: 10.1021/acs.jmedchem.5b00893] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Death-associated protein kinase 1 (DAPK1) is a 160 kDa serine/threonine protein kinase that belongs to the Ca(2+)/calmodulin-dependent protein kinase subfamily. DAPK1 is a possible target for the treatment of acute ischemic stroke and endometrial adenocarcinomas. In the present study, we investigated the binding characteristics of 17 natural flavonoids to DAPK1 using a 1-anilinonaphthalene-8-sulfonic acid competitive binding assay and revealed that morin was the strongest binder among the selected compounds. The crystallographic analysis of DAPK1 and 7 selected flavonoid complexes revealed the structure-binding affinity relationship in atomic-level detail. It was suggested that the high affinity of morin could be accounted for by the ionic interaction between 2'-OH and K42 and that such an interaction would not take place with either cyclin-dependent protein kinases or PIM kinases because of their broader entrance regions. Thus, morin would be a more selective inhibitor of DAPK1 than either of these other types of kinases. In addition, we found that the binding of kaempferol to DAPK1 was associated with a chloride ion. The present study provides a better understanding of the molecular properties of the ATP site of DAPK1 and may be useful for the design of specific DAPK1 inhibitors.
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Affiliation(s)
- Takeshi Yokoyama
- Faculty of Pharmaceutical Sciences, University of Toyama , 2630 Sugitani, Toyama 930-0914, Japan
| | - Yuto Kosaka
- Faculty of Pharmaceutical Sciences, University of Toyama , 2630 Sugitani, Toyama 930-0914, Japan
| | - Mineyuki Mizuguchi
- Faculty of Pharmaceutical Sciences, University of Toyama , 2630 Sugitani, Toyama 930-0914, Japan
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Lawrence HR, Mahajan K, Luo Y, Zhang D, Tindall N, Huseyin M, Gevariya H, Kazi S, Ozcan S, Mahajan NP, Lawrence NJ. Development of novel ACK1/TNK2 inhibitors using a fragment-based approach. J Med Chem 2015; 58:2746-63. [PMID: 25699576 DOI: 10.1021/jm501929n] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The tyrosine kinase ACK1, a critical signal transducer regulating survival of hormone-refractory cancers, is an important therapeutic target, for which there are no selective inhibitors in clinical trials to date. This work reports the discovery of novel and potent inhibitors for ACK1 tyrosine kinase (also known as TNK2) using an innovative fragment-based approach. Focused libraries were designed and synthesized by selecting fragments from reported ACK inhibitors to create hybrid structures in a mix and match process. The hybrid library was screened by enzyme-linked immunosorbent assay-based kinase inhibition and (33)P HotSpot assays. Systematic structure-activity relationship studies led to the identification of compound (R)-9b, which shows potent in vitro (IC50 = 56 nM, n = 3, (33)P HotSpot assay) and in vivo (IC50 < 2 μM, human cancer cell lines) ACK1 inhibition. Both (R)-9b and (S)-9b were stable in human plasma and displayed a long half-life (t(1/2) > 6 h).
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Affiliation(s)
- Harshani R Lawrence
- §Department of Oncologic Sciences, University of South Florida, Tampa, Florida 33620, United States
| | - Kiran Mahajan
- §Department of Oncologic Sciences, University of South Florida, Tampa, Florida 33620, United States
| | | | | | | | | | | | | | | | - Nupam P Mahajan
- §Department of Oncologic Sciences, University of South Florida, Tampa, Florida 33620, United States
| | - Nicholas J Lawrence
- §Department of Oncologic Sciences, University of South Florida, Tampa, Florida 33620, United States
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39
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Badrinarayan P, Sastry GN. Specificity rendering 'hot-spots' for aurora kinase inhibitor design: the role of non-covalent interactions and conformational transitions. PLoS One 2014; 9:e113773. [PMID: 25485544 PMCID: PMC4259475 DOI: 10.1371/journal.pone.0113773] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 10/29/2014] [Indexed: 11/19/2022] Open
Abstract
The present study examines the conformational transitions occurring among the major structural motifs of Aurora kinase (AK) concomitant with the DFG-flip and deciphers the role of non-covalent interactions in rendering specificity. Multiple sequence alignment, docking and structural analysis of a repertoire of 56 crystal structures of AK from Protein Data Bank (PDB) has been carried out. The crystal structures were systematically categorized based on the conformational disposition of the DFG-loop [in (DI) 42, out (DO) 5 and out-up (DOU) 9], G-loop [extended (GE) 53 and folded (GF) 3] and αC-helix [in (CI) 42 and out (CO) 14]. The overlapping subsets on categorization show the inter-dependency among structural motifs. Therefore, the four distinct possibilities a) 2W1C (DI, CI, GE) b) 3E5A (DI, CI, GF) c) 3DJ6 (DI, CO, GF) d) 3UNZ (DOU, CO, GF) along with their co-crystals and apo-forms were subjected to molecular dynamics simulations of 40 ns each to evaluate the variations of individual residues and their impact on forming interactions. The non-covalent interactions formed by the 157 AK co-crystals with different regions of the binding site were initially studied with the docked complexes and structure interaction fingerprints. The frequency of the most prominent interactions was gauged in the AK inhibitors from PDB and the four representative conformations during 40 ns. Based on this study, seven major non-covalent interactions and their complementary sites in AK capable of rendering specificity have been prioritized for the design of different classes of inhibitors.
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Affiliation(s)
- Preethi Badrinarayan
- Molecular Modeling Group, Organic Chemical Sciences, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad- 500 607, India
| | - G. Narahari Sastry
- Molecular Modeling Group, Organic Chemical Sciences, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad- 500 607, India
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40
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Carry JC, Clerc F, Minoux H, Schio L, Mauger J, Nair A, Parmantier E, Le Moigne R, Delorme C, Nicolas JP, Krick A, Abécassis PY, Crocq-Stuerga V, Pouzieux S, Delarbre L, Maignan S, Bertrand T, Bjergarde K, Ma N, Lachaud S, Guizani H, Lebel R, Doerflinger G, Monget S, Perron S, Gasse F, Angouillant-Boniface O, Filoche-Rommé B, Murer M, Gontier S, Prévost C, Monteiro ML, Combeau C. SAR156497, an exquisitely selective inhibitor of aurora kinases. J Med Chem 2014; 58:362-75. [PMID: 25369539 DOI: 10.1021/jm501326k] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The Aurora family of serine/threonine kinases is essential for mitosis. Their crucial role in cell cycle regulation and aberrant expression in a broad range of malignancies have been demonstrated and have prompted intensive search for small molecule Aurora inhibitors. Indeed, over 10 of them have reached the clinic as potential anticancer therapies. We report herein the discovery and optimization of a novel series of tricyclic molecules that has led to SAR156497, an exquisitely selective Aurora A, B, and C inhibitor with in vitro and in vivo efficacy. We also provide insights into its mode of binding to its target proteins, which could explain its selectivity.
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Affiliation(s)
- Jean-Christophe Carry
- Oncology Drug Discovery, ‡Structure Design Informatics, §Disposition Safety Animal Research, ∥Chemical Development, and ⊥Analytical Sciences, Sanofi , 13 Quai Jules Guesde, 94403 Vitry-sur-Seine, France
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41
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Gustafson WC, Meyerowitz JG, Nekritz EA, Chen J, Benes C, Charron E, Simonds EF, Seeger R, Matthay KK, Hertz NT, Eilers M, Shokat KM, Weiss WA. Drugging MYCN through an allosteric transition in Aurora kinase A. Cancer Cell 2014; 26:414-427. [PMID: 25175806 PMCID: PMC4160413 DOI: 10.1016/j.ccr.2014.07.015] [Citation(s) in RCA: 202] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 05/31/2014] [Accepted: 07/17/2014] [Indexed: 12/11/2022]
Abstract
MYC proteins are major drivers of cancer yet are considered undruggable because their DNA binding domains are composed of two extended alpha helices with no apparent surfaces for small-molecule binding. Proteolytic degradation of MYCN protein is regulated in part by a kinase-independent function of Aurora A. We describe a class of inhibitors that disrupts the native conformation of Aurora A and drives the degradation of MYCN protein across MYCN-driven cancers. Comparison of cocrystal structures with structure-activity relationships across multiple inhibitors and chemotypes, coupled with mechanistic studies and biochemical assays, delineates an Aurora A conformation-specific effect on proteolytic degradation of MYCN, rather than simple nanomolar-level inhibition of Aurora A kinase activity.
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Affiliation(s)
- William Clay Gustafson
- Department of Pediatrics, UCSF Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Justin Gabriel Meyerowitz
- Departments of Neurology and Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Erin A Nekritz
- Department of Pediatrics, UCSF Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Justin Chen
- Departments of Neurology and Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Cyril Benes
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02114, USA
| | - Elise Charron
- Department of Pediatrics, UCSF Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA 94158, USA; Departments of Neurology and Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Erin F Simonds
- Departments of Neurology and Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Robert Seeger
- Division of Hematology/Oncology, Children's Hospital Los Angeles, 4650 Sunset Boulevard, Mailstop #57, Los Angeles, CA 90027, USA
| | - Katherine K Matthay
- Department of Pediatrics, UCSF Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Nicholas T Hertz
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Martin Eilers
- Theodor Boveri Institute, Biocenter, University of Wurzburg, Am Hubland, 97074 Würzburg, Germany
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - William A Weiss
- Department of Pediatrics, UCSF Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA 94158, USA; Departments of Neurology and Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.
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Zorba A, Buosi V, Kutter S, Kern N, Pontiggia F, Cho YJ, Kern D. Molecular mechanism of Aurora A kinase autophosphorylation and its allosteric activation by TPX2. eLife 2014; 3:e02667. [PMID: 24867643 PMCID: PMC4032492 DOI: 10.7554/elife.02667] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
We elucidate the molecular mechanisms of two distinct activation strategies (autophosphorylation and TPX2-mediated activation) in human Aurora A kinase. Classic allosteric activation is in play where either activation loop phosphorylation or TPX2 binding to a conserved hydrophobic groove shifts the equilibrium far towards the active conformation. We resolve the controversy about the mechanism of autophosphorylation by demonstrating intermolecular autophosphorylation in a long-lived dimer by combining X-ray crystallography with functional assays. We then address the allosteric activation by TPX2 through activity assays and the crystal structure of a domain-swapped dimer of dephosphorylated Aurora A and TPX21−25. While autophosphorylation is the key regulatory mechanism in the centrosomes in the early stages of mitosis, allosteric activation by TPX2 of dephosphorylated Aurora A could be at play in the spindle microtubules. The mechanistic insights into autophosphorylation and allosteric activation by TPX2 binding proposed here, may have implications for understanding regulation of other protein kinases. DOI:http://dx.doi.org/10.7554/eLife.02667.001 The kinase, Aurora A, is a human protein that is needed for cells to divide normally. Kinases are enzymes that control other proteins by adding phosphate groups to these proteins; however, like other kinases, Aurora A must first be activated or ‘switched on’ before it can do this. Aurora A kinase can be switched on in two ways: by having a phosphate group added to its ‘activation loop’; or by binding to another protein called TPX2. Also like other kinases, Aurora A can self-activate, but the details of this process are not understood. Does a single Aurora A kinase add a phosphate group to its own activation loop, or does one Aurora A kinase activate a second? Furthermore, it is not clear how binding to TPX2 can activate an Aurora A kinase without adding a phosphate group to the activation loop. Zorba, Buosi et al. now show that Aurora A kinases that have been activated in different ways—via the addition of a phosphate group or binding to TPX2—are equally good at adding phosphate groups to other proteins. Zorba, Buosi et al. also worked out the three-dimensional shapes of the kinases activated in these two ways—since many proteins change shape when they are switched on—and found that they were also the same. Finally, it was shown that self-activation involves two Aurora A kinases binding to each other, and one kinase adding a phosphate group to the other, rather than a single kinase adding a phosphate group to itself. Since other protein kinases can be activated in similar ways to Aurora A, the findings of Zorba, Buosi et al. might also help us to understand how other protein kinases can be switched ‘on’ or ‘off’. And, as mutations in Aurora A have been linked to the development of cancer, uncovering how this kinase is controlled could help efforts to design new drugs to treat this disease. DOI:http://dx.doi.org/10.7554/eLife.02667.002
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Affiliation(s)
- Adelajda Zorba
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| | - Vanessa Buosi
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| | - Steffen Kutter
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| | - Nadja Kern
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| | - Francesco Pontiggia
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| | - Young-Jin Cho
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| | - Dorothee Kern
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
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Hari SB, Merritt EA, Maly DJ. Sequence determinants of a specific inactive protein kinase conformation. ACTA ACUST UNITED AC 2014; 20:806-15. [PMID: 23790491 DOI: 10.1016/j.chembiol.2013.05.005] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 04/18/2013] [Accepted: 05/09/2013] [Indexed: 02/07/2023]
Abstract
Only a small percentage of protein kinases have been shown to adopt a distinct inactive ATP-binding site conformation, called the Asp-Phe-Gly-out (DFG-out) conformation. Given the high degree of homology within this enzyme family, we sought to understand the basis of this disparity on a sequence level. We identified two residue positions that sensitize mitogen-activated protein kinases (MAPKs) to inhibitors that stabilize the DFG-out inactive conformation. After characterizing the structure and dynamics of an inhibitor-sensitive MAPK mutant, we demonstrated the generality of this strategy by sensitizing a kinase (apoptosis signal-regulating kinase 1) not in the MAPK family to several DFG-out stabilizing ligands, using the same residue positions. The use of specific inactive conformations may aid the study of noncatalytic roles of protein kinases, such as binding partner interactions and scaffolding effects.
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Affiliation(s)
- Sanjay B Hari
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
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44
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Lavogina D, Enkvist E, Viht K, Uri A. Long Residence Times Revealed by Aurora A Kinase-Targeting Fluorescent Probes Derived from Inhibitors MLN8237 and VX-689. Chembiochem 2014; 15:443-50. [DOI: 10.1002/cbic.201300613] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Indexed: 11/10/2022]
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Jørgensen R, Pesnot T, Lee HJ, Palcic MM, Wagner GK. Base-modified donor analogues reveal novel dynamic features of a glycosyltransferase. J Biol Chem 2013; 288:26201-26208. [PMID: 23836908 PMCID: PMC3764824 DOI: 10.1074/jbc.m113.465963] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Glycosyltransferases (GTs) are enzymes that are involved, as Nature's "glycosylation reagents," in many fundamental biological processes including cell adhesion and blood group biosynthesis. Although of similar importance to that of other large enzyme families such as protein kinases and proteases, the undisputed potential of GTs for chemical biology and drug discovery has remained largely unrealized to date. This is due, at least in part, to a relative lack of GT inhibitors and tool compounds for structural, mechanistic, and cellular studies. In this study, we have used a novel class of GT donor analogues to obtain new structural and enzymological information for a representative blood group GT. These analogues interfere with the folding of an internal loop and the C terminus, which are essential for catalysis. Our experiments have led to the discovery of an entirely new active site folding mode for this enzyme family, which can be targeted in inhibitor development, similar to the DFG motif in protein kinases. Taken together, our results provide new insights into substrate binding, dynamics, and utilization in this important enzyme family, which can very likely be harnessed for the rational development of new GT inhibitors and probes.
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Affiliation(s)
- René Jørgensen
- From the Department of Microbiology and Infection Control, Statens Serum Institut, DK-2300 Copenhagen S, Denmark,; the Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-1799 Copenhagen V, Denmark,.
| | - Thomas Pesnot
- the University of East Anglia, School of Pharmacy, Norwich NR47TJ, United Kingdom
| | - Ho Jun Lee
- the Department of Chemistry, University of Alberta, Edmonton, Alberta T6G2G2, Canada, and
| | - Monica M Palcic
- the Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-1799 Copenhagen V, Denmark
| | - Gerd K Wagner
- the King's College London, School of Biomedical Sciences, Institute of Pharmaceutical Science and Department of Chemistry, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom.
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Schonbrunn E, Betzi S, Alam R, Martin MP, Becker A, Han H, Francis R, Chakrasali R, Jakkaraj S, Kazi A, Sebti SM, Cubitt CL, Gebhard AW, Hazlehurst LA, Tash JS, Georg GI. Development of highly potent and selective diaminothiazole inhibitors of cyclin-dependent kinases. J Med Chem 2013; 56:3768-82. [PMID: 23600925 DOI: 10.1021/jm301234k] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cyclin-dependent kinases (CDKs) are serine/threonine protein kinases that act as key regulatory elements in cell cycle progression. We describe the development of highly potent diaminothiazole inhibitors of CDK2 (IC50 = 0.0009-0.0015 μM) from a single hit compound with weak inhibitory activity (IC50 = 15 μM), discovered by high-throughput screening. Structure-based design was performed using 35 cocrystal structures of CDK2 liganded with distinct analogues of the parent compound. The profiling of compound 51 against a panel of 339 kinases revealed high selectivity for CDKs, with preference for CDK2 and CDK5 over CDK9, CDK1, CDK4, and CDK6. Compound 51 inhibited the proliferation of 13 out of 15 cancer cell lines with IC50 values between 0.27 and 6.9 μM, which correlated with the complete suppression of retinoblastoma phosphorylation and the onset of apoptosis. Combined, the results demonstrate the potential of this new inhibitors series for further development into CDK-specific chemical probes or therapeutics.
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Affiliation(s)
- Ernst Schonbrunn
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, USA.
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Aurora kinase inhibitors reveal mechanisms of HURP in nucleation of centrosomal and kinetochore microtubules. Proc Natl Acad Sci U S A 2013; 110:E1779-87. [PMID: 23610398 DOI: 10.1073/pnas.1220523110] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The overexpression of Aurora kinases in multiple tumors makes these kinases appealing targets for the development of anticancer therapies. This study identified two small molecules with a furanopyrimidine core, IBPR001 and IBPR002, that target Aurora kinases and induce a DFG conformation change at the ATP site of Aurora A. Our results demonstrate the high potency of the IBPR compounds in reducing tumorigenesis in a colorectal cancer xenograft model in athymic nude mice. Human hepatoma up-regulated protein (HURP) is a substrate of Aurora kinase A, which plays a crucial role in the stabilization of kinetochore fibers. This study used the IBPR compounds as well as MLN8237, a proven Aurora A inhibitor, as chemical probes to investigate the molecular role of HURP in mitotic spindle formation. These compounds effectively eliminated HURP phosphorylation, thereby revealing the coexistence and continuous cycling of HURP between unphosphorylated and phosphorylated forms that are associated, respectively, with microtubules emanating from centrosomes and kinetochores. Furthermore, these compounds demonstrate a spatial hierarchical preference for HURP in the attachment of microtubules extending from the mother to the daughter centrosome. The finding of inequality in the centrosomal microtubules revealed by these small molecules provides a versatile tool for the discovery of new cell-division molecules for the development of antitumor drugs.
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48
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Le LTT, Vu HL, Nguyen CH, Molla A. Basal aurora kinase B activity is sufficient for histone H3 phosphorylation in prophase. Biol Open 2013; 2:379-86. [PMID: 23616922 PMCID: PMC3625866 DOI: 10.1242/bio.20133079] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 01/07/2013] [Indexed: 12/31/2022] Open
Abstract
Histone H3 phosphorylation is the hallmark of mitosis deposited by aurora kinase B. Benzo[e]pyridoindoles are a family of potent, broad, ATP-competitive aurora kinase inhibitors. However, benzo[e]pyridoindole C4 only inhibits histone H3 phosphorylation in prophase but not in metaphase. Under the C4 treatment, the cells enter into mitosis with dephosphorylated histone H3, assemble chromosomes normally and progress to metaphase, and then to anaphase. C4 also induces lagging chromosome in anaphase but we demonstrated that these chromosome compaction defects are not related to the absence of H3 phosphorylation in prophase. As a result of C4 action, mitosis lasts longer and the cell cycle is slowed down. We reproduced the mitotic defects with reduced concentrations of potent pan aurora kinase as well as with a specific aurora B ATP-competitive inhibitor; we therefore propose that histone H3 phosphorylation and anaphase chromosome compaction involve the basal activity of aurora kinase B. Our data suggest that aurora kinase B is progressively activated at mitosis entry and at anaphase onset. The full activation of aurora kinase B by its partners, in prometaphase, induces a shift in the catalytic domain of aurora B that modifies its affinity for ATP. These waves of activation/deactivation of aurora B correspond to different conformations of the chromosomal complex revealed by FRAP. The presence of lagging chromosomes may have deleterious consequences on the daughter cells and, unfortunately, the situation may be encountered in patients receiving treatment with aurora kinase inhibitors.
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Affiliation(s)
- Ly-Thuy-Tram Le
- CRI INSERM UJF U823, Institut Albert Bonniot, 38 706 La Tronche Cedex , France ; Permanent address: Da Nang University of Technology, Da Nang City, Vietnam
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Lawrence HR, Martin MP, Luo Y, Pireddu R, Yang H, Gevariya H, Ozcan S, Zhu JY, Kendig R, Rodriguez M, Elias R, Cheng JQ, Sebti SM, Schonbrunn E, Lawrence NJ. Development of o-chlorophenyl substituted pyrimidines as exceptionally potent aurora kinase inhibitors. J Med Chem 2012; 55:7392-7416. [PMID: 22803810 DOI: 10.1021/jm300334d] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The o-carboxylic acid substituted bisanilinopyrimidine 1 was identified as a potent hit (Aurora A IC(50) = 6.1 ± 1.0 nM) from in-house screening. Detailed structure-activity relationship (SAR) studies indicated that polar substituents at the para position of the B-ring are critical for potent activity. X-ray crystallography studies revealed that compound 1 is a type I inhibitor that binds the Aurora kinase active site in a DFG-in conformation. Structure-activity guided replacement of the A-ring carboxylic acid with halogens and incorporation of fluorine at the pyrimidine 5-position led to highly potent inhibitors of Aurora A that bind in a DFG-out conformation. B-Ring modifications were undertaken to improve the solubility and cell permeability. Compounds such as 9m with water-solubilizing moieties at the para position of the B-ring inhibited the autophosphorylation of Aurora A in MDA-MB-468 breast cancer cells.
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Affiliation(s)
- Harshani R Lawrence
- Department of Drug Discovery, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA.,Department of Chemical Biology Core, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA.,Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA
| | - Matthew P Martin
- Department of Drug Discovery, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Yunting Luo
- Department of Chemical Biology Core, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Roberta Pireddu
- Department of Drug Discovery, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Hua Yang
- Department of Drug Discovery, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Harsukh Gevariya
- Department of Drug Discovery, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Sevil Ozcan
- Department of Drug Discovery, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Jin-Yi Zhu
- Department of Drug Discovery, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Robert Kendig
- Department of Chemical Biology Core, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Mercedes Rodriguez
- Department of Chemical Biology Core, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA.,Department of Drug Discovery, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Roy Elias
- Department of Drug Discovery, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Jin Q Cheng
- Department of Molecular Oncology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA.,Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA
| | - Saïd M Sebti
- Department of Drug Discovery, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA.,Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA.,Department of Molecular Medicine, University of South Florida, Tampa, FL 33620, USA
| | - Ernst Schonbrunn
- Department of Drug Discovery, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA.,Department of Chemical Biology Core, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA.,Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA
| | - Nicholas J Lawrence
- Department of Drug Discovery, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA.,Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA
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Martin MP, Alam R, Betzi S, Ingles DJ, Zhu JY, Schönbrunn E. A novel approach to the discovery of small-molecule ligands of CDK2. Chembiochem 2012; 13:2128-36. [PMID: 22893598 DOI: 10.1002/cbic.201200316] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Indexed: 01/01/2023]
Abstract
In an attempt to identify novel small-molecule ligands of cyclin-dependent kinase 2 (CDK2) with potential as allosteric inhibitors, we have devised a robust and cost-effective fluorescence-based high-throughput screening assay. The assay is based on the specific interaction of CDK2 with the extrinsic fluorophore 8-anilino-1-naphthalene sulfonate (ANS), which binds to a large allosteric pocket adjacent to the ATP site. Hit compounds that displace ANS directly or indirectly from CDK2 are readily classified as ATP site binders or allosteric ligands through the use of staurosporine, which blocks the ATP site without displacing ANS. Pilot screening of 1453 compounds led to the discovery of 12 compounds with displacement activities (EC(50) values) ranging from 6 to 44 μM, all of which were classified as ATP-site-directed ligands. Four new type I inhibitor scaffolds were confirmed by X-ray crystallography. Although this small compound library contained only ATP-site-directed ligands, the application of this assay to large compound libraries has the potential to reveal previously unrecognized chemical scaffolds suitable for structure-based design of CDK2 inhibitors with new mechanisms of action.
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Affiliation(s)
- Mathew P Martin
- Drug Discovery Department, Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA
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