1
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Greber BJ. High-resolution cryo-EM of a small protein complex: The structure of the human CDK-activating kinase. Structure 2024:S0969-2126(24)00085-6. [PMID: 38565138 DOI: 10.1016/j.str.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/27/2023] [Accepted: 03/07/2024] [Indexed: 04/04/2024]
Abstract
The human CDK-activating kinase (CAK) is a multifunctional protein complex and key regulator of cell growth and division. Because of its critical functions in regulating the cell cycle and transcription initiation, it is a key target for multiple cancer drug discovery programs. However, the structure of the active human CAK, insights into its regulation, and its interactions with cellular substrates and inhibitors remained elusive until recently due to the lack of high-resolution structures of the intact complex. This review covers the progress in structure determination of the human CAK by cryogenic electron microscopy (cryo-EM), from early efforts to recent near-atomic resolution maps routinely resolved at 2Å or better. These results were enabled by the latest cryo-EM technologies introduced after the initial phase of the "resolution revolution" and allowed the application of high-resolution methods to new classes of molecular targets, including small protein complexes that were intractable using earlier technology.
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Affiliation(s)
- Basil J Greber
- Division of Structural Biology, The Institute of Cancer Research, London SW3 6JB, UK.
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2
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Cushing VI, Koh AF, Feng J, Jurgaityte K, Bondke A, Kroll SHB, Barbazanges M, Scheiper B, Bahl AK, Barrett AGM, Ali S, Kotecha A, Greber BJ. High-resolution cryo-EM of the human CDK-activating kinase for structure-based drug design. Nat Commun 2024; 15:2265. [PMID: 38480681 PMCID: PMC10937634 DOI: 10.1038/s41467-024-46375-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 02/23/2024] [Indexed: 03/17/2024] Open
Abstract
Rational design of next-generation therapeutics can be facilitated by high-resolution structures of drug targets bound to small-molecule inhibitors. However, application of structure-based methods to macromolecules refractory to crystallization has been hampered by the often-limiting resolution and throughput of cryogenic electron microscopy (cryo-EM). Here, we use high-resolution cryo-EM to determine structures of the CDK-activating kinase, a master regulator of cell growth and division, in its free and nucleotide-bound states and in complex with 15 inhibitors at up to 1.8 Å resolution. Our structures provide detailed insight into inhibitor interactions and networks of water molecules in the active site of cyclin-dependent kinase 7 and provide insights into the mechanisms contributing to inhibitor selectivity, thereby providing the basis for rational design of next-generation therapeutics. These results establish a methodological framework for the use of high-resolution cryo-EM in structure-based drug design.
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Affiliation(s)
- Victoria I Cushing
- The Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB, UK
| | - Adrian F Koh
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Achtseweg Noord 5, 5651, Eindhoven, The Netherlands
| | - Junjie Feng
- The Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB, UK
| | - Kaste Jurgaityte
- Division of Cancer, Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK
| | | | | | - Marion Barbazanges
- Department of Chemistry, Imperial College London, London, UK
- Institut Parisien de Chimie Moléculaire, Sorbonne Université, CNRS, 4 Place Jussieu, 75252, Paris Cedex 05, France
| | - Bodo Scheiper
- Department of Chemistry, Imperial College London, London, UK
| | - Ash K Bahl
- Carrick Therapeutics, Nova UCD, Bellfield Innovation Park, Dublin 4, Ireland
| | | | - Simak Ali
- Division of Cancer, Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK.
| | - Abhay Kotecha
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Achtseweg Noord 5, 5651, Eindhoven, The Netherlands.
| | - Basil J Greber
- The Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB, UK.
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3
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Zhu Y, Alqahtani S, Hu X. An Assessment of Dispersion-Corrected DFT Methods for Modeling Nonbonded Interactions in Protein Kinase Inhibitor Complexes. Molecules 2024; 29:304. [PMID: 38257217 DOI: 10.3390/molecules29020304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/30/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Accurate modeling of nonbonded interactions between protein kinases and their small molecule inhibitors is essential for structure-based drug design. Quantum chemical methods such as density functional theory (DFT) hold significant promise for quantifying the strengths of these key protein-ligand interactions. However, the accuracy of DFT methods can vary substantially depending on the choice of exchange-correlation functionals and associated basis sets. In this study, a comprehensive benchmarking of nine widely used DFT methods was carried out to identify an optimal approach for quantitative modeling of nonbonded interactions, balancing both accuracy and computational efficiency. From a database of 2139 kinase-inhibitor crystal structures, a diverse library of 49 nonbonded interaction motifs was extracted, encompassing CH-π, π-π stacking, cation-π, hydrogen bonding, and salt bridge interactions. The strengths of nonbonded interaction energies for all 49 motifs were calculated at the advanced CCSD(T)/CBS level of theory, which serve as references for a systematic benchmarking of BLYP, TPSS, B97, ωB97X, B3LYP, M062X, PW6B95, B2PLYP, and PWPB95 functionals with D3BJ dispersion correction alongside def2-SVP, def2-TZVP, and def2-QZVP basis sets. The RI, RIJK, and RIJCOSX approximations were used for selected functionals. It was found that the B3LYP/def2-TZVP and RIJK RI-B2PLYP/def2-QZVP methods delivered the best combination of accuracy and computational efficiency, making them well-suited for efficient modeling of nonbonded interactions responsible for molecular recognition of protein kinase inhibitors in their targets.
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Affiliation(s)
- Yan Zhu
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
| | - Saad Alqahtani
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
- Department of Chemistry, King Saud University, Riyadh 12372, Saudi Arabia
| | - Xiche Hu
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
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Czeleń P, Jeliński T, Skotnicka A, Szefler B, Szupryczyński K. ADMET and Solubility Analysis of New 5-Nitroisatine-Based Inhibitors of CDK2 Enzymes. Biomedicines 2023; 11:3019. [PMID: 38002019 PMCID: PMC10669656 DOI: 10.3390/biomedicines11113019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
The development of new substances with the ability to interact with a biological target is only the first stage in the process of the creation of new drugs. The 5-nitroisatin derivatives considered in this study are new inhibitors of cyclin-dependent kinase 2 (CDK2) intended for anticancer therapy. The research, carried out based on the ADMET (absorption, distribution, metabolism, excretion, toxicity) methods, allowed a basic assessment of the physicochemical parameters of the tested drugs to be made. The collected data clearly showed the good oral absorption, membrane permeability, and bioavailability of the tested substances. The analysis of the metabolite activity and toxicity of the tested drugs did not show any critical hazards in terms of the toxicity of the tested substances. The substances' low solubility in water meant that extended studies tested compounds were required, which helped to select solvents with a high dissolving capacity of the examined substances, such as DMSO or NMP. The use of aqueous binary mixtures based on these two solvents allowed a relatively high solubility with significantly reduced toxicity and environmental index compared to pure solvents to be maintained, which is important in the context of the search for green solvents for pharmaceutical use.
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Affiliation(s)
- Przemysław Czeleń
- Department of Physical Chemistry, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Kurpinskiego 5, 85-096 Bydgoszcz, Poland
| | - Tomasz Jeliński
- Department of Physical Chemistry, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Kurpinskiego 5, 85-096 Bydgoszcz, Poland
| | - Agnieszka Skotnicka
- Faculty of Chemical Technology and Engineering, Bydgoszcz University of Science and Technology, Seminaryjna 3, 85-326 Bydgoszcz, Poland
| | - Beata Szefler
- Department of Physical Chemistry, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Kurpinskiego 5, 85-096 Bydgoszcz, Poland
| | - Kamil Szupryczyński
- Doctoral School of Medical and Health Sciences, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Jagiellońska 13, 85-067 Bydgoszcz, Poland
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5
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Alshaye NA. Synthesis and in vitro anticancer activity of some 2-oxindoline derivatives as potential CDK2 inhibitors. J Biomol Struct Dyn 2023; 41:15009-15022. [PMID: 36927308 DOI: 10.1080/07391102.2023.2187222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 02/22/2023] [Indexed: 03/18/2023]
Abstract
Novel series of 2-oxindoline hydrazones 6a-h, 3-hydroxy-2-oxoindolines 9a-d and 2-oxoindolin-3-ylidenes 10a-d were prepared and assessed for their anticancer activity towards breast cancer cell line (MCF7). Compounds 6c, 6d, 6g, 9d, 10a and 10b (IC50 = 14.0 ± 0.7, 15.6 ± 0.7, 13.8 ± 0.7, 4.9 ± 0.2, 6.0 ± 0.3 and 10.8 ± 0.5 µM, respectively) showed the highest growth inhibition activity against MCF7 when compared to staurosporine (IC50 = 14.5 ± 0.7 µM). Cell cycle analysis exposed arrest at G1 phase for compounds 6c, 10 and 10b, at S phase for compounds 6d and 9d, and at G1/S phase for compound 6g. Apoptotic effect of compounds 6c, 6d, 6g, 9d, 10a and 10b was confirmed via their early and late apoptotic effects. A safety profile was revealed for compounds 6c, 6d, 6g, 9d, 10a and 10b on MCF10A treated normal cell. Also, compounds 6c and 10b displayed a promising CDK2 inhibition activity (IC50 = 0.22 ± 0.01, 0.25 ± 0.01 µM, respectively). Also, docking study revealed comparable interactions with the native ligand (5-bromoindirubin). ADMET computational studies forecast the promising pharmacokinetic profile of the targeted compounds.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Najla A Alshaye
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
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6
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Gupta A, Dagar G, Chauhan R, Sadida HQ, Almarzooqi SK, Hashem S, Uddin S, Macha MA, Akil ASAS, Pandita TK, Bhat AA, Singh M. Cyclin-dependent kinases in cancer: Role, regulation, and therapeutic targeting. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 135:21-55. [PMID: 37061333 DOI: 10.1016/bs.apcsb.2023.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Regulated cell division is one of the fundamental phenomena which is the basis of all life on earth. Even a single base pair mutation in DNA leads to the production of the dysregulated protein that can have catastrophic consequences. Cell division is tightly controlled and orchestrated by proteins called cyclins and cyclin-dependent kinase (CDKs), which serve as licensing factors during different phases of cell division. Dysregulated cell division is one of the most important hallmarks of cancer and is commonly associated with a mutation in cyclins and CDKs along with tumor suppressor proteins. Therefore, targeting the component of the cell cycle which leads to these characteristics would be an effective strategy for treating cancers. Specifically, Cyclin-dependent kinases (CDKs) involved in cell cycle regulation have been identified to be overexpressed in many cancers. Many studies indicate that oncogenesis occurs in cancerous cells by the overactivity of different CDKs, which impact cell cycle progression and checkpoint dysregulation which is responsible for development of tumor. The development of CDK inhibitors has emerged as a promising and novel approach for cancer treatment in both solid and hematological malignancies. Some of the novel CDK inhibitors have shown remarkable results in clinical trials, such as-Ribociclib®, Palbociclib® and Abemaciclib®, which are CDK4/6 inhibitors and have received FDA approval for the treatment of breast cancer. In this chapter, we discuss the molecular mechanism through which cyclins and CDKs regulate cell cycle progression and the emergence of cyclins and CDKs as rational targets in cancer. We also discuss recent advances in developing CDK inhibitors, which have emerged as a novel class of inhibitors, and their associated toxicities in recent years.
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Affiliation(s)
- Ashna Gupta
- Department of Medical Oncology, Dr B.R Ambedkar Institute Rotary Cancer Hospital All India Institute of Medical Sciences, New Delhi, India
| | - Gunjan Dagar
- Department of Medical Oncology, Dr B.R Ambedkar Institute Rotary Cancer Hospital All India Institute of Medical Sciences, New Delhi, India
| | - Ravi Chauhan
- Department of Medical Oncology, Dr B.R Ambedkar Institute Rotary Cancer Hospital All India Institute of Medical Sciences, New Delhi, India
| | - Hana Q Sadida
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Research Program, Sidra Medicine, Doha, Qatar
| | - Sara K Almarzooqi
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Research Program, Sidra Medicine, Doha, Qatar
| | - Sheema Hashem
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Shahab Uddin
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Muzafar A Macha
- Watson-Crick Centre for Molecular Medicine, Islamic University of Science and Technology, Awantipora, Jammu and Kashmir, India
| | - Ammira S Al-Shabeeb Akil
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Research Program, Sidra Medicine, Doha, Qatar
| | - Tej K Pandita
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, TX, United States
| | - Ajaz A Bhat
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Research Program, Sidra Medicine, Doha, Qatar.
| | - Mayank Singh
- Department of Medical Oncology, Dr B.R Ambedkar Institute Rotary Cancer Hospital All India Institute of Medical Sciences, New Delhi, India.
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7
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Designing and Synthesis of New Isatin Derivatives as Potential CDK2 Inhibitors. Int J Mol Sci 2022; 23:ijms23148046. [PMID: 35887396 PMCID: PMC9316372 DOI: 10.3390/ijms23148046] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/15/2022] [Accepted: 07/19/2022] [Indexed: 02/06/2023] Open
Abstract
Tumors are still one of the main causes of death; therefore, the search for new therapeutic agents that will enable the implementation of effective treatment is a significant challenge for modern pharmacy. One of the important factors contributing to the development of neoplastic diseases is the overexpression of enzymes responsible for the regulation of cell division processes such as cyclin-dependent kinases. Numerous studies and examples of already-developed drugs confirm that isatin is a convenient basis for the development of new groups of inhibitors for this class of enzyme. Therefore, in this work, a new group of potential inhibitors of the CDK2 enzyme, utilizing isatin derivatives and substituted benzoylhydrazines, has been designed based on the application of computational chemistry methods, such as docking and molecular dynamics, and their inhibiting ability was assessed. In the cases of the selected compounds, a synthesis method was developed, and the selected physicochemical properties of the newly synthesized derivatives were estimated. As part of the completed project, new compounds are developed which are potential inhibitors of the CDK2 enzyme.
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8
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Nurhayati APD, Rihandoko A, Fadlan A, Ghaissani SS, Jadid N, Setiawan E. Anti-cancer potency by induced apoptosis by molecular docking P53, caspase, cyclin D1, cytotoxicity analysis and phagocytosis activity of trisindoline 1,3 and 4. Saudi Pharm J 2022; 30:1345-1359. [PMID: 36249936 PMCID: PMC9563049 DOI: 10.1016/j.jsps.2022.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 06/17/2022] [Indexed: 11/27/2022] Open
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9
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Shi Z, Tian L, Qiang T, Li J, Xing Y, Ren X, Liu C, Liang C. From Structure Modification to Drug Launch: A Systematic Review of the Ongoing Development of Cyclin-Dependent Kinase Inhibitors for Multiple Cancer Therapy. J Med Chem 2022; 65:6390-6418. [PMID: 35485642 DOI: 10.1021/acs.jmedchem.1c02064] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Herein, we discuss more than 50 cyclin-dependent kinase (CDK) inhibitors that have been approved or have undergone clinical trials and their therapeutic application in multiple cancers. This review discusses the design strategies, structure-activity relationships, and efficacy performances of these selective or nonselective CDK inhibitors. The theoretical basis of early broad-spectrum CDK inhibitors is similar to the scope of chemotherapy, but because their toxicity is greater than the benefit, there is no clinical therapeutic window. The notion that selective CDK inhibitors have a safer therapeutic potential than pan-CDK inhibitors has been widely recognized during the research process. Four CDK4/6 inhibitors have been approved for the treatment of breast cancer or for prophylactic administration during chemotherapy to protect bone marrow and immune system function. Furthermore, the emerging strategies in the field of CDK inhibitors are summarized briefly, and CDKs continue to be widely pursued as emerging anticancer drug targets for drug discovery.
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Affiliation(s)
- Zhenfeng Shi
- Department of Urology Surgery Center, The People's Hospital of Xinjiang Uyghur Autonomous Region, Urumqi 830002, P. R. China
| | - Lei Tian
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China.,Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
| | - Taotao Qiang
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
| | - Jingyi Li
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
| | - Yue Xing
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
| | - Xiaodong Ren
- Medical College, Guizhou University, Guiyang 550025, P. R. China
| | - Chang Liu
- Zhuhai Jinan Selenium Source Nanotechnology Co., Ltd., Zhuhai 519030, P. R. China
| | - Chengyuan Liang
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an 710021, P. R. China
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10
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Ettl T, Schulz D, Bauer RJ. The Renaissance of Cyclin Dependent Kinase Inhibitors. Cancers (Basel) 2022; 14:293. [PMID: 35053461 PMCID: PMC8773807 DOI: 10.3390/cancers14020293] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/29/2021] [Accepted: 01/04/2022] [Indexed: 12/14/2022] Open
Abstract
Cyclin-dependent kinases (CDK) regulate cell cycle progression. During tumor development, altered expression and availability of CDKs strongly contribute to impaired cell proliferation, a hallmark of cancer. In recent years, targeted inhibition of CDKs has shown considerable therapeutic benefit in a variety of tumor entities. Their success is reflected in clinical approvals of specific CDK4/6 inhibitors for breast cancer. This review provides a detailed insight into the molecular mechanisms of CDKs as well as a general overview of CDK inhibition. It also summarizes the latest research approaches and current advances in the treatment of head and neck cancer with CDK inhibitors. Instead of monotherapies, combination therapies with CDK inhibitors may especially provide promising results in tumor therapy. Indeed, recent studies have shown a synergistic effect of CDK inhibition together with chemo- and radio- and immunotherapy in cancer treatment to overcome tumor evasion, which may lead to a renaissance of CDK inhibitors.
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Affiliation(s)
- Tobias Ettl
- Department of Oral and Maxillofacial Surgery, University Hospital Regensburg, 93053 Regensburg, Germany;
| | - Daniela Schulz
- Department of Oral and Maxillofacial Surgery, University Hospital Regensburg, 93053 Regensburg, Germany;
- Center for Medical Biotechnology, Department of Oral and Maxillofacial Surgery, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Richard Josef Bauer
- Department of Oral and Maxillofacial Surgery, University Hospital Regensburg, 93053 Regensburg, Germany;
- Center for Medical Biotechnology, Department of Oral and Maxillofacial Surgery, University Hospital Regensburg, 93053 Regensburg, Germany
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Eldehna WM, Al-Rashood ST, Al-Warhi T, Eskandrani RO, Alharbi A, El Kerdawy AM. Novel oxindole/benzofuran hybrids as potential dual CDK2/GSK-3β inhibitors targeting breast cancer: design, synthesis, biological evaluation, and in silico studies. J Enzyme Inhib Med Chem 2021; 36:270-285. [PMID: 33327806 PMCID: PMC7751407 DOI: 10.1080/14756366.2020.1862101] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 11/28/2020] [Accepted: 12/01/2020] [Indexed: 02/08/2023] Open
Abstract
The serine/threonine protein kinases CDK2 and GSK-3β are key oncotargets in breast cancer cell lines, therefore, in the present study three series of oxindole-benzofuran hybrids were designed and synthesised as dual CDK2/GSK-3β inhibitors targeting breast cancer (5a-g, 7a-h, and 13a-b). The N1 -unsubstituted oxindole derivatives, series 5, showed moderate to potent activity on both MCF-7 and T-47D breast cancer cell lines. Compounds 5d-f showed the most potent cytotoxic activity with IC50 of 3.41, 3.45 and 2.27 μM, respectively, on MCF-7 and of 3.82, 4.53 and 7.80 μM, respectively, on T-47D cell lines, in comparison to the used reference standard (staurosporine) IC50 of 4.81 and 4.34 μM, respectively. On the other hand, the N1 -substituted oxindole derivatives, series 7 and 13, showed moderate to weak cytotoxic activity on both breast cancer cell lines. CDK2 and GSK-3β enzyme inhibition assay of series 5 revealed that compounds 5d and 5f are showing potent dual CDK2/GSK-3β inhibitory activity with IC50 of 37.77 and 52.75 nM, respectively, on CDK2 and 32.09 and 40.13 nM, respectively, on GSK-3β. The most potent compounds 5d-f caused cell cycle arrest in the G2/M phase in MCF-7 cells inducing cell apoptosis because of the CDK2/GSK-3β inhibition. Molecular docking studies showed that the newly synthesised N1 -unsubstituted oxindole hybrids have comparable binding patterns in both CDK2 and GSK-3β. The oxindole ring is accommodated in the hinge region interacting through hydrogen bonding with the backbone CO and NH of the key amino acids Glu81 and Leu83, respectively, in CDK2 and Asp133 and Val135, respectively, in GSK-3β. Whereas, in series 7 and 13, the N1 -substitutions on the oxindole nucleus hinder the compounds from achieving these key interactions with hinge region amino acids what rationalises their moderate to low anti-proliferative activity.
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Affiliation(s)
- Wagdy M. Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafr El-Sheikh, Egypt
| | - Sara T. Al-Rashood
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Tarfah Al-Warhi
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Razan O. Eskandrani
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Amal Alharbi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ahmed M. El Kerdawy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, New Giza University, Cairo, Egypt
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12
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Wang H, Wang Z, Wei C, Wang J, Xu Y, Bai G, Yao Q, Zhang L, Chen Y. Anticancer potential of indirubins in medicinal chemistry: Biological activity, structural modification, and structure-activity relationship. Eur J Med Chem 2021; 223:113652. [PMID: 34161865 DOI: 10.1016/j.ejmech.2021.113652] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 06/13/2021] [Accepted: 06/13/2021] [Indexed: 10/21/2022]
Abstract
Indirubin is the crucial ingredient of Danggui Longhui Wan and Qing-Dai, traditional Chinese medicine herbal formulas used for the therapy of chronic myelocytic leukemia in China for hundreds of years. Although the monomeric indirubin has been used in China for the treatment human chronic myelocytic leukemia. However, due to low water solubility, poor pharmacokinetic properties and low therapeutic effects are the major obstacle, and had significantly limited its clinical application. Consequently, the attractive anticancer profile of indirubin has enthused numerous researchers to discover novel indirubin derivatives with improved pharmacodynamic activity as well as good pharmacokinetic property. In this paper, we comprehensively review the recent progress of anticancer potential of indirubins, structural modification and structure-activity relationship, which may provide useful direction for the further development of novel indirubins with improved pharmacological profiles for the treatment of various types of cancer.
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Affiliation(s)
- Hezhen Wang
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Key Laboratory of Basic Pharmacology of Ministry of Education, School of Pharmacy, Zunyi Medical University, 6 West Xuefu Road, Zunyi, 563000, PR China
| | - Zhiyuan Wang
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Key Laboratory of Basic Pharmacology of Ministry of Education, School of Pharmacy, Zunyi Medical University, 6 West Xuefu Road, Zunyi, 563000, PR China
| | - Chunyong Wei
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Key Laboratory of Basic Pharmacology of Ministry of Education, School of Pharmacy, Zunyi Medical University, 6 West Xuefu Road, Zunyi, 563000, PR China
| | - Jing Wang
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Key Laboratory of Basic Pharmacology of Ministry of Education, School of Pharmacy, Zunyi Medical University, 6 West Xuefu Road, Zunyi, 563000, PR China
| | - Yingshu Xu
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Key Laboratory of Basic Pharmacology of Ministry of Education, School of Pharmacy, Zunyi Medical University, 6 West Xuefu Road, Zunyi, 563000, PR China
| | - Guohui Bai
- Key Laboratory of Oral Disease of Higher Schools in Guizhou Province, Zunyi Medical University, 6 West Xuefu Road, Zunyi, 563000, PR China.
| | - Qizheng Yao
- School of Pharmacy, China Pharmaceutical University, 24 Tongjia Xiang, Nanjing, 210009, PR China.
| | - Lei Zhang
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Key Laboratory of Basic Pharmacology of Ministry of Education, School of Pharmacy, Zunyi Medical University, 6 West Xuefu Road, Zunyi, 563000, PR China.
| | - Yongzheng Chen
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Key Laboratory of Basic Pharmacology of Ministry of Education, School of Pharmacy, Zunyi Medical University, 6 West Xuefu Road, Zunyi, 563000, PR China.
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13
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Hassan A, Moustafa GO, Awad HM, Nossier ES, Mady MF. Design, Synthesis, Anticancer Evaluation, Enzymatic Assays, and a Molecular Modeling Study of Novel Pyrazole-Indole Hybrids. ACS OMEGA 2021; 6:12361-12374. [PMID: 34056388 PMCID: PMC8154124 DOI: 10.1021/acsomega.1c01604] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 04/21/2021] [Indexed: 05/14/2023]
Abstract
The molecular hybridization concept has recently emerged as a powerful approach in drug discovery. A series of novel indole derivatives linked to the pyrazole moiety were designed and developed via a molecular hybridization protocol as antitumor agents. The target compounds (5a-j and 7a-e) were prepared by the reaction of 5-aminopyrazoles (1a-e) with N-substituted isatin (4a,b) and 1H-indole-3-carbaldehyde (6), respectively. All products were characterized via several analytical and spectroscopic techniques. Compounds (5a-j and 7a-e) were screened for their cytotoxicity activities in vitro against four human cancer types [human colorectal carcinoma (HCT-116), human breast adenocarcinoma (MCF-7), human liver carcinoma (HepG2), and human lung carcinoma (A549)] using the MTT assay. The obtained results showed that the newly synthesized compounds displayed good-to-excellent antitumor activity. For example, 5-((1H-indol-3-yl)methyleneamino)-N-phenyl-3-(phenylamino)-1H-pyrazole-4-carboxamide (7a) and 5-((1H-indol-3-yl)methyleneamino)-3-(phenylamino)-N-(4-methylphenyl)-1H-pyrazole-4-carboxamide (7b) provided excellent anticancer inhibition performance against the HepG2 cancer cell line with IC50 values of 6.1 ± 1.9 and 7.9 ± 1.9 μM, respectively, compared to the standard reference drug, doxorubicin (IC50 = 24.7 ± 3.2 μM). The two powerful anticancer compounds (7a and 7b) were further subjected to cell cycle analysis and apoptosis investigation in HepG2 using flow cytometry. We have also studied the enzymatic assay of these two compounds against some enzymes, namely, caspase-3, Bcl-2, Bax, and CDK-2. Interestingly, the molecular docking study revealed that compounds 7a and 7b could well embed in the active pocket of the CDK-2 enzyme via different interactions. Overall, the prepared pyrazole-indole hybrids (7a and 7b) can be proposed as strong anticancer candidate drugs against various cancer cell lines.
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Affiliation(s)
- Ashraf
S. Hassan
- Organometallic
and Organometalloid Chemistry Department, National Research Centre, Dokki, Cairo 12622, Egypt
| | - Gaber O. Moustafa
- Peptide
Chemistry Department, National Research
Centre, Dokki, Cairo 12622, Egypt
| | - Hanem M. Awad
- Department
of Tanning Materials and Leather Technology, National Research Centre, Dokki, Cairo 12622, Egypt
| | - Eman S. Nossier
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo 11754, Egypt
| | - Mohamed F. Mady
- Department
of Chemistry, Bioscience and Environmental Engineering, Faculty of
Science and Technology, University of Stavanger, N-4036 Stavanger, Norway
- Green Chemistry
Department, National Research Centre, Dokki, Cairo 12622, Egypt
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14
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Al-Warhi T, Abo-Ashour MF, Almahli H, Alotaibi OJ, Al-Sanea MM, Al-Ansary GH, Ahmed HY, Elaasser MM, Eldehna WM, Abdel-Aziz HA. Novel [( N-alkyl-3-indolylmethylene)hydrazono]oxindoles arrest cell cycle and induce cell apoptosis by inhibiting CDK2 and Bcl-2: synthesis, biological evaluation and in silico studies. J Enzyme Inhib Med Chem 2020; 35:1300-1309. [PMID: 32522063 PMCID: PMC7717600 DOI: 10.1080/14756366.2020.1773814] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 05/03/2020] [Accepted: 05/17/2020] [Indexed: 12/21/2022] Open
Abstract
As a continuation for our previous work, a novel set of N-alkylindole-isatin conjugates (7, 8a-c, 9 and 10a-e) is here designed and synthesised with the prime aim to develop more efficient isatin-based antitumor candidates. Utilising the SAR outputs from the previous study, our design here is based on appending four alkyl groups with different length (ethyl and n-propyl), bulkiness (iso-propyl) and unsaturation (allyl) on N-1 of indole motif, with subsequent conjugation with different N-unsubstituted isatin moieties to furnish the target conjugates. As planned, the adopted strategy achieved a substantial improvement in the growth inhibitory profile for the target conjugates in comparison to the reported lead VI. The best results were obtained with N-propylindole -5-methylisatin hybrid 8a which displayed broad spectrum anti-proliferative action with efficient sub-panel GI50 (MG-MID) range from 1.33 to 4.23 µM, and promising full-panel GI50 (MG-MID) equals 3.10 µM, at the NCI five-dose assay. Also, hybrid 8a was able to provoke cell cycle disturbance and apoptosis in breast T-47D cells as evidenced by the DNA flow cytometry and Annexin V-FITC/PI assays. Furthermore, hybrid 8a exhibited good inhibitory action against cell cycle regulator CDK2 protein kinase and the anti-apoptotic Bcl-2 protein (IC50= 0.85 ± 0.03 and 0.46 ± 0.02 µM, respectively). Interestingly, molecular docking for hybrid 8a in CDK2 and Bcl-2 active sites unveiled that N-propyl group is involved in significant hydrophobic interactions. Taken together, the results suggested conjugate 8a as a promising lead for further development and optimisation as an efficient antitumor drug.
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Affiliation(s)
- Tarfah Al-Warhi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Mahmoud F. Abo-Ashour
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo, Egypt
| | - Hadia Almahli
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Ohoud J. Alotaibi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Mohammad M. Al-Sanea
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Aljouf, Saudi Arabia
| | - Ghada H. Al-Ansary
- Department of Pharmaceutical Chemistry, Pharmacy Program, Batterejee Medical College, Jeddah, Saudi Arabia
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Hanaa Y. Ahmed
- The Regional Center for Mycology and Biotechnology, Al-Azhar University, Cairo, Egypt
| | - Mahmoud M. Elaasser
- The Regional Center for Mycology and Biotechnology, Al-Azhar University, Cairo, Egypt
| | - Wagdy M. Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Hatem A. Abdel-Aziz
- Department of Applied Organic Chemistry, National Research Center, Dokki, Giza, Egypt
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15
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Bhowmick S, AlFaris NA, ALTamimi JZ, ALOthman ZA, Aldayel TS, Wabaidur SM, Islam MA. Screening and analysis of bioactive food compounds for modulating the CDK2 protein for cell cycle arrest: Multi-cheminformatics approaches for anticancer therapeutics. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128316] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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16
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Shriver JA, Wang KR, Patterson AC, DeYoung JR, Lipsius RJ. Exploring an anomaly: the synthesis of 7,7′-diazaindirubin through a 7-azaindoxyl intermediate. RSC Adv 2020; 10:36849-36852. [PMID: 35517962 PMCID: PMC9057083 DOI: 10.1039/d0ra07144g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 09/24/2020] [Indexed: 01/01/2023] Open
Abstract
Generation of 7-azaindoxyl under acidic conditions leads exclusively to 7,7′-diazaindirubin over 7,7′-diazaindigo through a condensation pathway.
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17
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Otten C, Knox J, Boulday G, Eymery M, Haniszewski M, Neuenschwander M, Radetzki S, Vogt I, Hähn K, De Luca C, Cardoso C, Hamad S, Igual Gil C, Roy P, Albiges-Rizo C, Faurobert E, von Kries JP, Campillos M, Tournier-Lasserve E, Derry WB, Abdelilah-Seyfried S. Systematic pharmacological screens uncover novel pathways involved in cerebral cavernous malformations. EMBO Mol Med 2019; 10:emmm.201809155. [PMID: 30181117 PMCID: PMC6180302 DOI: 10.15252/emmm.201809155] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Cerebral cavernous malformations (CCMs) are vascular lesions in the central nervous system causing strokes and seizures which currently can only be treated through neurosurgery. The disease arises through changes in the regulatory networks of endothelial cells that must be comprehensively understood to develop alternative, non-invasive pharmacological therapies. Here, we present the results of several unbiased small-molecule suppression screens in which we applied a total of 5,268 unique substances to CCM mutant worm, zebrafish, mouse, or human endothelial cells. We used a systems biology-based target prediction tool to integrate the results with the whole-transcriptome profile of zebrafish CCM2 mutants, revealing signaling pathways relevant to the disease and potential targets for small-molecule-based therapies. We found indirubin-3-monoxime to alleviate the lesion burden in murine preclinical models of CCM2 and CCM3 and suppress the loss-of-CCM phenotypes in human endothelial cells. Our multi-organism-based approach reveals new components of the CCM regulatory network and foreshadows novel small-molecule-based therapeutic applications for suppressing this devastating disease in patients.
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Affiliation(s)
- Cécile Otten
- Institute of Biochemistry and Biology, Potsdam University, Potsdam, Germany
| | - Jessica Knox
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Gwénola Boulday
- INSERM UMR-1161, Génétique et physiopathologie des maladies cérébro-vasculaires, Université Paris Diderot, Paris, France
| | - Mathias Eymery
- INSERM U1209, Grenoble, France.,Institute for Advanced Biosciences, Université Grenoble Alpes, Grenoble, France.,CNRS UMR 5309, Grenoble, France
| | - Marta Haniszewski
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Developmental and Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Silke Radetzki
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Ingo Vogt
- German Center for Diabetes Research, Neuherberg, Germany.,Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Kristina Hähn
- Institute of Biochemistry and Biology, Potsdam University, Potsdam, Germany
| | - Coralie De Luca
- INSERM UMR-1161, Génétique et physiopathologie des maladies cérébro-vasculaires, Université Paris Diderot, Paris, France
| | - Cécile Cardoso
- INSERM UMR-1161, Génétique et physiopathologie des maladies cérébro-vasculaires, Université Paris Diderot, Paris, France
| | - Sabri Hamad
- German Center for Diabetes Research, Neuherberg, Germany.,Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Carla Igual Gil
- Institute of Biochemistry and Biology, Potsdam University, Potsdam, Germany
| | - Peter Roy
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Corinne Albiges-Rizo
- INSERM U1209, Grenoble, France.,Institute for Advanced Biosciences, Université Grenoble Alpes, Grenoble, France.,CNRS UMR 5309, Grenoble, France
| | - Eva Faurobert
- INSERM U1209, Grenoble, France.,Institute for Advanced Biosciences, Université Grenoble Alpes, Grenoble, France.,CNRS UMR 5309, Grenoble, France
| | - Jens P von Kries
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Mónica Campillos
- German Center for Diabetes Research, Neuherberg, Germany.,Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Elisabeth Tournier-Lasserve
- INSERM UMR-1161, Génétique et physiopathologie des maladies cérébro-vasculaires, Université Paris Diderot, Paris, France.,AP-HP, Groupe hospitalier Saint-Louis, Lariboisière, Fernand-Widal, Service de génétique moléculaire neuro-vasculaire, Paris, France
| | - W Brent Derry
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Developmental and Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Salim Abdelilah-Seyfried
- Institute of Biochemistry and Biology, Potsdam University, Potsdam, Germany .,Institute of Molecular Biology, Hannover Medical School, Hannover, Germany
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18
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Kenny RG, Marmion CJ. Toward Multi-Targeted Platinum and Ruthenium Drugs-A New Paradigm in Cancer Drug Treatment Regimens? Chem Rev 2019; 119:1058-1137. [PMID: 30640441 DOI: 10.1021/acs.chemrev.8b00271] [Citation(s) in RCA: 390] [Impact Index Per Article: 78.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
While medicinal inorganic chemistry has been practised for over 5000 years, it was not until the late 1800s when Alfred Werner published his ground-breaking research on coordination chemistry that we began to truly understand the nature of the coordination bond and the structures and stereochemistries of metal complexes. We can now readily manipulate and fine-tune their properties. This had led to a multitude of complexes with wide-ranging biomedical applications. This review will focus on the use and potential of metal complexes as important therapeutic agents for the treatment of cancer. With major advances in technologies and a deeper understanding of the human genome, we are now in a strong position to more fully understand carcinogenesis at a molecular level. We can now also rationally design and develop drug molecules that can either selectively enhance or disrupt key biological processes and, in doing so, optimize their therapeutic potential. This has heralded a new era in drug design in which we are moving from a single- toward a multitargeted approach. This approach lies at the very heart of medicinal inorganic chemistry. In this review, we have endeavored to showcase how a "multitargeted" approach to drug design has led to new families of metallodrugs which may not only reduce systemic toxicities associated with modern day chemotherapeutics but also address resistance issues that are plaguing many chemotherapeutic regimens. We have focused our attention on metallodrugs incorporating platinum and ruthenium ions given that complexes containing these metal ions are already in clinical use or have advanced to clinical trials as anticancer agents. The "multitargeted" complexes described herein not only target DNA but also contain either vectors to enable them to target cancer cells selectively and/or moieties that target enzymes, peptides, and intracellular proteins. Multitargeted complexes which have been designed to target the mitochondria or complexes inspired by natural product activity are also described. A summary of advances in this field over the past decade or so will be provided.
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Affiliation(s)
- Reece G Kenny
- Centre for Synthesis and Chemical Biology, Department of Chemistry , Royal College of Surgeons in Ireland , 123 St. Stephen's Green , Dublin 2 , Ireland
| | - Celine J Marmion
- Centre for Synthesis and Chemical Biology, Department of Chemistry , Royal College of Surgeons in Ireland , 123 St. Stephen's Green , Dublin 2 , Ireland
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19
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Pacureanu L, Avram S, Bora A, Kurunczi L, Crisan L. Portraying the selectivity of GSK-3 inhibitors towards CDK-2 by 3D similarity and molecular docking. Struct Chem 2018. [DOI: 10.1007/s11224-018-1224-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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20
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Walter A, Chaikuad A, Helmer R, Loaëc N, Preu L, Ott I, Knapp S, Meijer L, Kunick C. Molecular structures of cdc2-like kinases in complex with a new inhibitor chemotype. PLoS One 2018; 13:e0196761. [PMID: 29723265 PMCID: PMC5933782 DOI: 10.1371/journal.pone.0196761] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 04/19/2018] [Indexed: 12/18/2022] Open
Abstract
Cdc2-like kinases (CLKs) represent a family of serine-threonine kinases involved in the regulation of splicing by phosphorylation of SR-proteins and other splicing factors. Although compounds acting against CLKs have been described, only a few show selectivity against dual-specificity tyrosine phosphorylation regulated-kinases (DYRKs). We here report a novel CLK inhibitor family based on a 6,7-dihydropyrrolo[3,4-g]indol-8(1H)-one core scaffold. Within the series, 3-(3-chlorophenyl)-6,7-dihydropyrrolo[3,4-g]indol-8(1H)-one (KuWal151) was identified as inhibitor of CLK1, CLK2 and CLK4 with a high selectivity margin towards DYRK kinases. The compound displayed a potent antiproliferative activity in an array of cultured cancer cell lines. The X-ray structure analyses of three members of the new compound class co-crystallized with CLK proteins corroborated a molecular binding mode predicted by docking studies.
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Affiliation(s)
- Anne Walter
- Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Braunschweig, Germany
- Center of Pharmaceutical Engeneering (PVZ), Technische Universität Braunschweig, Braunschweig, Germany
| | - Apirat Chaikuad
- Structural Genomics Consortium, Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
- Institute for Pharmaceutical Chemistry, Structural Genomics Consortium and Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Renate Helmer
- Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Nadège Loaëc
- ManRos Therapeutics, Hôtel de Recherche, Centre de Perharidy, Roscoff, France
| | - Lutz Preu
- Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Ingo Ott
- Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Braunschweig, Germany
- Center of Pharmaceutical Engeneering (PVZ), Technische Universität Braunschweig, Braunschweig, Germany
| | - Stefan Knapp
- Structural Genomics Consortium, Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
- Institute for Pharmaceutical Chemistry, Structural Genomics Consortium and Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Laurent Meijer
- ManRos Therapeutics, Hôtel de Recherche, Centre de Perharidy, Roscoff, France
- * E-mail: (CK); (LM)
| | - Conrad Kunick
- Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Braunschweig, Germany
- Center of Pharmaceutical Engeneering (PVZ), Technische Universität Braunschweig, Braunschweig, Germany
- * E-mail: (CK); (LM)
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21
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Tian W, Liang J. On quantification of geometry and topology of protein pockets and channels for assessing mutation effects. ... IEEE-EMBS INTERNATIONAL CONFERENCE ON BIOMEDICAL AND HEALTH INFORMATICS. IEEE-EMBS INTERNATIONAL CONFERENCE ON BIOMEDICAL AND HEALTH INFORMATICS 2018; 2018:263-266. [PMID: 30272056 PMCID: PMC6157619 DOI: 10.1109/bhi.2018.8333419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Geometric and topological features of proteins such as voids, pockets and channels are important for protein functions. We discuss a method for visualizing protein pockets and channels based on orthogonal spheres computed from alpha shapes of the protein structures, and how metric properties of channel surfaces can be mapped. In addition, we discuss how structurally prominent sites, such as constriction sties in channels, can be computed, which may help to understand protein functions and mutation effects, with implications in developing novel therapeutic interventions.
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Affiliation(s)
- Wei Tian
- Bioinformatics Program, Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Jie Liang
- Bioinformatics Program, Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
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22
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Yang CC, Hung CF, Chen BH. Preparation of coffee oil-algae oil-based nanoemulsions and the study of their inhibition effect on UVA-induced skin damage in mice and melanoma cell growth. Int J Nanomedicine 2017; 12:6559-6580. [PMID: 28919754 PMCID: PMC5592955 DOI: 10.2147/ijn.s144705] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Coffee grounds, a waste by-product generated after making coffee, contains approximately 15% coffee oil which can be used as a raw material in cosmetics. Algae oil rich in docosahexaenoic acid (DHA) has been demonstrated to possess anticancer and anti-inflammation functions. The objectives of this study were to develop a gas chromatography-mass spectrometry (GC-MS) method for the determination of fatty acids in coffee oil and algae oil and prepare a nanoemulsion for studying its inhibition effect on ultraviolet A-induced skin damage in mice and growth of melanoma cells B16-F10. A total of 8 and 5 fatty acids were separated and quantified in coffee oil and algae oil by GC-MS, respectively, with linoleic acid (39.8%) dominating in the former and DHA (33.9%) in the latter. A nanoemulsion with a particle size of 30 nm, zeta potential -72.72 mV, and DHA encapsulation efficiency 100% was prepared by using coffee oil, algae oil, surfactant (20% Span 80 and 80% Tween 80), and deionized water. Differential scanning calorimetry (DSC) analysis revealed a high stability of nanoemulsion when heated up to 110°C at a pH 6, whereas no significant changes in particle size distribution and pH occurred over a 90-day storage period at 4°C. Animal experiments showed that a dose of 0.1% coffee oil-algae oil nanoemulsion was effective in mitigating trans-epidermal water loss, skin erythema, melanin formation, and subcutaneous blood flow. Cytotoxicity test implied effective inhibition of melanoma cell growth by nanoemulsion with an IC50 value of 26.5 µg/mL and the cell cycle arrested at G2/M phase. A dose-dependent upregulation of p53, p21, cyclin B, and cyclin A expressions and downregulation of CDK1 and CDK2 occurred. Also, both Bax and cytochrome c expressions were upregulated and bcl-2 expression downregulated, accompanied by a rise in caspase-3, caspase-8, and caspase-9 activities for apoptosis execution. Collectively, the apoptosis pathway of melanoma cells B16-F10 may involve both mitochondria and death receptor.
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Affiliation(s)
| | - Chi-Feng Hung
- School of Medicine, Fu Jen Catholic University, Taipei, Taiwan
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23
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Czeleń P. Inhibition mechanism of CDK-2 and GSK-3β by a sulfamoylphenyl derivative of indoline-a molecular dynamics study. J Mol Model 2017; 23:230. [PMID: 28726150 PMCID: PMC5517586 DOI: 10.1007/s00894-017-3395-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 06/25/2017] [Indexed: 11/22/2022]
Abstract
A good understanding of the inhibition mechanism of enzymes exhibiting high levels of similarity is the first step to the discovery of new drugs with selective potential. Examples of such proteins include glycogen synthase kinase-3 (GSK-3β) and cyclin-dependent kinase 2 (CDK-2). This article reports the mechanism of such enzyme inhibition as analyzed by an indoline sulfamylophenyl derivative (CHEMBL410072). Previous work has shown that such compounds exhibit selective properties towards their biological targets. This study used a combined procedure involving docking and molecular dynamics simulations, which allowed identification of interactions responsible for stabilization of complexes, and analysis of the dynamic stability of the systems obtained. The initial data obtained during the molecular docking stage show that the ligand molecule exhibits a similar affinity towards both active sites, which was confirmed by quantification of identified interactions and energy values. However, the data do not cover dynamic aspects of the considered systems. Molecular dynamics simulations realized for both complexes indicate significant dissimilarities in dynamics properties of both side chains of the considered ligands, especially in the case of the part containing the sulfamide group. Such increased mobility of the analyzed systems disrupts the stability of binding in the stabilized complex with GSK-3β protein, which finally affects also the binding affinity of the ligand molecule towards this enzyme.
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Affiliation(s)
- Przemysław Czeleń
- Department of Physical Chemistry, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Kurpinskiego 5, 85-096, Bydgoszcz, Poland.
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24
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Cheng X, Merz KH, Vatter S, Zeller J, Muehlbeyer S, Thommet A, Christ J, Wölfl S, Eisenbrand G. Identification of a Water-Soluble Indirubin Derivative as Potent Inhibitor of Insulin-like Growth Factor 1 Receptor through Structural Modification of the Parent Natural Molecule. J Med Chem 2017; 60:4949-4962. [PMID: 28557430 DOI: 10.1021/acs.jmedchem.7b00324] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Indirubins have been identified as potent ATP-competitive protein kinase inhibitors. Structural modifications in the 5- and 3'-position have been extensively investigated, but the impact of substituents in 5'-position is not equally well-studied. Here, we report the synthesis of new indirubin 3'- and 5'-derivatives in the search of water-soluble indirubins by introducing basic centers. Antiproliferative activity of all compounds in tumor cells was evaluated along with kinase inhibition of selected compounds. The results show the 3'-position to tolerate large substituents without compromising activity, whereas bulk and rigid substituents in 5'-position appear unfavorable. Screening molecular targets of water-soluble 3'-oxime ethers revealed 6ha as preferential inhibitor of insulin-like growth factor 1 receptor (IGF-1R) in a panel of 22 protein kinases and in cells. Consistently, 6ha inhibited tumor cell growth in the NCI 60 cell line panel and induced apoptosis. The results indicate that the 5'-position provides limited space for chemical modifications and identify 6ha as a potent water-soluble indirubin-based IGF-1R inhibitor.
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Affiliation(s)
- Xinlai Cheng
- Department of Chemistry, Division of Food Chemistry and Toxicology, University of Kaiserslautern , Erwin-Schrödinger-Strasse 52, D-67663 Kaiserslautern, Germany.,Department of Pharmacy and Molecular Biotechnology, Division of Pharmaceutical Biology, University of Heidelberg , Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
| | - Karl-Heinz Merz
- Department of Chemistry, Division of Food Chemistry and Toxicology, University of Kaiserslautern , Erwin-Schrödinger-Strasse 52, D-67663 Kaiserslautern, Germany
| | - Sandra Vatter
- Department of Chemistry, Division of Food Chemistry and Toxicology, University of Kaiserslautern , Erwin-Schrödinger-Strasse 52, D-67663 Kaiserslautern, Germany
| | - Jochen Zeller
- Department of Chemistry, Division of Food Chemistry and Toxicology, University of Kaiserslautern , Erwin-Schrödinger-Strasse 52, D-67663 Kaiserslautern, Germany
| | - Stephan Muehlbeyer
- Department of Chemistry, Division of Food Chemistry and Toxicology, University of Kaiserslautern , Erwin-Schrödinger-Strasse 52, D-67663 Kaiserslautern, Germany
| | - Andrea Thommet
- Department of Chemistry, Division of Food Chemistry and Toxicology, University of Kaiserslautern , Erwin-Schrödinger-Strasse 52, D-67663 Kaiserslautern, Germany
| | - Jochen Christ
- Department of Chemistry, Division of Food Chemistry and Toxicology, University of Kaiserslautern , Erwin-Schrödinger-Strasse 52, D-67663 Kaiserslautern, Germany
| | - Stefan Wölfl
- Department of Pharmacy and Molecular Biotechnology, Division of Pharmaceutical Biology, University of Heidelberg , Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
| | - Gerhard Eisenbrand
- Department of Chemistry, Division of Food Chemistry and Toxicology, University of Kaiserslautern , Erwin-Schrödinger-Strasse 52, D-67663 Kaiserslautern, Germany
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Nekardová M, Vymětalová L, Khirsariya P, Kováčová S, Hylsová M, Jorda R, Kryštof V, Fanfrlík J, Hobza P, Paruch K. Structural Basis of the Interaction of Cyclin-Dependent Kinase 2 with Roscovitine and Its Analogues Having Bioisosteric Central Heterocycles. Chemphyschem 2017; 18:785-795. [DOI: 10.1002/cphc.201601319] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/24/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Michaela Nekardová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
- Faculty of Mathematics and Physics; Charles University in Prague; Ke Karlovu 3 Prague 2 121 16 Czech Republic
| | - Ladislava Vymětalová
- Laboratory of Growth Regulators, Faculty of Science of; Palacky University and Institute of Experimental Botany of the Czech Academy of Sciences; Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Prashant Khirsariya
- Department of Chemistry, CZ Openscreen; Masaryk University; Kamenice 5 62500 Brno Czech Republic
- International Center for Clinical Research; St. Anne's University Hospital Brno; Pekařská 53 656 91 Brno Czech Republic
| | - Silvia Kováčová
- Department of Chemistry, CZ Openscreen; Masaryk University; Kamenice 5 62500 Brno Czech Republic
| | - Michaela Hylsová
- Department of Chemistry, CZ Openscreen; Masaryk University; Kamenice 5 62500 Brno Czech Republic
| | - Radek Jorda
- Laboratory of Growth Regulators, Faculty of Science of; Palacky University and Institute of Experimental Botany of the Czech Academy of Sciences; Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Vladimír Kryštof
- Laboratory of Growth Regulators, Faculty of Science of; Palacky University and Institute of Experimental Botany of the Czech Academy of Sciences; Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Kamil Paruch
- Department of Chemistry, CZ Openscreen; Masaryk University; Kamenice 5 62500 Brno Czech Republic
- International Center for Clinical Research; St. Anne's University Hospital Brno; Pekařská 53 656 91 Brno Czech Republic
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Cheng X, Merz KH. The Role of Indirubins in Inflammation and Associated Tumorigenesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 929:269-290. [DOI: 10.1007/978-3-319-41342-6_12] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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27
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Molecular dynamics study on inhibition mechanism of CDK-2 and GSK-3β by CHEMBL272026 molecule. Struct Chem 2016. [DOI: 10.1007/s11224-016-0803-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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28
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The alpha-fetoprotein (AFP) third domain: a search for AFP interaction sites of cell cycle proteins. Tumour Biol 2016; 37:12697-12711. [DOI: 10.1007/s13277-016-5131-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 06/29/2016] [Indexed: 01/28/2023] Open
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Kilchmann F, Marcaida MJ, Kotak S, Schick T, Boss SD, Awale M, Gönczy P, Reymond JL. Discovery of a Selective Aurora A Kinase Inhibitor by Virtual Screening. J Med Chem 2016; 59:7188-211. [PMID: 27391133 DOI: 10.1021/acs.jmedchem.6b00709] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Here we report the discovery of a selective inhibitor of Aurora A, a key regulator of cell division and potential anticancer target. We used the atom category extended ligand overlap score (xLOS), a 3D ligand-based virtual screening method recently developed in our group, to select 437 shape and pharmacophore analogs of reference kinase inhibitors. Biochemical screening uncovered two inhibitor series with scaffolds unprecedented among kinase inhibitors. One of them was successfully optimized by structure-based design to a potent Aurora A inhibitor (IC50 = 2 nM) with very high kinome selectivity for Aurora kinases. This inhibitor locks Aurora A in an inactive conformation and disrupts binding to its activator protein TPX2, which impairs Aurora A localization at the mitotic spindle and induces cell division defects. This phenotype can be rescued by inhibitor-resistant Aurora A mutants. The inhibitor furthermore does not induce Aurora B specific effects in cells.
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Affiliation(s)
- Falco Kilchmann
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR Chemical Biology and NCCR TransCure, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland
| | - Maria J Marcaida
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR Chemical Biology and NCCR TransCure, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland
| | - Sachin Kotak
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, National Center of Competence in Research NCCR Chemical Biology, Swiss Federal Institute of Technology (EPFL) , CH-1015 Lausanne, Switzerland
| | - Thomas Schick
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR Chemical Biology and NCCR TransCure, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland
| | - Silvan D Boss
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR Chemical Biology and NCCR TransCure, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland
| | - Mahendra Awale
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR Chemical Biology and NCCR TransCure, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland
| | - Pierre Gönczy
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, National Center of Competence in Research NCCR Chemical Biology, Swiss Federal Institute of Technology (EPFL) , CH-1015 Lausanne, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR Chemical Biology and NCCR TransCure, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland
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Cheng X, Kim JY, Ghafoory S, Duvaci T, Rafiee R, Theobald J, Alborzinia H, Holenya P, Fredebohm J, Merz KH, Mehrabi A, Hafezi M, Saffari A, Eisenbrand G, Hoheisel JD, Wölfl S. Methylisoindigo preferentially kills cancer stem cells by interfering cell metabolism via inhibition of LKB1 and activation of AMPK in PDACs. Mol Oncol 2016; 10:806-24. [PMID: 26887594 PMCID: PMC5423166 DOI: 10.1016/j.molonc.2016.01.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 01/15/2016] [Accepted: 01/25/2016] [Indexed: 12/13/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) clinically has a very poor prognosis. No small molecule is available to reliably achieve cures. Meisoindigo is chemically related to the natural product indirubin and showed substantial efficiency in clinical chemotherapy for CML in China. However, its effect on PDAC is still unknown. Our results showed strong anti-proliferation effect of meisoindigo on gemcitabine-resistant PDACs. Using a recently established primary PDAC cell line, called Jopaca-1 with a larger CSCs population as model, we observed a reduction of CD133+ and ESA+/CD44+/CD24+ populations upon treatment and concomitantly a decreased expression of CSC-associated genes, and reduced cellular mobility and sphere formation. Investigating basic cellular metabolic responses, we detected lower oxygen consumption and glucose uptake, while intracellular ROS levels increased. This was effectively neutralized by the addition of antioxidants, indicating an essential role of the cellular redox balance. Further analysis on energy metabolism related signaling revealed that meisoindigo inhibited LKB1, but activated AMPK. Both of them were involved in cellular apoptosis. Additional in situ hybridization in tissue sections of PDAC patients reproducibly demonstrated co-expression and -localization of LKB1 and CD133 in malignant areas. Finally, we detected that CD133+/CD44+ were more vulnerable to meisoindigo, which could be mimicked by LKB1 siRNAs. Our results provide the first evidence, to our knowledge, that LKB1 sustains the CSC population in PDACs and demonstrate a clear benefit of meisoindigo in treatment of gemcitabine-resistant cells. This novel mechanism may provide a promising new treatment option for PDAC.
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Affiliation(s)
- Xinlai Cheng
- Institute of Pharmacy and Molecular Biotechnology, Pharmaceutical Biology, Heidelberg University, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany.
| | - Jee Young Kim
- Institute of Pharmacy and Molecular Biotechnology, Pharmaceutical Biology, Heidelberg University, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany.
| | - Shahrouz Ghafoory
- Institute of Pharmacy and Molecular Biotechnology, Pharmaceutical Biology, Heidelberg University, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany.
| | - Tijen Duvaci
- Institute of Pharmacy and Molecular Biotechnology, Pharmaceutical Biology, Heidelberg University, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany.
| | - Roya Rafiee
- Institute of Pharmacy and Molecular Biotechnology, Pharmaceutical Biology, Heidelberg University, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany.
| | - Jannick Theobald
- Institute of Pharmacy and Molecular Biotechnology, Pharmaceutical Biology, Heidelberg University, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany.
| | - Hamed Alborzinia
- Institute of Pharmacy and Molecular Biotechnology, Pharmaceutical Biology, Heidelberg University, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany.
| | - Pavlo Holenya
- Institute of Pharmacy and Molecular Biotechnology, Pharmaceutical Biology, Heidelberg University, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany.
| | - Johannes Fredebohm
- Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
| | - Karl-Heinz Merz
- Department of Chemistry, Division of Food Chemistry and Toxicology, University of Kaiserslautern, Erwin-Schrödinger-Str. 52, D-67663 Kaiserslautern, Germany.
| | - Arianeb Mehrabi
- Department of General, Visceral and Transplantation Surgery, Heidelberg University, Germany.
| | - Mohammadreza Hafezi
- Department of General, Visceral and Transplantation Surgery, Heidelberg University, Germany.
| | - Arash Saffari
- Department of General, Visceral and Transplantation Surgery, Heidelberg University, Germany.
| | - Gerhard Eisenbrand
- Department of Chemistry, Division of Food Chemistry and Toxicology, University of Kaiserslautern, Erwin-Schrödinger-Str. 52, D-67663 Kaiserslautern, Germany.
| | - Jörg D Hoheisel
- Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
| | - Stefan Wölfl
- Institute of Pharmacy and Molecular Biotechnology, Pharmaceutical Biology, Heidelberg University, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany.
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31
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Wu X, Chen X, Dan J, Cao Y, Gao S, Guo Z, Zerbe P, Chai Y, Diao Y, Zhang L. Characterization of anti-leukemia components from Indigo naturalis using comprehensive two-dimensional K562/cell membrane chromatography and in silico target identification. Sci Rep 2016; 6:25491. [PMID: 27150638 PMCID: PMC4858665 DOI: 10.1038/srep25491] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 04/18/2016] [Indexed: 12/30/2022] Open
Abstract
Traditional Chinese Medicine (TCM) has been developed for thousands of years and has formed an integrated theoretical system based on a large amount of clinical practice. However, essential ingredients in TCM herbs have not been fully identified, and their precise mechanisms and targets are not elucidated. In this study, a new strategy combining comprehensive two-dimensional K562/cell membrane chromatographic system and in silico target identification was established to characterize active components from Indigo naturalis, a famous TCM herb that has been widely used for the treatment of leukemia in China, and their targets. Three active components, indirubin, tryptanthrin and isorhamnetin, were successfully characterized and their anti-leukemia effects were validated by cell viability and cell apoptosis assays. Isorhamnetin, with undefined cancer related targets, was selected for in silico target identification. Proto-oncogene tyrosine-protein kinase (Src) was identified as its membrane target and the dissociation constant (Kd) between Src and isorhamnetin was 3.81 μM. Furthermore, anti-leukemia effects of isorhamnetin were mediated by Src through inducing G2/M cell cycle arrest. The results demonstrated that the integrated strategy could efficiently characterize active components in TCM and their targets, which may bring a new light for a better understanding of the complex mechanism of herbal medicines.
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Affiliation(s)
- Xunxun Wu
- School of Biomedical Science, Institute of Molecular Medicine, Huaqiao University, Quanzhou 362021, PR China.,School of Pharmacy, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200433, PR China
| | - Xiaofei Chen
- School of Pharmacy, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200433, PR China
| | - Jia Dan
- School of Pharmacy, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200433, PR China
| | - Yan Cao
- School of Pharmacy, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200433, PR China
| | - Shouhong Gao
- School of Pharmacy, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200433, PR China
| | - Zhiying Guo
- School of Biomedical Science, Institute of Molecular Medicine, Huaqiao University, Quanzhou 362021, PR China.,School of Pharmacy, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200433, PR China
| | - Philipp Zerbe
- Department of Plant Biology, University of California, Davis, CA 95616, USA
| | - Yifeng Chai
- School of Pharmacy, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200433, PR China
| | - Yong Diao
- School of Biomedical Science, Institute of Molecular Medicine, Huaqiao University, Quanzhou 362021, PR China
| | - Lei Zhang
- School of Pharmacy, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200433, PR China
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Begum J, Skamnaki VT, Moffatt C, Bischler N, Sarrou J, Skaltsounis AL, Leonidas DD, Oikonomakos NG, Hayes JM. An evaluation of indirubin analogues as phosphorylase kinase inhibitors. J Mol Graph Model 2015; 61:231-42. [PMID: 26364215 DOI: 10.1016/j.jmgm.2015.07.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 07/24/2015] [Accepted: 07/27/2015] [Indexed: 11/24/2022]
Abstract
Phosphorylase kinase (PhK) has been linked with a number of conditions such as glycogen storage diseases, psoriasis, type 2 diabetes and more recently, cancer (Camus et al., 2012 [6]). However, with few reported structural studies on PhK inhibitors, this hinders a structure based drug design approach. In this study, the inhibitory potential of 38 indirubin analogues have been investigated. 11 of these ligands had IC50 values in the range 0.170-0.360μM, with indirubin-3'-acetoxime (1c) the most potent. 7-Bromoindirubin-3'-oxime (13b), an antitumor compound which induces caspase-independent cell-death (Ribas et al., 2006 [20]) is revealed as a specific inhibitor of PhK (IC50=1.8μM). Binding assay experiments performed using both PhK-holo and PhK-γtrnc confirmed the inhibitory effects to arise from binding at the kinase domain (γ subunit). High level computations using QM/MM-PBSA binding free energy calculations were in good agreement with experimental binding data, as determined using statistical analysis, and support binding at the ATP-binding site. The value of a QM description for the binding of halogenated ligands exhibiting σ-hole effects is highlighted. A new statistical metric, the 'sum of the modified logarithm of ranks' (SMLR), has been defined which measures performance of a model for both the "early recognition" (ranking earlier/higher) of active compounds and their relative ordering by potency. Through a detailed structure activity relationship analysis considering other kinases (CDK2, CDK5 and GSK-3α/β), 6'(Z) and 7(L) indirubin substitutions have been identified to achieve selective PhK inhibition. The key PhK binding site residues involved can also be targeted using other ligand scaffolds in future work.
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Affiliation(s)
- Jaida Begum
- School of Physical Sciences & Computing, Division of Chemistry, University of Central Lancashire, Preston PR1 2HE, United Kingdom; School of Forensic & Investigative Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Vassiliki T Skamnaki
- Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Str., 41221 Larissa, Greece
| | - Colin Moffatt
- School of Forensic & Investigative Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Nicolas Bischler
- Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Ave., 116 35 Athens, Greece
| | - Josephine Sarrou
- Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Ave., 116 35 Athens, Greece
| | - Alexios-Leandros Skaltsounis
- Division of Pharmacognosy, Department of Pharmacy, University of Athens, Panepistimiopolis-Zografou, Athens 15771, Greece
| | - Demetres D Leonidas
- Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Str., 41221 Larissa, Greece
| | - Nikos G Oikonomakos
- Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Ave., 116 35 Athens, Greece
| | - Joseph M Hayes
- School of Physical Sciences & Computing, Division of Chemistry, University of Central Lancashire, Preston PR1 2HE, United Kingdom; School of Forensic & Investigative Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom.
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33
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Structure-based design of benzo[e]isoindole-1,3-dione derivatives as selective GSK-3β inhibitors to activate Wnt/β-catenin pathway. Bioorg Chem 2015; 61:21-7. [DOI: 10.1016/j.bioorg.2015.05.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Revised: 05/21/2015] [Accepted: 05/22/2015] [Indexed: 11/17/2022]
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Insights on Structural Characteristics and Ligand Binding Mechanisms of CDK2. Int J Mol Sci 2015; 16:9314-40. [PMID: 25918937 PMCID: PMC4463590 DOI: 10.3390/ijms16059314] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 04/01/2015] [Accepted: 04/15/2015] [Indexed: 12/20/2022] Open
Abstract
Cyclin-dependent kinase 2 (CDK2) is a crucial regulator of the eukaryotic cell cycle. However it is well established that monomeric CDK2 lacks regulatory activity, which needs to be aroused by its positive regulators, cyclins E and A, or be phosphorylated on the catalytic segment. Interestingly, these activation steps bring some dynamic changes on the 3D-structure of the kinase, especially the activation segment. Until now, in the monomeric CDK2 structure, three binding sites have been reported, including the adenosine triphosphate (ATP) binding site (Site I) and two non-competitive binding sites (Site II and III). In addition, when the kinase is subjected to the cyclin binding process, the resulting structural changes give rise to a variation of the ATP binding site, thus generating an allosteric binding site (Site IV). All the four sites are demonstrated as being targeted by corresponding inhibitors, as is illustrated by the allosteric binding one which is targeted by inhibitor ANS (fluorophore 8-anilino-1-naphthalene sulfonate). In the present work, the binding mechanisms and their fluctuations during the activation process attract our attention. Therefore, we carry out corresponding studies on the structural characterization of CDK2, which are expected to facilitate the understanding of the molecular mechanisms of kinase proteins. Besides, the binding mechanisms of CDK2 with its relevant inhibitors, as well as the changes of binding mechanisms following conformational variations of CDK2, are summarized and compared. The summary of the conformational characteristics and ligand binding mechanisms of CDK2 in the present work will improve our understanding of the molecular mechanisms regulating the bioactivities of CDK2.
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35
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Yan L, Lai F, Chen X, Xiao Z. Discovery of novel indirubin-3'-monoxime derivatives as potent inhibitors against CDK2 and CDK9. Bioorg Med Chem Lett 2015; 25:2447-51. [PMID: 25908517 DOI: 10.1016/j.bmcl.2015.03.066] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 03/06/2015] [Accepted: 03/24/2015] [Indexed: 10/23/2022]
Abstract
Indirubin-3'-monoxime (IM) is a potent cyclin-dependent kinase (CDK) inhibitor. Twenty novel IM derivatives were prepared to investigate the structure-activity relationships (SAR) of this compound class. Six compounds showed significant inhibition against both CDK2/cyclin E1 and CDK9/cyclin T1. The most potent compound 7t exhibited IC50 values at submicromolar level. Preliminary SAR trends were suggested and cytotoxicity of these compounds was investigated. Molecular docking studies on compounds 7l and 7t provided conducive clues for further structural optimization.
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Affiliation(s)
- Lei Yan
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Fangfang Lai
- Beijing Key Laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Xiaoguang Chen
- Beijing Key Laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Zhiyan Xiao
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
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36
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Czeleń P, Szefler B. Molecular dynamics study of the inhibitory effects of ChEMBL474807 on the enzymes GSK-3β and CDK-2. J Mol Model 2015; 21:74. [PMID: 25754137 PMCID: PMC4353878 DOI: 10.1007/s00894-015-2627-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 02/15/2015] [Indexed: 02/04/2023]
Abstract
Indirubin derivatives and analogs comprise a significant group of ATP-competitive inhibitors. The inhibitory effects of ChEMBL474807 (1-(4-amino-1,2,5-oxadiazol-3-yl)-5-(piperidin-1-ylmethyl)-N′-(pyridin-4-ylmethylene)-1H-1,2,3-triazole-4-carbohydrazide) on two enzymes, namely glycogen synthase kinase-3β (GSK-3β) and cyclin-dependent kinase-2 (CDK-2), were analyzed. The close resemblance of the amino acid sequences of these two enzymes (with 25 % identity and 41 % similarity) explains why indirubin derivatives are inhibitors of both of the enzymes studied. The docking and molecular dynamics investigation performed here led to the identification of the interactions responsible for stabilizing the ligand ChEMBL474807 at the active sites of the enzymes considered. The structural and energetic data collected during our investigations clearly indicate that there are important differences in the behavior of the ligand at the two active sites investigated here.
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Affiliation(s)
- Przemysław Czeleń
- Department of Physical Chemistry, Collegium Medicum, Nicolaus Copernicus University, Kurpinskiego 5, 85-950, Bydgoszcz, Poland,
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37
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Polyphony: superposition independent methods for ensemble-based drug discovery. BMC Bioinformatics 2014; 15:324. [PMID: 25265915 PMCID: PMC4261739 DOI: 10.1186/1471-2105-15-324] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 09/17/2014] [Indexed: 12/04/2022] Open
Abstract
Background Structure-based drug design is an iterative process, following cycles of structural biology, computer-aided design, synthetic chemistry and bioassay. In favorable circumstances, this process can lead to the structures of hundreds of protein-ligand crystal structures. In addition, molecular dynamics simulations are increasingly being used to further explore the conformational landscape of these complexes. Currently, methods capable of the analysis of ensembles of crystal structures and MD trajectories are limited and usually rely upon least squares superposition of coordinates. Results Novel methodologies are described for the analysis of multiple structures of a protein. Statistical approaches that rely upon residue equivalence, but not superposition, are developed. Tasks that can be performed include the identification of hinge regions, allosteric conformational changes and transient binding sites. The approaches are tested on crystal structures of CDK2 and other CMGC protein kinases and a simulation of p38α. Known interaction - conformational change relationships are highlighted but also new ones are revealed. A transient but druggable allosteric pocket in CDK2 is predicted to occur under the CMGC insert. Furthermore, an evolutionarily-conserved conformational link from the location of this pocket, via the αEF-αF loop, to phosphorylation sites on the activation loop is discovered. Conclusions New methodologies are described and validated for the superimposition independent conformational analysis of large collections of structures or simulation snapshots of the same protein. The methodologies are encoded in a Python package called Polyphony, which is released as open source to accompany this paper [http://wrpitt.bitbucket.org/polyphony/].
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Analogue-based design, synthesis and biological evaluation of 3-substituted-(methylenehydrazono)indolin-2-ones as anticancer agents. Eur J Med Chem 2014; 78:275-80. [PMID: 24686014 DOI: 10.1016/j.ejmech.2014.03.058] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 03/15/2014] [Accepted: 03/17/2014] [Indexed: 02/08/2023]
Abstract
The docking studies on CDK2 and GSK-3β inspired us to synthesis a series of indoline-2,3-dione hydrazones 10a-l. Treatment of indoline-2,3-dione derivatives 7a-d with hydrazine gave 3-hydrazonoindolin-2-ones 8a-d which were reacted with the appropriate aldehydes 9a-c to yield 3-substituted-(methylenehydrazono)indolin-2-ones 10a-l. Compounds 10a-l showed a significant anticancer activity against human breast cell line MCF-7. Compounds 10c, f, i exhibited the highest activity almost the same of doxorubicin (IC50 = 6.10 μM) with IC50 = 7.75, 6.75, 6.25 μM, respectively.
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39
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Carbain B, Paterson DJ, Anscombe E, Campbell AJ, Cano C, Echalier A, Endicott JA, Golding BT, Haggerty K, Hardcastle IR, Jewsbury PJ, Newell DR, Noble MEM, Roche C, Wang LZ, Griffin RJ. 8-Substituted O(6)-cyclohexylmethylguanine CDK2 inhibitors: using structure-based inhibitor design to optimize an alternative binding mode. J Med Chem 2014; 57:56-70. [PMID: 24304238 DOI: 10.1021/jm401555v] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Evaluation of the effects of purine C-8 substitution within a series of CDK1/2-selective O(6)-cyclohexylmethylguanine derivatives revealed that potency decreases initially with increasing size of the alkyl substituent. Structural analysis showed that C-8 substitution is poorly tolerated, and to avoid unacceptable steric interactions, these compounds adopt novel binding modes. Thus, 2-amino-6-cyclohexylmethoxy-8-isopropyl-9H-purine adopts a "reverse" binding mode where the purine backbone has flipped 180°. This provided a novel lead chemotype from which we have designed more potent CDK2 inhibitors using, in the first instance, quantum mechanical energy calculations. Introduction of an ortho-tolyl or ortho-chlorophenyl group at the purine C-8 position restored the potency of these "reverse" binding mode inhibitors to that of the parent 2-amino-6-cyclohexylmethoxy-9H-purine. By contrast, the corresponding 8-(2-methyl-3-sulfamoylphenyl)-purine derivative exhibited submicromolar CDK2-inhibitory activity by virtue of engineered additional interactions with Asp86 and Lys89 in the reversed binding mode, as confirmed by X-ray crystallography.
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Affiliation(s)
- Benoit Carbain
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, U.K
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Erben F, Michalik D, Feist H, Kleeblatt D, Hein M, Matin A, Iqbal J, Langer P. Synthesis and antiproliferative activity of (Z)-1-glycosyl-3-(5-oxo-2-thioxoimidazolidin-4-ylidene)indolin-2-ones and (Z)-3-(2-glycosylsulfanyl-4-oxo-4,5-dihydro-thiazol-5-ylidene)indolin-2-ones. RSC Adv 2014. [DOI: 10.1039/c3ra44362k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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41
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A colorful history: the evolution of indigoids. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2014; 99:69-145. [PMID: 25296438 DOI: 10.1007/978-3-319-04900-7_2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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42
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Kleeblatt D, Cordes CA, Lebrenz P, Hein M, Feist H, Matin A, Raza R, Iqbal J, Munshi O, Rahman Q, Villinger A, Langer P. Synthesis and antiproliferative activity of N-glycosyl-3,3-diaryloxindoles. RSC Adv 2014. [DOI: 10.1039/c4ra02627f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Cheng X, Merz KH, Vatter S, Christ J, Wölfl S, Eisenbrand G. 7,7'-Diazaindirubin--a small molecule inhibitor of casein kinase 2 in vitro and in cells. Bioorg Med Chem 2013; 22:247-55. [PMID: 24326279 DOI: 10.1016/j.bmc.2013.11.031] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 10/09/2013] [Accepted: 11/16/2013] [Indexed: 01/13/2023]
Abstract
Aza- and diaza-bisindoles were synthesized by coupling of 7-azaisatin, 7-azaoxindol, 7-azaindoxyl acetate, and their non-aza counterparts, respectively. Whereas 7,7'-diazaindigo (10) and 7,7'-diazaisoindigo (11) did not show antiproliferative activity in several human tumor cell lines up to 100 μM, 7-azaindirubin (12) and 7'-azaindirubin (13) were more active than the parent molecule, indirubin, in LXFL529L cells (human large cell lung tumor xenograft), and 7,7'-diazaindirubin (14) was exhibiting substantially enhanced growth inhibitory activity in these cells. In the NCI 60 cell line panel, 14 displayed antiproliferative activity preferentially in certain melanoma and non-small cell lung cancer cells. In contrast to the potent serine/threonine/tyrosine kinase inhibition observed for indirubins, kinase inhibition profiling of 14 in 220 kinases revealed largely a loss of kinase inhibitory activity towards most kinases, with retained inhibitory activity for just a few kinases. At 1 μM concentration, especially casein kinases CK1γ3, CK2α, CK2α2, and SIK were inhibited by more than 50%. In cell-based assays, 14 markedly affected CK2-mediated signaling in various human tumor cells. In MCF7 cells, 14 induced cell cycle arrest at G1 and G2/M and apoptosis, whereas CK2-deficient MCF7 cells were resistant. These findings reveal a novel key mechanism of action for 14, suggesting primarily CK2 inhibition to be causally related to growth inhibition of human tumor cells.
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Affiliation(s)
- Xinlai Cheng
- Department of Chemistry, Division of Food Chemistry and Toxicology, University of Kaiserslautern, Erwin-Schrödinger-Str. 52, D-67663 Kaiserslautern, Germany; Department of Pharmacy and Molecular Biotechnology, Division of Pharmaceutical Biology, University of Heidelberg, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany.
| | - Karl-Heinz Merz
- Department of Chemistry, Division of Food Chemistry and Toxicology, University of Kaiserslautern, Erwin-Schrödinger-Str. 52, D-67663 Kaiserslautern, Germany
| | - Sandra Vatter
- Department of Chemistry, Division of Food Chemistry and Toxicology, University of Kaiserslautern, Erwin-Schrödinger-Str. 52, D-67663 Kaiserslautern, Germany
| | - Jochen Christ
- Department of Chemistry, Division of Food Chemistry and Toxicology, University of Kaiserslautern, Erwin-Schrödinger-Str. 52, D-67663 Kaiserslautern, Germany
| | - Stefan Wölfl
- Department of Pharmacy and Molecular Biotechnology, Division of Pharmaceutical Biology, University of Heidelberg, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
| | - Gerhard Eisenbrand
- Department of Chemistry, Division of Food Chemistry and Toxicology, University of Kaiserslautern, Erwin-Schrödinger-Str. 52, D-67663 Kaiserslautern, Germany
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Brockhauser S, Svensson O, Bowler MW, Nanao M, Gordon E, Leal RMF, Popov A, Gerring M, McCarthy AA, Gotz A. The use of workflows in the design and implementation of complex experiments in macromolecular crystallography. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:975-84. [PMID: 22868763 PMCID: PMC3413211 DOI: 10.1107/s090744491201863x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Accepted: 04/25/2012] [Indexed: 11/10/2022]
Abstract
The automation of beam delivery, sample handling and data analysis, together with increasing photon flux, diminishing focal spot size and the appearance of fast-readout detectors on synchrotron beamlines, have changed the way that many macromolecular crystallography experiments are planned and executed. Screening for the best diffracting crystal, or even the best diffracting part of a selected crystal, has been enabled by the development of microfocus beams, precise goniometers and fast-readout detectors that all require rapid feedback from the initial processing of images in order to be effective. All of these advances require the coupling of data feedback to the experimental control system and depend on immediate online data-analysis results during the experiment. To facilitate this, a Data Analysis WorkBench (DAWB) for the flexible creation of complex automated protocols has been developed. Here, example workflows designed and implemented using DAWB are presented for enhanced multi-step crystal characterizations, experiments involving crystal reorientation with kappa goniometers, crystal-burning experiments for empirically determining the radiation sensitivity of a crystal system and the application of mesh scans to find the best location of a crystal to obtain the highest diffraction quality. Beamline users interact with the prepared workflows through a specific brick within the beamline-control GUI MXCuBE.
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Affiliation(s)
- Sandor Brockhauser
- European Molecular Biology Laboratory, 6 Rue Jules Horowitz, BP 181, 38042 Grenoble, France.
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Huang H, Zhao R, Dickson BM, Skeel RD, Post CB. αC helix as a switch in the conformational transition of Src/CDK-like kinase domains. J Phys Chem B 2012; 116:4465-75. [PMID: 22448785 DOI: 10.1021/jp301628r] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One mechanism of regulating the catalytic activity of protein kinases is through conformational transitions. Despite great diversity in the structural changes involved in the transitions, a certain set of changes within the kinase domain (KD) has been observed for many kinases including Src and CDK2. We investigated this conformational transition computationally to identify the topological features that are energetically critical to the transition. Results from both molecular dynamics sampling and transition path optimization highlight the displacement of the αC helix as the major energy barrier, mediating the switch of the KD between the active and down-regulated states. The critical role of the αC helix is noteworthy by providing a rationale for a number of activation and deactivation mechanisms known to occur in cells. We find that kinases with the αC helix displacement exist throughout the kinome, suggesting that this feature may have emerged early in evolution.
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Affiliation(s)
- He Huang
- Department of Medicinal Chemistry and Molecular Pharmacology, Markey Center for Structural Biology and Purdue Cancer Center, Purdue University, West Lafayette, Indiana 47907, United States
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Ginzinger W, Mühlgassner G, Arion VB, Jakupec MA, Roller A, Galanski M, Reithofer M, Berger W, Keppler BK. A SAR study of novel antiproliferative ruthenium and osmium complexes with quinoxalinone ligands in human cancer cell lines. J Med Chem 2012; 55:3398-413. [PMID: 22417128 DOI: 10.1021/jm3000906] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of ruthenium(II) arene complexes with 3-(1H-benzimidazol-2-yl)-1H-quinoxalin-2-one, bearing pharmacophoric groups of known protein kinase inhibitors, and related benzoxazole and benzothiazole derivatives have been synthesized. In addition, the corresponding osmium complexes of the unsubstituted ligands have also been prepared. The compounds have been characterized by NMR, UV-vis, and IR spectroscopy, ESI mass spectrometry, elemental analysis, and by X-ray crystallography. Antiproliferative activity in three human cancer cell lines (A549, CH1, SW480) was determined by MTT assays, yielding IC(50) values of 6-60 μM for three unsubstituted metal-free ligands, whereas values for the metal complexes vary in a broad range from 0.3 to 140 μM. Complexation with osmium of quinoxalinone derivatives with benzimidazole or benzothiazole results in a more consistent increase in cytotoxicity than complexation with ruthenium. For selected compounds, the capacity to induce apoptosis was confirmed by fluorescence microscopy and flow-cytometric analysis, whereas cell cycle effects are only moderate.
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Affiliation(s)
- Werner Ginzinger
- University of Vienna, Institute of Inorganic Chemistry, Währinger Strasse 42, A-1090 Vienna, Austria
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Abstract
Protein phosphorylation is a fundamental post-translational modification. It regulates a large number of critical cellular processes (differentiation, division, proliferation, apoptosis). Cell division is a process including a series of phases by which a parent cell divides into two daughter cells. The cells enter these stages then progress within the cell division under an accurate control by many proteins. These proteins are activated by phosphorylation. Cyclin-dependent kinases are responsible for this phosphorylation and therefore represent potential therapeutic targets especially in oncology.
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Synthesis of a dual functional anti-MDR tumor agent PH II-7 with elucidations of anti-tumor effects and mechanisms. PLoS One 2012; 7:e32782. [PMID: 22403708 PMCID: PMC3293869 DOI: 10.1371/journal.pone.0032782] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Accepted: 02/02/2012] [Indexed: 11/24/2022] Open
Abstract
Multidrug resistance mediated by P-glycoprotein in cancer cells has been a major issue that cripples the efficacy of chemotherapy agents. Aimed for improved efficacy against resistant cancer cells, we designed and synthesized 25 oxindole derivatives based on indirubin by structure-activity relationship analysis. The most potent one was named PH II-7, which was effective against 18 cancer cell lines and 5 resistant cell lines in MTT assay. It also significantly inhibited the resistant xenograft tumor growth in mouse model. In cell cycle assay and apoptosis assay conducted with flow cytometry, PH II-7 induced S phase cell cycle arrest and apoptosis even in resistant cells. Consistently revealed by real-time PCR, it modulates the expression of genes related to the cell cycle and apoptosis in these cells, which may contributes to its efficacy against them. By side-chain modification and FITC-labeling of PH II-7, we were able to show with confocal microscopy that not only it was not pumped by P-glycoprotein, it also attenuated the efflux of Adriamycin by P-glycoprotein in MDR tumor cells. Real-time PCR and western blot analysis showed that PH II-7 down-regulated MDR1 gene via protein kinase C alpha (PKCA) pathway, with c-FOS and c-JUN as possible mediators. Taken together, PH II-7 is a dual-functional compound that features both the cytotoxicity against cancer cells and the inhibitory effect on P-gp mediated drug efflux.
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Virtudazo EV, Suganami A, Tamura Y, Kawamoto S. Towards understanding cell cycle control in Cryptococcus neoformans: structure-function relationship of G1 and G1/S cyclins homologue CnCln1. Biochem Biophys Res Commun 2011; 416:217-21. [PMID: 22119191 DOI: 10.1016/j.bbrc.2011.11.040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2011] [Accepted: 11/08/2011] [Indexed: 12/18/2022]
Abstract
We have previously reported that only a single Cdk1-related G1 and G1/S cyclin homologue was found in the genome sequence of the pathogenic basidiomycetous yeast Cryptococcus neoformans (C. neoformans) and designated it CnCln1. Surprisingly, CnCln1 was not only able to complement the function of the G1 cyclins of the ascomycetous budding yeast Saccharomyces cerevisiae (S. cerevisiae), such as ScCln3, but also the G1/S cyclins of S. cerevisiae, such as ScCln1 and ScCln2. In this study, we investigated how CnCln1 cooperates with the cyclin-dependent kinases of S. cerevisiae (ScCdk1) and substitutes the function of G1 and G1/S cyclins of S. cerevisia from a point of view of their structure-function relationship. Our in silico analysis demonstrated that the CnCln1/ScCdk1 complex was more stable than any of the yeast cyclin and ScCdk1complexes. Thus, these results are consistent with in vitro analysis that has revealed the flexible functional capacity of CnCln1 as a Cdk1-related G1 and G1/S cyclins of S. cerevisiae.
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Affiliation(s)
- Eric V Virtudazo
- Division of Molecular Biology, Medical Mycology Research Center, Chiba University, Chiba 260-8673, Japan
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50
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Fischer JR, Lessel U, Rarey M. Improving Similarity-Driven Library Design: Customized Matching and Regioselective Feature Trees. J Chem Inf Model 2011; 51:2156-63. [DOI: 10.1021/ci200014g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J. Robert Fischer
- Center for Bioinformatics (ZBH), University of Hamburg, Hamburg, Germany
| | - Uta Lessel
- Department of Lead Identification and Optimization Support, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Matthias Rarey
- Center for Bioinformatics (ZBH), University of Hamburg, Hamburg, Germany
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