1
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Ueno H, Sano M, Hara M, Noji H. Digital Cascade Assays for ADP- or ATP-Producing Enzymes Using a Femtoliter Reactor Array Device. ACS Sens 2023; 8:3400-3407. [PMID: 37590841 PMCID: PMC10521141 DOI: 10.1021/acssensors.3c00587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/31/2023] [Indexed: 08/19/2023]
Abstract
Digital enzyme assays are emerging biosensing methods for highly sensitive quantitative analysis of biomolecules with single-molecule detection sensitivity. However, current digital enzyme assays require a fluorogenic substrate for detection, which limits the applicability of this method to certain enzymes. ATPases and kinases are representative enzymes for which fluorogenic substrates are not available; however, these enzymes form large domains and play a central role in biology. In this study, we implemented a fluorogenic cascade reaction in a femtoliter reactor array device to develop a digital bioassay platform for ATPases and kinases. The digital cascade assay enabled quantitative measurement of the single-molecule activity of F1-ATPase, the catalytic portion of ATP synthase. We also demonstrated a digital assay for human choline kinase α. Furthermore, we developed a digital cascade assay for ATP-synthesizing enzymes and demonstrated a digital assay for pyruvate kinase. These results show the high versatility of this assay platform. Thus, the digital cascade assay has great potential for the highly sensitive detection and accurate characterization of various ADP- and ATP-producing enzymes, such as kinases, which may serve as disease biomarkers.
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Affiliation(s)
| | - Mio Sano
- Department of Applied Chemistry,
Graduate School of Engineering, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Digital Bioanalysis Laboratory, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Mayu Hara
- Department of Applied Chemistry,
Graduate School of Engineering, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Digital Bioanalysis Laboratory, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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2
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Luque-Navarro PM, Carrasco-Jiménez MP, Goracci L, Paredes JM, Espinar-Barranco L, Valverde-Pozo J, Torretta A, Parisini E, Mariotto E, Marchioro C, Laso A, Marco C, Viola G, Lanari D, López Cara LC. New bioisosteric sulphur-containing choline kinase inhibitors with a tracked mode of action. Eur J Med Chem 2023; 246:115003. [PMID: 36493617 DOI: 10.1016/j.ejmech.2022.115003] [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: 09/01/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Since the identification of human choline kinase as a protein target against cancer progression, many compounds have been designed to inhibit its function and reduce the biosynthesis of phosphatidylcholine. Herein, we propose a series of bioisosteric inhibitors that are based on the introduction of sulphur and feature improved activity and lipophilic/hydrophilic balance. The evaluation of the inhibitory and of the antiproliferative properties of the PL (dithioethane) and FP (disulphide) libraries led to the identification of PL 48, PL 55 and PL 69 as the most active compounds of the series. Docking analysis using FLAP suggests that for hits to leads, binding mostly involves an interaction with the Mg2+ cofactor, or its destabilization. The most active compounds of the two series are capable of inducing apoptosis following the mitochondrial pathway and to significantly reduce the expression of anti-apoptotic proteins such as the Mcl-1. The fluorescence properties of the compounds of the PL library allowed the tracking of their mode of action, while PAINS (Pan Assays Interference Structures) filtration databases suggest the lack of any unspecific biological response.
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Affiliation(s)
- Pilar M Luque-Navarro
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, University of Granada, Campus of Cartuja s/n, Granada, 18071, Spain; Department of Pharmaceutical Sciences, University of Perugia, Perugia, 06123 Italy
| | - M Paz Carrasco-Jiménez
- Department of Biochemistry and Molecular Biology I, University of Granada, Campus of Fuentenueva s/n, Granada, 18071, Spain.
| | - Laura Goracci
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, 06123, Italy
| | - Jose M Paredes
- Department of Physical-Chemistry, Faculty of Pharmacy, University of Granada, Campus of Cartuja s/n, Granada, 18071, Spain
| | - Laura Espinar-Barranco
- Department of Physical-Chemistry, Faculty of Pharmacy, University of Granada, Campus of Cartuja s/n, Granada, 18071, Spain
| | - Javier Valverde-Pozo
- Department of Physical-Chemistry, Faculty of Pharmacy, University of Granada, Campus of Cartuja s/n, Granada, 18071, Spain
| | - Archimede Torretta
- Center for Nano Science and Technology @PoliMi, Istituto Italiano di Tecnologia, Via Pascoli 70/3, Milano, 20133, Italy
| | - Emilio Parisini
- Center for Nano Science and Technology @PoliMi, Istituto Italiano di Tecnologia, Via Pascoli 70/3, Milano, 20133, Italy; Department of Biotechnology, Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV, 1006, Latvia; Department of Chemistry "G. Ciamician", University of Bologna, Via Selmi 2, Bologna, 40126, Italy
| | - Elena Mariotto
- Department of Woman's and Child's Health, Laboratory of Oncohematology, University of Padova, Padova, 35128, Italy
| | - Chiara Marchioro
- Department of Woman's and Child's Health, Laboratory of Oncohematology, University of Padova, Padova, 35128, Italy
| | - Alejandro Laso
- Department of Biochemistry and Molecular Biology I, University of Granada, Campus of Fuentenueva s/n, Granada, 18071, Spain
| | - Carmen Marco
- Department of Biochemistry and Molecular Biology I, University of Granada, Campus of Fuentenueva s/n, Granada, 18071, Spain
| | - Giampietro Viola
- Department of Woman's and Child's Health, Laboratory of Oncohematology, University of Padova, Padova, 35128, Italy; Istituto di Ricerca Pediatrica (IRP) Fondazione Città della Speranza, Corso Stati Uniti 4, Padova, 35128, Italy.
| | - Daniela Lanari
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, 06123 Italy.
| | - Luisa Carlota López Cara
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, University of Granada, Campus of Cartuja s/n, Granada, 18071, Spain.
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3
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Moinul M, Khatun S, Amin SA, Jha T, Gayen S. Recent trends in fragment-based anticancer drug design strategies against different targets: A mini-review. Biochem Pharmacol 2022; 206:115301. [DOI: 10.1016/j.bcp.2022.115301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/02/2022]
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Ayotte Y, Woo S, LaPlante SR. Practical Considerations and Guidelines for Spectral Referencing for Fluorine NMR Ligand Screening. ACS OMEGA 2022; 7:13155-13163. [PMID: 35474811 PMCID: PMC9026065 DOI: 10.1021/acsomega.2c00613] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
Fluorine (19F) NMR strategies are increasingly being employed for evaluating ligand binding to macromolecules, among many other uses. 19F NMR offers many advantages as a result of its sensitive spin 1/2 nucleus, 100% natural abundance, and wide chemical shift range. Moreover, because of its absence from biological samples, one can directly monitor ligand binding without background interference from the macromolecule. Therefore, all these aforementioned features make it an attractive approach for screening compounds. However, the detection of ligand binding, especially those with weak affinities, can require interpretations of minor changes in chemical shifts. Thus, chemical shift referencing is critical for accurate measurements and interpretations. Unfortunately, one cannot rely on spectrometer indirect referencing alone, and internal chemical references have sample-dependent issues. Here, we evaluated 10 potential candidate compounds that could serve as 19F NMR chemical references. Multiple factors were systematically evaluated for each candidate to monitor the suitability for 19F NMR screening purposes. These factors include aqueous solubility, buffer compatibility, salt compatibility, aqueous stability, tolerability to pH changes, temperature changes, and compound pooling. It was concluded that there was no ideal candidate, but five compounds had properties that met the screening requirements.
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Affiliation(s)
- Yann Ayotte
- Centre
Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, 531 boulevard des Prairies, Laval, Québec H7V 1B7, Canada
- NMX
Research and Solutions Inc., 500 boulevard Cartier Ouest, Suite 6000, Laval, Québec H7V 5B7, Canada
| | - Simon Woo
- Centre
Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, 531 boulevard des Prairies, Laval, Québec H7V 1B7, Canada
- NMX
Research and Solutions Inc., 500 boulevard Cartier Ouest, Suite 6000, Laval, Québec H7V 5B7, Canada
| | - Steven R. LaPlante
- Centre
Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, 531 boulevard des Prairies, Laval, Québec H7V 1B7, Canada
- NMX
Research and Solutions Inc., 500 boulevard Cartier Ouest, Suite 6000, Laval, Québec H7V 5B7, Canada
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Fragment-to-lead tailored in silico design. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 40:44-57. [PMID: 34916022 DOI: 10.1016/j.ddtec.2021.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 06/25/2021] [Accepted: 08/11/2021] [Indexed: 02/07/2023]
Abstract
Fragment-based drug discovery (FBDD) emerged as a disruptive technology and became established during the last two decades. Its rationality and low entry costs make it appealing, and the numerous examples of approved drugs discovered through FBDD validate the approach. However, FBDD still faces numerous challenges. Perhaps the most important one is the transformation of the initial fragment hits into viable leads. Fragment-to-lead (F2L) optimization is resource-intensive and is therefore limited in the possibilities that can be actively pursued. In silico strategies play an important role in F2L, as they can perform a deeper exploration of chemical space, prioritize molecules with high probabilities of being active and generate non-obvious ideas. Here we provide a critical overview of current in silico strategies in F2L optimization and highlight their remarkable impact. While very effective, most solutions are target- or fragment- specific. We propose that fully integrated in silico strategies, capable of automatically and systematically exploring the fast-growing available chemical space can have a significant impact on accelerating the release of fragment originated drugs.
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Wang N, Brickute D, Braga M, Barnes C, Lu H, Allott L, Aboagye EO. Novel Non-Congeneric Derivatives of the Choline Kinase Alpha Inhibitor ICL-CCIC-0019. Pharmaceutics 2021; 13:1078. [PMID: 34371769 PMCID: PMC8309005 DOI: 10.3390/pharmaceutics13071078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/06/2021] [Accepted: 07/09/2021] [Indexed: 01/07/2023] Open
Abstract
Choline kinase alpha (CHKA) is a promising target for the development of cancer therapeutics. We have previously reported ICL-CCIC-0019, a potent CHKA inhibitor with high cellular activity but with some unfavorable pharmacological properties. In this work, we present an active analogue of ICL-CCIC-0019 bearing a piperazine handle (CK146) to facilitate further structural elaboration of the pharmacophore and thus improve the biological profile. Two different strategies were evaluated in this study: (1) a prodrug approach whereby selective CHKA inhibition could be achieved through modulating the activity of CK146, via the incorporation of an ε-(Ac) Lys motif, cleavable by elevated levels of histone deacetylase (HDAC) and cathepsin L (CTSL) in tumour cells; (2) a prostate-specific membrane antigen (PSMA) receptor targeted delivery strategy. Prodrug (CK145) and PSMA-targeted (CK147) derivatives were successfully synthesized and evaluated in vitro. While the exploitation of CK146 in those two strategies did not deliver the expected results, important and informative structure-activity relationships were observed and have been reported.
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Affiliation(s)
- Ning Wang
- Comprehensive Cancer Imaging Centre, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London W12 0NN, UK; (N.W.); (D.B.); (M.B.); (C.B.); (H.L.)
| | - Diana Brickute
- Comprehensive Cancer Imaging Centre, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London W12 0NN, UK; (N.W.); (D.B.); (M.B.); (C.B.); (H.L.)
| | - Marta Braga
- Comprehensive Cancer Imaging Centre, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London W12 0NN, UK; (N.W.); (D.B.); (M.B.); (C.B.); (H.L.)
| | - Chris Barnes
- Comprehensive Cancer Imaging Centre, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London W12 0NN, UK; (N.W.); (D.B.); (M.B.); (C.B.); (H.L.)
| | - Haonan Lu
- Comprehensive Cancer Imaging Centre, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London W12 0NN, UK; (N.W.); (D.B.); (M.B.); (C.B.); (H.L.)
| | - Louis Allott
- Comprehensive Cancer Imaging Centre, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London W12 0NN, UK; (N.W.); (D.B.); (M.B.); (C.B.); (H.L.)
- Positron Emission Tomography Research Centre, Faculty of Health Sciences, University of Hull, Kingston upon Hull HU6 7RX, UK
| | - Eric O. Aboagye
- Comprehensive Cancer Imaging Centre, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London W12 0NN, UK; (N.W.); (D.B.); (M.B.); (C.B.); (H.L.)
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Lacal JC, Zimmerman T, Campos JM. Choline Kinase: An Unexpected Journey for a Precision Medicine Strategy in Human Diseases. Pharmaceutics 2021; 13:788. [PMID: 34070409 PMCID: PMC8226952 DOI: 10.3390/pharmaceutics13060788] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/13/2021] [Accepted: 05/19/2021] [Indexed: 12/17/2022] Open
Abstract
Choline kinase (ChoK) is a cytosolic enzyme that catalyzes the phosphorylation of choline to form phosphorylcholine (PCho) in the presence of ATP and magnesium. ChoK is required for the synthesis of key membrane phospholipids and is involved in malignant transformation in a large variety of human tumours. Active compounds against ChoK have been identified and proposed as antitumor agents. The ChoK inhibitory and antiproliferative activities of symmetrical bispyridinium and bisquinolinium compounds have been defined using quantitative structure-activity relationships (QSARs) and structural parameters. The design strategy followed in the development of the most active molecules is presented. The selective anticancer activity of these structures is also described. One promising anticancer compound has even entered clinical trials. Recently, ChoKα inhibitors have also been proposed as a novel therapeutic approach against parasites, rheumatoid arthritis, inflammatory processes, and pathogenic bacteria. The evidence for ChoKα as a novel drug target for approaches in precision medicine is discussed.
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Affiliation(s)
- Juan Carlos Lacal
- Instituto de Investigaciones Biomédicas, CSIC, 28029 Madrid, Spain
- Instituto de Investigación Sanitaria Hospital La Paz, IDIPAZ, 28046 Madrid, Spain
| | - Tahl Zimmerman
- Food Microbiology and Biotechnology Laboratory, Department of Family and Consumer Sciences, College of Agriculture and Environmental Sciences, North Carolina University, 1601 East Market Street, Greensboro, NC 27411, USA;
| | - Joaquín M. Campos
- Departamento de Química Farmacéutica y Orgánica, Facultad de Farmacia, c/Campus de Cartuja, s/n, Universidad de Granada, 18071 Granada, Spain
- Instituto Biosanitario de Granada (ibs. GRANADA), SAS-Universidad de Granada, 18071 Granada, Spain
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Pacheco-Torres J, Penet MF, Mironchik Y, Krishnamachary B, Bhujwalla ZM. The PD-L1 metabolic interactome intersects with choline metabolism and inflammation. Cancer Metab 2021; 9:10. [PMID: 33608051 PMCID: PMC7893974 DOI: 10.1186/s40170-021-00245-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/08/2021] [Indexed: 12/14/2022] Open
Abstract
Background Harnessing the power of the immune system by using immune checkpoint inhibitors has resulted in some of the most exciting advances in cancer treatment. The full potential of this approach has, however, not been fully realized for treating many cancers such as pancreatic and breast cancer. Cancer metabolism influences many aspects of cancer progression including immune surveillance. An expanded understanding of how cancer metabolism can directly impact immune checkpoints may allow further optimization of immunotherapy. We therefore investigated, for the first time, the relationship between the overexpression of choline kinase-α (Chk-α), an enzyme observed in most cancers, and the expression of the immune checkpoint PD-L1. Methods We used small interfering RNA to downregulate Chk-α, PD-L1, or both in two triple-negative human breast cancer cell lines (MDA-MB-231 and SUM-149) and two human pancreatic ductal adenocarcinoma cell lines (Pa09C and Pa20C). The effects of the downregulation were studied at the genomic, proteomic, and metabolomic levels. The findings were compared with the results obtained by the analysis of public data from The Cancer Genome Atlas Program. Results We identified an inverse dependence between Chk-α and PD-L1 at the genomic, proteomic, and metabolomic levels. We also found that prostaglandin-endoperoxide synthase 2 (COX-2) and transforming growth factor beta (TGF-β) play an important role in this relationship. We independently confirmed this relationship in human cancers by analyzing data from The Cancer Genome Atlas Program. Conclusions Our data identified previously unknown roles of PD-L1 in cancer cell metabolic reprogramming, and revealed the immunosuppressive increased PD-L1 effect of Chk-α downregulation. These data suggest that PD-L1 regulation of metabolism may be mediated through Chk-α, COX-2, and TGF-β. The observations provide new insights that can be applied to the rational design of combinatorial therapies targeting immune checkpoints and cancer metabolism. Supplementary Information The online version contains supplementary material available at 10.1186/s40170-021-00245-w.
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Affiliation(s)
- Jesus Pacheco-Torres
- Division of Cancer Imaging Research, The Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Rm 208C Traylor Building, Baltimore, MD, 21205, USA
| | - Marie-France Penet
- Division of Cancer Imaging Research, The Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Rm 208C Traylor Building, Baltimore, MD, 21205, USA.,Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Yelena Mironchik
- Division of Cancer Imaging Research, The Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Rm 208C Traylor Building, Baltimore, MD, 21205, USA
| | - Balaji Krishnamachary
- Division of Cancer Imaging Research, The Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Rm 208C Traylor Building, Baltimore, MD, 21205, USA
| | - Zaver M Bhujwalla
- Division of Cancer Imaging Research, The Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, 720 Rutland Avenue, Rm 208C Traylor Building, Baltimore, MD, 21205, USA. .,Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. .,Department of Radiation Oncology and Molecular Radiation Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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Serrán-Aguilera L, Mariotto E, Rubbini G, Castro Navas FF, Marco C, Carrasco-Jiménez MP, Ballarotto M, Macchiarulo A, Hurtado-Guerrero R, Viola G, Lopez-Cara LC. Synthesis, biological evaluation, in silico modeling and crystallization of novel small monocationic molecules with potent antiproliferative activity by dual mechanism. Eur J Med Chem 2020; 207:112797. [PMID: 32977218 DOI: 10.1016/j.ejmech.2020.112797] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/28/2020] [Accepted: 08/30/2020] [Indexed: 12/28/2022]
Abstract
Seeking for new anticancer drugs with strong antiproliferative activity and simple molecular structure, we designed a novel series of compounds based on our previous reported pharmacophore model composed of five moieties. Antiproliferative assays on four tumoral cell lines and evaluation of Human Choline Kinase CKα1 enzymatic activity was performed for these compounds. Among tested molecules, those ones with biphenyl spacer showed betters enzymatic and antiproliferative activities (n-v). Docking and crystallization studies validate the hypothesis and confirm the results. The most active compound (t) induces a significant arrest of the cell cycle in G0/G1 phase that ultimately lead to apoptosis, following the mitochondrial pathway, as demonstrated for other choline kinase inhibitors. However additional assays reveal that the inhibition of choline uptake could also be involved in the antiproliferative outcome of this class of compounds.
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Affiliation(s)
- Lucía Serrán-Aguilera
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, Campus Cartuja S/n. University of Granada, 18010, Granada, Spain
| | - Elena Mariotto
- Department of Woman's and Child's Health, Laboratory of Oncohematology, University of Padova, 35128, Padova, Italy
| | - Gianluca Rubbini
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, Campus Cartuja S/n. University of Granada, 18010, Granada, Spain
| | - Francisco Fermín Castro Navas
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, Campus Cartuja S/n. University of Granada, 18010, Granada, Spain
| | - Carmen Marco
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, 18071, Granada, Spain
| | | | - Marco Ballarotto
- Department of Pharmaceutical Sciences, University of Perugia, Via Del Liceo 1, Perugia, 06123, Italy
| | - Antonio Macchiarulo
- Department of Pharmaceutical Sciences, University of Perugia, Via Del Liceo 1, Perugia, 06123, Italy
| | - Ramón Hurtado-Guerrero
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Institute for Biocomputation and Physics of Complex Systems (BIFI) and Laboratorio de Microscopías Avanzada (LMA), Mariano Esquillor S/n, Campus Rio Ebro, Edificio I+D; Fundacion ARAID, 50018, Zaragoza, Spain; Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, Copenhagen, Denmark
| | - Giampietro Viola
- Department of Woman's and Child's Health, Laboratory of Oncohematology, University of Padova, 35128, Padova, Italy
| | - Luisa Carlota Lopez-Cara
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, Campus Cartuja S/n. University of Granada, 18010, Granada, Spain.
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Khalil R, Usmani S, Nur-E-Alam M, Ahmed S, Ul-Haq Z. Site-directed Fragnomics and MD Simulations Approaches to Identify Interleukin-2 Inhibitors. Med Chem 2020; 17:407-417. [PMID: 33191887 DOI: 10.2174/1573406416999201113104501] [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: 04/22/2020] [Revised: 09/28/2020] [Accepted: 10/05/2020] [Indexed: 11/22/2022]
Abstract
INTRODUCTION The aberrant expression of Interleukin-2 (IL2), the chief regulator of immunity, is associated with many auto-immune diseases. At present, there is no FDA approved drug targeting IL2, which puts forth the need for small molecular inhibitors to block IL2 and its receptor interaction. METHODOLOGY Herein, we used the contemporary fragnomics approach to design novel drug-like inhibitors targeting IL2. Briefly, the RECAP (Retrosynthetic Combinatorial Analysis Procedure) package implemented in MOE (Molecular Operating Environment check) software suite was utilised to obtain fragments fulfilling the 'rule of three' criteria for fragments. The binding site of IL2 was divided into three smaller grooves, and the fragments were docked to screen their affinity for a particular site, followed by site-directed RECAP synthesis. RESULTS A focused library of 10,000 compounds was prepared by re-combining the fragments according to their affinity for a particular site as observed in docking. Docking and subsequent analysis of newly synthesised compounds identified 40 privileged leads, presenting hydrogen bonding with basic residues of the pocket. A QSAR model was implied to predict the IC50 of the compounds and to analyse the electrostatic and hydrophobic contour maps. The resulting hits were found to be modest IL2 inhibitors with predicted inhibitory activity in the range of 5.17-4.40 nM. Further Dynamic simulation studies were carried out to determine the stability of the inhibitor-IL2 complex. CONCLUSION Our findings underline the potential of the novel compounds as valuable pharmacological agents in diseases characterised by IL2 overexpression.
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Affiliation(s)
- Ruqaiya Khalil
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Saman Usmani
- Department of Pharmaceutical Chemistry, Institute of Pharmaceutical Sciences, Jinnah Sindh Medical University, Karachi, Pakistan
| | - Mohammad Nur-E-Alam
- Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O. Box. 2457, Riyadh 11451, Saudi Arabia
| | - Sarfaraz Ahmed
- Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O. Box. 2457, Riyadh 11451, Saudi Arabia
| | - Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
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11
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Rubio-Ruiz B, Serrán-Aguilera L, Hurtado-Guerrero R, Conejo-García A. Recent advances in the design of choline kinase α inhibitors and the molecular basis of their inhibition. Med Res Rev 2020; 41:902-927. [PMID: 33103259 DOI: 10.1002/med.21746] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/25/2020] [Accepted: 10/12/2020] [Indexed: 12/15/2022]
Abstract
Upregulated choline metabolism, characterized by an increase in phosphocholine (PCho), is a hallmark of oncogenesis and tumor progression. Choline kinase (ChoK), the enzyme responsible for PCho synthesis, has consequently become a promising drug target for cancer therapy and as such a significant number of ChoK inhibitors have been developed over the last few decades. More recently, due to the role of this enzyme in other pathologies, ChoK inhibitors have also been used in new therapeutic approaches against malaria and rheumatoid arthritis. Here, we review research results in the field of ChoKα inhibitors from their synthesis to the molecular basis of their binding mode. Strategies for the development of inhibitors and their selectivity on ChoKα over ChoKβ, the plasticity of the choline-binding site, the discovery of new exploitable binding sites, and the allosteric properties of this enzyme are highlighted. The outcomes summarized in this review will be a useful guide to develop new multifunctional potent drugs for the treatment of various human diseases.
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Affiliation(s)
- Belén Rubio-Ruiz
- Department of Medicinal and Organic Chemistry, Faculty of Pharmacy, University of Granada, Granada, Spain.,Pfizer-University of Granada-Andalusian Regional Government Centre for Genomics and Oncological Research (GENYO), Granada, Spain.,Biosanitary Institute of Granada (ibs.GRANADA), SAS-University of Granada, Granada, Spain
| | - Lucía Serrán-Aguilera
- Department of Medicinal and Organic Chemistry, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Ramón Hurtado-Guerrero
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain.,Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark.,Laboratorio de Microscopías Avanzada, University of Zaragoza, Zaragoza, Spain.,ARAID Foundation, Zaragoza, Spain
| | - Ana Conejo-García
- Department of Medicinal and Organic Chemistry, Faculty of Pharmacy, University of Granada, Granada, Spain.,Biosanitary Institute of Granada (ibs.GRANADA), SAS-University of Granada, Granada, Spain
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12
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Troelsen NS, Clausen MH. Library Design Strategies To Accelerate Fragment‐Based Drug Discovery. Chemistry 2020; 26:11391-11403. [DOI: 10.1002/chem.202000584] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/26/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Nikolaj S. Troelsen
- Center for Nanomedicine and Theranostics Department of Chemistry Technical University of Denmark Kemitorvet 207 2800 Kongens Lyngby Denmark
| | - Mads H. Clausen
- Center for Nanomedicine and Theranostics Department of Chemistry Technical University of Denmark Kemitorvet 207 2800 Kongens Lyngby Denmark
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13
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Zoeller RA, Geoghegan-Barek K. A cell-based high-throughput screen identifies tyrphostin AG 879 as an inhibitor of animal cell phospholipid and fatty acid biosynthesis. Biochem Biophys Rep 2019; 18:100621. [PMID: 30899803 PMCID: PMC6406593 DOI: 10.1016/j.bbrep.2019.100621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 02/18/2019] [Indexed: 01/02/2023] Open
Abstract
Inhibition of animal cell phospholipid biosynthesis has been proposed for anticancer and antiviral therapies. Using CHO—K1 derived cell lines, we have developed and used a cell-based high-throughput procedure to screen a 1280 compound, small molecule library for inhibitors of phospholipid biosynthesis. We identified tyrphostin AG 879 (AG879), which inhibited phospholipid biosynthesis by 85–90% at a concentration of 10 μM, displaying an IC50 of 1–3 μM. The synthesis of all phospholipid head group classes was heavily affected. Fatty acid biosynthesis was also dramatically inhibited (90%). AG879 inhibited phospholipid biosynthesis in all additional cell lines tested, including MDCK, HUH7, Vero, and HeLa cell lines. In CHO cells, AG879 was cytostatic; cells survived for at least four days during exposure and were able to divide following its removal. AG879 is an inhibitor of receptor tyrosine kinases (RTK) and inhibitors of signaling pathways known to be activated by RTK's also inhibited phospholipid biosynthesis. We speculate that inhibition of RTK by AG879 results in an inhibition of fatty acid biosynthesis with a resulting decrease in phospholipid biosynthesis and that AG879's effect on fatty acid synthesis and/or phospholipid biosynthesis may contribute to its known capacity as an effective antiviral/anticancer agent.
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Key Words
- 32Pi, [32P]orthophosphate
- AFU, Arbitrary fluorescence units
- AG879, Tyrphostin AG 879
- Anticancer
- Antiviral
- CE, Cholesterol ester
- CL, Cardiolipin
- Drug screening
- EGFR, Epidermal growth factor receptor
- Fatty acid biosynthesis
- HER2, Human epidermal growth factor receptor 2
- HTS, High-throughput screen
- P12, 12-(1′-pyrene) dodecanoic acid
- PA, Phosphatidic acid
- PC, Phosphatidylcholine
- PE, Phosphatidylethanolamine
- PI, Phosphatidylinositol
- PL, Phospholipid
- Phospholipid biosynthesis
- RTK, Receptor tyrosine kinase
- TG, Triacylglycerol
- Tyrphostin AG 879
- trkA, Tropomyosin analogue receptor kinase
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Affiliation(s)
- Raphael A Zoeller
- Department of Physiology & Biophysics, Boston University School of Medicine, 700 Albany Street, Room W302, Boston, MA, 02118, USA
| | - Kathleen Geoghegan-Barek
- Department of Physiology & Biophysics, Boston University School of Medicine, 700 Albany Street, Room W302, Boston, MA, 02118, USA
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14
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Jones DT, Valli A, Haider S, Zhang Q, Smethurst EA, Schug ZT, Peck B, Aboagye EO, Critchlow SE, Schulze A, Gottlieb E, Wakelam MJO, Harris AL. 3D Growth of Cancer Cells Elicits Sensitivity to Kinase Inhibitors but Not Lipid Metabolism Modifiers. Mol Cancer Ther 2019; 18:376-388. [PMID: 30478149 PMCID: PMC6611711 DOI: 10.1158/1535-7163.mct-17-0857] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 09/16/2018] [Accepted: 11/09/2018] [Indexed: 12/22/2022]
Abstract
Tumor cells exhibit altered lipid metabolism compared with normal cells. Cell signaling kinases are important for regulating lipid synthesis and energy storage. How upstream kinases regulate lipid content, versus direct targeting of lipid-metabolizing enzymes, is currently unexplored. We evaluated intracellular lipid concentrations in prostate and breast tumor spheroids, treated with drugs directly inhibiting metabolic enzymes fatty acid synthase (FASN), acetyl-CoA carboxylase (ACC), diacylglyceride acyltransferase (DGAT), and pyruvate dehydrogenase kinase (PDHK), or cell signaling kinase enzymes PI3K, AKT, and mTOR with lipidomic analysis. We assessed whether baseline lipid profiles corresponded to inhibitors' effectiveness in modulating lipid profiles in three-dimensional (3D) growth and their relationship to therapeutic activity. Inhibitors against PI3K, AKT, and mTOR significantly inhibited MDA-MB-468 and PC3 cell growth in two-dimensional (2D) and 3D spheroid growth, while moderately altering lipid content. Conversely, metabolism inhibitors against FASN and DGAT altered lipid content most effectively, while only moderately inhibiting growth compared with kinase inhibitors. The FASN and ACC inhibitors' effectiveness in MDA-MB-468, versus PC3, suggested the former depended more on synthesis, whereas the latter may salvage lipids. Although baseline lipid profiles did not predict growth effects, lipid changes on therapy matched the growth effects of FASN and DGAT inhibitors. Several phospholipids, including phosphatidylcholine, were also upregulated following treatment, possibly via the Kennedy pathway. As this promotes tumor growth, combination studies should include drugs targeting it. Two-dimensional drug screening may miss important metabolism inhibitors or underestimate their potency. Clinical studies should consider serial measurements of tumor lipids to prove target modulation. Pretherapy tumor classification by de novo lipid synthesis versus uptake may help demonstrate efficacy.
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Affiliation(s)
- Dylan T Jones
- Target Discovery Institute, NDM Research Building, Old Road Campus, Headington, Oxford, United Kingdom.
| | - Alessandro Valli
- Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Syed Haider
- Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, London, United Kingdom
| | - Qifeng Zhang
- Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Elizabeth A Smethurst
- Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- Cancer Research UK, Angel Building, Clerkenwell, London, United Kingdom
| | | | - Barrie Peck
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Eric O Aboagye
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, United Kingdom
| | - Susan E Critchlow
- Bioscience, Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, United Kingdom
| | - Almut Schulze
- Theodor-Boveri-Institute, Bicenter, Am Hubland, Würzburg, Germany; and Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - Eyal Gottlieb
- Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, Israel
| | | | - Adrian L Harris
- Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
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15
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Dalvit C, Vulpetti A. Ligand-Based Fluorine NMR Screening: Principles and Applications in Drug Discovery Projects. J Med Chem 2018; 62:2218-2244. [DOI: 10.1021/acs.jmedchem.8b01210] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | - Anna Vulpetti
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
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16
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Lead optimization-hit expansion of new asymmetrical pyridinium/quinolinium compounds as choline kinase α1 inhibitors. Future Med Chem 2018; 10:1769-1786. [PMID: 30043647 DOI: 10.4155/fmc-2018-0059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
AIM Choline kinase α inhibitors represent one of the newest classes of cytotoxic drugs for cancer treatment, since aberrant choline metabolism is a characteristic shared by many human cancers. RESULTS Here, we present a new class of asymmetrical pyridinium/quinolinium derivatives developed and designed based on drug optimization. CONCLUSION Among all compounds described here, compound 8, bearing a 7-chloro-4N-methyl-p-chloroaniline quinolinium moiety, exhibited the greatest inhibitory activity at the enzyme (IC50 = 0.29 μM) and antiproliferative activity in cellular assays (GI50 = 0.29-0.92 μM). Specifically, compound 8 strongly induces a cell-cycle arrest in G1 phase, but it does not significantly induce apoptosis while causing senescence in the MDA-MB-231 cell line.
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17
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Mariotto E, Bortolozzi R, Volpin I, Carta D, Serafin V, Accordi B, Basso G, Navarro PL, López-Cara LC, Viola G. EB-3D a novel choline kinase inhibitor induces deregulation of the AMPK-mTOR pathway and apoptosis in leukemia T-cells. Biochem Pharmacol 2018; 155:213-223. [PMID: 30006194 DOI: 10.1016/j.bcp.2018.07.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/09/2018] [Indexed: 11/26/2022]
Abstract
Choline kinase alpha 1 (ChoKα1) has recently become an interesting therapeutic target since its overexpression has been associated to tumorigenesis in many cancers. Nevertheless, little is known regarding hematological malignancies. In this manuscript, we investigated the effect of a novel and selective ChoKα inhibitor EB-3D in T acute lymphoblastic leukemia (T-ALL). The effect of EB-3D was evaluated in a panel of T-leukemia cell lines and ex-vivo primary cultures derived from pediatric T-ALL patients. We also evaluated in detail, using Reverse Phase Protein Array (RPPA), protein phosphorylation level changes in T-ALL cells upon treatment. The drug exhibits a potent antiproliferative activity in a panel of T-leukemia cell lines and primary cultures of pediatric patients. Moreover, the drug strongly induces apoptosis and more importantly it enhanced T-leukemia cell sensitivity to chemotherapeutic agents, such as dexamethasone and l-asparaginase. In addition, the compound induces an early activation of AMPK, the main regulator of cellular energy homeostasis, by its phosphorylation at residue T712 of catalytic subunit α, and thus repressing mTORC1 pathway, as shown by mTOR S2448 dephosphorylation. The inhibition of mTOR in turn affects the activity of several known downstream targets, such as 4E-BP1, p70S6K, S6 Ribosomal Protein and GSK3 that ultimately may lead to a reduction of protein synthesis and cell death. Taken together, our findings suggest that targeting ChoKα may be an interesting option for treating T-ALL and that EB-3D could represent a valuable therapeutic tool.
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Affiliation(s)
- Elena Mariotto
- Department of Woman's and Child's Health, Oncohematology Laboratory, University of Padova, 35128 Padova, Italy.
| | - Roberta Bortolozzi
- Department of Woman's and Child's Health, Oncohematology Laboratory, University of Padova, 35128 Padova, Italy
| | - Ilaria Volpin
- Department of Woman's and Child's Health, Oncohematology Laboratory, University of Padova, 35128 Padova, Italy
| | - Davide Carta
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy
| | - Valentina Serafin
- Department of Woman's and Child's Health, Oncohematology Laboratory, University of Padova, 35128 Padova, Italy
| | - Benedetta Accordi
- Department of Woman's and Child's Health, Oncohematology Laboratory, University of Padova, 35128 Padova, Italy
| | - Giuseppe Basso
- Department of Woman's and Child's Health, Oncohematology Laboratory, University of Padova, 35128 Padova, Italy
| | - Pilar Luque Navarro
- Departamento de Química Farmacéutica y Orgánica, Facultad de Farmacia, Campus de Cartuja, 18071 Granada, Spain
| | - Luisa Carlota López-Cara
- Departamento de Química Farmacéutica y Orgánica, Facultad de Farmacia, Campus de Cartuja, 18071 Granada, Spain
| | - Giampietro Viola
- Department of Woman's and Child's Health, Oncohematology Laboratory, University of Padova, 35128 Padova, Italy.
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18
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Hu L, Wang RY, Cai J, Feng D, Yang GZ, Xu QG, Zhai YX, Zhang Y, Zhou WP, Cai QP. Overexpression of CHKA contributes to tumor progression and metastasis and predicts poor prognosis in colorectal carcinoma. Oncotarget 2018; 7:66660-66678. [PMID: 27556502 PMCID: PMC5341828 DOI: 10.18632/oncotarget.11433] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 08/13/2016] [Indexed: 12/13/2022] Open
Abstract
Aberrant expression of choline kinase alpha (CHKA) has been reported in a variety of human malignancies including colorectal carcinoma (CRC). However, the role of CHKA in the progression and prognosis of CRC remains unknown. In this study, we found that CHKA was frequently upregulated in CRC clinical samples and CRC-derived cell lines and was significantly correlated with lymph node metastasis (p = 0.028), TNM stage (p = 0.009), disease recurrence (p = 0.004) and death (p < 0.001). Survival analyses indicated that patients with higher CHKA expression had a significantly shorter disease-free survival (DFS) and disease-specific survival (DSS) than those with lower CHKA expression. Multivariate analyses confirmed that increased CHKA expression was an independent unfavorable prognostic factor for CRC patients. In addition, combination of CHKA with TNM stage was a more powerful predictor of poor prognosis than either parameter alone. Functional study demonstrated that knockdown of CHKA expression profoundly suppressed the growth and metastasis of CRC cells both in vitro and in vivo. Mechanistic investigation revealed that EGFR/PI3K/AKT pathway was essential for mediating CHKA function. In conclusion, our results provide the first evidence that CHKA contributes to tumor progression and metastasis and may serve as a novel prognostic biomarker and potential therapeutic target in CRC.
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Affiliation(s)
- Liang Hu
- Anal-Colorectal Surgery Institute, 150th Hospital of PLA, Luoyang, China.,Department of Gastrointestine Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Ruo-Yu Wang
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Jian Cai
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Dan Feng
- Department of Oncology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Guang-Zhen Yang
- Department of Clinical Laboratory, 150th Hospital of PLA, Luoyang, China
| | - Qing-Guo Xu
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Yan-Xia Zhai
- Anal-Colorectal Surgery Institute, 150th Hospital of PLA, Luoyang, China
| | - Yu Zhang
- Anal-Colorectal Surgery Institute, 150th Hospital of PLA, Luoyang, China
| | - Wei-Ping Zhou
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Qing-Ping Cai
- Department of Gastrointestine Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
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19
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Kall SL, Delikatny EJ, Lavie A. Identification of a Unique Inhibitor-Binding Site on Choline Kinase α. Biochemistry 2018; 57:1316-1325. [PMID: 29389115 DOI: 10.1021/acs.biochem.7b01257] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Choline kinase α (ChoKα) is an enzyme that is upregulated in many types of cancer and has been shown to be tumorigenic. As such, it makes a promising target for inhibiting tumor growth. Though there have been several inhibitors synthesized for ChoKα, not all of them demonstrate the same efficacy in vivo, though the reasons behind this difference in potency are not clear. One particular inhibitor, designated TCD-717, has recently completed phase I clinical trials. Cell culture and in vitro studies support the powerful inhibitory effect TCD-717 has on ChoKα, but an examination of the inhibitor's interaction with the ChoKα enzyme has been missing prior to this work. Here we detail the 2.35 Å structure of ChoKα in complex with TCD-717. Examination of this structure in conjunction with kinetic assays reveals that TCD-717 does not bind directly in the choline pocket as do previously characterized ChoKα inhibitors, but rather in a proximal but novel location near the surface of the enzyme. The unique binding site identified for TCD-717 lends insight for the future design of more potent in vivo inhibitors for ChoKα.
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Affiliation(s)
- Stefanie L Kall
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago , Chicago, Illinois 60607, United States
| | - Edward J Delikatny
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania 19083, United States
| | - Arnon Lavie
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago , Chicago, Illinois 60607, United States.,The Jesse Brown VA Medical Center , Chicago, Illinois 60612, United States
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20
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Dalvit C, Knapp S. 19 F NMR isotropic chemical shift for efficient screening of fluorinated fragments which are racemates and/or display multiple conformers. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:1091-1095. [PMID: 28762528 DOI: 10.1002/mrc.4640] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 07/12/2017] [Accepted: 07/29/2017] [Indexed: 06/07/2023]
Abstract
Fluorine ligand-based NMR spectroscopy is now an established method for performing binding screening against a macromolecular target. Typically, the transverse relaxation rate of the fluorine signals is monitored in the absence and presence of the target. However, useful structural information can sometimes be obtained from the analysis of the fluorine isotropic chemical shift. This is particularly relevant for molecules that are racemates and/or display multiple conformers. The large difference in fluorine isotropic chemical shift between free and bound state deriving mainly from the breaking and/or making of intramolecular and/or intermolecular hydrogen bonds allows the detection of very weak affinity ligands. According to our experimental results, racemates should always be included in the generation of the fluorinated fragment libraries. The selection or the availability of only one of the enantiomers for the fluorinated screening library could result in missing relevant chemical scaffold motifs.
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Affiliation(s)
- Claudio Dalvit
- Faculty of Science, University of Neuchatel, 2000, Neuchatel, Switzerland
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Riedberg Campus, 60438, Frankfurt, Germany
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Oxford University, Oxford, OX3 7DQ, UK
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21
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Ángeles Canales M, Félix Espinosa J. Ligand-detected NMR Methods in Drug Discovery. BIOPHYSICAL TECHNIQUES IN DRUG DISCOVERY 2017. [DOI: 10.1039/9781788010016-00023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
This book chapter describes the basic principles of NMR-based techniques for detecting ligand binding and uses examples of the application of these techniques in drug discovery programs for screening, hit validation and optimization to illustrate their utility in characterizing ligand–protein interactions. The binding of small molecules to biological receptors can be observed directly by detecting changes in a particular NMR parameter when the protein is added to a sample containing the ligand, or indirectly, using a “spy” molecule in competitive NMR experiments. Combinations of different NMR experiments can be used to confirm binding and also to obtain structural information that can be used to guide medicinal chemistry decisions. Ligand-observed NMR methods are able to identify weak affinity ligands that cannot be detected by other biophysical techniques, which means that NMR-based methods are extremely valuable tools for fragment-based drug discovery approaches.
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Affiliation(s)
- María Ángeles Canales
- Department of Química Orgánica I, Universidad Complutense de Madrid Avd. Complutense s/n 28040 Madrid Spain
| | - Juan Félix Espinosa
- Centro de Investigación Lilly Avda. de la Industria 30 28108, Alcobendas, Madrid Spain
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22
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Johnson CN, Erlanson DA, Jahnke W, Mortenson PN, Rees DC. Fragment-to-Lead Medicinal Chemistry Publications in 2016. J Med Chem 2017; 61:1774-1784. [PMID: 29087197 DOI: 10.1021/acs.jmedchem.7b01298] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The popularity of fragment-based drug discovery (FBDD) is demonstrated by the number of recent successful fragment-to-lead (F2L) publications. This Miniperspective provides a tabulated summary of the F2L literature published in the year 2016, along with discussion of general trends. It uses the same format as our summary of the 2015 literature and is intended to be a resource for both FBDD practitioners and medicinal chemists in general.
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Affiliation(s)
- Christopher N Johnson
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge CB4 0QA , United Kingdom
| | - Daniel A Erlanson
- Carmot Therapeutics Inc. , 740 Heinz Avenue , Berkeley , California 94710 , United States
| | - Wolfgang Jahnke
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics , 4002 Basel , Switzerland
| | - Paul N Mortenson
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge CB4 0QA , United Kingdom
| | - David C Rees
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge CB4 0QA , United Kingdom
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23
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Rubio-Ruiz B, Ríos-Marco P, Carrasco-Jiménez MP, Espinosa A, Hurtado-Guerrero R, Marco C, Conejo-García A, Entrena A. Choline kinase inhibition and docking studies of a series of 6-(benzylthio)-9H-purin-9-yl-pyridinium derivatives. Med Chem Res 2017. [DOI: 10.1007/s00044-017-1979-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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24
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Dalvit C, Piotto M. 19 F NMR transverse and longitudinal relaxation filter experiments for screening: a theoretical and experimental analysis. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:106-114. [PMID: 27514284 DOI: 10.1002/mrc.4500] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 08/09/2016] [Indexed: 06/06/2023]
Abstract
Ligand-based 19 F NMR screening represents an efficient approach for performing binding assays. The high sensitivity of the methodology to receptor binding allows the detection of weak affinity ligands. The observable NMR parameters that are typically used are the 19 F transverse relaxation rate and isotropic chemical shift. However, there are few cases where the 19 F longitudinal relaxation rate should also be used. A theoretical and experimental analysis of the 19 F NMR transverse and longitudinal relaxation rates at different magnetic fields is presented along with proposed methods for improving the sensitivity and dynamic range of these experiments applied to fragment-based screening. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Claudio Dalvit
- Faculty of Science, University of Neuchatel, Neuchatel, Switzerland
- IDD/SDI, Sanofi, Vitry-sur-Seine, France
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25
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Chen X, Qiu H, Wang C, Yuan Y, Tickner J, Xu J, Zou J. Molecular structure and differential function of choline kinases CHKα and CHKβ in musculoskeletal system and cancer. Cytokine Growth Factor Rev 2016; 33:65-72. [PMID: 27769579 DOI: 10.1016/j.cytogfr.2016.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 10/04/2016] [Accepted: 10/06/2016] [Indexed: 12/20/2022]
Abstract
Choline, a hydrophilic cation, has versatile physiological roles throughout the body, including cholinergic neurotransmission, memory consolidation and membrane biosynthesis and metabolism. Choline kinases possess enzyme activity that catalyses the conversion of choline to phosphocholine, which is further converted to cytidine diphosphate-coline (CDP-choline) in the biosynthesis of phosphatidylcholine (PC). PC is a major constituent of the phospholipid bilayer which constitutes the eukaryotic cell membrane, and regulates cell signal transduction. Choline Kinase consists of three isoforms, CHKα1, CHKα2 and CHKβ, encoded by two separate genes (CHKA(Human)/Chka(Mouse) and CHKB(Human)/Chkb(Mouse)). Both isoforms have similar structures and enzyme activity, but display some distinct molecular structural domains and differential tissue expression patterns. Whilst Choline Kinase was discovered in early 1950, its pivotal role in the development of muscular dystrophy, bone deformities, and cancer has only recently been identified. CHKα has been proposed as a cancer biomarker and its inhibition as an anti-cancer therapy. In contrast, restoration of CHKβ deficiency through CDP-choline supplements like citicoline may be beneficial for the treatment of muscular dystrophy, bone metabolic diseases, and cognitive conditions. The molecular structure and expression pattern of Choline Kinase, the differential roles of Choline Kinase isoforms and their potential as novel therapeutic targets for muscular dystrophy, bone deformities, cognitive conditions and cancer are discussed.
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Affiliation(s)
- Xi Chen
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, PR China; School of Sports Science, Wenzhou Medical University, Wenzhou, 325035, PR China; School of Pathology and Laboratory Medicine, The University of Western Australia, Perth, Western Australia, 6009, Australia
| | - Heng Qiu
- School of Pathology and Laboratory Medicine, The University of Western Australia, Perth, Western Australia, 6009, Australia
| | - Chao Wang
- School of Pathology and Laboratory Medicine, The University of Western Australia, Perth, Western Australia, 6009, Australia
| | - Yu Yuan
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, PR China; School of Pathology and Laboratory Medicine, The University of Western Australia, Perth, Western Australia, 6009, Australia
| | - Jennifer Tickner
- School of Pathology and Laboratory Medicine, The University of Western Australia, Perth, Western Australia, 6009, Australia
| | - Jiake Xu
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, PR China; School of Pathology and Laboratory Medicine, The University of Western Australia, Perth, Western Australia, 6009, Australia.
| | - Jun Zou
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, PR China.
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26
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Bagnoli M, Granata A, Nicoletti R, Krishnamachary B, Bhujwalla ZM, Canese R, Podo F, Canevari S, Iorio E, Mezzanzanica D. Choline Metabolism Alteration: A Focus on Ovarian Cancer. Front Oncol 2016; 6:153. [PMID: 27446799 PMCID: PMC4916225 DOI: 10.3389/fonc.2016.00153] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/07/2016] [Indexed: 12/31/2022] Open
Abstract
Compared with normal differentiated cells, cancer cells require a metabolic reprograming to support their high proliferation rates and survival. Aberrant choline metabolism is a fairly new metabolic hallmark reflecting the complex reciprocal interactions between oncogenic signaling and cellular metabolism. Alterations of the involved metabolic network may be sustained by changes in activity of several choline transporters as well as of enzymes such as choline kinase-alpha (ChoK-α) and phosphatidylcholine-specific phospholipases C and D. Of note, the net outcome of these enzymatic alterations is an increase of phosphocholine and total choline-containing compounds, a "cholinic phenotype" that can be monitored in cancer by magnetic resonance spectroscopy. This review will highlight the molecular basis for targeting this pathway in epithelial ovarian cancer (EOC), a highly heterogeneous and lethal malignancy characterized by late diagnosis, frequent relapse, and development of chemoresistance. Modulation of ChoK-α expression impairs only EOC but not normal ovarian cells, thus supporting the hypothesis that "cholinic phenotype" is a peculiar feature of transformed cells and indicating ChoK-α targeting as a novel approach to improve efficacy of standard EOC chemotherapeutic treatments.
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Affiliation(s)
- Marina Bagnoli
- Unit of Molecular Therapies, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori , Milan , Italy
| | - Anna Granata
- Unit of Molecular Therapies, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori , Milan , Italy
| | - Roberta Nicoletti
- Unit of Molecular Therapies, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori , Milan , Italy
| | - Balaji Krishnamachary
- Russell H. Morgan Department of Radiology and Radiological Science, Division of Cancer Imaging Research, In Vivo Cellular and Molecular Imaging Center, The Johns Hopkins University School of Medicine , Baltimore, MD , USA
| | - Zaver M Bhujwalla
- Russell H. Morgan Department of Radiology and Radiological Science, Division of Cancer Imaging Research, In Vivo Cellular and Molecular Imaging Center, The Johns Hopkins University School of Medicine , Baltimore, MD , USA
| | - Rossella Canese
- Department of Cell Biology and Neurosciences, Istituto Superiore di Sanità , Rome , Italy
| | - Franca Podo
- Department of Cell Biology and Neurosciences, Istituto Superiore di Sanità , Rome , Italy
| | - Silvana Canevari
- Unit of Molecular Therapies, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy; Functional Genomics and Informatics, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Egidio Iorio
- Department of Cell Biology and Neurosciences, Istituto Superiore di Sanità , Rome , Italy
| | - Delia Mezzanzanica
- Unit of Molecular Therapies, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori , Milan , Italy
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27
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Trousil S, Kaliszczak M, Schug Z, Nguyen QD, Tomasi G, Favicchio R, Brickute D, Fortt R, Twyman FJ, Carroll L, Kalusa A, Navaratnam N, Adejumo T, Carling D, Gottlieb E, Aboagye EO. The novel choline kinase inhibitor ICL-CCIC-0019 reprograms cellular metabolism and inhibits cancer cell growth. Oncotarget 2016; 7:37103-37120. [PMID: 27206796 PMCID: PMC5095062 DOI: 10.18632/oncotarget.9466] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Accepted: 04/25/2016] [Indexed: 12/25/2022] Open
Abstract
The glycerophospholipid phosphatidylcholine is the most abundant phospholipid species of eukaryotic membranes and essential for structural integrity and signaling function of cell membranes required for cancer cell growth. Inhibition of choline kinase alpha (CHKA), the first committed step to phosphatidylcholine synthesis, by the selective small-molecule ICL-CCIC-0019, potently suppressed growth of a panel of 60 cancer cell lines with median GI50 of 1.12 μM and inhibited tumor xenograft growth in mice. ICL-CCIC-0019 decreased phosphocholine levels and the fraction of labeled choline in lipids, and induced G1 arrest, endoplasmic reticulum stress and apoptosis. Changes in phosphocholine cellular levels following treatment could be detected non-invasively in tumor xenografts by [18F]-fluoromethyl-[1,2-2H4]-choline positron emission tomography. Herein, we reveal a previously unappreciated effect of choline metabolism on mitochondria function. Comparative metabolomics demonstrated that phosphatidylcholine pathway inhibition leads to a metabolically stressed phenotype analogous to mitochondria toxin treatment but without reactive oxygen species activation. Drug treatment decreased mitochondria function with associated reduction of citrate synthase expression and AMPK activation. Glucose and acetate uptake were increased in an attempt to overcome the metabolic stress. This study indicates that choline pathway pharmacological inhibition critically affects the metabolic function of the cell beyond reduced synthesis of phospholipids.
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Affiliation(s)
- Sebastian Trousil
- Comprehensive Cancer Imaging Centre, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, UK
| | - Maciej Kaliszczak
- Comprehensive Cancer Imaging Centre, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, UK
| | - Zachary Schug
- Cancer Research UK, Beatson Institute, Garscube Estate, Glasgow, UK
| | - Quang-De Nguyen
- Comprehensive Cancer Imaging Centre, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, UK
| | - Giampaolo Tomasi
- Comprehensive Cancer Imaging Centre, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, UK
| | - Rosy Favicchio
- Comprehensive Cancer Imaging Centre, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, UK
| | - Diana Brickute
- Comprehensive Cancer Imaging Centre, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, UK
| | - Robin Fortt
- Comprehensive Cancer Imaging Centre, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, UK
| | - Frazer J. Twyman
- Comprehensive Cancer Imaging Centre, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, UK
| | - Laurence Carroll
- Comprehensive Cancer Imaging Centre, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, UK
| | - Andrew Kalusa
- Comprehensive Cancer Imaging Centre, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, UK
| | - Naveenan Navaratnam
- Cellular Stress Group, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, Hammersmith Campus, London, UK
| | - Thomas Adejumo
- Cellular Stress Group, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, Hammersmith Campus, London, UK
| | - David Carling
- Cellular Stress Group, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, Hammersmith Campus, London, UK
| | - Eyal Gottlieb
- Cancer Research UK, Beatson Institute, Garscube Estate, Glasgow, UK
| | - Eric O. Aboagye
- Comprehensive Cancer Imaging Centre, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, UK
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