1
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Dalwani S, Metz A, Huschmann FU, Weiss MS, Wierenga RK, Venkatesan R. Crystallographic fragment-binding studies of the Mycobacterium tuberculosis trifunctional enzyme suggest binding pockets for the tails of the acyl-CoA substrates at its active sites and a potential substrate-channeling path between them. Acta Crystallogr D Struct Biol 2024; 80:605-619. [PMID: 39012716 DOI: 10.1107/s2059798324006557] [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: 01/12/2024] [Accepted: 07/03/2024] [Indexed: 07/18/2024] Open
Abstract
The Mycobacterium tuberculosis trifunctional enzyme (MtTFE) is an α2β2 tetrameric enzyme in which the α-chain harbors the 2E-enoyl-CoA hydratase (ECH) and 3S-hydroxyacyl-CoA dehydrogenase (HAD) active sites, and the β-chain provides the 3-ketoacyl-CoA thiolase (KAT) active site. Linear, medium-chain and long-chain 2E-enoyl-CoA molecules are the preferred substrates of MtTFE. Previous crystallographic binding and modeling studies identified binding sites for the acyl-CoA substrates at the three active sites, as well as the NAD binding pocket at the HAD active site. These studies also identified three additional CoA binding sites on the surface of MtTFE that are different from the active sites. It has been proposed that one of these additional sites could be of functional relevance for the substrate channeling (by surface crawling) of reaction intermediates between the three active sites. Here, 226 fragments were screened in a crystallographic fragment-binding study of MtTFE crystals, resulting in the structures of 16 MtTFE-fragment complexes. Analysis of the 121 fragment-binding events shows that the ECH active site is the `binding hotspot' for the tested fragments, with 41 binding events. The mode of binding of the fragments bound at the active sites provides additional insight into how the long-chain acyl moiety of the substrates can be accommodated at their proposed binding pockets. In addition, the 20 fragment-binding events between the active sites identify potential transient binding sites of reaction intermediates relevant to the possible channeling of substrates between these active sites. These results provide a basis for further studies to understand the functional relevance of the latter binding sites and to identify substrates for which channeling is crucial.
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Affiliation(s)
- Subhadra Dalwani
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Alexander Metz
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Franziska U Huschmann
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Manfred S Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Berlin, Germany
| | - Rik K Wierenga
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Rajaram Venkatesan
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
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2
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Li Z, Jiang J, Ficarro SB, Beyett TS, To C, Tavares I, Zhu Y, Li J, Eck MJ, Jänne PA, Marto JA, Zhang T, Che J, Gray NS. Molecular Bidents with Two Electrophilic Warheads as a New Pharmacological Modality. ACS CENTRAL SCIENCE 2024; 10:1156-1166. [PMID: 38947214 PMCID: PMC11212140 DOI: 10.1021/acscentsci.3c01245] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 07/02/2024]
Abstract
A systematic strategy to develop dual-warhead inhibitors is introduced to circumvent the limitations of conventional covalent inhibitors such as vulnerability to mutations of the corresponding nucleophilic residue. Currently, all FDA-approved covalent small molecules feature one electrophile, leaving open a facile route to acquired resistance. We conducted a systematic analysis of human proteins in the protein data bank to reveal ∼400 unique targets amendable to dual covalent inhibitors, which we term "molecular bidents". We demonstrated this strategy by targeting two kinases: MKK7 and EGFR. The designed compounds, ZNL-8162 and ZNL-0056, are ATP-competitive inhibitors that form two covalent bonds with cysteines and retain potency against single cysteine mutants. Therefore, molecular bidents represent a new pharmacological modality with the potential for improved selectivity, potency, and drug resistance profile.
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Affiliation(s)
- Zhengnian Li
- Department
of Chemical and Systems Biology, Stanford Cancer Institute, ChEM-H, Stanford University, Stanford, California 94305, United States
| | - Jie Jiang
- Lowe
Center for Thoracic Oncology, Dana-Farber
Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Medical Oncology, Dana-Farber Cancer
Institute, Boston, Massachusetts 02215, United States
- Department
of Medicine, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Scott B. Ficarro
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Blais
Proteomics Center, Center for Emergent Drug
Targets, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Pathology, Brigham and Women’s
Hospital and Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Tyler S. Beyett
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Ciric To
- Lowe
Center for Thoracic Oncology, Dana-Farber
Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Medical Oncology, Dana-Farber Cancer
Institute, Boston, Massachusetts 02215, United States
- Department
of Medicine, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Isidoro Tavares
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Blais
Proteomics Center, Center for Emergent Drug
Targets, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Yingde Zhu
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Jiaqi Li
- Lowe
Center for Thoracic Oncology, Dana-Farber
Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Medical Oncology, Dana-Farber Cancer
Institute, Boston, Massachusetts 02215, United States
- Department
of Medicine, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Michael J. Eck
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Pasi A. Jänne
- Lowe
Center for Thoracic Oncology, Dana-Farber
Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Medical Oncology, Dana-Farber Cancer
Institute, Boston, Massachusetts 02215, United States
- Department
of Medicine, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Jarrod A. Marto
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Blais
Proteomics Center, Center for Emergent Drug
Targets, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Pathology, Brigham and Women’s
Hospital and Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Tinghu Zhang
- Department
of Chemical and Systems Biology, Stanford Cancer Institute, ChEM-H, Stanford University, Stanford, California 94305, United States
| | - Jianwei Che
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Nathanael S. Gray
- Department
of Chemical and Systems Biology, Stanford Cancer Institute, ChEM-H, Stanford University, Stanford, California 94305, United States
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3
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Yang R, Zhang L, Bu F, Sun F, Cheng B. AI-based prediction of protein-ligand binding affinity and discovery of potential natural product inhibitors against ERK2. BMC Chem 2024; 18:108. [PMID: 38831341 PMCID: PMC11145815 DOI: 10.1186/s13065-024-01219-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 05/29/2024] [Indexed: 06/05/2024] Open
Abstract
Determination of protein-ligand binding affinity (PLA) is a key technological tool in hit discovery and lead optimization, which is critical to the drug development process. PLA can be determined directly by experimental methods, but it is time-consuming and costly. In recent years, deep learning has been widely applied to PLA prediction, the key of which lies in the comprehensive and accurate representation of proteins and ligands. In this study, we proposed a multi-modal deep learning model based on the early fusion strategy, called DeepLIP, to improve PLA prediction by integrating multi-level information, and further used it for virtual screening of extracellular signal-regulated protein kinase 2 (ERK2), an ideal target for cancer treatment. Experimental results from model evaluation showed that DeepLIP achieved superior performance compared to state-of-the-art methods on the widely used benchmark dataset. In addition, by combining previously developed machine learning models and molecular dynamics simulation, we screened three novel hits from a drug-like natural product library. These compounds not only had favorable physicochemical properties, but also bound stably to the target protein. We believe they have the potential to serve as starting molecules for the development of ERK2 inhibitors.
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Affiliation(s)
- Ruoqi Yang
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250011, China.
- Shandong University of Traditional Chinese Medicine, Jinan, 250355, China.
| | - Lili Zhang
- Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, 250013, China
| | - Fanyou Bu
- Qingdao Municipal Hospital Group, Qingdao, 266000, China
| | - Fuqiang Sun
- Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Bin Cheng
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250011, China.
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4
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Anderson JW, Vaisar D, Jones DN, Pegram LM, Vigers GP, Chen H, Moffat JG, Ahn NG. Conformation selection by ATP-competitive inhibitors and allosteric communication in ERK2. eLife 2024; 12:RP91507. [PMID: 38537148 PMCID: PMC10972564 DOI: 10.7554/elife.91507] [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] [Indexed: 04/04/2024] Open
Abstract
Activation of the extracellular signal-regulated kinase-2 (ERK2) by phosphorylation has been shown to involve changes in protein dynamics, as determined by hydrogen-deuterium exchange mass spectrometry (HDX-MS) and NMR relaxation dispersion measurements. These can be described by a global exchange between two conformational states of the active kinase, named 'L' and 'R,' where R is associated with a catalytically productive ATP-binding mode. An ATP-competitive ERK1/2 inhibitor, Vertex-11e, has properties of conformation selection for the R-state, revealing movements of the activation loop that are allosterically coupled to the kinase active site. However, the features of inhibitors important for R-state selection are unknown. Here, we survey a panel of ATP-competitive ERK inhibitors using HDX-MS and NMR and identify 14 new molecules with properties of R-state selection. They reveal effects propagated to distal regions in the P+1 and helix αF segments surrounding the activation loop, as well as helix αL16. Crystal structures of inhibitor complexes with ERK2 reveal systematic shifts in the Gly loop and helix αC, mediated by a Tyr-Tyr ring stacking interaction and the conserved Lys-Glu salt bridge. The findings suggest a model for the R-state involving small movements in the N-lobe that promote compactness within the kinase active site and alter mobility surrounding the activation loop. Such properties of conformation selection might be exploited to modulate the protein docking interface used by ERK substrates and effectors.
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Affiliation(s)
- Jake W Anderson
- Department of Biochemistry, University of ColoradoBoulderUnited States
| | - David Vaisar
- Department of Biochemistry, University of ColoradoBoulderUnited States
| | - David N Jones
- Department of Pharmacology, University of Colorado Anschutz Medical CenterBoulderUnited States
| | - Laurel M Pegram
- Department of Biochemistry, University of ColoradoBoulderUnited States
| | | | - Huifen Chen
- Genentech, Inc.South San FranciscoUnited States
| | | | - Natalie G Ahn
- Department of Biochemistry, University of ColoradoBoulderUnited States
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5
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Gao T, Zhang M, Li M, Wang X, Yao W, Shu W, Tang W, Zhang X. Nuezhenoside G13 from Osmanthus fragrans fruit ameliorates Concanavalin A-induced autoimmune hepatitis by regulating the NF-κB/MAPK pathway. JOURNAL OF ETHNOPHARMACOLOGY 2024; 319:117257. [PMID: 37852338 DOI: 10.1016/j.jep.2023.117257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 09/06/2023] [Accepted: 09/17/2023] [Indexed: 10/20/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Osmanthus fragrans fruit (OFF) exhibits hepatoprotective function, and it is consumed as food and used in traditional medicine in China. Nuezhenoside G13 (G13) is present in the highest levels in OFF. Autoimmune hepatitis (AIH) is a manifestation of liver disease and seriously endangers health. However, it remains unclear whether G13 affects AIH. AIM OF THE STUDY To clarify the effect of G13 on AIH and its exact underlying mechanism from a new perspective. MATERIALS AND METHODS We used a Concanavalin A-induced AIH mouse model and lipopolysaccharide-treated Raw264.7 cells to quantify serum biochemical indicators and confirm whether G13 exhibited protective effects in the AIH mice. Furthermore, we evaluated the effect of G13 via hematoxylin and eosin and immunohistochemical staining. We used enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction to quantify the inflammatory factors. We confirmed that G13 inhibited apoptosis via terminal deoxynucleotidyl transferase dUTP nick end labeling staining. Molecular docking, immunofluorescence, and western blotting experiments of G13 and key proteins of the NF-κB/MAPK pathway revealed that G13 alleviated inflammation. In addition, Cell Counting Kit-8, ELISA, NO detection, and western blotting assays were performed. Finally, we used an inhibitor of the p38 MAPK to verify that G13 reduced inflammation through the NF-κB/MAPK pathway in Raw264.7 cells. RESULTS The in vivo experiments revealed that G13 improved oxidative stress and apoptosis. In addition, G13 decreased the expression levels of CD4+, CD8+, F4/80+, and Ly6G and the secretion of inflammatory factors. Interestingly, G13 reduced the phosphorylation levels of IκBα, NF-κB, JNK, ERK1/2, and p38. Additionally, the in vitro experiments revealed that G13 alleviated inflammation through the NF-κB/MAPK pathway in lipopolysaccharide-treated Raw264.7 cells. Furthermore, molecular docking demonstrated that the binding fraction of G13 with these proteins was high. CONCLUSION G13 suppressed oxidative stress, apoptosis, and inflammation in a Concanavalin A-induced AIH mouse model. Furthermore, G13 exerted its effect through the NF-κB/MAPK pathway.
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Affiliation(s)
- Ting Gao
- School of Functional Food and Wine, Shenyang Pharmaceutical University, Shenyang, 110016, PR China
| | - Meng Zhang
- School of Functional Food and Wine, Shenyang Pharmaceutical University, Shenyang, 110016, PR China
| | - Minjie Li
- School of Functional Food and Wine, Shenyang Pharmaceutical University, Shenyang, 110016, PR China
| | - Xiaoli Wang
- School of Functional Food and Wine, Shenyang Pharmaceutical University, Shenyang, 110016, PR China
| | - Wenhan Yao
- College of Biological and Chemical Engineering, Changsha University, Changsha, 410022, PR China
| | - Wenjie Shu
- College of Biological and Chemical Engineering, Changsha University, Changsha, 410022, PR China
| | - Weizhuo Tang
- College of Biological and Chemical Engineering, Changsha University, Changsha, 410022, PR China.
| | - Xiaoshu Zhang
- School of Functional Food and Wine, Shenyang Pharmaceutical University, Shenyang, 110016, PR China.
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6
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Zhang T, Sun S, Wang R, Li T, Gan B, Zhang Y. BioisoIdentifier: an online free tool to investigate local structural replacements from PDB. J Cheminform 2024; 16:7. [PMID: 38218937 PMCID: PMC10788035 DOI: 10.1186/s13321-024-00801-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/07/2024] [Indexed: 01/15/2024] Open
Abstract
Within the realm of contemporary medicinal chemistry, bioisosteres are empirically used to enhance potency and selectivity, improve adsorption, distribution, metabolism, excretion and toxicity profiles of drug candidates. It is believed that bioisosteric know-how may help bypass granted patents or generate novel intellectual property for commercialization. Beside the synthetic expertise, the drug discovery process also depends on efficient in silico tools. We hereby present BioisoIdentifier (BII), a web server aiming to uncover bioisosteric information for specific fragment. Using the Protein Data Bank as source, and specific substructures that the user attempt to surrogate as input, BII tries to find suitable fragments that fit well within the local protein active site. BII is a powerful computational tool that offers the ligand design ideas for bioisosteric replacing. For the validation of BII, catechol is conceived as model fragment attempted to be replaced, and many ideas are successfully offered. These outputs are hierarchically grouped according to structural similarity, and clustered based on unsupervised machine learning algorithms. In summary, we constructed a user-friendly interface to enable the viewing of top-ranking molecules for further experimental exploration. This makes BII a highly valuable tool for drug discovery. The BII web server is freely available to researchers and can be accessed at http://www.aifordrugs.cn/index/ . Scientific Contribution: By designing a more optimal computational process for mining bioisosteric replacements from the publicly accessible PDB database, then deployed on a web server for throughly free access for researchers. Additionally, machine learning methods are applied to cluster the bioisosteric replacements searched by the platform, making a scientific contribution to facilitate chemists' selection of appropriate bioisosteric replacements. The number of bioisosteric replacements obtained using BII is significantly larger than the currently available platforms, which expanding the search space for effective local structural replacements.
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Affiliation(s)
- Tinghao Zhang
- Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME), Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, China
| | - Shaohua Sun
- Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME), Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, China
| | - Runzhou Wang
- School of Management, Xi'an University of Architecture and Technology, Xi'an, 710055, China
| | - Ting Li
- Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME), Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, China
| | - Bicheng Gan
- College of Petroleum Engineering, Northeast Petroleum University, Daqing, 163318, Heilongjiang, China
| | - Yuezhou Zhang
- Xi'an Institute of Flexible Electronics (IFE) and Xi'an Institute of Biomedical Materials & Engineering (IBME), Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, China.
- Ningbo Institute of Northwestern Polytechnical University, Frontiers Science Center for Flexible Electronics (FSCFE), Key Laboratory of Flexible Electronics of Zhejiang Province, Ningbo Institute of Northwestern Polytechnical University, 218 Qingyi Road, Ningbo, 315103, China.
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7
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Liu Y, Ma T, Guo Z, Zhou L, Liu G, He Y, Ma L, Gao J, Bai J, Hollmann F, Jiang Y. Asymmetric α-benzylation of cyclic ketones enabled by concurrent chemical aldol condensation and biocatalytic reduction. Nat Commun 2024; 15:71. [PMID: 38167391 PMCID: PMC10761851 DOI: 10.1038/s41467-023-44452-z] [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: 05/15/2023] [Accepted: 12/13/2023] [Indexed: 01/05/2024] Open
Abstract
Chemoenzymatic cascade catalysis has emerged as a revolutionary tool for streamlining traditional retrosynthetic disconnections, creating new possibilities for the asymmetric synthesis of valuable chiral compounds. Here we construct a one-pot concurrent chemoenzymatic cascade by integrating organobismuth-catalyzed aldol condensation with ene-reductase (ER)-catalyzed enantioselective reduction, enabling the formal asymmetric α-benzylation of cyclic ketones. To achieve this, we develop a pair of enantiocomplementary ERs capable of reducing α-arylidene cyclic ketones, lactams, and lactones. Our engineered mutants exhibit significantly higher activity, up to 37-fold, and broader substrate specificity compared to the parent enzyme. The key to success is due to the well-tuned hydride attack distance/angle and, more importantly, to the synergistic proton-delivery triade of Tyr28-Tyr69-Tyr169. Molecular docking and density functional theory (DFT) studies provide important insights into the bioreduction mechanisms. Furthermore, we demonstrate the synthetic utility of the best mutants in the asymmetric synthesis of several key chiral synthons.
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Affiliation(s)
- Yunting Liu
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, 300130, China
| | - Teng Ma
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, 300130, China
| | - Zhongxu Guo
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, 300130, China
| | - Liya Zhou
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, 300130, China
| | - Guanhua Liu
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, 300130, China
| | - Ying He
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, 300130, China
| | - Li Ma
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, 300130, China
| | - Jing Gao
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, 300130, China
| | - Jing Bai
- College of Food Science and Biology, Hebei University of Science & Technology, Shijiazhuang, 050018, China
| | - Frank Hollmann
- Department of Biotechnology, Delft University of Technology, 2629 HZ, Delft, The Netherlands.
| | - Yanjun Jiang
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, 300130, China.
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8
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Bingham M, Pesnot T, Scott AD. Biophysical screening and characterisation in medicinal chemistry. PROGRESS IN MEDICINAL CHEMISTRY 2023; 62:61-104. [PMID: 37981351 DOI: 10.1016/bs.pmch.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
In the last two decades the use of biophysical assays and methods in medicinal chemistry has increased significantly, to meet the demands of the novel targets and modalities that drug discoverers are looking to tackle. The desire to obtain accurate affinities, kinetics, thermodynamics and structural data as early as possible in the drug discovery process has fuelled this innovation. This review introduces the principles underlying the techniques in common use and provides a perspective on the weaknesses and strengths of different methods. Case studies are used to further illustrate some of the applications in medicinal chemistry and a discussion of the emerging biophysical methods on the horizon is presented.
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9
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Pan P, He Y, Geng T, Li Z, Li Z, Meng X. Design, Synthesis, and Antitumor Activity Evaluation of Proteolysis-Targeting Chimeras as Degraders of Extracellular Signal-Regulated Kinases 1/2. Int J Mol Sci 2023; 24:16290. [PMID: 38003480 PMCID: PMC10671693 DOI: 10.3390/ijms242216290] [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: 10/23/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Inhibition of the extracellular signal-regulated kinases 1/2 (ERK1/2) alone or in combination with other targets has emerged as a promising treatment strategy for a variety of human tumors. In addition to the development of inhibitors, the development of ERK1/2 degraders is an alternative approach to decrease its activity. We synthesized proteolysis-targeting chimeras (PROTACs) as effective ERK1/2 degraders, among which B1-10J showed high degradative activity, with DC50 of 102 nM and cytotoxic IC50 of 2.2 μM against HCT116 cells. Moreover, B1-10J dose-dependently inhibited tumor cell migration. Xenograft experiments in nude mice demonstrated that B1-10J inhibited HCT116 tumor cell growth and achieved significant regression of tumors at a daily dose of 25 mg/kg.
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Affiliation(s)
- Pengming Pan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yichao He
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Tongtong Geng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zhongtang Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zhongjun Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xiangbao Meng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
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10
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Anderson JW, Vaisar D, Jones DN, Pegram LM, Vigers GP, Chen H, Moffat JG, Ahn NG. Conformation Selection by ATP-competitive Inhibitors and Allosteric Communication in ERK2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557258. [PMID: 37745518 PMCID: PMC10515847 DOI: 10.1101/2023.09.12.557258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Activation of the extracellular signal regulated kinase-2 (ERK2) by phosphorylation has been shown to involve changes in protein dynamics, as determined by hydrogen-deuterium exchange mass spectrometry (HDX-MS) and NMR relaxation dispersion measurements. These can be described by a global exchange between two conformational states of the active kinase, named "L" and "R", where R is associated with a catalytically productive ATP-binding mode. An ATP-competitive ERK1/2 inhibitor, Vertex-11e, has properties of conformation selection for the R-state, revealing movements of the activation loop that are allosterically coupled to the kinase active site. However, the features of inhibitors important for R-state selection are unknown. Here we survey a panel of ATP-competitive ERK inhibitors using HDX-MS and NMR and identify 14 new molecules with properties of R-state selection. They reveal effects propagated to distal regions in the P+1 and helix αF segments surrounding the activation loop, as well as helix αL16. Crystal structures of inhibitor complexes with ERK2 reveal systematic shifts in the Gly loop and helix αC, mediated by a Tyr-Tyr ring stacking interaction and the conserved Lys-Glu salt bridge. The findings suggest a model for the R-state involving small movements in the N-lobe that promote compactness within the kinase active site and alter mobility surrounding the activation loop. Such properties of conformation selection might be exploited to modulate the protein docking interface used by ERK substrates and effectors.
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Affiliation(s)
| | - David Vaisar
- Department of Biochemistry, University of Colorado, Boulder, CO
| | - David N. Jones
- Department of Pharmacology, University of Colorado Anschutz Medical Center, Aurora, CO
| | - Laurel M. Pegram
- Department of Biochemistry, University of Colorado, Boulder, CO
- Present address: Loxo Oncology, Louisville, CO 80027
| | - Guy P. Vigers
- Array BioPharma, Inc., Boulder, CO
- Present address: Allium Consulting LLC, Boulder, CO 80304
| | - Huifen Chen
- Genentech, Inc. South San Francisco, CA, USA
| | | | - Natalie G. Ahn
- Department of Biochemistry, University of Colorado, Boulder, CO
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11
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Payani S, Bhaskar M, Kumar GS, Pradeepkiran JA. A study on antimicrobial and anticancer properties of Cissus quadrangulris using lung cancer cell line. Cancer Treat Res Commun 2023; 36:100732. [PMID: 37379774 DOI: 10.1016/j.ctarc.2023.100732] [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: 05/22/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 06/30/2023]
Abstract
Cissus quadrangularis plant from Vitaceae family, native in India. Many parts of this plant have medicinal values but most precious is stem of this plant. In past years number of studies reported their activities and secondary metabolites in Cissus quadrangularis plant and their pharmacological activities and uses in traditional medicine system. It is reported to possess excellent medicinal properties and potent fracture healing properties, antimicrobial, antiulcer, antioxidative, cholinergic activity and beneficial effect on cardiovascular diseases, possesses antiulcer and cytoprotective property in indomethacin-induced gastric mucosal injury. The aim of this study was to determine the qualitative phytochemical analysis, antimicrobial activity, cell viability and in vitro anticancer activity of a potential of Cissus quadrangularis stem extract against A549 human lung cancer cell line. The disc diffusion method was employed to determine the antimicrobial activity of Cissus quadrangularis stem extract and showed potential antibacterial and antifungal activity against various microorganisms. Results have shown that Stem methanolic extract induced a significant decrease of tumour cell viability. The cell viability assay clearly showed that the cells treated with Cissus quadrangularis methanolic extract has significantly reduced the lung cancer cell viability in a dose dependant manner. The stem methanolic extract was tested for the in vitro antiproliferative potential on A549 human lung cancer cell line using different concentrations, namely 1000, 62.5 and 7.8 µg/ml. We observed the IC50 dose at 65.2 μg/ml concentration. In cell culture A549 cells treated with Cissus quadrangularis stem methanolic extract in 24 h the cells growth is controlled.
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Affiliation(s)
- Sholapuri Payani
- Department of Zoology, Division of Molecular Biology, Sri Venkateswara University, Tirupati, Andhra Pradesh, India
| | - Matcha Bhaskar
- Department of Zoology, Division of Molecular Biology, Sri Venkateswara University, Tirupati, Andhra Pradesh, India.
| | - Gandham Sandeep Kumar
- Department of Zoology, Division of Molecular Biology, Sri Venkateswara University, Tirupati, Andhra Pradesh, India
| | - Jangampalli Adi Pradeepkiran
- Department of Zoology, Division of Molecular Biology, Sri Venkateswara University, Tirupati, Andhra Pradesh, India; Deapartment of Internal Medicine, Texas Tech University of Health Science Centre, Lubbock, TX 79415, USA
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12
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Kumar A, Gupta R, Rashid H, Bhat AM, Sharma RR, Naikoo SH, Kaur S, Tasduq SA. Synthesis, molecular docking, and biological evaluation of [3,2- b]indole fused 18β-glycyrrhetinic acid derivatives against skin melanoma. RSC Adv 2023; 13:11130-11141. [PMID: 37056972 PMCID: PMC10086573 DOI: 10.1039/d2ra08023k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/19/2023] [Indexed: 04/15/2023] Open
Abstract
Melanoma, the most serious yet uncommon type of cancer, originates in melanocytes. Risk factors include UV radiation, genetic factors, tanning lamps and beds. Here, we described the synthesis and selective anti melanoma activity of [3,2-b]indole fused 18β-glycyrrhetinic acid, a derivative of 18β-glycyrrhetinic acid in murine B16F10 and A375 human melanoma cell lines. Among the 14 molecules, GPD-12 showed significant selective cytotoxic activity against A375 and B16F10 cell lines with IC50 of 13.38 μM and 15.20 μM respectively. GPD 12 induced the formation of reactive oxygen species in A375 cells that could trigger oxidative stress mediated cell death as is evident from the increased expression of apoptosis related proteins such as caspase-9 and caspase-3 and the increased ratio of Bax to Bcl2. The results showed that GPD 12 can be used as an effective therapeutic agent against melanoma.
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Affiliation(s)
- Amit Kumar
- Natural Product and Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine Jammu-180001 Jammu and Kashmir India
- Department of Pharmaceutical Sciences, Guru Nanak Dev University Amritsar-143005 India
| | - Ragni Gupta
- Pharmacology Division, CSIR-Indian Institute of Integrative Medicine Jammu-180001 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad-201002 India
| | - Haroon Rashid
- Sher-e-Kashmir Institute of Medical Sciences Soura Srinagar-190011 Jammu and Kashmir India
| | - Aalim Maqsood Bhat
- Pharmacology Division, CSIR-Indian Institute of Integrative Medicine Jammu-180001 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad-201002 India
| | - Raghu Rai Sharma
- Pharmacology Division, CSIR-Indian Institute of Integrative Medicine Jammu-180001 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad-201002 India
| | - Shahid Hussain Naikoo
- Pharmacology Division, CSIR-Indian Institute of Integrative Medicine Jammu-180001 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad-201002 India
| | - Sarabjit Kaur
- Department of Pharmaceutical Sciences, Guru Nanak Dev University Amritsar-143005 India
| | - Sheikh Abdullah Tasduq
- Pharmacology Division, CSIR-Indian Institute of Integrative Medicine Jammu-180001 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad-201002 India
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13
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Lotfaliansaremi S, Cornwell S, Casillas C, Sabio M, Tolias P, Windsor W, Paliwal S. Design and biological characterization of a series of dual mechanism ERK1/2 inhibitors with a Triazolopyridinone core. Chem Biol Drug Des 2023; 101:837-847. [PMID: 36434749 DOI: 10.1111/cbdd.14186] [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: 08/11/2022] [Revised: 11/07/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022]
Abstract
Oncology clinical development programs have targeted the RAS/RAF/MEK/ERK signaling pathway with small molecule inhibitors for a variety of cancers during the past decades, and most therapies have shown limited or minimal success. Specific BRAF and MEK inhibitors have shown clinical efficacy in patients for the treatment of BRAF-mutant melanoma. However, most cancers have shown treatment resistance after several months of inhibitor usage, and reports indicate resistance is often associated with the reactivation of the MAPK signaling pathway. It is widely accepted that an effective MAPK therapy will have a significant impact on curtailing cancer growth and improving patient survival. However, despite more than three decades of intense research and pharmaceutical industry efforts, an FDA-approved, effective anti-cancer ERK inhibitor has yet to be developed. Here, we present the design, optimization, and biological characterization of ERK1/2 inhibitors that block catalytic phosphorylation of downstream substrates such as RSK but also modulate the phosphorylation of ERK1/2 by MEK without directly inhibiting MEK. Our series of dual mechanism ERK1/2 inhibitors, in which we incorporated a triazolopyridinone core, may present potential benefits for enhancing efficacy and addressing the emergence of treatment resistance.
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Affiliation(s)
- Sajedeh Lotfaliansaremi
- Center for Healthcare Innovation, Stevens Institute of Technology, New Jersey, Hoboken, USA
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, New Jersey, Hoboken, USA
| | - Stephen Cornwell
- Center for Healthcare Innovation, Stevens Institute of Technology, New Jersey, Hoboken, USA
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, New Jersey, Hoboken, USA
| | - Candice Casillas
- Center for Healthcare Innovation, Stevens Institute of Technology, New Jersey, Hoboken, USA
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, New Jersey, Hoboken, USA
| | - Michael Sabio
- Center for Healthcare Innovation, Stevens Institute of Technology, New Jersey, Hoboken, USA
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, New Jersey, Hoboken, USA
| | - Peter Tolias
- Center for Healthcare Innovation, Stevens Institute of Technology, New Jersey, Hoboken, USA
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, New Jersey, Hoboken, USA
| | - William Windsor
- Center for Healthcare Innovation, Stevens Institute of Technology, New Jersey, Hoboken, USA
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, New Jersey, Hoboken, USA
| | - Sunil Paliwal
- Center for Healthcare Innovation, Stevens Institute of Technology, New Jersey, Hoboken, USA
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, New Jersey, Hoboken, USA
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14
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Aziz MN, Nguyen L, Chang Y, Gout D, Pan Z, Lovely CJ. Novel thiazolidines of potential anti-proliferation properties against esophageal squamous cell carcinoma via ERK pathway. Eur J Med Chem 2023; 246:114909. [PMID: 36508971 DOI: 10.1016/j.ejmech.2022.114909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 11/02/2022] [Accepted: 11/03/2022] [Indexed: 11/25/2022]
Abstract
The discovery of a new class of extracellular-signal-regulated kinase (ERK) inhibitors has been achieved via developing novel 2-imino-5-arylidene-thiazolidine analogues. A novel synthetic method employing a solid support-mediated reaction was used to construct the targeted thiazolidines through a cascade reaction with good yields. The chemical and physical stability of the new thiazolidine library has successfully been achieved by blocking the labile C5-position to aerobic oxidation. A cell viability study was performed using esophageal squamous cell carcinoma cell lines (KYSE-30 and KYSE-150) and non-tumorous esophageal epithelial cell lines (HET-1A and NES-G4T) through utilization of an MTT assay, revealing that (Z)-5-((Z)-4-bromobenzylidene)-N-(4-methoxy-2-nitrophenyl)-4,4-dimethylthiazolidin-2-imine (6g) was the best compound among the synthesized library in terms of selectivity. DAPI staining experiments were performed to visualize the morphological changes and to investigate the apoptotic activity. Moreover, western blots were used to probe the mechanism/pathway behind the observed activity/selectivity of thiazolidine 6g which established selective inhibition of phosphorylation in the ERK pathway. Molecular modeling techniques have been utilized to confirm the observed activity. A molecular docking study revealed similar binding interactions between the synthesized thiazolidines and reported co-crystalized inhibitors with ERK proteins. Thus, the present study provides a starting point for the development of interesting bioactive 2-imino-5-arylidene-thiazolidines.
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Affiliation(s)
- Marian N Aziz
- Department of Chemistry and Biochemistry, 700 Planetarium Place, University of Texas at Arlington, TX, 76019, USA; Department of Pesticide Chemistry, National Research Centre, Dokki, Giza, 12622, Egypt
| | - Linh Nguyen
- Dept. of Biology, College of Science, University of Texas at Arlington, TX, 76019, USA; Department of Graduate Nursing, College of Nursing and Health Innovation, University of Texas at Arlington, TX, 76019, USA
| | - Yan Chang
- Department of Graduate Nursing, College of Nursing and Health Innovation, University of Texas at Arlington, TX, 76019, USA; Bone and Muscle Research Center, University of Texas at Arlington, TX, 76019, USA
| | - Delphine Gout
- Department of Chemistry and Biochemistry, 700 Planetarium Place, University of Texas at Arlington, TX, 76019, USA
| | - Zui Pan
- Department of Graduate Nursing, College of Nursing and Health Innovation, University of Texas at Arlington, TX, 76019, USA; Bone and Muscle Research Center, University of Texas at Arlington, TX, 76019, USA
| | - Carl J Lovely
- Department of Chemistry and Biochemistry, 700 Planetarium Place, University of Texas at Arlington, TX, 76019, USA.
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15
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Hamdy AK, Sakamoto T, Toma T, Sakamoto M, Abourehab MAS, Otsuka M, Fujita M, Tateishi H, Radwan MO. New Insights into the Structural Requirements of Isatin-Derived Pro-Apoptotic Agents against Acute Myeloid Leukemia. Pharmaceuticals (Basel) 2022; 15:ph15121579. [PMID: 36559030 PMCID: PMC9784816 DOI: 10.3390/ph15121579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/13/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Searching for bioactive compounds within the huge chemical space is like trying to find a needle in a haystack. Isatin is a unique natural compound which is endowed with different bio-pertinent activities, especially in cancer therapy. Herein, we envisaged that adopting a hybrid strategy of isatin and α,β-unsaturated ketone would afford new chemical entities with strong chemotherapeutic potential. Of interest, compounds 5b and 5g demonstrated significant antiproliferative activities against different cancer genotypes according to NCI-60 screening. Concomitantly, their IC50 against HL-60 cells were 0.38 ± 0.08 and 0.57 ± 0.05 µM, respectively, demonstrating remarkable apoptosis and moderate cell cycle arrest at G1 phase. Intriguingly, an impressive safety profile for 5b was reflected by a 37.2 times selectivity against HL-60 over PBMC from a healthy donor. This provoked us to further explore their mechanism of action by in vitro and in silico tools. Conclusively, 5b and 5g stand out as strong chemotherapeutic agents that hold clinical promise against acute myeloid leukemia.
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Affiliation(s)
- Ahmed K. Hamdy
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan
- Department of Medicinal Chemistry, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Takashi Sakamoto
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan
| | - Tsugumasa Toma
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan
| | - Masaharu Sakamoto
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan
| | - Mohammed A. S. Abourehab
- Department of Pharmaceutics, College of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Masami Otsuka
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan
- Department of Drug Discovery, Science Farm, Ltd., Kumamoto 862-0976, Japan
| | - Mikako Fujita
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan
- Correspondence: (M.F.); (H.T.); (M.O.R.)
| | - Hiroshi Tateishi
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan
- Correspondence: (M.F.); (H.T.); (M.O.R.)
| | - Mohamed O. Radwan
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Giza 12622, Egypt
- Correspondence: (M.F.); (H.T.); (M.O.R.)
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16
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Design, synthesis and biological evaluation of novel 4-aminopiperidine derivatives as SMO/ERK dual inhibitors. Bioorg Med Chem 2022; 74:117051. [DOI: 10.1016/j.bmc.2022.117051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/22/2022] [Accepted: 10/04/2022] [Indexed: 11/18/2022]
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17
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Martin MP, Noble MEM. Exiting the tunnel of uncertainty: crystal soak to validated hit. Acta Crystallogr D Struct Biol 2022; 78:1294-1302. [PMID: 36322414 PMCID: PMC9629488 DOI: 10.1107/s2059798322009986] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 10/12/2022] [Indexed: 11/28/2022] Open
Abstract
Crystallographic fragment screens provide an efficient and effective way to identify small-molecule ligands of a crystallized protein. Due to their low molecular weight, such hits tend to have low, often unquantifiable, affinity for their target, complicating the twin challenges of validating the hits as authentic solution-phase ligands of the target and identifying the `best' hit(s) for further elaboration. In this article, approaches that address these challenges are assessed. Using retrospective analysis of a recent ATAD2 hit-identification campaign, alongside other examples of successful fragment-screening campaigns, it is suggested that hit validation and prioritization are best achieved by a `triangulation' approach in which the results of multiple available biochemical and biophysical techniques are correlated to develop qualitative structure-activity relationships (SARs). Such qualitative SARs may indeed be the only means by which to navigate a project through the tunnel of uncertainty that prevails before on-scale biophysical, biochemical and/or biological measurements become possible.
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Affiliation(s)
- Mathew P. Martin
- Cancer Research UK Drug Discovery Unit, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Martin E. M. Noble
- Cancer Research UK Drug Discovery Unit, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
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18
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Fu L, Chen S, He G, Chen Y, Liu B. Targeting Extracellular Signal-Regulated Protein Kinase 1/2 (ERK1/2) in Cancer: An Update on Pharmacological Small-Molecule Inhibitors. J Med Chem 2022; 65:13561-13573. [PMID: 36205714 DOI: 10.1021/acs.jmedchem.2c01244] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Extracellular signal-regulated protein kinase 1/2 (ERK1/2), the only known substrate of MEK1/2, is located downstream of the RAS-RAF-MEK-ERK (MAPK) pathway and is associated with the abnormal activation and poor prognosis of cancer. To date, several small-molecule inhibitors of RAS, RAF, and MEK have been reported to make rapid advances in cancer therapy; however, acquired resistance still occurs, thereby weakening the therapeutic efficacy of these inhibitors. Recently, selective inhibition of ERK1/2 has been regarded as a potential cancer therapeutic strategy that can not only effectively block the MAPK pathway but also overcome drug resistance caused by upstream mutations in RAS, RAF, and MEK. Herein, we summarize the oncogenic roles, key signaling network, and the single- and dual-target inhibitors of ERK1/2 in preclinical and clinical trials. Together, these inspiring findings shed new light on the discovery of more small-molecule inhibitors of ERK1/2 as candidate drugs to improve cancer therapeutics.
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Affiliation(s)
- Leilei Fu
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Siwei Chen
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Gu He
- Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yi Chen
- Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Bo Liu
- Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
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19
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St. Denis JD, Chessari G, Cleasby A, Cons BD, Cowan S, Dalton SE, East C, Murray CW, O’Reilly M, Peakman T, Rapti M, Stow JL. X-ray Screening of an Electrophilic Fragment Library and Application toward the Development of a Novel ERK 1/2 Covalent Inhibitor. J Med Chem 2022; 65:12319-12333. [DOI: 10.1021/acs.jmedchem.2c01044] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Jeffrey D. St. Denis
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Gianni Chessari
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Anne Cleasby
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Benjamin D. Cons
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Suzanna Cowan
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Samuel E. Dalton
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Charlotte East
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Christopher W. Murray
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Marc O’Reilly
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Torren Peakman
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Magdalini Rapti
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Jessie L. Stow
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
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20
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Pan X, Pei J, Wang A, Shuai W, Feng L, Bu F, Zhu Y, Zhang L, Wang G, Ouyang L. Development of small molecule extracellular signal-regulated kinases (ERKs) inhibitors for cancer therapy. Acta Pharm Sin B 2022; 12:2171-2192. [PMID: 35646548 PMCID: PMC9136582 DOI: 10.1016/j.apsb.2021.12.022] [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: 10/06/2021] [Revised: 12/18/2021] [Accepted: 12/22/2021] [Indexed: 01/09/2023] Open
Abstract
The mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase 1/2 (ERK1/2) signaling pathway is widely activated by a variety of extracellular stimuli, and its dysregulation is associated with the proliferation, invasion, and migration of cancer cells. ERK1/2 is located at the distal end of this pathway and rarely undergoes mutations, making it an attractive target for anticancer drug development. Currently, an increasing number of ERK1/2 inhibitors have been designed and synthesized for antitumor therapy, among which representative compounds have entered clinical trials. When ERK1/2 signal transduction is eliminated, ERK5 may provide a bypass route to rescue proliferation, and weaken the potency of ERK1/2 inhibitors. Therefore, drug research targeting ERK5 or based on the compensatory mechanism of ERK5 for ERK1/2 opens up a new way for oncotherapy. This review provides an overview of the physiological and biological functions of ERKs, focuses on the structure-activity relationships of small molecule inhibitors targeting ERKs, with a view to providing guidance for future drug design and optimization, and discusses the potential therapeutic strategies to overcome drug resistance.
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Affiliation(s)
- Xiaoli Pan
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Junping Pei
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Aoxue Wang
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Wen Shuai
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Lu Feng
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Faqian Bu
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Yumeng Zhu
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Lan Zhang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
- Corresponding authors. Tel./fax: +86 28 85503817.
| | - Guan Wang
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
- Corresponding authors. Tel./fax: +86 28 85503817.
| | - Liang Ouyang
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
- Corresponding authors. Tel./fax: +86 28 85503817.
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21
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Vafeiadou V, Hany D, Picard D. Hyperactivation of MAPK Induces Tamoxifen Resistance in SPRED2-Deficient ERα-Positive Breast Cancer. Cancers (Basel) 2022; 14:954. [PMID: 35205702 PMCID: PMC8870665 DOI: 10.3390/cancers14040954] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/07/2022] [Accepted: 02/10/2022] [Indexed: 02/07/2023] Open
Abstract
Breast cancer is the number one cause of cancer-related mortality in women worldwide. Most breast tumors depend on the expression of the estrogen receptor α (ERα) for their growth. For this reason, targeting ERα with antagonists such as tamoxifen is the therapy of choice for most patients. Although initially responsive to tamoxifen, about 40% of the patients will develop resistance and ultimately a recurrence of the disease. Thus, finding new biomarkers and therapeutic approaches to treatment-resistant tumors is of high significance. SPRED2, an inhibitor of the MAPK signal transduction pathway, has been found to be downregulated in various cancers. In the present study, we found that SPRED2 is downregulated in a large proportion of breast-cancer patients. Moreover, the knockdown of SPRED2 significantly increases cell proliferation and leads to tamoxifen resistance of breast-cancer cells that are initially tamoxifen-sensitive. We found that resistance occurs through increased activation of the MAPKs ERK1/ERK2, which enhances the transcriptional activity of ERα. Treatment of SPRED2-deficient breast cancer cells with a combination of the ERK 1/2 inhibitor ulixertinib and 4-hydroxytamoxifen (4-OHT) can inhibit cell growth and proliferation and overcome the induced tamoxifen resistance. Taken together, these results indicate that SPRED2 may also be a tumor suppressor for breast cancer and that it is a key regulator of cellular sensitivity to 4-OHT.
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Affiliation(s)
- Vasiliki Vafeiadou
- Département de Biologie Moléculaire et Cellulaire, Université de Genève, Sciences III, 1211 Genève 4, Switzerland; (V.V.); (D.H.)
| | - Dina Hany
- Département de Biologie Moléculaire et Cellulaire, Université de Genève, Sciences III, 1211 Genève 4, Switzerland; (V.V.); (D.H.)
- On leave from: Department of Pharmacology and Therapeutics, Faculty of Pharmacy, Pharos University in Alexandria, Alexandria 21311, Egypt
| | - Didier Picard
- Département de Biologie Moléculaire et Cellulaire, Université de Genève, Sciences III, 1211 Genève 4, Switzerland; (V.V.); (D.H.)
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22
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Niu Y, Ji H. Current developments in extracellular-regulated protein kinase (ERK1/2) inhibitors. Drug Discov Today 2022; 27:1464-1473. [DOI: 10.1016/j.drudis.2022.01.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/19/2021] [Accepted: 01/25/2022] [Indexed: 12/22/2022]
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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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24
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Pathania S, Singh PK, Narang RK, Rawal RK. Structure based designing of thiazolidinone-pyrimidine derivatives as ERK2 inhibitors: Synthesis and in vitro evaluation. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:793-816. [PMID: 34583590 DOI: 10.1080/1062936x.2021.1973094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
Breast cancer has been associated with an overexpression of various molecular targets; accordingly, various target-specific chemotherapeutic agents have been developed. Inhibition of ERK2, a member of MAPK pathway, is an important target involved in the treatment of both oestrogen receptor-positive and triple-negative breast cancer. Thus, in continuation of our previous work on the ERK2 target, we here report novel inhibitors of this kinase. Out of three lead molecules reported in our previous study, we selected the thiazolidinone-pyrimidine scaffold for further development of small molecule inhibitors of ERK2. Analogues of the lead molecule were docked in the target kinase, followed by molecular dynamic simulations and MM-GBSA calculations. Analogues maintaining key interactions with amino acid residues in the ATP-binding domain of ERK2 were selected and duly synthesized. In vitro biochemical evaluation of these molecules against ERK2 kinase disclosed that two molecules possess significant kinase inhibitory potential with IC50 values ≤ 0.5 µM.
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Affiliation(s)
- S Pathania
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, India
- Department of Pharmaceutical Sciences & Technology, Maharaja Ranjit Singh Punjab Technical University, Bathinda, India
| | - P K Singh
- Integrative Physiology and Pharmacology, Institute of Biomedicine, Faculty of Medicine, University of Turku, Turku, Finland
| | - R K Narang
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, India
| | - R K Rawal
- Department of Chemistry, Maharishi Markandeshwar (Deemed to Be University), Ambala, India
- CSIR-North East Institute of Science and Technology, Jorhat, India
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Chessari G, Grainger R, Holvey RS, Ludlow RF, Mortenson PN, Rees DC. C-H functionalisation tolerant to polar groups could transform fragment-based drug discovery (FBDD). Chem Sci 2021; 12:11976-11985. [PMID: 34667563 PMCID: PMC8457390 DOI: 10.1039/d1sc03563k] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/30/2021] [Indexed: 12/28/2022] Open
Abstract
We have analysed 131 fragment-to-lead (F2L) examples targeting a wide variety of protein families published by academic and industrial laboratories between 2015-2019. Our assessment of X-ray structural data identifies the most common polar functional groups involved in fragment-protein binding are: N-H (hydrogen bond donors on aromatic and aliphatic N-H, amides and anilines; totalling 35%), aromatic nitrogen atoms (hydrogen bond acceptors; totalling 23%), and carbonyl oxygen group atoms (hydrogen bond acceptors on amides, ureas and ketones; totalling 22%). Furthermore, the elaboration of each fragment into its corresponding lead is analysed to identify the nominal synthetic growth vectors. In ∼80% of cases, growth originates from an aromatic or aliphatic carbon on the fragment and more than 50% of the total bonds formed are carbon-carbon bonds. This analysis reveals that growth from carbocentric vectors is key and therefore robust C-H functionalisation methods that tolerate the innate polar functionality on fragments could transform fragment-based drug discovery (FBDD). As a further resource to the community, we have provided the full data of our analysis as well as an online overlay page of the X-ray structures of the fragment hit and leads: https://astx.com/interactive/F2L-2021/.
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Affiliation(s)
- Gianni Chessari
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | - Rachel Grainger
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | - Rhian S Holvey
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | | | - Paul N Mortenson
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | - David C Rees
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
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26
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Heightman TD, Berdini V, Bevan L, Buck IM, Carr MG, Courtin A, Coyle JE, Day JEH, East C, Fazal L, Griffiths-Jones CM, Howard S, Kucia-Tran J, Martins V, Muench S, Munck JM, Norton D, O'Reilly M, Palmer N, Pathuri P, Peakman TM, Reader M, Rees DC, Rich SJ, Shah A, Wallis NG, Walton H, Wilsher NE, Woolford AJA, Cooke M, Cousin D, Onions S, Shannon J, Watts J, Murray CW. Discovery of ASTX029, A Clinical Candidate Which Modulates the Phosphorylation and Catalytic Activity of ERK1/2. J Med Chem 2021; 64:12286-12303. [PMID: 34387469 DOI: 10.1021/acs.jmedchem.1c00905] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aberrant activation of the mitogen-activated protein kinase pathway frequently drives tumor growth, and the ERK1/2 kinases are positioned at a key node in this pathway, making them important targets for therapeutic intervention. Recently, a number of ERK1/2 inhibitors have been advanced to investigational clinical trials in patients with activating mutations in B-Raf proto-oncogene or Ras. Here, we describe the discovery of the clinical candidate ASTX029 (15) through structure-guided optimization of our previously published isoindolinone lead (7). The medicinal chemistry campaign focused on addressing CYP3A4-mediated metabolism and maintaining favorable physicochemical properties. These efforts led to the identification of ASTX029, which showed the desired pharmacological profile combining ERK1/2 inhibition with suppression of phospho-ERK1/2 (pERK) levels, and in addition, it possesses suitable preclinical pharmacokinetic properties predictive of once daily dosing in humans. ASTX029 is currently in a phase I-II clinical trial in patients with advanced solid tumors.
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Affiliation(s)
- Tom D Heightman
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Valerio Berdini
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Luke Bevan
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Ildiko M Buck
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Maria G Carr
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Aurélie Courtin
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Joseph E Coyle
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - James E H Day
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Charlotte East
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Lynsey Fazal
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | | | - Steven Howard
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Justyna Kucia-Tran
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Vanessa Martins
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Sandra Muench
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Joanne M Munck
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - David Norton
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Marc O'Reilly
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Nicholas Palmer
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Puja Pathuri
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Torren M Peakman
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Michael Reader
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - David C Rees
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Sharna J Rich
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Alpesh Shah
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Nicola G Wallis
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Hugh Walton
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Nicola E Wilsher
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | | | - Michael Cooke
- Sygnature Discovery Ltd., BioCity, Pennyfoot Street, Nottingham NG1 1GF, U.K
| | - David Cousin
- Sygnature Discovery Ltd., BioCity, Pennyfoot Street, Nottingham NG1 1GF, U.K
| | - Stuart Onions
- Sygnature Discovery Ltd., BioCity, Pennyfoot Street, Nottingham NG1 1GF, U.K
| | - Jonathan Shannon
- Sygnature Discovery Ltd., BioCity, Pennyfoot Street, Nottingham NG1 1GF, U.K
| | - John Watts
- Sygnature Discovery Ltd., BioCity, Pennyfoot Street, Nottingham NG1 1GF, U.K
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27
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Munck JM, Berdini V, Bevan L, Brothwood JL, Castro J, Courtin A, East C, Ferraldeschi R, Heightman TD, Hindley CJ, Kucia-Tran J, Lyons JF, Martins V, Muench S, Murray CW, Norton D, O'Reilly M, Reader M, Rees DC, Rich SJ, Richardson CJ, Shah AD, Stanczuk L, Thompson NT, Wilsher NE, Woolford AJA, Wallis NG. ASTX029, a Novel Dual-mechanism ERK Inhibitor, Modulates Both the Phosphorylation and Catalytic Activity of ERK. Mol Cancer Ther 2021; 20:1757-1768. [PMID: 34330842 DOI: 10.1158/1535-7163.mct-20-0909] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 02/11/2021] [Accepted: 07/19/2021] [Indexed: 11/16/2022]
Abstract
The MAPK signaling pathway is commonly upregulated in human cancers. As the primary downstream effector of the MAPK pathway, ERK is an attractive therapeutic target for the treatment of MAPK-activated cancers and for overcoming resistance to upstream inhibition. ASTX029 is a highly potent and selective dual-mechanism ERK inhibitor, discovered using fragment-based drug design. Because of its distinctive ERK-binding mode, ASTX029 inhibits both ERK catalytic activity and the phosphorylation of ERK itself by MEK, despite not directly inhibiting MEK activity. This dual mechanism was demonstrated in cell-free systems, as well as cell lines and xenograft tumor tissue, where the phosphorylation of both ERK and its substrate, ribosomal S6 kinase (RSK), were modulated on treatment with ASTX029. Markers of sensitivity were highlighted in a large cell panel, where ASTX029 preferentially inhibited the proliferation of MAPK-activated cell lines, including those with BRAF or RAS mutations. In vivo, significant antitumor activity was observed in MAPK-activated tumor xenograft models following oral treatment. ASTX029 also demonstrated activity in both in vitro and in vivo models of acquired resistance to MAPK pathway inhibitors. Overall, these findings highlight the therapeutic potential of a dual-mechanism ERK inhibitor such as ASTX029 for the treatment of MAPK-activated cancers, including those which have acquired resistance to inhibitors of upstream components of the MAPK pathway. ASTX029 is currently being evaluated in a first in human phase I-II clinical trial in patients with advanced solid tumors (NCT03520075).
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Affiliation(s)
| | | | - Luke Bevan
- Astex Pharmaceuticals, Cambridge, United Kingdom
| | | | - Juan Castro
- Astex Pharmaceuticals, Cambridge, United Kingdom
| | | | | | | | | | | | | | - John F Lyons
- Astex Pharmaceuticals, Cambridge, United Kingdom
| | | | | | | | - David Norton
- Astex Pharmaceuticals, Cambridge, United Kingdom
| | | | | | - David C Rees
- Astex Pharmaceuticals, Cambridge, United Kingdom
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28
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Benn CL, Dawson LA. Clinically Precedented Protein Kinases: Rationale for Their Use in Neurodegenerative Disease. Front Aging Neurosci 2020; 12:242. [PMID: 33117143 PMCID: PMC7494159 DOI: 10.3389/fnagi.2020.00242] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/13/2020] [Indexed: 12/12/2022] Open
Abstract
Kinases are an intensively studied drug target class in current pharmacological research as evidenced by the large number of kinase inhibitors being assessed in clinical trials. Kinase-targeted therapies have potential for treatment of a broad array of indications including central nervous system (CNS) disorders. In addition to the many variables which contribute to identification of a successful therapeutic molecule, drug discovery for CNS-related disorders also requires significant consideration of access to the target organ and specifically crossing the blood-brain barrier (BBB). To date, only a small number of kinase inhibitors have been reported that are specifically designed to be BBB permeable, which nonetheless demonstrates the potential for success. This review considers the potential for kinase inhibitors in the context of unmet medical need for neurodegenerative disease. A subset of kinases that have been the focus of clinical investigations over a 10-year period have been identified and discussed individually. For each kinase target, the data underpinning the validity of each in the context of neurodegenerative disease is critically evaluated. Selected molecules for each kinase are identified with information on modality, binding site and CNS penetrance, if known. Current clinical development in neurodegenerative disease are summarized. Collectively, the review indicates that kinase targets with sufficient rationale warrant careful design approaches with an emphasis on improving brain penetrance and selectivity.
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29
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Imatinib exhibit synergistic pleiotropy in the prevention of colorectal cancer by suppressing proinflammatory, cell survival and angiogenic signaling. Cell Signal 2020; 76:109803. [PMID: 33022360 DOI: 10.1016/j.cellsig.2020.109803] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/26/2020] [Accepted: 09/30/2020] [Indexed: 12/24/2022]
Abstract
Recent global incidences and mortality rates have placed colorectal cancer (CRC) at third and second positions, respectively, among both sexes of all ages. Resistance during chemotherapy is a big problem in the treatment and disease-free survival of CRC patients. Discovery of new anticancer drug(s) is a time taking process and therefore, invites studies for repurposing the known therapeutics. The present study was conceived to analyze the anticancer role of Imatinib in experimental CRC at early stages. Different experimental procedures e.g. tumor incidences or histoarchitectural changes, gene and protein expression analysis, estimations of intracellular calcium, ROS, mitochondrial membrane potential, apoptotic index and molecular docking was performed to support the hypothesis. It was observed that Imatinib could function as an immunomodulator by breaking the feed-back loop between the proinflammatory cytokines (IL-1β and TNF-α) and transcription factors (NF-κB, Jak3/Stat3) knowingly involved in increased cell proliferation during tumorigenesis via activating different intracellular signaling. Also, Imatinib could independently deregulate the other cell survival and proliferation signaling e.g. PI3-K/Akt/mTOR, Wnt/β-catenin and MAPK. Proinflammatory cytokines orchestrated intracellular signaling also involve angiogenic factors to be upregulated during CRC which were also seemed to be independently suppressed by Imatinib. Restoration of physiological apoptosis by increasing the release of intracellular calcium to generate ROS thereby reducing the mitochondrial membrane potential for the release of cytochrome c and activation of caspase-3 was also reported with Imatinib administration. Thus, it may be suggested that Imatinib show synergistic pleiotropy in suppressing the interlinked tumorigenic signaling pathways independently.
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30
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Wang H, Liang L, Guo Z, Peng H, Qiao S, Saha N, Zhu D, Zeng W, Chen Y, Huang P, Wen S. Highly Reactive Cyclic Monoaryl Iodoniums Tuned as Carbene Generators Couple with Nucleophiles under Metal-Free Conditions. iScience 2020; 23:101307. [PMID: 32634743 PMCID: PMC7338778 DOI: 10.1016/j.isci.2020.101307] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/05/2020] [Accepted: 06/18/2020] [Indexed: 12/29/2022] Open
Abstract
Cross-coupling reactions between aryl iodide and nucleophiles have been well developed. Iodoniums equipped with a reactive C-I(III) bond accelerate cross-coupling reactions of aryl iodide. Among them, cyclic diaryliodoniums are more atom economical; however; they are often in the trap of metal reliance and encounter regioselectivity issues. Now, we have developed a series of highly reactive cyclic monoaryl-vinyl iodoniums that can be tuned to construct C-N, C-O, and C-C bonds without metal catalysis. Under promotion of triethylamine, coupling reactions with aniline, phenol, aromatic acid, and indole proceed rapidly and regioselectively at room temperature. The carbene species is conceptualized as a key intermediate in our mechanism model. Furthermore, the coupling products enable diversity-oriented synthesis strategy to further build up a chemical library of diverse heterocyclic fragments that are in demand in the drug discovery field. Our current work provides a deep insight into the synthetic application of these highly reactive cyclic iodoniums.
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Affiliation(s)
- Haiwen Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou 510060, China
| | - Liyun Liang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou 510060, China
| | - Zhirong Guo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou 510060, China
| | - Hui Peng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou 510060, China
| | - Shuang Qiao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou 510060, China
| | - Nemai Saha
- Berhampore Girl's College, Berhampore, Murshidabad, West Bengal 742101, India
| | - Daqian Zhu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou 510060, China
| | - Wenbin Zeng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
| | - Yunyun Chen
- School of Pharmaceutical Science, Sun Yat-sen University, Guangzhou 510006, China
| | - Peng Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou 510060, China.
| | - Shijun Wen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou 510060, China.
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Guo S, Qiu L, Chen Y, Wang X, Ma B, Qu C, Cui J, Zhang H, Xing C, Zhan Y, An H. TMEM16A-inhibitor loaded pH-responsive nanoparticles: A novel dual-targeting antitumor therapy for lung adenocarcinoma. Biochem Pharmacol 2020; 178:114062. [PMID: 32492446 DOI: 10.1016/j.bcp.2020.114062] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 05/12/2020] [Accepted: 05/27/2020] [Indexed: 12/24/2022]
Abstract
To overcome the adverse effects of conventional chemotherapy for cancers, various nanoparticles based drug delivery systems have been developed. However, nanoparticles delivering drugs directly to kill tumor cells still faced with challenges, because tumors possessed adopt complex mechanism to resist damages, which compromised the therapeutic efficacy. TMEM16A/CaCCs (Calcium activates chloride channels) has been identified to be overexpressed in lung adenocarcinoma which can serve as a novel tumor specific drug target in our previous work. Here, we developed a novel dual-targeted antitumor strategy via designing a novel nano-assembled, pH-sensitive drug-delivery system loading with specific inhibitors of TMEM16A against lung adenocarcinoma. For validation, we assayed the novel dual-targeting therapy on xenograft mouse model which exhibited significant antitumor activity and not affect mouse body weight. The dual targeting therapy accomplished in this study will shed light on the development of advanced antitumor strategy.
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Affiliation(s)
- Shuai Guo
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin 300130, China; Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin 300130, China; Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Sciences, Hebei University of Technology, Tianjin 300401, China
| | - Liang Qiu
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Sciences, Hebei University of Technology, Tianjin 300401, China
| | - Yafei Chen
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Sciences, Hebei University of Technology, Tianjin 300401, China
| | - Xuzhao Wang
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin 300130, China; Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin 300130, China; Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Sciences, Hebei University of Technology, Tianjin 300401, China
| | - Biao Ma
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin 300130, China; Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin 300130, China; Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Sciences, Hebei University of Technology, Tianjin 300401, China
| | - Chang Qu
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin 300130, China; Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin 300130, China; Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Sciences, Hebei University of Technology, Tianjin 300401, China
| | - Jianmin Cui
- Department of Biomedical Engineering, Washington University, St Louis, MO 63130, USA
| | - Hailin Zhang
- Department of Pharmacology, Hebei Medical University, Shijiazhuang 050017, China
| | - Chengfen Xing
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Sciences, Hebei University of Technology, Tianjin 300401, China
| | - Yong Zhan
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin 300130, China; Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin 300130, China; Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Sciences, Hebei University of Technology, Tianjin 300401, China.
| | - Hailong An
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin 300130, China; Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin 300130, China; Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Sciences, Hebei University of Technology, Tianjin 300401, China.
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32
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Wang G, Zhao Y, Liu Y, Sun D, Zhen Y, Liu J, Fu L, Zhang L, Ouyang L. Discovery of a Novel Dual-Target Inhibitor of ERK1 and ERK5 That Induces Regulated Cell Death to Overcome Compensatory Mechanism in Specific Tumor Types. J Med Chem 2020; 63:3976-3995. [PMID: 32078308 DOI: 10.1021/acs.jmedchem.9b01896] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Guan Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Yuqian Zhao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Yao Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Dejuan Sun
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Yongqi Zhen
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Jie Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Leilei Fu
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Lan Zhang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Liang Ouyang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
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33
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Kidger AM, Munck JM, Saini HK, Balmanno K, Minihane E, Courtin A, Graham B, O'Reilly M, Odle R, Cook SJ. Dual-Mechanism ERK1/2 Inhibitors Exploit a Distinct Binding Mode to Block Phosphorylation and Nuclear Accumulation of ERK1/2. Mol Cancer Ther 2020; 19:525-539. [PMID: 31748345 DOI: 10.1158/1535-7163.mct-19-0505] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 10/04/2019] [Accepted: 11/13/2019] [Indexed: 11/16/2022]
Abstract
The RAS-regulated RAF-MEK1/2-ERK1/2 signaling pathway is frequently deregulated in cancer due to activating mutations of growth factor receptors, RAS or BRAF. Both RAF and MEK1/2 inhibitors are clinically approved and various ERK1/2 inhibitors (ERKi) are currently undergoing clinical trials. To date, ERKi display two distinct mechanisms of action (MoA): catalytic ERKi solely inhibit ERK1/2 catalytic activity, whereas dual mechanism ERKi additionally prevents the activating phosphorylation of ERK1/2 at its T-E-Y motif by MEK1/2. These differences may impart significant differences in biological activity because T-E-Y phosphorylation is the signal for nuclear entry of ERK1/2, allowing them to access many key transcription factor targets. Here, we characterized the MoA of five ERKi and examined their functional consequences in terms of ERK1/2 signaling, gene expression, and antiproliferative efficacy. We demonstrate that catalytic ERKi promote a striking nuclear accumulation of p-ERK1/2 in KRAS-mutant cell lines. In contrast, dual-mechanism ERKi exploits a distinct binding mode to block ERK1/2 phosphorylation by MEK1/2, exhibit superior potency, and prevent the nuclear accumulation of ERK1/2. Consequently, dual-mechanism ERKi exhibit more durable pathway inhibition and enhanced suppression of ERK1/2-dependent gene expression compared with catalytic ERKi, resulting in increased efficacy across BRAF- and RAS-mutant cell lines.
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Affiliation(s)
- Andrew M Kidger
- Signalling Laboratory, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom.
| | - Joanne M Munck
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, United Kingdom
| | - Harpreet K Saini
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, United Kingdom
| | - Kathryn Balmanno
- Signalling Laboratory, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Emma Minihane
- Signalling Laboratory, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Aurelie Courtin
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, United Kingdom
| | - Brent Graham
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, United Kingdom
| | - Marc O'Reilly
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, United Kingdom
| | - Richard Odle
- Signalling Laboratory, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Simon J Cook
- Signalling Laboratory, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom.
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Erlanson DA, de Esch IJP, Jahnke W, Johnson CN, Mortenson PN. Fragment-to-Lead Medicinal Chemistry Publications in 2018. J Med Chem 2020; 63:4430-4444. [PMID: 31913033 DOI: 10.1021/acs.jmedchem.9b01581] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This Perspective, the fourth in an annual series, summarizes fragment-to-lead (F2L) success stories published during 2018. Topics such as target class, screening methods, physicochemical properties, and ligand efficiency are discussed for the 2018 examples as well as for the combined 111 F2L examples covering 2015-2018. While the overall properties of fragments and leads have remained constant, a number of new trends are noted, for example, broadening of target class coverage and application of FBDD to covalent inhibitors. Moreover, several studies make use of fragment hits that were previously described in the literature, illustrating that fragments are versatile starting points that can be optimized to structurally diverse leads. By focusing on success stories, the hope is that this Perspective will identify and inform best practices in fragment-based drug discovery.
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Affiliation(s)
- Daniel A Erlanson
- Frontier Medicines, 151 Oyster Point Boulevard, South San Francisco, California 94080, United States
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Wolfgang Jahnke
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, 4002 Basel, Switzerland
| | - Christopher N Johnson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Paul N Mortenson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
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Ward RA, Anderton MJ, Bethel P, Breed J, Cook C, Davies EJ, Dobson A, Dong Z, Fairley G, Farrington P, Feron L, Flemington V, Gibbons FD, Graham MA, Greenwood R, Hanson L, Hopcroft P, Howells R, Hudson J, James M, Jones CD, Jones CR, Li Y, Lamont S, Lewis R, Lindsay N, McCabe J, McGuire T, Rawlins P, Roberts K, Sandin L, Simpson I, Swallow S, Tang J, Tomkinson G, Tonge M, Wang Z, Zhai B. Discovery of a Potent and Selective Oral Inhibitor of ERK1/2 (AZD0364) That Is Efficacious in Both Monotherapy and Combination Therapy in Models of Nonsmall Cell Lung Cancer (NSCLC). J Med Chem 2019; 62:11004-11018. [DOI: 10.1021/acs.jmedchem.9b01295] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Richard A. Ward
- Oncology and Discovery Sciences R&D, AstraZeneca, Darwin Building and Hodgkin Building, c/o Darwin Building, 310 Cambridge Science Park, Milton Rd, Cambridge CB4 0WG, U.K
| | - Mark J. Anderton
- Oncology and Discovery Sciences R&D, AstraZeneca, Darwin Building and Hodgkin Building, c/o Darwin Building, 310 Cambridge Science Park, Milton Rd, Cambridge CB4 0WG, U.K
| | - Paul Bethel
- Chemical Development, Pharmaceutical Technology & Development, AstraZeneca, Macclesfield Campus, Macclesfield SK10 2NA, U.K
| | - Jason Breed
- Oncology and Discovery Sciences R&D, AstraZeneca, Darwin Building and Hodgkin Building, c/o Darwin Building, 310 Cambridge Science Park, Milton Rd, Cambridge CB4 0WG, U.K
| | - Calum Cook
- Oncology and Discovery Sciences R&D, AstraZeneca, Darwin Building and Hodgkin Building, c/o Darwin Building, 310 Cambridge Science Park, Milton Rd, Cambridge CB4 0WG, U.K
| | - Emma J. Davies
- Oncology and Discovery Sciences R&D, AstraZeneca, Darwin Building and Hodgkin Building, c/o Darwin Building, 310 Cambridge Science Park, Milton Rd, Cambridge CB4 0WG, U.K
| | - Andrew Dobson
- Chemical Development, Pharmaceutical Technology & Development, AstraZeneca, Macclesfield Campus, Macclesfield SK10 2NA, U.K
| | - Zhiqiang Dong
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Gary Fairley
- Oncology and Discovery Sciences R&D, AstraZeneca, Darwin Building and Hodgkin Building, c/o Darwin Building, 310 Cambridge Science Park, Milton Rd, Cambridge CB4 0WG, U.K
| | - Paul Farrington
- Bioscience, Oncology R&D, AstraZeneca, Alderley Park, Macclesfield SK10 4TG, U.K
| | - Lyman Feron
- Oncology and Discovery Sciences R&D, AstraZeneca, Darwin Building and Hodgkin Building, c/o Darwin Building, 310 Cambridge Science Park, Milton Rd, Cambridge CB4 0WG, U.K
| | - Vikki Flemington
- Oncology and Discovery Sciences R&D, AstraZeneca, Darwin Building and Hodgkin Building, c/o Darwin Building, 310 Cambridge Science Park, Milton Rd, Cambridge CB4 0WG, U.K
| | - Francis D. Gibbons
- DMPK, Oncology R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
| | - Mark A. Graham
- Chemical Development, Pharmaceutical Technology & Development, AstraZeneca, Macclesfield Campus, Macclesfield SK10 2NA, U.K
| | - Ryan Greenwood
- Oncology and Discovery Sciences R&D, AstraZeneca, Darwin Building and Hodgkin Building, c/o Darwin Building, 310 Cambridge Science Park, Milton Rd, Cambridge CB4 0WG, U.K
| | - Lyndsey Hanson
- Bioscience, Oncology R&D, AstraZeneca, Alderley Park, Macclesfield SK10 4TG, U.K
| | - Philip Hopcroft
- Oncology and Discovery Sciences R&D, AstraZeneca, Darwin Building and Hodgkin Building, c/o Darwin Building, 310 Cambridge Science Park, Milton Rd, Cambridge CB4 0WG, U.K
| | - Rachel Howells
- Oncology and Discovery Sciences R&D, AstraZeneca, Darwin Building and Hodgkin Building, c/o Darwin Building, 310 Cambridge Science Park, Milton Rd, Cambridge CB4 0WG, U.K
| | | | | | | | | | - Yongchao Li
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Scott Lamont
- Oncology and Discovery Sciences R&D, AstraZeneca, Darwin Building and Hodgkin Building, c/o Darwin Building, 310 Cambridge Science Park, Milton Rd, Cambridge CB4 0WG, U.K
| | - Richard Lewis
- Medicinal Chemistry, Respiratory, Inflammation and Autoimmune (RIA), BioPharmaceuticals R&D, AstraZeneca, Gothenburg 431 50, Sweden
| | - Nicola Lindsay
- Oncology and Discovery Sciences R&D, AstraZeneca, Darwin Building and Hodgkin Building, c/o Darwin Building, 310 Cambridge Science Park, Milton Rd, Cambridge CB4 0WG, U.K
| | - James McCabe
- Chemical Development, Pharmaceutical Technology & Development, AstraZeneca, Macclesfield Campus, Macclesfield SK10 2NA, U.K
| | - Thomas McGuire
- Oncology and Discovery Sciences R&D, AstraZeneca, Darwin Building and Hodgkin Building, c/o Darwin Building, 310 Cambridge Science Park, Milton Rd, Cambridge CB4 0WG, U.K
| | - Philip Rawlins
- Oncology and Discovery Sciences R&D, AstraZeneca, Darwin Building and Hodgkin Building, c/o Darwin Building, 310 Cambridge Science Park, Milton Rd, Cambridge CB4 0WG, U.K
| | - Karen Roberts
- Oncology and Discovery Sciences R&D, AstraZeneca, Darwin Building and Hodgkin Building, c/o Darwin Building, 310 Cambridge Science Park, Milton Rd, Cambridge CB4 0WG, U.K
| | | | | | - Steve Swallow
- Chemical Development, Pharmaceutical Technology & Development, AstraZeneca, Macclesfield Campus, Macclesfield SK10 2NA, U.K
| | - Jia Tang
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Gary Tomkinson
- Chemical Development, Pharmaceutical Technology & Development, AstraZeneca, Macclesfield Campus, Macclesfield SK10 2NA, U.K
| | - Michael Tonge
- Oncology and Discovery Sciences R&D, AstraZeneca, Darwin Building and Hodgkin Building, c/o Darwin Building, 310 Cambridge Science Park, Milton Rd, Cambridge CB4 0WG, U.K
| | - Zhenhua Wang
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Baochang Zhai
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P.R. China
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Halder AK, Giri AK, Cordeiro MNDS. Multi-Target Chemometric Modelling, Fragment Analysis and Virtual Screening with ERK Inhibitors as Potential Anticancer Agents. Molecules 2019; 24:molecules24213909. [PMID: 31671605 PMCID: PMC6864583 DOI: 10.3390/molecules24213909] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/21/2019] [Accepted: 10/25/2019] [Indexed: 02/07/2023] Open
Abstract
Two isoforms of extracellular regulated kinase (ERK), namely ERK-1 and ERK-2, are associated with several cellular processes, the aberration of which leads to cancer. The ERK-1/2 inhibitors are thus considered as potential agents for cancer therapy. Multitarget quantitative structure–activity relationship (mt-QSAR) models based on the Box–Jenkins approach were developed with a dataset containing 6400 ERK inhibitors assayed under different experimental conditions. The first mt-QSAR linear model was built with linear discriminant analysis (LDA) and provided information regarding the structural requirements for better activity. This linear model was also utilised for a fragment analysis to estimate the contributions of ring fragments towards ERK inhibition. Then, the random forest (RF) technique was employed to produce highly predictive non-linear mt-QSAR models, which were used for screening the Asinex kinase library and identify the most potential virtual hits. The fragment analysis results justified the selection of the hits retrieved through such virtual screening. The latter were subsequently subjected to molecular docking and molecular dynamics simulations to understand their possible interactions with ERK enzymes. The present work, which utilises in-silico techniques such as multitarget chemometric modelling, fragment analysis, virtual screening, molecular docking and dynamics, may provide important guidelines to facilitate the discovery of novel ERK inhibitors.
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Affiliation(s)
- Amit Kumar Halder
- Department of Chemistry and Biochemistry, University of Porto, 4169-007 Porto, Portugal.
| | - Amal Kanta Giri
- Department of Chemistry and Biochemistry, University of Porto, 4169-007 Porto, Portugal.
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Miao L, Tian H. Development of ERK1/2 inhibitors as a therapeutic strategy for tumour with MAPK upstream target mutations. J Drug Target 2019; 28:154-165. [PMID: 31340679 DOI: 10.1080/1061186x.2019.1648477] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Extracellular signal-regulated kinases 1 and 2 (ERK1/2) phosphorylate a variety of substrates that play key roles in promoting cell survival and proliferation. Many inhibitors, acting on upstream of the ERK pathway, exhibit excellent antitumor activity. However, drug-resistant tumour cells invariably emerge after their use due to the reactivation of ERK1/2 signalling. ERK1/2 inhibitors have shown clinical efficacy as a therapeutic strategy for the treatment of tumours with mitogen-activated protein kinase (MAPK) upstream target mutations. These inhibitors may be effective against cancers with altered MAPK upstream pathway and may be used as a possible strategy to overcome acquired resistance to MAPK inhibitors. In this review, we describe the mechanism and types of ERK1/2 inhibitors, summarise the current development status of small-molecule ERK1/2 inhibitors, including the preclinical data and clinical study progress, and discuss the future research directions for the application of ERK1/2 inhibitors.
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Affiliation(s)
- Longfei Miao
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Science & Peking Union Medical College, Tianjin, China
| | - Hongqi Tian
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Science & Peking Union Medical College, Tianjin, China
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Selective ERK1/2 agonists isolated from Melia azedarach with potent anti-leukemic activity. BMC Cancer 2019; 19:764. [PMID: 31375085 PMCID: PMC6679490 DOI: 10.1186/s12885-019-5914-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 07/09/2019] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND MAPK/ERK kinases transmit signals from many growth factors/kinase receptors during normal cell growth/differentiation, and their dysregulation is a hallmark of diverse types of cancers. A plethora of drugs were developed to block this kinase pathway for clinical application. With the exception of a recently identified agent, EQW, most of these inhibitors target upstream factors but not ERK1/2; no activator of ERK1/2 is currently available. METHOD A library of compounds isolated from medicinal plants of China was screened for anti-cancer activities. Three limonoid compounds, termed A1541-43, originally isolated from the plant Melia azedarach, exhibiting strong anti-leukemic activity. The anti-neoplastic activity and the biological target of these compounds were explored using various methods, including western blotting, flow cytometry, molecular docking and animal model for leukemia. RESULTS Compounds A1541-43, exhibiting potent anti-leukemic activity, was shown to induce ERK1/2 phosphorylation. In contrast, the natural product Cedrelone, which shares structural similarities with A1541-43, functions as a potent inhibitor of ERK1/2. We provided evidence that A1541-43 and Cedrelone specifically target ERK1/2, but not the upstream MAPK/ERK pathway. Computational docking analysis predicts that compounds A1541-43 bind a region in ERK1/2 that is distinct from that to which Cedrelone and EQW bind. Interestingly, both A1541-43, which act as ERK1/2 agonists, and Cedrelone, which inhibit these kinases, exerted strong anti-proliferative activity against multiple leukemic cell lines, and induced robust apoptosis as well as erythroid and megakaryocytic differentiation in erythroleukemic cell lines. These compounds also suppressed tumor progression in a mouse model of erythroleukemia. CONCLUSIONS This study identifies for the first time activators of ERK1/2 with therapeutic potential for the treatment of cancers driven by dysregulation of the MAPK/ERK pathway and possibly for other disorders.
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O'Reilly M, Cleasby A, Davies TG, Hall RJ, Ludlow RF, Murray CW, Tisi D, Jhoti H. Crystallographic screening using ultra-low-molecular-weight ligands to guide drug design. Drug Discov Today 2019; 24:1081-1086. [PMID: 30878562 DOI: 10.1016/j.drudis.2019.03.009] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/06/2019] [Accepted: 03/08/2019] [Indexed: 02/06/2023]
Abstract
We present a novel crystallographic screening methodology (MiniFrags) that employs high-concentration aqueous soaks with a chemically diverse and ultra-low-molecular-weight library (heavy atom count 5-7) to identify ligand-binding hot and warm spots on proteins. We propose that MiniFrag screening represents a highly effective method for guiding optimisation of fragment-derived lead compounds or chemical tools and that the high screening hit rates reflect enhanced sampling of chemical space.
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Affiliation(s)
- Marc O'Reilly
- Astex Pharmaceuticals,436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, UK
| | - Anne Cleasby
- Astex Pharmaceuticals,436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, UK
| | - Thomas G Davies
- Astex Pharmaceuticals,436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, UK
| | - Richard J Hall
- Astex Pharmaceuticals,436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, UK
| | - R Frederick Ludlow
- Astex Pharmaceuticals,436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, UK
| | - Christopher W Murray
- Astex Pharmaceuticals,436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, UK
| | - Dominic Tisi
- Astex Pharmaceuticals,436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, UK
| | - Harren Jhoti
- Astex Pharmaceuticals,436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, UK.
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40
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Roskoski R. Targeting ERK1/2 protein-serine/threonine kinases in human cancers. Pharmacol Res 2019; 142:151-168. [PMID: 30794926 DOI: 10.1016/j.phrs.2019.01.039] [Citation(s) in RCA: 190] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 01/18/2019] [Indexed: 12/17/2022]
Abstract
ERK1 and ERK2 are key protein kinases that contribute to the Ras-Raf-MEK-ERK MAP kinase signalling module. This pathway participates in the control of numerous processes including apoptosis, cell proliferation, the immune response, nervous system function, and RNA synthesis and processing. MEK1/2 activate human ERK1/2 by first catalyzing the phosphorylation of Y204/187 and then T202/185, both residues of which occur within the activation segment. The phosphorylation of both residues is required for enzyme activation. The only Raf substrates are MEK1/2 and the only MEK1/2 substrates are ERK1/2. In contrast, ERK1/2 catalyze the phosphorylation of many cytoplasmic and nuclear substrates including transcription factors and regulatory molecules. The linear MAP kinase pathway branches extensively at the ERK1/2 node. ERK1/2 are proline-directed kinases that preferentially catalyze the phosphorylation of substrates containing a PxS/TP sequence. The dephosphorylation and inactivation of ERK1/2 is catalyzed by dual specificity phosphatases, protein-tyrosine specific phosphatases, and protein-serine/threonine phosphatases. The combined functions of kinases and phosphatases make the overall process reversible. To provide an idea of the complexities involved in these reactions, somatic cell cycle progression involves the strict timing of more than 32,000 phosphorylation and dephosphorylation events as determined by mass spectrometry. The MAP kinase cascade is perhaps the most important oncogenic driver of human cancers and the blockade of this signalling module by targeted inhibitors is an important anti-tumor strategy. Although numerous cancers are driven by MAP kinase pathway activation, thus far the only orally effective approved drugs that target this signaling module are used for the treatment of BRAF-mutant melanomas. The best treatments include the combination of B-Raf and MEK inhibitors (dabrafenib and trametinib, encorafenib and binimetinib, vemurafenib and cobimetanib). However, resistance to these antagonists occurs within one year and additional treatment options are necessary. Owing to the large variety of malignancies that are driven by dysregulation of the MAP kinase pathway, additional tumor types should be amenable to MAP kinase pathway inhibitor therapy. In addition to new B-Raf and MEK inhibitors, the addition of ERK inhibitors should prove helpful. Ulixertinib, MK-8353, and GDC-0994 are orally effective, potent, and specific inhibitors of ERK1/2 that are in early clinical trials for the treatment of various advanced/metastatic solid tumors. These agents are effective against cell lines that are resistant to B-Raf and MEK1/2 inhibitor therapy. Although MK-8353 does not directly inhibit MEK1/2, it decreases the phosphorylation of ERK1/2 as well as the phosphorylation of RSK, an ERK1/2 substrate. The decrease in RSK phosphorylation appears to be a result of ERK inhibition and the decrease in ERK1/2 phosphorylation is related to the inability of MEK to catalyze the phosphorylation of the ERK-MK-8353 complex; these decreases characterize the ERK dual mechanism inhibition paradigm. Additional work will be required to determine whether ERK inhibitors will be successful in the clinic and are able to forestall the development of drug resistance of the MAP kinase pathway.
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Affiliation(s)
- Robert Roskoski
- Blue Ridge Institute for Medical Research, 3754 Brevard Road, Suite 116, Box 19, Horse Shoe, NC, 28742-8814, United States.
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Kurczab R, Canale V, Satała G, Zajdel P, Bojarski AJ. Amino Acid Hot Spots of Halogen Bonding: A Combined Theoretical and Experimental Case Study of the 5-HT 7 Receptor. J Med Chem 2018; 61:8717-8733. [PMID: 30188719 DOI: 10.1021/acs.jmedchem.8b00828] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A computational approach combining a structure-activity relationship library of halogenated and the corresponding unsubstituted ligands (called XSAR) with QM-based molecular docking and binding free energy calculations was used to search for amino acids frequently targeted by halogen bonding (hot spots) in a 5-HT7R as a case study. The procedure identified two sets of hot spots, extracellular (D2.65, T2.64, and E7.35) and transmembrane (C3.36, T5.39, and S5.42), which were further verified by a synthesized library of halogenated arylsulfonamide derivatives of (aryloxy)ethylpiperidines. It was found that a halogen bond formed between T5.39 and a bromine atom at 3-position of the aryloxy fragment caused the most remarkable, 35-fold increase in binding affinity for 5-HT7R when compared to the nonhalogenated analog. The proposed paradigm of halogen bonding hot spots was additionally verified on D4 dopamine receptor showing that it can be used in rational drug design/optimization for any protein target.
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Affiliation(s)
- Rafał Kurczab
- Department of Medicinal Chemistry , Institute of Pharmacology, Polish Academy of Sciences , 12 Smętna Street , 31-343 Krakow , Poland
| | - Vittorio Canale
- Department of Medicinal Chemistry , Jagiellonian University Medical College , 9 Medyczna Street , 30-688 Krakow , Poland
| | - Grzegorz Satała
- Department of Medicinal Chemistry , Institute of Pharmacology, Polish Academy of Sciences , 12 Smętna Street , 31-343 Krakow , Poland
| | - Paweł Zajdel
- Department of Medicinal Chemistry , Jagiellonian University Medical College , 9 Medyczna Street , 30-688 Krakow , Poland
| | - Andrzej J Bojarski
- Department of Medicinal Chemistry , Institute of Pharmacology, Polish Academy of Sciences , 12 Smętna Street , 31-343 Krakow , Poland
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