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Abstract
Pseudokinases are members of the protein kinase superfamily but signal primarily through noncatalytic mechanisms. Many pseudokinases contribute to the pathologies of human diseases, yet they remain largely unexplored as drug targets owing to challenges associated with modulation of their biological functions. Our understanding of the structure and physiological roles of pseudokinases has improved substantially over the past decade, revealing intriguing similarities between pseudokinases and their catalytically active counterparts. Pseudokinases often adopt conformations that are analogous to those seen in catalytically active kinases and, in some cases, can also bind metal cations and/or nucleotides. Several clinically approved kinase inhibitors have been shown to influence the noncatalytic functions of active kinases, providing hope that similar properties in pseudokinases could be pharmacologically regulated. In this Review, we discuss known roles of pseudokinases in disease, their unique structural features and the progress that has been made towards developing pseudokinase-directed therapeutics.
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102
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Gagic Z, Ruzic D, Djokovic N, Djikic T, Nikolic K. In silico Methods for Design of Kinase Inhibitors as Anticancer Drugs. Front Chem 2020; 7:873. [PMID: 31970149 PMCID: PMC6960140 DOI: 10.3389/fchem.2019.00873] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 12/04/2019] [Indexed: 12/11/2022] Open
Abstract
Rational drug design implies usage of molecular modeling techniques such as pharmacophore modeling, molecular dynamics, virtual screening, and molecular docking to explain the activity of biomolecules, define molecular determinants for interaction with the drug target, and design more efficient drug candidates. Kinases play an essential role in cell function and therefore are extensively studied targets in drug design and discovery. Kinase inhibitors are clinically very important and widely used antineoplastic drugs. In this review, computational methods used in rational drug design of kinase inhibitors are discussed and compared, considering some representative case studies.
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Affiliation(s)
- Zarko Gagic
- Department of Pharmaceutical Chemistry, Faculty of Medicine, University of Banja Luka, Banja Luka, Bosnia and Herzegovina
| | - Dusan Ruzic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Nemanja Djokovic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Teodora Djikic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Katarina Nikolic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
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103
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Abdeldayem A, Raouf YS, Constantinescu SN, Moriggl R, Gunning PT. Advances in covalent kinase inhibitors. Chem Soc Rev 2020; 49:2617-2687. [DOI: 10.1039/c9cs00720b] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This comprehensive review details recent advances, challenges and innovations in covalent kinase inhibition within a 10 year period (2007–2018).
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Affiliation(s)
- Ayah Abdeldayem
- Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Canada
- Department of Chemistry
| | - Yasir S. Raouf
- Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Canada
- Department of Chemistry
| | | | - Richard Moriggl
- Institute of Animal Breeding and Genetics
- University of Veterinary Medicine
- 1210 Vienna
- Austria
| | - Patrick T. Gunning
- Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Canada
- Department of Chemistry
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104
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Roskoski R. The role of fibroblast growth factor receptor (FGFR) protein-tyrosine kinase inhibitors in the treatment of cancers including those of the urinary bladder. Pharmacol Res 2020; 151:104567. [DOI: 10.1016/j.phrs.2019.104567] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 11/20/2019] [Indexed: 12/31/2022]
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105
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Exploring receptor tyrosine kinases-inhibitors in Cancer treatments. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2019. [DOI: 10.1186/s43042-019-0035-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
AbstractBackgroundReceptor tyrosine kinases (RTKs) are signaling enzymes responsible for the transfer of Adenosine triphosphate (ATP) γ-phosphate to the tyrosine residues substrates. RTKs demonstrate essential roles in cellular growth, metabolism, differentiation, and motility. Anomalous expression of RTK customarily leads to cell growth dysfunction, which is connected to tumor takeover, angiogenesis, and metastasis. Understanding the structure, mechanisms of adaptive and acquired resistance, optimizing inhibition of RTKs, and eradicating cum minimizing the havocs of quiescence cancer cells is paramount.MainTextTyrosine kinase inhibitors (TKIs) vie with RTKs ATP-binding site for ATP and hitherto reduce tyrosine kinase phosphorylation, thus hampering the growth of cancer cells. TKIs can either be monoclonal antibodies that compete for the receptor’s extracellular domain or small molecules that inhibit the tyrosine kinase domain and prevent conformational changes that activate RTKs. Progression of cancer is related to aberrant activation of RTKs due to due to mutation, excessive expression, or autocrine stimulation.ConclusionsUnderstanding the modes of inhibition and structures of RTKs is germane to the design of novel and potent TKIs. This review shed light on the structures of tyrosine kinases, receptor tyrosine kinases, tyrosine kinase inhibitors, minimizing imatinib associated toxicities, optimization of tyrosine kinase inhibition in curtailing quiescence in cancer cells and the prospects of receptor tyrosine kinase based treatments.
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106
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Lakkaniga NR, Balasubramaniam M, Zhang S, Frett B, Li HY. Structural Characterization of the Aurora Kinase B "DFG-flip" Using Metadynamics. AAPS JOURNAL 2019; 22:14. [PMID: 31853739 DOI: 10.1208/s12248-019-0399-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/13/2019] [Indexed: 11/30/2022]
Abstract
Aurora kinase B (AKB), a Ser/Thr kinase that plays a crucial role in mitosis, is overexpressed in several cancers. Clinical inhibitors targeting AKB bind to the active DFG "in" conformation of the kinase. It would be beneficial, however, to understand if AKB is susceptible to type II kinase inhibitors that bind to the inactive, DFG "out" conformation, since type II inhibitors achieve higher kinome selectivity and higher potency in vivo. The DFG "out" conformation of AKB is not yet experimentally determined which makes the design of type II inhibitors exceedingly difficult. An alternate approach is to simulate the DFG "out" conformation from the experimentally determined DFG "in" conformation using atomistic molecular dynamics (MD) simulation. In this work, we employed metadynamics (MTD) approach to simulate the DFG "out" conformation of AKB by choosing the appropriate collective variables. We examined structural changes during the DFG-flip and determined the interactions crucial to stabilize the kinase in active and inactive states. Interestingly, the MTD approach also identified a unique transition state (DFG "up"), which can be targeted by small molecule inhibitors. Structural insights about these conformations is essential for structure-guided design of next-generation AKB inhibitors. This work also emphasizes the usefulness of MTD simulations in predicting macromolecular conformational changes at reduced computational costs.
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Affiliation(s)
- Naga Rajiv Lakkaniga
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas, 72205, USA
| | | | - Shuxing Zhang
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas, 77225, USA
| | - Brendan Frett
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas, 72205, USA
| | - Hong-Yu Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas, 72205, USA.
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107
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Roskoski R. Properties of FDA-approved small molecule protein kinase inhibitors: A 2020 update. Pharmacol Res 2019; 152:104609. [PMID: 31862477 DOI: 10.1016/j.phrs.2019.104609] [Citation(s) in RCA: 349] [Impact Index Per Article: 69.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 12/16/2019] [Indexed: 02/07/2023]
Abstract
Because genetic alterations including mutations, overexpression, translocations, and dysregulation of protein kinases are involved in the pathogenesis of many illnesses, this enzyme family is currently the subject of many drug discovery programs in the pharmaceutical industry. The US FDA approved four small molecule protein kinase antagonists in 2019; these include entrectinib, erdafitinib, pexidartinib, and fedratinib. Entrectinib binds to TRKA/B/C and ROS1 and is prescribed for the treatment of solid tumors with NTRK fusion proteins and for ROS1-postive non-small cell lung cancers. Erdafitinib inhibits fibroblast growth factor receptors 1-4 and is used in the treatment of urothelial bladder cancers. Pexidartinib is a CSF1R antagonist that is prescribed for the treatment of tenosynovial giant cell tumors. Fedratinib blocks JAK2 and is used in the treatment of myelofibrosis. Overall, the US FDA has approved 52 small molecule protein kinase inhibitors, nearly all of which are orally effective with the exceptions of temsirolimus (which is given intravenously) and netarsudil (an eye drop). Of the 52 approved drugs, eleven inhibit protein-serine/threonine protein kinases, two are directed against dual specificity protein kinases, eleven target non-receptor protein-tyrosine kinases, and 28 block receptor protein-tyrosine kinases. The data indicate that 46 of these drugs are used in the treatment of neoplastic diseases (eight against non-solid tumors such as leukemias and 41 against solid tumors including breast and lung cancers; some drugs are used against both tumor types). Eight drugs are employed in the treatment of non-malignancies: fedratinib, myelofibrosis; ruxolitinib, myelofibrosis and polycythemia vera; fostamatinib, chronic immune thrombocytopenia; baricitinib, rheumatoid arthritis; sirolimus, renal graft vs. host disease; nintedanib, idiopathic pulmonary fibrosis; netarsudil, glaucoma; and tofacitinib, rheumatoid arthritis, Crohn disease, and ulcerative colitis. Moreover, sirolimus and ibrutinib are used for the treatment of both neoplastic and non-neoplastic diseases. Entrectinib and larotrectinib are tissue-agnostic anti-cancer small molecule protein kinase inhibitors. These drugs are prescribed for the treatment of any solid cancer harboring NTRK1/2/3 fusion proteins regardless of the organ, tissue, anatomical location, or histology type. Of the 52 approved drugs, seventeen are used in the treatment of more than one disease. Imatinib, for example, is approved for the treatment of eight disparate disorders. The most common drug targets of the approved pharmaceuticals include BCR-Abl, B-Raf, vascular endothelial growth factor receptors (VEGFR), epidermal growth factor receptors (EGFR), and ALK. Most of the approved small molecule protein kinase antagonists (49) bind to the protein kinase domain and six of them bind covalently. In contrast, everolimus, temsirolimus, and sirolimus are larger molecules (MW ≈ 1000) that bind to FK506 binding protein-12 (FKBP-12) to generate a complex that inhibits the mammalian target of rapamycin (mTOR) protein kinase complex. This review presents the physicochemical properties of all of the FDA-approved small molecule protein kinase inhibitors. Twenty-two of the 52 drugs have molecular weights greater than 500, exceeding a Lipinski rule of five criterion. Excluding the macrolides (everolimus, sirolimus, temsirolimus), the average molecular weight of the approved drugs is 480 with a range of 306 (ruxolitinib) to 615 (trametinib). More than half of the antagonists (29) have lipophilic efficiency values of less than five while the recommended optima range from 5 to 10. One of the troublesome problems with both targeted and cytotoxic drugs in the treatment of malignant diseases is the near universal development of resistance to every therapeutic modality.
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Affiliation(s)
- Robert Roskoski
- Blue Ridge Institute for Medical Research, 3754 Brevard Road, Suite 116, Box 19, Horse Shoe, North Carolina, 28742-8814, United States.
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108
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Ung PMU, DeVita RJ, Schlessinger A. Encounter and React: Computer-Guided Design of Covalent Inhibitors. Cell Chem Biol 2019; 26:6-8. [PMID: 30658111 DOI: 10.1016/j.chembiol.2018.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Covalent inhibitors can obtain optimal selectivity and extended residence time. In this issue of Cell Chemical Biology, Shraga et al. (2019) take a comprehensive computational and experimental approach to modulate the JNK-Jun pathway through design of MKK7 covalent inhibitors. This study highlights a promising and emerging strategy for therapeutic discovery.
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Affiliation(s)
- Peter Man-Un Ung
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Robert J DeVita
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Drug Discovery Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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109
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A Systematic Review of Recently Reported Marine Derived Natural Product Kinase Inhibitors. Mar Drugs 2019; 17:md17090493. [PMID: 31450856 PMCID: PMC6780990 DOI: 10.3390/md17090493] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/16/2019] [Accepted: 08/18/2019] [Indexed: 12/13/2022] Open
Abstract
Protein kinases are validated drug targets for a number of therapeutic areas, as kinase deregulation is known to play an essential role in many disease states. Many investigated protein kinase inhibitors are natural product small molecules or their derivatives. Many marine-derived natural products from various marine sources, such as bacteria and cyanobacteria, fungi, animals, algae, soft corals, sponges, etc. have been found to have potent kinase inhibitory activity, or desirable pharmacophores for further development. This review covers the new compounds reported from the beginning of 2014 through the middle of 2019 as having been isolated from marine organisms and having potential therapeutic applications due to kinase inhibitory and associated bioactivities. Moreover, some existing clinical drugs based on marine-derived natural product scaffolds are also discussed.
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110
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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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111
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Schehr M, Ianes C, Weisner J, Heintze L, Müller MP, Pichlo C, Charl J, Brunstein E, Ewert J, Lehr M, Baumann U, Rauh D, Knippschild U, Peifer C, Herges R. 2-Azo-, 2-diazocine-thiazols and 2-azo-imidazoles as photoswitchable kinase inhibitors: limitations and pitfalls of the photoswitchable inhibitor approach. Photochem Photobiol Sci 2019; 18:1398-1407. [PMID: 30924488 DOI: 10.1039/c9pp00010k] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In photopharmacology, photoswitchable compounds including azobenzene or other diarylazo moieties exhibit bioactivity against a target protein typically in the slender E-configuration, whereas the rather bulky Z-configuration usually is pharmacologically less potent. Herein we report the design, synthesis and photochemical/inhibitory characterization of new photoswitchable kinase inhibitors targeting p38α MAPK and CK1δ. A well characterized inhibitor scaffold was used to attach arylazo- and diazocine moieties. When the isolated isomers, or the photostationary state (PSS) of isomers, were tested in commonly used in vitro kinase assays, however, only small differences in activity were observed. X-ray analyses of ligand-bound p38α MAPK and CK1δ complexes revealed dynamic conformational adaptations of the protein with respect to both isomers. More importantly, irreversible reduction of the azo group to the corresponding hydrazine was observed. Independent experiments revealed that reducing agents such as DTT (dithiothreitol) and GSH (glutathione) that are typically used for protein stabilization in biological assays were responsible. Two further sources of error are the concentration dependence of the E-Z-switching efficiency and artefacts due to incomplete exclusion of light during testing. Our findings may also apply to a number of previously investigated azobenzene-based photoswitchable inhibitors.
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Affiliation(s)
- Miriam Schehr
- Otto Diels-Institute of Organic Chemistry, Christian Albrechts University Kiel, Otto-Hahn-Platz 4, 24118 Kiel, Germany.
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112
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Astl L, Verkhivker GM. Data-driven computational analysis of allosteric proteins by exploring protein dynamics, residue coevolution and residue interaction networks. Biochim Biophys Acta Gen Subj 2019:S0304-4165(19)30179-5. [PMID: 31330173 DOI: 10.1016/j.bbagen.2019.07.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 07/15/2019] [Accepted: 07/17/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Computational studies of allosteric interactions have witnessed a recent renaissance fueled by the growing interest in modeling of the complex molecular assemblies and biological networks. Allosteric interactions in protein structures allow for molecular communication in signal transduction networks. METHODS In this work, we performed a large scale comprehensive and multi-faceted analysis of >300 diverse allosteric proteins and complexes with allosteric modulators. By modeling and exploring coarse-grained dynamics, residue coevolution, and residue interaction networks for allosteric proteins, we have determined unifying molecular signatures shared by allosteric systems. RESULTS The results of this study have suggested that allosteric inhibitors and allosteric activators may differentially affect global dynamics and network organization of protein systems, leading to diverse allosteric mechanisms. By using structural and functional data on protein kinases, we present a detailed case study that that included atomic-level analysis of coevolutionary networks in kinases bound with allosteric inhibitors and activators. CONCLUSIONS We have found that coevolutionary networks can form direct communication pathways connecting functional regions and can recapitulate key regulatory sites and interactions responsible for allosteric signaling in the studied protein systems. The results of this computational investigation are compared with the experimental studies and reveal molecular signatures of known regulatory hotspots in protein kinases. GENERAL SIGNIFICANCE This study has shown that allosteric inhibitors and allosteric activators can have a different effect on residue interaction networks and can exploit distinct regulatory mechanisms, which could open up opportunities for probing allostery and new drug combinations with broad range of activities.
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Affiliation(s)
- Lindy Astl
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, United States of America
| | - Gennady M Verkhivker
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, United States of America; Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States of America.
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113
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Apsel Winger B, Cortopassi WA, Garrido Ruiz D, Ding L, Jang K, Leyte-Vidal A, Zhang N, Esteve-Puig R, Jacobson MP, Shah NP. ATP-Competitive Inhibitors Midostaurin and Avapritinib Have Distinct Resistance Profiles in Exon 17-Mutant KIT. Cancer Res 2019; 79:4283-4292. [PMID: 31270078 DOI: 10.1158/0008-5472.can-18-3139] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 05/05/2019] [Accepted: 06/26/2019] [Indexed: 01/08/2023]
Abstract
KIT is a type-3 receptor tyrosine kinase that is frequently mutated at exon 11 or 17 in a variety of cancers. First-generation KIT tyrosine kinase inhibitors (TKI) are ineffective against KIT exon 17 mutations, which favor an active conformation that prevents these TKIs from binding. The ATP-competitive inhibitors, midostaurin and avapritinib, which target the active kinase conformation, were developed to inhibit exon 17-mutant KIT. Because secondary kinase domain mutations are a common mechanism of TKI resistance and guide ensuing TKI design, we sought to define problematic KIT kinase domain mutations for these emerging therapeutics. Midostaurin and avapritinib displayed different vulnerabilities to secondary kinase domain substitutions, with the T670I gatekeeper mutation being selectively problematic for avapritinib. Although gatekeeper mutations often directly disrupt inhibitor binding, we provide evidence that T670I confers avapritinib resistance indirectly by inducing distant conformational changes in the phosphate-binding loop. These findings suggest combining midostaurin and avapritinib may forestall acquired resistance mediated by secondary kinase domain mutations. SIGNIFICANCE: This study identifies potential problematic kinase domain mutations for next-generation KIT inhibitors midostaurin and avapritinib.
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Affiliation(s)
- Beth Apsel Winger
- Division of Hematology/Oncology, Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Wilian A Cortopassi
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California
| | - Diego Garrido Ruiz
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California
| | - Lucky Ding
- Department of Medicine, Division of Hematology/Oncology, University of California San Francisco, San Francisco, California
| | - Kibeom Jang
- Department of Medicine, Division of Hematology/Oncology, University of California San Francisco, San Francisco, California
| | - Ariel Leyte-Vidal
- Department of Medicine, Division of Hematology/Oncology, University of California San Francisco, San Francisco, California
| | - Na Zhang
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California.,Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing, China
| | - Rosaura Esteve-Puig
- Department of Dermatology, University of California San Francisco, San Francisco, California
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California
| | - Neil P Shah
- Department of Medicine, Division of Hematology/Oncology, University of California San Francisco, San Francisco, California.
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114
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Jenardhanan P, Panneerselvam M, Mathur PP. Targeting Kinase Interaction Networks: A New Paradigm in PPI Based Design of Kinase Inhibitors. Curr Top Med Chem 2019; 19:467-485. [PMID: 31184298 DOI: 10.2174/1568026619666190304155711] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 01/20/2019] [Accepted: 02/06/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND Kinases are key modulators in regulating diverse range of cellular activities and are an essential part of the protein-protein interactome. Understanding the interaction of kinases with different substrates and other proteins is vital to decode the cell signaling machinery as well as causative mechanism for disease onset and progression. OBJECTIVE The objective of this review is to present all studies on the structure and function of few important kinases and highlight the protein-protein interaction (PPI) mechanism of kinases and the kinase specific interactome databases and how such studies could be utilized to develop anticancer drugs. METHODS The article is a review of the detailed description of the various domains in kinases that are involved in protein-protein interactions and specific inhibitors developed targeting these PPI domains. RESULTS The review has surfaced in depth the interacting domains in key kinases and their features and the roles of PPI in the human kinome and the various signaling cascades that are involved in certain types of cancer. CONCLUSION The insight availed into the mechanism of existing peptide inhibitors and peptidomimetics against kinases will pave way for the design and generation of domain specific peptide inhibitors with better productivity and efficiency and the various software and servers available can be of great use for the identification and analysis of protein-protein interactions.
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Affiliation(s)
| | - Manivel Panneerselvam
- Department of Biotechnology, BJM School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Premendu P Mathur
- Department of Biochemistry & Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
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115
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Dai S, Zhou Z, Chen Z, Xu G, Chen Y. Fibroblast Growth Factor Receptors (FGFRs): Structures and Small Molecule Inhibitors. Cells 2019; 8:E614. [PMID: 31216761 PMCID: PMC6627960 DOI: 10.3390/cells8060614] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 06/11/2019] [Accepted: 06/12/2019] [Indexed: 12/05/2022] Open
Abstract
Fibroblast growth factor receptors (FGFRs) are a family of receptor tyrosine kinases expressed on the cell membrane that play crucial roles in both developmental and adult cells. Dysregulation of FGFRs has been implicated in a wide variety of cancers, such as urothelial carcinoma, hepatocellular carcinoma, ovarian cancer and lung adenocarcinoma. Due to their functional importance, FGFRs have been considered as promising drug targets for the therapy of various cancers. Multiple small molecule inhibitors targeting this family of kinases have been developed, and some of them are in clinical trials. Furthermore, the pan-FGFR inhibitor erdafitinib (JNJ-42756493) has recently been approved by the U.S. Food and Drug Administration (FDA) for the treatment of metastatic or unresectable urothelial carcinoma (mUC). This review summarizes the structure of FGFR, especially its kinase domain, and the development of small molecule FGFR inhibitors.
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Affiliation(s)
- Shuyan Dai
- NHC Key Laboratory of Cancer Proteomics & Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
| | - Zhan Zhou
- NHC Key Laboratory of Cancer Proteomics & Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
| | - Zhuchu Chen
- NHC Key Laboratory of Cancer Proteomics & Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
| | - Guangyu Xu
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, Hunan, China.
| | - Yongheng Chen
- NHC Key Laboratory of Cancer Proteomics & Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
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116
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Sammons RM, Ghose R, Tsai KY, Dalby KN. Targeting ERK beyond the boundaries of the kinase active site in melanoma. Mol Carcinog 2019; 58:1551-1570. [PMID: 31190430 DOI: 10.1002/mc.23047] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/30/2019] [Accepted: 05/10/2019] [Indexed: 12/14/2022]
Abstract
Extracellular signal-regulated kinase 1/2 (ERK1/2) constitute a point of convergence for complex signaling events that regulate essential cellular processes, including proliferation and survival. As such, dysregulation of the ERK signaling pathway is prevalent in many cancers. In the case of BRAF-V600E mutant melanoma, ERK inhibition has emerged as a viable clinical approach to abrogate signaling through the ERK pathway, even in cases where MEK and Raf inhibitor treatments fail to induce tumor regression due to resistance mechanisms. Several ERK inhibitors that target the active site of ERK have reached clinical trials, however, many critical ERK interactions occur at other potentially druggable sites on the protein. Here we discuss the role of ERK signaling in cell fate, in driving melanoma, and in resistance mechanisms to current BRAF-V600E melanoma treatments. We explore targeting ERK via a distinct site of protein-protein interaction, known as the D-recruitment site (DRS), as an alternative or supplementary mode of ERK pathway inhibition in BRAF-V600E melanoma. Targeting the DRS with inhibitors in melanoma has the potential to not only disrupt the catalytic apparatus of ERK but also its noncatalytic functions, which have significant impacts on spatiotemporal signaling dynamics and cell fate.
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Affiliation(s)
- Rachel M Sammons
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas.,Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas
| | - Ranajeet Ghose
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York
| | - Kenneth Y Tsai
- Departments of Anatomic Pathology and Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas.,Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, Texas
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117
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Roskoski R. Properties of FDA-approved small molecule protein kinase inhibitors. Pharmacol Res 2019; 144:19-50. [DOI: 10.1016/j.phrs.2019.03.006] [Citation(s) in RCA: 290] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 03/07/2019] [Indexed: 12/14/2022]
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118
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Schaffner A, Li X, Gomez-Llorente Y, Leandrou E, Memou A, Clemente N, Yao C, Afsari F, Zhi L, Pan N, Morohashi K, Hua X, Zhou MM, Wang C, Zhang H, Chen SG, Elliott CJ, Rideout H, Ubarretxena-Belandia I, Yue Z. Vitamin B 12 modulates Parkinson's disease LRRK2 kinase activity through allosteric regulation and confers neuroprotection. Cell Res 2019; 29:313-329. [PMID: 30858560 PMCID: PMC6462009 DOI: 10.1038/s41422-019-0153-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 02/09/2019] [Indexed: 12/12/2022] Open
Abstract
Missense mutations in Leucine-Rich Repeat Kinase 2 (LRRK2) cause the majority of familial and some sporadic forms of Parkinson's disease (PD). The hyperactivity of LRRK2 kinase induced by the pathogenic mutations underlies neurotoxicity, promoting the development of LRRK2 kinase inhibitors as therapeutics. Many potent and specific small-molecule LRRK2 inhibitors have been reported with promise. However, nearly all inhibitors are ATP competitive-some with unwanted side effects and unclear clinical outcome-alternative types of LRRK2 inhibitors are lacking. Herein we identify 5'-deoxyadenosylcobalamin (AdoCbl), a physiological form of the essential micronutrient vitamin B12 as a mixed-type allosteric inhibitor of LRRK2 kinase activity. Multiple assays show that AdoCbl directly binds LRRK2, leading to the alterations of protein conformation and ATP binding in LRRK2. STD-NMR analysis of a LRRK2 homologous kinase reveals the contact sites in AdoCbl that interface with the kinase domain. Furthermore, we provide evidence that AdoCbl modulates LRRK2 activity through disrupting LRRK2 dimerization. Treatment with AdoCbl inhibits LRRK2 kinase activity in cultured cells and brain tissue, and prevents neurotoxicity in cultured primary rodent neurons as well as in transgenic C. elegans and D. melanogaster expressing LRRK2 disease variants. Finally, AdoCbl alleviates deficits in dopamine release sustainability caused by LRRK2 disease variants in mouse models. Our study uncovers vitamin B12 as a novel class of LRRK2 kinase modulator with a distinct mechanism, which can be harnessed to develop new LRRK2-based PD therapeutics in the future.
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Affiliation(s)
- Adam Schaffner
- Department of Neurology and Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Xianting Li
- Department of Neurology and Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Yacob Gomez-Llorente
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Emmanouela Leandrou
- Division of Basic Neurosciences, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Anna Memou
- Division of Basic Neurosciences, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Nicolina Clemente
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Chen Yao
- Department of Pathology, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Farinaz Afsari
- Department of Biology, University of York, York, YO1 5DD, UK
| | - Lianteng Zhi
- Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Nina Pan
- Department of Neurology and Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Keita Morohashi
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Xiaoluan Hua
- Department of Neurology and Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ming-Ming Zhou
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Chunyu Wang
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Hui Zhang
- Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Shu G Chen
- Department of Pathology, Case Western Reserve University, Cleveland, OH, 44106, USA
| | | | - Hardy Rideout
- Division of Basic Neurosciences, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Iban Ubarretxena-Belandia
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, Leioa, Spain
| | - Zhenyu Yue
- Department of Neurology and Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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119
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Damm-Ganamet KL, Arora N, Becart S, Edwards JP, Lebsack AD, McAllister HM, Nelen MI, Rao NL, Westover L, Wiener JJM, Mirzadegan T. Accelerating Lead Identification by High Throughput Virtual Screening: Prospective Case Studies from the Pharmaceutical Industry. J Chem Inf Model 2019; 59:2046-2062. [DOI: 10.1021/acs.jcim.8b00941] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
| | | | | | | | | | | | - Marina I. Nelen
- Discovery Sciences, Janssen Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477, United States
| | | | - Lori Westover
- Discovery Sciences, Janssen Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477, United States
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120
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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: 182] [Impact Index Per Article: 36.4] [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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121
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Koudelková L, Pataki AC, Tolde O, Pavlik V, Nobis M, Gemperle J, Anderson K, Brábek J, Rosel D. Novel FRET-Based Src Biosensor Reveals Mechanisms of Src Activation and Its Dynamics in Focal Adhesions. Cell Chem Biol 2019; 26:255-268.e4. [DOI: 10.1016/j.chembiol.2018.10.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 09/12/2018] [Accepted: 10/26/2018] [Indexed: 10/27/2022]
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122
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Roskoski R. Cyclin-dependent protein serine/threonine kinase inhibitors as anticancer drugs. Pharmacol Res 2019; 139:471-488. [DOI: 10.1016/j.phrs.2018.11.035] [Citation(s) in RCA: 157] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 02/07/2023]
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123
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Astl L, Tse A, Verkhivker GM. Interrogating Regulatory Mechanisms in Signaling Proteins by Allosteric Inhibitors and Activators: A Dynamic View Through the Lens of Residue Interaction Networks. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:187-223. [DOI: 10.1007/978-981-13-8719-7_9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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124
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Rodon Ahnert J, Gray N, Mok T, Gainor J. What It Takes to Improve a First-Generation Inhibitor to a Second- or Third-Generation Small Molecule. Am Soc Clin Oncol Educ Book 2019; 39:196-205. [PMID: 31099659 DOI: 10.1200/edbk_242209] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Since the first generation of small molecules was included in the armamentarium of treatment of solid tumors (imatinib, erlotinib, etc.), there has been an expansion of anticancer small molecules, mostly kinase inhibitors, in development. Some of these drugs may not be a real breakthrough but may be similar in pharmacologic properties and marginal benefit over previously existing agents for the same indication (i.e., me-too drugs). Other drugs, however, have been specifically designed to solve an unmet medical need. Overcoming the problems of the blood-brain barrier and brain metastasis, emerging resistance mutations (such as gatekeeper mutations), or increasing selectivity/potency can be addressed with modern drug design. In this article, we discuss the advancements in the field of drug discovery, drug development, and clinical development that have enabled solving some of these issues. The evolution of the different generations of EGFR and anaplastic lymphoma kinase inhibitors exemplifies recent advancements in pharmacology that are driving the field of anticancer small molecules as a whole.
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Affiliation(s)
| | | | - Tony Mok
- 3 Chinese University of Hong Kong, Hong Kong, China
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125
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Leroux AE, Gross LZF, Sacerdoti M, Biondi RM. Allosteric Regulation of Protein Kinases Downstream of PI3-Kinase Signalling. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:279-311. [PMID: 31707708 DOI: 10.1007/978-981-13-8719-7_12] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Allostery is a basic principle that enables proteins to process and transmit cellular information. Protein kinases evolved allosteric mechanisms to transduce cellular signals to downstream signalling components or effector molecules. Protein kinases catalyse the transfer of the terminal phosphate from ATP to protein substrates upon specific stimuli. Protein kinases are targets for the development of small molecule inhibitors for the treatment of human diseases. Drug development has focussed on ATP-binding site, while there is increase interest in the development of drugs targeting alternative sites, i.e. allosteric sites. Here, we review the mechanism of regulation of protein kinases, which often involve the allosteric modulation of the ATP-binding site, enhancing or inhibiting activity. We exemplify the molecular mechanism of allostery in protein kinases downstream of PI3-kinase signalling with a focus on phosphoinositide-dependent protein kinase 1 (PDK1), a model kinase where small compounds can allosterically modulate the conformation of the kinase bidirectionally.
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Affiliation(s)
- Alejandro E Leroux
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Lissy Z F Gross
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Mariana Sacerdoti
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Ricardo M Biondi
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina.
- Department of Internal Medicine I, Universitätsklinikum Frankfurt, Frankfurt, Germany.
- DKTK German Cancer Consortium (DKTK), Frankfurt, Germany.
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
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126
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Roskoski R. Small molecule inhibitors targeting the EGFR/ErbB family of protein-tyrosine kinases in human cancers. Pharmacol Res 2018; 139:395-411. [PMID: 30500458 DOI: 10.1016/j.phrs.2018.11.014] [Citation(s) in RCA: 284] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 11/07/2018] [Indexed: 02/07/2023]
Abstract
The EGFR family is among the most investigated receptor protein-tyrosine kinase groups owing to its general role in signal transduction and in oncogenesis. This family consists of four members that belong to the ErbB lineage of proteins (ErbB1-4). The ErbB proteins function as homo and heterodimers. These receptors contain an extracellular domain that consists of four parts: domains I and III are leucine-rich segments that participate in growth factor binding (except for ErbB2) and domains II and IV contain multiple disulfide bonds. Moreover, domain II participates in both homo and heterodimer formation within the ErbB/HER family of proteins. Seven ligands bind to EGFR including epidermal growth factor and transforming growth factor-α, none bind to ErbB2, two bind to ErbB3, and seven ligands bind to ErbB4. The extracellular domain is followed by a single transmembrane segment of about 25 amino acid residues and an intracellular portion of about 550 amino acid residues that contains (i) a short juxtamembrane segment, (ii) a protein kinase domain, and (iii) a carboxyterminal tail. ErbB2 lacks a known activating ligand and ErbB3 is kinase impaired. Surprisingly, the ErbB2-ErbB3 heterodimer complex is the most active dimer in the family. These receptors are implicated in the pathogenesis of a large proportion of lung and breast cancers, which rank first and second, respectively, in the incidence of all types of cancers (excluding skin) worldwide. On the order of 20% of non-small cell lung cancers bear activating mutations in EGFR. More than 90% of these patients have exon-19 deletions (746ELREA750) or the exon-21 L858R substitution. Gefitinib and erlotinib are orally effective type I reversible EGFR mutant inhibitors; type I inhibitors bind to an active enzyme conformation. Unfortunately, secondary resistance to these drugs occurs within about one year owing to a T790M gatekeeper mutation. Osimertinib is an irreversible type VI inhibitor that forms a covalent bond with C797 of EGFR and is FDA-approved for the treatment of patients with this mutation; type VI inhibitors generally form a covalent adduct with their target protein. Resistance also develops to this and related type VI inhibitory drugs owing to a C797S mutation; the serine residue is unable to react with the drugs to form a covalent bond. Approximately 20% of breast cancer patients exhibit ErbB2/HER2 gene amplification on chromosome 17q. One of the earliest targeted treatments in cancer involved the development of trastuzumab, a monoclonal antibody that interacts with the extracellular domain ErbB2/HER2 causing its down regulation. Surgery, radiation therapy, chemotherapy with cytotoxic drugs, and hormonal modulation are the mainstays in the treatment of breast cancer. Moreover, lapatinib and neratinib are FDA-approved small molecule ErbB2/HER2 antagonists used in the treatment of selected breast cancer patients. Of the approximate three dozen FDA-approved small molecule protein kinase inhibitors, five are type VI irreversible inhibitors and four of them including afatinib, osimertinib, dacomitinib, and neratinib are directed against the ErbB family of receptors (ibrutinib is the fifth and it targets Bruton tyrosine kinase). Avitinib, olmutinib, and pelitinib are additional type VI inhibitors in clinical trials for non-small cell lung cancer that target EGFR. Secondary resistance to both targeted and cytotoxic drugs is the norm, and devising and implementing strategies for minimizing or overcoming resistance is an important goal in cancer therapeutics.
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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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127
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Type IIA - Type IIB protein tyrosine kinase inhibitors hybridization as an efficient approach for potent multikinase inhibitor development: Design, synthesis, anti-proliferative activity, multikinase inhibitory activity and molecular modeling of novel indolinone-based ureides and amides. Eur J Med Chem 2018; 163:37-53. [PMID: 30503942 DOI: 10.1016/j.ejmech.2018.11.061] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 11/05/2018] [Accepted: 11/23/2018] [Indexed: 11/21/2022]
Abstract
Pursuing on our efforts regarding development of novel multikinase inhibitors, herein we report the design and synthesis of novel 2-indolinone-based ureides 6a-u and amides 10a-j. In this work we adopt a hybridization strategy between type IIA PTK inhibitor (sorafenib) and type IIB PTK inhibitors (sunitinib and nintedanib). This was implemented via linking the indolinone core, in both sunitinib and nintedanib, which is well-fitted in the hinge region in the kinase domain front cleft and the biaryl urea extension, in sorafenib, which is accommodated in the gate area and the hydrophobic back pocket. Molecular docking of the designed hybrid compounds in VEGFR-2 and FGFR-1 active sites revealed, as planned, their ability to establish the binding interactions achieved by both original type IIA and type IIB inhibitors. The designed compounds were evaluated for their multikinase inhibitory activity towards VEGFR-2, PDGFR-b and FGFR-1 and anti-proliferative activity towards HepG2, MCF-7, A549 and A498 cancer cell lines. The ureido analogue 6u emerged as the most potent multikinase inhibitor in the ureido series with VEGFR-2, FGFR-1 and PDGFR-b IC50 of 0.18, 0.23 and 0.10 μM, respectively. Whereas, the amido congener 10j emerged as the most potent multikinase inhibitor in the amide series with VEGFR-2, FGFR-1 and PDGFR-b IC50 of 0.28, 0.46 and 0.09 μM, respectively. While, indolinone 6u was the most potent derivative towards HepG2 cells (IC50 = 2.67 ± 0.14 μM), 6r stood out as the most potent indolinone against A498 cells (IC50 = 0.78 ± 0.02 μM). Additionally, the target indolinones displayed non-significant cytotoxic impact towards human normal melanocyte (HFB4). ADME prediction study of the designed compounds showed that they are not only with promising multikinase inhibitory activity but also with favorable pharmacokinetic and drug-likeness properties. Compounds 6r and 10j are revealed to be the best compounds in terms of multikinase activity and pharmacokinetics.
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128
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Shen C, Wang Z, Yao X, Li Y, Lei T, Wang E, Xu L, Zhu F, Li D, Hou T. Comprehensive assessment of nine docking programs on type II kinase inhibitors: prediction accuracy of sampling power, scoring power and screening power. Brief Bioinform 2018; 21:282-297. [PMID: 30379986 DOI: 10.1093/bib/bby103] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/08/2018] [Accepted: 09/26/2018] [Indexed: 12/16/2022] Open
Abstract
Protein kinases have been regarded as important therapeutic targets for many diseases. Currently, a total of 41 kinase inhibitors have been approved by the Food and Drug Administration, along with a large number of kinase inhibitors being evaluated in clinical and preclinical trials. Among all, allosteric inhibitors, such as type II kinase inhibitors, have attracted extensive attention owing to their potential high selectivity. Nowadays, molecular docking has become a powerful tool to search for novel kinase inhibitors. However, as for type II kinase inhibitors, their allosteric characteristics may exert a deep influence on docking accuracy. In this study, a comprehensive assessment was conducted to evaluate the effectiveness of nine docking algorithms towards type II kinase inhibitors. The calculation results showed that most tested docking programs, especially Glide with XP scoring, LeDock and Surflex-Dock, succeeded in the accurate identification of near-native binding poses, with the success rates ranging from 0.80 to 0.90, and the scoring functions in GOLD and LeDock outperformed the others in the prediction of relative binding affinities. In terms of the P-values, areas under the curve and enrichment factors, Glide with XP scoring, Surflex-Dock, GOLD with Astex Statistical Potential scoring and LeDock had better screening power to discriminate between active compounds and decoys. However, the screening power is sensitive to different initial conformations of the same target. It is expected that our study can provide some guidance for docking-based virtual screening to discover novel type II kinase inhibitors, as well as other allosteric inhibitors.
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Affiliation(s)
- Chao Shen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Zhe Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Xiaojun Yao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health,Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau (SAR), P. R. China
| | - Youyong Li
- Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu, P. R. China
| | - Tailong Lei
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Ercheng Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, P. R. China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Dan Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
- State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang, P. R. China
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129
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Ma N, Lippert LG, Devamani T, Levy B, Lee S, Sandhu M, Vaidehi N, Sivaramakrishnan S. Bitopic Inhibition of ATP and Substrate Binding in Ser/Thr Kinases through a Conserved Allosteric Mechanism. Biochemistry 2018; 57:6387-6390. [PMID: 30339352 DOI: 10.1021/acs.biochem.8b00729] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein kinases achieve substrate selective phosphorylation through their conformational flexibility and dynamic interaction with the substrate. Designing substrate selective or kinase selective small molecule inhibitors remains a challenge because of a lack of understanding of the dynamic mechanism by which substrates are selected by the kinase. Using a combination of all-atom molecular dynamics simulations and FRET sensors, we have delineated an allosteric mechanism that results in interaction among the DFG motif, G-loop, and activation loop and structurally links the nucleotide and substrate binding interfaces in protein kinase Cα and three other Ser/Thr kinases. ATP-competitive staurosporine analogues engage this allosteric switch region located just outside the ATP binding site to displace substrate binding to varying degrees. These inhibitors function as bitopic ligands by occupying the ATP binding site and interacting with the allosteric switch region. The conserved mechanism identified in this study can be exploited to select and design bitopic inhibitors for kinases.
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Affiliation(s)
- Ning Ma
- Department of Computational and Quantitative Medicine , Beckman Research Institute of the City of Hope , Duarte , California 91010 , United States
| | - Lisa G Lippert
- Department of Genetics, Cell Biology, and Development , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Titu Devamani
- Department of Genetics, Cell Biology, and Development , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Benjamin Levy
- Department of Computational and Quantitative Medicine , Beckman Research Institute of the City of Hope , Duarte , California 91010 , United States
| | - Sangbae Lee
- Department of Computational and Quantitative Medicine , Beckman Research Institute of the City of Hope , Duarte , California 91010 , United States
| | - Manbir Sandhu
- Department of Computational and Quantitative Medicine , Beckman Research Institute of the City of Hope , Duarte , California 91010 , United States
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine , Beckman Research Institute of the City of Hope , Duarte , California 91010 , United States
| | - Sivaraj Sivaramakrishnan
- Department of Genetics, Cell Biology, and Development , University of Minnesota , Minneapolis , Minnesota 55455 , United States
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130
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Ocasio CA, Warkentin AA, McIntyre PJ, Barkovich KJ, Vesely C, Spencer J, Shokat KM, Bayliss R. Type II Kinase Inhibitors Targeting Cys-Gatekeeper Kinases Display Orthogonality with Wild Type and Ala/Gly-Gatekeeper Kinases. ACS Chem Biol 2018; 13:2956-2965. [PMID: 30239186 DOI: 10.1021/acschembio.8b00592] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Analogue-sensitive (AS) kinases contain large to small mutations in the gatekeeper position rendering them susceptible to inhibition with bulky analogues of pyrazolopyrimidine-based Src kinase inhibitors (e.g., PP1). This "bump-hole" method has been utilized for at least 85 of ∼520 kinases, but many kinases are intolerant to this approach. To expand the scope of AS kinase technology, we designed type II kinase inhibitors, ASDO2/6 (analogue-sensitive "DFG-out" kinase inhibitors 2 and 6), that target the "DFG-out" conformation of Cys-gatekeeper kinases with submicromolar potency. We validated this system in vitro against Greatwall kinase (GWL), Aurora-A kinase, and cyclin-dependent kinase-1 and in cells using M110C-GWL-expressing mouse embryonic fibroblasts. These Cys-gatekeeper kinases were sensitive to ASDO2/6 inhibition but not AS kinase inhibitor 3MB-PP1 and vice versa. These compounds, with AS kinase inhibitors, have the potential to inhibit multiple AS kinases independently with applications in systems level and translational kinase research as well as the rational design of type II kinase inhibitors targeting endogenous kinases.
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Affiliation(s)
- Cory A Ocasio
- Genome Damage and Stability Centre, School of Life Sciences , University of Sussex , Falmer, Brighton BN1 9RQ , U.K
| | - Alexander A Warkentin
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology , University of California, San Francisco , 600 16th Street , San Francisco , California 94158-2280 , United States
| | - Patrick J McIntyre
- Department of Molecular and Cell Biology , University of Leicester , Henry Wellcome Building , Leicester LE1 9HN , U.K
| | - Krister J Barkovich
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology , University of California, San Francisco , 600 16th Street , San Francisco , California 94158-2280 , United States
| | - Clare Vesely
- Genome Damage and Stability Centre, School of Life Sciences , University of Sussex , Falmer, Brighton BN1 9RQ , U.K
| | - John Spencer
- Department of Chemistry, School of Life Sciences , University of Sussex , Falmer, Brighton BN1 9QJ , U.K
| | - Kevan M Shokat
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology , University of California, San Francisco , 600 16th Street , San Francisco , California 94158-2280 , United States
| | - Richard Bayliss
- School of Molecular and Cellular Biology, Faculty of Biological Sciences , University of Leeds , Leeds LS2 9JT , U.K
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131
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Schöning V, Krähenbühl S, Drewe J. The hepatotoxic potential of protein kinase inhibitors predicted with Random Forest and Artificial Neural Networks. Toxicol Lett 2018; 299:145-148. [PMID: 30315951 DOI: 10.1016/j.toxlet.2018.10.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 10/01/2018] [Accepted: 10/08/2018] [Indexed: 01/29/2023]
Abstract
Protein kinases (PKs) play a role in many pivotal aspects of cellular function. Dysregulation and mutations of protein kinases are involved in the development of different diseases, which might be treated by inhibition of the corresponding kinase. Protein kinase inhibitors (PKIs) are generally well tolerated, but unexpected and serious adverse events on the heart, lung, kidney and liver were observed clinically. In this study, the structure-activity relationship of PKIs in relation to hepatotoxicity was investigated. A dataset of 165 PKIs was compiled and the probability of human hepatotoxicity with two different machine learning algorithms (Random Forest and Artificial Neural Networks) was analysed. The estimated probability of hepatotoxicity was generally high for single PKIs. However, depending on the target kinase of the PKI, a difference in hepatotoxic potential could be observed. The similarity of the PKIs to each other is caused by the conserved site of action of the protein kinases. Hepatotoxicity may therefore always be an issue in PKIs.
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Affiliation(s)
- Verena Schöning
- Department of Clinical Pharmacology, University Hospital Basel, CH 4031 Basel, Switzerland
| | - Stephan Krähenbühl
- Department of Clinical Pharmacology, University Hospital Basel, CH 4031 Basel, Switzerland
| | - Jürgen Drewe
- Department of Clinical Pharmacology, University Hospital Basel, CH 4031 Basel, Switzerland.
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132
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Lombard CK, Davis AL, Inukai T, Maly DJ. Allosteric Modulation of JNK Docking Site Interactions with ATP-Competitive Inhibitors. Biochemistry 2018; 57:5897-5909. [PMID: 30211540 DOI: 10.1021/acs.biochem.8b00776] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The c-Jun N-terminal kinases (JNKs) play a wide variety of roles in cellular signaling processes, dictating important, and even divergent, cellular fates. These essential kinases possess docking surfaces distal to their active sites that interact with diverse binding partners, including upstream activators, downstream substrates, and protein scaffolds. Prior studies have suggested that the interactions of certain protein-binding partners with one such JNK docking surface, termed the D-recruitment site (DRS), can allosterically influence the conformational state of the ATP-binding pocket of JNKs. To further explore the allosteric relationship between the ATP-binding pockets and DRSs of JNKs, we investigated how the interactions of the scaffolding protein JIP1, as well as the upstream activators MKK4 and MKK7, are allosterically influenced by the ATP-binding site occupancy of the JNKs. We show that the affinity of the JNKs for JIP1 can be divergently modulated with ATP-competitive inhibitors, with a >50-fold difference in dissociation constant observed between the lowest- and highest-affinity JNK1-inhibitor complexes. Furthermore, we found that we could promote or attenuate phosphorylation of JNK1's activation loop by MKK4 and MKK7, by varying the ATP-binding site occupancy. Given that JIP1, MKK4, and MKK7 all interact with JNK DRSs, these results demonstrate that there is functional allostery between the ATP-binding sites and DRSs of these kinases. Furthermore, our studies suggest that ATP-competitive inhibitors can allosterically influence the intracellular binding partners of the JNKs.
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Affiliation(s)
- Chloe K Lombard
- Department of Chemistry , University of Washington , Seattle , Washington 98117 , United States
| | - Audrey L Davis
- Department of Chemistry , University of Washington , Seattle , Washington 98117 , United States
| | - Takayuki Inukai
- Medicinal Chemistry Research Laboratories , Ono Pharmaceutical Company, Ltd. , 3-1-1 Sakurai , Shimamoto, Mishima, Osaka 618-8585 , Japan
| | - Dustin J Maly
- Department of Chemistry , University of Washington , Seattle , Washington 98117 , United States.,Department of Biochemistry , University of Washington , Seattle , Washington 98117 , United States
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133
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Optimization of Aminoimidazole Derivatives as Src Family Kinase Inhibitors. Molecules 2018; 23:molecules23092369. [PMID: 30227617 PMCID: PMC6225123 DOI: 10.3390/molecules23092369] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/12/2018] [Accepted: 09/13/2018] [Indexed: 01/20/2023] Open
Abstract
Protein kinases have emerged as crucial targets for cancer therapy over the last decades. Since 2001, 40 and 39 kinase inhibitors have been approved by FDA and EMA, respectively, and the majority are antineoplastic drugs. Morevoer, many candidates are currently in clinical trials. We previously reported a small library of 4-aminoimidazole and 2-aminothiazole derivatives active as Src family kinase (SFK) inhibitors. Starting from these results, we decided to perform an optimization study applying a mix and match strategy to identify a more potent generation of 4-aminoimidazoles. Firstly, a computational study has been performed, then compounds showing the best predicted docking scores were synthesized and screened in a cell-free assay for their SFK inhibitory activity. All the new chemical entities showed IC50s in the nanomolar range, with 2–130 fold increased activities compared to the previously reported inhibitors. Finally, the most active compounds have been tested on three cancer cell lines characterized by Src hyperactivation. Compounds 4k and 4l showed an interesting antiproliferative activity on SH-SY5Y neuroblastoma (NB) cell line. In this assay, the compounds resulted more potent than dasatinib, a tyrosine kinase inhibitor approved for the treatment of leukemias and in clinical trials for NB.
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134
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Targeting oncogenic Raf protein-serine/threonine kinases in human cancers. Pharmacol Res 2018; 135:239-258. [DOI: 10.1016/j.phrs.2018.08.013] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 08/13/2018] [Indexed: 02/07/2023]
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135
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Ohbayashi N, Murayama K, Kato‐Murayama M, Kukimoto‐Niino M, Uejima T, Matsuda T, Ohsawa N, Yokoyoma S, Nojima H, Shirouzu M. Structural Basis for the Inhibition of Cyclin G-Associated Kinase by Gefitinib. ChemistryOpen 2018; 7:721-727. [PMID: 30214852 PMCID: PMC6129943 DOI: 10.1002/open.201800177] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Indexed: 02/03/2023] Open
Abstract
Gefitinib is the molecular target drug for advanced non-small-cell lung cancer. The primary target of gefitinib is the positive mutation of epidermal growth factor receptor, but it also inhibits cyclin G-associated kinase (GAK). To reveal the molecular bases of GAK and gefitinib binding, structure analyses were conducted and determined two forms of the gefitinib-bound nanobody⋅GAK kinase domain complex structures. The first form, GAK_1, has one gefitinib at the ATP binding pocket, whereas the second form, GAK_2, binds one each in the ATP binding site and a novel binding site adjacent to the activation segment C-terminal helix, a unique element of the Numb-associated kinase family. In the novel binding site, gefitinib binds in the hydrophobic groove around the activation segment, disrupting the conserved hydrogen bonds for the catalytic activity. These structures suggest possibilities for the development of selective GAK inhibitors for viral infections, such as the hepatitis C virus.
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Affiliation(s)
- Naomi Ohbayashi
- Division of Structural and Synthetic BiologyRIKEN Center for Life Science Technologies1-7-22 Suehiro-cho, TsurumiYokohama230-0045Japan
| | - Kazutaka Murayama
- RIKEN Center for Biosystems Dynamics Research1-7-22 Suehiro-cho, TsurumiYokohama230-0045Japan
- Graduate School of Biomedical EngineeringTohoku University2-1 Seiryomachi, AobaSendai980-8575Japan
| | - Miyuki Kato‐Murayama
- RIKEN Center for Biosystems Dynamics Research1-7-22 Suehiro-cho, TsurumiYokohama230-0045Japan
| | - Mutsuko Kukimoto‐Niino
- RIKEN Center for Biosystems Dynamics Research1-7-22 Suehiro-cho, TsurumiYokohama230-0045Japan
| | - Tamami Uejima
- RIKEN Center for Biosystems Dynamics Research1-7-22 Suehiro-cho, TsurumiYokohama230-0045Japan
| | - Takayoshi Matsuda
- Division of Structural and Synthetic BiologyRIKEN Center for Life Science Technologies1-7-22 Suehiro-cho, TsurumiYokohama230-0045Japan
| | - Noboru Ohsawa
- Division of Structural and Synthetic BiologyRIKEN Center for Life Science Technologies1-7-22 Suehiro-cho, TsurumiYokohama230-0045Japan
| | - Shigeyuki Yokoyoma
- RIKEN Structural Biology Laboratory1-7-22 Suehiro-cho, TsurumiYokohama230-0045Japan
| | - Hiroshi Nojima
- Department of Molecular GeneticsOsaka University3-1 Yamadaoka, SuitaOsaka565-0871Japan
| | - Mikako Shirouzu
- RIKEN Center for Biosystems Dynamics Research1-7-22 Suehiro-cho, TsurumiYokohama230-0045Japan
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136
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Kasak L, Näks M, Eek P, Piirsoo A, Bhadoria R, Starkov P, Saarma M, Kasvandik S, Piirsoo M. Characterization of Protein Kinase ULK3 Regulation by Phosphorylation and Inhibition by Small Molecule SU6668. Biochemistry 2018; 57:5456-5465. [DOI: 10.1021/acs.biochem.8b00356] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Lagle Kasak
- Department of Chemistry & Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
| | - Mihkel Näks
- Department of Chemistry & Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
| | - Priit Eek
- Department of Chemistry & Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
| | - Alla Piirsoo
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
| | - Rohit Bhadoria
- Department of Chemistry & Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
| | - Pavel Starkov
- Department of Chemistry & Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
| | - Merilin Saarma
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
| | - Sergo Kasvandik
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
| | - Marko Piirsoo
- Department of Chemistry & Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
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137
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Roskoski R. The role of small molecule Kit protein-tyrosine kinase inhibitors in the treatment of neoplastic disorders. Pharmacol Res 2018; 133:35-52. [DOI: 10.1016/j.phrs.2018.04.020] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 04/23/2018] [Indexed: 12/25/2022]
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138
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Neri D, Lerner RA. DNA-Encoded Chemical Libraries: A Selection System Based on Endowing Organic Compounds with Amplifiable Information. Annu Rev Biochem 2018; 87:479-502. [PMID: 29328784 PMCID: PMC6080696 DOI: 10.1146/annurev-biochem-062917-012550] [Citation(s) in RCA: 265] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The discovery of organic ligands that bind specifically to proteins is a central problem in chemistry, biology, and the biomedical sciences. The encoding of individual organic molecules with distinctive DNA tags, serving as amplifiable identification bar codes, allows the construction and screening of combinatorial libraries of unprecedented size, thus facilitating the discovery of ligands to many different protein targets. Fundamentally, one links powers of genetics and chemical synthesis. After the initial description of DNA-encoded chemical libraries in 1992, several experimental embodiments of the technology have been reduced to practice. This review provides a historical account of important milestones in the development of DNA-encoded chemical libraries, a survey of relevant ongoing research activities, and a glimpse into the future.
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Affiliation(s)
- Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), 8093 Zürich, Switzerland;
| | - Richard A Lerner
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA;
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139
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Ung PMU, Rahman R, Schlessinger A. Redefining the Protein Kinase Conformational Space with Machine Learning. Cell Chem Biol 2018; 25:916-924.e2. [PMID: 29861272 DOI: 10.1016/j.chembiol.2018.05.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 02/28/2018] [Accepted: 05/01/2018] [Indexed: 02/07/2023]
Abstract
Protein kinases are dynamic, adopting different conformational states that are critical for their catalytic activity. We assess a range of structural features derived from the conserved αC helix and DFG motif to define the conformational space of the catalytic domain of protein kinases. We then construct Kinformation, a random forest classifier, to annotate the conformation of 3,708 kinase structures in the PDB. Our classification scheme captures known active and inactive kinase conformations and defines an additional conformational state, thereby refining the current understanding of the kinase conformational space. Furthermore, network analysis of the small molecules recognized by each conformation captures chemical substructures that are associated with each conformation type. Our description of the kinase conformational space is expected to improve modeling of protein kinase structures, as well as guide the development of conformation-specific kinase inhibitors with optimal pharmacological profiles.
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Affiliation(s)
- Peter Man-Un Ung
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Rayees Rahman
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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140
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Sturm N, Tinivella A, Rastelli G. Exploration and Comparison of the Geometrical and Physicochemical Properties of an αC Allosteric Pocket in the Structural Kinome. J Chem Inf Model 2018; 58:1094-1103. [DOI: 10.1021/acs.jcim.7b00735] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Noé Sturm
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Annachiara Tinivella
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Giulio Rastelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
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141
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Dite TA, Langendorf CG, Hoque A, Galic S, Rebello RJ, Ovens AJ, Lindqvist LM, Ngoei KRW, Ling NXY, Furic L, Kemp BE, Scott JW, Oakhill JS. AMP-activated protein kinase selectively inhibited by the type II inhibitor SBI-0206965. J Biol Chem 2018; 293:8874-8885. [PMID: 29695504 DOI: 10.1074/jbc.ra118.003547] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Indexed: 12/30/2022] Open
Abstract
Inhibition of the metabolic regulator AMP-activated protein kinase (AMPK) is increasingly being investigated for its therapeutic potential in diseases where AMPK hyperactivity results in poor prognoses, as in established cancers and neurodegeneration. However, AMPK-inhibitory tool compounds are largely limited to compound C, which has a poor selectivity profile. Here we identify the pyrimidine derivative SBI-0206965 as a direct AMPK inhibitor. SBI-0206965 inhibits AMPK with 40-fold greater potency and markedly lower kinase promiscuity than compound C and inhibits cellular AMPK signaling. Biochemical characterization reveals that SBI-0206965 is a mixed-type inhibitor. A co-crystal structure of the AMPK kinase domain/SBI-0206965 complex shows that the drug occupies a pocket that partially overlaps the ATP active site in a type IIb inhibitor manner. SBI-0206965 has utility as a tool compound for investigating physiological roles for AMPK and provides fresh impetus to small-molecule AMPK inhibitor therapeutic development.
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Affiliation(s)
- Toby A Dite
- From the Metabolic Signalling Laboratory and
| | - Christopher G Langendorf
- Protein Chemistry and Metabolism Unit, St. Vincent's Institute of Medical Research, University of Melbourne, Fitzroy 3065, Victoria, Australia
| | | | - Sandra Galic
- Protein Chemistry and Metabolism Unit, St. Vincent's Institute of Medical Research, University of Melbourne, Fitzroy 3065, Victoria, Australia
| | - Richard J Rebello
- the Prostate Cancer Translational Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.,the Cancer Program, Biomedicine Discovery Institute, and Department of Anatomy and Developmental Biology, Monash University, Clayton 3800, Victoria, Australia
| | | | - Lisa M Lindqvist
- the Cell Signalling and Cell Death Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Kevin R W Ngoei
- Protein Chemistry and Metabolism Unit, St. Vincent's Institute of Medical Research, University of Melbourne, Fitzroy 3065, Victoria, Australia
| | | | - Luc Furic
- the Prostate Cancer Translational Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.,the Cancer Program, Biomedicine Discovery Institute, and Department of Anatomy and Developmental Biology, Monash University, Clayton 3800, Victoria, Australia.,the Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3010, Australia, and
| | - Bruce E Kemp
- Protein Chemistry and Metabolism Unit, St. Vincent's Institute of Medical Research, University of Melbourne, Fitzroy 3065, Victoria, Australia.,the Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, Victoria 3000, Australia
| | - John W Scott
- Protein Chemistry and Metabolism Unit, St. Vincent's Institute of Medical Research, University of Melbourne, Fitzroy 3065, Victoria, Australia.,the Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, Victoria 3000, Australia
| | - Jonathan S Oakhill
- From the Metabolic Signalling Laboratory and .,the Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, Victoria 3000, Australia
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142
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Rampogu S, Baek A, Zeb A, Lee KW. Exploration for novel inhibitors showing back-to-front approach against VEGFR-2 kinase domain (4AG8) employing molecular docking mechanism and molecular dynamics simulations. BMC Cancer 2018. [PMID: 29514608 PMCID: PMC5842552 DOI: 10.1186/s12885-018-4050-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background Angiogenesis is a process of formation of new blood vessels and is an important criteria demonstrated by cancer cells. Over a period of time, these cancer cells infect the other parts of the healthy body by a process called progression. The objective of the present article is to identify a drug molecule that inhibits angiogenesis and progression. Methods In this pursuit, ligand based pharmacophore virtual screening was employed, generating a pharmacophore model, Hypo1 consisting of four features. Furthermore, this Hypo1 was validated recruiting, Fischer’s randomization, test set method and decoy set method. Later, Hypo1 was allowed to screen databases such as Maybridge, Chembridge, Asinex and NCI and were further filtered by ADMET filters and Lipinski’s Rule of Five. A total of 699 molecules that passed the above criteria, were challenged against 4AG8, an angiogenic drug target employing GOLD v5.2.2. Results The results rendered by molecular docking, DFT and the MD simulations showed only one molecule (Hit) obeyed the back-to-front approach. This molecule displayed a dock score of 89.77, involving the amino acids, Glu885 and Cys919, Asp1046, respectively and additionally formed several important hydrophobic interactions. Furthermore, the identified lead molecule showed interactions with key residues when challenged with CDK2 protein, 1URW. Conclusion The lead candidate showed several interactions with the crucial residues of both the targets. Furthermore, we speculate that the residues Cys919 and Leu83 are important in the development of dual inhibitor. Therefore, the identified lead molecule can act as a potential inhibitor for angiogenesis and progression. Electronic supplementary material The online version of this article (10.1186/s12885-018-4050-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shailima Rampogu
- Division of Applied Life Science (BK21 Plus Program), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Ayoung Baek
- Division of Applied Life Science (BK21 Plus Program), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Amir Zeb
- Division of Applied Life Science (BK21 Plus Program), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Keun Woo Lee
- Division of Applied Life Science (BK21 Plus Program), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, Republic of Korea.
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143
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Ankenbruck N, Courtney T, Naro Y, Deiters A. Optochemical Control of Biological Processes in Cells and Animals. Angew Chem Int Ed Engl 2018; 57:2768-2798. [PMID: 28521066 PMCID: PMC6026863 DOI: 10.1002/anie.201700171] [Citation(s) in RCA: 293] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 05/06/2017] [Indexed: 12/13/2022]
Abstract
Biological processes are naturally regulated with high spatial and temporal control, as is perhaps most evident in metazoan embryogenesis. Chemical tools have been extensively utilized in cell and developmental biology to investigate cellular processes, and conditional control methods have expanded applications of these technologies toward resolving complex biological questions. Light represents an excellent external trigger since it can be controlled with very high spatial and temporal precision. To this end, several optically regulated tools have been developed and applied to living systems. In this review we discuss recent developments of optochemical tools, including small molecules, peptides, proteins, and nucleic acids that can be irreversibly or reversibly controlled through light irradiation, with a focus on applications in cells and animals.
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Affiliation(s)
- Nicholas Ankenbruck
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Taylor Courtney
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Yuta Naro
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
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144
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Roskoski R. The role of small molecule platelet-derived growth factor receptor (PDGFR) inhibitors in the treatment of neoplastic disorders. Pharmacol Res 2018; 129:65-83. [DOI: 10.1016/j.phrs.2018.01.021] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 01/29/2018] [Indexed: 12/15/2022]
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145
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Bhullar KS, Lagarón NO, McGowan EM, Parmar I, Jha A, Hubbard BP, Rupasinghe HPV. Kinase-targeted cancer therapies: progress, challenges and future directions. Mol Cancer 2018; 17:48. [PMID: 29455673 PMCID: PMC5817855 DOI: 10.1186/s12943-018-0804-2] [Citation(s) in RCA: 687] [Impact Index Per Article: 114.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 02/01/2018] [Indexed: 02/06/2023] Open
Abstract
The human genome encodes 538 protein kinases that transfer a γ-phosphate group from ATP to serine, threonine, or tyrosine residues. Many of these kinases are associated with human cancer initiation and progression. The recent development of small-molecule kinase inhibitors for the treatment of diverse types of cancer has proven successful in clinical therapy. Significantly, protein kinases are the second most targeted group of drug targets, after the G-protein-coupled receptors. Since the development of the first protein kinase inhibitor, in the early 1980s, 37 kinase inhibitors have received FDA approval for treatment of malignancies such as breast and lung cancer. Furthermore, about 150 kinase-targeted drugs are in clinical phase trials, and many kinase-specific inhibitors are in the preclinical stage of drug development. Nevertheless, many factors confound the clinical efficacy of these molecules. Specific tumor genetics, tumor microenvironment, drug resistance, and pharmacogenomics determine how useful a compound will be in the treatment of a given cancer. This review provides an overview of kinase-targeted drug discovery and development in relation to oncology and highlights the challenges and future potential for kinase-targeted cancer therapies.
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Affiliation(s)
- Khushwant S Bhullar
- Department of Pharmacology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Naiara Orrego Lagarón
- Department of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Eileen M McGowan
- Chronic Disease Solutions Team, School of Life Science, University of Technology, New South Wales, Australia
| | - Indu Parmar
- Division of Product Development, Radient Technologies, Edmonton, AB, Canada
| | - Amitabh Jha
- Department of Chemistry, Acadia University, Wolfville, NS, Canada
| | - Basil P Hubbard
- Department of Pharmacology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - H P Vasantha Rupasinghe
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada.
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada.
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146
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Ankenbruck N, Courtney T, Naro Y, Deiters A. Optochemische Steuerung biologischer Vorgänge in Zellen und Tieren. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201700171] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Nicholas Ankenbruck
- Department of Chemistry University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
| | - Taylor Courtney
- Department of Chemistry University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
| | - Yuta Naro
- Department of Chemistry University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
| | - Alexander Deiters
- Department of Chemistry University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
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147
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Roskoski R, Sadeghi-Nejad A. Role of RET protein-tyrosine kinase inhibitors in the treatment RET-driven thyroid and lung cancers. Pharmacol Res 2017; 128:1-17. [PMID: 29284153 DOI: 10.1016/j.phrs.2017.12.021] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 12/21/2017] [Indexed: 01/10/2023]
Abstract
RET is a transmembrane receptor protein-tyrosine kinase that is required for the development of the nervous system and several other tissues. The mechanism of activation of RET by its glial-cell derived neurotrophic factor (GDNF) ligands differs from that of all other receptor protein-tyrosine kinases owing to the requirement for additional GDNF family receptor-α (GFRα) co-receptors (GFRα1/2/3/4). RET point mutations have been reported in multiple endocrine neoplasia (MEN2A, MEN2B) and medullary thyroid carcinoma. In contrast, RET fusion proteins have been reported in papillary thyroid and non-small cell lung adenocarcinomas. More than a dozen fusion partners of RET have been described in papillary thyroid carcinomas, most frequently CCDC6-RET and NCOA4-RET. RET-fusion proteins, commonly KIF5B-RET, have also been found in non-small cell lung cancer (NSCLC). Several drugs targeting RET have been approved by the FDA for the treatment of cancer: (i) cabozantinib and vandetanib for medullary thyroid carcinomas and (ii) lenvatinib and sorafenib for differentiated thyroid cancers. In addition, alectinib and sunitinib are approved for the treatment of other neoplasms. Each of these drugs is a multikinase inhibitor that has activity against RET. Previous X-ray studies indicated that vandetanib binds within the ATP-binding pocket and forms a hydrogen bond with A807 within the RET hinge and it makes hydrophobic contact with L881 of the catalytic spine which occurs in the floor of the adenine-binding pocket. Our molecular modeling studies indicate that the other antagonists bind in a similar fashion. All of these antagonists bind to the active conformation of RET and are therefore classified as type I inhibitors. The drugs also make variable contacts with other residues of the regulatory and catalytic spines. None of these drugs was designed to bind preferentially to RET and it is hypothesized that RET-specific antagonists might produce even better clinical outcomes. Currently the number of new cases of neoplasms bearing RET mutations or RET-fusion proteins is estimated to be about 10,000 per year in the United States. This is about the same as the incidence of chronic myelogenous leukemia for which imatinib and second and third generation BCR-Abl non-receptor protein-tyrosine kinase antagonists have proven clinically efficacious and which are commercially successful. These findings warrant the continued development of specific antagonists targeting RET-driven neoplasms.
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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.
| | - Abdollah Sadeghi-Nejad
- Department of Pediatrics, Tufts Medical Center, Tufts University School of Medicine, 800 Washington Street, Boston, MA 02111-1552, United States.
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148
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Jukič M, Konc J, Gobec S, Janežič D. Identification of Conserved Water Sites in Protein Structures for Drug Design. J Chem Inf Model 2017; 57:3094-3103. [DOI: 10.1021/acs.jcim.7b00443] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Marko Jukič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI−1000, Ljubljana, Slovenia
| | - Janez Konc
- National Institute of Chemistry, Hajdrihova 19, SI−1000, Ljubljana, Slovenia
- Faculty of
Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, SI−6000 Koper, Slovenia
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI−1000, Ljubljana, Slovenia
| | - Dušanka Janežič
- Faculty of
Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, SI−6000 Koper, Slovenia
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149
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Lin B, Harris DR, Kirkman LMD, Perez AM, Qian Y, Schermerhorn JT, Hong MY, Winston DS, Xu L, Brandt GS. FIKK Kinase, a Ser/Thr Kinase Important to Malaria Parasites, Is Inhibited by Tyrosine Kinase Inhibitors. ACS OMEGA 2017; 2:6605-6612. [PMID: 30023525 PMCID: PMC6044879 DOI: 10.1021/acsomega.7b00997] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/27/2017] [Indexed: 06/08/2023]
Abstract
A relatively high-affinity inhibitor of FIKK kinase from the malaria parasite Plasmodium vivax was identified by in vitro assay of recombinant kinase. The FIKK kinase family is unique to parasitic organisms of the Apicomplexan order and has been shown to be critical in malaria parasites. The recombinant kinase domain was expressed and screened against a small molecule library, revealing a number of tyrosine kinase inhibitors that block FIKK kinase activity. A family of tyrphostins was further investigated, to begin exploring the FIKK kinase pharmacophore. Finally, emodin was identified as a relatively high-affinity FIKK kinase inhibitor, identifying this family of anthraquinones as potential lead compounds for the development of antimalarials targeting the FIKK kinase.
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150
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Modulation of mitogen‑activated protein kinase attenuates sepsis‑induced acute lung injury in acute respiratory distress syndrome rats. Mol Med Rep 2017; 16:9652-9658. [PMID: 29039541 DOI: 10.3892/mmr.2017.7811] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 08/10/2017] [Indexed: 11/05/2022] Open
Abstract
Sepsis is the most important predisposing cause inducing acute respiratory distress syndrome (ARDS); however, the mechanism of sepsis leading to the development of ARDS remains to be elucidated. Suppression of the mitogen‑activated protein kinase (MAPK) signal by blocking the phosphorylation of Jun N‑terminal kinase (JNK) and p38 in lung tissues could alleviate acute lung injury induced by sepsis. MAPK signaling may have a crucial role in development of the sepsis‑induced acute lung injury. The specific inhibitors of JNK and p38 MAPK, SP600125 and SB203580, were administrated by intragastric injection 4 h before induction of ARDS after cecal ligation and puncture (CLP). Rats were sacrificed at 1, 6 or 24 h after CLP challenge. The histological evaluation, lung water content, and biochemical analysis were performed. The results revealed that the JNK and p38 MAPK inhibitor improved lung permeability, attenuated system inflammation, further alleviated the lung injury induced by sepsis. In conclusion, JNK and p38 MAPK signaling are essential for the development of ARDS following sepsis. Further studies are needed to illuminate the detailed mechanisms of JNK and p38 MAPK signaling in sepsis‑induced ARDS.
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