151
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Xu Y, Shi W, He X, Wu X, Li X, Ma H. Facile and Sensitive Method for Protein Kinase A Activity Assay Based on Fluorescent Off-On PolyU-peptide Assembly. Anal Chem 2017; 89:10980-10984. [PMID: 28937207 DOI: 10.1021/acs.analchem.7b02815] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Phosphorylation mediated by protein kinases plays a pivotal role in metabolic and cell-signaling processes, and the dysfunction of protein kinases such as protein kinase A (PKA) may induce several human diseases. Therefore, it is of great significance to develop a facile and effective method for PKA activity assay and high-throughput screening of inhibitors. Herein, we develop a new fluorescent off-on method for PKA assay based on the assembly of anionic polyuridylic acid (polyU) and cationic fluorescent peptide. The phosphorylation of the peptide disrupts its electrostatic binding with polyU, suppresses the concentration quenching effect of polyU, and thus causes fluorescence recovery. The recovered fluorescence intensity at 585 nm is directly proportional to the PKA activity in the range of 0.1-3.2 U/mL with a detection limit of 0.05 U/mL. Using our method, the PKA activity in HeLa cell lysate is determined to be 58.2 ± 5.1 U/mg protein. The method has also been employed to evaluate the inhibitory effect of PKA inhibitors with satisfactory results and may be expected to be a promising candidate for facile and cost-effective assay of kinase activity and high-throughput inhibitor screening.
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Affiliation(s)
- Yanhui Xu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China.,University of Chinese Academy of Sciences , Beijing 100049, China
| | - Wen Shi
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China.,University of Chinese Academy of Sciences , Beijing 100049, China
| | - Xinyuan He
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
| | - Xiaofeng Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
| | - Xiaohua Li
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
| | - Huimin Ma
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China.,University of Chinese Academy of Sciences , Beijing 100049, China
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152
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Lin BC, Harris DR, Kirkman LMD, Perez AM, Qian Y, Schermerhorn JT, Hong MY, Winston DS, Xu L, Lieber AM, Hamilton M, Brandt GS. The anthraquinone emodin inhibits the non-exported FIKK kinase from Plasmodium falciparum. Bioorg Chem 2017; 75:217-223. [PMID: 28987877 DOI: 10.1016/j.bioorg.2017.09.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 09/13/2017] [Accepted: 09/15/2017] [Indexed: 01/08/2023]
Abstract
The FIKK family of kinases is unique to parasites of the Apicomplexan order, which includes all malaria parasites. Plasmodium falciparum, the most virulent form of human malaria, has a family of 19 FIKK kinases, most of which are exported into the host red blood cell during malaria infection. Here, we confirm that FIKK 8 is a non-exported member of the FIKK kinase family. Through expression and purification of the recombinant kinase domain, we establish that emodin is a relatively high-affinity (IC50=2μM) inhibitor of PfFk8. Closely related anthraquinones do not inhibit PfFk8, suggesting that the particular substitution pattern of emodin is critical to the inhibitory pharmacophore. This first report of a P. falciparum FIKK kinase inhibitor lays the groundwork for developing specific inhibitors of the various members of the FIKK kinase family in order to probe their physiological function.
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Affiliation(s)
- Benjamin C Lin
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States
| | - Darcy R Harris
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States
| | - Lucy M D Kirkman
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States
| | - Astrid M Perez
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States
| | - Yiwen Qian
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States
| | - Janse T Schermerhorn
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States
| | - Min Y Hong
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States
| | - Dennis S Winston
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States
| | - Lingyin Xu
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States
| | - Alexander M Lieber
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States
| | - Matthew Hamilton
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States
| | - Gabriel S Brandt
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, United States.
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153
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Zheng PP, Li J, Kros JM. Breakthroughs in modern cancer therapy and elusive cardiotoxicity: Critical research-practice gaps, challenges, and insights. Med Res Rev 2017; 38:325-376. [PMID: 28862319 PMCID: PMC5763363 DOI: 10.1002/med.21463] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 07/14/2017] [Accepted: 07/15/2017] [Indexed: 12/16/2022]
Abstract
To date, five cancer treatment modalities have been defined. The three traditional modalities of cancer treatment are surgery, radiotherapy, and conventional chemotherapy, and the two modern modalities include molecularly targeted therapy (the fourth modality) and immunotherapy (the fifth modality). The cardiotoxicity associated with conventional chemotherapy and radiotherapy is well known. Similar adverse cardiac events are resurging with the fourth modality. Aside from the conventional and newer targeted agents, even the most newly developed, immune‐based therapeutic modalities of anticancer treatment (the fifth modality), e.g., immune checkpoint inhibitors and chimeric antigen receptor (CAR) T‐cell therapy, have unfortunately led to potentially lethal cardiotoxicity in patients. Cardiac complications represent unresolved and potentially life‐threatening conditions in cancer survivors, while effective clinical management remains quite challenging. As a consequence, morbidity and mortality related to cardiac complications now threaten to offset some favorable benefits of modern cancer treatments in cancer‐related survival, regardless of the oncologic prognosis. This review focuses on identifying critical research‐practice gaps, addressing real‐world challenges and pinpointing real‐time insights in general terms under the context of clinical cardiotoxicity induced by the fourth and fifth modalities of cancer treatment. The information ranges from basic science to clinical management in the field of cardio‐oncology and crosses the interface between oncology and onco‐pharmacology. The complexity of the ongoing clinical problem is addressed at different levels. A better understanding of these research‐practice gaps may advance research initiatives on the development of mechanism‐based diagnoses and treatments for the effective clinical management of cardiotoxicity.
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Affiliation(s)
- Ping-Pin Zheng
- Cardio-Oncology Research Group, Erasmus Medical Center, Rotterdam, the Netherlands.,Department of Pathology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Jin Li
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Johan M Kros
- Department of Pathology, Erasmus Medical Center, Rotterdam, the Netherlands
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154
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Aptamers as Valuable Molecular Tools in Neurosciences. J Neurosci 2017; 37:2517-2523. [PMID: 28275062 DOI: 10.1523/jneurosci.1969-16.2017] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/18/2017] [Accepted: 01/30/2017] [Indexed: 01/19/2023] Open
Abstract
Aptamers are short nucleic acids that interact with a variety of targets with high affinity and specificity. They have been shown to inhibit biological functions of cognate target proteins, and they are identifiable by an in vitro selection process, also termed SELEX (Systematic Evolution of Ligands by EXponential enrichment). Being nucleic acids, aptamers can be synthesized chemically or enzymatically. The latter renders RNA aptamers compatible with the cell's own transcription machinery and, thus, expressable inside cells. The synthesis of aptamers by chemical approaches opens up the possibility of producing aptamers on a large scale and enables a straightforward access to introduce modifications in a site-specific manner (e.g., fluorophores or photo-labile groups). These characteristics make aptamers broadly applicable (e.g., as an analytical, diagnostic, or separation tool). In this TechSight, we provide a brief overview on aptamer technology and the potential of aptamers as valuable research tools in neurosciences.
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155
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Yamada K, Levell J, Yoon T, Kohls D, Yowe D, Rigel DF, Imase H, Yuan J, Yasoshima K, DiPetrillo K, Monovich L, Xu L, Zhu M, Kato M, Jain M, Idamakanti N, Taslimi P, Kawanami T, Argikar UA, Kunjathoor V, Xie X, Yagi YI, Iwaki Y, Robinson Z, Park HM. Optimization of Allosteric With-No-Lysine (WNK) Kinase Inhibitors and Efficacy in Rodent Hypertension Models. J Med Chem 2017; 60:7099-7107. [PMID: 28771350 DOI: 10.1021/acs.jmedchem.7b00708] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The observed structure-activity relationship of three distinct ATP noncompetitive With-No-Lysine (WNK) kinase inhibitor series, together with a crystal structure of a previously disclosed allosteric inhibitor bound to WNK1, led to an overlay hypothesis defining core and side-chain relationships across the different series. This in turn enabled an efficient optimization through scaffold morphing, resulting in compounds with a good balance of selectivity, cellular potency, and pharmacokinetic profile, which were suitable for in vivo proof-of-concept studies. When dosed orally, the optimized compound reduced blood pressure in mice overexpressing human WNK1, and induced diuresis, natriuresis and kaliuresis in spontaneously hypertensive rats (SHR), confirming that this mechanism of inhibition of WNK kinase activity is effective at regulating cardiovascular homeostasis.
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Affiliation(s)
- Ken Yamada
- Novartis Institutes for BioMedical Research, Inc. , Cambridge, Massachusetts 02139-4133, United States.,Novartis Institutes for BioMedical Research, Novartis Pharma K.K. , Tsukuba, Ibaraki 300-2611, Japan
| | - Julian Levell
- Novartis Institutes for BioMedical Research, Inc. , Cambridge, Massachusetts 02139-4133, United States
| | - Taeyong Yoon
- Novartis Institutes for BioMedical Research, Inc. , Cambridge, Massachusetts 02139-4133, United States
| | - Darcy Kohls
- Novartis Institutes for BioMedical Research, Inc. , Cambridge, Massachusetts 02139-4133, United States
| | - David Yowe
- Novartis Institutes for BioMedical Research, Inc. , Cambridge, Massachusetts 02139-4133, United States
| | - Dean F Rigel
- Novartis Institutes for BioMedical Research, Novartis Pharmaceuticals Corporation , East Hanover, New Jersey 07936-1080, United States
| | - Hidetomo Imase
- Novartis Institutes for BioMedical Research, Inc. , Cambridge, Massachusetts 02139-4133, United States
| | - Jun Yuan
- Novartis Institutes for BioMedical Research, Inc. , Cambridge, Massachusetts 02139-4133, United States
| | - Kayo Yasoshima
- Novartis Institutes for BioMedical Research, Inc. , Cambridge, Massachusetts 02139-4133, United States.,Novartis Institutes for BioMedical Research, Novartis Pharma K.K. , Tsukuba, Ibaraki 300-2611, Japan
| | - Keith DiPetrillo
- Novartis Institutes for BioMedical Research, Novartis Pharmaceuticals Corporation , East Hanover, New Jersey 07936-1080, United States
| | - Lauren Monovich
- Novartis Institutes for BioMedical Research, Inc. , Cambridge, Massachusetts 02139-4133, United States
| | - Lingfei Xu
- Novartis Institutes for BioMedical Research, Novartis Pharmaceuticals Corporation , East Hanover, New Jersey 07936-1080, United States
| | - Meicheng Zhu
- Novartis Institutes for BioMedical Research, Inc. , Cambridge, Massachusetts 02139-4133, United States
| | - Mitsunori Kato
- Novartis Institutes for BioMedical Research, Inc. , Cambridge, Massachusetts 02139-4133, United States.,Novartis Institutes for BioMedical Research, Novartis Pharma K.K. , Tsukuba, Ibaraki 300-2611, Japan
| | - Monish Jain
- Novartis Institutes for BioMedical Research, Inc. , Cambridge, Massachusetts 02139-4133, United States
| | - Neeraja Idamakanti
- Novartis Institutes for BioMedical Research, Inc. , Cambridge, Massachusetts 02139-4133, United States
| | - Paul Taslimi
- Novartis Institutes for BioMedical Research, Inc. , Cambridge, Massachusetts 02139-4133, United States
| | - Toshio Kawanami
- Novartis Institutes for BioMedical Research, Inc. , Cambridge, Massachusetts 02139-4133, United States.,Novartis Institutes for BioMedical Research, Novartis Pharma K.K. , Tsukuba, Ibaraki 300-2611, Japan
| | - Upendra A Argikar
- Novartis Institutes for BioMedical Research, Inc. , Cambridge, Massachusetts 02139-4133, United States
| | - Vidya Kunjathoor
- Novartis Institutes for BioMedical Research, Inc. , Cambridge, Massachusetts 02139-4133, United States
| | - Xiaoling Xie
- Novartis Institutes for BioMedical Research, Inc. , Cambridge, Massachusetts 02139-4133, United States
| | - Yukiko I Yagi
- Novartis Institutes for BioMedical Research, Novartis Pharma K.K. , Tsukuba, Ibaraki 300-2611, Japan
| | - Yuki Iwaki
- Novartis Institutes for BioMedical Research, Inc. , Cambridge, Massachusetts 02139-4133, United States
| | - Zachary Robinson
- Novartis Institutes for BioMedical Research, Inc. , Cambridge, Massachusetts 02139-4133, United States
| | - Hyi-Man Park
- Novartis Institutes for BioMedical Research, Inc. , Cambridge, Massachusetts 02139-4133, United States.,Novartis Institutes for BioMedical Research, Novartis Pharma K.K. , Tsukuba, Ibaraki 300-2611, Japan
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156
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Triptolide-Assisted Phosphorylation of p53 Suppresses Inflammation-Induced NF-κB Survival Pathways in Cancer Cells. Mol Cell Biol 2017; 37:MCB.00149-17. [PMID: 28533220 DOI: 10.1128/mcb.00149-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 05/16/2017] [Indexed: 12/25/2022] Open
Abstract
Chronic inflammation plays important roles in cancer initiation and progression. Resolving chronic inflammation or blocking inflammatory signal transduction may prevent cancer development. Here, we report that the combined low-dose use of two anti-inflammatory drugs, aspirin and triptolide, reduces spontaneous lung cancer incidence from 70% to 10% in a mouse model. Subsequent studies reveal that such treatment has little effect on resolving chronic inflammatory conditions in the lung, but it significantly blocks the NF-κB-mediated expression of proliferation and survival genes in cancer cells. Furthermore, triptolide and aspirin induce distinct mechanisms to potentiate each other to block NF-κB nuclear localization stimulated by inflammatory cytokines. While aspirin directly inhibits IκB kinases (IKKs) to phosphorylate IκBα for NF-κB activation, triptolide does not directly target IKKs or other factors that mediate IKK activation. Instead, it requires p53 to inhibit IκBα phosphorylation and degradation. Triptolide binds to and activates p38α and extracellular signal-regulated kinase 1/2 (ERK1/2), which phosphorylate and stabilize p53. Subsequently, p53 competes with IκBα for substrate binding to IKKβ and thereby blocks IκBα phosphorylation and NF-κB nuclear translocation. Inhibition of p38α and ERK1/2 or p53 mutations could abolish the inhibitory effects of triptolide on NF-κB. Our study defines a new p53-dependent mechanism for blocking NF-κB survival pathways in cancer cells.
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157
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Zha JS, Zhu BL, Liu L, Lai YJ, Long Y, Hu XT, Deng XJ, Wang XF, Yan Z, Chen GJ. Phorbol esters dPPA/dPA promote furin expression involving transcription factor CEBPβ in neuronal cells. Oncotarget 2017; 8:60159-60172. [PMID: 28947961 PMCID: PMC5601129 DOI: 10.18632/oncotarget.18569] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 06/10/2017] [Indexed: 02/03/2023] Open
Abstract
Using high-throughput small molecule screening targeting furin gene, we identified that phorbol esters dPPA (12-Deoxyphorbol 13-phenylacetate 20-acetate) and dPA (12-Deoxyphorbol 13-acetate) significantly increased furin protein and mRNA expression in SH-SY5Y cells. This effect was prevented by PKC (protein kinase C) inhibitor calphostin C but not Ro318220, suggesting that the C1 domain, rather than the catalytic domain of PKC plays an important role. Luciferase assay revealed that nucleotides -7925 to -7426 were sufficient to mediate dPPA/dPA enhancement of furin P1 promoter activity. RNA interference of transcriptional factors CEBPβ (CCAAT/enhancer-binding protein β) and GATA1 revealed that knockdown of CEBPβ significantly attenuated the effect of dPPA on furin expression. Pharmacological inhibition of ERK and PI3K but not TGFβ receptor diminished the up-regulation of furin by dPPA. These results suggested that in neuronal cells, transcriptional activation of furin by dPPA/dPA may be initiated by C1 domain containing proteins including PKC; the intracellular signaling involves ERK and PI3K and transcription factor CEBPβ.
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Affiliation(s)
- Jing-Si Zha
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, Chongqing 400016, China
| | - Bing-Lin Zhu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, Chongqing 400016, China
| | - Lu Liu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, Chongqing 400016, China
| | - Yu-Jie Lai
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, Chongqing 400016, China
| | - Yan Long
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, Chongqing 400016, China
| | - Xiao-Tong Hu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, Chongqing 400016, China
| | - Xiao-Juan Deng
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, Chongqing 400016, China
| | - Xue-Feng Wang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, Chongqing 400016, China
| | - Zhen Yan
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY, 14214, USA
| | - Guo-Jun Chen
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, Chongqing 400016, China
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158
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Wang W, Krosky D, Ahn K. Discovery of Inactive Conformation-Selective Kinase Inhibitors by Utilizing Cascade Assays. Biochemistry 2017; 56:4449-4456. [DOI: 10.1021/acs.biochem.7b00521] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Weixue Wang
- Molecular & Cellular Pharmacology, Lead Discovery, Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States
| | - Daniel Krosky
- Molecular & Cellular Pharmacology, Lead Discovery, Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States
| | - Kay Ahn
- Molecular & Cellular Pharmacology, Lead Discovery, Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States
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159
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Nakano H, Hasegawa T, Kojima H, Okabe T, Nagano T. Design and Synthesis of Potent and Selective PIM Kinase Inhibitors by Targeting Unique Structure of ATP-Binding Pocket. ACS Med Chem Lett 2017; 8:504-509. [PMID: 28523101 DOI: 10.1021/acsmedchemlett.6b00518] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 04/02/2017] [Indexed: 01/23/2023] Open
Abstract
In the development of kinase inhibitors, one of the major concerns is selectivity. An effective strategy to achieve high selectivity is to utilize structural differences among kinases to inform inhibitor design. Here, we set out to improve the PIM (proviral integration site for Moloney murine leukemia virus) kinase-inhibitory selectivity of our previously reported 7-azaindole derivative 2, which has promising ADMET properties, by targeting a unique bulge in the ATP-binding pocket. 6-Substituted 7-azaindoles, especially the 6-chlorinated derivatives, proved to be potent and selective PIM kinase inhibitors and appear to be promising lead compounds for future drug discovery.
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Affiliation(s)
- Hirofumi Nakano
- Drug Discovery
Initiative, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tsukasa Hasegawa
- Drug Discovery
Initiative, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hirotatsu Kojima
- Drug Discovery
Initiative, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayoshi Okabe
- Drug Discovery
Initiative, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tetsuo Nagano
- Drug Discovery
Initiative, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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160
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Kim J, Ahuja LG, Chao FA, Xia Y, McClendon CL, Kornev AP, Taylor SS, Veglia G. A dynamic hydrophobic core orchestrates allostery in protein kinases. SCIENCE ADVANCES 2017; 3:e1600663. [PMID: 28435869 PMCID: PMC5384802 DOI: 10.1126/sciadv.1600663] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 03/15/2017] [Indexed: 05/05/2023]
Abstract
Eukaryotic protein kinases (EPKs) constitute a class of allosteric switches that mediate a myriad of signaling events. It has been postulated that EPKs' active and inactive states depend on the structural architecture of their hydrophobic cores, organized around two highly conserved spines: C-spine and R-spine. How the spines orchestrate the transition of the enzyme between catalytically uncommitted and committed states remains elusive. Using relaxation dispersion nuclear magnetic resonance spectroscopy, we found that the hydrophobic core of the catalytic subunit of protein kinase A, a prototypical and ubiquitous EPK, moves synchronously to poise the C subunit for catalysis in response to binding adenosine 5'-triphosphate. In addition to completing the C-spine, the adenine ring fuses the β structures of the N-lobe and the C-lobe. Additional residues that bridge the two spines (I150 and V104) are revealed as part of the correlated hydrophobic network; their importance was validated by mutagenesis, which led to inactivation. Because the hydrophobic architecture of the catalytic core is conserved throughout the EPK superfamily, the present study suggests a universal mechanism for dynamically driven allosteric activation of kinases mediated by coordinated signal transmission through ordered motifs in their hydrophobic cores.
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Affiliation(s)
- Jonggul Kim
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Lalima G. Ahuja
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Fa-An Chao
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Youlin Xia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Christopher L. McClendon
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
| | - Alexandr P. Kornev
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Susan S. Taylor
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
| | - Gianluigi Veglia
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
- Corresponding author.
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161
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162
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Roskoski R. Allosteric MEK1/2 inhibitors including cobimetanib and trametinib in the treatment of cutaneous melanomas. Pharmacol Res 2017; 117:20-31. [PMID: 27956260 DOI: 10.1016/j.phrs.2016.12.009] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 12/08/2016] [Indexed: 02/07/2023]
Abstract
The Ras-Raf-MEK-ERK (Map kinase) cellular pathway is a highly conserved eukaryotic signaling module that transduces extracellular signals from growth factors and cytokines into intracellular regulatory events that are involved in cell growth and proliferation or the contrary pathway of cell differentiation. Dysregulation of this pathway occurs in more than one-third of all malignancies, a process that has fostered the development of targeted Map kinase pathway inhibitors. Cutaneous melanomas, which arise from skin melanocytes, are the most aggressive form of skin cancer. Mutations that activate the Map kinase pathway occur in more than 90% of these melanomas. This has led to the development of the combination of dabrafenib and trametinib or vemurafenib and cobimetanib for the treatment of BRAF V600E mutant melanomas. Dabrafenib and vemurafenib target V600E/K BRAF mutants while trametinib and cobimetanib target MEK1/2. The latter two agents bind to MEK1/2 at a site that is adjacent to, but separate from, the ATP-binding site and are therefore classified as type III allosteric protein kinase inhibitors. These agents form a hydrogen bond with a conserved β3-lysine and they make numerous hydrophobic contacts with residues within the αC-helix, the β5 strand, and within the activation segment, regions of the protein kinase domain that exhibit greater diversity than those found within the ATP-binding site. One advantage of such allosteric inhibitors is that they do not have to compete with millimolar concentrations of cellular ATP, which most FDA-approved small molecule competitive inhibitors such as imatinib must do. Owing to the wide spread activation of this pathway in numerous neoplasms, trametinib and cobimetinib are being studied in combination with other targeted and cytotoxic drugs in a variety of clinical situations. Except for BRAF and NRAS mutations, there are no other biomarkers correlated with treatment responses following MEK1/2 inhibition and the discovery of such biomarkers would represent an important therapeutic breakthrough.
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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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163
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Long MJC, Parvez S, Zhao Y, Surya SL, Wang Y, Zhang S, Aye Y. Akt3 is a privileged first responder in isozyme-specific electrophile response. Nat Chem Biol 2017; 13:333-338. [PMID: 28114274 PMCID: PMC5586141 DOI: 10.1038/nchembio.2284] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 11/29/2016] [Indexed: 12/25/2022]
Abstract
Isozyme-specific post-translational regulation fine tunes signaling events. However, redundancy in sequence or activity renders links between isozyme-specific modifications and downstream functions uncertain. Methods to study this phenomenon are underdeveloped. Here we use a redox-targeting screen to reveal that Akt3 is a first-responding isozyme sensing native electrophilic lipids. Electrophile modification of Akt3 modulated downstream pathway responses in cells and Danio rerio (zebrafish) and markedly differed from Akt2-specific oxidative regulation. Digest MS sequencing identified Akt3 C119 as the privileged cysteine that senses 4-hydroxynonenal. A C119S Akt3 mutant was hypomorphic for all downstream phenotypes shown by wild-type Akt3. This study documents isozyme-specific and chemical redox signal-personalized physiological responses.
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Affiliation(s)
- Marcus J. C. Long
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, NY, 14850, United States
| | - Saba Parvez
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, NY, 14850, United States
| | - Yi Zhao
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, NY, 14850, United States
| | - Sanjna L. Surya
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, NY, 14850, United States
| | - Yiran Wang
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, NY, 14850, United States
| | - Sheng Zhang
- Proteomics and Mass Spectrometry Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14850, United States
| | - Yimon Aye
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, NY, 14850, United States
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, United States
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164
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Weerapana E. Taking AKTion on HNEs. Nat Chem Biol 2017; 13:244-245. [DOI: 10.1038/nchembio.2311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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165
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Roskoski R. Anaplastic lymphoma kinase (ALK) inhibitors in the treatment of ALK-driven lung cancers. Pharmacol Res 2017; 117:343-356. [DOI: 10.1016/j.phrs.2017.01.007] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 01/06/2017] [Indexed: 12/24/2022]
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166
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Sullenberger C, Piqué D, Ogata Y, Mensa-Wilmot K. AEE788 Inhibits Basal Body Assembly and Blocks DNA Replication in the African Trypanosome. Mol Pharmacol 2017; 91:482-498. [PMID: 28246189 PMCID: PMC5399642 DOI: 10.1124/mol.116.106906] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 02/17/2017] [Indexed: 12/15/2022] Open
Abstract
Trypanosoma brucei causes human African trypanosomiasis (HAT). The pyrrolopyrimidine AEE788 (a hit for anti-HAT drug discovery) associates with three trypanosome protein kinases. Herein we delineate the effects of AEE788 on T. brucei using chemical biology strategies. AEE788 treatment inhibits DNA replication in the kinetoplast (mitochondrial nucleoid) and nucleus. In addition, AEE788 blocks duplication of the basal body and the bilobe without affecting mitosis. Thus, AEE788 prevents entry into the S-phase of the cell division cycle. To study the kinetics of early events in trypanosome division, we employed an "AEE788 block and release" protocol to stage entry into the S-phase. A time-course of DNA synthesis (nuclear and kinetoplast DNA), duplication of organelles (basal body, bilobe, kinetoplast, nucleus), and cytokinesis was obtained. Unexpected findings include the following: 1) basal body and bilobe duplication are concurrent; 2) maturation of probasal bodies, marked by TbRP2 recruitment, is coupled with nascent basal body assembly, monitored by localization of TbSAS6 at newly forming basal bodies; and 3) kinetoplast division is observed in G2 after completion of nuclear DNA synthesis. Prolonged exposure of trypanosomes to AEE788 inhibited transferrin endocytosis, altered cell morphology, and decreased cell viability. To discover putative effectors for the pleiotropic effects of AEE788, proteome-wide changes in protein phosphorylation induced by the drug were determined. Putative effectors include an SR protein kinase, bilobe proteins, TbSAS4, TbRP2, and BILBO-1. Loss of function of one or more of these effectors can, from published literature, explain the polypharmacology of AEE788 on trypanosome biology.
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Affiliation(s)
- Catherine Sullenberger
- Department of Cellular Biology, and Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia (C.S., D.P., K.M.-W.); and the Proteomics Facility, Fred Hutchinson Cancer Research Center, Seattle, Washington (Y.O.)
| | - Daniel Piqué
- Department of Cellular Biology, and Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia (C.S., D.P., K.M.-W.); and the Proteomics Facility, Fred Hutchinson Cancer Research Center, Seattle, Washington (Y.O.)
| | - Yuko Ogata
- Department of Cellular Biology, and Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia (C.S., D.P., K.M.-W.); and the Proteomics Facility, Fred Hutchinson Cancer Research Center, Seattle, Washington (Y.O.)
| | - Kojo Mensa-Wilmot
- Department of Cellular Biology, and Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia (C.S., D.P., K.M.-W.); and the Proteomics Facility, Fred Hutchinson Cancer Research Center, Seattle, Washington (Y.O.)
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167
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Bataille CJR, Brennan MB, Byrne S, Davies SG, Durbin M, Fedorov O, Huber KVM, Jones AM, Knapp S, Liu G, Nadali A, Quevedo CE, Russell AJ, Walker RG, Westwood R, Wynne GM. Thiazolidine derivatives as potent and selective inhibitors of the PIM kinase family. Bioorg Med Chem 2017; 25:2657-2665. [PMID: 28341403 DOI: 10.1016/j.bmc.2017.02.056] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 02/23/2017] [Accepted: 02/25/2017] [Indexed: 12/31/2022]
Abstract
The PIM family of serine/threonine kinases have become an attractive target for anti-cancer drug development, particularly for certain hematological malignancies. Here, we describe the discovery of a series of inhibitors of the PIM kinase family using a high throughput screening strategy. Through a combination of molecular modeling and optimization studies, the intrinsic potencies and molecular properties of this series of compounds was significantly improved. An excellent pan-PIM isoform inhibition profile was observed across the series, while optimized examples show good selectivity over other kinases. Two PIM-expressing leukemic cancer cell lines, MV4-11 and K562, were employed to evaluate the in vitro anti-proliferative effects of selected inhibitors. Encouraging activities were observed for many examples, with the best example (44) giving an IC50 of 0.75μM against the K562 cell line. These data provide a promising starting point for further development of this series as a new cancer therapy through PIM kinase inhibition.
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Affiliation(s)
- Carole J R Bataille
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Méabh B Brennan
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Simon Byrne
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Stephen G Davies
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK.
| | - Matthew Durbin
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Oleg Fedorov
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, UK
| | - Kilian V M Huber
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Alan M Jones
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Stefan Knapp
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, UK
| | - Gu Liu
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Anna Nadali
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK
| | - Camilo E Quevedo
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Angela J Russell
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK; Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK.
| | - Roderick G Walker
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK
| | - Robert Westwood
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Graham M Wynne
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
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168
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Wilson D, Li JW, Branda NR. Visible-Light-Triggered Activation of a Protein Kinase Inhibitor. ChemMedChem 2017; 12:284-287. [DOI: 10.1002/cmdc.201600632] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Indexed: 12/26/2022]
Affiliation(s)
- Danielle Wilson
- 4D LABS; Department of Chemistry; Simon Fraser University; 8888 University Drive Burnaby BC V5A 1S6 Canada
| | - Jason W. Li
- 4D LABS; Department of Chemistry; Simon Fraser University; 8888 University Drive Burnaby BC V5A 1S6 Canada
| | - Neil R. Branda
- 4D LABS; Department of Chemistry; Simon Fraser University; 8888 University Drive Burnaby BC V5A 1S6 Canada
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169
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Yamada K, Zhang JH, Xie X, Reinhardt J, Xie AQ, LaSala D, Kohls D, Yowe D, Burdick D, Yoshisue H, Wakai H, Schmidt I, Gunawan J, Yasoshima K, Yue QK, Kato M, Mogi M, Idamakanti N, Kreder N, Drueckes P, Pandey P, Kawanami T, Huang W, Yagi YI, Deng Z, Park HM. Discovery and Characterization of Allosteric WNK Kinase Inhibitors. ACS Chem Biol 2016; 11:3338-3346. [PMID: 27712055 DOI: 10.1021/acschembio.6b00511] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein kinases are known for their highly conserved adenosine triphosphate (ATP)-binding site, rendering the discovery of selective inhibitors a major challenge. In theory, allosteric inhibitors can achieve high selectivity by targeting less conserved regions of the kinases, often with an added benefit of retaining efficacy under high physiological ATP concentration. Although often overlooked in favor of ATP-site directed approaches, performing a screen at high ATP concentration or stringent hit triaging with high ATP concentration offers conceptually simple methods of identifying inhibitors that bind outside the ATP pocket. Here, we applied the latter approach to the With-No-Lysine (K) (WNK) kinases to discover lead molecules for a next-generation antihypertensive that requires a stringent safety profile. This strategy yielded several ATP noncompetitive WNK1-4 kinase inhibitors, the optimization of which enabled cocrystallization with WNK1, revealing an allosteric binding mode consistent with the observed exquisite specificity for WNK1-4 kinases. The optimized compound inhibited rubidium uptake by sodium chloride cotransporter 1 (NKCC1) in HT29 cells, consistent with the reported physiology of WNK kinases in renal electrolyte handling.
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Affiliation(s)
- Ken Yamada
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
- Novartis Institutes for BioMedical Research, Novartis
Pharma K.K., Tsukuba, Ibaraki 300-2611, Japan
| | - Ji-Hu Zhang
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
| | - Xiaoling Xie
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
| | - Juergen Reinhardt
- Novartis Institutes for BioMedical Research, Novartis
Pharma AG, Basel, 4002, Switzerland
| | - Amy Qiongshu Xie
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
| | - Daniel LaSala
- Novartis Institutes for BioMedical Research, Novartis
Pharmaceuticals Corporation, East
Hanover, New Jersey 07936-1080, United States
| | - Darcy Kohls
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
| | - David Yowe
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
| | - Debra Burdick
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
| | - Hajime Yoshisue
- Novartis Institutes for BioMedical Research, Novartis
Pharma K.K., Tsukuba, Ibaraki 300-2611, Japan
| | - Hiromichi Wakai
- Novartis Institutes for BioMedical Research, Novartis
Pharma K.K., Tsukuba, Ibaraki 300-2611, Japan
| | - Isabel Schmidt
- Novartis Institutes for BioMedical Research, Novartis
Pharma AG, Basel, 4002, Switzerland
| | - Jason Gunawan
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
| | - Kayo Yasoshima
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
- Novartis Institutes for BioMedical Research, Novartis
Pharma K.K., Tsukuba, Ibaraki 300-2611, Japan
| | - Q. Kimberley Yue
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
| | - Mitsunori Kato
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
- Novartis Institutes for BioMedical Research, Novartis
Pharma K.K., Tsukuba, Ibaraki 300-2611, Japan
| | - Muneto Mogi
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
- Novartis Institutes for BioMedical Research, Novartis
Pharma K.K., Tsukuba, Ibaraki 300-2611, Japan
| | - Neeraja Idamakanti
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
| | - Natasha Kreder
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
| | - Peter Drueckes
- Novartis Institutes for BioMedical Research, Novartis
Pharma AG, Basel, 4002, Switzerland
| | - Pramod Pandey
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
| | - Toshio Kawanami
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
- Novartis Institutes for BioMedical Research, Novartis
Pharma K.K., Tsukuba, Ibaraki 300-2611, Japan
| | - Waanjeng Huang
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
| | - Yukiko I. Yagi
- Novartis Institutes for BioMedical Research, Novartis
Pharma K.K., Tsukuba, Ibaraki 300-2611, Japan
| | - Zhan Deng
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
| | - Hyi-Man Park
- Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139-4133, United States
- Novartis Institutes for BioMedical Research, Novartis
Pharma K.K., Tsukuba, Ibaraki 300-2611, Japan
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170
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Chan CYX, Gritsenko MA, Smith RD, Qian WJ. The current state of the art of quantitative phosphoproteomics and its applications to diabetes research. Expert Rev Proteomics 2016; 13:421-33. [PMID: 26960075 DOI: 10.1586/14789450.2016.1164604] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Protein phosphorylation is a fundamental regulatory mechanism in many cellular processes and aberrant perturbation of phosphorylation has been implicated in various human diseases. Kinases and their cognate inhibitors have been considered as hotspots for drug development. Therefore, the emerging tools, which enable a system-wide quantitative profiling of phosphoproteome, would offer a powerful impetus in unveiling novel signaling pathways, drug targets and/or biomarkers for diseases of interest. This review highlights recent advances in phosphoproteomics, the current state of the art of the technologies and the challenges and future perspectives of this research area. Finally, some exemplary applications of phosphoproteomics in diabetes research are underscored.
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Affiliation(s)
- Chi Yuet X'avia Chan
- a Biological Sciences Division and Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Marina A Gritsenko
- a Biological Sciences Division and Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Richard D Smith
- a Biological Sciences Division and Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Wei-Jun Qian
- a Biological Sciences Division and Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA , USA
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171
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Ismail NS, Ali GM, Ibrahim DA, Elmetwali AM. Medicinal attributes of pyrazolo[1,5-a]pyrimidine based scaffold derivatives targeting kinases as anticancer agents. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2016. [DOI: 10.1016/j.fjps.2016.08.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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172
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Exploring Molecular Mechanisms of Paradoxical Activation in the BRAF Kinase Dimers: Atomistic Simulations of Conformational Dynamics and Modeling of Allosteric Communication Networks and Signaling Pathways. PLoS One 2016; 11:e0166583. [PMID: 27861609 PMCID: PMC5115767 DOI: 10.1371/journal.pone.0166583] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/31/2016] [Indexed: 12/14/2022] Open
Abstract
The recent studies have revealed that most BRAF inhibitors can paradoxically induce kinase activation by promoting dimerization and enzyme transactivation. Despite rapidly growing number of structural and functional studies about the BRAF dimer complexes, the molecular basis of paradoxical activation phenomenon is poorly understood and remains largely hypothetical. In this work, we have explored the relationships between inhibitor binding, protein dynamics and allosteric signaling in the BRAF dimers using a network-centric approach. Using this theoretical framework, we have combined molecular dynamics simulations with coevolutionary analysis and modeling of the residue interaction networks to determine molecular determinants of paradoxical activation. We have investigated functional effects produced by paradox inducer inhibitors PLX4720, Dabrafenib, Vemurafenib and a paradox breaker inhibitor PLX7904. Functional dynamics and binding free energy analyses of the BRAF dimer complexes have suggested that negative cooperativity effect and dimer-promoting potential of the inhibitors could be important drivers of paradoxical activation. We have introduced a protein structure network model in which coevolutionary residue dependencies and dynamic maps of residue correlations are integrated in the construction and analysis of the residue interaction networks. The results have shown that coevolutionary residues in the BRAF structures could assemble into independent structural modules and form a global interaction network that may promote dimerization. We have also found that BRAF inhibitors could modulate centrality and communication propensities of global mediating centers in the residue interaction networks. By simulating allosteric communication pathways in the BRAF structures, we have determined that paradox inducer and breaker inhibitors may activate specific signaling routes that correlate with the extent of paradoxical activation. While paradox inducer inhibitors may facilitate a rapid and efficient communication via an optimal single pathway, the paradox breaker may induce a broader ensemble of suboptimal and less efficient communication routes. The central finding of our study is that paradox breaker PLX7904 could mimic structural, dynamic and network features of the inactive BRAF-WT monomer that may be required for evading paradoxical activation. The results of this study rationalize the existing structure-functional experiments by offering a network-centric rationale of the paradoxical activation phenomenon. We argue that BRAF inhibitors that amplify dynamic features of the inactive BRAF-WT monomer and intervene with the allosteric interaction networks may serve as effective paradox breakers in cellular environment.
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173
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Ma B, Marcotte D, Paramasivam M, Michelsen K, Wang T, Bertolotti-Ciarlet A, Jones JH, Moree B, Butko M, Salafsky J, Sun X, McKee T, Silvian LF. ATP-Competitive MLKL Binders Have No Functional Impact on Necroptosis. PLoS One 2016; 11:e0165983. [PMID: 27832137 PMCID: PMC5104457 DOI: 10.1371/journal.pone.0165983] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 10/20/2016] [Indexed: 01/18/2023] Open
Abstract
MLKL is a pore forming pseudokinase involved in the final stage of necroptosis, a form of programmed cell death. Its phosphorylation by RIPK3 is necessary for triggering necroptosis but not for triggering apoptosis, which makes it a unique target for pharmacological inhibition to block necroptotic cell death. This mechanism has been described as playing a role in disease progression in neurodegenerative and inflammatory diseases. A type II kinase inhibitor (cpd 1) has been described that reportedly binds to the MLKL pseudokinase domain and prevents necroptosis. Here we describe five compounds that bind to the MLKL ATP-binding site, however the four MLKL-selective compounds have no activity in rescuing cells from necroptosis. We use kinase selectivity panels, crystallography and a new conformationally sensitive method of measuring protein conformational changes (SHG) to confirm that the one previously reported compound that can rescue cells (cpd 1) is a non-selective type II inhibitor that also inhibits the upstream kinase RIPK1. Although this compound can shift the GFE motif of the activation loop to an “out” position, the accessibility of the key residue Ser358 in the MLKL activation loop is not affected by compound binding to the MLKL active site. Our studies indicate that an ATP-pocket inhibitor of the MLKL pseudokinase domain does not have any impact on the necroptosis pathway, which is contrary to a previously reported study.
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Affiliation(s)
- Bin Ma
- Drug Discovery, Biogen Inc., Cambridge, MA, 02142, United States of America
| | - Doug Marcotte
- Drug Discovery, Biogen Inc., Cambridge, MA, 02142, United States of America
| | | | - Klaus Michelsen
- Drug Discovery, Biogen Inc., Cambridge, MA, 02142, United States of America
| | - Ti Wang
- Drug Discovery, Biogen Inc., Cambridge, MA, 02142, United States of America
| | | | - John Howard Jones
- Drug Discovery, Biogen Inc., Cambridge, MA, 02142, United States of America
| | - Ben Moree
- Biodesy Inc., South San Francisco, CA, 94080, United States of America
| | - Margaret Butko
- Biodesy Inc., South San Francisco, CA, 94080, United States of America
| | - Joshua Salafsky
- Biodesy Inc., South San Francisco, CA, 94080, United States of America
| | - Xin Sun
- Drug Discovery, Biogen Inc., Cambridge, MA, 02142, United States of America
| | - Timothy McKee
- Drug Discovery, Biogen Inc., Cambridge, MA, 02142, United States of America
| | - Laura F. Silvian
- Drug Discovery, Biogen Inc., Cambridge, MA, 02142, United States of America
- * E-mail:
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174
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Roskoski R. Ibrutinib inhibition of Bruton protein-tyrosine kinase (BTK) in the treatment of B cell neoplasms. Pharmacol Res 2016; 113:395-408. [DOI: 10.1016/j.phrs.2016.09.011] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 09/12/2016] [Indexed: 12/12/2022]
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175
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Long MJC, Aye Y. The Die Is Cast: Precision Electrophilic Modifications Contribute to Cellular Decision Making. Chem Res Toxicol 2016; 29:1575-1582. [PMID: 27617777 PMCID: PMC5069682 DOI: 10.1021/acs.chemrestox.6b00261] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
![]()
This perspective sets out to critically
evaluate the scope of reactive
electrophilic small molecules as unique chemical signal carriers in
biological information transfer cascades. We consider these electrophilic
cues as a new volatile cellular currency and compare them to canonical
signaling circulation such as phosphate in terms of chemical properties,
biological specificity, sufficiency, and necessity. The fact that
nonenzymatic redox sensing properties are found in proteins undertaking
varied cellular tasks suggests that electrophile signaling is a moonlighting
phenomenon manifested within a privileged set of sensor proteins.
The latest interrogations into these on-target electrophilic responses
set forth a new horizon in the molecular mechanism of redox signal
propagation wherein direct low-occupancy electrophilic modifications
on a single sensor target are biologically sufficient to drive functional
redox responses with precision timing. We detail how the various mechanisms
through which redox signals function could contribute to their interesting
phenotypic responses, including hormesis.
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Affiliation(s)
- Marcus J C Long
- Department of Chemistry & Chemical Biology, Cornell University , 244 Baker Laboratory, Ithaca, New York 14850, United States
| | - Yimon Aye
- Department of Chemistry & Chemical Biology, Cornell University , 244 Baker Laboratory, Ithaca, New York 14850, United States.,Department of Biochemistry, Weill Cornell Medicine , 1300 York Avenue, New York, New York 10065, United States
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176
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Christmann-Franck S, van Westen GJP, Papadatos G, Beltran Escudie F, Roberts A, Overington JP, Domine D. Unprecedently Large-Scale Kinase Inhibitor Set Enabling the Accurate Prediction of Compound-Kinase Activities: A Way toward Selective Promiscuity by Design? J Chem Inf Model 2016; 56:1654-75. [PMID: 27482722 PMCID: PMC5039764 DOI: 10.1021/acs.jcim.6b00122] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Drug discovery programs frequently target members of the human kinome and try to identify small molecule protein kinase inhibitors, primarily for cancer treatment, additional indications being increasingly investigated. One of the challenges is controlling the inhibitors degree of selectivity, assessed by in vitro profiling against panels of protein kinases. We manually extracted, compiled, and standardized such profiles published in the literature: we collected 356 908 data points corresponding to 482 protein kinases, 2106 inhibitors, and 661 patents. We then analyzed this data set in terms of kinome coverage, results reproducibility, popularity, and degree of selectivity of both kinases and inhibitors. We used the data set to create robust proteochemometric models capable of predicting kinase activity (the ligand-target space was modeled with an externally validated RMSE of 0.41 ± 0.02 log units and R02 0.74 ± 0.03), in order to account for missing or unreliable measurements. The influence on the prediction quality of parameters such as number of measurements, Murcko scaffold frequency or inhibitor type was assessed. Interpretation of the models enabled to highlight inhibitors and kinases properties correlated with higher affinities, and an analysis in the context of kinases crystal structures was performed. Overall, the models quality allows the accurate prediction of kinase-inhibitor activities and their structural interpretation, thus paving the way for the rational design of compounds with a targeted selectivity profile.
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Affiliation(s)
| | - Gerard J P van Westen
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus , Hinxton, Cambridgeshire CB10 1SD, U.K
| | - George Papadatos
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus , Hinxton, Cambridgeshire CB10 1SD, U.K
| | | | | | - John P Overington
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus , Hinxton, Cambridgeshire CB10 1SD, U.K
| | - Daniel Domine
- Merck Serono , Chemin des Mines 9, 1202 Genève, Switzerland
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177
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El-Ansary AK, Kamal AM, Al-Ghorafi MAH. Design, Synthesis and Biological Evaluation of Some 5-Arylthieno[2,3-d]pyrimidines as Potential Anti-cancer Agents. Chem Pharm Bull (Tokyo) 2016; 64:1172-80. [PMID: 27477657 DOI: 10.1248/cpb.c16-00291] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Structure-based design, synthesis and biological evaluation of new small molecules anti-cancer agents were described. On continuation of applying scaffold hopping theory, a series of 5-arylthieno[2,3-d]pyrimidines based on the structural features of lapatinib was designed, synthesized and characterized using IR, (1)H-NMR, (13)C-NMR, mass and microanalyses. Biological evaluation of the cytotoxic activity against MCF-7 cell line and the inhibition of the enzymatic activity of epidermal growth factor tyrosine kinase were carried out in vitro for the target compounds. Substituting the 4-anilino-5-arylthieno[2,3-d]pyrimidines with different pharmacophoric groups at ortho, meta and/or para positions led to discovery of two potent lead compounds 3b and f with excellent cytotoxic activity and enzymatic inhibition activity.
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Affiliation(s)
- Afaf Kamal El-Ansary
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University
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178
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Abstract
Chromatin is the universal template of genetic information in all eukaryotic organisms. Chemical modifications of the DNA-packaging histone proteins and the DNA bases are crucial signaling events in directing the use and readout of eukaryotic genomes. The enzymes that install and remove these chromatin modifications as well as the proteins that bind these marks govern information that goes beyond the sequence of DNA. Therefore, these so-called epigenetic regulators are intensively studied and represent promising drug targets in modern medicine. We summarize and discuss recent advances in the field of chemical biology that have provided chromatin research with sophisticated tools for investigating the composition, activity, and target sites of chromatin modifying enzymes and reader proteins.
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Affiliation(s)
- Wolfgang Fischle
- King Abdullah University of Science and Technology (KAUST), Environmental Epigenetics Program, Thuwal 23955-6900, Saudi Arabia
- Max Planck Institute for Biophysical Chemistry, Laboratory of Chromatin Biochemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Dirk Schwarzer
- Interfaculty
Institute of Biochemistry (IFIB), University of Tübingen, Hoppe-Seyler-Str.
4, 72076 Tübingen, Germany
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179
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Yuan H, Marmorstein R. Histone acetyltransferases: Rising ancient counterparts to protein kinases. Biopolymers 2016; 99:98-111. [PMID: 23175385 DOI: 10.1002/bip.22128] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 07/01/2012] [Accepted: 07/06/2012] [Indexed: 01/19/2023]
Abstract
Protein kinases catalyze phosphorylation, a posttranslational modification widely utilized in cell signaling. Histone acetyltransferases (HATs) catalyze a counterpart posttranslational modification of acetylation which marks histones for epigenetic signaling but in some cases modifies non-histone proteins to mediate other cellular activities. In addition, recent proteomic studies have revealed that thousands of proteins are acetylated throughout the cell to regulate diverse biological processes, thus placing acetyltransferases on the same playing field as kinases. Emerging biochemical and structural data further supports mechanistic and biological links between the two enzyme families. In this article, we will review what is known to date about the structure, catalysis and mode of regulation of HAT enzymes and draw analogies, where relevant, to protein kinases. This comparison reveals that HATs may be rising ancient counterparts to protein kinases.
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Affiliation(s)
- Hua Yuan
- Program in Gene Expression and Regulation, The Wistar Institute, Philadelphia, PA 19104
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180
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Zhan T, Cao C, Li L, Gu N, Civin CI, Zhan X. MIM regulates the trafficking of bone marrow cells via modulating surface expression of CXCR4. Leukemia 2016; 30:1327-34. [PMID: 26965284 PMCID: PMC4889520 DOI: 10.1038/leu.2016.39] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 10/15/2015] [Accepted: 02/15/2016] [Indexed: 12/21/2022]
Abstract
Missing in metastasis (MIM) is abundantly expressed in hematopoietic cells. Here we characterized the impact of MIM deficiency on murine bone marrow (BM) cells. Although MIM-/- cells proliferated similarly to wild type (WT), they exhibited stronger response to chemokine SDF-1, increase in surface expression of CXCR4, impaired CXCR4 internalization and constitutive activation of Rac, Cdc42 and p38. Transplantation of MIM-/- BM cells into lethally irradiated mice showed enhanced homing to BM, which was abolished when mice were pretreated with a p38 antagonist. Interestingly, MIM-/- BM cells, including hematopoietic stem and progenitor cells (HSPCs), showed 2 to 5-fold increase in mobilization into the peripheral blood upon treatment with AMD3100. In vitro, MIM-/- leukocytes were susceptible to AMD3100 and maintained increased response to AMD3100 for mobilization even after transfer into wild type mice. MIM-/- mice had also a higher level of SDF-1 in the circulation. Our data highlighted an unprecedented role of MIM in the homoeostasis of BM cells, including HSPCs, through modulation of the CXCR4/SDF-1 axis and interactions of BM leukocytes with their microenvironments.
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Affiliation(s)
- T Zhan
- Department of Pathology, Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, USA
| | - C Cao
- Department of Pathology, Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, USA.,Department of Physiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - L Li
- Department of Pathology, Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, USA.,China Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, China
| | - N Gu
- China Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, China
| | - C I Civin
- Department of Pediatrics, Center for Stem Cell Biology and Regenerative Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.,Departments of Pediatrics and Physiology, Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - X Zhan
- Department of Pathology, Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, USA.,Departments of Pediatrics and Physiology, Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA.,Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA
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181
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Design strategies, structure activity relationship and mechanistic insights for purines as kinase inhibitors. Eur J Med Chem 2016; 112:298-346. [PMID: 26907156 DOI: 10.1016/j.ejmech.2016.02.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Revised: 02/04/2016] [Accepted: 02/05/2016] [Indexed: 12/22/2022]
Abstract
Kinases control a diverse set of cellular processes comprising of reversible phosphorylation of proteins. Protein kinases play a pivotal role in human tumor cell proliferation, migration and survival of neoplasia. In the recent past, purine based molecules have emerged as significantly potent kinase inhibitors. In view of their promising potential for the inhibition of kinases, this review article focuses on purines which have progressed as kinase inhibitors during the last five years. A detailed account of the design strategies employed for the synthesis of purine analogs exerting inhibitory effects on diverse kinases has been presented. Apart from presenting the design strategies, the article also highlights the structure activity relationship along with mechanistic insights revealed during the biological evaluation of the purine analogs for kinase inhibition. The interactions with the amino acid residues responsible for kinase inhibitory potential of purine based molecules have also been discussed. In this assemblage, purine based protein kinase inhibitors patented in the past have also been summarized in the tabular form. This compilation will be of great interest for the researchers working in the area of protein kinase inhibitors.
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182
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Kim J, Li G, Walters MA, Taylor SS, Veglia G. Uncoupling Catalytic and Binding Functions in the Cyclic AMP-Dependent Protein Kinase A. Structure 2016; 24:353-63. [PMID: 26833386 DOI: 10.1016/j.str.2015.11.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/12/2015] [Accepted: 11/13/2015] [Indexed: 01/07/2023]
Abstract
The canonical function of kinases is to transfer a phosphoryl group to substrates, initiating a signaling cascade; while their non-canonical role is to bind other kinases or substrates, acting as scaffolds, competitors, and signal integrators. Here, we show how to uncouple kinases' dual function by tuning the binding cooperativity between nucleotide (or inhibitors) and substrate allosterically. We demonstrate this new concept for the C subunit of protein kinase A (PKA-C). Using thermocalorimetry and nuclear magnetic resonance, we found a linear correlation between the degree of cooperativity and the population of the closed state of PKA-C. The non-hydrolyzable ATP analog (ATPγC) does not follow this correlation, suggesting that changing the chemical groups around the phosphoester bond can uncouple kinases' dual function. Remarkably, this uncoupling was also found for two ATP-competitive inhibitors, H89 and balanol. Since the mechanism for allosteric cooperativity is not conserved in different kinases, these results may suggest new approaches for designing selective kinase inhibitors.
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Affiliation(s)
- Jonggul Kim
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Geoffrey Li
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Michael A Walters
- Department of Medicinal Chemistry, Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Susan S Taylor
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
| | - Gianluigi Veglia
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
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183
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Mehdizadeh A, Somi MH, Darabi M, Jabbarpour-Bonyadi M. Extracellular signal-regulated kinase 1 and 2 in cancer therapy: a focus on hepatocellular carcinoma. Mol Biol Rep 2016; 43:107-16. [DOI: 10.1007/s11033-016-3943-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 01/05/2016] [Indexed: 12/30/2022]
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184
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Mondolfi AP, Singh RR. Genotyping of Frequent Mutations in Solid Tumors by PCR-Based Single-Base Extension and MassARRAY Analysis. Methods Mol Biol 2016; 1392:83-101. [PMID: 26843049 DOI: 10.1007/978-1-4939-3360-0_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Over the last decade, cancer genome sequencing has revealed in detail the genomic landscapes of an increasing number of common solid human tumors. This has greatly impacted the clinical care of cancer patients based on the fact that many of these tumors exhibit activating mutations in driver genes that are prone to target therapy, largely impacting cancer management strategies. Genomic heterogeneity of tumors is becoming an increasingly recognized phenomenon relevant to genome-based medicine. Because a large number tumors may display several mutations at the same time, multiplexing has become the preferred approach to reveal the mutational landscape in patient samples and to better design a targeted approach to their illness.
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Affiliation(s)
- Alberto Paniz Mondolfi
- Microbiology Laboratory, Department of Laboratory Medicine,Yale New Haven Hospital, Yale University School of Medicine, New Haven, CT, USA.
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 8515 Fannin Street, Houston, TX, 77054, USA.
| | - Rajesh R Singh
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 8515 Fannin Street, Houston, TX, 77054, USA.
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185
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Verkhivker GM. Molecular dynamics simulations and modelling of the residue interaction networks in the BRAF kinase complexes with small molecule inhibitors: probing the allosteric effects of ligand-induced kinase dimerization and paradoxical activation. MOLECULAR BIOSYSTEMS 2016; 12:3146-65. [DOI: 10.1039/c6mb00298f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The computational analysis of residue interaction networks dissects the allosteric effects of inhibitor-induced BRAF kinase dimerization and paradoxical activation.
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Affiliation(s)
- G. M. Verkhivker
- Graduate Program in Computational and Data Sciences
- Department of Computational Sciences
- Schmid College of Science and Technology
- Chapman University
- Orange
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186
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Hammarén HM, Virtanen AT, Silvennoinen O. Nucleotide-binding mechanisms in pseudokinases. Biosci Rep 2015; 36:e00282. [PMID: 26589967 PMCID: PMC4718504 DOI: 10.1042/bsr20150226] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 11/11/2015] [Accepted: 11/20/2015] [Indexed: 01/01/2023] Open
Abstract
Pseudokinases are classified by the lack of one or several of the highly conserved motifs involved in nucleotide (nt) binding or catalytic activity of protein kinases (PKs). Pseudokinases represent ∼10% of the human kinome and they are found in all evolutionary classes of kinases. It has become evident that pseudokinases, which were initially considered somewhat peculiar dead kinases, are important components in several signalling cascades. Furthermore, several pseudokinases have been linked to human diseases, particularly cancer, which is raising interest for therapeutic approaches towards these proteins. The ATP-binding pocket is a well-established drug target and elucidation of the mechanism and properties of nt binding in pseudokinases is of significant interest and importance. Recent studies have demonstrated that members of the pseudokinase family are very diverse in structure as well as in their ability and mechanism to bind nts or perform phosphoryl transfer reactions. This diversity also precludes prediction of pseudokinase function, or the importance of nt binding for said function, based on primary sequence alone. Currently available data indicate that ∼40% of pseudokinases are able to bind nts, whereas only few are able to catalyse occasional phosphoryl transfer. Pseudokinases employ diverse mechanisms to bind nts, which usually occurs at low, but physiological, affinity. ATP binding serves often a structural role but in most cases the functional roles are not precisely known. In the present review, we discuss the various mechanisms that pseudokinases employ for nt binding and how this often low-affinity binding can be accurately analysed.
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Affiliation(s)
- Henrik M Hammarén
- School of Medicine, University of Tampere, Biokatu 8, FI-33014 Tampere, Finland
| | - Anniina T Virtanen
- School of Medicine, University of Tampere, Biokatu 8, FI-33014 Tampere, Finland
| | - Olli Silvennoinen
- School of Medicine, University of Tampere, Biokatu 8, FI-33014 Tampere, Finland Clinical Hematology, Department of Internal Medicine, Tampere University Hospital, Medisiinarinkatu 3, FI-33520 Tampere, Finland
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187
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Roskoski R. Classification of small molecule protein kinase inhibitors based upon the structures of their drug-enzyme complexes. Pharmacol Res 2015; 103:26-48. [PMID: 26529477 DOI: 10.1016/j.phrs.2015.10.021] [Citation(s) in RCA: 520] [Impact Index Per Article: 57.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Revised: 10/26/2015] [Accepted: 10/27/2015] [Indexed: 01/04/2023]
Abstract
Because dysregulation and mutations of protein kinases play causal roles in human disease, this family of enzymes has become one of the most important drug targets over the past two decades. The X-ray crystal structures of 21 of the 27 FDA-approved small molecule inhibitors bound to their target protein kinases are depicted in this paper. The structure of the enzyme-bound antagonist complex is used in the classification of these inhibitors. Type I inhibitors bind to the active protein kinase conformation (DFG-Asp in, αC-helix in). Type I½ inhibitors bind to a DFG-Asp in inactive conformation while Type II inhibitors bind to a DFG-Asp out inactive conformation. Type I, I½, and type II inhibitors occupy part of the adenine binding pocket and form hydrogen bonds with the hinge region connecting the small and large lobes of the enzyme. Type III inhibitors bind next to the ATP-binding pocket and type IV inhibitors do not bind to the ATP or peptide substrate binding sites. Type III and IV inhibitors are allosteric in nature. Type V inhibitors bind to two different regions of the protein kinase domain and are therefore bivalent inhibitors. The type I-V inhibitors are reversible. In contrast, type VI inhibitors bind covalently to their target enzyme. Type I, I½, and II inhibitors are divided into A and B subtypes. The type A inhibitors bind in the front cleft, the back cleft, and near the gatekeeper residue, all of which occur within the region separating the small and large lobes of the protein kinase. The type B inhibitors bind in the front cleft and gate area but do not extend into the back cleft. An analysis of the limited available data indicates that type A inhibitors have a long residence time (minutes to hours) while the type B inhibitors have a short residence time (seconds to minutes). The catalytic spine includes residues from the small and large lobes and interacts with the adenine ring of ATP. Nearly all of the approved protein kinase inhibitors occupy the adenine-binding pocket; thus it is not surprising that these inhibitors interact with nearby catalytic spine (CS) residues. Moreover, a significant number of approved drugs also interact with regulatory spine (RS) residues.
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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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188
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Concha NO, Smallwood A, Bonnette W, Totoritis R, Zhang G, Federowicz K, Yang J, Qi H, Chen S, Campobasso N, Choudhry AE, Shuster LE, Evans KA, Ralph J, Sweitzer S, Heerding DA, Buser CA, Su DS, DeYoung MP. Long-Range Inhibitor-Induced Conformational Regulation of Human IRE1α Endoribonuclease Activity. Mol Pharmacol 2015; 88:1011-23. [PMID: 26438213 DOI: 10.1124/mol.115.100917] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 09/25/2015] [Indexed: 12/21/2022] Open
Abstract
Activation of the inositol-requiring enzyme-1 alpha (IRE1α) protein caused by endoplasmic reticulum stress results in the homodimerization of the N-terminal endoplasmic reticulum luminal domains, autophosphorylation of the cytoplasmic kinase domains, and conformational changes to the cytoplasmic endoribonuclease (RNase) domains, which render them functional and can lead to the splicing of X-box binding protein 1 (XBP 1) mRNA. Herein, we report the first crystal structures of the cytoplasmic portion of a human phosphorylated IRE1α dimer in complex with (R)-2-(3,4-dichlorobenzyl)-N-(4-methylbenzyl)-2,7-diazaspiro(4.5)decane-7-carboxamide, a novel, IRE1α-selective kinase inhibitor, and staurosporine, a broad spectrum kinase inhibitor. (R)-2-(3,4-dichlorobenzyl)-N-(4-methylbenzyl)-2,7-diazaspiro(4.5)decane-7-carboxamide inhibits both the kinase and RNase activities of IRE1α. The inhibitor interacts with the catalytic residues Lys599 and Glu612 and displaces the kinase activation loop to the DFG-out conformation. Inactivation of IRE1α RNase activity appears to be caused by a conformational change, whereby the αC helix is displaced, resulting in the rearrangement of the kinase domain-dimer interface and a rotation of the RNase domains away from each other. In contrast, staurosporine binds at the ATP-binding site of IRE1α, resulting in a dimer consistent with RNase active yeast Ire1 dimers. Activation of IRE1α RNase activity appears to be promoted by a network of hydrogen bond interactions between highly conserved residues across the RNase dimer interface that place key catalytic residues poised for reaction. These data implicate that the intermolecular interactions between conserved residues in the RNase domain are required for activity, and that the disruption of these interactions can be achieved pharmacologically by small molecule kinase domain inhibitors.
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Affiliation(s)
- Nestor O Concha
- Oncology R&D (K.F., J.Y., L.E.S., K.A.E., J.R., D.A.H., C.A.B., D.S.S, M.P.D.), Biological Sciences (R.T., G.Z., H.Q., S.C., A.E.C., S.S.), and Chemical Sciences, GlaxoSmithKline Research and Development, Collegeville, Pennsylvania (N.O.C., A.S., W.B., N.C.)
| | - Angela Smallwood
- Oncology R&D (K.F., J.Y., L.E.S., K.A.E., J.R., D.A.H., C.A.B., D.S.S, M.P.D.), Biological Sciences (R.T., G.Z., H.Q., S.C., A.E.C., S.S.), and Chemical Sciences, GlaxoSmithKline Research and Development, Collegeville, Pennsylvania (N.O.C., A.S., W.B., N.C.)
| | - William Bonnette
- Oncology R&D (K.F., J.Y., L.E.S., K.A.E., J.R., D.A.H., C.A.B., D.S.S, M.P.D.), Biological Sciences (R.T., G.Z., H.Q., S.C., A.E.C., S.S.), and Chemical Sciences, GlaxoSmithKline Research and Development, Collegeville, Pennsylvania (N.O.C., A.S., W.B., N.C.)
| | - Rachel Totoritis
- Oncology R&D (K.F., J.Y., L.E.S., K.A.E., J.R., D.A.H., C.A.B., D.S.S, M.P.D.), Biological Sciences (R.T., G.Z., H.Q., S.C., A.E.C., S.S.), and Chemical Sciences, GlaxoSmithKline Research and Development, Collegeville, Pennsylvania (N.O.C., A.S., W.B., N.C.)
| | - Guofeng Zhang
- Oncology R&D (K.F., J.Y., L.E.S., K.A.E., J.R., D.A.H., C.A.B., D.S.S, M.P.D.), Biological Sciences (R.T., G.Z., H.Q., S.C., A.E.C., S.S.), and Chemical Sciences, GlaxoSmithKline Research and Development, Collegeville, Pennsylvania (N.O.C., A.S., W.B., N.C.)
| | - Kelly Federowicz
- Oncology R&D (K.F., J.Y., L.E.S., K.A.E., J.R., D.A.H., C.A.B., D.S.S, M.P.D.), Biological Sciences (R.T., G.Z., H.Q., S.C., A.E.C., S.S.), and Chemical Sciences, GlaxoSmithKline Research and Development, Collegeville, Pennsylvania (N.O.C., A.S., W.B., N.C.)
| | - Jingsong Yang
- Oncology R&D (K.F., J.Y., L.E.S., K.A.E., J.R., D.A.H., C.A.B., D.S.S, M.P.D.), Biological Sciences (R.T., G.Z., H.Q., S.C., A.E.C., S.S.), and Chemical Sciences, GlaxoSmithKline Research and Development, Collegeville, Pennsylvania (N.O.C., A.S., W.B., N.C.)
| | - Hongwei Qi
- Oncology R&D (K.F., J.Y., L.E.S., K.A.E., J.R., D.A.H., C.A.B., D.S.S, M.P.D.), Biological Sciences (R.T., G.Z., H.Q., S.C., A.E.C., S.S.), and Chemical Sciences, GlaxoSmithKline Research and Development, Collegeville, Pennsylvania (N.O.C., A.S., W.B., N.C.)
| | - Stephanie Chen
- Oncology R&D (K.F., J.Y., L.E.S., K.A.E., J.R., D.A.H., C.A.B., D.S.S, M.P.D.), Biological Sciences (R.T., G.Z., H.Q., S.C., A.E.C., S.S.), and Chemical Sciences, GlaxoSmithKline Research and Development, Collegeville, Pennsylvania (N.O.C., A.S., W.B., N.C.)
| | - Nino Campobasso
- Oncology R&D (K.F., J.Y., L.E.S., K.A.E., J.R., D.A.H., C.A.B., D.S.S, M.P.D.), Biological Sciences (R.T., G.Z., H.Q., S.C., A.E.C., S.S.), and Chemical Sciences, GlaxoSmithKline Research and Development, Collegeville, Pennsylvania (N.O.C., A.S., W.B., N.C.)
| | - Anthony E Choudhry
- Oncology R&D (K.F., J.Y., L.E.S., K.A.E., J.R., D.A.H., C.A.B., D.S.S, M.P.D.), Biological Sciences (R.T., G.Z., H.Q., S.C., A.E.C., S.S.), and Chemical Sciences, GlaxoSmithKline Research and Development, Collegeville, Pennsylvania (N.O.C., A.S., W.B., N.C.)
| | - Leanna E Shuster
- Oncology R&D (K.F., J.Y., L.E.S., K.A.E., J.R., D.A.H., C.A.B., D.S.S, M.P.D.), Biological Sciences (R.T., G.Z., H.Q., S.C., A.E.C., S.S.), and Chemical Sciences, GlaxoSmithKline Research and Development, Collegeville, Pennsylvania (N.O.C., A.S., W.B., N.C.)
| | - Karen A Evans
- Oncology R&D (K.F., J.Y., L.E.S., K.A.E., J.R., D.A.H., C.A.B., D.S.S, M.P.D.), Biological Sciences (R.T., G.Z., H.Q., S.C., A.E.C., S.S.), and Chemical Sciences, GlaxoSmithKline Research and Development, Collegeville, Pennsylvania (N.O.C., A.S., W.B., N.C.)
| | - Jeff Ralph
- Oncology R&D (K.F., J.Y., L.E.S., K.A.E., J.R., D.A.H., C.A.B., D.S.S, M.P.D.), Biological Sciences (R.T., G.Z., H.Q., S.C., A.E.C., S.S.), and Chemical Sciences, GlaxoSmithKline Research and Development, Collegeville, Pennsylvania (N.O.C., A.S., W.B., N.C.)
| | - Sharon Sweitzer
- Oncology R&D (K.F., J.Y., L.E.S., K.A.E., J.R., D.A.H., C.A.B., D.S.S, M.P.D.), Biological Sciences (R.T., G.Z., H.Q., S.C., A.E.C., S.S.), and Chemical Sciences, GlaxoSmithKline Research and Development, Collegeville, Pennsylvania (N.O.C., A.S., W.B., N.C.)
| | - Dirk A Heerding
- Oncology R&D (K.F., J.Y., L.E.S., K.A.E., J.R., D.A.H., C.A.B., D.S.S, M.P.D.), Biological Sciences (R.T., G.Z., H.Q., S.C., A.E.C., S.S.), and Chemical Sciences, GlaxoSmithKline Research and Development, Collegeville, Pennsylvania (N.O.C., A.S., W.B., N.C.)
| | - Carolyn A Buser
- Oncology R&D (K.F., J.Y., L.E.S., K.A.E., J.R., D.A.H., C.A.B., D.S.S, M.P.D.), Biological Sciences (R.T., G.Z., H.Q., S.C., A.E.C., S.S.), and Chemical Sciences, GlaxoSmithKline Research and Development, Collegeville, Pennsylvania (N.O.C., A.S., W.B., N.C.)
| | - Dai-Shi Su
- Oncology R&D (K.F., J.Y., L.E.S., K.A.E., J.R., D.A.H., C.A.B., D.S.S, M.P.D.), Biological Sciences (R.T., G.Z., H.Q., S.C., A.E.C., S.S.), and Chemical Sciences, GlaxoSmithKline Research and Development, Collegeville, Pennsylvania (N.O.C., A.S., W.B., N.C.)
| | - M Phillip DeYoung
- Oncology R&D (K.F., J.Y., L.E.S., K.A.E., J.R., D.A.H., C.A.B., D.S.S, M.P.D.), Biological Sciences (R.T., G.Z., H.Q., S.C., A.E.C., S.S.), and Chemical Sciences, GlaxoSmithKline Research and Development, Collegeville, Pennsylvania (N.O.C., A.S., W.B., N.C.)
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190
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Horbert R, Pinchuk B, Davies P, Alessi D, Peifer C. Photoactivatable Prodrugs of Antimelanoma Agent Vemurafenib. ACS Chem Biol 2015; 10:2099-107. [PMID: 26061392 DOI: 10.1021/acschembio.5b00174] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this study, we report on novel photoactivatable caged prodrugs of vemurafenib. This kinase inhibitor was the first approved drug for the personalized treatment of BRAF-mutated melanoma and showed impressive results in clinical studies. However, the occurrence of severe side effects and drug resistance illustrates the urgent need for innovative therapeutic approaches. To conquer these limitations, we implemented photoremovable protecting groups into vemurafenib. In general, this caging concept provides spatial and temporal control over the activation of molecules triggered by ultraviolet light. Thus, higher inhibitor concentrations in tumor tissues might be reached with less systemic effects. Our study describes the first development of caged vemurafenib prodrugs useful as pharmacological tools. We investigated their photochemical characteristics and photoactivation. In vitro evaluation proved the intended loss-of-function and the light-dependent recovery of efficacy in kinase and cellular assays. The reported vemurafenib photo prodrugs represent a powerful biological tool for novel pharmacological approaches in cancer research.
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Affiliation(s)
- Rebecca Horbert
- Pharmaceutical
Chemistry, Christian Albrechts University, Gutenbergstraße 76, 24118 Kiel, Germany
| | - Boris Pinchuk
- Pharmaceutical
Chemistry, Christian Albrechts University, Gutenbergstraße 76, 24118 Kiel, Germany
| | - Paul Davies
- MRC
Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, U.K
| | - Dario Alessi
- MRC
Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, U.K
| | - Christian Peifer
- Pharmaceutical
Chemistry, Christian Albrechts University, Gutenbergstraße 76, 24118 Kiel, Germany
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191
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Anscombe E, Meschini E, Mora-Vidal R, Martin MP, Staunton D, Geitmann M, Danielson UH, Stanley WA, Wang LZ, Reuillon T, Golding BT, Cano C, Newell DR, Noble MEM, Wedge SR, Endicott JA, Griffin RJ. Identification and Characterization of an Irreversible Inhibitor of CDK2. CHEMISTRY & BIOLOGY 2015; 22:1159-64. [PMID: 26320860 PMCID: PMC4579270 DOI: 10.1016/j.chembiol.2015.07.018] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 07/02/2015] [Accepted: 07/24/2015] [Indexed: 01/04/2023]
Abstract
Irreversible inhibitors that modify cysteine or lysine residues within a protein kinase ATP binding site offer, through their distinctive mode of action, an alternative to ATP-competitive agents. 4-((6-(Cyclohexylmethoxy)-9H-purin-2-yl)amino)benzenesulfonamide (NU6102) is a potent and selective ATP-competitive inhibitor of CDK2 in which the sulfonamide moiety is positioned close to a pair of lysine residues. Guided by the CDK2/NU6102 structure, we designed 6-(cyclohexylmethoxy)-N-(4-(vinylsulfonyl)phenyl)-9H-purin-2-amine (NU6300), which binds covalently to CDK2 as shown by a co-complex crystal structure. Acute incubation with NU6300 produced a durable inhibition of Rb phosphorylation in SKUT-1B cells, consistent with it acting as an irreversible CDK2 inhibitor. NU6300 is the first covalent CDK2 inhibitor to be described, and illustrates the potential of vinyl sulfones for the design of more potent and selective compounds.
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Affiliation(s)
- Elizabeth Anscombe
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Elisa Meschini
- Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Regina Mora-Vidal
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Mathew P Martin
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - David Staunton
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | | | - U Helena Danielson
- Beactica AB, Box 567, 751 22 Uppsala, Sweden; Department of Chemistry-BMC, Uppsala University, 751 23 Uppsala, Sweden
| | - Will A Stanley
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Lan Z Wang
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Tristan Reuillon
- Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Bernard T Golding
- Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
| | - Celine Cano
- Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - David R Newell
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Martin E M Noble
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Stephen R Wedge
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Jane A Endicott
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| | - Roger J Griffin
- Newcastle Cancer Centre, Northern Institute for Cancer Research, School of Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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192
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Wang Q, Zorn JA, Kuriyan J. A structural atlas of kinases inhibited by clinically approved drugs. Methods Enzymol 2015; 548:23-67. [PMID: 25399641 DOI: 10.1016/b978-0-12-397918-6.00002-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The aberrant activation of protein kinases is associated with many human diseases, most notably cancer. Due to this link between kinase deregulation and disease progression, kinases are one of the most targeted protein families for small-molecule inhibition. Within the last 15 years, the U.S. Food and Drug Administration has approved over 20 small-molecule inhibitors of protein kinases for use in the clinic. These inhibitors target the kinase active site and represent the successful hurdling by medicinal chemists of the formidable challenge posed by the high similarity among the active sites of the approximately 500 human kinases. We review the conserved structural features of kinases that are important for inhibitor binding as well as for catalysis. Many clinically approved drugs elicit selectivity by exploiting subtle variation within the kinase active site. We highlight some of the crystallographic studies on the kinase-inhibitor complexes that have provided valuable guidance for the development of these drugs as well as for future drug design efforts.
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Affiliation(s)
- Qi Wang
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, California, USA
| | - Julie A Zorn
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, California, USA
| | - John Kuriyan
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, California, USA; Howard Hughes Medical Institute, University of California, Berkeley, California, USA; Department of Chemistry, University of California, Berkeley, California, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
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193
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New spleen tyrosine kinase inhibitors: patent applications published during 2011-2013. Pharm Pat Anal 2015; 3:523-41. [PMID: 25374321 DOI: 10.4155/ppa.14.34] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Spleen tyrosine kinase (SYK) is one of the more advanced small-molecule targets with regard to clinical development for treatment of inflammatory diseases. In this review we continue our analysis of the patent literature covering the time period 2011-2013. The analysis relates to any organization that has filed applications that explicitly discloses SYK as the intended target. In the last 2 years there has been a surge of application with a few new entries in a crowded field with the structural theme of compounds in these applications being a traditional type I ATP competitive inhibitor [ 1 ]. This overview of the SYK patent literature and the learning's of the inhibitors substitution patterns would be an important reading for anyone working in the area of SYK inhibitors.
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194
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Murray JI, Woscholski R, Spivey AC. Highly efficient and selective phosphorylation of amino acid derivatives and polyols catalysed by 2-aryl-4-(dimethylamino)pyridine-N-oxides--towards kinase-like reactivity. Chem Commun (Camb) 2015; 50:13608-11. [PMID: 25248055 DOI: 10.1039/c4cc05388e] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The chemoselective phosphorylation of hydroxyl containing amino acid derivatives and polyols by phosphoryl chlorides catalyzed by 2-aryl-4-(dimethylamino)pyridine-N-oxides is described.
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Affiliation(s)
- James I Murray
- Department of Chemistry, South Kensington Campus, Imperial College London, SW7 2AZ, UK.
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195
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Hsu KC, Sung TY, Lin CT, Chiu YY, Hsu JTA, Hung HC, Sun CM, Barve I, Chen WL, Huang WC, Huang CT, Chen CH, Yang JM. Anchor-based classification and type-C inhibitors for tyrosine kinases. Sci Rep 2015; 5:10938. [PMID: 26077136 PMCID: PMC4468516 DOI: 10.1038/srep10938] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 05/08/2015] [Indexed: 12/13/2022] Open
Abstract
Tyrosine kinases regulate various biological processes and are drug targets for cancers. At present, the design of selective and anti-resistant inhibitors of kinases is an emergent task. Here, we inferred specific site-moiety maps containing two specific anchors to uncover a new binding pocket in the C-terminal hinge region by docking 4,680 kinase inhibitors into 51 protein kinases, and this finding provides an opportunity for the development of kinase inhibitors with high selectivity and anti-drug resistance. We present an anchor-based classification for tyrosine kinases and discover two type-C inhibitors, namely rosmarinic acid (RA) and EGCG, which occupy two and one specific anchors, respectively, by screening 118,759 natural compounds. Our profiling reveals that RA and EGCG selectively inhibit 3% (EGFR and SYK) and 14% of 64 kinases, respectively. According to the guide of our anchor model, we synthesized three RA derivatives with better potency. These type-C inhibitors are able to maintain activities for drug-resistant EGFR and decrease the invasion ability of breast cancer cells. Our results show that the type-C inhibitors occupying a new pocket are promising for cancer treatments due to their kinase selectivity and anti-drug resistance.
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Affiliation(s)
- Kai-Cheng Hsu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Tzu-Ying Sung
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Chih-Ta Lin
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Yi-Yuan Chiu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - John T-A Hsu
- 1] Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan [2] Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, Taiwan
| | - Hui-Chen Hung
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, Taiwan
| | - Chung-Ming Sun
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu, Taiwan
| | - Indrajeet Barve
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu, Taiwan
| | - Wen-Liang Chen
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | - Wen-Chien Huang
- Department of Thoracic Surgery, Mackay Memorial Hospital, Taipei City, Taiwan
| | - Chin-Ting Huang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, Taiwan
| | - Chun-Hwa Chen
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, Taiwan
| | - Jinn-Moon Yang
- 1] Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan [2] Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
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196
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Zindler M, Pinchuk B, Renn C, Horbert R, Döbber A, Peifer C. Design, Synthesis, and Characterization of a Photoactivatable Caged Prodrug of Imatinib. ChemMedChem 2015; 10:1335-8. [DOI: 10.1002/cmdc.201500163] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Indexed: 12/26/2022]
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197
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Tse A, Verkhivker GM. Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution. PLoS One 2015; 10:e0130203. [PMID: 26075886 PMCID: PMC4468085 DOI: 10.1371/journal.pone.0130203] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/17/2015] [Indexed: 12/20/2022] Open
Abstract
Quantifying binding specificity and drug resistance of protein kinase inhibitors is of fundamental importance and remains highly challenging due to complex interplay of structural and thermodynamic factors. In this work, molecular simulations and computational alanine scanning are combined with the network-based approaches to characterize molecular determinants underlying binding specificities of the ABL kinase inhibitors. The proposed theoretical framework unveiled a relationship between ligand binding and inhibitor-mediated changes in the residue interaction networks. By using topological parameters, we have described the organization of the residue interaction networks and networks of coevolving residues in the ABL kinase structures. This analysis has shown that functionally critical regulatory residues can simultaneously embody strong coevolutionary signal and high network centrality with a propensity to be energetic hot spots for drug binding. We have found that selective (Nilotinib) and promiscuous (Bosutinib, Dasatinib) kinase inhibitors can use their energetic hot spots to differentially modulate stability of the residue interaction networks, thus inhibiting or promoting conformational equilibrium between inactive and active states. According to our results, Nilotinib binding may induce a significant network-bridging effect and enhance centrality of the hot spot residues that stabilize structural environment favored by the specific kinase form. In contrast, Bosutinib and Dasatinib can incur modest changes in the residue interaction network in which ligand binding is primarily coupled only with the identity of the gate-keeper residue. These factors may promote structural adaptability of the active kinase states in binding with these promiscuous inhibitors. Our results have related ligand-induced changes in the residue interaction networks with drug resistance effects, showing that network robustness may be compromised by targeted mutations of key mediating residues. This study has outlined mechanisms by which inhibitor binding could modulate resilience and efficiency of allosteric interactions in the kinase structures, while preserving structural topology required for catalytic activity and regulation.
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Affiliation(s)
- Amanda Tse
- Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Gennady M. Verkhivker
- Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
- Chapman University School of Pharmacy, Irvine, California, United States of America
- * E-mail:
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198
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Mendez AS, Alfaro J, Morales-Soto MA, Dar AC, McCullagh E, Gotthardt K, Li H, Acosta-Alvear D, Sidrauski C, Korennykh AV, Bernales S, Shokat KM, Walter P. Endoplasmic reticulum stress-independent activation of unfolded protein response kinases by a small molecule ATP-mimic. eLife 2015; 4. [PMID: 25986605 PMCID: PMC4436593 DOI: 10.7554/elife.05434] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 03/25/2015] [Indexed: 12/21/2022] Open
Abstract
Two ER membrane-resident transmembrane kinases, IRE1 and PERK, function as stress sensors in the unfolded protein response. IRE1 also has an endoribonuclease activity, which initiates a non-conventional mRNA splicing reaction, while PERK phosphorylates eIF2α. We engineered a potent small molecule, IPA, that binds to IRE1's ATP-binding pocket and predisposes the kinase domain to oligomerization, activating its RNase. IPA also inhibits PERK but, paradoxically, activates it at low concentrations, resulting in a bell-shaped activation profile. We reconstituted IPA-activation of PERK-mediated eIF2α phosphorylation from purified components. We estimate that under conditions of maximal activation less than 15% of PERK molecules in the reaction are occupied by IPA. We propose that IPA binding biases the PERK kinase towards its active conformation, which trans-activates apo-PERK molecules. The mechanism by which partial occupancy with an inhibitor can activate kinases may be wide-spread and carries major implications for design and therapeutic application of kinase inhibitors. DOI:http://dx.doi.org/10.7554/eLife.05434.001 Cells contain thousands of proteins that carry out the essential tasks needed for survival. Before they can work, proteins must first fold into specific three-dimensional shapes. The endoplasmic reticulum, a cellular compartment that specializes in properly folding newly made proteins into their native states, is critical for this protein maturation process. If folding-enzymes in the endoplasmic reticulum are not properly balanced with the load of proteins they must fold, the endoplasmic reticulum can be overwhelmed with unfolded proteins that accumulate, leading to ‘endoplasmic reticulum stress’. The cell copes with endoplasmic reticulum stress by triggering the ‘unfolded protein response’ (UPR). This response helps to clear the unfolded proteins by increasing the size of the endoplasmic reticulum and the concentration of folding enzymes within it, and by decreasing the influx of newly made protein into the endoplasmic reticulum. The UPR engages signaling molecules in the endoplasmic reticulum membrane, among them two signaling enzymes called IRE1 and PERK. Drugs that activate these signaling enzymes could help the cell to deal with unfolded proteins, prevent toxicity resulting from endoplasmic reticulum stress, and ward off the diseases that result from it. Mendez, Alfaro, Morales-Soto et al. developed a small molecule, called IPA (short for IRE1/PERK Activator), that was designed to bind to and activate IRE1. Serendipitously, IPA not only activated IRE1 but also activated PERK. Surprisingly, PERK activation was only observed at low IPA concentrations in which IPA occupied the active sites in only a few PERK molecules, whereas at higher concentrations and full occupancy IPA completely inhibited PERK. Mendez, Alfaro, Morales-Soto et al. proposed that, under conditions of partial IPA occupancy, a minority of IPA-bound PERK molecules assume an activated state that propagates to adjacent PERK molecules that have no IPA bound to them, and activates them. Similar dose-dependent activation was previously observed for a clinically used drug designed to inhibit a similar signaling enzyme that is important in cancer progression. Together with the observations of Mendez, Alfaro, Morales-Soto et al., these results suggest that research into similar treatments must consider that a ‘minimal dose’ can exist, below which drugs may have the opposite effect to what is desired. Further work is still needed to fully understand the mechanisms that produce such behavior. DOI:http://dx.doi.org/10.7554/eLife.05434.002
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Affiliation(s)
- Aaron S Mendez
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | | | | | - Arvin C Dar
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | | | - Katja Gotthardt
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Han Li
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Diego Acosta-Alvear
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Carmela Sidrauski
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Alexei V Korennykh
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | | | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Peter Walter
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
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199
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Wang LJ, Yang Y, Zhang CY. Phosphorylation-Directed Assembly of a Single Quantum Dot Based Nanosensor for Protein Kinase Assay. Anal Chem 2015; 87:4696-703. [DOI: 10.1021/ac504358q] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Li-juan Wang
- Single-Molecule
Detection and Imaging
Laboratory, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Guangdong 518055, China
| | - Yong Yang
- Single-Molecule
Detection and Imaging
Laboratory, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Guangdong 518055, China
| | - Chun-yang Zhang
- Single-Molecule
Detection and Imaging
Laboratory, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Guangdong 518055, China
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200
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Kelley MR, Logsdon D, Fishel ML. Targeting DNA repair pathways for cancer treatment: what's new? Future Oncol 2015; 10:1215-37. [PMID: 24947262 DOI: 10.2217/fon.14.60] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Disruptions in DNA repair pathways predispose cells to accumulating DNA damage. A growing body of evidence indicates that tumors accumulate progressively more mutations in DNA repair proteins as cancers progress. DNA repair mechanisms greatly affect the response to cytotoxic treatments, so understanding those mechanisms and finding ways to turn dysregulated repair processes against themselves to induce tumor death is the goal of all DNA repair inhibition efforts. Inhibition may be direct or indirect. This burgeoning field of research is replete with promise and challenge, as more intricacies of each repair pathway are discovered. In an era of increasing concern about healthcare costs, use of DNA repair inhibitors can prove to be highly effective stewardship of R&D resources and patient expenses.
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Affiliation(s)
- Mark R Kelley
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
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