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Gao X, Mazière AD, Beard R, Klumperman J, Hannoush RN. Fatty acylation enhances the cellular internalization and cytosolic distribution of a cystine-knot peptide. iScience 2021; 24:103220. [PMID: 34712919 PMCID: PMC8529511 DOI: 10.1016/j.isci.2021.103220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/14/2021] [Accepted: 09/30/2021] [Indexed: 02/07/2023] Open
Abstract
Delivering peptides into cells could open up possibilities for targeting intracellular proteins. Although fatty acylation of peptide therapeutics improves their systemic half-life, it remains unclear how it influences their cellular uptake. Here, we demonstrate that a fatty acylated peptide exhibits enhanced cellular internalization and cytosolic distribution compared to the un-acylated version. By using a cystine-knot peptide as a model system, we report an efficient strategy for site-specific conjugation of fatty acids. Peptides modified with fatty acids of different chain lengths entered cells through clathrin-mediated and macropinocytosis pathways. The cellular uptake was mediated by the length of the hydrocarbon chain, with myristic acid conjugates displaying the highest distribution across the cytoplasm including the cytosol, and endomembranes of the ER, Golgi and mitochondria. Our studies demonstrate how fatty acylation improves the cellular uptake of peptides, and lay the groundwork for future development of bioactive peptides with enhanced intracellular distribution. A synthetic strategy comprises site-specific conjugation of fatty acids to peptides Fatty acylation of a peptide enhances its cellular uptake and cytosolic distribution Myristoylated peptides display a high cytoplasmic distribution Fatty acylated peptides are internalized via multiple endocytic routes
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Affiliation(s)
- Xinxin Gao
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA, USA
| | - Ann De Mazière
- Department of Cell Biology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Rhiannon Beard
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA, USA
| | - Judith Klumperman
- Department of Cell Biology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Rami N Hannoush
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA, USA
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52
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Liu J, Tokheim C, Lee JD, Gan W, North BJ, Liu XS, Pandolfi PP, Wei W. Genetic fusions favor tumorigenesis through degron loss in oncogenes. Nat Commun 2021; 12:6704. [PMID: 34795215 PMCID: PMC8602260 DOI: 10.1038/s41467-021-26871-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 10/27/2021] [Indexed: 12/12/2022] Open
Abstract
Chromosomal rearrangements can generate genetic fusions composed of two distinct gene sequences, many of which have been implicated in tumorigenesis and progression. Our study proposes a model whereby oncogenic gene fusions frequently alter the protein stability of the resulting fusion products, via exchanging protein degradation signal (degron) between gene sequences. Computational analyses of The Cancer Genome Atlas (TCGA) identify 2,406 cases of degron exchange events and reveal an enrichment of oncogene stabilization due to loss of degrons from fusion. Furthermore, we identify and experimentally validate that some recurrent fusions, such as BCR-ABL, CCDC6-RET and PML-RARA fusions, perturb protein stability by exchanging internal degrons. Likewise, we also validate that EGFR or RAF1 fusions can be stabilized by losing a computationally-predicted C-terminal degron. Thus, complementary to enhanced oncogene transcription via promoter swapping, our model of degron loss illustrates another general mechanism for recurrent fusion proteins in driving tumorigenesis.
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Affiliation(s)
- Jing Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Collin Tokheim
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Jonathan D Lee
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
- Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Wenjian Gan
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Brian J North
- Department of Biomedical Sciences, Creighton University, Omaha, NE, 68178, USA
| | - X Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
| | - Pier Paolo Pandolfi
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, 10124, Italy.
- Renown Institute for Cancer, Nevada System of Higher Education, Reno, NV, 89502, USA.
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.
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53
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Hoch M, Zack J, Quinlan M, Huth F, Forte S, Dodd S, Aimone P, Hourcade-Potelleret F. Pharmacokinetics of Asciminib When Taken With Imatinib or With Food. Clin Pharmacol Drug Dev 2021; 11:207-219. [PMID: 34609077 DOI: 10.1002/cpdd.1019] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 08/03/2021] [Indexed: 12/17/2022]
Abstract
Asciminib, a first-in-class, Specifically Targeting the Abelson kinase Myristoyl Pocket (STAMP) inhibitor with the potential to overcome resistance to adenosine triphosphate-competitive tyrosine kinase inhibitors, is being investigated in leukemia as monotherapy and in combination with tyrosine kinase inhibitors including imatinib. This phase 1 study in healthy volunteers assessed the pharmacokinetics of asciminib (40 mg single dose) under 2 conditions: when taken with imatinib (steady state; 400 mg once daily) and a low-fat meal (according to imatinib prescription information), or when taken as single-agent under different food conditions. Asciminib plus imatinib with a low-fat meal increased asciminib area under the plasma concentration-time curve from time 0 to infinity and maximum plasma concentration (geometric mean ratios [90% confidence interval], 2.08 [1.93-2.24] and 1.59 [1.45-1.75], respectively) compared with asciminib alone under the same food conditions. Asciminib plus food decreased asciminib area under the plasma concentration-time curve from time 0 to infinity compared with asciminib taken under fasted conditions (geometric mean ratios: low-fat meal, 0.7 [0.631-0.776]; high-fat meal, 0.377 [0.341-0.417]). Asciminib plus imatinib was well tolerated with no new safety signals. Overall, coadministration of asciminib with imatinib and a low-fat meal results in a moderate increase in asciminib exposure compared with asciminib alone under the same food condition. Food itself decreases asciminib exposure, indicating that single-agent asciminib should be administered in the fasted state to prevent potential suboptimal exposures.
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Affiliation(s)
- Matthias Hoch
- Novartis Pharma AG, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Julia Zack
- Novartis Pharmaceuticals, East Hanover, New Jersey, USA
| | | | - Felix Huth
- Novartis Pharma AG, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | | | - Stephanie Dodd
- Novartis Pharmaceuticals, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
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54
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Johnson TK, Bochar DA, Vandecan NM, Furtado J, Agius MP, Phadke S, Soellner MB. Synergy and Antagonism between Allosteric and Active-Site Inhibitors of Abl Tyrosine Kinase. Angew Chem Int Ed Engl 2021; 60:20196-20199. [PMID: 34292655 PMCID: PMC8405588 DOI: 10.1002/anie.202105351] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/05/2021] [Indexed: 11/06/2022]
Abstract
Allosteric inhibitors of Abl kinase are being explored in the clinic, often in combination with ATP-site inhibitors of Abl kinase. However, there are conflicting data on whether both ATP-competitive inhibitors and myristoyl-site allosteric inhibitors can simultaneously bind Abl kinase. Here, we determine whether there is synergy or antagonism between ATP-competitive inhibitors and allosteric inhibitors of Abl. We observe that clinical ATP-competitive inhibitors are not synergistic with allosteric ABL inhibitors, however, conformation-selective ATP-site inhibitors that modulate the global conformation of Abl can afford synergy. We demonstrate that kinase conformation is the key driver to simultaneously bind two compounds to Abl kinase. Finally, we explore the interaction of allosteric and conformation selective ATP-competitive inhibitors in a series of biochemical and cellular assays.
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Affiliation(s)
- Taylor K Johnson
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 48109, USA
| | - Daniel A Bochar
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 48109, USA
| | - Nathalie M Vandecan
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 48109, USA
| | - Jessica Furtado
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 48109, USA
| | - Michael P Agius
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 48109, USA
| | - Sameer Phadke
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 48109, USA
| | - Matthew B Soellner
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 48109, USA
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55
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Johnson TK, Bochar DA, Vandecan NM, Furtado J, Agius MP, Phadke S, Soellner MB. Synergy and Antagonism between Allosteric and Active‐Site Inhibitors of Abl Tyrosine Kinase. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105351] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Taylor K. Johnson
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
| | - Daniel A. Bochar
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
| | - Nathalie M. Vandecan
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
| | - Jessica Furtado
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
| | - Michael P. Agius
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
| | - Sameer Phadke
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
| | - Matthew B. Soellner
- Department of Chemistry University of Michigan 930 N. University Ave. Ann Arbor MI 48109 USA
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56
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Lee ES, Park JH, Wi SD, Chae HB, Paeng SK, Bae SB, Phan KAT, Kim MG, Kwak SS, Kim WY, Yun DJ, Lee SY. Demyristoylation of the Cytoplasmic Redox Protein Trx-h2 Is Critical for Inducing a Rapid Cold Stress Response in Plants. Antioxidants (Basel) 2021; 10:antiox10081287. [PMID: 34439534 PMCID: PMC8389195 DOI: 10.3390/antiox10081287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/09/2021] [Accepted: 08/11/2021] [Indexed: 12/27/2022] Open
Abstract
In Arabidopsis, the cytosolic redox protein thioredoxin h2 (Trx-h2) is anchored to the cytoplasmic endomembrane through the myristoylated second glycine residue (Gly2). However, under cold stress, the cytosolic Trx-h2 is rapidly translocated to the nucleus, where it interacts with and reduces the cold-responsive C-repeat-binding factors (CBFs), thus activating cold-responsive (COR) genes. In this study, we investigated the significance of fatty acid modification of Trx-h2 under cold conditions by generating transgenic Arabidopsis lines in the trx-h2 mutant background, overexpressing Trx-h2 (Trx-h2OE/trx-h2) and its point mutation variant Trx-h2(G/A) [Trx-h2(G/A)OE/trx-h2], in which the Gly2 was replaced by alanine (Ala). Due to the lack of Gly2, Trx-h2(G/A) was incapable of myristoylation, and a part of Trx-h2(G/A) localized to the nucleus even under warm temperature. As no time is spent on the demyristoylation and subsequent nuclear translocation of Trx-h2(G/A) under a cold snap, the ability of Trx-h2(G/A) to protect plants from cold stress was greater than that of Trx-h2. Additionally, COR genes were up-regulated earlier in Trx-h2(G/A)2OE/trx-h2 plants than in Trx-h2OE/trx-h2 plants under cold stress. Consequently, Trx-h2(G/A)2OE/trx-h2 plants showed greater cold tolerance than Col-0 (wild type) and Trx-h2OE/trx-h2 plants. Overall, our results clearly demonstrate the significance of the demyristoylation of Trx-h2 in enhancing plant cold/freezing tolerance.
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Affiliation(s)
- Eun Seon Lee
- Division of Applied Life Science (BK21+) and PMBBRC, Gyeongsang National University, Jinju 52828, Korea; (E.S.L.); (J.H.P.); (S.D.W.); (H.B.C.); (S.K.P.); (S.B.B.); (K.A.T.P.); (W.-Y.K.)
| | - Joung Hun Park
- Division of Applied Life Science (BK21+) and PMBBRC, Gyeongsang National University, Jinju 52828, Korea; (E.S.L.); (J.H.P.); (S.D.W.); (H.B.C.); (S.K.P.); (S.B.B.); (K.A.T.P.); (W.-Y.K.)
| | - Seong Dong Wi
- Division of Applied Life Science (BK21+) and PMBBRC, Gyeongsang National University, Jinju 52828, Korea; (E.S.L.); (J.H.P.); (S.D.W.); (H.B.C.); (S.K.P.); (S.B.B.); (K.A.T.P.); (W.-Y.K.)
| | - Ho Byoung Chae
- Division of Applied Life Science (BK21+) and PMBBRC, Gyeongsang National University, Jinju 52828, Korea; (E.S.L.); (J.H.P.); (S.D.W.); (H.B.C.); (S.K.P.); (S.B.B.); (K.A.T.P.); (W.-Y.K.)
| | - Seol Ki Paeng
- Division of Applied Life Science (BK21+) and PMBBRC, Gyeongsang National University, Jinju 52828, Korea; (E.S.L.); (J.H.P.); (S.D.W.); (H.B.C.); (S.K.P.); (S.B.B.); (K.A.T.P.); (W.-Y.K.)
| | - Su Bin Bae
- Division of Applied Life Science (BK21+) and PMBBRC, Gyeongsang National University, Jinju 52828, Korea; (E.S.L.); (J.H.P.); (S.D.W.); (H.B.C.); (S.K.P.); (S.B.B.); (K.A.T.P.); (W.-Y.K.)
| | - Kieu Anh Thi Phan
- Division of Applied Life Science (BK21+) and PMBBRC, Gyeongsang National University, Jinju 52828, Korea; (E.S.L.); (J.H.P.); (S.D.W.); (H.B.C.); (S.K.P.); (S.B.B.); (K.A.T.P.); (W.-Y.K.)
| | - Min Gab Kim
- College of Pharmacy, Gyeongsang National University, Jinju 52828, Korea;
| | - Sang-Soo Kwak
- Plant Systems Engineering Research Center, KRIBB, Daejeon 34141, Korea;
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21+) and PMBBRC, Gyeongsang National University, Jinju 52828, Korea; (E.S.L.); (J.H.P.); (S.D.W.); (H.B.C.); (S.K.P.); (S.B.B.); (K.A.T.P.); (W.-Y.K.)
| | - Dae-Jin Yun
- Department of Biomedical Science & Engineering, Konkuk University, Seoul 05029, Korea;
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21+) and PMBBRC, Gyeongsang National University, Jinju 52828, Korea; (E.S.L.); (J.H.P.); (S.D.W.); (H.B.C.); (S.K.P.); (S.B.B.); (K.A.T.P.); (W.-Y.K.)
- Correspondence: ; Tel.: +82-55-772-1351; Fax: +82-55-759-9363
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57
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Lee ES, Park JH, Wi SD, Kang CH, Chi YH, Chae HB, Paeng SK, Ji MG, Kim WY, Kim MG, Yun DJ, Stacey G, Lee SY. Redox-dependent structural switch and CBF activation confer freezing tolerance in plants. NATURE PLANTS 2021; 7:914-922. [PMID: 34155371 DOI: 10.1038/s41477-021-00944-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 05/12/2021] [Indexed: 05/20/2023]
Abstract
The activities of cold-responsive C-repeat-binding transcription factors (CBFs) are tightly controlled as they not only induce cold tolerance but also regulate normal plant growth under temperate conditions1-4. Thioredoxin h2 (Trx-h2)-a cytosolic redox protein identified as an interacting partner of CBF1-is normally anchored to cytoplasmic endomembranes through myristoylation at the second glycine residue5,6. However, after exposure to cold conditions, the demyristoylated Trx-h2 is translocated to the nucleus, where it reduces the oxidized (inactive) CBF oligomers and monomers. The reduced (active) monomers activate cold-regulated gene expression. Thus, in contrast to the Arabidopsis trx-h2 (AT5G39950) null mutant, Trx-h2 overexpression lines are highly cold tolerant. Our findings reveal the mechanism by which cold-mediated redox changes induce the structural switching and functional activation of CBFs, therefore conferring plant cold tolerance.
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Affiliation(s)
- Eun Seon Lee
- Division of Applied Life Science (BK21+) and PMBBRC, Gyeongsang National University, Jinju, Korea
| | - Joung Hun Park
- Division of Applied Life Science (BK21+) and PMBBRC, Gyeongsang National University, Jinju, Korea
| | - Seong Dong Wi
- Division of Applied Life Science (BK21+) and PMBBRC, Gyeongsang National University, Jinju, Korea
| | - Chang Ho Kang
- Division of Applied Life Science (BK21+) and PMBBRC, Gyeongsang National University, Jinju, Korea
| | - Yong Hun Chi
- Division of Applied Life Science (BK21+) and PMBBRC, Gyeongsang National University, Jinju, Korea
| | - Ho Byoung Chae
- Division of Applied Life Science (BK21+) and PMBBRC, Gyeongsang National University, Jinju, Korea
| | - Seol Ki Paeng
- Division of Applied Life Science (BK21+) and PMBBRC, Gyeongsang National University, Jinju, Korea
| | - Myung Geun Ji
- Division of Applied Life Science (BK21+) and PMBBRC, Gyeongsang National University, Jinju, Korea
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21+) and PMBBRC, Gyeongsang National University, Jinju, Korea
| | - Min Gab Kim
- College of Pharmacy, Gyeongsang National University, Jinju, Korea
| | - Dae-Jin Yun
- Department of Biomedical Science & Engineering, Konkuk University, Seoul, Korea
| | - Gary Stacey
- Divisions of Plant Science and Biochemistry, University of Missouri, Columbia, MO, USA
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21+) and PMBBRC, Gyeongsang National University, Jinju, Korea.
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China.
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58
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Wu K, Wu H, Lyu W, Kim Y, Furdui CM, Anderson KS, Koleske AJ. Platelet-derived growth factor receptor beta activates Abl2 via direct binding and phosphorylation. J Biol Chem 2021; 297:100883. [PMID: 34144039 PMCID: PMC8259415 DOI: 10.1016/j.jbc.2021.100883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/07/2021] [Accepted: 06/14/2021] [Indexed: 11/27/2022] Open
Abstract
Abl family kinases are nonreceptor tyrosine kinases activated by diverse cellular stimuli that regulate cytoskeleton organization, morphogenesis, and adhesion. The catalytic activity of Abl family kinases is tightly regulated in cells by a complex set of intramolecular and intermolecular interactions and post-translational modifications. For example, the platelet-derived growth factor receptor beta (PDGFRβ), important for cell proliferation and chemotaxis, is a potent activator of Abl family kinases. However, the molecular mechanism by which PDGFRβ engages and activates Abl family kinases is not known. We show here that the Abl2 Src homology 2 domain directly binds to phosphotyrosine Y771 in the PDGFRβ cytoplasmic domain. PDGFRβ directly phosphorylates multiple novel sites on the N-terminal half of Abl2, including Y116, Y139, and Y161 within the Src homology 3 domain, and Y299, Y303, and Y310 on the kinase domain. Y116, Y161, Y272, and Y310 are all located at or near the Src homology 3/Src homology 2-kinase linker interface, which helps maintain Abl family kinases in an autoinhibited conformation. We also found that PDGFRβ-mediated phosphorylation of Abl2 in vitro activates Abl2 kinase activity, but mutation of these four tyrosines (Y116, Y161, Y272, and Y310) to phenylalanine abrogated PDGFRβ-mediated activation of Abl2. These findings reveal how PDGFRβ engages and phosphorylates Abl2 leading to activation of the kinase, providing a framework to understand how growth factor receptors engage and activate Abl family kinases.
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Affiliation(s)
- Kuanlin Wu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Hanzhi Wu
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Wanqing Lyu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Youngjoo Kim
- Department of Pharmacology, Yale University, New Haven, Connecticut, USA
| | - Cristina M Furdui
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Karen S Anderson
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA; Department of Pharmacology, Yale University, New Haven, Connecticut, USA
| | - Anthony J Koleske
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA; Department of Neuroscience, Yale University, New Haven, Connecticut, USA.
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59
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Hoch M, Sato M, Zack J, Quinlan M, Sengupta T, Allepuz A, Aimone P, Hourcade-Potelleret F. Pharmacokinetics of Asciminib in Individuals With Hepatic or Renal Impairment. J Clin Pharmacol 2021; 61:1454-1465. [PMID: 34115385 DOI: 10.1002/jcph.1926] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/12/2021] [Accepted: 06/08/2021] [Indexed: 12/17/2022]
Abstract
Asciminib is an investigational, first-in-class, specifically targeting the ABL myristoyl pocket (STAMP) inhibitor of BCR-ABL1 with a new mechanism of action compared with approved ATP-competitive tyrosine kinase inhibitors. This report describes the findings from 2 phase 1 studies assessing the pharmacokinetic (PK) profile of a single dose of asciminib (40 mg) in individuals with impaired renal function (based on absolute glomerular filtration rate; NCT03605277) or impaired hepatic function (based on Child-Pugh classification; NCT02857868). Individuals with severe renal impairment exhibited 49%-56% higher exposure (area under the curve [AUC]), with similar maximum plasma concentration (Cmax ), than matched healthy controls. Based on these findings, as per the protocol, the PK of asciminib in individuals with mild or moderate renal impairment was not assessed. In individuals with mild and severe hepatic impairment, asciminib AUC was 21%-22% and 55%-66% higher, respectively, and Cmax was 26% and 29% higher, respectively, compared with individuals with normal hepatic function. Individuals with moderate hepatic impairment had similar asciminib AUC and Cmax than matched healthy controls. The increase in asciminib AUC and Cmax in the mild hepatic impairment cohort was mainly driven by 1 participant with particularly high exposure. Asciminib was generally well tolerated, and the safety data were consistent with its known safety profile. In summary, these findings indicate that renal or hepatic impairment has no clinically meaningful effect on the exposure or safety profile of asciminib, and support its use in patients with varying degrees of renal or hepatic dysfunction.
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Affiliation(s)
- Matthias Hoch
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Masahiko Sato
- Novartis Institutes for Biomedical Research, Novartis Pharma K.K, Tokyo, Japan
| | - Julia Zack
- Novartis Pharmaceuticals, East Hanover, New Jersey, USA
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60
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Mian AA, Haberbosch I, Khamaisie H, Agbarya A, Pietsch L, Eshel E, Najib D, Chiriches C, Ottmann OG, Hantschel O, Biondi RM, Ruthardt M, Mahajna J. Crizotinib acts as ABL1 inhibitor combining ATP-binding with allosteric inhibition and is active against native BCR-ABL1 and its resistance and compound mutants BCR-ABL1 T315I and BCR-ABL1 T315I-E255K. Ann Hematol 2021; 100:2023-2029. [PMID: 34110462 PMCID: PMC8285356 DOI: 10.1007/s00277-020-04357-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 11/18/2020] [Indexed: 12/30/2022]
Abstract
Resistance remains the major clinical challenge for the therapy of Philadelphia chromosome-positive (Ph+) leukemia. With the exception of ponatinib, all approved tyrosine kinase inhibitors (TKIs) are unable to inhibit the common "gatekeeper" mutation T315I. Here we investigated the therapeutic potential of crizotinib, a TKI approved for targeting ALK and ROS1 in non-small cell lung cancer patients, which inhibited also the ABL1 kinase in cell-free systems, for the treatment of advanced and therapy-resistant Ph+ leukemia. By inhibiting the BCR-ABL1 kinase, crizotinib efficiently suppressed growth of Ph+ cells without affecting growth of Ph- cells. It was also active in Ph+ patient-derived long-term cultures (PD-LTCs) independently of the responsiveness/resistance to other TKIs. The efficacy of crizotinib was confirmed in vivo in syngeneic mouse models of BCR-ABL1- or BCR-ABL1T315I-driven chronic myeloid leukemia-like disease and in BCR-ABL1-driven acute lymphoblastic leukemia (ALL). Although crizotinib binds to the ATP-binding site, it also allosterically affected the myristol binding pocket, the binding site of GNF2 and asciminib (former ABL001). Therefore, crizotinib has a seemingly unique double mechanism of action, on the ATP-binding site and on the myristoylation binding pocket. These findings strongly suggest the clinical evaluation of crizotinib for the treatment of advanced and therapy-resistant Ph+ leukemia.
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Affiliation(s)
- Afsar Ali Mian
- Department of Hematology, Division of Cancer and Genetics, and Experimental Clinical Medical Center (ECMC), Medical School, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.,Center for Regenerative Medicine and Stem Cell Research, Aga Khan University, Karachi, Pakistan
| | | | - Hazem Khamaisie
- Department of Nutrition and Natural Products, Migal-Galilee Technology Center, PO Box 831, 11016, Kiryat Shmona, Israel
| | - Abed Agbarya
- Oncology Department, Bnai Zion MC, Haifa, Israel
| | - Larissa Pietsch
- Department of Internal Medicine I, Clinic of Goethe University, Frankfurt, Germany.,German Cancer Consortium (DKTK), Frankfurt, Germany
| | - Elizabeh Eshel
- Hematology Institute, Ziv Medical Center, Azrieli Faculty of Medicine, Bar Ilan University, Zfat, Israel
| | - Dally Najib
- Hematology Institute, Ziv Medical Center, Azrieli Faculty of Medicine, Bar Ilan University, Zfat, Israel
| | - Claudia Chiriches
- Department of Hematology, Division of Cancer and Genetics, and Experimental Clinical Medical Center (ECMC), Medical School, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Oliver Gerhard Ottmann
- Department of Hematology, Division of Cancer and Genetics, and Experimental Clinical Medical Center (ECMC), Medical School, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Oliver Hantschel
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, École polytechnique fédérale de Lausanne, Lausanne, Switzerland.,Medical Biochemistry and Pharmacology Center, Institute for Physiological Chemistry, Philipps-University, Marburg, Germany
| | - Ricardo M Biondi
- Department of Internal Medicine I, Clinic of Goethe University, Frankfurt, Germany.,German Cancer Consortium (DKTK), Frankfurt, Germany.,Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Martin Ruthardt
- Department of Hematology, Division of Cancer and Genetics, and Experimental Clinical Medical Center (ECMC), Medical School, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
| | - Jamal Mahajna
- Department of Nutrition and Natural Products, Migal-Galilee Technology Center, PO Box 831, 11016, Kiryat Shmona, Israel. .,The Department of Nutritional Sciences, Tel Hai Academic College, Kiryat Shmona, Israel.
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61
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Myristoylation-mediated phase separation of EZH2 compartmentalizes STAT3 to promote lung cancer growth. Cancer Lett 2021; 516:84-98. [PMID: 34102285 DOI: 10.1016/j.canlet.2021.05.035] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 01/27/2023]
Abstract
N-myristoylation is a crucial signaling and pathogenic modification process that confers hydrophobicity to cytosolic proteins. Although different large-scale approaches have been applied, a large proportion of myristoylated proteins remain to be identified. EZH2 is overexpressed in lung cancer cells and exerts oncogenic effects via its intrinsic methyltransferase activity. Using a well-established click chemistry approach, we found that EZH2 can be modified by myristoylation at its N-terminal glycine in lung cancer cells. Hydrophobic interaction is one of the main forces driving or stabilizing liquid-liquid phase separation (LLPS), raising the possibility that myristoylation can modulate LLPS by mediating hydrophobic interactions. Indeed, myristoylation facilitates EZH2 to form phase-separated liquid droplets in lung cancer cells and in vitro. Furthermore, we provide evidence that myristoylation-mediated LLPS of EZH2 compartmentalizes its non-canonical substrate, STAT3, and activates STAT3 signaling, ultimately resulting in accelerated lung cancer cell growth. Thus, targeting EZH2 myristoylation may have significant therapeutic efficacy in the treatment of lung cancer. Altogether, these observations not only extend the list of myristoylated proteins, but also indicate that hydrophobic lipidation may serve as a novel incentive to induce or maintain LLPS.
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62
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Luttman JH, Colemon A, Mayro B, Pendergast AM. Role of the ABL tyrosine kinases in the epithelial-mesenchymal transition and the metastatic cascade. Cell Commun Signal 2021; 19:59. [PMID: 34022881 PMCID: PMC8140471 DOI: 10.1186/s12964-021-00739-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/16/2021] [Indexed: 12/20/2022] Open
Abstract
The ABL kinases, ABL1 and ABL2, promote tumor progression and metastasis in various solid tumors. Recent reports have shown that ABL kinases have increased expression and/or activity in solid tumors and that ABL inactivation impairs metastasis. The therapeutic effects of ABL inactivation are due in part to ABL-dependent regulation of diverse cellular processes related to the epithelial to mesenchymal transition and subsequent steps in the metastatic cascade. ABL kinases target multiple signaling pathways required for promoting one or more steps in the metastatic cascade. These findings highlight the potential utility of specific ABL kinase inhibitors as a novel treatment paradigm for patients with advanced metastatic disease. Video abstract.
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Affiliation(s)
- Jillian Hattaway Luttman
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, 308 Research Drive, C-233A LSRC Bldg., P.O. Box 3813, Durham, NC 27710 USA
| | - Ashley Colemon
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, 308 Research Drive, C-233A LSRC Bldg., P.O. Box 3813, Durham, NC 27710 USA
| | - Benjamin Mayro
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, 308 Research Drive, C-233A LSRC Bldg., P.O. Box 3813, Durham, NC 27710 USA
| | - Ann Marie Pendergast
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, 308 Research Drive, C-233A LSRC Bldg., P.O. Box 3813, Durham, NC 27710 USA
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63
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Blakes AJM, Gaul E, Lam W, Shannon N, Knapp KM, Bicknell LS, Jackson MR, Wade EM, Robertson S, White SM, Heller R, Chase A, Baralle D, Douglas AGL. Pathogenic variants causing ABL1 malformation syndrome cluster in a myristoyl-binding pocket and increase tyrosine kinase activity. Eur J Hum Genet 2021; 29:593-603. [PMID: 33223528 PMCID: PMC8115115 DOI: 10.1038/s41431-020-00766-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 11/24/2022] Open
Abstract
ABL1 is a proto-oncogene encoding a nonreceptor tyrosine kinase, best known in the somatic BCR-ABL fusion gene associated with chronic myeloid leukaemia. Recently, germline missense variants in ABL1 have been found to cause an autosomal dominant developmental syndrome with congenital heart disease, skeletal malformations and characteristic facies. Here, we describe a series of six new unrelated individuals with heterozygous missense variants in ABL1 (including four novel variants) identified via whole exome sequencing. All the affected individuals in this series recapitulate the phenotype of the ABL1 developmental syndrome and additionally we affirm that hearing impairment is a common feature of the condition. Four of the variants cluster in the myristoyl-binding pocket of ABL1, a region critical for auto-inhibitory regulation of the kinase domain. Bio-informatic analysis of transcript-wide conservation and germline/somatic variation reveals that this pocket region is subject to high missense constraint and evolutionary conservation. Functional work to investigate ABL1 kinase activity in vitro by transient transfection of HEK293T cells with variant ABL1 plasmid constructs revealed increased phosphorylation of ABL1-specific substrates compared to wild-type. The increased tyrosine kinase activity was suppressed by imatinib treatment. This case series of six new patients with germline heterozygous ABL1 missense variants further delineates the phenotypic spectrum of this condition and recognises microcephaly as a common finding. Our analysis supports an ABL1 gain-of-function mechanism due to loss of auto-inhibition, and demonstrates the potential for pharmacological inhibition using imatinib.
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Affiliation(s)
- Alexander J M Blakes
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Emily Gaul
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Wayne Lam
- South East of Scotland Clinical Genetics Service, Western General Hospital, Crewe Road, Edinburgh, UK
| | - Nora Shannon
- Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Hucknall Road, Nottingham, UK
| | - Karen M Knapp
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Louise S Bicknell
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Meremaihi R Jackson
- Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Emma M Wade
- Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Stephen Robertson
- Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Raoul Heller
- Genetic Health Service NZ - Northern Hub, Auckland District Health Board, Auckland City Hospital, Auckland, New Zealand
| | - Andrew Chase
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Diana Baralle
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Andrew G L Douglas
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK.
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK.
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64
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SRC Signaling in Cancer and Tumor Microenvironment. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1270:57-71. [PMID: 33123993 DOI: 10.1007/978-3-030-47189-7_4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Pioneering experiments performed by Harold Varmus and Mike Bishop in 1976 led to one of the most influential discoveries in cancer research and identified the first cancer-causing oncogene called Src. Later experimental and clinical evidence suggested that Src kinase plays a significant role in promoting tumor growth and progression and its activity is associated with poor patient survival. Thus, several Src inhibitors were developed and approved by FDA for treatment of cancer patients. Tumor microenvironment (TME) is a highly complex and dynamic milieu where significant cross-talk occurs between cancer cells and TME components, which consist of tumor-associated macrophages, fibroblasts, and other immune and vascular cells. Growth factors and chemokines activate multiple signaling cascades in TME and induce multiple kinases and pathways, including Src, leading to tumor growth, invasion/metastasis, angiogenesis, drug resistance, and progression. Here, we will systemically evaluate recent findings regarding regulation of Src and significance of targeting Src in cancer therapy.
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65
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Meng F, Liang Z, Zhao K, Luo C. Drug design targeting active posttranslational modification protein isoforms. Med Res Rev 2020; 41:1701-1750. [PMID: 33355944 DOI: 10.1002/med.21774] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/29/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022]
Abstract
Modern drug design aims to discover novel lead compounds with attractable chemical profiles to enable further exploration of the intersection of chemical space and biological space. Identification of small molecules with good ligand efficiency, high activity, and selectivity is crucial toward developing effective and safe drugs. However, the intersection is one of the most challenging tasks in the pharmaceutical industry, as chemical space is almost infinity and continuous, whereas the biological space is very limited and discrete. This bottleneck potentially limits the discovery of molecules with desirable properties for lead optimization. Herein, we present a new direction leveraging posttranslational modification (PTM) protein isoforms target space to inspire drug design termed as "Post-translational Modification Inspired Drug Design (PTMI-DD)." PTMI-DD aims to extend the intersections of chemical space and biological space. We further rationalized and highlighted the importance of PTM protein isoforms and their roles in various diseases and biological functions. We then laid out a few directions to elaborate the PTMI-DD in drug design including discovering covalent binding inhibitors mimicking PTMs, targeting PTM protein isoforms with distinctive binding sites from that of wild-type counterpart, targeting protein-protein interactions involving PTMs, and hijacking protein degeneration by ubiquitination for PTM protein isoforms. These directions will lead to a significant expansion of the biological space and/or increase the tractability of compounds, primarily due to precisely targeting PTM protein isoforms or complexes which are highly relevant to biological functions. Importantly, this new avenue will further enrich the personalized treatment opportunity through precision medicine targeting PTM isoforms.
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Affiliation(s)
- Fanwang Meng
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Zhongjie Liang
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Kehao Zhao
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China
| | - Cheng Luo
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
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66
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Kjaergaard M, Glavina J, Chemes LB. Predicting the effect of disordered linkers on effective concentrations and avidity with the "C eff calculator" app. Methods Enzymol 2020; 647:145-171. [PMID: 33482987 DOI: 10.1016/bs.mie.2020.09.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Linkers are crucial to the functions of multidomain proteins as they couple functional units to encode regulation such as auto-inhibition, enzyme targeting or tuning of interaction strength. A linker changes reactions from bimolecular to unimolecular, and the equilibrium and kinetics is thus determined by the properties of the linker rather than concentrations. We present a theoretical workflow for estimating the functional consequences of tethering by a linker. We discuss how to: (1) Identify flexible linkers from sequence. (2) Model the end-to-end distance distribution for a flexible linker using a worm-like chain. (3) Estimate the effective concentration of a ligand tethered by a flexible linker. (4) Calculate the decrease in binding affinity caused by auto-inhibition. (5) Calculate the expected avidity enhancement of a bivalent interaction from effective concentration. The worm-like chain modeling is available through a web application called the "Ceff calculator" (http://ceffapp.chemeslab.org), which will allow user-friendly prediction of experimentally inaccessible parameters.
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Affiliation(s)
- Magnus Kjaergaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark; The Danish Research Institute for Translational Neuroscience (DANDRITE), Aarhus, Denmark; Center for Proteins in Memory (PROMEMO), Aarhus, Denmark.
| | - Juliana Glavina
- Instituto de Investigaciones Biotecnológicas "Dr. Rodolfo A. Ugalde", IIB-UNSAM, IIBIO-CONICET, Universidad Nacional de San Martín, San Martín, Argentina
| | - Lucia Beatriz Chemes
- Instituto de Investigaciones Biotecnológicas "Dr. Rodolfo A. Ugalde", IIB-UNSAM, IIBIO-CONICET, Universidad Nacional de San Martín, San Martín, Argentina.
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67
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Foltz L, Palacios-Moreno J, Mayfield M, Kinch S, Dillon J, Syrenne J, Levy T, Grimes M. PAG1 directs SRC-family kinase intracellular localization to mediate receptor tyrosine kinase-induced differentiation. Mol Biol Cell 2020; 31:2269-2282. [PMID: 32726167 PMCID: PMC7550700 DOI: 10.1091/mbc.e20-02-0135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 07/15/2020] [Accepted: 07/21/2020] [Indexed: 12/30/2022] Open
Abstract
All receptor tyrosine kinases (RTKs) activate similar downstream signaling pathways through a common set of effectors, yet it is not fully understood how different receptors elicit distinct cellular responses to cause cell proliferation, differentiation, or other cell fates. We tested the hypothesis that regulation of SRC family kinase (SFK) signaling by the scaffold protein, PAG1, influences cell fate decisions following RTK activation. We generated a neuroblastoma cell line expressing a PAG1 fragment that lacks the membrane-spanning domain (PAG1TM-) and localized to the cytoplasm. PAG1TM- cells exhibited higher amounts of active SFKs and increased growth rate. PAG1TM- cells were unresponsive to TRKA and RET signaling, two RTKs that induce neuronal differentiation, but retained responses to EGFR and KIT. Under differentiation conditions, PAG1TM- cells continued to proliferate and did not extend neurites or increase β-III tubulin expression. FYN and LYN were sequestered in multivesicular bodies (MVBs), and dramatically more FYN and LYN were in the lumen of MVBs in PAG1TM- cells. In particular, activated FYN was sequestered in PAG1TM- cells, suggesting that disruption of FYN localization led to the observed defects in differentiation. The results demonstrate that PAG1 directs SFK intracellular localization to control activity and to mediate signaling by RTKs that induce neuronal differentiation.
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Affiliation(s)
- Lauren Foltz
- Division of Biological Sciences, Center for Biomolecular Structure and Dynamics, and Center for Structural and Functional Neuroscience, University of Montana, Missoula, MT 59812
| | | | - Makenzie Mayfield
- Division of Biological Sciences, Center for Biomolecular Structure and Dynamics, and Center for Structural and Functional Neuroscience, University of Montana, Missoula, MT 59812
| | - Shelby Kinch
- Division of Biological Sciences, Center for Biomolecular Structure and Dynamics, and Center for Structural and Functional Neuroscience, University of Montana, Missoula, MT 59812
| | - Jordan Dillon
- Division of Biological Sciences, Center for Biomolecular Structure and Dynamics, and Center for Structural and Functional Neuroscience, University of Montana, Missoula, MT 59812
| | - Jed Syrenne
- Division of Biological Sciences, Center for Biomolecular Structure and Dynamics, and Center for Structural and Functional Neuroscience, University of Montana, Missoula, MT 59812
| | - Tyler Levy
- Cell Signaling Technology, Danvers, MA 01923
| | - Mark Grimes
- Division of Biological Sciences, Center for Biomolecular Structure and Dynamics, and Center for Structural and Functional Neuroscience, University of Montana, Missoula, MT 59812
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68
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Carofiglio F, Trisciuzzi D, Gambacorta N, Leonetti F, Stefanachi A, Nicolotti O. Bcr-Abl Allosteric Inhibitors: Where We Are and Where We Are Going to. Molecules 2020; 25:E4210. [PMID: 32937901 PMCID: PMC7570842 DOI: 10.3390/molecules25184210] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/08/2020] [Accepted: 09/10/2020] [Indexed: 12/12/2022] Open
Abstract
The fusion oncoprotein Bcr-Abl is an aberrant tyrosine kinase responsible for chronic myeloid leukemia and acute lymphoblastic leukemia. The auto-inhibition regulatory module observed in the progenitor kinase c-Abl is lost in the aberrant Bcr-Abl, because of the lack of the N-myristoylated cap able to bind the myristoyl binding pocket also conserved in the Bcr-Abl kinase domain. A way to overcome the occurrence of resistance phenomena frequently observed for Bcr-Abl orthosteric drugs is the rational design of allosteric ligands approaching the so-called myristoyl binding pocket. The discovery of these allosteric inhibitors although very difficult and extremely challenging, represents a valuable option to minimize drug resistance, mostly due to the occurrence of mutations more frequently affecting orthosteric pockets, and to enhance target selectivity with lower off-target effects. In this perspective, we will elucidate at a molecular level the structural bases behind the Bcr-Abl allosteric control and will show how artificial intelligence can be effective to drive the automated de novo design towards off-patent regions of the chemical space.
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Affiliation(s)
- Francesca Carofiglio
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
| | - Daniela Trisciuzzi
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
- Molecular Horizon srl, Via Montelino 32, 06084 Bettona, Italy
| | - Nicola Gambacorta
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
| | - Francesco Leonetti
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
| | - Angela Stefanachi
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
| | - Orazio Nicolotti
- Dipartimento di Farmacia Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, 70125 Bari, Italy; (F.C.); (D.T.); (N.G.); (F.L.)
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69
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Domain Organization in Plant Blue-Light Receptor Phototropin2 of Arabidopsis thaliana Studied by Small-Angle X-ray Scattering. Int J Mol Sci 2020; 21:ijms21186638. [PMID: 32927860 PMCID: PMC7555306 DOI: 10.3390/ijms21186638] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/06/2020] [Accepted: 09/07/2020] [Indexed: 01/10/2023] Open
Abstract
Phototropin2 (phot2) is a blue-light (BL) receptor protein that regulates the BL-dependent activities of plants for efficient photosynthesis. Phot2 is composed of two light-oxygen-voltage sensing domains (LOV1 and LOV2) to absorb BL, and a kinase domain. Photo-activated LOV domains, especially LOV2, play a major role in photo-dependent increase in the phosphorylation activity of the kinase domain. The atomic details of the overall structure of phot2 and the intramolecular mechanism to convert BL energy to a phosphorylation signal remain unknown. We performed structural studies on the LOV fragments LOV1, LOV2, LOV2-linker, and LOV2-kinase, and full-length phot2, using small-angle X-ray scattering (SAXS). The aim of the study was to understand structural changes under BL irradiation and discuss the molecular mechanism that enhance the phosphorylation activity under BL. SAXS is a suitable technique for visualizing molecular structures of proteins in solution at low resolution and is advantageous for monitoring their structural changes in the presence of external physical and/or chemical stimuli. Structural parameters and molecular models of the recombinant specimens were obtained from SAXS profiles in the dark, under BL irradiation, and after dark reversion. LOV1, LOV2, and LOV2-linker fragments displayed minimal structural changes. However, BL-induced rearrangements of functional domains were noted for LOV2-kinase and full-length phot2. Based on the molecular model together with the absorption measurements and biochemical assays, we discuss the intramolecular interactions and domain motions necessary for BL-enhanced phosphorylation activity of phot2.
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70
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Yuan M, Song ZH, Ying MD, Zhu H, He QJ, Yang B, Cao J. N-myristoylation: from cell biology to translational medicine. Acta Pharmacol Sin 2020; 41:1005-1015. [PMID: 32203082 PMCID: PMC7468318 DOI: 10.1038/s41401-020-0388-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 02/20/2020] [Indexed: 02/07/2023] Open
Abstract
Various lipids and lipid metabolites are bound to and modify the proteins in eukaryotic cells, which are known as ‘protein lipidation’. There are four major types of the protein lipidation, i.e. myristoylation, palmitoylation, prenylation, and glycosylphosphatidylinositol anchor. N-myristoylation refers to the attachment of 14-carbon fatty acid myristates to the N-terminal glycine of proteins by N-myristoyltransferases (NMT) and affects their physiology such as plasma targeting, subcellular tracking and localization, thereby influencing the function of proteins. With more novel pathogenic N-myristoylated proteins are identified, the N-myristoylation will attract great attentions in various human diseases including infectious diseases, parasitic diseases, and cancers. In this review, we summarize the current understanding of N-myristoylation in physiological processes and discuss the hitherto implication of crosstalk between N-myristoylation and other protein modification. Furthermore, we mention several well-studied NMT inhibitors mainly in infectious diseases and cancers and generalize the relation of NMT and cancer progression by browsing the clinic database. This review also aims to highlight the further investigation into the dynamic crosstalk of N-myristoylation in physiological processes as well as the potential application of protein N-myristoylation in translational medicine.
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71
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Yang Y, Gao H, Sun X, Sun Y, Qiu Y, Weng Q, Rao Y. Global PROTAC Toolbox for Degrading BCR-ABL Overcomes Drug-Resistant Mutants and Adverse Effects. J Med Chem 2020; 63:8567-8583. [PMID: 32657579 DOI: 10.1021/acs.jmedchem.0c00967] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The BCR-ABL fusion oncoprotein causes chronic myeloid leukemia or acute lymphoblastic leukemia in Ph+ patients because the ABL kinase is constitutively activated. However, current clinical treatment with ABL inhibitors is seriously limited by drug resistance and adverse effects. Although the emerging proteolysis-targeting chimeras (PROTACs) have been introduced to degrade BCR-ABL, most of them showed limited activity and could not overcome the common drug-resistant mutants, especially for T315I mutant. Herein, we systematically designed a set of unique PROTACs by globally targeting all the three binding sites of BCR-ABL, including dasatinib-, ponatinib-, and asciminib-based PROTACs. Our ponatinib-based PROTACs showed practical activity as dasatinib-based PROTACs, while no reported ponatinib-based PROTACs could degrade BCR-ABL before. As a proof of concept, some additional dasatinib-based PROTACs were then designed to degrade T315I mutant too. We provided a global PROTAC toolbox for degrading both wild-type and T315I-mutated BCR-ABL from each binding site. More importantly, these PROTACs showed better selectivity and less adverse effects than the inhibitors, indicating that PROTACs had great potential for overcoming clinical drug resistance and safety issues.
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Affiliation(s)
- Yiqing Yang
- MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China.,Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China
| | - Hongying Gao
- MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China.,Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China
| | - Xiuyun Sun
- MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China.,Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China
| | - Yonghui Sun
- MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China.,Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China
| | - Yueping Qiu
- Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qinjie Weng
- Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Center for Drug Safety Evaluation and Research, Zhejiang University, Hangzhou 310058, China
| | - Yu Rao
- MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
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72
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Chen CA, Crutcher E, Gill H, Nelson TN, Robak LA, Jongmans MCJ, Pfundt R, Prasad C, Berard RA, Fannemel M, Frengen E, Misceo D, Ramsey K, Yang Y, Schaaf CP, Wang X. The expanding clinical phenotype of germline ABL1-associated congenital heart defects and skeletal malformations syndrome. Hum Mutat 2020; 41:1738-1744. [PMID: 32643838 DOI: 10.1002/humu.24075] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 06/23/2020] [Accepted: 07/02/2020] [Indexed: 11/07/2022]
Abstract
Congenital heart defects and skeletal malformations syndrome (CHDSKM) is a rare autosomal dominant disorder characterized by congenital heart disease, skeletal abnormalities, and failure to thrive. CHDSKM is caused by germline mutations in ABL1. To date, three variants have been in association with CHDSKM. In this study, we describe three de novo missense variants, c.407C>T (p.Thr136Met), c.746C>T (p.Pro249Leu), and c.1573G>A (p.Val525Met), and one recurrent variant, c.1066G>A (p.Ala356Thr), in six patients, thereby expanding the phenotypic spectrum of CHDSKM to include hearing impairment, lipodystrophy-like features, renal hypoplasia, and distinct ocular abnormalities. Functional investigation of the three novel variants showed an increased ABL1 kinase activity. The cardiac findings in additional patients with p.Ala356Thr contribute to the accumulating evidence that patients carrying either one of the recurrent variants, p.Tyr245Cys and p.Ala356Thr, have a high incidence of cardiac abnormalities. The phenotypic expansion has implications for the clinical diagnosis of CHDSKM in patients with germline ABL1 variants.
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Affiliation(s)
- Chun-An Chen
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas
| | - Emeline Crutcher
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas
- Development, Disease Models, and Therapeutics Graduate Program, Baylor College of Medicine, Houston, Texas
| | - Harinder Gill
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Provincial Medical Genetics Program, BC Women's Hospital and Health Centre, Vancouver, British Columbia, Canada
| | - Tanya N Nelson
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, BC Children's Hospital, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Laurie A Robak
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Marjolijn C J Jongmans
- Department of Human Genetics, Radboud University Medical Center and Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center and Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Chitra Prasad
- Genetics and Development, Children's Health Research Institute, London, Ontario, Canada
- Department of Pediatrics, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Roberta A Berard
- Genetics and Development, Children's Health Research Institute, London, Ontario, Canada
- Department of Pediatrics, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
- Division of Rheumatology, Children's Hospital, London, Ontario, Canada
| | - Madeleine Fannemel
- Department of Medical Genetics, Rikshospitalet, Oslo University Hospital, Oslo, Norway
| | - Eirik Frengen
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Doriana Misceo
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Keri Ramsey
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona
| | - Yaping Yang
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics, Houston, Texas
- AiLife Diagnostics, Pearland, Texas
| | - Christian P Schaaf
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Xia Wang
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
- Baylor Genetics, Houston, Texas
- AiLife Diagnostics, Pearland, Texas
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73
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Kosciuk T, Lin H. N-Myristoyltransferase as a Glycine and Lysine Myristoyltransferase in Cancer, Immunity, and Infections. ACS Chem Biol 2020; 15:1747-1758. [PMID: 32453941 DOI: 10.1021/acschembio.0c00314] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein myristoylation, the addition of a 14-carbon saturated acyl group, is an abundant modification implicated in biological events as diverse as development, immunity, oncogenesis, and infections. N-Myristoyltransferase (NMT) is the enzyme that catalyzes this modification. Many elegant studies have established the rules guiding the catalysis including substrate amino acid sequence requirements with the indispensable N-terminal glycine, and a co-translational mode of action. Recent advances in technology such as the development of fatty acid analogs, small molecule inhibitors, and new proteomic strategies, allowed a deeper insight into the NMT activity and function. Here we focus on discussing recent work demonstrating that NMT is also a lysine myristoyltransferase, the enzyme's regulation by a previously unnoticed solvent channel, and the mechanism of NMT regulation by protein-protein interactions. We also summarize recent findings on NMT's role in cancer, immunity, and infections and the advances in pharmacological targeting of myristoylation. Our analyses highlight opportunities for further understanding and discoveries.
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Affiliation(s)
- Tatsiana Kosciuk
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, United States
| | - Hening Lin
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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74
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Fang L, Vilas-Boas J, Chakraborty S, Potter ZE, Register AC, Seeliger MA, Maly DJ. How ATP-Competitive Inhibitors Allosterically Modulate Tyrosine Kinases That Contain a Src-like Regulatory Architecture. ACS Chem Biol 2020; 15:2005-2016. [PMID: 32479050 DOI: 10.1021/acschembio.0c00429] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Small molecule kinase inhibitors that stabilize distinct ATP binding site conformations can differentially modulate the global conformation of Src-family kinases (SFKs). However, it is unclear which specific ATP binding site contacts are responsible for modulating the global conformation of SFKs and whether these inhibitor-mediated allosteric effects generalize to other tyrosine kinases. Here, we describe the development of chemical probes that allow us to deconvolute which features in the ATP binding site are responsible for the allosteric modulation of the global conformation of Src. We find that the ability of an inhibitor to modulate the global conformation of Src's regulatory domain-catalytic domain module relies mainly on the influence it has on the conformation of a structural element called helix αC. Furthermore, by developing a set of orthogonal probes that target a drug-sensitized Src variant, we show that stabilizing Src's helix αC in an active conformation is sufficient to promote a Src-mediated, phosphotransferase-independent alteration in cell morphology. Finally, we report that ATP-competitive, conformation-selective inhibitors can influence the global conformation of tyrosine kinases beyond the SFKs, suggesting that the allosteric networks we observe in Src are conserved in kinases that have a similar regulatory architecture. Our study highlights that an ATP-competitive inhibitor's interactions with helix αC can have a major influence on the global conformation of some tyrosine kinases.
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Affiliation(s)
| | - Jessica Vilas-Boas
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794-8651, United States
| | | | | | | | - Markus A. Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794-8651, United States
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75
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Jones JK, Thompson EM. Allosteric Inhibition of ABL Kinases: Therapeutic Potential in Cancer. Mol Cancer Ther 2020; 19:1763-1769. [PMID: 32606014 DOI: 10.1158/1535-7163.mct-20-0069] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/21/2020] [Accepted: 06/09/2020] [Indexed: 11/16/2022]
Abstract
Tyrosine kinase inhibitors have revolutionized the world of cancer treatment in recent years, profoundly improving survival of patients with chronic myeloid leukemia (CML) and beyond. However, off-target toxicities of these inhibitors are well-described, and resistance has become a paramount concern. Novel allosteric inhibitors of the Abelson (ABL) family of tyrosine kinases, including GNF-2, GNF-5, and ABL-001, are equipped to overcome these issues. Several contemporary studies have demonstrated their potential efficacy in three key areas: primary hematologic and solid malignancies, metastasis, and combination with other small molecules. Further, ongoing clinical trials are investigating the efficacy of ABL-001 for the treatment of CML and recurrent solid tumors. This work reviews the current literature of the preclinical testing of GNF-2 and GNF-5 and the preclinical and clinical testing of ABL-001. Future research will continue to evaluate these promising inhibitors as both first-line therapy for solid tumors and salvage therapy when more traditional drugs such as imatinib fail.
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Affiliation(s)
- Jill K Jones
- Trinity College of Arts & Sciences, Duke University, Durham, North Carolina
| | - Eric M Thompson
- Department of Neurosurgery, Duke University, Durham, North Carolina. .,Preston Robert Tisch Brain Tumor Center, Duke University, Durham, North Carolina
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76
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Marasco M, Carlomagno T. Specificity and regulation of phosphotyrosine signaling through SH2 domains. JOURNAL OF STRUCTURAL BIOLOGY-X 2020; 4:100026. [PMID: 32647828 PMCID: PMC7337045 DOI: 10.1016/j.yjsbx.2020.100026] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/14/2020] [Accepted: 05/15/2020] [Indexed: 10/26/2022]
Abstract
Phosphotyrosine (pY) signaling is instrumental to numerous cellular processes. pY recognition occurs through specialized protein modules, among which the Src-homology 2 (SH2) domain is the most common. SH2 domains are small protein modules with an invariant fold, and are present in more than a hundred proteins with different function. Here we ask the question of how such a structurally conserved, small protein domain can recognize distinct phosphopeptides with the breath of binding affinity, specificity and kinetic parameters necessary for proper control of pY-dependent signaling and rapid cellular response. We review the current knowledge on structure, thermodynamics and kinetics of SH2-phosphopeptide complexes and conclude that selective phosphopeptide recognition is governed by both structure and dynamics of the SH2 domain, as well as by the kinetics of the binding events. Further studies on the thermodynamic and kinetic properties of SH2-phosphopeptide complexes, beyond their structure, are required to understand signaling regulation.
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Affiliation(s)
- Michelangelo Marasco
- Leibniz University Hannover, Institute of Organic Chemistry and Centre for Biomolecular Drug Research, Schneiderberg 38, 30167 Hannover, Germany
| | - Teresa Carlomagno
- Leibniz University Hannover, Institute of Organic Chemistry and Centre for Biomolecular Drug Research, Schneiderberg 38, 30167 Hannover, Germany.,Helmholtz Centre for Infection Research, Group of Structural Chemistry, Inhoffenstrasse 7, 38124 Braunschweig, Germany
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77
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Btk SH2-kinase interface is critical for allosteric kinase activation and its targeting inhibits B-cell neoplasms. Nat Commun 2020; 11:2319. [PMID: 32385234 PMCID: PMC7210950 DOI: 10.1038/s41467-020-16128-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 04/15/2020] [Indexed: 02/07/2023] Open
Abstract
Bruton’s tyrosine kinase (Btk) is critical for B-cell maturation and activation. Btk loss-of-function mutations cause human X-linked agammaglobulinemia (XLA). In contrast, Btk signaling sustains growth of several B-cell neoplasms which may be treated with tyrosine kinase inhibitors (TKIs). Here, we uncovered the structural mechanism by which certain XLA mutations in the SH2 domain strongly perturb Btk activation. Using a combination of molecular dynamics (MD) simulations and small-angle X-ray scattering (SAXS), we discovered an allosteric interface between the SH2 and kinase domain required for Btk activation and to which multiple XLA mutations map. As allosteric interactions provide unique targeting opportunities, we developed an engineered repebody protein binding to the SH2 domain and able to disrupt the SH2-kinase interaction. The repebody prevents activation of wild-type and TKI-resistant Btk, inhibiting Btk-dependent signaling and proliferation of malignant B-cells. Therefore, the SH2-kinase interface is critical for Btk activation and a targetable site for allosteric inhibition. Constitutive Btk signaling drives several B-cell cancers. Here the authors demonstrate key allosteric intramolecular interactions between the SH2 domain and the kinase domain of Btk, and propose an alternative approach for inhibition of both wild-type and tyrosine kinase inhibitor-resistant Btk.
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78
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Braun TP, Eide CA, Druker BJ. Response and Resistance to BCR-ABL1-Targeted Therapies. Cancer Cell 2020; 37:530-542. [PMID: 32289275 PMCID: PMC7722523 DOI: 10.1016/j.ccell.2020.03.006] [Citation(s) in RCA: 225] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 03/06/2020] [Accepted: 03/09/2020] [Indexed: 12/22/2022]
Abstract
Chronic myeloid leukemia (CML), caused by constitutively active BCR-ABL1 fusion tyrosine kinase, has served as a paradigm for successful application of molecularly targeted cancer therapy. The development of the tyrosine kinase inhibitor (TKI) imatinib allows patients with CML to experience near-normal life expectancy. Specific point mutations that decrease drug binding affinity can produce TKI resistance, and second- and third-generation TKIs largely mitigate this problem. Some patients develop TKI resistance without known resistance mutations, with significant heterogeneity in the underlying mechanism, but this is relatively uncommon, with the majority of patients with chronic phase CML achieving long-term disease control. In contrast, responses to TKI treatment are short lived in advanced phases of the disease or in BCR-ABL1-positive acute lymphoblastic leukemia, with relapse driven by both BCR-ABL1 kinase-dependent and -independent mechanisms. Additionally, the frontline CML treatment with second-generation TKIs produces deeper molecular responses, driving disease burden below the detection limit for a greater number of patients. For patients with deep molecular responses, up to half have been able to discontinue therapy. Current efforts are focused on identifying therapeutic strategies to drive deeper molecular responses, enabling more patients to attempt TKI discontinuation.
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MESH Headings
- Drug Resistance, Neoplasm/genetics
- Fusion Proteins, bcr-abl/antagonists & inhibitors
- Fusion Proteins, bcr-abl/genetics
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Molecular Targeted Therapy
- Protein Kinase Inhibitors/therapeutic use
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Affiliation(s)
- Theodore P Braun
- Division of Hematology/Medical Oncology, Knight Cancer Insitute, Oregon Health & Science University, Portland, OR, USA.
| | - Christopher A Eide
- Division of Hematology/Medical Oncology, Knight Cancer Insitute, Oregon Health & Science University, Portland, OR, USA
| | - Brian J Druker
- Division of Hematology/Medical Oncology, Knight Cancer Insitute, Oregon Health & Science University, Portland, OR, USA
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79
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Ji Y, Mishra RK, Davuluri RV. In silico analysis of alternative splicing on drug-target gene interactions. Sci Rep 2020; 10:134. [PMID: 31924844 PMCID: PMC6954184 DOI: 10.1038/s41598-019-56894-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 12/18/2019] [Indexed: 12/24/2022] Open
Abstract
Identifying and evaluating the right target are the most important factors in early drug discovery phase. Most studies focus on one protein ignoring the multiple splice-variant or protein-isoforms, which might contribute to unexpected therapeutic activity or adverse side effects. Here, we present computational analysis of cancer drug-target interactions affected by alternative splicing. By integrating information from publicly available databases, we curated 883 FDA approved or investigational stage small molecule cancer drugs that target 1,434 different genes, with an average of 5.22 protein isoforms per gene. Of these, 618 genes have ≥5 annotated protein-isoforms. By analyzing the interactions with binding pocket information, we found that 76% of drugs either miss a potential target isoform or target other isoforms with varied expression in multiple normal tissues. We present sequence and structure level alignments at isoform-level and make this information publicly available for all the curated drugs. Structure-level analysis showed ligand binding pocket architectures differences in size, shape and electrostatic parameters between isoforms. Our results emphasize how potentially important isoform-level interactions could be missed by solely focusing on the canonical isoform, and suggest that on- and off-target effects at isoform-level should be investigated to enhance the productivity of drug-discovery research.
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Affiliation(s)
- Yanrong Ji
- Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Rama K Mishra
- The Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, IL, USA.,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.,Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ramana V Davuluri
- Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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80
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Röhm S, Krämer A, Knapp S. Function, Structure and Topology of Protein Kinases. PROTEINKINASE INHIBITORS 2020. [DOI: 10.1007/7355_2020_97] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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81
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Benz PM, Ding Y, Stingl H, Loot AE, Zink J, Wittig I, Popp R, Fleming I. AKAP12 deficiency impairs VEGF-induced endothelial cell migration and sprouting. Acta Physiol (Oxf) 2020; 228:e13325. [PMID: 31162891 PMCID: PMC6916389 DOI: 10.1111/apha.13325] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 05/31/2019] [Accepted: 05/31/2019] [Indexed: 12/12/2022]
Abstract
Aim Protein kinase (PK) A anchoring protein (AKAP) 12 is a scaffolding protein that anchors PKA to compartmentalize cyclic AMP signalling. This study assessed the consequences of the downregulation or deletion of AKAP12 on endothelial cell migration and angiogenesis. Methods The consequences of siRNA‐mediated downregulation AKAP12 were studied in primary cultures of human endothelial cells as well as in endothelial cells and retinas from wild‐type versus AKAP12−/− mice. Molecular interactions were investigated using a combination of immunoprecipitation and mass spectrometry. Results AKAP12 was expressed at low levels in confluent endothelial cells but its expression was increased in actively migrating cells, where it localized to lamellipodia. In the postnatal retina, AKAP12 was expressed by actively migrating tip cells at the angiogenic front, and its deletion resulted in defective extension of the vascular plexus. In migrating endothelial cells, AKAP12 was co‐localized with the PKA type II‐α regulatory subunit as well as multiple key regulators of actin dynamics and actin filament‐based movement; including components of the Arp2/3 complex and the vasodilator‐stimulated phosphoprotein (VASP). Fitting with the evidence of a physical VASP/AKAP12/PKA complex, it was possible to demonstrate that the VEGF‐stimulated and PKA‐dependent phosphorylation of VASP was dependent on AKAP12. Indeed, AKAP12 colocalized with phospho‐Ser157 VASP at the leading edge of migrating endothelial cells. Conclusion The results suggest that compartmentalized AKAP12/PKA signalling mediates VASP phosphorylation at the leading edge of migrating endothelial cells to translate angiogenic stimuli into altered actin dynamics and cell movement.
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Affiliation(s)
- Peter M. Benz
- Institute for Vascular Signalling, Centre for Molecular Medicine Goethe University Frankfurt am Main Germany
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain Frankfurt am Main Germany
| | - Yindi Ding
- Institute for Vascular Signalling, Centre for Molecular Medicine Goethe University Frankfurt am Main Germany
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain Frankfurt am Main Germany
| | - Heike Stingl
- Institute for Vascular Signalling, Centre for Molecular Medicine Goethe University Frankfurt am Main Germany
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain Frankfurt am Main Germany
| | - Annemarieke E. Loot
- Institute for Vascular Signalling, Centre for Molecular Medicine Goethe University Frankfurt am Main Germany
| | - Joana Zink
- Institute for Vascular Signalling, Centre for Molecular Medicine Goethe University Frankfurt am Main Germany
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain Frankfurt am Main Germany
| | - Ilka Wittig
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain Frankfurt am Main Germany
- Functional Proteomics, SFB 815 Core Unit, Faculty of Medicine Goethe University Frankfurt am Main Germany
| | - Rüdiger Popp
- Institute for Vascular Signalling, Centre for Molecular Medicine Goethe University Frankfurt am Main Germany
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain Frankfurt am Main Germany
| | - Ingrid Fleming
- Institute for Vascular Signalling, Centre for Molecular Medicine Goethe University Frankfurt am Main Germany
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain Frankfurt am Main Germany
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82
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Spassov DS, Ruiz-Saenz A, Piple A, Moasser MM. A Dimerization Function in the Intrinsically Disordered N-Terminal Region of Src. Cell Rep 2019; 25:449-463.e4. [PMID: 30304684 PMCID: PMC6226010 DOI: 10.1016/j.celrep.2018.09.035] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 07/09/2018] [Accepted: 09/12/2018] [Indexed: 01/30/2023] Open
Abstract
The mode of regulation of Src kinases has been elucidated by crystallographic studies identifying conserved structured protein modules involved in an orderly set of intramolecular associations and ligand interactions. Despite these detailed insights, much of the complex behavior and diversity in the Src family remains unexplained. A key missing piece is the function of the unstructured N-terminal region. We report here the function of the N-terminal region in binding within a hydrophobic pocket in the kinase domain of a dimerization partner. Dimerization substantially enhances autophosphorylation and phosphorylation of selected substrates, and interfering with dimerization is disruptive to these functions. Dimerization and Y419 phosphorylation are codependent events creating a bistable switch. Given the versatility inherent in this intrinsically disordered region, its multisite phosphorylations, and its divergence within the family, the unique domain likely functions as a central signaling hub overseeing much of the activities and unique functions of Src family kinases. Spassov et al. report that Src exists in cells and functions as a dimer and that dimerization and autophosphorylation are codependent events. Through a comprehensive structure-function analysis, they show that the dimer is an asymmetric dimer held through the interaction of the myristoylated N-terminal unique domain of one partner with a hydrophobic pocket in the kinase domain of another.
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Affiliation(s)
- Danislav S Spassov
- Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ana Ruiz-Saenz
- Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Amit Piple
- Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mark M Moasser
- Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA.
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83
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Chichirau BE, Diechler S, Posselt G, Wessler S. Tyrosine Kinases in Helicobacter pylori Infections and Gastric Cancer. Toxins (Basel) 2019; 11:toxins11100591. [PMID: 31614680 PMCID: PMC6832112 DOI: 10.3390/toxins11100591] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/02/2019] [Accepted: 10/09/2019] [Indexed: 12/11/2022] Open
Abstract
Helicobacter pylori (H. pylori) has been identified as a leading cause of gastric cancer, which is one of the most frequent and malignant types of tumor. It is characterized by its rapid progression, distant metastases, and resistance to conventional chemotherapy. A number of receptor tyrosine kinases and non-receptor tyrosine kinases have been implicated in H. pylori-mediated pathogenesis and tumorigenesis. In this review, recent findings of deregulated EGFR, c-Met, JAK, FAK, Src, and c-Abl and their functions in H. pylori pathogenesis are summarized.
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Affiliation(s)
- Bianca E Chichirau
- Department of Biosciences, Paris-Lodron University of Salzburg, 5020 Salzburg, Austria.
| | - Sebastian Diechler
- Department of Biosciences, Paris-Lodron University of Salzburg, 5020 Salzburg, Austria.
| | - Gernot Posselt
- Department of Biosciences, Paris-Lodron University of Salzburg, 5020 Salzburg, Austria.
| | - Silja Wessler
- Cancer Cluster Salzburg, Department of Biosciences, Paris-Lodron University of Salzburg, 5020 Salzburg, Austria.
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84
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de Oliveira GAP, Cordeiro Y, Silva JL, Vieira TCRG. Liquid-liquid phase transitions and amyloid aggregation in proteins related to cancer and neurodegenerative diseases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 118:289-331. [PMID: 31928729 DOI: 10.1016/bs.apcsb.2019.08.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Liquid-liquid phase separation (LLPS) and phase transition (LLPT) of proteins and nucleic acids have emerged as a new paradigm in cell biology. Here we will describe the recent findings about LLPS and LLPT, including the molecular and physical determinants leading to their formation, the resulting functions and their implications in cell physiology and disease. Amyloid aggregation is implicated in many neurodegenerative diseases and cancer, and LLPS of proteins involved in these diseases appear to be related to their function in different cell contexts. Amyloid formation would correspond to an irreversible liquid-to-solid transition, as clearly observed in the case of PrP, TDP43, FUS/TLS and tau protein in neurodegenerative pathologies as well as with the mutant tumor suppressor p53 in cancer. Nucleic acids play a modulatory effect on both LLPS and amyloid aggregation. Understanding the molecular events regulating how the demixing process advances to solid-like fibril materials is crucial for the development of novel therapeutic strategies against cancer and neurodegenerative maladies.
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Affiliation(s)
- Guilherme A P de Oliveira
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil; Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - Yraima Cordeiro
- Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro-RJ, Brazil
| | - Jerson L Silva
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Tuane C R G Vieira
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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85
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Dynamic regulatory features of the protein tyrosine kinases. Biochem Soc Trans 2019; 47:1101-1116. [PMID: 31395755 DOI: 10.1042/bst20180590] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/15/2019] [Accepted: 07/17/2019] [Indexed: 12/20/2022]
Abstract
The SRC, Abelson murine leukemia viral oncogene homolog 1, TEC and C-terminal SRC Kinase families of non-receptor tyrosine kinases (collectively the Src module kinases) mediate an array of cellular signaling processes and are therapeutic targets in many disease states. Crystal structures of Src modules kinases provide valuable insights into the regulatory mechanisms that control activation and generate a framework from which drug discovery can advance. The conformational ensembles visited by these multidomain kinases in solution are also key features of the regulatory machinery controlling catalytic activity. Measurement of dynamic motions within kinases substantially augments information derived from crystal structures. In this review, we focus on a body of work that has transformed our understanding of non-receptor tyrosine kinase regulation from a static view to one that incorporates how fluctuations in conformational ensembles and dynamic motions influence activation status. Regulatory dynamic networks are often shared across and between kinase families while specific dynamic behavior distinguishes unique regulatory mechanisms for select kinases. Moreover, intrinsically dynamic regions of kinases likely play important regulatory roles that have only been partially explored. Since there is clear precedence that kinase inhibitors can exploit specific dynamic features, continued efforts to define conformational ensembles and dynamic allostery will be key to combating drug resistance and devising alternate treatments for kinase-associated diseases.
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86
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[Recommendations from the French CML Study Group (Fi-LMC) for BCR-ABL1 kinase domain mutation analysis in chronic myeloid leukemia]. Bull Cancer 2019; 107:113-128. [PMID: 31353136 DOI: 10.1016/j.bulcan.2019.05.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/22/2019] [Accepted: 05/27/2019] [Indexed: 11/22/2022]
Abstract
In the context of chronic myeloid leukemia (CML) resistant to tyrosine kinase inhibitors (TKIs), BCR-ABL1 tyrosine kinase domain (TKD) mutations still remain the sole biological marker that directly condition therapeutic decision. These recommendations aim at updating the use of BCR-ABL1 mutation testing with respect to new available therapeutic options and at repositioning different testing methods at the era of next generation sequencing (NGS). They have been written by a panel of experts from the French Study Group on CML (Fi-LMC), after a critical review of relevant publications. TKD mutation testing is recommended in case of treatment failure but not in case of optimal response. For patients in warning situation, mutation testing must be discussed depending on the type of TKI used, lasting of the treatment, kinetic evolution of BCR-ABL1 transcripts along time and necessity for switching treatment. The kind and the frequency of TKD mutations occasioning resistance mainly depend on the TKI in use and disease phase. Because of its better sensitivity, NGS methods are recommended for mutation testing rather than Sanger's. Facing a given TKD mutation, therapeutic decision should be taken based on in vitro sensitivity and clinical efficacy data. Identification by sequencing of a TKD mutation known to induce resistance must lead to a therapeutic change. The clinical value of testing methods more sensitive than NGS remains to be assessed.
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87
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Chung JK, Nocka LM, Decker A, Wang Q, Kadlecek TA, Weiss A, Kuriyan J, Groves JT. Switch-like activation of Bruton's tyrosine kinase by membrane-mediated dimerization. Proc Natl Acad Sci U S A 2019; 116:10798-10803. [PMID: 31076553 PMCID: PMC6561188 DOI: 10.1073/pnas.1819309116] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The transformation of molecular binding events into cellular decisions is the basis of most biological signal transduction. A fundamental challenge faced by these systems is that reliance on protein-ligand chemical affinities alone generally results in poor sensitivity to ligand concentration, endangering the system to error. Here, we examine the lipid-binding pleckstrin homology and Tec homology (PH-TH) module of Bruton's tyrosine kinase (Btk). Using fluorescence correlation spectroscopy (FCS) and membrane-binding kinetic measurements, we identify a phosphatidylinositol (3-5)-trisphosphate (PIP3) sensing mechanism that achieves switch-like sensitivity to PIP3 levels, surpassing the intrinsic affinity discrimination of PIP3:PH binding. This mechanism employs multiple PIP3 binding as well as dimerization of Btk on the membrane surface. Studies in live cells confirm that mutations at the dimer interface and peripheral site produce effects comparable to that of the kinase-dead Btk in vivo. These results demonstrate how a single protein module can institute an allosteric counting mechanism to achieve high-precision discrimination of ligand concentration. Furthermore, this activation mechanism distinguishes Btk from other Tec family member kinases, Tec and Itk, which we show are not capable of dimerization through their PH-TH modules. This suggests that Btk plays a critical role in the stringency of the B cell response, whereas T cells rely on other mechanisms to achieve stringency.
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Affiliation(s)
- Jean K Chung
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Laura M Nocka
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Aubrianna Decker
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Qi Wang
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Theresa A Kadlecek
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143
| | - Arthur Weiss
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA 94143
- The Howard Hughes Medical Institute, University of California, San Francisco, CA 94143
| | - John Kuriyan
- Department of Chemistry, University of California, Berkeley, CA 94720;
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
| | - Jay T Groves
- Department of Chemistry, University of California, Berkeley, CA 94720;
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88
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A Combined Approach Reveals a Regulatory Mechanism Coupling Src's Kinase Activity, Localization, and Phosphotransferase-Independent Functions. Mol Cell 2019; 74:393-408.e20. [PMID: 30956043 DOI: 10.1016/j.molcel.2019.02.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 11/20/2018] [Accepted: 01/31/2019] [Indexed: 02/06/2023]
Abstract
Multiple layers of regulation modulate the activity and localization of protein kinases. However, many details of kinase regulation remain incompletely understood. Here, we apply saturation mutagenesis and a chemical genetic method for allosterically modulating kinase global conformation to Src kinase, providing insight into known regulatory mechanisms and revealing a previously undiscovered interaction between Src's SH4 and catalytic domains. Abrogation of this interaction increased phosphotransferase activity, promoted membrane association, and provoked phosphotransferase-independent alterations in cell morphology. Thus, Src's SH4 domain serves as an intramolecular regulator coupling catalytic activity, global conformation, and localization, as well as mediating a phosphotransferase-independent function. Sequence conservation suggests that the SH4 domain regulatory interaction exists in other Src-family kinases. Our combined approach's ability to reveal a regulatory mechanism in one of the best-studied kinases suggests that it could be applied broadly to provide insight into kinase structure, regulation, and function.
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89
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Molecular dynamics investigation on the Asciminib resistance mechanism of I502L and V468F mutations in BCR-ABL. J Mol Graph Model 2019; 89:242-249. [PMID: 30927708 DOI: 10.1016/j.jmgm.2019.03.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 02/23/2019] [Accepted: 03/18/2019] [Indexed: 01/29/2023]
Abstract
Asciminib, a highly selective non-ATP competitive inhibitor of BCR-ABL, has demonstrated to be a promising drug for patients with chronic myeloid leukemia. It is a pity that two resistant mutations (I502L and V468F) have been found during the clinical trial, which is a challenge for the curative effect of Asciminib. In this study, molecular dynamics simulations and molecular mechanics generalized Born surface area (MM-GB/SA) calculations were performed to investigate the molecular mechanism of Asciminib resistance induced by the two mutants. The obtained results indicate that the mutations have adversely influence on the binding of Asciminib to BCR-ABL, as the nonpolar contributions decline in the two mutants. In addition, I502L mutation causes α-helix I' (αI') to shift away from the helical bundle composed of αE, αF, and αH, making the distance between αI' and Asciminib increased. For V468F mutant, the side chain of Phe468 occupies the bottom of the myristoyl pocket (MP), which drives Asciminib to shift toward the outside of MP. Our results provide the molecular insights of Asciminib resistance mechanism in BCR-ABL mutants, which may help the design of novel inhibitors.
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90
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Zhu XG, Nicholson Puthenveedu S, Shen Y, La K, Ozlu C, Wang T, Klompstra D, Gultekin Y, Chi J, Fidelin J, Peng T, Molina H, Hang HC, Min W, Birsoy K. CHP1 Regulates Compartmentalized Glycerolipid Synthesis by Activating GPAT4. Mol Cell 2019; 74:45-58.e7. [PMID: 30846317 DOI: 10.1016/j.molcel.2019.01.037] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 11/26/2018] [Accepted: 01/25/2019] [Indexed: 01/10/2023]
Abstract
Cells require a constant supply of fatty acids to survive and proliferate. Fatty acids incorporate into membrane and storage glycerolipids through a series of endoplasmic reticulum (ER) enzymes, but how these enzymes are regulated is not well understood. Here, using a combination of CRISPR-based genetic screens and unbiased lipidomics, we identified calcineurin B homologous protein 1 (CHP1) as a major regulator of ER glycerolipid synthesis. Loss of CHP1 severely reduces fatty acid incorporation and storage in mammalian cells and invertebrates. Mechanistically, CHP1 binds and activates GPAT4, which catalyzes the initial rate-limiting step in glycerolipid synthesis. GPAT4 activity requires CHP1 to be N-myristoylated, forming a key molecular interface between the two proteins. Interestingly, upon CHP1 loss, the peroxisomal enzyme, GNPAT, partially compensates for the loss of ER lipid synthesis, enabling cell proliferation. Thus, our work identifies a conserved regulator of glycerolipid metabolism and reveals plasticity in lipid synthesis of proliferating cells.
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Affiliation(s)
- Xiphias Ge Zhu
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Shirony Nicholson Puthenveedu
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Institute of Pathology, Medical University of Graz, Auenbruggerplatz 25, Graz 8036, Austria
| | - Yihui Shen
- Department of Chemistry and Kavli Institute for Brain Science, Columbia University, New York, NY 10027, USA
| | - Konnor La
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Can Ozlu
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Tim Wang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Diana Klompstra
- Laboratory of Developmental Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Yetis Gultekin
- Laboratory of Apoptosis and Cancer Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Jingyi Chi
- Laboratory of Molecular Metabolism, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Justine Fidelin
- The Proteomics Resource Center, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Tao Peng
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Henrik Molina
- The Proteomics Resource Center, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Howard C Hang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Wei Min
- Department of Chemistry and Kavli Institute for Brain Science, Columbia University, New York, NY 10027, USA
| | - Kıvanç Birsoy
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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91
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Simpson GL, Bertrand SM, Borthwick JA, Campobasso N, Chabanet J, Chen S, Coggins J, Cottom J, Christensen SB, Dawson HC, Evans HL, Hobbs AN, Hong X, Mangatt B, Munoz-Muriedas J, Oliff A, Qin D, Scott-Stevens P, Ward P, Washio Y, Yang J, Young RJ. Identification and Optimization of Novel Small c-Abl Kinase Activators Using Fragment and HTS Methodologies. J Med Chem 2019; 62:2154-2171. [PMID: 30689376 DOI: 10.1021/acs.jmedchem.8b01872] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abelson kinase (c-Abl) is a ubiquitously expressed, nonreceptor tyrosine kinase which plays a key role in cell differentiation and survival. It was hypothesized that transient activation of c-Abl kinase via displacement of the N-terminal autoinhibitory "myristoyl latch", may lead to an increased hematopoietic stem cell differentiation. This would increase the numbers of circulating neutrophils and so be an effective treatment for chemotherapy-induced neutropenia. This paper describes the discovery and optimization of a thiazole series of novel small molecule c-Abl activators, initially identified by a high throughput screening. Subsequently, a scaffold-hop, which exploited the improved physicochemical properties of a dihydropyrazole analogue, identified through fragment screening, delivered potent, soluble, cell-active c-Abl activators, which demonstrated the intracellular activation of c-Abl in vivo.
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Affiliation(s)
- Graham L Simpson
- Medicines Research Centre , GlaxoSmithKline R&D , Gunnels Wood Road , Stevenage , Hertfordshire SG1 2NY , U.K
| | - Sophie M Bertrand
- Medicines Research Centre , GlaxoSmithKline R&D , Gunnels Wood Road , Stevenage , Hertfordshire SG1 2NY , U.K
| | - Jennifer A Borthwick
- Medicines Research Centre , GlaxoSmithKline R&D , Gunnels Wood Road , Stevenage , Hertfordshire SG1 2NY , U.K
| | - Nino Campobasso
- GlaxoSmithKline R&D , 1250 South Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | - Julien Chabanet
- Medicines Research Centre , GlaxoSmithKline R&D , Gunnels Wood Road , Stevenage , Hertfordshire SG1 2NY , U.K
| | | | - Julia Coggins
- Medicines Research Centre , GlaxoSmithKline R&D , Gunnels Wood Road , Stevenage , Hertfordshire SG1 2NY , U.K
| | - Josh Cottom
- GlaxoSmithKline R&D , 1250 South Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | | | - Helen C Dawson
- Medicines Research Centre , GlaxoSmithKline R&D , Gunnels Wood Road , Stevenage , Hertfordshire SG1 2NY , U.K
| | - Helen L Evans
- Medicines Research Centre , GlaxoSmithKline R&D , Gunnels Wood Road , Stevenage , Hertfordshire SG1 2NY , U.K
| | - Andrew N Hobbs
- Medicines Research Centre , GlaxoSmithKline R&D , Gunnels Wood Road , Stevenage , Hertfordshire SG1 2NY , U.K
| | - Xuan Hong
- GlaxoSmithKline R&D , 1250 South Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | - Biju Mangatt
- GlaxoSmithKline R&D , 1250 South Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | - Jordi Munoz-Muriedas
- Medicines Research Centre , GlaxoSmithKline R&D , Gunnels Wood Road , Stevenage , Hertfordshire SG1 2NY , U.K
| | - Allen Oliff
- GlaxoSmithKline R&D , 1250 South Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | - Donghui Qin
- Medicines Research Centre , GlaxoSmithKline R&D , Gunnels Wood Road , Stevenage , Hertfordshire SG1 2NY , U.K
| | - Paul Scott-Stevens
- Medicines Research Centre , GlaxoSmithKline R&D , Gunnels Wood Road , Stevenage , Hertfordshire SG1 2NY , U.K
| | - Paris Ward
- GlaxoSmithKline R&D , 1250 South Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | - Yoshiaki Washio
- Medicines Research Centre , GlaxoSmithKline R&D , Gunnels Wood Road , Stevenage , Hertfordshire SG1 2NY , U.K
| | - Jingsong Yang
- GlaxoSmithKline R&D , 1250 South Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | - Robert J Young
- Medicines Research Centre , GlaxoSmithKline R&D , Gunnels Wood Road , Stevenage , Hertfordshire SG1 2NY , U.K
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92
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Posselt G, Wiesauer M, Chichirau BE, Engler D, Krisch LM, Gadermaier G, Briza P, Schneider S, Boccellato F, Meyer TF, Hauser-Kronberger C, Neureiter D, Müller A, Wessler S. Helicobacter pylori-controlled c-Abl localization promotes cell migration and limits apoptosis. Cell Commun Signal 2019; 17:10. [PMID: 30704478 PMCID: PMC6357398 DOI: 10.1186/s12964-019-0323-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 01/22/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Deregulated c-Abl activity has been intensively studied in a variety of solid tumors and leukemia. The class-I carcinogen Helicobacter pylori (Hp) activates the non-receptor tyrosine kinase c-Abl to phosphorylate the oncoprotein cytotoxin-associated gene A (CagA). The role of c-Abl in CagA-dependent pathways is well established; however, the knowledge of CagA-independent c-Abl processes is scarce. METHODS c-Abl phosphorylation and localization were analyzed by immunostaining and immunofluorescence. Interaction partners were identified by tandem-affinity purification. Cell elongation and migration were analyzed in transwell-filter experiments. Apoptosis and cell survival were examined by FACS analyses and MTT assays. In mice experiments and human biopsies, the involvement of c-Abl in Hp pathogenesis was investigated. RESULTS Here, we investigated the activity and subcellular localization of c-Abl in vitro and in vivo and unraveled the contribution of c-Abl in CagA-dependent and -independent pathways to gastric Hp pathogenesis. We report a novel mechanism and identified strong c-Abl threonine 735 phosphorylation (pAblT735) mediated by the type-IV secretion system (T4SS) effector D-glycero-β-D-manno-heptose-1,7-bisphosphate (βHBP) and protein kinase C (PKC) as a new c-Abl kinase. pAblT735 interacted with 14-3-3 proteins, which caused cytoplasmic retention of c-Abl, where it potentiated Hp-mediated cell elongation and migration. Further, the nuclear exclusion of pAblT735 attenuated caspase-8 and caspase-9-dependent apoptosis. Importantly, in human patients suffering from Hp-mediated gastritis c-Abl expression and pAblT735 phosphorylation were drastically enhanced as compared to type C gastritis patients or healthy individuals. Pharmacological inhibition using the selective c-Abl kinase inhibitor Gleevec confirmed that c-Abl plays an important role in Hp pathogenesis in a murine in vivo model. CONCLUSIONS In this study, we identified a novel regulatory mechanism in Hp-infected gastric epithelial cells by which Hp determines the subcellular localization of activated c-Abl to control Hp-mediated EMT-like processes while decreasing cell death.
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Affiliation(s)
- Gernot Posselt
- Department of Biosciences, Division of Microbiology, University of Salzburg, Paris-Lodron University of Salzburg, Billroth Str. 11, A-5020, Salzburg, Austria
| | - Maria Wiesauer
- Department of Biosciences, Division of Microbiology, University of Salzburg, Paris-Lodron University of Salzburg, Billroth Str. 11, A-5020, Salzburg, Austria
| | - Bianca E Chichirau
- Department of Biosciences, Division of Microbiology, University of Salzburg, Paris-Lodron University of Salzburg, Billroth Str. 11, A-5020, Salzburg, Austria
| | - Daniela Engler
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Linda M Krisch
- Department of Biosciences, Division of Microbiology, University of Salzburg, Paris-Lodron University of Salzburg, Billroth Str. 11, A-5020, Salzburg, Austria
| | - Gabriele Gadermaier
- Department of Biosciences, Division of Allergy and Immunology, University of Salzburg, Paris-Lodron University of Salzburg, Hellbrunner Str. 34, A-5020, Salzburg, Austria
| | - Peter Briza
- Department of Biosciences, Division of Allergy and Immunology, University of Salzburg, Paris-Lodron University of Salzburg, Hellbrunner Str. 34, A-5020, Salzburg, Austria
| | - Sabine Schneider
- Paul-Ehrlich-Institute, Paul-Ehrlich-Str. 51-59, D-63225, Langen, Germany
| | - Francesco Boccellato
- Max Planck Institute for Infection Biology, Charitéplatz 1, D-10117, Berlin, Germany
| | - Thomas F Meyer
- Max Planck Institute for Infection Biology, Charitéplatz 1, D-10117, Berlin, Germany
| | - Cornelia Hauser-Kronberger
- Department of Pathology, Paracelsus Medical University Salzburg, Müllner Hauptstraße 48, A-5020, Salzburg, Austria
| | - Daniel Neureiter
- Department of Pathology, Paracelsus Medical University Salzburg, Müllner Hauptstraße 48, A-5020, Salzburg, Austria.,Cancer Cluster Salzburg, University of Salzburg, A-5020, Salzburg, Austria
| | - Anne Müller
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Silja Wessler
- Department of Biosciences, Division of Microbiology, University of Salzburg, Paris-Lodron University of Salzburg, Billroth Str. 11, A-5020, Salzburg, Austria. .,Cancer Cluster Salzburg, University of Salzburg, A-5020, Salzburg, Austria.
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93
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Agnello S, Brand M, Chellat MF, Gazzola S, Riedl R. A Structural View on Medicinal Chemistry Strategies against Drug Resistance. Angew Chem Int Ed Engl 2019; 58:3300-3345. [PMID: 29846032 DOI: 10.1002/anie.201802416] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/24/2018] [Indexed: 12/31/2022]
Abstract
The natural phenomenon of drug resistance is a widespread issue that hampers the performance of drugs in many major clinical indications. Antibacterial and antifungal drugs are affected, as well as compounds for the treatment of cancer, viral infections, or parasitic diseases. Despite the very diverse set of biological targets and organisms involved in the development of drug resistance, the underlying molecular mechanisms have been identified to understand the emergence of resistance and to overcome this detrimental process. Detailed structural information on the root causes for drug resistance is nowadays frequently available, so next-generation drugs can be designed that are anticipated to suffer less from resistance. This knowledge-based approach is essential for fighting the inevitable occurrence of drug resistance.
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Affiliation(s)
- Stefano Agnello
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Michael Brand
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Mathieu F Chellat
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Silvia Gazzola
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Rainer Riedl
- Institute of Chemistry and Biotechnology, Center for Organic and Medicinal Chemistry, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
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94
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Agnello S, Brand M, Chellat MF, Gazzola S, Riedl R. Eine strukturelle Evaluierung medizinalchemischer Strategien gegen Wirkstoffresistenzen. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201802416] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Stefano Agnello
- Institut für Chemie und Biotechnologie; FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
| | - Michael Brand
- Institut für Chemie und Biotechnologie; FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
| | - Mathieu F. Chellat
- Institut für Chemie und Biotechnologie; FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
| | - Silvia Gazzola
- Institut für Chemie und Biotechnologie; FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
| | - Rainer Riedl
- Institut für Chemie und Biotechnologie; FS Organische Chemie und Medizinalchemie; Zürcher Hochschule für Angewandte Wissenschaften (ZHAW); Einsiedlerstrasse 31 CH-8820 Wädenswil Schweiz
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95
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Understanding molecular mechanisms in cell signaling through natural and artificial sequence variation. Nat Struct Mol Biol 2018; 26:25-34. [PMID: 30598552 DOI: 10.1038/s41594-018-0175-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 11/16/2018] [Indexed: 02/08/2023]
Abstract
The functionally tolerated sequence space of proteins can now be explored in an unprecedented way, owing to the expansion of genomic databases and the development of high-throughput methods to interrogate protein function. For signaling proteins, several recent studies have shown how the analysis of sequence variation leverages the available protein-structure information to provide new insights into specificity and allosteric regulation. In this Review, we discuss recent work that illustrates how this emerging approach is providing a deeper understanding of signaling proteins.
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96
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The biochemical basis of disease. Essays Biochem 2018; 62:619-642. [PMID: 30509933 PMCID: PMC6279435 DOI: 10.1042/ebc20170054] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/26/2018] [Accepted: 10/04/2018] [Indexed: 12/19/2022]
Abstract
This article gives the reader an insight into the role of biochemistry in some of the current global health and disease problems. It surveys the biochemical causes of disease in an accessible and succinct form while also bringing in aspects of pharmacology, cell biology, pathology and physiology which are closely aligned with biochemistry. The discussion of the selected diseases highlights exciting new developments and illuminates key biochemical pathways and commonalities. The article includes coverage of diabetes, atherosclerosis, cancer, microorganisms and disease, nutrition, liver disease and Alzheimer’s disease, but does not attempt to be comprehensive in its coverage of disease, since this is beyond its remit and scope. Consequently there are many fascinating biochemical aspects of diseases, both common and rare, that are not addressed here that can be explored in the further reading cited. Techniques and biochemical procedures for studying disease are not covered in detail here, but these can be found readily in a range of biochemical methods sources.
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Gomes EV, Bortolossi JC, Sanches PR, Mendes NS, Martinez-Rossi NM, Rossi A. STE20/PAKA Protein Kinase Gene Releases an Autoinhibitory Domain through Pre-mRNA Alternative Splicing in the Dermatophyte Trichophyton rubrum. Int J Mol Sci 2018; 19:ijms19113654. [PMID: 30463281 PMCID: PMC6274995 DOI: 10.3390/ijms19113654] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 10/30/2018] [Accepted: 11/16/2018] [Indexed: 12/31/2022] Open
Abstract
Signaling pathways are highly diverse in filamentous fungi, allowing the cells to receive and process ambient information. Interaction of components from different pathways results in signaling networks. The mitogen-activated protein kinase (MAPK) pathway is dependent on phosphorylation that is accomplished by kinase proteins. Thus, the STE/PAK protein kinase family plays essential roles in MAPK signal transduction, regulating several cellular functions. The STE/PAK protein displays an autoinhibitory (Cdc42/Rac interactive binding-CRIB) domain on its N-terminal portion, which interacts with the C-terminal catalytic kinase domain. Based on current knowledge, for the STE/PAK kinase to be activated, molecular signals (e.g., interaction with the activated form of Rac1 and Cdc42 proteins) or proteolytic cleavage by caspase 3 is necessary. Both mechanisms release the kinase domain from the CRIB interaction. Here, we hypothesize a novel molecular mechanism for the activation of STE20/PAKA kinase in Trichophyton rubrum based on an alternative pre-mRNA splicing process. Our data suggest that, because of the retention of intron 1 of this gene, it is theoretically possible that the translation of STE20/PAKA kinase will be free of its autoinhibitory CRIB domain. These findings indicate a rapid response system to environmental changes. Furthermore, STE20/PAKA may be a potential T. rubrum virulence factor and an interesting target for new drugs against dermatophytes.
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Affiliation(s)
- Eriston V Gomes
- Department of Genetics, Ribeirão Preto Medical School, São Paulo University, Ribeirão Preto, São Paulo 14049-900, Brazil.
- Department of Biofunctional, Center of Higher Education Morgana Potrich Eireli, Morgana Potrich College, Mineiros, Goiás 75830-000, Brazil.
| | - Julio C Bortolossi
- Department of Genetics, Ribeirão Preto Medical School, São Paulo University, Ribeirão Preto, São Paulo 14049-900, Brazil.
| | - Pablo R Sanches
- Department of Genetics, Ribeirão Preto Medical School, São Paulo University, Ribeirão Preto, São Paulo 14049-900, Brazil.
| | - Niege S Mendes
- Department of Genetics, Ribeirão Preto Medical School, São Paulo University, Ribeirão Preto, São Paulo 14049-900, Brazil.
| | - Nilce M Martinez-Rossi
- Department of Genetics, Ribeirão Preto Medical School, São Paulo University, Ribeirão Preto, São Paulo 14049-900, Brazil.
| | - Antonio Rossi
- Department of Genetics, Ribeirão Preto Medical School, São Paulo University, Ribeirão Preto, São Paulo 14049-900, Brazil.
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98
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Zhang K, Lyu W, Yu J, Koleske AJ. Abl2 is recruited to ventral actin waves through cytoskeletal interactions to promote lamellipodium extension. Mol Biol Cell 2018; 29:2863-2873. [PMID: 30256707 PMCID: PMC6249870 DOI: 10.1091/mbc.e18-01-0044] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 08/28/2018] [Accepted: 09/19/2018] [Indexed: 01/05/2023] Open
Abstract
Abl family nonreceptor tyrosine kinases regulate changes in cell shape and migration. Abl2 localizes to dynamic actin-rich protrusions, such as lamellipodia in fibroblasts and dendritic spines in neurons. Abl2 interactions with cortactin, an actin filament stabilizer, are crucial for the formation and stability of actin-rich structures, but Abl2:cortactin-positive structures have not been characterized with high spatiotemporal resolution in cells. Using total internal reflection fluorescence microscopy, we demonstrate that Abl2 colocalizes with cortactin at wave-like structures within lamellum and lamellipodium tips. Abl2 and cortactin within waves are focal and transient, extend to the outer edge of lamella, and serve as the base for lamellipodia protrusions. Abl2-positive foci colocalize with integrin β3 and paxillin, adhesive markers of the lamellum-lamellipodium interface. Cortactin-positive waves still form in Abl2 knockout cells, but the lamellipodium size is significantly reduced. This deficiency is restored following Abl2 reexpression. Complementation analyses revealed that the Abl2 C-terminal half, which contains domains that bind actin and microtubules, is necessary and sufficient for recruitment to the wave-like structures and to support normal lamellipodium size, while the kinase domain-containing N-terminal half does not impact lamellipodium size. Together, this work demonstrates that Abl2 is recruited with cortactin to actin waves through cytoskeletal interactions to promote lamellipodium extension.
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Affiliation(s)
- Ke Zhang
- Department of Cell Biology, Yale University, New Haven, CT 06520
| | - Wanqing Lyu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Ji Yu
- Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, CT 06030
| | - Anthony J. Koleske
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
- Department of Neuroscience, Yale University, New Haven, CT 06520
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99
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Shah NH, Amacher JF, Nocka LM, Kuriyan J. The Src module: an ancient scaffold in the evolution of cytoplasmic tyrosine kinases. Crit Rev Biochem Mol Biol 2018; 53:535-563. [PMID: 30183386 PMCID: PMC6328253 DOI: 10.1080/10409238.2018.1495173] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Tyrosine kinases were first discovered as the protein products of viral oncogenes. We now know that this large family of metazoan enzymes includes nearly one hundred structurally diverse members. Tyrosine kinases are broadly classified into two groups: the transmembrane receptor tyrosine kinases, which sense extracellular stimuli, and the cytoplasmic tyrosine kinases, which contain modular ligand-binding domains and propagate intracellular signals. Several families of cytoplasmic tyrosine kinases have in common a core architecture, the "Src module," composed of a Src-homology 3 (SH3) domain, a Src-homology 2 (SH2) domain, and a kinase domain. Each of these families is defined by additional elaborations on this core architecture. Structural, functional, and evolutionary studies have revealed a unifying set of principles underlying the activity and regulation of tyrosine kinases built on the Src module. The discovery of these conserved properties has shaped our knowledge of the workings of protein kinases in general, and it has had important implications for our understanding of kinase dysregulation in disease and the development of effective kinase-targeted therapies.
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Affiliation(s)
- Neel H. Shah
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Jeanine F. Amacher
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Laura M. Nocka
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - John Kuriyan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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100
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Desuppression of TGF-β signaling via nuclear c-Abl-mediated phosphorylation of TIF1γ/TRIM33 at Tyr-524, -610, and -1048. Oncogene 2018; 38:637-655. [PMID: 30177833 DOI: 10.1038/s41388-018-0481-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 07/30/2018] [Accepted: 08/07/2018] [Indexed: 01/26/2023]
Abstract
Protein-tyrosine kinases regulate a broad range of intracellular processes occurring primarily just beneath the plasma membrane. With the greatest care to prevent dephosphorylation, we have shown that nuclear tyrosine phosphorylation regulates global chromatin structural states. However, the roles for tyrosine phosphorylation in the nucleus are poorly understood. Here we identify transcriptional intermediary factor 1-γ (TIF1γ/TRIM33/Ectodermin), which suppresses transforming growth factor-β (TGF-β) signaling through the association with Smad2/3 transcription factor, as a new nuclear substrate of c-Abl tyrosine kinase. Replacement of the three tyrosine residues Tyr-524, -610, and -1048 with phenylalanine (3YF) inhibits c-Abl-mediated phosphorylation of TIF1γ and enhances TIF1γ's association with Smad3. Importantly, knockdown-rescue experiments show that 3YF strengthens TIF1γ's ability to suppress TGF-β signaling. Intriguingly, activation of c-Abl by epidermal growth factor (EGF) induces desuppression of TGF-β signaling via enhancing the tyrosine phosphorylation level of TIF1γ. TGF-β together with EGF synergistically provokes desuppressive responses of epithelial-to-mesenchymal transition through tyrosine phosphorylation of TIF1γ. These results suggest that nuclear c-Abl-mediated tyrosine phosphorylation of TIF1γ has a desuppressive role in TGF-β-Smad2/3 signaling.
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