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Yu JX, Craig AJ, Duffy ME, Villacorta-Martin C, Miguela V, Ruiz de Galarreta M, Scopton AP, Silber L, Maldonado AY, Rialdi A, Guccione E, Lujambio A, Villanueva A, Dar AC. Phenotype-Based Screens with Conformation-Specific Inhibitors Reveal p38 Gamma and Delta as Targets for HCC Polypharmacology. Mol Cancer Ther 2019; 18:1506-1519. [PMID: 31213506 PMCID: PMC7017390 DOI: 10.1158/1535-7163.mct-18-0571] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 03/14/2019] [Accepted: 06/12/2019] [Indexed: 12/24/2022]
Abstract
The approved kinase inhibitors for hepatocellular carcinoma (HCC) are not matched to specific mutations within tumors. This has presented a daunting challenge; without a clear target or mechanism, no straightforward path has existed to guide the development of improved therapies for HCC. Here, we combine phenotypic screens with a class of conformation-specific kinase inhibitors termed type II to identify a multikinase inhibitor, AD80, with antitumoral activity across a variety of HCC preclinical models, including mouse xenografts. Mass spectrometry profiling found a number of kinases as putative targets for AD80, including several receptor and cytoplasmic protein kinases. Among these, we found p38 gamma and delta as direct targets of AD80. Notably, a closely related analog of AD80 lacking p38δ/γ activity, but retaining several other off-target kinases, lost significant activity in several HCC models. Moreover, forced and sustained MKK6 → p38→ATF2 signaling led to a significant reduction of AD80 activity within HCC cell lines. Together with HCC survival data in The Cancer Genome Atlas and RNA-seq analysis, we suggest p38 delta and gamma as therapeutic targets in HCC and an "AD80 inhibition signature" as identifying those patients with best clinical outcomes.
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Affiliation(s)
- Jia Xin Yu
- Department of Oncological Sciences, The Tisch Cancer Institute, The Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Pharmacological Sciences, The Tisch Cancer Institute, The Icahn School of Medicine at Mount Sinai, New York, New York
- Graduate School of Biomedical Sciences at Icahn School of Medicine at Mount Sinai, New York, New York
| | - Amanda J Craig
- Graduate School of Biomedical Sciences at Icahn School of Medicine at Mount Sinai, New York, New York
- Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Mary E Duffy
- Department of Oncological Sciences, The Tisch Cancer Institute, The Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Pharmacological Sciences, The Tisch Cancer Institute, The Icahn School of Medicine at Mount Sinai, New York, New York
- Graduate School of Biomedical Sciences at Icahn School of Medicine at Mount Sinai, New York, New York
| | - Carlos Villacorta-Martin
- Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Verónica Miguela
- Department of Oncological Sciences, The Tisch Cancer Institute, The Icahn School of Medicine at Mount Sinai, New York, New York
- Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Precision Immunology Institute at Icahn School of Medicine at Mount Sinai, New York, New York
| | - Marina Ruiz de Galarreta
- Department of Oncological Sciences, The Tisch Cancer Institute, The Icahn School of Medicine at Mount Sinai, New York, New York
- Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Precision Immunology Institute at Icahn School of Medicine at Mount Sinai, New York, New York
| | - Alexander P Scopton
- Department of Oncological Sciences, The Tisch Cancer Institute, The Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Pharmacological Sciences, The Tisch Cancer Institute, The Icahn School of Medicine at Mount Sinai, New York, New York
| | - Lisa Silber
- Department of Oncological Sciences, The Tisch Cancer Institute, The Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Pharmacological Sciences, The Tisch Cancer Institute, The Icahn School of Medicine at Mount Sinai, New York, New York
| | - Andres Y Maldonado
- Department of Oncological Sciences, The Tisch Cancer Institute, The Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Pharmacological Sciences, The Tisch Cancer Institute, The Icahn School of Medicine at Mount Sinai, New York, New York
| | - Alexander Rialdi
- Department of Oncological Sciences, The Tisch Cancer Institute, The Icahn School of Medicine at Mount Sinai, New York, New York
- Graduate School of Biomedical Sciences at Icahn School of Medicine at Mount Sinai, New York, New York
- Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ernesto Guccione
- Department of Oncological Sciences, The Tisch Cancer Institute, The Icahn School of Medicine at Mount Sinai, New York, New York
- Graduate School of Biomedical Sciences at Icahn School of Medicine at Mount Sinai, New York, New York
- Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Amaia Lujambio
- Department of Oncological Sciences, The Tisch Cancer Institute, The Icahn School of Medicine at Mount Sinai, New York, New York.
- Graduate School of Biomedical Sciences at Icahn School of Medicine at Mount Sinai, New York, New York
- Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Precision Immunology Institute at Icahn School of Medicine at Mount Sinai, New York, New York
| | - Augusto Villanueva
- Graduate School of Biomedical Sciences at Icahn School of Medicine at Mount Sinai, New York, New York.
- Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Arvin C Dar
- Department of Oncological Sciences, The Tisch Cancer Institute, The Icahn School of Medicine at Mount Sinai, New York, New York.
- Department of Pharmacological Sciences, The Tisch Cancer Institute, The Icahn School of Medicine at Mount Sinai, New York, New York
- Graduate School of Biomedical Sciences at Icahn School of Medicine at Mount Sinai, New York, New York
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Sonoshita M, Scopton AP, Ung PMU, Murray MA, Silber L, Maldonado AY, Real A, Schlessinger A, Cagan RL, Dar AC. A whole-animal platform to advance a clinical kinase inhibitor into new disease space. Nat Chem Biol 2018; 14:291-298. [PMID: 29355849 PMCID: PMC5931369 DOI: 10.1038/nchembio.2556] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 11/28/2017] [Indexed: 01/07/2023]
Abstract
Synthetic tailoring of approved drugs for new indications is often difficult, as the most appropriate targets may not be readily apparent, and therefore few roadmaps exist to guide chemistry. Here, we report a multidisciplinary approach for accessing novel target and chemical space starting from an FDA-approved kinase inhibitor. By combining chemical and genetic modifier screening with computational modeling, we identify distinct kinases that strongly enhance ('pro-targets') or limit ('anti-targets') whole-animal activity of the clinical kinase inhibitor sorafenib in a Drosophila medullary thyroid carcinoma (MTC) model. We demonstrate that RAF-the original intended sorafenib target-and MKNK kinases function as pharmacological liabilities because of inhibitor-induced transactivation and negative feedback, respectively. Through progressive synthetic refinement, we report a new class of 'tumor calibrated inhibitors' with unique polypharmacology and strongly improved therapeutic index in fly and human MTC xenograft models. This platform provides a rational approach to creating new high-efficacy and low-toxicity drugs.
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Affiliation(s)
- Masahiro Sonoshita
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Systems Neuropharmacology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Alex P Scopton
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Peter M U Ung
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Matthew A Murray
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Biomedical Sciences, Florida State University, Tallahassee, Florida, USA
| | - Lisa Silber
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Andres Y Maldonado
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Alexander Real
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ross L Cagan
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Arvin C Dar
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Israelow B, Mullokandov G, Agudo J, Sourisseau M, Bashir A, Maldonado AY, Dar AC, Brown BD, Evans MJ. Hepatitis C virus genetics affects miR-122 requirements and response to miR-122 inhibitors. Nat Commun 2014; 5:5408. [PMID: 25403145 PMCID: PMC4236719 DOI: 10.1038/ncomms6408] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Accepted: 09/29/2014] [Indexed: 12/19/2022] Open
Abstract
Hepatitis C virus (HCV) replication is dependent on a liver-specific microRNA (miRNA), miR-122. A recent clinical trial reported that transient inhibition of miR-122 reduced viral titers in HCV infected patients. Here we set out to better understand how miR-122 inhibition influences HCV replication over time. Unexpectedly, we observed the emergence of a HCV variant that is resistant to miR-122 knockdown. Next-generation sequencing revealed that this was due to a single nucleotide change at position 28 (G28A) of the HCV genome, which falls between the two miR-122 seed-binding sites. Naturally occurring HCV isolates encoding G28A are similarly resistant to miR-122 inhibition, indicating that subtle differences in viral sequence, even outside the seed-binding site, greatly influence HCV’s miR-122 concentration requirement. Additionally, we found that HCV itself reduces miR-122’s activity in the cell, possibly through binding and sequestering miR-122. Our study provides insight into the interaction between miR-122 and HCV, including viral adaptation to reduced miR-122 bioavailability, and has implications for the development of anti-miR-122-based HCV drugs.
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Affiliation(s)
- Benjamin Israelow
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1124, New York, New York 10029, USA
| | - Gavriel Mullokandov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1124, New York, New York 10029, USA
| | - Judith Agudo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1124, New York, New York 10029, USA
| | - Marion Sourisseau
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1124, New York, New York 10029, USA
| | - Ali Bashir
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1124, New York, New York 10029, USA
| | - Andres Y Maldonado
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1124, New York, New York 10029, USA
| | - Arvin C Dar
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1124, New York, New York 10029, USA
| | - Brian D Brown
- 1] Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1124, New York, New York 10029, USA [2] Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1124, New York, New York 10029, USA [3] Diabetes, Metabolism and Obesity Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1124, New York, New York 10029, USA [4] Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1124, New York, New York 10029, USA
| | - Matthew J Evans
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1124, New York, New York 10029, USA
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Abstract
The Mycobacterium tuberculosis proteasome is required for maximum virulence and to resist killing by the host immune system. The prokaryotic ubiquitin-like protein, Pup-GGE, targets proteins for proteasome-mediated degradation. We demonstrate that Pup-GGQ, a precursor of Pup-GGE, is not a substrate for proteasomal degradation. Using STINT-NMR, an in-cell NMR technique, we studied the interactions between Pup-GGQ, mycobacterial proteasomal ATPase, Mpa, and Mtb proteasome core particle (CP) inside a living cell at amino acid residue resolution. We showed that under in-cell conditions, in the absence of the proteasome CP, Pup-GGQ interacts with Mpa only weakly, primarily through its C-terminal region. When Mpa and non-stoichiometric amounts of proteasome CP are present, both the N-terminal and C-terminal regions of Pup-GGQ bind strongly to Mpa. This suggests a mechanism by which transient binding of Mpa to the proteasome CP controls the fate of Pup.
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Affiliation(s)
- Andres Y. Maldonado
- Department of Chemistry, State University of New York at Albany, Albany, New York, United States of America
| | - David S. Burz
- Department of Chemistry, State University of New York at Albany, Albany, New York, United States of America
| | - Sergey Reverdatto
- Department of Chemistry, State University of New York at Albany, Albany, New York, United States of America
| | - Alexander Shekhtman
- Department of Chemistry, State University of New York at Albany, Albany, New York, United States of America
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