1
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Paternot S, Raspé E, Meiller C, Tarabichi M, Assié J, Libert F, Remmelink M, Bisteau X, Pauwels P, Blum Y, Le Stang N, Tabone‐Eglinger S, Galateau‐Sallé F, Blanquart C, Van Meerbeeck JP, Berghmans T, Jean D, Roger PP. Preclinical evaluation of CDK4 phosphorylation predicts high sensitivity of pleural mesotheliomas to CDK4/6 inhibition. Mol Oncol 2024; 18:866-894. [PMID: 36453028 PMCID: PMC10994244 DOI: 10.1002/1878-0261.13351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 11/04/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022] Open
Abstract
Malignant pleural mesothelioma (MPM) is an aggressive cancer with limited therapeutic options. We evaluated the impact of CDK4/6 inhibition by palbociclib in 28 MPM cell lines including 19 patient-derived ones, using various approaches including RNA-sequencing. Palbociclib strongly and durably inhibited the proliferation of 23 cell lines, indicating a unique sensitivity of MPM to CDK4/6 inhibition. When observed, insensitivity to palbociclib was mostly explained by the lack of active T172-phosphorylated CDK4. This was associated with high p16INK4A (CDKN2A) levels that accompany RB1 defects or inactivation, or (unexpectedly) CCNE1 overexpression in the presence of wild-type RB1. Prolonged palbociclib treatment irreversibly inhibited proliferation despite re-induction of cell cycle genes upon drug washout. A senescence-associated secretory phenotype including various potentially immunogenic components was irreversibly induced. Phosphorylated CDK4 was detected in 80% of 47 MPMs indicating their sensitivity to CDK4/6 inhibitors. Its absence in some highly proliferative MPMs was linked to very high p16 (CDKN2A) expression, which was also observed in public datasets in tumours from short-survival patients. Our study supports the evaluation of CDK4/6 inhibitors for MPM treatment, in monotherapy or combination therapy.
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Affiliation(s)
- Sabine Paternot
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM)Université Libre de BruxellesBelgium
- ULB‐Cancer Research Center (U‐CRC)Université Libre de BruxellesBelgium
| | - Eric Raspé
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM)Université Libre de BruxellesBelgium
- ULB‐Cancer Research Center (U‐CRC)Université Libre de BruxellesBelgium
| | - Clément Meiller
- Université de ParisCentre de Recherche des Cordeliers, Inserm, Sorbonne Université, Functional Genomics of Solid TumorsFrance
| | - Maxime Tarabichi
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM)Université Libre de BruxellesBelgium
- ULB‐Cancer Research Center (U‐CRC)Université Libre de BruxellesBelgium
| | - Jean‐Baptiste Assié
- Université de ParisCentre de Recherche des Cordeliers, Inserm, Sorbonne Université, Functional Genomics of Solid TumorsFrance
- CEpiA (Clinical Epidemiology and Ageing), EA 7376‐IMRBUniversity Paris‐Est CréteilFrance
- GRC OncoThoParisEst, Service de Pneumologie, CHI Créteil, UPECCréteilFrance
| | - Frederick Libert
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM)Université Libre de BruxellesBelgium
- ULB‐Cancer Research Center (U‐CRC)Université Libre de BruxellesBelgium
- BRIGHTCore, ULBBrusselsBelgium
| | - Myriam Remmelink
- Department of Pathology, Erasme HospitalUniversité Libre de BruxellesBelgium
| | - Xavier Bisteau
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM)Université Libre de BruxellesBelgium
- ULB‐Cancer Research Center (U‐CRC)Université Libre de BruxellesBelgium
| | - Patrick Pauwels
- Center for Oncological Research (CORE)Integrated Personalized and Precision Oncology Network (IPPON)WilrijkBelgium
- Department of PathologyAntwerp University HospitalEdegemBelgium
| | - Yuna Blum
- Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre Le CancerParisFrance
- Present address:
IGDR UMR 6290, CNRS, Université de Rennes 1France
| | - Nolwenn Le Stang
- MESOBANK, Department of Biopathology, Centre Léon BérardLyonFrance
| | | | - Françoise Galateau‐Sallé
- MESOBANK, Department of Biopathology, Centre Léon BérardLyonFrance
- Cancer Research Center INSERM U1052‐CNRS 5286RLyonFrance
| | | | | | - Thierry Berghmans
- Clinic of Thoracic OncologyInstitut Jules Bordet, Université Libre de BruxellesBrusselsBelgium
| | - Didier Jean
- Université de ParisCentre de Recherche des Cordeliers, Inserm, Sorbonne Université, Functional Genomics of Solid TumorsFrance
| | - Pierre P. Roger
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM)Université Libre de BruxellesBelgium
- ULB‐Cancer Research Center (U‐CRC)Université Libre de BruxellesBelgium
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2
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Schmitt DL, Dranchak P, Parajuli P, Blivis D, Voss T, Kohnhorst CL, Kyoung M, Inglese J, An S. High-throughput screening identifies cell cycle-associated signaling cascades that regulate a multienzyme glucosome assembly in human cells. PLoS One 2023; 18:e0289707. [PMID: 37540718 PMCID: PMC10403072 DOI: 10.1371/journal.pone.0289707] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 07/25/2023] [Indexed: 08/06/2023] Open
Abstract
We have previously demonstrated that human liver-type phosphofructokinase 1 (PFK1) recruits other rate-determining enzymes in glucose metabolism to organize multienzyme metabolic assemblies, termed glucosomes, in human cells. However, it has remained largely elusive how glucosomes are reversibly assembled and disassembled to functionally regulate glucose metabolism and thus contribute to human cell biology. We developed a high-content quantitative high-throughput screening (qHTS) assay to identify regulatory mechanisms that control PFK1-mediated glucosome assemblies from stably transfected HeLa Tet-On cells. Initial qHTS with a library of pharmacologically active compounds directed following efforts to kinase-inhibitor enriched collections. Consequently, three compounds that were known to inhibit cyclin-dependent kinase 2, ribosomal protein S6 kinase and Aurora kinase A, respectively, were identified and further validated under high-resolution fluorescence single-cell microscopy. Subsequent knockdown studies using small-hairpin RNAs further confirmed an active role of Aurora kinase A on the formation of PFK1 assemblies in HeLa cells. Importantly, all the identified protein kinases here have been investigated as key signaling nodes of one specific cascade that controls cell cycle progression in human cells. Collectively, our qHTS approaches unravel a cell cycle-associated signaling network that regulates the formation of PFK1-mediated glucosome assembly in human cells.
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Affiliation(s)
- Danielle L. Schmitt
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), Baltimore, Maryland, United States of America
| | - Patricia Dranchak
- National Institutes of Health, National Center for Advancing Translational Sciences, Rockville, Maryland, United States of America
| | - Prakash Parajuli
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), Baltimore, Maryland, United States of America
| | - Dvir Blivis
- National Institutes of Health, National Center for Advancing Translational Sciences, Rockville, Maryland, United States of America
| | - Ty Voss
- National Institutes of Health, National Center for Advancing Translational Sciences, Rockville, Maryland, United States of America
| | - Casey L. Kohnhorst
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), Baltimore, Maryland, United States of America
| | - Minjoung Kyoung
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), Baltimore, Maryland, United States of America
- Program in Oncology, Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, Maryland, United States of America
| | - James Inglese
- National Institutes of Health, National Center for Advancing Translational Sciences, Rockville, Maryland, United States of America
- National Institutes of Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Songon An
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), Baltimore, Maryland, United States of America
- Program in Oncology, Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, Maryland, United States of America
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3
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Hong S, Jeon M, Kwon J, Park H, Lee G, Kim K, Ahn S. Targeting RAF Isoforms and Tumor Microenvironments in RAS or BRAF Mutant Colorectal Cancers with SJ-C1044 for Anti-Tumor Activity. Curr Issues Mol Biol 2023; 45:5865-5878. [PMID: 37504287 PMCID: PMC10378394 DOI: 10.3390/cimb45070371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 07/09/2023] [Accepted: 07/10/2023] [Indexed: 07/29/2023] Open
Abstract
Colorectal cancer (CRC) is a significant global health issue characterized by a high prevalence of KRAS gene mutations. The RAS/MAPK pathway, involving KRAS, plays a crucial role in CRC progression. Although some RAS inhibitors have been approved, their efficacy in CRC is limited. To overcome these limitations, pan-RAF inhibitors targeting A-Raf, B-Raf, and C-Raf have emerged as promising therapeutic strategies. However, resistance to RAF inhibition and the presence of an immunosuppressive tumor microenvironment (TME) pose additional obstacles to effective therapy. Here, we evaluated the potential of a novel pan-RAF inhibitor, SJ-C1044, for targeting mutant KRAS-mediated signaling and inhibiting CRC cell proliferation. Notably, SJ-C1044 also exhibited inhibitory effects on immunokinases, specifically, CSF1R, VEGFR2, and TIE2, which play crucial roles in immune suppression. SJ-C1044 demonstrated potent antitumor activity in xenograft models of CRC harboring KRAS or BRAF mutations. Importantly, treatment with SJ-C1044 resulted in increased infiltration of T cells and reduced presence of tumor-associated macrophages and regulatory T cells within the TME. Thus, SJ-C1044 shows immunomodulatory potential and the ability to enhance antitumor responses. The study underscores the therapeutic potential of SJ-C1044 as a novel pan-RAF inhibitor capable of targeting oncogenic signaling pathways and overcoming immune suppression in CRC.
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Affiliation(s)
- Sungpyo Hong
- Institute for New Drug Development, Division of Life Sciences, Incheon National University, Incheon 22012, Republic of Korea; (S.H.)
| | - Myeongjin Jeon
- Research Center, Samjin Pharm. Co., Ltd., Seoul 07794, Republic of Korea; (M.J.); (G.L.)
| | - Jeonghee Kwon
- Institute for New Drug Development, Division of Life Sciences, Incheon National University, Incheon 22012, Republic of Korea; (S.H.)
| | - Hanbyeol Park
- Institute for New Drug Development, Division of Life Sciences, Incheon National University, Incheon 22012, Republic of Korea; (S.H.)
| | - Goeun Lee
- Research Center, Samjin Pharm. Co., Ltd., Seoul 07794, Republic of Korea; (M.J.); (G.L.)
| | - Kilwon Kim
- Institute for New Drug Development, Division of Life Sciences, Incheon National University, Incheon 22012, Republic of Korea; (S.H.)
| | - Soonkil Ahn
- Institute for New Drug Development, Division of Life Sciences, Incheon National University, Incheon 22012, Republic of Korea; (S.H.)
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4
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Roy A, Chakraborty AR, Nomanbhoy T, DePamphilis ML. PIP5K1C phosphoinositide kinase deficiency distinguishes PIKFYVE-dependent cancer cells from non-malignant cells. Autophagy 2023:1-21. [PMID: 36803256 PMCID: PMC10392749 DOI: 10.1080/15548627.2023.2182594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
Although PIKFYVE phosphoinositide kinase inhibitors can selectively eliminate PIKFYVE-dependent human cancer cells in vitro and in vivo, the basis for this selectivity has remained elusive. Here we show that the sensitivity of cells to the PIKFYVE inhibitor WX8 is not linked to PIKFYVE expression, macroautophagic/autophagic flux, the BRAFV600E mutation, or ambiguous inhibitor specificity. PIKFYVE dependence results from a deficiency in the PIP5K1C phosphoinositide kinase, an enzyme required for conversion of phosphatidylinositol-4-phosphate (PtdIns4P) into phosphatidylinositol-4,5-bisphosphate (PtdIns[4,5]P2/PIP2), a phosphoinositide associated with lysosome homeostasis, endosome trafficking, and autophagy. PtdIns(4,5)P2 is produced via two independent pathways. One requires PIP5K1C; the other requires PIKFYVE and PIP4K2C to convert PtdIns3P into PtdIns(4,5)P2. In PIKFYVE-dependent cells, low concentrations of WX8 specifically inhibit PIKFYVE in situ, thereby increasing the level of its substrate PtdIns3P while suppressing PtdIns(4,5)P2 synthesis and inhibiting lysosome function and cell proliferation. At higher concentrations, WX8 inhibits both PIKFYVE and PIP4K2C in situ, which amplifies these effects to further disrupt autophagy and induce cell death. WX8 did not alter PtdIns4P levels. Consequently, inhibition of PIP5K1C in WX8-resistant cells transformed them into sensitive cells, and overexpression of PIP5K1C in WX8-sensitive cells increased their resistance to WX8. This discovery suggests that PIKFYVE-dependent cancers could be identified clinically by low levels of PIP5K1C and treated with PIKFYVE inhibitors.
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Affiliation(s)
- Ajit Roy
- Division of Developmental Biology, National Institute of Child Health & Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Arup R Chakraborty
- Division of Developmental Biology, National Institute of Child Health & Human Development, National Institutes of Health, Bethesda, MD, USA
| | | | - Melvin L DePamphilis
- Division of Developmental Biology, National Institute of Child Health & Human Development, National Institutes of Health, Bethesda, MD, USA
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5
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Sharma V, Gupta M. Designing of kinase hinge binders: A medicinal chemistry perspective. Chem Biol Drug Des 2022; 100:968-980. [PMID: 35112799 DOI: 10.1111/cbdd.14024] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 01/16/2022] [Accepted: 01/29/2022] [Indexed: 01/25/2023]
Abstract
Protein kinases are key regulators of cellular signaling and play a critical role in oncogenesis. Inhibitors of protein kinases are pursued by both industry and academia as a promising target for cancer therapy. Within the protein kinases, the ATP site has produced more than 40 FDA-approved drugs. The ATP site is broadly composed of a hinge region, gatekeeper residues, DFG-loop, ribose pocket, and other hydrophobic regions. The hinge region in the ATP site can be used for designing potent inhibitors. In this review, we discuss some representative studies that will highlight the interactions of heterocyclic compounds with hinge regions of different kinases like BRAF kinase, EGRF kinase, MAP kinase, and Mps1 kinase.
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Affiliation(s)
- Vikas Sharma
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, India
| | - Mohit Gupta
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Portland, Oregon, USA.,GreenLight Biosciences, Woburn, MA, United States
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6
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Channathodiyil P, May K, Segonds-Pichon A, Smith PD, Cook S, Houseley J. Escape from G1 arrest during acute MEK inhibition drives the acquisition of drug resistance. NAR Cancer 2022; 4:zcac032. [PMID: 36267209 PMCID: PMC9575185 DOI: 10.1093/narcan/zcac032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 09/08/2022] [Accepted: 10/04/2022] [Indexed: 11/13/2022] Open
Abstract
Mutations and gene amplifications that confer drug resistance emerge frequently during chemotherapy, but their mechanism and timing are poorly understood. Here, we investigate BRAFV600E amplification events that underlie resistance to the MEK inhibitor selumetinib (AZD6244/ARRY-142886) in COLO205 cells, a well-characterized model for reproducible emergence of drug resistance, and show that BRAF amplifications acquired de novo are the primary cause of resistance. Selumetinib causes long-term G1 arrest accompanied by reduced expression of DNA replication and repair genes, but cells stochastically re-enter the cell cycle during treatment despite continued repression of pERK1/2. Most DNA replication and repair genes are re-expressed as cells enter S and G2; however, mRNAs encoding a subset of factors important for error-free replication and chromosome segregation, including TIPIN, PLK2 and PLK3, remain at low abundance. This suggests that DNA replication following escape from G1 arrest in drug is more error prone and provides a potential explanation for the DNA damage observed under long-term RAF-MEK-ERK1/2 pathway inhibition. To test the hypothesis that escape from G1 arrest in drug promotes de novo BRAF amplification, we exploited the combination of palbociclib and selumetinib. Combined treatment with selumetinib and a dose of palbociclib sufficient to reinforce G1 arrest in selumetinib-sensitive cells, but not to impair proliferation of resistant cells, delays the emergence of resistant colonies, meaning that escape from G1 arrest is critical in the formation of resistant clones. Our findings demonstrate that acquisition of MEK inhibitor resistance often occurs through de novo gene amplification and can be suppressed by impeding cell cycle entry in drug.
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Affiliation(s)
| | - Kieron May
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 4NT, UK
| | | | - Paul D Smith
- Oncology R&D, AstraZeneca CRUK Cambridge Institute, Cambridge, CB2 0AA, UK
| | - Simon J Cook
- Signalling Programme, Babraham Institute, Cambridge, CB22 4NT, UK
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7
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Polisety A, Misra G, Rajawat J, Katiyar A, Singh H, Bhatt AN. Therapeutic natural compounds Enzastaurin and Palbociclib inhibit MASTL kinase activity preventing breast cancer cell proliferation. Med Oncol 2022; 39:100. [PMID: 35599277 PMCID: PMC9124600 DOI: 10.1007/s12032-022-01701-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/01/2022] [Indexed: 11/29/2022]
Abstract
Microtubule-associated serine/threonine kinase-like (MASTL) regulates mitotic progression and is an attractive target for the development of new anticancer drugs. In this study, novel inhibitory molecules were screened against MASTL kinase, a protein involved in cell proliferation in breast cancer. Natural source-derived drugs Enzastaurin and Palbociclib were selected to identify their role as MASTL kinase inhibitors. Cytotoxic activity, kinase activity, and other cell-based assays of Enzastaurin and Palbociclib were evaluated on human breast cancer (MCF-7) cells. The potential natural compounds caused cytotoxicity in MCF-7 cells in a dose- and time-dependent manner. Further analysis by Annexin V and PI staining indicated that both drugs are potent inducers of apoptosis. Enzastaurin induced G2/M phase arrest, while Palbociclib caused G1 arrest. MASTL kinase activity was significantly abrogated with both the compounds showing EC50 values of 17.13 µM and 10.51 µM, respectively. Taken together, these data strongly suggest that Enzastaurin and Palbociclib possess the ability to inhibit MASTL kinase activity and induce cell death in breast cancer cells, thus exhibiting significant therapeutic potential.
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Affiliation(s)
- Aneesha Polisety
- Molecular Diagnostic & Covid-19 Kit Testing Laboratory, National Institute of Biologicals (NIB), A-32, Sector-62, Institutional Area Noida, Noida, 201309, UP, India
| | - Gauri Misra
- Molecular Diagnostic & Covid-19 Kit Testing Laboratory, National Institute of Biologicals (NIB), A-32, Sector-62, Institutional Area Noida, Noida, 201309, UP, India.
| | - Jyotika Rajawat
- Department of Zoology, University of Lucknow, Lucknow, India
| | - Amit Katiyar
- CCRF: Bioinformatics Facility, All India Institute of Medical Sciences, Delhi, India
| | - Harpreet Singh
- Division of Biomedical Informatics, Data Management Laboratory, ICMR-AIIMS Computational Genomics Centre, Indian Council of Medical Research, New Delhi, India
| | - Anant Narayan Bhatt
- Division of Radiation Biosciences, Institute of Nuclear Medicine and Allied Sciences, Delhi, India
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8
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Wang B, Wu H, Hu C, Wang H, Liu J, Wang W, Liu Q. An overview of kinase downregulators and recent advances in discovery approaches. Signal Transduct Target Ther 2021; 6:423. [PMID: 34924565 PMCID: PMC8685278 DOI: 10.1038/s41392-021-00826-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 10/28/2021] [Accepted: 11/05/2021] [Indexed: 12/17/2022] Open
Abstract
Since the clinical approval of imatinib, the discovery of protein kinase downregulators entered a prosperous age. However, challenges still exist in the discovery of kinase downregulator drugs, such as the high failure rate during development, side effects, and drug-resistance problems. With the progress made through multidisciplinary efforts, an increasing number of new approaches have been applied to solve the above problems during the discovery process of kinase downregulators. In terms of in vitro and in vivo drug evaluation, progress was also made in cellular and animal model platforms for better and more clinically relevant drug assessment. Here, we review the advances in drug design strategies, drug property evaluation technologies, and efficacy evaluation models and technologies. Finally, we discuss the challenges and perspectives in the development of kinase downregulator drugs.
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Affiliation(s)
- Beilei Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Hong Wu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Chen Hu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Haizhen Wang
- Hefei PreceDo pharmaceuticals Co., Ltd, Hefei, Anhui, 230088, People's Republic of China
| | - Jing Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Wenchao Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Qingsong Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China.
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China.
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9
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Coulonval K, Vercruysse V, Paternot S, Pita JM, Corman R, Raspé E, Roger PP. Monoclonal antibodies to activated CDK4: use to investigate normal and cancerous cell cycle regulation and involvement of phosphorylations of p21 and p27. Cell Cycle 2021; 21:12-32. [PMID: 34913830 PMCID: PMC8837260 DOI: 10.1080/15384101.2021.1984663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Cyclin-dependent kinase 4 (CDK4) is a master integrator that couples mitogenic/oncogenic signaling with the cell division cycle. It is deregulated in most cancers and inhibitors of CDK4 have become standard of care drugs for metastatic estrogen-receptor positive breast cancers and are being evaluated in a variety of other cancers. We previously characterized the T-loop phosphorylation at T172 of CDK4 as the highly regulated step that determines the activity of cyclin D-CDK4 complexes. Moreover we demonstrated that the highly variable detection of T172-phosphorylated CDK4 signals the presence or absence of the active CDK4 targeted by the CDK4/6 inhibitory drugs, which predicts the tumor cell sensitivity to these drugs including palbociclib. To date, the phosphorylation of CDK4 has been very poorly studied because only few biochemical techniques and reagents are available for it. In addition, the available ones including 2D-IEF separation of CDK4 modified forms are considered too tedious. The present report describes the generation, selection and characterization of the first monoclonal antibodies that specifically recognize the active CDK4 phosphorylated on its T172 residue. One key to this success was the immunization with a long phosphopeptide corresponding to the complete activation segment of CDK4. These monoclonal antibodies specifically recognize T172-phosphorylated CDK4 in a variety of assays, including western blotting, immunoprecipitation and, as a capture antibody, a sensitive ELISA from cell lysates. The specific immunoprecipitation of T172-phosphorylated CDK4 allowed to clarify the involvement of phosphorylations of co-immunoprecipitated p21 and p27, showing a privileged interaction of T172-phosphorylated CDK4 with S130-phosphorylated p21 and S10-phosphorylated p27.
Abbreviations:
2D: two-dimensional; CAK: CDK-activating kinase; CDK: cyclin-dependent kinase; HAT: Hypoxanthine-Aminopterin-Thymidine; FBS: fetal bovine serum; IP: immunoprecipitation; ID: immunodetection; mAb: monoclonal antibody; PAGE: polyacrylamide gel electrophoresis; PBS: phosphate buffer saline; pRb: retinoblastoma susceptibility protein; SDS: sodium dodecyl sulfate; DTT: dithiotreitol; TET: tetracyclin repressor; Avi: Avi tag; TEV: tobacco etch virus cleavage site; EGFP: enhanced green fluorescent protein; BirA: bifunctional protein biotin ligase BirA; IRES: internal ribosome entry site; HIS: poly-HIS purification tag; DELFIA: dissociation-enhanced lanthanide fluorescent immunoassay; 3-MBPP1: 1-(1,1-dimethylethyl)-3[(3-methylphenyl) methyl]-1H-pyrazolo[3,4-d] pyrimidin-4-amine; BSA: bovine serum albumin; ECL: Enhanced chemiluminescence
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Affiliation(s)
- Katia Coulonval
- Institute of Interdisciplinary Research (Iribhm) and ULB-Cancer Research Center (U-crc), Université Libre de Bruxelles, Campus Erasme, Brussels, Belgium
| | - Vincent Vercruysse
- Institute of Interdisciplinary Research (Iribhm) and ULB-Cancer Research Center (U-crc), Université Libre de Bruxelles, Campus Erasme, Brussels, Belgium
| | - Sabine Paternot
- Institute of Interdisciplinary Research (Iribhm) and ULB-Cancer Research Center (U-crc), Université Libre de Bruxelles, Campus Erasme, Brussels, Belgium
| | - Jaime M Pita
- Institute of Interdisciplinary Research (Iribhm) and ULB-Cancer Research Center (U-crc), Université Libre de Bruxelles, Campus Erasme, Brussels, Belgium
| | - Robert Corman
- Kaneka Eurogentec, Liège Science Park, Seraing, Belgium
| | - Eric Raspé
- Institute of Interdisciplinary Research (Iribhm) and ULB-Cancer Research Center (U-crc), Université Libre de Bruxelles, Campus Erasme, Brussels, Belgium
| | - Pierre P Roger
- Institute of Interdisciplinary Research (Iribhm) and ULB-Cancer Research Center (U-crc), Université Libre de Bruxelles, Campus Erasme, Brussels, Belgium
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10
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Wu X, Yang X, Xiong Y, Li R, Ito T, Ahmed TA, Karoulia Z, Adamopoulos C, Wang H, Wang L, Xie L, Liu J, Ueberheide B, Aaronson SA, Chen X, Buchanan SG, Sellers WR, Jin J, Poulikakos PI. Distinct CDK6 complexes determine tumor cell response to CDK4/6 inhibitors and degraders. NATURE CANCER 2021; 2:429-443. [PMID: 34568836 PMCID: PMC8462800 DOI: 10.1038/s43018-021-00174-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 01/21/2021] [Indexed: 12/26/2022]
Abstract
CDK4/6 inhibitors (CDK4/6i) are effective in metastatic breast cancer, but they have been only modestly effective in most other tumor types. Here we show that tumors expressing low CDK6 rely on CDK4 function, and are exquisitely sensitive to CDK4/6i. In contrast, tumor cells expressing both CDK4 and CDK6 have increased reliance on CDK6 to ensure cell cycle progression. We discovered that CDK4/6i and CDK4/6 degraders potently bind and inhibit CDK6 selectively in tumors in which CDK6 is highly thermo-unstable and strongly associated with the HSP90/CDC37 complex. In contrast, CDK4/6i and CDK4/6 degraders are ineffective in antagonizing tumor cells expressing thermostable CDK6, due to their weaker binding to CDK6 in these cells. Thus, we uncover a general mechanism of intrinsic resistance to CDK4/6i and CDK4/6i-derived degraders and the need for novel inhibitors targeting the CDK4/6i-resistant, thermostable form of CDK6 for application as cancer therapeutics.
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Affiliation(s)
- Xuewei Wu
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xiaobao Yang
- Department of Pharmacological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yan Xiong
- Department of Pharmacological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruitong Li
- The Broad Institute of Harvard and MIT, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Takahiro Ito
- The Broad Institute of Harvard and MIT, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Tamer A Ahmed
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zoi Karoulia
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christos Adamopoulos
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hong Wang
- Eli Lilly and Company, Indianapolis, IN, USA
| | - Li Wang
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA
| | - Ling Xie
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA
| | - Jing Liu
- Department of Pharmacological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Beatrix Ueberheide
- Department of Biochemistry and Molecular Pharmacology, New York University, New York, NY, USA
| | - Stuart A Aaronson
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xian Chen
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA
| | | | - William R Sellers
- The Broad Institute of Harvard and MIT, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Jian Jin
- Department of Pharmacological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Poulikos I Poulikakos
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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11
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Monaco KA, Delach S, Yuan J, Mishina Y, Fordjour P, Labrot E, McKay D, Guo R, Higgins S, Wang HQ, Liang J, Bui K, Green J, Aspesi P, Ambrose J, Mapa F, Griner L, Jaskelioff M, Fuller J, Crawford K, Pardee G, Widger S, Hammerman PS, Engelman JA, Stuart DD, Cooke VG, Caponigro G. LXH254, a Potent and Selective ARAF-Sparing Inhibitor of BRAF and CRAF for the Treatment of MAPK-Driven Tumors. Clin Cancer Res 2020; 27:2061-2073. [DOI: 10.1158/1078-0432.ccr-20-2563] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/02/2020] [Accepted: 12/16/2020] [Indexed: 11/16/2022]
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12
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Xiao L, Salem JE, Clauss S, Hanley A, Bapat A, Hulsmans M, Iwamoto Y, Wojtkiewicz G, Cetinbas M, Schloss MJ, Tedeschi J, Lebrun-Vignes B, Lundby A, Sadreyev RI, Moslehi J, Nahrendorf M, Ellinor PT, Milan DJ. Ibrutinib-Mediated Atrial Fibrillation Attributable to Inhibition of C-Terminal Src Kinase. Circulation 2020; 142:2443-2455. [PMID: 33092403 DOI: 10.1161/circulationaha.120.049210] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND Ibrutinib is a Bruton tyrosine kinase inhibitor with remarkable efficacy against B-cell cancers. Ibrutinib also increases the risk of atrial fibrillation (AF), which remains poorly understood. METHODS We performed electrophysiology studies on mice treated with ibrutinib to assess inducibility of AF. Chemoproteomic analysis of cardiac lysates identified candidate ibrutinib targets, which were further evaluated in genetic mouse models and additional pharmacological experiments. The pharmacovigilance database, VigiBase, was queried to determine whether drug inhibition of an identified candidate kinase was associated with increased reporting of AF. RESULTS We demonstrate that treatment of mice with ibrutinib for 4 weeks results in inducible AF, left atrial enlargement, myocardial fibrosis, and inflammation. This effect was reproduced in mice lacking Bruton tyrosine kinase, but not in mice treated with 4 weeks of acalabrutinib, a more specific Bruton tyrosine kinase inhibitor, demonstrating that AF is an off-target side effect. Chemoproteomic profiling identified a short list of candidate kinases that was narrowed by additional experimentation leaving CSK (C-terminal Src kinase) as the strongest candidate for ibrutinib-induced AF. Cardiac-specific Csk knockout in mice led to increased AF, left atrial enlargement, fibrosis, and inflammation, phenocopying ibrutinib treatment. Disproportionality analyses in VigiBase confirmed increased reporting of AF associated with kinase inhibitors blocking Csk versus non-Csk inhibitors, with a reporting odds ratio of 8.0 (95% CI, 7.3-8.7; P<0.0001). CONCLUSIONS These data identify Csk inhibition as the mechanism through which ibrutinib leads to AF. Registration: URL: https://ww.clinicaltrials.gov; Unique identifier: NCT03530215.
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Affiliation(s)
- Ling Xiao
- Cardiovascular Research Center (L.X., S.C., A.H., A.B., J.T., M.N., P.T.E., D.J.M.), Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Joe-Elie Salem
- Clinical Pharmacology, Sorbonne University, INSERM, APHP, UNICO-GRECO Cardio-oncology Program (J-E.S., B.L-V.), Sorbonne University, ISERM, APHP, UNICO-GRECO Cardio-oncology Program, Hospital Pitié-Salpêtrière, Paris, France.,Clinical Investigation Center, Paris, France (J-E.S.).,Vanderbilt University Medical Center, Cardio-Oncology Program, Division of Cardiovascular Medicine, Nashville, TN (J-E.S., J.M.)
| | - Sebastian Clauss
- Cardiovascular Research Center (L.X., S.C., A.H., A.B., J.T., M.N., P.T.E., D.J.M.), Massachusetts General Hospital and Harvard Medical School, Boston, MA.,Department of Medicine I, Klinikum Grosshadern, University of Munich, Germany (S.C.).,DZHK (German Centre for Cardiovascular Research), Partner Site Munich, Munich Heart Alliance, Germany (S.C.)
| | - Alan Hanley
- Cardiovascular Research Center (L.X., S.C., A.H., A.B., J.T., M.N., P.T.E., D.J.M.), Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Aneesh Bapat
- Cardiovascular Research Center (L.X., S.C., A.H., A.B., J.T., M.N., P.T.E., D.J.M.), Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Maarten Hulsmans
- Center for Systems Biology, Department of Radiology (M.H., Y.I., G.W., M.J.S., M.N.), Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Yoshiko Iwamoto
- Center for Systems Biology, Department of Radiology (M.H., Y.I., G.W., M.J.S., M.N.), Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Gregory Wojtkiewicz
- Center for Systems Biology, Department of Radiology (M.H., Y.I., G.W., M.J.S., M.N.), Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Murat Cetinbas
- Department of Molecular Biology(M.C.), Massachusetts General Hospital and Harvard Medical School, Boston, MA.,Department of Genetics, Harvard Medical School, Boston, MA (M.C.)
| | - Maximilian J Schloss
- Center for Systems Biology, Department of Radiology (M.H., Y.I., G.W., M.J.S., M.N.), Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Justin Tedeschi
- Cardiovascular Research Center (L.X., S.C., A.H., A.B., J.T., M.N., P.T.E., D.J.M.), Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Bénédicte Lebrun-Vignes
- Clinical Pharmacology, Sorbonne University, INSERM, APHP, UNICO-GRECO Cardio-oncology Program (J-E.S., B.L-V.), Sorbonne University, ISERM, APHP, UNICO-GRECO Cardio-oncology Program, Hospital Pitié-Salpêtrière, Paris, France.,Clinical Pharmacology and Regional Pharmacovigilance Center (B.L-V.), Sorbonne University, ISERM, APHP, UNICO-GRECO Cardio-oncology Program, Hospital Pitié-Salpêtrière, Paris, France.,Université Paris Est (UPEC), IRMB- EA 7379 EpiDermE (Epidemiology in Dermatology and Evaluation of Therapeutics), F-94010, Créteil, France (B.L-V.)
| | - Alicia Lundby
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences and NNF Center for Protein Research, Københavns Universitet, Copenhagen, Denmark (A.L.)
| | - Ruslan I Sadreyev
- Department of Pathology (R.I.S.), Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Javid Moslehi
- Vanderbilt University Medical Center, Cardio-Oncology Program, Division of Cardiovascular Medicine, Nashville, TN (J-E.S., J.M.)
| | - Matthias Nahrendorf
- Cardiovascular Research Center (L.X., S.C., A.H., A.B., J.T., M.N., P.T.E., D.J.M.), Massachusetts General Hospital and Harvard Medical School, Boston, MA.,Center for Systems Biology, Department of Radiology (M.H., Y.I., G.W., M.J.S., M.N.), Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Patrick T Ellinor
- Cardiovascular Research Center (L.X., S.C., A.H., A.B., J.T., M.N., P.T.E., D.J.M.), Massachusetts General Hospital and Harvard Medical School, Boston, MA.,Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA (P.T.E.)
| | - David J Milan
- Cardiovascular Research Center (L.X., S.C., A.H., A.B., J.T., M.N., P.T.E., D.J.M.), Massachusetts General Hospital and Harvard Medical School, Boston, MA.,Leducq Foundation, Boston, MA (D.J.M.)
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13
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Teng M, Jiang J, He Z, Kwiatkowski NP, Donovan KA, Mills CE, Victor C, Hatcher JM, Fischer ES, Sorger PK, Zhang T, Gray NS. Development of CDK2 and CDK5 Dual Degrader TMX‐2172. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Mingxing Teng
- Department of Cancer Biology Dana-Farber Cancer Institute Harvard Medical School Boston MA USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School Boston MA USA
| | - Jie Jiang
- Department of Cancer Biology Dana-Farber Cancer Institute Harvard Medical School Boston MA USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School Boston MA USA
| | - Zhixiang He
- Department of Cancer Biology Dana-Farber Cancer Institute Harvard Medical School Boston MA USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School Boston MA USA
| | - Nicholas P. Kwiatkowski
- Department of Cancer Biology Dana-Farber Cancer Institute Harvard Medical School Boston MA USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School Boston MA USA
| | - Katherine A. Donovan
- Department of Cancer Biology Dana-Farber Cancer Institute Harvard Medical School Boston MA USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School Boston MA USA
| | - Caitlin E. Mills
- Laboratory of Systems Pharmacology Department of Systems Biology Harvard Medical School Boston MA USA
| | - Chiara Victor
- Laboratory of Systems Pharmacology Department of Systems Biology Harvard Medical School Boston MA USA
| | - John M. Hatcher
- Department of Cancer Biology Dana-Farber Cancer Institute Harvard Medical School Boston MA USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School Boston MA USA
| | - Eric S. Fischer
- Department of Cancer Biology Dana-Farber Cancer Institute Harvard Medical School Boston MA USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School Boston MA USA
| | - Peter K. Sorger
- Laboratory of Systems Pharmacology Department of Systems Biology Harvard Medical School Boston MA USA
| | - Tinghu Zhang
- Department of Cancer Biology Dana-Farber Cancer Institute Harvard Medical School Boston MA USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School Boston MA USA
| | - Nathanael S. Gray
- Department of Cancer Biology Dana-Farber Cancer Institute Harvard Medical School Boston MA USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School Boston MA USA
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14
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Teng M, Jiang J, He Z, Kwiatkowski NP, Donovan KA, Mills CE, Victor C, Hatcher JM, Fischer ES, Sorger PK, Zhang T, Gray NS. Development of CDK2 and CDK5 Dual Degrader TMX-2172. Angew Chem Int Ed Engl 2020; 59:13865-13870. [PMID: 32415712 DOI: 10.1002/anie.202004087] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/13/2020] [Indexed: 12/12/2022]
Abstract
Cyclin-dependent kinase 2 (CDK2) is a potential therapeutic target for the treatment of cancer. Development of CDK2 inhibitors has been extremely challenging as its ATP-binding site shares high similarity with CDK1, a related kinase whose inhibition causes toxic effects. Here, we report the development of TMX-2172, a heterobifunctional CDK2 degrader with degradation selectivity for CDK2 and CDK5 over not only CDK1, but transcriptional CDKs (CDK7 and CDK9) and cell cycle CDKs (CDK4 and CDK6) as well. In addition, we demonstrate that antiproliferative activity in ovarian cancer cells (OVCAR8) depends on CDK2 degradation and correlates with high expression of cyclin E1 (CCNE1), which functions as a regulatory subunit of CDK2. Collectively, our work provides evidence that TMX-2172 represents a lead for further development and that CDK2 degradation is a potentially valuable therapeutic strategy in ovarian and other cancers that overexpress CCNE1.
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Affiliation(s)
- Mingxing Teng
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jie Jiang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Zhixiang He
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Nicholas P Kwiatkowski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Caitlin E Mills
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Chiara Victor
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - John M Hatcher
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Tinghu Zhang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
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15
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An atlas of the catalytically active liver and spleen kinases in chicken identified by chemoproteomics. J Proteomics 2020; 225:103850. [PMID: 32502695 DOI: 10.1016/j.jprot.2020.103850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 05/08/2020] [Accepted: 05/27/2020] [Indexed: 12/16/2022]
Abstract
Phosphorylation is a post-translational protein modification regulating most known cellular processes. While protein kinases constitute a large family of highly conserved enzymes, identification of active kinases is challenging due to a low abundance of some of these signaling molecules. Although chicken is the first agricultural animal to have a sequenced genome, annotation of the kinome, i.e., a complement of all protein kinases in the genome is limited. We used chemical probes consisting of ATP and ADP derivatives binding to specific lysine (Lys) residues within the ATP-binding pocket of kinases, combined with proteomics, to identify 267 peptides labeled with the ATP and ADP acyl derivatives and 188 corresponding chicken kinases in chicken spleen and liver. Our description of active chicken kinases and ATP binding sites will support future studies focused on identifying the role of this important class of enzymes in chicken health and disease. SIGNIFICANCE: Advances made in understanding chicken enzymes are critical for the improved knowledge of the regulatory pathways controlling physiological processes in chicken. Since protein phosphorylation controls multiple aspects of cell fate, it is often linked to pathological conditions, and understanding of the kinase expression in chicken is essential for future therapeutic approaches. We coupled proteomics and labeling with active-site probes binding to Lys residues within the ATP-binding pocket of kinases to identify 188 kinases and corresponding 267 peptides labeled with the ATP and ADP acyl derivatives in chicken spleen and liver. Results of the present study describing catalytically active kinases is a starting point for chemoproteomic-based interrogation of kinases in chicken exposed to different conditions. Kinases identified in this study are available through the Chickspress genome browser that has previously published mRNA, miRNA, and shotgun proteomics data.
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16
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Kennedy AL, Rai R, Isingizwe ZR, Zhao YD, Lightfoot SA, Benbrook DM. Complementary Targeting of Rb Phosphorylation and Growth in Cervical Cancer Cell Cultures and a Xenograft Mouse Model by SHetA2 and Palbociclib. Cancers (Basel) 2020; 12:cancers12051269. [PMID: 32429557 PMCID: PMC7281234 DOI: 10.3390/cancers12051269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/08/2020] [Accepted: 05/15/2020] [Indexed: 12/11/2022] Open
Abstract
Cervical cancer is caused by high-risk human papillomavirus (HPV) types and treated with conventional chemotherapy with surgery and/or radiation. HPV E6 and E7 proteins increase phosphorylation of retinoblastoma (Rb) by cyclin D1/cyclin dependent kinase (CDK)4/6 complexes. We hypothesized that cyclin D1 degradation by the SHetA2 drug in combination with palbociclib inhibition of CDK4/6 activity synergistically reduces phosphorylated Rb (phospho-Rb) and inhibits cervical cancer growth. The effects of these drugs, alone, and in combination, were evaluated in SiHa and CaSki HPV-positive and C33A HPV-negative cervical cancer cell lines using cell culture, western blots and ELISA, and in a SiHa xenograft model. Endpoints were compared by isobolograms, ANOVA, and Chi-Square. In all cell lines, combination indexes documented synergistic interaction of SHetA2 and palbociclib in association SHetA2 reduction of cyclin D1 and phospho-Rb, palbociclib reduction of phospho-Rb, and enhanced phospho-Rb reduction upon drug combination. Both drugs significantly reduced phospho-Rb and growth of SiHa xenograft tumors as single agents and acted additively when combined, with no evidence of toxicity. Dilated CD31-negative blood vessels adjacent to, or within, areas of necrosis and apoptosis were observed in all drug-treated tumors. These results justify development of the SHetA2 and palbociclib combination for targeting phospho-Rb in cervical cancer treatment.
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Affiliation(s)
- Amy L. Kennedy
- Department of Pathology, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
| | - Rajani Rai
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
| | - Zitha Redempta Isingizwe
- Department of Pharmaceutical Sciences, College of Pharmacy University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
| | - Yan Daniel Zhao
- Department of Biostatistics and Epidemiology, College of Public Health University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
| | - Stanley A. Lightfoot
- Center for Cancer Prevention and Drug Development, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
| | - Doris M. Benbrook
- Department of Pathology, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
- Department of Pharmaceutical Sciences, College of Pharmacy University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
- Department of Biostatistics and Epidemiology, College of Public Health University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
- Center for Cancer Prevention and Drug Development, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
- Correspondence:
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17
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Abdeldayem A, Raouf YS, Constantinescu SN, Moriggl R, Gunning PT. Advances in covalent kinase inhibitors. Chem Soc Rev 2020; 49:2617-2687. [DOI: 10.1039/c9cs00720b] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This comprehensive review details recent advances, challenges and innovations in covalent kinase inhibition within a 10 year period (2007–2018).
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Affiliation(s)
- Ayah Abdeldayem
- Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Canada
- Department of Chemistry
| | - Yasir S. Raouf
- Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Canada
- Department of Chemistry
| | | | - Richard Moriggl
- Institute of Animal Breeding and Genetics
- University of Veterinary Medicine
- 1210 Vienna
- Austria
| | - Patrick T. Gunning
- Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Canada
- Department of Chemistry
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18
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Sadek K, Abouzed T, Nasr S, Shoukry M. Licochalcone B Ameliorates Liver Cancer via Targeting of Apoptotic Genes, DNA Repair Systems, and Cell Cycle Control. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2020; 19:372-386. [PMID: 33841550 PMCID: PMC8019863 DOI: 10.22037/ijpr.2020.1101292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Apurinic/apyrimidinic endonuclease 1/redox factor-1 (APE1/Ref-1) is a ubiquitous multifunctional protein required in the DNA base excision repair pathway and a noteworthy reducing-oxidizing factor that regulates the activity of various transcription factors. Cyclin-dependent kinases (CDKs) assume a key role in directing the progression of the cell- cycle. The present study evaluated the synergistic efficacy of using licochalcone B (LCB) and fullerene C60 (FnC60) nanoparticles against diethylnitrosamine (DEN)-induced hepatocarcinoma in rats and relevant signaling pathways, with APE1/Ref-1 and CDK-4, as novel anti-cancer- targeting. LCB alone and in combination with FnC60 significantly decreased DNA fragmentation, oxidative DNA damage (8-hydroxy-2'-deoxyguanosine levels), APE1/Ref-1, CDK-4, retinoblastoma, B- cell lymphoma-2 (Bcl-2), B-cell lymphoma-xL (Bcl-xL), and β-arrestin-2 mRNA expression, and APE1/Ref-1 and CDK-4 protein expression. In contrast, these treatments significantly increased the expression of protein 53 (p53), Bcl-2-associated X protein (Bax), and caspase-3. These data suggest that LCB either alone or in combination with FnC60 elicited significant protective effects against DEN-induced hepatocarcinogenesis, which may have occurred because of the regulation of enzymes involved in DNA repair and cell-cycle control at S phase progression as well as the induction of apoptosis at the gene and protein expression levels. Furthermore, FnC60 potentiated the effect of LCB at the molecular level, possibly through targeting of cancerous cells.
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Affiliation(s)
- Kadry Sadek
- Department of Biochemistry, Faculty of Veterinary Medicine, Damanhur University, Egypt.
| | - Tarek Abouzed
- Department of Biochemistry, Faculty of Veterinary Medicine, Kafr El-Sheikh University, Egypt.
| | - Sherif Nasr
- Department of Molecular Biology and Genetic Engineering, Faculty of Veterinary Medicine, Damanhur University, Egypt.
| | - Moustafa Shoukry
- Department of Physiology, Faculty of Veterinary Medicine, Kafr El-Sheikh University, Egypt.
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19
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Maynard J, Hart P. The Opportunities and Use of Imaging to Measure Target Engagement. SLAS DISCOVERY 2019; 25:127-136. [PMID: 31885303 DOI: 10.1177/2472555219897270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Lack of efficacy and poor safety outcomes are deemed to be the greatest causes of clinical failure of novel therapeutics. The use of biomarkers that give accurate information on target engagement, providing confidence that pharmacological activity in the target organ is being achieved, is key in optimizing clinical success. Without a measurement of target engagement, it can be very difficult to discern the basis for any lack of efficacy of a drug molecule within the pharmaceutical industry. Target engagement can be measured in both an in vitro and in vivo setting, and in recent years imaging measurements have been used frequently in drug discovery and development to assess target engagement and receptor occupancy in both human and animal models. From this perspective, we assess and look at the advancements in both in vivo and ex vivo imaging to demonstrate the enormous potential that imaging has as an application to provide a greater understanding of target engagement with a correlative therapeutic impact.
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Affiliation(s)
| | - Philippa Hart
- Medicines Discovery Catapult, Alderley Park, Cheshire, UK
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20
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Chen X, Xu D, Li X, Zhang J, Xu W, Hou J, Zhang W, Tang J. Latest Overview of the Cyclin-Dependent Kinases 4/6 Inhibitors in Breast Cancer: The Past, the Present and the Future. J Cancer 2019; 10:6608-6617. [PMID: 31777590 PMCID: PMC6856891 DOI: 10.7150/jca.33079] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 08/26/2019] [Indexed: 12/13/2022] Open
Abstract
Endocrine resistance in hormone receptor positive breast cancer patients urges us to develop novel approaches such as inhibitors of the cyclin-dependent kinases (CDK) 4/6 to reverse its resistance. Nowadays, three selective CDK4/6 inhibitors (Palbociclib, Ribociclib and Abemaciclib) are approved by Federal Drug Administration and the European Medicines Agency for the treatment of advanced and metastatic HR+/HER2- breast cancer. However, no consistent conclusion has been reached to its application in other types of breast cancer. Therefore, the purpose of our study was to overview the clinical trials about the beneficial effects of Palbociclib, Ribociclib and Abemaciclib in breast cancer with their tolerable adverse effects, and discuss their resistant mechanisms thus looking for useful biomarkers to predict the efficiency of the CDK4/6 inhibitors. The CDK4/6 inhibitors application after the support of preclinic and clinic data will be helpful to provide other alternatively suitable strategies for different types of breast cancer patients.
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Affiliation(s)
- Xiu Chen
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Di Xu
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xingjiang Li
- Changzhou Wujin People's Hospital, Changzhou, Jiangsu, China
| | - Jian Zhang
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Weilin Xu
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Junchen Hou
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wei Zhang
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jinhai Tang
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
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21
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Hafner M, Mills CE, Subramanian K, Chen C, Chung M, Boswell SA, Everley RA, Liu C, Walmsley CS, Juric D, Sorger PK. Multiomics Profiling Establishes the Polypharmacology of FDA-Approved CDK4/6 Inhibitors and the Potential for Differential Clinical Activity. Cell Chem Biol 2019; 26:1067-1080.e8. [PMID: 31178407 DOI: 10.1016/j.chembiol.2019.05.005] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 03/14/2019] [Accepted: 05/13/2019] [Indexed: 11/28/2022]
Abstract
The target profiles of many drugs are established early in their development and are not systematically revisited at the time of FDA approval. Thus, it is often unclear whether therapeutics with the same nominal targets but different chemical structures are functionally equivalent. In this paper we use five different phenotypic and biochemical assays to compare approved inhibitors of cyclin-dependent kinases 4/6-collectively regarded as breakthroughs in the treatment of hormone receptor-positive breast cancer. We find that transcriptional, proteomic, and phenotypic changes induced by palbociclib, ribociclib, and abemaciclib differ significantly; abemaciclib in particular has advantageous activities partially overlapping those of alvocidib, an older polyselective CDK inhibitor. In cells and mice, abemaciclib inhibits kinases other than CDK4/6 including CDK2/cyclin A/E-implicated in resistance to CDK4/6 inhibition-and CDK1/cyclin B. The multifaceted experimental and computational approaches described here therefore uncover underappreciated differences in CDK4/6 inhibitor activities with potential importance in treating human patients.
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Affiliation(s)
- Marc Hafner
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Caitlin E Mills
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Kartik Subramanian
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Chen Chen
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Mirra Chung
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Sarah A Boswell
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Robert A Everley
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Changchang Liu
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Charlotte S Walmsley
- Termeer Center for Targeted Therapies, Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA
| | - Dejan Juric
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Termeer Center for Targeted Therapies, Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA.
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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22
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Green JL, Okerberg ES, Sejd J, Palafox M, Monserrat L, Alemayehu S, Wu J, Sykes M, Aban A, Serra V, Nomanbhoy T. Direct CDKN2 Modulation of CDK4 Alters Target Engagement of CDK4 Inhibitor Drugs. Mol Cancer Ther 2019; 18:771-779. [DOI: 10.1158/1535-7163.mct-18-0755] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 11/14/2018] [Accepted: 02/22/2019] [Indexed: 11/16/2022]
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23
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Kinome rewiring reveals AURKA limits PI3K-pathway inhibitor efficacy in breast cancer. Nat Chem Biol 2018; 14:768-777. [PMID: 29942081 PMCID: PMC6051919 DOI: 10.1038/s41589-018-0081-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 04/13/2018] [Indexed: 02/07/2023]
Abstract
Dysregulation of the PI3K-AKT-mTOR signaling network is a prominent feature of breast cancers. However, clinical responses to drugs targeting this pathway have been modest, possibly because of dynamic changes in cellular signaling that drive resistance and limit drug efficacy. Using a quantitative chemoproteomics approach, we mapped kinome dynamics in response to inhibitors of this pathway and identified signaling changes that correlate with drug sensitivity. Maintenance of AURKA after drug treatment was associated with resistance in breast cancer models. Incomplete inhibition of AURKA was a common source of therapy failure, and combinations of PI3K, AKT or mTOR inhibitors with the AURKA inhibitor MLN8237 were highly synergistic and durably suppressed mTOR signaling, resulting in apoptosis and tumor regression in vivo. This signaling map identifies survival factors whose presence limits the efficacy of targeted therapies and reveals new drug combinations that may unlock the full potential of PI3K-AKT-mTOR pathway inhibitors in breast cancer.
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24
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Joachimiak Ł, Błażewska KM. Phosphorus-Based Probes as Molecular Tools for Proteome Studies: Recent Advances in Probe Development and Applications. J Med Chem 2018; 61:8536-8562. [DOI: 10.1021/acs.jmedchem.8b00249] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Łukasz Joachimiak
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego Street 116, 90-924 Łódź, Poland
| | - Katarzyna M. Błażewska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego Street 116, 90-924 Łódź, Poland
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25
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Hatcher JM, Wu G, Zeng C, Zhu J, Meng F, Patel S, Wang W, Ficarro SB, Leggett AL, Powell CE, Marto JA, Zhang K, Ngo JCK, Fu XD, Zhang T, Gray NS. SRPKIN-1: A Covalent SRPK1/2 Inhibitor that Potently Converts VEGF from Pro-angiogenic to Anti-angiogenic Isoform. Cell Chem Biol 2018; 25:460-470.e6. [PMID: 29478907 PMCID: PMC5973797 DOI: 10.1016/j.chembiol.2018.01.013] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 11/03/2017] [Accepted: 01/26/2018] [Indexed: 01/07/2023]
Abstract
The SRPK family of kinases regulates pre-mRNA splicing by phosphorylating serine/arginine (SR)-rich splicing factors, signals splicing control in response to extracellular stimuli, and contributes to tumorigenesis, suggesting that these splicing kinases are potential therapeutic targets. Here, we report the development of the first irreversible SRPK inhibitor, SRPKIN-1, which is also the first kinase inhibitor that forms a covalent bond with a tyrosine phenol group in the ATP-binding pocket. Kinome-wide profiling demonstrates its selectivity for SRPK1/2, and SRPKIN-1 attenuates SR protein phosphorylation at submicromolar concentrations. Vascular endothelial growth factor (VEGF) is a known target for SRPK-regulated splicing and, relative to the first-generation SRPK inhibitor SRPIN340 or small interfering RNA-mediated SRPK knockdown, SRPKIN-1 is more potent in converting the pro-angiogenic VEGF-A165a to the anti-angiogenic VEGF-A165b isoform and in blocking laser-induced neovascularization in a murine retinal model. These findings encourage further development of SRPK inhibitors for treatment of age-related macular degeneration.
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Affiliation(s)
- John M. Hatcher
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Guowei Wu
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Chuyue Zeng
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region NA, China
| | - Jie Zhu
- Shiley Eye Institute, Institute for Engineering in Medicine, Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA,Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Fan Meng
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sherrina Patel
- Shiley Eye Institute, Institute for Engineering in Medicine, Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Wenqiu Wang
- Shiley Eye Institute, Institute for Engineering in Medicine, Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Scott B. Ficarro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA,Department of Oncologic Pathology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA,Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Alan L. Leggett
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Chelsea E. Powell
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jarrod A. Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA,Department of Oncologic Pathology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA,Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kang Zhang
- Shiley Eye Institute, Institute for Engineering in Medicine, Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jacky Chi Ki Ngo
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region NA, China
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA,Correspondence: (X.-D.F.), (T.Z.), (N.S.G.)
| | - Tinghu Zhang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA,Correspondence: (X.-D.F.), (T.Z.), (N.S.G.)
| | - Nathanael S. Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA,Correspondence: (X.-D.F.), (T.Z.), (N.S.G.)
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26
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Pharmacological perturbation of CDK9 using selective CDK9 inhibition or degradation. Nat Chem Biol 2017; 14:163-170. [PMID: 29251720 DOI: 10.1038/nchembio.2538] [Citation(s) in RCA: 334] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 11/09/2017] [Indexed: 01/06/2023]
Abstract
Cyclin-dependent kinase 9 (CDK9), an important regulator of transcriptional elongation, is a promising target for cancer therapy, particularly for cancers driven by transcriptional dysregulation. We characterized NVP-2, a selective ATP-competitive CDK9 inhibitor, and THAL-SNS-032, a selective CDK9 degrader consisting of a CDK-binding SNS-032 ligand linked to a thalidomide derivative that binds the E3 ubiquitin ligase Cereblon (CRBN). To our surprise, THAL-SNS-032 induced rapid degradation of CDK9 without affecting the levels of other SNS-032 targets. Moreover, the transcriptional changes elicited by THAL-SNS-032 were more like those caused by NVP-2 than those induced by SNS-032. Notably, compound washout did not significantly reduce levels of THAL-SNS-032-induced apoptosis, suggesting that CDK9 degradation had prolonged cytotoxic effects compared with CDK9 inhibition. Thus, our findings suggest that thalidomide conjugation represents a promising strategy for converting multi-targeted inhibitors into selective degraders and reveal that kinase degradation can induce distinct pharmacological effects compared with inhibition.
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27
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Huang HT, Dobrovolsky D, Paulk J, Yang G, Weisberg EL, Doctor ZM, Buckley DL, Cho JH, Ko E, Jang J, Shi K, Choi HG, Griffin JD, Li Y, Treon SP, Fischer ES, Bradner JE, Tan L, Gray NS. A Chemoproteomic Approach to Query the Degradable Kinome Using a Multi-kinase Degrader. Cell Chem Biol 2017; 25:88-99.e6. [PMID: 29129717 DOI: 10.1016/j.chembiol.2017.10.005] [Citation(s) in RCA: 258] [Impact Index Per Article: 36.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 09/11/2017] [Accepted: 10/17/2017] [Indexed: 12/16/2022]
Abstract
Heterobifunctional molecules that recruit E3 ubiquitin ligases, such as cereblon, for targeted protein degradation represent an emerging pharmacological strategy. A major unanswered question is how generally applicable this strategy is to all protein targets. In this study, we designed a multi-kinase degrader by conjugating a highly promiscuous kinase inhibitor with a cereblon-binding ligand, and used quantitative proteomics to discover 28 kinases, including BTK, PTK2, PTK2B, FLT3, AURKA, AURKB, TEC, ULK1, ITK, and nine members of the CDK family, as degradable. This set of kinases is only a fraction of the intracellular targets bound by the degrader, demonstrating that successful degradation requires more than target engagement. The results guided us to develop selective degraders for FLT3 and BTK, with potentials to improve disease treatment. Together, this study demonstrates an efficient approach to triage a gene family of interest to identify readily degradable targets for further studies and pre-clinical developments.
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Affiliation(s)
- Hai-Tsang Huang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Dennis Dobrovolsky
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Joshiawa Paulk
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Guang Yang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Bing Center for Waldenström's Macroglobulinemia, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Ellen L Weisberg
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Zainab M Doctor
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Dennis L Buckley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Joong-Heui Cho
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, Korea
| | - Eunhwa Ko
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, Korea
| | - Jaebong Jang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Kun Shi
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hwan Geun Choi
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, Korea
| | - James D Griffin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Ying Li
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Steven P Treon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Bing Center for Waldenström's Macroglobulinemia, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Li Tan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China.
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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