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Gubat J, Selvaraju K, Sjöstrand L, Kumar Singh D, Turkina MV, Schmierer B, Sabatier P, Zubarev RA, Linder S, D’Arcy P. Comprehensive Target Screening and Cellular Profiling of the Cancer-Active Compound b-AP15 Indicate Abrogation of Protein Homeostasis and Organelle Dysfunction as the Primary Mechanism of Action. Front Oncol 2022; 12:852980. [PMID: 35530310 PMCID: PMC9076133 DOI: 10.3389/fonc.2022.852980] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/17/2022] [Indexed: 12/11/2022] Open
Abstract
Dienone compounds have been demonstrated to display tumor-selective anti-cancer activity independently of the mutational status of TP53. Previous studies have shown that cell death elicited by this class of compounds is associated with inhibition of the ubiquitin-proteasome system (UPS). Here we extend previous findings by showing that the dienone compound b-AP15 inhibits proteasomal degradation of long-lived proteins. We show that exposure to b-AP15 results in increased association of the chaperones VCP/p97/Cdc48 and BAG6 with proteasomes. Comparisons between the gene expression profile generated by b-AP15 to those elicited by siRNA showed that knock-down of the proteasome-associated deubiquitinase (DUB) USP14 is the closest related to drug response. USP14 is a validated target for b-AP15 and we show that b-AP15 binds covalently to two cysteines, Cys203 and Cys257, in the ubiquitin-binding pocket of the enzyme. Consistent with this, deletion of USP14 resulted in decreased sensitivity to b-AP15. Targeting of USP14 was, however, found to not fully account for the observed proteasome inhibition. In search for additional targets, we utilized genome-wide CRISPR/Cas9 library screening and Proteome Integral Solubility Alteration (PISA) to identify mechanistically essential genes and b-AP15 interacting proteins respectively. Deletion of genes encoding mitochondrial proteins decreased the sensitivity to b-AP15, suggesting that mitochondrial dysfunction is coupled to cell death induced by b-AP15. Enzymes known to be involved in Phase II detoxification such as aldo-ketoreductases and glutathione-S-transferases were identified as b-AP15-targets using PISA. The finding that different exploratory approaches yielded different results may be explained in terms of a “target” not necessarily connected to the “mechanism of action” thus highlighting the importance of a holistic approach in the identification of drug targets. We conclude that b-AP15, and likely also other dienone compounds of the same class, affect protein degradation and proteasome function at more than one level.
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Affiliation(s)
- Johannes Gubat
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Karthik Selvaraju
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Linda Sjöstrand
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Dhananjay Kumar Singh
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Department of Pharmacy, Central University of South Bihar, Gaya, India
| | - Maria V. Turkina
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Bernhard Schmierer
- Department of Medical Biochemistry and Biophysics, Division of Chemical Biology, Karolinska Institutet, Stockholm, Sweden
| | - Pierre Sabatier
- Department of Medical Biochemistry and Biophysics, Division of Physiological Chemistry I, Karolinska Institutet, Stockholm, Sweden
| | - Roman A. Zubarev
- Department of Medical Biochemistry and Biophysics, Division of Physiological Chemistry I, Karolinska Institutet, Stockholm, Sweden
- Department of Pharmacological and Technological Chemistry, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Stig Linder
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Pádraig D’Arcy
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- *Correspondence: Pádraig D’Arcy,
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Selvaraju K, Lotfi K, Gubat J, Miquel M, Nilsson A, Hill J, Jensen LD, Linder S, D’Arcy P. Sensitivity of Acute Myelocytic Leukemia Cells to the Dienone Compound VLX1570 Is Associated with Inhibition of the Ubiquitin-Proteasome System. Biomolecules 2021; 11:biom11091339. [PMID: 34572552 PMCID: PMC8470745 DOI: 10.3390/biom11091339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/02/2021] [Accepted: 09/02/2021] [Indexed: 12/16/2022] Open
Abstract
Dienone compounds with a 1,5-diaryl-3-oxo-1,4-pentadienyl pharmacophore have been widely reported to show tumor cell selectivity. These compounds target the ubiquitin-proteasome system (UPS), known to be essential for the viability of tumor cells. The induction of oxidative stress, depletion of glutathione, and induction of high-molecular-weight (HMW) complexes have also been reported. We here examined the response of acute myeloid leukemia (AML) cells to the dienone compound VLX1570. AML cells have relatively high protein turnover rates and have also been reported to be sensitive to depletion of reduced glutathione. We found AML cells of diverse cytogenetic backgrounds to be sensitive to VLX1570, with drug exposure resulting in an accumulation of ubiquitin complexes, induction of ER stress, and the loss of cell viability in a dose-dependent manner. Caspase activation was observed but was not required for the loss of cell viability. Glutathione depletion was also observed but did not correlate to VLX1570 sensitivity. Formation of HMW complexes occurred at higher concentrations of VLX1570 than those required for the loss of cell viability and was not enhanced by glutathione depletion. To study the effect of VLX1570 we developed a zebrafish PDX model of AML and confirmed antigrowth activity in vivo. Our results show that VLX1570 induces UPS inhibition in AML cells and encourage further work in developing compounds useful for cancer therapeutics.
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Affiliation(s)
- Karthik Selvaraju
- Department of Biomedical and Clinical Sciences (BKV), Linköping University, SE-581 85 Linköping, Sweden; (K.S.); (K.L.); (J.G.); (M.M.); (A.N.); (J.H.); (S.L.)
| | - Kourosh Lotfi
- Department of Biomedical and Clinical Sciences (BKV), Linköping University, SE-581 85 Linköping, Sweden; (K.S.); (K.L.); (J.G.); (M.M.); (A.N.); (J.H.); (S.L.)
- Department of Hematology, Linköping University Hospital, SE-581 85 Linköping, Sweden
| | - Johannes Gubat
- Department of Biomedical and Clinical Sciences (BKV), Linköping University, SE-581 85 Linköping, Sweden; (K.S.); (K.L.); (J.G.); (M.M.); (A.N.); (J.H.); (S.L.)
| | - Maria Miquel
- Department of Biomedical and Clinical Sciences (BKV), Linköping University, SE-581 85 Linköping, Sweden; (K.S.); (K.L.); (J.G.); (M.M.); (A.N.); (J.H.); (S.L.)
| | - Amanda Nilsson
- Department of Biomedical and Clinical Sciences (BKV), Linköping University, SE-581 85 Linköping, Sweden; (K.S.); (K.L.); (J.G.); (M.M.); (A.N.); (J.H.); (S.L.)
| | - Julia Hill
- Department of Biomedical and Clinical Sciences (BKV), Linköping University, SE-581 85 Linköping, Sweden; (K.S.); (K.L.); (J.G.); (M.M.); (A.N.); (J.H.); (S.L.)
| | - Lasse D. Jensen
- Department of Health, Medical and Caring Sciences (HMV), Linköping University, SE-581 85 Linköping, Sweden;
| | - Stig Linder
- Department of Biomedical and Clinical Sciences (BKV), Linköping University, SE-581 85 Linköping, Sweden; (K.S.); (K.L.); (J.G.); (M.M.); (A.N.); (J.H.); (S.L.)
- Department of Oncology-Pathology, Karolinska Institute, SE-171 76 Stockholm, Sweden
| | - Pádraig D’Arcy
- Department of Biomedical and Clinical Sciences (BKV), Linköping University, SE-581 85 Linköping, Sweden; (K.S.); (K.L.); (J.G.); (M.M.); (A.N.); (J.H.); (S.L.)
- Correspondence:
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Mofers A, Selvaraju K, Gubat J, D'Arcy P, Linder S. Identification of proteasome inhibitors using analysis of gene expression profiles. Eur J Pharmacol 2020; 889:173709. [PMID: 33166494 DOI: 10.1016/j.ejphar.2020.173709] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/14/2020] [Accepted: 10/29/2020] [Indexed: 12/29/2022]
Abstract
Inhibitors of the 20S proteasome such as bortezomib (Velcade®) and carfilzomib (Kypriolis®) are in clinical use for the treatment of patients with multiple myeloma and mantle cell lymphoma. In an attempt to identify novel inhibitors of the ubiquitin-proteasome system (UPS) we used the connectivity map (CMap) resource, based on alterations of gene expression profiles by perturbagens, and performed COMPARE analyses of drug sensitivity patterns in the NCI60 panel. Cmap analysis identified a large number of small molecules with strong connectivity to proteasome inhibition, including both well characterized inhibitors of the 20S proteasome and molecules previously not described to inhibit the UPS. A number of these compounds have been reported to be cytotoxic to tumor cells and were tested for their ability to decrease processing of proteasome substrates. The antibiotic thiostrepton and the natural products celastrol and curcumin induced strong accumulation of polyubiquitinated proteasome substrates in exposed cells. Other compounds elicited modest increases of proteasome substrates, including the protein phosphatase inhibitor BCI-Cl and the farnesyltransferase inhibitor manumycin A, suggesting that these compounds inhibit proteasome function. Induction of chaperone expression in the absence of proteasome inhibition was observed by a number of compounds, suggesting other effects on the UPS. We conclude that the combination of bioinformatic analyses and cellular assays resulted in the identification of compounds with potential to inhibit the UPS.
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Affiliation(s)
- Arjan Mofers
- Biomedical and Clinical Sciences, Linköping University, SE-58183, Linköping, Sweden
| | - Karthik Selvaraju
- Biomedical and Clinical Sciences, Linköping University, SE-58183, Linköping, Sweden
| | - Johannes Gubat
- Biomedical and Clinical Sciences, Linköping University, SE-58183, Linköping, Sweden
| | - Padraig D'Arcy
- Biomedical and Clinical Sciences, Linköping University, SE-58183, Linköping, Sweden
| | - Stig Linder
- Biomedical and Clinical Sciences, Linköping University, SE-58183, Linköping, Sweden; Department of Oncology-Pathology, Karolinska Institutet, SE-17176, Stockholm, Sweden.
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