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Tomazini A, Shifman JM. Targeting Ras with protein engineering. Oncotarget 2023; 14:672-687. [PMID: 37395750 DOI: 10.18632/oncotarget.28469] [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: 07/04/2023] Open
Abstract
Ras proteins are small GTPases that regulate cell growth and division. Mutations in Ras genes are associated with many types of cancer, making them attractive targets for cancer therapy. Despite extensive efforts, targeting Ras proteins with small molecules has been extremely challenging due to Ras's mostly flat surface and lack of small molecule-binding cavities. These challenges were recently overcome by the development of the first covalent small-molecule anti-Ras drug, sotorasib, highlighting the efficacy of Ras inhibition as a therapeutic strategy. However, this drug exclusively inhibits the Ras G12C mutant, which is not a prevalent mutation in most cancer types. Unlike the G12C variant, other Ras oncogenic mutants lack reactive cysteines, rendering them unsuitable for targeting via the same strategy. Protein engineering has emerged as a promising method to target Ras, as engineered proteins have the ability to recognize various surfaces with high affinity and specificity. Over the past few years, scientists have engineered antibodies, natural Ras effectors, and novel binding domains to bind to Ras and counteract its carcinogenic activities via a variety of strategies. These include inhibiting Ras-effector interactions, disrupting Ras dimerization, interrupting Ras nucleotide exchange, stimulating Ras interaction with tumor suppressor genes, and promoting Ras degradation. In parallel, significant advancements have been made in intracellular protein delivery, enabling the delivery of the engineered anti-Ras agents into the cellular cytoplasm. These advances offer a promising path for targeting Ras proteins and other challenging drug targets, opening up new opportunities for drug discovery and development.
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Affiliation(s)
- Atilio Tomazini
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Julia M Shifman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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2
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Eliminating oncogenic RAS: back to the future at the drawing board. Biochem Soc Trans 2023; 51:447-456. [PMID: 36688434 PMCID: PMC9987992 DOI: 10.1042/bst20221343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 01/24/2023]
Abstract
RAS drug development has made enormous strides in the past ten years, with the first direct KRAS inhibitor being approved in 2021. However, despite the clinical success of covalent KRAS-G12C inhibitors, we are immediately confronted with resistances as commonly found with targeted drugs. Previously believed to be undruggable due to its lack of obvious druggable pockets, a couple of new approaches to hit this much feared oncogene have now been carved out. We here concisely review these approaches to directly target four druggable sites of RAS from various angles. Our analysis focuses on the lessons learnt during the development of allele-specific covalent and non-covalent RAS inhibitors, the potential of macromolecular binders to facilitate the discovery and validation of targetable sites on RAS and finally an outlook on a future that may engage more small molecule binders to become drugs. We foresee that the latter could happen mainly in two ways: First, non-covalent small molecule inhibitors may be derived from the development of covalent binders. Second, reversible small molecule binders could be utilized for novel targeting modalities, such as degraders of RAS. Provided that degraders eliminate RAS by recruiting differentially expressed E3-ligases, this approach could enable unprecedented tissue- or developmental stage-specific destruction of RAS with potential advantages for on-target toxicity. We conclude that novel creative ideas continue to be important to exterminate RAS in cancer and other RAS pathway-driven diseases, such as RASopathies.
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Hempfling JP, Sekera ER, Sarkar A, Hummon AB, Pei D. Generation of Proteins with Free N-Terminal Cysteine by Aminopeptidases. J Am Chem Soc 2022; 144:21763-21771. [PMID: 36378906 PMCID: PMC9923720 DOI: 10.1021/jacs.2c10194] [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] [Indexed: 11/16/2022]
Abstract
Efficient, site-specific, and bio-orthogonal conjugation of chemical functionalities to proteins is of great utility in fundamental research as well as industrial processes (e.g., the production of antibody-drug conjugates and immobilization of enzymes for biocatalysis). A popular approach involves reacting a free N-terminal cysteine with a variety of electrophilic reagents. However, current methods for generating proteins with N-terminal cysteines have significant limitations. Herein we report a novel, efficient, and convenient method for producing recombinant proteins with free N-terminal cysteines by genetically fusing a Met-Pro-Cys sequence to the N-terminus of a protein of interest and subjecting the recombinant protein to the sequential action of methionine and proline aminopeptidases. The resulting protein was site-specifically labeled at the N-terminus with fluorescein and a cyclic cell-penetrating peptide through native chemical ligation and a 2-cyanobenzothiazole moiety, respectively. In addition, the optimal recognition sequence of Aeromonas sobria proline aminopeptidase was determined by screening a combinatorial peptide library and incorporated into the N-terminus of a protein of interest for most efficient N-terminal processing.
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Affiliation(s)
- Jordan P. Hempfling
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, United States
| | - Emily R. Sekera
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, OH 43210, United States
| | - Amar Sarkar
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, OH 43210, United States
| | - Amanda B. Hummon
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, United States
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, OH 43210, United States
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, United States
| | - Dehua Pei
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, United States
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, OH 43210, United States
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4
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Weeks R, Zhou X, Yuan TL, Zhang J. Fluorescent Biosensor for Measuring Ras Activity in Living Cells. J Am Chem Soc 2022; 144:17432-17440. [PMID: 36122391 PMCID: PMC10031818 DOI: 10.1021/jacs.2c05203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The small GTPase Ras is a critical regulator of cell growth and proliferation. Its activity is frequently dysregulated in cancers, prompting decades of work to pharmacologically target Ras. Understanding Ras biology and developing effective Ras therapeutics both require probing Ras activity in its native context, yet tools to measure its activities in cellulo are limited. Here, we developed a ratiometric Ras activity reporter (RasAR) that provides quantitative measurement of Ras activity in living cells with high spatiotemporal resolution. We demonstrated that RasAR can probe live-cell activities of all the primary isoforms of Ras. Given that the functional roles of different isoforms of Ras are intimately linked to their subcellular distribution and regulation, we interrogated the spatiotemporal regulation of Ras utilizing subcellularly targeted RasAR and uncovered the role of Src kinase as an upstream regulator to inhibit HRas. Furthermore, we showed that RasAR enables capture of KRasG12C inhibition dynamics in living cells upon treatment with KRasG12C covalent inhibitors, including ARS1620, Sotorasib, and Adagrasib. We found in living cells a residual Ras activity lingers for hours in the presence of these inhibitors. Together, RasAR represents a powerful molecular tool to enable live-cell interrogation of Ras activity and facilitate the development of Ras inhibitors.
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Affiliation(s)
- Ryan Weeks
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Xin Zhou
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Tina L. Yuan
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Correspondence: Jin Zhang, 9500 Gilman Drive, BRF-II 1120, La Jolla, CA 92093-0702, phone (858) 246-0602,
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5
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Surve S, Watkins SC, Sorkin A. EGFR-RAS-MAPK signaling is confined to the plasma membrane and associated endorecycling protrusions. J Cell Biol 2021; 220:212639. [PMID: 34515735 PMCID: PMC8563293 DOI: 10.1083/jcb.202107103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/21/2021] [Accepted: 08/24/2021] [Indexed: 12/16/2022] Open
Abstract
The subcellular localization of RAS GTPases defines the operational compartment of the EGFR-ERK1/2 signaling pathway within cells. Hence, we used live-cell imaging to demonstrate that endogenous KRAS and NRAS tagged with mNeonGreen are predominantly localized to the plasma membrane. NRAS was also present in the Golgi apparatus and a tubular, plasma-membrane derived endorecycling compartment, enriched in recycling endosome markers (TERC). In EGF-stimulated cells, there was essentially no colocalization of either mNeonGreen-KRAS or mNeonGreen-NRAS with endosomal EGFR, which, by contrast, remained associated with endogenous Grb2-mNeonGreen, a receptor adaptor upstream of RAS. ERK1/2 activity was diminished by blocking cell surface EGFR with cetuximab, even after most ligand-bound, Grb2-associated EGFRs were internalized. Endogenous mCherry-tagged RAF1, an effector of RAS, was recruited to the plasma membrane, with subsequent accumulation in mNG-NRAS–containing TERCs. We propose that a small pool of surface EGFRs sustain signaling within the RAS-ERK1/2 pathway and that RAS activation persists in TERCs, whereas endosomal EGFR does not significantly contribute to ERK1/2 activity.
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Affiliation(s)
- Sachin Surve
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Simon C Watkins
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Alexander Sorkin
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
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Engineered variants of the Ras effector protein RASSF5 (NORE1A) promote anticancer activities in lung adenocarcinoma. J Biol Chem 2021; 297:101353. [PMID: 34717958 PMCID: PMC8605244 DOI: 10.1016/j.jbc.2021.101353] [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] [Received: 06/03/2021] [Revised: 10/12/2021] [Accepted: 10/25/2021] [Indexed: 11/24/2022] Open
Abstract
Within the superfamily of small GTPases, Ras appears to be the master regulator of such processes as cell cycle progression, cell division, and apoptosis. Several oncogenic Ras mutations at amino acid positions 12, 13, and 61 have been identified that lose their ability to hydrolyze GTP, giving rise to constitutive signaling and eventually development of cancer. While disruption of the Ras/effector interface is an attractive strategy for drug design to prevent this constitutive activity, inhibition of this interaction using small molecules is impractical due to the absence of a cavity to which such molecules could bind. However, proteins and especially natural Ras effectors that bind to the Ras/effector interface with high affinity could disrupt Ras/effector interactions and abolish procancer pathways initiated by Ras oncogene. Using a combination of computational design and in vitro evolution, we engineered high-affinity Ras-binding proteins starting from a natural Ras effector, RASSF5 (NORE1A), which is encoded by a tumor suppressor gene. Unlike previously reported Ras oncogene inhibitors, the proteins we designed not only inhibit Ras-regulated procancer pathways, but also stimulate anticancer pathways initiated by RASSF5. We show that upon introduction into A549 lung carcinoma cells, the engineered RASSF5 mutants decreased cell viability and mobility to a significantly greater extent than WT RASSF5. In addition, these mutant proteins induce cellular senescence by increasing acetylation and decreasing phosphorylation of p53. In conclusion, engineered RASSF5 variants provide an attractive therapeutic strategy able to oppose cancer development by means of inhibiting of procancer pathways and stimulating anticancer processes.
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Buyanova M, Cai S, Cooper J, Rhodes C, Salim H, Sahni A, Upadhyaya P, Yang R, Sarkar A, Li N, Wang QE, Pei D. Discovery of a Bicyclic Peptidyl Pan-Ras Inhibitor. J Med Chem 2021; 64:13038-13053. [PMID: 34415745 DOI: 10.1021/acs.jmedchem.1c01130] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The Ras subfamily of small GTPases is mutated in ∼30% of human cancers and represents compelling yet challenging anticancer drug targets owing to their flat protein surface. We previously reported a bicyclic peptidyl inhibitor, cyclorasin B3, which binds selectively to Ras-GTP with modest affinity and blocks its interaction with downstream effector proteins in vitro but lacks cell permeability or biological activity. In this study, optimization of B3 yielded a potent pan-Ras inhibitor, cyclorasin B4-27, which binds selectively to the GTP-bound forms of wild-type and mutant Ras isoforms (KD = 21 nM for KRasG12V-GppNHp) and is highly cell-permeable and metabolically stable (serum t1/2 > 24 h). B4-27 inhibits Ras signaling in vitro and in vivo by blocking Ras from interacting with downstream effector proteins and induces apoptosis of Ras-mutant cancer cells. When administered systemically (i.v.), B4-27 suppressed tumor growth in two different mouse xenograft models at 1-5 mg/kg of daily doses.
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Affiliation(s)
- Marina Buyanova
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Shurui Cai
- Department of Radiation Oncology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jahan Cooper
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Curran Rhodes
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Heba Salim
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Ashweta Sahni
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Punit Upadhyaya
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Rui Yang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Amar Sarkar
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Na Li
- Department of Radiation Oncology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Qi-En Wang
- Department of Radiation Oncology, The Ohio State University, Columbus, Ohio 43210, United States.,Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States.,Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
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Nomura TK, Heishima K, Sugito N, Sugawara R, Ueda H, Yukihiro A, Honda R. Specific inhibition of oncogenic RAS using cell-permeable RAS-binding domains. Cell Chem Biol 2021; 28:1581-1589.e6. [PMID: 33964212 DOI: 10.1016/j.chembiol.2021.04.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/17/2021] [Accepted: 04/20/2021] [Indexed: 10/21/2022]
Abstract
Oncogenic RAS proteins, common oncogenic drivers in many human cancers, have been refractory to conventional small-molecule and macromolecule inhibitors due to their intracellular localization and the lack of druggable pockets. Here, we present a feasible strategy for designing RAS inhibitors that involves intracellular delivery of RAS-binding domain (RBD), a nanomolar-affinity specific ligand of RAS. Screening of 51 different combinations of RBD and cell-permeable peptides has identified Pen-cRaf-v1 as a cell-permeable pan-RAS inhibitor capable of targeting both G12C and non-G12C RAS mutants. Pen-cRaf-v1 crosses the cell membrane via endocytosis, competitively inhibits RAS-effector interaction, and thereby exerts anticancer activity against several KRAS-mutant cancer cell lines. Moreover, Pen-cRaf-v1 exhibits excellent activity comparable with a leading pan-RAS inhibitor (BI-2852), as well as high target specificity in transcriptome analysis and alanine mutation analysis. These findings demonstrate that specific inhibition of oncogenic RAS, and possibly treatment of RAS-mutant cancer, is feasible by intracellular delivery of RBD.
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Affiliation(s)
- Teiko Komori Nomura
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan
| | - Kazuki Heishima
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan
| | - Nobuhiko Sugito
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan
| | - Ryota Sugawara
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan
| | - Hiroshi Ueda
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan
| | - Akao Yukihiro
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan
| | - Ryo Honda
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1193, Japan.
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9
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Fukuda K, Lu F, Qin J. Molecular basis for Ras suppressor-1 binding to PINCH-1 in focal adhesion assembly. J Biol Chem 2021; 296:100685. [PMID: 33891945 PMCID: PMC8141872 DOI: 10.1016/j.jbc.2021.100685] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/14/2021] [Accepted: 04/19/2021] [Indexed: 10/29/2022] Open
Abstract
Ras suppressor-1 (Rsu-1) is a leucine-rich repeat (LRR)-containing protein that is crucial for regulating cell adhesion and is involved in such physiological and pathological processes as focal adhesion assembly and tumor metastasis. Rsu-1 interacts with zinc-finger type multi-LIM domain-containing adaptor protein PINCH-1, known to be involved in the integrin-mediated consensus adhesome, but not with its highly homologous family member PINCH-2. However, the structural basis for and regulatory mechanisms of this specific interaction remain unclear. Here, we determined the crystal structures of Rsu-1 and its complex with the PINCH-1 LIM4-5 domains. Rsu-1 displays an arc-shaped solenoid architecture, with eight LRRs shielded by N- and C-terminal capping modules. We showed that the conserved concave surface of the Rsu-1 LRR domain binds and stabilizes the PINCH-1 LIM5 domain via salt bridge and hydrophobic interactions, while the C-terminal non-LIM region of PINCH-2 sterically disfavors Rsu-1 binding. We also showed that Rsu-1 can be assembled, via PINCH-1-binding, into a heteropentamer complex comprising Rsu-1, PINCH-1, ILK, Parvin, and Kindlin-2, which constitute a major consensus integrin adhesome crucial for focal adhesion assembly. Our mutagenesis and cell biological data emphasize the significance of the Rsu-1/PINCH-1 interaction in focal adhesion assembly and cell spreading, providing crucial molecular insights into Rsu-1-mediated cell adhesion with implications for disease development.
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Affiliation(s)
- Koichi Fukuda
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Ohio, USA
| | - Fan Lu
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Ohio, USA; Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jun Qin
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Ohio, USA; Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.
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10
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Zhang L, Liang J, Liu X, Wu J, Tan D, Hu W. Aloperine Exerts Antitumor Effects on Bladder Cancer in vitro. Onco Targets Ther 2020; 13:10351-10360. [PMID: 33116615 PMCID: PMC7568640 DOI: 10.2147/ott.s260215] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/07/2020] [Indexed: 12/22/2022] Open
Abstract
Background Human bladder cancer is the most common malignant tumor of the urinary system and one of the 10 most common tumors of the whole body. Although most patients with bladder cancer exhibit a good prognosis with standard treatment, effective therapies for patients with a recurrent or advanced bladder cancer are unavailable. Therefore, highly effective drugs to treat such patients need to be developed. Aloperine (ALO), a natural compound isolated from Sophora alopecuroides, has antitumor properties. However, the role of ALO in human bladder cancer remains unclear. Methods In the present study, MTT was used to detect the cytotoxic effect of ALO on human BC cell line EJ and human urothelium cell line SV-HUC-1cells. Meanwhile, in order to investigate the effects of ALO on the proliferation, apoptosis, migration, and invasion of BC EJ cells and its mechanism by Cell Counting Kit-8 (CCK-8) assay, immunofluorescence, Hoechst 33342 staining, wound scratch assay, transwell migration and invasion assay, Western blot analysis. Results ALO can inhibit the proliferation and invasion of human bladder cancer EJ cells, and is low-toxic to human urothelium cells. Moreover, it can promote cellular apoptosis in vitro. Further analysis demonstrated the involvement of Caspase-dependent apoptosis following ALO treatment. ALO also downregulated the protein expression levels of Ras, p-Raf1 and p-Erk1/2. Conclusion ALO is a potential drug for human bladder cancer therapy.
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Affiliation(s)
- Lijun Zhang
- Department of Urology, Minda Hospital Affiliated to Hubei Minzu University, Enshi, Hubei Province, People's Republic of China
| | - Jun Liang
- Department of Urology, Minda Hospital Affiliated to Hubei Minzu University, Enshi, Hubei Province, People's Republic of China
| | - Xiaohua Liu
- Department of Urology, Minda Hospital Affiliated to Hubei Minzu University, Enshi, Hubei Province, People's Republic of China
| | - Jianhua Wu
- Department of Urology, Minda Hospital Affiliated to Hubei Minzu University, Enshi, Hubei Province, People's Republic of China
| | - Daqing Tan
- Department of Urology, Minda Hospital Affiliated to Hubei Minzu University, Enshi, Hubei Province, People's Republic of China
| | - Wei Hu
- Department of Urology, The First Affiliated Hospital of University of South of China, Hengyang, Hunan Province, People's Republic of China
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11
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Maculins T, Garcia-Pardo J, Skenderovic A, Gebel J, Putyrski M, Vorobyov A, Busse P, Varga G, Kuzikov M, Zaliani A, Rahighi S, Schaeffer V, Parnham MJ, Sidhu SS, Ernst A, Dötsch V, Akutsu M, Dikic I. Discovery of Protein-Protein Interaction Inhibitors by Integrating Protein Engineering and Chemical Screening Platforms. Cell Chem Biol 2020; 27:1441-1451.e7. [PMID: 32726587 DOI: 10.1016/j.chembiol.2020.07.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/24/2020] [Accepted: 07/09/2020] [Indexed: 02/06/2023]
Abstract
Protein-protein interactions (PPIs) govern intracellular life, and identification of PPI inhibitors is challenging. Roadblocks in assay development stemming from weak binding affinities of natural PPIs impede progress in this field. We postulated that enhancing binding affinity of natural PPIs via protein engineering will aid assay development and hit discovery. This proof-of-principle study targets PPI between linear ubiquitin chains and NEMO UBAN domain, which activates NF-κB signaling. Using phage display, we generated ubiquitin variants that bind to the functional UBAN epitope with high affinity, act as competitive inhibitors, and structurally maintain the existing PPI interface. When utilized in assay development, variants enable generation of robust cell-based assays for chemical screening. Top compounds identified using this approach directly bind to UBAN and dampen NF-κB signaling. This study illustrates advantages of integrating protein engineering and chemical screening in hit identification, a development that we anticipate will have wide application in drug discovery.
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Affiliation(s)
- Timurs Maculins
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany.
| | - Javier Garcia-Pardo
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | | | - Jakob Gebel
- Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany
| | - Mateusz Putyrski
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Andrew Vorobyov
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Philipp Busse
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Gabor Varga
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Maria Kuzikov
- Fraunhofer Institute for Molecular Biology and Applied Ecology Screening Port, Hamburg, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Molecular Biology and Applied Ecology Screening Port, Hamburg, Germany
| | - Simin Rahighi
- Chapman University School of Pharmacy (CUSP), Harry and Diane Rinker Health Science Campus, Chapman University, Irvine, CA 92618, USA
| | | | - Michael J Parnham
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Sachdev S Sidhu
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Andreas Ernst
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany
| | - Masato Akutsu
- Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany.
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12
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Putyrski M, Vakhrusheva O, Bonn F, Guntur S, Vorobyov A, Brandts C, Dikic I, Ernst A. Disrupting the LC3 Interaction Region (LIR) Binding of Selective Autophagy Receptors Sensitizes AML Cell Lines to Cytarabine. Front Cell Dev Biol 2020; 8:208. [PMID: 32296703 PMCID: PMC7137635 DOI: 10.3389/fcell.2020.00208] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/10/2020] [Indexed: 12/26/2022] Open
Abstract
Short linear motifs (SLiMs) located in disordered regions of multidomain proteins are important for the organization of protein-protein interaction networks. By dynamic association with their binding partners, SLiMs enable assembly of multiprotein complexes, pivotal for the regulation of various aspects of cell biology in higher organisms. Despite their importance, there is a paucity of molecular tools to study SLiMs of endogenous proteins in live cells. LC3 interacting regions (LIRs), being quintessential for orchestrating diverse stages of autophagy, are a prominent example of SLiMs and mediate binding to the ubiquitin-like LC3/GABARAP family of proteins. The role of LIRs ranges from the posttranslational processing of their binding partners at early stages of autophagy to the binding of selective autophagy receptors (SARs) to the autophagosome. In order to generate tools to study LIRs in cells, we engineered high affinity binders of LIR motifs of three archetypical SARs: OPTN, p62, and NDP52. In an array of in vitro and cellular assays, the engineered binders were shown to have greatly improved affinity and specificity when compared with the endogenous LC3/GABARAP family of proteins, thus providing a unique possibility for modulating LIR interactions in living systems. We exploited these novel tools to study the impact of LIR inhibition on the fitness and the responsiveness to cytarabine treatment of THP-1 cells - a model for studying acute myeloid leukemia (AML). Our results demonstrate that inhibition of LIR of a single autophagy receptor is insufficient to sensitize the cells to cytarabine, while simultaneous inhibition of three LIR motifs in three distinct SARs reduces the IC50 of the chemotherapeutic.
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Affiliation(s)
- Mateusz Putyrski
- Institute of Biochemistry II, Medical Faculty, Goethe-University, Frankfurt, Germany.,Project Group Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Frankfurt, Germany
| | - Olesya Vakhrusheva
- Department of Medicine, Hematology/Oncology, Goethe-University, Frankfurt, Germany
| | - Florian Bonn
- Institute of Biochemistry II, Medical Faculty, Goethe-University, Frankfurt, Germany
| | - Suchithra Guntur
- Institute of Biochemistry II, Medical Faculty, Goethe-University, Frankfurt, Germany
| | - Andrew Vorobyov
- Project Group Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Frankfurt, Germany
| | - Christian Brandts
- Department of Medicine, Hematology/Oncology, Goethe-University, Frankfurt, Germany.,German Cancer Consortium and German Cancer Research Center, Heidelberg, Germany.,University Cancer Center Frankfurt, Goethe-University, Frankfurt, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Medical Faculty, Goethe-University, Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Frankfurt, Germany
| | - Andreas Ernst
- Institute of Biochemistry II, Medical Faculty, Goethe-University, Frankfurt, Germany.,Project Group Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Frankfurt, Germany
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