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Mauro M, Berretta M, Palermo G, Cavalieri V, La Rocca G. The Multiplicity of Argonaute Complexes in Mammalian Cells. J Pharmacol Exp Ther 2023; 384:1-9. [PMID: 35667689 PMCID: PMC9827513 DOI: 10.1124/jpet.122.001158] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 01/12/2023] Open
Abstract
Argonautes (AGOs) are a highly conserved family of proteins found in most eukaryotes and involved in mechanisms of gene regulation, both at the transcriptional and post-transcriptional level. Among other functions, AGO proteins associate with microRNAs (miRNAs) to mediate the post-transcriptional repression of protein-coding genes. In this process, AGOs associate with members of the trinucleotide repeat containing 6 protein (TNRC6) family to form the core of the RNA-induced silencing complex (RISC), the effector machinery that mediates miRNA function. However, the description of the exact composition of the RISC has been a challenging task due to the fact the AGO's interactome is dynamically regulated in a cell type- and condition-specific manner. Here, we summarize some of the most significant studies that have identified AGO complexes in mammalian cells, as well as the approaches used to characterize them. Finally, we discuss possible opportunities to exploit what we have learned on the properties of the RISC to develop novel anti-cancer therapies. SIGNIFICANCE STATEMENT: The RNA-induced silencing complex (RISC) is the molecular machinery that mediates miRNA function in mammals. Studies over the past two decades have shed light on important biochemical and functional properties of this complex. However, many aspects of this complex await further elucidation, mostly due to technical limitations that have hindered full characterization. Here, we summarize some of the most significant studies on the mammalian RISC and discuss possible sources of biases in the approaches used to characterize it.
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Affiliation(s)
- Maurizio Mauro
- Department of Medicine, Albert Einstein College of Medicine, New York, New York (M.M.); Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy (M.B.); Gruppo Oncologico Ricercatori Italiani, GORI ONLUS, Pordenone, Italy (M.B.); Department of Biomedical and Biotechnological Sciences, University of Catania, Catania Italy (G.P.); Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy (V.C.); and Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York (G.L.R.)
| | - Massimiliano Berretta
- Department of Medicine, Albert Einstein College of Medicine, New York, New York (M.M.); Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy (M.B.); Gruppo Oncologico Ricercatori Italiani, GORI ONLUS, Pordenone, Italy (M.B.); Department of Biomedical and Biotechnological Sciences, University of Catania, Catania Italy (G.P.); Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy (V.C.); and Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York (G.L.R.)
| | - Giuseppe Palermo
- Department of Medicine, Albert Einstein College of Medicine, New York, New York (M.M.); Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy (M.B.); Gruppo Oncologico Ricercatori Italiani, GORI ONLUS, Pordenone, Italy (M.B.); Department of Biomedical and Biotechnological Sciences, University of Catania, Catania Italy (G.P.); Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy (V.C.); and Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York (G.L.R.)
| | - Vincenzo Cavalieri
- Department of Medicine, Albert Einstein College of Medicine, New York, New York (M.M.); Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy (M.B.); Gruppo Oncologico Ricercatori Italiani, GORI ONLUS, Pordenone, Italy (M.B.); Department of Biomedical and Biotechnological Sciences, University of Catania, Catania Italy (G.P.); Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy (V.C.); and Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York (G.L.R.)
| | - Gaspare La Rocca
- Department of Medicine, Albert Einstein College of Medicine, New York, New York (M.M.); Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy (M.B.); Gruppo Oncologico Ricercatori Italiani, GORI ONLUS, Pordenone, Italy (M.B.); Department of Biomedical and Biotechnological Sciences, University of Catania, Catania Italy (G.P.); Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy (V.C.); and Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York (G.L.R.)
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2
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Peng T, He Y, Wang T, Yu J, Ma X, Zhou Z, Sheng Y, Li L, Peng H, Li S, Zou J, Yuan Y, Zhao Y, Shi H, Li F, Liu W, Hu K, Lu X, Zhang G, Wang F. Discovery of a Novel Small-Molecule Inhibitor Disrupting TRBP-Dicer Interaction against Hepatocellular Carcinoma via the Modulation of microRNA Biogenesis. J Med Chem 2022; 65:11010-11033. [PMID: 35695407 DOI: 10.1021/acs.jmedchem.2c00189] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
MicroRNAs (miRNAs) are key players in human hepatocellular carcinoma (HCC) tumorigenesis. Therefore, small molecules targeting components of miRNA biogenesis may provide new therapeutic means for HCC treatment. By a high-throughput screening and structural simplification, we identified a small molecule, CIB-3b, which suppresses the growth and metastasis of HCC in vitro and in vivo by modulating expression profiles of miRNAome and proteome in HCC cells. Mechanistically, CIB-3b physically binds to transactivation response (TAR) RNA-binding protein 2 (TRBP) and disrupts the TRBP-Dicer interaction, thereby altering the activity of Dicer and mature miRNA production. Structure-activity relationship study via the synthesis of 45 CIB-3b derivatives showed that some compounds exhibited a similar inhibitory effect on miRNA biogenesis to CIB-3b. These results support TRBP as a potential therapeutic target in HCC and warrant further development of CIB-3b along with its analogues as a novel therapeutic strategy for the treatment of HCC.
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Affiliation(s)
- Ting Peng
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.,Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610052, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yujiao He
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.,Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu 610052, China
| | - Tao Wang
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Jialing Yu
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaofang Ma
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Zongyuan Zhou
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuwen Sheng
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lingyu Li
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huipan Peng
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Sheng Li
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Jiawei Zou
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Yi Yuan
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Yongyun Zhao
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Hailong Shi
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fu Li
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Wanli Liu
- Ministry of Education Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Life Sciences, Institute for Immunology, Tsinghua University, Beijing 100084, China
| | - Kaifeng Hu
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Xiaoxia Lu
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Guolin Zhang
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.,Xiongan Institute of Innovation, Chinese Academy of Sciences, Hebei 071700, China
| | - Fei Wang
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.,Xiongan Institute of Innovation, Chinese Academy of Sciences, Hebei 071700, China
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3
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Gindi N, Grossman H, Bar-Joseph H, Miller I, Nemerovsky L, Hadas R, Nevo N, Galiani D, Dekel N, Shalgi R. Fyn and argonaute 2 participate in maternal-mRNA degradation during mouse oocyte maturation. Cell Cycle 2022; 21:792-804. [PMID: 35104175 PMCID: PMC8973342 DOI: 10.1080/15384101.2022.2031427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Fertilization triggers physiological degradation of maternal-mRNAs, which are then replaced by embryonic transcripts. Ample evidence suggests that Argonaut 2 (AGO2) is a possible post-fertilization regulator of maternal-mRNAs degradation; but its role in degradation of maternal-mRNAs during oocyte maturation remains obscure. Fyn, a member of the Src family kinases (SFKs), and an essential factor in oocyte maturation, was reported to inhibit AGO2 activity in oligodendrocytes. Our aim was to examine the role of Fyn and AGO2 in degradation of maternal-mRNAs during oocyte maturation by either suppressing their activity with SU6656 - an SFKs inhibitor; or by microinjecting DN-Fyn RNA for suppression of Fyn and BCl-137 for suppression of AGO2. Batches of fifteen mouse oocytes or embryos were analyzed by qPCR to measure the expression level of nine maternal-mRNAs that were selected for their known role in oocyte growth, maturation and early embryogenesis. We found that Fyn/SFKs are involved in maintaining the stability of at least four pre-transcribed mRNAs in oocytes at the germinal vesicle (GV) stage, whereas AGO2 had no role at this stage. During in-vivo oocyte maturation, eight maternal-mRNAs were significantly degraded. Inhibition of AGO2 prevented the degreadation of at least five maternal-mRNAs, whereas inhibition of Fyn/SFK prevented degradation of at least five Fyn maternal-mRNAs and two SFKs maternal-mRNAs; pointing at their role in promoting the physiological degradation which occurs during in-vivo oocyte maturation. Our findings imply the involvement of Fyn/SFKs in stabilization of maternal-mRNA at the GV stage and the involvement of Fyn, SFKs and AGO2 in degradation of maternal mRNAs during oocyte maturation.
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Affiliation(s)
- Natalie Gindi
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-AvivIsrael
| | - Hadas Grossman
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-AvivIsrael
| | - Hadas Bar-Joseph
- The Unit for Tmcr, Sackler Faculty of Medicine, Tel-Aviv University, Tel-AvivIsrael
| | - Irit Miller
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-AvivIsrael
| | - Luba Nemerovsky
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-AvivIsrael
| | - Ron Hadas
- Department of Biological Regulation, Weizmann Institute of Science, RehovotIsrael
| | - Nava Nevo
- Department of Biological Regulation, Weizmann Institute of Science, RehovotIsrael
| | - Dalia Galiani
- Department of Biological Regulation, Weizmann Institute of Science, RehovotIsrael
| | - Nava Dekel
- Department of Biological Regulation, Weizmann Institute of Science, RehovotIsrael
| | - Ruth Shalgi
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-AvivIsrael,CONTACT Ruth Shalgi Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv69978, Israel
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4
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Nguyen LD, Chau RK, Krichevsky AM. Small Molecule Drugs Targeting Non-Coding RNAs as Treatments for Alzheimer's Disease and Related Dementias. Genes (Basel) 2021; 12:2005. [PMID: 34946953 PMCID: PMC8701955 DOI: 10.3390/genes12122005] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/24/2022] Open
Abstract
Despite the enormous burden of Alzheimer's disease and related dementias (ADRD) on patients, caregivers, and society, only a few treatments with limited efficacy are currently available. While drug development conventionally focuses on disease-associated proteins, RNA has recently been shown to be druggable for therapeutic purposes as well. Approximately 70% of the human genome is transcribed into non-protein-coding RNAs (ncRNAs) such as microRNAs, long ncRNAs, and circular RNAs, which can adopt diverse structures and cellular functions. Many ncRNAs are specifically enriched in the central nervous system, and their dysregulation is implicated in ADRD pathogenesis, making them attractive therapeutic targets. In this review, we first detail why targeting ncRNAs with small molecules is a promising therapeutic strategy for ADRD. We then outline the process from discovery to validation of small molecules targeting ncRNAs in preclinical studies, with special emphasis on primary high-throughput screens for identifying lead compounds. Screening strategies for specific ncRNAs will also be included as examples. Key challenges-including selecting appropriate ncRNA targets, lack of specificity of small molecules, and general low success rate of neurological drugs and how they may be overcome-will be discussed throughout the review.
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Affiliation(s)
- Lien D Nguyen
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Rachel K Chau
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Anna M Krichevsky
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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Self-assembling ferritin-dendrimer nanoparticles for targeted delivery of nucleic acids to myeloid leukemia cells. J Nanobiotechnology 2021; 19:172. [PMID: 34107976 PMCID: PMC8190868 DOI: 10.1186/s12951-021-00921-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 05/31/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND In recent years, the use of ferritins as nano-vehicles for drug delivery is taking center stage. Compared to other similar nanocarriers, Archaeoglobus fulgidus ferritin is particularly interesting due to its unique ability to assemble-disassemble under very mild conditions. Recently this ferritin was engineered to get a chimeric protein targeted to human CD71 receptor, typically overexpressed in cancer cells. RESULTS Archaeoglobus fulgidus chimeric ferritin was used to generate a self-assembling hybrid nanoparticle hosting an aminic dendrimer together with a small nucleic acid. The positively charged dendrimer can indeed establish electrostatic interactions with the chimeric ferritin internal surface, allowing the formation of a protein-dendrimer binary system. The 4 large triangular openings on the ferritin shell represent a gate for negatively charged small RNAs, which access the internal cavity attracted by the dense positive charge of the dendrimer. This ternary protein-dendrimer-RNA system is efficiently uptaken by acute myeloid leukemia cells, typically difficult to transfect. As a proof of concept, we used a microRNA whose cellular delivery and induced phenotypic effects can be easily detected. In this article we have demonstrated that this hybrid nanoparticle successfully delivers a pre-miRNA to leukemia cells. Once delivered, the nucleic acid is released into the cytosol and processed to mature miRNA, thus eliciting phenotypic effects and morphological changes similar to the initial stages of granulocyte differentiation. CONCLUSION The results here presented pave the way for the design of a new family of protein-based transfecting agents that can specifically target a wide range of diseased cells.
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Nowak I, Sarshad AA. Argonaute Proteins Take Center Stage in Cancers. Cancers (Basel) 2021; 13:cancers13040788. [PMID: 33668654 PMCID: PMC7918559 DOI: 10.3390/cancers13040788] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary The dysregulation of RNA interference (RNAi) has often been observed in cancers, where the main focus of research has been on the small RNA molecules directing RNAi. In this review, we focus on the activity of Argonaute proteins, central components of RNAi, in tumorigenesis, and also highlight their potential applications in grading tumors and anti-cancer therapies. Abstract Argonaute proteins (AGOs) play crucial roles in RNA-induced silencing complex (RISC) formation and activity. AGOs loaded with small RNA molecules (miRNA or siRNA) either catalyze endoribonucleolytic cleavage of target RNAs or recruit factors responsible for translational silencing and target destabilization. miRNAs are well characterized and broadly studied in tumorigenesis; nevertheless, the functions of the AGOs in cancers have lagged behind. Here, we discuss the current state of knowledge on the role of AGOs in tumorigenesis, highlighting canonical and non-canonical functions of AGOs in cancer cells, as well as the biomarker potential of AGO expression in different of tumor types. Furthermore, we point to the possible application of the AGOs in development of novel therapeutic approaches.
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Affiliation(s)
- Iwona Nowak
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden;
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Aishe A. Sarshad
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden;
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden
- Correspondence:
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7
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Fabbiano F, Corsi J, Gurrieri E, Trevisan C, Notarangelo M, D'Agostino VG. RNA packaging into extracellular vesicles: An orchestra of RNA-binding proteins? J Extracell Vesicles 2020; 10:e12043. [PMID: 33391635 PMCID: PMC7769857 DOI: 10.1002/jev2.12043] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 11/17/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022] Open
Abstract
Extracellular vesicles (EVs) are heterogeneous membranous particles released from the cells through different biogenetic and secretory mechanisms. We now conceive EVs as shuttles mediating cellular communication, carrying a variety of molecules resulting from intracellular homeostatic mechanisms. The RNA is a widely detected cargo and, impressively, a recognized functional intermediate that elects EVs as modulators of cancer cell phenotypes, determinants of disease spreading, cell surrogates in regenerative medicine, and a source for non-invasive molecular diagnostics. The mechanistic elucidation of the intracellular events responsible for the engagement of RNA into EVs will significantly improve the comprehension and possibly the prediction of EV "quality" in association with cell physiology. Interestingly, the application of multidisciplinary approaches, including biochemical as well as cell-based and computational strategies, is increasingly revealing an active RNA-packaging process implicating RNA-binding proteins (RBPs) in the sorting of coding and non-coding RNAs. In this review, we provide a comprehensive view of RBPs recently emerging as part of the EV biology, considering the scenarios where: (i) individual RBPs were detected in EVs along with their RNA substrates, (ii) RBPs were detected in EVs with inferred RNA targets, and (iii) EV-transcripts were found to harbour sequence motifs mirroring the activity of RBPs. Proteins so far identified are members of the hnRNP family (hnRNPA2B1, hnRNPC1, hnRNPG, hnRNPH1, hnRNPK, and hnRNPQ), as well as YBX1, HuR, AGO2, IGF2BP1, MEX3C, ANXA2, ALIX, NCL, FUS, TDP-43, MVP, LIN28, SRP9/14, QKI, and TERT. We describe the RBPs based on protein domain features, current knowledge on the association with human diseases, recognition of RNA consensus motifs, and the need to clarify the functional significance in different cellular contexts. We also summarize data on previously identified RBP inhibitor small molecules that could also be introduced in EV research as potential modulators of vesicular RNA sorting.
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Affiliation(s)
- Fabrizio Fabbiano
- Department of CellularComputational and Integrative Biology (CIBIO)University of TrentoTrentoItaly
| | - Jessica Corsi
- Department of CellularComputational and Integrative Biology (CIBIO)University of TrentoTrentoItaly
| | - Elena Gurrieri
- Department of CellularComputational and Integrative Biology (CIBIO)University of TrentoTrentoItaly
| | - Caterina Trevisan
- Department of CellularComputational and Integrative Biology (CIBIO)University of TrentoTrentoItaly
| | - Michela Notarangelo
- Department of CellularComputational and Integrative Biology (CIBIO)University of TrentoTrentoItaly
| | - Vito G. D'Agostino
- Department of CellularComputational and Integrative Biology (CIBIO)University of TrentoTrentoItaly
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8
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Hentzschel F, Obrova K, Marti M. No evidence for Ago2 translocation from the host erythrocyte into the Plasmodium parasite. Wellcome Open Res 2020; 5:92. [PMID: 33501380 PMCID: PMC7808052 DOI: 10.12688/wellcomeopenres.15852.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2020] [Indexed: 12/13/2022] Open
Abstract
Background: Plasmodium parasites rely on various host factors to grow and replicate within red blood cells (RBC). While many host proteins are known that mediate parasite adhesion and invasion, few examples of host enzymes co-opted by the parasite during intracellular development have been described. Recent studies suggested that the host protein Argonaute 2 (Ago2), which is involved in RNA interference, can translocate into the parasite and affect its development. Here, we investigated this hypothesis. Methods: We used several different monoclonal antibodies to test for Ago2 localisation in the human malaria parasite, P. falciparum and rodent P. berghei parasites. In addition, we biochemically fractionated infected red blood cells to localize Ago2. We also quantified parasite growth and sexual commitment in the presence of the Ago2 inhibitor BCI-137. Results: Ago2 localization by fluorescence microscopy produced inconclusive results across the three different antibodies, suggesting cross-reactivity with parasite targets. Biochemical separation of parasite and RBC cytoplasm detected Ago2 only in the RBC cytoplasm and not in the parasite. Inhibition of Ago2 using BCl-137 did not result in altered parasite development. Conclusion: Ago2 localization in infected RBCs by microscopy is confounded by non-specific binding of antibodies. Complementary results using biochemical fractionation and Ago2 detection by western blot did not detect the protein in the parasite cytosol, and growth assays using a specific inhibitor demonstrated that its catalytical activity is not required for parasite development. We therefore conclude that previous data localising Ago2 to parasite ring stages are due to antibody cross reactivity, and that Ago2 is not required for intracellular Plasmodium development.
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Affiliation(s)
- Franziska Hentzschel
- Wellcome Center for Integrative Parasitology; Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
- Center for Infectious Diseases, Parasitology Unit, Heidelberg University Hospital, Heidelberg, 69120, Germany
| | - Klara Obrova
- Center for Infectious Diseases, Parasitology Unit, Heidelberg University Hospital, Heidelberg, 69120, Germany
| | - Matthias Marti
- Wellcome Center for Integrative Parasitology; Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
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Lazar S, Wurtzel JGT, Chen X, Ma P, Goldfinger LE. High-efficiency unassisted transfection of platelets with naked double-stranded miRNAs modulates signal-activated translation and platelet function. Platelets 2020; 32:794-806. [PMID: 32838617 DOI: 10.1080/09537104.2020.1809642] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We sought novel approaches to improve transfection efficiencies of microRNAs (miRNAs) in platelets, and to apply these approaches to investigate the roles of miRNAs in regulating signal-activated protein translation and functional effects. We found that ex vivo human platelets support gymnosis---internalization of ectopic miRNAs following co-incubation in the absence of conventional transfection reagents or schemes---and subsequently incorporate transfected miRNA into ARGONAUTE2 (AGO2)-based RNA-induced silencing complexes (RISC). Thrombin/fibrinogen stimulation activated translation of miR-223-3p target SEPTIN2, which was suppressed by miR-223-3p transfection in an AGO2/RISC-dependent manner. Thrombin/fibrinogen-induced exosome and microvesicle generation was inhibited by miR-223-3p transfection, and this effect was reversed with a RISC inhibitor. Platelet gymnosis of naked miRNAs appeared to be mediated in part by endocytic pathways including clathrin-dependent and fluid-phase endocytosis and caveolae. These results demonstrate the ability of ex vivo platelets to internalize ectopic miRNAs by unassisted transfection, and utilize them to modulate signal-activated translation and platelet function. Our results identify new roles for miR-223-3p in extracellular vesicle generation in stimulated platelets. High-efficiency gymnotic transfection of miRNAs in ex vivo platelets may be a broadly useful tool for exploring molecular genetic regulation of platelet function.
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Affiliation(s)
- Sophia Lazar
- Cardeza Foundation for Hematologic Research, Department of Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Jeremy G T Wurtzel
- Cardeza Foundation for Hematologic Research, Department of Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Xi Chen
- Cardeza Foundation for Hematologic Research, Department of Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Peisong Ma
- Cardeza Foundation for Hematologic Research, Department of Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Lawrence E Goldfinger
- Cardeza Foundation for Hematologic Research, Department of Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
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10
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Harumoto T, Sato A, Takayama Y, Miyagi H, Saito JI, Shinohara F. Structure-guided screening strategy combining surface plasmon resonance with nuclear magnetic resonance for identification of small-molecule Argonaute 2 inhibitors. PLoS One 2020; 15:e0236710. [PMID: 32735606 PMCID: PMC7394379 DOI: 10.1371/journal.pone.0236710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 07/13/2020] [Indexed: 01/07/2023] Open
Abstract
Argonaute (AGO) proteins are the key component of the RNA interference machinery that suppresses gene expression by forming an RNA-induced silencing complex (RISC) with microRNAs (miRNAs). Each miRNA is involved in various cellular processes, such as development, differentiation, tumorigenesis, and viral infection. Thus, molecules that regulate miRNA function are expected to have therapeutic potential. In addition, the biogenesis of miRNA is a multistep process involving various proteins, although the complete pathway remains to be elucidated. Therefore, identification of molecules that can specifically modulate each step will help understand the mechanism of gene suppression. To date, several AGO2 inhibitors have been identified. However, these molecules were identified through a single screening method, and no studies have specifically evaluated a combinatorial strategy. Here, we demonstrated a combinatorial screening (SCR) approach comprising an in silico molecular docking study, surface plasmon resonance (SPR) analysis, and nuclear magnetic resonance (NMR) analysis, focusing on the strong binding between the 5'-terminal phosphate of RNA and the AGO2 middle (MID) domain. By combining SPR and NMR, we identified binding modes of amino acid residues binding to AGO2. First, using a large chemical library (over 6,000,000 compounds), 171 compounds with acidic functional groups were screened using in silico SCR. Next, we constructed an SPR inhibition system that could analyze only the 5'-terminal binding site of RNA, and nine molecules that strongly bound to the AGO2 MID domain were selected. Finally, using NMR, three molecules that bound to the desired site were identified. The RISC inhibitory ability of the “hit” compounds was analyzed in human cell lysate, and all three hit compounds strongly inhibited the binding between double-stranded RNA and AGO2.
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Affiliation(s)
- Toshimasa Harumoto
- Research Functions Unit, R&D Division, Kyowa Kirin Co., Ltd., Machida-shi, Tokyo, Japan
- * E-mail:
| | - Atsuko Sato
- Research Functions Unit, R&D Division, Kyowa Kirin Co., Ltd., Nagaizumi-cho, Suntou-gun, Shizuoka, Japan
| | - Yuki Takayama
- Research Functions Unit, R&D Division, Kyowa Kirin Co., Ltd., Nagaizumi-cho, Suntou-gun, Shizuoka, Japan
| | - Hikaru Miyagi
- Research Functions Unit, R&D Division, Kyowa Kirin Co., Ltd., Machida-shi, Tokyo, Japan
| | - Jun-ichi Saito
- Research Functions Unit, R&D Division, Kyowa Kirin Co., Ltd., Nagaizumi-cho, Suntou-gun, Shizuoka, Japan
| | - Fumikazu Shinohara
- Research Functions Unit, R&D Division, Kyowa Kirin Co., Ltd., Otemachi, Chiyoda-ku, Tokyo, Japan
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11
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From the Argonauts Mythological Sailors to the Argonautes RNA-Silencing Navigators: Their Emerging Roles in Human-Cell Pathologies. Int J Mol Sci 2020; 21:ijms21114007. [PMID: 32503341 PMCID: PMC7312461 DOI: 10.3390/ijms21114007] [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: 05/15/2020] [Revised: 06/01/2020] [Accepted: 06/01/2020] [Indexed: 12/27/2022] Open
Abstract
Regulation of gene expression has emerged as a fundamental element of transcript homeostasis. Key effectors in this process are the Argonautes (AGOs), highly specialized RNA-binding proteins (RBPs) that form complexes, such as the RNA-Induced Silencing Complex (RISC). AGOs dictate post-transcriptional gene-silencing by directly loading small RNAs and repressing their mRNA targets through small RNA-sequence complementarity. The four human highly-conserved family-members (AGO1, AGO2, AGO3, and AGO4) demonstrate multi-faceted and versatile roles in transcriptome’s stability, plasticity, and functionality. The post-translational modifications of AGOs in critical amino acid residues, the nucleotide polymorphisms and mutations, and the deregulation of expression and interactions are tightly associated with aberrant activities, which are observed in a wide spectrum of pathologies. Through constantly accumulating information, the AGOs’ fundamental engagement in multiple human diseases has recently emerged. The present review examines new insights into AGO-driven pathology and AGO-deregulation patterns in a variety of diseases such as in viral infections and propagations, autoimmune diseases, cancers, metabolic deficiencies, neuronal disorders, and human infertility. Altogether, AGO seems to be a crucial contributor to pathogenesis and its targeting may serve as a novel and powerful therapeutic tool for the successful management of diverse human diseases in the clinic.
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12
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Hentzschel F, Obrova K, Marti M. No evidence for Ago2 translocation from the host erythrocyte into the Plasmodium parasite. Wellcome Open Res 2020; 5:92. [PMID: 33501380 PMCID: PMC7808052 DOI: 10.12688/wellcomeopenres.15852.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2020] [Indexed: 02/15/2024] Open
Abstract
Background: Plasmodium parasites rely on various host factors to grow and replicate within red blood cells (RBC). While many host proteins are known that mediate parasite adhesion and invasion, few examples of host enzymes co-opted by the parasite during intracellular development have been described. Recent studies suggested that the host protein Argonaute 2 (Ago2), which is involved in RNA interference, can translocate into the parasite and affect its development. Here, we investigated this hypothesis. Methods: We used several different monoclonal antibodies to test for Ago2 localisation in the human malaria parasite, P. falciparum and rodent P. berghei parasites. In addition, we biochemically fractionated infected red blood cells to localize Ago2. We also quantified parasite growth and sexual commitment in the presence of the Ago2 inhibitor BCI-137. Results: Ago2 localization by fluorescence microscopy produced inconclusive results across the three different antibodies, suggesting cross-reactivity with parasite targets. Biochemical separation of parasite and RBC cytoplasm detected Ago2 only in the RBC cytoplasm and not in the parasite. Inhibition of Ago2 using BCl-137 did not result in altered parasite development. Conclusion: Ago2 localization in infected RBCs by microscopy is confounded by non-specific binding of antibodies. Complementary results using biochemical fractionation and Ago2 detection by western blot did not detect the protein in the parasite cytosol, and growth assays using a specific inhibitor demonstrated that its catalytical activity is not required for parasite development. We therefore conclude that previous data localising Ago2 to parasite ring stages are due to antibody cross reactivity, and that Ago2 is not required for intracellular Plasmodium development.
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Affiliation(s)
- Franziska Hentzschel
- Wellcome Center for Integrative Parasitology; Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
- Center for Infectious Diseases, Parasitology Unit, Heidelberg University Hospital, Heidelberg, 69120, Germany
| | - Klara Obrova
- Center for Infectious Diseases, Parasitology Unit, Heidelberg University Hospital, Heidelberg, 69120, Germany
| | - Matthias Marti
- Wellcome Center for Integrative Parasitology; Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
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13
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Van Meter EN, Onyango JA, Teske KA. A review of currently identified small molecule modulators of microRNA function. Eur J Med Chem 2020; 188:112008. [DOI: 10.1016/j.ejmech.2019.112008] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 12/06/2019] [Accepted: 12/20/2019] [Indexed: 12/13/2022]
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14
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Gholikhani-Darbroud R. MicroRNA and retinoic acid. Clin Chim Acta 2019; 502:15-24. [PMID: 31812758 DOI: 10.1016/j.cca.2019.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/02/2019] [Accepted: 12/03/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND OBJECTIVE Retinoic acid is a metabolite of vitamin A that is necessary to maintain health in human and most of the other vertebrates. MicroRNAs (miR or miRNAs) are small, non-coding RNA particles that diminish mRNA translation of various genes and so can regulate critical cell processes including cell death, proliferation, development, etc. The aim of this review is to study interrelations between retinoic acid with miRNAs. METHODS We reviewed and summarized all published articles in PubMed, Europe PMC, and Embase databases with any relationship between retinoic acid and miRNAs from Jun 2003 to Dec 2018 that includes 126 articles. RESULTS Results showed direct and indirect relationships between retinoic acid and miRNAs in various levels including effects of retinoic acid on expression of various miRNAs and miRNA-biogenesis enzymes, and effect of miRNAs on metabolism of retinoic acid. DISCUTION AND CONCLUSION This review indicates that retinoic acid has inter-correlations with various miRNA members and their metabolism in health and disease may require implications of the other.
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Affiliation(s)
- Reza Gholikhani-Darbroud
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute, Urmia University of Medical Sciences, Urmia 5714783734, Iran.
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15
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Mahernia S, Hassanzadeh M, Sarvari S, Amanlou M. Targeting the microRNA binding domain of argonaute 2: rational inhibitor design and study of mutation effects on protein-ligand interaction. J Biomol Struct Dyn 2019; 38:4710-4717. [PMID: 31684811 DOI: 10.1080/07391102.2019.1688688] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Based on the accumulative evidences during recent decades, miRNAs have been found overexpressed in several human cancer types and also in Down syndrome patients, contributing to the neuropathology of Down syndrome. From this point of view, investigations on the structure and dynamic mechanisms related to the Argonaute 2 miRNAs binding in which silencing of the mRNA occurs, have inspired many clinical researchers to target this complex to inhibit the silencing process. In the current research, we have virtually screened the OTAVA_CNS_library to introduce new inhibitor compounds for the Ago2/miRNA complex. Ten hit compounds were obtained, with just one of them nominated as the best compound. Following the interaction analysis, by utilizing molecular dynamics (MD) simulations, effects of two mutations (Thr526 to isoleucine and Gln545 to alanine) on the dynamic properties of Ago2 in the complex with the best inhibitor compound were investigated. RMSD, RMSF and h-bond number beside other analyses, highlighted the importance of the Thr526 and Gln545 mutations for the stability and flexibility of the (Ago2)/ligand complex.[Formula: see text]Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shabnam Mahernia
- The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
| | - Malihe Hassanzadeh
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Sajad Sarvari
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Massoud Amanlou
- The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran.,Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran.,Experimental Medicine Research Center, Tehran University of Medical Sciences, Tehran, Iran
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16
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Salem ESB, Vonberg AD, Borra VJ, Gill RK, Nakamura T. RNAs and RNA-Binding Proteins in Immuno-Metabolic Homeostasis and Diseases. Front Cardiovasc Med 2019; 6:106. [PMID: 31482095 PMCID: PMC6710452 DOI: 10.3389/fcvm.2019.00106] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 07/17/2019] [Indexed: 12/16/2022] Open
Abstract
The increasing prevalence of worldwide obesity has emerged as a major risk factor for type 2 diabetes (T2D), hepatosteatosis, and cardiovascular disease. Accumulating evidence indicates that obesity has strong inflammatory underpinnings tightly linked to the development of metabolic diseases. However, the molecular mechanisms by which obesity induces aberrant inflammation associated with metabolic diseases are not yet clearly defined. Recently, RNAs have emerged as important regulators of stress responses and metabolism. RNAs are subject to changes in modification status, higher-order structure, and cellular localization; all of which could affect the affinity for RNA-binding proteins (RBPs) and thereby modify the RNA-RBP networks. Proper regulation and management of RNA characteristics are fundamental to cellular and organismal homeostasis, as well as paramount to health. Identification of multiple single nucleotide polymorphisms (SNPs) within loci of fat mass- and obesity-associated protein (FTO) gene, an RNA demethylase, through genome-wide association studies (GWAS) of T2D, and functional assessments of FTO in mice, support the concept that disruption in RNA modifications leads to the development of human diseases including obesity and metabolic disorder. In obesity, dynamic alterations in modification and localization of RNAs appear to modulate the RNA-RBP networks and activate proinflammatory RBPs, such as double-stranded RNA (dsRNA)-dependent protein kinase (PKR), Toll-like receptor (TLR) 3 and TLR7, and RNA silencing machinery. These changes induce aberrant inflammation and the development of metabolic diseases. This review will describe the current understanding of the underlying causes of these common and altered characteristics of RNA-RBP networks which will pave the way for developing novel approaches to tackle the pandemic issue of obesity.
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Affiliation(s)
- Esam S B Salem
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Andrew D Vonberg
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Vishnupriya J Borra
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Rupinder K Gill
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Takahisa Nakamura
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Department of Metabolic Bioregulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
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17
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Argonaute 2 drives miR-145-5p-dependent gene expression program in breast cancer cells. Cell Death Dis 2019; 10:17. [PMID: 30622242 PMCID: PMC6325137 DOI: 10.1038/s41419-018-1267-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 11/25/2018] [Accepted: 12/04/2018] [Indexed: 12/21/2022]
Abstract
To perform their regulatory functions, microRNAs (miRNAs) must assemble with any of the four mammalian Argonaute (Ago) family of proteins, Ago1–4, into an effector complex known as the RNA-induced silencing complex (RISC). While the mature miRNA guides the RISC complex to its target mRNA, the Ago protein represses mRNA translation. The specific roles of the various Ago members in mediating miRNAs activity, however, haven’t been clearly established. In this study, we investigated the contribution of Ago2, the only human Ago protein endowed with nuclease activity, to the function of tumor-suppressor miR-145-5p in breast cancer (BC). We show that miR-145-5p and Ago2 protein are concomitantly downregulated in BC tissues and that restoration of miR-145-5p expression in BC cells leads to Ago2 protein induction through the loosening of Ago2 mRNA translational repression. Functionally, miR-145-5p exerts its inhibitory activity on cell migration only in presence of Ago2, while, upon Ago2 depletion, we observed increased miR-145/Ago1 complex and enhanced cell motility. Profiling by microarray of miR-145-5p target mRNAs, in BC cells depleted or not of Ago2, revealed that miR-145-5p drives Ago2-dependent and -independent activities. Our results highlight that the Ago2 protein in cancer cells strictly dictates miR-145-5p tumor suppressor activity.
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18
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Abstract
Only 20 years after the discovery of small non-coding, single-stranded ribonucleic acids, so-called microRNAs (miRNAs), as post-transcriptional gene regulators, the first miRNA-targeting drug Miravirsen for the treatment of hepatitis C has been successfully tested in clinical Phase II trials. Addressing miRNAs as drug targets may enable the cure, or at least the treatment of diseases, which presently seems impossible. However, due to miRNAs' chemical structure, generation of potential drug molecules with necessary pharmacokinetic properties is still challenging and requires a re-thinking of the drug discovery process. Therefore, this chapter highlights the potential of miRNAs as drug targets, discusses the challenges, and tries to give a complete overview of recent strategies in miRNA drug discovery.
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Affiliation(s)
- Marco F Schmidt
- BEROCEUTICA GmbH, c/o Universität Potsdam, August-Bebel-Strasse 89, 14482, Potsdam, Germany.
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19
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Bellissimo T, Masciarelli S, Poser E, Genovese I, Del Rio A, Colotti G, Fazi F. Small Molecules Targeting the miRNA-Binding Domain of Argonaute 2: From Computer-Aided Molecular Design to RNA Immunoprecipitation. Methods Mol Biol 2017; 1517:211-221. [PMID: 27924485 DOI: 10.1007/978-1-4939-6563-2_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The development of small-molecule-based target therapy design for human disease and cancer is object of growing attention. Recently, specific microRNA (miRNA) mimicking compounds able to bind the miRNA-binding domain of Argonaute 2 protein (AGO2) to inhibit miRNA loading and its functional activity were described. Computer-aided molecular design techniques and RNA immunoprecipitation represent suitable approaches to identify and experimentally determine if a compound is able to impair the loading of miRNAs on AGO2 protein. Here, we describe these two methodologies that we recently used to select a specific compound able to interfere with the AGO2 functional activity and able to improve the retinoic acid-dependent myeloid differentiation of leukemic cells.
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Affiliation(s)
- Teresa Bellissimo
- Department of Anatomical, Histological, Forensic & Orthopaedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Via A. Scarpa, 14-16, 00161, Rome, Italy
| | - Silvia Masciarelli
- Department of Anatomical, Histological, Forensic & Orthopaedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Via A. Scarpa, 14-16, 00161, Rome, Italy
| | - Elena Poser
- Pathology, Italian National Research Council, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, 00161, Rome, Italy
| | - Ilaria Genovese
- Pathology, Italian National Research Council, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, 00161, Rome, Italy
| | - Alberto Del Rio
- CNR-National Research Council of Italy, Institute for Organic Chemistry and Photoreactivity, Via P. Gobetti 101, 40129, Bologna, Italy. .,Innovamol Srls, Viale A. Corassori 24, 41124, Modena, Italy.
| | - Gianni Colotti
- Pathology, Italian National Research Council, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, 00161, Rome, Italy.
| | - Francesco Fazi
- Department of Anatomical, Histological, Forensic & Orthopaedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Via A. Scarpa, 14-16, 00161, Rome, Italy.
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20
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Approaches for the Discovery of Small Molecule Ligands Targeting microRNAs. TOPICS IN MEDICINAL CHEMISTRY 2017. [DOI: 10.1007/7355_2017_3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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21
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Surface Plasmon Resonance: A Useful Strategy for the Identification of Small Molecule Argonaute 2 Protein Binders. Methods Mol Biol 2017; 1517:223-237. [PMID: 27924486 DOI: 10.1007/978-1-4939-6563-2_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Surface plasmon resonance (SPR) is one of the most important techniques for the detection and the characterization of molecular interactions. SPR technology is a label-free approach for monitoring biomolecular interactions in real time. The binding of analytes to molecules immobilized on a thin metal film (ligand) determines a change in the refractive index and, therefore in the angle of extinction of light, is reflected when polarized light hits the film, monitored in real time as a change in the position of the dip in reflected intensity. Since SPR detects mass, the technique is label-free.Here, we describe the use of SPR techniques to study the interaction between Argonaute 2 and small molecular compounds selected by means of high-throughput docking screening.
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22
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Liu T, Men Q, Wu G, Yu C, Huang Z, Liu X, Li W. Tetrandrine induces autophagy and differentiation by activating ROS and Notch1 signaling in leukemia cells. Oncotarget 2016; 6:7992-8006. [PMID: 25797266 PMCID: PMC4480730 DOI: 10.18632/oncotarget.3505] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 02/01/2015] [Indexed: 12/19/2022] Open
Abstract
All-trans retinoic acid (ATRA) is a differentiating agent for the treatment of acute promyelocytic leukemia (APL). However, the therapeutic efficacy of ATRA has limitations. Tetrandrine is a traditional Chinese medicinal herb extract with antitumor effects. In this study, we investigated the effects of tetrandrine on human PML-RARα-positive acute promyelocytic leukemia cells. Tetrandrine inhibited tumors in vivo. It induced autophagy and differentiation by triggering ROS generation and activating Notch1 signaling. Tetrandrine induced autophagy and differentiation in M5 type patient primary leukemia cells. The in vivo results indicated that low concentrations of tetrandrine inhibited leukemia cells proliferation and induced autophagy and then facilitated their differentiation, by activating ROS and Notch1 signaling. We suggest that tetrandrine is a potential agent for the treatment of APL by inducing differentiation of leukemia cells.
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Affiliation(s)
- Ting Liu
- College of Life Sciences, Wuhan University, Wuhan, P. R. China
| | - Qiuxu Men
- Ministry of Education Laboratory of Combinatorial Biosynthesis and Drug Discovery, College of Pharmacy, Wuhan University, Wuhan, P. R. China
| | - Guixian Wu
- College of Life Sciences, Wuhan University, Wuhan, P. R. China
| | - Chunrong Yu
- College of Life Sciences, Wuhan University, Wuhan, P. R. China
| | - Zan Huang
- College of Life Sciences, Wuhan University, Wuhan, P. R. China
| | - Xin Liu
- Ministry of Education Laboratory of Combinatorial Biosynthesis and Drug Discovery, College of Pharmacy, Wuhan University, Wuhan, P. R. China
| | - Wenhua Li
- College of Life Sciences, Wuhan University, Wuhan, P. R. China
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23
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Beheshti A, Babadi SS, Nozarian K, Heidarizadeh F, Ghamari N, Mayer P, Motamedi H. Crystal structure, microbiological activity and theoretical studies of Ag(I) and Cu(I) coordination polymers with 1,1′-(butane-1,4-diyl)bis(3-methylimidazoline-2-thione) ligand. Polyhedron 2016. [DOI: 10.1016/j.poly.2016.02.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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24
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Small-molecule approaches toward the targeting of oncogenic miRNAs: roadmap for the discovery of RNA modulators. Future Med Chem 2016; 8:803-16. [DOI: 10.4155/fmc-2016-0018] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
miRNAs are a recently discovered class of small noncoding RNAs implicated in the regulation of gene expression. The deregulation of miRNAs levels has been linked to the development of various cancers where oncogenic miRNAs are overexpressed and tumor suppressor miRNAs are underexpressed. Here we report the three main strategies developed in order to discover small-molecule drugs able to selectively interfere with oncogenic miRNAs: the high throughput screening of large libraries of compounds, the focused screening of small libraries of molecules that are known to be able to interact with RNA thus being supposed modulators of miRNAs pathway and the design of small molecules based on the secondary structure of targeted RNA and/or three-dimensional structure of enzymes involved in miRNAs pathway.
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25
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Xia T, Li J, Cheng H, Zhang C, Zhang Y. Small-Molecule Regulators of MicroRNAs in Biomedicine. Drug Dev Res 2015; 76:375-81. [PMID: 26450362 DOI: 10.1002/ddr.21271] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Preclinical Research MicroRNAs (miRNAs) can regulate gene expression at the post-transcriptional level and have been implicated in the development of various human diseases, including cancer. The regulatory networks of miRNAs play a vital role not only in normal physiology but also in pathology and may represent novel targets for drug discovery. Regulation of miRNAs and the elucidation of miRNA networks will advance miRNA-targeted research but are challenging due to a shortage of appropriate tools. Using different assay systems, diverse small molecules with unique miRNA regulatory activity have been identified. These bioactive small molecules not only showed regulation on different miRNAs but revealed previously unknown miRNA networks. Treatment of cancer both in vitro and in vivo with small-molecule regulators of miRNAs has demonstrated their therapeutic potential. In this review, we discuss assay systems for the identification of small-molecule regulators of miRNAs and reported small molecules, and discuss their applications as probes and candidate drug leads.
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Affiliation(s)
- Tingting Xia
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing Advanced Institute for Life Sciences (NAILS), Nanjing University School of Life Sciences, Nanjing, Jiangsu, 210093, China.,Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, 22 Hankou Road, Nanjing, Jiangsu, 210093, China
| | - Jinbo Li
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing Advanced Institute for Life Sciences (NAILS), Nanjing University School of Life Sciences, Nanjing, Jiangsu, 210093, China.,Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, 22 Hankou Road, Nanjing, Jiangsu, 210093, China.,School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China
| | - Hao Cheng
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China
| | - Chenyu Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing Advanced Institute for Life Sciences (NAILS), Nanjing University School of Life Sciences, Nanjing, Jiangsu, 210093, China.,Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, 22 Hankou Road, Nanjing, Jiangsu, 210093, China
| | - Yan Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing Advanced Institute for Life Sciences (NAILS), Nanjing University School of Life Sciences, Nanjing, Jiangsu, 210093, China.,Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, 22 Hankou Road, Nanjing, Jiangsu, 210093, China.,School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China
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26
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Andreoli F, Del Rio A. Computer-aided Molecular Design of Compounds Targeting Histone Modifying Enzymes. Comput Struct Biotechnol J 2015; 13:358-65. [PMID: 26082827 PMCID: PMC4459771 DOI: 10.1016/j.csbj.2015.04.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 04/24/2015] [Accepted: 04/30/2015] [Indexed: 02/06/2023] Open
Abstract
Growing evidences show that epigenetic mechanisms play crucial roles in the genesis and progression of many physiopathological processes. As a result, research in epigenetic grew at a fast pace in the last decade. In particular, the study of histone post-translational modifications encountered an extraordinary progression and many modifications have been characterized and associated to fundamental biological processes and pathological conditions. Histone modifications are the catalytic result of a large set of enzyme families that operate covalent modifications on specific residues at the histone tails. Taken together, these modifications elicit a complex and concerted processing that greatly contribute to the chromatin remodeling and may drive different pathological conditions, especially cancer. For this reason, several epigenetic targets are currently under validation for drug discovery purposes and different academic and industrial programs have been already launched to produce the first pre-clinical and clinical outcomes. In this scenario, computer-aided molecular design techniques are offering important tools, mainly as a consequence of the increasing structural information available for these targets. In this mini-review we will briefly discuss the most common types of known histone modifications and the corresponding operating enzymes by emphasizing the computer-aided molecular design approaches that can be of use to speed-up the efforts to generate new pharmaceutically relevant compounds.
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Affiliation(s)
- Federico Andreoli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum, University of Bologna, Via S. Giacomo 14, 40126 Bologna, Italy
| | - Alberto Del Rio
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum, University of Bologna, Via S. Giacomo 14, 40126 Bologna, Italy
- Institute of Organic Synthesis and Photoreactivity, National Research Council, Via P. Gobetti, 101 40129 Bologna, Italy
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Schmidt MF. Drug target miRNAs: chances and challenges. Trends Biotechnol 2014; 32:578-585. [PMID: 25304465 DOI: 10.1016/j.tibtech.2014.09.002] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/09/2014] [Accepted: 09/09/2014] [Indexed: 11/28/2022]
Abstract
miRNAs, short ribonucleic acid gene regulators, are increasingly popular drug targets. Traditionally 'undruggable' proteins can be targeted via their miRNA gene regulators, enabling the treatment of diseases that, at present, seem impossible to cure. However, addressing miRNAs requires innovation at the level of drug discovery. This review article outlines the potential of miRNAs as drug targets, focuses on the challenges of developing miRNA-targeting drugs, and surveys new advances. The aim is to provide an orientation guide for scientists, as well business analysts, to help them navigate the jungle of different approaches in miRNA drug discovery.
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Affiliation(s)
- Marco F Schmidt
- University Chemical Laboratory, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, UK.
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