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Rocca R, Grillone K, Citriniti EL, Gualtieri G, Artese A, Tagliaferri P, Tassone P, Alcaro S. Targeting non-coding RNAs: Perspectives and challenges of in-silico approaches. Eur J Med Chem 2023; 261:115850. [PMID: 37839343 DOI: 10.1016/j.ejmech.2023.115850] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/08/2023] [Accepted: 09/29/2023] [Indexed: 10/17/2023]
Abstract
The growing information currently available on the central role of non-coding RNAs (ncRNAs) including microRNAs (miRNAS) and long non-coding RNAs (lncRNAs) for chronic and degenerative human diseases makes them attractive therapeutic targets. RNAs carry out different functional roles in human biology and are deeply deregulated in several diseases. So far, different attempts to therapeutically target the 3D RNA structures with small molecules have been reported. In this scenario, the development of computational tools suitable for describing RNA structures and their potential interactions with small molecules is gaining more and more interest. Here, we describe the most suitable strategies to study ncRNAs through computational tools. We focus on methods capable of predicting 2D and 3D ncRNA structures. Furthermore, we describe computational tools to identify, design and optimize small molecule ncRNA binders. This review aims to outline the state of the art and perspectives of computational methods for ncRNAs over the past decade.
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Affiliation(s)
- Roberta Rocca
- Department of Health Science, Magna Graecia University, Catanzaro, Italy; Net4Science srl, Academic Spinoff, Magna Græcia University, Catanzaro, Italy
| | - Katia Grillone
- Department of Experimental and Clinical Medicine, Magna Græcia University, Catanzaro, Italy
| | | | | | - Anna Artese
- Department of Health Science, Magna Graecia University, Catanzaro, Italy; Net4Science srl, Academic Spinoff, Magna Græcia University, Catanzaro, Italy.
| | | | - Pierfrancesco Tassone
- Department of Experimental and Clinical Medicine, Magna Græcia University, Catanzaro, Italy
| | - Stefano Alcaro
- Department of Health Science, Magna Graecia University, Catanzaro, Italy; Net4Science srl, Academic Spinoff, Magna Græcia University, Catanzaro, Italy
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2
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Canale P, Campolo J, Borghini A, Andreassi MG. Long Telomeric Repeat-Containing RNA (TERRA): Biological Functions and Challenges in Vascular Aging and Disease. Biomedicines 2023; 11:3211. [PMID: 38137431 PMCID: PMC10740775 DOI: 10.3390/biomedicines11123211] [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: 10/26/2023] [Revised: 11/29/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
Telomere dysfunction is implicated in vascular aging and shorter leucocyte telomeres are associated with an increased risk of atherosclerosis, myocardial infarction, and heart failure. Another pathophysiological mechanism that explains the causal relationship between telomere shortening and atherosclerosis development focuses on the clonal hematopoiesis of indeterminate potential (CHIP), which represents a new and independent risk factor in atherosclerotic cardiovascular diseases. Since telomere attrition has a central role in driving vascular senescence, understanding telomere biology is essential to modulate the deleterious consequences of vascular aging and its cardiovascular disease-related manifestations. Emerging evidence indicates that a class of long noncoding RNAs transcribed at telomeres, known as TERRA for "TElomeric Repeat-containing RNA", actively participates in the mechanisms regulating telomere maintenance and chromosome end protection. However, the multiple biological functions of TERRA remain to be largely elucidated. In particular, the role of TERRA in vascular biology is surprisingly unknown. In this review, we discuss the current knowledge of TERRA and its roles in telomere biology. Additionally, we outline the pieces of evidence that exist regarding the relationship between TERRA dysregulation and disease. Finally, we speculate on how a comprehensive understanding of TERRA transcription in the cardiovascular system may provide valuable insights into telomere-associated vascular aging, offering great potential for new therapeutic approaches.
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Affiliation(s)
- Paola Canale
- CNR Institute of Clinical Physiology, 56124 Pisa, Italy; (P.C.); (A.B.)
- Health Science Interdisciplinary Center, Sant’Anna School of Advanced Studies, 56124 Pisa, Italy
| | - Jonica Campolo
- CNR Institute of Clinical Physiology, ASST Grande Ospedale Metropolitano Niguarda, 20142 Milano, Italy;
| | - Andrea Borghini
- CNR Institute of Clinical Physiology, 56124 Pisa, Italy; (P.C.); (A.B.)
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3
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Rocca R, Polerà N, Juli G, Grillone K, Maruca A, Di Martino MT, Artese A, Amato J, Pagano B, Randazzo A, Tagliaferri P, Tassone P, Alcaro S. Hit identification of novel small molecules interfering with MALAT1 triplex by a structure-based virtual screening. Arch Pharm (Weinheim) 2023; 356:e2300134. [PMID: 37309243 DOI: 10.1002/ardp.202300134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/02/2023] [Accepted: 05/03/2023] [Indexed: 06/14/2023]
Abstract
Nowadays, RNA is an attractive target for the design of new small molecules with different pharmacological activities. Among several RNA molecules, long noncoding RNAs (lncRNAs) are extensively reported to be involved in cancer pathogenesis. In particular, the overexpression of lncRNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) plays an important role in the development of multiple myeloma (MM). Starting from the crystallographic structure of the triple-helical stability element at the 3'-end of MALAT1, we performed a structure-based virtual screening of a large commercial database, previously filtered according to the drug-like properties. After a thermodynamic analysis, we selected five compounds for the in vitro assays. Compound M5, characterized by a diazaindene scaffold, emerged as the most promising molecule enabling the destabilization of the MALAT1 triplex structure and antiproliferative activity on in vitro models of MM. M5 is proposed as a lead compound to be further optimized for improving its affinity toward MALAT1.
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Affiliation(s)
- Roberta Rocca
- Department of Experimental and Clinical Medicine, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Catanzaro, Italy
- Net4science srl, Università degli Studi "Magna Graecia" di Catanzaro, Catanzaro, Italy
| | - Nicoletta Polerà
- Department of Experimental and Clinical Medicine, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Catanzaro, Italy
| | - Giada Juli
- Department of Experimental and Clinical Medicine, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Catanzaro, Italy
| | - Katia Grillone
- Department of Experimental and Clinical Medicine, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Catanzaro, Italy
| | - Annalisa Maruca
- Net4science srl, Università degli Studi "Magna Graecia" di Catanzaro, Catanzaro, Italy
| | - Maria Teresa Di Martino
- Department of Experimental and Clinical Medicine, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Catanzaro, Italy
| | - Anna Artese
- Net4science srl, Università degli Studi "Magna Graecia" di Catanzaro, Catanzaro, Italy
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Catanzaro, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Pietrosandro Tagliaferri
- Department of Experimental and Clinical Medicine, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Catanzaro, Italy
| | - Pierfrancesco Tassone
- Department of Experimental and Clinical Medicine, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Catanzaro, Italy
| | - Stefano Alcaro
- Net4science srl, Università degli Studi "Magna Graecia" di Catanzaro, Catanzaro, Italy
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Catanzaro, Italy
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4
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Selective Ligands for Non-Canonical DNA Structures: Do They Have a Future in Medicinal Chemistry? Int J Mol Sci 2022; 23:ijms231911984. [PMID: 36233283 PMCID: PMC9570084 DOI: 10.3390/ijms231911984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 10/02/2022] [Indexed: 11/30/2022] Open
Abstract
Winning the war against cancer represents a major goal currently [...].
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Cyclic Triimidazoles as Stabilizers for Gene Promoter and Human Telomeric DNA G‐Quadruplexes. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Zou T, Sato Y, Kaneyoshi S, Mano K, Yasukawa R, Nakano Y, Fujii S, Sato S, Takenaka S. Naphthalene Diimides Carrying Two β-Cyclodextrins Prefer Telomere RNA G-Quadruplex Recognition. Molecules 2022; 27:molecules27134053. [PMID: 35807292 PMCID: PMC9268153 DOI: 10.3390/molecules27134053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 11/16/2022] Open
Abstract
Newly synthesized naphthalene diimide carrying two β-cyclodextrins (NDI-β-CyDs) showed improved specificity for the parallel G-quadruplex structure alongside the hybrid G-quadruplex structure. Specifically, the highest binding affinity of NDI-β-CyDs for the telomere RNA G-quadruplex was observed. The binding simulation indicated that β-cyclodextrins might be available for loop nucleobase inclusion under its complex.
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Affiliation(s)
- Tingting Zou
- Department of Applied Chemistry, Kyushu Institute of Technology, Fukuoka 804-8550, Japan; (T.Z.); (Y.S.); (S.K.); (K.M.); (R.Y.); (Y.N.)
| | - Yuka Sato
- Department of Applied Chemistry, Kyushu Institute of Technology, Fukuoka 804-8550, Japan; (T.Z.); (Y.S.); (S.K.); (K.M.); (R.Y.); (Y.N.)
| | - Shuma Kaneyoshi
- Department of Applied Chemistry, Kyushu Institute of Technology, Fukuoka 804-8550, Japan; (T.Z.); (Y.S.); (S.K.); (K.M.); (R.Y.); (Y.N.)
| | - Kota Mano
- Department of Applied Chemistry, Kyushu Institute of Technology, Fukuoka 804-8550, Japan; (T.Z.); (Y.S.); (S.K.); (K.M.); (R.Y.); (Y.N.)
| | - Rui Yasukawa
- Department of Applied Chemistry, Kyushu Institute of Technology, Fukuoka 804-8550, Japan; (T.Z.); (Y.S.); (S.K.); (K.M.); (R.Y.); (Y.N.)
| | - Yoshifumi Nakano
- Department of Applied Chemistry, Kyushu Institute of Technology, Fukuoka 804-8550, Japan; (T.Z.); (Y.S.); (S.K.); (K.M.); (R.Y.); (Y.N.)
| | - Satoshi Fujii
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Fukuoka 820-8502, Japan;
| | - Shinobu Sato
- Department of Applied Chemistry, Kyushu Institute of Technology, Fukuoka 804-8550, Japan; (T.Z.); (Y.S.); (S.K.); (K.M.); (R.Y.); (Y.N.)
- Correspondence: (S.S.); (S.T.)
| | - Shigeori Takenaka
- Department of Applied Chemistry, Kyushu Institute of Technology, Fukuoka 804-8550, Japan; (T.Z.); (Y.S.); (S.K.); (K.M.); (R.Y.); (Y.N.)
- Correspondence: (S.S.); (S.T.)
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7
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Rocca R, Scionti F, Nadai M, Moraca F, Maruca A, Costa G, Catalano R, Juli G, Di Martino MT, Ortuso F, Alcaro S, Tagliaferri P, Tassone P, Richter SN, Artese A. Chromene Derivatives as Selective TERRA G-Quadruplex RNA Binders with Antiproliferative Properties. Pharmaceuticals (Basel) 2022; 15:ph15050548. [PMID: 35631373 PMCID: PMC9147070 DOI: 10.3390/ph15050548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 11/30/2022] Open
Abstract
In mammalian cells, telomerase transcribes telomeres in large G-rich non-coding RNA, known as telomeric repeat-containing RNA (TERRA), which folds into noncanonical nucleic acid secondary structures called G-quadruplexes (G4s). Since TERRA G4 has been shown to be involved in telomere length and translation regulation, it could provide valuable insight into fundamental biological processes, such as cancer growth, and TERRA G4 binders could represent an innovative strategy for cancer treatment. In this work, the three best candidates identified in our previous virtual screening campaign on bimolecular DNA/RNA G4s were investigated on the monomolecular Tel DNA and TERRA G4s by means of molecular modelling simulations and in vitro and in cell analysis. The results obtained in this work highlighted the stabilizing power of all the three candidates on TERRA G4. In particular, the two compounds characterized by a chromene scaffold were selective TERRA G4 binders, while the compound with a naphthyridine core acted as a dual Tel/TERRA G4-binder. A biophysical investigation by circular dichroism confirmed the relative stabilization efficiency of the compounds towards TERRA and Tel G4s. The TERRA G4 stabilizing hits showed good antiproliferative activity against colorectal and lung adenocarcinoma cell lines. Lead optimization to increase TERRA G4 stabilization may provide new powerful tools against cancer.
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Affiliation(s)
- Roberta Rocca
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Campus “Salvatore Venuta”, Viale Europa, 88100 Catanzaro, Italy; (R.R.); (G.J.); (M.T.D.M.); (P.T.); (P.T.)
- Net4science Srl, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (F.M.); (A.M.); (G.C.); (R.C.); (F.O.); (S.A.)
| | - Francesca Scionti
- Institute for Biomedical Research and Innovation (IRIB), National Research Council of Italy (CNR), 98164 Messina, Italy;
| | - Matteo Nadai
- Department of Molecular Medicine, University of Padua, Via A. Gabelli 63, 35121 Padua, Italy;
| | - Federica Moraca
- Net4science Srl, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (F.M.); (A.M.); (G.C.); (R.C.); (F.O.); (S.A.)
- Department of Pharmacy, University of Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Annalisa Maruca
- Net4science Srl, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (F.M.); (A.M.); (G.C.); (R.C.); (F.O.); (S.A.)
- Department of Health Sciences, Magna Graecia University of Catanzaro, Campus “Salvatore Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Giosuè Costa
- Net4science Srl, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (F.M.); (A.M.); (G.C.); (R.C.); (F.O.); (S.A.)
- Department of Health Sciences, Magna Graecia University of Catanzaro, Campus “Salvatore Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Raffaella Catalano
- Net4science Srl, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (F.M.); (A.M.); (G.C.); (R.C.); (F.O.); (S.A.)
- Department of Health Sciences, Magna Graecia University of Catanzaro, Campus “Salvatore Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Giada Juli
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Campus “Salvatore Venuta”, Viale Europa, 88100 Catanzaro, Italy; (R.R.); (G.J.); (M.T.D.M.); (P.T.); (P.T.)
| | - Maria Teresa Di Martino
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Campus “Salvatore Venuta”, Viale Europa, 88100 Catanzaro, Italy; (R.R.); (G.J.); (M.T.D.M.); (P.T.); (P.T.)
| | - Francesco Ortuso
- Net4science Srl, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (F.M.); (A.M.); (G.C.); (R.C.); (F.O.); (S.A.)
- Department of Health Sciences, Magna Graecia University of Catanzaro, Campus “Salvatore Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Net4science Srl, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (F.M.); (A.M.); (G.C.); (R.C.); (F.O.); (S.A.)
- Department of Health Sciences, Magna Graecia University of Catanzaro, Campus “Salvatore Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Pierosandro Tagliaferri
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Campus “Salvatore Venuta”, Viale Europa, 88100 Catanzaro, Italy; (R.R.); (G.J.); (M.T.D.M.); (P.T.); (P.T.)
| | - Pierfrancesco Tassone
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Campus “Salvatore Venuta”, Viale Europa, 88100 Catanzaro, Italy; (R.R.); (G.J.); (M.T.D.M.); (P.T.); (P.T.)
| | - Sara N. Richter
- Department of Molecular Medicine, University of Padua, Via A. Gabelli 63, 35121 Padua, Italy;
- Correspondence: (S.N.R.); (A.A.)
| | - Anna Artese
- Net4science Srl, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; (F.M.); (A.M.); (G.C.); (R.C.); (F.O.); (S.A.)
- Department of Health Sciences, Magna Graecia University of Catanzaro, Campus “Salvatore Venuta”, Viale Europa, 88100 Catanzaro, Italy
- Correspondence: (S.N.R.); (A.A.)
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8
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Vertecchi E, Rizzo A, Salvati E. Telomere Targeting Approaches in Cancer: Beyond Length Maintenance. Int J Mol Sci 2022; 23:ijms23073784. [PMID: 35409143 PMCID: PMC8998427 DOI: 10.3390/ijms23073784] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/25/2022] [Accepted: 03/26/2022] [Indexed: 12/19/2022] Open
Abstract
Telomeres are crucial structures that preserve genome stability. Their progressive erosion over numerous DNA duplications determines the senescence of cells and organisms. As telomere length homeostasis is critical for cancer development, nowadays, telomere maintenance mechanisms are established targets in cancer treatment. Besides telomere elongation, telomere dysfunction impinges on intracellular signaling pathways, in particular DNA damage signaling and repair, affecting cancer cell survival and proliferation. This review summarizes and discusses recent findings in anticancer drug development targeting different “telosome” components.
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Affiliation(s)
- Eleonora Vertecchi
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy, c/o Department of Biology and Biotechnology, Sapienza University of Rome, Via degli Apuli 4, 00185 Rome, Italy;
| | - Angela Rizzo
- Oncogenomic and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy;
| | - Erica Salvati
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy, c/o Department of Biology and Biotechnology, Sapienza University of Rome, Via degli Apuli 4, 00185 Rome, Italy;
- Correspondence:
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