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Refael T, Sudman M, Golan G, Pnueli L, Naik S, Preger-Ben Noon E, Henn A, Kaplan A, Melamed P. An i-motif-regulated enhancer, eRNA and adjacent lncRNA affect Lhb expression through distinct mechanisms in a sex-specific context. Cell Mol Life Sci 2024; 81:361. [PMID: 39158745 PMCID: PMC11335282 DOI: 10.1007/s00018-024-05398-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/21/2024] [Accepted: 08/05/2024] [Indexed: 08/20/2024]
Abstract
Genome-wide studies have demonstrated regulatory roles for diverse non-coding elements, but their precise and interrelated functions have often remained enigmatic. Addressing the need for mechanistic insight, we studied their roles in expression of Lhb which encodes the pituitary gonadotropic hormone that controls reproduction. We identified a bi-directional enhancer in gonadotrope-specific open chromatin, whose functional eRNA (eRNA2) supports permissive chromatin at the Lhb locus. The central untranscribed region of the enhancer contains an iMotif (iM), and is bound by Hmgb2 which stabilizes the iM and directs transcription specifically towards the functional eRNA2. A distinct downstream lncRNA, associated with an inducible G-quadruplex (G4) and iM, also facilitates Lhb expression, following its splicing in situ. GnRH activates Lhb transcription and increased levels of all three RNAs, eRNA2 showing the highest response, while estradiol, which inhibits Lhb, repressed levels of eRNA2 and the lncRNA. The levels of these regulatory RNAs and Lhb mRNA correlate highly in female mice, though strikingly not in males, suggesting a female-specific function. Our findings, which shed new light on the workings of non-coding elements and non-canonical DNA structures, reveal novel mechanisms regulating transcription which have implications not only in the central control of reproduction but also for other inducible genes.
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Affiliation(s)
- Tal Refael
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Maya Sudman
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Gil Golan
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Lilach Pnueli
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Sujay Naik
- Department of Genetics and Developmental Biology, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, 3109601, Israel
| | - Ella Preger-Ben Noon
- Department of Genetics and Developmental Biology, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, 3109601, Israel
| | - Arnon Henn
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Ariel Kaplan
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Philippa Melamed
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel.
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2
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Alam P, Clovis NS, Chand AK, Khan MF, Sen S. Effect of molecular crowders on ligand binding kinetics with G-quadruplex DNA probed by fluorescence correlation spectroscopy. Methods Appl Fluoresc 2024; 12:045002. [PMID: 39013401 DOI: 10.1088/2050-6120/ad63f5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 07/16/2024] [Indexed: 07/18/2024]
Abstract
Guanine-rich single-stranded DNA folds into G-quadruplex DNA (GqDNA) structures, which play crucial roles in various biological processes. These structures are also promising targets for ligands, potentially inducing antitumor effects. While thermodynamic parameters of ligand/DNA interactions are well-studied, the kinetics of ligand interaction with GqDNA, particularly in cell-like crowded environments, remain less explored. In this study, we investigate the impact of molecular crowding agents (glucose, sucrose, and ficoll 70) at physiologically relevant concentrations (20% w/v) on the association and dissociation rates of the benzophenoxazine-core based ligand, cresyl violet (CV), with human telomeric antiparallel-GqDNA. We utilized fluorescence correlation spectroscopy (FCS) along with other techniques. Our findings reveal that crowding agents decrease the binding affinity of CV to GqDNA, with the most significant effect-a nearly three-fold decrease-observed with ficoll 70. FCS measurements indicate that this decrease is primarily due to a viscosity-induced slowdown of ligand association in the crowded environment. Interestingly, dissociation rates remain largely unaffected by smaller crowders, with only small effect observed in presence of ficoll 70 due to direct but weak interaction between the ligand and ficoll. These results along with previously reported data provide valuable insights into ligand/GqDNA interactions in cellular contexts, suggesting a conserved mechanism of saccharide crowder influence, regardless of variations in GqDNA structure and ligand binding mode. This underscores the importance of considering crowding effects in the design and development of GqDNA-targeted drugs for potential cancer treatment.
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Affiliation(s)
- Parvez Alam
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ndege Simisi Clovis
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ajay Kumar Chand
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Mohammad Firoz Khan
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sobhan Sen
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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3
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Sharma P, Sweta Jha N. Enhanced antioxidant and cytotoxic activity of ferrocenyl-substituted curcumin via stabilization of promoter c-MYC silencer element. J Biomol Struct Dyn 2023; 41:9539-9550. [PMID: 36345790 DOI: 10.1080/07391102.2022.2143424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/29/2022] [Indexed: 11/11/2022]
Abstract
We are reporting a successful attachment of ferrocenyl moiety at the active methylene carbon atom of β-diketone of curcumin via Knoevenagel condensation reaction, to utilize the optimum selectivity toward biological targets. The formation of ferrocenyl curcumin (i.e., Fc-cur) has been confirmed by 1H NMR, 13C NMR, and FT-IR spectra analysis. Further, circular dichroism (CD) spectroscopy, thermal denaturation, absorption, and fluorescence spectroscopy have been used to understand the association of ligand (i.e., Fc-cur) with G-quadruplex. Based on these analysis, the binding mechanism of the ligand i.e., Fc-cur to the parallel and hybrid topology present in different G-quadruplex has been proposed. Further, the binding and modes of the interaction of Fc-cur with Pu27 c-MYC silencer element and H-telo G-quadruplex have unravelled selective and stronger binding via intercalation with the parallel topology of c-MYC G-quadruplex rather than the hybrid topology of H-telo quadruplex. The manifestation of better antioxidant activity of Fc-cur has been demonstrated by showing a stronger radical scavenging capability than pristine curcumin. The cytotoxicity analysis of the proposed ligand i.e., Fc-cur against Vero and HeLa cells have clearly reflected the nontoxicity toward Vero cells and quite effective against the HeLa cells which reduces the cancer cells more effectively than the already reported for curcumin.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Padma Sharma
- Department of Chemistry, National Institute of Technology, Patna, India
| | - Niki Sweta Jha
- Department of Chemistry, National Institute of Technology, Patna, India
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4
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Platella C, Criscuolo A, Riccardi C, Gaglione R, Arciello A, Musumeci D, DellaGreca M, Montesarchio D. Exploring the Binding of Natural Compounds to Cancer-Related G-Quadruplex Structures: From 9,10-Dihydrophenanthrenes to Their Dimeric and Glucoside Derivatives. Int J Mol Sci 2023; 24:ijms24097765. [PMID: 37175474 PMCID: PMC10178421 DOI: 10.3390/ijms24097765] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/19/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
In-depth studies on the interaction of natural compounds with cancer-related G-quadruplex structures have been undertaken only recently, despite their high potential as anticancer agents, especially due to their well-known and various bioactivities. In this frame, aiming at expanding the repertoire of natural compounds able to selectively recognize G-quadruplexes, and particularly focusing on phenanthrenoids, a mini-library including dimeric (1-3) and glucoside (4-5) analogues of 9,10-dihydrophenanthrenes, a related tetrahydropyrene glucoside (6) along with 9,10-dihydrophenanthrene 7 were investigated here by several biophysical techniques and molecular docking. Compounds 3 and 6 emerged as the most selective G-quadruplex ligands within the investigated series. These compounds proved to mainly target the grooves/flanking residues of the hybrid telomeric and parallel oncogenic G-quadruplex models exploiting hydrophobic, hydrogen bond and π-π interactions, without perturbing the main folds of the G-quadruplex structures. Notably, a binding preference was found for both ligands towards the hybrid telomeric G-quadruplex. Moreover, compounds 3 and 6 proved to be active on different human cancer cells in the low micromolar range. Overall, these compounds emerged as useful ligands able to target G-quadruplex structures, which are of interest as promising starting scaffolds for the design of analogues endowed with high and selective anticancer activity.
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Affiliation(s)
- Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126 Naples, Italy
| | - Andrea Criscuolo
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126 Naples, Italy
| | - Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126 Naples, Italy
| | - Rosa Gaglione
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126 Naples, Italy
| | - Angela Arciello
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126 Naples, Italy
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126 Naples, Italy
- Institute of Biostructures and Bioimages, CNR, 80134 Naples, Italy
| | - Marina DellaGreca
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126 Naples, Italy
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126 Naples, Italy
- CINMPIS-Consorzio Interuniversitario Nazionale di Ricerca in Metodologie e Processi Innovativi di Sintesi, Via E. Orabona 4, 70125 Bari, Italy
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5
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Selective Targeting of Cancer-Related G-Quadruplex Structures by the Natural Compound Dicentrine. Int J Mol Sci 2023; 24:ijms24044070. [PMID: 36835480 PMCID: PMC9959918 DOI: 10.3390/ijms24044070] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
Aiming to identify highly effective and selective G-quadruplex ligands as anticancer candidates, five natural compounds were investigated here, i.e., the alkaloids Canadine, D-Glaucine and Dicentrine, as well as the flavonoids Deguelin and Millettone, selected as analogs of compounds previously identified as promising G-quadruplex-targeting ligands. A preliminary screening with the G-quadruplex on the Controlled Pore Glass assay proved that, among the investigated compounds, Dicentrine is the most effective ligand of telomeric and oncogenic G-quadruplexes, also showing good G-quadruplex vs. duplex selectivity. In-depth studies in solution demonstrated the ability of Dicentrine to thermally stabilize telomeric and oncogenic G-quadruplexes without affecting the control duplex. Interestingly, it showed higher affinity for the investigated G-quadruplex structures over the control duplex (Kb~106 vs. 105 M-1), with some preference for the telomeric over the oncogenic G-quadruplex model. Molecular dynamics simulations indicated that Dicentrine preferentially binds the G-quadruplex groove or the outer G-tetrad for the telomeric and oncogenic G-quadruplexes, respectively. Finally, biological assays proved that Dicentrine is highly effective in promoting potent and selective anticancer activity by inducing cell cycle arrest through apoptosis, preferentially targeting G-quadruplex structures localized at telomeres. Taken together, these data validate Dicentrine as a putative anticancer candidate drug selectively targeting cancer-related G-quadruplex structures.
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6
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Selective light-up of dimeric G-quadruplex forming aptamers for efficient VEGF165 detection. Int J Biol Macromol 2022; 224:344-357. [DOI: 10.1016/j.ijbiomac.2022.10.128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/08/2022] [Accepted: 10/13/2022] [Indexed: 11/05/2022]
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7
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Meier-Stephenson V. G4-quadruplex-binding proteins: review and insights into selectivity. Biophys Rev 2022; 14:635-654. [PMID: 35791380 PMCID: PMC9250568 DOI: 10.1007/s12551-022-00952-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 04/04/2022] [Indexed: 02/06/2023] Open
Abstract
There are over 700,000 putative G4-quadruplexes (G4Qs) in the human genome, found largely in promoter regions, telomeres, and other regions of high regulation. Growing evidence links their presence to functionality in various cellular processes, where cellular proteins interact with them, either stabilizing and/or anchoring upon them, or unwinding them to allow a process to proceed. Interest in understanding and manipulating the plethora of processes regulated by these G4Qs has spawned a new area of small-molecule binder development, with attempts to mimic and block the associated G4-binding protein (G4BP). Despite the growing interest and focus on these G4Qs, there is limited data (in particular, high-resolution structural information), on the nature of these G4Q-G4BP interactions and what makes a G4BP selective to certain G4Qs, if in fact they are at all. This review summarizes the current literature on G4BPs with regards to their interactions with G4Qs, providing groupings for binding mode, drawing conclusions around commonalities and highlighting information on specific interactions where available.
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Affiliation(s)
- Vanessa Meier-Stephenson
- Department of Medicine, Division of Infectious Diseases, University of Alberta, Edmonton, AB Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB Canada
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8
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Platella C, Capasso D, Riccardi C, Musumeci D, DellaGreca M, Montesarchio D. Natural compounds from Juncus plants interacting with telomeric and oncogene G-quadruplex structures as potential anticancer agents. Org Biomol Chem 2021; 19:9953-9965. [PMID: 34747958 DOI: 10.1039/d1ob01995c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Aiming at discovering novel, putative anticancer drugs featuring low-to-null side effects, natural compounds isolated from Juncaceae were studied here for their ability to target G-quadruplex structures originating from cancer-related telomeric and oncogene DNA sequences. Particularly, various dihydrophenanthrene, benzocoumarin and dihydrodibenzoxepin derivatives were firstly screened by the affinity chromatography-based G4-CPG assay, and the compound with the highest affinity and selectivity for G-quadruplexes (named J10) was selected for further studies. Fluorescence spectroscopy and circular dichroism experiments corroborated its capability to selectively recognize and stabilize G-quadruplexes over duplex DNA, also showing a preference for parallel G-quadruplexes. Molecular docking proved that the selective G-quadruplex interactions over duplex interactions could be due to the ability of J10 to bind to the grooves of the telomeric and oncogene G-quadruplex structures. Finally, biological assays demonstrated that J10 induces significant antiproliferative effects on human leukemia cells, with no relevant effects on healthy human fibroblasts. Interestingly, J10 exerts its antiproliferative action on tumor cells by activating the apoptotic pathway.
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Affiliation(s)
- Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, via Cintia, 21, 80126 Naples, Italy.
| | - Domenica Capasso
- CIRPEB, University of Naples Federico II, Naples, Italy.,CESTEV, University of Naples Federico II, Naples, Italy
| | - Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, via Cintia, 21, 80126 Naples, Italy.
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, via Cintia, 21, 80126 Naples, Italy. .,Institute of Biostructures and Bioimaging (IBB) - CNR, Naples, Italy
| | - Marina DellaGreca
- Department of Chemical Sciences, University of Naples Federico II, via Cintia, 21, 80126 Naples, Italy.
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia, 21, 80126 Naples, Italy.
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9
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Di Porzio A, Galli U, Amato J, Zizza P, Iachettini S, Iaccarino N, Marzano S, Santoro F, Brancaccio D, Carotenuto A, De Tito S, Biroccio A, Pagano B, Tron GC, Randazzo A. Synthesis and Characterization of Bis-Triazolyl-Pyridine Derivatives as Noncanonical DNA-Interacting Compounds. Int J Mol Sci 2021; 22:11959. [PMID: 34769387 PMCID: PMC8584640 DOI: 10.3390/ijms222111959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/31/2021] [Accepted: 11/01/2021] [Indexed: 02/07/2023] Open
Abstract
Besides the well-known double-helical conformation, DNA is capable of folding into various noncanonical arrangements, such as G-quadruplexes (G4s) and i-motifs (iMs), whose occurrence in gene promoters, replication origins, and telomeres highlights the breadth of biological processes that they might regulate. Particularly, previous studies have reported that G4 and iM structures may play different roles in controlling gene transcription. Anyway, molecular tools able to simultaneously stabilize/destabilize those structures are still needed to shed light on what happens at the biological level. Herein, a multicomponent reaction and a click chemistry functionalization were combined to generate a set of 31 bis-triazolyl-pyridine derivatives which were initially screened by circular dichroism for their ability to interact with different G4 and/or iM DNAs and to affect the thermal stability of these structures. All the compounds were then clustered through multivariate data analysis, based on such capability. The most promising compounds were subjected to a further biophysical and biological characterization, leading to the identification of two molecules simultaneously able to stabilize G4s and destabilize iMs, both in vitro and in living cells.
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Affiliation(s)
- Anna Di Porzio
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (A.D.P.); (J.A.); (N.I.); (S.M.); (F.S.); (D.B.); (A.C.); (B.P.)
| | - Ubaldina Galli
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2/3, 28100 Novara, Italy;
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (A.D.P.); (J.A.); (N.I.); (S.M.); (F.S.); (D.B.); (A.C.); (B.P.)
| | - Pasquale Zizza
- Oncogenomic and Epigenetic Unit, IRCCS-Regina Elena National Cancer Institute, 00144 Rome, Italy; (P.Z.); (S.I.); (A.B.)
| | - Sara Iachettini
- Oncogenomic and Epigenetic Unit, IRCCS-Regina Elena National Cancer Institute, 00144 Rome, Italy; (P.Z.); (S.I.); (A.B.)
| | - Nunzia Iaccarino
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (A.D.P.); (J.A.); (N.I.); (S.M.); (F.S.); (D.B.); (A.C.); (B.P.)
| | - Simona Marzano
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (A.D.P.); (J.A.); (N.I.); (S.M.); (F.S.); (D.B.); (A.C.); (B.P.)
| | - Federica Santoro
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (A.D.P.); (J.A.); (N.I.); (S.M.); (F.S.); (D.B.); (A.C.); (B.P.)
| | - Diego Brancaccio
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (A.D.P.); (J.A.); (N.I.); (S.M.); (F.S.); (D.B.); (A.C.); (B.P.)
| | - Alfonso Carotenuto
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (A.D.P.); (J.A.); (N.I.); (S.M.); (F.S.); (D.B.); (A.C.); (B.P.)
| | - Stefano De Tito
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK;
- Institute of Experimental Endocrinology and Oncology, National Research Council, 80131 Naples, Italy
| | - Annamaria Biroccio
- Oncogenomic and Epigenetic Unit, IRCCS-Regina Elena National Cancer Institute, 00144 Rome, Italy; (P.Z.); (S.I.); (A.B.)
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (A.D.P.); (J.A.); (N.I.); (S.M.); (F.S.); (D.B.); (A.C.); (B.P.)
| | - Gian Cesare Tron
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2/3, 28100 Novara, Italy;
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (A.D.P.); (J.A.); (N.I.); (S.M.); (F.S.); (D.B.); (A.C.); (B.P.)
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Identification of Effective Anticancer G-Quadruplex-Targeting Chemotypes through the Exploration of a High Diversity Library of Natural Compounds. Pharmaceutics 2021; 13:pharmaceutics13101611. [PMID: 34683905 PMCID: PMC8537501 DOI: 10.3390/pharmaceutics13101611] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/21/2021] [Accepted: 09/26/2021] [Indexed: 12/14/2022] Open
Abstract
In the quest for selective G-quadruplex (G4)-targeting chemotypes, natural compounds have been thus far poorly explored, though representing appealing candidates due to the high structural diversity of their scaffolds. In this regard, a unique high diversity in-house library composed of ca. one thousand individual natural products was investigated. The combination of molecular docking-based virtual screening and the G4-CPG experimental screening assay proved to be useful to quickly and effectively identify-out of many natural compounds-five hit binders of telomeric and oncogenic G4s, i.e., Bulbocapnine, Chelidonine, Ibogaine, Rotenone and Vomicine. Biophysical studies unambiguously demonstrated the selective interaction of these compounds with G4s compared to duplex DNA. The rationale behind the G4 selective recognition was suggested by molecular dynamics simulations. Indeed, the selected ligands proved to specifically interact with G4 structures due to peculiar interaction patterns, while they were unable to firmly bind to a DNA duplex. From biological assays, Chelidonine and Rotenone emerged as the most active compounds of the series against cancer cells, also showing good selectivity over normal cells. Notably, the anticancer activity correlated well with the ability of the two compounds to target telomeric G4s.
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11
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Targeting of Telomeric Repeat-Containing RNA G-Quadruplexes: From Screening to Biophysical and Biological Characterization of a New Hit Compound. Int J Mol Sci 2021; 22:ijms221910315. [PMID: 34638655 PMCID: PMC8508872 DOI: 10.3390/ijms221910315] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/10/2021] [Accepted: 09/22/2021] [Indexed: 12/19/2022] Open
Abstract
DNA G-quadruplex (G4) structures, either within gene promoter sequences or at telomeres, have been extensively investigated as potential small-molecule therapeutic targets. However, although G4s forming at the telomeric DNA have been extensively investigated as anticancer targets, few studies focus on the telomeric repeat-containing RNA (TERRA), transcribed from telomeres, as potential pharmacological targets. Here, a virtual screening approach to identify a library of drug-like putative TERRA G4 binders, in tandem with circular dichroism melting assay to study their TERRA G4-stabilizing properties, led to the identification of a new hit compound. The affinity of this compound for TERRA RNA and some DNA G4s was analyzed through several biophysical techniques and its biological activity investigated in terms of antiproliferative effect, DNA damage response (DDR) activation, and TERRA RNA expression in high vs. low TERRA-expressing human cancer cells. The selected hit showed good affinity for TERRA G4 and no binding to double-stranded DNA. In addition, biological assays showed that this compound is endowed with a preferential cytotoxic effect on high TERRA-expressing cells, where it induces a DDR at telomeres, probably by displacing TERRA from telomeres. Our studies demonstrate that the identification of TERRA G4-targeting drugs with potential pharmacological effects is achievable, shedding light on new perspectives aimed at discovering new anticancer agents targeting these G4 structures.
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Santos T, Salgado GF, Cabrita EJ, Cruz C. G-Quadruplexes and Their Ligands: Biophysical Methods to Unravel G-Quadruplex/Ligand Interactions. Pharmaceuticals (Basel) 2021; 14:769. [PMID: 34451866 PMCID: PMC8401999 DOI: 10.3390/ph14080769] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/31/2021] [Accepted: 08/03/2021] [Indexed: 12/12/2022] Open
Abstract
Progress in the design of G-quadruplex (G4) binding ligands relies on the availability of approaches that assess the binding mode and nature of the interactions between G4 forming sequences and their putative ligands. The experimental approaches used to characterize G4/ligand interactions can be categorized into structure-based methods (circular dichroism (CD), nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography), affinity and apparent affinity-based methods (surface plasmon resonance (SPR), isothermal titration calorimetry (ITC) and mass spectrometry (MS)), and high-throughput methods (fluorescence resonance energy transfer (FRET)-melting, G4-fluorescent intercalator displacement assay (G4-FID), affinity chromatography and microarrays. Each method has unique advantages and drawbacks, which makes it essential to select the ideal strategies for the biological question being addressed. The structural- and affinity and apparent affinity-based methods are in several cases complex and/or time-consuming and can be combined with fast and cheap high-throughput approaches to improve the design and development of new potential G4 ligands. In recent years, the joint use of these techniques permitted the discovery of a huge number of G4 ligands investigated for diagnostic and therapeutic purposes. Overall, this review article highlights in detail the most commonly used approaches to characterize the G4/ligand interactions, as well as the applications and types of information that can be obtained from the use of each technique.
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Affiliation(s)
- Tiago Santos
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal;
| | - Gilmar F. Salgado
- ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR 5320, IECB, 33607 Pessac, France;
| | - Eurico J. Cabrita
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal;
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | - Carla Cruz
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal;
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13
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Cadoni E, Magalhães PR, Emídio RM, Mendes E, Vítor J, Carvalho J, Cruz C, Victor BL, Paulo A. New (Iso)quinolinyl-pyridine-2,6-dicarboxamide G-Quadruplex Stabilizers. A Structure-Activity Relationship Study. Pharmaceuticals (Basel) 2021; 14:ph14070669. [PMID: 34358095 PMCID: PMC8308870 DOI: 10.3390/ph14070669] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/06/2021] [Accepted: 07/09/2021] [Indexed: 12/15/2022] Open
Abstract
G-quadruplex (G4)-interactive small molecules have a wide range of potential applications, not only as drugs, but also as sensors of quadruplex structures. The purpose of this work is the synthesis of analogues of the bis-methylquinolinium-pyridine-2,6-dicarboxamide G4 ligand 360A, to identify relevant structure-activity relationships to apply to the design of other G4-interactive small molecules bearing bis-quinoline or bis-isoquinoline moieties. Thermal denaturation experiments revealed that non-methylated derivatives with a relative 1,4 position between the amide linker and the nitrogen of the quinoline ring are moderate G4 stabilizers, with a preference for the hybrid h-Telo G4, a 21-nt sequence present in human telomeres. Insertion of a positive charge upon methylation of quinoline/isoquinoline nitrogen increases compounds' ability to selectively stabilize G4s compared to duplex DNA, with a preference for parallel structures. Among these, compounds having a relative 1,3-position between the charged methylquinolinium/isoquinolinium nitrogen and the amide linker are the best G4 stabilizers. More interestingly, these ligands showed different capacities to selectively block DNA polymerization in a PCR-stop assay and to induce G4 conformation switches of hybrid h-Telo G4. Molecular dynamic simulations with the parallel G4 formed by a 21-nt sequence present in k-RAS gene promoter, showed that the relative spatial orientation of the two methylated quinoline/isoquinoline rings determines the ligands mode and strength of binding to G4s.
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Affiliation(s)
- Enrico Cadoni
- Faculty of Pharmacy, Research Institute for Medicines (iMed.ULisboa), Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (E.C.); (E.M.)
| | - Pedro R. Magalhães
- Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal; (P.R.M.); (R.M.E.); (B.L.V.)
| | - Rita M. Emídio
- Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal; (P.R.M.); (R.M.E.); (B.L.V.)
| | - Eduarda Mendes
- Faculty of Pharmacy, Research Institute for Medicines (iMed.ULisboa), Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (E.C.); (E.M.)
- Department of Pharmaceutical Sciences and Medicines, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Jorge Vítor
- Department of Pharmacy, Pharmacology and Health Technologies, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal;
| | - Josué Carvalho
- CICS-UBI-Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal; (J.C.); (C.C.)
| | - Carla Cruz
- CICS-UBI-Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal; (J.C.); (C.C.)
| | - Bruno L. Victor
- Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal; (P.R.M.); (R.M.E.); (B.L.V.)
| | - Alexandra Paulo
- Faculty of Pharmacy, Research Institute for Medicines (iMed.ULisboa), Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal; (E.C.); (E.M.)
- Department of Pharmaceutical Sciences and Medicines, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
- Correspondence:
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14
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D’Aria F, Pagano B, Petraccone L, Giancola C. KRAS Promoter G-Quadruplexes from Sequences of Different Length: A Physicochemical Study. Int J Mol Sci 2021; 22:ijms22010448. [PMID: 33466280 PMCID: PMC7795837 DOI: 10.3390/ijms22010448] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/23/2020] [Accepted: 12/31/2020] [Indexed: 11/16/2022] Open
Abstract
DNA G-quadruplexes (G4s) form in relevant genomic regions and intervene in several biological processes, including the modulation of oncogenes expression, and are potential anticancer drug targets. The human KRAS proto-oncogene promoter region contains guanine-rich sequences able to fold into G4 structures. Here, by using circular dichroism and differential scanning calorimetry as complementary physicochemical methodologies, we compared the thermodynamic stability of the G4s formed by a shorter and a longer version of the KRAS promoter sequence, namely 5′-AGGGCGGTGTGGGAATAGGGAA-3′ (KRAS 22RT) and 5′-AGGGCGGTGTGGGAAGAGGGAAGAGGGGGAGG-3′ (KRAS 32R). Our results show that the unfolding mechanism of KRAS 32R is more complex than that of KRAS 22RT. The different thermodynamic stability is discussed based on the recently determined NMR structures. The binding properties of TMPyP4 and BRACO-19, two well-known G4-targeting anticancer compounds, to the KRAS G4s were also investigated. The present physicochemical study aims to help in choosing the best G4 target for potential anticancer drugs.
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Affiliation(s)
- Federica D’Aria
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (F.D.); (B.P.)
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (F.D.); (B.P.)
| | - Luigi Petraccone
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126 Naples, Italy;
| | - Concetta Giancola
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (F.D.); (B.P.)
- Correspondence:
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15
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Platella C, Trajkovski M, Doria F, Freccero M, Plavec J, Montesarchio D. On the interaction of an anticancer trisubstituted naphthalene diimide with G-quadruplexes of different topologies: a structural insight. Nucleic Acids Res 2020; 48:12380-12393. [PMID: 33170272 PMCID: PMC7708068 DOI: 10.1093/nar/gkaa1001] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/29/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022] Open
Abstract
Naphthalene diimides showed significant anticancer activity in animal models, with therapeutic potential related to their ability to strongly interact with G-quadruplexes. Recently, a trifunctionalized naphthalene diimide, named NDI-5, was identified as the best analogue of a mini-library of novel naphthalene diimides for its high G-quadruplex binding affinity along with marked, selective anticancer activity, emerging as promising candidate drug for in vivo studies. Here we used NMR, dynamic light scattering, circular dichroism and fluorescence analyses to investigate the interactions of NDI-5 with G-quadruplexes featuring either parallel or hybrid topology. Interplay of different binding modes of NDI-5 to G-quadruplexes was observed for both parallel and hybrid topologies, with end-stacking always operative as the predominant binding event. While NDI-5 primarily targets the 5'-end quartet of the hybrid G-quadruplex model (m-tel24), the binding to a parallel G-quadruplex model (M2) occurs seemingly simultaneously at the 5'- and 3'-end quartets. With parallel G-quadruplex M2, NDI-5 formed stable complexes with 1:3 DNA:ligand binding stoichiometry. Conversely, when interacting with hybrid G-quadruplex m-tel24, NDI-5 showed multiple binding poses on a single G-quadruplex unit and/or formed different complexes comprising two or more G-quadruplex units. NDI-5 produced stabilizing effects on both G-quadruplexes, forming complexes with dissociation constants in the nM range.
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Affiliation(s)
- Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy
| | - Marko Trajkovski
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Filippo Doria
- Department of Chemistry, University of Pavia, Viale Taramelli 10, I-27100 Pavia, Italy
| | - Mauro Freccero
- Department of Chemistry, University of Pavia, Viale Taramelli 10, I-27100 Pavia, Italy
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- EN→FIST Centre of Excellence, Trg OF 13, SI-1000 Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy
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16
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Pirota V, Platella C, Musumeci D, Benassi A, Amato J, Pagano B, Colombo G, Freccero M, Doria F, Montesarchio D. On the binding of naphthalene diimides to a human telomeric G-quadruplex multimer model. Int J Biol Macromol 2020; 166:1320-1334. [PMID: 33166559 DOI: 10.1016/j.ijbiomac.2020.11.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 02/07/2023]
Abstract
To selectively target telomeric G-quadruplex (G4) DNA, monomeric and dimeric naphthalene diimides (NDIs) were investigated as binders of multimeric G4 structures able to discriminate duplex DNA. These NDIs were analysed by the affinity chromatography-based screening G4-CPG (G-quadruplex on Controlled Pore Glass), using the sequence d[AGGG(TTAGGG)7] (tel46), folding into two consecutive G4s, as model of the human telomeric G4 multimer. In parallel, a telomeric G4 monomer (tel26) and a duplex structure (ds27) were used as controls. According to G4-CPG screening, NDI-5 proved to be the best ligand in terms of dimeric G4 vs. duplex DNA selectivity and was analysed by circular dichroism (CD), gel electrophoresis, isothermal titration calorimetry (ITC) and fluorescence spectroscopy in its interactions with tel46. NDI-5 strongly binds and stabilizes tel46 G4, favouring a hybrid folding in K+-containing buffer. Under these conditions, the binding process comprises a first event involving three molecules of NDI-5 and a second one in which other six molecules bind to the DNA. In a metal cation-free system, NDI-5 induces tel46 G4 folding, as indicated by CD and PAGE, favouring an antiparallel structuring. Docking simulations showed that NDI-5 can effectively bind to the pocket between two G4 units, representing a promising ligand for multimeric G4s.
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Affiliation(s)
- Valentina Pirota
- Department of Chemistry, University of Pavia, 27100 Pavia, Italy
| | - Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | | | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
| | - Giorgio Colombo
- Department of Chemistry, University of Pavia, 27100 Pavia, Italy
| | - Mauro Freccero
- Department of Chemistry, University of Pavia, 27100 Pavia, Italy
| | - Filippo Doria
- Department of Chemistry, University of Pavia, 27100 Pavia, Italy.
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy.
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17
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Ogloblina AM, Iaccarino N, Capasso D, Di Gaetano S, Garzarella EU, Dolinnaya NG, Yakubovskaya MG, Pagano B, Amato J, Randazzo A. Toward G-Quadruplex-Based Anticancer Agents: Biophysical and Biological Studies of Novel AS1411 Derivatives. Int J Mol Sci 2020; 21:E7781. [PMID: 33096752 PMCID: PMC7590035 DOI: 10.3390/ijms21207781] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 12/16/2022] Open
Abstract
Certain G-quadruplex forming guanine-rich oligonucleotides (GROs), including AS1411, are endowed with cancer-selective antiproliferative activity. They are known to bind to nucleolin protein, resulting in the inhibition of nucleolin-mediated phenomena. However, multiple nucleolin-independent biological effects of GROs have also been reported, allowing them to be considered promising candidates for multi-targeted cancer therapy. Herein, with the aim of optimizing AS1411 structural features to find GROs with improved anticancer properties, we have studied a small library of AS1411 derivatives differing in the sequence length and base composition. The AS1411 derivatives were characterized by using circular dichroism and nuclear magnetic resonance spectroscopies and then investigated for their enzymatic resistance in serum and nuclear extract, as well as for their ability to bind nucleolin, inhibit topoisomerase I, and affect the viability of MCF-7 human breast adenocarcinoma cells. All derivatives showed higher thermal stability and inhibitory effect against topoisomerase I than AS1411. In addition, most of them showed an improved antiproliferative activity on MCF-7 cells compared to AS1411 despite a weaker binding to nucleolin. Our results support the hypothesis that the antiproliferative properties of GROs are due to multi-targeted effects.
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Affiliation(s)
- Anna M. Ogloblina
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health, 115478 Moscow, Russia; (A.M.O.); (M.G.Y.)
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Nunzia Iaccarino
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Domenica Capasso
- Center for Life Sciences and Technologies (CESTEV), University of Naples Federico II, Via A. De Amicis 95, 80145 Naples, Italy;
| | - Sonia Di Gaetano
- Institute of Biostructures and Bioimaging, National Research Council, Via Mezzocannone 16, 80134 Naples, Italy;
| | - Emanuele U. Garzarella
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Nina G. Dolinnaya
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Marianna G. Yakubovskaya
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health, 115478 Moscow, Russia; (A.M.O.); (M.G.Y.)
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
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18
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Amato J, Mashima T, Kamatari YO, Kuwata K, Novellino E, Randazzo A, Giancola C, Katahira M, Pagano B. Improved Anti-Prion Nucleic Acid Aptamers by Incorporation of Chemical Modifications. Nucleic Acid Ther 2020; 30:414-421. [PMID: 32991255 DOI: 10.1089/nat.2020.0899] [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] [Indexed: 12/28/2022] Open
Abstract
Nucleic acid aptamers are innovative and promising candidates to block the hallmark event in the prion diseases, that is the conversion of prion protein (PrP) into an abnormal form; however, they need chemical modifications for effective therapeutic activity. This communication reports on the development and biophysical characterization of a small library of chemically modified G-quadruplex-forming aptamers targeting the cellular PrP and the evaluation of their anti-prion activity. The results show the possibility of enhancing anti-prion aptamer properties through straightforward modifications.
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Affiliation(s)
- Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Tsukasa Mashima
- Institute of Advanced Energy, Kyoto University, Uji, Japan.,Graduate School of Energy Science, Kyoto University, Uji, Japan
| | | | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | - Ettore Novellino
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Concetta Giancola
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Masato Katahira
- Institute of Advanced Energy, Kyoto University, Uji, Japan.,Graduate School of Energy Science, Kyoto University, Uji, Japan
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
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19
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D'Aria F, D'Amore VM, Di Leva FS, Amato J, Caterino M, Russomanno P, Salerno S, Barresi E, De Leo M, Marini AM, Taliani S, Da Settimo F, Salgado GF, Pompili L, Zizza P, Shirasawa S, Novellino E, Biroccio A, Marinelli L, Giancola C. Targeting the KRAS oncogene: Synthesis, physicochemical and biological evaluation of novel G-Quadruplex DNA binders. Eur J Pharm Sci 2020; 149:105337. [PMID: 32311457 DOI: 10.1016/j.ejps.2020.105337] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/30/2020] [Accepted: 04/01/2020] [Indexed: 02/07/2023]
Abstract
The oncogene KRAS is involved in the pathogenesis of many tumors such as pancreatic, lung and colorectal cancers, thereby representing a relevant target for the treatment of these diseases. The KRAS P1 promoter contains a nuclease hypersensitive, guanine-rich sequence able to fold into a G-quadruplex motif (G4). The stabilization of this G4 structure by small molecules is emerging as a feasible approach to downregulate KRAS expression. Here, a set of novel stabilizing molecules was identified through a virtual screening campaign on the NMR structure of the 22-mer KRAS G4. The most promising hits were then submitted to structure-activity relationships studies which allowed improving their binding affinity and selectivity over double helix DNA and different G4 topologies. The best derivative (19) underwent fluorescence titration experiments and further computational studies to disclose its binding mechanism to KRAS G4. Finally, biological assays showed that this compound is capable to reduce the viability of colorectal cancer cells in which mutated KRAS acts as a driver oncogene. Thus, 19 might represent the prototype of a new class of drugs for the treatment of tumors that, expressing mutated forms of KRAS, are refractory to current therapeutic regimens.
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Affiliation(s)
- Federica D'Aria
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Napoli, Italy
| | - Vincenzo Maria D'Amore
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Napoli, Italy
| | | | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Napoli, Italy
| | - Marco Caterino
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Napoli, Italy
| | - Pasquale Russomanno
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Napoli, Italy
| | - Silvia Salerno
- Department of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Elisabetta Barresi
- Department of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Marinella De Leo
- Department of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Anna Maria Marini
- Department of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Sabrina Taliani
- Department of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Federico Da Settimo
- Department of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Gilmar F Salgado
- ARNA Laboratory, IECB, University of Bordeaux, Inserm U1212, CNRS UMR 5320, F-33600 Pessac, France
| | - Luca Pompili
- Oncogenomic and Epigenetic Unit, IRCCS - Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy
| | - Pasquale Zizza
- Oncogenomic and Epigenetic Unit, IRCCS - Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy
| | - Senji Shirasawa
- Central Research Institute for Advanced Molecular Medicine, Fukuoka University, Fukuoka, Japan
| | - Ettore Novellino
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Napoli, Italy
| | - Annamaria Biroccio
- Oncogenomic and Epigenetic Unit, IRCCS - Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy
| | - Luciana Marinelli
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Napoli, Italy
| | - Concetta Giancola
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Napoli, Italy.
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20
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Amato J, Miglietta G, Morigi R, Iaccarino N, Locatelli A, Leoni A, Novellino E, Pagano B, Capranico G, Randazzo A. Monohydrazone Based G-Quadruplex Selective Ligands Induce DNA Damage and Genome Instability in Human Cancer Cells. J Med Chem 2020; 63:3090-3103. [PMID: 32142285 PMCID: PMC7997572 DOI: 10.1021/acs.jmedchem.9b01866] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
Targeting
G-quadruplex structures is currently viewed as a promising
anticancer strategy. Searching for potent and selective G-quadruplex
binders, here we describe a small series of new monohydrazone derivatives
designed as analogues of a lead which was proved to stabilize G-quadruplex
structures and increase R loop levels in human cancer cells. To investigate
the G-quadruplex binding properties of the new molecules, in vitro biophysical studies were performed employing both
telomeric and oncogene promoter G-quadruplex-forming sequences. The
obtained results allowed the identification of a highly selective
G-quadruplex ligand that, when studied in human cancer cells, proved
to be able to stabilize both G-quadruplexes and R loops and showed
a potent cell killing activity associated with the formation of micronuclei,
a clear sign of genome instability.
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Affiliation(s)
- Jussara Amato
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Giulia Miglietta
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, 40126 Bologna, Italy
| | - Rita Morigi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, 40126 Bologna, Italy
| | - Nunzia Iaccarino
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Alessandra Locatelli
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, 40126 Bologna, Italy
| | - Alberto Leoni
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, 40126 Bologna, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, 40126 Bologna, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
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21
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Trifunctionalized Naphthalene Diimides and Dimeric Analogues as G-Quadruplex-Targeting Anticancer Agents Selected by Affinity Chromatography. Int J Mol Sci 2020; 21:ijms21061964. [PMID: 32183038 PMCID: PMC7139804 DOI: 10.3390/ijms21061964] [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: 01/31/2020] [Revised: 03/02/2020] [Accepted: 03/10/2020] [Indexed: 12/14/2022] Open
Abstract
A focused library of newly designed monomeric and dimeric naphthalene diimides (NDIs) was analyzed in its ability to recognize specific G-quadruplex (G4) structures discriminating duplex DNA. The best G4 ligands—according to an affinity chromatography-based screening method named G4-CPG—were tested on human cancer and healthy cells, inducing DNA damage at telomeres, and in parallel, showing selective antiproliferative activity on HeLa cancer cells with IC50 values in the low nanomolar range. CD and fluorescence spectroscopy studies allowed detailed investigation of the interaction in solution with different G4 and duplex DNA models of the most promising NDI of the series, as determined by combining the biophysical and biological assays’ data.
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22
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Caterino M, D'Aria F, Kustov AV, Belykh DV, Khudyaeva IS, Starseva OM, Berezin DB, Pylina YI, Usacheva T, Amato J, Giancola C. Selective binding of a bioactive porphyrin-based photosensitizer to the G-quadruplex from the KRAS oncogene promoter. Int J Biol Macromol 2019; 145:244-251. [PMID: 31870869 DOI: 10.1016/j.ijbiomac.2019.12.152] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/07/2019] [Accepted: 12/17/2019] [Indexed: 01/24/2023]
Abstract
BACKGROUND The G-quadruplex-forming sequence within the KRAS proto-oncogene P1 promoter is a promising target for anticancer therapy. Porphyrin derivatives are among the most rewarding G-quadruplex binders. They can also behave as photosensitizers. METHODS Three water-soluble, positively charged porphyrin-like compounds were synthesized and tested for their interaction with the KRAS G-quadruplex by circular dichroism, fluorescence, and molecular docking calculations. For a comparison of ligands binding affinity and selectivity, TMPyP4 was taken as a reference. RESULTS One out of the three tested compounds proved biological activity and selectivity for G-quadruplex over duplex DNA. It also showed to discriminate between different G-quadruplex topologies, with a preference for the parallel over antiparallel conformation. Molecular docking studies suggested a preferential binding to the 3'-end of the KRAS G-quadruplex driven through π-π stacking interactions. Biological assays also revealed a good photodynamic-induced cytotoxicity on HeLa cells. CONCLUSIONS The reported results show that these porphyrin-like compounds could actually give the basis for the development of G-quadruplex ligands with effective photodynamic-induced cytotoxicity on cancer cells. GENERAL SIGNIFICANCE The possibility of obtaining photosensitizers with improved physico-chemical features and able to selectively target G-quadruplexes is a very interesting perspective to develop new therapeutic agents.
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Affiliation(s)
- Marco Caterino
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Federica D'Aria
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Andrey V Kustov
- Krestov Institute of Solution Chemistry of Russian Academy of Sciences, Ivanovo, Russian Federation; Ivanovo State University of Chemistry and Technology, Institute of Macroheterocyclic Compounds, Ivanovo, Russian Federation
| | - Dmitrii V Belykh
- Institute of Chemistry of Komi Science Center of the Ural Branch of the Russian Academy of Sciences, Syktyvkar, Russian Federation
| | - Irina S Khudyaeva
- Institute of Chemistry of Komi Science Center of the Ural Branch of the Russian Academy of Sciences, Syktyvkar, Russian Federation
| | - Olga M Starseva
- Institute of Chemistry of Komi Science Center of the Ural Branch of the Russian Academy of Sciences, Syktyvkar, Russian Federation
| | - Dmitriy B Berezin
- Ivanovo State University of Chemistry and Technology, Institute of Macroheterocyclic Compounds, Ivanovo, Russian Federation
| | - Yana I Pylina
- Institute of Biology of Komi Scientific Center of the Ural Branch of the Russian Academy of Sciences, Syktyvkar, Russian Federation
| | - Tatiana Usacheva
- Ivanovo State University of Chemistry and Technology, Department of General Chemical Technology, Ivanovo, Russian Federation
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy.
| | - Concetta Giancola
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy.
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23
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Amato J, Cerofolini L, Brancaccio D, Giuntini S, Iaccarino N, Zizza P, Iachettini S, Biroccio A, Novellino E, Rosato A, Fragai M, Luchinat C, Randazzo A, Pagano B. Insights into telomeric G-quadruplex DNA recognition by HMGB1 protein. Nucleic Acids Res 2019; 47:9950-9966. [PMID: 31504744 PMCID: PMC6765150 DOI: 10.1093/nar/gkz727] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 08/02/2019] [Accepted: 08/15/2019] [Indexed: 01/21/2023] Open
Abstract
HMGB1 is a ubiquitous non-histone protein, which biological effects depend on its expression and subcellular location. Inside the nucleus, HMGB1 is engaged in many DNA events such as DNA repair, transcription and telomere maintenance. HMGB1 has been reported to bind preferentially to bent DNA as well as to noncanonical DNA structures like 4-way junctions and, more recently, to G-quadruplexes. These are four-stranded conformations of nucleic acids involved in important cellular processes, including telomere maintenance. In this frame, G-quadruplex recognition by specific proteins represents a key event to modulate physiological or pathological pathways. Herein, to get insights into the telomeric G-quadruplex DNA recognition by HMGB1, we performed detailed biophysical studies complemented with biological analyses. The obtained results provided information about the molecular determinants for the interaction and showed that the structural variability of human telomeric G-quadruplex DNA may have significant implications in HMGB1 recognition. The biological data identified HMGB1 as a telomere-associated protein in both telomerase-positive and -negative tumor cells and showed that HMGB1 gene silencing in such cells induces telomere DNA damage foci. Altogether, these findings provide a deeper understanding of telomeric G-quadruplex recognition by HMGB1 and suggest that this protein could actually represent a new target for cancer therapy.
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Affiliation(s)
- Jussara Amato
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence, via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
| | - Diego Brancaccio
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Stefano Giuntini
- Magnetic Resonance Center (CERM), University of Florence, via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
| | - Nunzia Iaccarino
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Pasquale Zizza
- Oncogenomic and Epigenetic Unit, IRCCS - Regina Elena National Cancer Institute, via Elio Chianesi 53, 00144 Rome, Italy
| | - Sara Iachettini
- Oncogenomic and Epigenetic Unit, IRCCS - Regina Elena National Cancer Institute, via Elio Chianesi 53, 00144 Rome, Italy
| | - Annamaria Biroccio
- Oncogenomic and Epigenetic Unit, IRCCS - Regina Elena National Cancer Institute, via Elio Chianesi 53, 00144 Rome, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Antonio Rosato
- Magnetic Resonance Center (CERM), University of Florence, via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
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24
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Amato J, Madanayake TW, Iaccarino N, Novellino E, Randazzo A, Hurley LH, Pagano B. HMGB1 binds to the KRAS promoter G-quadruplex: a new player in oncogene transcriptional regulation? Chem Commun (Camb) 2018; 54:9442-9445. [PMID: 30079419 PMCID: PMC6234227 DOI: 10.1039/c8cc03614d] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This communication reports on a possible distinct role of HMGB1 protein. Biophysical studies revealed that HMGB1 binds and stabilizes the G-quadruplex of the KRAS promoter element that is responsible for most of the transcriptional activity. Biological data showed that inhibition of HMGB1 increases KRAS expression. These results suggest that HMGB1 could play a role in the gene transcriptional regulation via the functional recognition of the G-quadruplex.
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Affiliation(s)
- Jussara Amato
- Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy.
| | - Thushara W. Madanayake
- College of Pharmacy, University of Arizona, 1703 East Mabel Street, Tucson, Arizona 85721, United States
| | - Nunzia Iaccarino
- Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy.
| | - Ettore Novellino
- Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy.
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy.
| | - Laurence H. Hurley
- College of Pharmacy, University of Arizona, 1703 East Mabel Street, Tucson, Arizona 85721, United States
| | - Bruno Pagano
- Department of Pharmacy, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy.
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25
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The estimation of H-bond and metal ion-ligand interaction energies in the G-Quadruplex ⋯ Mn+ complexes. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.02.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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26
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Amato J, Pagano A, Capasso D, Di Gaetano S, Giustiniano M, Novellino E, Randazzo A, Pagano B. Targeting the BCL2 Gene Promoter G-Quadruplex with a New Class of Furopyridazinone-Based Molecules. ChemMedChem 2018; 13:406-410. [PMID: 29345419 DOI: 10.1002/cmdc.201700749] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/17/2018] [Indexed: 12/11/2022]
Abstract
Targeting of G-quadruplex-forming DNA in the BCL2 gene promoter to inhibit the expression of anti-apoptotic Bcl-2 protein is an attractive approach to cancer treatment. So far, efforts made in the discovery of molecules that are able to target the BCL2 G-quadruplex have succeeded mainly in the identification of ligands with poor drug-like properties. Here, a small series of furo[2,3-d]pyridazin-4(5H)-one derivatives were evaluated as a new class of drug-like G-quadruplex-targeting compounds. Biophysical studies showed that two derivatives could effectively bind to BCL2 G-quadruplex with good selectivity. Moreover, one such ligand was found to appreciably inhibit BCL2 gene transcription, with a substantial decrease in protein expression levels, and also showed significant cytotoxicity toward the Jurkat human T-lymphoblastoid cell line.
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Affiliation(s)
- Jussara Amato
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131, Naples, Italy
| | - Alessia Pagano
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131, Naples, Italy
| | - Domenica Capasso
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131, Naples, Italy
| | - Sonia Di Gaetano
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, 80134, Naples, Italy
| | - Mariateresa Giustiniano
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131, Naples, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131, Naples, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131, Naples, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131, Naples, Italy
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27
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Salvati E, Botta L, Amato J, Di Leva FS, Zizza P, Gioiello A, Pagano B, Graziani G, Tarsounas M, Randazzo A, Novellino E, Biroccio A, Cosconati S. Lead Discovery of Dual G-Quadruplex Stabilizers and Poly(ADP-ribose) Polymerases (PARPs) Inhibitors: A New Avenue in Anticancer Treatment. J Med Chem 2017; 60:3626-3635. [PMID: 28445046 DOI: 10.1021/acs.jmedchem.6b01563] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
G-quadruplex stabilizers are an established opportunity in anticancer chemotherapy. To circumvent the antiproliferative effects of G4 ligands, cancer cells recruit PARP enzymes at telomeres. Herein, starting from the structural similarity of a potent G4 ligand previously discovered by our group and a congeneric PARP inhibitor, a library of derivatives was synthesized to discover the first dual G4/PARP ligand. We demonstrate that a properly decorated thieno[3,2-c]quinolin-4(5H)-one stabilizes the G4 fold in vitro and in cells, induces a DNA damage response localized to telomeres, inhibits PARylation in cells, and has an antiproliferative effect in BRCA2 deficient tumor cells.
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Affiliation(s)
- Erica Salvati
- Oncogenomic and Epigenetic Unit, Regina Elena National Cancer Institute , 00158 Rome, Italy
| | - Lorenzo Botta
- Department of Pharmacy, University of Naples "Federico II" , 80131 Naples, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples "Federico II" , 80131 Naples, Italy
| | | | - Pasquale Zizza
- Oncogenomic and Epigenetic Unit, Regina Elena National Cancer Institute , 00158 Rome, Italy
| | - Antimo Gioiello
- Department of Pharmaceutical Science, University of Perugia , I-06123 Perugia, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples "Federico II" , 80131 Naples, Italy
| | - Grazia Graziani
- Department of Systems Medicine, University of "Tor Vergata" , 00173 Rome, Italy
| | - Madalena Tarsounas
- Genome Stability and Tumourigenesis Group, Department of Oncology, CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford , Old Road Campus Research Building, Oxford OX3 7DQ, U.K
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples "Federico II" , 80131 Naples, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples "Federico II" , 80131 Naples, Italy
| | - Annamaria Biroccio
- Oncogenomic and Epigenetic Unit, Regina Elena National Cancer Institute , 00158 Rome, Italy
| | - Sandro Cosconati
- DiSTABiF, University of Campania Luigi Vanvitelli , 81100 Caserta, Italy
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28
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Dolinnaya NG, Ogloblina AM, Yakubovskaya MG. Structure, Properties, and Biological Relevance of the DNA and RNA G-Quadruplexes: Overview 50 Years after Their Discovery. BIOCHEMISTRY (MOSCOW) 2017; 81:1602-1649. [PMID: 28260487 PMCID: PMC7087716 DOI: 10.1134/s0006297916130034] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
G-quadruplexes (G4s), which are known to have important roles in regulation of key biological processes in both normal and pathological cells, are the most actively studied non-canonical structures of nucleic acids. In this review, we summarize the results of studies published in recent years that change significantly scientific views on various aspects of our understanding of quadruplexes. Modern notions on the polymorphism of DNA quadruplexes, on factors affecting thermodynamics and kinetics of G4 folding–unfolding, on structural organization of multiquadruplex systems, and on conformational features of RNA G4s and hybrid DNA–RNA G4s are discussed. Here we report the data on location of G4 sequence motifs in the genomes of eukaryotes, bacteria, and viruses, characterize G4-specific small-molecule ligands and proteins, as well as the mechanisms of their interactions with quadruplexes. New information on the structure and stability of G4s in telomeric DNA and oncogene promoters is discussed as well as proof being provided on the occurrence of G-quadruplexes in cells. Prominence is given to novel experimental techniques (single molecule manipulations, optical and magnetic tweezers, original chemical approaches, G4 detection in situ, in-cell NMR spectroscopy) that facilitate breakthroughs in the investigation of the structure and functions of G-quadruplexes.
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Affiliation(s)
- N G Dolinnaya
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119991, Russia.
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29
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Ligand binding to telomeric G-quadruplex DNA investigated by funnel-metadynamics simulations. Proc Natl Acad Sci U S A 2017; 114:E2136-E2145. [PMID: 28232513 PMCID: PMC5358390 DOI: 10.1073/pnas.1612627114] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A thorough characterization of the binding interaction between a drug and its molecular target is fundamental to successfully lead drug design. We demonstrate that this characterization is also possible using the recently developed method of funnel-metadynamics (FM), here applied to investigate the binding of berberine to DNA G-quadruplex. We computed a quantitatively well-characterized free-energy landscape that allows identifying two low-energy ligand binding modes and the presence of higher energy prebinding states. We validated the accuracy of our calculations by steady-state fluorescence experiments. The good agreement between the theoretical and experimental binding free-energy value demonstrates that FM is a most reliable method to study ligand/DNA interaction. G-quadruplexes (G4s) are higher-order DNA structures typically present at promoter regions of genes and telomeres. Here, the G4 formation decreases the replicative DNA at each cell cycle, finally leading to apoptosis. The ability to control this mitotic clock, particularly in cancer cells, is fascinating and passes through a rational understanding of the ligand/G4 interaction. We demonstrate that an accurate description of the ligand/G4 binding mechanism is possible using an innovative free-energy method called funnel-metadynamics (FM), which we have recently developed to investigate ligand/protein interaction. Using FM simulations, we have elucidated the binding mechanism of the anticancer alkaloid berberine to the human telomeric G4 (d[AG3(T2AG3)3]), computing also the binding free-energy landscape. Two ligand binding modes have been identified as the lowest energy states. Furthermore, we have found prebinding sites, which are preparatory to reach the final binding mode. In our simulations, the ions and the water molecules have been explicitly represented and the energetic contribution of the solvent during ligand binding evaluated. Our theoretical results provide an accurate estimate of the absolute ligand/DNA binding free energy (ΔGb0 = −10.3 ± 0.5 kcal/mol) that we validated through steady-state fluorescence binding assays. The good agreement between the theoretical and experimental value demonstrates that FM is a most powerful method to investigate ligand/DNA interaction and can be a useful tool for the rational design also of G4 ligands.
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30
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Musumeci D, Amato J, Zizza P, Platella C, Cosconati S, Cingolani C, Biroccio A, Novellino E, Randazzo A, Giancola C, Pagano B, Montesarchio D. Tandem application of ligand-based virtual screening and G4-OAS assay to identify novel G-quadruplex-targeting chemotypes. Biochim Biophys Acta Gen Subj 2017; 1861:1341-1352. [PMID: 28130159 DOI: 10.1016/j.bbagen.2017.01.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Revised: 01/16/2017] [Accepted: 01/23/2017] [Indexed: 11/29/2022]
Abstract
BACKGROUND G-quadruplex (G4) structures are key elements in the regulation of cancer cell proliferation and their targeting is deemed to be a promising strategy in anticancer therapy. METHODS A tandem application of ligand-based virtual screening (VS) calculations together with the experimental G-quadruplex on Oligo Affinity Support (G4-OAS) assay was employed to discover novel G4-targeting compounds. The interaction of the selected compounds with the investigated G4 in solution was analysed through a series of biophysical techniques and their biological activity investigated by immunofluorescence and MTT assays. RESULTS A focused library of 60 small molecules, designed as putative G4 groove binders, was identified through the VS. The G4-OAS experimental screening led to the selection of 7 ligands effectively interacting with the G4-forming human telomeric DNA. Evaluation of the biological activity of the selected compounds showed that 3 ligands of this sub-library induced a marked telomere-localized DNA damage response in human tumour cells. CONCLUSIONS The combined application of virtual and experimental screening tools proved to be a successful strategy to identify new bioactive chemotypes able to target the telomeric G4 DNA. These compounds may represent useful leads for the development of more potent and selective G4 ligands. GENERAL SIGNIFICANCE Expanding the repertoire of the available G4-targeting chemotypes with improved physico-chemical features, in particular aiming at the discovery of novel, selective G4 telomeric ligands, can help in developing effective anti-cancer drugs with fewer side effects. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
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Affiliation(s)
- Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, Naples 80126, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Pasquale Zizza
- Oncogenomic and Epigenetic Unit, Regina Elena National Cancer Institute, Rome 00144, Italy
| | - Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, Naples 80126, Italy
| | | | - Chiara Cingolani
- Oncogenomic and Epigenetic Unit, Regina Elena National Cancer Institute, Rome 00144, Italy
| | - Annamaria Biroccio
- Oncogenomic and Epigenetic Unit, Regina Elena National Cancer Institute, Rome 00144, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Concetta Giancola
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy.
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, Naples 80126, Italy.
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31
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Kang HJ, Cui Y, Yin H, Scheid A, Hendricks WPD, Schmidt J, Sekulic A, Kong D, Trent JM, Gokhale V, Mao H, Hurley LH. A Pharmacological Chaperone Molecule Induces Cancer Cell Death by Restoring Tertiary DNA Structures in Mutant hTERT Promoters. J Am Chem Soc 2016; 138:13673-13692. [PMID: 27643954 DOI: 10.1021/jacs.6b07598] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Activation of human telomerase reverse transcriptase (hTERT) is necessary for limitless replication in tumorigenesis. Whereas hTERT is transcriptionally silenced in normal cells, most tumor cells reactivate hTERT expression by alleviating transcriptional repression through diverse genetic and epigenetic mechanisms. Transcription-activating hTERT promoter mutations have been found to occur at high frequencies in multiple cancer types. These mutations have been shown to form new transcription factor binding sites that drive hTERT expression, but this model cannot fully account for differences in wild-type (WT) and mutant promoter activation and has not yet enabled a selective therapeutic strategy. Here, we demonstrate a novel mechanism by which promoter mutations activate hTERT transcription, which also sheds light on a unique therapeutic opportunity. Promoter mutations occur in a core promoter region that forms tertiary structures consisting of a pair of G-quadruplexes involved in transcriptional silencing. We show that promoter mutations exert a detrimental effect on the folding of one of these G-quadruplexes, resulting in a nonfunctional silencer element that alleviates transcriptional repression. We have also identified a small drug-like pharmacological chaperone (pharmacoperone) molecule, GTC365, that acts at an early step in the G-quadruplex folding pathway to redirect mutant promoter G-quadruplex misfolding, partially reinstate the correct folding pathway, and reduce hTERT activity through transcriptional repression. This transcription-mediated repression produces cancer cell death through multiple routes including both induction of apoptosis through inhibition of hTERT's role in regulating apoptosis-related proteins and induction of senescence by decreasing telomerase activity and telomere length. We demonstrate the selective therapeutic potential of this strategy in melanoma cells that overexpress hTERT.
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Affiliation(s)
- Hyun-Jin Kang
- University of Arizona , College of Pharmacy, 1703 East Mabel Street, Tucson, Arizona 85721, United States
| | - Yunxi Cui
- Department of Chemistry and Biochemistry and School of Biomedical Sciences, Kent State University , Kent, Ohio 44242, United States
| | - Holly Yin
- Translational Genomics Research Institute , 445 North Fifth Street, Phoenix, Arizona 85004, United States
| | - Amy Scheid
- College of Science, University of Arizona , 1040 East Fourth Street, Tucson, Arizona 85721, United States
| | - William P D Hendricks
- Translational Genomics Research Institute , 445 North Fifth Street, Phoenix, Arizona 85004, United States
| | - Jessica Schmidt
- Department of Dermatology, Mayo Clinic , 13400 East Shea Boulevard, Scottsdale, Arizona 85259, United States
| | - Aleksandar Sekulic
- Department of Dermatology, Mayo Clinic , 13400 East Shea Boulevard, Scottsdale, Arizona 85259, United States
| | - Deming Kong
- State Key Laboratory of Medicinal Chemical Biology, College of Chemistry, Nankai University , Tianjin 300071, People's Republic of China
| | - Jeffrey M Trent
- Translational Genomics Research Institute , 445 North Fifth Street, Phoenix, Arizona 85004, United States
| | - Vijay Gokhale
- BIO5 Institute , 1657 East Helen Street, Tucson, Arizona 85721, United States
| | - Hanbin Mao
- Department of Chemistry and Biochemistry and School of Biomedical Sciences, Kent State University , Kent, Ohio 44242, United States
| | - Laurence H Hurley
- University of Arizona , College of Pharmacy, 1703 East Mabel Street, Tucson, Arizona 85721, United States.,BIO5 Institute , 1657 East Helen Street, Tucson, Arizona 85721, United States.,Arizona Cancer Center , 1515 North Campbell Avenue, Tucson, Arizona 85724, United States
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32
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Carvalho J, Ferreira J, Pereira P, Coutinho E, Guédin A, Nottelet P, Salgado GF, Mergny JL, Queiroz J, Sousa F, Cabrita EJ, Cruz C. Stabilization of novel immunoglobulin switch regions G-quadruplexes by naphthalene and quinoline-based ligands. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.01.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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33
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Zhang Q, Liu YC, Kong DM, Guo DS. Tetraphenylethene Derivatives with Different Numbers of Positively Charged Side Arms have Different Multimeric G-Quadruplex Recognition Specificity. Chemistry 2015; 21:13253-60. [DOI: 10.1002/chem.201501847] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Indexed: 01/10/2023]
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34
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Cerofolini L, Amato J, Borsi V, Pagano B, Randazzo A, Fragai M. Probing the interaction of distamycin A with S100β: the "unexpected" ability of S100β to bind to DNA-binding ligands. J Mol Recognit 2015; 28:376-84. [PMID: 25694263 DOI: 10.1002/jmr.2452] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 11/20/2014] [Accepted: 11/24/2014] [Indexed: 11/11/2022]
Abstract
DNA-minor-groove-binding ligands are potent antineoplastic molecules. The antibiotic distamycin A is the prototype of one class of these DNA-interfering molecules that have been largely used in vitro. The affinity of distamycin A for DNA is well known, and the structural details of the complexes with some B-DNA and G-quadruplex-forming DNA sequences have been already elucidated. Here, we show that distamycin A binds S100β, a protein involved in the regulation of several cellular processes. The reported affinity of distamycin A for the calcium(II)-loaded S100β reinforces the idea that some biological activities of the DNA-minor-groove-binding ligands arise from the binding to cellular proteins.
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Affiliation(s)
- Linda Cerofolini
- Giotto Biotech, Via Madonna del Piano 6, Sesto Fiorentino, Florence, 50019, Italy
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35
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Pagano B, Amato J, Iaccarino N, Cingolani C, Zizza P, Biroccio A, Novellino E, Randazzo A. Looking for efficient G-quadruplex ligands: evidence for selective stabilizing properties and telomere damage by drug-like molecules. ChemMedChem 2015; 10:640-9. [PMID: 25694275 DOI: 10.1002/cmdc.201402552] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Indexed: 01/02/2023]
Abstract
There is currently significant interest in the development of G-quadruplex-interactive compounds, given the relationship between the ability to stabilize these non-canonical DNA structures and anticancer activity. In this study, a set of biophysical assays was applied to evaluate the binding of six drug-like ligands to DNA G-quadruplexes with different folding topologies. Interestingly, two of the investigated ligands showed selective G-quadruplex-stabilizing properties and biological activity. These compounds may represent useful leads for the development of more potent and selective ligands.
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Affiliation(s)
- Bruno Pagano
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131, Napoli (Italy)
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36
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Prato G, Silvent S, Saka S, Lamberto M, Kosenkov D. Thermodynamics of binding of di- and tetrasubstituted naphthalene diimide ligands to DNA G-quadruplex. J Phys Chem B 2015; 119:3335-47. [PMID: 25635929 DOI: 10.1021/jp509637y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Naphthalene diimide ligands have the potential to stabilize human telomeric G-quadruplex DNA via noncovalent interactions. Stabilization of G-quadruplex high order structures has become an important strategy to develop novel anticancer therapeutics. In this study four naphthalene diimide based ligands were analyzed in order to elucidate the principal factors determining contributions to G-quadruplex-ligand binding. Three possible modes of binding and their respective Gibbs free energies for two naphthalene diimide based di-N-alkylpyridinium substituted ligands have been determined using a molecular docking technique and compared to experimental results. The structures obtained from the molecular docking calculations, were analyzed using the ab initio based fragment molecular orbital (FMO) method in order to determine the major enthalpic contributions to the binding and types of interactions between the ligand and specific residues of the G-quadruplex. A computational methodology for the efficient and inexpensive ligand optimization as compared to fully ab initio methods based on the estimation of binding affinities of the naphthalene diimide derived ligands to G-quadruplex is proposed.
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Affiliation(s)
- Gary Prato
- Department of Chemistry and Physics, Monmouth University , 400 Cedar Avenue, West Long Branch, New Jersey 07764, United States
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37
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Fotticchia I, Fotticchia T, Mattia CA, Netti PA, Vecchione R, Giancola C. Thermodynamic signature of secondary nano-emulsion formation by isothermal titration calorimetry. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:14427-14433. [PMID: 25396753 DOI: 10.1021/la503558w] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The stabilization of oil in water nano-emulsions by means of a polymer coating is extremely important; it prolongs the shelf life of the product and makes it suitable for a variety of applications ranging from nutraceutics to cosmetics and pharmaceutics. To date, an effective methodology to assess the best formulations in terms of thermodynamic stability has yet to be designed. Here, we perform a complete physicochemical characterization based on isothermal titration calorimetry (ITC) compared to conventional dynamic light scattering (DLS) to identify polymer concentration domains that are thermodynamically stable and to define the degree of stability through thermodynamic functions depending upon any relevant parameter affecting the stability itself, such as type of polymer coating, droplet distance, etc. For instance, the method was proven by measuring the energetics in the case of two different biopolymers, chitosan and poly-L-lysine, and for different concentrations of the emulsion coated with poly-L-lysine.
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Affiliation(s)
- Iolanda Fotticchia
- Dipartimento di Farmacia, Università di Napoli Federico II , via Domenico Montesano 49, 80131 Naples, Italy
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38
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Amato J, Iaccarino N, Pagano B, Morigi R, Locatelli A, Leoni A, Rambaldi M, Zizza P, Biroccio A, Novellino E, Randazzo A. Bis-indole derivatives with antitumor activity turn out to be specific ligands of human telomeric G-quadruplex. Front Chem 2014; 2:54. [PMID: 25105115 PMCID: PMC4109613 DOI: 10.3389/fchem.2014.00054] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 07/04/2014] [Indexed: 01/04/2023] Open
Abstract
Bis-indolinone derivatives having either 2,6-disubstituted pyridine core (1a and 1b) or 1,10-disubstituted phenanthroline core (2a and 2b), already known to have antitumor activity, have been tested as potential G-quadruplex binders. Compounds 2a and 2b are able to selectively stabilize G-quadruplex over duplex DNA, and also to discriminate among different G-quadruplex structures, having a particular affinity for the parallel form of the human telomeric G-quadruplex. Both compounds are also able to induce telomeric DNA damage that may explain the activity of these compounds.
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Affiliation(s)
- Jussara Amato
- Department of Pharmacy, University of Naples "Federico II" Naples, Italy
| | - Nunzia Iaccarino
- Department of Pharmacy, University of Naples "Federico II" Naples, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples "Federico II" Naples, Italy
| | - Rita Morigi
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna Bologna, Italy
| | - Alessandra Locatelli
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna Bologna, Italy
| | - Alberto Leoni
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna Bologna, Italy
| | - Mirella Rambaldi
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna Bologna, Italy
| | - Pasquale Zizza
- Experimental Chemotherapy Laboratory, Regina Elena National Cancer Institute Rome, Italy
| | - Annamaria Biroccio
- Experimental Chemotherapy Laboratory, Regina Elena National Cancer Institute Rome, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples "Federico II" Naples, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples "Federico II" Naples, Italy
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39
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Musumeci D, Amato J, Randazzo A, Novellino E, Giancola C, Montesarchio D, Pagano B. G-Quadruplex on Oligo Affinity Support (G4-OAS): An Easy Affinity Chromatography-Based Assay for the Screening of G-Quadruplex Ligands. Anal Chem 2014; 86:4126-30. [DOI: 10.1021/ac500444m] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Domenica Musumeci
- Department
of Chemical Sciences, University of Naples Federico II, via Cintia 4, I-80126 Napoli, Italy
| | - Jussara Amato
- Department
of Pharmacy, University of Naples Federico II, via D. Montesano 49, I-80131 Napoli, Italy
| | - Antonio Randazzo
- Department
of Pharmacy, University of Naples Federico II, via D. Montesano 49, I-80131 Napoli, Italy
| | - Ettore Novellino
- Department
of Pharmacy, University of Naples Federico II, via D. Montesano 49, I-80131 Napoli, Italy
| | - Concetta Giancola
- Department
of Pharmacy, University of Naples Federico II, via D. Montesano 49, I-80131 Napoli, Italy
| | - Daniela Montesarchio
- Department
of Chemical Sciences, University of Naples Federico II, via Cintia 4, I-80126 Napoli, Italy
| | - Bruno Pagano
- Department
of Pharmacy, University of Naples Federico II, via D. Montesano 49, I-80131 Napoli, Italy
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40
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Maji B, Bhattacharya S. Advances in the molecular design of potential anticancer agents via targeting of human telomeric DNA. Chem Commun (Camb) 2014; 50:6422-38. [DOI: 10.1039/c4cc00611a] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Telomerase is an attractive drug target to develop new generation drugs against cancer.
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Affiliation(s)
- Basudeb Maji
- Department of Organic Chemistry
- Indian Institute of Science
- Bangalore-560012, India
| | - Santanu Bhattacharya
- Department of Organic Chemistry
- Indian Institute of Science
- Bangalore-560012, India
- Chemical Biology Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
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41
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Di Leva FS, Zizza P, Cingolani C, D'Angelo C, Pagano B, Amato J, Salvati E, Sissi C, Pinato O, Marinelli L, Cavalli A, Cosconati S, Novellino E, Randazzo A, Biroccio A. Exploring the chemical space of G-quadruplex binders: discovery of a novel chemotype targeting the human telomeric sequence. J Med Chem 2013; 56:9646-54. [PMID: 24256368 DOI: 10.1021/jm401185b] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Recent findings have unambiguously demonstrated that DNA G-rich sequences can adopt a G-quadruplex folding in living cells, thus further validating them as crucial targets for anticancer therapy. Herein, to identify new potent G4 binders as antitumor drug candidates, we have targeted a 24-nt G4-forming telomeric sequence employing a receptor-based virtual screening approach. Among the best candidates, in vitro binding experiments allowed identification of three novel G4 ligands. Among them, the best compound features an unprecedented binding selectivity for the human telomeric DNA G-quadruplex with no detectable binding for other G4-forming sequences present at different genomic sites. This behavior correlates with the detected ability to generate DNA damage response in tumor cells at the telomeric level and efficient antiproliferative effect on different tumor cell lines at low micromolar concentrations.
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Affiliation(s)
- Francesco Saverio Di Leva
- Department of Drug Discovery and Development, Istituto Italiano di Tecnologia , via Morego 30, 16163 Genova, Italy
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