1
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Tao S, Run Y, Monchaud D, Zhang W. i-Motif DNA: identification, formation, and cellular functions. Trends Genet 2024:S0168-9525(24)00133-1. [PMID: 38902139 DOI: 10.1016/j.tig.2024.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/29/2024] [Accepted: 05/29/2024] [Indexed: 06/22/2024]
Abstract
An i-motif (iM) is a four-stranded (quadruplex) DNA structure that folds from cytosine (C)-rich sequences. iMs can fold under many different conditions in vitro, which paves the way for their formation in living cells. iMs are thought to play key roles in various DNA transactions, notably in the regulation of genome stability, gene transcription, mRNA translation, DNA replication, telomere and centromere functions, and human diseases. We summarize the different techniques used to assess the folding of iMs in vitro and provide an overview of the internal and external factors that affect their formation and stability in vivo. We describe the possible biological relevance of iMs and propose directions towards their use as target in biology.
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Affiliation(s)
- Shentong Tao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production (CIC-MCP), Nanjing Agricultural University, 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Yonghang Run
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production (CIC-MCP), Nanjing Agricultural University, 1 Weigang, Nanjing, Jiangsu 210095, China
| | - David Monchaud
- Institut de Chimie Moleculaire de l'Université de Bourgogne (ICMUB), Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 6302, Université Bourgogne Franche Comté (UBFC), Dijon, France
| | - Wenli Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production (CIC-MCP), Nanjing Agricultural University, 1 Weigang, Nanjing, Jiangsu 210095, China.
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2
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Laigre E, Bonnet H, Beauvineau C, Lavergne T, Verga D, Defrancq E, Dejeu J, Teulade-Fichou MP. Systematic Evaluation of Benchmark G4 Probes and G4 Clinical Drugs using three Biophysical Methods: A Guideline to Evaluate Rapidly G4-Binding Affinity. Chembiochem 2024; 25:e202400210. [PMID: 38619969 DOI: 10.1002/cbic.202400210] [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: 04/08/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/17/2024]
Abstract
G-quadruplex DNA structures (G4) are proven to interfere with most genetic and epigenetic processes. Small molecules binding these structures (G4 ligands) are invaluable tools to probe G4-biology and address G4-druggability in various diseases (cancer, viral infections). However, the large number of reported G4 ligands (>1000) could lead to confusion while selecting one for a given application. Herein we conducted a systematic affinity ranking of 11 popular G4 ligands vs 5 classical G4 sequences using FRET-melting, G4-FID assays and SPR. Interestingly SPR data globally align with the rankings obtained from the two semi-quantitative assays despite discrepancies due to limits and characteristics of each assay. In the whole, PhenDC3 emerges as the most potent binder irrespective of the G4 sequence. Immediately below PDS, PDC-360A, BRACO19, TMPyP4 and RHPS4 feature strong to medium binding again with poor G4 topology discrimination. More strikingly, the G4 drugs Quarfloxin, CX5461 and c-PDS exhibit weak affinity with all G4s studied. Finally, NMM and Cu-ttpy showed heterogeneous behaviors due, in part, to their physicochemical particularities poorly compatible with screening conditions. The remarkable properties of PhenDC3 led us to propose its use for benchmarking FRET-melting and G4-FID assays for rapid G4-affinity evaluation of newly developed ligands.
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Affiliation(s)
- E Laigre
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405, Orsay, France
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France
| | - H Bonnet
- DCM, UMR 5250, Univ. Grenoble Alpes, CNRS, 570 Rue de la Chimie, 38000, Grenoble, France
| | - C Beauvineau
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405, Orsay, France
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France
| | - T Lavergne
- DCM, UMR 5250, Univ. Grenoble Alpes, CNRS, 570 Rue de la Chimie, 38000, Grenoble, France
| | - D Verga
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405, Orsay, France
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France
| | - E Defrancq
- DCM, UMR 5250, Univ. Grenoble Alpes, CNRS, 570 Rue de la Chimie, 38000, Grenoble, France
| | - J Dejeu
- DCM, UMR 5250, Univ. Grenoble Alpes, CNRS, 570 Rue de la Chimie, 38000, Grenoble, France
- SUPMICROTECH, Université Franche-Comté, CNRS, Institut FEMTO-ST, 25000, Besançon, France
| | - M-P Teulade-Fichou
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405, Orsay, France
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France
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3
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Guneri D, Waller ZAE. Utility of intercalator displacement assays for screening of ligands for i-motif DNA structures. Methods Enzymol 2024; 695:221-232. [PMID: 38521586 DOI: 10.1016/bs.mie.2023.12.004] [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] [Indexed: 03/25/2024]
Abstract
Cytosine rich sequences can form intercalated, i-motif DNA structures stabilized by hemi-protonated cytosine:cytosine base pairing. These sequences are often located in regulatory regions of genes such as promoters. Ligands targeting i-motif structures may provide potential leads for treatments for genetic disease. The focus on ligands interacting with i-motif DNA has been increasing in recent years. Here, we describe the fluorescent intercalator displacement (FID) assay using thiazole orange binding i-motif DNA and assess the binding affinity of a ligand to the i-motif DNA by displacing thiazole orange. This provides a time and cost-effective high throughput screening of ligands against secondary DNA structures for hit identification.
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Affiliation(s)
- Dilek Guneri
- School of Pharmacy, University College London, London, United Kingdom.
| | - Zoë A E Waller
- School of Pharmacy, University College London, London, United Kingdom.
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Alexandrou E, Guneri D, Neidle S, Waller ZAE. QN-302 demonstrates opposing effects between i-motif and G-quadruplex DNA structures in the promoter of the S100P gene. Org Biomol Chem 2023; 22:55-58. [PMID: 37970888 PMCID: PMC10732280 DOI: 10.1039/d3ob01464a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 10/24/2023] [Indexed: 11/19/2023]
Abstract
GC-rich sequences can fold into G-quadruplexes and i-motifs and are known to control gene expression in many organisms. The potent G-quadruplex experimental anticancer drug QN-302 down-regulates a number of cancer-related genes, in particular S100P. Here we show this ligand has strong opposing effects with i-motif DNA structures and is one of the most potent i-motif destabilising agents reported to date. QN-302 down-regulates the expression of numerous cancer-related genes by pan-quadruplex targeting. QN-302 exhibits exceptional combined synergistic effects compared to many other G-quadruplex and i-motif interacting compounds. This work further emphasises the importance of considering G-quadruplex and i-motif DNA structures as one dynamic system.
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Affiliation(s)
- Effrosyni Alexandrou
- School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK.
| | - Dilek Guneri
- School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK.
| | - Stephen Neidle
- School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK.
| | - Zoë A E Waller
- School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK.
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5
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Yazdani K, Seshadri S, Tillo D, Yang M, Sibley CD, Vinson C, Schneekloth JS. Decoding complexity in biomolecular recognition of DNA i-motifs with microarrays. Nucleic Acids Res 2023; 51:12020-12030. [PMID: 37962331 PMCID: PMC10711443 DOI: 10.1093/nar/gkad981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 09/28/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
DNA i-motifs (iMs) are non-canonical C-rich secondary structures implicated in numerous cellular processes. Though iMs exist throughout the genome, our understanding of iM recognition by proteins or small molecules is limited to a few examples. We designed a DNA microarray containing 10976 genomic iM sequences to examine the binding profiles of four iM-binding proteins, mitoxantrone and the iMab antibody. iMab microarray screens demonstrated that pH 6.5, 5% BSA buffer was optimal, and fluorescence was correlated with iM C-tract length. hnRNP K broadly recognizes diverse iM sequences, favoring 3-5 cytosine repeats flanked by thymine-rich loops of 1-3 nucleotides. Array binding mirrored public ChIP-Seq datasets, in which 35% of well-bound array iMs are enriched in hnRNP K peaks. In contrast, other reported iM-binding proteins had weaker binding or preferred G-quadruplex (G4) sequences instead. Mitoxantrone broadly binds both shorter iMs and G4s, consistent with an intercalation mechanism. These results suggest that hnRNP K may play a role in iM-mediated regulation of gene expression in vivo, whereas hnRNP A1 and ASF/SF2 are possibly more selective in their binding preferences. This powerful approach represents the most comprehensive investigation of how biomolecules selectively recognize genomic iMs to date.
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Affiliation(s)
- Kamyar Yazdani
- Chemical Biology Laboratory, National Cancer Institute, 1050 Boyle St., Frederick, MD 21702, USA
| | - Srinath Seshadri
- Chemical Biology Laboratory, National Cancer Institute, 1050 Boyle St., Frederick, MD 21702, USA
| | - Desiree Tillo
- Genome Analysis Unit, National Cancer Institute, 37 Convent Dr., Bethesda, MD 20892, USA
| | - Mo Yang
- Chemical Biology Laboratory, National Cancer Institute, 1050 Boyle St., Frederick, MD 21702, USA
| | - Christopher D Sibley
- Chemical Biology Laboratory, National Cancer Institute, 1050 Boyle St., Frederick, MD 21702, USA
| | - Charles Vinson
- Laboratory of Metabolism, National Cancer Institute, 37 Convent Dr., Bethesda, MD 20892, USA
| | - John S Schneekloth
- Chemical Biology Laboratory, National Cancer Institute, 1050 Boyle St., Frederick, MD 21702, USA
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6
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Boissieras J, Granzhan A. Potentiometric titrations to study ligand interactions with DNA i-motifs. Methods Enzymol 2023; 695:233-254. [PMID: 38521587 DOI: 10.1016/bs.mie.2023.11.005] [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] [Indexed: 03/25/2024]
Abstract
i-Motifs are non-canonical secondary structures of DNA formed by mutual intercalation of hemi-protonated cytosine-cytosine base pairs, most typically in slightly acidic conditions (pH<7.0). These structures are well-studied in vitro and have recently been suggested to exist in cells. Despite nearly a decade of active research, the quest for small-molecule ligands that could selectively bind to and stabilize i-motifs continues, and no reference, bona fide i-motif ligand is currently available. This is, at least in part, due to the lack of robust methods to assess the interaction of ligands with i-motifs, since many techniques well-established for studies of other secondary structures (such as CD-, UV-, and FRET-melting) may generate artifacts when applied to i-motifs. Here, we describe an implementation of automated, potentiometric (pH) titrations as a robust isothermal method to assess the impact of ligands or cosolutes on thermodynamic stability of i-motifs. This approach is validated through the use of a cosolute previously known to stabilize i-motifs (PEG2000) and three small-molecule ligands that are able to stabilize, destabilize, or have no effect on the stability of i-motifs, respectively.
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Affiliation(s)
- Joseph Boissieras
- CMBC, CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, Orsay, France; CMBC, CNRS UMR9187, INSERM U1196, Université Paris Saclay, Orsay, France
| | - Anton Granzhan
- CMBC, CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, Orsay, France; CMBC, CNRS UMR9187, INSERM U1196, Université Paris Saclay, Orsay, France.
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7
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Cadoni E, De Paepe L, Colpaert G, Tack R, Waegeman D, Manicardi A, Madder A. A red light-triggered chemical tool for sequence-specific alkylation of G-quadruplex and I-motif DNA. Nucleic Acids Res 2023; 51:4112-4125. [PMID: 36971129 PMCID: PMC10201448 DOI: 10.1093/nar/gkad189] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/03/2023] [Accepted: 03/12/2023] [Indexed: 08/21/2023] Open
Abstract
The importance of non-canonical DNA structures such as G-quadruplexes (G4) and intercalating-motifs (iMs) in the fine regulation of a variety of cellular processes has been recently demonstrated. As the crucial roles of these structures are being unravelled, it is becoming more and more important to develop tools that allow targeting these structures with the highest possible specificity. While targeting methodologies have been reported for G4s, this is not the case for iMs, as evidenced by the limited number of specific ligands able to bind the latter and the total absence of selective alkylating agents for their covalent targeting. Furthermore, strategies for the sequence-specific covalent targeting of G4s and iMs have not been reported thus far. Herein, we describe a simple methodology to achieve sequence-specific covalent targeting of G4 and iM DNA structures based on the combination of (i) a peptide nucleic acid (PNA) recognizing a specific sequence of interest, (ii) a pro-reactive moiety enabling a controlled alkylation reaction, and (iii) a G4 or iM ligand orienting the alkylating warhead to the reactive residues. This multi-component system allows for the targeting of specific G4 or iM sequences of interest in the presence of competing DNA sequences and under biologically relevant conditions.
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Affiliation(s)
- Enrico Cadoni
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Lessandro De Paepe
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Gertjan Colpaert
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Ruben Tack
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Dries Waegeman
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Alex Manicardi
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
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8
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Rodriguez J, Domínguez A, Aviñó A, Borgonovo G, Eritja R, Mazzini S, Gargallo R. Exploring the stabilizing effect on the i-motif of neighboring structural motifs and drugs. Int J Biol Macromol 2023; 242:124794. [PMID: 37182626 DOI: 10.1016/j.ijbiomac.2023.124794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/18/2023] [Accepted: 04/25/2023] [Indexed: 05/16/2023]
Abstract
Cytosine-rich DNA sequences may fold into a structure known as i-motif, with potential in vivo modulation of gene expression. The stability of the i-motif is residual at neutral pH values. To increase it, the addition of neighboring moieties, such as Watson-Crick stabilized loops, tetrads, or non-canonical base pairs have been proposed. Taking a recently described i-motif structure as a model, the relative effect of these structural moieties, as well as several DNA ligands, on the stabilization of the i-motif has been studied. To this end, not only the original sequence but different mutants were considered. Spectroscopic techniques, PAGE, and multivariate data analysis methods have been used to model the folding/unfolding equilibria induced by changes of pH, temperature, and the presence of ligands. The results have shown that the duplex is the moiety that is responsible of the stabilization of the i-motif structure at neutral pH. The T:T base pair, on the contrary, shows little stabilization of the i-motif. From several selected DNA-binding ligands, the G-quadruplex ligand BA41 is shown to interact with the duplex moiety, whereas non-specific interaction and little stabilization has been observed within the i-motif.
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Affiliation(s)
- Judit Rodriguez
- Department of Chemical Engineering and Analytical Chemistry, Faculty of Chemistry, University of Barcelona, Marti i Franqués 1-11, E-08028 Barcelona, Spain
| | - Arnau Domínguez
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain
| | - Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain
| | - Gigliola Borgonovo
- Department of Food, Environmental and Nutritional Sciences (DEFENS), University of Milan (Università degli Studi di Milano), Milan, Italy
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain
| | - Stefania Mazzini
- Department of Food, Environmental and Nutritional Sciences (DEFENS), University of Milan (Università degli Studi di Milano), Milan, Italy
| | - Raimundo Gargallo
- Department of Chemical Engineering and Analytical Chemistry, Faculty of Chemistry, University of Barcelona, Marti i Franqués 1-11, E-08028 Barcelona, Spain.
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9
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Yazdani K, Seshadri S, Tillo D, Vinson C, Schneekloth JS. DECODING COMPLEXITY IN BIOMOLECULAR RECOGNITION OF DNA I-MOTIFS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.19.537548. [PMID: 37131644 PMCID: PMC10153190 DOI: 10.1101/2023.04.19.537548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
DNA i-motifs (iMs) are non-canonical C-rich secondary structures implicated in numerous cellular processes. Though iMs exist throughout the genome, our understanding of iM recognition by proteins or small molecules is limited to a few examples. We designed a DNA microarray containing 10,976 genomic iM sequences to examine the binding profiles of four iM-binding proteins, mitoxantrone, and the iMab antibody. iMab microarray screens demonstrated that pH 6.5, 5% BSA buffer was optimal, and fluorescence was correlated with iM C-tract length. hnRNP K broadly recognizes diverse iM sequences, favoring 3-5 cytosine repeats flanked by thymine-rich loops of 1-3 nucleotides. Array binding mirrored public ChIP-Seq datasets, in which 35% of well-bound array iMs are enriched in hnRNP K peaks. In contrast, other reported iM-binding proteins had weaker binding or preferred G-quadruplex (G4) sequences instead. Mitoxantrone broadly binds both shorter iMs and G4s, consistent with an intercalation mechanism. These results suggest that hnRNP K may play a role in iM-mediated regulation of gene expression in vivo, whereas hnRNP A1 and ASF/SF2 are possibly more selective in their binding preferences. This powerful approach represents the most comprehensive investigation of how biomolecules selectively recognize genomic iMs to date.
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Affiliation(s)
- Kamyar Yazdani
- Chemical Biology Laboratory, National Cancer Institute, 1050 Boyle St., Frederick, MD 21702
| | - Srinath Seshadri
- Chemical Biology Laboratory, National Cancer Institute, 1050 Boyle St., Frederick, MD 21702
| | - Desiree Tillo
- Genome Analysis Unit, National Cancer Institute, 37 Convent Dr., Bethesda, MD 20892
| | - Charles Vinson
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, 37 Convent Dr., Bethesda MD 20892
| | - John S Schneekloth
- Chemical Biology Laboratory, National Cancer Institute, 1050 Boyle St., Frederick, MD 21702
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Ambrosio MR, Migliaccio T, Napolitano F, Di Somma S, Maneli G, Amato J, Pagano B, Randazzo A, Portella G, Formisano P, Malfitano AM. Targeting G-quadruplex motifs interferes with differentiation of adipose-derived mesenchymal stem cells. Stem Cell Res Ther 2023; 14:98. [PMID: 37076894 PMCID: PMC10116735 DOI: 10.1186/s13287-023-03320-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 03/29/2023] [Indexed: 04/21/2023] Open
Abstract
BACKGROUND G-quadruplex (G4) motifs are nucleic acid secondary structures observed in mammalian genomes and transcriptomes able to regulate various cellular processes. Several small molecules have been developed so far to modulate G4 stability, frequently associated with anticancer activity. However, how G4 structures are regulated over homeostatic conditions is mostly unexplored. Here, we used human adipose-derived mesenchymal stem cells (ASCs) to address the role of G4 motifs during adipogenic differentiation. METHODS Adipocyte differentiation of ASCs was investigated in the presence or absence of a well-known G4 ligand, Braco-19. Cell viability was determined by sulforhodamine B assay. Cell dimension and granularity, DNA G4 motifs and cell cycle were detected by flow cytometry. Lipid droplet accumulation was assessed by Oil Red O staining. Cell senescence was evaluated by β-galactosidase staining. Gene expression was measured by qPCR. Protein release in the extracellular medium was quantified by ELISA. RESULTS Braco-19 used at non-cytotoxic concentrations induced morphological changes in mature adipocytes partially restoring an undifferentiated-like status. Braco-19 reduced lipid vacuolization and PPARG, AP2, LEP and TNFA mRNA levels in terminally differentiated cells. No effect was observed in cell senescence, fibrotic markers, IL-6 and IL-8 production, while the secretion of VEGF was dose-dependently reduced. Interestingly, G4 structures were increased in differentiated adipocytes compared to their precursors. Braco-19 treatment reduced G4 content in mature adipocytes. CONCLUSIONS Our data highlight a new role of G4 motifs as genomic structural elements related to human ASC differentiation into mature adipocytes, with potential implications in physio-pathological processes.
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Affiliation(s)
- Maria Rosaria Ambrosio
- Department of Translational Medical Sciences, University "Federico II", 80131, Naples, Italy
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, 80131, Naples, Italy
| | - Teresa Migliaccio
- Department of Translational Medical Sciences, University "Federico II", 80131, Naples, Italy
| | - Fabiana Napolitano
- Department of Translational Medical Sciences, University "Federico II", 80131, Naples, Italy
| | - Sarah Di Somma
- Department of Translational Medical Sciences, University "Federico II", 80131, Naples, Italy
| | - Giovanni Maneli
- Department of Translational Medical Sciences, University "Federico II", 80131, 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
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, 80131, Naples, Italy
| | - Giuseppe Portella
- Department of Translational Medical Sciences, University "Federico II", 80131, Naples, Italy
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, 80131, Naples, Italy
| | - Pietro Formisano
- Department of Translational Medical Sciences, University "Federico II", 80131, Naples, Italy.
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, 80131, Naples, Italy.
| | - Anna Maria Malfitano
- Department of Translational Medical Sciences, University "Federico II", 80131, Naples, Italy.
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11
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Luo X, Zhang J, Gao Y, Pan W, Yang Y, Li X, Chen L, Wang C, Wang Y. Emerging roles of i-motif in gene expression and disease treatment. Front Pharmacol 2023; 14:1136251. [PMID: 37021044 PMCID: PMC10067743 DOI: 10.3389/fphar.2023.1136251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 02/27/2023] [Indexed: 03/22/2023] Open
Abstract
As non-canonical nucleic acid secondary structures consisting of cytosine-rich nucleic acids, i-motifs can form under certain conditions. Several i-motif sequences have been identified in the human genome and play important roles in biological regulatory functions. Due to their physicochemical properties, these i-motif structures have attracted attention and are new targets for drug development. Herein, we reviewed the characteristics and mechanisms of i-motifs located in gene promoters (including c-myc, Bcl-2, VEGF, and telomeres), summarized various small molecule ligands that interact with them, and the possible binding modes between ligands and i-motifs, and described their effects on gene expression. Furthermore, we discussed diseases closely associated with i-motifs. Among these, cancer is closely associated with i-motifs since i-motifs can form in some regions of most oncogenes. Finally, we introduced recent advances in the applications of i-motifs in multiple areas.
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Affiliation(s)
| | | | | | | | | | | | | | - Chang Wang
- *Correspondence: Chang Wang, ; Yuqing Wang,
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12
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Gorini F, Ambrosio S, Lania L, Majello B, Amente S. The Intertwined Role of 8-oxodG and G4 in Transcription Regulation. Int J Mol Sci 2023; 24:ijms24032031. [PMID: 36768357 PMCID: PMC9916577 DOI: 10.3390/ijms24032031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/11/2023] [Accepted: 01/14/2023] [Indexed: 01/22/2023] Open
Abstract
The guanine base in nucleic acids is, among the other bases, the most susceptible to being converted into 8-Oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) when exposed to reactive oxygen species. In double-helix DNA, 8-oxodG can pair with adenine; hence, it may cause a G > T (C > A) mutation; it is frequently referred to as a form of DNA damage and promptly corrected by DNA repair mechanisms. Moreover, 8-oxodG has recently been redefined as an epigenetic factor that impacts transcriptional regulatory elements and other epigenetic modifications. It has been proposed that 8-oxodG exerts epigenetic control through interplay with the G-quadruplex (G4), a non-canonical DNA structure, in transcription regulatory regions. In this review, we focused on the epigenetic roles of 8-oxodG and the G4 and explored their interplay at the genomic level.
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Affiliation(s)
- Francesca Gorini
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy
| | - Susanna Ambrosio
- Department of Biology, University of Naples Federico II, 80138 Naples, Italy
| | - Luigi Lania
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy
| | - Barbara Majello
- Department of Biology, University of Naples Federico II, 80138 Naples, Italy
| | - Stefano Amente
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy
- Correspondence:
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13
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Berthiol F, Boissieras J, Bonnet H, Pierrot M, Philouze C, Poisson JF, Granzhan A, Dejeu J, Defrancq E. Novel Synthesis of IMC-48 and Affinity Evaluation with Different i-Motif DNA Sequences. Molecules 2023; 28:molecules28020682. [PMID: 36677740 PMCID: PMC9865601 DOI: 10.3390/molecules28020682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/12/2023] Open
Abstract
During the last decade, the evidence for the biological relevance of i-motif DNA (i-DNA) has been accumulated. However, relatively few molecules were reported to interact with i-DNA, and a controversy concerning their binding mode, affinity, and selectivity persists in the literature. In this context, the cholestane derivative IMC-48 has been reported to modulate bcl-2 gene expression by stabilizing an i-motif structure in its promoter. In the present contribution, we report on a novel, more straightforward, synthesis of IMC-48 requiring fewer steps compared to the previous approach. Furthermore, the interaction of IMC-48 with four different i-motif DNA sequences was thoroughly investigated by bio-layer interferometry (BLI) and circular dichroism (CD) spectroscopy. Surprisingly, our results show that IMC-48 is a very weak ligand of i-DNA as no quantifiable interaction or significant stabilization of i-motif structures could be observed, stimulating a quest for an alternative mechanism of its biological activity.
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Affiliation(s)
- Florian Berthiol
- Department of Molecular Chemistry (DCM), CNRS, UMR 5250, Université Grenoble-Alpes, 38000 Grenoble, France
- Correspondence: (F.B.); (J.D.); (E.D.)
| | - Joseph Boissieras
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405 Orsay, France
- CNRS UMR9187, INSERM U1196, Université Paris Saclay, F-91405 Orsay, France
| | - Hugues Bonnet
- Department of Molecular Chemistry (DCM), CNRS, UMR 5250, Université Grenoble-Alpes, 38000 Grenoble, France
| | - Marie Pierrot
- Department of Molecular Chemistry (DCM), CNRS, UMR 5250, Université Grenoble-Alpes, 38000 Grenoble, France
| | - Christian Philouze
- Department of Molecular Chemistry (DCM), CNRS, UMR 5250, Université Grenoble-Alpes, 38000 Grenoble, France
| | - Jean-François Poisson
- Department of Molecular Chemistry (DCM), CNRS, UMR 5250, Université Grenoble-Alpes, 38000 Grenoble, France
| | - Anton Granzhan
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405 Orsay, France
- CNRS UMR9187, INSERM U1196, Université Paris Saclay, F-91405 Orsay, France
| | - Jérôme Dejeu
- Department of Molecular Chemistry (DCM), CNRS, UMR 5250, Université Grenoble-Alpes, 38000 Grenoble, France
- FEMTO-ST Institute, CNRS UMR-6174, Université de Bourgogne Franche-Comté, F-25000 Besançon, France
- Correspondence: (F.B.); (J.D.); (E.D.)
| | - Eric Defrancq
- Department of Molecular Chemistry (DCM), CNRS, UMR 5250, Université Grenoble-Alpes, 38000 Grenoble, France
- Correspondence: (F.B.); (J.D.); (E.D.)
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14
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Alexander A, Pillai AS, Akash BA, Ananthi N, Pal H, Enoch IV, Sayed M. Supramolecular association of a diguanidine derivative with a porphyrin-cyclodextrin conjugate and its binding to G-Quadruplex DNA. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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15
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Teng Y, Zhu M, Chi Y, Li L, Jin Y. Can G-quadruplex become a promising target in HBV therapy? Front Immunol 2022; 13:1091873. [PMID: 36591216 PMCID: PMC9797731 DOI: 10.3389/fimmu.2022.1091873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
The chronic infection with hepatitis B virus (HBV) is an important health problem that affects millions of people worldwide. Current therapies for HBV always suffer from a poor response rate, common side effects, and the need for lifelong treatment. Novel therapeutic targets are expected. Interestingly, non-canonical structures of nucleic acids play crucial roles in the regulation of gene expression. Especially the formation of G-quadruplexes (G4s) in G-rich strands has been demonstrated to affect many bioprocesses including replication, transcription, and translation, showing great potential as targets in anticancer and antiviral therapies. In this review, we summarize recent antiviral studies about G4s and discuss the potential roles of G4 structures in antiviral therapy for HBV.
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Affiliation(s)
- Ye Teng
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Ming Zhu
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Yuan Chi
- Pharmaceutical Department, The Affiliated Hospital of Changchun University of Chinese Medicine, Changchun, China
| | - Lijing Li
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China,*Correspondence: Lijing Li, ; Ye Jin,
| | - Ye Jin
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China,*Correspondence: Lijing Li, ; Ye Jin,
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16
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Suganthi S, Alexander A, Pillai AS, Enoch IVMV, Yousuf S. Naphtholylimino-tether on β-cyclodextrin: Selective G-quadruplex DNA binding. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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17
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Bansal A, Kaushik S, Kukreti S. Non-canonical DNA structures: Diversity and disease association. Front Genet 2022; 13:959258. [PMID: 36134025 PMCID: PMC9483843 DOI: 10.3389/fgene.2022.959258] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/25/2022] [Indexed: 11/18/2022] Open
Abstract
A complete understanding of DNA double-helical structure discovered by James Watson and Francis Crick in 1953, unveil the importance and significance of DNA. For the last seven decades, this has been a leading light in the course of the development of modern biology and biomedical science. Apart from the predominant B-form, experimental shreds of evidence have revealed the existence of a sequence-dependent structural diversity, unusual non-canonical structures like hairpin, cruciform, Z-DNA, multistranded structures such as DNA triplex, G-quadruplex, i-motif forms, etc. The diversity in the DNA structure depends on various factors such as base sequence, ions, superhelical stress, and ligands. In response to these various factors, the polymorphism of DNA regulates various genes via different processes like replication, transcription, translation, and recombination. However, altered levels of gene expression are associated with many human genetic diseases including neurological disorders and cancer. These non-B-DNA structures are expected to play a key role in determining genetic stability, DNA damage and repair etc. The present review is a modest attempt to summarize the available literature, illustrating the occurrence of non-canonical structures at the molecular level in response to the environment and interaction with ligands and proteins. This would provide an insight to understand the biological functions of these unusual DNA structures and their recognition as potential therapeutic targets for diverse genetic diseases.
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Affiliation(s)
- Aparna Bansal
- Nucleic Acid Research Lab, Department of Chemistry, University of Delhi, Delhi, India
- Department of Chemistry, Hansraj College, University of Delhi, Delhi, India
| | - Shikha Kaushik
- Nucleic Acid Research Lab, Department of Chemistry, University of Delhi, Delhi, India
- Department of Chemistry, Rajdhani College, University of Delhi, New Delhi, India
| | - Shrikant Kukreti
- Nucleic Acid Research Lab, Department of Chemistry, University of Delhi, Delhi, India
- *Correspondence: Shrikant Kukreti,
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18
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Zhai LY, Liu JF, Zhao JJ, Su AM, Xi XG, Hou XM. Targeting the RNA G-Quadruplex and Protein Interactome for Antiviral Therapy. J Med Chem 2022; 65:10161-10182. [PMID: 35862260 DOI: 10.1021/acs.jmedchem.2c00649] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In recent years, G-quadruplexes (G4s), types of noncanonical four-stranded nucleic acid structures, have been identified in many viruses that threaten human health, such as HIV and Epstein-Barr virus. In this context, G4 ligands were designed to target the G4 structures, among which some have shown promising antiviral effects. In this Perspective, we first summarize the diversified roles of RNA G4s in different viruses. Next, we introduce small-molecule ligands developed as G4 modulators and highlight their applications in antiviral studies. In addition to G4s, we comprehensively review the medical intervention of G4-interacting proteins from both the virus (N protein, viral-encoded helicases, severe acute respiratory syndrome-unique domain, and Epstein-Barr nuclear antigen 1) and the host (heterogeneous nuclear ribonucleoproteins, RNA helicases, zinc-finger cellular nucelic acid-binding protein, and nucleolin) by inhibitors as an alternative way to disturb the normal functions of G4s. Finally, we discuss the challenges and opportunities in G4-based antiviral therapy.
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Affiliation(s)
- Li-Yan Zhai
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
| | - Jing-Fan Liu
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
| | - Jian-Jin Zhao
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
| | - Ai-Min Su
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
| | - Xu-Guang Xi
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China.,Laboratory of Biology and Applied Pharmacology, CNRS UMR 8113, IDA FR3242, ENS Paris-Saclay, Université Paris-Saclay, Gif-sur-Yvette 91190, France
| | - Xi-Miao Hou
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
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19
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Santos T, Lopes-Nunes J, Alexandre D, Miranda A, Figueiredo J, Silva MS, Mergny JL, Cruz C. Stabilization of a DNA aptamer by ligand binding. Biochimie 2022; 200:8-18. [PMID: 35550917 DOI: 10.1016/j.biochi.2022.05.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/03/2022] [Accepted: 05/05/2022] [Indexed: 12/17/2022]
Abstract
G-rich aptamers such as AS1411 are small oligonucleotides that present several benefits comparatively to monoclonal antibodies, since they are easier to manufacture and store, have small size and do not stimulate an immune response. We analyzed AT11-B1, a modified sequence of AT11 (itself a modified version of AS1411), in which one thymine was removed from the bulge region. We studied G-quadruplex (G4) formation/stabilization using PhenDC3, PDS, BRACO-19, TMPyP4 and 360A ligands by different biophysical techniques, namely circular dichroism (CD), Förster resonance energy transfer (FRET-melting) and nuclear magnetic resonance (NMR). The CD spectra showed that AT11-B1 adopts a predominant G4 of parallel topology when the buffer contains KCl or when ligands are added. PhenDC3 induced a ΔTm of 30 °C or more of the G4 structure as shown by CD- and FRET-melting experiments. The ligands demonstrate high affinity for AT11-B1 G4 and the NMR studies revealed that the AT11-B1 G4 involves four G-tetrad layers. The in silico studies suggest that all ligands bind AT11-B1 G4, namely, by stacking interactions, except PDS that may bind to the loop/groove interface. In addition, molecular dynamics simulations revealed that nucleolin (NCL) interacts with the AT11-B1 G4 structure through the RNA binding domain (RBD) 2 and the 12-residue linker between RBD1,2. Moreover, AT11-B1 G4 was internalized into a NCL-positive tongue squamous cell carcinoma cell line. In a nutshell, this study may help the identification of the ligands scaffolds to bind and stabilize AT11-B1, improving the targeting towards NCL that is overexpressed in cancer cells.
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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, Covilhã, Portugal
| | - Jéssica Lopes-Nunes
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal
| | - Daniela Alexandre
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal
| | - André Miranda
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal
| | - Joana Figueiredo
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal
| | - Micael S Silva
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal
| | - Jean-Louis Mergny
- Institute of Biophysics of the CAS, v.v.i, Královopolská 135, 612 65, Brno, Czech Republic; Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128, Palaiseau, France
| | - Carla Cruz
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal.
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20
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Bonnet H, Morel M, Devaux A, Boissieras J, Granzhan A, Elias B, Lavergne T, Dejeu J, Defrancq E. Assessment of presumed small-molecule ligands of telomeric i-DNA by biolayer interferometry (BLI). Chem Commun (Camb) 2022; 58:5116-5119. [PMID: 35380138 DOI: 10.1039/d2cc00836j] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Biolayer interferometry (BLI) and circular dichroism (CD) spectroscopy were used to investigate the interaction between previously reported i-motif DNA (i-DNA) ligands and folded or unfolded i-DNA in acidic (pH 5.5) and near-neutral (pH 6.5) conditions. We observed that although several ligands, in particular macrocyclic bis-acridine (BisA) and pyridostatin (PDS), showed good affinities for the telomeric i-motif forming sequence, none of the ligands displayed selective interactions with the i-DNA structure nor was able to promote its formation.
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Affiliation(s)
- Hugues Bonnet
- Université Grenoble Alpes, Département de Chimie Moléculaire, UMR CNRS 5250, CS 40700-38058 Grenoble, France.
| | - Maéva Morel
- Université Grenoble Alpes, Département de Chimie Moléculaire, UMR CNRS 5250, CS 40700-38058 Grenoble, France.
| | - Alexandre Devaux
- Université Grenoble Alpes, Département de Chimie Moléculaire, UMR CNRS 5250, CS 40700-38058 Grenoble, France.
| | - Joseph Boissieras
- Institut Curie, CNRS UMR 9187, INSERM U1196, Université Paris Saclay, 91405 Orsay, France
| | - Anton Granzhan
- Institut Curie, CNRS UMR 9187, INSERM U1196, Université Paris Saclay, 91405 Orsay, France
| | - Benjamin Elias
- Institut de la Matière Condensée et des Nanosciences (IMCN), Molecular Chemistry, Materials and Catalysis (MOST), Université catholique de Louvain (UCLouvain), Place Louis Pasteur 1, 1348 Louvain-la-Neuve, Belgium
| | - Thomas Lavergne
- Université Grenoble Alpes, Département de Chimie Moléculaire, UMR CNRS 5250, CS 40700-38058 Grenoble, France.
| | - Jérôme Dejeu
- Université Grenoble Alpes, Département de Chimie Moléculaire, UMR CNRS 5250, CS 40700-38058 Grenoble, France. .,FEMTO-ST Institute, CNRS UMR-6174, Université de Bourgogne Franche-Comté, F-25000 Besançon, France
| | - Eric Defrancq
- Université Grenoble Alpes, Département de Chimie Moléculaire, UMR CNRS 5250, CS 40700-38058 Grenoble, France.
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21
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Jamroskovic J, Deiana M, Sabouri N. Probing the folding pathways of four-stranded intercalated cytosine-rich motifs at single base-pair resolution. Biochimie 2022; 199:81-91. [PMID: 35452743 DOI: 10.1016/j.biochi.2022.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 04/13/2022] [Accepted: 04/13/2022] [Indexed: 11/24/2022]
Abstract
Cytosine-rich DNA can fold into four-stranded intercalated structures called i-motifs (iMs) under acidic conditions through the formation of hemi-protonated C:C+ base pairs. However, the folding and stability of iMs rely on many other factors that are not yet fully understood. Here, we combined biochemical and biophysical approaches to determine the factors influencing iM stability under a wide range of experimental conditions. By using high-resolution primer extension assays, circular dichroism, and absorption spectroscopies, we demonstrate that the stabilities of three different biologically relevant iMs are not dependent on molecular crowding agents. Instead, some of the crowding agents affected overall DNA synthesis. We also tested a range of small molecules to determine their effect on iM stabilization at physiological temperature and demonstrated that the G-quadruplex-specific molecule CX-5461 is also a promising candidate for selective iM stabilization. This work provides important insights into the requirements needed for different assays to accurately study iM stabilization, which will serve as important tools for understanding the contribution of iMs in cell regulation and their potential as therapeutic targets.
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Affiliation(s)
- Jan Jamroskovic
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87, Umeå, Sweden.
| | - Marco Deiana
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87, Umeå, Sweden
| | - Nasim Sabouri
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87, Umeå, Sweden.
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22
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Vertecchi E, Rizzo A, Salvati E. Telomere Targeting Approaches in Cancer: Beyond Length Maintenance. Int J Mol Sci 2022; 23:ijms23073784. [PMID: 35409143 PMCID: PMC8998427 DOI: 10.3390/ijms23073784] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/25/2022] [Accepted: 03/26/2022] [Indexed: 12/19/2022] Open
Abstract
Telomeres are crucial structures that preserve genome stability. Their progressive erosion over numerous DNA duplications determines the senescence of cells and organisms. As telomere length homeostasis is critical for cancer development, nowadays, telomere maintenance mechanisms are established targets in cancer treatment. Besides telomere elongation, telomere dysfunction impinges on intracellular signaling pathways, in particular DNA damage signaling and repair, affecting cancer cell survival and proliferation. This review summarizes and discusses recent findings in anticancer drug development targeting different “telosome” components.
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Affiliation(s)
- Eleonora Vertecchi
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy, c/o Department of Biology and Biotechnology, Sapienza University of Rome, Via degli Apuli 4, 00185 Rome, Italy;
| | - Angela Rizzo
- Oncogenomic and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy;
| | - Erica Salvati
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy, c/o Department of Biology and Biotechnology, Sapienza University of Rome, Via degli Apuli 4, 00185 Rome, Italy;
- Correspondence:
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23
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Stability and context of intercalated motifs (i-motifs) for biological applications. Biochimie 2022; 198:33-47. [PMID: 35259471 DOI: 10.1016/j.biochi.2022.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/21/2022] [Accepted: 03/03/2022] [Indexed: 11/24/2022]
Abstract
DNA is naturally dynamic and can self-assemble into alternative secondary structures including the intercalated motif (i-motif), a four-stranded structure formed in cytosine-rich DNA sequences. Until recently, i-motifs were thought to be unstable in physiological cellular environments. Studies demonstrating their existence in the human genome and role in gene regulation are now shining light on their biological relevance. Herein, we review the effects of epigenetic modifications on i-motif structure and stability, and biological factors that affect i-motif formation within cells. Furthermore, we highlight recent progress in targeting i-motifs with structure-specific ligands for biotechnology and therapeutic purposes.
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24
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Mendes E, Aljnadi IM, Bahls B, Victor BL, Paulo A. Major Achievements in the Design of Quadruplex-Interactive Small Molecules. Pharmaceuticals (Basel) 2022; 15:ph15030300. [PMID: 35337098 PMCID: PMC8953082 DOI: 10.3390/ph15030300] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/17/2022] Open
Abstract
Organic small molecules that can recognize and bind to G-quadruplex and i-Motif nucleic acids have great potential as selective drugs or as tools in drug target discovery programs, or even in the development of nanodevices for medical diagnosis. Hundreds of quadruplex-interactive small molecules have been reported, and the challenges in their design vary with the intended application. Herein, we survey the major achievements on the therapeutic potential of such quadruplex ligands, their mode of binding, effects upon interaction with quadruplexes, and consider the opportunities and challenges for their exploitation in drug discovery.
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Affiliation(s)
- Eduarda Mendes
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
| | - Israa M. Aljnadi
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
- Faculty of Sciences, BioISI, Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Bárbara Bahls
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
- Faculty of Sciences, BioISI, Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Bruno L. Victor
- Faculty of Sciences, BioISI, Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Alexandra Paulo
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
- Correspondence:
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25
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Muturi E, Meng F, Liu H, Jiang M, Wei H, Yang H. Comprehensive Analysis of G-Quadruplexes in African Swine Fever Virus Genome Reveals Potential Antiviral Targets by G-Quadruplex Stabilizers. Front Microbiol 2022; 12:798431. [PMID: 34975822 PMCID: PMC8718096 DOI: 10.3389/fmicb.2021.798431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 11/11/2021] [Indexed: 12/24/2022] Open
Abstract
African Swine Fever Virus (ASFV), a lethal hemorrhagic fever of the swine, poses a major threat to the world's swine population and has so far resulted in devastating socio-economic consequences. The situation is further compounded by the lack of an approved vaccine or antiviral drug. Herein, we investigated a novel anti-ASFV approach by targeting G-Quadruplexes (G4s) in the viral genome. Bioinformatics analysis of putative G-quadruplex-forming sequences (PQSs) in the genome of ASFV BA71V strain revealed 317 PQSs on the forward strand and 322 PQSs on the reverse strand of the viral genome, translating to a density of 3.82 PQSs/kb covering 9.52% of the entire genome, which means that 85% of genes in the ASFV genome have at least 1 PQS on either strand. Biochemical characterization showed that 8 out of 13 conserved PQSs could form stable G4s in the presence of K+, and 4 of them could be stabilized by G4 ligands, N-Methyl Mesoporphyrin (NMM), and pyridostatin (PDS) in vitro. An enhanced green fluorescent protein (EGFP)-based reporter system revealed that the expression of two G4-containing genes, i.e., P1192R and D117L, could be significantly suppressed by NMM and PDS in 293T cells. In addition, a virus infection model showed that NMM could inhibit the replication of ASFV in Porcine Alveolar Macrophages (PAM) cells with an EC50 value of 1.16 μM. Altogether, the present study showed that functional PQSs existent in the promoters, CDS, 3' and 5' UTRs of the ASFV genome could be stabilized by G4 ligands, such as NMM and PDS, and could serve as potential targets for antivirals.
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Affiliation(s)
- Elishiba Muturi
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Fei Meng
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Huan Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Mengwei Jiang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hang Yang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
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26
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Maliszewska HK, Arnau Del Valle C, Xia Y, Marín MJ, Waller ZAE, Muñoz MP. Precious metal complexes of bis(pyridyl)allenes: synthesis and catalytic and medicinal applications. Dalton Trans 2021; 50:16739-16750. [PMID: 34761768 DOI: 10.1039/d1dt02929k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The incorporation of donor-type substituents on the allene core opens up the possibility of coordination complexes in which the metal is bonded to the donor groups, with or without interaction with the double bond system. Despite the challenges in the synthesis of such allene-containing metal complexes, their unique 3D environments and dual functionality (allene and metal) could facilitate catalysis and interaction with chemical and biological systems. Bis(pyridyl)allenes are presented here as robust ligands for novel Pd(II), Pt(IV) and Au(III) complexes. Their synthesis, characterisation and first application as catalysts of benchmark reactions for Pd, Pt and Au are presented with interesting reactivity and selectivities. The complexes have also been probed as antimicrobial and anticancer agents with promising activities, and the first studies on their unusual interaction with several DNA structures will open new avenues for research in the area of metallodrugs with new mechanisms of action.
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Affiliation(s)
- Hanna K Maliszewska
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Carla Arnau Del Valle
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Ying Xia
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - María J Marín
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Zoë A E Waller
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,UCL School of Pharmacy, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - María Paz Muñoz
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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27
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Ruiz N, Jarosova P, Taborsky P, Gargallo R. Study of the interaction of the palmatine alkaloid with hybrid G-quadruplex/duplex and i-motif/duplex DNA structures. Biophys Chem 2021; 281:106715. [PMID: 34784553 DOI: 10.1016/j.bpc.2021.106715] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/22/2021] [Accepted: 11/04/2021] [Indexed: 11/19/2022]
Abstract
There is an increasing interest in the study of guanine or cytosine-rich sequences that may fold into G-quadruplex (G4) or i-motif (iM) structures showing a short hairpin (or stem-loop) stabilized by Watson-Crick base pairs. These hybrid spatial arrangements may be target of ligands that have been shown to interact strongly with B-DNA. In this work, the interaction of the palmatine alkaloid with several sequences forming different G4s, iMs, and hybrid structures has been studied by means of spectroscopic and separation techniques, as well as multivariate data analysis methods. At the experimental conditions used in this work, the results have shown that this ligand strongly stabilizes parallel G4 structures, whereas a weaker interaction was observed with the antiparallel G4 adopted by the thrombin-binding aptamer or iMs. The presence of hairpins within the loops scarcely affects the affinity of this ligand for the hybrid G4/duplex or iM/duplex structures. Fluorescence measurements have provided evidence of a certain interaction with iMs at pH 5.1, despite the absence of thermal stabilization effects.
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Affiliation(s)
- Noelia Ruiz
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Martí I Franqués 1-11, E-08028 Barcelona, Spain
| | - Petra Jarosova
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Petr Taborsky
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic.
| | - Raimundo Gargallo
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Martí I Franqués 1-11, E-08028 Barcelona, Spain.
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28
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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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Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
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Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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30
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Amato J, D'Aria F, Marzano S, Iaccarino N, Randazzo A, Giancola C, Pagano B. On the thermodynamics of folding of an i-motif DNA in solution under favorable conditions. Phys Chem Chem Phys 2021; 23:15030-15037. [PMID: 34151914 DOI: 10.1039/d1cp01779a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Under slightly acidic conditions, cytosine-rich DNA sequences can form non-canonical secondary structures called i-motifs, which occur as four stretches of cytosine repeats form hemi-protonated C·C+ base pairs. The growing interest in the i-motif structures as important components in functional DNA-based nanotechnology or as potential targets of anticancer drugs, increases the need for a deep understanding of the energetics of their structural transitions. Here, a combination of spectroscopic and calorimetric techniques is used to unravel the thermodynamics of folding of an i-motif DNA under favorable conditions. The results give new insights into the energetic aspects of i-motifs and show that thermodynamic and thermal stability are related but not identical properties of such DNA structures.
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Affiliation(s)
- Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
| | - Federica D'Aria
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
| | - Simona Marzano
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
| | - Nunzia Iaccarino
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
| | - Concetta Giancola
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
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31
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Sanchez-Martin V, Soriano M, Garcia-Salcedo JA. Quadruplex Ligands in Cancer Therapy. Cancers (Basel) 2021; 13:3156. [PMID: 34202648 PMCID: PMC8267697 DOI: 10.3390/cancers13133156] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/18/2021] [Accepted: 06/20/2021] [Indexed: 02/07/2023] Open
Abstract
Nucleic acids can adopt alternative secondary conformations including four-stranded structures known as quadruplexes. To date, quadruplexes have been demonstrated to exist both in human chromatin DNA and RNA. In particular, quadruplexes are found in guanine-rich sequences constituting G-quadruplexes, and in cytosine-rich sequences forming i-Motifs as a counterpart. Quadruplexes are associated with key biological processes ranging from transcription and translation of several oncogenes and tumor suppressors to telomeres maintenance and genome instability. In this context, quadruplexes have prompted investigations on their possible role in cancer biology and the evaluation of small-molecule ligands as potential therapeutic agents. This review aims to provide an updated close-up view of the literature on quadruplex ligands in cancer therapy, by grouping together ligands for DNA and RNA G-quadruplexes and DNA i-Motifs.
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Affiliation(s)
- Victoria Sanchez-Martin
- Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain;
- Microbiology Unit, Biosanitary Research Institute IBS, University Hospital Virgen de las Nieves, 18014 Granada, Spain
- Department of Biochemistry, Molecular Biology III and Immunology, University of Granada, 18016 Granada, Spain
| | - Miguel Soriano
- Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain;
- Centre for Intensive Mediterranean Agrosystems and Agri-Food Biotechnology (CIAMBITAL), University of Almeria, 04001 Almeria, Spain
| | - Jose Antonio Garcia-Salcedo
- Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain;
- Microbiology Unit, Biosanitary Research Institute IBS, University Hospital Virgen de las Nieves, 18014 Granada, Spain
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32
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Tsvetkov VB, Turaev AV, Petrunina NA, Melnik DM, Khodarovich YM, Pozmogova GE, Zatsepin TS, Varizhuk AM, Aralov AV. Phenoxazine pseudonucleotides in DNA i-motifs allow precise profiling of small molecule binders by fluorescence monitoring. Analyst 2021; 146:4436-4440. [PMID: 34132709 DOI: 10.1039/d1an00660f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The lack of high throughput screening (HTS) techniques for small molecules that stabilize DNA iMs limits their development as perspective drug candidates. Here we showed that fluorescence monitoring for probing the effects of ligands on the iM stability using the FAM-BHQ1 pair provides incorrect results due to additional dye-related interactions. We developed an alternative system with fluorescent phenoxazine pseudonucleotides in loops that do not alter iM unfolding. At the same time, the fluorescence of phenoxazine residues is sensitive to iM unfolding that enables accurate evaluation of ligand-induced changes of iM stability. Our results provide the basis for new approaches for HTS of iM ligands.
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Affiliation(s)
- Vladimir B Tsvetkov
- Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia and World-Class Research Center "Digital biodesign and personalized healthcare", Sechenov First Moscow State Medical University, 8/2 Trubetskaya Str., Moscow, 119146, Russia and A.V. Topchiev Institute of Petrochemical Synthesis RAS, Moscow, 119071, Russia
| | - Anton V Turaev
- Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Nataliia A Petrunina
- Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia and Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Denis M Melnik
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy boulevard 30b1, Moscow, 121205, Russia
| | - Yuriy M Khodarovich
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia.
| | - Galina E Pozmogova
- Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Timofei S Zatsepin
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy boulevard 30b1, Moscow, 121205, Russia and Lomonosov Moscow State University, Department of Chemistry, Leninskie Gory Str. 1-3, 119992 Moscow, Russia
| | - Anna M Varizhuk
- Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia and Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia and Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia.
| | - Andrey V Aralov
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia and Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia.
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33
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Chaudhuri R, Fatma K, Dash J. Regulation of gene expression by targeting DNA secondary structures. J CHEM SCI 2021. [DOI: 10.1007/s12039-021-01898-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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34
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Tikhomirov AS, Abdelhamid MAS, Nadysev GY, Zatonsky GV, Bykov EE, Chueh PJ, Waller ZAE, Shchekotikhin AE. Water-Soluble Heliomycin Derivatives to Target i-Motif DNA. JOURNAL OF NATURAL PRODUCTS 2021; 84:1617-1625. [PMID: 33974416 DOI: 10.1021/acs.jnatprod.1c00162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Heliomycin (also known as resistomycin) is an antibiotic with a broad spectrum of biological activities. However, low aqueous solubility and poor knowledge of its chemical properties have limited the development of this natural product. Here, we present an original scheme for the introduction of aminoalkylamine residues at positions 3, 5, and 7 of heliomycin and, using this, have prepared a series of novel water-soluble derivatives. The addition of side chains to the heliomycin scaffold significantly improves their interaction with different DNA secondary structures. One derivative, 7-deoxy-7-(2-aminoethyl)amino-10-O-methylheliomycin (8e), demonstrated affinity, stabilization potential, and good selectivity toward i-motif-forming DNA sequences over the duplex and G-quadruplex. Heliomycin derivatives therefore represent promising molecular scaffolds for further development as DNA-i-motif interacting ligands and potential chemotherapeutic agents.
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Affiliation(s)
- Alexander S Tikhomirov
- Laboratory of Chemical Transformation of Antibiotics, Gause Institute of New Antibiotics, 11 B. Pirogovskaya Street, Moscow 119021, Russia
| | | | - Georgy Y Nadysev
- Laboratory of Chemical Transformation of Antibiotics, Gause Institute of New Antibiotics, 11 B. Pirogovskaya Street, Moscow 119021, Russia
| | - George V Zatonsky
- Laboratory of Chemical Transformation of Antibiotics, Gause Institute of New Antibiotics, 11 B. Pirogovskaya Street, Moscow 119021, Russia
| | - Eugene E Bykov
- Laboratory of Chemical Transformation of Antibiotics, Gause Institute of New Antibiotics, 11 B. Pirogovskaya Street, Moscow 119021, Russia
| | - Pin Ju Chueh
- Institute of Biomedical Sciences, National Chung Hsing University, Taichung, Taiwan, Republic of China
| | - Zoë A E Waller
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Andrey E Shchekotikhin
- Laboratory of Chemical Transformation of Antibiotics, Gause Institute of New Antibiotics, 11 B. Pirogovskaya Street, Moscow 119021, Russia
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Iaccarino N, Cheng M, Qiu D, Pagano B, Amato J, Di Porzio A, Zhou J, Randazzo A, Mergny J. Effects of Sequence and Base Composition on the CD and TDS Profiles of i‐DNA. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Nunzia Iaccarino
- Department of Pharmacy University of Naples Federico II Via D. Montesano 49 80131 Naples Italy
| | - Mingpan Cheng
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry & Chemical Engineering Nanjing University Nanjing 210023 China
- ARNA Laboratory Université de Bordeaux Inserm U 1212, CNRS UMR5320 IECB 33607 Pessac France
| | - Dehui Qiu
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry & Chemical Engineering Nanjing University Nanjing 210023 China
| | - Bruno Pagano
- Department of Pharmacy University of Naples Federico II Via D. Montesano 49 80131 Naples Italy
| | - Jussara Amato
- Department of Pharmacy University of Naples Federico II Via D. Montesano 49 80131 Naples Italy
| | - Anna Di Porzio
- Department of Pharmacy University of Naples Federico II Via D. Montesano 49 80131 Naples Italy
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry & Chemical Engineering Nanjing University Nanjing 210023 China
| | - Antonio Randazzo
- Department of Pharmacy University of Naples Federico II Via D. Montesano 49 80131 Naples Italy
| | - Jean‐Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry & Chemical Engineering Nanjing University Nanjing 210023 China
- ARNA Laboratory Université de Bordeaux Inserm U 1212, CNRS UMR5320 IECB 33607 Pessac France
- Laboratoire d'Optique et Biosciences Ecole Polytechnique CNRS INSERM Institut Polytechnique de Paris 91128 Palaiseau France
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36
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Iaccarino N, Cheng M, Qiu D, Pagano B, Amato J, Di Porzio A, Zhou J, Randazzo A, Mergny J. Effects of Sequence and Base Composition on the CD and TDS Profiles of i-DNA. Angew Chem Int Ed Engl 2021; 60:10295-10303. [PMID: 33617090 PMCID: PMC8251954 DOI: 10.1002/anie.202016822] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Indexed: 12/19/2022]
Abstract
The i-motif DNA, also known as i-DNA, is a non-canonical DNA secondary structure formed by cytosine-rich sequences, consisting of two intercalated parallel-stranded duplexes held together by hemi-protonated cytosine-cytosine+ (C:C+ ) base pairs. The growing interest in the i-DNA structure as a target in anticancer therapy increases the need for tools for a rapid and meaningful interpretation of the spectroscopic data of i-DNA samples. Herein, we analyzed the circular dichroism (CD) and thermal difference UV-absorbance spectra (TDS) of 255 DNA sequences by means of multivariate data analysis, aiming at unveiling peculiar spectral regions that could be used as diagnostic features during the analysis of i-DNA-forming sequences.
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Affiliation(s)
- Nunzia Iaccarino
- Department of PharmacyUniversity of Naples Federico IIVia D. Montesano 4980131NaplesItaly
| | - Mingpan Cheng
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry & Chemical EngineeringNanjing UniversityNanjing210023China
- ARNA LaboratoryUniversité de BordeauxInserm U 1212, CNRS UMR5320IECB33607PessacFrance
| | - Dehui Qiu
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry & Chemical EngineeringNanjing UniversityNanjing210023China
| | - Bruno Pagano
- Department of PharmacyUniversity of Naples Federico IIVia D. Montesano 4980131NaplesItaly
| | - Jussara Amato
- Department of PharmacyUniversity of Naples Federico IIVia D. Montesano 4980131NaplesItaly
| | - Anna Di Porzio
- Department of PharmacyUniversity of Naples Federico IIVia D. Montesano 4980131NaplesItaly
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry & Chemical EngineeringNanjing UniversityNanjing210023China
| | - Antonio Randazzo
- Department of PharmacyUniversity of Naples Federico IIVia D. Montesano 4980131NaplesItaly
| | - Jean‐Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life ScienceSchool of Chemistry & Chemical EngineeringNanjing UniversityNanjing210023China
- ARNA LaboratoryUniversité de BordeauxInserm U 1212, CNRS UMR5320IECB33607PessacFrance
- Laboratoire d'Optique et BiosciencesEcole PolytechniqueCNRSINSERMInstitut Polytechnique de Paris91128PalaiseauFrance
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37
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Gargallo R, Aviñó A, Eritja R, Jarosova P, Mazzini S, Scaglioni L, Taborsky P. Study of alkaloid berberine and its interaction with the human telomeric i-motif DNA structure. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 248:119185. [PMID: 33234477 DOI: 10.1016/j.saa.2020.119185] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/30/2020] [Accepted: 11/01/2020] [Indexed: 06/11/2023]
Abstract
The alkaloid berberine presents many biological activities related to its potential to bind DNA structures, such as duplex or G-quadruplex. Recently, it has been proposed that berberine may interact with i-motif structures formed from the folding of cytosine-rich sequences. In the present work, the interaction of this alkaloid with the i-motif formed by the human telomere cytosine-rich sequence, as well as with several positive and negative controls, has been studied. Molecular fluorescence and circular dichroism spectroscopies, as well as nuclear magnetic resonance spectrometry and competitive dialysis, have been used with this purpose. The results shown here reveal that the interaction of berberine with this i-motif is weak, mostly electrostatics in nature and takes place with bases not involved in C·C+ base pairs. Moreover, this ligand is not selective for i-motif structures, as binds equally to both, folded structure, and unfolded strand, without producing any stabilization of the i-motif. As a conclusion, the development of analytical methods based on the interaction of fluorescent ligands, such as berberine, with i-motif structures should consider the thermodynamic aspects related with the interaction, as well as the selectivity of the proposed ligands with different DNA structures, including unfolded strands.
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Affiliation(s)
- R Gargallo
- Dept. of Chemical Engineering and Analytical Chemistry, University of Barcelona, Marti i Franquès 1, E-08028 Barcelona, Spain.
| | - A Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), CIBER-BBN, Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - R Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), CIBER-BBN, Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - P Jarosova
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - S Mazzini
- Department of Food, Environmental and Nutritional Sciences (DEFENS), Section of Chemical and Biomolecular Sciences, University of Milan, Via Celoria 2, 20133 Milan, Italy
| | - L Scaglioni
- Department of Food, Environmental and Nutritional Sciences (DEFENS), Section of Chemical and Biomolecular Sciences, University of Milan, Via Celoria 2, 20133 Milan, Italy
| | - P Taborsky
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic.
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Kosiol N, Juranek S, Brossart P, Heine A, Paeschke K. G-quadruplexes: a promising target for cancer therapy. Mol Cancer 2021; 20:40. [PMID: 33632214 PMCID: PMC7905668 DOI: 10.1186/s12943-021-01328-4] [Citation(s) in RCA: 215] [Impact Index Per Article: 71.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/01/2021] [Indexed: 12/13/2022] Open
Abstract
DNA and RNA can fold into a variety of alternative conformations. In recent years, a particular nucleic acid structure was discussed to play a role in malignant transformation and cancer development. This structure is called a G-quadruplex (G4). G4 structure formation can drive genome instability by creating mutations, deletions and stimulating recombination events. The importance of G4 structures in the characterization of malignant cells was currently demonstrated in breast cancer samples. In this analysis a correlation between G4 structure formation and an increased intratumor heterogeneity was identified. This suggests that G4 structures might allow breast cancer stratification and supports the identification of new personalized treatment options. Because of the stability of G4 structures and their presence within most human oncogenic promoters and at telomeres, G4 structures are currently tested as a therapeutic target to downregulate transcription or to block telomere elongation in cancer cells. To date, different chemical molecules (G4 ligands) have been developed that aim to target G4 structures. In this review we discuss and compare G4 function and relevance for therapeutic approaches and their impact on cancer development for three cancer entities, which differ significantly in their amount and type of mutations: pancreatic cancer, leukemia and malignant melanoma. G4 structures might present a promising new strategy to individually target tumor cells and could support personalized treatment approaches in the future.
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Affiliation(s)
- Nils Kosiol
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127, Bonn, Germany
| | - Stefan Juranek
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127, Bonn, Germany
| | - Peter Brossart
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127, Bonn, Germany
| | - Annkristin Heine
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127, Bonn, Germany
| | - Katrin Paeschke
- Department of Oncology, Hematology, Rheumatology and Immune-Oncology, University Hospital Bonn, 53127, Bonn, Germany.
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Sengupta P, Bose D, Chatterjee S. The Molecular Tête-à-Tête between G-Quadruplexes and the i-motif in the Human Genome. Chembiochem 2021; 22:1517-1537. [PMID: 33355980 DOI: 10.1002/cbic.202000703] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/16/2020] [Indexed: 12/22/2022]
Abstract
G-Quadruplex (GQ) and i-motif structures are the paradigmatic examples of nonclassical tetrastranded nucleic acids having multifarious biological functions and widespread applications in therapeutics and material science. Recently, tetraplexes emerged as promising anticancer targets due to their structural robustness, gene-regulatory roles, and predominant distribution at specific loci of oncogenes. However, it is arguable whether the i-motif evolves in the complementary single-stranded region after GQ formation in its opposite strand and vice versa. In this review, we address the prerequisites and significance of the simultaneous and/or mutually exclusive formation of GQ and i-motif structures at complementary and sequential positions in duplexes in the cellular milieu. We discussed how their dynamic interplay Sets up cellular homeostasis and exacerbates carcinogenesis. The review gives insights into the spatiotemporal formation of GQ and i-motifs that could be harnessed to design different types of reporter systems and diagnostic platforms for potential bioanalytical and therapeutic intervention.
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Affiliation(s)
- Pallabi Sengupta
- Department of Biophysics, Bose Institute, Centenary Campus, P-1/12, C.I.T. Scheme VIIM, Kankurgachi, Kolkata, 700054, West Bengal, India
| | - Debopriya Bose
- Department of Biophysics, Bose Institute, Centenary Campus, P-1/12, C.I.T. Scheme VIIM, Kankurgachi, Kolkata, 700054, West Bengal, India
| | - Subhrangsu Chatterjee
- Department of Biophysics, Bose Institute, Centenary Campus, P-1/12, C.I.T. Scheme VIIM, Kankurgachi, Kolkata, 700054, West Bengal, India
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Brown SL, Kendrick S. The i-Motif as a Molecular Target: More Than a Complementary DNA Secondary Structure. Pharmaceuticals (Basel) 2021; 14:ph14020096. [PMID: 33513764 PMCID: PMC7911047 DOI: 10.3390/ph14020096] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/20/2021] [Accepted: 01/22/2021] [Indexed: 12/25/2022] Open
Abstract
Stretches of cytosine-rich DNA are capable of adopting a dynamic secondary structure, the i-motif. When within promoter regions, the i-motif has the potential to act as a molecular switch for controlling gene expression. However, i-motif structures in genomic areas of repetitive nucleotide sequences may play a role in facilitating or hindering expansion of these DNA elements. Despite research on the i-motif trailing behind the complementary G-quadruplex structure, recent discoveries including the identification of a specific i-motif antibody are pushing this field forward. This perspective reviews initial and current work characterizing the i-motif and providing insight into the biological function of this DNA structure, with a focus on how the i-motif can serve as a molecular target for developing new therapeutic approaches to modulate gene expression and extension of repetitive DNA.
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41
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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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42
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Miglietta G, Russo M, Capranico G. G-quadruplex-R-loop interactions and the mechanism of anticancer G-quadruplex binders. Nucleic Acids Res 2020; 48:11942-11957. [PMID: 33137181 PMCID: PMC7708042 DOI: 10.1093/nar/gkaa944] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/05/2020] [Accepted: 10/08/2020] [Indexed: 12/17/2022] Open
Abstract
Genomic DNA and cellular RNAs can form a variety of non-B secondary structures, including G-quadruplex (G4) and R-loops. G4s are constituted by stacked guanine tetrads held together by Hoogsteen hydrogen bonds and can form at key regulatory sites of eukaryote genomes and transcripts, including gene promoters, untranslated exon regions and telomeres. R-loops are 3-stranded structures wherein the two strands of a DNA duplex are melted and one of them is annealed to an RNA. Specific G4 binders are intensively investigated to discover new effective anticancer drugs based on a common rationale, i.e.: the selective inhibition of oncogene expression or specific impairment of telomere maintenance. However, despite the high number of known G4 binders, such a selective molecular activity has not been fully established and several published data point to a different mode of action. We will review published data that address the close structural interplay between G4s and R-loops in vitro and in vivo, and how these interactions can have functional consequences in relation to G4 binder activity. We propose that R-loops can play a previously-underestimated role in G4 binder action, in relation to DNA damage induction, telomere maintenance, genome and epigenome instability and alterations of gene expression programs.
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Affiliation(s)
- Giulia Miglietta
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126 Bologna, Italy
| | - Marco Russo
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126 Bologna, Italy
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126 Bologna, Italy
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43
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Sanchez-Martin V, Lopez-Pujante C, Soriano-Rodriguez M, Garcia-Salcedo JA. An Updated Focus on Quadruplex Structures as Potential Therapeutic Targets in Cancer. Int J Mol Sci 2020; 21:ijms21238900. [PMID: 33255335 PMCID: PMC7734589 DOI: 10.3390/ijms21238900] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/13/2020] [Accepted: 11/20/2020] [Indexed: 02/06/2023] Open
Abstract
Non-canonical, four-stranded nucleic acids secondary structures are present within regulatory regions in the human genome and transcriptome. To date, these quadruplex structures include both DNA and RNA G-quadruplexes, formed in guanine-rich sequences, and i-Motifs, found in cytosine-rich sequences, as their counterparts. Quadruplexes have been extensively associated with cancer, playing an important role in telomere maintenance and control of genetic expression of several oncogenes and tumor suppressors. Therefore, quadruplex structures are considered attractive molecular targets for cancer therapeutics with novel mechanisms of action. In this review, we provide a general overview about recent research on the implications of quadruplex structures in cancer, firstly gathering together DNA G-quadruplexes, RNA G-quadruplexes as well as DNA i-Motifs.
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Affiliation(s)
- Victoria Sanchez-Martin
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016 Granada, Spain; (V.S.-M.); (C.L.-P.)
- Microbiology Unit, University Hospital Virgen de las Nieves, Biosanitary Research Institute IBS, Granada, 18014 Granada, Spain
- Department of Biochemistry, Molecular Biology III and Immunology, University of Granada, 18016 Granada, Spain
| | - Carmen Lopez-Pujante
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016 Granada, Spain; (V.S.-M.); (C.L.-P.)
| | - Miguel Soriano-Rodriguez
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016 Granada, Spain; (V.S.-M.); (C.L.-P.)
- Centre for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAMBITAL), University of Almeria, 04001 Almeria, Spain
- Correspondence: (M.S.-R.); (J.A.G.-S.); Tel.: +34-958715500 (M.S.-R.); +34-958715500 (J.A.G.-S.)
| | - Jose A. Garcia-Salcedo
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016 Granada, Spain; (V.S.-M.); (C.L.-P.)
- Microbiology Unit, University Hospital Virgen de las Nieves, Biosanitary Research Institute IBS, Granada, 18014 Granada, Spain
- Correspondence: (M.S.-R.); (J.A.G.-S.); Tel.: +34-958715500 (M.S.-R.); +34-958715500 (J.A.G.-S.)
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44
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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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45
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Thorne BN, Ellenbroek BA, Day DJ. Evaluation of i-Motif Formation in the Serotonin Transporter-Linked Polymorphic Region. Chembiochem 2020; 22:349-353. [PMID: 32840058 DOI: 10.1002/cbic.202000513] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 08/23/2020] [Indexed: 01/30/2023]
Abstract
Neuropsychiatric disorders such as major depressive disorder (MDD) arise from a complex set of genetic and environmental factors. The serotonin transporter (SERT) is a key regulator of synaptic serotonin (5-HT), and its inhibition is an important pharmacological target for treating MDD. The SERT-linked polymorphic region (5-HTTLPR) contains two major variants (short and long) that have been implicated in modulating susceptibility to MDD by altering the level of expression of SERT. Both variants contain C-rich repeats that conform to consensus i-motif folding sequences. i-Motifs are quadruplex DNA structures that have been proposed to have a role in transcription regulation. With spectroscopic techniques, we demonstrate that both alleles are able to form i-motifs at acidic pH, and at neutral pH under conditions of molecular crowding. This highlights the potential for i-motif formation to contribute to transcriptional regulation of the serotonin transporter, with a potential role in the pathophysiology of neuropsychiatric disorders.
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Affiliation(s)
- Bryony N Thorne
- School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Wellington, 6012, New Zealand
| | - Bart A Ellenbroek
- School of Psychology, Victoria University of Wellington, Faculty of Science, Wellington, 6012, New Zealand
| | - Darren J Day
- School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Wellington, 6012, New Zealand
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46
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Baranowski MR, Warminski M, Jemielity J, Kowalska J. 5'-fluoro(di)phosphate-labeled oligonucleotides are versatile molecular probes for studying nucleic acid secondary structure and interactions by 19F NMR. Nucleic Acids Res 2020; 48:8209-8224. [PMID: 32514551 PMCID: PMC7470941 DOI: 10.1093/nar/gkaa470] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/19/2020] [Accepted: 05/22/2020] [Indexed: 01/03/2023] Open
Abstract
The high sensitivity of 19F nucleus to changes in the chemical environment has promoted the use of fluorine-labeled molecular probes to study structure and interactions of nucleic acids by 19F NMR. So far, most efforts have focused on incorporating the fluorine atom into nucleobase and ribose moieties using either monomer building blocks for solid-phase synthesis, or nucleoside triphosphates for enzymatic synthesis. Here, we report a simple and efficient synthesis of 5'-fluoromonophosphorylated and 5'-fluorodiphosphorylated oligodeoxyribonucleotides, which combines solid-phase and in-solution synthesis methods and requires only commercially available nucleoside phosphoramidites, followed by their evaluation as 19F NMR probes. We confirmed that the fluorine atom at the oligonucleotide 5' end did not alter the secondary structure of DNA fragments. Moreover, at the same time, it enabled real-time 19F NMR monitoring of various DNA-related biophysical processes, such as oligonucleotide hybridization (including mismatch identification), G-quadruplex folding/unfolding and its interactions with thrombin, as well as formation of an i-motif structure and its interaction with small-molecule ligands.
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Affiliation(s)
- Marek R Baranowski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Ludwika Pasteura 5, 02-093 Warsaw, Poland
| | - Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Ludwika Pasteura 5, 02-093 Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Stefana Banacha 2c, 02-097 Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Ludwika Pasteura 5, 02-093 Warsaw, Poland
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47
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Školáková P, Badri Z, Foldynová-Trantírková S, Ryneš J, Šponer J, Fojtová M, Fajkus J, Marek R, Vorlíčková M, Mergny JL, Trantírek L. Composite 5-methylations of cytosines modulate i-motif stability in a sequence-specific manner: Implications for DNA nanotechnology and epigenetic regulation of plant telomeric DNA. Biochim Biophys Acta Gen Subj 2020; 1864:129651. [DOI: 10.1016/j.bbagen.2020.129651] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/23/2020] [Accepted: 05/28/2020] [Indexed: 12/14/2022]
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48
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Maleki P, Mustafa G, Gyawali P, Budhathoki JB, Ma Y, Nagasawa K, Balci H. Quantifying the impact of small molecule ligands on G-quadruplex stability against Bloom helicase. Nucleic Acids Res 2020; 47:10744-10753. [PMID: 31544934 PMCID: PMC6847008 DOI: 10.1093/nar/gkz803] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 08/28/2019] [Accepted: 09/09/2019] [Indexed: 01/28/2023] Open
Abstract
G-quadruplex (GQ) stabilizing small molecule (SM) ligands have been used to stabilize human telomeric GQ (hGQ) to inhibit telomerase activity, or non-telomeric GQs to manipulate gene expression at transcription or translation level. GQs are known to inhibit DNA replication unless destabilized by helicases, such as Bloom helicase (BLM). Even though the impact of SM ligands on thermal stability of GQs is commonly used to characterize their efficacy, how these ligands influence helicase-mediated GQ unfolding is not well understood. Three prominent SM ligands (an oxazole telomestatin derivative, pyridostatin, and PhenDC3), which thermally stabilize hGQ at different levels, were utilized in this study. How these ligands influence BLM-mediated hGQ unfolding was investigated using two independent single-molecule approaches. While the frequency of dynamic hGQ unfolding events was used as the metric in the first approach, the second approach was based on quantifying the cumulative unfolding activity as a function of time. All three SM ligands inhibited BLM activity at similar levels, 2–3 fold, in both approaches. Our observations suggest that the impact of SM ligands on GQ thermal stability is not an ideal predictor for their inhibition of helicase-mediated unfolding, which is physiologically more relevant.
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Affiliation(s)
- Parastoo Maleki
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | - Golam Mustafa
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | - Prabesh Gyawali
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | | | - Yue Ma
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH 44242, USA
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Di Fonzo S, Amato J, D'Aria F, Caterino M, D'Amico F, Gessini A, Brady JW, Cesàro A, Pagano B, Giancola C. Ligand binding to G-quadruplex DNA: new insights from ultraviolet resonance Raman spectroscopy. Phys Chem Chem Phys 2020; 22:8128-8140. [PMID: 32246758 DOI: 10.1039/d0cp01022g] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
G-Quadruplexes (G4s) are noncanonical nucleic acid structures involved in the regulation of several biological processes of many organisms. The rational design of G4-targeting molecules developed as potential anticancer and antiviral therapeutics is a complex problem intrinsically due to the structural polymorphism of these peculiar DNA structures. The aim of the present work is to show how Ultraviolet Resonance Raman (UVRR) spectroscopy can complement other techniques in providing valuable information about ligand/G4 interactions in solution. Here, the binding of BRACO-19 and Pyridostatin - two of the most potent ligands - to selected biologically relevant G4s was investigated by polarized UVRR scattering at 266 nm. The results give new insights into the binding mode of these ligands to G4s having different sequences and topologies by performing an accurate analysis of peaks assigned to specific groups and their changes upon binding. Indeed, the UVRR data not only show that BRACO-19 and Pyridostatin interact with different G4 sites, but also shed light on the ligand and G4 chemical groups really involved in the interaction. In addition, UVRR results complemented by circular dichroism data clearly indicate that the binding mode of a ligand can also depend on the conformation(s) of the target G4. Overall, these findings demonstrate the utility of using UVRR spectroscopy in the investigation of G4s and G4-ligand interactions in solution.
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Affiliation(s)
- Silvia Di Fonzo
- Elettra-Sincrotrone Trieste S. C. p. A., Science Park, Trieste, I-34149, Italy.
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
| | - Federica D'Aria
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
| | - Marco Caterino
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
| | - Francesco D'Amico
- Elettra-Sincrotrone Trieste S. C. p. A., Science Park, Trieste, I-34149, Italy.
| | - Alessandro Gessini
- Elettra-Sincrotrone Trieste S. C. p. A., Science Park, Trieste, I-34149, Italy.
| | - John W Brady
- Department of Food Science, Cornell University, Ithaca, New York, NY 14853, USA
| | - Attilio Cesàro
- Elettra-Sincrotrone Trieste S. C. p. A., Science Park, Trieste, I-34149, Italy. and Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, I-34127, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
| | - Concetta Giancola
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
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50
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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
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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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