{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,19]],"date-time":"2025-10-19T06:11:11Z","timestamp":1760854271131,"version":"build-2065373602"},"reference-count":28,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2022,2,18]],"date-time":"2022-02-18T00:00:00Z","timestamp":1645142400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Applied Sciences"],"abstract":"<jats:p>In the last decade, progress has been made in G-quadruplex (G4) ligands development, but for most compounds, the ligand binding mode is speculative or based on low resolution methods, with its discovery based on structure-based approaches. Herein, we report the synthesis of small (MW &lt; 400 Da) heterocycle compounds, containing different aromatic scaffolds, such as phenyl, quinoline, naphthalene, phenanthroline and acridine moieties, in order to explore their stabilization effect towards different DNA G4s, such as those found in c-MYC, KRAS21 and VEGF promoters, 21G human telomeric motif and pre-MIR150. The fluorescence resonance energy transfer (FRET) melting assay indicates that the acridine moiety is the most active scaffold, followed by phenanthroline. The different scaffolds are promising in terms of drug-like properties and, in general, the IC50 values of the respective heterocycle compounds are lower in a cancer cell line, when compared with a normal cell line. The acridine derivative C5NH2 has the most favorable cytotoxic profile in terms of cell selectivity.<\/jats:p>","DOI":"10.3390\/app12042170","type":"journal-article","created":{"date-parts":[[2022,2,21]],"date-time":"2022-02-21T08:14:46Z","timestamp":1645431286000},"page":"2170","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Screening of Scaffolds for the Design of G-Quadruplex Ligands"],"prefix":"10.3390","volume":"12","author":[{"given":"Joana","family":"Figueiredo","sequence":"first","affiliation":[{"name":"Centro de Investiga\u00e7\u00e3o em Ci\u00eancias da Sa\u00fade, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilh\u00e3, Portugal"}]},{"given":"David","family":"Peitinho","sequence":"additional","affiliation":[{"name":"Centro de Ci\u00eancias e Tecnologias Nucleares, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Estrada Nacional 10 (km 139.7), 2695-066 Bobadela, Portugal"}]},{"given":"Maria Paula Cabral","family":"Campello","sequence":"additional","affiliation":[{"name":"Centro de Ci\u00eancias e Tecnologias Nucleares, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Estrada Nacional 10 (km 139.7), 2695-066 Bobadela, Portugal"}]},{"given":"Maria Cristina","family":"Oliveira","sequence":"additional","affiliation":[{"name":"Centro de Ci\u00eancias e Tecnologias Nucleares, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Estrada Nacional 10 (km 139.7), 2695-066 Bobadela, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9164-0913","authenticated-orcid":false,"given":"Ant\u00f3nio","family":"Paulo","sequence":"additional","affiliation":[{"name":"Centro de Ci\u00eancias e Tecnologias Nucleares, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Estrada Nacional 10 (km 139.7), 2695-066 Bobadela, Portugal"}]},{"given":"Jean-Louis","family":"Mergny","sequence":"additional","affiliation":[{"name":"Institute of Biophysics of the CAS, v.v.i., Kr\u00e1lovopolsk\u00e1 135, 612 65 Brno, Czech Republic"},{"name":"Laboratoire d\u2019Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6630-1242","authenticated-orcid":false,"given":"Carla","family":"Cruz","sequence":"additional","affiliation":[{"name":"Centro de Investiga\u00e7\u00e3o em Ci\u00eancias da Sa\u00fade, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilh\u00e3, Portugal"}]}],"member":"1968","published-online":{"date-parts":[[2022,2,18]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Figueiredo, J., Santos, T., Miranda, A., Alexandre, D., Teixeira, B., Sim\u00f5es, P., Lopes-Nunes, J., and Cruz, C. (2021). Ligands as Stabilizers of G-Quadruplexes in Non-Coding RNAs. Molecules, 26.","DOI":"10.3390\/molecules26206164"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1124\/pharmrev.120.000230","article-title":"Unlocking G-Quadruplexes as Antiviral Targets","volume":"73","author":"Abiri","year":"2021","journal-title":"Pharmacol. Rev."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"2113","DOI":"10.1021\/jm970199z","article-title":"Inhibition of human telomerase by a G-Quadruplex-Interactive compound","volume":"40","author":"Sun","year":"1997","journal-title":"J. Med. Chem."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"3261","DOI":"10.1021\/ja973792e","article-title":"Cationic porphyrins as telomerase inhibitors: The interaction of tetra-(N-methyl-4-pyridyl)porphine with quadruplex DNA","volume":"120","author":"Wheelhouse","year":"1998","journal-title":"J. Am. Chem. Soc."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"15425","DOI":"10.1021\/bi9913808","article-title":"Cationic 5,10,15,20-Tetrakis(N-methylpyridinium-4-yl)porphyrin Fully Intercalates at 5\u2032-CG-3\u2032 Steps of Duplex DNA in Solution","volume":"38","author":"Guliaev","year":"1999","journal-title":"Biochemistry"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"8106","DOI":"10.1021\/ja034499j","article-title":"Binding of meso-Tetrakis(N-methylpyridium-4-yl)porphyrin to Triplex Oligonucleotides: Evidence for the Porphyrin Stacking in the Major Groove","volume":"125","author":"Lee","year":"2003","journal-title":"J. Am. Chem. Soc."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"2098","DOI":"10.1021\/ja017308q","article-title":"Telomestatin, a potent telomerase inhibitor that interacts quite specifically with the human telomeric intramolecular G-quadruplex","volume":"124","author":"Kim","year":"2002","journal-title":"J. Am. Chem. Soc."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1707","DOI":"10.1016\/j.bmcl.2005.12.001","article-title":"Natural and synthetic G-quadruplex interactive berberine derivatives","volume":"16","author":"Franceschin","year":"2006","journal-title":"Bioorg. Med. Chem. Lett."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1038\/nbt.3295","article-title":"High-throughput sequencing of DNA G-quadruplex structures in the human genome","volume":"33","author":"Chambers","year":"2015","journal-title":"Nat. Biotechnol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"14432","DOI":"10.1038\/ncomms14432","article-title":"CX-5461 is a DNA G-quadruplex stabilizer with selective lethality in BRCA1\/2 deficient tumours","volume":"8","author":"Xu","year":"2017","journal-title":"Nat. Commun."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1418","DOI":"10.1158\/0008-5472.CAN-10-1728","article-title":"Targeting RNA Polymerase I with an Oral Small Molecule CX-5461 Inhibits Ribosomal RNA Synthesis and Solid Tumor Growth","volume":"71","author":"Drygin","year":"2011","journal-title":"Cancer Res."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Das, R., Chevret, E., Desplat, V., Rubio, S., Mergny, J.-L., and Guillon, J. (2017). Design, Synthesis and Biological Evaluation of New Substituted Diquinolinyl-Pyridine Ligands as Anticancer Agents by Targeting G-Quadruplex. Molecules, 23.","DOI":"10.3390\/molecules23010081"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"8745","DOI":"10.1002\/anie.201103422","article-title":"An Acyclic Oligoheteroaryle That Discriminates Strongly between Diverse G-Quadruplex Topologies","volume":"50","author":"Hamon","year":"2011","journal-title":"Angew. Chem. Int. Ed."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1016\/j.biochi.2015.06.002","article-title":"Assessment of selectivity of G-quadruplex ligands via an optimised FRET melting assay","volume":"115","author":"Mergny","year":"2015","journal-title":"Biochimie"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1281","DOI":"10.1016\/j.bbagen.2016.11.024","article-title":"Phenanthroline-bis-oxazole ligands for binding and stabilization of G-quadruplexes","volume":"1861","author":"Salgado","year":"2017","journal-title":"Biochim. Biophys. Acta Gen. Subj."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"6114","DOI":"10.1021\/ic049694t","article-title":"Synthesis and H+, Cu2+, and Zn2+ Coordination Behavior of a Bis(fluorophoric) Bibrachial Lariat Aza-Crown","volume":"43","author":"Clares","year":"2004","journal-title":"Inorg. Chem."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1270","DOI":"10.1016\/j.cclet.2010.05.030","article-title":"A new and convenient synthesis of phendiones oxidated by KBrO3\/H2SO4 at room temperature","volume":"21","author":"Zheng","year":"2010","journal-title":"Chin. Chem. Lett."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1002\/jhet.5570370125","article-title":"Synthesis of some novel derivatives of 1,10-phenanthroline","volume":"37","author":"Garas","year":"2000","journal-title":"J. Heterocycl. Chem."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"15270","DOI":"10.1021\/acs.inorgchem.8b02564","article-title":"Development of the Smartphone-Assisted Colorimetric Detection of Thorium by Using New Schiff\u2019s Base and Its Applications to Real Time Samples","volume":"57","author":"R","year":"2018","journal-title":"Inorg. Chem."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"42544","DOI":"10.1038\/srep42544","article-title":"Evaluation of Acridine Orange Derivatives as DNA-Targeted Radiopharmaceuticals for Auger Therapy: Influence of the Radionuclide and Distance to DNA","volume":"7","author":"Pereira","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"4066","DOI":"10.1021\/acs.jmedchem.5b00104","article-title":"pkCSM: Predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures","volume":"58","author":"Pires","year":"2015","journal-title":"J. Med. Chem."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"D1115","DOI":"10.1093\/nar\/gks1101","article-title":"G4LDB: A database for discovering and studying G-quadruplex ligands","volume":"41","author":"Li","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1016\/S1056-8719(00)00107-6","article-title":"Drug-like properties and the causes of poor solubility and poor permeability","volume":"44","author":"Lipinski","year":"2000","journal-title":"J. Pharmacol. Toxicol. Methods"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"2615","DOI":"10.1021\/jm020017n","article-title":"Molecular properties that influence the oral bioavailability of drug candidates","volume":"45","author":"Veber","year":"2002","journal-title":"J. Med. Chem."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/j.ymeth.2006.10.004","article-title":"Fluorescence-based melting assays for studying quadruplex ligands","volume":"42","author":"Guittat","year":"2007","journal-title":"Methods"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"114418","DOI":"10.1016\/j.bcp.2021.114418","article-title":"Targeting nucleolin by RNA G-quadruplex-forming motif","volume":"189","author":"Figueiredo","year":"2021","journal-title":"Biochem. Pharmacol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1016\/j.biochi.2017.11.004","article-title":"Fluorescent light-up acridine orange derivatives bind and stabilize KRAS-22RT G-quadruplex","volume":"144","author":"Carvalho","year":"2018","journal-title":"Biochimie"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"114208","DOI":"10.1016\/j.bcp.2020.114208","article-title":"Recognition of nucleolin through interaction with RNA G-quadruplex","volume":"189","author":"Santos","year":"2021","journal-title":"Biochem. Pharmacol."}],"container-title":["Applied Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-3417\/12\/4\/2170\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T22:22:52Z","timestamp":1760134972000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-3417\/12\/4\/2170"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,2,18]]},"references-count":28,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2022,2]]}},"alternative-id":["app12042170"],"URL":"https:\/\/doi.org\/10.3390\/app12042170","relation":{},"ISSN":["2076-3417"],"issn-type":[{"type":"electronic","value":"2076-3417"}],"subject":[],"published":{"date-parts":[[2022,2,18]]}}}