Herein, we report, for the first time, the screening of several ligands in terms of their ability to bind and stabilize G-quadruplexes (G4) found in seven human Papillomavirus (HPV) genomes. Using a variety of biophysical assays, HPV G-quadruplexes were shown to possess a high degree of structural polymorphism upon ligand binding, which may have an impact on transcription, replication, and viral protein production. A sequence found in high-risk HPV16 genotype folds into multiple non-canonical DNA structures; it was converted into a major G4 conformation upon interaction with a well-characterized highly selective G4 ligand, PhenDC3, which may have an impact on the viral infection. Likewise, HPV57 and 58, which fold into multiple G4 structures, were found to form single stable complexes in the presence of two other G4 ligands, C8 and pyridostatin, respectively. In addition, one of the selected compounds, the acridine derivative C8, demonstrated a significant antiviral effect in HPV18-infected organotypic raft cultures. Altogether, these results indicate that targeting HPV G4s may be an alternative route for the development of novel antiviral therapies.
Get full access to this article
View all access options for this article.
References
1.
SchiffmanM, DoorbarJ, WentzensenN, De SanjoséS, FakhryC, MonkBJ, StanleyMA and Franceschi.S (2016). Carcinogenic human papillomavirus infection. Nat Rev Dis Primers, 2:16086.
2.
MarušičM, HošnjakL, KrafčikovaP, PoljakM, ViglaskyV and PlavecJ. (2017). The effect of single nucleotide polymorphisms in G-rich regions of high-risk human papillomaviruses on structural diversity of DNA. Biochim Biophys Acta, 1861:1229–1236.
3.
EdwardsTG, KoellerKJ, SlomczynskaU, FokK, HelmusM, BashkinJK and FisherC. (2011). HPV episome levels are potently decreased by pyrrole–imidazole polyamides. Antivir Res, 91:177–186.
4.
BiryukovJ, and CMeyers. (2015). Papillomavirus infectious pathways: a comparison of systems. Viruses, 7:4303–4325.
5.
AsamitsuS, ObataS, YuZ, BandoT and H.Sugiyama (2019). Recent progress of targeted G-quadruplex-preferred ligands toward cancer therapy. Molecules, 24:429.
6.
NeidleS. (2016). Quadruplex nucleic acids as novel therapeutic targets. J Med Chem, 59:5987–6011.
7.
GonzálezV, GuoK, HurleyL and DSun. (2009). Identification and Characterization of Nucleolin as a c- myc G-quadruplex-binding Protein. J Biol Chem, 284:23622–23635.
8.
TosoniE, FrassonI, ScalabrinM, PerroneR, ButovskayaE, NadaiM, PalùG., FabrisD and RichterSN. (2015). Nucleolin stabilizes G-quadruplex structures folded by the LTR promoter and silences HIV-1 viral transcription. Nucleic Acids Res, 43:8884–8897.
9.
ButovskayaE, SoldàP, ScalabrinM, NadaiM and RichterSN. (2019). HIV-1 Nucleocapsid Protein Unfolds Stable RNA G-Quadruplexes in the Viral Genome and Is Inhibited by G-Quadruplex Ligands. ACS Infect Dis, 5:2127–2135.
10.
RuggieroE, and RichterSN. (2018). G-quadruplexes and G-quadruplex ligands: targets and tools in antiviral therapy. Nucleic Acids Res, 46:3270–3283.
11.
MetifiotM, AmraneS, LitvakS and M.-LAndreola. (2014). G-quadruplexes in viruses: function and potential therapeutic applications. Nucleic Acids Res, 42:12352–12366.
12.
FlemingAM, DingY, AlenkoA and BurrowsCJ. (2016). Zika virus genomic RNA possesses conserved G-quadruplexes characteristic of the flaviviridae family. ACS Infect Dis, 2:674–681.
13.
RuggieroE, TassinariM, PerroneR, NadaiM and RichterSN. (2019). Stable and conserved G-quadruplexes in the long terminal repeat promoter of retroviruses. ACS Infect Dis, 5:1150–1159.
14.
BiswasB, KumariP and PVivekanandan. (2018). Pac1 signals of human herpesviruses contain a highly conserved G-Quadruplex Motif. ACS Infect Dis, 4:744–751.
15.
MadireddyA, PurushothamanP, LoosbroockCP, RobertsonES, SchildkrautCL and VermaSC. (2016). G-quadruplex-interacting compounds alter latent DNA replication and episomal persistence of KSHV. Nucleic Acids Res, 44:3675–3694.
16.
TlučkováK, MarušičM, TóthováP, BauerL, P Šket, PlavecJ and VViglasky. (2013). Human papillomavirus G-quadruplexes. Biochemistry, 52:7207–7216.
17.
MarušičM, and J.Plavec (2019). Towards understanding of polymorphism of the G-rich region of human papillomavirus type 52. Molecules, 24:1294.
18.
HarrisLM, and MerrickCJ. (2015). G-Quadruplexes in Pathogens: common route to virulence control? PLoS Pathogens, 11:1–15.
19.
ShanmugasundaramS, and J.You (2017). Targeting persistent human papillomavirus infection. Viruses, 9:229.
20.
De CianA, DeLemosE, MergnyJ.-L., Teulade-FichouM-PP and DMonchaud. (2007). Highly efficient G-quadruplex recognition by bisquinolinium compounds. J Am Chem Soc, 129:1856–1857.
21.
CarvalhoJ, QuintelaT, GueddoudaNM, BourdoncleA, MergnyJ-L, SalgadoGF, QueirozJA and CruzC. (2018). Phenanthroline polyazamacrocycles as G-quadruplex DNA binders. Org Biomol Chem, 16:2776–2786.
22.
ReadM, HarrisonRJ, RomagnoliB, TaniousFA, GowanSH, ReszkaAP, WilsonWD, KellandLR and SNeidle. (2001). Structure-based design of selective and potent G quadruplex-mediated telomerase inhibitors. Proc Natl Acad Sci U S A, 98:4844–4849.
23.
CarvalhoJ, PereiraE, MarquevielleJ, CampelloMPC, MergnyJ.-L., PauloA, SalgadoGF, QueirozJA and CCruz. (2018). Fluorescent light-up acridine orange derivatives bind and stabilize KRAS-22RT G-quadruplex. Biochimie, 144:144–152.
24.
RodriguezR, MüllerS., YeomanJA, TrentesauxC, RiouJ-F and SBalasubramanian. (2008). A novel small molecule that alters shelterin integrity and triggers a DNA-damage response at telomeres. J Am Chem Soc, 130:15758–15759.
25.
GranotierC, PennarunG, RiouL, HoffschirF, GauthierLR, De CianA, GomezD, MandineE, RiouJF, MergnyJL, MaillietP, DutrillauxB and BoussinFD. (2005). Preferential binding of a G-quadruplex ligand to human chromosome ends. Nucleic Acids Res, 33:4182–4190.
26.
HanFX, WheelhouseRT and HurleyLH. (1999). Interactions of TMPyP4 and TMPyP2 with quadruplex DNA. Structural basis for the differential effects on telomerase inhibition. J Am Chem Soc, 121:3561–3570.
27.
RenčiukD, ZhouJ, BeaurepaireL, GuédinA, BourdoncleA and J.-LMergny. (2012). A FRET-based screening assay for nucleic acid ligands. Methods, 57:122–128.
28.
MeyersC. (1996). Organotypic (raft) epithelial tissue culture system for the differentiation-dependent replication of papillomavirus. Methods Cell Sci, 18:201–210.
29.
ConwayMJ, and Meyers, C. (2009). Replication and assembly of human papillomaviruses. J Dental Res, 88:307–317.
30.
BiryukovJ, CruzL, RyndockEJ and CMeyers. (2015). Native human papillomavirus production, quantification, and infectivity analysis. Methods Mol Biol, 1249:317–331.
31.
BedratA, LacroixL and J.-LMergny. (2016). Re-evaluation of G-quadruplex propensity with G4Hunter. Nucleic Acids Res, 44:1746–1759.
32.
RuanTL, DavisSJ, PowellBM, HarbeckCP, HabdasJ, HabdasP and YatsunykLA. (2017). Lowering the overall charge on TMPyP4 improves its selectivity for G-quadruplex DNA. Biochimie, 132:121–130.
33.
del Villar-GuerraR, TrentJO and ChairesJB. (2018). G-quadruplex secondary structure obtained from circular dichroism spectroscopy. Angew Chem Int Ed Engl, 57:7171–7175.
34.
BončinaM, Č Podlipnik, PiantanidaI, EilmesJ, Teulade-FichouMP, VesnaverG and JLah. (2015). Thermodynamic fingerprints of ligand binding to human telomeric G-quadruplexes. Nucleic Acids Res, 43:10376–10386.
35.
TranPLT, LargyE, HamonF, Teulade-FichouM-P and J.-LMergny. (2011). Fluorescence intercalator displacement assay for screening G4 ligands towards a variety of G-quadruplex structures. Biochimie, 93:1288–1296.
36.
LargyE, HamonF and M.-PTeulade-Fichou. (2011). Development of a high-throughput G4-FID assay for screening and evaluation of small molecules binding quadruplex nucleic acid structures. Anal Bioanal Chem, 400:3419–3427.
37.
Webba da SilvaM. (2007). NMR methods for studying quadruplex nucleic acids. Methods, 43:264–277.
38.
BessiI, Wirmer-BartoschekJ, DashJ and HSchwalbe. (2017). Targeting G-quadruplex with Small Molecules: An NMR View. In: Modern Magnetic Resonance. Webb GA, ed. Springer, New York, NY, pp. 1–22.
39.
DaiJ, CarverM, HurleyLH and DYang. (2011). Solution structure of a 2:1 quindoline-c-MYC G-quadruplex: insights into G-quadruplex-interactive small molecule drug design. J Am Chem Soc, 133:17673–17680.
40.
AdrianM, HeddiB and PhanAT. (2012). NMR spectroscopy of G-quadruplexes. Methods, 57:11–24.
41.
De Rache A and J.-LMergny. (2015). Assessment of selectivity of G-quadruplex ligands via an optimised FRET melting assay. Biochimie, 115:194–202.
42.
DrubinDA, McLaughlin-DrubinME, ClawsonGA and CMeyers. (2006). A Protease Inhibitor Specifically Inhibits Growth of HPV-Infected Keratinocytes. Mol Ther, 13:1142–1148.
43.
Sanjib BanerjeeN, MooreDW, BrokerTR and ChowLT. (2018). Vorinostat, a pan-HDAC inhibitor, abrogates productive HPV-18 DNA amplification. Proc Natl Acad Sci U S A, 115:E11138–E11147.
44.
ListaMJ, MartinsRP, BillantO, ContesseMA, FindaklyS, PochardP, DaskalogianniC, BeauvineauC, GuettaC, JaminC, Teulade-FichouMP, FåhraeusR, VoissetC and M.Blondel (2017). Nucleolin directly mediates Epstein-Barr virus immune evasion through binding to G-quadruplexes of EBNA1 mRNA. Nat Commun, 8:16043.
45.
GrinsteinE, WernetP, PSnijdersJFF, RöslF, WeinertI, JiaW, KraftR, ScheweC, SchwabeM, HauptmannS, DietelM, CJLMeijerMLM and H.-DRoyer. (2002). Nucleolin as activator of human papillomavirus type 18 oncogene transcription in cervical cancer. J Exp Med, 196:1067–1078.
46.
ArtusiS, PerroneR, LagoS, RaffaP, Di IorioE, PalùG and RichterSN. (2016). Visualization of DNA G-quadruplexes in herpes simplex virus 1-infected cells. Nucleic Acids Res, 44:10343–10353.
47.
El-SabbaghOI and RadyHM. (2009). Synthesis of new acridines and hydrazones derived from cyclic β-diketone for cytotoxic and antiviral evaluation. Eur J Med Chem, 44:3680–3686.
48.
GoodellJR, MadhokAA, HiasaH and FergusonDM. (2006). Synthesis and evaluation of acridine- and acridone-based anti-herpes agents with topoisomerase activity. Bioorg Med Chem, 14:5467–5480.
49.
RuparJ, DobričićV, AleksićM, Brborić and ČudinaJ, O. (2018). A review of published data on acridine derivatives with different biological activities. Kragujevac J Sci, 40:83–101.
50.
TonelliM, VettorettiG, TassoB, NovelliF, BoidoV, SparatoreF, BusoneraB, OuhtitA, FarciP, BloisS, Giliberti and La CollaG, P. (2011). Acridine derivatives as anti-BVDV agents. Antivir Res, 91:133–141.
51.
HuZ, and DMa. (2018). The precision prevention and therapy of HPV-related cervical cancer: new concepts and clinical implications. Cancer Med, 7:5217–5236.
52.
Piekna-PrzybylskaD, SharmaG, MaggirwarSB and BambaraRA. (2017). Deficiency in DNA damage response, a new characteristic of cells infected with latent HIV-1. Cell Cycle, 16:968–978.
Supplementary Material
Please find the following supplemental material available below.
For Open Access articles published under a Creative Commons License, all supplemental material carries the same license as the article it is associated with.
For non-Open Access articles published, all supplemental material carries a non-exclusive license, and permission requests for re-use of supplemental material or any part of supplemental material shall be sent directly to the copyright owner as specified in the copyright notice associated with the article.
