Medicinal Chemistry Research

, Volume 27, Issue 5, pp 1517–1527 | Cite as

Synthesis of nucleobase-neomycin conjugates and evaluation of their DNA binding, cytotoxicities, and antibacterial properties

  • Siwen Wang
  • Mandeep Singh
  • Mingheng Ling
  • Danni Li
  • Krege M. Christison
  • Joan Lin-Cereghino
  • Geoff P. Lin-Cereghino
  • Liang Xue
Original Research


Neomycin is known to preferentially bind to A-form nucleic acid structures including triplex DNA, DNA and RNA hybrid, and duplex RNA. Tethering a DNA intercalator moiety to the C5” position of the ring III of neomycin is a practical approach to develop potent binders targeting various nucleic acid secondary structures via a synergistic effect; however, the minimal stacking surface of the intercalating moiety required to exhibit the effect remains unclear. In the present work, we synthesized four nucleobase and neomycin conjugates via click chemistry. All four conjugates stabilized a DNA oligonucleotide triplex in the thermal denaturation experiments monitored by UV. The guanine-neomycin conjugate (6b) showed a better triplex stabilization effect than neomycin. All the conjugates, as well as neomycin, exhibited no thermal stabilization effect on a human telomeric DNA G-quadruplex. These results suggest that the synergistic effect of binding is vastly dependent on the surface area of the stacking moiety of the conjugates. In addition, tethering a nucleobase to the C5” position of neomycin enhanced the cytotoxicity of neomycin toward MCF-7 and HeLa cancer cells but decreased the antibacterial effect of neomycin against several Gram-negative and Gram-positive bacterial species.


Neomycin DNA binding ligands Cell viability Antibacterial effect 





ribosomal RNA


trans-activation response element


aminoglycoside-modifying enzymes




dimethyl sulfoxide


3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide


half maximal inhibitory concentration


minimum inhibitory concentration


nuclear magnetic resonance


ultra-high-performance liquid chromatography




electrospray ionization


high-resolution mass spectrometry


time of flight


fetal bovine serum


Dulbecco’s modified eagle’s medium

KB test

Kirby–Bauer test


optical density



This work was supported by the University of the Pacific. We also thank Dr. William K. Chan for providing MCF-7 and HeLa cells.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

44_2018_2169_MOESM1_ESM.docx (6.4 mb)
Supplementary Data


  1. Ambrus A, Chen D, Dai J, Bialis T, Jones RA, Yang D (2006) Human telomeric sequence forms a hybrid-type intramolecular g-quadruplex structure with mixed parallel/antiparallel strands in potassium solution. Nucleic Acids Res 34:2723–2735CrossRefPubMedPubMedCentralGoogle Scholar
  2. Arya DP, Micovic L, Charles I, Coffee Jr. RL, Willis B, Xue L (2003a) Neomycin binding to Watson-Hoogsteen (W-H) DNA triplex groove: a model. J Am Chem Soc 125:3733–3744CrossRefPubMedGoogle Scholar
  3. Arya DP, Xue L, Tennant P (2003b) Combining the best in triplex recognition: synthesis and nucleic acid binding of a BQQ-neomycin conjugate. J Am Chem Soc 125:8070–8071CrossRefPubMedGoogle Scholar
  4. Arya DP, Xue L, Willis B (2003c) Aminoglycoside (neomycin) preference is for a-form nucleic acids, not just RNA: results for a competition dialysis study. J Am Chem Soc 125:10148–10149CrossRefPubMedGoogle Scholar
  5. Balouiri M, Sadiki M, Ibnsouda SK (2016) Methods for in vitro evaluating antimicrobial activity: a review. J Pharm Anal 6:71–79CrossRefPubMedGoogle Scholar
  6. Blount KF, Tor Y (2006) A tale of two targets: differential RNA selectivity of nucleobase-aminoglycoside conjugates. ChemBioChem 7:1612–1621CrossRefPubMedGoogle Scholar
  7. Degtyareva NN, Gong C, Story S, Levinson NS, Oyelere AK, Green KD, Garneau-Tsodikova S, Arya DP (2017) Antimicrobial activity, AME resistance, and A-site binding studies of anthraquinone-neomycin conjugates. ACS Infect Dis 3:206–215CrossRefPubMedGoogle Scholar
  8. Edward Lindsell W, Murray C, Preston PN, Woodman TAJ (2000) Synthesis of 1,3-diynes in the purine, pyrimidine, 1,3,5-triazine and acridine series. Tetrahedron 56:1233–1245CrossRefGoogle Scholar
  9. Fourmy D, Recht MI, Puglisi JD (1998) Binding of neomycin-class aminoglycoside antibiotics to the a-site of 16 s rrna. J Mol Biol 277:347–362CrossRefPubMedGoogle Scholar
  10. Fridman M, Belakhov V, Yaron S, Baasov T (2003) A new class of branched aminoglycosides: pseudo-pentasaccharide derivatives of neomycin b. Org Lett 5:3575–3578CrossRefPubMedGoogle Scholar
  11. Grau-Campistany A, Massaguer A, Carrion-Salip D, Barragan F, Artigas G, Lopez-Senin P, Moreno V, Marchan V (2013) Conjugation of a ru(ii) arene complex to neomycin or to guanidinoneomycin leads to compounds with differential cytotoxicities and accumulation between cancer and normal cells. Mol Pharm 10:1964–1976CrossRefPubMedGoogle Scholar
  12. Green KD, Chen W, Houghton JL, Fridman M, Garneau-Tsodikova S (2010) Exploring the substrate promiscuity of drug-modifying enzymes for the chemoenzymatic generation of n-acylated aminoglycosides. ChemBioChem 11:119–126CrossRefPubMedGoogle Scholar
  13. Guckian KM, Schweitzer BA, Ren RX, Sheils CJ, Tahmassebi DC, Kool ET (2000) Factors contributing to aromatic stacking in water: evaluation in the context of DNA. J Am Chem Soc 122:2213–2222CrossRefPubMedPubMedCentralGoogle Scholar
  14. Guthrie OW (2008) Aminoglycoside induced ototoxicity. Toxicology 249:91–96CrossRefPubMedGoogle Scholar
  15. Houghton JL, Green KD, Chen W, Garneau-Tsodikova S (2010) The future of aminoglycosides: the end or renaissance? ChemBioChem 11:880–902CrossRefPubMedGoogle Scholar
  16. Kirk SR, Luedtke NW, Tor Y (2000) Neomycin−acridine conjugate: a potent inhibitor of rev-rre binding. J Am Chem Soc 122:980–981CrossRefGoogle Scholar
  17. Liu M, Haddad J, Azucena E, Kotra LP, Kirzhner M, Mobashery S (2000) Tethered bisubstrate derivatives as probes for mechanism and as inhibitors of aminoglycoside 3‘-phosphotransferases. J Org Chem 65:7422–7431CrossRefPubMedGoogle Scholar
  18. Liu W, Minier MA, Franz AH, Curtis M, Xue L (2011) Synthesis of nucleobase-calix[4]arenes via click chemistry and evaluation of their complexation with alkali metal ions and molecular assembly. Supramol Chem 23:806–818CrossRefGoogle Scholar
  19. Liu W, Wang S, Dotsenko IA, Samoshin VV, Xue L (2017) Arylsulfanyl groups-suitable side chains for 5-substituted 1,10-phenanthroline and nickel complexes as g4 ligands and telomerase inhibitors. J Inorg Biochem 173:12–20CrossRefPubMedGoogle Scholar
  20. Lu W, Sengupta S, Petersen JL, Akhmedov NG, Shi X (2007) Mitsunobu coupling of nucleobases and alcohols: An efficient, practical synthesis for novel nonsugar carbon nucleosides. J Org Chem 72:5012–5015CrossRefPubMedGoogle Scholar
  21. Oliveira JF, Silva CA, Barbieri CD, Oliveira GM, Zanetta DM, Burdmann EA (2009) Prevalence and risk factors for aminoglycoside nephrotoxicity in intensive care units. Antimicrob Agents Chemother 53:2887–2891CrossRefPubMedPubMedCentralGoogle Scholar
  22. Ramirez MS, Tolmasky ME (2010) Aminoglycoside modifying enzymes. Drug Resist Updat 13:151–171CrossRefPubMedPubMedCentralGoogle Scholar
  23. Vakulenko SB, Mobashery S (2003) Versatility of aminoglycosides and prospects for their future. Clin Microbiol Rev 16:430–450CrossRefPubMedPubMedCentralGoogle Scholar
  24. Wellenzohn B, Flader W, Winger RH, Hallbrucker A, Mayer E, Liedl KR (2001) Exocyclic groups in the minor groove influence the backbone conformation of DNA. Nucleic Acids Res 29:5036–5043CrossRefPubMedPubMedCentralGoogle Scholar
  25. Wong C-H, Hendrix M, Scott Priestley E, Greenberg WA (1998) Specificity of aminoglycoside antibiotics for the A-site of the decoding region of ribosomal RNA. Chem Biol 5:397–406CrossRefPubMedGoogle Scholar
  26. Xue L, Charles I, Arya DP (2002) Pyrene–neomycin conjugate: dual recognition of a DNA triple helix. Chem Commun 70–71Google Scholar
  27. Xue L, Ling M, Wang S (2017) A reliable method to measure the melting temperatures of DNA oligonucleotide triplexes. J Undergrad Chem Res 16:19–23Google Scholar
  28. Xue L, Ranjan N, Arya DP (2011) Synthesis and spectroscopic studies of the aminoglycoside (neomycin)--perylene conjugate binding to human telomeric DNA. Biochemistry 50:2838–2849CrossRefPubMedGoogle Scholar
  29. Zhang J, Keller K, Takemoto JY, Bensaci M, Litke A, Czyryca PG, Chang CW (2009) Synthesis and combinational antibacterial study of 5”-modified neomycin. J Antibiot 62:539–544CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of ChemistryUniversity of the PacificStocktonUSA
  2. 2.Department of Biological SciencesUniversity of the PacificStocktonUSA

Personalised recommendations