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Spectroscopy, Thermodynamics and Molecular Docking of Fraxinellone with DNA

Abstract

Fraxinellone is an important botanical lactone compound and has been demonstrated to have insecticidal activity. To provide theoretical support to the assessment on the safety of utilizing fraxinellone as a natural insecticidal agent, the interactions between fraxinellone and armyworm DNA, salmon sperm DNA and calf thymus DNA were investigated using UV–Vis absorption spectroscopy, isothermal titration calorimetry, and molecular docking. Results showed that there were two types of combinations between fraxinellone and three kinds of DNA. Type I combination had an equilibrium constant of combination (Ka1) of about 105 and binding sites (n1) of 0.40–0.70, while type II combination had an equilibrium constant of combination (Ka2) of 103 and binding sites (n2) of 1.35–3.15. Results of molecular docking showed that there were non-classical embedding type interactions between fraxinellone and three kinds of DNA, with the reaction taking place in small groove areas of the DNA structure, resulting in relatively weak interactive forces.

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References

  1. Akhmedzhanova VI, Bessonova IA, Yunusov SY (1978) The roots of Dictamnus angustifolius. Chem Nat Compd 14:404–406

    Article  Google Scholar 

  2. Biavatti MW, Vieira PC, Da SM et al (2001) Limonoids from the endemic Brazilian species Raulinoa echinata. Zeitschrift Für Naturforschung C J Biosci 56:570–574

    CAS  Article  Google Scholar 

  3. Biavatti MW, Westerlon R, Vieira PC et al (2005) Leaf-cutting ants toxicity of limonexic acid and degraded limonoids from Raulinoa echinata. X-ray structure of epoxy-fraxinellone. J Braz Chem Soc 16:1443–1447

    Article  Google Scholar 

  4. Boustie J, Moulis C, Gleye J et al (1990) A degraded limonoid from Fagaropsis glabra. Phytochemistry 29:1699–1701

    CAS  Article  Google Scholar 

  5. Braakman RBH, Karel B, Sieuwerts AM et al (2015) Integrative analysis of genomics and proteomics data on clinical breast cancer tissue specimens extracted with Acid guanidinium thiocyanate-phenol-chloroform. J Proteome Res 14:1627–1636

    Article  Google Scholar 

  6. Fathizadeh A, Schiessel H, Ejtehadi MR et al (2014) Molecular dynamics simulation of supercoiled DNA rings. Macromolecules 48:164–172

    Article  Google Scholar 

  7. Gindt YM, Edani BH, Olejnikova A et al (2016) The missing electrostatic interactions between DNA substrate and sulfolobus solfataricus DNA photolyase: what is the role of charged amino acids in thermophilic DNA binding proteins? J Phys Chem B 120(39):10234–10242

    CAS  Article  Google Scholar 

  8. Gu HM, Xu H, Zhong ZZ et al (2011) Fraxinellone. Acta Crystallogr 67:1472

    Article  Google Scholar 

  9. Guo Y, Xu H, Zhong ZZ et al (2012a) Synthesis and insecticidal activity of some novel fraxinellone-based esters. J Agric Food Chem 60:7016–7021

    CAS  Article  Google Scholar 

  10. Guo Y, YanY Y, Yang C et al (2012b) Regioselective synthesis of fraxinellone-based hydrazone derivatives as insecticidal agents. Bioorg Med Chem Lett 22:5384–5387

    CAS  Article  Google Scholar 

  11. Guo Y, Qu H, Zhi X et al (2013) Semisynthesis and insecticidal activity of some fraxinellone derivatives modified in the B ring. J Agric Food Chem 61:11937–11944

    CAS  Article  Google Scholar 

  12. Guo Y, Wang X, Fan J et al (2017) Semisynthesis and insecticidal activity of some novel fraxinellone-based thioethers containing 1,3,4-oxadiazole moiety. R Soc Open Sci 13:1–4

    Google Scholar 

  13. Haris P, Varughese M, Haridas M et al (2015) Energetics, thermodynamics, and molecular recognition of piperine with dNA. J Chem Inf Model 55:2644–2656

    CAS  Article  Google Scholar 

  14. Hu CQ, Song GQ, Yin DX (1989) Limonoids from Dictamnus angustifolius. Acta Bot Sin 31(6):453–458

    CAS  Google Scholar 

  15. Jeong Seon Y, Hyun SS, Young Choong K et al (2008) Neuroprotective limonoids of root bark of Dictamnus dasycarpus. J Nat Prod 71:208–211

    Article  Google Scholar 

  16. Katrin S, Ursula R, Paolo C (2006) Duocarmycins binding to DNA investigated by molecular simulation. J Phys Chem B 110:3647–3660

    Google Scholar 

  17. Kumar CV, Asuncion EH (1993) DNA binding studies and site selective fluorescence sensitization of an anthryl probe. J Am Chem Soc 115(19):8547–8553

    CAS  Article  Google Scholar 

  18. Lee J, Kim JS, Seok C (2010) Cooperativity and specificity of Cys2His2 zinc finger protein-DNA interactions: a molecular dynamics simulation study. J Phys Chem B 114(22):7662–7671

    CAS  Article  Google Scholar 

  19. Li ZX, Zhao WW, Pu XH (2011) Thermodynamic properties of resveratrol in dimethyl sulfoxide. J Therm Anal Calorim 110:1249–1252

    Article  Google Scholar 

  20. Li Q, Huang X, Li S et al (2016) Semisynthesis of esters of fraxinellone C4/10-oxime and their pesticidal activities. J Agric Food Chem 64(27):5472–5478

    CAS  Article  Google Scholar 

  21. Li JH, Bian L, Tian SY et al (2017) Spectroscopic study on the interaction of human cytoglobin with copper (II) ion. Spectrosc Spectral Anal 37(1):321–326

    CAS  Google Scholar 

  22. Lian MP, Marc L, Winnik F O M et al (2009) New insights into chitosan-DNA interactions using isothermal titration microcalorimetry. Biomacromolecules 10:1490–1499

    Article  Google Scholar 

  23. Lindsay SW, Hossainl MI, Bennett S et al (2010) Preliminary studies on the insecticidal activity and wash-fastness of twelve pyrethroid treatments impregnated into bednetting assayed against mosquitoes. Pest Manag Sci 32:397–411

    Article  Google Scholar 

  24. Lomzov AA, Vorobjev YN, Pyshnyi DV (2015) Evaluation of the gibbs free energy changes and melting temperatures of DNA/DNA duplexes using hybridization enthalpy calculated by molecular dynamics simulation. J Phys Chem B 119:15221–15234

    CAS  Article  Google Scholar 

  25. Long EC, Barton JK (1990) On demonstrating DNA intercalation. Acc Chem Res 23(9):271–273

    CAS  Article  Google Scholar 

  26. Long LZ, Jian XY, Jien W et al (2002) Feeding deterrents from Dictamnus dasycarpus Turcz against two stored-product insects. J Agric Food Chem 50(6):1447–1450

    Article  Google Scholar 

  27. Lv M, Wu WJ, Liu HX et al (2014) Effects of fraxinellone on the midgut enzyme activities of the 5th instar larvae of oriental armyworm, mythimna separata walker. Toxins 6(9):2708–2718

    Article  Google Scholar 

  28. Mishra AS, Krishna EM, Maiti S (2016) Influence of ionic liquids on thermodynamics of small molecule-DNA interaction: the binding of ethidium bromide to Calf Thymus DNA. J Phys Chem B 120(10):2691–2700

    CAS  Article  Google Scholar 

  29. Nakatani M, Huang RC, Okamura H et al (1998) Degraded limonoids from Melia azedarach. Phytochemistry 49(6):1773–1776

    CAS  Article  Google Scholar 

  30. Silva MALD, Medeiros Z, Soares CRP et al (2014) A comparison of four DNA extraction protocols for the analysis of urine from patients with visceral leishmaniasis. Rev Soc Bras Med Trop 47(2):193–197

    Article  Google Scholar 

  31. Yoshiyasu F, Momoko N, Tomoko Y et al (2006) Degraded and oxetane-bearing limonoids from the roots of Melia azedarach. Chem Pharm Bull 54(8):1219–1222

    Article  Google Scholar 

  32. Zhang Z, Liu J (2016) Molecularly imprinted polymers with DNA aptamer fragments as macromonomers. ACS Appl Mater Interfaces 8(10):6371–6378

    CAS  Article  Google Scholar 

  33. Zhao W, Wolfender JL, Hostettmann K et al (1998) Antifungal alkaloids and limonoid derivatives from Dictamnus dasycarpus. Phytochemistry 47(1):7–11

    CAS  Article  Google Scholar 

Download references

Funding

This work was funded by the Natural Science Foundation of Shaanxi Province (No. 2019JQ-582) and the Doctoral Scientific Research Starting Foundation of Baoji University of Arts and Science (No. ZK2018048 and No. ZK2017045).

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Correspondence to Ji Lei or Zongxiao Li.

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Lei, J., Gou, X., Wei, S. et al. Spectroscopy, Thermodynamics and Molecular Docking of Fraxinellone with DNA. Bull Environ Contam Toxicol 104, 864–870 (2020). https://doi.org/10.1007/s00128-020-02860-7

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Keywords

  • Fraxinellone
  • DNA
  • Isothermal titration calorimetry
  • Molecular docking
  • Botanical insecticide