Document Type : Final File

Authors

1 Iranian Research Institute of Plant Protection (IRIPP), Tehran, Islamic Republic of Iran

2 2 Department of Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Islamic Republic of Iran

3 3 Department of Pesticides, Iranian Research Institute of Plant Protection, Arak, Islamic Republic of Iran

4 4 Drug Design and Development Research Center, Tehran University of Medical Sciences, Tehran, Islamic Republic of Iran

5 5 Department of Medicinal Chemistry, Faculty of Pharmacy and Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Islamic Republic of Iran

6 6 Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran, Islamic Republic of Iran

Abstract

The binding interaction of novel podophyllotoxin derivative, (3R,4R)-4-((benzo[d][1,3]dioxol-5-yl)methyl)-dihydro-3-(hydroxy(3,4-dimethoxyphenyl) methyl) furan-2(3H)-one (PPT), with calf thymus DNA (ctDNA) has been examined using UV-Visible absorption spectrophotometry, fluorescence spectroscopy, viscosity measurement and molecular docking studies. UV-Vis absorption results showed hyperchromic effect and low binding constant value (1.01×104 M-1), indicating non-intercalative interaction as a binding mode. The competitive fluorescence study also confirmed the obtained results from UV-Vis absorption spectra. Small changes in the viscosity of DNA exhibited that the interaction of PPT with DNA is based on groove binding mode. Molecular docking study showed minor groove interaction and -7.08 kcal/mol as a calculated energy.
 

Keywords

  1. Ducasse H., Arnal A., Vittecoq M., Daoust S.P., Ujvari B., Jacqueline C., Tissot T., Ewald P., Gatenby R.A., King K.C., Bonhomme F., Brodeur J., Renaud F., Solary E., Roche B. and Thomas F. Cancer: an emergent property of disturbed resource-rich environments? Ecology meets personalized medicine. Evol. Appl. 8: 527-540 (2015).
  2. Rescifina A., Zagni C., Varrica M.G., Pistarà V.  and Corsaro A. Recent advances in small organic molecules as DNA intercalating agents: Synthesis, activity, and modeling. Eur. J. Med. Chem. 74: 95-115 (2014).
  3. Roos W.P. and Kaina B. DNA damage-induced cell death by apoptosis. Trends Mol. Med. 12: 440-450 (2006).
  4. Zhang G., Guo J., Zhao N. and Wang J. Study of interaction between kaempferol-Eu3+ complex and DNA with the use of the Neutral Red dye as a fluorescence probe. Sensors Actuat. B Chem. 144: 239-246 (2010).
  5. Lerman L.S. Structural considerations in the interaction of DNA and acridines. J. Mol. Biol. 3: 18-30 (1961).
  6. Bauer W. and Vinograd J. The interaction of closed circular DNA with intercalative dyes. 3. Dependence of the buoyant density upon superhelix density and base composition. J. Mol. Biol. 54: 281-298 (1970).
  7. Sirajuddin M., Ali S. and Badshah A. Drug-DNA interactions and their study by UV-Visible, fluorescence spectroscopies and cyclic voltammetry. J. Photochem. Photobiol. B. 124: 1-19 (2013).
  8. Kikandi S.N., Musah S., Lee K., Hassani J., Rajan S., Zhou A. and Sadik O.A. Comparative Studies of Quercetin Interactions with Monophosphate Nucleotides Using UV-Vis Spectroscopy and Electrochemical Techniques. Electroanalysis 19: 2131-2140 (2007).
  9. Silvestri A., Barone G., Ruisi G., Lo Giudice M.T. and Tumminello S. The interaction of native DNA with iron(III)-N,N′-ethylene-bis(salicylideneiminato)-chloride. J. Inorg. Biochem. 98: 589-594 (2004).

10. Wang L., Lin L. and Ye B. Electrochemical studies of the interaction of the anticancer herbal drug emodin with DNA. J. Pharm. Biomed. Anal. 42: 625-629 (2006).

11. Lin H.W., Kwok K.H. and Doran P.M. Production of podophyllotoxin using cross-species coculture of Linum flavum hairy roots and Podophyllum hexandrum cell suspensions. Biotechnol. Prog. 19: 1417-1426 (2003).

12. Inamori Y., Kubo M., Tsujibo H., Ogawa M., Baba K., Kozawa M. and Fujita E. The biological activities of podophyllotoxin compounds. Chem. Pharm. Bull. 34: 3928-3932 (1986).

13. Castro M.A., Del corral J.M., Garcia P.A., Rojo M.V., La Iglesia-Vincete J., Mollinedo F., Cuevas C. and San Feliciano A. Synthesis and biological evaluation of new podophyllic aldehyde derivatives with cytotoxic and apoptosis-inducing activities. J. Med. Chem. 53: 983-993 (2010).

14. Stahelin H.F. and Wartburg A.V. The Chemical and Biological Route from Podophyllotoxin Glucoside to Etoposide: Ninth Cain Memorial Award Lecture. Cancer Res. 51: 5-15 (1991).

15. Baldwin E.L. and Osheroff N. Etoposide, Topoisomerase II and Cancer. Anticancer Agents Med. Chem. 5: 363-372 (2005).

16. Gordaliza M., MaMiguel del Corral J., Castro M.A., Lopez-Vazquez M., Garcia P.A., San Feliciano A. and Garcia-Gravalos M. Selective cytotoxic cyclolignans. Bioorg. Med. Chem. Lett. 5: 2465-2468 (1995).

17. Kamal A., Hssaini S.M.A., Rahim A. and Riyaz S. Podophyllotoxin derivatives: a patent review (2012-2014). Expert Opin. Ther. Pat. 25: 1025-1034 (2015).

18. You Y. Podophyllotoxin derivatives: current synthetic approaches for new anticancer agents. Curr. Pharm. Des. 11: 1695-1717 (2005).

19. Heidary Alizadeh B., Emami S., Dehghan G., Foroumadi A. and Shafiee A. Synthesis of Cytotoxic Isodeoxypodophyllotoxin Analogs. J. Heterocyclic Chem. DOI: 10.1002/jhet.2618  (2016).

20. Dehghan G., Dolatabadi J.E.N., Jouyban A., Zeynali K.A., Ahmadi S.M. and Kashanian S. Spectroscopic Studies on the Interaction of Quercetin–Terbium(III) Complex with Calf Thymus DNA. DNA Cell Biol. 30: 195-201 (2011).

21. Glasel J.A. Validity of nucleic acid purities monitored by 260nm/280nm absorbance ratios. Biotechniques, 18: 62-63 (1995).

22. Subastri A., Ramamurthy C.H., Suyavaran A., Mareeswaran R., Rao P.L., Harikrishna M., Kumar M.S., Sujatha V. and Thirunavukkarasu C. Spectroscopic and molecular docking studies on the interaction of troxerutin with DNA. Int. J. Biol. Macromolec. 78: 122-129 (2015).

23. Pettersen E.F., Goddard T.D., Huang C.C., Couch G.S., Greenblatt D.M., Meng E.C. and Ferrin T.E. UCSF Chimera--a visualization system for exploratory research and analysis. J. Comput. Chem. 25: 1605-1612 (2004).

24. Parveen M., Ahmad F., Malla A.M., Sohrab Khan M., Ur Rehman S., Tabish M., Silva M.R. and Pereira Silva P.S. Structure elucidation and DNA binding specificity of natural compounds from Cassia siamea leaves: A biophysical approach. J. Photochem. Photobiol. B. 159: 218-228 (2016).

25. Jangir D.K., Charak S., Mehrotra R. and Kundu S. FTIR and circular dichroism spectroscopic study of interaction of 5-fluorouracil with DNA. J. Photochem. Photobiol. B. 105: 143-148 (2011).

26. Shahabadi N. and Maghsudi M. Multi-spectroscopic and molecular modeling studies on the interaction of antihypertensive drug; methyldopa with calf thymus DNA. Mol. BioSyst. 10: 338-347 (2014).

27. Tomer E., Goren R. and Monselise S.P. Isolation and identification of seselin in Citrus roots. Phytochemistry, 8: 1315-1316 (1969).

28. Bauri A.K., Foro S., Lindner H.J. and Nayak S.K. Reinvestigation of seselin. Acta Cryst. E. 62: 1340-1341 (2006).

29. Nafisi S., Saboury A.A., Keramat N., Neault J.F. and Tajmir-Riahi H.A. Stability and structural features of DNA intercalation with ethidium bromide, acridine orange and methylene blue. J. Mol. Struct. 827: 35-43 (2007).

30. Kashanian S., Shahabadi N., Roshanfekr H., Shalmashi K. and Omidfar K.  DNA binding studies of PdCl2(LL)(LL = chelating diamine ligand: N,N-dimethyl trimethylenediamine) complex. Biochemistry, 73: 929-936 (2008).

31. Kashanian S., Javanmardi A., Chitsazan D., Paknejad M. and Omidfar K. Fluorometric study of fluoxetine DNA binding. J. Photochem. Photobiol. B. 113: 1-6 (2012).

32. Douthart R.J., Burnett J.P., Beasley F.W. and Frank B.H. Binding of ethidium bromide to double-stranded ribonucleic acid. Biochemistry, 12: 214-220 (1973).

33. Shahabadi N., Kashanian S., Khosravi M. and Mahdavi M. ultispectroscopic DNA interaction studies of a water-soluble nickel(II) complex containing different dinitrogen aromatic ligands. Transit. Metal Chem. 35: 699-705 (2010).

34.

 

Shahabadi N., Kashanian S. and Purfoulad M. DNA interaction studies of a platinum(II) complex, PtCl2(NN) (NN = 4,7-dimethyl-1,10-phenanthroline), using different instrumental methods. Spectrochim. Acta A. Mol. Biomol. Spectrosc. 72: 757-761 (2009).

35. Zhao T., Bi S., Wang Y., Wang T., Pang B. and Gu T.  In vitro studies on the behavior of salmeterol xinafoate and its interaction with calf thymus DNA by multi-spectroscopic techniques. Spectrochim. Acta A. Mol. Biomol. Spectrosc. 132: 198-204 (2014).

36. Husain M.A., Sarwar T., Rehman S.U., Ishqi H.M. and Tabish M. Ibuprofen causes photocleavage through ROS generation and intercalates with DNA: a combined biophysical and molecular docking approach. Phys. Chem. Chem. Phys. 17: 13837-13850 (2015).

37. Husain M., Dehghan G., Jouyban A., Sistani P. and Arvin M. Studies of interaction between terbium(III)-deferasirox and double helix DNA by spectral and electrochemical methods. Spectrochim. Acta A Mol. Biomol. Spectrosc. 120: 467-472 (2014).

38. Sarwar T., Rehman S.U., Husain M.A., Ishqi H.M. and Tabish M. Interaction of coumarin with calf thymus DNA: Deciphering the mode of binding by in vitro studies. Int. J. Biol. Macromolec.73: 9-16 (2015).

39. Satyanarayana S., Dabrowiak J.C. and Chaires J.B. Neither. DELTA. nor. LAMBDA. tris(phenanthroline) ruthenium(II) binds to DNA by classical intercalation. Biochemistry, 31: 9319-9324 (1992).

40. Charak S., Shandilya M., Tyagi G. and Mehrotra R. Spectroscopic and molecular docking studies on chlorambucil interaction with DNA. Int. J. Biol. Macromolec. 51: 406-411 (2012).