135
Views
3
CrossRef citations to date
0
Altmetric
Research Articles

In vitro and in silico binding studies of phytochemical isochroman with calf thymus DNA using multi-spectroscopic and computational modelling techniques

, , &
Pages 8795-8809 | Received 07 Jun 2022, Accepted 11 Oct 2022, Published online: 25 Oct 2022

References

  • Afrin, S., Rahman, Y., Sarwar, T., Husain, M. A., Ali, A., & Tabish, M. (2017). Molecular spectroscopic and thermodynamic studies on the interaction of anti-platelet drug ticlopidine with calf thymus DNA. Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy, 186, 66–75., https://doi.org/10.1016/j.saa.2017.05.073
  • Ahmadi, F., Valadbeigi, S., Sajjadi, S. E., Shokoohinia, Y., Azizian, H., & Taheripak, G. (2016). Grandivittin as a natural minor groove binder extracted from Ferulago macrocarpa to ct-DNA, experimental and in silico analysis. Chemico-Biological Interactions, 258, 89–101. https://doi.org/10.1016/j.cbi.2016.08.020
  • Al Qumaizi, K. I., Anwer, R., Ahmad, N., Alosaimi, S. M., & Fatma, T. (2018). Study on the interaction of antidiabetic drug Pioglitazone with calf thymus DNA using spectroscopic techniques. Journal of Molecular Recognition, 31(11), e2735–2744. https://doi.org/10.1002/jmr.2735
  • Aleksic, M., & Kapetanovic, V. (2014). An overview of the optical and electrochemical methods for detection of DNA-drug interactions. Acta Chimica Slovenica, 61(3), 555–573.
  • Ameen, F., Siddiqui, S., Jahan, I., Nayeem, S. M., ur Rehman, S., & Tabish, M. (2022). Studying the interaction of scopolamine with calf-thymus DNA: An in-vitro and in-silico approach and genotoxicity. Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy, 265, 120391–120403. https://doi.org/10.1016/j.saa.2021.120391
  • Ameen, F., Siddiqui, S., Kausar, T., Nayeem, S. M., Sarwar, T., Rizvi, M. M. A., Rehman, S. U., & Tabish, M. (2022). Interaction of memantine with calf thymus DNA: an in-vitro and in-silico approach and cytotoxic effect on the cancerous cell lines. Journal of Biomolecular Structure and Dynamics, 40(3), 1216–1229. https://doi.org/10.1080/07391102.2020.1823886
  • Banerjee, P., Eckert, A. O., Schrey, A. K., & Preissner, R. (2018). ProTox-II: a webserver for the prediction of toxicity of chemicals. Nucleic Acids Research, 46(W1), W257–W263.
  • Berendsen, H. J., van der Spoel, D., & van Drunen, R. (1995). GROMACS: A message-passing parallel molecular dynamics implementation. Computer Physics Communications, 91(1-3), 43–56. https://doi.org/10.1016/0010-4655(95)00042-E
  • Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, IN., & Bourne, P. E. (2000). The protein data bank. Nucleic Acids Research, 28(1), 235–242. https://doi.org/10.1093/nar/28.1.235
  • Bi, S., Zhao, T., Wang, Y., Zhou, H., Pang, B., & Gu, T. (2015). Binding studies of terbutaline sulfate to calf thymus DNA using multispectroscopic and molecular docking techniques. Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy, 150, 921–927. https://doi.org/10.1016/j.saa.2015.06.042
  • Bonincontro, A., Falivene, M., La Mesa, C., Risuleo, G., & Ruiz Peña, M. (2008). Dynamics of DNA adsorption on and release from SDS − DDAB Cat − anionic vesicles: a multitechnique study. Langmuir: The ACS Journal of Surfaces and Colloids, 24(5), 1973–1978. https://doi.org/10.1021/la701730h
  • Chang, Y. M., Chen, C. K. M., & Hou, M. H. (2012). Conformational changes in DNA upon ligand binding monitored by circular dichroism. International Journal of Molecular Sciences, 13(3), 3394–3413. https://doi.org/10.3390/ijms13033394
  • Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7(1), 42717–42713. https://doi.org/10.1038/srep42717
  • Enmozhi, S. K., Raja, K., Sebastine, I., & Joseph, J. (2021). Andrographolide as a potential inhibitor of SARS-CoV-2 main protease: an in silico approach. Journal of Biomolecular Structure & Dynamics, 39(9), 3092–3098. https://doi.org/10.1080/07391102.2020.1760136
  • Fei, Y., Lu, G., Fan, G., & Wu, Y. (2009). Spectroscopic studies on the binding of a new quinolone antibacterial agent: sinafloxacin to DNA. Analytical Sciences: The International Journal of the Japan Society for Analytical Chemistry, 25(11), 1333–1338. https://doi.org/10.2116/analsci.25.1333
  • Fouedjou, R. T., Chtita, S., Bakhouch, M., Belaidi, S., Ouassaf, M., Djoumbissie, L. A., Tapondjou, L. A., & Abul Qais, F. (2021). Cameroonian medicinal plants as potential candidates of SARS-CoV-2 inhibitors. Journal of Biomolecular Structure and Dynamics, 1–15. https://doi.org/10.1080/07391102.2021.1914170
  • Hanwell, M. D., Curtis, D. E., Lonie, D. C., Vandermeersch, T., Zurek, E., & Hutchison, G. R. (2012). Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. Journal of Cheminformatics, 4(1), 17–17. https://doi.org/10.1186/1758-2946-4-17
  • Hashmi, M. A., Khan, A., Hanif, M., Farooq, U., & Perveen, S. (2015). Traditional uses, phytochemistry, and pharmacology of Olea europaea (olive). Evidence-Based Complementary and Alternative Medicine: eCAM, 2015, 541591. https://doi.org/10.1155/2015/541591
  • Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., & Simmerling, C. (2006). Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins, 65(3), 712–725. https://doi.org/10.1002/prot.21123
  • Husain, M. A., Ishqi, H. M., Sarwar, T., Rehman, S. U., & Tabish, M. (2017). Interaction of indomethacin with calf thymus DNA: a multi-spectroscopic, thermodynamic and molecular modelling approach. MedChemComm, 8(6), 1283–1296. https://doi.org/10.1039/c7md00094d
  • Hussain, I., Fatima, S., Ahmed, S., & Tabish, M. (2022a). Deciphering the biomolecular interaction of β-resorcylic acid with human lysozyme: A biophysical and bioinformatics outlook. Journal of Molecular Liquids, 346, 117885. https://doi.org/10.1016/j.molliq.2021.117885
  • Hussain, I., Fatima, S., Ahmed, S., & Tabish, M. (2022b). Biophysical and molecular modelling analysis of the binding of β-resorcylic acid with bovine serum albumin. Food Hydrocolloids, 135, 108175. https://doi.org/10.1016/j.foodhyd.2022.108175
  • Hussain, I., Fatima, S., Siddiqui, S., Ahmed, S., & Tabish, M. (2021). Exploring the binding mechanism of β-resorcylic acid with calf thymus DNA: Insights from multi-spectroscopic, thermodynamic and bioinformatics approaches. Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy, 260, 119952–119965. https://doi.org/10.1016/j.saa.2021.119952
  • Islam, M. M., Chakraborty, M., Pandya, P., Al Masum, A., Gupta, N., & Mukhopadhyay, S. (2013). Binding of DNA with Rhodamine B: Spectroscopic and molecular modeling studies. Dyes and Pigments, 99(2), 412–422. https://doi.org/10.1016/j.dyepig.2013.05.028
  • Jayaram, B., Singh, T., Mukherjee, G., Mathur, A., Shekhar, S., & Shekhar, V. (2012). Sanjeevini: a freely accessible web-server for target directed lead molecule discovery. BMC Bioinformatics, 13(S17), 1–13. https://doi.org/10.1186/1471-2105-13-S17-S7
  • Kashanian, S., & Dolatabadi, J. E. N. (2010). In vitro studies on calf thymus DNA interaction and 2-tert-butyl-4-methylphenol food additive. European Food Research and Technology, 230(6), 821–825. https://doi.org/10.1007/s00217-010-1226-6
  • Kashanian, S., Zeidali, S. H., Omidfar, K., & Shahabadi, N. (2012). Multi-spectroscopic DNA interaction studies of sunset yellow food additive. Molecular Biology Reports, 39(12), 10045–10051. https://doi.org/10.1007/s11033-012-1873-8
  • Kim, S. K., & Norden, B. (1993). Methyl green: A DNA major‐groove binding drug. FEBS Letters, 315(1), 61–64. https://doi.org/10.1016/0014-5793(93)81133-K
  • Kumar, C. V., Turner, R. S., & Asuncion, E. H. (1993). Groove binding of a styrylcyanine dye to the DNA double helix: the salt effect. Journal of Photochemistry and Photobiology A: Chemistry, 74(2-3), 231–238. https://doi.org/10.1016/1010-6030(93)80121-O
  • Kumar, J. S. (2021). In silico studies comparing the adjuvant therapies approved for Parkinson’s disease(S). Journal of Drug Delivery and Therapeutics, 11(3), 104–110.
  • Liao, S. Y., Mo, G. Q., Chen, J. C., & Zheng, K. C. (2014). Exploration of the binding mode between (−)-zampanolide and tubulin using docking and molecular dynamics simulation. Journal of Molecular Modeling, 20(2), 2070–2079. https://doi.org/10.1007/s00894-014-2070-6
  • MacDonald, M. L., Lamerdin, J., Owens, S., Keon, B. H., Bilter, G. K., Shang, Z., Huang, Z., Yu, H., Dias, J., Minami, T., Michnick, S. W., & Westwick, J. K. (2006). Identifying off-target effects and hidden phenotypes of drugs in human cells. Nature Chemical Biology, 2(6), 329–337. https://doi.org/10.1038/nchembio790
  • Maheswari, P. U., & Palaniandavar, M. (2004). DNA binding and cleavage properties of certain tetrammine ruthenium (II) complexes of modified 1, 10-phenanthrolines–effect of hydrogen-bonding on DNA-binding affinity. Journal of Inorganic Biochemistry, 98(2), 219–230. https://doi.org/10.1016/j.jinorgbio.2003.09.003
  • Markaryan, E. A., & Samodurova, A. G. (1989). Advances in the chemistry of isochroman. Russian Chemical Reviews, 58(5), 479–493. https://doi.org/10.1070/RC1989v058n05ABEH003455
  • Min, J., Meng-Xia, X., Dong, Z., Yuan, L., Xiao-Yu, L., & Xing, C. (2004). Spectroscopic studies on the interaction of cinnamic acid and its hydroxyl derivatives with human serum albumin. Journal of Molecular Structure, 692(1-3), 71–80. https://doi.org/10.1016/j.molstruc.2004.01.003
  • Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/10.1002/jcc.21256
  • Mostafavinia, S. E., & Hoshyar, R. (2016). Spectroscopic studies on the interaction of anti cancer rosemary with ctDNA. Gene, Cell and Tissue, 3(2), 35368–35372. https://doi.org/10.17795/gct-35638
  • Mukherjee, A., Lavery, R., Bagchi, B., & Hynes, J. T. (2008). On the molecular mechanism of drug intercalation into DNA: a simulation study of the intercalation pathway, free energy, and DNA structural changes. Journal of the American Chemical Society, 130(30), 9747–9755. https://doi.org/10.1021/ja8001666
  • Ozluer, C., & Kara, H. E. S. (2014). In vitro DNA binding studies of anticancer drug idarubicin using spectroscopic techniques. Journal of Photochemistry and Photobiology. B, Biology, 138, 36–42. https://doi.org/10.1016/j.jphotobiol.2014.05.015
  • Parveen, M., Azeem, M., Aslam, A., Azam, M., Siddiqui, S., Tabish, M., Malla, A. M., Min, K., Rodrigues, V. H., Al-Resayes, S. I., & Alam, M. (2022). Isolation, identification, spectral studies and X-ray crystal structures of two compounds from Bixa orellana, DFT calculations and DNA binding studies. Crystals, 12(3), 380–401. https://doi.org/10.3390/cryst12030380
  • Paul, P., Hossain, M., Yadav, R. C., & Kumar, G. S. (2010). Biophysical studies on the base specificity and energetics of the DNA interaction of photoactive dye thionine: spectroscopic and calorimetric approach. Biophysical Chemistry, 148(1-3), 93–103. https://doi.org/10.1016/j.bpc.2010.02.015
  • Perveen, F., Qureshi, R., Ansari, F. L., Kalsoom, S., & Ahmed, S. (2011). Investigations of drug–DNA interactions using molecular docking, cyclic voltammetry and UV–Vis spectroscopy. Journal of Molecular Structure, 1004(1-3), 67–73. https://doi.org/10.1016/j.molstruc.2011.07.027
  • Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera—a visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084
  • Phadte, A. A., Banerjee, S., Mate, N. A., & Banerjee, A. (2019). Spectroscopic and viscometric determination of DNA-binding modes of some bioactive dibenzodioxins and phenazines. Biochemistry and Biophysics Reports, 18, 100629–100635. https://doi.org/10.1016/j.bbrep.2019.100629
  • Qais, F. A., Abdullah, K. M., Alam, M. M., Naseem, I., & Ahmad, I. (2017). Interaction of capsaicin with calf thymus DNA: A multi-spectroscopic and molecular modelling study. International Journal of Biological Macromolecules, 97, 392–402. https://doi.org/10.1016/j.ijbiomac.2017.01.022
  • Qureshi, A. M., & Javed, S. (2020). Structural dynamics studies on the binding of aflatoxin B1 to chicken egg albumin using spectroscopic techniques and molecular docking. Journal of Biomolecular Structure & Dynamics, 38(11), 3144–3155. https://doi.org/10.1080/07391102.2019.1652690
  • Rahman, Y., Afrin, S., Husain, M. A., Sarwar, T., Ali, A., & Tabish, M.. (2017). Unravelling the interaction of pirenzepine, a gastrointestinal disorder drug, with calf thymus DNA: An in vitro and molecular modelling study. Archives of Biochemistry and Biophysics, 625-626, 1–12. https://doi.org/10.1016/j.abb.2017.05.014
  • Ramana, M. M. V., Betkar, R., Nimkar, A., Ranade, P., Mundhe, B., & Pardeshi, S. (2015). In vitro DNA binding studies of antiretroviral drug nelfinavir using ethidium bromide as fluorescence probe. Journal of Photochemistry and Photobiology. B, Biology, 151, 194–200. https://doi.org/10.1016/j.jphotobiol.2015.08.012
  • Reha, D., Kabelác, M., Ryjácek, F., Šponer, J., Šponer, J. E., Elstner, M., Suhai, S., & Hobza, P. (2002). Intercalators. 1. Nature of stacking interactions between intercalators (ethidium, daunomycin, ellipticine, and 4 ‘, 6-diaminide-2-phenylindole) and DNA base pairs. Ab initio quantum chemical, density functional theory, and empirical potential study. Journal of the American Chemical Society, 124(13), 3366–3376. https://doi.org/10.1021/ja011490d
  • Rehman, S. U., Sarwar, T., Ishqi, H. M., Husain, M. A., Hasan, Z., & Tabish, M. (2015). Deciphering the interactions between chlorambucil and calf thymus DNA: a multi-spectroscopic and molecular docking study. Archives of Biochemistry and Biophysics, 566, 7–14. https://doi.org/10.1016/j.abb.2014.12.013
  • Samreen, Qais, F. A., & Ahmad, I. (2022). In silico screening and in vitro validation of phytocompounds as multidrug efflux pump inhibitor against E. coli. Journal of Biomolecular Structure and Dynamics, 1–13. https://doi.org/10.1080/07391102.2022.2029564
  • Sarwar, T., Husain, M. A., Rehman, S. U., Ishqi, H. M., & Tabish, M. (2015). Multi-spectroscopic and molecular modelling studies on the interaction of esculetin with calf thymus DNA. Molecular bioSystems, 11(2), 522–531. https://doi.org/10.1039/c4mb00636d
  • Sarwar, T., Ishqi, H. M., Rehman, S. U., Husain, M. A., Rahman, Y., & Tabish, M. (2017). Caffeic acid binds to the minor groove of calf thymus DNA: A multi-spectroscopic, thermodynamics and molecular modelling study. International Journal of Biological Macromolecules, 98, 319–328. https://doi.org/10.1016/j.ijbiomac.2017.02.014
  • Shahabadi, N., & Maghsudi, M. (2014). Multi-spectroscopic and molecular modeling studies on the interaction of antihypertensive drug; methyldopa with calf thymus DNA. Molecular bioSystems, 10(2), 338–347. https://doi.org/10.1039/c3mb70340a
  • Siddiqui, S., Ameen, F., Kausar, T., Nayeem, S. M., Rehman, S. U., & Tabish, M. (2021). Biophysical insight into the binding mechanism of doxofylline to bovine serum albumin: An in vitro and in silico approach. Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy, 249, 119296. https://doi.org/10.1016/j.saa.2020.119296
  • Siddiqui, S., Mujeeb, A., Ameen, F., Ishqi, H. M., Rehman, S. U., & Tabish, M. (2021). Investigating the mechanism of binding of nalidixic acid with deoxyribonucleic acid and serum albumin: A biophysical and molecular docking approaches. Journal of Biomolecular Structure and Dynamics, 39(2), 570–585. https://doi.org/10.1080/07391102.2020.1711808
  • Silva, J., Rocha, M. N., & Marinho, E. M. (2021). Evaluation of the ADME, toxicological analysis and molecular docking studies of the anacardic acid derivatives with potential antibacterial effects against staphylococcus aureus. Journal of Analytical & Pharmaceutical RESEARCH, 10(5), 177–194.
  • Silva, M. M., Nascimento, E. O. O., Silva, E. F., Araújo, J. X. d., Santana, C. C., Grillo, L. A. M., de Oliveira, R. S., R R Costa, P., Buarque, C. D., Santos, J. C. C., & Figueiredo, I. M. (2017). Interaction between bioactive compound 11a-N-tosyl-5-deoxi-pterocarpan (LQB-223) and Calf thymus DNA: Spectroscopic approach, electrophoresis and theoretical studies. International Journal of Biological Macromolecules, 96, 223–233. https://doi.org/10.1016/j.ijbiomac.2016.12.044
  • Silva, M. M., Savariz, F. C., Silva-Júnior, E. F., Aquino, T. M. d., Sarragiotto, M. H., Santos, J. C. C., & Figueiredo, I. M. (2016). Interaction of β-Carbolines with DNA: spectroscopic studies, correlation with biological activity and molecular docking. Journal of the Brazilian Chemical Society, 27, 1558–1568. https://doi.org/10.5935/0103-5053.20160035
  • Sirajuddin, M., Ali, S., & Badshah, A. (2013). Drug–DNA interactions and their study by UV–Visible, fluorescence spectroscopies and cyclic voltametry. Journal of Photochemistry and Photobiology. B, Biology, 124, 1–19. https://doi.org/10.1016/j.jphotobiol.2013.03.013
  • Sousa da Silva, A. W., & Vranken, W. F. (2012). ACPYPE-Antechamber python parser interface. BMC Research Notes, 5(1), 367–368. https://doi.org/10.1186/1756-0500-5-367
  • Spackova, N. A., Cheatham, T. E., Ryjacek, F., Lankas, F., Van Meervelt, L., Hobza, P., & Sponer, J. (2003). Molecular dynamics simulations and thermodynamics analysis of DNA − drug complexes. Minor groove binding between 4‘, 6-diamidino-2-phenylindole and DNA duplexes in solution. Journal of the American Chemical Society, 125(7), 1759–1769. https://doi.org/10.1021/ja025660d
  • Tao, M., Zhang, G., Pan, J., & Xiong, C. (2016). Deciphering the groove binding modes of tau-fluvalinate and flumethrin with calf thymus DNA. Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy, 155, 28–37. https://doi.org/10.1016/j.saa.2015.11.006
  • Wei, W., Gao, S. G., & Shi, N. N. (2006). Study on the interaction between gatifloxacin mesylate and salmon sperm DNA by fluorescence method. Journal of the Chinese Chemical Society, 53(3), 721–726. https://doi.org/10.1002/jccs.200600095
  • Zhang, G., Hu, X., & Fu, P. (2012). Spectroscopic studies on the interaction between carbaryl and calf thymus DNA with the use of ethidium bromide as a fluorescence probe. Journal of Photochemistry and Photobiology. B, Biology, 108, 53–61. https://doi.org/10.1016/j.jphotobiol.2011.12.011
  • Zhang, G., Hu, X., Zhao, N., Li, W., & He, L. (2010). Studies on the interaction of aminocarb with calf thymus DNA by spectroscopic methods. Pesticide Biochemistry and Physiology, 98(2), 206–212. https://doi.org/10.1016/j.pestbp.2010.06.008

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.