Molecular docking study of oligonucleotides with D-mannitol

  • V. Shchodryi Institute of molecular biology and genetics NASU, Ukraine, 03143, Kyiv, 150 Zabolotnogo street
  • D. Lozhko Institute of molecular biology and genetics NASU, Ukraine, 03143, Kyiv, 150 Zabolotnogo street
  • Z. Tkachuk Institute of molecular biology and genetics NASU, Ukraine, 03143, Kyiv, 150 Zabolotnogo street
DOI: https://doi.org/10.7124/visnyk.utgis.15.1.714

Abstract

Aim. Complex of yeast RNA and D-mannitol has a specific antiviral activity. This complex inhibits the
neuraminidase and hemagglutinin activity of viruses such as influenza, parainfluenza and thus it blocks virus entry into the cell and his replication. So, nowadays, study of the interaction of this compound is an important task. Study interaction of the oligoribonucleotides and oligodesoxynucleotides with D mannitol molecule. Methods. Molecular modeling structure of oligoribonucleotides and oligodesoxynucleotides were done by using «Hyperchem» software package. The AutoDock program was used to perform accuracy molecular docking. Results. Were obtained binding energies of D-mannitol molecule with oligoribonucleotides and oligodesoxynucleotides. We have shown the possible connections between atoms of oligonucleotides and D-mannitol molecule. Conclusions. The modeling results should give more detailed information about nature of the oligonucleotides binding with a shugar alcohol D-mannitol.

Keywords: molecular docking, oligonucleotides, D-mannitol, binding energies.

References

Sullenger B. A., Gilboa E. Emerging clinical applications of RNA. Nature. 2002. Vol. 418(6894). P. 252-258. doi: 10.1038/418252a

Burnett J.C., Rossi J.J. RNA-Based therapeurics: current progress and future prospects. Chem Biol. 2012. Vol. 19(1). P. 60-71. doi: 10.1016/j.chembiol.2011.12.008

Tkachuk Z. Multiantivirus compound, composition and method for treatment of virus disease. US patent 2014. May,13. No 8722642. B2. P. 61.

Vivcharyk M.M., Ilchenko O.O., Levchenko S.M., Tkachuk Z.Yu. Complexation of RNA with mannitol, its spectral characteristics and biological activity. Dopov. Nac. akad. nauk Ukr. 2016. No 10. P. 78-83. doi: 10.15407/dopovidi2016.10.078

Ye P., Byron T. Characterization of D-Mannitol by Thermal Analysis, FTIR, and RamanSpectroscopy. American Laboratory. 2008. Vol. 40(14). P. 24-27.

Maurin C., Bailly F., Cotelle P. Structure-activity relationships of HIV-1 integrase inhibitors enzyme-ligand interactions. Curr. Med. Chem. 2003. Vol. 10(18). P. 1795-1810.

Morris G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., Olson, A. J. AutoDock 4 and AutoDockTools4: automated docking with selective receptor flexiblity. J. Comput. Chem. 2009. Vol. 30(16). P. 2785-2791. doi: 10.1002/jcc.21256

HyperChem(TM) Professional 7.51, Hypercube, Inc., 1115 NW 4th Street, Gainesville, Florida 32601, USA

Mustard D., Ritchie D.W. Docking essential dynamics eigenstructures. Proteins. 2005. Vol. 60(2). P. 269-274. doi: 10.1002/prot.20569