effect of G-quadruplex on aromaticity of phenanthroline based ligands: mlecular dynamics simulation and density functional theory methods

Document Type : Original Article

Authors

• Mohadese Bazobandi ¹
• Mohammad Reza Bozorgmehr ²
• Ali Mahmoudi ³
• Ali Morsali ⁴

¹ student,, IAU

² Rahnamaee Road, No. 24

³ Associate prof. IAU

⁴ Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran

Abstract

G-quadruplexes are biostructures that are used as biomarkers. These compounds are composed of four guanine sheets. Studying the interaction of G-quadruplex with planar ligands is very important. In this work, the effect of G-quadruplex on the aromaticity of three phenanthroline based ligands was studied by molecular dynamics simulation and density functional theory. The investigated ligands are: N,N'-(dibenzo [b,j] [1,7]phenanthroline-2,10-diylbis (methylene)) die-thanamine (L1), N,N'-(dibenzo [b,j] [1,7] phenanthroline-2,10diylbis (methylene)) bis (N-methylpropan-1-amine) (L2) and N1-(dibenzo [b, j] [1,7] phenanthroline-7-ylmethyl)-N3 -methy lpropane-1,3-diamine (L3) which have 5 aromatic rings in their structure. To check the effect of temperature, calculations were repeated at four temperatures of 20, 40, 60 and 80 degrees Celsius. The HOMA index was calculated as an index of the aromaticity of the rings. The obtained results show that the L1 ligand has higher aromaticity than the other two ligands. Also, as the temperature increases, the aromaticity of the ligand rings decreases. On the other hand, the terminal two rings of the ligands are more affected by G-quadruplex. In general, the aromaticity of the five-membered rings of the ligands increases with the interaction with the G-quadruplex.

Keywords

• nucleic acid
• aromaticity
• biosensor
• phenantroline
• quadruplex

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