Molecular Dynamics simulation study of interaction of Ru-complex and calf thymus DNA

Ashwini Mali1∗, Avinash Kumbhar2∗, Bhalchandra Pujari3∗

1,3 Centre for Modeling and Simulation and

2Department of Chemistry,

∗Savitribai Phule Pune University, Pune-7

Need for discovery of new organometallic compounds in pharmaceutical industry, has been established for quite a long now. One of the emerging classes of these are of Ruthenium(Ru) complex compounds. Ru complex com- pounds have potential to replace the conventional platinum organometallic pharmaceuticals. Our study gives interaction of calf thymus DNA with Ru- complex computationally. All the calculations are performed using GROMACS- 2018 package. Structure of Ru-compound is provided by experimental group, and DNA structure is used from protein data bank(PDB), with PDB ID- 1BNA [d(CGCGAAT T CGCG)2]. Ru compound is first optimized using GAUSSIAN package and AmberTools is used to generate force field param- eters for Ru-DNA complex. The potential parameters for the system were derived using AMBER99SB force field implemented in gromacs code.

Our systems consist of three DNA stands with and without Ru-compound. RMSD analysis shows the increase in stability of DNAs in presence of Ru- compound and Helicity paramaters analysis shows increased bending of DNAs with the presence of Ru-compound as compared to the free standing DNAs. Hence, RMSD studies shows that in presence of Ru-compound DNA attains the stable form as compared to the free standing DNAs. Helicity parameter analysis highlights the deformation of the DNA structure, and stability.

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