Docking analysis of aryl derivatives of diepoxide alkylating agents

In this research, molecular structural manipulation of treosulfan alkylating agent and resultant changes in binding is studied to assist in designing derivatives of treosulfan for synthesis. Molecular docking has been conducted on simulated heterocyclic polyaromatic alkylating diepoxide derivatives of treosulfan with DNA nucleobases of dodecamer duplex of sequences d(CGCGAATTCGCG) and d(CGCGAATTCGCG) using Autodock vina package. Two series of simulated diepoxide molecules were designed with increasing aryl ring chain in linear and fused aryl way between the two epoxide reactive rings. Relationship between increasing no. of aryl rings (both linear and fused) between epoxide moieties on the binding energy values was evaluated. We also identified that designed molecules bind specifically to Guanine and Cytosine (GC) base pairs on DNA. Mode of interaction and resultant behavior as an alkylating agent or as minor groove binder was also found to be dependent up on the no. of aryl rings and their connectivity in the molecule. Both linearly bonded and fused aryl rings in higher number, between the epoxide rings, gave the strongest binding with the binding energy up to -8.1 and -8.7 Kcal/mol, respectively. These relationships can immensely help in designing and synthesis of derivatives of treosulfan like diepoxide based alkylating agents.