Drug design and molecular modelling of boron compounds

Boron and aromatic compounds are biologically active molecules. Molecular dynamics simulations are the cheapest and the fastest way to illuminate the biochemical reactions associated with such molecules. The performing of molecular simulations depends on the force field files. In this study, parameters required for the simulations of both boron compounds, containing aromatic structure, and boronate derivatives were produced and tested under the names BAFF1 and BAFF2, in accordance with the Amber simulation program which is the most used in the market. To develop force field parameters, all of the frequency and potential energy surface scans were performed at the B3LYP / 6,311G ++ (2d, 2p) level, the RESP charges were calculated at the HF/6-31G* level. Then obtained parameters were combined in the force field file. The power of the novel boron force field to reproduce the experimental structure was tested against x-ray structures taken from the Cambridge Crystallographic Data Center and the results showed that the experimental X-ray structures and optimized geometries with force field are in very good agreement. In the second test, the ligand, proven to have the anti-cancer property against MCF-7 breast cancer by experimental data in the literature, was simulated with DNA. It was observed that the minor cavity binding position where the ligand was bound to the DNA by docking process did not change for 10 ns. This result showed that experimental data has been supported by the simulation. Consequently, two sperate force fields were generated, called BAFF1 and BAFF2, and molecular dynamics simulations of boron compounds were carried out, making it possible to use them in drug design.