Development and Validation of Empirical Force Field Parameters for Netropsin

• Published in: Journal of chemical information and modeling 2005-11, Vol.45 (6), p.1546-1552
• Main Authors: Bren, Urban, Hodošček, Milan, Koller, Jože
• Format: Article
• Language: English
• Subjects: Algorithms; CAD; Chemical Phenomena; Chemistry, Physical; Computer aided design; Deoxyribonucleic acid; DNA; Gene expression; Geometry; Ligands; Models, Molecular; Molecular Conformation; Molecules; Netropsin - chemistry; Reproducibility of Results; Spectroscopy, Fourier Transform Infrared; Tumors
• ISSN: 1549-9596; 1549-960X
• DOI: 10.1021/ci050151r

The netropsin molecule preferentially binds to the four consecutive A·T base pairs of the DNA minor groove and could therefore inhibit the expression of specific genes. The understanding of its binding on a molecular level is indispensable for computer-aided design of new antitumor agents. This knowledge could be obtained via molecular dynamics (MD) and docking simulations, but in this case appropriate force field parameters for the netropsin molecule should be explicitly defined. Our parametrization was based on the results of quantum chemical calculations. The resulting set of parameters was able to reproduce bond lengths, bond angles, torsional angles of the ab initio minimized geometry within 0.03 Å, 3 deg and 5 deg, respectively, and its vibrational frequencies with a relative error of 4.3% for low and 2.8% for high energy modes. To show the accuaracy of the developed parameters we calculated an IR spectrum of the netropsin molecule using MD simulation and found it to be in good agreement with the experimental one. Finally, we performed a 10 ns long MD simulation of the netropsin−DNA complex immersed in explicit water. The overall complex conformation remained stable at all times, and its secondary structure was well retained.