The interaction pattern between PTP1B (one kind of protein tyrosine phosphatase) and its inhibitors (1,2 naphthoquinone derivatives) was investigated by using molecular mechanics and molecular dynamics. From the calculations, it can be found that the van der Waals interactions, the hydrophobic interactions, as well as the H bonding interactions are crucial for ligand binding. Meanwhile, the calculated results show that the interaction energy, ΔE, is closely correlated with the activity of inhibitors. In addition, from the calculation of contribution of the van der Waals and electrostatic interactions to ΔE and the analyses of the predicted structures of the complex, we found that the difference of the activities of inhibitors is attributed to the hydrophobic interaction, which afford us important information for designing non acid PTP1B inhibitors.

Key words: PTP1B, 1, 22naphthoquinone derivative, MD simulation, inhibitor