Molecular dynamics simulation method was used to study the complex structure of HIV-1 integrase and its inhibitor aurintricarboxylic acid (Aurin). The HIV-1 integrase core domain (IN-A) with a Mg²⁺ and inhibitor Aurin molecule are docked as a complex with the program Autodock. A 950 ps molecular dynamics simulation was carried out on the complex system. The simulation shows the stability of the complex. It was found that there are two stable hydrogen bonds between IN-A and Aurin in the predicted complex structure. The Mg²⁺ is also chelated with an oxygen atom of Aurin. The mean electrostatic interaction and the mean van der Waals interaction between IN-A and Aurin are -205.8 and -162.7 kJ/mol, respectively. The result of our simulation and the predicted complex structure will be useful in designing anti HIV-1 integrase inhibitor.

Key words: HIV-1 integrase, aurintricarboxylic acid, docking, melocular dynamics