Abstract: To rationally design inhibitors targeting at HIV-1 transmembrane protein-gp41,molecular docking,molecular dynamic(MD) simulation and free energy calculation are adopted to explore the binding mode between gp41 and its inhibitor NB-2. A de novo drug design method inhibitors of gp41,and two main binding modes between NB-2 and gp41 are attained by molecular docking. The results obtained with MD simulation and binding energy calculation indicate that Mode 1 is superior to another and is proposed to be the rational binding mode. Based on this mode,103 new compounds were designed and evaluated for their binding affinities into gp41. These compounds possess structural features not seen in known HIV-1 gp41 inhibitors and most of them bind into gp41 with lower binding free energy than NB-2. The binding modes reasonably interpret the interactions between NB-2 and gp41.