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Molecular Dynamics Studies of the Wild-Type and Double Mutant HIV-1 Integrase Complexed with the 5CITEP Inhibitor: Mechanism for Inhibition and Drug Resistance

Maria L. Barreca^*, Keun Woo Lee, Alba Chimirri^* and James M. Briggs

^*Dipartimento Farmaco-Chimico, Università di Messina, 98168 Messina, Italy; and Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001 USA

Correspondence: Address reprint requests to Dr. James Briggs, Dept. of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001. Tel.: 713-743-8366; Fax: 713-743-8351; E-mail: jbriggs{at}uh.edu.

The human immunodeficiency virus type 1 (HIV-1) integrase (IN) is an essential enzyme in the life cycle of the virus and is an attractive target for the development of new drugs useful in acquired immunodeficiency syndrome multidrug therapy. Starting from the crystal structure of the 5CITEP inhibitor bound to the active site in the catalytic domain of the HIV-1 IN, two different molecular dynamics simulations in water have been carried out. In the first simulation the wild-type IN was used, whereas in the second one the double mutation T66I/M154I, described to lead to drug resistance, was introduced in the protein. Compelling differences have been observed in these two structures during analyses of the molecular dynamics trajectories, particularly in the inhibitor binding modes and in the conformational flexibility of the loop (residues 138–149) located near the three catalytic residues in the active site (Asp⁶⁴, Asp¹¹⁶, Glu¹⁵²). Because the conformational flexibility of this region is important for efficient biological activity and its behavior is quite different in the two models, we suggest a hypothetical mechanism for the inhibition and drug resistance of HIV-1 IN. These results can be useful for the rational design of more potent and selective integrase inhibitors and may allow for the design of inhibitors that will be more robust against known resistance mutations.

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