A Study on Docking Mode of HIV Protease and Their Inhibitors

Eiichi AKAHOa*, Garret MORRISb, David GOODSELLb, David WONGb and Arthur OLSONb

aFaculty of Pharmaceutical Sciences, Kobe Gakuin University
518 Arise, Ikawadani-cho, Nishi-ku, Kobe 651-2180 JAPAN
bDepartment of Molecular Biology, the Scripps Research Institute
10666 North Torrey Pines Road, La Jolla CA 92037-5025 USA

(Received: September 20, 2000; Accepted for publication: December 6, 2000; Published on Web: January 30, 2001)

The capability to propose feasible ways of binding a putative ligand inhibitor to a known receptor site is crucial to the successful structure-based drug design. A computer docking approach is to position or "dock" ligand and receptor molecules together in many different ways and then score each orientation by applying a reasonable evaluation function. AutoDock3.0 is an unbiased type docking program in which a user does not have to direct a ligand to an active site, but the system finds an optimal position after a ligand is placed in a random manner. Synthesized derivatives of the intact inhibitor (inh1) of HIV protease were investigated for their docking modes as compared with their Ki values. Among the derivatives, inh3trans and inh6H were found to be more powerful inhibitors of HIV protease than the others. Gibbs free energy calculated by applying molecular mechanics interaction energies was compared with the one obtained by using experimental inhibitory potencies for a series of HIV protease inhibitors, and a fairly good correlation was found between the two. Based on this favorable correlationship between the computational and the experimental results, the computational experiments were pursued for the compounds drawn by Sybyl taking into consideration the fact that unexploited carbon affinity regions (or hydrophobic regions) with sizable volume were detected on the docking study of inh1 and inh8 against HIV protease. Those were compounds with a t-butyl substituted by various hydrophobic side chains. Among those a compound with a benzyl group exhibited the lowest docking energy. Since one of the goals of this paper was to perform the computational drug-design experiment to investigate potential HIV protease inhibitors, the authors would like to leave the clinical investigational work for the expertise of those areas.

Keywords: Computer docking, Drug design, HIV protease, Gibbs free energy, Ligand inhibitor

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