Structural Basis for a New Mechanism of Inhibition of H I V-1 Integrase Identified by Fragment Screening and Structure-Based Design

Avexa Ltd, Richmond, Australia.
Antiviral chemistry & chemotherapy 04/2011; 21(4):155-68. DOI: 10.3851/IMP1716
Source: PubMed


HIV-1 integrase is a clinically validated therapeutic target for the treatment of HIV-1 infection, with one approved therapeutic currently on the market. This enzyme represents an attractive target for the development of new inhibitors to HIV-1 that are effective against the current resistance mutations.
A fragment-based screening method employing surface plasmon resonance and NMR was initially used to detect interactions between integrase and fragments. The binding sites of the fragments were elucidated by crystallography and the structural information used to design and synthesize improved ligands.
The location of binding of fragments to the catalytic core of integrase was found to be in a previously undescribed binding site, adjacent to the mobile loop. Enzyme assays confirmed that formation of enzyme-fragment complexes inhibits the catalytic activity of integrase and the structural data was utilized to further develop these fragments into more potent novel enzyme inhibitors.
We have defined a new site in integrase as a valid region for the structure-based design of allosteric integrase inhibitors. Using a structure-based design process we have improved the activity of the initial fragments 45-fold.

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    • "The ability to reproducibly generate high quality CCD IN crystals allowed us to generate all complex structures by soaking in the compounds with preformed HIV IN CCD crystals. The protein was crystallized as described previously [10]. Briefly, purified hexa-His core3H protein was concentrated to 5.5 mg/ml in 40 mM Tris pH 8.0, 250 mM NaCl, 30 mM MgCl2 and 5 mM DTT. Drops were set up in SD-2 (IDEX Corp) sitting drop plates using a Phoenix robot (Art Robbins Industries) with 50 µl of crystallant in the reservoir and droplets consisting of 200 nl of the reservoir and 200 nl of the protein sample. "
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