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.

Download full-text


Available from: Gregory Paul Savage,
  • Source
    • "Due to the lack of exact crystallographic data on the full integrase or integration complex, this mechanism is only a strong hypothesis. Other possible mechanisms should also be considered including the allosteric interaction of inhibitors with the integration complex [96] [97] [98]. Nevertheless, there are several data that have confirmed this approach. "
    [Show abstract] [Hide abstract]
    ABSTRACT: HIV integrase became an important target for drug development more than twenty years ago. However, progress has been hampered by the lack of assays suitable for high throughput screening, a reliable crystal structure or pharmacophore. Thus, a real breakthrough was only observed in 2007 with the introduction of the first integrase inhibitor, raltegravir, into treatment. To date, the armament of integrase inhibitors is broad and covers several drugs from different classes that are under clinical trials. Among them, quinoline-based compounds and analogues occupy an important place. This review is focused on those compounds that have a quinoline scaffold and attempts to answer the question of whether quinoline is privileged for these activities. In fact, quinoline has been claimed as a privileged structure several times for different fields of activities. A closer look at its structural features may reveal the prerequisites responsible for the popularity of quinoline-based inhibitors of HIV integrase.
    Current pharmaceutical design 10/2012; 19(10). DOI:10.2174/1381612811319100008 · 3.45 Impact Factor
  • Source
    • "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. "
    [Show abstract] [Hide abstract]
    ABSTRACT: A fragment-based screen against human immunodeficiency virus type 1 (HIV) integrase led to a number of compounds that bound to the lens epithelium derived growth factor (LEDGF) binding site of the integrase catalytic core domain. We determined the crystallographic structures of complexes of the HIV integrase catalytic core domain for 10 of these compounds and quantitated the binding by surface plasmon resonance. We demonstrate that the compounds inhibit the interaction of LEDGF with HIV integrase in a proximity AlphaScreen assay, an assay for the LEDGF enhancement of HIV integrase strand transfer and in a cell based assay. The compounds identified represent a potential framework for the development of a new series of HIV integrase inhibitors that do not bind to the catalytic site of the enzyme.
    PLoS ONE 07/2012; 7(7):e40147. DOI:10.1371/journal.pone.0040147 · 3.23 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: An optimised method of solution cyclisation gave us access to a series of peptides including SLKIDNLD (2). We investigated the crystallographic complexes of the HIV integrase (HIV-IN) catalytic core domain with 13 of the peptides and identified multiple interactions at the binding site, including hydrogen bonds with residues Thr125 and Gln95, that have not previously been described as being accessible within the binding site. We show that the peptides inhibit the interaction of lens epithelium-derived growth factor (LEDGF) with HIV-IN in a proximity AlphaScreen assay and in an assay for the LEDGF enhancement of HIV-IN strand transfer. The interactions identified represent a potential framework for the development of new HIV-IN inhibitors.
    ChemBioChem 10/2011; 12(15):2311-5. DOI:10.1002/cbic.201100350 · 3.09 Impact Factor
Show more