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

Abstract

Background: 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. Methods: 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. Results: 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. Conclusions: 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.

Crystal Structures of Novel Allosteric Peptide Inhibitors of HIV Integrase Identify New Interactions at the LEDGF Binding Site

“…HIV-IN has been proven to be a clinically valid target; however, resistance to inhibition by active-site inhibitors, including raltegravir (Isentress), has been observed to be rapid in the clinic even in the presence of optimised, highly active antiretroviral therapy (HAART) regimens. [1] Therefore, other strategies for inhibiting the essential integration process are being considered and include the targeting of novel pockets [2] and blocking the interactions of the host cofactor cell lens epithelium-derived growth factor (LEDGF, also known as p75) with HIV-IN. [3][4][5] Several viral and host cofactors have been identified that regulate the function of HIV-IN as part of the preintegration complex (PIC).…”

Fueling HIV-1 integrase drug design with structural insights

“…In recent years, there has been a steady release of high-resolution IN CCD cocrystal structures containing small molecules or fragments derived from SPR and STD-NMR fragment-based screens. These ligands bind various pockets on the IN surface and delineate local pharmacophoric features [12][13][14]. Although binding to some of these sites has not yet been shown to interfere with IN activity (either directly or indirectly), the conserved nature and pleiotropic effects associated with these sites together with the data support strategies to develop novel potent compounds.…”

“…2a). In a series of papers, Wielens and Rhodes describe their application of (Saturation Transfer Difference) Nuclear Magnetic Resonance (STD-NMR), Surface Plasmon Resonance (SPR) and high resolution X-ray crystallography in a fragment-based screen for IN CCD binders [12][13][14].…”

“…In another paper, Rhodes et al investigate a pocket sitting right behind CCD helix 4 (containing E152 of the catalytic DDE motif, Fig. 2d) [14]. Starting from an identified N-benzyl indolinone, the authors applied structure-based drug design to elaborate this fragment into a series of compounds.…”

“…LEDGINS also have the benefit of inhibiting IN catalytic activity allosterically [20][21][22]. Other, purely allosteric inhibitors of IN have been reported as well and various starting points for in silico optimization are present in the literature [12][13][14]. A further strategy to inhibit IN activity is to perturb its crucial oligomerization equilibrium, either by shifting it to the inactive monomer or to a certain other species like the dimer or tetramer [11,22,23].…”