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Rational design of small-molecule inhibitors of the LEDGF/p75-integrase interaction and HIV replication

Nature Chemical Biology volume 6, pages 442–448 (2010)Cite this article

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Abstract

Lens epithelium–derived growth factor (LEDGF/p75) is a cellular cofactor of HIV-1 integrase that promotes viral integration by tethering the preintegration complex to the chromatin. By virtue of its crucial role in the early steps of HIV replication, the interaction between LEDGF/p75 and integrase represents an attractive target for antiviral therapy. We have rationally designed a series of 2-(quinolin-3-yl)acetic acid derivatives (LEDGINs) that act as potent inhibitors of the LEDGF/p75-integrase interaction and HIV-1 replication at submicromolar concentration by blocking the integration step. A 1.84-Å resolution crystal structure corroborates the binding of the inhibitor in the LEDGF/p75-binding pocket of integrase. Together with the lack of cross-resistance with two clinical integrase inhibitors, these findings define the 2-(quinolin-3-yl)acetic acid derivatives as the first genuine allosteric HIV-1 integrase inhibitors. Our work demonstrates the feasibility of rational design of small molecules inhibiting the protein-protein interaction between a viral protein and a cellular host factor.

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Figure 1: Virtual screening of small molecules that inhibit the LEDGF/p75-IN interaction.
Figure 2: Resistance selection to 6.
Figure 3: Analysis of the mechanism of action of 6 by Q-PCR.
Figure 4: Crystal structure of 6 bound to the LEDGF/p75 binding pocket of the IN-core.

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Acknowledgements

We acknowledge A. Calleja for performing analytical chemistry on the compounds, M. Michiels for macrophage and integrase assays and L. Desender for performing large-scale protein purifications. We thank A. Jonckheer for information and communication technology support. X-ray diffraction data collection was done at the X06DA beamline of the Swiss Light Source, Paul Scherrer Institut, Villigen, Switzerland. We thank R. Clayton of Tibotec for providing raltegravir and elvitegravir as well as HXB2D-INN155H E92Q Q148H. Research was funded by the CellCoVir SBO grant (60813) of the Flemish Agentschap voor Innovatie door Wetenschap en Technologie, the FWO grant G.0530.08, the EC grant THINC (HEALTH-F3-2008-201032), the Research Fund and the Industrieel Onderzoeksfonds Program of the K.U. Leuven. A.V. is supported by a grant from the Institute for the Promotion of Innovation through Science and Technology in Flanders. F.C. is funded by an Industrieel Onderzoeksfonds mandate, and B.A.D. is funded by a Bijzonder Onderzoeksfonds-PhD scholarship for international cooperation with non-EEA countries outside the EEA.

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Author notes

  1. Frauke Christ, Arnout Voet and Arnaud Marchand: These authors contributed equally to this work.

Authors and Affiliations

  1. Division of Molecular Medicine, Laboratory for Molecular Virology and Gene Therapy, Katholieke Universiteit Leuven (KULeuven), Leuven, Belgium

    Frauke Christ, Belete A Desimmie, Nam Joo Van der Veken, Barbara Van Remoortel & Zeger Debyser

  2. Department of Chemistry, Division of Biochemistry, Laboratory for Biomolecular Modelling, Molecular and Structural Biology, KULeuven, Heverlee, Belgium

    Arnout Voet & Marc De Maeyer

  3. Department of Pharmaceutical Sciences, Laboratory for Biocrystallography, KULeuven, Leuven, Belgium

    Stefan Nicolet & Sergei V Strelkov

  4. Centre for Drug Design and Development, KULeuven R&D, KULeuven, Leuven, Belgium

    Patrick Chaltin

  5. Centre for Innovation and Stimulation of Medicines Development, Leuven, Belgium

    Arnaud Marchand, Damien Marchand, Dorothée Bardiot & Patrick Chaltin

  6. M.E. Müller Institute for Structural Biology, Biozentrum, University of Basel, CH-4056 Basel, Switzerland

    Stefan Nicolet

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Contributions

F.C. established the specific high-throughput screening tools for the LEDGF/p75-IN interaction, purified proteins and designed and guided the biological characterization of the compounds; A.V. designed and executed the modeling strategy; A.M. and P.C. guided and coordinated the medicinal chemistry; D.M. and D.B. performed organic synthesis; S.N. performed the cocrystallization studies; B.A.D. performed Q-PCR analysis, resistance selection and, together with B.V.R., antiviral testing; B.V.R. performed antiviral testing in T cells and primary cells; N.J.V.d.V. performed AlphaScreen assays; S.V.S. guided the crystallography; M.D.M. guided the modeling; Z.D. coordinated the project and designed experiments; F.C. and Z.D. prepared the manuscript.

Corresponding author

Correspondence to Zeger Debyser.

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Christ, F., Voet, A., Marchand, A. et al. Rational design of small-molecule inhibitors of the LEDGF/p75-integrase interaction and HIV replication. Nat Chem Biol 6, 442–448 (2010). https://doi.org/10.1038/nchembio.370

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