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Selection of gp41-mediated HIV-1 cell entry inhibitors from biased combinatorial libraries of non-natural binding elements

Nature Structural Biology volume 6, pages 953–960 (1999)Cite this article

Abstract

The trimeric, α-helical coiled-coil core of the HIV-1 gp41 ectodomain is thought to be part of a transient, receptor-triggered intermediate in the refolding of the envelope glycoprotein into a fusion-active conformation. In an effort to discover small organic inhibitors that block gp41 activation, we have generated a biased combinatorial chemical library of non-natural binding elements targeted to the gp41 core. From this library of 61,275 potential ligands, we have identified elements that, when covalently attached to a peptide derived from the gp41 outer-layer α-helix, contribute to the formation of a stable complex with the inner core and to inhibition of gp41-mediated cell fusion.

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Figure 1: Stereo view of contacts near the N-terminus of the outer helix of gp41.
Figure 2: A structure-based combinatorial approach to identifiy inhibitiors of gp41-mediated viral entry.
Figure 3: Optimization of an on-bead affinity-based assay for the determination of a biasing peptide sequence.
Figure 4: Building blocks used to construct the library.
Figure 5: Results of deconvoluting the library of non-peptide elements biased to interact with the gp41 inner core.
Figure 6: In vitro refolding of gp41 inner core–outer helix complexes.
Figure 7: Inhibition of gp41-mediated cell-cell fusion by outer helix peptides and peptide-hybrids.

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Acknowledgements

We thank N. Sinitskaya for technical assistance. M.F. acknowledges a fellowship from the Ministry of Education (Spain). The work was supported by NIH grants to D.O., D.C.W., and S.C.H. S.L.S., D.C.W., and S.C.H. are Investigators in the HHMI.

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Authors and Affiliations

  1. Department of Molecular and Cellular Biology, Harvard University, 7 Divinity Ave., Cambridge, 02138, Massachusetts, USA

    Marc Ferrer, Don C. Wiley & Stephen C. Harrison

  2. Department of Chemistry and Chemical Biology, Harvard University, 16 Oxford St., Cambridge, 02138, Massachusetts, USA

    Tarun M. Kapoor & Stuart L. Schreiber

  3. Department of Biochemistry, Brandeis University, 415 South St., Waltham, 02454, , Massachusetts, USA

    Tim Strassmaier & Dan Oprian

  4. Laboratory of Molecular Medicine, The Children's Hospital, 320 Longwood Ave., Boston, 02215, Massachusetts , USA

    Winfried Weissenhorn, Don C. Wiley & Stephen C. Harrison

  5. Howard Hughes Medical Institute.,

    Winfried Weissenhorn, Stuart L. Schreiber, Don C. Wiley & Stephen C. Harrison

  6. National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK

    John J. Skehel

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Correspondence to Stephen C. Harrison.

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Ferrer, M., Kapoor, T., Strassmaier, T. et al. Selection of gp41-mediated HIV-1 cell entry inhibitors from biased combinatorial libraries of non-natural binding elements. Nat Struct Mol Biol 6, 953–960 (1999). https://doi.org/10.1038/13324

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