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


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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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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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).

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