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Logo of nihpaAbout Author manuscriptsSubmit a manuscriptHHS Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
J Am Chem Soc. Author manuscript; available in PMC 2010 May 19.
Published in final edited form as:
PMCID: PMC2873035

Inhibiting HIV Fusion with a β-Peptide Foldamer

Linear peptides derived from the HIV gp41 C-terminus (C-peptides), such as the 36-residue Fuzeon, are potent HIV fusion inhibitors.1 These molecules bind to the N-peptide region of gp41 and act as dominant negative inhibitors of an intramolecular protein–protein interaction that powers fusion of the viral and host cell membranes.24 The gp41 N-peptide region contains a surface pocket35 that is less prone to mutation than other gp41 regions or HIV enzymes.6 This pocket is occupied in the post-fusion state by three α-helical residues found near the gp41 C-terminus: Trp628, Trp631, and Ile635; together, these residues comprise the WWI epitope.35 Simple7,8 and constrained9,10 α-peptides, aromatic foldamers,11 peptide–small molecule conjugates,12 and small molecules13 that bind this pocket inhibit gp41-mediated fusion. Here, we describe a set of β3-decapeptides, βWWI-1–4, in which the WWI epitope is presented on one face of a short 14-helix (Figure 1).14 βWWI-1–4 bind to a validated gp41 model in vitro and inhibit viral fusion in cell culture. Our work suggests that β-peptide 14-helices, which are likely to be metabolically stable and protease resistant,1517 can function as in vivo inhibitors of intramolecular protein–protein interactions.18

Figure 1
Sequences of βWWI-1–4 and βWAI-1. β3-homoamino acids are identified by the single letter code used for the corresponding α-amino acid. O signifies ornithine.

We synthesized19 four β3-peptides (βWWI-1–4) containing the WWI epitope in both possible orientations on each available face of a β3-decapeptide14 possessing significant 14-helix stability in aqueous solution due to electrostatic macrodipole stabilization20 and side chain–side chain salt bridges.21,22 We also prepared βWAI-1 as a control, as previous work has documented the significant contribution of the central Trp631 to gp41 affinity and viral infectivity.7 The circular dichroism spectra of βWWI-1–4 and βWAI-1 all display the expected minima at 214 nm (Figure 2A).14,20,23 The spectra of βWWI-1–4, but not βWAI-1, also show a transition at 227 nm, which may result from distortions in the 14-helix or the presence of two tryptophan residues in close proximity.24 Two-dimensional NMR spectroscopy in CD3OH confirmed the presence of 14-helix structure in βWWI-1; NOESY spectra showed five of seven possible Cα(i) → Cβ(i+3) NOEs and three of six possible (CN(i) → Cβ(i+3) NOEs, and no NOEs inconsistent with 14-helical structure were observed.19

Figure 2
(A) CD spectra of βWWI-1–4 and βWAI-1 at 5 μM in PBC buffer. (B) Fluorescence polarization analysis of the binding of IZN17 and (C) the inhibition of C14wtFlu• IZN17 complexation by βWWI-1–4 and ...

Each β-peptide was fluorescently labeled19 at the N-terminus and used in direct fluorescence polarization (FP) experiments to determine its affinity for the gp41 model IZN17.25 IZN17, which exists as a stable trimer in solution,25 contains 24 residues of an isoleucine zipper26 fused in register to 17 residues from gp41 containing the pocket for the WWI functional epitope.25 All four β-peptides, βWWI-1–4Flu, bound IZN17 well, with equilibrium affinities of 0.75 ± 0.1, 1.0 ± 0.3, 2.4 ± 0.7, and 1.5 ± 0.4 μM, respectively (Figure 2A). Interestingly, in this case, IZN17 affinity is relatively insensitive to the orientation of the WWI epitope relative to either the 14-helix macrodipole or the salt-bridging face.14 The affinity of βWWI-1–4 for IZN17 is nearly identical to that of the highest affinity α-peptide of comparable size (Kd = 1.2 μM).10 Also, βWWI-1 binds IZN17 with significantly higher affinity than it binds carbonic anhydrase II (Kd ≥ 115 μM) or calmodulin (Kd > 100 μM), two globular proteins that recognize hydrophobic and/or helical molecules.19

Two experiments were performed to investigate the binding mode of βWWI-1–4. First we performed competition fluorescence polarization experiments to assess whether βWWI-1–4 competed with C14wtFlu (suc-MTWMEWDR EINNYTCFlu), a fluorescent analogue of a gp41 ligand10 that binds IZN17 with an affinity of 4.1 μM. βWWI-1–4 competed well, with IC50 values of 4.0 ± 0.7, 4.6 ± 0.4, 13 ± 4.1, and 3.3 ± 1.4 μM, respectively (Figure 2C). We also synthesized the βWWI-1 analogue βWAI-1 with alanine in place of the central tryptophan of the WWI epitope. βWAI-1Flu bound IZN17 with lower affinity (Kd ≥ 20 μM) than βWWI-1 and βWAI-1 and competed poorly with C14wtFlu for IZN17 (IC50 = 72.9 ± 5.0 μM).27 These data suggest that the affinity of βWWI-1–4 for IZN17 results from interactions between the WWI epitope and the targeted IZN17 pocket.

βWWI-1–4 were then evaluated for their ability to inhibit gp41-mediated cell–cell fusion in an assay that accurately predicts potency in HIV infectivity assays.9 HeLa cells that express CD4 and a tat inducible β-gal gene28 were co-cultured in the presence of varying concentrations of β-peptides with HXB2 Env-expressing CHO cells29 that express HIV-1 env, tat, and rev. Without inhibitors, these cells fuse and form syncytia that express β-galactosidase and can be detected with 5-bromo-4-chloro-3-indoyl-β-D-galactoside.28 β-Peptides βWWI-1–4 inhibited cell–cell fusion with EC50 values of 27 ± 2.5, 15 ± 1.6, 13 ± 1.9, and 5.3 ± 0.5 μM, respectively, whereas βWAI-1 did not (Figure 2).19 The EC50 values measured for βWWI-1–4 are equal if not better than those measured for L-peptides,10 cyclic D-peptides,9 aromatic foldamers,11 or small molecules.13 Although less potent than Fuzeon (IC50 = 0.11 nM),1 βWWI-1–4 are one-third the size, likely metabolically stable,15 and can be optimized combinatorially. These results suggest that short β-peptide 14-helices can inhibit intramolecular protein–protein interactions in vivo. Molecules, such as βWWI-1–4, could represent leads toward inhibitors or antigens effective against HIV or other viruses, such as SARS,30 Ebola, HRSV, and influenza,31 that employ common fusion mechanisms.

Supplementary Material

Supporting Information


This work was supported by the NIH (GM65453 and GM74756 to A.S., P01 GM066521 to M.K.), the National Foundation for Cancer Research, the Robert Leet and Clara Guthrie Patterson Trust, and in part by a grant to Yale University, in support of A.S., from the Howard Hughes Medical Institute. B.W. was supported by an NIH training grant in Biological Chemistry. CD4+ HeLa cells were obtained from the AIDS Research and Reference Reagent Program (M. Emerman). HXB2 Env-expressing CHO cells were a gift of M. Krieger.


Supporting Information Available: β-peptide synthesis and binding and cell fusion assays. This material is available free of charge via the Internet at


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