Rational engineering of a miniprotein that reproduces the core of the CD4 site interacting with HIV-1 envelope glycoprotein

Abstract

Protein-protein interacting surfaces are usually large and intricate, making the rational design of small mimetics of these interfaces a daunting problem. On the basis of a structural similarity between the CDR2-like loop of CD4 and the ␤-hairpin region of a short scorpion toxin, scyllatoxin, we transferred the side chains of nine residues of CD4, central in the binding to HIV-1 envelope glycoprotein (gp120), to a structurally homologous region of the scorpion toxin scaffold. In competition experiments, the resulting 27-amino acid miniprotein inhibited binding of CD4 to gp120 with a 40 M IC50. Structural analysis by NMR showed that both the backbone of the chimeric ␤-hairpin and the introduced side chains adopted conformations similar to those of the parent CD4. Systematic single mutations suggested that most CD4 residues from the CDR2-like loop were reproduced in the miniprotein, including the critical Phe-43. The structural and functional analysis performed suggested five additional mutations that, once incorporated in the miniprotein, increased its affinity for gp120 by 100-fold to an IC50 of 0.1-1.0 M, depending on viral strains. The resulting mini-CD4 inhibited infection of CD4 ؉ cells by different virus isolates. Thus, core regions of large protein-protein interfaces can be reproduced in miniprotein scaffolds, offering possibilities for the development of inhibitors of protein-protein interactions that may represent useful tools in biology and in drug discovery. T he interaction of the gp120 envelope glycoprotein of HIV-1 with CD4 represents the initial step of virus entry into its target cells (1, 2) and triggers gp120 conformational changes that increase binding affinity for CCR5 (3, 4), the chemokine receptor used as coreceptor by most HIV-1 primary isolates (5, 6). X-ray structure analysis (7) of gp120 in complex with CD4 and the Fab of a neutralizing monoclonal antibody has revealed that CD4 binds to a large (800-Å 2 ) depression on gp120 by using a 742-Å 2 surface involving 22 residues in the span of amino acids 25-64 of the CD4 D1 domain and centered on the CDR2-like 36-47 loop (Fig. 1A). Phe-43, the side chain of which protrudes from the 36-47 loop and plugs the entrance of a deep cavity in gp120, Arg-59 (at the end of strand D), which makes multiple contacts with gp120, and strand C'', which interacts with strand ␤15 of gp120 in a ␤-sheet alignment, are critical elements in the CD4 interface (7). The involvement of these CD4 structural elements in gp120 binding is in agreement with previous mutational analyses that identified most residues of CDR2-like loop as important recognition elements (8-12).The large size and complexity of the CD4 surface interacting with gp120 (7) explains the difficulties encountered in deriving gp120 ligands based on CD4 structure that could effectively block virus entry. Peptides derived from the envelope glycoprotein gp41 (13) have been shown to trap gp41 in a fusionnoncompetent conformation after gp120 has interacted with cellular receptors (14), thereby preventing in...

Small-molecule inhibitors of HIV-1 entry block receptor-induced conformational changes in the viral envelope glycoproteins

“…Our data agree with those of Lin et al (23) and Guo et al (24) on these important points. Several other gp120-directed inhibitors have been reported, but are either significantly larger than BMS-806 (e.g., CD4 miniproteins and 12p1 peptide) (33,37) or bind multiple sites on gp120 because of electrostatic or lectin-carbohydrate interactions (e.g., sulfated polymers and cyanovirin) (38,39). These considerations make BMS-806 much more attractive as a potential antiviral drug and as a probe to study HIV-1 entry.…”

The Ixodes scapularis salivary protein, salp15, prevents the association of HIV-1 gp120 and CD4

“…Scyllatoxin is a scorpion toxin with structural similarities in the hairpin region with the CDR2-like loop of CD4. A series of amino acid interchanges and point mutations resulted in peptides structurally similar to the parent CD4 molecule with the capacity to mimic the gp120 binding region of CD4 [29,30]. CD4M9 had an IC 50 of 0.1-1.0 μM, depending on viral strains, and inhibited the infection of CD4 + cells [30].…”

“…A series of amino acid interchanges and point mutations resulted in peptides structurally similar to the parent CD4 molecule with the capacity to mimic the gp120 binding region of CD4 [29,30]. CD4M9 had an IC 50 of 0.1-1.0 μM, depending on viral strains, and inhibited the infection of CD4 + cells [30]. We coated a 96-well plate with 25 nM of soluble gp120 or 1 μM of Salp15 and incubated the wells with 2 μM of biotin-tagged CD4M9.…”

“…The Salp15 overlapping peptides (P1-P11) were previously described [18]. The peptide CD4M9 (CNLARCQLRCKSLGLLGKCAGSFCACGP) [19,20] …”

β‒hairpin polypeptides by design and selection

“…This was done in the context of a 10-residue peptide with cysteine residues at position 1 and 10, threonine residues at position 2 and 9 (this amino acid tends to favor an extended backbone [35,51]), and a Glu-Gly-AsnLys sequence for residues 4-7 as it should have a moderate tendency to form a type II reverse turn [24]. Position 8 was initially chosen to be leucine, and naturally-occurring amino acids were substituted at [41][42][43][44][45][46][47][48][49][50][51][52][53][54][55][56]; ∆∆G estimated assuming additivity of data for trpzip4, 5 and 6. b Spaces separate strand from turn residues; substitutions in the gb1 C-terminal peptide are indicated bold and underlined. position 3 (the X3L8-series), with the aim of identifying the residue that most stabilized the β-hairpin structure [10].…”