Figure 1.
The chemical structures of NBD analogues that target the CD4 binding site of gp120.
The general structure of the NBD congeners is shown, defining Regions I (blue), II (red), and III (green). The diverse Region III scaffolds crystalographically characterized in complex with gp120 are shown below.
Figure 2.
Structures of HIV-1 gp120 core in complex with NBD-557.
(A) YU2 gp120 coreV3s (surface representation in grey) in complex with NBD-557 (stick representation in green) and Fab 48d depicted in a ribbon diagram (light chain in light blue and heavy chain in blue). (B) NBD-557 (stick representation in cyan) binds the Phe 43CD4 cavity on clade A/E93TH057 gp120 coree. Area colored red represents N-terminal residues (44–89), which are missing in gp120 core in (A). CD4 footprints on gp120 are colored in yellow in (A) and (B). (C) Superposition of NBD-557- and Fab 48d- bound YU2 gp120, NBD-557-bound clade A/E93TH057 gp120 core, and the CD4-bound gp120. Two NBD-557 (green and cyan) and the side chain of Phe 43CD4 (yellow) in the cavity are highlighted.
Table 1.
Data collection and refinement statistics.
Figure 3.
Detailed interactions of NBD-557 with gp120.
(A) The chemical structure of NBD-557, defining Regions I, II, and III. (B, C) NBD-557 interactions with clade A/E93TH057 gp120 in the cavity. (D) The tetramethylpiperidine ring resides in the cavity vestibule and does not make optimal contacts with gp120 surface.
Figure 4.
Comparison of Region I and II of NBD analogues in the Phe 43 cavity.
(A) The para-bromo substituted phenyl ring of NBD-557. (B) The para-chloro and meta-fluoro substituted phenyl ring of AS-I-261. The fluorine substitution at the meta position of AS-I-261 fills the space formed near Ser 256 and Thr 257 in NBD-557 bound Phe 43 cavity (A). Ortho substitution of the aromatic ring would not be tolerated in either complex, because of steric clash with gp120. (C–E) Residues on gp120 that make contacts with the Region I and II of AS-I-261. Hydrogen bonds are noted in red dotted lines, and atoms that are within the van der Waals radius (>5 Å) are noted in blue dotted lines.
Figure 5.
Diverse interaction modes of NBD-analogue Region III with gp120.
Close-up views of NBD-557 (A, B), AS-II-37 (C, D), AS-I-261 (E, F), MAE-II-167 (G, H), and MAE-II-188 (I, J) in the Phe 43 cavity. Region I and II reside inside the Phe 43 cavity. The Region III of the analogues protrudes outside the cavity in diverse conformations. All atoms on gp120 within 5 Å distance to the Region III of the analogues are shown with dotted lines; hydrogen bonds in red and two atoms within the van der Waals radius in green dotted lines. (B, D, F, H, and J) NBD analogues in 2fo-fc electron density map colored by the B-factor. The color scale ranges from blue to red for B-factors of >40 to <150 Å2.
Figure 6.
Superposition of MAE-II-167 (blue) and MAE-II-188 (cyan) at the Phe 43 cavity suggests a model compound that forms a hydrogen bond with Asp 368 in Area A. The model makes hydrophobic contacts with the tip of β20/21 in Area B. A successful design strategy for a potent drug should include additions of an amine group that will interact with Asp 368 by a salt bridge, a longer hydrophobic tail that will satisfy hydrophobic interactions in Area B, and a moiety that expands contacts in Area C.
Figure 7.
NBD analogue binding to gp120 enhances 17b-gp120 interaction.
(A–D) 100 nM of gp120 coremin or full-length gp120 in the presence of 0–100 µM of NBD analogues was passed over 17b antibody immobilized on a CM5 chip. The binding of gp120 to 17b increased, in a concentration dependent manner, in response to treatment with the NBD analogues. (E) In contrast, the presence of BMS-806, a small molecule inhibitor that has known not to induce gp120 conformation, did not enhance gp120-17b interaction.
Figure 8.
NBD analogues are unable to bind Ser 375 variants of gp120s.
(A) Clade BYU2 gp120 coree binds both NBD-556(Ligand:1) and sCD4. Ser 375 was shown in the NBD-557 bound cavity. (B) Clade A/E93TH057 gp120 coree does not show detectable binding to NBD-556 immobilized onto a CM5, but binds to sCD4. NBD-557 modeled into the Phe 43 cavity of clade A/E gp120 clashes with His 375. (C) Clade AKER2008 gp120 coree does not bind NBD-556, but does bind sCD4. Met 375 modeled into NBD-557-bound YU2 gp120 clashes with NBD-557. (D) Clade CRF34_1OUR2478P gp120 coree does not bind NBD-556, but binds sCD4. NBD-557 clashes with Trp 375 in the Phe 43 cavity.