N-Substituted Pyrrole Derivatives as Novel Human Immunodeficiency Virus Type 1 Entry Inhibitors That Interfere with the gp41 Six-Helix Bundle Formation and Block Virus Fusion

Abstract

A recently approved peptidic human immunodeficiency virus type 1 (HIV-1) fusion inhibitor, T-20 (Fuzeon; Trimeris Inc.), has shown significant promise in clinical application for treating HIV-1-infected individuals who have failed to respond to the currently available antiretroviral drugs. However, T-20 must be injected twice daily and is too expensive. Therefore, it is essential to develop orally available small molecule HIV-1 fusion inhibitors. By screening a chemical library consisting of "drug-like" compounds, we identified two N-substituted pyrroles, designated NB-2 and NB-64, that inhibited HIV-1 replication at a low micromolar range. The absence of the COOH group in NB-2 and NB-64 resulted in a loss of anti-HIV-1 activity, suggesting that this acid group plays an important role in mediating the antiviral activity. NB-2 and NB-64 inhibited HIV-1 fusion and entry by interfering with the gp41 six-helix bundle formation and disrupting the ␣-helical conformation. They blocked a D-peptide binding to the hydrophobic pocket on surface of the gp41 internal trimeric coiled-coil domain. Computer-aided molecular docking analysis has shown that they fit inside the hydrophobic pocket and that their COOH group interacts with a positively charged residue (K574) around the pocket to form a salt bridge. These results suggest that NB-2 and NB-64 may bind to the gp41 hydrophobic pocket through hydrophobic and ionic interactions and block the formation of the fusion-active gp41 core, thereby inhibiting HIV-1-mediated membrane fusion and virus entry. Therefore, NB-2 and NB-64 can be used as lead compounds toward designing and developing more potent small molecule HIV-1 fusion inhibitors targeting gp41.

High-Throughput HIV–Cell Fusion Assay for Discovery of Virus Entry Inhibitors

“…In the final 6-helix bundle structure (6HB), three HR1 and three HR2 coalesce forming a highly stable antiparallel helical bundle. A number of small-molecule inhibitors of HIV-1 fusion that interfere with CD4-induced conformational changes in gp120, 8,9 coreceptor binding, [10][11][12] and the gp41 6HB formation [13][14][15][16][17][18][19][20][21][22][23][24] have been identified by high-throughput screening (HTS). Currently, only two HIV-1 fusion inhibitors (enfuvirtide and maraviroc) have been approved for clinical use.…”

Viral surface glycoproteins, gp120 and gp41, as potential drug targets against HIV-1: Brief overview one quarter of a century past the approval of zidovudine, the first anti-retroviral drug

“…This way, Jiang et al [115] identified two N-substituted pyrroles, NB-2 and NB-64 ( Fig. 13a and b, respectively), that block HIV-1 fusion and entry against both laboratory-adapted and primary HIV-1 strains at low micromolar levels.…”

“…Another group, Jiang et al, also used computer-aided molecular docking analysis to show that NB-2 and NB-64 (see Fig. 13a and b) bind to the gp41 hydrophobic cavity region through hydrophobic and ionic interactions and blocks the formation of the fusion-active gp41 core [115].…”

Artificial Ion Channel Biosensor in Human Immunodeficiency Virus gp41 Drug Sensing

“…As demonstrated above, the affinity of negatively charged analytes was overestimated, by a factor that appeared to correlate with analyte pI or pKa. The interaction of inhibitors in the gp41 hydrophobic pocket involves both hydrophobic and electrostatic contacts [38][39][40] , and the charge on the inhibitors plays a crucial role in binding 41,42 . It is impossible to avoid the effect of analyte charge on the ICS response 21 .…”