Discovery of a Distinct Chemical and Mechanistic Class of Allosteric HIV-1 Integrase Inhibitors with Antiretroviral Activity

Abstract

Allosteric integrase inhibitors (ALLINIs) bind to the lens epithelial-derived growth factor (LEDGF) pocket on HIV-1 integrase (IN) and possess potent antiviral effects. Rather than blocking proviral integration, ALLINIs trigger IN conformational changes that have catastrophic effects on viral maturation, rendering the virions assembled in the presence of ALLINIs noninfectious. A high-throughput screen for compounds that disrupt the IN·LEDGF interaction was executed, and extensive triage led to the identification of a t-butylsulfonamide series, as exemplified by 1. The chemical, biochemical, and virological characterization of this series revealed that 1 and its analogs produce an ALLINI-like phenotype through engagement of IN sites distinct from the LEDGF pocket. Key to demonstrating target engagement and differentiating this new series from the existing ALLINIs was the development of a fluorescence polarization probe of IN (FLIPPIN) based on the t-butylsulfonamide series. These findings further solidify the late antiviral mechanism of ALLINIs and point toward opportunities to develop structurally and mechanistically novel antiretroviral agents with unique resistance patterns.

Multifaceted HIV integrase functionalities and therapeutic strategies for their inhibition

“…Novel tert-butylsulfonamide (t-BSF) compound 1 inhibited the late phase of HIV-1 infection 6-fold more potently than the early phase, indicating bona fide ALLINI activity (270). Whereas the T174I substitution in the LEDGF/p75 IBD binding pocket conferred about 500-fold resistance to a control quinoline ALLINI compound, the mutant virus was 5-fold more sensitive to inhibition by t-BSF ALLINI compound 1, indicating engagement of the IN CCD dimer at a location other than the LEDGF/p75-binding pocket (270). The binding of a predecessor ALLINI compound, which inhibited IN subunit exchange in solution, mapped to the CCD dimer interface adjacent to the LEDGF/p75-binding pocket (271).…”

Multimerization of HIV-1 integrase hinges on conserved SH3-docking platforms

“…The fact that IN regulates not only viral integration but also the assembly and maturation of virus particles (9,22), accentuates the prominence of this target. Whereas the peptide used in this study may not, per se, provide a lead hit for this anti-IN strategy, our work underscores the overlooked SH3-docking platform of HIV-1 IN as a potential therapeutic target for future anti-IN allosteric inhibitors.…”

“…Fragment-based screening and structural studies have revealed the capability of all three pockets (Y3, FBP and LEDGF) to bind numerous small molecules (21). Most recently, a new class of LEDGINs has been shown to distinctively bind to undefined interfaces of both CCD and CTD of IN (22). Therefore, IN harbors several allosteric hotspots that can be explored for novel anti-multimerization intervention strategies.…”

Augmenting Hit Identification by Virtual Screening Techniques in Small Molecule Drug Discovery

“…Further complicating matters, the antiviral assay used to characterize the virtual hits included 10% fetal bovine serum, which can significantly lower the unbound concentration of hydrophobic molecules, and compounds required cellular permeability in order to reveal any antiviral activity. Perhaps due to a combination of these factors, none of the virtual hits displayed the existing antiviral activity …”