Structure of a HIV-1 IN-Allosteric inhibitor complex at 2.93 Å resolution: Routes to inhibitor optimization

Abstract

HIV integrase (IN) inserts viral DNA into the host genome and is the target of the strand transfer inhibitors (STIs), a class of small molecules currently in clinical use. Another potent class of antivirals is the allosteric inhibitors of integrase, or ALLINIs. ALLINIs promote IN aggregation by stabilizing an interaction between the catalytic core domain (CCD) and carboxy-terminal domain (CTD) that undermines viral particle formation in late replication. Ongoing challenges with inhibitor potency, toxicity, and viral resistance motivate research to understand their mechanism. Here, we report a 2.93 Å X-ray crystal structure of the minimal ternary complex between CCD, CTD, and the ALLINI BI-224436. This structure reveals an asymmetric ternary complex with a prominent network of π-mediated interactions that suggest specific avenues for future ALLINI development and optimization.

Oligomeric HIV-1 Integrase Structures Reveal Functional Plasticity for Intasome Assembly and RNA Binding

“…This engagement is anti-parallel, which differs from the original dimeric CTD solution NMR structure (PDB 1IHV) 47 , but resembles recently described crystallographic packing interactions within IN assemblies containing bound ALLINI (PDB 8CTA) 48 ( Figure 2c , bottom right). Notably, the fact that the anti-parallel CTD:CTD interface is now observed within the IN tetramer indicates that this interaction mode is biologically relevant, which could not be concluded from packing assemblies observed crystallographically 48 . Such diverse contacts contributed by CTDs help stabilize and maintain the tetrameric conformation and add to our understanding of the promiscuity of the CTD, which additionally engages with other protein domains and/or nucleic acids in the intasome 8 .…”

“…Lastly, the CTDs engage one another at the twofold axis through hydrophobic contacts ( Figure 2c , bottom left). This engagement is anti-parallel, which differs from the original dimeric CTD solution NMR structure (PDB 1IHV) 47 , but resembles recently described crystallographic packing interactions within IN assemblies containing bound ALLINI (PDB 8CTA) 48 ( Figure 2c , bottom right). Notably, the fact that the anti-parallel CTD:CTD interface is now observed within the IN tetramer indicates that this interaction mode is biologically relevant, which could not be concluded from packing assemblies observed crystallographically 48 .…”

“…( c ) The structure of the tetramer is displayed in the center, with key interactions interfaces shown within inset panels. The interaction mediated by the central CTD:CTD dimer (bottom left panel) resides in an anti-parallel configuration, which is distinct from the parallel configuration previously encountered in CCD-CTD oligomeric assemblies with bound inhibitors 30 or within dimeric CTD:CTD structures in solution 67 , but resembles the crystal packing interactions observed in PDB 8CTA 48 . The CTD also mediates other diverse interactions, including with the NTD (upper left) and with the CCD-CTD linker (upper right) within the IN tetramer.…”

Biological and Structural Analyses of New Potent Allosteric Inhibitors of HIV-1 Integrase

“…In their mode of binding to HIV-1 IN, INLAIs mimic the LEDGF/p75 integrase binding domain (IBD), which engages the same pocket on the CCD dimer interface ( 38 ). Recent X-ray crystallography and biochemical studies revealed that INLAIs act as molecular glues, promoting formation of a pathological interface involving the HIV-1 CCD dimer and a C-terminal domain (CTD) ( 39 – 42 ). While HIV-1 IN forms stable tetramers ( 24 , 43 , 44 ) under physiological conditions, the formation of the additional, drug-induced IN-IN interface leads to uncontrolled multimerization of the viral protein.…”

The structural and mechanistic bases for the viral resistance to allosteric HIV-1 integrase inhibitor pirmitegravir

“…Upon binding to the V-shaped cavity at the CCD dimer interface, ALLINIs act as molecular glues to recruit CTD (31)(32)(33). Therefore, we tested how Y99H/A128T IN mutations affected formation of the CCD-PIR-CTD complex.…”