HIV-1 integrase multimerization as a therapeutic target

Abstract

Multimeric HIV-1 integrase (IN) plays an essential, multifunctional role in virus replication and serves as an important therapeutic target. Structural and biochemical studies have revealed the importance of the ordered interplay between IN molecules for its function. In the presence of viral DNA ends, individual IN subunits assemble into a tetramer and form a stable synaptic complex (SSC), which mediates integration of the reverse transcribed HIV-1 genome into chromatin. Cellular chromatin-associated protein LEDGF/p75 engages the IN tetramer in the SSC and directs HIV-1 integration into active genes. A mechanism to deregulate the productive interplay between IN subunits with small molecule inhibitors has recently received considerable attention. Most notably, allosteric IN inhibitors (ALLINIs) have been shown to bind to the IN dimer interface at the LEDGF/p75 binding pocket, stabilize interacting IN subunits, and promote aberrant, higher order IN multimerization. Consequently, these compounds impair formation of the SSC and associated LEDGF/p75-independent IN catalytic activities as well as inhibit LEDGF/p75 binding to the SSC in vitro. However, in infected cells, ALLINIs more potently impaired correct maturation of virus particles than the integration step. ALLINI treatments induced aberrant, higher order IN multimerization in virions and resulted in eccentric, non-infectious virus particles. These studies have suggested that the correctly ordered IN structure is important for virus particle morphogenesis and highlighted IN multimerization as a plausible therapeutic target for developing new inhibitors to enhance treatment options for HIV-1-infected patients.

Fig. 1

Domain organization of HIV-1 IN. a A schematic to show organization of individual domains in the full-length protein. b The crystal structure of the two domain NTD–CCD tetramer. Individual IN subunits are colored yellow, green, magenta, and cyan. Active-site residues Asp64, Asp116, and Glu152 are shown as red spheres. Of importance are the interactions between CCD (shown in yellow and cyan) with NTD of the other CCD–CCD dimer (shown in cyan and yellow respectively) in addition to the canonical CCD–CCD interactions. c The crystal structure of the two domain CCD–CTD dimer. Individual IN subunits are colored yellow and green, and active-site residues Asp64, Asp116, and Glu152 are depicted as red spheres

Fig. 2

A molecular model for the functional complex between IN tetramer, viral DNA ends, and LEDGF/IBD. In the presence of viral DNA substrates, individual IN subunits assemble into a tetramer to form the SSC. Two inner subunits colored green and magenta directly bind viral DNA, whereas two outer subunits colored yellow and cyan engage the inner subunits through the canonical CCD–CCD interactions. Two LEDGF/IBD molecules colored gray bind the SSC by bridging between two IN dimers through interactions with the CCD dimers (one dimer shown in yellow and green and one dimer in magenta and cyan) and the NTD of the opposite dimer (shown in magenta and green, respectively)

Fig. 3

Two adjacent small molecule binding pockets (indicated by circles) at the HIV-1 IN CCD dimer interface. a A molecular model of compound 1 bound to IN showing that the inhibitor bridges between two subunits. b A zoomed-in view to depict compound 1 interactions with subunit 2 (colored yellow) residues Lys173 and Tyr99, and subunit 1 (colored green) residues Glu87, Glu96, and Lys103. c The crystal structure of ALLINI BI-1001 bound to the HIV-1 IN CCD dimer. d A zoomed-in view to show the hydrogen bonding and hydrophobic interactions of ALLINI BI-1001 with subunit 2 (colored yellow) and subunit 1 (colored green), respectively. Hydrogen bonding between ALLINI BI-1001 carboxylic acid and the backbone amides of IN residues Glu170 and His171 as well as between the methoxy group and the side chain of Thr174 are indicated by dash lines. The quinoline rings extend toward the A128 residue, which allows the evolution of HIV-1 IN A128T escape mutation. e A schematic to show ALLINI-induced aberrant IN multimerization. In the absence of the inhibitor, IN is in a dynamic equilibrium between monomers, dimers, and possibly tetramers (for clarity only monomers and dimers are shown). ALLINI binds at the IN CCD dimer interface, stabilizes interacting IN subunits, and consequently shifts the thermodynamic equilibrium toward aberrant, higher order multimerization