The molecular biology of HIV integrase

Abstract

Integration of viral DNA into cellular DNA is an essential step in the replication cycle of HIV and other retroviruses. The first antiviral drugs that target integrase, the viral enzyme that catalyzes DNA integration, have recently been approved and more are in the pipeline. These drugs bind to an intermediate in DNA integration called the intasome, in which a pair of viral DNA ends are synapsed by a tetramer of integrase, rather than free integrase enzyme. We discuss the biochemical mechanism of integration, which is now quite well understood, and recent progress towards obtaining atomic-resolution structures of HIV intasomes in complex with inhibitors. Such structures are ultimately required to understand the detailed mechanism of inhibition and the mechanisms by which mutations in integrase confer resistance. The path from early biochemical studies to therapeutic inhibitors of integrase highlights the value of basic science in fighting human diseases.

Figure 1. DNA cutting and joining steps of retroviral DNA integration

(A) The viral DNA synthesized by reverse transcription is initially blunt ended. (B) The 3′ end processing reaction removes two nucleotides from each 3′ end. (C) Next, in the DNA strand transfer reaction, the 3′ hydroxyls at the ends of the viral DNA attack a pair of phosphodiester bonds in the target DNA; in the case of HIV, the sites of attack are separated by five nucleotides on the two target DNA strands. (D) The result is the integration intermediate, in which the 3′ ends of the viral DNA are joined to the 5′ ends of the target DNA at the site of integration. The integration intermediate is then repaired by cellular enzymes to complete the integration process.

Figure 2. In vitro catalytic activities of HIV integrase

(A) Integrase catalyzes 3′ end processing on an oligonucleotide DNA substrate mimicking the ends of HIV DNA. The GT dinucleotide is released, exposing the conserved CA that is to be joined to the target DNA. (B) Integrase also catalyzes DNA strand transfer, in which the 3′ end of the viral DNA attacks a phosphodiester bond in the target DNA, covalently joining the viral to target DNA. Integration can occur at essentially any location in the target DNA. Note that, in vitro with oligonucleotide DNA substrates, most of the reaction products result from joining only one viral DNA end into one strand of target DNA, rather than concerted integration of a pair of viral DNA ends as occurs in vivo.

Figure 3. Cartoon representation of the prototype foamy virus intasome structure

The integrase monomers in the intasome are distinguished by their colors. The CCD, NTD, CTD and NED are distinguished by shape. The pair of viral DNA ends are represented as helices. All the contacts between integrase and viral DNA are with the inner subunits. The CTD, NTD and NED of the outer subunits are disordered. CCD: Catalytic core domain; CTD: C-terminal domain; NED: N-terminal extension domain; NTD: N-terminal domain. Adapted with permission from [81].