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HIV-1 Integrase: A Promising Therapeutic Target Against AIDS

Dr. Chandravanu Dash

In the absence of an effective vaccine, a combination of inhibitors of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase and protease provides strong support for continued development of potent and selective therapeutic agents to control HIV infection. There are three classes of antiretrovirals: inhibitors of the HIV-1 reverse transcriptase (RT) and protease (PR) enzymes and inhibitors of HIV entry, including receptor and coreceptor binding and cell fusion.

Recently, inhibitors of HIV-1 Integrase (IN) are also making considerable progress as potential drugs against HIV. IN is an attractive drug target because it is essential for a stable and productive HIV-1 infection and unlike other HIV-1 enzymes there is no mammalian homologue of IN.

HIV-1 IN is encoded in the pol gene of the virus and is translated as part of a large Gag-Pol polyprotein. This polyprotein is processed by the virus-encoded protease generating the mature IN. HIV-1 IN is a 32 KDa protein with 288 amino acid residues folding into three distinct domains: the N-terminal domain, the core domain and the C-terminal domain.

During HIV-1 replication, the RNA genome is reverse transcribed into integration competent double stranded DNA by HIV-1 RT and this DNA is subsequently integrated into the host genome by the HIV-1 IN. This integration mechanism is catalyzed by virally encoded IN enzyme in two-steps: 3'-processing followed by strand transfer. But still the detailed mechanism involved is unclear due to lack of a high resolution structure of the intact IN.

Since IN plays an essential role in HIV-1 replication, it is an attractive target for developing new antiviral drugs. However, progress in the development of IN inhibitors had been slow, largely because of the absence of: a) crystal structure of intact IN and IN:DNA complex, b) good lead compounds, and c) reliable in vitro screening assays. Despite these impediments, several classes of integrase inhibitors have been reported in recently. An overview of the inhibitors against HIV-1 IN is discussed below. 

a) DNA binding agents: DNA intercalators and DNA groove binders have been identified as non-selective DNA binders, which also target the host genome. Some examples include doxorubicin, chloroquine, dihydroxynaphthoquinones and anthraquinones.

b) Hydroxylated aromatic compounds: The main structural feature of this class responsible for integrase inhibition is the presence of a catecholic moiety and includes quercetagetin, caffeic-acid penethyl ester (CAPE) and its derivatives, tyrphostins. It is hypothesized that the phenolic groups in these compounds are involved in the chelation of the divalent cation, which is a cofactor for integrase.

c) Sulfones, sulfonamides, and sulfonates: Many diaryl sulfones have been found to be integrase inhibitors but most of them lack antiviral activity. Suramin, a polyanionic sulfonate was among the first integrase inhibitors reported. 2- Mercaptobenzenesulfonamides is another class that has potent integrase inhibitory as well as antiviral activities.

d) Nucleotides: Since integrase uses polynucleotides as its substrates, nucleotides can be used to inhibit integrase activity. Zidovudine nucleotides inhibit integrase strand transfer activity. Mononucleotides are thought to inhibit integrase by occupying the DNA substrate binding site. Zintevir is a short (17-mer) GT containing polynucleotide, currently undergoing Phase I /II trials, and is well tolerated.

e) Diketo acids: These classes of inhibitors are one of the promising inhibitors of HIV-1 IN. Several diketo acid serve as specific inhibitors of integration with potent antiviral activity. These compounds show a preference for the strand transfer reaction in vitro and inhibit integration without affecting processing of the viral DNA in infected cells. Several diketo acids are currently undergoing Phase II clinical trials.

f) Peptides and proteins: A hexapeptide inhibitor (HCKFWW) of integrase was identified using a combinatorial library screening method. The exact binding site of this inhibitor however, remains to be elucidated. Two plant proteins-MAP30 (Momordica aomordica anti-HIV-protein of 30Kda) and GAP31 (Gelonium anti-HIV-protein of 31 Kda) have been identified as HIV-1 integrase inhibitors. These proteins were isolated from Momordica charantia and Gelonium multiflorum, respectively. Both proteins exhibit dose-dependent inhibition of HIV-1 integrase.

In addition to these inhibitors, which are the outcome of high-throughput or random screenings, other inhibitors such as: ligand based pharmacophores and receptor based pharmacophores also contribute towards the development of promising compounds against HIV-1 IN. Recent advances in computational methodologies such as QSAR and de novo drug design programs are contributing immensely towards the development of compounds with potency towards HIV-1 IN. Although pharmacophore-based methods have been successful in discovering novel molecules by database searches, knowledge of the details of protein-ligand interactions could greatly facilitate the new drug discovery of IN inhibitors. For example, the structure of HIV-1 IN in complex with 5CITEP (1-(5-chloroindol-3-yl)-3-(tetrazolyl)-1,3-propane- dione enol) can serve as a platform for the structure based drug design of IN inhibitors.

Challenges and Future Directions
Tremendous progress has been made in understanding the details of the structure and function of HIV-1 IN, which helps in determining the strategies for targeting HIV integration. While it has taken longer for integrase inhibitors to make it into human testing than the current reverse transcriptase and protease inhibitors, the recent discoveries on potent HIV-1 IN inhibitors is highly encouraging. The discoveries of these leads also corroborate the potential of integrase to serve as an antiviral target. Although, these discoveries provide a great potential of antiviral therapy, similar to other drug targets, resistance to the HIV-1 IN arises from the selection of viral variants with genetic mutations that change the target enzyme. Before IN inhibitors can be successfully translate into anti-HIV drugs, understanding the resistance mechanism posses a great hurdle to the HIV researchers. However, the hope is that a combination of therapies targeting different enzymes, including integrase, will convey lasting benefit to the HIV infected patients by decreasing replication rate of HIV, and thereby reducing the emergence of mutant strains.
 

Dr. Chandravanu Dash is a talented researcher at National Cancer Institute (NCI), Frederick, USA.