Wednesday, May 18, 2011

HIV-1 Integrase: The beauty of weakness

HIV is currently responsible for 33 million infections worldwide, and to date no universal cure has been developed. The most promising treatment currently available for HIV is Highly Active Antiretroviral Therapy (HAART), which attempts to inhibit the replication of the virus. While not capable of eradicating the virus, HAART does prevent the spread of the virus, thus preserving the immune system of HIV+ patients and prolonging the progression of AIDS.

The first antiretroviral drugs developed were meant to target HIV protease and HIV reverse transcriptase activity. While moderately successful, it turns out that the high mutation rate of HIV led to the development of resistance to these drugs individually as quickly as 2 months post-treatment. In order to prevent this resistance combinatorial drug regimens of 3-5 different drugs had to be used, a regimen that is highly toxic to the body.

What does all this have to do with integrase you may ask? Well, it just so happens that integrase is another protein (along with protease and reverse transcriptase) that is necessary for viral replication. It also just so happens that it has become the greatest weakness to HIV's fitness.

Here is a picture of integrase doing its thing: incoporating HIV DNA into the host genome (this is actually a tetramer of the enzyme):

Now, the regions of the enzyme that are bound to the DNA (yellow) are called catalytic core domains (CCDs), and they are necessary for the fuction of the integrase (see previous post). It also just so happens that these CCDs are highly conserved regions, meaning that they cannot be mutated or altered significantly without creating a disfunctional enzyme.

So, imagine the excitement of the HIV researching community when somebody did this:

Do you see it? The space filling spheres and the protein cartoon are a zoomed in view of the CCD of integrase. The orange and blue stick diagram is a chemical called raltegravir. Raltegravir has been put on the market as an antiretroviral drug, because as this image is attempting to show, it binds quite will over the CCD of integrase, thereby inhibiting the DNA integration reaction.

What's even more exciting, because the CCD of integrase has to be highly conserved to maintain function, far less resistance related to integrase inhibitors has been noticed in HIV+ patients, especially when used in a combinatorial drug regimen.

While integrase inhibitors are not effective enough to be used as a single drug for HAART, their effectiveness has allowed patients to be moved from HAART regimens of 4 or 5 drugs to only 2, a move that has reduced side effects considerably.

So here's to integrase: Because of its intricacy, because of the specificity of its CCD, we now have the most effective target for the treatment of HIV infection in the history of HIV research.


1. Alian, A., Griner, S.L., Chiang, V., Tsiang, M., Jones, G., Birkus, G., Geleziunas, R., Leavitt, A.D., Stroud, R.M., 2009. Catalytically-active complex of HIV-1 integrase with a viral DNA substrate binds anti-integrase drugs. Proceedings of the National Academy of Sciences United States of America 106, 8192–8197.

2. Arribas, J.R., Pozniak, A.L., Gallant, J.E., Dejesus, E., Gazzard, B., Campo, R.E., Chen, S.S., McColl, D., Holmes, C.B., Enejosa, J., Toole, J.J., Cheng, A.K., 2008. Tenofovir disoproxil fumarate, emtricitabine, and efavirenz compared with zidovudine/lamivudine and efavirenz in treatment-naive patients: 144-week analysis. Journal of Acquired Immune Deficiency Syndromes (JAIDS) 47, 74–78.

3. Bartlett, J.A., Chen, S.S., Quinn, J.B., 2007. Comparative efficacy of nucleoside/ nucleotide reverse transcriptase inhibitors in combination with efavirenz: results of a systematic overview. HIV Clinical Trials 8, 221–226.

4. Sherman, P.A., Fyfe, J.A., 1990. Human immunodeficiency virus integration protein expressed in Escherichia coli possesses selective DNA cleaving activity. Proceedings of the National Academy of Sciences United States of America 87, 5119–5123.

Assignment #2

1. Yang Luo and Mark A Muesing. Prospective strategies for targeting HIV-1 integrase function. Future Med Chem. 2010 July 1; 2(7): 1055–1060. doi:10.4155/fmc.10.205.

This review provides a good summary of the function and mechanism of HIV-1 Integrase. The protein has two catalytic activities: 3’ endonucleitic processing and strand transfer. The 3’ processing can occur in integrase’s dimer form, and the protein removes two nucleotides from the HIV viral DNA (vDNA) in order to prepare the vDNA for integration into the host genome. The next activity that occurs is the process of integration, and this requires a tetramer of the integrase protein (one dimer necessary to process each 3’ end of the vDNA). The end result of the catalysis is the insertion of the vDNA into the host genome, which allows for HIV to be replicated using host transcription machinery.

Integrase dimer

Integrase Tetramer

2. McColl, DJ, and Chen X. Strand transfer inhibitors of HIV-1 integrase: bringing IN a new era of antiretroviral therapy. Antiviral Res. 2010 Jan;85(1):101-18. Epub 2009 Nov 17.

This review provides a thorough analysis of the different inhibitors of the strand transfer reaction of HIV-1 integrase. The most promising of these inhibitors in the clinical setting are raltegravir and elvitegravir. These inhibitors act through the blockage of the active site of the integrase tetramer, or the catalytic core domain (CCD). This CCD is highly conserved within HIV-1, and provides an extremely effective target for antiretroviral therapy. The development of integrase inhibitors such as raltegravir has been extremely important to combat drug resistance in HIV-1, as the high mutation rate of the virus has lead to resistance to both protease inhibitors and reverse transcriptase inhibitors.

Raltegravir bound to the Catalytic Core Domain of Integrase

3. Sandy Azzi, Vincent Parissi, Richard G. Maroun, Pierre Eid, Olivier Mauffret, and Serge Fermandjian. The HIV-1 Integrase α4-Helix Involved in LTR-DNA Recognition Is also a Highly Antigenic Peptide Element. PLoS One. 2010; 5(12): e16001.

In this study, the activity of the α4-Helix of the integrase Catalytic Core Domain was found through a method that utilizes monoclonal antibodies. Taking the peptide fragment responsible for the α4-Helix, the researchers created monoclonal antibodies reactive to the peptide fragment by mouse immunization. These antibodies were first shown to be reactive to the α4-Helix found in the CCD. Once this was established, through competitive inhibition experiments the researcher were able to show that the CCD of integrase interacts with Long Terminal Repeats of the host DNA. Through such a technique, the researchers are able to further characterize the nature and location of the integrase CCD interaction with host DNA.