HIV Pathogenesis and Drug Resistance

By Jason Socrates Bardi

By the middle of the last decade, several pharmaceutical companies had developed HIV drugs (commonly called antiretrovirals) and had successfully brought these drugs to market.

The first antiretroviral was AZT, a type of chemical known as a nucleoside analogue, which targets the HIV enzyme called reverse transcriptase. AZT was approved by the U.S. Food and Drug Administration (FDA) in 1987. Later, the FDA approved several other drugs in the same class.

In the1990s, another major class of HIV drugs began appearing on the market—protease inhibitors. According to AIDSinfo, a service of the U.S. Department of Health and Human Services, seven protease inhibitors have been approved to treat HIV—amprenavir, atazanavir, indinavir, lopinavir, nelfinavir, ritonavir, and saquinavir.

These protease inhibitors function by preventing the maturation of an HIV virion. HIV codes for a handful of structural genes, which encapsulate the RNA and are produced by a gene called gag. The protease and a few other necessary enzymes are encoded by a viral pol gene. Both gag and pol code for several proteins, and in an infected cell, the virus produces a large Gag polyprotein and a Gag-Pol polyprotein. The Gag-Pol polyproteins are chopped up inside a budding virion into their constituent pieces by the all-important HIV protease.

Once folded and active, the protease has a binding pocket that targets particular sequences along these polyproteins. Whenever there is a tyrosine amino acid followed by a proline (Tyr–Pro), or when there is a phenylalanine followed by a proline (Phe–Pro), the protease acts like a pair of molecular scissors.

When the protease active site comes into contact with one of these sequences, it draws a flexible flap down on the peptide chain, transfers a few electrons around, and cuts the peptide in a precise location.

Protease inhibitors block this interaction by occupying the active sites of the protease enzymes and preventing them from processing the polyproteins. This prevents the virions from maturing completely and effectively prevents that virion from infecting a human cell.

But the effectiveness of protease inhibitors is undermined by drug resistance.

Drug Resistance

In HIV, the problem of drug resistance is a consequence of the virus' propensity to mutate.

HIV has an RNA genome of around 10,000 bases that is packaged in a protein and lipid capsid and coat. The infectious particle, called a virion, binds to receptors on the surface of particular types of human cells and gains entry. Once inside a human cell, the virus does something known as reverse transcription—where it uses its own enzyme called reverse transcriptase to convert its viral RNA into corresponding DNA (it's called "reverse" transcription because transcription, in biology, is where pieces of RNA are made out of DNA genes).

Mutations arise because HIV's replication machinery lacks what is known as a proofreading mechanism.

Such proofreading mechanisms exist in humans, along with other mechanisms, to ensure that whenever human DNA is replicated, it is copied with such high fidelity that a mistake or mutation is made on an average of only once every million bases copied. Since HIV has no proofreading mechanism, it copies itself with such notoriously low fidelity that it makes a mistake about once every 10,000 bases—in general, the virus may make one mistake every time it replicates.

As a patient starts to take an HIV protease inhibitor, the viral "load" or amount of HIV that is in the bloodstream may fall dramatically, helping the patient fight infections.

However, because of the propensity of the virus to mutate, new strains arise all the time. Some of these mutations change the amino acid sequence of the protease enzyme, which can disrupt the binding of the enzyme and the inhibitor.

Protease inhibitors, in general, look like the natural protein "substrate" that the protease targets. These inhibitors mimic the peptides in their affinity for the active site of the protease, and if they are powerful inhibitors they sit tightly in the active site.

But if the protease enzyme is mutated, the interaction between the drug and the protease is no longer strong enough for the drug to be able to stop the virus from replicating.

The Ice Man Cometh

The problem of designing a drug that will block the HIV protease is that the HIV protease is not a stationary target but a moving one.

Several years of treating HIV with highly active antiretroviral therapies like AZT in combination with protease inhibitors has shown that resistance to drugs can rapidly emerge in an infected person. There are countless mutant strains, and over a hundred that have been isolated with resistance to some type of antiretroviral.

If a patient takes a drug that prevents one strain of HIV from replicating, there will likely be other strains in the patient's body already that have randomly acquired mutations that confer resistance. The drug then acts as a selective tool that holds back the sensitive virus more than the mutant virus. Perhaps these mutant strains don't flourish in the patient's body, but they may be replicating nevertheless. And when they do they may acquire more mutations and more resistance to the drugs.

The mutant strains may then cause the patient's viral load to rebound, resulting in further loss of immune cells, placing the patient at greater risk of developing life-threatening infections and AIDS. And treatment with the same drugs may no longer be effective

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The Global HIV/AIDS Epidemic Today

The Joint United Nations Program on AIDS (UNAIDS) estimates that as of December 2003, some 40 million people worldwide were living with HIV/AIDS. Shown here is the breakdown of cases by region. These numbers are approximations that represent the midpoints of range estimates compiled by UNAIDS. Graphic by Kevin Fung.