Interact Differently with Drugs
Naturally occurring genetic variations in HIV-A and HIV-C, the two subtypes of HIV prevalent in Africa, make it harder for inhibitory drugs to bind to the protease, a key protein involved in viral maturation, according to a new report by biologists in The Krieger School of Arts and Sciences of The Johns Hopkins University.
Ernesto Freire (pictured at right), the Henry A. Walters professor of biology, emphasized that the new findings, published in The Proceedings of the National Academy of Sciences, are based on in-vitro tests of basic biochemical properties, and therefore cannot be used to assess the effectiveness of inhibitor drugs in patient treatments.
Instead, Freire suggested that the results add new support to the argument that scientists need to broaden the focus of HIV drug development, which has been almost exclusively centered on HIV-B.
"More than two-thirds of all AIDS cases today are in Africa, and those cases are predominantly HIV-A and HIV-C," says Freire. "Those different subtypes can vary genetically from the B subtype as much as 10 to 30 percent along their entire genome, and this new report proves that variation can affect interactions between drugs and HIV proteins at a very basic biochemical level. We need to broaden drug development efforts to include these subtypes."
For the research, Freire's group created recombinant forms of the proteases from HIV-A and HIV-C, using information from viral gene databases (GenBank) in Africa to recreate the proteins. HIV-A dominates in the northern part of Sub-Saharan Africa, while HIV-C is prevalent in southern regions.
Freire's lab measured the proteases' efficiency and biochemical fitness through factors related to catalysis, a chemical term for a process where one substance (the protease) accelerates a chemical reaction in another substance (the substrate) without being changed itself. The catalytic action of the protease is vital in viral maturation, which has made it a key target for drug development.
Measurements of the catalytic factors were taken in the absence and in the presence of indinavir, ritonavir, saquinavir, and nelfinavir, four protease inhibitor drugs that are part of the drug "cocktails"currently used to control AIDS.
Proteases from the A and C subtype consistently scored better than the normal B subtype, meaning that they were better able to perform their catalytic functions in the presence of inhibitory drugs. Researchers also tested the structural stability of the various proteases, and found that A and C proteases could remain stable at higher temperatures than the B protease.
Genetic variations in the subtypes of HIV cause amino acid polymorphisms -- differences in the sequence of amino acids that are put together to make up a protein. Polymorphisms can occur both through natural genetic variations and through mutations that occur after exposure to inhibitory drugs. The latter form the basis of drug resistance.
In the protease, the effects of the polymorphisms vary.
In some instances, there's no change in the chemical nature or polarity of the binding site for inhibitor drugs, but instead a change in the geometry of the site that inhibitors can't adapt to," says Freire. "It's even possible for the effects of polymorphisms elsewhere in the protein to propagate through the protein to the binding site, where they may again distort the geometry of that site or alter the energy required to elicit the conformational change associated with inhibitor binding.
"An additional cause for concern is the fact that we're starting to get some initial reports of drug resistance in HIV-A and HIV-C, and we don't know how those mutations are going to interact with the naturally occurring polymorphisms already present in those subtypes," says Freire.
Other authors on the paper are Adrian Velazquez-Campoy, a postdoctoral fellow; Matthew Todd, an associate research scientist now at 3D Pharmaceuticals; and Sonia Vega, a visiting scientist. The research was supported by the National Institutes of Health and the National Science Foundation. Velazquez-Campoy, the lead author, was partially supported by a postdoctoral fellowship from the Universidad de Granada, Spain.
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