Molecular Evolution: HIV Drug Targets and Resistance

Keywords Molecularevolution.Sequencealignment.Drugresistance.HIV.Inquiry.ActivelearningHIV Evolution: Drug Targets and ResistanceStudent ActivityBackgroundOnce the human immunodeficiency virus (HIV) binds to ahost immune cell through the interactions of the envelopeprotein with CD4 and a coreceptor, the host and virusmembranes fuse and the HIV core, called the matrix/capsid,containing its RNA genome and related proteins enter thecell. The matrix/capsid core breaks down and releasesHIV's two single-stranded RNA genome molecules into thecell's cytoplasm. Reverse transcriptase then synthesizes aDNA copy of HIV's RNA genome. The double-strandedDNA copy is then transported to the nucleus where it isintegrated into the host's genome by the enzyme integrase.This integrated copy is called a provirus. Once theseprovirus copies are integrated, there is no way to removethem from the host's genome.Using the host cell's protein machinery, includingribosomes and other proteins involved in the translationprocess, the provirus is transcribed into RNA moleculesand translated into HIV proteins. Once synthesized, theHIV components assemble near the cell membrane. Duringthis process, the immature polypeptide chains are cleavedand processed by protease, another HIV enzyme, resultingin mature, functional HIV proteins. Millions of new virusparticles, each potentially capable of infecting other cells,can be produced from one infected CD4-positive cell.Scientists are trying to develop drugs that can interfere witheach step in the HIV lifecycle to stop the release of newviral progeny.A potential target for antiretroviral drugs is the HIVprotein, protease. When HIV progeny are released, they are‘immature’ and noninfectious until protease cleaves certainproteins ‘maturing’ the virion. The structure of the proteaseenzyme is a homodimer, composed of two identical proteinsubunitsthatcometogethertoformanactivesite(seeFig.1).Each protein chain subunit is 99 amino acids long. Oncefolded properly, amino acid residues in the active site of theenzyme include the Asp–Thr–Gly sequence at positions 25to 27, which are important for its enzymatic action, andVal82 and Ile84, which are accessible in the active site. Ifprotease activity is blocked, ‘new’ viruses remain immature(Boden and Markowitz 1998; Resch et al. 2005).Currently, nine protease inhibitors are available to treatHIV-infected individuals (http://www.aidsmeds.com). Rito-navir is one of these inhibitors. Research has shown thatamino acid residues Val82 and Ile84 among others areimportant for ritonavir to bind to protease.For another example, the first antiretroviral drug devel-oped for HIV, AZT, is a chemical compound similar instructure to DNA nucleotides. AZT blocks the action of thereverse transcriptase enzyme. Early testing of AZT inpatients resulted in decreased viral loads and decreasedHIVreplication. However, this inhibition lasted only a shorttime as HIV evolved so that reverse transcriptase couldfunction even in the presence of the inhibitor. HIV canevolve resistance to any monotherapy currently in use. Theappearance of these drug-resistant strains are a growingconcern for researchers and HIV-infected patients, as thesestrains can be passed on to others, making the fight againstHIV even more difficult (HIV Drug Resistance Database,http://hivdb.stanford.edu). Today, numerous antiretroviral