A novel substrate-based HIV-1 protease inhibitor drug resistance mechanism

• Published in: PLoS medicine Vol. 4; no. 1; p. e36
• Main Authors: Nijhuis, Monique, van Maarseveen, Noortje M, Lastere, Stephane, Schipper, Pauline, Coakley, Eoin, Glass, Bärbel, Rovenska, Mirka, de Jong, Dorien, Chappey, Colombe, Goedegebuure, Irma W, Heilek-Snyder, Gabrielle, Dulude, Dominic, Cammack, Nick, Brakier-Gingras, Lea, Konvalinka, Jan, Parkin, Neil, Kräusslich, Hans-Georg, Brun-Vezinet, Francoise, Boucher, Charles A B
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01-01-2007; Public Library of Science (PLoS)
• Subjects: Acquired immune deficiency syndrome; AIDS; Amino Acid Sequence; Base Sequence; Biochemistry; Blotting, Western; Care and treatment; Cell Line; Chronic Disease Management; Codon - genetics; Drug resistance; Drug Resistance, Viral - genetics; Drugs and adverse drug reactions; Frameshift Mutation; Gene Products, gag - genetics; Gene Products, gag - metabolism; Genome, Viral; HIV; HIV infection; HIV Infection/AIDS; HIV Protease - genetics; HIV Protease - metabolism; HIV Protease Inhibitors - pharmacology; HIV Reverse Transcriptase - genetics; HIV Reverse Transcriptase - metabolism; HIV-1 - drug effects; HIV-1 - genetics; Human immunodeficiency virus; Humans; Immunoblotting; Infectious Diseases; Microbiology; Molecular Sequence Data; Mutation; Protease inhibitors; Ritonavir - pharmacology; RNA, Viral - genetics; Substrate Specificity; Transfection; Virology; Viruses; United States > US; HIV-1; Amino Acid Sequence; Cell Line; Genome, Viral; Frameshift Mutation; Ritonavir; Humans; Drug Resistance, Viral; HIV Protease; Molecular Sequence Data; Substrate Specificity; Immunoblotting; Gene Products, gag; HIV Protease Inhibitors; Blotting, Western; Codon; Transfection; Base Sequence; RNA, Viral; HIV Reverse Transcriptase; Mutation
• ISSN: 1549-1676; 1549-1277; 1549-1676
• DOI: 10.1371/journal.pmed.0040036

HIV protease inhibitor (PI) therapy results in the rapid selection of drug resistant viral variants harbouring one or two substitutions in the viral protease. To combat PI resistance development, two approaches have been developed. The first is to increase the level of PI in the plasma of the patient, and the second is to develop novel PI with high potency against the known PI-resistant HIV protease variants. Both approaches share the requirement for a considerable increase in the number of protease mutations to lead to clinical resistance, thereby increasing the genetic barrier. We investigated whether HIV could yet again find a way to become less susceptible to these novel inhibitors.
We have performed in vitro selection experiments using a novel PI with an increased genetic barrier (RO033-4649) and demonstrated selection of three viruses 4- to 8-fold resistant to all PI compared to wild type. These PI-resistant viruses did not have a single substitution in the viral protease. Full genomic sequencing revealed the presence of NC/p1 cleavage site substitutions in the viral Gag polyprotein (K436E and/or I437T/V) in all three resistant viruses. These changes, when introduced in a reference strain, conferred PI resistance. The mechanism leading to PI resistance is enhancement of the processing efficiency of the altered substrate by wild-type protease. Analysis of genotypic and phenotypic resistance profiles of 28,000 clinical isolates demonstrated the presence of these NC/p1 cleavage site mutations in some clinical samples (codon 431 substitutions in 13%, codon 436 substitutions in 8%, and codon 437 substitutions in 10%). Moreover, these cleavage site substitutions were highly significantly associated with reduced susceptibility to PI in clinical isolates lacking primary protease mutations. Furthermore, we used data from a clinical trial (NARVAL, ANRS 088) to demonstrate that these NC/p1 cleavage site changes are associated with virological failure during PI therapy.
HIV can use an alternative mechanism to become resistant to PI by changing the substrate instead of the protease. Further studies are required to determine to what extent cleavage site mutations may explain virological failure during PI therapy.