High-affinity RNA Aptamers Against the HIV-1 Protease Inhibit Both in Vitro Protease Activity and Late Events of Viral Replication

Sonald Duclair, Archana Gautam, Andrew Ellington, Vinayaka R. Prasad

Research output: Contribution to journalArticlepeer-review

41 Scopus citations


HIV-1 aspartyl protease (PR) plays a key role in virion morphogenesis, underscoring the effectiveness of protease inhibitors (PI). Despite their utility, side effects and drug-resistance remains a problem. We report the development of RNA aptamers as inhibitors of HIV-1 PR for potential use in anti-HIV gene therapy. Employing Systematic Evolution of Ligands by Exponential Enrichment (SELEX), we isolated four unique families of anti-HIV-1 PR RNA aptamers displaying moderate binding affinities (Kd = 92-140 nmol/l) and anti-PR inhibitory activity (Kis = 138-647 nmol/l). Second-generation RNA aptamers selected from partially randomized pools based on two of the aptamer sequences displayed striking enhancements in binding (Kds = 2-22 nmol/l) and inhibition (Kis = 31-49 nmol/l). The aptamers were specific in that they did not bind either the related HIV-2 protease, or the cellular aspartyl protease, Cathepsin D. Site-directed mutagenesis of a second-generation aptamer to probe the predicted secondary structure indicated that the stem-loops SL2 and SL3 and the stem P1 were essential for binding and that only the 3′-most 17 nucleotides were dispensable. Anti-PR aptamers inhibited HIV replication in vitro and the degree of inhibition was higher for second-generation aptamers with greater affinity and the inhibition was abrogated for a nonbinding aptamer variant.

Original languageEnglish (US)
Article numbere228
Pages (from-to)e228
JournalMolecular Therapy - Nucleic Acids
Issue number2
StatePublished - Feb 17 2015


  • HIV-1 PR inhibitor
  • HIV-1 inhibitor
  • RNA aptamer
  • RNA aptamer structure
  • anti-HIV-1 gene therapy

ASJC Scopus subject areas

  • Molecular Medicine
  • Drug Discovery


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