Structure based design of potent inhibitors against multidrug-resistant HIV-1 protease variants

The current study is focused on designing potent inhibitors against multidrug-resistant strains of HIV-1 protease, a critical enzyme required for the viral replication, maturation and infectivity. Due to the error prone rapid replication of the virus, mutations are randomly incorporated into the viral proteins. Accumulation of mutations leads to changes in the secondary structure of the viral proteins that may hinder the viral replication as well as cause drug resistance. HIV-1 protease is a small homodimeric aspartic protease which cleaves the long viral polyproteins into mature individual proteins that are packed into a functional infective virion. Due to its critical role, the viral protease is a very important drug target. Currently there are ten FDA approved inhibitors against HIV-1 protease that are used as a part of the combination therapy. Due to the accumulation of various mutations, drug resistant variants of HIV-1 protease are selected during the therapy. Some of these clinical isolates are multidrug-resistant (MDR) variants.;One such MDRHIV-1 protease was chosen as the drug target in the current study. Structure-function studies of an ensemble of MDR protease variants revealed that there is a conserved trend in active site expansion with wide-open flaps. Some mutants even showed proline switch (reported for the first time) that might even worsen the drug resistance problem. Crystal structures of these mutants show loss of contacts mainly due to lack of induced fit conformational changes in the protease upon ligand binding. FRET based enzyme assays showed that MDR769 HIV-1 protease is ten fold resistant against the current drugs.;The expanded active site cavity of the MDR protease was scanned using a library of heptapeptides that mimic the CA/p2 cleavage site. Among the library of nine peptides, one was identified as a lead peptide with a subnanomolar inhibition capability. This peptide was further studied and was used as a template to design potent compounds that can be used as inhibitors against such ensemble of MDR protease variants. These compounds are to be synthesized and tested in future. The pharmacological properties of these drugs are to be further studied in order to use them as a part of combination therapy.