3 years ago

How Mutations Can Resist Drug Binding yet Keep HIV-1 Protease Functional

How Mutations Can Resist Drug Binding yet Keep HIV-1 Protease Functional
Sanjib Senapati, Rajeswari Appadurai
Human immunodeficiency virus-1 (HIV-1) protease is an important drug target for acquired immune deficiency syndrome therapy. Nearly 10 small molecule drugs have been approved by the Food and Drug Administration (FDA). However, prolonged use of these drugs produced protease mutants that are not susceptible to many of these drugs. The mutated proteases, however, continue to cleave the substrate peptides and thus remain largely functional. This poses a major challenge for the treatment strategies. Thus, it has become imperative to understand how these mutations induce drug resistance while maintaining the enzymatic activity of this protein. Here, we perform a comprehensive study of the wild type (WT) and clinically relevant mutated protease bound to a series of FDA-approved drugs and substrates of varying sequences to unravel the mechanism of unhindered activity of the drug-resistant protease variants. Our results from large molecular dynamics simulations suggest that while binding of the substrate to WT and protease mutants involves multiple H-bonding interactions between substrate subsites and the protease’s main chain atoms, the drug binds primarily through the hydrophobic interactions with the side chains of protease’s active site and flap residues. This implies that any side chain variations caused by mutations in protease could greatly modulate the binding affinity of inhibitors, but not of the substrates. The significantly weaker free energy of binding of the drugs could also be attributed to the limited number of interaction subsites present in the inhibitor structures compared to the substrates. These findings in combination with the identified protease flap and active site residues that contribute to ligand recognition and strong binding can help in the design of future resistance-evading HIV-1 protease inhibitors.

Publisher URL: http://dx.doi.org/10.1021/acs.biochem.7b00139

DOI: 10.1021/acs.biochem.7b00139

You might also like
Never Miss Important Research

Researcher is an app designed by academics, for academics. Create a personalised feed in two minutes.
Choose from over 15,000 academics journals covering ten research areas then let Researcher deliver you papers tailored to your interests each day.

  • Download from Google Play
  • Download from App Store
  • Download from AppInChina

Researcher displays publicly available abstracts and doesn’t host any full article content. If the content is open access, we will direct clicks from the abstracts to the publisher website and display the PDF copy on our platform. Clicks to view the full text will be directed to the publisher website, where only users with subscriptions or access through their institution are able to view the full article.