Hiv-1 Protease Complexed With A Macrocyclic Peptidomimetic Inhibitor

HIV protease is a tetrameric protein with two active sites. However, for simplicity, this image shows only two of the chains complexed to an inhibitor that mimics the region of the protein to be cleaved. 

The inhibitor shown, called a macrocycle, possesses two amides and an aromatic group within 15-17 membered rings designed to replace N- or C-terminal tripeptides from peptidic inhibitors of HIV protease. These cyclic analogues are potent inhibitors of HIV protease, and the crystal structures show them to be structural mimics of acyclic peptides. They bind to the active site of the protease via the same interactions. Each macrocycle  adopts a beta-strand conformation which is pre-organized for protease binding. An unusual feature of the binding of C-terminal macrocyclic inhibitors is the interaction between a positively charged secondary amine and a catalytic aspartate of HIV protease

Use the buttons in the table to highlight the individual chains of the protease as required. 

Space fill the inhibitor here [On Off ]. Highlight the aspartate residues at the active site [On  Off ]. You will see that although each chain contains four aspartates [On Off  ]. only two are involved in the catalytic process. Isoleucine 50 of each chain also interacts with the substrate [ On   Off ] via a water molecule. You may want to look closer by zooming in [ In Out ] and rotating [On Off  ]

HIV protease, like the other proteins of this virus, is subject to rapid mutation that allows the virus to become resistant to the drug. Three HIV-1 protease mutant species, glycine 48 converted to valine, leucine 90 converted to methionine and G48V/L90M double mutant, are associated in vivo with resistance to the drug saquinavir. Kinetic studies on these mutants demonstrate a 13.5-, 3-, and 419-fold increase in Ki values, respectively, compared to the wild-type enzyme. To see why mutations at these sites alter the interaction with the drug, highlight glycine 48 (gray) [Rotate On Off  ].  In order to accommodate a valine side chain (which is much larger than glycine, the smallest amino acid) at position 48, the inhibitor moves away from the protease, resulting in the formation of larger gaps between the inhibitor and the enzyme. Now highlight leucine 90 (cyan) . You will see that it does not contact the substrate but if you turn the aspartates off    and highlight  asparatate 25 (violet), a critical catalytic residue at the enzyme's active site, you can see that leucine 90 interacts with this residue. A new methionine side chain at position 90 has van der Waals interactions with main-chain atoms of the active site residues resulting in a decrease in the volume and the structural flexibility of the substrate binding pockets.

You have now made a lot of changes to the image at the right. You may want to reset the original image here     If you have rotated the image you should reload/refresh the page with the browser button.

As you have seen the protease is made of two polypeptide chains. The substrate is held in a tunnel that is formed between the two chains. To see this rotate the molecule here . Spacefill glycine 48 of the blue chain   and spacefill the substrate/inhibitor .  See how this residue interacts with the substrate and note the small size of the glycine residue. Let's now change the blue chain to backbone to make things simpler . You can see the pocket in the blue chain that accommodates the substrate. Allow the molecule to rotate  

Now see what happens when we have a mutation that converts glycine to valine at position 48 . Again spacefill the residue at position 48 . It goes to a magenta color. It is now a valine   and you can see that it protrudes much more from the backbone. Spacefill the substrate (The substrate is now Saquinavir. Resistance to this drug occurs when the valine is present at position 48). Note how the drug is pushed away from the chain by the larger valine. Allow the molecule to rotate .

You can reset this image here   or start again by using the reload/refresh button of the browser

To compare the size of valine and glycine which is the basis of Saquinavir resistance, go here .  Glycine is gray and valine is magenta. See Saquinavir here .

Finally, let's put Saquinavir back into the protease .Only one chain of the protease is shown. The protease is green and the  Saquinavir is in cpk color (gray, red, blue) as it was in the enlarged image of the drug that you just saw. The valine at residue 48 is magenta and the active site residues are orange.

Read more about this in the abstract of the original paper here

Further changes and selection may be made using the Chime menu. Right click on the molecule to show the Chime menu. The buttons below replicate the functions in the text.

Protein Database file for first image (1D4L) is here   -   Protein database for second image (1FB7) is here   -   Get Chime here

The chime images of amino acids are from Dr Don Harden, Georgia State University

© Richard Hunt, University of South Carolina School of Medicine