Fragments vs HIV-1 Protease: Pocket-to-Lead

The drugging of HIV-1 protease is a classic structure-based design success story, as discussed in a guest post by Glyn Williams from the early days of the SARS-CoV-2 pandemic. The peptide origins of approved inhibitors such as saquinavir are obvious, and the residual structural features can present problems for oral bioavailability. Although there have been fragment screens against the enzyme, the hits do not seem to have been pursued, perhaps in part to the number of approved drugs. But viruses never stop mutating, and developing new chemical matter is prudent. In a recent J. Med. Chem. paper, Yuki Tachibana and colleagues at Shionogi describe a fragment-based approach.

 

The researchers started by performing a virtual screen, but none of the hits were active when tested in a biochemical assay. The active site of HIV-1 protease contains four hydrophobic subsites, and none of the virtual hits filled all four of them. Thus, the researchers chose to focus on fragments that could make some of the interactions while providing growth vectors to additional subsites. They call this a “pocket-to-lead” strategy.

 

Fragment 5 docked nicely into the active site; the hydroxyl group makes interactions with the catalytic aspartic acid residues, while the phenyl ring tucks into the S2 pocket. Growing into the S2’ and S1’ pockets led to molecules such as compound 9, which showed weak but detectable activity. (Astute readers will notice that the stereochemistry around the hydroxyl moiety has changed; both diastereomers are active.) A crystal structure of compound 9 bound to HIV-1 protease confirmed the predicted binding mode

 

Examination of the crystal structure revealed that the parafluorobenzyl substituent was not completely filling the S1’ pocket, and was also in a strained conformation. Replacing this with an alkyl substituent led to low micromolar compound 12. Finally, growing into the S1 subsite led to compound 14, a low nanomolar inhibitor with sub-micromolar antiviral activity.

 

This is a nice example of structure-guided, computationally-enabled fragment-based lead discovery that bears some similarity to the V-SYNTHES method we highlighted earlier this year. As the researchers note, the cyclic lactam found in fragment 5 had been used previously in HIV-1 protease inhibitors. It might have been possible to get to something similar to compound 14 from that earlier molecule. But regardless, compound 14 is emphatically non-peptidic. Whether it will lead to superior drugs remains to be seen, but the paper does say that further optimization is underway.