6PU8

Room temperature X-ray structure of HIV-1 protease triple mutant (V32I,I47V,V82I) with tetrahedral intermediate of keto-darunavir

Summary for 6PU8

• Entry DOI: 10.2210/pdb6pu8/pdb
• Descriptor: HIV-1 protease, (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(2S)-4-{[(4-aminophenyl)sulfonyl](2-methylpropyl)amino}-3,3-dihydroxy-1-phenylbutan-2-yl]carbamate (3 entities in total)
• Functional Keywords: hiv-1 protease, aspartic protease, tetrahedral intermediate inhibitor, homodimer, hydrolase
• Biological source: Human immunodeficiency virus 1
• Total number of polymer chains: 2
• Total formula weight: 22073.07

Authors

Kovalevsky, A.,Das, A. (deposition date: 2019-07-17, release date: 2020-06-24, Last modification date: 2023-10-11)

Primary citation

Kumar, M.,Mandal, K.,Blakeley, M.P.,Wymore, T.,Kent, S.B.H.,Louis, J.M.,Das, A.,Kovalevsky, A.
Visualizing Tetrahedral Oxyanion Bound in HIV-1 Protease Using Neutrons: Implications for the Catalytic Mechanism and Drug Design.
Acs Omega, 5:11605-11617, 2020

PubMed Abstract: HIV-1 protease is indispensable for virus propagation and an important therapeutic target for antiviral inhibitors to treat AIDS. As such inhibitors are transition-state mimics, a detailed understanding of the enzyme mechanism is crucial for the development of better anti-HIV drugs. Here, we used room-temperature joint X-ray/neutron crystallography to directly visualize hydrogen atoms and map hydrogen bonding interactions in a protease complex with peptidomimetic inhibitor KVS-1 containing a reactive nonhydrolyzable ketomethylene isostere, which, upon reacting with the catalytic water molecule, is converted into a tetrahedral intermediate state, KVS-1. We unambiguously determined that the resulting tetrahedral intermediate is an oxyanion, rather than the -diol, and both catalytic aspartic acid residues are protonated. The oxyanion tetrahedral intermediate appears to be unstable, even though the negative charge on the oxyanion is delocalized through a strong n → π* hyperconjugative interaction into the nearby peptidic carbonyl group of the inhibitor. To better understand the influence of the ketomethylene isostere as a protease inhibitor, we have also examined the protease structure and binding affinity with keto-darunavir (keto-DRV), which similar to KVS-1 includes the ketomethylene isostere. We show that keto-DRV is a significantly less potent protease inhibitor than DRV. These findings shed light on the reaction mechanism of peptide hydrolysis catalyzed by HIV-1 protease and provide valuable insights into further improvements in the design of protease inhibitors.

PubMed: 32478251
DOI: 10.1021/acsomega.0c00835

Experimental method

X-RAY DIFFRACTION (1.8 Å)