6PTP

Joint X-ray/neutron structure of HIV-1 protease triple mutant (V32I,I47V,V82I) with tetrahedral intermediate mimic KVS-1

Summary for 6PTP

• Entry DOI: 10.2210/pdb6ptp/pdb
• Descriptor: HIV-1 Protease, N~2~-[(2R,5S)-5-({(2S,3S)-2-[(N-acetyl-L-threonyl)amino]-3-methylpent-4-enoyl}amino)-2-butyl-4,4-dihydroxynonanoyl]-L-glutaminyl-L-argininamide (3 entities in total)
• Functional Keywords: hiv-1 protease, aspartic protease, homodimer, hydrolase
• Biological source: Human immunodeficiency virus 1
• Total number of polymer chains: 2
• Total formula weight: 22310.39

Authors

Kovalevsky, A.,Das, A. (deposition date: 2019-07-16, release date: 2020-06-10, Last modification date: 2023-10-25)

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

NEUTRON DIFFRACTION (2.2 Å)
X-RAY DIFFRACTION (1.85 Å)