6OGT

X-ray crystal structure of darunavir-resistant HIV-1 protease (P51) in complex with GRL-001

Summary for 6OGT

• Entry DOI: 10.2210/pdb6ogt/pdb
• Descriptor: Protease, GLYCEROL, (3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl [(2S,3R)-4-[{[2-(cyclopropylamino)-1,3-benzothiazol-6-yl]sulfonyl}(2-methylpropyl)amino]-1-(3-fluorophenyl)-3-hydroxybutan-2-yl]carbamate, ... (5 entities in total)
• Functional Keywords: inhibitor, viral protein, viral protein-inhibitor complex, viral protein/inhibitor
• Biological source: Human immunodeficiency virus 1
• Total number of polymer chains: 1
• Total formula weight: 11718.71

Authors

Bulut, H.,Hattori, S.I.,Aoki-Ogata, H.,Hayashi, H.,Aoki, M.,Ghosh, A.K.,Mitsuya, H. (deposition date: 2019-04-03, release date: 2020-04-08, Last modification date: 2023-10-11)

Primary citation

Bulut, H.,Hattori, S.I.,Aoki-Ogata, H.,Hayashi, H.,Das, D.,Aoki, M.,Davis, D.A.,Rao, K.V.,Nyalapatla, P.R.,Ghosh, A.K.,Mitsuya, H.
Single atom changes in newly synthesized HIV protease inhibitors reveal structural basis for extreme affinity, high genetic barrier, and adaptation to the HIV protease plasticity.
Sci Rep, 10:10664-10664, 2020

PubMed Abstract: HIV-1 protease inhibitors (PIs), such as darunavir (DRV), are the key component of antiretroviral therapy. However, HIV-1 often acquires resistance to PIs. Here, seven novel PIs were synthesized, by introducing single atom changes such as an exchange of a sulfur to an oxygen, scission of a single bond in P2'-cyclopropylaminobenzothiazole (or -oxazole), and/or P1-benzene ring with fluorine scan of mono- or bis-fluorine atoms around DRV's scaffold. X-ray structural analyses of the PIs complexed with wild-type Protease (PR) and highly-multi-PI-resistance-associated PR revealed that the PIs better adapt to structural plasticity in PR with resistance-associated amino acid substitutions by formation of optimal sulfur bond and adaptation of cyclopropyl ring in the S2'-subsite. Furthermore, these PIs displayed increased cell permeability and extreme anti-HIV-1 potency compared to DRV. Our work provides the basis for developing novel PIs with high potency against PI-resistant HIV-1 variants with a high genetic barrier.

PubMed: 32606378
DOI: 10.1038/s41598-020-65993-z

Experimental method

X-RAY DIFFRACTION (1.21 Å)