X-ray crystal structure of wild type HIV-1 protease in complex with GRL-084-13

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

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Novel Central Nervous System (CNS)-Targeting Protease Inhibitors for Drug-Resistant HIV Infection and HIV-Associated CNS Complications.

Amano, M.Salcedo-Gomez, P.M.Yedidi, R.S.Zhao, R.Hayashi, H.Hasegawa, K.Nakamura, T.Martyr, C.D.Ghosh, A.K.Mitsuya, H.

(2019) Antimicrob Agents Chemother 63

  • DOI: https://doi.org/10.1128/AAC.00466-19
  • Primary Citation of Related Structures:  
    6D0D, 6D0E

  • PubMed Abstract: 

    There is currently no specific therapeutics for the HIV-1-related central nervous system (CNS) complications. Here we report that three newly designed CNS-targeting HIV-1 protease inhibitors (PIs), GRL-083-13, GRL-084-13, and GRL-087-13, which contain a P1-3,5- bis -fluorophenyl or P1- para -monofluorophenyl ring, and P2- bis -tetrahydrofuran ( bis -THF) or P2-tetrahydropyrano-tetrahydrofuran ( Tp -THF), with a sulfonamide isostere, are highly active against wild-type HIV-1 strains and primary clinical isolates (50% effective concentration [EC 50 ], 0.0002 to ∼0.003 μM), with minimal cytotoxicity. These CNS-targeting PIs efficiently suppressed the replication of HIV-1 variants (EC 50 , 0.002 to ∼0.047 μM) that had been selected to propagate at high concentrations of conventional HIV-1 PIs. Such CNS-targeting PIs maintained their antiviral activity against HIV-2 ROD as well as multidrug-resistant clinical HIV-1 variants isolated from AIDS patients who no longer responded to existing antiviral regimens after long-term therapy. Long-term drug selection experiments revealed that the emergence of resistant-HIV-1 against these CNS-targeting PIs was substantially delayed. In addition, the CNS-targeting PIs showed the most favorable CNS penetration properties among the tested compounds, including various FDA-approved anti-HIV-1 drugs, as assessed with the in vitro blood-brain barrier reconstruction system. Crystallographic analysis demonstrated that the bicyclic rings at the P2 moiety of the CNS-targeting PIs form strong hydrogen-bond interactions with HIV-1 protease (PR) active site. Moreover, both the P1-3,5- bis -fluorophenyl and P1- para -monofluorophenyl rings sustain greater van der Waals contacts with PR than in the case of darunavir (DRV). The data suggest that the present CNS-targeting PIs have desirable features for treating patients infected with wild-type and/or multidrug-resistant HIV-1 strains and might serve as promising preventive and/or therapeutic candidates for HIV-1-associated neurocognitive disorders (HAND) and other CNS complications.

  • Organizational Affiliation

    Department of Infectious Diseases, Kumamoto University School of Medicine, Kumamoto, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
99Human immunodeficiency virus 1Mutation(s): 0 
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03366
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FQ1

Download Ideal Coordinates CCD File 
C [auth B](3aS,4S,7aR)-hexahydro-4H-furo[2,3-b]pyran-4-yl [(2S,3R)-1-(3,5-difluorophenyl)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}butan-2-yl]carbamate
C29 H38 F2 N2 O8 S
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.686α = 90
b = 62.686β = 90
c = 82.181γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-01
    Type: Initial release
  • Version 1.1: 2019-05-29
    Changes: Data collection, Database references
  • Version 1.2: 2019-07-10
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Refinement description