6D0D

X-ray crystal structure of wild type HIV-1 protease in complex with GRL-087-13


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1128/AAC.00466-19
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Presently, no specific therapeutics for the HIV-1-related central nervous system (CNS) complications exists. Here we report that three newly-designed CNS-targeting HIV-1 protease inhibitors (PIs), GRL-083-13, -084-13, and -087-13, which contain P1-3, ...

    Presently, no specific therapeutics for the HIV-1-related central nervous system (CNS) complications exists. Here we report that three newly-designed CNS-targeting HIV-1 protease inhibitors (PIs), GRL-083-13, -084-13, and -087-13, which contain 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-1s and primary clinical isolates (EC 50 : 0.0002∼0.003 μM) with minimal cytotoxicity. These CNS-targeting PIs efficiently suppressed the replication of HIV-1 variants (EC 50 : 0.002∼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 multi-drug-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 contact surfaces and form 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 multi-drug-resistant HIV-1s, and might serve as promising preventive and/or therapeutic candidates for HIV-1-associated neurocognitive disorders (HAND) and other CNS complications.


    Organizational Affiliation

    Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.,Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, Hyogo, Japan.,Departments of Infectious Diseases and Hematology, Kumamoto University School of Medicine, Kumamoto 860-8556, Japan mitsuyah@nih.gov.,Departments of Infectious Diseases and Hematology, Kumamoto University School of Medicine, Kumamoto 860-8556, Japan.,National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan.,Departments of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protease
A, B
99Human immunodeficiency virus type 1 group M subtype B (isolate BH10)Mutation(s): 0 
Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Go to UniProtKB:  P03366
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FQ4
Query on FQ4

Download SDF File 
Download CCD File 
B
(3aS,4S,7aR)-hexahydro-4H-furo[2,3-b]pyran-4-yl [(2S,3R)-1-(4-fluorophenyl)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}butan-2-yl]carbamate
C29 H39 F N2 O8 S
NIQHANOAJHWKET-AJIIGFCHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.191 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 62.592α = 90.00
b = 62.592β = 90.00
c = 82.372γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
MOLREPphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

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