4O0J

HIV-1 Integrase Catalytic Core Domain Complexed with Allosteric Inhibitor (2S)-tert-butoxy[4-(4-chlorophenyl)-6-(3,4-dimethylphenyl)-2,5-dimethylpyridin-3-yl]ethanoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A New Class of Multimerization Selective Inhibitors of HIV-1 Integrase.

Sharma, A.Slaughter, A.Jena, N.Feng, L.Kessl, J.J.Fadel, H.J.Malani, N.Male, F.Wu, L.Poeschla, E.Bushman, F.D.Fuchs, J.R.Kvaratskhelia, M.

(2014) Plos Pathog. 10: e1004171-e1004171

  • DOI: 10.1371/journal.ppat.1004171
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The quinoline-based allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) are promising candidates for clinically useful antiviral agents. Studies using these compounds have highlighted the role of IN in both early and late stages of virus replication ...

    The quinoline-based allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) are promising candidates for clinically useful antiviral agents. Studies using these compounds have highlighted the role of IN in both early and late stages of virus replication. However, dissecting the exact mechanism of action of the quinoline-based ALLINIs has been complicated by the multifunctional nature of these inhibitors because they both inhibit IN binding with its cofactor LEDGF/p75 and promote aberrant IN multimerization with similar potencies in vitro. Here we report design of small molecules that allowed us to probe the role of HIV-1 IN multimerization independently from IN-LEDGF/p75 interactions in infected cells. We altered the rigid quinoline moiety in ALLINIs and designed pyridine-based molecules with a rotatable single bond to allow these compounds to bridge between interacting IN subunits optimally and promote oligomerization. The most potent pyridine-based inhibitor, KF116, potently (EC50 of 0.024 ┬ÁM) blocked HIV-1 replication by inducing aberrant IN multimerization in virus particles, whereas it was not effective when added to target cells. Furthermore, KF116 inhibited the HIV-1 IN variant with the A128T substitution, which confers resistance to the majority of quinoline-based ALLINIs. A genome-wide HIV-1 integration site analysis demonstrated that addition of KF116 to target or producer cells did not affect LEDGF/p75-dependent HIV-1 integration in host chromosomes, indicating that this compound is not detectably inhibiting IN-LEDGF/p75 binding. These findings delineate the significance of correctly ordered IN structure for HIV-1 particle morphogenesis and demonstrate feasibility of exploiting IN multimerization as a therapeutic target. Furthermore, pyridine-based compounds present a novel class of multimerization selective IN inhibitors as investigational probes for HIV-1 molecular biology.


    Organizational Affiliation

    Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, Ohio, United States of America.,Perelman School of Medicine, Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.,Center for Retrovirus Research and Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, United States of America.,Department of Molecular Medicine & Division of Infectious Diseases, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America.,Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Integrase
A
163Human immunodeficiency virus type 1 group M subtype B (isolate NY5)Mutation(s): 0 
Gene Names: gag-pol
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Go to UniProtKB:  P12497
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
LF8
Query on LF8

Download SDF File 
Download CCD File 
A
(2S)-tert-butoxy[4-(4-chlorophenyl)-6-(3,4-dimethylphenyl)-2,5-dimethylpyridin-3-yl]ethanoic acid
C27 H30 Cl N O3
DQQCEFPUGHRAEE-VWLOTQADSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CAF
Query on CAF
A
L-PEPTIDE LINKINGC5 H12 As N O3 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LF8Kd: 40 nM (98) BINDINGDB
LF8IC50: 13000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.184 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 72.223α = 90.00
b = 72.223β = 90.00
c = 65.227γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-2000data scaling
HKL-2000data reduction
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-02
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Refinement description