5OI2

Dissociation of biochemical and antiretroviral activities of Integrase-LEDGF Allosteric Inhibitors revealed by resistance of A125 polymorphic HIV-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure-function analyses unravel distinct effects of allosteric inhibitors of HIV-1 integrase on viral maturation and integration.

Bonnard, D.Le Rouzic, E.Eiler, S.Amadori, C.Orlov, I.Bruneau, J.M.Brias, J.Barbion, J.Chevreuil, F.Spehner, D.Chasset, S.Ledoussal, B.Moreau, F.Saib, A.Klaholz, B.P.Emiliani, S.Ruff, M.Zamborlini, A.Benarous, R.

(2018) J. Biol. Chem. 293: 6172-6186

  • DOI: 10.1074/jbc.M117.816793
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Recently, a new class of HIV-1 integrase (IN) inhibitors with a dual mode of action, called IN-LEDGF/p75 allosteric inhibitors (INLAIs), was described. Designed to interfere with the IN-LEDGF/p75 interaction during viral integration, unexpectedly, th ...

    Recently, a new class of HIV-1 integrase (IN) inhibitors with a dual mode of action, called IN-LEDGF/p75 allosteric inhibitors (INLAIs), was described. Designed to interfere with the IN-LEDGF/p75 interaction during viral integration, unexpectedly, their major impact was on virus maturation. This activity has been linked to induction of aberrant IN multimerization, whereas inhibition of the IN-LEDGF/p75 interaction accounts for weaker antiretroviral effect at integration. Because these dual activities result from INLAI binding to IN at a single binding site, we expected that these activities co-evolved together, driven by the affinity for IN. Using an original INLAI, MUT-A, and its activity on an Ala-125 (A125) IN variant, we found that these two activities on A125-IN can be fully dissociated: MUT-A-induced IN multimerization and the formation of eccentric condensates in viral particles, which are responsible for inhibition of virus maturation, were lost, whereas inhibition of the IN-LEDGF/p75 interaction and consequently integration was fully retained. Hence, the mere binding of INLAI to A125 IN is insufficient to promote the conformational changes of IN required for aberrant multimerization. By analyzing the X-ray structures of MUT-A bound to the IN catalytic core domain (CCD) with or without the Ala-125 polymorphism, we discovered that the loss of IN multimerization is due to stabilization of the A125-IN variant CCD dimer, highlighting the importance of the CCD dimerization energy for IN multimerization. Our study reveals that affinity for the LEDGF/p75-binding pocket is not sufficient to induce INLAI-dependent IN multimerization and the associated inhibition of viral maturation.


    Organizational Affiliation

    the Institut Cochin, Inserm U1016, 75014 Paris, France.,Inserm U944, CNRS UMR 7212, Université Paris Diderot, Conservatoire National des Arts et Métiers, 75010 Paris.,Inserm U944, CNRS UMR 7212, Université Paris Diderot, Conservatoire National des Arts et Métiers, 75010 Paris, alessia.zamborlini@lecnam.net.,From Biodim Mutabilis, 93230 Romainville, benarous.r@wanadoo.fr.,From Biodim Mutabilis, 93230 Romainville, damien.bonnard@mutabilis.fr.,From Biodim Mutabilis, 93230 Romainville.,the Centre for Integrative Biology, IGBMC, Inserm, CNRS, Université de Strasbourg, 67404 Illkirch, and ruff@igbmc.fr.,the Centre for Integrative Biology, IGBMC, Inserm, CNRS, Université de Strasbourg, 67404 Illkirch, and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Integrase
A
182Human 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 3 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
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
9VN
Query on 9VN

Download SDF File 
Download CCD File 
A
(2~{S})-2-[4-(4,4-dimethylcyclohexen-1-yl)-2-methyl-5-pyridin-4-yl-thiophen-3-yl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid
C24 H31 N O3 S
AOGLTJVFULDNHV-FQEVSTJZSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CAS
Query on CAS
A
L-PEPTIDE LINKINGC5 H12 As N O2 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
9VNIC50: 170 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.174 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 72.194α = 90.00
b = 72.194β = 90.00
c = 65.935γ = 120.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-07-18 
  • Released Date: 2018-03-07 
  • Deposition Author(s): Ruff, M., Benarous, R.

Revision History 

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2018-03-14
    Type: Database references
  • Version 1.2: 2018-05-02
    Type: Data collection, Database references
  • Version 1.3: 2019-10-16
    Type: Data collection