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Author Notes:

Corresponding author: Dr. James P. Snyder jsnyder@emory.edu

We are grateful to OpenEye Scientific Software (Santa Fe, New Mexico) for kindly providing us with access to the ROCS software.

We would also like to thank Dr. Shaoxiong Wu, director of the Emory NMR facilities, for his assistance.



  • NMR spectroscopy
  • chemokine receptors
  • computational chemistry
  • conformational analysis
  • molecular modeling
  • Anti-HIV Agents
  • Binding Sites
  • Crystallography, X-Ray
  • Heterocyclic Compounds, 1-Ring
  • Models, Molecular
  • Molecular Structure
  • Peptides
  • Receptors, CXCR4
  • Small Molecule Libraries
  • Structure-Activity Relationship

Anti-HIV small-molecule binding in the peptide subpocket of the CXCR4:CVX15 crystal structure


Journal Title:



Volume 15, Number 11


, Pages 1614-1620

Type of Work:

Article | Post-print: After Peer Review


The CXC chemokine receptor 4 (CXCR4) is involved in chemotaxis and serves as a coreceptor for T-tropic HIV-1 viral entry, thus making this receptor an attractive drug target. Recently, crystal structures of CXCR4 were reported as complexes with the small molecule IT1t and the CVX15 peptide. Follow-up efforts to model different antagonists into the small molecule CXCR4:IT1t crystal structure did not generate poses consistent with either the X-ray crystal structure or site-directed mutagenesis (SDM). Here, we compare the binding pockets of the two CXCR4 crystal structures, revealing differences in helices IV, V, VI, and VII, with major differences for the His203 residue buried in the binding pocket. The small molecule antagonist AMD11070 was docked into both CXCR4 crystal structures. An AMD11070 pose identified from the CXCR4:CVX15 model presented interactions with Asp171, Glu288, Trp94, and Asp97, consistent with published SDM data, thus suggesting it is the bioactive pose. A CXCR4 receptor model was optimized around this pose of AMD11070, and the resulting model correlated HIV-1 inhibition with MM-GBSA docking scores for a congeneric AMD11070-like series. Subsequent NAMFIS NMR results successfully linked the proposed binding pose to an independent experimental structure. These results strongly suggest that not all small molecules will bind to CXCR4 in a similar manner as IT1t. Instead, the CXCR4:CVX15 crystal structure may provide a binding locus for small organic molecules that is more suitable than the secondary IT1t site. This work is expected to provide modeling insights useful for future CXCR4 antagonist and X4-tropic HIV-1 based drug design efforts.

Copyright information:

© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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