Biomolecules at Kenyon  HHMI at Kenyon  Jmol Home  Biology Dept  COMMENTS and CORRECTIONS

HIV Capsid Protein

Kelly Wahl '12 and Kiersten Bell '13


I. Introduction

The HIV genome and its core proteins are protected by an outer cell membrane-derived envelope and an inner viral protein shell, or capsid. HIV's fullerene or cone-shaped capsid offers both structure and support. The entire multimeric capsid is composed of the HIV capsid protein (CA). 12 pentamers and 250 hexamers of CA link together in a higly ordered manner to form the capsid. 

Model of HIV fullerene and CA pentamer and hexamer

The capsid is a potential drug target due to its vital role in the HIV life cycle. If capsid assembly or disassembly is disrupted, viral replication, and consequently transmission, can be stopped.  A new class of HIV inhibitors has recently been discovered that bind to the N-terminus domain (NTD) of CA interrupting both uncoating of the viral genome after entry into the cell and prevents assembly of the capsid during viral replication. One of these new potential HIV capsid inhibitors is PF-3450074 . Presented here are two HIV-1 CA NTDs bound to the potential HIV inhibitor PF-3450074

II. CA Structure

CA is comprosed of a c-terminus domain (CTD) and a NTD briged by a short linker region. The NTD is comprised of seven alpha helices , with a flexible linker between helix 4 and 5 . The helices pack together to give the entire monomer a flat, roughly triangular shape. The NTD also contains a short, antiparallel 13 residue beta sheet . This beta sheet packs against helix 6 through hydrophobic contacts . The amino group of proline 1 of the beta sheet and the carbonyl group of asparagine 51 form a salt bridge that stabilizes the structure .

III. Capsid Structure

CA monomers are oriented in the same way and have the protein interactions wherther they are forming a hexamer or pentamer. The linker domain appears to be the key feature that allows both hexameric and pentameric faces to form out of CA. This linker is found between the CTD and NTD domains of a monomer. The NTDs act like “spokes on a wheel” and the outward facing CTDS interact with each other to form the “rim” of the wheel and hold the NTD "spokes" in place so CTD-CTD interactions with other faces can occur.

NTD ring formation is mediated by three a-helices: helix 1 and 3 of one CA's NTD bind to helix 2 of another CA's NTD . The side chains methionine 55; valine 59, 27, 26, and 24; leucine 56, 52, 20, and 52; alanine 31, 22, and 65; and tryptophan 23   form a hydrophobic region, stabilizing helix interactions to help create a rigid, wheel like hexameric or pentameric face CTD-CTD binding differs slightly depending on which face, pentamer or hexamer, is formed. No interamolecular interactions occur between the CTD and the NTD of a monomer.

IV. PF-3450074

The drug sits in a preformed pocket of the NTD, made up of helices 3, 4, 5, and 7 . The hydrophobic interactions between the two benzene substituents of PF-3450074 and the binding pocket anchor the drug to the NTD of CA . The other ringed structure of the drug interacts with lysine 70 of helix 4 further stabilizing the drug-protein interactions. PF-3450074 binding at the hydrophobic pocket limits the flexibility of the linker domain connecting the CTD and the NTD. When  the drug binds at the hydrophobic pocket, tyrosine 145 changes orientation . This prevednts NTD and CTD interactions between CA monomers resulting in the premature dissolution of the capsid after viral entry. It also prevents pentameric and hexameric face formation during capsid assembly.

Mutant CA's with amino acid substitutions at in the NTD region were constructed to determine drug-protein interactions.  When threonine107 is exchanged for an asparagine,  there is a 6-fold reduction in viral susceptibility to the drug. Additional mutations Q67H, K7OR, and L111I resulted in a >60-fold reduction in susceptibility, highlighting the importance of the NTD binding pocket in CA’s interaction with PF-3450074 .

PF-3450074 represents a new class of HIV inhibitors that prevent HIV replication by interfering with capsid formation. Other classes of HIV inhibitors work by blocking viral reverse transcriptase and protease activity.

Although select substitutions of amino acids in the binding pocket resulted in HIV strains resistant to PF-3450074, this drug still has the potential to be a powerful drug in the treatment of HIV. PF-345007 would most likely be used in a cocktail with other classes of HIV inhibitors, decreasing the odds of widespread resistance developing  quickly and therefore prolonging its use.

VI. References

Blair, W.S., C. Pickford, S.L. Irving, D.G. Brown, M. Anderson, R. Bazin, J. Cao, G. Ciaramella, J. Issacson, L. Jackson, R. Hunt, A. Kjerrstrom, J.A. Nieman, A.K. Patick, M. Perros, A.D. Scott, K. Whitby, H. Wu, and S.L. Butler. 2010. HIV capsid is a tractable target for small molecule therapeutic intervention. PloS Pathogens 6:12.

Fikes, B. (2011, January 19). Scripps Research Details HIV Capsid Structure, Potential Drug. Blogs . Retrieved from

Du, S., L. Betts, R. Yang, H. Shi, J. Concel, J. Ahn, C. Aiken, P. Zhang, and J.I. Yeh. 2011. Structure of the HIV-1 full-length capsid protein in a conformationally trapped unassembled state induced by small-molecule binding. Journal of Molecular Biology 406: 371-386.

Pornillos, O., B.K. Ganser-Pornillos, and M. Yeager. 2011. Atomic level modeling of the HIV capsid. Nature 469: 424-427.

Yeager, M. 2011. Design of in Vitro symmetric complexes and analysis by hybrid methods reveal mechanisms of HIV capsid assembly. Journal of Molecular Biology 410: 534-552.

Shi, J., J. Zhou, V.B. Shah, C. Aiken, and K. Whitby. 2011. Small-molecule inhibition of human immunodeficiency virus type 1 infection by virus capsid destabilization. Journal of Virology 85: 542-549.

Back to Top