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. 2009 Nov;83(21):10892-907.
doi: 10.1128/JVI.01142-09. Epub 2009 Aug 19.

Mechanism of human immunodeficiency virus type 1 resistance to monoclonal antibody B12 that effectively targets the site of CD4 attachment

Xueling Wu  1 , Tongqing Zhou, Sijy O'Dell, Richard T Wyatt, Peter D Kwong, John R Mascola
Affiliations

Mechanism of human immunodeficiency virus type 1 resistance to monoclonal antibody B12 that effectively targets the site of CD4 attachment

Xueling Wu et al. J Virol. 2009 Nov.

Abstract

The region of the human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein gp120 that engages its primary cellular receptor CD4 forms a site of vulnerability to neutralizing antibodies. The monoclonal antibody b12 exploits the conservation and accessibility of the CD4-binding site to neutralize many, though not all, HIV-1 isolates. To understand the basis of viral resistance to b12, we used the atomic-level definition of b12-gp120 contact sites to study a panel of diverse circulating viruses. A combination of sequence analysis, computational modeling, and site-directed mutagenesis was used to determine the influence of amino acid variants on binding and neutralization by b12. We found that several substitutions within the dominant b12 contact surface, called the CD4-binding loop, mediated b12 resistance, and that these substitutions resided just proximal to the known CD4 contact surface. Hence, viruses varied in key b12 contact residues that are proximal to, but not part of, the CD4 contact surface. This explained how viral isolates were able to evade b12 neutralization while maintaining functional binding to CD4. In addition, some viruses were resistant to b12 despite minimal sequence variation at b12 contact sites. Such neutralization resistance usually could be reversed by alterations at residues thought to influence the quaternary configuration of the viral envelope spike. To design immunogens that elicit neutralizing antibodies directed to the CD4-binding site, researchers need to address the antigenic variation within this region of gp120 and the restricted access to the CD4-binding site imposed by the native configuration of the trimeric viral envelope spike.

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Figures

FIG. 1.
FIG. 1.
HIV-1 gp120 sequence variation displayed in dendrogram format and mapped on the three-dimensional structure of the core of gp120. (A) Maximum-likelihood trees for HIV-1 group M (left), clade B (middle), and clade C (right). A value of 0.1 indicates the distance scale. The 19 clade B and 18 clade C reference viruses are highlighted with blue and red squares, respectively. (B) Sequence variation from HXBc2 in the context of the b12 epitope and gp120 core structure. The top row, from left to right, shows the molecular surface of the HXBc2 core gp120 in blue, with the b12 contact surface highlighted in green. Subsequent images display protein sequence variability from HXBc2 for group M, clade B, and clade C strains. Variability is displayed utilizing a white-to-red color gradient, which corresponds to 0 to 100% variation from the HXBc2 sequence. Hence, a 100% value for a specific site among clade C viruses indicates that all clade C viruses contained an amino acid that is different from that found in the HXBc2 isolate. Note that although the intrinsic variation within group M is greater than that of clade C, the average variation of clade C from the HXBc2 isolate is greater. To aid visualization, the borders of the b12 epitope are highlighted with a green outline. Some regions of the gp120 core display high variation (bright red), while the b12 epitope is relatively conserved except in the CD4-binding loop, where there is substantial variation. The middle row shows ribbon representations corresponding to the top-row surface representation. The dash boxes highlight the CD4-binding loop. The bottom row is a close-up, with Cα atoms of residues of the CD4-binding loop displayed in spheres and selectively marked according to the HXBc2 residue numbers. Note the level of variation (in red) near residues 364, 369, and 373.
FIG. 2.
FIG. 2.
Sequence of the HXBc2 gp120 core and residue-by-residue fractional variation. The fraction of non-HXBc2 sequences at each residue for HIV-1 group M (blue column), clade B (green column), and clade C (red column) are plotted along the primary sequence of the HXBc2 core of gp120. Variable loops V1-V2 and V3 were replaced with Gly-Ala-Gly tripeptides, and V4 was deleted because of unreliable alignment. Sequence numbering follows the HXBc2 convention. Symbols under the HXBc2 sequence in green and orange depict gp120 contacts with b12 and CD4, respectively. Open circles, gp120 main-chain contacts; open circles with rays, gp120 side chain contacts; filled circles, gp120 main- and side-chain contacts. The CD4-binding loop, which is the prominent b12 and CD4 contact surface on gp120, is highlighted with a red box.
FIG. 3.
FIG. 3.
Amino acid variants within the CD4-binding loop in the context of b12- and CD4-bound structures of the gp120 core. (A) Structure-based computational models display likely side-chain rotomers for natural variants 364H, 369L, and 373 M (shown with carbon atoms in magenta), which are predicted to be incompatible with b12 binding. These models are displayed in the context of the b12-gp120 core structure, shown in stick representation, with gp120 residues shown with blue carbon atoms and b12 residues with green carbon atoms. Potential clashes are highlighted in gold. These clashes may occur with other gp120 residues within the b12-bound conformation and/or with b12 residues such as Asn31, Tyr98, and Trp100. (B) The locations of residues 364, 369, and 373 (highlighted in purple) in CD4-bound (left) and b12-bound (right) structures of the gp120 core are shown in both ribbon diagrams (top row) and close-up surface representations (bottom row) of the CD4-binding loop. The CD4 and b12 contact sites are colored yellow and green, respectively. Boxed areas in the top row are magnified in the indicated insets. In the bottom row, portions of CD4 (orange) and b12 complementarity-determining regions (CDRs) CDR-H1, CDR-H2, and CDR-H3 (orange) are shown as a ribbon diagram, and portions of the borders of their contact sites on the CD4-binding loop of gp120 are marked with red lines. CD4 interacts with only one side of the CD4-binding loop, while the CDRs of b12 grab on both sides of the CD4-binding loop. Residues 364, 369, and 373, with naturally occurring mutations, reside outside of the conserved CD4-binding site (yellow) but are contained within the b12 contact surface (green). Although residue 364 appears to be outside the b12 epitope in the viewing angle shown in the middle bottom panel, its side chain actually falls within the b12 contact area on the other side of the CD4-binding loop, as shown in the bottom right panel.
FIG. 4.
FIG. 4.
Effect of amino acid variants within the CD4-binding loop on b12 binding to monomeric gp120 (A, C, and E) and viral neutralization sensitivity to b12 (B, D, and F). ELISA binding curves show monoclonal antibody (Ab) 17b binding in black, as a control for the capture of wild-type (WT) and mutated gp120, and b12 binding in red. Solid symbols are WT gp120, and open symbols are the indicated point mutants. Control 17b binding was performed in the presence of sCD4. OD450, optical density at 450 nm.
FIG. 5.
FIG. 5.
Statistical analysis of b12 binding and neutralization. (A) Comparison of b12 binding to gp120 from b12 neutralization-sensitive (b12S) and -resistant (b12R) viruses from clade B and C (left). The middle and right panels show the linear regression of b12 binding of gp120s and the neutralization of Env pseudoviruses from clade B and C. (B) Comparison of sCD4 neutralization sensitivity between b12S and b12R viruses from clade B and C (left). The middle and right panels show the linear regression of sCD4 and b12 neutralization activity against Env pseudoviruses from clade B and C. (C) Comparisons of b12 binding to clade B and C gp120 (left), b12 (middle), and sCD4 (right) neutralization activity against clade B and C Env pseudoviruses. The horizontal bars show geometric means. P values were derived by the Mann-Whitney test. The b12 and sCD4 neutralization IC50s used in these plots were converted from micrograms/milliliter to nanomolars using a molecular mass of 148 kDa for b12 and 46 kDa for sCD4.
FIG. 6.
FIG. 6.
Effect of mutations outside the b12 epitope such as Δ197, Δ301, and gp41 (569 and 675) on b12 binding to monomeric gp120 (A, C, and E) and on viral neutralization sensitivity to b12 (B, D, and F). ELISA binding curves show monoclonal antibody (Ab) 17b binding in black as a control for the capture of wild-type (WT) and mutated gp120 and b12 binding in red. Solid symbols are WT gp120, and open symbols are the indicated point mutants. OD450, optical density at 450 nm. (G) Illustration of the altered conformation of the Env spike by mutations outside the b12 epitope. Glycans at 197 and 301 appear to restrict the quaternary flexibility of gp120 within the viral Env spike, thus limiting the Env movement required for the exposure of the b12 epitope. Glycan removal at these sites likely alters the quaternary restriction of conformational changes, and this appears to allow for increased accessibility to the b12 contact surface. A similar effect may occur with alterations in gp41 residues 569 and 675.
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References

    1. Arendrup, M., C. Nielsen, J. E. Hansen, C. Pedersen, L. Mathiesen, and J. O. Nielsen. 1992. Autologous HIV-1 neutralizing antibodies: emergence of neutralization-resistant escape virus and subsequent development of escape virus neutralizing antibodies. J. Acquir. Immune Defic. Syndr. 5:303-307. - PubMed
    1. Barbas, C. F., III, E. Bjorling, F. Chiodi, N. Dunlop, D. Cababa, T. M. Jones, S. L. Zebedee, M. A. Persson, P. L. Nara, E. Norrby, et al. 1992. Recombinant human Fab fragments neutralize human type 1 immunodeficiency virus in vitro. Proc. Natl. Acad. Sci. USA 89:9339-9343. - PMC - PubMed
    1. Beaumont, T., E. Quakkelaar, A. van Nuenen, R. Pantophlet, and H. Schuitemaker. 2004. Increased sensitivity to CD4 binding site-directed neutralization following in vitro propagation on primary lymphocytes of a neutralization-resistant human immunodeficiency virus IIIB strain isolated from an accidentally infected laboratory worker. J. Virol. 78:5651-5657. - PMC - PubMed
    1. Binley, J. M., E. A. Lybarger, E. T. Crooks, M. S. Seaman, E. Gray, K. L. Davis, J. M. Decker, D. Wycuff, L. Harris, N. Hawkins, B. Wood, C. Nathe, D. Richman, G. D. Tomaras, F. Bibollet-Ruche, J. E. Robinson, L. Morris, G. M. Shaw, D. C. Montefiori, and J. R. Mascola. 2008. Profiling the specificity of neutralizing antibodies in a large panel of plasmas from patients chronically infected with human immunodeficiency virus type 1 subtypes B and C. J. Virol. 82:11651-11668. - PMC - PubMed
    1. Binley, J. M., T. Wrin, B. Korber, M. B. Zwick, M. Wang, C. Chappey, G. Stiegler, R. Kunert, S. Zolla-Pazner, H. Katinger, C. J. Petropoulos, and D. R. Burton. 2004. Comprehensive cross-clade neutralization analysis of a panel of anti-human immunodeficiency virus type 1 monoclonal antibodies. J. Virol. 78:13232-13252. - PMC - PubMed

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