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Structural and Physical Basis for Anti-IgE Therapy.

Wright JD, Chu HM, Huang CH, Ma C, Chang TW, Lim C - Sci Rep (2015)

Bottom Line: Mutagenesis studies indicate overlapping FcεRI and omalizumab-binding sites in the Cε3 domain, but crystallographic studies show FcεRI and CD23-binding sites that are far apart, so how can omalizumab block IgE from binding both receptors?These results provide a structural and physical basis as to why omalizumab cannot bind receptor-bound IgE and why omalizumab-bound IgE cannot bind to CD23/FcεRI.They reveal the key IgE residues and their roles in binding omalizumab, CD23, and FcεRI.

View Article: PubMed Central - PubMed

Affiliation: 1] Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan [2] The Genomics Research Center, Academia Sinica 115, Taiwan.

ABSTRACT
Omalizumab, an anti-IgE antibody, used to treat severe allergic asthma and chronic idiopathic urticaria, binds to IgE in blood or membrane-bound on B lymphocytes but not to IgE bound to its high (FcεRI) or low (CD23) affinity receptor. Mutagenesis studies indicate overlapping FcεRI and omalizumab-binding sites in the Cε3 domain, but crystallographic studies show FcεRI and CD23-binding sites that are far apart, so how can omalizumab block IgE from binding both receptors? We report a 2.42-Å omalizumab-Fab structure, a docked IgE-Fc/omalizumab-Fab structure consistent with available experimental data, and the free energy contributions of IgE residues to binding omalizumab, CD23, and FcεRI. These results provide a structural and physical basis as to why omalizumab cannot bind receptor-bound IgE and why omalizumab-bound IgE cannot bind to CD23/FcεRI. They reveal the key IgE residues and their roles in binding omalizumab, CD23, and FcεRI.

No MeSH data available.


Related in: MedlinePlus

Why omalizumab-bound IgE cannot bind CD23 or FcεRI and why omalizumab cannot bind to receptor-bound IgE.(a) CD23 (tangerine) clashes with omalizumab–Fab (green) after the IgE Cε3 domains from omalizumab-bound IgE are separately superimposed onto that from CD23-bound IgE (PDB 4gko), and displaying only the omalizumab-Fv. The IgE-Cε2 domains in the extended position are modeled by superimposing the IgE Cε3-4 domains from PDB 4j4p onto those in CD23-bound IgE and displaying only the IgE Cε2 domains. Omalizumab heavy atoms within 2.5 Å of heavy atoms in CD23 are depicted as spheres. (b) FcεRI (scarlet) clashes with the IgE-Cε2 domains (cyan) in the extended position after each IgE Cε3 domain from omalizumab-bound IgE is separately superimposed onto that from FcεRI-bound IgE (PDB 2y7q), and displaying only omalizumab-Fv. The IgE-Cε2 domains were modeled in an extended position by superimposing the IgE-Cε3-4 domains from PDB 4j4p over the FcεRI-bound IgE and displaying only the Cε2 domains in the 4j4p structure, while hiding the IgE-Cε2 domains from 2y7q. Omalizumab and IgE-Cε2 heavy atoms within 2.5 Å of heavy atoms from FcεRI are depicted as spheres. (c) FcεRI (scarlet) clashes with omalizumab–Fv (green) after each Cε3 domain from omalizumab-bound IgE is separately superimposed onto that from FcεRI-bound IgE (PDB 2y7q), and displaying only omalizumab-Fv. Omalizumab heavy atoms within 2.5 Å of heavy atoms from FcεRI or IgE-Cε2 are depicted as spheres. (d) Omalizumab–Fv (green) clashes with CD23 or the Cε2 domain after each Cε3 domain from omalizumab-bound IgE is separately superimposed onto that from the 1:1 IgE-Fc/CD23 complex (see text), and displaying only omalizumab-Fv. Omalizumab heavy atoms within 2.5 Å of heavy atoms from CD23 or IgE-Cε2 are depicted as spheres.
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f7: Why omalizumab-bound IgE cannot bind CD23 or FcεRI and why omalizumab cannot bind to receptor-bound IgE.(a) CD23 (tangerine) clashes with omalizumab–Fab (green) after the IgE Cε3 domains from omalizumab-bound IgE are separately superimposed onto that from CD23-bound IgE (PDB 4gko), and displaying only the omalizumab-Fv. The IgE-Cε2 domains in the extended position are modeled by superimposing the IgE Cε3-4 domains from PDB 4j4p onto those in CD23-bound IgE and displaying only the IgE Cε2 domains. Omalizumab heavy atoms within 2.5 Å of heavy atoms in CD23 are depicted as spheres. (b) FcεRI (scarlet) clashes with the IgE-Cε2 domains (cyan) in the extended position after each IgE Cε3 domain from omalizumab-bound IgE is separately superimposed onto that from FcεRI-bound IgE (PDB 2y7q), and displaying only omalizumab-Fv. The IgE-Cε2 domains were modeled in an extended position by superimposing the IgE-Cε3-4 domains from PDB 4j4p over the FcεRI-bound IgE and displaying only the Cε2 domains in the 4j4p structure, while hiding the IgE-Cε2 domains from 2y7q. Omalizumab and IgE-Cε2 heavy atoms within 2.5 Å of heavy atoms from FcεRI are depicted as spheres. (c) FcεRI (scarlet) clashes with omalizumab–Fv (green) after each Cε3 domain from omalizumab-bound IgE is separately superimposed onto that from FcεRI-bound IgE (PDB 2y7q), and displaying only omalizumab-Fv. Omalizumab heavy atoms within 2.5 Å of heavy atoms from FcεRI or IgE-Cε2 are depicted as spheres. (d) Omalizumab–Fv (green) clashes with CD23 or the Cε2 domain after each Cε3 domain from omalizumab-bound IgE is separately superimposed onto that from the 1:1 IgE-Fc/CD23 complex (see text), and displaying only omalizumab-Fv. Omalizumab heavy atoms within 2.5 Å of heavy atoms from CD23 or IgE-Cε2 are depicted as spheres.

Mentions: The 1:2 IgE/omalizumab complex cannot bind to CD23 and FcεRI because the key IgE residues involved in binding both IgE receptors are bound or blocked by the two omalizumabs. The 408RASGK415 motif makes a significant free energy contribution to binding CD23, but is occupied by omalizumab. Furthermore, Glu450 and Glu452, which form hydrogen bonds with CD23:Arg188/Arg224 and CD23:His186, respectively, are locked by intramolecular interactions when IgE is bound by two omalizumabs (Fig. 7a). On the other hand, the 461PHLPR465 motif in the FG loop makes a large free energy contribution to binding FcεRI (Fig. 5), but these residues in both IgE chains are bound by two omalizumabs. Furthermore, the extended conformation of the Cε2 domains in the 1:2 IgE/omalizumab complex also obstructs FcεRI binding (Fig. 7b).


Structural and Physical Basis for Anti-IgE Therapy.

Wright JD, Chu HM, Huang CH, Ma C, Chang TW, Lim C - Sci Rep (2015)

Why omalizumab-bound IgE cannot bind CD23 or FcεRI and why omalizumab cannot bind to receptor-bound IgE.(a) CD23 (tangerine) clashes with omalizumab–Fab (green) after the IgE Cε3 domains from omalizumab-bound IgE are separately superimposed onto that from CD23-bound IgE (PDB 4gko), and displaying only the omalizumab-Fv. The IgE-Cε2 domains in the extended position are modeled by superimposing the IgE Cε3-4 domains from PDB 4j4p onto those in CD23-bound IgE and displaying only the IgE Cε2 domains. Omalizumab heavy atoms within 2.5 Å of heavy atoms in CD23 are depicted as spheres. (b) FcεRI (scarlet) clashes with the IgE-Cε2 domains (cyan) in the extended position after each IgE Cε3 domain from omalizumab-bound IgE is separately superimposed onto that from FcεRI-bound IgE (PDB 2y7q), and displaying only omalizumab-Fv. The IgE-Cε2 domains were modeled in an extended position by superimposing the IgE-Cε3-4 domains from PDB 4j4p over the FcεRI-bound IgE and displaying only the Cε2 domains in the 4j4p structure, while hiding the IgE-Cε2 domains from 2y7q. Omalizumab and IgE-Cε2 heavy atoms within 2.5 Å of heavy atoms from FcεRI are depicted as spheres. (c) FcεRI (scarlet) clashes with omalizumab–Fv (green) after each Cε3 domain from omalizumab-bound IgE is separately superimposed onto that from FcεRI-bound IgE (PDB 2y7q), and displaying only omalizumab-Fv. Omalizumab heavy atoms within 2.5 Å of heavy atoms from FcεRI or IgE-Cε2 are depicted as spheres. (d) Omalizumab–Fv (green) clashes with CD23 or the Cε2 domain after each Cε3 domain from omalizumab-bound IgE is separately superimposed onto that from the 1:1 IgE-Fc/CD23 complex (see text), and displaying only omalizumab-Fv. Omalizumab heavy atoms within 2.5 Å of heavy atoms from CD23 or IgE-Cε2 are depicted as spheres.
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f7: Why omalizumab-bound IgE cannot bind CD23 or FcεRI and why omalizumab cannot bind to receptor-bound IgE.(a) CD23 (tangerine) clashes with omalizumab–Fab (green) after the IgE Cε3 domains from omalizumab-bound IgE are separately superimposed onto that from CD23-bound IgE (PDB 4gko), and displaying only the omalizumab-Fv. The IgE-Cε2 domains in the extended position are modeled by superimposing the IgE Cε3-4 domains from PDB 4j4p onto those in CD23-bound IgE and displaying only the IgE Cε2 domains. Omalizumab heavy atoms within 2.5 Å of heavy atoms in CD23 are depicted as spheres. (b) FcεRI (scarlet) clashes with the IgE-Cε2 domains (cyan) in the extended position after each IgE Cε3 domain from omalizumab-bound IgE is separately superimposed onto that from FcεRI-bound IgE (PDB 2y7q), and displaying only omalizumab-Fv. The IgE-Cε2 domains were modeled in an extended position by superimposing the IgE-Cε3-4 domains from PDB 4j4p over the FcεRI-bound IgE and displaying only the Cε2 domains in the 4j4p structure, while hiding the IgE-Cε2 domains from 2y7q. Omalizumab and IgE-Cε2 heavy atoms within 2.5 Å of heavy atoms from FcεRI are depicted as spheres. (c) FcεRI (scarlet) clashes with omalizumab–Fv (green) after each Cε3 domain from omalizumab-bound IgE is separately superimposed onto that from FcεRI-bound IgE (PDB 2y7q), and displaying only omalizumab-Fv. Omalizumab heavy atoms within 2.5 Å of heavy atoms from FcεRI or IgE-Cε2 are depicted as spheres. (d) Omalizumab–Fv (green) clashes with CD23 or the Cε2 domain after each Cε3 domain from omalizumab-bound IgE is separately superimposed onto that from the 1:1 IgE-Fc/CD23 complex (see text), and displaying only omalizumab-Fv. Omalizumab heavy atoms within 2.5 Å of heavy atoms from CD23 or IgE-Cε2 are depicted as spheres.
Mentions: The 1:2 IgE/omalizumab complex cannot bind to CD23 and FcεRI because the key IgE residues involved in binding both IgE receptors are bound or blocked by the two omalizumabs. The 408RASGK415 motif makes a significant free energy contribution to binding CD23, but is occupied by omalizumab. Furthermore, Glu450 and Glu452, which form hydrogen bonds with CD23:Arg188/Arg224 and CD23:His186, respectively, are locked by intramolecular interactions when IgE is bound by two omalizumabs (Fig. 7a). On the other hand, the 461PHLPR465 motif in the FG loop makes a large free energy contribution to binding FcεRI (Fig. 5), but these residues in both IgE chains are bound by two omalizumabs. Furthermore, the extended conformation of the Cε2 domains in the 1:2 IgE/omalizumab complex also obstructs FcεRI binding (Fig. 7b).

Bottom Line: Mutagenesis studies indicate overlapping FcεRI and omalizumab-binding sites in the Cε3 domain, but crystallographic studies show FcεRI and CD23-binding sites that are far apart, so how can omalizumab block IgE from binding both receptors?These results provide a structural and physical basis as to why omalizumab cannot bind receptor-bound IgE and why omalizumab-bound IgE cannot bind to CD23/FcεRI.They reveal the key IgE residues and their roles in binding omalizumab, CD23, and FcεRI.

View Article: PubMed Central - PubMed

Affiliation: 1] Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan [2] The Genomics Research Center, Academia Sinica 115, Taiwan.

ABSTRACT
Omalizumab, an anti-IgE antibody, used to treat severe allergic asthma and chronic idiopathic urticaria, binds to IgE in blood or membrane-bound on B lymphocytes but not to IgE bound to its high (FcεRI) or low (CD23) affinity receptor. Mutagenesis studies indicate overlapping FcεRI and omalizumab-binding sites in the Cε3 domain, but crystallographic studies show FcεRI and CD23-binding sites that are far apart, so how can omalizumab block IgE from binding both receptors? We report a 2.42-Å omalizumab-Fab structure, a docked IgE-Fc/omalizumab-Fab structure consistent with available experimental data, and the free energy contributions of IgE residues to binding omalizumab, CD23, and FcεRI. These results provide a structural and physical basis as to why omalizumab cannot bind receptor-bound IgE and why omalizumab-bound IgE cannot bind to CD23/FcεRI. They reveal the key IgE residues and their roles in binding omalizumab, CD23, and FcεRI.

No MeSH data available.


Related in: MedlinePlus