Journal:Acta Cryst D:S2059798319006995

Structural insight into a matured humanized monoclonal antibody HuA21 against HER2-overexpressing cancer cells

Zhenyi Wang, Liansheng Cheng, Gongrui Guo, Baoyun Cheng, Siyi Hu, Hongmin Zhang, Zhongliang Zhu and Liwen Niu ^[1]

Molecular Tour
HER2, a member of the epidermal growth factor receptor (EGFR) family, has been associated with human breast, ovarian, and gastric cancers. We previously developed a chimeric antibody chA21 that specifically inhibits the growth of HER2-overexpressing cancer cells both in vitro and in vivo. To reduce potential human anti-mouse immune response, humanized antibody HuA21 was developed on the basis of chA21. The crystal structure of HuA21-scFv in complex with the extracellular domain (ECD) of HER2 was determined, which demonstrates that HuA21 binds almost the same epitope as chA21 and also provides insight into how substitutions in HuA21 improve the binding affinity compared with chA21. The binding epitopes of antibodies could contribute to understand their anti-tumor activities. Our HuA21-HER2 structure clearly shows that the epitope of HuA21 is located at the C-terminal part of subdomain I of HER2. This is a new epitope distinct from those described for Trastuzumab and Pertuzumab, which are located at subdomains IV and II, respectively.

Overall structure of HuA21 scFv in complex with HER2 ECD (PDB entry 6j71). In ECD, the subdomains I, II, III and IV are colored red, green, blue and yellow, respectively. The light chain (V_L) and heavy chain (V_H) of HuA21 scFv are colored magenta and cyan, respectively. HuA21 consists of two immunoglobulin domains formed by the VH and VL fragments, respectively. The extracellular domain of HER2 is composed of four subdomains designated I, II, III and IV.

The Interface of the HuA21-HER2 Complex

The CDRs are labelled L1, L2, L3, H1, H2 and H3 and colored paleyellow, limegreen, lightorange, palegreen, palecyan and lightpink, respectively. The other parts of HuA21 scFv are colored light gray. The three loops containing the epitope of HER2 are labelled Loop I, Loop II and Loop III and colored lemon, orange and cyan. The three loops containing the epitope of HER2 lie on the HuA21 surface. The important residues on HER2 are shown as sticks and labelled with white characters. The key residues on HuA21 are colored the same as in the previous scene and labelled with red characters.

Compared to chA21, HuA21 shows higher affinity towards HER2 ECD. While most interactions keep the same between chA21 and HuA21, structural superposition reveals that two important regions should contribute to the affinity improvement. One is the K41W mutation in CDR loop L1 which forms hydrophobic interaction with residues P194 and P197 in loop III as well as hydrogen bond with the main chain carbonyl oxygen of residue C195 (Loop III). The newly formed hydrogen bond between Ne of W41 (L1) and the carbonyl oxygen of residue C195 (Loop III) pulls residue W41 (L1) near loop III and helps W41 (L1) forms extra hydrophobic interaction with residue P194 and P197 (Loop III). The important residues on HER2-chA21 are shown as sticks and labelled with white characters. The key residues on HER2-HuA21 are shown as sticks and labelled with red characters. The other important mutation is G170Q in CDR loop H1. As mentioned above, the side chain of residue Q170 (H1) forms bidentate hydrogen bonds with the main chain carbonyl oxygen of residue T186 (Loop III) and side chain carbonyl oxygen of residue N187 (Loop III). These extra hydrophobic interaction and hydrogen bonds should greatly enhance the interaction between HuA21 and HER2.

The overview of the distinct epitopes of HuA21, Trastuzumab and Pertuzumab. HuA21, Trastuzumab and Pertuzumab are labelled and colored slate, magenta and cyan, respectively. The HER2 subdomains I, II, III and IV are colored red, green, blue and yellow, respectively.

PDB reference: HuA21-scFv in complex with the extracellular domain (ECD) of HER2 6j71.

References

1. ↑ Wang Z, Cheng L, Guo G, Cheng B, Hu S, Zhang H, Zhu Z, Niu L. Structural insight into a matured humanized monoclonal antibody HuA21 against HER2-overexpressing cancer cells. Acta Crystallogr D Struct Biol. 2019 Jun 1;75(Pt 6):554-563. doi:, 10.1107/S2059798319006995. Epub 2019 May 31. PMID:31205018 doi:http://dx.doi.org/10.1107/S2059798319006995