Skip to main content
SpringerLink
Log in

Rational Identification of Conformational and Linear EGFR Epitopes Recognized Specifically by, Respectively, Type-I and Type-II Anti-EGFR Antibodies and Molecular Design of Linear Epitope-Derived Peptidic Mimotopes to Elicit Type-II Antibody

  • Published:
International Journal of Peptide Research and Therapeutics Aims and scope Submit manuscript

Abstract

Human epidermal growth factor receptor (EGFR) has been established as a promising therapeutic target of diverse tumors and many antibody drugs have been developed to target the third subdomain III (TSDIII) of EGFR extracellular domain. Here, by systematically examining the crystal complex structures of EGFR ETSIII domain with a variety of antibody drugs we classified the EGFR-targeted antibodies into type-I and type-II, which can recognize and interact with two distinct epitopes in EGFR ETSIII domain, namely conformational wrist epitope and linear knuckle epitope that cover discrete and continuous protein segments on the domain surface, respectively. The knuckle-to-type-II was found to have lower absolute binding energy but higher relative binding energy than wrist-to-type-I. Subsequently, an 18-mer linear peptidic mimotope K-peptide was derived from the knuckle epitope, which, however, cannot spontaneously maintain in its native ordered conformation as that in the protein context of EGFR ETSIII domain. A disulfide stapling strategy was used to cyclize and constrain the flexible (disordered) K-peptide into a desired (roughly ordered) native-like structure, which can significantly minimize the unfavorable indirect readout effect upon binding to its cognate antibody. Further binding analysis confirmed that the stapling can moderately or significantly improve the affinity of linear K-peptide to type-I antibody by ~ 2–12-folds. The designed cyclic cK-peptide[449–466] was measured to have the highest affinity, which was improved by 11.5-fold from the linear K-peptide. In addition, both the knuckle-derived linear and cyclic peptidic mimotopes exhibited a good selectivity for type-II over type-I antibodies; cyclization can improve the selectivity.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

References

  • Anandakrishnan R, Aguilar B, Onufriev AV (2012) H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations. Nucleic Acids Res 40:W537–W541

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bai Z, Hou S, Zhang S, Li Z, Zhou P (2017) Targeting self-binding peptides as a novel strategy to regulate protein activity and function: a case study on the proto-oncogene tyrosine protein kinase c-Src. J Chem Inf Model 57:835–845

    Article  CAS  PubMed  Google Scholar 

  • Behrendt R, White P, Offer J (2016) Advances in Fmoc solid-phase peptide synthesis. J Pept Sci 22:4–27

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bennasroune A, Gardin A, Aunis D, Crémel G, Hubert P (2004) Tyrosine kinase receptors as attractive targets of cancer therapy. Crit Rev Oncol Hematol 50:23–38

    Article  PubMed  Google Scholar 

  • Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucleic Acids Res 28:235–242

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Case D (1994) Normal mode analysis of protein dynamics. Curr Opin Struct Biol 4:285–290

    Article  CAS  Google Scholar 

  • Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, Merz KM, Onufriev A, Simmerling C, Wang B, Woods RJ (2005) The Amber biomolecular simulation programs. J Comput Chem 26:1668–1688

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen K, Huang L, Shen B (2019) Rational cyclization-based minimization of entropy penalty upon the binding of Nrf2-derived linear peptides to Keap1: a new strategy to improve therapeutic peptide activity against sepsis. Biophys Chem 244:22–28

    Article  CAS  PubMed  Google Scholar 

  • Chen K, Ge L, Liu G (2023) Integrated in silico-in vitro rational design of oncogenic EGFR-derived specific monoclonal antibody-binding peptide mimotopes. J Bioinform Comput Biol 21:2350007

    Article  CAS  PubMed  Google Scholar 

  • Chua YJ, Cunningham D (2006) Panitumumab. Drugs Today 42:711–719

    Article  CAS  Google Scholar 

  • Darden T, York D, Pedersen L (1993) Particle mesh Ewald: an N∙log(N) method for Ewald sums in large systems. J Chem Phys 98:10089–10092

    Article  CAS  Google Scholar 

  • Dassonville O, Bozec A, Fischel JL, Milano G (2007) EGFR targeting therapies: monoclonal antibodies versus tyrosine kinase inhibitors. Similarities and differences. Crit Rev Oncol Hematol 62:53–61

    Article  PubMed  Google Scholar 

  • Garnock-Jones KP (2016) Necitumumab: first global approval. Drugs 76:283–289

    Article  CAS  PubMed  Google Scholar 

  • Harding J, Burtness B (2005) Cetuximab: an epidermal growth factor receptor chemeric human-murine monoclonal antibody. Drugs Today 41:107–127

    Article  CAS  Google Scholar 

  • Hartmann C, Müller N, Blaukat A, Koch J, Benhar I, Wels WS (2010) Peptide mimotopes recognized by antibodies cetuximab and matuzumab induce a functionally equivalent anti-EGFR immune response. Oncogene 29:4517–4527

    Article  CAS  PubMed  Google Scholar 

  • Holash J, Davis S, Papadopoulos N, Croll SD, Ho L, Russell M, Boland P, Leidich R, Hylton D, Burova E, Ioffe E, Huang T, Radziejewski C, Bailey K, Fandl JP, Daly T, Wiegand SJ, Yancopoulos GD, Rudge JS (2002) VEGF-Trap: a VEGF blocker with potent antitumor effects. Proc Natl Acad Sci USA 99:11393–11398

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Homeyer N (2012) Gohlke H (2012) Free energy calculations by the molecular mechanics Poisson-Boltzmann surface area method. Mol Inf 31:114–122

    Article  CAS  Google Scholar 

  • Huang SM, Harari PM (1999) Epidermal growth factor receptor inhibition in cancer therapy: biology, rationale and preliminary clinical results. Invest New Drugs 17:259–269

    Article  CAS  PubMed  Google Scholar 

  • Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Phys Chem 79:926

    Article  CAS  Google Scholar 

  • Kirsch T, Sebald W, Dreyer MK (2000) Crystal structure of the BMP-2-BRIA ectodomain complex. Nat Struct Biol 7:492–496

    Article  CAS  PubMed  Google Scholar 

  • Klein DE, Nappi VM, Reeves GT, Shvartsman SY, Lemmon MA (2004) Argos inhibits epidermal growth factor receptor signalling by ligand sequestration. Nature 430:1040–1044

    Article  CAS  PubMed  Google Scholar 

  • Ko J, Park H, Heo L, Seok C (2012) GalaxyWEB server for protein structure prediction and refinement. Nucleic Acids Res 40:W294–W297

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kortemme T, Kim DE, Baker D (2004) Computational alanine scanning of protein-protein interfaces. Sci STKE 2004:pl2

    Article  PubMed  Google Scholar 

  • Li Z, Miao Q, Yan F, Meng Y, Zhou P (2019) Machine learning in quantitative protein–peptide affinity prediction: implications for therapeutic peptide design. Curr Drug Metab 20:170–176

    Article  CAS  PubMed  Google Scholar 

  • Lim Y, Yoo J, Kim MS, Hur M, Lee EH, Hur HS, Lee JC, Lee SN, Park TW, Lee K, Chang KH, Kim K, Kang Y, Hong KW, Kim SH, Kim YG, Yoon Y, Nam DH, Yang H, Kim DG, Cho HS, Won J (2016) GC1118, an anti-EGFR antibody with a distinct binding epitope and superior inhibitory activity against high-affinity EGFR ligands. Mol Cancer Ther 15:251–263

    Article  CAS  PubMed  Google Scholar 

  • Lin L, Bivona TG (2012) Mechanisms of resistance to epidermal growth factor receptor inhibitors and novel therapeutic strategies to overcome resistance in NSCLC patients. Chemother Res Pract 2012:817297

    PubMed  PubMed Central  Google Scholar 

  • Lin J, Wang S, Wen L, Ye H, Shang S, Li J, Shu J, Zhou P (2023a) Targeting peptide-mediated interactions in omics. Proteomics 2023(23):e2200175

    Article  Google Scholar 

  • Lin J, Wen L, Zhou Y, Wang S, Ye H, Su J, Li J, Shu J, Huang J, Zhou P (2023b) PepQSAR: a comprehensive data source and information platform for peptide quantitative structure-activity relationships. Amino Acids 55:235–242

    Article  CAS  PubMed  Google Scholar 

  • Liu Q, Lin J, Wen L, Wang S, Zhou P, Mei L, Shang S (2022) Systematic modeling, prediction, and comparison of domain–peptide affinities: does it work effectively with the peptide QSAR methodology? Front Genet 12:800857

    Article  PubMed  PubMed Central  Google Scholar 

  • Maier JA, Martinez C, Kasavajhala K, Wickstrom L, Hauser KE, Simmerling C (2015) ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB. J Chem Theory Comput 11:3696–3713

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mazzarella L, Guida A, Curigliano G (2018) Cetuximab for treating non-small cell lung cancer. Expert Opin Biol Ther 18:483–493

    Article  CAS  PubMed  Google Scholar 

  • Mei L, Shang S, Wang S, Ye H, Zhou P (2023) Machine annealing-guided navigation of antihypertensive food peptide selectivity between human ACE N- and C-domains in structurally interacting diversity space. J Mol Recognit 36:e3014

    Article  CAS  PubMed  Google Scholar 

  • Miller BR, McGee TD, Swails JM, Homeyer N, Gohlke H, Roitberg AE (2012) MMPBSA.py: an efficient program for end-state free energy calculations. J Chem Theory Comput 8:3314–3321

    Article  CAS  PubMed  Google Scholar 

  • Nicholson RI, Gee JM, Harper ME (2001) EGFR and cancer prognosis. Eur J Cancer 37:S9–S15

    Article  CAS  PubMed  Google Scholar 

  • Normanno N, De Luca A, Bianco C, Strizzi L, Mancino M, Maiello MR, Carotenuto A, De Feo G, Caponigro F, Salomon DS (2006) Epidermal growth factor receptor (EGFR) signaling in cancer. Gene 366:2–16

    Article  CAS  PubMed  Google Scholar 

  • Ohashi K, Maruvka YE, Michor F, Pao W (2013) Epidermal growth factor receptor tyrosine kinase inhibitor –– resistant disease. J Clin Oncol 31:1070–1080

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Riemer AB, Kurz H, Klinger M, Scheiner O, Zielinski CC, Jensen-Jarolim E (2005) Vaccination with cetuximab mimotopes and biological properties of induced anti-epidermal growth factor receptor antibodies. J Natl Cancer Inst 97:1663–1670

    Article  CAS  PubMed  Google Scholar 

  • Rocha-Lima CM, Soares HP, Raez LE, Singal R (2007) EGFR targeting of solid tumors. Cancer Control 14:295–304

    Article  PubMed  Google Scholar 

  • Ryckaert JP, Ciccotti G, Berendsen HJC (1997) Numerical integration of the Cartesian equations of motion of a system with constraints molecular dynamics of n-alkanes. J Comput Phys 23:327–341

    Article  Google Scholar 

  • Ryu J, Lee M, Cha J, Laskowski RA, Ryu SE, Kim DS (2016) BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization. Nucleic Acids Res 44:W416–W423

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sachdeva S, Joo H, Tsai J, Jasti B, Li X (2019) A rational approach for creating peptides mimicking antibody binding. Sci Rep 9:997

    Article  PubMed  PubMed Central  Google Scholar 

  • Schiller JH (2008) Developments in epidermal growth factor receptor-targeting therapy for solid tumors: focus on matuzumab (EMD 72000). Cancer Invest 26:81–95

    Article  CAS  PubMed  Google Scholar 

  • Schmiedel J, Blaukat A, Li S, Knöchel T, Ferguson KM (2008) Matuzumab binding to EGFR prevents the conformational rearrangement required for dimerization. Cancer Cell 13:365–373

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schöning-Stierand K, Diedrich K, Fährrolfes R, Flachsenberg F, Meyder A, Nittinger E, Steinegger R, Rarey M (2020) ProteinsPlus: interactive analysis of protein-ligand binding interfaces. Nucleic Acids Res 48:W48–W53

    Article  PubMed  PubMed Central  Google Scholar 

  • Seiden MV, Burris HA, Matulonis U, Hall JB, Armstrong DK, Speyer J, Weber JD, Muggia F (2007) A phase II trial of EMD72000 (matuzumab), a humanized anti-EGFR monoclonal antibody, in patients with platinum-resistant ovarian and primary peritoneal malignancies. Gynecol Oncol 104:727–731

    Article  CAS  PubMed  Google Scholar 

  • Shu J, Li J, Wang S, Lin J, Wen L, Ye H, Zhou P (2023) Systematic analysis and comparison of peptide specificity and selectivity between their cognate receptors and noncognate decoys. J Mol Recognit 36:e3006

    Article  CAS  PubMed  Google Scholar 

  • Voigt M, Braig F, Göthel M, Schulte A, Lamszus K, Bokemeyer C, Binder M (2012) Functional dissection of the epidermal growth factor receptor epitopes targeted by panitumumab and cetuximab. Neoplasia 14:1023–1031

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang A, Cui M, Qu H, Di J, Wang Z, Xing J, Wu F, Wu W, Wang X, Shen L, Jiang B, Su X (2016) Induction of anti-EGFR immune response with mimotopes identified from a phage display peptide library by panitumumab. Oncotarget 7:75293–75306

    Article  PubMed  PubMed Central  Google Scholar 

  • Yang C, Zhang S, He P, Wang C, Huang J, Zhou P (2015) Self-binding peptides: folding or binding? J Chem Inf Model 5:329–342

    Article  Google Scholar 

  • Yu H, Zhou P, Deng M, Shang Z (2014) Indirect readout in protein-peptide recognition: a different story from classical biomolecular recognition. J Chem Inf Model 54:2022–2032

    Article  CAS  PubMed  Google Scholar 

  • Zhang Y, Schulten K, Gruebele M, Bansal PS, Wilson D, Daly NL (2016) Disulfide bridges: bringing together frustrated structure in a bioactive peptide. Biophys J 110:1744–1752

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang D, He D, Huang L, Xu Y, Liu L (2018) Rational design and cyclization of MIG6 peptide to restore its binding affinity for ErbB family receptor tyrosine kinases. Int J Pept Res Ther 24:71–76

    Article  CAS  Google Scholar 

  • Zhang D, He D, Pan X, Xu Y, Liu L (2019) Structural analysis and rational design of orthogonal stacking system in an E. coli DegP PDZ1–peptide complex. Chem Pap 73:2469–2476

    Article  CAS  Google Scholar 

  • Zhang D, He D, Pan X, Liu L (2020) Rational design and intramolecular cyclization of hotspot peptide segments at YAP–TEAD4 complex interface. Protein Pept Lett 27:999–1006

    Article  CAS  PubMed  Google Scholar 

  • Zhang W, Liu J, Zhang C, Yu X, Zhong B (2021) Structural definition of the discrete hotspot sites of BMP-2 conformational wrist epitope and rational design of the hotspot-derived osteogenic peptides against chondrocyte senescence. Bioorg Chem 116:105382

    Article  CAS  PubMed  Google Scholar 

  • Zhang XC, Chang N, Zhang XQ (2023) Orthogonal threading-through-β-sheet design of lung cancer EGFR extracellular domain-derived peptidic mimotopes binding to anti-EGFR antibody. Chem Biol Drug Des 101:848–854

    Article  CAS  PubMed  Google Scholar 

  • Zhou P, Wang C, Ren Y, Yang C, Tian F (2013) Computational peptidology: a new and promising approach to therapeutic peptide design. Curr Med Chem 20:1985–1996

    Article  CAS  PubMed  Google Scholar 

  • Zhou P, Miao Q, Yan F, Li Z, Jiang Q, Wen L, Meng Y (2019) Is protein context responsible for peptide-mediated interactions? Mol Omics 15:280–295

    Article  CAS  PubMed  Google Scholar 

  • Zhou P, Liu Q, Wu T, Miao Q, Shang S, Wang H, Chen Z, Wang S, Wang H (2021) Systematic comparison and comprehensive evaluation of 80 amino acid descriptors in peptide QSAR modeling. J Chem Inf Model 61:1718–1731

    Article  CAS  PubMed  Google Scholar 

  • Zhou P, Wen L, Lin J, Mei L, Liu Q, Shang S, Li J, Shu J (2022) Integrated unsupervised-supervised modeling and prediction of protein–peptide affinities at structural level. Brief Bioinform 23:bbac097

    Article  PubMed  Google Scholar 

Download references

Acknowledgements

This work was supported by the Jiangxi Provincial Natural Science Foundation (Grant No. 20202BABL206111), the Jiangxi Provincial Educational Reform Research Program (Grant No. JXJG-14-9-31), and the Jinggangshan University Startup Fund for Doctor Research (Grant No. JZB11035).

Author information

Authors and Affiliations

  1. School of Chemistry and Chemical Engineering, Jinggangshan University, No.28, Xueyuan Road, Ji’an, 343009, China

    Deyong He, Rongyuan Yuan & Lijun Liu

Authors
  1. Deyong He
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Rongyuan Yuan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Lijun Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

DH and RY performed the researches; DH and LL wrote the main manuscript text; LL proposed and supervised the researches; all authors reviewed the manuscript.

Corresponding author

Correspondence to Lijun Liu.

Ethics declarations

Conflict of interest

The authors declare no competing interests.

Informed Consent

Not applicable.

Research involving Human and Animal Rights

Not applicable.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

He, D., Yuan, R. & Liu, L. Rational Identification of Conformational and Linear EGFR Epitopes Recognized Specifically by, Respectively, Type-I and Type-II Anti-EGFR Antibodies and Molecular Design of Linear Epitope-Derived Peptidic Mimotopes to Elicit Type-II Antibody. Int J Pept Res Ther 29, 45 (2023). https://doi.org/10.1007/s10989-023-10520-7

Download citation

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s10989-023-10520-7

Keywords

Search

Navigation