Binding Affinity of Trastuzumab and Pertuzumab Monoclonal Antibodies to Extracellular HER2 Domain †
Abstract
:1. Introduction
2. Results
2.1. Experimental Findings
2.2. In Silico Binding
3. Discussion
3.1. Binding Affinity
3.2. Antigen–Antibody Complexes’ Stoichiometry
4. Materials and Methods
4.1. Experimental Details
4.1.1. Samples
4.1.2. Basic Hydrodynamic Characterization of e-HER2 Receptor and mAbs
4.1.3. Molecular Weight and Concentration of g-eHER2 Receptor, mAbs, and Complexes
4.2. In Silico Methods
4.2.1. Molecular Dynamics Simulations
4.2.2. PRODIGY QSAR Model
4.2.3. Models for Antigen–Antibody Complexes’ Stoichiometry
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Cesca, M.G.; Vian, L.; Cristóvão-Ferreira, S.; Pondé, N.; de Azambuja, E. HER2-Positive Advanced Breast Cancer Treatment in 2020. Cancer Treat. Rev. 2020, 88, 102033. [Google Scholar] [CrossRef]
- Cho, H.S.; Mason, K.; Ramyar, K.X.; Stanley, A.M.; Gabelli, S.B.; Denney, D.W.; Leahy, D.J. Structure of the Extracellular Region of HER2 Alone and in Complex with the Herceptin Fab. Nature 2003, 421, 756–760. [Google Scholar] [CrossRef]
- Franklin, M.C.; Carey, K.D.; Vajdos, F.F.; Leahy, D.J.; de Vos, A.M.; Sliwkowski, M.X. Insights into ErbB Signaling from the Structure of the ErbB2-Pertuzumab Complex. Cancer Cell 2004, 5, 317–328. [Google Scholar] [CrossRef] [Green Version]
- Troise, F.; Cafaro, V.; Giancola, C.; D’Alessio, G.; De Lorenzo, C. Differential Binding of Human Immunoagents and Herceptin to the ErbB2 Receptor. FEBS J. 2008, 275, 4967–4979. [Google Scholar] [CrossRef] [PubMed]
- Lua, W.H.; Gan, S.K.E.; Lane, D.P.; Verma, C.S. A Search for Synergy in the Binding Kinetics of Trastuzumab and Pertuzumab Whole and F(Ab) to Her2. Npj Breast Cancer 2015, 1, 15012. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Spiegelberg, D.; Stenberg, J.; Richalet, P.; Vanhove, M.K.D. Determination from Time-Resolved Experiments on Live Cells with LigandTracer and Reconciliation with End-Point Flow Cytometry Measurements. Eur. Biophys. J. 2021, 50, 979–991. [Google Scholar] [CrossRef]
- Hao, Y.; Yu, X.; Bai, Y.; McBride, H.J.; Huang, X. Cryo-EM Structure of HER2-Trastuzumab-Pertuzumab Complex. PLoS ONE 2019, 14, e0216095. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Fuentes, G.; Scaltriti, M.; Baselga, J.; Verma, C.S. Synergy between Trastuzumab and Pertuzumab for Human Epidermal Growth Factor 2 (Her2) from Colocalization: An in Silico Based Mechanism. Breast Cancer Res. 2011, 13, R54. [Google Scholar] [CrossRef]
- Samsudin, F.; Yeo, J.Y.; Gan, S.K.E.; Bond, P.J. Not All Therapeutic Antibody Isotypes Are Equal: The Case of IgM: Versus IgG in Pertuzumab and Trastuzumab. Chem. Sci. 2020, 11, 2843–2854. [Google Scholar] [CrossRef] [Green Version]
- Vega, J.F.; Ramos, J.; Cruz, V.L.; Vicente-Alique, E.; Sanchez-Sanchez, E.; Sanchez-Fernandez, A.; Wang, Y.; Hu, P.; Cortes, J.; Martinez-Salazar, J. Molecular and Hydrodynamic Properties of Human Epidermal Growth Factor Receptor HER2 Extracellular Domain and Its Homodimer: Experiments and Multi-Scale Simulations. Biochim. Biophys. Acta Gen. Subj. 2017, 1861, 2406–2416. [Google Scholar] [CrossRef]
- Oda, M.; Uchiyama, S.; Noda, M.; Nishi, Y.; Koga, M.; Mayanagi, K.; Robinson, C.V.; Fukui, K.; Kobayashi, Y.; Morikawa, K.; et al. Effects of Antibody Affinity and Antigen Valence on Molecular Forms of Immune Complexes. Mol. Immunol. 2009, 47, 357–364. [Google Scholar] [CrossRef] [PubMed]
- Vangone, A.; Bonvin, A.M.J.J. Contacts-Based Prediction of Binding Affinity in Protein–Protein Complexes. Elife 2015, 4, e07454. [Google Scholar] [CrossRef] [PubMed]
- Ramos, J.; Vega, J.F.; Cruz, V.; Sanchez-Sanchez, E.; Cortes, J.; Martinez-Salazar, J. Hydrodynamic and Electrophoretic Properties of Trastuzumab/HER2 Extracellular Domain Complexes as Revealed by Experimental Techniques and Computational Simulations. Int. J. Mol. Sci. 2019, 20, 1076. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Vicente-Alique, E.; Núñez-Ramírez, R.; Vega, J.F.; Hu, P.; Martínez-Salazar, J. Size and Conformational Features of ErbB2 and ErbB3 Receptors: A TEM and DLS Comparative Study. Eur. Biophys. J. 2011, 40, 835–842. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Gill, S.C.; von Hippel, P.H. Calculation of Protein Extinction Coefficients from Amino Acid Sequence Data. Anal. Biochem. 1989, 182, 319–326, Erratum in Anal. Biochem. 1990, 189, 283. [Google Scholar] [CrossRef]
- Goldberg, R.J. A Theory of Antibody-Antigen Reactions. II. Theory for Reactions of Multivalent Antigen with Multivalent Antibody. J. Am. Chem. Soc. 1953, 75, 3127–3131. [Google Scholar] [CrossRef]
- Karagiannis, P.; Singer, J.; Hunt, J.; Gan, S.K.E.; Rudman, S.M.; Mechtcheriakova, D.; Knittelfelder, R.; Daniels, T.R.; Hobson, P.S.; Beavil, A.J.; et al. Characterisation of an Engineered Trastuzumab IgE Antibody and Effector Cell Mechanisms Targeting HER2/Neu-Positive Tumour Cells. Cancer Immunol. Immunother. 2009, 58, 915–930. [Google Scholar] [CrossRef] [Green Version]
- Thompson, R.J.; Jackson, A.P. Cyclic Complexes and High Avidity Antibodies. Trends Biochem. Sci. 1984, 9, 1–3. [Google Scholar] [CrossRef]
- Chakraborty, A.; Biswas, A. Structure, Stability and Chaperone Function of Mycobacterium Leprae Heat Shock Protein 18 Are Differentially Affected upon Interaction with Gold and Silver Nanoparticles. Int. J. Biol. Macromol. 2020, 152, 250–260. [Google Scholar] [CrossRef]
- Dassault Systèmes BIOVIA. Discovery Studio Modeling Environment, Release 2022; Dassault Systèmes: San Diego, CA, USA, 2022. [Google Scholar]
- Maier, J.A.; Martinez, C.; Kasavajhala, K.; Wickstrom, L.; Hauser, K.E.; Simmerling, C. Ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from Ff99SB. J. Chem. Theory Comput. 2015, 11, 3696–3713. [Google Scholar] [CrossRef] [Green Version]
- Case, D.A.; Walker, R.C.; Darden, T.; Wang, J. Amber 2016 Reference Manual Principal Contributors to the Current Codes; University of California: San Francisco, CA, USA, 2016. [Google Scholar]
- Xue, L.C.; Rodrigues, J.P.; Kastritis, P.L.; Bonvin, A.M.; Vangone, A. PRODIGY: A Web Server for Predicting the Binding Affinity of Protein-Protein Complexes. Bioinformatics 2016, 32, 3676–3678. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Kastritis, P.L.; Rodrigues, J.P.G.L.M.; Folkers, G.E.; Boelens, R.; Bonvin, A.M.J.J. Proteins Feel More than They See: Fine-Tuning of Binding Affinity by Properties of the Non-Interacting Surface. J. Mol. Biol. 2014, 426, 2632–2652. [Google Scholar] [CrossRef] [PubMed]
Sample | Ka (Mole Fraction−1) × 10−7 s.d. < 2% | ΔG (kcal·mol−1) s.d. < 2% |
---|---|---|
HER2/Trastuzumab | 2.49 | −10.4 |
HER2/Pertuzumab | 3.17 | −10.6 |
System | ΔGbind (kcal·mol−1) | |
---|---|---|
Crystal Structures | MD Structures | |
HER2/Trastuzumab | −10.3 | −11.0 ± 0.8 |
HER2/Pertuzumab | −12.0 | −12.2 ± 0.9 |
QSAR Component | HER2/Trastuzumab | HER2/Pertuzumab | ||
---|---|---|---|---|
Crystal | MD | Crystal | MD | |
NIS charged (%) | 21 | 20 ± 1 | 21 | 20 ± 1 |
NIS apolar (%) | 36 | 38 ± 1 | 37 | 38 ± 1 |
Number of ICs per property | ||||
ICs charged–charged | 7 | 8 ± 4 | 3 | 3 ± 1 |
ICs charged–polar | 7 | 12 ± 5 | 13 | 12 ± 2 |
ICs charged–apolar | 16 | 20 ± 5 | 23 | 22 ± 4 |
ICs polar–polar | 2 | 5 ± 3 | 10 | 6 ± 1 |
ICs polar–apolar | 8 | 12 ± 3 | 24 | 20 ± 3 |
ICs apolar–apolar | 21 | 29 ± 2 | 17 | 17 ± 4 |
Sample | Mw (kDa) s.d. < 2% | [η] (cm3·g−1) s.d. ± 0.2 | dA/dc (mLg−1cm−1) s.d. ± 0.02 | Ds × 107 (μm2·s−1) s.d. ± 0.2 | rh (nm) s.d. ± 0.1 |
---|---|---|---|---|---|
Trastuzumab—TZM | 147.0 | 6.5 | 1.38 (1.40) | 58.1 | 5.5 |
Pertuzumab—PZM | 146.4 | 6.4 | 1.29 (1.36) | 58.2 | 5.5 |
g-eHER2 | 86.4 | 6.5 | 0.90 (0.90) | 44.6 * | 4.7 * |
HER2/TZM | 234.0 | 7.4 * | n.d. | 31.6 * | 6.8 * |
HER2/PZM/HER2 | 320.0 | 8.6 | n.d. | n.d. | 7.4 |
Initial Concentrations a s.d. < 2% | Equilibrium Concentrations s.d. < 2% | |||||
---|---|---|---|---|---|---|
Sample | mAb | g-eHER2 | Complex 1 | Complex 2 | Free mAb | Free g-eHER2 |
HER2/TZM | 4.78 | 1.46 | 1.12 | 0.26 | 3.37 | 0.08 |
HER2/PZM | 4.76 | 1.16 | 0.42 | 0.68 | 3.36 | 0.04 |
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content. |
© 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Cruz, V.L.; Souza-Egipsy, V.; Gion, M.; Pérez-García, J.; Cortes, J.; Ramos, J.; Vega, J.F. Binding Affinity of Trastuzumab and Pertuzumab Monoclonal Antibodies to Extracellular HER2 Domain. Int. J. Mol. Sci. 2023, 24, 12031. https://doi.org/10.3390/ijms241512031
Cruz VL, Souza-Egipsy V, Gion M, Pérez-García J, Cortes J, Ramos J, Vega JF. Binding Affinity of Trastuzumab and Pertuzumab Monoclonal Antibodies to Extracellular HER2 Domain. International Journal of Molecular Sciences. 2023; 24(15):12031. https://doi.org/10.3390/ijms241512031
Chicago/Turabian StyleCruz, Victor L., Virginia Souza-Egipsy, María Gion, José Pérez-García, Javier Cortes, Javier Ramos, and Juan F. Vega. 2023. "Binding Affinity of Trastuzumab and Pertuzumab Monoclonal Antibodies to Extracellular HER2 Domain" International Journal of Molecular Sciences 24, no. 15: 12031. https://doi.org/10.3390/ijms241512031