EphA2 is displayed on the cell surface, making it an ideal target for the design of immunotoxins. To develop an anti-EphA2 immunotoxin, we selected ricin as the toxin moiety. This protein toxin has already been used to generate other immunotoxins. Its small size is advantageous for cell internalization. Although ricin consists of two chains, A and B, only the A chain is required to kill cancer cells. The cytotoxic mechanism is related to the inhibition of the translation process inside the cells (
23).
Several factors should be considered when designing an immunotoxin (
17). The critical considerations include vector size, expression, and solubility in the bacterial host, purification strategy, stability of mRNA and protein expressed from the construct, protein structure, binding ability of the immunotoxin to the cell surface, and its allergenic or antigenic potential. A smaller immunotoxin is preferable since a smaller vector is easier to construct using molecular cloning techniques (
24), and the expressed protein is more likely to be soluble in the bacterial host (
25). In this study, we aimed to generate two immunotoxins composed of subunit A of ricin and an antibody fragment (scFv) against the EphA2 receptor. Subunit A of ricin can be fused to the antibody at either its N- or C-terminal region. It has been shown that the orientation of the fused toxin relative to the antibody can significantly impact the efficiency of immunotoxins (
26).
Using bioinformatics tools to evaluate immunotoxin design and construction before experimental validation is highly beneficial. It is more cost-effective, saves time, and avoids ethical concerns related to the use of animal models for hypothesis testing. Experimental setups are expensive, and trial-and-error approaches are not advisable (
16). Since the only difference between the two immunotoxins in this study is the orientation of the toxin relative to the antibody, we expect many physicochemical properties to be similar. Therefore, the aim of this study is to compare these two immunotoxins using bioinformatics approaches and identify the most promising candidate for combating breast cancer.
The stability of the 3D structures of the designed immunotoxins is a crucial property. The structures obtained from 3D structure prediction tools demonstrated acceptable quality, indicating the accuracy of the predicted models. The low number of outlier amino acids within the generated Ramachandran plots further supports the accuracy of the predictions. However, the results suggest that the conformation of the protein expressed from construct 2 is slightly more favorable. Along with structural accuracy, the high binding potency of the designed immunotoxins to the target receptor is essential (
27). Our analyses demonstrated that both immunotoxins are capable of binding to the EphA2 receptor with high affinity. However, construct 2 exhibited a stronger binding affinity to the EphA2 receptor and formed a greater number of stronger bonds with it. The MD simulation results further confirmed the stable binding between the designed immunotoxins and the EphA2 receptor.
Based on these observations, it can be concluded that both designed immunotoxins could serve as suitable therapeutic candidates, but construct 2 exhibits more promising properties. The stability of the mRNA expressed from both constructs was assessed using the mFold software, and the results indicate sufficient stability. Based on thermodynamic properties, the mRNA expressed from construct 2 appears to be more stable. For the best model, the ΔG value for construct 1 was -613.69 kcal/mol, while for construct 2, it was -624.88 kcal/mol. Furthermore, the absence of experimentally proven IgE epitopes confirms the safety of the designed immunotoxins.
The obtained results in our study resemble the findings of the in silico sections of various studies. Ataee et al. conducted a bioinformatics study on the single-chain fragment variable of the rovalpituzumab antibody fused to granzyme B (Rova-GrB) and PltA of typhoid toxin (Rova-Typh) as immunotoxins. Their docking analysis demonstrated that the binding domain of the immunotoxins could bind to the N-terminal region of delta-like ligand 3 (DLL3). The bioinformatics analysis revealed that Rova-GrB and Rova-Typh possessed hydrophilic properties, their codon optimization parameters were within standard ranges, and their validation parameters were enhanced following immunotoxin refinement. They concluded that recombinant immunotoxins targeting DLL3 may serve as effective treatment options for small-cell lung cancer (SCLC) (
28).
In a similar study, Rezaie et al. assessed the characteristics of a proposed immunotoxin composed of an EphA2-specific scFv linked to PE38KDEL. They evaluated the binding potency, cytotoxic effects, apoptosis induction capacity, and internalization of the designed immunotoxin on an EphA2-overexpressing breast cancer cell line. Flow cytometry analysis demonstrated that, in contrast to the normal cell line (HEK-293) or the EphA2-low-expressing cell line (MCF-7), the immunotoxin could bind significantly (approximately 99%) to the EphA2-overexpressing breast cancer cell line (MDA-MB-231) at a low concentration (2.5 ng/μL). Moreover, significant cytotoxicity and apoptosis induction were observed in MDA-MB-231 cells at varying doses (
10).
In another study, Goleij et al. used recombinant DNA technology to fuse the HER2 monoclonal antibody (mAb) (Herceptin) to PE38, producing a novel recombinant immunotoxin. Their results showed that, in contrast to MCF-7 cells, SKBR-3 cells exhibited dose-dependent cytotoxicity when treated with this immunotoxin. The findings suggest that the immunotoxin may bind to HER2-positive breast cancer cells, undergo internalization, and induce apoptosis to eliminate the cancer cells (
29).
Furthermore, Mohammadi et al. (
30) developed a unique recombinant anti-CD22 scFv.Bim fusion protein. They employed flow cytometry, microscopy, and the MTT assay to assess the binding capacity, cytotoxicity, and apoptotic activity of the purified recombinant protein against the CD22+ Raji cell line. Their analysis confirmed that anti-CD22 scFv.Bim exhibited apoptotic activity against Raji cells but not Jurkat cells. Additionally, in silico analyses demonstrated the good stereochemical quality of the 3D model and its molecular interactions with CD22. The researchers concluded that the pro-apoptotic peptide BIM could be effectively delivered to target cells by this novel recombinant anti-CD22 scFv.Bim fusion protein, making it a promising candidate for the treatment of B-cell malignancies.
In light of these studies, it can be anticipated that the designed immunotoxins in our study may exert similar effects in eliminating appropriate cell lines and could potentially function as effective anti-cancer agents.
5.1. Conclusions
In this in silico study, we utilized bioinformatics analyses through various tools and web servers to evaluate the design and construction of two immunotoxins, construct 1 and construct 2. We assessed key parameters crucial for immunotoxin design, including protein structure, docking, MD simulation, mRNA stability, allergenicity, and antigenicity. Based on our analyses, construct 2 demonstrated superior properties, making it a more promising immunotoxin candidate. This construct exhibited better structural properties, higher binding affinity, and improved stability. We recommend that construct 2 undergo further experimental validation, including expression in a suitable bacterial host, purification, and in vitro testing on breast cancer cell lines to evaluate its therapeutic potential.