Simulation and Stability Assessment of Anti-EpCAM Immunotoxin for Cancer Therapy

Abstract

Purpose: Epithelial cell adhesion molecule (EpCAM) is a dominant antigen in human colon carcinoma tissue. Topology features of this antigen are different in normal and malignant conditions; for instance, EpCAM is much less accessible to antibodies in normal cells than in cancerous tissues. Hence, EpCAM has been considered as a suitable candidate for cancer target therapy via immunotoxins (ITs) development. In this study, attention was focused on the stability assessment of anti-EpCAM-IT (anti-Ep-IT) to design a novel IT.Methods: The 3D structures of the antibody template and the toxin segment of anti-Ep-IT were retrieved from PDB. Discovery Studio3.0 was used to separate the ligands and water molecules. The antibody (Ab) fragment of anti-Ep-IT was aligned using protein blast (BLAST-p), and SWISS-MODEL database was used for Ab modeling. IT modeling was accomplished using MODELLER 9.15. Also, GROMACS 5.07 was used for molecular dynamic (MD) simulation step. Moreover, ERRAT and RAMPAGE databases were used for quality assessment of the structures.Results: BLAST-p results indicated that antibody moiety of IT has the highest E-value and query coverage scores to the monoclonal antibody (mAb) 4D5MOC-B. Modeling by SWISS-MODEL provided a reasonable template for Ab portion compared to MODELLER. The best modeled full-length IT with the lowest RMSD values was selected. Finally, RMSD plot for MD stage demonstrated constant values from 7000ps to 20000ps.Conclusion: In general, both modeling results and their quality evaluations were satisfactory for designing IT. Moreover, RMSD plot revealed that IT stability was preserved during the simulation. Overall, our findings led to modeling and simulation of the anti-Ep-IT with more structural stability.

Evolution of Thyroglobulin Loop Kinetics in EpCAM

“…Though many studies have modeled EpCAM [ 3 , 10 , 28 , 29 , 30 , 31 ], we have not found reported evidence of the TY loop-CTD binding site. This is understandable given that these studies have mostly focused on predicting EpCAM interactions with therapeutics targeting the physiological cis -dimer form [ 10 , 29 , 31 ].…”

“…Though many studies have modeled EpCAM [ 3 , 10 , 28 , 29 , 30 , 31 ], we have not found reported evidence of the TY loop-CTD binding site. This is understandable given that these studies have mostly focused on predicting EpCAM interactions with therapeutics targeting the physiological cis -dimer form [ 10 , 29 , 31 ]. Likewise, researchers have focused on characterizing other EpCAM domains such as the intramembrane [ 3 ] and intracellular [ 30 ] regions.…”

“…Though many studies have modeled EpCAM [3,10,[28][29][30][31], we have not found reported evidence of the TY loop-CTD binding site. This is understandable given that these Fish Fish + HTY ratio of each residue at the CTD site for the fish and fish + HTY systems.…”

Immunotoxins: Targeted Toxin Delivery for Cancer Therapy

“…VB4-845 (or oportuzumab monatox, Proxinium) is a recombinant fusion protein that combines the specificity of an anti-EpCAM ScFv with the toxicity of PE 40. [61][62][63] Mesothelin, expressed on mesotheliomas, ovarian, pancreatic, and lung cancers, has been targeted with PE toxin and was found to have a synergistic effect with chemotherapeutic agents in a mice model. 44,49,64 One of the more interesting ITs is SS1P or antimesothelin (Fv)-PE38.…”