In Silico Evaluation of the Interactions Among Novel Phage Display-Selected Single Chain Variable Fragment (scFv) with CD24 Marker

Abstract

Background: Antibody is a considerable approach in the pharmaceutical industry, and many studies have been done on antibody fragment engineering. Objectives: The objective of this study is to evaluate the interaction between antigens and antibodies, which is a necessary step for designing an efficient antibody with suitable properties for targeting cancer cells. Methods: In the current study, the 3-dimensional structure of the displayed-selected scFv antibody was constructed, using Sabpred Antibody Builder. The analysis of interactions between scFv and Cluster of differentiation 24 (CD24) was performed by computational docking and molecular dynamics (MD) simulation. Firstly, docking CD24 antigen to the new scFv antibody was done, using the ClusPro 2.0 web server, and residues involved in the interaction were identified. Secondly, using the GROMACS 4.5.3 package, MD simulations were performed. Results: By analyzing the antigen-antibody complex, the critical amino acids involved in these interactions were recognized. Thus, 15 hydrogen bonds between amino acids in light and heavy chains of antibodies and antigens were identified; most of the amino acids belonged to the complementarity-determining regions (CDRs) regions. Tyr148, which belongs to CDR1 of the VL chain by forming 4 hydrogen bonds with amino acids of the CD24 antigen, was considered an important amino acid in the CD24-scFv complex. Conclusions: Our bioinformatics study identified critical residues involved in antigen-antibody interaction, which could be considered an effective strategy for creating novel efficient fragmented antibodies with improved affinities for the CD24 receptor.