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Production of a Ribosome-Displayed Mouse scFv Antibody Against CD133, Analysis of Its Molecular Docking, and Molecular Dynamic Simulations of Their Interactions

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Abstract

The pentaspan transmembrane glycoprotein CD133, prominin-1, is expressed in cancer stem cells in many tumors and is promising as a novel target for the delivery of cytotoxic drugs to cancer-initiating cells. In this study, we prepared a mouse library of single-chain variable fragment (scFv) antibodies using mRNAs isolated from mice immunized with the third extracellular domain of a recombinant CD133 (D-EC3). First, the scFvs were directly exposed to D-EC3 to select a new specific scFv with high affinity against CD133 using the ribosome display method. Then, the selected scFv was characterized by the indirect enzyme-linked immunosorbent assay (ELISA), immunocytochemistry (ICC), and in silico analyses included molecular docking and molecular dynamics simulations. Based on ELISA results, scFv 2 had a higher affinity for recombinant CD133, and it was considered for further analysis. Next, the immunocytochemistry and flow cytometry experiments confirmed that the obtained scFv could bind to the CD133 expressing HT-29 cells. Furthermore, the results of in silico analysis verified the ability of the scFv 2 antibody to bind and detect the D-EC3 antigen through key residues employed in antigen–antibody interactions. Our results suggest that ribosome display could be applied as a rapid and valid method for isolation of scFv with high affinity and specificity. Also, studying the mechanism of interaction between CD133’s scFv and D-EC3 with two approaches of experimental and in silico analysis has potential importance for the design and development of antibody with improved properties.

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Data Availability

The datasets generated during the current study are available in the GenBank accession number: LC655309.

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Funding

This research is supported by the Iran National Science Foundation (INSF) (Grant No. 98000339) as a flowship for PhD dissertation of Sepideh Ghani and this article is extracted from Dr. Ghani’s PhD thesis.

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SG wrote original draft and performed the experiment and data analysis. MB supervised the study and provided the funding and project administration. FY, KB, and BK conducted guidance and review and editing. All authors read and approved the final manuscript.

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Correspondence to Mojgan Bandehpour or Fatemeh Yarian.

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All animal experiments were conducted in accordance with the guideline approved by the ethics committee of Shahid Beheshti University of Medical Sciences (Ethics code: IR.SBMU.REC.1397.129).

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Ghani, S., Bandehpour, M., Yarian, F. et al. Production of a Ribosome-Displayed Mouse scFv Antibody Against CD133, Analysis of Its Molecular Docking, and Molecular Dynamic Simulations of Their Interactions. Appl Biochem Biotechnol 196, 1399–1418 (2024). https://doi.org/10.1007/s12010-023-04609-4

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