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Original Article

Korean J Physiol Pharmacol 2024; 28(5): 457-467

Published online September 1, 2024 https://doi.org/10.4196/kjpp.2024.28.5.457

Copyright © Korean J Physiol Pharmacol.

Construction and validation of a synthetic phage-displayed nanobody library

Minju Kim1,2,#, Xuelian Bai3,#, Hyewon Im4, Jisoo Yang1,2, Youngju Kim1,2, Minjoo MJ Kim1,2, Yeonji Oh3, Yuna Jeon3, Hayoung Kwon5, Seunghyun Lee3,*, and Chang-Han Lee1,2,4,5,6,7,8,*

1Department of Biomedical Sciences, 2BK21 FOUR Biomedical Science Project, Seoul National University College of Medicine, Seoul 03080, 3Research Center, EPD Biotherapeutics Inc., Seoul 08378, 4Cancer Research Institute, 5Department of Pharmacology, Seoul National University College of Medicine, Seoul 03080, 6Wide River Institute of Immunology, Seoul National University, Hongcheon 25159, 7SNU Dementia Research Center, College of Medicine, Seoul National University, 8Seoul National University Hospital, Seoul 03080, Korea

Correspondence to:Seunghyun Lee
E-mail: sh.lee@epdbio.com
Chang-Han Lee
E-mail: chlee-antibody@snu.ac.kr

#These authors contributed equally to this work.

Author contributions: C.H.L. and S.L. conceptualized the study. C.H.L., S.L., X.B., Y.O., and Y.J. were responsible for the design of nanobody library. M.K., H.I., J.Y., Y.K., and M.M.K. constructed nanobody library. M.K., H.I., X.B., Y.O., and Y.J. carried out the biopanning experiments. M.K. and H.I. preformed the protein purification and ELISA experiments. In silico analysis was conducted by M.K., and C.H.L., S.L., M.K., H.I., and H.K. analyzed the data. C.H.L., S.L., and M.K. wrote the manuscript.

Received: April 10, 2024; Revised: April 17, 2024; Accepted: April 22, 2024

Abstract

Nanobodies derived from camelids and sharks offer unique advantages in therapeutic applications due to their ability to bind to epitopes that were previously inaccessible. Traditional methods of nanobody development face challenges such as ethical concerns and antigen toxicity. Our study presents a synthetic, phagedisplayed nanobody library using trinucleotide-directed mutagenesis technology, which allows precise amino acid composition in complementarity-determining regions (CDRs), with a focus on CDR3 diversity. This approach avoids common problems such as frameshift mutations and stop codon insertions associated with other synthetic antibody library construction methods. By analyzing FDA-approved nanobodies and Protein Data Bank sequences, we designed sub-libraries with different CDR3 lengths and introduced amino acid substitutions to improve solubility. The validation of our library through the successful isolation of nanobodies against targets such as PD-1, ATXN1 and STAT3 demonstrates a versatile and ethical platform for the development of high specificity and affinity nanobodies and represents a significant advance in biotechnology.

Keywords: Ataxin-1, Nanobodies, Phage display peptide library, Programmed cell death 1 receptor, Signal transducer and activator of transcription 3, Synthetic peptide libraries

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