Synthetic antibodies designed on natural sequence landscapes

Zhai, Wenwu; Glanville, Jacob; Fuhrmann, Markus; Mei, Li; Ni, Irene; Sundar, Purnima D.; Van Blarcom, Thomas; Abdiche, Yasmina; Lindquist, Kevin; Strohner, Ralf; Telman, Dilduz; Cappuccilli, Guido; Finlay, William J.J.; Van den Brulle, Jan; Cox, David R.; Pons, Jaume; Rajpal, Arvind

doi:10.1016/j.jmb.2011.07.018

Cited by 93Monoclonal and Polyclonal Antibodies ResearchChemical Synthesis and Analysisvaccines and immunoinformatics approaches

Synthetic antibodies designed on natural sequence landscapes

Zhai, Wenwu, Glanville, Jacob, Fuhrmann, Markus, Mei, Li, Ni, Irene, Sundar, Purnima D., Van Blarcom, Thomas, Abdiche, Yasmina +9 more·2011·Journal of Molecular Biology

DOI 10.1016/j.jmb.2011.07.018

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Abstract

We present a method for synthetic antibody library generation that combines the use of high-throughput immune repertoire analysis and a novel synthetic technology. The library design recapitulates positional amino acid frequencies observed in natural antibody repertoires. V-segment diversity in four heavy (V(H)) and two kappa (V(κ)) germlines was introduced based on the analysis of somatically hypermutated donor-derived repertoires. Complementarity-determining region 3 length and amino acid designs were based on aggregate frequencies of all V(H) and V(κ) sequences in the data set. The designed libraries were constructed through an adaptation of a novel gene synthesis technology that enables precise positional control of amino acid composition and incorporation frequencies. High-throughput pyrosequencing was used to monitor the fidelity of construction and characterize genetic diversity in the final 3.6×10(10) transformants. The library exhibited Fab expression superior to currently reported synthetic approaches of equivalent diversity, with greater than 93% of clones observed to successfully display both a correctly folded heavy chain and a correctly folded light chain. Genetic diversity in the library was high, with 95% of 7.0×10(5) clones sequenced observed only once. The obtained library diversity explores a comparable sequence space as the donor-derived natural repertoire and, at the same time, is able to access novel recombined diversity due to lack of segmental linkage. The successful isolation of low- and subnanomolar-affinity antibodies against a diverse panel of receptors, growth factors, enzymes, antigens from infectious reagents, and peptides confirms the functional viability of the design strategy.

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Natural preferences in antibody repertoires can be used as a reference to assess the biophysical properties of therapeutic antibodies or to develop naturally focused surface display libraries.
“Among others, such natural preferences can be used as a reference to assess the biophysical properties of therapeutic antibodies [13] or to develop naturally focused surface display libraries [26].”
From Computational approaches to therapeutic antibody design: established methods and emerging trends (2020) · cites this paper as [26]
Analysis of antibodies derived from 600 donors followed by construction of a library based on natural positional preferences has demonstrated that such constraints can be adapted to library construction and used to identify binding antibodies.
“This has already been demonstrated to some extent through analysis of antibodies derived from 600 donors [24] followed by construction of a library based on natural positional preferences [26].”
From Computational approaches to therapeutic antibody design: established methods and emerging trends (2020) · cites this paper as [26]

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Computational approaches to therapeutic antibody design: established methods and emerging trends
Norman, R. A., Ambrosetti, F., Bonvin, A. M. J. J., Colwell, L. J., Kelm, S., Kumar, S., & Krawczyk, K. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbz095 · Cited by 219 · see citing works
“This has already been demonstrated to some extent through analysis of antibodies derived from 600 donors [24] followed by construction of a library based on natural positional preferences [26].”
Background
Prediction of delayed retention of antibodies in hydrophobic interaction chromatography from sequence using machine learning
Jain, T., Boland, T., Lilov, A., Burnina, I., Brown, M., Xu, Y., & Vásquez, M. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx519 · Cited by 61 · see citing works

Authors: Zhai, W., Glanville, J., Fuhrmann, M., Mei, L., Ni, I., Sundar, P. D., Van Blarcom, T., Abdiche, Y., Lindquist, K., Strohner, R., Telman, D., Cappuccilli, G., Finlay, W. J. J., Van den Brulle, J., Cox, D. R., Pons, J., & Rajpal, A.
Affiliations: Pfizer (United States) (US)
MorphoSys (Germany) (DE)
AREA Science Park (IT)
Pfizer (Ireland) (IE)
Corresponding author: Pons, Jaume
Rajpal, Arvind
ORCID: Mei, Li
Ni, Irene
Sundar, Purnima D.
Abdiche, Yasmina
Lindquist, Kevin
Cox, David R.
Pons, Jaume
Venue: Journal of Molecular Biology
Publisher: Elsevier BV
Published: 2011-09
Volume: 412
Issue: 1
Pages: 55-71
ISSN: 0022-2836 (ISSN-L)
DOI: 10.1016/j.jmb.2011.07.018
OpenAlex: W2073308880
Cited by: 93
References: 41
Citations by year: 2026: 3 · 2025: 4 · 2024: 5 · 2023: 4 · 2022: 6 · 2021: 2 · 2020: 3 · 2019: 5 · 2018: 5 · 2017: 13 · 2016: 6 · 2015: 13 · 2014: 5 · 2013: 8 · 2012: 10
FWCI: 5.86
Type: journal article
Language: en
Open access: closed
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations: Journal of Molecular Biology (publishedVersion)
PubMed (publishedVersion)
Topics: Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Monoclonal and Polyclonal Antibodies Research
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chemical Synthesis and Analysis
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
Keywords: synthetic antibody libraries, somatic hypermutation, germline sequences, CDR3 length, gene synthesis, library diversity, affinity maturation
MeSH terms: Antibodies, Enzyme-Linked Immunosorbent Assay, Humans, Models, Theoretical, Genetic Variation, Biosensing Techniques, Peptide Library

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Synthetic antibodies designed on natural sequence landscapes

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