Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023:2552:333-359.
doi: 10.1007/978-1-0716-2609-2_19.

Antibody Affinity Maturation Using Computational Methods: From an Initial Hit to Small-Scale Expression of Optimized Binders

Barbara Medagli  1 , Miguel A Soler  2   3 , Rita De Zorzi  4 , Sara Fortuna  5   6
Affiliations
Free article

Antibody Affinity Maturation Using Computational Methods: From an Initial Hit to Small-Scale Expression of Optimized Binders

Barbara Medagli et al. Methods Mol Biol. 2023.
Free article

Abstract

Nanobodies (VHHs) are engineered fragments of the camelid single-chain immunoglobulins. The VHH domain contains the highly variable segments responsible for antigen recognition. VHHs can be easily produced as recombinant proteins. Their small size is a good advantage for in silico approaches. Computer methods represent a valuable strategy for the optimization and improvement of their binding affinity. They also allow for epitope selection offering the possibility to design new VHHs for regions of a target protein that are not naturally immunogenic. Here we present an in silico mutagenic protocol developed to improve the binding affinity of nanobodies together with the first step of their in vitro production. The method, already proven successful in improving the low Kd of a nanobody hit obtained by panning, can be employed for the ex novo design of antibody fragments against selected protein target epitopes.

Keywords: Antigen; Binding affinity; In silico protocol; Nanobodies (VHH).

PubMed Disclaimer

References

    1. Melarkode Vattekatte A, Shinada NK, Narwani TJ et al (2020) Discrete analysis of camelid variable domains: sequences, structures, and in-silico structure prediction. PeerJ 8:e8408. https://doi.org/10.7717/peerj.8408 - DOI - PubMed - PMC
    1. Mitchell LS, Colwell LJ (2018) Comparative analysis of nanobody sequence and structure data. Proteins Struct Funct Bioinforma 86:697–706. https://doi.org/10.1002/prot.25497 - DOI
    1. Zavrtanik U, Lukan J, Loris R et al (2018) Structural basis of epitope recognition by heavy-chain camelid antibodies. J Mol Biol 430:4369–4386. https://doi.org/10.1016/j.jmb.2018.09.002 - DOI - PubMed
    1. Arbabi-Ghahroudi M (2017) Camelid single-domain antibodies: historical perspective and future outlook. Front Immunol 8:1–8. https://doi.org/10.3389/fimmu.2017.01589 - DOI
    1. Wang Y, Fan Z, Shao L et al (2016) Nanobody-derived nanobiotechnology tool kits for diverse biomedical and biotechnology applications. Int J Nanomedicine 11:3287–3303. https://doi.org/10.2147/IJN.S107194 - DOI - PubMed - PMC

Publication types

LinkOut - more resources