Cargando…
Design of nanobody-based bispecific constructs by in silico affinity maturation and umbrella sampling simulations
Random mutagenesis is the natural opportunity for proteins to evolve and biotechnologically it has been exploited to create diversity and identify variants with improved characteristics in the mutant pools. Rational mutagenesis based on biophysical assumptions and supported by computational power ha...
Autores principales: | , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Research Network of Computational and Structural Biotechnology
2022
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9822835/ https://www.ncbi.nlm.nih.gov/pubmed/36659922 http://dx.doi.org/10.1016/j.csbj.2022.12.021 |
_version_ | 1784866033613406208 |
---|---|
author | Bai, Zixuan Wang, Jiewen Li, Jiaqi Yuan, Haibin Wang, Ping Zhang, Miao Feng, Yuanhang Cao, Xiangtong Cao, Xiangan Kang, Guangbo de Marco, Ario Huang, He |
author_facet | Bai, Zixuan Wang, Jiewen Li, Jiaqi Yuan, Haibin Wang, Ping Zhang, Miao Feng, Yuanhang Cao, Xiangtong Cao, Xiangan Kang, Guangbo de Marco, Ario Huang, He |
author_sort | Bai, Zixuan |
collection | PubMed |
description | Random mutagenesis is the natural opportunity for proteins to evolve and biotechnologically it has been exploited to create diversity and identify variants with improved characteristics in the mutant pools. Rational mutagenesis based on biophysical assumptions and supported by computational power has been proposed as a faster and more predictable strategy to reach the same aim. In this work we confirm that substantial improvements in terms of both affinity and stability of nanobodies can be obtained by using combinations of algorithms, even for binders with already high affinity and elevated thermal stability. Furthermore, in silico approaches allowed the development of an optimized bispecific construct able to bind simultaneously the two clinically relevant antigens TNF-α and IL-23 and, by means of its enhanced avidity, to inhibit effectively the apoptosis of TNF-α-sensitive L929 cells. The results revealed that salt bridges, hydrogen bonds, aromatic-aromatic and cation-pi interactions had a critical role in increasing affinity. We provided a platform for the construction of high-affinity bispecific constructs based on nanobodies that can have relevant applications for the control of all those biological mechanisms in which more than a single antigen must be targeted to increase the treatment effectiveness and avoid resistance mechanisms. |
format | Online Article Text |
id | pubmed-9822835 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Research Network of Computational and Structural Biotechnology |
record_format | MEDLINE/PubMed |
spelling | pubmed-98228352023-01-18 Design of nanobody-based bispecific constructs by in silico affinity maturation and umbrella sampling simulations Bai, Zixuan Wang, Jiewen Li, Jiaqi Yuan, Haibin Wang, Ping Zhang, Miao Feng, Yuanhang Cao, Xiangtong Cao, Xiangan Kang, Guangbo de Marco, Ario Huang, He Comput Struct Biotechnol J Research Article Random mutagenesis is the natural opportunity for proteins to evolve and biotechnologically it has been exploited to create diversity and identify variants with improved characteristics in the mutant pools. Rational mutagenesis based on biophysical assumptions and supported by computational power has been proposed as a faster and more predictable strategy to reach the same aim. In this work we confirm that substantial improvements in terms of both affinity and stability of nanobodies can be obtained by using combinations of algorithms, even for binders with already high affinity and elevated thermal stability. Furthermore, in silico approaches allowed the development of an optimized bispecific construct able to bind simultaneously the two clinically relevant antigens TNF-α and IL-23 and, by means of its enhanced avidity, to inhibit effectively the apoptosis of TNF-α-sensitive L929 cells. The results revealed that salt bridges, hydrogen bonds, aromatic-aromatic and cation-pi interactions had a critical role in increasing affinity. We provided a platform for the construction of high-affinity bispecific constructs based on nanobodies that can have relevant applications for the control of all those biological mechanisms in which more than a single antigen must be targeted to increase the treatment effectiveness and avoid resistance mechanisms. Research Network of Computational and Structural Biotechnology 2022-12-16 /pmc/articles/PMC9822835/ /pubmed/36659922 http://dx.doi.org/10.1016/j.csbj.2022.12.021 Text en © 2022 The Authors https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Research Article Bai, Zixuan Wang, Jiewen Li, Jiaqi Yuan, Haibin Wang, Ping Zhang, Miao Feng, Yuanhang Cao, Xiangtong Cao, Xiangan Kang, Guangbo de Marco, Ario Huang, He Design of nanobody-based bispecific constructs by in silico affinity maturation and umbrella sampling simulations |
title | Design of nanobody-based bispecific constructs by in silico affinity maturation and umbrella sampling simulations |
title_full | Design of nanobody-based bispecific constructs by in silico affinity maturation and umbrella sampling simulations |
title_fullStr | Design of nanobody-based bispecific constructs by in silico affinity maturation and umbrella sampling simulations |
title_full_unstemmed | Design of nanobody-based bispecific constructs by in silico affinity maturation and umbrella sampling simulations |
title_short | Design of nanobody-based bispecific constructs by in silico affinity maturation and umbrella sampling simulations |
title_sort | design of nanobody-based bispecific constructs by in silico affinity maturation and umbrella sampling simulations |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9822835/ https://www.ncbi.nlm.nih.gov/pubmed/36659922 http://dx.doi.org/10.1016/j.csbj.2022.12.021 |
work_keys_str_mv | AT baizixuan designofnanobodybasedbispecificconstructsbyinsilicoaffinitymaturationandumbrellasamplingsimulations AT wangjiewen designofnanobodybasedbispecificconstructsbyinsilicoaffinitymaturationandumbrellasamplingsimulations AT lijiaqi designofnanobodybasedbispecificconstructsbyinsilicoaffinitymaturationandumbrellasamplingsimulations AT yuanhaibin designofnanobodybasedbispecificconstructsbyinsilicoaffinitymaturationandumbrellasamplingsimulations AT wangping designofnanobodybasedbispecificconstructsbyinsilicoaffinitymaturationandumbrellasamplingsimulations AT zhangmiao designofnanobodybasedbispecificconstructsbyinsilicoaffinitymaturationandumbrellasamplingsimulations AT fengyuanhang designofnanobodybasedbispecificconstructsbyinsilicoaffinitymaturationandumbrellasamplingsimulations AT caoxiangtong designofnanobodybasedbispecificconstructsbyinsilicoaffinitymaturationandumbrellasamplingsimulations AT caoxiangan designofnanobodybasedbispecificconstructsbyinsilicoaffinitymaturationandumbrellasamplingsimulations AT kangguangbo designofnanobodybasedbispecificconstructsbyinsilicoaffinitymaturationandumbrellasamplingsimulations AT demarcoario designofnanobodybasedbispecificconstructsbyinsilicoaffinitymaturationandumbrellasamplingsimulations AT huanghe designofnanobodybasedbispecificconstructsbyinsilicoaffinitymaturationandumbrellasamplingsimulations |