Open Access
Molecules, volume 28, issue 17, pages 6358
Interface-Based Design of High-Affinity Affibody Ligands for the Purification of RBD from Spike Proteins
Publication type: Journal Article
Publication date: 2023-08-30
Organic Chemistry
Drug Discovery
Physical and Theoretical Chemistry
Pharmaceutical Science
Molecular Medicine
Analytical Chemistry
Chemistry (miscellaneous)
Abstract
The outbreak of coronavirus disease 2019 (COVID-19) has sparked an urgent demand for advanced diagnosis and vaccination worldwide. The discovery of high-affinity ligands is of great significance for vaccine and diagnostic reagent manufacturing. Targeting the receptor binding domain (RBD) from the spike protein of severe acute respiratory syndrome-coronavirus 2, an interface at the outer surface of helices on the Z domain from protein A was introduced to construct a virtual library for the screening of ZRBD affibody ligands. Molecular docking was performed using HADDOCK software, and three potential ZRBD affibodies, ZRBD-02, ZRBD-04, and ZRBD-07, were obtained. Molecular dynamics (MD) simulation verified that the binding of ZRBD affibodies to RBD was driven by electrostatic interactions. Per-residue free energy decomposition analysis further substantiated that four residues with negative-charge characteristics on helix α1 of the Z domain participated in this process. Binding affinity analysis by microscale thermophoresis showed that ZRBD affibodies had high affinity for RBD binding, and the lowest dissociation constant was 36.3 nmol/L for ZRBD-07 among the three potential ZRBD affibodies. Herein, ZRBD-02 and ZRBD-07 affibodies were selected for chromatographic verifications after being coupled to thiol-activated Sepharose 6 Fast Flow (SepFF) gel. Chromatographic experiments showed that RBD could bind on both ZRBD SepFF gels and was eluted by 0.1 mol/L NaOH. Moreover, the ZRBD-07 SepFF gel had a higher affinity for RBD. This research provided a new idea for the design of affibody ligands and validated the potential of affibody ligands in the application of RBD purification from complex feedstock.
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Journal of Chromatography A
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Russian Chemical Reviews
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Elsevier
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Autonomous Non-profit Organization Editorial Board of the journal Uspekhi Khimii
1 publication, 25%
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Song S., Shi Q. Interface-Based Design of High-Affinity Affibody Ligands for the Purification of RBD from Spike Proteins // Molecules. 2023. Vol. 28. No. 17. p. 6358.
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Song S., Shi Q. Interface-Based Design of High-Affinity Affibody Ligands for the Purification of RBD from Spike Proteins // Molecules. 2023. Vol. 28. No. 17. p. 6358.
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TY - JOUR
DO - 10.3390/molecules28176358
UR - https://doi.org/10.3390/molecules28176358
TI - Interface-Based Design of High-Affinity Affibody Ligands for the Purification of RBD from Spike Proteins
T2 - Molecules
AU - Song, Siyuan
AU - Shi, Qinghong
PY - 2023
DA - 2023/08/30 00:00:00
PB - Multidisciplinary Digital Publishing Institute (MDPI)
SP - 6358
IS - 17
VL - 28
SN - 1420-3049
SN - 1420-3049
ER -
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@article{2023_Song,
author = {Siyuan Song and Qinghong Shi},
title = {Interface-Based Design of High-Affinity Affibody Ligands for the Purification of RBD from Spike Proteins},
journal = {Molecules},
year = {2023},
volume = {28},
publisher = {Multidisciplinary Digital Publishing Institute (MDPI)},
month = {aug},
url = {https://doi.org/10.3390/molecules28176358},
number = {17},
pages = {6358},
doi = {10.3390/molecules28176358}
}
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Song, Siyuan, et al. “Interface-Based Design of High-Affinity Affibody Ligands for the Purification of RBD from Spike Proteins.” Molecules, vol. 28, no. 17, Aug. 2023, p. 6358. https://doi.org/10.3390/molecules28176358.