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Zong X, Liu P, Wang Z, Zhu H, Zhong C, Zhong P, Jiang H, Liu J, Ma Z, Liu X, Liu R, Ding Y. Structural insights into the binding of nanobodies to the Staphylococcal enterotoxin B. Int J Biol Macromol 2024; 276:133957. [PMID: 39029852 DOI: 10.1016/j.ijbiomac.2024.133957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/21/2024] [Accepted: 07/16/2024] [Indexed: 07/21/2024]
Abstract
Staphylococcal Enterotoxin Type B (SEB), produced by Staphylococcus aureus bacteria, is notorious for inducing severe food poisoning and toxic shock syndrome. While nanobody-based treatments hold promises for combating SEB-induced diseases, the lack of structural information between SEB and nanobodies has hindered the development of nanobody-based therapeutics. Here, we present crystal structures of SEB-Nb3, SEB-Nb6, SEB-Nb8, SEB-Nb11, and SEB-Nb20 at resolutions ranging from 1.59 Å to 2.33 Å. Crystallographic analysis revealed that Nb3, Nb8, Nb11, and Nb20 bind to SEB at the T-cell receptor (TCR) interface, while Nb6 binds at the major histocompatibility complex (MHC) interface, suggesting their potential to inhibit SEB function by disrupting interactions with TCR or MHC molecules. Molecular biological analyses confirmed the thermodynamic and kinetic parameters of Nb3, Nb5, Nb6, Nb8, Nb11, Nb15, Nb18, and Nb20 to SEB. The competitive inhibition was further confirmed by cell-based experiments demonstrating nanobody neutralization. These findings elucidate the structural basis for developing specific nanobodies to neutralize SEB threats, providing crucial insights into the underlying mechanisms and offering significant assistance for further optimization towards future therapeutic strategies.
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Affiliation(s)
- Xin Zong
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Peng Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Ziying Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Haoran Zhu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Chao Zhong
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Peiyu Zhong
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - He Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jiayuan Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Zhiqiang Ma
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Xihuan Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Rui Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China; Quzhou Fudan Institute, Quzhou, Zhejiang 324002, China.
| | - Yu Ding
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China; Quzhou Fudan Institute, Quzhou, Zhejiang 324002, China.
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Liu ML, Liang XM, Jin MY, Huang HW, Luo L, Wang H, Shen X, Xu ZL. Food-Borne Biotoxin Neutralization in Vivo by Nanobodies: Current Status and Prospects. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:10753-10771. [PMID: 38706131 DOI: 10.1021/acs.jafc.4c02257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Food-borne biotoxins from microbes, plants, or animals contaminate unclean, spoiled, and rotten foods, posing significant health risks. Neutralizing such toxins is vital for human health, especially after food poisoning. Nanobodies (Nbs), a type of single-domain antibodies derived from the genetic cloning of a variable domain of heavy chain antibodies (VHHs) in camels, offer unique advantages in toxin neutralization. Their small size, high stability, and precise binding enable effective neutralization. The use of Nbs in neutralizing food-borne biotoxins offers numerous benefits, and their genetic malleability allows tailored optimization for diverse toxins. As nanotechnology continues to evolve and improve, Nbs are poised to become increasingly efficient and safer tools for toxin neutralization, playing a pivotal role in safeguarding human health and environmental safety. This review not only highlights the efficacy of these agents in neutralizing toxins but also proposes innovative solutions to address their current challenges. It lays a solid foundation for their further development in this crucial field and propels their commercial application, thereby contributing significantly to advancements in this domain.
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Affiliation(s)
- Min-Ling Liu
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Research Center for Green Development of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Xiao-Min Liang
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Research Center for Green Development of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Ming-Yu Jin
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Research Center for Green Development of Agriculture, South China Agricultural University, Guangzhou 510642, China
- School of Life and Health Technology, Dongguan, University of Technology, Dongguan 523808, China
| | - Hui-Wei Huang
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Research Center for Green Development of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Lin Luo
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Research Center for Green Development of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Hong Wang
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Research Center for Green Development of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Xing Shen
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Research Center for Green Development of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Zhen-Lin Xu
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Research Center for Green Development of Agriculture, South China Agricultural University, Guangzhou 510642, China
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Ming K, Xing B, Hu Y, Mei M, Huang W, Hu X, Wei Z. De novo design of a protein binder against Staphylococcus enterotoxin B. Int J Biol Macromol 2024; 257:128666. [PMID: 38070805 DOI: 10.1016/j.ijbiomac.2023.128666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/03/2023] [Accepted: 12/06/2023] [Indexed: 01/26/2024]
Abstract
Staphylococcus enterotoxin B (SEB) interacts with MHC-II molecules to overactivate immune cells and thereby to produce excessive pro-inflammatory cytokines. Disrupting the interactions between SEB and MHC-II helps eliminate the lethal threat posed by SEB. In this study, a de novo computational approach was used to design protein binders targeting SEB. The MHC-II binding domain of SEB was selected as the target, and the possible promising binding mode was broadly explored. The obtained original binder was folded into triple-helix bundles and contained 56 amino acids with molecular weight 5.9 kDa. The interface of SEB and the binder was highly hydrophobic. ProteinMPNN optimization further enlarged the hydrophobic region of the binder and improved the stability of the binder-SEB complex. In vitro study demonstrated that the optimized binder significantly inhibited the inflammatory response induced by SEB. Overall, our research demonstrated the applicability of this approach in de novo designing protein binders against SEB, and thereby providing potential therapeutics for SEB induced diseases.
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Affiliation(s)
- Ke Ming
- School of life sciences, Hubei University, Wuhan, Hubei, PR China; State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, PR China; Hubei Jiangxia Laboratory, Wuhan, Hubei, PR China
| | - Banbin Xing
- School of life sciences, Hubei University, Wuhan, Hubei, PR China; State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, PR China
| | - Yang Hu
- School of life sciences, Hubei University, Wuhan, Hubei, PR China; State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, PR China
| | - Meng Mei
- School of life sciences, Hubei University, Wuhan, Hubei, PR China; State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, PR China
| | - Wenli Huang
- School of life sciences, Hubei University, Wuhan, Hubei, PR China; State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, PR China
| | - Xiaoyu Hu
- School of life sciences, Hubei University, Wuhan, Hubei, PR China; State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, PR China
| | - Zigong Wei
- School of life sciences, Hubei University, Wuhan, Hubei, PR China; State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, PR China; Hubei Jiangxia Laboratory, Wuhan, Hubei, PR China; Hubei Province Key Laboratory of Biotechnology of Chinese Traditional Medicine, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of life sciences, Hubei University, Wuhan, Hubei, PR China.
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