Structural basis of nanobodies neutralizing SARS-CoV-2 variants

Shi, Zhenzhong; Li, Xiyang; Wang, Lucy; Sun, Zengchao; Zhang, Haiwei; Chen, Xiaochen; Cui, Qianqian; Qiao, Huarui; Lan, Zhongyun; Zhang, Xin; Li, Xianheng; Li, Lingyun; Xu, Jianfeng; Gong, Rui; Fan, Chengpeng; Geng, Yong

doi:10.1016/j.str.2022.02.011

Cited by 14 publications

(6 citation statements)

References 46 publications

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“…So far, several Nbs have been developed with promising diagnostic and therapeutic applications [ 20 , 50 , 51 , 52 , 53 , 54 ]. Both monomeric Nbs and engineered molecules showed strong neutralizing activity to the different VOCs that have emerged, including the Omicron subvariants [ 52 , 55 , 56 , 57 , 58 , 59 , 60 , 61 ]. The intense production of new recombinant Nbs highlights the relevance of this technological platform, which is expected to reach clinical use for SARS-CoV-2 and other viral diseases in the near future [ 62 ].…”

Section: Discussionmentioning

confidence: 99%

SARS-CoV-2 Specific Nanobodies Neutralize Different Variants of Concern and Reduce Virus Load in the Brain of h-ACE2 Transgenic Mice

Pavan,

Bok,

Betanzos San Juan

et al. 2024

Viruses

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Since the beginning of the COVID-19 pandemic, there has been a significant need to develop antivirals and vaccines to combat the disease. In this work, we developed llama-derived nanobodies (Nbs) directed against the receptor binding domain (RBD) and other domains of the Spike (S) protein of SARS-CoV-2. Most of the Nbs with neutralizing properties were directed to RBD and were able to block S-2P/ACE2 interaction. Three neutralizing Nbs recognized the N-terminal domain (NTD) of the S-2P protein. Intranasal administration of Nbs induced protection ranging from 40% to 80% after challenge with the WA1/2020 strain in k18-hACE2 transgenic mice. Interestingly, protection was associated with a significant reduction in virus replication in nasal turbinates and a reduction in virus load in the brain. Employing pseudovirus neutralization assays, we identified Nbs with neutralizing capacity against the Alpha, Beta, Delta, and Omicron variants, including a Nb capable of neutralizing all variants tested. Furthermore, cocktails of different Nbs performed better than individual Nbs at neutralizing two Omicron variants (B.1.529 and BA.2). Altogether, the data suggest the potential of SARS-CoV-2 specific Nbs for intranasal treatment of COVID-19 encephalitis.

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Section: Discussionmentioning

confidence: 99%

SARS-CoV-2 Specific Nanobodies Neutralize Different Variants of Concern and Reduce Virus Load in the Brain of h-ACE2 Transgenic Mice

Pavan,

Bok,

Betanzos San Juan

et al. 2024

Viruses

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show abstract

“…So far, several Nbs have been developed with promising diagnostic and therapeutic applications [20,38]. Both monomeric Nbs and engineered molecules showed strong neutralizing activity to the different VOCs that have emerged, including the Omicron variants [39][40][41][42][43][44][45][46]. The intense production of new recombinant Nbs highlights the relevance of this technological platform, which is expected to reach clinical use for SARS-CoV-2 and other viral diseases in the near future [47].…”

Section: Discussionmentioning

confidence: 99%

Nanobodies against SARS-CoV-2 reduced virus load in the brain of challenged mice and neutralized Wuhan, Delta and Omicron Variants

Pavan

Bok

Juan

et al. 2023

Preprint

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In this work, we developed llama-derived nanobodies (Nbs) directed to the receptor binding domain (RBD) and other domains of the Spike (S) protein of SARS-CoV-2. Nanobodies were selected after the biopanning of two Nb-libraries, one of which was generated after the immunization of a llama (lama glama) with the bovine coronavirus (BCoV) Mebus, and another with the full-length pre-fused locked S protein (S-2P) and the RBD from the SARS-CoV-2 Wuhan strain (WT). Most of the neutralizing Nbs selected with either RBD or S-2P from SARS-CoV-2 were directed to RBD and were able to block S2P/ACE2 interaction. Three Nbs recognized the N-terminal domain (NTD) of the S-2P protein as measured by competition with biliverdin, while some non-neutralizing Nbs recognize epitopes in the S2 domain. One Nb from the BCoV immune library was directed to RBD but was non-neutralizing. Intranasal administration of Nbs induced protection ranging from 40% to 80% against COVID-19 death in k18-hACE2 mice challenged with the WT strain. Interestingly, protection was not only associated with a significant reduction of virus replication in nasal turbinates and lungs, but also with a reduction of virus load in the brain. Employing pseudovirus neutralization assays, we were able to identify Nbs with neutralizing capacity against the Alpha, Beta, Delta and Omicron variants. Furthermore, cocktails of different Nbs performed better than individual Nbs to neutralize two Omicron variants (B.1.529 and BA.2). Altogether, the data suggest these Nbs can potentially be used as a cocktail for intranasal treatment to prevent or treat COVID-19 encephalitis, or modified for prophylactic administration to fight this disease.

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“…The amino acid repertoires resulting from these codons vary from 2 to 16 aa, with most of the sets having only 4 or 6 aa. Even so, the theoretical diversity is huge, in the order of 10 18 .…”

Section: Discussionmentioning

confidence: 99%

“…An important issue to consider in Nb library design is the length of CDR3. It has been shown that nanobodies can recognize clefts and cryptic epitopes in proteins that are less accessible to conventional antibodies [16][17][18]. This important capability is due to the compact prolate shape of Nbs together with their usually long CDR3 loop that folds over the framework region, generating a convex paratope.…”

Section: Introductionmentioning

confidence: 99%

Design and Construction of a Synthetic Nanobody Library: Testing Its Potential with a Single Selection Round Strategy

et al. 2023

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Nanobodies (Nbs) are single domain antibody fragments derived from heavy-chain antibodies found in members of the Camelidae family. They have become a relevant class of biomolecules for many different applications because of several important advantages such as their small size, high solubility and stability, and low production costs. On the other hand, synthetic Nb libraries are emerging as an attractive alternative to animal immunization for the selection of antigen-specific Nbs. Here, we present the design and construction of a new synthetic nanobody library using the phage display technology, following a structure-based approach in which the three hypervariable loops were subjected to position-specific randomization schemes. The constructed library has a clonal diversity of 108 and an amino acid variability that matches the codon distribution set by design at each randomized position. We have explored the capabilities of the new library by selecting nanobodies specific for three antigens: vascular endothelial growth factor (VEGF), tumor necrosis factor (TNF) and the glycoprotein complex (GnGc) of Andes virus. To test the potential of the library to yield a variety of antigen-specific Nbs, we introduced a biopanning strategy consisting of a single selection round using stringent conditions. Using this approach, we obtained several binders for each of the target antigens. The constructed library represents a promising nanobody source for different applications.

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Structural basis of nanobodies neutralizing SARS-CoV-2 variants

Cited by 14 publications

References 46 publications

SARS-CoV-2 Specific Nanobodies Neutralize Different Variants of Concern and Reduce Virus Load in the Brain of h-ACE2 Transgenic Mice

SARS-CoV-2 Specific Nanobodies Neutralize Different Variants of Concern and Reduce Virus Load in the Brain of h-ACE2 Transgenic Mice

Nanobodies against SARS-CoV-2 reduced virus load in the brain of challenged mice and neutralized Wuhan, Delta and Omicron Variants

Design and Construction of a Synthetic Nanobody Library: Testing Its Potential with a Single Selection Round Strategy

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