A bispecific monomeric nanobody induces spike trimer dimers and neutralizes SARS-CoV-2 in vivo

Hanke, Leo; Das, Hrishikesh; Sheward, Daniel J.; Vidakovics, Laura Perez; Urgard, Egon; Morro, Ainhoa Moliner; Kim, Chang-Il; Karl, Vivien; Pankow, Alec; Smith, Natalie; Porębski, Bartłomiej; Fernández-Capetillo, Óscar; Sezgin, Erdinç; Pedersen, Gabriel Kristian; Coquet, Jonathan M.; Hållberg, Bengt; Murrell, Ben; McInerney, Gerald M.

doi:10.1038/s41467-021-27610-z

Cited by 61 publications

(76 citation statements)

References 61 publications

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“…All-atom MD simulations totaling 27.6 µs in length using the recently solved structures of the RBD of SARS-CoV-2 S protein in complex with nanobodies H11-H4 [145], H11-D4, and Ty1 revealed interactions between RBD and the nanobodies and estimated that the binding strength of the nanobodies to RBD is similar to that of ACE2 [145]. Together, our MD simulations suggest that H11-H4 and Ty1 abrogate ACE2 binding via different mechanisms, whereas H11-D4 is the least effective inhibitor among the three examined nanobodies, which is consistent with the experimental studies showing the lowest K D value for Ty1 and the highest for H11-D4 nanobody [89,95].…”

Section: Computational Studies Of Sars-cov-2 S Protein Binding Mechan...supporting

confidence: 88%

“…Many other recent studies have demonstrated and confirmed the potential of linker-based bi-paratopic or multi-paratopic nanobodies for enhanced blocking and neutralization of SARS-CoV-2 variants. The avidity effect was also observed by Hanke and colleagues that presented a bispecific monomeric nanobody that can promote the formation of the S trimer dimers and neutralizes SARS-CoV-2 in vivo [ 95 ]. This study demonstrated that multimerization of nanobodies can substantially improve virus neutralization potency, and the cryo-EM structure of the Fu2-spike complex with S protein revealed a remarkable head-to-head dimerization of the trimeric spike, bound by six molecules of Fu2 [ 95 ].…”

Section: Biophysical Characterization and Protein Engineering Of Sars...mentioning

confidence: 78%

“…The avidity effect was also observed by Hanke and colleagues that presented a bispecific monomeric nanobody that can promote the formation of the S trimer dimers and neutralizes SARS-CoV-2 in vivo [ 95 ]. This study demonstrated that multimerization of nanobodies can substantially improve virus neutralization potency, and the cryo-EM structure of the Fu2-spike complex with S protein revealed a remarkable head-to-head dimerization of the trimeric spike, bound by six molecules of Fu2 [ 95 ]. Another strategy to increase sybody potency by bi-paratopic fusion was proposed [ 105 ] using a sybody SR31 that binds RBD with high affinity, but does not perturb ACE2 binding.…”

Section: Biophysical Characterization and Protein Engineering Of Sars...mentioning

confidence: 78%

“…The X-ray crystal structures of sybodies (synthetic nanobodies) that effectively inhibit the ACE2 binding interaction and neutralize viral infectivity were reported and a bispecific construct, Sb15-Sb68 blocked ACE2 binding ( Figure 3 and Figure 4 ) [ 94 ]. A bispecific monomeric nanobody that induces SARS-CoV02 S trimer dimers and neutralizes SARS-CoV-2 in vivo was reported [ 95 ]. The engineered Fu2 nanobody interacts simultaneously with two RBDs from different SARS-CoV-2 S trimers inducing the highly unusual mode of binding and formation of spike dimers, leading to potent neutralization of the virus as well as the B.1.351 and B.1.617.2 variants.…”

Section: Structural Biology Of the Sars-cov-2 S Protein Complexes Wit...mentioning

confidence: 99%

“…The engineered Fu2 nanobody interacts simultaneously with two RBDs from different SARS-CoV-2 S trimers inducing the highly unusual mode of binding and formation of spike dimers, leading to potent neutralization of the virus as well as the B.1.351 and B.1.617.2 variants. Remarkably, not only does the F2 nanobody act by targeting two epitopes, but it also locks in the S trimers in very constrained conformations that completely block spike function [ 95 ].…”

Section: Structural Biology Of the Sars-cov-2 S Protein Complexes Wit...mentioning

confidence: 99%

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Structural and Computational Studies of the SARS-CoV-2 Spike Protein Binding Mechanisms with Nanobodies: From Structure and Dynamics to Avidity-Driven Nanobody Engineering

Verkhivker

2022

IJMS

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Nanobodies provide important advantages over traditional antibodies, including their smaller size and robust biochemical properties such as high thermal stability, high solubility, and the ability to be bioengineered into novel multivalent, multi-specific, and high-affinity molecules, making them a class of emerging powerful therapies against SARS-CoV-2. Recent research efforts on the design, protein engineering, and structure-functional characterization of nanobodies and their binding with SARS-CoV-2 S proteins reflected a growing realization that nanobody combinations can exploit distinct binding epitopes and leverage the intrinsic plasticity of the conformational landscape for the SARS-CoV-2 S protein to produce efficient neutralizing and mutation resistant characteristics. Structural and computational studies have also been instrumental in quantifying the structure, dynamics, and energetics of the SARS-CoV-2 spike protein binding with nanobodies. In this review, a comprehensive analysis of the current structural, biophysical, and computational biology investigations of SARS-CoV-2 S proteins and their complexes with distinct classes of nanobodies targeting different binding sites is presented. The analysis of computational studies is supplemented by an in-depth examination of mutational scanning simulations and identification of binding energy hotspots for distinct nanobody classes. The review is focused on the analysis of mechanisms underlying synergistic binding of multivalent nanobodies that can be superior to single nanobodies and conventional nanobody cocktails in combating escape mutations by effectively leveraging binding avidity and allosteric cooperativity. We discuss how structural insights and protein engineering approaches together with computational biology tools can aid in the rational design of synergistic combinations that exhibit superior binding and neutralization characteristics owing to avidity-mediated mechanisms.

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Section: Computational Studies Of Sars-cov-2 S Protein Binding Mechan...supporting

confidence: 88%

Section: Biophysical Characterization and Protein Engineering Of Sars...mentioning

confidence: 78%

Section: Biophysical Characterization and Protein Engineering Of Sars...mentioning

confidence: 78%

Section: Structural Biology Of the Sars-cov-2 S Protein Complexes Wit...mentioning

confidence: 99%

Section: Structural Biology Of the Sars-cov-2 S Protein Complexes Wit...mentioning

confidence: 99%

See 3 more Smart Citations

Structural and Computational Studies of the SARS-CoV-2 Spike Protein Binding Mechanisms with Nanobodies: From Structure and Dynamics to Avidity-Driven Nanobody Engineering

Verkhivker

2022

IJMS

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A novel nanobody broadly neutralizes SARS‐CoV‐2 via induction of spike trimer dimers conformation

Yang,

Zhang,

Zhang

et al. 2023

Exploration

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The ongoing mutations of the SARS‐CoV‐2 pose serious challenges to the efficacy of the available antiviral drugs, and new drugs with fantastic efficacy are always deserved investigation. Here, a nanobody called IBT‐CoV144 is reported, which exhibits broad neutralizing activity against SARS‐CoV‐2 by inducing the conformation of spike trimer dimers. IBT‐CoV144 was isolated from an immunized alpaca using the RBD of wild‐type SARS‐CoV‐2, and it showed strong cross‐reactive binding and neutralizing potency against diverse SARS‐CoV‐2 variants, including Omicron subvariants. Moreover, the prophylactically and therapeutically intranasal administration of IBT‐CoV144 confers fantastic protective efficacy against the challenge of Omicron BA.1 variant in BALB/c mice model. The structure analysis of the complex between spike (S) protein, conducted using Cryo‐EM, revealed a special conformation known as the trimer dimers. This conformation is formed by two trimers, with six RBDs in the “up” state and bound by six VHHs. IBT‐CoV144 binds to the lateral region of the RBD on the S protein, facilitating the aggregation of S proteins. This aggregation results in steric hindrance, which disrupts the recognition of the virus by ACE2 on host cells. The discovery of IBT‐CoV144 will provide valuable insights for the development of advanced therapeutics and the design of next‐generation vaccines.

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The Potential of Nanobodies for COVID-19 Diagnostics and Therapeutics

Naidoo

Chuturgoon

2023

Mol Diagn Ther

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The infectious severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the causative agent for coronavirus disease 2019 (COVID-19). Globally, there have been millions of infections and fatalities. Unfortunately, the virus has been persistent and a contributing factor is the emergence of several variants. The urgency to combat COVID-19 led to the identification/development of various diagnosis (polymerase chain reaction and antigen tests) and treatment (repurposed drugs, convalescent plasma, antibodies and vaccines) options. These treatments may treat mild symptoms and decrease the risk of life-threatening disease. Although these options have been fairly beneficial, there are some challenges and limitations, such as cost of tests/drugs, specificity, large treatment dosages, intravenous administration, need for trained personal, lengthy production time, high manufacturing costs, and limited availability. Therefore, the development of more efficient COVID-19 diagnostic and therapeutic options are vital. Nanobodies (Nbs) are novel monomeric antigen-binding fragments derived from camelid antibodies. Advantages of Nbs include low immunogenicity, high specificity, stability and affinity. These characteristics allow for rapid Nb generation, inexpensive large-scale production, effective storage, and transportation, which is essential during pandemics. Additionally, the potential aerosolization and inhalation delivery of Nbs allows for targeted treatment delivery as well as patient self-administration. Therefore, Nbs are a viable option to target SARS-CoV-2 and overcome COVID-19. In this review we discuss (1) COVID-19; (2) SARS-CoV-2; (3) the present conventional COVID-19 diagnostics and therapeutics, including their challenges and limitations; (4) advantages of Nbs; and (5) the numerous Nbs generated against SARS-CoV-2 as well as their diagnostic and therapeutic potential.

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A bispecific monomeric nanobody induces spike trimer dimers and neutralizes SARS-CoV-2 in vivo

Cited by 61 publications

References 61 publications

Structural and Computational Studies of the SARS-CoV-2 Spike Protein Binding Mechanisms with Nanobodies: From Structure and Dynamics to Avidity-Driven Nanobody Engineering

Structural and Computational Studies of the SARS-CoV-2 Spike Protein Binding Mechanisms with Nanobodies: From Structure and Dynamics to Avidity-Driven Nanobody Engineering

A novel nanobody broadly neutralizes SARS‐CoV‐2 via induction of spike trimer dimers conformation

The Potential of Nanobodies for COVID-19 Diagnostics and Therapeutics

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