Binding mechanism of neutralizing Nanobodies targeting SARS-CoV-2 Spike Glycoprotein

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Gür

2021

Preprint

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The Omicron variant (B.1.1.529) comprises 30 mutations on the spike glycoprotein (S), 15 of which are located on its receptor-binding domain (RBD_Omicron). RBD interacts with the peptidase domain (PD) of angiotensin-converting enzyme 2 (ACE2) receptors and plays a critical role in the host cell entry of the virus. We performed all-atom simulations of the RBD_Omicron-PD in the presence of explicit water and ions. Simulations showed a considerably more extensive interactions network between RBD_Omicron and PD compared to RBD_WT, comprising a 250%, 10% and -25% change in the total number of salt bridges, hydrophobic interactions, hydrogen bonds at the S-ACE2 interface, respectively. Using the conformations sampled in each our MD trajectories, binding energies of two sets of RBD_WT-PD and four sets of RBD_Omicron-PD simulations were calculated via the Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) method, estimating ~44% stronger binding energy for RBD_Omicron compared to RBD_WT. Our results suggest that an increase in the number of salt bridges in the S-ACE2 interface result in a higher binding strength of RBD to PD, which may result in a higher efficiency of the SARS-CoV-2 virus to infect host cells. Furthermore, RBD_Omicron exhibits a more dispersed interaction network on both sides of the RBD-PD interaction surface compared to WT.

Section: Methodsmentioning

confidence: 99%

Omicron BA.1 and BA.2 Variants Increase the Interactions of SARS-CoV-2 Spike Glycoprotein with ACE2

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2021

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“…[46][47][48] Observation frequencies were classified as high and moderate for interactions that occur in 49% and above and between 15% and 48% of the total trajectory, respectively. 29,49 All reported changes in interactions frequency classifications due to the Delta mutations were statistically different from that of the WT RBD (Student's t-test, p<0.05). 29,49 Pairwise interactions with observation frequencies below 15% were excluded from further analysis.…”

Section: Simulation Detailsmentioning

confidence: 87%

“…29,49 All reported changes in interactions frequency classifications due to the Delta mutations were statistically different from that of the WT RBD (Student's t-test, p<0.05). 29,49 Pairwise interactions with observation frequencies below 15% were excluded from further analysis. SMD Simulations.…”

Section: Simulation Detailsmentioning

confidence: 87%

“…In addition, H11-H4 was dislocated from its RBD binding pose in all three simulations (Supplementary Movie S2) due to the repulsion of identically charged residues of ACE2 and H11-H4 (ACE2 D67 with H11-H4 E44 and ACE2 K68 with H11-H4 R45, Figure 4) when ACE2 and H11-H4 are bound to RBD side by side. Therefore, while ACE2 loses the electrostatic tug-of-war against H11-H4 to bind RBDWT, 29 it outcompetes H11-H4 on RBDDelta because of its increased and H11-H4's decreased interaction network with the RBD surface in the Delta variant. Electrostatic repulsion between ACE2 and H11-H4 upon H11-H4 docking on (A) RBDWT 29,49 and (B) RBDDelta.…”

Section: Table 1 Net Changes In the Number Of Detected High Frequency...mentioning

confidence: 99%

“…20,[26][27][28] The molecular mechanism underlying loss in antibody and nanobody effectivity have been investigated for various SARS-CoV-2 variants, including Alpha and Beta. [29][30][31] However, the underlying mechanism of the reduced effectiveness of the nanobodies against the Delta variant is not well understood.…”

Section: Introductionmentioning

confidence: 99%

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SARS-Cov-2 Delta Variant Decreases Nanobody Binding and ACE2 Blocking Effectivity

Hacisuleyman

Yilmaz

et al. 2022

Preprint

Self Cite

The Delta variant spreads more rapidly than previous variants of SARS-CoV-2. This variant comprises several mutations on the receptor-binding domain (RBD_Delta) of its spike (S) glycoprotein, which binds to the peptidase domain (PD) of angiotensin-converting enzyme 2 (ACE2) receptors in host cells. The RBD-PD interaction has been targeted by antibodies and nanobodies to prevent viral infection, but their effectiveness against the Delta variant remains unclear. Here, we investigated RBD_Delta-PD interactions in the presence and absence of nanobodies H11-H4, H11-D4, and Ty1 by performing 21.8 µs of all-atom molecular dynamics (MD) simulations. Unbiased simulations revealed that Delta variant mutations strengthen RBD binding to ACE2 by increasing the hydrophobic interactions and salt bridge formation, but weaken interactions with H11-H4, H11-D4, and Ty1. Among these nanobodies H11-H4 and H11-D4 bind RBD without overlapping ACE2. They were unable to dislocate ACE2 from RBD_Delta when bound side by side with ACE2 on RBD. Steered MD simulations at comparable loading rates to atomic force microscopy (AFM) experiments estimated lower rupture forces of the nanobodies from RBD_Delta compared to ACE2. Our results suggest that existing nanobodies are less effective to inhibit RBD_Delta-PD interactions and a new generation of nanobodies will be needed to neutralize the Delta variant.

SARS-CoV-2 Delta Variant Decreases Nanobody Binding and ACE2 Blocking Effectivity

Hacisuleyman

Yilmaz

et al. 2022

J. Chem. Inf. Model.

Self Cite

The Delta variant spreads more rapidly than previous variants of SARS-CoV-2. This variant comprises several mutations on the receptor-binding domain (RBD Delta ) of its spike glycoprotein, which binds to the peptidase domain (PD) of angiotensin-converting enzyme 2 (ACE2) receptors in host cells. The RBD–PD interaction has been targeted by antibodies and nanobodies to prevent viral infection, but their effectiveness against the Delta variant remains unclear. Here, we investigated RBD Delta –PD interactions in the presence and absence of nanobodies H11-H4, H11-D4, and Ty1 by performing 21.8 μs of all-atom molecular dynamics simulations. Unbiased simulations revealed that Delta variant mutations strengthen RBD binding to ACE2 by increasing the hydrophobic interactions and salt bridge formation, but weaken interactions with H11-H4, H11-D4, and Ty1. Among these nanobodies H11-H4 and H11-D4 bind RBD without overlapping ACE2. They were unable to dislocate ACE2 from RBD Delta when bound side by side with ACE2 on RBD. Steered molecular dynamics simulations at comparable loading rates to high-speed atomic force microscopy (AFM) experiments estimated lower rupture forces of the nanobodies from RBD Delta compared to ACE2. Our results suggest that existing nanobodies are less effective to inhibit RBD Delta –PD interactions and a new generation of nanobodies is needed to neutralize the Delta variant.