A Tethered Ligand Assay to Probe the SARS-CoV-2 ACE2 Interaction under Constant Force

Bauer, Magnus S.; Gruber, Sophia; Milles, Lukas F.; Nicolaus, Thomas; Schendel, Leonard C.; Gaub, Hermann E.; Lipfert, Jan

doi:10.1101/2020.09.27.315796

Cited by 8 publications

(6 citation statements)

References 69 publications

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“…The structure of the RBD–ACE2 complex showed that extensive interactions are formed between RBD and ACE2 ( Lu et al, 2020 ; Bauer et al, 2020 ). To understand the potential role of the RBD mutations in binding to ACE2, we combined a cell-surface-binding assay, a kinetics study, a single-molecule biophysical method, and steered molecular dynamics (SMD) simulations to study the interaction of RBD mutants and ACE2 ( Figure 1D,E ).…”

Section: Introductionmentioning

confidence: 99%

N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2

Tian

Tong

Sun

et al. 2021

eLife

299

220

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SARS-CoV-2 has been spreading around the world for the past year. Recently, several variants such as B.1.1.7 (alpha), B.1.351 (beta), and P.1 (gamma), which share a key mutation N501Y on the receptor-binding domain (RBD), appear to be more infectious to humans. To understand the underlying mechanism, we used a cell surface-binding assay, a kinetics study, a single-molecule technique, and a computational method to investigate the interaction between these RBD (mutations) and ACE2. Remarkably, RBD with the N501Y mutation exhibited a considerably stronger interaction, with a faster association rate and a slower dissociation rate. Atomic force microscopy (AFM)-based single-molecule force microscopy (SMFS) consistently quantified the interaction strength of RBD with the mutation as having increased binding probability and requiring increased unbinding force. Molecular dynamics simulations of RBD–ACE2 complexes indicated that the N501Y mutation introduced additional π-π and π-cation interactions that could explain the changes observed by force microscopy. Taken together, these results suggest that the reinforced RBD–ACE2 interaction that results from the N501Y mutation in the RBD should play an essential role in the higher rate of transmission of SARS-CoV-2 variants, and that future mutations in the RBD of the virus should be under surveillance.

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Section: Introductionmentioning

confidence: 99%

N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2

Tian

Tong

Sun

et al. 2021

eLife

299

220

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“…The presence of mucin also does not impair the binding of the polymer. In turn, one could predict that the dissociation constant for polyP is even lower than the KD value of the RBD to the cellular ACE2 receptor, which is in the range of ~ 1-100 nM [167]. A cartoon about the binding of mucin-polyP coacervate on the surface of the SARS-CoV-2 is given in Figure 7.I.E-F.…”

Section: Interaction With Mucinmentioning

confidence: 99%

The therapeutic potential of inorganic polyphosphate: A versatile physiological polymer to control coronavirus disease (COVID-19)

Schepler¹,

Wang²,

Neufurth³

et al. 2021

Theranostics

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Rationale:The pandemic caused by the novel coronavirus SARS-CoV-2 is advancing rapidly. In particular, the number of severe courses of the disease is still dramatically high. An efficient drug therapy that helps to improve significantly the fatal combination of damages in the airway epithelia, in the extensive pulmonary microvascularization and finally multiorgan failure, is missing. The physiological, inorganic polymer, polyphosphate (polyP) is a molecule which could prevent the initial phase of the virus life cycle, the attachment of the virus to the target cells, and improve the epithelial integrity as well as the mucus barrier. Results: Surprisingly, polyP matches perfectly with the cationic groove on the RBD. Subsequent binding studies disclosed that polyP, with a physiological chain length of 40 phosphate residues, abolishes the binding propensity of the RBD to the ACE2 receptor. In addition to this first mode of action of polyP, this polymer causes in epithelial cells an increased gene expression of the major mucins in the airways, of MUC5AC and MUC1, as well as a subsequent glycoprotein production. MUC5AC forms a gel-like mucus layer trapping inhaled particles which are then transported out of the airways, while MUC1 constitutes the periciliary liquid layer and supports ciliary beating. As a third mode of action, polyP undergoes enzymatic hydrolysis of the anhydride bonds in the airway system by alkaline phosphatase, releasing metabolic energy. Conclusions: This review summarizes the state of the art of the biotherapeutic potential of the polymer polyP and the findings from basic research and outlines future biomedical applications.

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“…For instance, the characterization of the mechanical stability of the RBD of Acute Respiratory Syndrome-novel Coronavirus 2 (SARS-CoV-2) has shown it to be stiffer (greater by 50 pN) compared to SARS-CoV [16]. This result has important consequences during binding to ACE2 (pre-fusion state) [17], as it can withstand Brownian and cellular forces and yet maintains close contact while priming of the spike protein by transmembrane protease serine 2 (TMPRSS2) occurs as part of S1 dissociation from S2 that enables the post-fusion mechanism [17,18]. In addition, in silico studies found a space correlation between the polybasic furin cleavage site Q 677 TNSPRRAR↓SV 687 and surface residues located in the RBD region that recognize the ACE2 in SARS-CoV-2.…”

Section: Introductionmentioning

confidence: 99%

Characterization of Structural and Energetic Differences between Conformations of the SARS-CoV-2 Spike Protein

et al. 2020

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The novel coronavirus disease 2019 (COVID-19) pandemic has disrupted modern societies and their economies. The resurgence in COVID-19 cases as part of the second wave is observed across Europe and the Americas. The scientific response has enabled a complete structural characterization of the Severe Acute Respiratory Syndrome—novel Coronavirus 2 (SARS-CoV-2). Among the most relevant proteins required by the novel coronavirus to facilitate the cell entry mechanism is the spike protein. This protein possesses a receptor-binding domain (RBD) that binds the cellular angiotensin-converting enzyme 2 (ACE2) and then triggers the fusion of viral and host cell membranes. In this regard, a comprehensive characterization of the structural stability of the spike protein is a crucial step to find new therapeutics to interrupt the process of recognition. On the other hand, it has been suggested that the participation of more than one RBD is a possible mechanism to enhance cell entry. Here, we discuss the protein structural stability based on the computational determination of the dynamic contact map and the energetic difference of the spike protein conformations via the mapping of the hydration free energy by the Poisson–Boltzmann method. We expect our result to foster the discussion of the number of RBD involved during recognition and the repurposing of new drugs to disable the recognition by discovering new hotspots for drug targets apart from the flexible loop in the RBD that binds the ACE2.

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A Tethered Ligand Assay to Probe the SARS-CoV-2 ACE2 Interaction under Constant Force

Cited by 8 publications

References 69 publications

N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2

N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2

The therapeutic potential of inorganic polyphosphate: A versatile physiological polymer to control coronavirus disease (COVID-19)

Characterization of Structural and Energetic Differences between Conformations of the SARS-CoV-2 Spike Protein

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