A Functional Interaction Between the SARS-CoV-2 Spike Protein and the Human α7 Nicotinic Receptor

Abstract Coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Infection relies on the binding of the viral spike protein (S) to angiotensin-converting enzyme 2 in host cells. The S protein has been suggested to interact with nicotinic acetylcholine receptors (nAChRs), and a potential contribution of nAChRs to COVID-19 pathophysiology has been proposed. α7 nAChR is an interesting candidate target since it is present in neuronal and non-neuronal cells, including immune cells, and has anti-inflammatory actions. We here identified a novel direct functional interaction between the α7 nAChR and the Y674-R685 S region. The S fragment exerts a dual effect, acting as a low-efficacy agonist and a non-competitive inhibitor. It activates the α7 nAChR, in line with our previous molecular dynamics simulations showing favorable binding of this accessible region of the S protein to the nAChR agonist binding pocket. However, activation requires the presence of positive allosteric modulators that enhance channel opening probability, indicating very low activation efficacy. The S fragment also induces an overlapped non-competitive inhibition, which may be the predominant effect on α7 responses. This study provides unequivocal evidence supporting a functional α7-S protein interaction, which opens doors for exploring the involvement of nAChRs in COVID-19 pathophysiology.

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Simulations support the interaction of the SARS-CoV-2 spike protein with nicotinic acetylcholine receptors

10.1101/2020.07.16.206680 ◽

2020 ◽

Cited By ~ 3

Author(s):

A. Sofia F. Oliveira ◽

Amaurys Avila Ibarra ◽

Isabel Bermudez ◽

Lorenzo Casalino ◽

Zied Gaieb ◽

...

Keyword(s):

Binding Energy ◽

Nicotinic Acetylcholine Receptors ◽

Acetylcholine Receptors ◽

Binding Pocket ◽

Spike Protein ◽

Receptor Subtype ◽

Nicotinic Acetylcholine ◽

S Protein ◽

Open Conformation ◽

Potential Binding

AbstractChangeux et al. recently suggested that the SARS-CoV-2 spike (S) protein may interact with nicotinic acetylcholine receptors (nAChRs). Such interactions may be involved in pathology and infectivity. Here, we use molecular simulations of validated atomically detailed structures of nAChRs, and of the S protein, to investigate this ‘nicotinic hypothesis’. We examine the binding of the Y674-R685 loop of the S protein to three nAChRs, namely the human α4β2 and α7 subtypes and the muscle-like αβγd receptor from Tetronarce californica. Our results indicate that Y674-R685 has affinity for nAChRs and the region responsible for binding contains the PRRA motif, a four-residue insertion not found in other SARS-like coronaviruses. In particular, R682 has a key role in the stabilisation of the complexes as it forms interactions with loops A, B and C in the receptor’s binding pocket. The conformational behaviour of the bound Y674-R685 region is highly dependent on the receptor subtype, adopting extended conformations in the α4β2 and α7 complexes and more compact ones when bound to the muscle-like receptor. In the α4β2 and αβγd complexes, the interaction of Y674-R685 with the receptors forces the loop C region to adopt an open conformation similar to other known nAChR antagonists. In contrast, in the α7 complex, Y674-R685 penetrates deeply into the binding pocket where it forms interactions with the residues lining the aromatic box, namely with TrpB, TyrC1 and TyrC2. Estimates of binding energy suggest that Y674-R685 forms stable complexes with all three nAChR subtypes. Analyses of the simulations of the full-length S protein show that the Y674-R685 region is accessible for binding, and suggest a potential binding orientation of the S protein with nAChRs.

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Repurposing Therapeutics for COVID-19: Supercomputer-Based Docking to the SARS-CoV-2 Viral Spike Protein and Viral Spike Protein-Human ACE2 Interface

10.26434/chemrxiv.11871402.v3 ◽

2020 ◽

Cited By ~ 13

Author(s):

Micholas Smith ◽

Jeremy C. Smith

Keyword(s):

Small Molecules ◽

High Throughput Screening ◽

Protein S ◽

Host Cells ◽

Spike Protein ◽

The Novel ◽

S Protein ◽

Host Virus Interactions ◽

Virus Interactions ◽

Ranked List

The novel Wuhan coronavirus (SARS-CoV-2) has been sequenced, and the virus shares substantial similarity with SARS-CoV. Here, using a computational model of the spike protein (S-protein) of SARS-CoV-2 interacting with the human ACE2 receptor, we make use of the world's most powerful supercomputer, SUMMIT, to enact an ensemble docking virtual high-throughput screening campaign and identify small-molecules which bind to either the isolated Viral S-protein at its host receptor region or to the S protein-human ACE2 interface. We hypothesize the identified small-molecules may be repurposed to limit viral recognition of host cells and/or disrupt host-virus interactions. A ranked list of compounds is given that can be tested experimentally.<br>

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Repurposing Therapeutics for COVID-19: Supercomputer-Based Docking to the SARS-CoV-2 Viral Spike Protein and Viral Spike Protein-Human ACE2 Interface

10.26434/chemrxiv.11871402.v4 ◽

2020 ◽

Cited By ~ 26

Author(s):

Micholas Smith ◽

Jeremy C. Smith

Keyword(s):

Small Molecules ◽

High Throughput Screening ◽

Protein S ◽

Host Cells ◽

Spike Protein ◽

The Novel ◽

S Protein ◽

Host Virus Interactions ◽

Virus Interactions ◽

Ranked List

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Deletion of ER-retention motif on SARS-CoV-2 spike protein reduces cell hybrid during cell–cell fusion

Cell & Bioscience ◽

10.1186/s13578-021-00626-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Xuening Wang ◽

Chih-Hsiung Chen ◽

Saiaditya Badeti ◽

Jong Hyun Cho ◽

Alireza Naghizadeh ◽

...

Keyword(s):

Cell Fusion ◽

Cell Lines ◽

Cell Hybrid ◽

Host Cells ◽

Spike Protein ◽

Expression Vectors ◽

S Protein ◽

Er Retention ◽

Syncytia Formation ◽

Cell Cell

Abstract Background The novel SARS-CoV-2 has quickly become a global pandemic since the first reported case in December 2019, with the virus infecting millions of people to date. The spike (S) protein of the SARS-CoV-2 virus plays a key role in binding to angiotensin-converting enzyme 2 (ACE2), a host cell receptor for SARS-CoV-2. S proteins that are expressed on the cell membrane can initiate receptor-dependent syncytia formation that is associated with extensive tissue damage. Formation of syncytia have been previously observed in cells infected with various other viruses (e.g., HIV, Ebola, Influenza, and Herpesviruses). However, this phenomenon is not well documented and the mechanisms regulating the formation of the syncytia by SARS-CoV-2 are not fully understood. Results In this study, we investigated the possibility that cell fusion events mediated by the S protein of SARS-CoV-2 and ACE2 interaction can occur in different human cell lines that mimic different tissue origins. These cell lines were transduced with either wild-type (WT-S) S protein or a mutated variant where the ER-retention motif was removed (Δ19-S), as well as human ACE2 expression vectors. Different co-culture combinations of spike-expressing 293T, A549, K562, and SK-Hep1 cells with hACE2-expressing cells revealed cell hybrid fusion. However, only certain cells expressing S protein can form syncytial structures as this phenomenon cannot be observed in all co-culture combinations. Thus, SARS-CoV-2 mediated cell–cell fusion represents a cell type-dependent process which might rely on a different set of parameters. Recently, the Δ19-S variant is being widely used to increase SARS-CoV-2 pseudovirus production for in vitro assays. Comparison of cell fusion occurring via Δ19-S expressing cells shows defective nuclear fusion and syncytia formation compared to WT-S. Conclusions This distinction between the Δ19-S variant and WT-S protein may have downstream implications for studies that utilize pseudovirus-based entry assays. Additionally, this study suggest that spike protein expressed by vaccines may affect different ACE2-expressing host cells after SARS-CoV-2 vaccine administration. The long-term effects of these vaccines should be monitored carefully. Δ19-S mRNA may represent a safer mRNA vaccine design in the future.

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The Spike of SARS-CoV-2: Uniqueness and Applications

Frontiers in Immunology ◽

10.3389/fimmu.2021.663912 ◽

2021 ◽

Vol 12 ◽

Author(s):

Ranjith Kumavath ◽

Debmalya Barh ◽

Bruno Silva Andrade ◽

Madangchanok Imchen ◽

Flavia Figueira Aburjaile ◽

...

Keyword(s):

Vaccine Development ◽

Point Of Care ◽

Meta Analysis ◽

Host Cells ◽

Spike Protein ◽

Detection Methods ◽

S Protein ◽

Recent Advances ◽

Research Findings ◽

Effect Transistor

The Spike (S) protein of the SARS-CoV-2 virus is critical for its ability to attach and fuse into the host cells, leading to infection, and transmission. In this review, we have initially performed a meta-analysis of keywords associated with the S protein to frame the outline of important research findings and directions related to it. Based on this outline, we have reviewed the structure, uniqueness, and origin of the S protein of SARS-CoV-2. Furthermore, the interactions of the Spike protein with host and its implications in COVID-19 pathogenesis, as well as drug and vaccine development, are discussed. We have also summarized the recent advances in detection methods using S protein-based RT-PCR, ELISA, point‐of‐care lateral flow immunoassay, and graphene-based field-effect transistor (FET) biosensors. Finally, we have also discussed the emerging Spike mutants and the efficacy of the Spike-based vaccines against those strains. Overall, we have covered most of the recent advances on the SARS-CoV-2 Spike protein and its possible implications in countering this virus.

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Deletion of ER-retention Motif on SARS-CoV-2 Spike Protein Reduces Cell Hybrid During Cell-cell Fusion

10.21203/rs.3.rs-380389/v1 ◽

2021 ◽

Author(s):

Chih-Hsiung Chen ◽

Saiaditya Badeti ◽

Jong Hyun Cho ◽

Alireza Naghizadeh ◽

Xuening Wang ◽

...

Keyword(s):

Cell Fusion ◽

Cell Lines ◽

Cell Hybrid ◽

Host Cells ◽

Spike Protein ◽

In Vitro Assays ◽

S Protein ◽

Er Retention ◽

Syncytia Formation ◽

Cell Cell

Abstract The novel SARS-CoV-2 has quickly become a global pandemic since the first reported case in December 2019, with the virus infecting millions of people to date. The spike (S) protein of the SARS-CoV-2 virus plays a key role in binding to angiotensin-converting enzyme 2 (ACE2), a host cell receptor for SARS-CoV-2. S proteins that are expressed on the cell membrane can initiate receptor-dependent syncytia formation that is associated with extensive tissue damage. Formation of syncytia have been previously observed in cells infected with various other viruses (e.g., HIV, Ebola, Influenza, and Herpesviruses). However, this phenomenon is not well documented and the mechanisms regulating the formation of these syncytia by SARS-CoV-2 are not fully understood. In this study, we investigated the possibility that cell fusion events mediated by the S protein of SARS-CoV-2 and ACE2 interaction can occur in different human cell lines that mimic different tissue origins. These cell lines were stably transduced with either wild-type (WT-S) S protein or a mutated variant where the ER-retention motif was removed (Δ19-S), or human ACE2 vectors. Different co-culture combinations of spike-expressing 293T, A549, K562, and SK-Hep1 cells with hACE2-expressing cells revealed cell hybrid fusion. However, only certain cells expressing S protein can form syncytial structures as this phenomenon cannot be observed in all co-culture combinations. Thus, SARS-CoV-2 mediated cell-cell fusion represents a cell type-dependent process which might rely on a different set of parameters. Recently, the Δ19-S variant is being widely used to increase SARS-CoV-2 pseudovirus production for in vitro assays. Comparison of cell fusion occurring via Δ19-S expressing cells shows defective nuclear fusion and syncytia formation compared to WT-S. This distinction between the Δ19-S variant and WT-S protein may have downstream implications for studies that utilize pseudovirus-based entry assays. Additionally, this study suggest that spike protein expressed by vaccines may affect different ACE2-expressing host cells after SARS-CoV-2 vaccine administration. The long-term effects of these vaccines should be monitored carefully.

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Evolutionary Origin of SARS-CoV-2 (COVID-19 Virus) and SARS Viruses through the Identification of Novel Protein/DNA Sequence Features Specific for Different Clades of Sarbecoviruses

10.20944/preprints202006.0165.v1 ◽

2020 ◽

Author(s):

Radhey S. Gupta ◽

Bijendra Khadka

Keyword(s):

Host Cells ◽

Spike Protein ◽

The Novel ◽

Terminal Sequence ◽

S Protein ◽

Origin And Evolution ◽

Novel Interactions ◽

Surface Loops ◽

Relationship Of ◽

Novel Protein

Both SARS-CoV-2 (COVID-19) and SARS coronaviruses (CoVs) are members of the subgenus Sarbecovirus. To understand the origin of SARS-CoV-2 and its relation to other viruses, protein sequences from sarbecoviruses were analyzed to identify conserved inserts or deletions (termed CSIs) demarcating either particular clusters/lineages of sarbecoviruses or those shared by specific lineages shedding light on their interrelationships. We report several clade-specific CSIs in the spike (S) and nucleocapsid (N) proteins that reliably demarcate distinct sarbecoviruses clades providing important insights into the origin and evolution of SARS-CoV-2. Two CSIs in the N-terminal domain (NTD) of S-protein are uniquely shared by SARS-CoV-2, BatCoV-RaTG13 and most pangolin CoVs (SARS-CoV-2r cluster); another CSI supports a closer relationship of SARS-CoV-2 to BatCov-RaTG13. Three additional CSIs in the NTD are specific for two Bat-SARS-like CoVs (viz. CoVZXC21 and CoVZC45; CoVZC cluster) which form an outgroup of the SARS-CoV-2r cluster. Interestingly, one of the pangolin-CoV-MP789 also shares these CSIs but lack the CSIs specific for the SARS-CoV-2r cluster. The N-terminal sequence (aa 1-320) of the S-protein for pangolin-CoV-MP789 shows highest similarity (85.94%) to the CoVZC cluster, while its C-terminal region including the receptor binding domain (RBD) is most similar (97-98% identity) to the SARS-CoV-2 virus. These observations indicate that the spike protein sequence for the strain MP789 is of chimeric origin. Multiple CSIs described here also distinguish two bat SARS-CoVs strains (BM48-31/BGR/2008 and SARS_BtKY72) from all others. Our work also clarifies that two large CSIs (5 aa and 13 aa) found in the RBD of S-protein are mainly specific for the SARS and SARS-CoV-2r clusters of CoVs. The surface loops formed by these CSIs are predicted to be important in the binding of S-protein with the human ACE-2 receptor. Lastly, we have mapped the locations of different CSIs in the structure of the S-protein. These studies reveal that the three CSIs specific for the SARS-CoV-2r cluster form distinct surface-exposed loops/patches on the S-protein. As the surface-exposed loops play important roles in mediating novel interactions, the novel lobes/patches formed by the SARS-CoV-2-specific CSIs in the spike protein are predicted to play important roles in the interaction of this protein with other surface-exposed components in the host cells thereby enhancing the binding/infectivity of this virus to humans.

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The antidepressant drug vilazodone is an allosteric inhibitor of the serotonin transporter

Nature Communications ◽

10.1038/s41467-021-25363-3 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Per Plenge ◽

Dongxue Yang ◽

Kristine Salomon ◽

Louise Laursen ◽

Iris E. Kalenderoglou ◽

...

Keyword(s):

Serotonin Transporter ◽

Selective Serotonin Reuptake Inhibitors ◽

Competitive Inhibition ◽

Common Mental Disorder ◽

Antidepressant Drug ◽

Binding Pocket ◽

Competitive Inhibitor ◽

Limited Information ◽

Allosteric Site ◽

Binding Characteristics

AbstractDepression is a common mental disorder. The standard medical treatment is the selective serotonin reuptake inhibitors (SSRIs). All characterized SSRIs are competitive inhibitors of the serotonin transporter (SERT). A non-competitive inhibitor may produce a more favorable therapeutic profile. Vilazodone is an antidepressant with limited information on its molecular interactions with SERT. Here we use molecular pharmacology and cryo-EM structural elucidation to characterize vilazodone binding to SERT. We find that it exhibits non-competitive inhibition of serotonin uptake and impedes dissociation of [3H]imipramine at low nanomolar concentrations. Our SERT structure with bound imipramine and vilazodone reveals a unique binding pocket for vilazodone, expanding the boundaries of the extracellular vestibule. Characterization of the binding site is substantiated with molecular dynamics simulations and systematic mutagenesis of interacting residues resulting in decreased vilazodone binding to the allosteric site. Our findings underline the versatility of SERT allosteric ligands and describe the unique binding characteristics of vilazodone.

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Metabolism of an Alkyl Polyamine Analog by a Polyamine Oxidase from the Microsporidian Encephalitozoon cuniculi

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00267-08 ◽

2009 ◽

Vol 53 (6) ◽

pp. 2599-2604 ◽

Cited By ~ 6

Author(s):

Cyrus J. Bacchi ◽

Nigel Yarlett ◽

Evangeline Faciane ◽

Xiangdong Bi ◽

Donna Rattendi ◽

...

Keyword(s):

Oxidase Activity ◽

Competitive Inhibition ◽

Amine Oxidase ◽

Reaction Rates ◽

Competitive Inhibitor ◽

Host Cells ◽

Nuclear Magnetic Resonance Analysis ◽

Encephalitozoon Cuniculi ◽

Resonance Analysis ◽

Polyamine Analog

ABSTRACT Encephalitozoon cuniculi is a microsporidium responsible for systemic illness in mammals. In the course of developing leads to new therapy for microsporidiosis, we found that a bis(phenylbenzyl)3-7-3 analog of spermine, 1,15-bis{N-[o-(phenyl)benzylamino}-4,12-diazapentadecane (BW-1), was a substrate for an E. cuniculi amine oxidase activity. The primary natural substrate for this oxidase activity was N′-acetylspermine, but BW-1 had activity comparable to that of the substrate. As the sole substrate, BW-1 gave linear reaction rates over 15 min and K m of 2 μM. In the presence of N′-acetylspermine, BW-1 acted as a competitive inhibitor of oxidase activity and may be a subversive substrate, resulting in increased peroxide production. By use of 13C-labeled BW-1 as a substrate and nuclear magnetic resonance analysis, two products were determined to be oxidative metabolites, a hydrated aldehyde or dicarboxylate and 2(phenyl)benzylamine. These products were detected after exposure of 13C-labeled BW-1 to E. cuniculi preemergent spore preparations and to uninfected host cells. In previous studies, BW-1 was curative in a rodent model of infection with E. cuniculi. The results in this study demonstrate competitive inhibition of oxidase activity by BW-1 and support further studies of this oxidase activity by the parasite and host.

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