The Free Fatty Acid-Binding Pocket is a Conserved Hallmark in Pathogenic β-Coronavirus Spike Proteins from SARS-CoV to Omicron

Toelzer, Christine; Gupta, Kapil; Yadav, Sathish K. N.; Hodgson, Lorna; Williamson, Maia Kavanagh; Buzas, Dora; Borucu, Ufuk; Powers, Kyle T.; Stenner, Richard; Vasileiou, Kate; Garzoni, Frédéric; Fitzgerald, Daniel J.; Payré, Christine; Lambeau, Gérard; Davidson, Andrew D.; Verkade, Paul; Frank, Martin; Berger, Imre; Schaffitzel, Christiane

doi:10.1101/2022.04.22.489083

Cited by 4 publications

(13 citation statements)

References 57 publications

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Section: Discussionmentioning

confidence: 82%

“…S10 ). Of note, during preparation of this manuscript, a preprint reported a subpopulation of purified insect cell expressed (presumably expressed in low-pH insect cell media) SARS-CoV-1 spike ectodomain adopted a locked-2 conformation with lipid bound in RBD (Toelzer et al , 2022). We speculate that unlike SARS-CoV-2 S, where Domain D-loops are disordered in closed and open conformations, breaking interactions involving the ordered Domain D-loops in closed and open conformations represents a barrier to revert closed/open spike to locked conformations for SARS-CoV-1 S. This difference reflects how changes in Domain D may affect dynamics of Sarbecovirus spikes.…”

Section: Discussionmentioning

confidence: 99%

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Disulfide stabilization reveals conserved dynamic features between SARS-CoV-1 and SARS-CoV-2 spikes

Zhang

et al. 2022

Preprint

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SARS-CoV-2 spike protein (S) is structurally dynamic and has been observed by cryo-EM to adopt a variety of prefusion conformations that can be categorized as locked, closed and open. The locked conformations feature tightly packed trimers with structural elements incompatible with RBD in "up" position. For SARS-CoV-2 S, it has been shown that the locked conformations are transient under neutral pH. Probably due to their transience, locked conformations remain largely uncharacterized for SARS-CoV-1 S. Intriguingly, locked conformations were the only conformations captured for S proteins of bat and pangolin origin SARS-related coronaviruses. In this study, we introduced x1, x2, and x3 disulfides into SARS-CoV-1 S. Some of these disulfides have been shown to preserve rare locked conformations when introduced to SARS-CoV-2 S. Introduction of these disulfides allowed us to image a variety of locked and other rare conformations for SARS-CoV-1 S by cryo-EM. We identified bound cofactors and structural features that are associated with SARS-CoV-1 S locked conformations. We compare newly determined structures to other available spike structures of Sarbecoviruses to identify conserved features and discuss their possible functions.

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Section: Discussionmentioning

confidence: 82%

Section: Discussionmentioning

confidence: 99%

Disulfide stabilization reveals conserved dynamic features between SARS-CoV-1 and SARS-CoV-2 spikes

Zhang

et al. 2022

Preprint

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“…The crystal structure of HKU1-hCoV spike RBD indicates that the entrance to the hydrophobic pocket is obstructed by a glutamate residue (Ou et al, 2017). Notably, mutation of the glutamate residue to an alanine at the pocket entrance restores LA binding (Toelzer et al, 2022). Cryo-EM structures of OC43-hCoV spike also showed a hydrophobic pocket within the B domain, but it appears to be spatially too restricted to allow LA binding (Tortorici et al, 2019;Bangaru et al, 2022).…”

Section: Evolutionary Conservation Of La Binding To the Hydrophobic P...mentioning

confidence: 98%

“…Sequence alignments of spike proteins of the other human betacoronaviruses SARS-CoV, MERS-CoV, HKU1-hCoV and OC43-hCoV indicated that the hydrophobic pocket in the RBD (named the B domain in HKU1-hCoV and OC43-hCoV) is conserved (Toelzer et al, 2020). Importantly, the pocket is also conserved in all SARS-CoV-2 variants of concern (VOCs) to date, including the current VOC Omicron (Toelzer et al, 2022). Using surface plasmon resonance, betacoronavirus spike RBD proteins were tested for LA binding.…”

Section: Evolutionary Conservation Of La Binding To the Hydrophobic P...mentioning

confidence: 99%

“…It was shown that the highly pathogenic SARS-CoV, MERS-CoV and SARS-CoV-2 VOCs indeed bind LA with similar affinity as wild-type SARS-CoV-2 (Wuhan). In marked contrast, HKU1-hCoV, which causes a common cold, has a hydrophobic pocket in the spike RBD but cannot bind LA (Toelzer et al, 2022). The crystal structure of HKU1-hCoV spike RBD indicates that the entrance to the hydrophobic pocket is obstructed by a glutamate residue (Ou et al, 2017).…”

Section: Evolutionary Conservation Of La Binding To the Hydrophobic P...mentioning

confidence: 99%

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Cryo-EM reveals binding of linoleic acid to SARS-CoV-2 spike glycoprotein, suggesting an antiviral treatment strategy

Toelzer¹,

Gupta²,

Berger³

et al. 2023

Acta Cryst Sect D Struct Biol

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The COVID-19 pandemic and concomitant lockdowns presented a global health challenge and triggered unprecedented research efforts to elucidate the molecular mechanisms and pathogenicity of SARS-CoV-2. The spike glycoprotein decorating the surface of SARS-CoV-2 virions is a prime target for vaccine development, antibody therapy and serology as it binds the host cell receptor and is central for viral cell entry. The electron cryo-microscopy structure of the spike protein revealed a hydrophobic pocket in the receptor-binding domain that is occupied by an essential fatty acid, linoleic acid (LA). The LA-bound spike protein adopts a non-infectious locked conformation which is more stable than the infectious form and shields important immunogenic epitopes. Here, the impact of LA binding on viral infectivity and replication, and the evolutionary conservation of the pocket in other highly pathogenic coronaviruses, including SARS-CoV-2 variants of concern (VOCs), are reviewed. The importance of LA metabolic products, the eicosanoids, in regulating the human immune response and inflammation is highlighted. Lipid and fatty-acid binding to a hydrophobic pocket in proteins on the virion surface appears to be a broader strategy employed by viruses, including picornaviruses and Zika virus. Ligand binding stabilizes their protein structure and assembly, and downregulates infectivity. In the case of rhinoviruses, this has been exploited to develop small-molecule antiviral drugs that bind to the hydrophobic pocket. The results suggest a COVID-19 antiviral treatment based on the LA-binding pocket.

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Therapeutic strategy targeting host lipolysis limits infection by SARS-CoV-2 and influenza A virus

Baek

Kwon

Sharif

et al. 2022

Sig Transduct Target Ther

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The biosynthesis of host lipids and/or lipid droplets (LDs) has been studied extensively as a putative therapeutic target in diverse viral infections. However, directly targeting the LD lipolytic catabolism in virus-infected cells has not been widely investigated. Here, we show the linkage of the LD-associated lipase activation to the breakdown of LDs for the generation of free fatty acids (FFAs) at the late stage of diverse RNA viral infections, which represents a broad-spectrum antiviral target. Dysfunction of membrane transporter systems due to virus-induced cell injury results in intracellular malnutrition at the late stage of infection, thereby making the virus more dependent on the FFAs generated from LD storage for viral morphogenesis and as a source of energy. The replication of SARS-CoV-2 and influenza A virus (IAV), which is suppressed by the treatment with LD-associated lipases inhibitors, is rescued by supplementation with FFAs. The administration of lipase inhibitors, either individually or in a combination with virus-targeting drugs, protects mice from lethal IAV infection and mitigates severe lung lesions in SARS-CoV-2-infected hamsters. Moreover, the lipase inhibitors significantly reduce proinflammatory cytokine levels in the lungs of SARS-CoV-2- and IAV-challenged animals, a cause of a cytokine storm important for the critical infection or mortality of COVID-19 and IAV patients. In conclusion, the results reveal that lipase-mediated intracellular LD lipolysis is commonly exploited to facilitate RNA virus replication and furthermore suggest that pharmacological inhibitors of LD-associated lipases could be used to curb current COVID-19- and future pandemic outbreaks of potentially troublesome RNA virus infection in humans.

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The Free Fatty Acid-Binding Pocket is a Conserved Hallmark in Pathogenic β-Coronavirus Spike Proteins from SARS-CoV to Omicron

Cited by 4 publications

References 57 publications

Disulfide stabilization reveals conserved dynamic features between SARS-CoV-1 and SARS-CoV-2 spikes

Disulfide stabilization reveals conserved dynamic features between SARS-CoV-1 and SARS-CoV-2 spikes

Cryo-EM reveals binding of linoleic acid to SARS-CoV-2 spike glycoprotein, suggesting an antiviral treatment strategy

Therapeutic strategy targeting host lipolysis limits infection by SARS-CoV-2 and influenza A virus

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