Identifying SARS-CoV-2 Entry Inhibitors through Drug Repurposing Screens of SARS-S and MERS-S Pseudotyped Particles

Chen, Catherine Z.; Xu, Miao; Pradhan, Manisha; Gorshkov, Kirill; Petersen, Jennifer D.; Straus, Marco R.; Zhu, Wei; Shinn, Paul; Guo, Hui; Shen, Min; Klumpp‐Thomas, Carleen; Michael, Samuel G.; Zimmerberg, Joshua; Zheng, Wei; Whittaker, Gary R.

doi:10.1021/acsptsci.0c00112

Cited by 107 publications

(137 citation statements)

References 42 publications

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“…These include cell cycle inhibitors ABE targeting Cdk4, AZ1 targeting Usp25/28, HAR targeting Dyrk1A, NIN targeting Fgfr1/2/3, and UC2 targeting p21; the endocytosis inhibitor PMZ targeting Wdr81; and the Tbk1 inhibitor AMX. Chen et al recently reported similar activity of ABE against SARS-CoV-2 (31), validating our findings. To our knowledge, the discovery that AMX, AZ1, HAR, NIN, PMZ, and UC2 possess antiviral activity against SARS-CoV-2 has not been reported.…”

Section: Discussionsupporting

confidence: 92%

Genome-scale CRISPR Screens Identify Host Factors that Promote Human Coronavirus Infection

Grodzki

Schäfer

et al. 2021

Preprint

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The COVID-19 pandemic has resulted in 153 million infections and 3.2 million deaths as of May 2021. While effective vaccines are being administered globally, there is still a great need for antiviral therapies as potentially antigenically distinct SARS-CoV-2 variants continue to emerge across the globe. Viruses require host factors at every step in their life cycle, representing a rich pool of candidate targets for antiviral drug design. To identify host factors that promote SARS-CoV-2 infection with potential for broad-spectrum activity across the coronavirus family, we performed genome-scale CRISPR knockout screens in two cell lines (Vero E6 and HEK293T ectopically expressing ACE2) with SARS-CoV-2 and the common cold-causing human coronavirus OC43. While we identified multiple genes and functional pathways that have been previously reported to promote human coronavirus replication, we also identified a substantial number of novel genes and pathways. Of note, host factors involved in cell cycle regulation were enriched in our screens as were several key components of the programmed mRNA decay pathway. Finally, we identified novel candidate antiviral compounds targeting a number of factors revealed by our screens. Overall, our studies substantiate and expand the growing body of literature focused on understanding key human coronavirus-host cell interactions and exploit that knowledge for rational antiviral drug development.

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Section: Discussionsupporting

confidence: 92%

Genome-scale CRISPR Screens Identify Host Factors that Promote Human Coronavirus Infection

Grodzki

Schäfer

et al. 2021

Preprint

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“…Cepharantine was approved in Japan to treat alopecia [ 40 ], which was proposed in the last months as anti-COVID-19 therapy based on theoretical and in vitro results [ 11 ]. Our in silico results showed that cepharantine could be a potential inhibitor of furin and TPC2, being its biological action involved not only in first entry phases but also in the escape from late endosomes, a mechanism that is compatible with the results obtained in the surrogate model of viral entry here presented ( Figure 4 B) and a recently published report [ 41 ]. Moreover, in the last months, cepharantine has been identified as an experimental inhibitor of TPC2 [ 42 ].…”

Section: Discussionsupporting

confidence: 91%

Host-Directed FDA-Approved Drugs with Antiviral Activity against SARS-CoV-2 Identified by Hierarchical In Silico/In Vitro Screening Methods

et al. 2021

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The unprecedent situation generated by the COVID-19 global emergency has prompted us to actively work to fight against this pandemic by searching for repurposable agents among FDA approved drugs to shed light into immediate opportunities for the treatment of COVID-19 patients. In the attempt to proceed toward a proper rationalization of the search for new antivirals among approved drugs, we carried out a hierarchical in silico/in vitro protocol which successfully combines virtual and biological screening to speed up the identification of host-directed therapies against COVID-19 in an effective way. To this end a multi-target virtual screening approach focused on host-based targets related to viral entry, followed by the experimental evaluation of the antiviral activity of selected compounds, has been carried out. As a result, five different potentially repurposable drugs interfering with viral entry—cepharantine, clofazimine, metergoline, imatinib and efloxate—have been identified.

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“…To probe the mechanism of SARS-CoV-2 infection inhibition, we utilized the SARS-CoV-2 spike pseudotyped particle (PP) assay in HEK239T cells stably transfected with ACE2 fused to green fluorescent protein (ACE2-GFP) that are permissive to spike-mediated PP entry and transduction of luciferase. 33 All compounds inhibited PP entry, and while some toxicity was observed as measured by ATP content, the CC 50 /EC 50 ratio, or SI, indicated an efficacy independent of compound toxicity ( Figure 5 , Table 2 ). The data suggested these compounds blocked the cellular entry of SARS-CoV-2 PPs that rely on spike-mediated endocytosis and fusion in ACE2-expressing cells.…”

Section: Resultsmentioning

confidence: 95%

The SARS-CoV-2 Cytopathic Effect Is Blocked by Lysosome Alkalizing Small Molecules

et al. 2020

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Understanding the SARS-CoV-2 virus’ pathways of infection, virus–host–protein interactions, and mechanisms of virus-induced cytopathic effects will greatly aid in the discovery and design of new therapeutics to treat COVID-19. Chloroquine and hydroxychloroquine, extensively explored as clinical agents for COVID-19, have multiple cellular effects including alkalizing lysosomes and blocking autophagy as well as exhibiting dose-limiting toxicities in patients. Therefore, we evaluated additional lysosomotropic compounds to identify an alternative lysosome-based drug repurposing opportunity. We found that six of these compounds blocked the cytopathic effect of SARS-CoV-2 in Vero E6 cells with half-maximal effective concentration (EC 50 ) values ranging from 2.0 to 13 μM and selectivity indices (SIs; SI = CC 50 /EC 50 ) ranging from 1.5- to >10-fold. The compounds (1) blocked lysosome functioning and autophagy, (2) prevented pseudotyped particle entry, (3) increased lysosomal pH, and (4) reduced (ROC-325) viral titers in the EpiAirway 3D tissue model. Consistent with these findings, the siRNA knockdown of ATP6V0D1 blocked the HCoV-NL63 cytopathic effect in LLC-MK2 cells. Moreover, an analysis of SARS-CoV-2 infected Vero E6 cell lysate revealed significant dysregulation of autophagy and lysosomal function, suggesting a contribution of the lysosome to the life cycle of SARS-CoV-2. Our findings suggest the lysosome as a potential host cell target to combat SARS-CoV-2 infections and inhibitors of lysosomal function could become an important component of drug combination therapies aimed at improving treatment and outcomes for COVID-19.

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Identifying SARS-CoV-2 Entry Inhibitors through Drug Repurposing Screens of SARS-S and MERS-S Pseudotyped Particles

Cited by 107 publications

References 42 publications

Genome-scale CRISPR Screens Identify Host Factors that Promote Human Coronavirus Infection

Genome-scale CRISPR Screens Identify Host Factors that Promote Human Coronavirus Infection

Host-Directed FDA-Approved Drugs with Antiviral Activity against SARS-CoV-2 Identified by Hierarchical In Silico/In Vitro Screening Methods

The SARS-CoV-2 Cytopathic Effect Is Blocked by Lysosome Alkalizing Small Molecules

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