Drug repurposing screens identify chemical entities for the development of COVID-19 interventions

Abstract

The ongoing pandemic caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), necessitates strategies to identify prophylactic and therapeutic drug candidates for rapid clinical deployment. Here, we describe a screening pipeline for the discovery of efficacious SARS-CoV-2 inhibitors. We screen a best-in-class drug repurposing library, ReFRAME, against two high-throughput, high-content imaging infection assays: one using HeLa cells expressing SARS-CoV-2 receptor ACE2 and the other using lung epithelial Calu-3 cells. From nearly 12,000 compounds, we identify 49 (in HeLa-ACE2) and 41 (in Calu-3) compounds capable of selectively inhibiting SARS-CoV-2 replication. Notably, most screen hits are cell-line specific, likely due to different virus entry mechanisms or host cell-specific sensitivities to modulators. Among these promising hits, the antivirals nelfinavir and the parent of prodrug MK-4482 possess desirable in vitro activity, pharmacokinetic and human safety profiles, and both reduce SARS-CoV-2 replication in an orthogonal human differentiated primary cell model. Furthermore, MK-4482 effectively blocks SARS-CoV-2 infection in a hamster model. Overall, we identify direct-acting antivirals as the most promising compounds for drug repurposing, additional compounds that may have value in combination therapies, and tool compounds for identification of viral host cell targets.

Combination Treatment With Remdesivir and Ivermectin Exerts Highly Synergistic and Potent Antiviral Activity Against Murine Coronavirus Infection

“…For direct comparison versus MHV, future detailed studies are thus warranted to evaluate the potential utility of this drug combination against SARS-CoV-2 and other coronaviruses (e.g. SARS-CoV, MERS-CoV, HCoV-229E, HCoV-OC43), such as multi-dose checkerboard experiments to ascertain additive effects of drugs (Bakowski et al, 2021). This caveat is also critically important given the observations of cell line-dependent compound efficacy against SARS-CoV-2 infection reported in many previous SARS-CoV-2 antiviral studies.…”

Application of Artificial Intelligence in COVID-19 Diagnosis and Therapeutics

“…The fragment-based drug discovery approach facilitates the identification of lead compounds, and their crystallographic screening approach identified 71 hits [82] (Figure 2). For drug repurposing or repositioning, protein-protein interaction networks have been identified by expressing 26 out of 29 SARS-CoV-2 proteins in human cells [83] and two high-throughput repurposing screenings using HeLa cells expressing ACE2 and lung epithelial Calu-3 cell lines [84]. To screen anti-viral drugs for COVID-19, matrix completion techniques have been used to predict the drug-virus association for drug repositioning using a manually curated comprehensive dataset [85].…”

“…This may be due to people intentionally or inadvertently violating policies or infecting others without being detected as infected themselves, resulting in the rapid spread of mild cases worldwide and an increasing number of deaths [98,99]. The progress of the infection has also varied For drug repurposing or repositioning, protein-protein interaction networks have been identified by expressing 26 out of 29 SARS-CoV-2 proteins in human cells [83] and two high-throughput repurposing screenings using HeLa cells expressing ACE2 and lung epithelial Calu-3 cell lines [84]. To screen anti-viral drugs for COVID-19, matrix completion techniques have been used to predict the drug-virus association for drug repositioning using a manually curated comprehensive dataset [85].…”

A Bioluminescent 3CLPro Activity Assay to Monitor SARS-CoV-2 Replication and Identify Inhibitors

“…The reported phenotypic screens used to identify SARS-CoV-2 inhibitors essentially rely on host cell viability as an indicator of viral growth [ 4 , 5 , 6 ], assessing the inhibition of the virus cytopathic effect after multicyclic replication at relatively late timepoints. More direct measures of viral infection by immunostaining and fluorescence imaging have been used but are often more challenging to implement in a format suitable for testing hundreds of molecules and require automated microscopes for data acquisition [ 7 , 8 ]. Interestingly, the SARS-CoV-2 genome encodes a 3C-like protease (3CL Pro ; nsP5) that is responsible for the cis- and trans-processing of the viral polyprotein and the destruction of host protein targets ( Figure 1 A).…”