A new platform for the discovery of antiviral drugs for the treatment of COVID-19

By Martin Michaelis and Mark Wass. This blog refers to a study that was performed in collaboration with researchers from other institutions, in particular with the research group of Jindrich Cinatl (Goethe-University, Frankfurt am Main, Germany; Dr. Petra Joh-Haus, Frankfurt am Main, Germany).

COVID-19 currently causes fewer disruptions to the health services and society than in the past, which is largely due to the immune protection provided by vaccinations and previous infections. However, each new variant, in particular each new Omicron subvariant, becomes better at infecting people who have been vaccinated and/ or infected in the past. Hence, there is concern that a new variant may fill up hospitals again and cause many deaths.

Moreover, there is a substantial number of individuals with immune defects, who cannot protect themselves from COVID-19 via vaccination. These individuals depend on antiviral drugs that inhibit the replication of SARS-CoV-2, the coronavirus that causes COVID-19. Currently, three antiviral drugs (remdesivir, molnupiravir, nirmatrelvir) and a number of antibody preparations are available for the treatment of SARS-CoV-2-infected individuals at high risk of COVID-19.

However, there are concerns that the circulating viruses will develop resistance if antiviral drugs are regularly used. Notably, some of the antibody preparations have already lost their activity against the currently circulating Omicron subvariants. Thus, antiviral drugs will remain relevant for the treatment of COVID-19, and a wide range of different antiviral drugs with different mechanisms of action will be needed to keep COVID-19 at bay.

To facilitate the identification of antiviral drugs for the treatment of COVID-19, we have developed a novel screening platform for anti-SARS-CoV-2 agents that can be widely used by researchers, even those with limited experience of drug screens. The platform is based on a unique cell line (Caco-2-F03) that can be used for all available SARS-CoV-2 isolates (and other coronaviruses). In contrast to other cell lines used for SARS-CoV-2 cultivation, Caco-2-F03 cells did not produce false-positive hits due to a drug-induced process called ‘phospholipidosis’.

As a side effect, our study also explained why there are conflicting data about the SARS-CoV-2-susceptibility of Caco-2 cells. We have used Caco-2 to cultivate SARS-CoV (the virus that caused the SARS outbreak in the early 2000’s) since 2003 and SARS-CoV-2 since 2020. However, other research groups could not effectively propagate these viruses in Caco-2 cells. When we used fresh Caco-2 cell lines from different sources, they were indeed poorly susceptible to SARS-CoV-2, but we were able to establish clonal Caco-2 subpopulations in which SARS-CoV-2 replicated to high titres. Therefore, we seem to have inadvertently generated a Caco-2 cell line, in which the SARS-CoV-2-susceptible cells are enriched. We now call this highly SARS-CoV-2 permissive subline Caco-2-F03.

The study also showed that this new platform can be used to identify resistant virus strains and to identify novel agents that are still effective against resistant viruses. Moreover, it can be used to detect whether an individual has antibodies that protect them from a certain virus variant.

Finally, a proof-of-concept screen of 1796 potential drugs, identified a compound called NCT-503 as an additional drug candidate. In contrast to the already available antiviral drugs, which target viral proteins, NCT-503 targets cellular processes that are only changed in virus-infected cells. Notably, the risk of resistance formation is considered to be reduced for compounds like NCT-503 that have cellular targets.

Now, we hope that our new platform will facilitate, improve, and speed up the discovery of additional drugs for the treatment of COVID-19.


More information on the study:

Title: Identification of novel antiviral drug candidates using an optimized SARS-CoV-2 phenotypic screening platform

Authors: Richard Stack, Mark Wass, Martin Michaelis – University of Kent; Denisa Bojkova, Philipp Reus, Leona Panosch, Marco Bechtel, Tamara Rothenburger, Joshua Kandler, Annika Pfeifer, Julian Wagner, Mariana Shumliakivska, Stefanie Dimmeler, Tuna Toptan, Richard Zehner, Holger Rabenau, Sandra Ciesek, Jindrich Cinatl – Goethe-University Frankfurt; Florian Rothweiler, Dr Petra Joh Research Institute; Ruth Olmer, Ulrich Martin, Julian Vondran – Medizinische Hochschule Hannover; Karen Osman, Steven Pullan – UK Health Security Agency; Miles Carroll – University of Oxford.

Journal iScience.