Exploiting the SARS-CoV-2 nsp14 3'-5'-exoribonuclease as a target for antiviral chemotherapy

Many viruses can mutate, or change, their genetic material rapidly. This means that they can avoid our immune system or become resistant to antiviral drugs. This is not the case for coronaviruses as they possess a protein that corrects the errors made by the virus during the production of new viral genetic material. This also means that they are resistant to some antiviral drugs that work by increasing the rate of mutation, inducing fatal errors. This project will use a computer-based approach to identify drugs that can inhibit this error-correcting protein. The structure of the error-correcting protein is known and we will use sophisticated computer algorithms to screen large collections of drugs to identify those that are able to bind to the protein and block its function. Such drugs could be used in combination with mutation-inducing drugs to effectively prevent the virus from growing and thus have clinical benefit for patients suffering from COVID-19 disease, caused by the SARS-CoV-2 coronavirus

RNA viruses exhibit high mutation rates due to the lack of proof-reading by their RNA-dependent RNA polymerases, imposing a restriction on genome size. In contrast to other positive-strand RNA viruses, coronaviruses have large genomes (~30kb). To ensure high fidelity replication the coronavirus non-structural protein 14 (nsp14) possesses 3'-5'-exoribonuclease (ExoN) activity, which also renders coronaviruses resistant to mutagenic nucleoside analogues (eg ribavirin).
Nsp14 ExoN activity is stimulated by nsp10 binding, and structures of the SARS-CoV nsp14:nsp10 complex have been determined to 3.2Å resolution. Importantly, SARS-CoV and SARS-CoV-2 nsp14:nsp10 exhibit 95% amino-acid conservation, allowing us to build a homology model of SARS-CoV-2 nsp14:nsp10. In conjunction with protein dynamic simulations, this model will be subjected to virtual screening to identify small molecules able to bind to either the ExoN active site, or the nsp14:nsp10 interface. Compounds will be tested in combination with mutagenic nucleoside analogues for effects on the replication of SARS-CoV-2, exploiting in-house BSL-3 containment facilities. Specificity and mode of action of compounds will be confirmed by virological and biochemical assays.
Our priority is to seek existing clinically approved compounds that inhibit the SARS-CoV-2 ExoN, and could be rapidly repurposed to treat SARS-CoV-2 infection. To this end, we will interrogate the DrugBank database of approved or investigational drugs. This will be followed by an expansion of virtual screening to an in-house library, and a ZINC library subset, comprising available drug-like compounds. In the longer term these could lead to early-stage drug discovery to provide further therapeutic options for SARS-CoV-2, or other future emerging coronaviruses.