A library of nucleotide analogues terminate RNA synthesis catalyzed by polymerases of coronaviruses that cause SARS and COVID-19.

SARS-CoV-2, a member of the coronavirus family, is responsible for the current COVID-19 worldwide pandemic. We previously demonstrated that five nucleotide analogues inhibit the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp), including the active triphosphate forms of Sofosbuvir, Alovudine, Zidovudine, Tenofovir alafenamide and Emtricitabine. We report here the evaluation of a library of nucleoside triphosphate analogues with a variety of structural and chemical features as inhibitors of the RdRps of SARS-CoV and SARS-CoV-2. These features include modifications on the sugar (2' or 3' modifications, carbocyclic, acyclic, or dideoxynucleotides) or on the base. The goal is to identify nucleotide analogues that not only terminate RNA synthesis catalyzed by these coronavirus RdRps, but also have the potential to resist the viruses' exonuclease activity. We examined these nucleotide analogues for their ability to be incorporated by the RdRps in the polymerase reaction and to prevent further incorporation. While all 11 molecules tested displayed incorporation, 6 exhibited immediate termination of the polymerase reaction (triphosphates of Carbovir, Ganciclovir, Stavudine and Entecavir; 3'-OMe-UTP and Biotin-16-dUTP), 2 showed delayed termination (Cidofovir diphosphate and 2'-OMe-UTP), and 3 did not terminate the polymerase reaction (2'-F-dUTP, 2'-NH2-dUTP and Desthiobiotin-16-UTP). The coronaviruses possess an exonuclease that apparently requires a 2'-OH at the 3'-terminus of the growing RNA strand for proofreading. In this study, all nucleoside triphosphate analogues evaluated form Watson-Crick-like base pairs. The nucleotide analogues demonstrating termination either lack a 2'-OH, have a blocked 2'-OH, or show delayed termination. Thus, these nucleotide analogues are of interest for further investigation to evaluate whether they can evade the viral exonuclease activity. Prodrugs of five of these nucleotide analogues (Cidofovir, Abacavir, Valganciclovir/Ganciclovir, Stavudine and Entecavir) are FDA-approved medications for treatment of other viral infections, and their safety profiles are well established. After demonstrating potency in inhibiting viral replication in cell culture, candidate molecules can be rapidly evaluated as potential therapies for COVID-19.

Validation of an assay for quantifying ganciclovir in dried blood spots.

Valganciclovir (VGC) is an orally available mono-valyl ester pro drug of the nucleoside analog (NA) ganciclovir (GCV) used to treat cytomegalovirus (CMV). Congenital CMV infection in the newborn is associated with progressive sensorineural hearing loss; however, effective CMV therapy with VGC can improve audiologic outcomes. Ongoing studies to demonstrate the effect of VGC in this setting are hampered by a poor understanding of the pharmacology of VGC and GCV in newborns, and the low blood volumes that can be safely collected from this population. We describe a simple method for determining systemic GCV concentrations using dried blood spot (DBS) samples. GCV was extracted from a single 6 mm punch via sonication in methanol, then quantified using liquid chromatography-tandem mass spectrometry. The assay was accurate and precise in the dynamic range of 10-10,000 ng/mL. GCV concentrations determined in DBS agreed well with GCV concentrations observed in serum. The assay was successfully applied to patient samples, and will be used to support pharmacokinetic studies in an ongoing clinical trial of VGC in infants with CMV-mediated hearing loss.