Nucleoside Analogs That Inhibit SARS-CoV-2 Replication by Blocking Interaction of Virus Polymerase with RNA

Abstract

The SARS-CoV-2 betacoronavirus pandemic has claimed more than 6.5 million lives and, despite the development and use of COVID-19 vaccines, remains a major global public health problem. The development of specific drugs for the treatment of this disease remains a very urgent task. In the context of a repurposing strategy, we previously screened a library of nucleoside analogs showing different types of biological activity against the SARS-CoV-2 virus. The screening revealed compounds capable of inhibiting the reproduction of SARS-CoV-2 with EC50 values in the range of 20–50 µM. Here we present the design and synthesis of various analogs of the leader compounds, the evaluation of their cytotoxicity and antiviral activity against SARS-CoV-2 in cell cultures, as well as experimental data on RNA-dependent RNA polymerase inhibition. Several compounds have been shown to prevent the interaction between the SARS-CoV-2 RNA-dependent RNA polymerase and the RNA substrate, likely inhibiting virus replication. Three of the synthesized compounds have also been shown to inhibit influenza virus. The structures of these compounds can be used for further optimization in order to develop an antiviral drug.

Phenotypic Test of Benzo[4,5]imidazo[1,2-c]pyrimidinone-Based Nucleoside and Non-Nucleoside Derivatives against DNA and RNA Viruses, Including Coronaviruses

“…These values significantly differ from the data on antiviral activity for compound 3a, which has a much lower EC 50 value than 3b (by at least one order of magnitude) (Table 3). In contrast to our results, several previously tested nucleoside inhibitors had close values of EC 50 and IC 50 , measured in almost the same in vitro system [26]. Thus, RdRp may not be the primary target for 3a, suggesting the presence of other viral or cellular targets.…”

“…A series of furanopyrimidinone derivatives with exclusive activity against VZV can only be phosphorylated by VZV kinases, but their target and further metabolic fate remain unknown [25]. Pyrrolopyrimidinones are capable of inhibiting the activity of coronavirus polymerase without incorporation into the growing chain [26]. At the same time, both pyrrolo-and furanopyrimidinones can influence liquid-liquid phase separation (LLPS) of the viral nucleocapsid protein (N) and viral genomic RNA (vgRNA) [27].…”

“…For this purpose, we purified the RdRp holoenzyme, consisting of the catalytic subunit nsp12 and two accessory subunits (nsp7 and nsp), and tested its activity with a double-stranded RNA substrate containing a radiolabeled primer and the template strand in the presence of various inhibitor concentrations. Previously, we showed that the system could be used as a good model for studying substrate specificity and testing RdRp inhibitors [26,41]. We examined the effect of the inhibitors on RdRp activity in concentrations ranging from 1 µM to 10 mM (Figure 3).…”

New Flexible Analogues of 8-Aza-7-deazapurine Nucleosides as Potential Antibacterial Agents

“…At the same time, biological properties not associated with phosphorylation are retained. This feature also helps to exclude classical nucleoside polymerases inhibition [40], but at the same time several 5 -norcarbocyclic nucleoside analogues have been shown to act as nonnucleoside inhibitors of viral RNA polymerases [41] or reverse transcriptase [42,43].…”

Recent Advances in Molecular Mechanisms of Nucleoside Antivirals

“…Examples of non-incorporating inhibitors of viral RdRp include pyrrolopyrimidinone-based NAs [ 77 ]. The inhibitory action on coronavirus RdRp is only observed upon pre-incubation RdRp with NAs, while an inhibitory effect is not observed when NAs are added to the in vitro-assembled RdRp:RNA complex.…”