Scientists are anxiously searching for an effective antiviral to combat severe or critical COVID-19, which has already caused over one million deaths worldwide. A new study published on the Preliminary Publication “server” bioRxiv* reports elucidation of the mechanism of SARS-CoV-2 inhibition by a non-nucleotide inhibitor called suramin. This is the first such compound to be shown to have such activity and shows promise for use as a repurposed drug against COVID-19.
Compared to the earlier highly pathogenic SAR-Co’s and MERS-CoV, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has much greater transmissibility and therefore has caused a pandemic rather than a local outbreak. Suramin is a drug that has been used to treat African sleeping sickness and river blindness for over a hundred years. Suramin has also been shown to be an inhibitor against a wide variety of viruses, including Zika and Chikungunya viruses, indicating its diverse mechanisms of action against multiple viruses.
For example, it can prevent viral attachment, entry and release into host cells by its interactions with viral capsid proteins. Recent research has shown it to be an in vitro inhibitor of SARS-CoV-2 infection in cell culture by preventing viral entry. The current study shows this to be due to its potent inhibition of SARS-CoV-2 RNA-dependent RNA polymerase (RdRp), an essential viral life cycle enzyme. Suramin is 20 or more times more potent than remdesivir, which is the only current approved anti-COVID-19 drug.
cryoEM studies reveal the binding of suramin to the catalytic site of RdRp to prevent RNA and background binding. This serves as a rational explanation to repurpose suramin for this virus as well as provides a template for designing a structure that can be tweaked for newer suramin derivatives.
Inhibition of RdRp by suramin
SARS-CoV-2 has a memory RNA polymerase composed of the non-structural protein nsp12 and two accessory subunits nsp7 and nsp8. This complex is necessary for RNA-based RNA synthesis. This is almost entirely inhibited by μM 8-32 suramin compared to μM 100-1000 of remdesivir triphosphate module (RDV-TP). The same trend was seen when it comes to complete abolition of RdRp-RNA complex formation, which required 100 μM of suramin but >5 μM of RDV-TP. The half-maximum inhibition concentration (IC50) of suramin is 0.26 μM but 6.21 μM for RDV-TP.
This indicates that suramin is 20-fold or more potent than RDV-TP. In cell culture, the former was shown to inhibit virus duplication in Vero cells, the effective half-maximum concentration (EC50) which is ~2.9 μM comparable to that of remdesivir.
Why does suramin show the weakest effects in cell culture? Researchers speculate that this is due to the high negativity of this molecule, which decreases its uptake by host cells. The CC50 (drug concentrations required to decrease cell viability by 50%) of suramin is over 1000 μM, indicating its high margin of safety.
The structure of the RdRp-suramin complex
Using cryo-EM, current researchers have found that the RdRp-suramin complex has a very similar structure to the apo RdRp complex. Nsp 12 has the same right palmetto configuration with a catalytic active site comprising seven motifs (AG) that are highly conserved among coronaviruses. Two molecules of suramin fit into the catalytic chamber, one consisting of the G motif and the B motif.
Chemically, suramin has a dual symmetry with a urea linker in the center. However, only half of is clearly defined on the EM map, lacking the urea linker. Interactions between RdRp and suramin include hydrogen bonds, charge interactions, and hydrophobic packing interactions.
A study of alignment with RdRp from several viruses suggests that residues contacting suramin are conserved, indicating the broad applicability of suramin to multiple viral infections.
Suramin Inhibits SARS-CoV-2 RdRp
Comparing the RdRp-suramin complex to the direct remdesivir complex of RdRp shows that the two suramin molecules occupy specific positions on the RNA strand and background hand strand, blocking the binding of the RNA template-bottom hand duplex strand to the active site of the enzyme. It simultaneously prevented the entry of nucleotide triphosphate into the catalytic site. This directly blocked the catalytic activity of RdRp.
This mechanism is related to the inhibition of SARS-CoV-2 RdRp, which is different from the suramin-mediated inhibition of norovirus RdRp, although the latter also involves the binding of two suramin molecules. Both suramin binding sites have half the suramin molecule, but compared to the previous enzyme, only one of the two sites has partial overlap. In the latter case, there is indirect inhibition of RdRp polymerization because one binding site overlaps with the proposed nucleotide entry channel.
When other suramin derivatives are used, they bind in different orientations and conformations and thus may also inhibit RdRp of SARS-CoV-2.
Suramin derivatives inhibit the RdRp of SARS-CoV-2
Suramin-based drugs have been tested for chemotherapy of cancers and parasitic infestations. In in vitro screening, all eight compounds tested were found to be effective inhibitors of RdRp, with a relative potency at least five times that of Suramin. With the effective micromolar concentrations, cytotoxicity was low, indicating their potential utility for the treatment of COVID-19. However, the previously observed discrepancy in biochemical potency in cell-based assays is still present, indicating that these compounds are not well taken up in living host cells. Thus, the use of glycol-based chitosan nanoparticles to deliver these drug particles into cells may improve their bioavailability in lung tissue and their potency as viral inhibitors.
The researchers report that suramin is a potent direct viral inhibitor of RdRp by direct inhibition, with structural analysis showing the mechanism of association and inhibition. This is the first non-nucleotide inhibitor of SARS-CoV-2 RdRp and indicates the possibility of developing suramin analogues and drug formulations as potent and effective inhibitors of viral replication.
Yin, W. et al. (2020). Structural Basis For Repurposing A 100-Years-Old Drug Suramin For Treating COVID-19. bioRxiv preprint. doi: https://doi.org/10.1101/2020.10.06.328336. https://www.biorxiv.org/content/10.1101/2020.10.06.328336v1