New natural compounds may help treat COVID-19 disease, study suggests

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the devastating 2019 coronavirus disease (COVID-19) pandemic. the global outbreak of COVID-19 has killed millions of people, and while vaccine rollout is well underway, the end of the pandemic is far from certain.

New and more infectious variants of SARS-CoV-2 have shown the potential to resist antibody neutralisation induced by older strains and vaccines currently in use, threatening the ability to ultimately stop the spread of the virus. Therefore, the rapid development of effective, safe and targeted treatments for those who are severely unwell remains as important as ever.

A new study in the European Journal of Chemistry reports on two natural compounds identified through virtual screening and computational modelling that hold great promise for the development of drugs against SARS-CoV-2.

Non-structural proteins

SARS-CoV-2 uses ribonucleic acid (RNA) as its genetic material and encodes several structural and non-structural proteins (NSPs) required for viral replication and the assembly of new viral particles.
The viral spike mediates attachment to host cells via the angiotensin-converting enzyme 2 (ACE2) receptor on the host cell. However, this requires elicitation by the TMPRSS2 enzyme, a serine protease that cleaves the spike in the S1/S2 structural domain.
Following successful viral attachment, the virus-host membrane fuses and the virus enters the cell to begin replication, indicating that productive infection has been established.
NSPs play many important roles in viral replication. For example, NSP1 shuts down protein synthesis in the host ribosome, thereby preventing an innate immune response against the virus. nSP3 binds to NSP4, forming a complex that is essential for the formation of the replication/transcription complex (RTC). nSP3 is also essential for cleavage of the large polypeptide formed by open reading frame 1ab into a variety of proteins.
NSP3 also impairs host defences. nSP5 encodes the viral master protease (Mpro) enzyme, which inhibits antiviral interferon and thus impairs antiviral defences.
NSP10 is the protein scaffold for NSP14 and NSP16, while NSP12 functions as an RNA-dependent RNA polymerase along with cofactors NSP7 and 8. NSP14 proofreads the viral genome, while NSP16 shields it from recognition by host cells and reduces innate immunity.
NSP16 adds a protective cap to the 5' end of the viral RNA genome to prevent its breakdown, and NSP10 is a cofactor. The latter encodes a 2′-O-methyltransferase (2′-O-MTase) that can selectively add the N7-methylguanine RNA cap alone. This feature is only found in SARS-CoV-2.
The binding of NSP-16-NSP10 is mediated by an activation face of the latter, which allows NSP16 to bind to the RNA molecule as well as to the actual cap donor S-adenosyl-L-methionine (SAM). The result is a stabilisation of the binding pocket of the donor molecule and a conformational change that expands the binding groove of the capped RNA.

Recently, these three sites (SAM binding site, NSP10-NSP16 interface and RNA binding groove) have been shown to be medicinally available sites. The current study focuses on the first of these.

Molecules that resemble drugs

The researchers used the InterBioScreen (IBS) database of small molecules to search for possible candidates. They identified two possible lead compounds, STOCK1N-45683 and STOCK1N-71493, which interact with the protein with high affinity at important residues.
These two compounds showed good pharmacokinetic properties. This was predicted by the ADMET tool, an acronym that stands for absorption, distribution, metabolism, excretion and toxicity properties of a compound. This means that the compounds are well absorbed, widely distributed and non-toxic after oral administration.
They also meet the criteria for a drug-like molecule (Lipinski's Rule of Five), which means that they are predicted to have high bioavailability after oral administration. Such compounds have a high probability of surviving the long drug development process.
To ensure that they are physically and chemically stable and can be synthesised on a commercial basis, they have also been tested by the SwissADME model, further highlighting their feasibility.

High binding affinity

Molecular dynamics simulation (MDS) studies are performed to analyse the stability of proteins bound to these ligands.MDS also helps to understand how binding occurs in the binding pocket.
Binding affinity, or stability of binding, is measured by several parameters such as root mean square deviation (RMSD), binding mode analysis, intermolecular interactions, hydrogen bonding analysis and interaction energy.
It has been observed that these compounds exhibit high binding affinity for the active site of the protein.
The first of these, STOCKIN-45683, interacts with key residues on NSP16 via hydrogen bonding and alkyl-alkyl-π interactions. One such residue, Leu6898, has already gained attention for its interactions with other compounds. Therefore, it may be a potential SARS-CoV-2 inhibitor bound to NSP16.
Another compound, STOCK1N-71493, binds to multiple residues that are responsible for holding SAM in the binding pocket of NSP16. These bonds include hydrogen bonds as well as π-sulphur interactions.
Importantly, these residues are not only essential for their activity, but also for maintaining their properties during binding to SAM or this compound. Thus, STOCK1N-71493 is likely to be an inhibitor of viruses by preventing RNA capping and thus rendering viral RNA susceptible to catabolism.

What is the significance of this?

Earlier reports suggest that compounds like Raltegravir and Maraviroc, selected for their ability to inhibit the viral MT enzyme through their ability to target it, could inhibit this enzyme. Some like sinefungin (SFG) were selected through a virtual screen based on their similarity to the enzyme.
Similarly, synbiotics, Rimegepant and other compounds were reported as potential inhibitors.
The current study identified compounds with different spatial conformations and with good drug-like properties as well as pharmacokinetics suitable for drug development.
The researchers suggest that these compounds could be used not only as part of a COVID-19 treatment regimen, but also as scaffolds for the design of new drug candidates.