Novel natural compounds may help treat COVID-19, study suggests

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a pandemic of coronavirus disease 2019 (COVID-19) of devastating proportions. The global outbreak of COVID-19 has already cost millions of deaths and, while vaccine rollouts have gotten well underway, the end of the pandemic is far from certain.

New and more infectious variants of SARS-CoV-2 that have shown potential to resist neutralization by antibodies elicited by older strains and the vaccines now being administered, threaten the ability to stop the spread of the virus definitively. Thus, the rapid development of effective, safe and targeted treatments for those who become severely unwell remains as important as ever.

A new study in the journal Chemistry Europe reports two natural compounds identified by virtual screening and computational modeling as having great promise for the development of drugs against SARS-CoV-2.

Non-structural proteins

The SARS-CoV-2 has ribonucleic acid (RNA) as its genetic material, encoding several structural and non-structural proteins (NSPs) required for viral replication and assembly of new viral particles.

The viral spike mediates attachment to the host cell via the angiotensin-converting enzyme 2 (ACE2) receptor on the latter. However, this requires priming through the TMPRSS2 enzyme, a serine protease that cleaves the spike in the S1/S2 domain.

Successful viral attachment is followed by virus-host membrane fusion and viral entry into the cell to begin replication, indicating that productive infection has been established.

The NSPs play many important roles in viral replication. For instance, NSP1 closes protein synthesis at host ribosomes, thus preventing antiviral innate immune responses. NSP3 binds NSP4, forming a complex which is vital for the formation of the replication/transcription complex (RTC). NSP3 is also essential for cleaving the large polypeptide formed from the open reading frame 1ab to multiple proteins.

NSP3 also impairs host defenses. NSP5 encodes the viral main protease (Mpro) enzyme, inhibits antiviral interferons and thus impair antiviral defenses.

NSP10 are protein scaffolds for NSP14 and NSP16, while NSP12 functions as the RNA-dependent RNA polymerase, along with cofactors NSP7 and 8. NSP14 proofreads the viral genome, while NSP16 shields it from host cell recognition and downregulates innate immunity.

NSP16 adds a protective cap at the 5’ end of the viral RNA genome to prevent its breakdown, with NSP10 as a cofactor. The latter encodes the 2′-O-methyltransferase (2′-O-MTase) enzyme, which allows the selective addition of N7-methyl guanine RNA caps alone. This feature is found only in SARS-CoV-2.

NSP-16-NSP10 binding is mediated by an activation surface on the latter, which allows NSP16 binding to the RNA molecule as well as to the actual cap donor, S-adenosyl-l-methionine (SAM). The result is stabilization of the donor molecule’s binding pocket and a conformational change that enlarges the binding groove for the capped RNA.

Recently, these three sites (the SAM binding site, the NSP10-NSP16 interface, and the RNA-binding groove) were shown to be druggable sites. The current study focused on the first of these.

Drug-like molecules

The researchers used the InterBioScreen (IBS) database of small molecules to search out possible candidates. They identified two possible lead compounds, STOCK1N-45683 and STOCK1N-71493, that interact with this protein at important residues at high affinities.

These two compounds showed good pharmacokinetic properties. This is predicted by the ADMET tool. ADMET is an acronym that represents the absorption, distribution, metabolism, excretion and toxicity properties of a compound. That is, these compounds are well absorbed after oral administration, widely distributed, and not toxic.

They also fulfilled drug-like molecule criteria (the Lipinski’s Rule of five), which means they were predicted to be highly bioavailable after being taken orally. Such compounds have a high probability of surviving the long drug development process.

To ensure that they were stable, physically and chemically, and could be synthesized on a commercial basis, they were also tested by the SwissADME model, further highlighting their viability.

High binding affinity

Molecular dynamics simulation (MDS) studies were to analyze the stability of binding of the protein to these ligands. MDS also helps understand how binding occurs at the binding pocket.

The binding affinity, or stability of binding, is measured in terms of multiple parameters, such as root mean square deviation (RMSD), binding mode analysis, intermolecular interactions, hydrogen bond analysis and the interaction energy.

These compounds were observed to show a high binding affinity for the active site of the proteins.

The first of them, STOCKIN-45683, interacts with key residues on the NSP16 via hydrogen bonds and alkyl-alkyl pi interactions. One such residue, Leu6898, has already gained attention for its interactions with other compounds. Thus, it could be a potential NSP16-binding SARS-CoV-2 inhibitor.

The other compound, STOCK1N-71493, binds multiple residues that are responsible for keeping SAM in the binding pocket of NSP16. These bonds include both hydrogen bonds as well as pi-sulfur interactions.

Importantly, these residues are not only key to its activity but also maintain their identity as such during binding with either SAM or this compound. Thus, STOCK1N-71493 is likely to be an inhibitor of the virus by preventing RNA capping, and thus rendering the viral RNA susceptible to breakdown.  

What are the implications?

Earlier reports indicated that compounds like Raltegravir and Maraviroc, selected by their ability to target the viral MTase, could inhibit this enzyme. Some like sinefungin (SFG) were selected based on their similarity to the enzyme by virtual screening.

Again, hesperidin, Rimegepant, and other compounds were reported as potential inhibitors.

The current study identified compounds with a different spatial conformation and with good drug-like characteristics as well as pharmacokinetic suitability for drug development.

To sum up, we suggest the two natural compounds from IBS database as probable SARS-CoV-2 inhibitors targeting nsp16. These compounds have not been assessed against SARS-CoV-2 or any other disease or target. This finding endorses the novelty of the compounds suggesting that these can be taken up for in vitro assessment.”

Not only could these be used as part of COVID-19 treatment protocols, suggest the researchers, but they may be used as a scaffold for the designing of new drug candidates.

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