Phycobilins found to inhibit SARS-CoV-2 enzymes in vitro

The search for effective antivirals to counter or prevent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, the pathogen that causes coronavirus disease 2019 (COVID-19), continues.

Researchers from Tennesee State University and Meharry Medical College in the United States have released an interesting new study on the preprint bioRxiv* server in November 2020 that describes the broad-spectrum of antiviral activity that phycobilins can have. Phycobilins, which are bioactive plant compounds, were found to inhibit two coronavirus enzymes.

3D rendering of SARS-CoV-2 microbe. Image Credit: joshimerbin / Shutterstock
3D rendering of SARS-CoV-2 microbe. Image Credit: joshimerbin / Shutterstock

Seven viruses from the coronavirus family are known to cause infectious human disease, four of them causing seasonal common colds, and three causing potentially lethal respiratory syndromes. Among the latter three, SARS-CoV-2 has already killed over 1.42 million people worldwide within a year, while the number of infections globally has crossed 60.5 million.

COVID-19 has proved difficult to contain because of SARS-CoV-2’s high transmissibility and a lack of vaccines or therapeutic agents that can effectively fight against it. While many old and new drugs are being tried out, there is a severe lack of clinical data on which to base treatment decisions. The current study is an example of an approach that focuses on identifying broad-spectrum antivirals that can inhibit not just this virus but a range of others, both coronaviruses and other novel viral pathogens.

Broad-spectrum antivirals

Broad-spectrum antivirals (BSA) fall into one of two classes: those which inhibit viral entry by engaging viruses before they enter the host cell, and those which prevent viral replication such that the virus within the host cell cannot initiate productive infection.

In the case of coronaviruses, the spike (S) protein differs significantly between the other human coronaviruses and is therefore not a fit target for the first class of BSA. However, the coronavirus nonstructural proteins (nsps) that are key to viral replication are highly conserved; their structure remaining the same between different viruses of this family.

Several researchers have reported SARS-CoV-2 nsps that can be targeted by antivirals, including the main protease MPro, the papain-like protease PLPro, RNA dependent RNA polymerase RdRp, and nsps 14-16. Among these, MPro and PLPro cleave viral polyproteins into functional nsps.

MPro acts on 11 or more cleavage sites of replicase 1ab. At the same time, PLPro catalyzes proteolysis of the peptide linkage at the P1 position to produce nsps 1, 2 and 3, all of which are essential for viral replication.

The study

The current study focuses on phytochemicals, which are less toxic than synthetic drugs in many cases, and have been reported to have antiviral activity against multiple viruses, including coronaviruses. Selecting 15 phytochemicals of various chemical classes based on existing knowledge of their antiviral activity, the researchers studied their binding interactions with the SARS-CoV-2 MPro and PLPro.

These compounds include flavonols like quercetin, flavins like riboflavins, isoflavones such as daidzein and genistein, phenolic ketones like gingerol, and phenolic alkaloids such as capsaicin, all of which are well-known plant compounds.

The study’s findings

Their interactions with the viral enzymes were examined by docking studies. These showed that the phycobilins (PCB) docked with the best score or binding energy for MPro, followed by riboflavin, cyanidin, daidzein and genistein in a close cluster. There were 12 important residues at the active site involved in these interactions with the phytochemicals.

The docking studies for PLPro were carried out in dimer form, when PCB again had the best score and binding energy. This involved 11 key residues in chain A and 13 in chain B of the enzyme.

These in silico experiments were validated by in vitro studies comparing the potential inhibitors with established inhibitory compounds for each of the enzymes. With the positive control containing the enzyme without the inhibitor, its activity was set at 100%. The six phytochemicals with the best docking score, as mentioned above, were tested against MPro. In the first phase, PCB was found to have the highest inhibitory activity, with half-maximal inhibitory concentration (IC50) less than half that of the second-place quercetin (71 versus 145 μM).

Again, for PLPro, four of these compounds were screened, again showing PCB to have the most potent inhibitory activity with IC50 of 62 μM. Thus, PCB is shown to have powerful inhibitory activity against both these enzymes.

The ability of PCB to inhibit other coronavirus MPro and PLPro enzymes was assessed using the crystal structures of these enzymes in various human and animal coronaviruses. Docking studies were carried out on both dimeric and monomeric forms. PCB was found to have a high docking affinity for MERS MPro and PLPro. However, for the latter, the dimeric form of the enzyme had a higher binding affinity relative to the monomeric enzyme.

When only monomers were compared, the highest docking score for PCB was with MERS-CoV, TGEV and SARS-CoV-2, indicating its potential to be a broad-spectrum inhibitor.

When other phycobilins, such as phycourobilin (PUB), Phycoerythrobilin (PEB) and Phycoviolobilin (PVB), were explored, they all bound strongly to the binding pockets of these enzymes at specific amino acids, with PCB having the highest or almost the highest docking score for both enzymes. It is notable that these compounds also have other powerful therapeutic properties such as scavenging oxidative radicals, inhibiting cancer cell division and platelet aggregation. They can also be used orally in the form of the phycobilin-protein complex, phycobiliprotein. Once ingested, it is digested in the human gut, and free PCB is released there, which may account for the therapeutic properties of this complex.


The researchers call for “in-vivo studies on inhibition of CoVs infectivity using human cells and animal models.”

Moreover, they suggest that more phycobilin lead compounds could be developed by structure-guided development to “rapidly lead to the discovery of a single agent with clinical potential against existing and possible future emerging CoV-associated diseases.”

*Important Notice

bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Journal reference:
Dr. Liji Thomas

Written by

Dr. Liji Thomas

Dr. Liji Thomas is an OB-GYN, who graduated from the Government Medical College, University of Calicut, Kerala, in 2001. Liji practiced as a full-time consultant in obstetrics/gynecology in a private hospital for a few years following her graduation. She has counseled hundreds of patients facing issues from pregnancy-related problems and infertility, and has been in charge of over 2,000 deliveries, striving always to achieve a normal delivery rather than operative.


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