Interaction of small molecules with the SARS-CoV-2 main protease in silico and in vitro validation of potential lead compounds using an enzyme-linked immunosorbent assay
“…Although hypericin has a binding affinity that is weaker than other compounds, it is important to consider its position, orientation and the interactions that are formed with the protein residues within the PL pro binding site. Hypericin has also been examined as a lead compound for the SARS-CoV-2 spike protein and M pro ( 114 , 115 ). Figure 2 Docking of lead compounds to the naphthalene inhibitor binding pocket and PL pro and blind docking.…”
“…Although hypericin has a binding affinity that is weaker than other compounds, it is important to consider its position, orientation and the interactions that are formed with the protein residues within the PL pro binding site. Hypericin has also been examined as a lead compound for the SARS-CoV-2 spike protein and M pro ( 114 , 115 ). Figure 2 Docking of lead compounds to the naphthalene inhibitor binding pocket and PL pro and blind docking.…”
“…Natural compounds have been screened for their ability to target SARS-CoV-2 proteins. This includes extracts of medicinal herbs and several studies have focused on their inhibitory effects on key proteins, such as the spike glycoprotein and the main protease (M pro ) (Mani et al, 2020 ; Pitsillou et al, 2020 ; Russo et al, 2020 ; Smith and Smith, 2020 ). In a recent paper by Alamri et al a structured-based computational approach was utilized to identify compounds that may act as pan-PL pro inhibitors and could be developed further as antiviral agents (Alamri et al, in press ).…”
COVID-19 is an ongoing pandemic caused by the SARS-CoV-2 virus with important political, socio-economic, and public health consequences. Inhibiting replication represents an important antiviral approach, and in this context two viral proteases, the SARS-CoV-2 main and papain-like proteases (PLpro), which cleave pp1a and pp1ab polypeptides, are critical. Along with protease activity, the PLpro possesses deubiquitinating activity, which is important in immune regulation. Naphthalene-based inhibitors, such as the well-investigated GRL-0617 compound, have been shown to possess dual effects, inhibiting both protease and deubiquitinating activity of the PLpro. Rather than binding to the canonical catalytic triad, these type of non-covalent inhibitors target an adjacent pocket, the naphthalene-inhibitor binding site. Using a high-throughput screen, we have previously identified the dietary hypericin, rutin, and cyanidin-3-O-glucoside compounds as potential protease inhibitors targeting the naphthalene-inhibitor binding site. Here, our aim was to investigate the binding characteristics of these compounds to the PLpro, and to evaluate deubiquitinating activity, by analyzing seven different PLpro crystal structures. Molecular docking highlighted the relatively high affinity of GRL-0617 and dietary compounds. In contrast binding of the small molecules was abolished in the presence of ubiquitin in the palm subdomain of the PLpro. Further, docking the small molecules in the naphthalene-inhibitor binding site, followed by protein-protein docking revealed displacement of ubiquitin in a conformation inconsistent with functional activity. Finally, the deubiquitinating activity was validated in vitro using an enzymatic activity assay. The findings indicated that the dietary compounds inhibited deubiquitinase activity in the micromolar range with an order of activity of GRL-0167, hypericin >> rutin, cyanidin-3-O-glucoside > epigallocatechin gallate, epicatechin gallate, and cefotaxime. Our findings are in accordance with mechanisms and potential antiviral effects of the naphthalene-based, GRL-0617 inhibitor, which is currently progressing in preclinical trials. Further, our findings indicate that in particular hypericin, rutin, and cyanidin-3-O-glucoside, represent suitable candidates for subsequent evaluation as PLpro inhibitors.
“…and accelerates processes involved in cell cycle arrest [ 20 , 30 , 31 , 32 , 33 ]. PLpro, which is involved in viral replication, modulates signaling that alters immune defenses and contributes to the cytokine storm (e.g., nuclear factor kappa B and interferon 1) through its deubiquitinating (DUB) activity and removal of interferon-stimulated gene 15 from cellular proteins [ 34 ]. In addition, a few amino acid residues in S1 and S2 subunits of S protein, known as short linear motifs (SLiMs) LxxLxE, recruit protein phosphatase 2A (PP2A) by binding its B56 subunit [ 2 ].…”
Section: Sars-cov-2 and Associated Immune Responsementioning
Despite the virulence and high fatality of coronavirus disease 2019 (COVID-19), no specific antiviral treatment exists until the current moment. Natural agents with immune-promoting potentials such as bee products are being explored as possible treatments. Bee honey and propolis are rich in bioactive compounds that express strong antimicrobial, bactericidal, antiviral, anti-inflammatory, immunomodulatory, and antioxidant activities. This review examined the literature for the anti-COVID-19 effects of bee honey and propolis, with the aim of optimizing the use of these handy products as prophylactic or adjuvant treatments for people infected with severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). Molecular simulations show that flavonoids in propolis and honey (e.g., rutin, naringin, caffeic acid phenyl ester, luteolin, and artepillin C) may inhibit viral spike fusion in host cells, viral-host interactions that trigger the cytokine storm, and viral replication. Similar to the potent antiviral drug remdesivir, rutin, propolis ethanolic extract, and propolis liposomes inhibited non-structural proteins of SARS-CoV-2 in vitro, and these compounds along with naringin inhibited SARS-CoV-2 infection in Vero E6 cells. Propolis extracts delivered by nanocarriers exhibit better antiviral effects against SARS-CoV-2 than ethanolic extracts. In line, hospitalized COVID-19 patients receiving green Brazilian propolis or a combination of honey and Nigella sativa exhibited earlier viral clearance, symptom recovery, discharge from the hospital as well as less mortality than counterparts receiving standard care alone. Thus, the use of bee products as an adjuvant treatment for COVID-19 may produce beneficial effects. Implications for treatment outcomes and issues to be considered in future studies are discussed.
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