Natural Compounds Inhibit SARS-CoV-2 nsp13 Unwinding and ATPase Enzyme Activities

Abstract

SARS-CoV-2 infection is still spreading worldwide, and new antiviral therapies are an urgent need to complement the approved vaccine preparations. SARS-CoV-2 nps13 helicase is a validated drug target participating in the viral replication complex and possessing two associated activities: RNA unwinding and 5′-triphosphatase. In the search of SARS-CoV-2 direct antiviral agents, we established biochemical assays for both SARS-CoV-2 nps13-associated enzyme activities and screened both in silico and in vitro a small in-house library of natural compounds. Myricetin, quercetin, kaempferol, and flavanone were found to inhibit the SARS-CoV-2 nps13 unwinding activity at nanomolar concentrations, while licoflavone C was shown to block both SARS-CoV-2 nps13 activities at micromolar concentrations. Mode of action studies showed that all compounds are nsp13 noncompetitive inhibitors versus ATP, while computational studies suggested that they can bind both nucleotide and 5′-RNA nsp13 binding sites, with licoflavone C showing a unique pattern of interaction with nsp13 amino acid residues. Overall, we report for the first time natural flavonoids as selective inhibitors of SARS-CoV-2 nps13 helicase with low micromolar activity.

Potential COVID-19 Therapies from Computational Repurposing of Drugs and Natural Products against the SARS-CoV-2 Helicase

“…For example, a group developed a novel fluorescence resonance energy transfer-based strand displacement assay for monitoring SARS-CoV-2 helicase activity and used this assay to screen a custom chemical library of over 5000 approved and investigational compounds for novel helicase inhibitors, identifying three novel compounds and confirming suramin-like compounds as helicase inhibitors [ 60 ]. Another group established biochemical assays for SARS-CoV-2 nps13-associated enzyme activities on RNA unwinding and 5′-triphosphatase activity and used these to screen a small in-house library of natural compounds identifying myricetin, quercetin, kaempferol, and flavanone as inhibitors of RNA unwinding activity and licoflavone C as an inhibitor of both helicase activities [ 61 ]. A compound based on a 2-phenylquinoline scaffold was shown to have potent in vitro activity against SARS-CoV-2 helicase [ 62 ].…”

Recent advances in applying G-quadruplex for SARS-CoV-2 targeting and diagnosis: A review

“…Recently, lumacaftor and cepharanthine were shown to inhibit SARS-CoV-2 Nsp13 ATPase activity [78] . Natural flavonoids were also identified as selective inhibitors of SARS-CoV-2 Nsp13 [79] . Together, these pieces of evidence reflect that targeting Nsp13 could be one of the major areas of anti-SARS-CoV-2 research.…”

Some natural compounds and their analogues having potent anti- SARS-CoV-2 and anti-proteases activities as lead molecules in drug discovery for COVID-19

“…Baicalein also inhibited the SARS-CoV-2 nsp13 associated unwinding activity in viral translation with an IC 50 value of 2.90 μM. The docking analysis suggested that baicalein binds to both orthosteric and allosteric binding sites of helicase nsp13 to prevent the unwinding activity [ 72 ]. Several studies on the antiviral activities of natural flavonoids reported that baicalein showed antiviral activity against a wide range of enveloped RNA viruses including influenza A-, Dengue-, Japanese encephalitis-, chikungunya-, human immunodeficiency- and Zika-viruses and non-enveloped RNA viruses, such as enteroviruses.…”

“…Quercetin potently inhibited the SARS-CoV-2 nsp13 helicase RNA unwinding activity with an IC 50 value of 0.53 μM and another flavonoid myricetin showed a better activity with an IC 50 value of 0.41 μM. Molecular docking analysis showed that both quercetin and myricetin have good binding affinity for 5′-RNA-binding site of the virus RNA [ 72 ]. In a clinical trial, quercetin phytosome ® (QP), a lecithin-based novel bioavailable form of quercetin, with 200 mg quercetin in 500 mg capsule, on treatment (1 capsule thrice a day for 7 days followed by 2 capsules per day for next 7 days) to subjects with mild COVID-19, significantly reduced viral load (negative SARS-CoV-2 in RT-PCR test) and improved the blood parameters in reduction of LDH, ferritin, CRP and D-dimer levels in the patients [ 76 ].…”