Kinetic Characterization of SARS-CoV-2 nsp13 ATPase Activity and Discovery of Small-Molecule Inhibitors

Yazdi, Aliakbar Khalili; Pakarian, Paknoosh; Perveen, Sumera; Santhakumar, V.; Bolotokova, Albina; Li, Fengling; Vedadi, Masoud

doi:10.1021/acsinfecdis.2c00165

Cited by 11 publications

(11 citation statements)

References 48 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Disulfiram is known as a “zinc-ejector” and has been shown to specifically target conserved zinc-bound cysteine residues [ 125 , 126 ]. This mechanism allows it to target the highly-conserved non-structural proteins nsp13 and nsp14 [ 128 ], critical enzymes that function in viral replication as a helicase [ 129 ] and an exoribonuclease, respectively. A study of disulfiram against viral pseudo-particles (Vpps) of multiple SARS-CoV-2 strains showed that disulfiram potently blocked viral entry via the inhibition of the interaction between the spike protein and its ACE2 receptor [ 130 ].…”

Section: Resultsmentioning

confidence: 99%

Disulfiram: Mechanisms, Applications, and Challenges

et al. 2023

View full text Add to dashboard Cite

Background: Since disulfiram’s discovery in the 1940s and its FDA approval for alcohol use disorder, other indications have been investigated. This review describes potential clinical applications, associated risks, and challenges. Methods: For this narrative review, a PubMed search was conducted for articles addressing in vivo studies of disulfiram with an emphasis on drug repurposing for the treatment of human diseases. The key search terms were “disulfiram” and “Antabuse”. Animal studies and in vitro studies highlighting important mechanisms and safety issues were also included. Results: In total, 196 sources addressing our research focus spanning 1948–2022 were selected for inclusion. In addition to alcohol use disorder, emerging data support a potential role for disulfiram in the treatment of other addictions (e.g., cocaine), infections (e.g., bacteria such as Staphylococcus aureus and Borrelia burgdorferi, viruses, parasites), inflammatory conditions, neurological diseases, and cancers. The side effects range from minor to life-threatening, with lower doses conveying less risk. Caution in human use is needed due to the considerable inter-subject variability in disulfiram pharmacokinetics. Conclusions: While disulfiram has promise as a “repurposed” agent in human disease, its risk profile is of concern. Animal studies and well-controlled clinical trials are needed to assess its safety and efficacy for non-alcohol-related indications.

show abstract

Section: Resultsmentioning

confidence: 99%

Disulfiram: Mechanisms, Applications, and Challenges

et al. 2023

View full text Add to dashboard Cite

show abstract

“…Structural, crystallographic, and mechanistic studies have identified two pockets where ATP and RNA bind [ 83 ]. These pockets and ATPase activity have been the target of multiple studies, resulting in several drugs and metabolites having the potential to bind to them, reducing the activity of NSP13 helicase [ 83 , 84 ]. Moreover, studies by Sui et al [ 85 ] showed that NSP13 is capable of inhibiting the production of type I IFN, allowing the virus to evade the innate immune response, shedding lighter on the importance of this protein in the pathogenesis of the virus and reinforcing its potential as a therapeutic target.…”

Section: Resultsmentioning

confidence: 99%

Can Probiotics, Particularly Limosilactobacillus fermentum UCO-979C and Lacticaseibacillus rhamnosus UCO-25A, Be Preventive Alternatives against SARS-CoV-2?

Valdebenito-Navarrete

Fuentes-Barrera

Smith

et al. 2023

Biology

View full text Add to dashboard Cite

COVID-19, an infection produced by the SARS-CoV-2 virus in humans, has rapidly spread to become a high-mortality pandemic. SARS-CoV-2 is a single-stranded RNA virus characterized by infecting epithelial cells of the intestine and lungs, binding to the ACE2 receptor present on epithelial cells. COVID-19 treatment is based on antivirals and antibiotics against symptomatology in addition to a successful preventive strategy based on vaccination. At this point, several variants of the virus have emerged, altering the effectiveness of treatments and thereby attracting attention to several alternative therapies, including immunobiotics, to cope with the problem. This review, based on articles, patents, and an in silico analysis, aims to address our present knowledge of the COVID-19 disease, its symptomatology, and the possible beneficial effects for patients if probiotics with the characteristics of immunobiotics are used to confront this disease. Moreover, two probiotic strains, L. fermentum UCO-979C and L. rhamnosus UCO-25A, with different effects demonstrated at our laboratory, are emphasized. The point of view of this review highlights the possible benefits of probiotics, particularly those associated with immunomodulation as well as the production of secondary metabolites, and their potential targets during SARS-CoV-2 infection.

show abstract

“…SARS-CoV-2 Nsp13 helicase is less studied, especially in comparison to the main protease (Mpro, or 3CLpro), and there are relatively few known inhibitors of SARS-CoV-2 Nsp13 helicase, and even fewer belonging to SAR, as summarized in Table S2 [ 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 ]. Inhibitors including repurposed drugs were shown to bind the SARS-CoV-2 Nsp13 helicase ATP binding site in recent studies [ 24 , 53 ]. Following Molecular Dynamics simulations (MDS) for in silico validation of target specificity, antiviral activity of N -functionalized 2-aminocyclobutanone hits and analogs was confirmed in vitro using a cell survival assay, and inherent cellular toxicity was assessed.…”

Section: Discussionmentioning

confidence: 99%

In Silico Binding of 2-Aminocyclobutanones to SARS-CoV-2 Nsp13 Helicase and Demonstration of Antiviral Activity

Mohammad

Gupta

Reidl

et al. 2023

IJMS

View full text Add to dashboard Cite

The landscape of viral strains and lineages of SARS-CoV-2 keeps changing and is currently dominated by Delta and Omicron variants. Members of the latest Omicron variants, including BA.1, are showing a high level of immune evasion, and Omicron has become a prominent variant circulating globally. In our search for versatile medicinal chemistry scaffolds, we prepared a library of substituted ɑ-aminocyclobutanones from an ɑ-aminocyclobutanone synthon (11). We performed an in silico screen of this actual chemical library as well as other virtual 2-aminocyclobutanone analogs against seven SARS-CoV-2 nonstructural proteins to identify potential drug leads against SARS-CoV-2, and more broadly against coronavirus antiviral targets. Several of these analogs were initially identified as in silico hits against SARS-CoV-2 nonstructural protein 13 (Nsp13) helicase through molecular docking and dynamics simulations. Antiviral activity of the original hits as well as ɑ-aminocyclobutanone analogs that were predicted to bind more tightly to SARS-CoV-2 Nsp13 helicase are reported. We now report cyclobutanone derivatives that exhibit anti-SARS-CoV-2 activity. Furthermore, the Nsp13 helicase enzyme has been the target of relatively few target-based drug discovery efforts, in part due to a very late release of a high-resolution structure accompanied by a limited understanding of its protein biochemistry. In general, antiviral agents initially efficacious against wild-type SARS-CoV-2 strains have lower activities against variants due to heavy viral loads and greater turnover rates, but the inhibitors we are reporting have higher activities against the later variants than the wild-type (10–20X). We speculate this could be due to Nsp13 helicase being a critical bottleneck in faster replication rates of the new variants, so targeting this enzyme affects these variants to an even greater extent. This work calls attention to cyclobutanones as a useful medicinal chemistry scaffold, and the need for additional focus on the discovery of Nsp13 helicase inhibitors to combat the aggressive and immune-evading variants of concern (VOCs).

show abstract

Kinetic Characterization of SARS-CoV-2 nsp13 ATPase Activity and Discovery of Small-Molecule Inhibitors

Cited by 11 publications

References 48 publications

Disulfiram: Mechanisms, Applications, and Challenges

Disulfiram: Mechanisms, Applications, and Challenges

Can Probiotics, Particularly Limosilactobacillus fermentum UCO-979C and Lacticaseibacillus rhamnosus UCO-25A, Be Preventive Alternatives against SARS-CoV-2?

In Silico Binding of 2-Aminocyclobutanones to SARS-CoV-2 Nsp13 Helicase and Demonstration of Antiviral Activity

Contact Info

Product

Resources

About