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

Abstract

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).

Cyclobutanone Inhibitors of Diaminopimelate Desuccinylase (DapE) as Potential New Antibiotics

“…We reported the facile preparation of a protected 2-aminocyclobutanone synthon, enabling rapid formation of peptidomimetic 2-amido-and 2-sulfonamidocyclobutanones as a potential toward enzyme inhibitor lead molecules that are tunable for recognition by different proteases and esterases with therapeutic potential. Very recently, we reported cyclobutanone inhibitors against SARS-CoV-2 helicase with antiviral activity, identified through in silico screening [17]. Herein, we describe the preparation of a small cyclobutanone library, which we screened against the antibiotic target DapE, identifying a number of 2-aminocyclobutanone derivatives with micromolar inhibitory potency.…”

Mycolactone: A Broad Spectrum Multitarget Antiviral Active in the Picomolar Range for COVID-19 Prevention and Cure

“…Our group has shown the usefulness of heparin as a viral fusion inhibitor by targeting spike protein early on in the pandemic [ 9 ]. Owing to its complicated pharmacodynamics, contraindications, and lack of topical formulations [ 9 , 10 , 11 ], we have further developed lead molecules against essential SARS-CoV-2 enzymes [ 12 ] such as 3Clpro, NendoU, and Helicase [ 13 , 14 , 15 ]. An alternate approach to the COVID-19 R&D of drugs and vaccines would be blocking the host cell’s entry and exit mechanisms with safer compounds, and mycolactone (MLN) could be such a candidate [ 16 ].…”