A Proteomics-MM/PBSA Dual Approach for the Analysis of SARS-CoV-2 Main Protease Substrate Peptide Specificity
The main protease Mpro of SARS-CoV-2 is a well-studied major drug target. Additionally, it has been linked to this virus’ pathogenicity, possibly through off-target effects. It is also an interesting diagnostic target. To obtain more data on possible substrates as well as to assess the enzyme’s primary specificity a two-step approach was introduced. First, Terminal Amine Isobaric Labeling of Substrates (TAILS) was employed to identify novel Mpro cleavage sites in a mouse lung proteome library. In a second step, using a structural homology model, the MM/PBSA variant MM/GBSA (Molecular Mechanics Poisson-Boltzmann/Generalized Born Surface Area) free binding energy calculations were carried out to determine relevant interacting amino acids. As a result, 58 unique cleavage sites were detected, including six that displayed glutamine at the P1 position. Furthermore, modeling results indicated that Mpro has a far higher potential promiscuity towards substrates than expected. The combination of proteomics and MM/PBSA modeling analysis can thus be useful for elucidating the specificity of Mpro, and thus open novel perspectives for the development of future peptidomimetic drugs against COVID-19, as well as diagnostic tools.
Gallo, G., Barcick, U., Coelho, C., Salardani, M., Camacho, M.F., Cajado-Carvalho, D., Loures, F. V., Serrano, S.M.T., Hardy, L., Zelanis, A., & Wurtele, M. (2022). A Proteomics-MM/PBSA Dual Approach for the Analysis of SARS-CoV-2 Main Protease Substrate Peptide Specificity. Peptides, 1-24. https://doi.org/10.1016/j.peptides.2022.170814
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