Abstract
The main protease M pro 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 M pro 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 M pro 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 M pro , and thus open novel perspectives for the development of future peptidomimetic drugs against COVID-19, as well as diagnostic tools.
Keywords: COVID-19; Free energy calculations; MM/PBSA; Main protease; Proteomics; TAILS.
【저자키워드】 COVID-19, proteomics, main protease, Free energy calculations, MM/PBSA, TAILS., 【초록키워드】 SARS-CoV-2, proteomics, variant, diagnostic, lung, drug, protease, virus, binding energy, free energy, Free energy calculations, specificity, amino acids, drug target, proteome, surface, pathogenicity, Glutamine, Molecular mechanics, MM/PBSA, Combination, Analysis, surface area, Mechanics, enzyme, Perspective, M pro, cleavage site, substrate, substrates, terminal, structural homology, Effects, approach, identify, carried, indicated, determine, introduced, unique, expected, Area, Amine, 【제목키워드】 peptide, SARS-CoV-2 main protease, specificity, Analysis, approach,