TY - JOUR
T1 - A proteomics-MM/PBSA dual approach for the analysis of SARS-CoV-2 main protease substrate peptide specificity
AU - Gallo, Gloria
AU - Barcick, Uilla
AU - Coelho, Camila
AU - Salardani, Murilo
AU - Camacho, Maurício F.
AU - Cajado-Carvalho, Daniela
AU - Loures, Flávio V.
AU - Serrano, Solange M.T.
AU - Hardy, Leon
AU - Zelanis, André
AU - Würtele, Martin
N1 - Publisher Copyright:
© 2022 Elsevier Inc.
PY - 2022/8
Y1 - 2022/8
N2 - 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.
AB - 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.
KW - COVID-19
KW - Free energy calculations
KW - Main protease
KW - MM/PBSA
KW - Proteomics
KW - TAILS
UR - http://www.scopus.com/inward/record.url?scp=85131919689&partnerID=8YFLogxK
U2 - 10.1016/j.peptides.2022.170814
DO - 10.1016/j.peptides.2022.170814
M3 - Article
C2 - 35644302
AN - SCOPUS:85131919689
SN - 0196-9781
VL - 154
JO - Peptides
JF - Peptides
M1 - 170814
ER -