A proteomics-MM/PBSA dual approach for the analysis of SARS-CoV-2 main protease substrate peptide specificity

Author(s):Show less -

Gallo, Gloria ; Barcick, Uilla ; Coelho, Camila ; Salardani, Murilo ; Camacho, Mauricio F. ; Cajado-Carvalho, Daniela ; Loures, Flavio V. ; Serrano, Solange M. T. ; Hardy, Leon ; Zelanis, Andre ; Wurtele, Martin

• Document type: Journal article
• Source: Peptides; v. 154, p. 8-pg., 2022-08-01.

Abstract

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. (AU)

• FAPESP's process: 13/07467-1 - CeTICS - Center of Toxins, Immune-Response and Cell Signaling
• Grantee: Hugo Aguirre Armelin
• Support Opportunities: Research Grants - Research, Innovation and Dissemination Centers - RIDC
• FAPESP's process: 19/07282-8 - Prospection of markers associated to proteolytic processing in plasma samples of patients with melanoma
• Grantee: André Zelanis Palitot Pereira
• Support Opportunities: Regular Research Grants