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

Autor(es):Mostrar menos -

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

• Tipo de documento: Artigo Científico
• Fonte: Peptides; v. 154, p. 8-pg., 2022-08-01.

Resumo

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)

• Processo FAPESP: 11/50963-4 - Biologia estrutural de proteinas processadoras de acidos nucleicos em bacterias com elevada relevancia biomedica
• Beneficiário: Martin Rodrigo Alejandro Wurtele Alfonso
• Modalidade de apoio: Auxílio à Pesquisa - Regular
• Processo FAPESP: 13/07467-1 - CeTICS - Centro de Toxinas, Imuno-Resposta e Sinalização Celular
• Beneficiário: Hugo Aguirre Armelin
• Modalidade de apoio: Auxílio à Pesquisa - Centros de Pesquisa, Inovação e Difusão - CEPIDs
• Processo FAPESP: 19/07282-8 - Prospecção de marcadores associados a processamento proteolítico em amostras de plasma de pacientes com melanoma
• Beneficiário: André Zelanis Palitot Pereira
• Modalidade de apoio: Auxílio à Pesquisa - Regular