In silico and in vitro studies of organoselenium compounds interaction with Mpro and PLpro from SARS-CoV-2
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2023-02-24Primeiro coorientador
Orian, Laura
Primeiro membro da banca
Rodriguez, Ihosvany Camps
Segundo membro da banca
Bellanda, Massimo
Terceiro membro da banca
Scott, Ana Ligia Barbour
Quarto membro da banca
Sancineto, Luca
Metadatos
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The SARS-CoV-2 pandemic has prompted global efforts to develop therapeutics. The main protease of SARS-CoV-
2 (Mpro) and the papain-like protease (PLpro) are essential for viral replication and are key targets for therapeutic
development. These two proteases have no equivalent enzymatic analogs in humans and thus no similar cleavage
specificity, implying that their inhibition will likely have low or no toxicity. The Mpro activity has more than 11
cleavage sites on larger polyproteins, cleaving the C-terminus of replicase polyproteins with recognition sequence
Ile-Leu-Met-Val-Phe-Gln**Ser-Gly-Ala,Cys-Asn where the symbol ** marks the cleavage sites. Inhibiting the
activity of Mpro will block viral replication. The enzyme mechanism is via a catalytic dyad formed by a nucleophilic
Cysteine (Cys145) activated by a His41 residue. Attacks on substrate leads to a tetrahedral intermediate from which
the actual peptide bond cleavage occurs thanks to the back-proton-transfer from His45 of Mpro leading to a thioester
after a preliminary proton transfer from Cys145 to His41, which greatly increases the nucleophilic strength of the
former residue. PLpro is responsible for cleavages located at the N-terminus of the replicase polyprotein, possessing
deubiquitinating/deISGylating activity. Cys111, His272, and Asp286 residues form a catalytic triad in the active
site of PLpro, with Cys111 acting as the critical nucleophile in the peptide bond cleavage from the pp1a and pp1ab.
The two proteases have very similar mechanisms, and as our results show, there is more to these proteases than
meets the eye. Several in vitro assays have revealed that organochalcogen compounds, such as ebselen, inhibit Mpro
and PLpro as well as having antiviral activity. However, much remains unknown about the whys and the important
role that organochalcogen plays in these mechanisms, which are embedded within the binding site’s structure,
dynamics, and energetics. To investigate this, we use a wide range of computational chemistry approaches, including
molecular docking, virtual screening, kmeans analysis, molecular dynamics, molecular mechanics, quantum
mechanics, and hybrid methods focusing on reactivity. Among the organochalcogens explored, diphenyldiselenide
(PhSe)2, a parent compound of diaryl diselenide with a low electrophilic potential, serves as a prototype model for
a diselenide as well as a potential therapeutic agent. In Vero cells, the inhibitory concentration of (PhSe)2against
SARS-CoV-2 is in the low micromolar range. The free energy landscape for the mechanism of inhibition was
computed using a combined molecular dynamic and Density Functional Theory (DFT) approach. We investigated
two possible routes of diselenide inhibition in proteases: non-covalent inhibition via pi-stacking interactions with
His-41 of Mpro and His-272 of PLpro, and covalent inhibition via the protease-Cys-SePh inhibitor complex. The
findings highlight the benefits and drawbacks of diselenide and offer recommendations for rational drug design of
bioorganic selenium-based inhibitors.
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