Identification of triazolopyrimidinyl scaffold SARS-CoV-2 papain-like protease (PL$^{pro}$) inhibitor

Kralj, Sebastjan (author), Jukič, Marko (author), Bahun, Miha (author), Kranjc, Luka (author), Kolarič, Anja (author), Hodošček, Milan (author), Poklar Ulrih, Nataša (author), Bren, Urban (author)

The global impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its companion disease, COVID-19, has reminded us of the importance of basic coronaviral research. In this study, a comprehensive approach using molecular docking, in vitro assays, and molecular dynamics simulations was applied to identify potential inhibitors for SARS-CoV-2 papain-like protease (PL$^{pro}$), a key and underexplored viral enzyme target. A focused protease inhibitor library was initially created and molecular docking was performed using CmDock software (v0.2.0), resulting in the selection of hit compounds for in vitro testing on the isolated enzyme. Among them, compound 372 exhibited promising inhibitory properties against PL$^{pro}$, with an IC50 value of 82 ± 34 µM. The compound also displayed a new triazolopyrimidinyl scaffold not yet represented within protease inhibitors. Molecular dynamics simulations demonstrated the favorable binding properties of compound 372. Structural analysis highlighted its key interactions with PL$^{pro}$, and we stress its potential for further optimization. Moreover, besides compound 372 as a candidate for PL$^{pro}$ inhibitor development, this study elaborates on the PL$^{pro}$ binding site dynamics and provides a valuable contribution for further efforts in pan-coronaviral PL$^{pro}$ inhibitor development.

• Language: English
• Keywords: drug design, protease inhibitor, SARS-CoV-2, papain-like protease, PL$^{pro}$, antiviral design, in silico drug design, CADD, virtual screening, HTVS, structure-based design
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: BF - Biotechnical Faculty
• Publication status: Published
• Publication version: Version of Record
• Year: 2024
• Number of pages: 13 str.
• Numbering: Vol. 16, iss. 2, art. 169
• PID: 20.500.12556/RUL-164981
• UDC: 60:543.2/.9
• ISSN on article: 1999-4923
• DOI: 10.3390/pharmaceutics16020169
• COBISS.SI-ID: 182627331
• Publication date in RUL: 19.11.2024

Record is a part of a journal

• Title: Pharmaceutics
• Shortened title: Pharmaceutics
• Publisher: MDPI
• ISSN: 1999-4923
• COBISS.SI-ID: 517949977

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.

Secondary language

• Language: Slovenian
• Keywords: zdravila, inhibitorji proteaze, proteaza