Targeted structural design of molecular scaffolds for dual-action peptidomimetic inhibitors against SARS-CoV-2 MPRO and PLPRO

Authors

DOI:

https://doi.org/10.15587/2519-4852.2025.337951

Keywords:

SARS-CoV-2, Mpro protease, PLpro protease, peptidomimetics, dual inhibitors, molecular docking

Abstract

The two proteases of SARS-CoV-2 coronavirus – the main protease (Mpro or 3CLpro) and the papain-like protease (PLpro) – are essential enzymes required for the successful replication of the virus within cells. Both proteases have become major targets in the development of antiviral drugs against SARS-CoV-2. The potential to achieve a dual inhibitory effect has sparked significant interest in creating dual inhibitors as complex therapeutic agents for this virus. In this article, we discuss the development and in silico evaluation of a series of new peptidomimetic molecules designed as dual-action inhibitors of both SARS-CoV-2 Mpro and PLpro, along with their synthesis. We implemented a combined approach that began with developing a basic molecular model, considering the substrate specificity of the active centers of each protease. Through rational in silico design, we created a series of peptidomimetics. Further analysis of how these compounds bound to the active sites of both proteases enabled us to identify several new structural hits, including hydantoin derivatives, as potential dual inhibitors of Mpro and PLpro.

The aim of the study. This study aims to establish a common molecular framework for designing dual-action inhibitors targeting the SARS-CoV-2 Mpro and PLpro proteases. The research includes receptor-oriented molecular docking, in silico optimization, and the selection and synthesis of the most active candidate structures for further in vitro experimental studies.

Materials and methods. LigandScout 4.5 software is used for 3D pharmacophore analysis, visualization, and molecular docking. AutoDock Vina 1.1 provides tools for molecular docking. The PLIP (Protein-Ligand Interaction Profiler) web servers are utilized to study molecular binding mechanisms. DataWarrior 6.0 software helps create a library of molecular structures, calculate physicochemical properties, and analyze molecular frameworks. SwissADME web server is used to predict ADME parameters and assess the pharmacokinetic properties of small molecules as potential drugs.

Results. We analyzed the substrate specificity of the binding sites of the Mpro and PLpro proteases, which enabled us to identify a common amino acid sequence containing shared recognition elements for both proteases. By rationally modifying the functional groups in this initial base structure, utilizing the principle of isosteric replacement and incorporating non-classical bioisosteres, we developed a series of peptidomimetic frameworks. Molecular docking conducted at the active sites of both Mpro and PLpro, along with the assessment of their binding energy values (in kcal/mol), identified several structures with potential for dual inhibition. Notably, hydantoin derivatives demonstrated the strongest binding affinity to the active sites of both proteases.

Conclusions. We have identified promising peptidomimetic molecular structures that demonstrate dual inhibitory activity against the SARS-CoV-2 proteases through in silico analysis. Specifically, we discovered a novel class of hydantoin derivatives that act as inhibitors for both SARS-CoV-2 Mpro and PLpro. The synthesis methods we developed allow for the preparation of these compounds for further in vitro studies

Supporting Agency

  • Grant No. 96/0062 (2021.01/0062) “Molecular design, synthesis and screening of new potential antiviral pharmaceutical ingredients for the treatment of infectious diseases COVID-19” from the National Research Foundation of Ukraine

Author Biographies

Larysa Yevsieieva, V. N. Karazin Kharkiv National University

Senior Lecturer

Education and Research Institute of Chemistry

Alexander Kyrychenko, V. N. Karazin Kharkiv National University

Doctor of Chemical Sciences, Head of Department

Education and Research Institute of Chemistry

Pavlo Trostianko, V. N. Karazin Kharkiv National University

PhD Student

Education and Research Institute of Chemistry

Volodymyr Ivanov, V. N. Karazin Kharkiv National University

Doctor of Chemical Sciences, Professor

Education and Research Institute of Chemistry

Sergiy M. Kovalenko, V. N. Karazin Kharkiv National University

Doctor of Chemical Sciences, Professor

Education and Research Institute of Chemistry

Oleg Kalugin, V. N. Karazin Kharkiv National University

Doctor of Chemical Sciences, Professor

Education and Research Institute of Chemistry

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Targeted structural design of molecular scaffolds for dual-action peptidomimetic inhibitors against SARS-CoV-2 MPRO and PLPRO

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2025-10-27

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Yevsieieva, L., Kyrychenko, A., Trostianko, P., Ivanov, V., Kovalenko, S. M., & Kalugin, O. (2025). Targeted structural design of molecular scaffolds for dual-action peptidomimetic inhibitors against SARS-CoV-2 MPRO and PLPRO. ScienceRise: Pharmaceutical Science, (5 (57), 56–67. https://doi.org/10.15587/2519-4852.2025.337951

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No. 5 (57) (2025)

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Pharmaceutical Science

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Copyright (c) 2025 Larysa Yevsieieva, Alexander Kyrychenko, Pavlo Trostianko, Volodymyr Ivanov, Sergiy M. Kovalenko, Oleg Kalugin

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