Thiophene-fused γ-lactams inhibit the SARS-CoV-2 main protease via reversible covalent acylation

Gayatri, Lennart Brewitz, Lewis Ibbotson, Eidarus Salah, Shyam Basak, Hani Choudhry and Christopher J. Schofield

Chem. Sci., 2024, 15, 7667
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Inhibition of SARS-CoV-2 3CLpro by chemically modified tyrosinase from Agaricus bisporus

David Aguilera-Rodriguez, David Ortega-Alarcon, Angela Vazquez-Calvo, Veronica Ricci, Olga Abian, Adrian Velazquez-Campoy, Antonio Alcami and Jose M. Palomo

RSC Med. Chem., 2024, 15, 4159
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Towards the discovery of molecules with anti-COVID-19 activity: Relationships between screening and docking results

Dmytro Anokhin, Sergiy Kovalenko, Pavlo Trostianko, Alexander Kyrychenko, Anton Zakharov, Tetiana Zubatiuk, Volodymyr Ivanov and Oleg Kalugin

Chemical Series, 2024, 6
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Native Folding Stability of the Main Protease of Coronavirus SARS-CoV-2 on a Gold Surface

Alexander Kyrychenko, Mykyta V. Prud, Kateryna O. Lohachova, Oleg V. Prezhdo and Oleg N. Kalugin

J. Phys. Chem. Lett., 2025, 16, 11222
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Evolving SARS-CoV-2 Vaccines: From Current Solutions to Broad-Spectrum Protection

Rui Qiao, Jiayan Li, Jiami Gong, Yuchen Shao, Jizhen Yu, Yumeng Chen, Yinying Lu, Luxuan Yang, Luanfeng Lin, Zixin Hu, Pengfei Wang, Xiaoyu Zhao and Wenhong Zhang

Vaccines, 2025, 13, 635
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Studying Ligand-Protein Interactions in the Era of Artificial Intelligence: Benchmarking Boltz-1 for 3D-Structure Prediction of Biomolecular Complexes

Mykyta Prud and Alexander Kyrychenko

Chemical Series, 2025, 57
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Evolutionary Structure Optimization of Ensitrelvir as Non-Covalent Inhibitor of SARS-CoV-2 Main Protease Mpro

Kateryna Lohachova, Anastasiia Sviatenko, Alexander Kyrychenko and Oleg Kalugin

Chemical Series, 2024, 26
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Support Enzyme Loading Influences the Effect of Aldehyde Dextran Modification on the Specificity of Immobilized Ficin for Large Proteins

El Hocine Siar, Pedro Abellanas-Perez, Javier Rocha-Martin and Roberto Fernandez-Lafuente

Molecules, 2024, 29, 3674
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Inhibitors Targeting SARS‐CoV‐2 Papain‐Like Protease: Screening, Design, Synthesis, and Biological Evaluation

Elena‐Oriana Iuga, Nilu Gone, Mariana Ortiz de Godoy, Gabriel Correa Verissimo, Giovanna de Jesus Agostinetto, Liam Urich, Nadine Krüger, Thales Kronenberger, Rafael Victorio Carvalho Guido, Anthony J. O’Donoghue, Stefan A. Laufer and Thanigaimalai Pillaiyar

ChemMedChem, 2026, 21
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Computational Discovery of Natural Dual Inhibitors Targeting SARS‐CoV‐2 Main and Papain‐Like Proteases

Imane Yamari, Lamiae ElBouamri, Abdelkbir Errougui, Mohammed Talbi, Mohammed Bouachrine, M'Hammed El Kouali and Samir Chtita

ChemistrySelect, 2025, 10
DOI: 10.1002/slct.202501293

Integrating biochemical, computational, and randomized clinical trials to evaluate the efficacy of herbal formulation against SARS-CoV-2

Sudhir Dadram Patsute, Suchitra Ganeshacharya, Sarita Singh, William Rananaware, Sandeep Kumar Thakur, Kshipra Rajoria, Sarvesh Kumar Singh and Pawan Kumar Singh

Journal of Investigative Medicine, 2026
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From ML300 to Novel Non-covalent Inhibitors of SARS‑CoV‑2 Main Protease via Evolutionary De Novo Design, Virtual Screening, Molecular Dynamics, and Retrosynthetic Strategies

Anna Geleverya, Alexander Kyrychenko, Volodymyr V. Ivanov, Larysa V. Yevsieieva, Volodymyr Fetyukhin, Sergiy M. Kovalenko and Oleg N. Kalugin

Polycyclic Aromatic Compounds, 2026, 1
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Benchmarking Google DeepMind’s AlphaFold 3 Performance for Protein 3D-Structure Prediction

Yelyzaveta Duma and Alexander Kyrychenko

Chemical Series, 2024, 6
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Benchmarking biomolecular force fields for molecular dynamics simulations of native fold and enzymatic activity of SARS-CoV-2 papain-like protease

Kateryna O. Lohachova, Alexander Kyrychenko and Oleg N. Kalugin

Heliyon, 2025, 11, e43578
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Computational evaluation and benchmark study of 342 crystallographic holo-structures of SARS-CoV-2 Mpro enzyme

Hamlet Khachatryan, Mher Matevosyan, Vardan Harutyunyan, Smbat Gevorgyan, Anastasiya Shavina, Irina Tirosyan, Yeva Gabrielyan, Marusya Ayvazyan, Marine Bozdaganyan, Zeynab Fakhar, Sajjad Gharaghani and Hovakim Zakaryan

Sci Rep, 2024, 14
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Towards the computational design of organic molecules with specified properties

Anton B. Zakharov, Mariia Kyrpa, Alexander V. Kyrychenko, Sergiy M. Kovalenko, Oleg N. Kalugin, Volodymyr V. Ivanov and Ludwik Adamowicz

Struct Chem, 2025, 36, 723
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Rerouting therapeutic peptides and unlocking their potential against SARS-CoV2

Namrata Prashar, Saharuddin Bin Mohammed, N. S. Raja and Habeeb Shaik Mohideen

3 Biotech, 2025, 15
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Nanoparticles of natural product-derived medicines: Beyond the pandemic

Yedi Herdiana

Heliyon, 2025, 11, e42739
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Critical assessment of popular biomolecular force fields for molecular dynamics simulations of folding and enzymatic activity of main protease of coronavirus SARS-CoV-2

Kateryna O. Lohachova, Alexander Kyrychenko and Oleg N. Kalugin

Biophysical Chemistry, 2024, 311, 107258
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Integrated Exploration of Pyranocoumarin Derivatives as Synergistic Inhibitors of Dual-target for Mpro and PLpro Proteins of SARS-CoV- 2 through Molecular Docking, ADMET Analysis, and Molecular Dynamics Simulation

Imane Yamari, Lamiae El Bouamri, Oussama Abchir, Mohammed Bouachrine, Mhammed El Kouali, Abdelouahid Samadi and Samir Chtita

CMC, 2025, 32, 5530
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Design, synthesis, and binding analysis of target-specific covalent inhibitors of SARS-CoV-2 papain-like protease

Martynas Bagdonas, Laimonas Stančaitis, Ernestas Urniežius, Audrius Zakšauskas, Aurelija Mickevičiūtė, Rūta Kananavičiūtė, Audronė Rukšėnaitė, Vaida Juozapaitienė, Jurgita Matulienė, Visvaldas Kairys, Franz-Josef Meyer-Almes, Asta Zubrienė and Daumantas Matulis

European Journal of Medicinal Chemistry Reports, 2025, 15, 100306
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Discovery of 3-phenyl-1H-5-pyrazolylamides as PLpro inhibitors through virtual screening and structure optimization

Chengwei Wu, Mengdie Ou, Bo Qin, Shuo Wang, Peng Li, Sheng Cui, Haihong Huang and Gang Li

Bioorganic & Medicinal Chemistry Letters, 2025, 127, 130293
DOI: 10.1016/j.bmcl.2025.130293

Comparative Evaluation of Computational Methods for Modeling SARS-CoV-2 Spike Protein RBD - Antibody Complexes

Vira Morozova, Mykyta Prud and Alexander Kyrychenko

Kharkov University Bulletin Chemical Series, 2025, 21
DOI: 10.26565/2220-637X-2025-45-02