Comprehensive fitness landscape of SARS-CoV-2 Mpro reveals insights into viral resistance mechanisms

JM Flynn, N Samant, G Schneider-Nachum, DT Barkan… - Elife, 2022 - elifesciences.org
With the continual evolution of new strains of severe acute respiratory syndrome coronavirus-
2 (SARS-CoV-2) that are more virulent, transmissible, and able to evade current vaccines …

Pre‐exascale HPC approaches for molecular dynamics simulations. Covid‐19 research: A use case

M Wieczor, V Genna, J Aranda… - Wiley …, 2023 - Wiley Online Library
Exascale computing has been a dream for ages and is close to becoming a reality that will
impact how molecular simulations are being performed, as well as the quantity and quality of …

Supervised Molecular Dynamics (SuMD) Insights into the mechanism of action of SARS-CoV-2 main protease inhibitor PF-07321332

M Pavan, G Bolcato, D Bassani… - Journal of Enzyme …, 2021 - Taylor & Francis
The chemical structure of PF-07321332, the first orally available Covid-19 clinical candidate,
has recently been revealed by Pfizer. No information has been provided about the …

Virus structure and structure-based antivirals

Z Plavec, I Pöhner, A Poso, SJ Butcher - Current opinion in virology, 2021 - Elsevier
Highlights•Drug repurposing for corona-virus and picorna-virus protease broad range
inhibitors.•Promising developments in RNA-dependent RNA polymerase broad range …

The H163A mutation unravels an oxidized conformation of the SARS-CoV-2 main protease

N Tran, S Dasari, SAE Barwell, MJ McLeod… - Nature …, 2023 - nature.com
The main protease of SARS-CoV-2 (Mpro) is an important target for developing COVID-19
therapeutics. Recent work has highlighted Mpro's susceptibility to undergo redox-associated …

Diphenyl Diselenide and SARS-CoV-2: in silico Exploration of the Mechanisms of Inhibition of Main Protease (Mpro) and Papain-like Protease (PLpro)

FB Omage, A Madabeni, AR Tucci… - Journal of Chemical …, 2023 - ACS Publications
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 …

[HTML][HTML] Multi-ligand molecular docking, simulation, free energy calculations and wavelet analysis of the synergistic effects between natural compounds baicalein and …

H Li, A Komori, M Li, X Chen, AWH Yang, X Sun… - Journal of Molecular …, 2023 - Elsevier
Combination drugs have been used for several diseases for many years since they produce
better therapeutic effects. However, it is still a challenge to discover candidates to form a …

[HTML][HTML] SARS-CoV-2 proteases Mpro and PLpro: Design of inhibitors with predicted high potency and low mammalian toxicity using artificial neural networks, ligand …

RS Tumskiy, AV Tumskaia, IN Klochkova… - Computers in Biology …, 2023 - Elsevier
The main (Mpro) and papain-like (PLpro) proteases are highly conserved viral proteins
essential for replication of the COVID-19 virus, SARS-COV-2. Therefore, a logical plan for …

Identification of pyrazole derivatives of usnic acid as novel inhibitor of SARS-CoV-2 main protease through virtual screening approaches

M Roney, G Singh, AKMM Huq, MS Forid… - Molecular …, 2024 - Springer
The infection produced by the SARS-CoV-2 virus remains a significant health crisis
worldwide. The lack of specific medications for COVID-19 necessitates a concerted effort to …

Novel covalent and non-covalent complex-based pharmacophore models of SARS-CoV-2 main protease (Mpro) elucidated by microsecond MD simulations

Y Hayek-Orduz, AF Vásquez, MF Villegas-Torres… - Scientific Reports, 2022 - nature.com
As the world enters its second year of the pandemic caused by SARS-CoV-2, intense efforts
have been directed to develop an effective diagnosis, prevention, and treatment strategies …