English (United Kingdom)

https://curated-unify.zendy.io/wp-json/zendy-region/v1/featured_content/oa?rat=en

https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

Global: Zendy Tools annual

Presents the keyphrase highlighting as premium feature

Keyphrase Highlighting

Presents the summarisation as premium feature

Summarisation

Insights

Presents the pdf analysis as premium feature

PDF Analysis

Presents the zaia usage as premium feature

ZAIA

Global: Zendy Tools monthly

Global: Zendy Plus monthly

Presents the access of premium content as premium feature

Premium Content

Global: Zendy Plus annual

Global: Zendy Free Plan

Molecular dynamics simulations with the QM(DFT)/MM potentials are utilized to discriminate between reactive and nonreactive complexes of the SARS-CoV-2 main protease and its substrates. Classification of frames along the molecular dynamic trajectories is utilized by analysis of the 2D maps of the Laplacian of electron density. Those are calculated in the plane formed by the carbonyl group of the substrate and a nucleophilic sulfur atom of the cysteine residue that initiates enzymatic reaction. Utilization of the GPU-based DFT code allows fast and accurate simulations with the hybrid functional PBE0 and double-zeta basis set. Exclusion of the polarization functions accelerates the calculations 2-fold, however this does not describe the substrate activation. Larger basis set with d-functions on heavy atoms and p-functions on hydrogen atoms enables to disclose equilibrium between the reactive and nonreactive species along the MD trajectory. The suggested approach can be utilized to choose covalent inhibitors that will readily interact with the catalytic residue of the selected enzyme.

Computational Characterization of the Substrate Activation in the Active Site of SARS-CoV-2 Main Protease