Open AccessStatistical interaction analyses between SARS-CoV-2 main protease and inhibitor N3 by combining molecular dynamics simulation and fragment molecular orbital calculation
Author(s) -
Ryo Hatada,
Koji Okuwaki,
Kazuki Akisawa,
Yuji Mochizuki,
Yuma Handa,
Kaori Fukuzawa,
Yuto Komeiji,
Yoshio Okiyama,
Shigenori Tanaka
Publication year - 2021
Publication title -
applied physics express
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.911
H-Index - 94
eISSN - 1882-0786
pISSN - 1882-0778
DOI - 10.35848/1882-0786/abdac6
Subject(s) - fragment molecular orbital , molecular dynamics , protease , fragment (logic) , amino acid residue , ab initio , chemistry , computational chemistry , molecular orbital , statistical physics , physics , molecule , enzyme , peptide sequence , biochemistry , computer science , algorithm , organic chemistry , gene
A combination of classical molecular dynamics (MD) simulation and ab initio fragment molecular orbital (FMO) calculation was applied to a complex formed between the main protease of the new coronavirus and the inhibitor N3 to calculate interactions within the complex while incorporating structural fluctuations mimicking physiological conditions. Namely, a statistical evaluation of interaction energies between N3 and amino acid residues was performed by processing a thousand of structure samples. It was found that relative importance of each residue is altered by the structural fluctuation. The MD-FMO combination should be promising to simulate protein related systems in a more realistic way.