Statistical interaction analyses between SARS-CoV-2 main protease and inhibitor N3 by combining molecular dynamics simulation and fragment molecular orbital calculation | Zendy

Ryo Hatada | Zendy; Koji Okuwaki | Zendy; Kazuki Akisawa | Zendy; Yuji Mochizuki | Zendy; Yuma Handa | Zendy; Kaori Fukuzawa | Zendy; Yuto Komeiji | Zendy; Yoshio Okiyama | Zendy; Shigenori Tanaka | Zendy

Open Access

Statistical 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 , fragment (logic) , amino acid residue , protease , ab initio , molecular orbital , computational chemistry , statistical physics , chemistry , covid-19 , physics , biological system , computational biology , molecule , biology , enzyme , peptide sequence , biochemistry , computer science , algorithm , gene , quantum mechanics , medicine , disease , pathology , infectious disease (medical specialty)

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.

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