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COVID-19-6LU7-complex-FMO-analyses-2020316-a.pdf (1.37 MB)
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Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease - Inhibitor N3 Complex (PDB ID:6LU7)

preprint
submitted on 16.03.2020 and posted on 17.03.2020 by Ryo Hatada, Koji Okuwaki, Yuji Mochizuki, Kaori Fukuzawa, Yuto Komeiji, Yoshio Okiyama, Shigenori Tanaka
The worldwide spread of COVID-19 (new coronavirus found in Wuhan in 2019) is an emergent issue to be tackled. In fact, a great amount of works in various fields have been made in rather short period. Here, we report a fragment molecular orbital (FMO) based interaction analysis on a complex between the SARS-CoV-2 main protease (Mpro) and its peptide-like inhibitor N3 (PDB ID: 6LU7). The target inhibitor molecule was segmented into five fragments in order to capture site specific interactions with amino acid residues of the protease. The interaction energies were decomposed into several contributions, and then the characteristics of hydrogen bonding and dispersion stabilization were made clear. Furthermore, the hydration effect was incorporated by the Poisson-Boltzmann (PB) scheme. From the present FMO study, His41, His163, His164, and Glu166 were found to be the most important amino acid residues of Mpro in interacting with the inhibitor, mainly due to hydrogen bonding. A guideline for optimizations of the inhibitor molecule was suggested as well based on the FMO analysis.

Funding

A social and scientific priority issue #6 (Accelerated Development of Innovative Clean Energy Systems) to be tackled by using post-K computer ("Fugaku")

Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS) from Japan Agency for Medical Research and Development (AMED) under grant number JP19am0101113

Rikkyo SFR

History

Email Address of Submitting Author

fullmoon@rikkyo.ac.jp

Institution

Rikkyo University

Country

Japan

ORCID For Submitting Author

0000-0002-7310-5183

Declaration of Conflict of Interest

No conflict of interest

Version Notes

2020/3/16, JST - 1st version 2020/3/17, JST - minor update of 1st version

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