Due to the good clinical efficacy in treating Novel Coronavirus Pneumonia (NCP) resulted from

SARS-CoV-2, as the traditional Chinese medicine(TCM) prescription, Lianhua Qingwen Formula

(LQF) was composed into the Diagnosis and Treatment Programs of 2019 New Coronavirus

Pneumonia (from fourth to seventh editions) formulated by the National Health Commission of China.

Aiming to prevent and treat viral influenza, LQF was patented from 2003 in China, and passed the

Phase II clinical trial by FDA in the United States in 2015. However, the molecular mechanism of LQF

anti SARS-CoV-2 pneumonia is still not clear. It is shown that the docking scores of three components

in LQF including Rutin, Forsythoside E, and Hyperoside to main protease of SARS-CoV-2 are very

large as -9.1, -9.0 and -8.7 kcal/mol, respectively, which are even better than those of Lopinavir at -7.3

kcal/mol. Importantly, the binding modes between active compounds and protein were verified via

molecular dynamics (MD) simulation and calculation all the binding free energies at MM-PBSA level.

Note that these donor-acceptor systems were stabilized by non-polar interactions including hydrogen

bonds and hydrophobic interactions. At last, from the constructed component-target-pathway network,

it is shown that the components in LQF are related important pathways to improve the human immunity

such as T cell, B cell receptor signaling, natural killer cell mediated cytotoxicity, as well as anti

inflammatory pathways including Fc epsilon RI, ErbB, MAPK signaling and so on. The present

investigation represents the first report on the molecular mechanism of LQF as NCP inhibitor

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