Molecular docking and molecular dynamics study Lianhua Qingwen granules (LHQW) treats COVID-19 by inhibiting inflammatory response and regulating cell survival

Abstract

Purpose2019 Coronavirus disease (COVID-19) is endangering health of populations worldwide. Latest research has proved that Lianhua Qingwen granules (LHQW) can reduce tissue damage caused by inflammatory reactions and relieve patients’ clinical symptoms. However, the mechanism of LHQW treats COVID-19 is currently lacking. Therefore, we employed computer simulations to investigate the mechanism of LHQW treats COVID-19 by modulating inflammatory response.MethodsWe employed bioinformatics to screen active ingredients in LHQW and intersection gene targets. PPI, GO and KEGG was used to analyze relationship of intersection gene targets. Molecular dynamics simulations validated the binding stability of active ingredients and target proteins. Binding free energy, radius of gyration and the solvent accessible surface area were analyzed by supercomputer platform.ResultsCOVID-19 had 4628 gene targets, LHQW had 1409 gene targets, intersection gene targets were 415. Bioinformatics analysis showed that intersection targets were closely related to inflammation and immunomodulatory. Molecular docking suggested that active ingredients (including: licopyranocoumarin, Glycyrol and 3-3-Oxopropanoic acid) in LHQW played a role in treating COVID-19 by acting on CSF2, CXCL8, CCR5, NLRP3, IFNG and TNF. Molecular dynamics was used to prove the binding stability of active ingredients and protein targets.ConclusionThe mechanism of active ingredients in LHQW treats COVID-19 was investigated by computer simulations. We found that active ingredients in LHQW not only reduce cell damage and tissue destruction by inhibiting the inflammatory response through CSF2, CXCL8, CCR5 and IFNG, but also regulate cell survival and growth through NLRP3 and TNF thereby reducing apoptosis.

Identification of A Potential Inhibitor for Anticancer Target MTHFD2 by Consensus Docking and Molecular Dynamics

“…As demonstrated in prior research, the analysis of the docked conformations of virtual screened ligands, when compared to experimentally confirmed binding poses, serves as a valuable validation step for assessing the reliability of the docking protocol [38]. The binding mode examination reveals that both ligands occupy the binding pocket of the established ligands B01 and D56, but present slightly different binding modes.…”

Potential herb–drug interactions between anti-COVID-19 drugs and traditional Chinese medicine

“…The active metabolites of Remdesivir and Molnupiravir selectively inhibit RdRp, which delays viral RNA chain termination and inhibits SARS-CoV-2 replication 24 . Previous studies revealed that many herbs and their bioactive ingredients could bind to ACE2, 3CLpro, and RdRp and inhibit their activities 486 , 487 . Compared with antiviral drug treatment alone, JHQG combined with antiviral drugs was superior in relieving fever and poor appetite in patients with COVID-19 488 .…”

“…A meta-analysis indicated that LHQW combined with conventional therapy could effectively reduce the severity in patients with mild or moderate COVID-19 490 . LHQW significantly inhibited SARS-CoV-2 replication in Vero E6 cells, and three ingredients (rutin, forsythoside E, and hyperoside) in LHQW were better bound to 3CLpro than Lopinavir based on the docking scores 271 , 487 . Baicalein and quercetin, as the top two ingredients of HSBD, have shown high affinity to 3CLpro and ACE2, which was further suggested in a study that showed that HSFD strengthened the efficacy of lopinavir–ritonvir in the treatment of 60 patients with COVID-19 491 .…”

Efficacy and safety of Lianhua Qingwen granule combined with azithromycin for mycoplasma pneumoniae pneumonia in children: a systematic review with meta-analysis and trial sequential analysis

“…Pharmacological studies have confirmed the antiviral, antibacterial, anti-inflammatory, and immunomodulatory properties of LHQW ( Hu et al, 2022 ). Furthermore, LHQW has been found to reduce tissue damage caused by inflammatory responses and alleviate pulmonary symptoms ( Shen and Yin, 2021 ; Cao et al, 2022 ). Compared to traditional decoction, LHQW granule offers the advantages of convenience in carrying, storing, and administration, making it more suitable for children.…”