The Potential Bioactive Components of Nine TCM Prescriptions Against COVID-19 in Lung Cancer Were Explored Based on Network Pharmacology and Molecular Docking

Abstract

ObjectiveThe purpose of this study was to screen active components and molecular targets of nine prescriptions recommended by the National Health Commission (NHC) of China by network pharmacology, and to explore the potential mechanism of the core active components against COVID-19 with molecular docking.MethodsDifferentially expressed genes of lung adenocarcinoma (LUAD) screened by edgeR analysis were overlapped with immune-related genes in MMPORT and COVID-19-related genes in GeneCards. The overlapped genes were also COVID-19 immune-related genes in LUAD. TCMSP platform was used to identify active ingredients of the prescription, potential targets were identified by the UniProt database, and the cross genes with COVID-19 immune-related genes in LUAD were used to construct a Chinese Medicine-Logy-immune target network. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed on the target genes of each prescription. Finally, the key active components were selected for molecular docking simulation with ACE2.ResultsWe obtained 15 overlapping immunization target genes from FPQXZ, HSYFZ, HSZFZ, and QFPDT, 16 overlapping immunization target genes from QYLFZ, SDYFZ, SRYFZ, and YDBFZ, and 17 overlapping immunization target genes from QYLXZ. ADRB2, FOS, HMOX1, ICAM1, IL6, JUN, NFKBIA, and STAT1 also had the highest-ranked therapeutic targets for 9 prescriptions, and their expressions were positively correlated with TME-related stromal score, immune score, and ESTIMATE score. Among 9 compounds with the highest frequency of occurrence in the 9 prescriptions, baicalein had the highest ACE2 binding affinity and can be well-combined into the active pocket of ACE2 It is stabilized by forming hydrogen bonds with ASN290 and ILE291 in ACE2 and hydrophobic interaction with PHE438, ILE291, and PRO415.ConclusionThe nine Chinese medicine prescriptions may play an anti-SARS-CoV-2 role via regulating viral transcription and immune function through multi-component, multi-target, and multi-pathway.

Exploration of molecular targets and mechanisms of Chinese medicinal formula Acacia Catechu ‐Scutellariae Radix in the treatment of COVID‐19 by a systems pharmacology strategy

“…Particularly, we identified that baicalein had good affinity for ACE2 and 3CLpro, mainly through hydrogen bonds and hydrophobic interactions, with measured IC 50 values against SARS‐CoV‐2 3CLpro and ACE2 to be 11.3 and 138.2 μM, respectively, which indicate that baicalein may directly inhibit SARS‐CoV‐2 replication and transcription. Du et al ( 2022 ) also confirmed that baicalein has good binding activity with ACE2 and that hydrogen bonding plays a key role in the recognition and stability of the active ingredients and proteins. In addition, baicalein is the first identified non‐covalent, non‐peptidomimetic inhibitors of SARS‐CoV‐2 3CLpro (Liu et al, 2021 ; Su et al, 2020 ).…”

“…The three‐dimensional (3D) structure of the key target protein was downloaded from the RCSB PDB protein structure database ( https://www.rcsb.org/ ). AutoDock Vina (version 1.5.6) was used to remove the water molecules, isolate proteins, add the nonpolar hydrogen, and calculate Gasteiger charges for the structure (Du et al, 2022 ; Trott & Olson, 2010 ). Then, the corresponding format components and target proteins were signed in http://www.swissdock.ch/docking website to conduct the molecular docking experiment, and the docking binding energy [Estimated ΔG (kcal mol −1 )] was predicted.…”

“…rcsb.org/). AutoDock Vina (version 1.5.6) was used to remove the water molecules, isolate proteins, add the nonpolar hydrogen, and calculate Gasteiger charges for the structure (Du et al, 2022;Trott & Olson, 2010).…”

“…thus further evaluation of the two compounds as potential SARS-CoV-2 ACE2 inhibitors may be warranted. Particularly, we identified that baicalein had good affinity for ACE2 and 3CLpro, mainly through hydrogen bonds and hydrophobic interactions, with measured IC 50 values against SARS-CoV-2 3CLpro and ACE2 to be 11.3 and 138.2 μM, respectively, which indicate that baicalein may directly inhibit SARS-CoV-2 replication and transcription Du et al (2022). also confirmed that baicalein has good binding activity with ACE2 and that hydrogen bonding plays a key role in the recognition and stability of the active ingredients and proteins.…”

Exploring the mechanism of active components from ginseng to manage diabetes mellitus based on network pharmacology and molecular docking

“…We inputted the intersection targets into STRING 11.0 ( https://string-db.org/ ) to obtain their reciprocal relationships 19 . Selection parameters were set to “Homo sapiens”, and the confidence level was set at 0.400 for the minimum required interaction score, and hid ligand disconnected nodes in the network.…”