A review on computational approaches that support the researches on traditional Chinese medicines (TCM) against COVID-19

Ruchawapol, Chattarin; Fu, Wenwei; Xu, Hong‐Xi

doi:10.1016/j.phymed.2022.154324

Cited by 5 publications

(3 citation statements)

References 179 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The active site of M pro is an extensively studied drug target situated in the crevice between structural domains 2 and 3 . This active site encompasses five crucial subsites for substrate recognition: S1′, S1, S2, S4. , Numerous small molecules targeting the active site of M pro have been discovered. , Among them, Ensitreivir stands out as the first orally administered clinical candidate, belonging to the category of noncovalent nonpeptidic inhibitors. , Structural modifications of small-molecule inhibitors against this target have been a thriving area of research, aiming to circumvent patents, enhance drug activity, or reduce resistance arising from viral mutations. − …”

Section: Resultsmentioning

confidence: 99%

“…51,52 Numerous small molecules targeting the active site of M pro have been discovered. 53,54 Among them, Ensitreivir stands out as the first orally administered clinical candidate, belonging to the category of noncovalent nonpeptidic inhibitors. 43,54 Structural modifications of small-molecule inhibitors against this target have been a thriving area of research, aiming to circumvent patents, enhance drug activity, or reduce resistance arising from viral mutations.…”

Section: Pocket Scoring and Automatic Pocketmentioning

confidence: 99%

See 1 more Smart Citation

Subpocket-Based Analysis Approach for the Protein Pocket Dynamics

Lv,

Cao

2024

J. Chem. Theory Comput.

View full text Add to dashboard Cite

Structural and dynamic characteristics of protein pockets remarkably influence their biological functions and are also important for enzyme engineering and new drug research and development. To date, several softwares have been developed to analyze the dynamic properties of protein pockets. However, due to the complexity and diversity of the pocket information during the kinetic relaxation, further improvement and capacity expansion of current tools are required. Here, we developed a platform software AlphaTraj in which a computational strategy that divides the whole protein pocket into subpockets and examines various properties of the subpockets such as survival time, stability, and correlation was proposed and implemented. We also proposed a scoring function for the subpockets as well as the whole pocket to visualize the quality of the pocket. Furthermore, we implemented automated conformational search functions for ligand docking and ligand optimization. These functions may help us to gain a deep understanding of the dynamic properties of protein pockets and accelerate the protein engineering and the design of inhibitors and small-molecule drugs. The software is freely available at under the GNU GPL license.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Pocket Scoring and Automatic Pocketmentioning

confidence: 99%

Subpocket-Based Analysis Approach for the Protein Pocket Dynamics

Lv,

Cao

2024

J. Chem. Theory Comput.

View full text Add to dashboard Cite

show abstract

“…1 In addition, network pharmacology integrates the interaction into a network and analyzes the action of traditional Chinese medicine (TCM) from a systematic perspective. 2 Meanwhile, some problems such as the difficulty of data integration for network pharmacology remain to be overcome. The signed random walk with restart (SRWR) has been developed to simulate the propagation of activation or inhibition effects of the drug on the signaling network.…”

Section: Introductionmentioning

confidence: 99%

Network Pharmacology Revealed the Mechanisms of Action of Lithospermum erythrorhizon Sieb on Atopic Dermatitis

Wang¹,

Wang²,

Zhao³

et al. 2023

CCID

View full text Add to dashboard Cite

The application of network analysis algorithms promoted the development of network pharmacology. This study aimed to combine network pharmacology and signed random walk with restart (SRWR) to reveal the mechanism by which Lithospermum erythrorhizon Sieb (LES) exerts effects on atopic dermatitis (AD). Methods: The compounds and targets of LES were retrieved from Traditional Chinese Medicine Integrated Database (TCMID) and Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), and important compounds and targets were identified by intersection analysis and protein-protein interaction (PPI) network. Results: We found that active LES-derived compounds such as caffeic acid, Isovaleric acid, Arnebinol, and Alannan may inhibit PTGS2, HSP90AA1 and MAPK14, which are key mediators involved in PI3K-Akt pathway, vascular endothelial growth factor signaling pathway, Fc epsilon RI signaling pathway, and calcium signaling pathway. Conclusion:The application of SRWR could identify potential targets of LES with a low false-positive rate and help elucidate the mechanism of action of traditional Chinese medicine.

show abstract