Target identification of anticancer natural products using a chemical proteomics approach

Bhukta, Swadhapriya; Gopinath, Pushparathinam; Dandela, Rambabu

doi:10.1039/d1ra04283a

Cited by 8 publications

(1 citation statement)

References 108 publications

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“…Te search for target genes is a very important part of the drug discovery process. Intriguingly, mounting molecules, compounds, and drugs have been noted to share complex relationships with a large quantity of genes and proteins [47][48][49]. TCM and natural compounds contain a large number of active ingredients, which provides more possibilities and opportunities for drug development and use.…”

Section: Discussionmentioning

confidence: 99%

The Regulatory Network of Gastric Cancer Pathogenesis and Its Potential Therapeutic Active Ingredients of Traditional Chinese Medicine Based on Bioinformatics, Molecular Docking, and Molecular Dynamics Simulation

Yang

Liu

2022

Evidence-Based Complementary and Alternative Medicine

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Objective. This study aims to investigate the functional gene network in gastric carcinogenesis by using bioinformatics; besides, the diagnostic utility of key genes and potential active ingredients of traditional Chinese medicine (TCM) for treatment in gastric cancer have been explored. Methods. The Cancer Genome Atlas and Gene Expression Omnibus databases have been applied to analyze the differentially expressed genes (DEGs) between gastric cancer and normal gastric tissues. Then, the DEGs underwent Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses using the Metascape database. The STRING database and the Cytoscape software were utilized for the protein-protein interaction network of DEGs and hub genes screening. Furthermore, survival and expression analyses of hub genes were conducted using Gene Expression Profiling Interactive Analysis and Human Protein Atlas databases. By using the Comparative Toxicogenomics Database, the hub genes interconnected with active ingredients of TCM were analyzed to provide potential information for the treatment of gastric cancer. After the molecular docking of the active ingredients of TCM to specific hub gene receptor proteins, the molecular dynamics simulation GROMACS was applied to validate the conformation of the strongest binding ability in the molecular docking. Results. A total of 291 significant DEGs were found, from which 12 hub genes were screened out. Among these hub genes, the expressions of five hub genes including COL1A1, COL5A2, MMP12, SERPINE1, and VCAN were significantly correlated with the overall survival. Furthermore, four potential therapeutic active ingredients of TCM were acquired, including quercetin, resveratrol, emodin, and schizandrin B. In addition, the molecular docking results exhibited that the active ingredients of TCM formed stable binding with the hub gene targets. SERPINE1 (3UT3)-Emodin and COL1A1 (7DV6)-Quercetin were subjected to molecular dynamics simulations as conformations of continuing research significance, and both were found to be stably bound as a result of the interaction of van der Waals potentials, electrostatic, and hydrogen bonding. Conclusion. Our findings may provide novel insights and references for the screening of biomarkers, the prognostic evaluation, and the identification of potential active ingredients of TCM for gastric cancer treatment.

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Section: Discussionmentioning

confidence: 99%

The Regulatory Network of Gastric Cancer Pathogenesis and Its Potential Therapeutic Active Ingredients of Traditional Chinese Medicine Based on Bioinformatics, Molecular Docking, and Molecular Dynamics Simulation

Yang

Liu

2022

Evidence-Based Complementary and Alternative Medicine

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Stereo‐Controlled Synthesis of Vicinal Tertiary Carbinols: Application in the Synthesis of a Diol Substructure of Zaragozic Acid, Pactamycin and Ryanodol

Kim,

Puthukanoori,

Martha

et al. 2023

Chemistry A European J

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A novel and flexible approach for the stereo‐controlled synthesis of vicinal tertiary carbinols is reported. The developed strategy featured a highly diastereoselective singlet‐oxygen (O21) [4+2] cycloaddition of rationally designed cyclohexadienones (derived from oxidative dearomatization of the corresponding carboxylic‐acid appended phenol precursors), followed by programmed “O−O” and “C−C” bond cleavage. In doing so, a highly functionalized and versatile intermediate was identified and prepared in synthetically useful quantity as a plausible precursor to access a variety of designed and naturally occurring vicinal tertiary carbinol containing compounds. Most notably, the developed strategy was successfully applied in the stereo‐controlled synthesis of advanced core structures of zaragozic acid, pactamycin and ryanodol.

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Synthesis, biological evaluation and cellular localization study of fluorescent derivatives of Jiyuan Oridonin A

Zhou

Zhang

Liu

et al. 2022

European Journal of Medicinal Chemistry

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Target identification of anticancer natural products using a chemical proteomics approach

Abstract: Natural products are one of the most effective therapeutic candidates in cancer treatment. In this review, we briefly discuss the target identification of anticancer natural products in different cancer cell lines through a chemical proteomics approach.

Cited by 8 publications

References 108 publications

The Regulatory Network of Gastric Cancer Pathogenesis and Its Potential Therapeutic Active Ingredients of Traditional Chinese Medicine Based on Bioinformatics, Molecular Docking, and Molecular Dynamics Simulation

The Regulatory Network of Gastric Cancer Pathogenesis and Its Potential Therapeutic Active Ingredients of Traditional Chinese Medicine Based on Bioinformatics, Molecular Docking, and Molecular Dynamics Simulation

Stereo‐Controlled Synthesis of Vicinal Tertiary Carbinols: Application in the Synthesis of a Diol Substructure of Zaragozic Acid, Pactamycin and Ryanodol

Synthesis, biological evaluation and cellular localization study of fluorescent derivatives of Jiyuan Oridonin A

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