Fluorescent delivery vehicle containing cobalt oxide–umbelliferone nanoconjugate: DNA/protein interaction studies and anticancer activity on MF7 cancer cell line
“…The fluorescent cobalt oxide (CoO) umbelliferone nanoconjugate having anti-cancer activity can be used both as a drug and carrier. Ali et al have conducted molecular docking studies applying the protein docking program, HEX 8.0.0 using Spherical Polar Fourier Correlations technique to find the binding interactions of the CoO-drug nanoconjugate with the B-DNA dodecamer (also called as Calf thymus DNA (CT-DNA)), a DNA duplex having the sequence (CGCGAATTCGCG) 2 (PDB ID: 1BNA) and human serum albumin (HSA) (PDB ID: 1H9Z) protein separately [ 117 – 119 ]. The most stable docking results with least binding energies of the CoO-drug nanoconjugate against the DNA molecule and interactions in the binding cavity of the CT-DNA are shown in Fig.…”
Section: Docking In Organic Inorganic and Hybrid Systemsmentioning
confidence: 99%
“… Fig. 18 A Molecular docking complex of calf thymus DNA (CT-DNA) (PDB ID: 1BNA) and cobalt oxide (CoO) umbelliferone drug nanoconjugate using HEX 8.0.0 [ 117 , 118 ]. DNA is represented in carton and surface view.…”
Section: Docking In Organic Inorganic and Hybrid Systemsmentioning
confidence: 99%
“…The drug nanoconjugate, a mixture of CoO nanoparticle (blue and red sphered view) and umbelliferone drug (green, red, and white sphered view). B Non-covalent interactions of DNA bases with the nanoconjugate depicted by dashed lines [ 117 ]. (Color figure online) Fig.…”
Section: Docking In Organic Inorganic and Hybrid Systemsmentioning
Molecular docking simulation is a very popular and well-established computational approach and has been extensively used to understand molecular interactions between a natural organic molecule (ideally taken as a receptor) such as an enzyme, protein, DNA, RNA and a natural or synthetic organic/inorganic molecule (considered as a ligand). But the implementation of docking ideas to synthetic organic, inorganic, or hybrid systems is very limited with respect to their use as a receptor despite their huge popularity in different experimental systems. In this context, molecular docking can be an efficient computational tool for understanding the role of intermolecular interactions in hybrid systems that can help in designing materials on mesoscale for different applications. The current review focuses on the implementation of the docking method in organic, inorganic, and hybrid systems along with examples from different case studies. We describe different resources, including databases and tools required in the docking study and applications. The concept of docking techniques, types of docking models, and the role of different intermolecular interactions involved in the docking process to understand the binding mechanisms are explained. Finally, the challenges and limitations of dockings are also discussed in this review.
Graphical abstract
“…The fluorescent cobalt oxide (CoO) umbelliferone nanoconjugate having anti-cancer activity can be used both as a drug and carrier. Ali et al have conducted molecular docking studies applying the protein docking program, HEX 8.0.0 using Spherical Polar Fourier Correlations technique to find the binding interactions of the CoO-drug nanoconjugate with the B-DNA dodecamer (also called as Calf thymus DNA (CT-DNA)), a DNA duplex having the sequence (CGCGAATTCGCG) 2 (PDB ID: 1BNA) and human serum albumin (HSA) (PDB ID: 1H9Z) protein separately [ 117 – 119 ]. The most stable docking results with least binding energies of the CoO-drug nanoconjugate against the DNA molecule and interactions in the binding cavity of the CT-DNA are shown in Fig.…”
Section: Docking In Organic Inorganic and Hybrid Systemsmentioning
confidence: 99%
“… Fig. 18 A Molecular docking complex of calf thymus DNA (CT-DNA) (PDB ID: 1BNA) and cobalt oxide (CoO) umbelliferone drug nanoconjugate using HEX 8.0.0 [ 117 , 118 ]. DNA is represented in carton and surface view.…”
Section: Docking In Organic Inorganic and Hybrid Systemsmentioning
confidence: 99%
“…The drug nanoconjugate, a mixture of CoO nanoparticle (blue and red sphered view) and umbelliferone drug (green, red, and white sphered view). B Non-covalent interactions of DNA bases with the nanoconjugate depicted by dashed lines [ 117 ]. (Color figure online) Fig.…”
Section: Docking In Organic Inorganic and Hybrid Systemsmentioning
Molecular docking simulation is a very popular and well-established computational approach and has been extensively used to understand molecular interactions between a natural organic molecule (ideally taken as a receptor) such as an enzyme, protein, DNA, RNA and a natural or synthetic organic/inorganic molecule (considered as a ligand). But the implementation of docking ideas to synthetic organic, inorganic, or hybrid systems is very limited with respect to their use as a receptor despite their huge popularity in different experimental systems. In this context, molecular docking can be an efficient computational tool for understanding the role of intermolecular interactions in hybrid systems that can help in designing materials on mesoscale for different applications. The current review focuses on the implementation of the docking method in organic, inorganic, and hybrid systems along with examples from different case studies. We describe different resources, including databases and tools required in the docking study and applications. The concept of docking techniques, types of docking models, and the role of different intermolecular interactions involved in the docking process to understand the binding mechanisms are explained. Finally, the challenges and limitations of dockings are also discussed in this review.
Graphical abstract
“…It can also act as a tumor suppressor and anti-cancer cell metastasis agent. Most studies have shown that umbelliferone reduces the expression of matrix metalloproteinase 9 (Ali et al, 2019; Kandil et al, 2016; Karthikeyan et al, 2016), while decreasing the levels of hyaluronic acid and glucose in the tumor microenvironment and inhibiting tumorigenesis in vitro and in vivo . However, there are no data on umbelliferone’s ability to suppress tumor growth through inhibiting glycolysis.…”
Section: Introductionmentioning
confidence: 99%
“…It is now employed as an inhibitor of hyaluronic acid formation and has anti-inflammatory properties. Recent research has demonstrated that umbelliferone has positive effects on breast cancer (Ali et al, 2019; Kandil et al, 2016), patocellular carcinoma (Yu et al, 2015), prostate carcinoma (Shen et al, 2017), oral carcinoma (Vijayalakshmi & Sindhu, 2017), and more. It can also act as a tumor suppressor and anti-cancer cell metastasis agent.…”
Background and Objectives Both primary and secondary cancers require the involvement of glycolytic pathways. Cancer cell proliferation leads to the upregulation of glycolysis, which results in increased glucose consumption. For demonstrating that umbelliferone can effectively bind to several proteins involved in the glycolytic pathway, thereby inhibiting glycolysis and reducing cancer cell proliferation. Materials and Methods This study uses transcriptomics, network pharmacology, and molecular docking to predict the potential targets and possible pathways of umbelliferone against cancer and microscale thermophoresis (MST) to detect the affinity between umbelliferone and potential targets. Results Transcriptomic analysis revealed that differentially expressed genes were primarily associated with glycolytic and other metabolic pathways and proteins. According to network pharmacology and molecular docking results, glycolysis-related proteins such as glucose-6-phosphate isomerase (GPI), glycerol-3-phosphate dehydrogenase, mitochondrial (GPD2), phosphoglycerate kinase 2 (PGK2), and heat shock protein HSP-90 alpha (Hsp90AA1) are potential targets of umbelliferone against tumors. MST confirmed that umbelliferous lactone binds strongly to GPI, GPD2, and PGK2 but not to Hsp90AA1. Conclusion By binding to the glycolysis-related proteins such as GPI, GPD2, and PGK2, umbelliferone acts as an anti-tumor agent by inhibiting glycolysis, cutting off the energy supply to tumor tissue, and reducing tumor growth. It was suggested that umbelliferone might be a brand-new tumor glycolysis inhibitor and that these glycolysis-related proteins might be potential new targets for cancer therapy. This finding helped to establish a solid foundation for the anti-cancer action of umbelliferone.
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