Dynamics of Binding of Lysozyme with Gold Nanoparticles: Corona Formation and its Correlation with a Naked-Eye-Based Colorimetric Approach

NANO ◽  
2020 ◽  
Vol 15 (01) ◽  
pp. 2050008
Author(s):  
D. Aich ◽  
S. Saha ◽  
R. N. Mondal ◽  
T. Kamilya
Keyword(s):  
Gold Nanoparticles ◽  
Molecular Docking ◽  
Electrostatic Interaction ◽  
Docking Simulation ◽  
Peak Position ◽  
Stoichiometric Ratio ◽  
Molecular Docking Simulation ◽  
Naked Eye ◽  
Corona Formation ◽  
Citrate Ions

The interaction between colloidal gold nanoparticles (AuNPs) and lysozyme (Lyz) has been studied through spectroscopic and microscopic measurements, molecular docking simulation and colorimetric measurements to investigate corona formation and the mechanism, affinity, number of sites and stoichiometry of binding. Molecular docking simulation endorses that, at physiological pH, the interaction between basic NH2 group of arginine and citrate ions is predominant than the interaction between citrate ions and the positive surface charge of the bare AuNPs that result in the desorption of citrate ions from Au surfaces and finally, electrostatic interaction between [Formula: see text] group of arginine and positive charge surface of AuNPs results in the adsorption of Lyz on Au surfaces. As observed from Benesi–Hildebrand and fluorescence analyses, the ground state complex formation between Lyz and AuNPs requires several minutes, which is approximately 11 min in the present work to attain stoichiometric ratio 1:1. CD spectra indicate insignificant or no conformational change in the secondary structure of Lyz in the presence of AuNPs. The time variation of LSPR peak position and peak height in the presence of Lyz have been studied extensively through spectroscopic and microscopic measurements. Detailed discussion on the probable time-specific roles of change in local dielectric constant, plasmon coupling and electrostatic interaction on these variations has been presented. Colorimetric change of the AuNPs-Lyz system with time has been analyzed by measuring the red, blue and green color fractions as well as its correlation with the process of corona formation and aggregation has been investigated to propose a novel naked eye colorimetric approach of studying these processes in AuNPs-Lyz system.

Design, Molecular docking, Synthesis and Biological evaluation of 5, 7 dimethyl pyrido(2, 3-d)pyrimidin-4-one and 4,5 dihydro pyrazolo (3, 4-d) pyrimidines for cytotoxic activity

2021 ◽  
pp. 3029-3038
Author(s):  
M. Sathish Kumar ◽  
M. Vijey Aanandhi
Keyword(s):  
Molecular Docking ◽  
Docking Simulation ◽  
Docking Studies ◽  
Biological Evaluation ◽  
Hep G2 ◽  
Molecular Docking Simulation ◽  
Hela Cell Lines ◽  
Benzene Diazonium ◽  
Synthesis And Biological Evaluation ◽  
Mcf 7

The fused pyrimidine derivatives are potent tyrosine kinase and thymidylate synthase inhibitors. The compound 3-(4-sulphonyl amino)-2-methyl thio-6-phenyl azo-5, 7-dimethyl pyrido(2,3-d)pyrimidin-4-one was synthesized from Ethyl 2-amino-4,6-dimethylpyridine-3-carboxylate, benzene diazonium chloride, benzene sulphonyl amino isothiocyanate in subsequent reactions. 1-(1, 3-benzothiazol-2-yl)-3-methyl-4-phenyl-1H-pyrazolo[3,4-d]pyrimidines were synthesized from 1, 3-benzothiazole, 2-thiol, Hydrazine Hydrate, 2-hydrazinyl-1, 3-benzothiazole and aldehydes in subsequent reactions. Twenty-five derivatives pyrimidine scaffolds were designed and performed molecular docking studies for the ability to inhibit the target protein using molecular docking simulation, selective compounds were synthesized and characterized by spectral methods. All the synthesized compounds evaluated for their antioxidant activity and MTT assay exhibited compounds 13c, 13e and 14d can be potential anticancer candidates against MCF-7, Hep G2 and Hela cell lines respectively. Based on all the studies conclude that good agreement was observed between the top-ranked docking scores and top experimental inhibitors when compared with standards ascorbic acid and imatinib. Hence, the compounds could be considered as new anticancer hits for further lead optimization.

Binding Investigation of Integrin αvβ3 With Its Inhibitors by SPR Technology and Molecular Docking Simulation

2010 ◽  
Vol 15 (2) ◽  
pp. 131-137 ◽  
Author(s):  
Yaqin Liu ◽  
Yuanjiang Pan ◽  
Yuhong Xu
Keyword(s):  
Molecular Docking ◽  
Binding Sites ◽  
Structural Model ◽  
Docking Simulation ◽  
Integrin Αvβ3 ◽  
Equilibrium Dissociation Constant ◽  
Molecular Docking Simulation ◽  
Spr Biosensor ◽  
Inhibitor Discovery ◽  
Equilibrium Dissociation

Integrins play critical roles in the process of angiogenesis and are attractive targets for anticancer therapies. It is desirable to develop new types of small-molecule inhibitors of integrin. Herein, the binding features of several inhibitors to integrin αvβ3 have been studied by surface plasmon resonance (SPR) biosensor technology and molecular docking analyses. The SPR results indicated that the equilibrium dissociation constant (KD) values are evaluated for the inhibitors and showed that the KD value of cyclopeptide c-Lys is much lower than the reference molecule. In addition, the 3D structural model of integrin αvβ3 was generated according to the crystal structure of the integrin αvβ3 complex, and the molecular docking simulation analyses revealed that the predicted binding sites for the most active cyclopeptide c-Lys were consistent with the reported structure. These results thus implied that cyclopeptide c-Lys could be developed as a novel inhibitor for integrin αvβ3. The current work has potential for application in structure-based integrin αvβ3 inhibitor discovery.

scholarly journals Discovery of GPX4 inhibitor by molecular docking simulation as a potential ferroptosis inducer

2020 ◽  
Vol 10 (1) ◽  
pp. 4929-4933
Keyword(s):  
Molecular Docking ◽  
Therapeutic Strategy ◽  
Docking Simulation ◽  
Drug Candidate ◽  
Synthetic Compounds ◽  
Molecular Docking Simulation ◽  
Docking Simulations ◽  
Lipinski’S Rule ◽  
Mercaptosuccinic Acid ◽  
Significant Public Health

As one of the most complex diseases in the world, cancer continues as one of the significant public health problems. It was recorded by 2014 that cancer caused 1,551,000 death in Indonesia. One type of programmed cell death (PCD) that played a role in cancer cell treatment is Ferroptosis. Ferroptosis is PCD on iron and characterized by the inactivation of glutathione-dependent peroxidase (GPx4). In this research, a new therapeutic strategy for cancer was developed through the computational approach on synthetic compounds to discover its potential as an inhibitor of GPx4. About 688 compounds derivative from mercaptosuccinic acid acquired from the Zinc15 database. These compounds screened through the Lipinski’s Rule of Three and pharmacological prediction to eliminate ligands with undesired molecular properties. After that, the ligands underwent both rigid and flexible molecular docking simulations to predict their inhibition activity toward GPx4. From molecular docking simulation, (2S)-2-[(Z)-3-phenylprop-2-enyl]sulfanylbutanedioic acid show favorable characteristics as a drug candidate.

PTP1B inhibitors from Selaginella tamariscina (Beauv.) Spring and their kinetic properties and molecular docking simulation

2017 ◽  
Vol 72 ◽  
pp. 273-281 ◽  
Author(s):  
Duc Dat Le ◽  
Duc Hung Nguyen ◽  
Bing Tian Zhao ◽  
Su Hui Seong ◽  
Jae Sue Choi ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Docking Simulation ◽  
Kinetic Properties ◽  
Molecular Docking Simulation ◽  
Selaginella Tamariscina ◽  
Ptp1b Inhibitors

scholarly journals Mechanisms of Compound Kushen Injection for the Treatment of Lung Cancer Based on Network Pharmacology

2019 ◽  
Vol 2019 ◽  
pp. 1-15 ◽  
Author(s):  
Ziqi Meng ◽  
Xinkui Liu ◽  
Jiarui Wu ◽  
Wei Zhou ◽  
Kaihuan Wang ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Molecular Docking ◽  
Small Cell Lung Cancer ◽  
Docking Simulation ◽  
Small Cell ◽  
Network Pharmacology ◽  
Small Cell Lung ◽  
Molecular Docking Simulation ◽  
Target Network ◽  
Compound Kushen Injection

Background. Compound Kushen Injection (CKI) is a Chinese patent drug that shows good efficacy in treating lung cancer (LC). However, its underlying mechanisms need to be further clarified.Methods. In this study, we adopted a network pharmacology method to gather compounds, predict targets, construct networks, and analyze biological functions and pathways. Moreover, molecular docking simulation was employed to assess the binding potential of selected target-compound pairs.Results. Four networks were established, including the compound-putative target network, protein-protein interaction (PPI) network of LC targets, compound-LC target network, and herb-compound-target-pathway network. Network analysis showed that 8 targets (CHRNA3, DRD2, PRKCA, CDK1, CDK2, CHRNA5, MMP1, and MMP9) may be the therapeutic targets of CKI in LC. In addition, molecular docking simulation indicated that CHRNA3, DRD2, PRKCA, CDK1, CDK2, MMP1, and MMP9 had good binding activity with the corresponding compounds. Furthermore, enrichment analysis indicated that CKI might exert a therapeutic role in LC by regulating some important pathways, namely, pathways in cancer, proteoglycans in cancer, PI3K-Akt signaling pathway, non-small-cell lung cancer, and small cell lung cancer.Conclusions. This study validated and predicted the mechanism of CKI in treating LC. Additionally, this study provides a good foundation for further experimental studies and promotes the reasonable application of CKI in the clinical treatment of LC.

Molecular docking simulation and in vitro studies on estrogenic activities of flavonoids from leaves of Carya cathayensis Sarg

Steroids ◽  
2020 ◽  
Vol 163 ◽  
pp. 108726
Author(s):  
Jing-Jing Lu ◽  
Fang-Mei Zhou ◽  
Xu-Jiao Hu ◽  
Jing-Jing Fang ◽  
Cai-Xia Liu ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Docking Simulation ◽  
In Vitro Studies ◽  
Molecular Docking Simulation ◽  
Carya Cathayensis ◽  
Carya Cathayensis Sarg
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