Point mutation consideration in CcO protein of the electron transfer chain by MD simulation

Shojapour, Mahnaz; Farahmand, Somayeh

doi:10.1016/j.jmgm.2022.108309

Cited by 6 publications

(3 citation statements)

References 43 publications

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“…The dynamic stability and binding energy of the complexes were further analyzed by molecular dynamics (MD) simulations. RMSD was used to determine the average deviation of the complex conformation from the original conformation at a given time and to assess whether the complex system had reached a steady state [ 55 ]. As shown in Figure 5 a, both 2-(3,5-dihydroxyphenyl)-5,7-dihydroxy-4 H -chromen-4-one and 2-(2,5-dihydroxyphenyl)-5,7-dihydroxy-4 H -chromen-4-one systems reached equilibrium at 20,000 ps, and their RMSD values remained stable at 0.12 and 0.14 nm, respectively.…”

Section: Resultsmentioning

confidence: 99%

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Construction of an MLR-QSAR Model Based on Dietary Flavonoids and Screening of Natural α-Glucosidase Inhibitors

Yang

Pan

et al. 2022

Foods

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Postprandial hyperglycemia can be reduced by inhibiting α-glucosidase activity. Common α-glucosidase inhibitors such as acarbose may have various side effects. Therefore, it is important to find natural products that are non-toxic and have high α-glucosidase-inhibitory activity. In the present study, a comprehensive computational analysis of 27 dietary flavonoid compounds with α-glucosidase-inhibitory activity was performed. These included flavonoids, flavanones, isoflavonoids, dihydrochalcone, flavan-3-ols, and anthocyanins. Firstly, molecular fingerprint similarity clustering analysis was performed on the target molecules. Secondly, multiple linear regression quantitative structure–activity relationship (MLR-QSAR) models of dietary flavonoids (2D descriptors and 3D descriptors optimized), with R2 of 0.927 and 0.934, respectively, were constructed using genetic algorithms. Finally, the MolNatSim tool based on the COCONUT database was used to match the similarity of each flavonoid in this study, and to sequentially perform molecular enrichment, similarity screening, and QSAR prediction. After screening, five kinds of natural product molecule (2-(3,5-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one, norartocarpetin, 2-(2,5-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one, 2-(3,4-dihydroxyphenyl)-5-hydroxy-4H-chromen-4-one, and morelosin) were finally obtained. Their IC50pre values were 8.977, 31.949, 78.566, 87.87, and 94.136 µM, respectively. Pharmacokinetic predictions evaluated the properties of the new natural products, such as bioavailability and toxicity. Molecular docking analysis revealed the interaction of candidate novel natural flavonoid compounds with the amino acid residues of α-glucosidase. Molecular dynamics (MD) simulations and molecular mechanics/generalized Born surface area (MMGBSA) further validated the stability of these novel natural compounds bound to α-glucosidase. The present findings may provide new directions in the search for novel natural α-glucosidase inhibitors.

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Section: Resultsmentioning

confidence: 99%

“…RMSF can be used to characterize the stability of a composite system by evaluating the fluctuation of conformational change from the original conformation [ 55 ]. Figure 5 b shows the RMSF values of the five natural product–α-glucosidase complex molecules as a function of residue number.…”

Section: Resultsmentioning

confidence: 99%

Construction of an MLR-QSAR Model Based on Dietary Flavonoids and Screening of Natural α-Glucosidase Inhibitors

Yang

Pan

et al. 2022

Foods

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“…MD simulations of the target compounds were performed using the GROMACS 2019 software package and analyzed using different trajectories. The RMSD trajectory curves can determine the average deviation between the complex conformation and the original conformation over a certain time period and evaluate whether the system has reached a steady state [38].…”

Section: Molecular Dynamics Simulation Analysismentioning

confidence: 99%

Construction of a QSAR Model Based on Flavonoids and Screening of Natural Pancreatic Lipase Inhibitors

Yuan,

Pan,

Zhu

et al. 2023

Nutrients

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Pancreatic lipase (PL) is a key hydrolase in lipid metabolism. Inhibition of PL activity can intervene in obesity, a global sub-health disease. The natural product is considered a good alternative to chemically synthesized drugs due to its advantages, such as low side effects. However, traditional experimental screening methods are labor-intensive and cost-consuming, and there is an urgent need to develop high-throughput screening methods for the discovery of anti-PL natural products. In this study, a high-throughput virtual screening process for anti-PL natural products is provided. Firstly, a predictable anti-PL natural product QSAR model (R2train = 0.9444, R2test = 0.8962) were developed using the artificial intelligence drug design software MolAIcal based on genetic algorithms and their conformational relationships. 1068 highly similar (FS > 0.8) natural products were rapidly enriched based on the structure-activity similarity principle, combined with the QSAR model and the ADMET model, for rapid prediction of a total of five potentially efficient anti-PL natural products (IC50pre < 2 μM). Subsequently, molecular docking, molecular dynamics simulation, and MMGBSA free energy calculation were performed to not only reveal the interaction of candidate novel natural products with the amino acid residues of PL but also to validate the stability of these novel natural compounds bound to PL. In conclusion, this study greatly simplifies the screening and discovery of anti-PL natural products and accelerates the development of novel anti-obesity functional foods.

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Prediction and validation of monoclonal antibodies separation in aqueous two-phase system using molecular dynamic simulation

Guo

Chen

Yang

et al. 2023

Journal of Chromatography A

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Point mutation consideration in CcO protein of the electron transfer chain by MD simulation

Cited by 6 publications

References 43 publications

Construction of an MLR-QSAR Model Based on Dietary Flavonoids and Screening of Natural α-Glucosidase Inhibitors

Construction of an MLR-QSAR Model Based on Dietary Flavonoids and Screening of Natural α-Glucosidase Inhibitors

Construction of a QSAR Model Based on Flavonoids and Screening of Natural Pancreatic Lipase Inhibitors

Prediction and validation of monoclonal antibodies separation in aqueous two-phase system using molecular dynamic simulation

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