3D-QSAR studies on the structure–bitterness analysis of citrus flavonoids

Chen, Lufang; Lin, Yanling; Yan, Xiu‐Ping; Ni, Hui; Chen, Feng; HE, FAN

doi:10.1039/d3fo00601h

Cited by 10 publications

(2 citation statements)

References 43 publications

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“…Models with q 2 >0.3 are considered to be over 95 % reliable, with a probability of less than 5 %. Additionally, models with q 2 >0.5 and a non‐cross‐validation coefficient r 2 >0.6 are statistically highly significant and have excellent predictive abilities [26] . Following this, non‐validation method was used to predict biological activity data.…”

Section: Methodsmentioning

confidence: 99%

“…Additionally, models with q 2 > 0.5 and a non-cross-validation coefficient r 2 > 0.6 are statistically highly significant and have excellent predictive abilities. [26] Following this, non-validation method was used to predict biological activity data. The predictive capability of the QSAR model was evaluated based on the correlation coefficient r, standard deviation S, and Fisher's test value F. The closer r is to 1, the smaller S is, and the larger F is, the better the model fits.…”

Section: Pls Analysismentioning

confidence: 99%

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Design of New Second‐Generation TRK Inhibitors Targeting Tropomyosin Receptor Kinases by Using Molecular Docking, Molecular Dynamics Simulations and ADMET Properties

Zhao,

Cui,

Tang

et al. 2024

ChemistrySelect

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TRK, as a type of cell surface protein, plays a critical role in various biological processes, particularly as a key target for cancer treatment. We explored the correlation between the structure and activity of indole‐2‐one derivatives through investigations involving 3D‐QSAR molecular modelling, molecular docking, molecular dynamics, and ADMET property research. The statistical data from the CoMFA and CoMSIA models exhibit excellent internal stability (CoMFA: q2=0.622, r2=0.992; CoMSIA: q2=0.740, r2=0.972). Further molecular docking unveiled the interaction mechanism between small molecules and receptor proteins, demonstrating that the hydrogen bonding between amino acids Met590 and Glu592 and small molecules could enhance the ligand‐receptor binding affinity. Based on the 3D‐QSAR model and molecular docking, we designed and predicted the activity of eight new molecules, which displayed high expected activity. Subsequently, through 100 ns MD simulations and binding free energy calculations, we affirmed the stability of the molecular docking results. Finally, we employed ADMET to predict the pharmacokinetic properties of the newly designed molecules, validating their commendable drug‐like characteristics. These research findings provide valuable references for the design and development of novel TRK inhibitors, offering fresh perspectives for subsequent drug design.

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Section: Methodsmentioning

confidence: 99%

Section: Pls Analysismentioning

confidence: 99%

Design of New Second‐Generation TRK Inhibitors Targeting Tropomyosin Receptor Kinases by Using Molecular Docking, Molecular Dynamics Simulations and ADMET Properties

Zhao,

Cui,

Tang

et al. 2024

ChemistrySelect

View full text Add to dashboard Cite

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Design of Novel Naphthalimidopropanediol Derivatives as Staphylococcus Aureus Antibacterial Agents Utilizing 3D‐QSAR, ADMET, Molecular Docking, and Dynamics Simulations

Xiong,

Xu,

Wang

2024

ChemistrySelect

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Staphylococcus aureus is a prevalent foodborne pathogen, and its resistance has become more pronounced due to antibiotic overuse. In this paper, we constructed a 3D‐QSAR model using 47 naphthalimidopropanediols derivatives (NIOLs). The results indicate that the CoMFA model (q2 = 0.771, r2 = 0.998) and CoMSIA‐ASH model (q2 = 0.638, r2 = 0.995) exhibit favorable predictive capabilities, leading to the design of 11 novel NIOLs as antibacterial agents. ADMET was used to validate their pharmacokinetic characteristics, molecular docking was performed to validate the binding capability of the designed molecules, dynamics simulations, and binding free energy were employed to verify the accuracy of docking results. The results demonstrate excellent performance of the designed novel molecules, which may provide significant references for the development of novel and effective antibacterial agents against S. aureus.

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Synthesis, anticancer evaluation, preliminary mechanism study of novel 1, 2, 3-triazole-piperlongumine derivatives

Feng,

Qiu,

et al. 2024

Mol Divers

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3D-QSAR studies on the structure–bitterness analysis of citrus flavonoids

Abstract: Despite important bioactivities, the unpleasant bitter taste of citrus-derived flavonoids limits their application in food industry. While the structure-bitterness relationship of flavonoids is still far from clear. In this study,...

Cited by 10 publications

References 43 publications

Design of New Second‐Generation TRK Inhibitors Targeting Tropomyosin Receptor Kinases by Using Molecular Docking, Molecular Dynamics Simulations and ADMET Properties

Design of New Second‐Generation TRK Inhibitors Targeting Tropomyosin Receptor Kinases by Using Molecular Docking, Molecular Dynamics Simulations and ADMET Properties

Design of Novel Naphthalimidopropanediol Derivatives as Staphylococcus Aureus Antibacterial Agents Utilizing 3D‐QSAR, ADMET, Molecular Docking, and Dynamics Simulations

Synthesis, anticancer evaluation, preliminary mechanism study of novel 1, 2, 3-triazole-piperlongumine derivatives

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