In silico evaluation of geroprotective phytochemicals as potential sirtuin 1 interactors

Medoro, Alessandro; Jafar, Tassadaq Hussain; Alì, Sawan; Trung, Truong Tan; Sorrenti, Vincenzo; Intrieri, Mariano; Scapagnini, Giovanni; Davinelli, Sergio

doi:10.1016/j.biopha.2023.114425

Cited by 7 publications

(4 citation statements)

References 82 publications

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“…The gmx_distance utility was used to determine the center of mass distance between the protein and ligand during the simulation. Finally, the VMD molecular graphics program was used to visualize the trajectories and analyze the frequency of protein–ligand contacts [37] …”

Section: Methodsmentioning

confidence: 99%

“…top), and MD‐parameter file ( . mdp) used to generate the binary run input file were obtained from the MD process [37] …”

Section: Methodsmentioning

confidence: 99%

“…Finally, the VMD molecular graphics program was used to visualize the trajectories and analyze the frequency of protein-ligand contacts. [37] Binding Free Energy (MM/PBSA Calculations)…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

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Exploring Structure–Toxicity Relationships in Nitrobenzene and Derivatives: A Multifaceted Biochemical Investigation Using 3D–QSPR, HQSPR, Molecular Docking, and MD Simulation

Ouabane,

Zaki,

Alaqarbeh

et al. 2024

ChemistrySelect

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Nitrobenzene derivatives present an environmental concern to aquatic organisms, as well as a potential adverse effects on human health due to their toxicity. Therefore, monitoring nitrobenzene contamination levels is critical to protect both the ecosystem and the public. This study aims to quantitatively correlate the toxicity of nitrobenzene derivatives to their chemical structures using computational chemistry methods such as 3D‐QSPR, HQSPR, Molecular Docking and MD simulation. Additionally, to investigate the type of interactions and stability of nitrobenzene derivatives with the PP2 protein involved in the Phloem protein 2 (PP2). From each computational method a prediction model was extracted HQSPR (Atomic, Bonds, Donor/Acceptor, 3D‐QSPR (Steric, Electrostatic, Hydrophobic, Acceptor), and used for the design of X1 and X2 new nitrobenzene derivatives, which showed remarkable stability and better interactions. This study contributes to the understanding of the nitrobenzene derivatives’ toxicity and offers materials towards the understanding of the mechanism of action of these substances in protein–ligand interactions.

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Section: Methodsmentioning

confidence: 99%

“…top), and MD‐parameter file ( . mdp) used to generate the binary run input file were obtained from the MD process [37] …”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Exploring Structure–Toxicity Relationships in Nitrobenzene and Derivatives: A Multifaceted Biochemical Investigation Using 3D–QSPR, HQSPR, Molecular Docking, and MD Simulation

Ouabane,

Zaki,

Alaqarbeh

et al. 2024

ChemistrySelect

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show abstract

“…Furthermore, the energy gap (Eg) and several other important parameters, which as ionization potential (IP), electron a nity (EA), electronegativity (χ), chemical hardnesses (η), electronic chemical potential (µ), chemical softness (S), and electrophilicity (ω) were calculated by using Eqs. ( 1)-( 8) (Medoro et al, 2023).…”

Section: Density Functional Theory (Dft)mentioning

confidence: 99%

Apoptosis induction of kadsuric acid from Vietnamese Kadsura coccinea (Lem.) A. C. Smith in human pancreatic cancer cells: in vitro and in silico approach

Nguyen,

Tran,

Truong

et al. 2024

Preprint

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Kadsuric acid, a major triterpenoid isolated from the leaves of Vietnamese Kadsura coccinea, exhibited potent cytotoxic effects in some human cancer cells. In this study, the effects of kadsuric acid on pancreatic cancer cells PANC-1 were investigated. The results showed that kadsuric acid exhibited dose-dependent cytotoxicity against PANC-1 with an IC50 value of 14.5 ± 0.8 µM. Kadsuric acid effectively activated caspase-3 by increasing the level of enzyme cleavage by 1–2 times after 12 and 24 h, and by more than 3–4 times compared to the negative control. In addition, this compound enhanced both two types of cysteine-aspartic acid proteases, including caspase-3 and caspase-9 through protein expressions. Western blot analysis also indicated that kadsuric acid reduced Poly [ADP-ribose] polymerase 1 (PARP1) expression in PANC-1 cells. For underlying mechanism insights, molecular modeling methods were applied to investigate the binding interaction between kadsuric acid and PARP1. Compared to the co-crystallized ligand, kadsuric acid displayed a stronger binding affinity (-9.3 kcal/mol). A molecular dynamics simulation showed that the complex is stable over 200 ns. Taken together, it can be determined that kadsuric acid can interact with the DNA of human pancreatic cancer cells through the intrinsic caspase/PARP-1 pathway. This study can guide future research on kadsuric acid as PARP1 inhibitor for cancer treatment.

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Quality Control of Coumarins, Furocoumarins and Polymethoxyflavones in Citrus Essential Oils: In Silico Analysis

Ouabane.,

Alaqarbeh,

Hajji

et al. 2024

ChemistrySelect

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Citrus essential oils (EOs) contain a variety of secondary metabolites, including coumarins (Cs), furocoumarins (FCs) and polymethoxyflavones (PMFs), all with different biological activities. While Regulation (EC) No 1334/2008 strictly regulates the use of coumarins, undesirable side effects of consuming furocoumarins remain without established maximum toxicity limits for human dietary intake. This study is based on an in‐silico approach aimed at determining these toxicity limits for the oxygenated heterocyclic compounds of citrus EOs approved for use in food. In addition, an innovative quantitative structure‐property relationship (QSPR) using the linear retention index system was explored to characterize the oxygenated heterocyclic compounds (COHs) present in these essential oils. Molecular docking of the studied compounds provided crucial insights into the structure‐odor relationships, offering insights into their mechanisms of action. In addition, an analysis of the pharmacokinetic and pharmacodynamic properties through ADME‐Tox deconstruction provides insight into the potential side effects of their consumption. The results are consolidated by dynamic simulations, providing crucial data for the development of regulations on the maximum toxicity limits of citrus EOs, given the health implications of the various compounds such as coumarins, furocoumarins and polymethoxyflavones present in these essential oils.

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In silico evaluation of geroprotective phytochemicals as potential sirtuin 1 interactors

Cited by 7 publications

References 82 publications

Exploring Structure–Toxicity Relationships in Nitrobenzene and Derivatives: A Multifaceted Biochemical Investigation Using 3D–QSPR, HQSPR, Molecular Docking, and MD Simulation

Exploring Structure–Toxicity Relationships in Nitrobenzene and Derivatives: A Multifaceted Biochemical Investigation Using 3D–QSPR, HQSPR, Molecular Docking, and MD Simulation

Apoptosis induction of kadsuric acid from Vietnamese Kadsura coccinea (Lem.) A. C. Smith in human pancreatic cancer cells: in vitro and in silico approach

Quality Control of Coumarins, Furocoumarins and Polymethoxyflavones in Citrus Essential Oils: In Silico Analysis

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