Investigation of small inhibitor effects on methane hydrate formation in a carbon nanotube using molecular dynamics simulation

Abbaspour, Mohsen; Fotourechi, Fateme; Akbarzadeh, Hamed; Salemi, Sirous

doi:10.1039/d2ra06518e

Cited by 4 publications

(2 citation statements)

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“…In RDF analysis, we can observe the distribution of drug molecules (cisplatin) around MOFs and estimate the extent of their diffusion aggregation. , Figure illustrates the RDF analysis graph for cisplatin and MOFs at different pH values . The RDF analysis provides insights into the adsorption criteria by evaluating the maximum value and visualizing the positions of the drug and nanocarrier within the simulation box . The vertical axis represents the maximum value in the graph .…”

Section: Resultsmentioning

confidence: 99%

“… 59 The RDF analysis provides insights into the adsorption criteria by evaluating the maximum value and visualizing the positions of the drug and nanocarrier within the simulation box. 60 The vertical axis represents the maximum value in the graph. 57 A higher maximum value in the graph indicates a stronger connection and closer proximity between the drug and nanocarrier molecules.…”

Section: Resultsmentioning

confidence: 99%

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Metal–Organic Frameworks for Cisplatin Delivery to Cancer Cells: A Molecular Dynamics Simulation

Mashayekh,

Ghiasi,

Bhia

et al. 2024

ACS Omega

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Metal−organic frameworks (MOFs) are utilized as nanocarriers to enhance the efficiency of chemotherapy drugs, including cisplatin, which exhibit limitations such as side effects and resistance mechanisms. To evaluate the role of MOFs, we employed a molecular dynamics simulation, which, unlike other experiments, is cost-effective, less dangerous, and provides accurate results. Furthermore, we conducted molecular docking simulations to understand the interaction between cisplatin and MOF, as well as their internal interactions and how they bind to each other. Cisplatin and MOF molecules were parametrized using the Avogadro software and x2top command in GROMACS 5.1.2 and optimized by CP2K software; the Charmm-GUI site parametrized the cell cancer membrane. Three molecular dynamics simulations were conducted in four stages at various pHs, followed by simulated umbrella sampling. The simulations analyzed the pH responsiveness, total energy, Gibbs free energy, gyration radius, radial distribution function (RDF), solvent accessible surface area, and nanoparticles' toxicity. Results demonstrated that a neutral pH level (7.4) has greater adsorption and interaction compared to acidic pH values (6.4 and 5.4) because it displays the highest total energy (−17.1 kJ/mol), the highest RDF value (6.66), and the shortest distance (0.51 nm). Furthermore, the combination of cisplatin and MOFs displayed increased penetration compared to that of their individual forms. This study highlights the suitability of MOFs as nanocarriers and identifies the optimal pH values for desirable outcomes. Thus, it provides future studies with appropriate data to conduct their experiments in assessing MOFs.

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