Two statins and cromolyn as possible drugs against the cytotoxicity of Aβ(31–35) and Aβ(25–35) peptides: a comparative study by advanced computer simulation methods

Ermilova, Inna; Blomgren, Fredrik; Pacut, Dawid Wojciech; Chrobak, Wojciech; Rodin, Alexander; Swenson, Jan

doi:10.1039/d2ra01963a

Cited by 1 publication

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References 83 publications

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“…First, the free energy value was negative, indicating that the binding phenomenon was spontaneous. Second, the lower the free energy value, the higher the bonding strength between two molecules and the more pronounced the affinity . The free energy results between different cations and proteins are shown in Figure c.…”

Section: Resultsmentioning

confidence: 99%

“…Second, the lower the free energy value, the higher the bonding strength between two molecules and the more pronounced the affinity. 54 The free energy results between different cations and proteins are shown in Figure 5c. It is easy to see in the figure that the short-chain cation bound with a value of around 30 kJ/mol.…”

Section: Thermodynamic Analysis Of Cations Bound Into the Rbd Protein...mentioning

confidence: 99%

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Molecular Insights into the Binding Behavior of Imidazolium Ionic Liquids to the Receptor Binding Domain of the SARS-CoV-2 Spike Protein

Liu,

Li,

Liu

et al. 2023

J. Phys. Chem. B

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The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein is considered as a key target for the design and development of COVID-19 drugs and inhibitors. Due to their unique structure and properties, ionic liquids (ILs) have many special interactions with proteins, showing great potential in biomedicine. Nevertheless, few research studies have been carried out on ILs and the spike RBD protein. Here, we explore the interaction of ILs and the RBD protein through large-scale molecular dynamics simulations (4 μs in total). It was found that IL cations with long alkyl chain lengths (n chain ) could spontaneously bind to the cavity region of the RBD protein. The longer the alkyl chain is, the stabler the cations bind to the protein. The binding free energy (ΔG) had the same trend, peaking at n chain = 12 with −101.19 kJ/mol. The cationic chain lengths and their fit to the pocket are decisive factors that influence the binding strength of cations and proteins. The cationic imidazole ring has a high contact frequency with phenylalanine and tryptophan, and the hydrophobic residues phenylalanine, valine, leucine, and isoleucine are the most interacting residues with side chains of cations. Meanwhile, through analysis of the interaction energy, the hydrophobic and π−π interactions are the main contributors to the high affinity between cations and the RBD protein. In addition, the long-chain ILs would also act on the protein through clustering. These studies not only provide insights into the molecular interaction between ILs and the RBD of SARS-CoV-2 but also contribute to the rational design of IL-based drugs, drug carriers, and selective inhibitors as a therapeutic for SARS-CoV-2.

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Section: Resultsmentioning

confidence: 99%

Section: Thermodynamic Analysis Of Cations Bound Into the Rbd Protein...mentioning

confidence: 99%

Molecular Insights into the Binding Behavior of Imidazolium Ionic Liquids to the Receptor Binding Domain of the SARS-CoV-2 Spike Protein

Liu,

Li,

Liu

et al. 2023

J. Phys. Chem. B

View full text Add to dashboard Cite

show abstract

Two statins and cromolyn as possible drugs against the cytotoxicity of Aβ(31–35) and Aβ(25–35) peptides: a comparative study by advanced computer simulation methods

Abstract: In this work, possible effective mechanisms of cromolyn, atorvastatin and lovastatin on the cytotoxicity of Aβ(31–35) and Aβ(25–35) peptides were investigated by classical molecular dynamics and well-tempered metadynamics simulations.

Cited by 1 publication

References 83 publications

Molecular Insights into the Binding Behavior of Imidazolium Ionic Liquids to the Receptor Binding Domain of the SARS-CoV-2 Spike Protein

Molecular Insights into the Binding Behavior of Imidazolium Ionic Liquids to the Receptor Binding Domain of the SARS-CoV-2 Spike Protein

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