DFT and molecular docking studies of self-assembly of sulfone analogues and graphene

Al‐Otaibi, Jamelah S.; Almuqrin, Aljawhara H.; Mary, Y. Sheena; Mary, Y. Shyma; Alsenoy, C. Van

doi:10.1007/s00894-020-04546-7

Cited by 37 publications

(6 citation statements)

References 75 publications

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“…MEP is a helpful tool for predicting the chemical reactivity of a compound. The knowledge of a compound’s chemical reactivity can be used to describe the interaction of drugs with proteins [ 41 ]. The calculated MEP for EVO and RUT are plotted in Figure 2 .…”

Section: Resultsmentioning

confidence: 99%

Evodiamine and Rutaecarpine as Potential Anticancer Compounds: A Combined Computational Study

Liu¹,

Guo²,

Zhou³

et al. 2022

IJMS

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Evodiamine (EVO) and rutaecarpine (RUT) are the main active compounds of the traditional Chinese medicinal herb Evodia rutaecarpa. Here, we fully optimized the molecular geometries of EVO and RUT at the B3LYP/6-311++G (d, p) level of density functional theory. The natural population analysis (NPA) charges, frontier molecular orbitals, molecular electrostatic potentials, and the chemical reactivity descriptors for EVO and RUT were also investigated. Furthermore, molecular docking, molecular dynamics simulations, and the analysis of the binding free energies of EVO and RUT were carried out against the anticancer target topoisomerase 1 (TOP1) to clarify their anticancer mechanisms. The docking results indicated that they could inhibit TOP1 by intercalating into the cleaved DNA-binding site to form a TOP1–DNA–ligand ternary complex, suggesting that they may be potential TOP1 inhibitors. Molecular dynamics (MD) simulations evaluated the binding stability of the TOP1–DNA–ligand ternary complex. The calculation of binding free energy showed that the binding ability of EVO with TOP1 was stronger than that of RUT. These results elucidated the structure–activity relationship and the antitumor mechanism of EVO and RUT at the molecular level. It is suggested that EVO and RUT may be potential compounds for the development of new anticancer drugs.

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Section: Resultsmentioning

confidence: 99%

Evodiamine and Rutaecarpine as Potential Anticancer Compounds: A Combined Computational Study

Liu¹,

Guo²,

Zhou³

et al. 2022

IJMS

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“…The values of relaxed NCs revealed that AlP with low kinetic consistency have more reactivity than the others. The HOMO and LUMO energies for VLA were -7.7222 and -0.4177 eV [34,35]. Except for BP, the electrophilicity index increased with VLA adsorption resulting with a higher tendency to accept electrons.…”

Section: Resultsmentioning

confidence: 98%

DFT analysis of valproic acid adsorption onto Al12/B12-N12/P12 nanocages with solvent effects

Al‐Otaibi

Mary²,

Mary³

2022

Preprint

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Using density functional theory, the adsorption of valproic acid onto the surface of fullerene-like nanocages was investigated. Valproic acid interact the nanocages through the carboxylic group with energies of -144.14, -109.71, -105.22 and -84.96 kcal/mol. The FMOs energy levels were considerably altered upon adsorption, resulting in a reduction in energy gap and increase in electrical conductivity. This suggests that nanocages could be used as sensors as well as options for drug administration in biological systems. Solvation effects in water are also reported.

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“…The values of relaxed NCs revealed that AlP with low kinetic consistency have more reactivity than the others. The HOMO and LUMO energies for VLA were -7.7222 and -0.4177 eV [34,35]. Hardness decreased in VLA-NCS, indicating higher reactivity than that of NCs, allowing for more VLA to be adsorbed (tables 1 and 3).…”

Section: Resultsmentioning

confidence: 99%

DFT analysis of valproic acid adsorption onto Al12/B12-N12/P12 nanocages with solvent effects

Al‐Otaibi

Mary²,

Mary³

2022

J Mol Model

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DFT and molecular docking studies of self-assembly of sulfone analogues and graphene

Cited by 37 publications

References 75 publications

Evodiamine and Rutaecarpine as Potential Anticancer Compounds: A Combined Computational Study

Evodiamine and Rutaecarpine as Potential Anticancer Compounds: A Combined Computational Study

DFT analysis of valproic acid adsorption onto Al12/B12-N12/P12 nanocages with solvent effects

DFT analysis of valproic acid adsorption onto Al12/B12-N12/P12 nanocages with solvent effects

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