Insights from molecular dynamics and DFT calculations into the interaction of 1,4-benzodiazepines with 2-hydroxypropyl-βCD in a theoretical study

Koli, Mokhtar Ganjali; Malekshah, Rahime Eshaghi; Hajiabadi, H.

doi:10.1038/s41598-023-36385-w

Cited by 10 publications

(9 citation statements)

References 79 publications

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“…Initially, Coulombic solute–solvent interactions were turned off at a larger λ value compared to vdW terms 43 in order to avoid unstable Coulombic interactions that could lead to unreliable energies and unstable configurations. Soft-core potentials with specific parameters (α = 0.5, σ = 0.3, and p = 1) 42 , 44 were implemented to prevent the overlap of atoms between the solute and solvent at low λ values. The starting point for the free energy calculations was obtained from the final configuration of each simulated system, and each simulation had a duration time of 5 ns.…”

Section: Computational Detailsmentioning

confidence: 99%

Exploring the role of cyclodextrins as a cholesterol scavenger: a molecular dynamics investigation of conformational changes and thermodynamics

Ganjali Koli,

Fogolari

2023

Sci Rep

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This study presents a comprehensive analysis of the cholesterol binding mechanism and conformational changes in cyclodextrin (CD) carriers, namely βCD, 2HPβCD, and MβCD. The results revealed that the binding of cholesterol to CDs was spontaneous and thermodynamically favorable, with van der Waals interactions playing a dominant role, while Coulombic interactions have a negligible contribution. The solubility of cholesterol/βCD and cholesterol/MβCD complexes was lower compared to cholesterol/2HPβCD complex due to stronger vdW and Coulombic repulsion between water and CDs. Hydrogen bonding was found to have a minor role in the binding process. The investigation of mechanisms and kinetics of binding demonstrated that cholesterol permeates into the CD cavities completely. Replicas consideration indicated that while the binding to 2HPβCD occurred perpendicularly and solely through positioning cholesterol's oxygen toward the primary hydroxyl rim (PHR), the mechanism of cholesterol binding to βCD and MβCD could take place with the orientation of oxygen towards both rims. Functionalization resulted in decreased cavity polarity, increased constriction tendency, and altered solubility and configuration of the carrier. Upon cholesterol binding, the CDs expanded, increasing the cavity volume in cholesterol-containing systems. The effects of cholesterol on the relative shape anisotropy (κ2) and asphericity parameter (b) in cyclodextrins were investigated. βCD exhibited a spherical structure regardless of cholesterol presence, while 2HPβCD and MβCD displayed more pronounced non-sphericity in the absence of cholesterol. Loading cholesterol transformed 2HPβCD and MβCD into more spherical shapes, with increased probabilities of higher κ2. MβCD showed a higher maximum peak of κ2 compared to 2HPβCD after cholesterol loading, while 2HPβCD maintained a significant maximum peak at 0.2 for b.

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Section: Computational Detailsmentioning

confidence: 99%

Exploring the role of cyclodextrins as a cholesterol scavenger: a molecular dynamics investigation of conformational changes and thermodynamics

Ganjali Koli,

Fogolari

2023

Sci Rep

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“…The adsorption free energy obtained from MC simulation for the Nar/β-CD/CS/ GP complex was negative, suggesting a spontaneous process, revealing that negative adsorption energy was energetically desirable for adsorption process (Figure a–d). Furthermore, the negative value of the Nar/β-CD complex was more stable than that of the CS/ GP and Nar/β-CD owing to more energy of the Nar/β-CD/CS/ GP complex as compared with Nar/β-CD complex …”

Section: Resultsmentioning

confidence: 96%

“…Furthermore, the negative value of the Nar/β-CD complex was more stable than that of the CS/ GP and Nar/β-CD owing to more energy of the Nar/β-CD/CS/ GP complex as compared with Nar/β-CD complex. 54 …”

Section: Resultsmentioning

confidence: 99%

Bioactive Wound Healing 3D Structure Based on Chitosan Hydrogel Loaded with Naringin/Cyclodextrin Inclusion Nanocomplex

Bian,

Pilehvar,

Kousha

et al. 2024

ACS Omega

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The current assay aimed to fabricate and analyze a potent wound healing structure based on a naringin (Nar)/β-cyclodextrin (β-CD)-loaded chitosan hydrogel. Using the simulation studies, we assessed the interactions among the Nar, β-CD, and the formation of the inclusion complex. Then, the formation of the hydrogel nanocomplex was simulated and evaluated using the in silico methods. The results showed that after optimization of the structures by DMol3 based on DFT-D, the total energies of Nar, GP, CD, and β-CD were calculated at −2100. 159, −912.192, −3778.370, and −4273.078 Ha, respectively. The encapsulation energy of Nar on β-CD in the solvent phase was calculated at −93.626 kcal/mol, and the Nar structure was located inside β-CD in solution. The negative interaction energy value for the encapsulation of Nar on β-CD suggests the exothermic adsorption process and a stable structure between Nar and β-CD. Monte Carlo method was applied to obtain adsorption of CS/GP on Nar/β-CD. Its value of the obtained interaction energy was calculated at −1.423 × 103 kcal/mol. The characterization confirmed the formation of a Nar/β-CD inclusion complex. The Zeta potential of the pristine β-CD changed from −4.60 ± 1.1 to −17.60 ± 2.34 mV after interaction with Nar, and the heightened surface negativity can be attributed to the existence of electron-rich naringin molecules, as well as the orientation of the hydroxyl (OH) group of the β-CD toward the surface in an aqueous solution. The porosity of the fabricated hydrogels was in the range of 70−90% and during 14 days around 47.0 ± 3.1% of the pure hydrogel and around 56.4 ± 5.1 of hydrogel nanocomposite was degraded. The MTT assay showed that the hydrogels were biocompatible, and the wound contraction measurement (in an animal model) showed that the closure of the induced wound in the hydrogel nanocomposite treatment was faster than that of the control group (wound without treatment). The results of this study indicate that the developed bioactive wound healing 3D structure, which is composed of a chitosan hydrogel containing a Nar/β-CD inclusion nanocomplex, has potential as an effective material for wound dressing applications.

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“…The process was stable physico-sorption and spontaneous, and Cr(VI) can be effectively adsorbed on H 4 BTC-PANI/pC 3 N 4 . The outcome of Monte Carlo (MC) simulation supported experimental studies due to its negative result …”

Section: Resultsmentioning

confidence: 99%

1,2,4,5-Benzene Tetracarboxylic Acid-Doped Polyaniline/Protonated Carbon Nitride Nanostructures for Cr(VI) Adsorption in Water

Hsini,

Haounati,

Imgharn

et al. 2024

ACS Appl. Nano Mater.

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This work outlines the fabrication of a nanocomposite, namely, 1,2,4,5-benzene tetracarboxylic acid-doped polyaniline/protonated carbon nitride (H 4 BTC-PANI/pC 3 N 4 ) through a straightforward two-step process. Various advanced analytical tools validated the formation of the composite. Subsequently, the adsorption characteristics of the prepared composite for the uptake of Cr(VI) ions were assessed via batch adsorption experiments. Removal equilibrium and kinetic approaches clearly demonstrated the simulation of adsorption data via Langmuir and pseudo-second-order models. The thermodynamic analysis disclosed that the removal of Cr(VI) ions by the H 4 BTC-PANI/pC 3 N 4 material was a spontaneous, endothermic procedure associated with an increase in surface site availability randomness. It was found that by using 0.25 g/L of adsorbent dose at pH 2, almost 97.1% of the chromium was eliminated within an equilibrium time of 90 min. Furthermore, the maximum adsorbed amount was 1229 mg•g −1 , exceeding the capabilities of most similar adsorbents. The composites retained a significant adsorption capacity for Cr(VI) even after undergoing five regeneration cycles, demonstrating excellent reusability. Monte Carlo (MC) calculations were executed to search for the most stable configuration and adsorption energies of H 4 BTC on pC 3 N 4 , PANI on H 4 BTC/pC 3 N 4 , and Cr(VI) removal on H 4 BTC-PANI/pC 3 N 4 surfaces in the aqueous system. The experimental findings indicated that H 4 BTC-PANI/pC 3 N 4 holds significant promise as a cost-effective material for removing hexavalent chromium from wastewater, showcasing considerable potential for practical use.

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Insights from molecular dynamics and DFT calculations into the interaction of 1,4-benzodiazepines with 2-hydroxypropyl-βCD in a theoretical study

Cited by 10 publications

References 79 publications

Exploring the role of cyclodextrins as a cholesterol scavenger: a molecular dynamics investigation of conformational changes and thermodynamics

Exploring the role of cyclodextrins as a cholesterol scavenger: a molecular dynamics investigation of conformational changes and thermodynamics

Bioactive Wound Healing 3D Structure Based on Chitosan Hydrogel Loaded with Naringin/Cyclodextrin Inclusion Nanocomplex

1,2,4,5-Benzene Tetracarboxylic Acid-Doped Polyaniline/Protonated Carbon Nitride Nanostructures for Cr(VI) Adsorption in Water

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