Binding modes of cibacron blue with albumin in affinity chromatography using docking tools

Kılıç, Seçkin; Andaç, Müge; Deni̇zli̇, Adil

doi:10.1016/j.ijbiomac.2021.04.142

Cited by 16 publications

(7 citation statements)

References 21 publications

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“…The interaction between AST and protein complexes was visualized in 2D and 3D structures using Molecular Operating Environment MOE 2015.10 software and PyMol. 30…”

Section: Methodsmentioning

confidence: 99%

Astaxanthin targets IL-6 and alleviates the LPS-induced adverse inflammatory response of macrophages

Wu,

Bashir,

Shao

et al. 2024

Food Funct.

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“…The interaction between AST and protein complexes was visualized in 2D and 3D structures using Molecular Operating Environment MOE 2015.10 software and PyMol. 30…”

Section: Methodsmentioning

confidence: 99%

Astaxanthin targets IL-6 and alleviates the LPS-induced adverse inflammatory response of macrophages

Wu,

Bashir,

Shao

et al. 2024

Food Funct.

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Section: Computational Approach For Ligand Evaluationmentioning

confidence: 99%

“…Molecular modeling applications are used to predict the protein-ligand interactions and design the highly selective biomimetic dye ligands for the target molecules . For instance, Kılıç et al used computational methods to investigate the appropriate complexes between CB and human serum albumin (HSA).…”

Section: Computational Approach For Ligand Evaluationmentioning

confidence: 99%

“…51,52 Molecular modeling applications are used to predict the protein-ligand interactions and design the highly selective biomimetic dye ligands for the target molecules. 53 For instance, Kılıçet al 53 used computational methods to investigate the appropriate complexes between CB and human serum albumin (HSA). For this purpose, the AutoDock v4.2.6 software was used, and six conformations of CB were investigated using molecular docking software to predict the binding preference of the biomimetic dye and the target protein (Figure 5).…”

Section: Other Biomimetic Ligandsmentioning

confidence: 99%

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Inspirations of Biomimetic Affinity Ligands: A Review

et al. 2022

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Affinity chromatography is a well-known method dependent on molecular recognition and is used to purify biomolecules by mimicking the specific interactions between the biomolecules and their substrates. Enzyme substrates, cofactors, antigens, and inhibitors are generally utilized as bioligands in affinity chromatography. However, their cost, instability, and leakage problems are the main drawbacks of these bioligands. Biomimetic affinity ligands can recognize their target molecules with high selectivity. Their cost-effectiveness and chemical and biological stabilities make these antibody analogs favorable candidates for affinity chromatography applications. Biomimetics applies to nature and aims to develop nanodevices, processes, and nanomaterials. Today, biomimetics provides a design approach to the biomimetic affinity ligands with the aid of computational methods, rational design, and other approaches to meet the requirements of the bioligands and improve the downstream process. This review highlighted the recent trends in designing biomimetic affinity ligands and summarized their binding interactions with the target molecules with computational approaches.

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“…4,5 Several studies have been reported before to address the binding properties of CB in complex with HSA. 3,[6][7][8][9] Although several studies on the binding nature of CB interacting with a few proteins, including HSA, have been published in literature 3,6,7,9,10 a full insight into the experimental details of the thermodynamic binding properties of CB in complex with HSA currently remains mysterious.…”

Section: Introductionmentioning

confidence: 99%

Isothermal titration calorimetry binding properties of Cibacron Blue F3GA in complex with human serum albumin

Andac

Çağlar

Deni̇zli̇

et al. 2023

J of Molecular Recognition

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Binding interactions between Cibacron Blue-F3GA (CB-F3GA) and human serum albumin (HSA, at physiologically ten-fold lower concentration) was studied by isothermal titration calorimetry (ITC) and in-silico docking computations. ITC experiments revealed two separate binding sites on HSA with different binding affinities for CB-F3GA. The high-affinity binding site (PBS-II) on HSA binds CB-F3GA at nanomolar scale (K D1 = 118 ± 107 nM) with favorable binding enthalpy (ΔH o 1 = À 6.47 ± 0.44 kcal/mol) and entropy (ÀTΔS o 1 = À2.98 kcal/mol) energies. CB-F3GA binds to the low-affinity binding site (PBS-I) at μM scale (K D2 = 31.20 ± 18.40 μM) with favorable binding enthalpy (ΔH o 1 = À 5.03 ± 3.86 Â 10 À2 kcal/mol) and entropy (ÀTΔS o 1 = À1.12 kcal/mol) energies. ITC binding data strongly suggest that CB-F3GA binding to PBS-II site increases the formation of dimeric-HSA clusters (N 1 = 2.43 ± 0.50), while binding to PBS-I leads to tetrameric-HSA clusters (N 2 = 4.61 ± 0.90). These results suggest that a higher degree of HSA aggregation upon drug binding may be expected under physiological conditions, a notion that should be further investigated for the delivery and toxicity of drugÀHSA interactions.

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Binding modes of cibacron blue with albumin in affinity chromatography using docking tools

Cited by 16 publications

References 21 publications

Astaxanthin targets IL-6 and alleviates the LPS-induced adverse inflammatory response of macrophages

Astaxanthin targets IL-6 and alleviates the LPS-induced adverse inflammatory response of macrophages

Inspirations of Biomimetic Affinity Ligands: A Review

Isothermal titration calorimetry binding properties of Cibacron Blue F3GA in complex with human serum albumin

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