A molecular simulation approach towards the development of universal nanocarriers by studying the pH- and electrostatic-driven changes in the dynamic structure of albumin

Srivastav, Amit Kumar; Gupta, Sanjeev K.; Kumar, Umesh

doi:10.1039/d0ra00803f

Cited by 13 publications

(7 citation statements)

References 46 publications

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“…We performed the MD simulation and free energy of binding for the BSA with fucoxanthin in the presence of rhamnolipid. All MD simulation studies were performed in GROMACS 2020 30 with OPLS‐AA/L all‐atom force field 31 following the procedure of our previous theoretical work based on BSA 32 . All simulated protein–ligand complexes were analyzed at the same simulation condition which includes energy minimization steps, NVT‐NPT ensembles, 33 trajectory analysis, and analysis of the free binding energies through MM‐PB(GB)SA method 34,35 .…”

Section: Methodsmentioning

confidence: 99%

“…All MD simulation studies were performed in GROMACS 2020 30 with OPLS-AA/L all-atom force field 31 following the procedure of our previous theoretical work based on BSA. 32 All simulated protein-ligand complexes were analyzed at the same simulation condition which includes energy minimization steps, NVT-NPT ensembles, 33 trajectory analysis, and analysis of the free binding energies through MM-PB(GB)SA method. 34,35 All the complex systems were enclosed in a dodecahedral box with SPC/E water model for MD simulation.…”

Section: Molecular Dynamic Simulation and Free Energy Of Binding Calc...mentioning

confidence: 99%

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Synthesis and physicochemical characterization of rhamnolipid fabricated fucoxanthin loaded bovine serum albumin nanoparticles supported by simulation studies

et al. 2022

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BACKGROUND: Fucoxanthin is a hydrophobic carotenoid with many beneficial biological activities. However, due to low aqueous solubility their clinical efficacy is limited thus leading to poor oral bioavailability. To address this issue, we encapsulated fucoxanthin in rhamnolipid fabricated bovine serum albumin (BSA) loaded nanoparticles (LNPs) for improving solubility dependent bioavailability of fucoxanthin.RESULTS: These synthesized LNPs were characterized by dynamic light scattering (DLS), ultraviolet (UV)-visible spectrophotometry, high-performance liquid chromatography (HPLC), Fourier-transform infrared (FTIR), scanning electron microscopy (SEM), differential scanning calorimetry (DSC). Our results showed that LNPs were spherical in shape with particle size around 180 nm along with positive zeta potential. The encapsulation efficiency and loading efficiency calculated for LNPs were 69.66 ± 1.5% and 14 ± 0.2%, respectively. The antioxidant assay of LNPs indicate high radical scavenging activity compared to pure fucoxanthin. Besides this, our release studies indicates that drug release occur from the matrix of nanocarrier system through diffusion based on concentration. Thus, these findings indicate successful encapsulation of fucoxanthin, with improved solubility thereby leading to increased bioavailability. This nano formulation is derived from components which are FDA approved that could be exploited for encapsulating other vital nutraceutical molecules. CONCLUSION: Overall, our results showed successful synthesis of biodegradable nanocarrier for delivering fucoxanthin supported by molecular docking, molecular dynamics simulation and thermodynamics of free binding energy studies.

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Section: Methodsmentioning

confidence: 99%

Section: Molecular Dynamic Simulation and Free Energy Of Binding Calc...mentioning

confidence: 99%

Synthesis and physicochemical characterization of rhamnolipid fabricated fucoxanthin loaded bovine serum albumin nanoparticles supported by simulation studies

et al. 2022

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“…Both R g and RMSD agree well with circular dichroism often used to examine the secondary structure of proteins and are therefore well recognized quantifiers of conformational changes in proteins ,,− which could be used to characterize the changes in HSA conformation upon interaction with the AuNR passivated with different surface ligands.…”

Section: Resultsmentioning

confidence: 52%

Dynamics of Human Serum Albumin Corona Formation on Gold Nanorods with Different Surface Ligands In Silico

2021

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The interaction between human serum albumin (HSA) and nanoparticles (NPs) to form HSA corona has widely been studied since endogenous functions of albumin are highly attractive for drug delivery. However, a full understanding of the molecular dynamics and factors behind the formation of HSA corona, including interactions between HSA and different surface ligands and between neighboring HSA molecules, resulting in conformational change of HSA is presently lacking. Here, we assembled 14 HSA molecules around gold nanorods (AuNRs) with different surface chemistries (bare gold surface, cetyltrimethylammonium bromide (CTAB), polystyrene sulfonate (PSS), and polydiallyldimethylammonium chloride (PDADMAC)) in silico and examined the dynamics of HSA corona formation using coarse-grained molecular dynamics for 300 ns of simulation. We observed that PDADMAC, being more flexible than PSS, resulted in all HSA molecules moving toward AuNR−PDADMAC, while the instability of CTAB on AuNR resulted in fewer HSA molecules moving toward AuNR−CTAB compared to AuNR−PSS. HSA molecules around AuNR−PDADMAC also exhibited the largest conformational change in terms of their radius of gyration (R g ) and root mean square deviation (RMSD). In the absence of surface ligands, HSA molecules around the bare AuNR were susceptible to steric hindrance with conformational change observed in terms of their RMSD but not their R g unlike that of HSA molecules around AuNR−PDADMAC. The insights gained from the inclusion of neighboring HSA molecules in the simulation of corona formation could be more representative than examining a single adsorbed HSA molecule on AuNRs with different surface passivations.

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“…The docking mechanism of proteins or receptor shows rigid molecular behavior that do not reflect their conformational or structural changes occurred during the docking process with ligands. MD simulation is helpful for studying and analyzing the conformational and structural changes occurred during receptor-ligand interactions (Srivastav et al, 2020).…”

Section: Interaction Of Multilayer Graphene With Sars-mentioning

confidence: 99%

Synthesis of exfoliated multilayer graphene and its putative interactions with SARS-CoV-2 virus investigated through computational studies

Raval

Srivastav

Gupta

et al. 2020

Journal of Biomolecular Structure and Dynamics

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Our work investigates the interaction of synthesized graphene with the SARS-CoV-2 virus using molecular docking and molecular dynamics (MD) simulation method. The layer dependent inhibitory effect of graphene nanosheets on spike receptor-binding domain of 6LZG, complexed with host receptor i.e. angiotensin-converting enzyme 2 (ACE2) of SARS-CoV-2 was investigated through computational study. Graphene sample was synthesized using mechanical exfoliation with shear stress and its mechanism of inhibition towards the SARS-CoV-2 virus was explored by molecular docking and molecular dynamics (MD) simulation method. The thermodynamics study for the free binding energy of graphene towards the SARS-CoV-2 virus was analyzed. The binding energy of graphene towards the virus increased with an increasing number of layers. It shows the highest affinity of À17.5 Kcal/mol in molecular docking while DG binding is in the order of À28.01 ± 0.04 5 Kcal/mol for the seven-layers structure. The increase in carbon layers is associated with an increasing number of edge sp 3-type carbon, providing greater curvature, further increase the surface reactivity responsible for high binding efficiency. The MD simulation data reveals the high inhibition efficiency of the synthesized graphene towards SARS-CoV-2 virus which would help to design future in-vitro studies. The graphene system could find potential applications in personal protective equipment and diagnostic kits.

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A molecular simulation approach towards the development of universal nanocarriers by studying the pH- and electrostatic-driven changes in the dynamic structure of albumin

Abstract: Role of pH and electrostatic charges on the conformations and dynamics of albumin structure by molecular dynamic study.

Cited by 13 publications

References 46 publications

Synthesis and physicochemical characterization of rhamnolipid fabricated fucoxanthin loaded bovine serum albumin nanoparticles supported by simulation studies

Synthesis and physicochemical characterization of rhamnolipid fabricated fucoxanthin loaded bovine serum albumin nanoparticles supported by simulation studies

Dynamics of Human Serum Albumin Corona Formation on Gold Nanorods with Different Surface Ligands In Silico

Synthesis of exfoliated multilayer graphene and its putative interactions with SARS-CoV-2 virus investigated through computational studies

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