The RGD tripeptide anticancer drug carrier: DFT computations and molecular dynamics simulations

Nikfar, Zahra; Shariatinia‬, Zahra

doi:10.1016/j.molliq.2019.02.114

Cited by 34 publications

(10 citation statements)

References 96 publications

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“…At the main optimization step, we used GROMACS 2019.3 (OPLS-AA force field) in the EM (10 kJ/mol/nm minimum force), NVT (500 ps), NPT (500 ps) and then MD (100 ns) simulation in 2 fs time steps. All cases contained 30600 water molecules (SPC/E water model) in boxes with a dimension of 3 × 3 × 30 nm 3 .This size of box was only to optimize the chain length of polymer structures, because their non-optimized chain length was about 28 nm.…”

Section: Methodsmentioning

confidence: 99%

“…The triamino acid peptide is another important ligand in the targeted drug delivery field which is composed of three sequences of arginine-glycine-aspartate, known as RGD, the simplest member of a big family. [2] Due to its molecular structure and the presence of amino groups in its formulation, its affinity towards the acidic environment of the tumor cells is enhanced that can be utilized in cancer treatments [3] and the inhibition of tumor metastasis and inducing the cell apoptosis. [4] Despite the developments in this field, control of the polymeric NPs size is considered as a remaining challenge.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Microfluidic Engineering of RGD^[1]‐Terminated Nanocarriers Micellization and In‐Situ Docetaxel Encapsulation: An Atomistic Insight

Khedri

Moraveji

2022

ChemistrySelect

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The interactions between ligands and polymers are of great interest to drug delivery researches. In this work for the first time, Poly (lactic-co-glycolic acid) based polymers with arginine-glycine-aspartate (RGD) peptide ligands which are immediately self-assembled into micellar nanoparticles (NPs) in contact with water have been investigated in the atomistic level. In this regard, the effect of polymer and RGD concentrations on the stability, size, interaction energies and other molecular properties of nanocarriers has been investigated using molecular dynamics simulation. In the next step, the microfluidic micellization and docetaxel (DTX) encapsulation has been simulated in comparison to bulk micellization. Results indicated that by employing only 20 wt % RGD-conjugated polymer, the particles reach the stable properties and compactness without DTX. But, when the DTX was added, 30 wt.% of RGD-conjugated polymers that assembled in microfluidic system is the best state nanocarrier for the smart target drug delivery for transfer of DTX drug into the Cancer cell. Comparisons of the results acquired in the current paper confirmed that engineering and tuning the self-assembly in the interface of phases in microchennel resulted in a precise control on the particle size and resulted in the preparation of smaller and more stable NPs that can be exploited as ultrasmall, smart drug carriers.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Microfluidic Engineering of RGD^[1]‐Terminated Nanocarriers Micellization and In‐Situ Docetaxel Encapsulation: An Atomistic Insight

Khedri

Moraveji

2022

ChemistrySelect

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“…B3LYP-D3(BJ)/6-311G* is calculated about HOMO-LUMO gaps. The calculation formulas of related parameters are as follows [30,31] :…”

Section: Highest Occupied Molecular Orbital and Lowest Unoccupied Mol...mentioning

confidence: 99%

The mechanisms and molecular properties about isomerization of resin acids, synthesis of acrylopimaric acid based on density functional theory calculation

Lai

Jiang

et al. 2022

J of Physical Organic Chem

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Acrylopimaric acid is considered a possible substitute for petroleum‐based polymeric monomers. Resin acids were isomerized to form levopimaric acid(4), which reacted with acrylic acid to synthesize isomers of acrylopimaric acid. Density functional theory calculations were carried out to investigate the reaction mechanisms with seven reaction paths. In terms of dynamics, the energy barrier in the isomerization of palustric acid(2) to levopimaric acid(4) was the lowest, whereas the highest energy barrier was the isomerization of neoabietic acid(3) to levopimaric acid(4). The addition reaction of levopimaric acid(4) and acrylic acid(5) to acrylopimaric acid c(8) was the optimal reaction path dynamically. However, the energy of acrylopimaric acid c(8) was higher than that of acrylopimaric acid d(9). Highest occupied molecular orbital and lowest unoccupied molecular orbital (HOMO–LUMO) were analyzed for eight kinds of molecules. For acylpyimaric acid, the nonplanar six‐memed ring and the C–C double bonds were easily attacked by nucleophile, whereas the nonplanar six‐memed ring and the carboxyl group are easily reacted with electrophiles. The electrostatic surface potential were analyzed for molecules.

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“…Biomolecular materials containing the arginine-glycine-aspartate (RGD) sequence are always at the center of biophysics research in their application such as in the bone scaffold, synthesis, and regeneration of tissue and cartilage [ 1 , 2 ], in imaging as radiotracers [ 3 , 4 , 5 , 6 ], for cancer therapy [ 7 , 8 , 9 ], and in targeted drug delivery [ 10 , 11 , 12 , 13 , 14 , 15 ]. The RGD motif peptide serves as a primary integrin recognition site in extracellular matrix proteins since it has a strong binding affinity to integrins, which are heterodimeric cell surface receptors and mediate cell-extracellular matrix adhesion [ 16 , 17 , 18 , 19 ].…”

Section: Introductionmentioning

confidence: 99%

“…To explore the details of peptide solvation properties, molecular dynamics (MD), molecular mechanics, and Monte Carlo methods, all based on specific force field parameters, are widely used. Nevertheless, the information on the role played by the hydrogen bond (HB) within RGD and at the RGD-water interface is in general still missing, as are the relevant ab initio MD (AIMD) studies [ 12 , 25 , 26 , 27 ]. Classical MD studies cannot provide a quantitative description of essentially quantum HBs (O–H and N–H) since they depend on the details of the force field parameterization.…”

Section: Introductionmentioning

confidence: 99%

Solvent Effect on the Structure and Properties of RGD Peptide (1FUV) at Body Temperature (310 K) Using Ab Initio Molecular Dynamics

et al. 2021

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The structure and properties of the arginine-glycine-aspartate (RGD) sequence of the 1FUV peptide at 0 K and body temperature (310 K) are systematically investigated in a dry and aqueous environment using more accurate ab initio molecular dynamics and density functional theory calculations. The fundamental properties, such as electronic structure, interatomic bonding, partial charge distribution, and dielectric response function at 0 and 310 K are analyzed, comparing them in dry and solvated models. These accurate microscopic parameters determined from highly reliable quantum mechanical calculations are useful to define the range and strength of complex molecular interactions occurring between the RGD peptide and the integrin receptor. The in-depth bonding picture analyzed using a novel quantum mechanical metric, the total bond order (TBO), quantifies the role played by hydrogen bonds in the internal cohesion of the simulated structures. The TBO at 310 K decreases in the dry model but increases in the solvated model. These differences are small but extremely important in the context of conditions prevalent in the human body and relevant for health issues. Our results provide a new level of understanding of the structure and properties of the 1FUV peptide and help in advancing the study of RGD containing other peptides.

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The RGD tripeptide anticancer drug carrier: DFT computations and molecular dynamics simulations

Cited by 34 publications

References 96 publications

Microfluidic Engineering of RGD^[1]‐Terminated Nanocarriers Micellization and In‐Situ Docetaxel Encapsulation: An Atomistic Insight

Microfluidic Engineering of RGD^[1]‐Terminated Nanocarriers Micellization and In‐Situ Docetaxel Encapsulation: An Atomistic Insight

The mechanisms and molecular properties about isomerization of resin acids, synthesis of acrylopimaric acid based on density functional theory calculation

Solvent Effect on the Structure and Properties of RGD Peptide (1FUV) at Body Temperature (310 K) Using Ab Initio Molecular Dynamics

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The RGD tripeptide anticancer drug carrier: DFT computations and molecular dynamics simulations

Cited by 34 publications

References 96 publications

Microfluidic Engineering of RGD[1]‐Terminated Nanocarriers Micellization and In‐Situ Docetaxel Encapsulation: An Atomistic Insight

Microfluidic Engineering of RGD[1]‐Terminated Nanocarriers Micellization and In‐Situ Docetaxel Encapsulation: An Atomistic Insight

The mechanisms and molecular properties about isomerization of resin acids, synthesis of acrylopimaric acid based on density functional theory calculation

Solvent Effect on the Structure and Properties of RGD Peptide (1FUV) at Body Temperature (310 K) Using Ab Initio Molecular Dynamics

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Product

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Microfluidic Engineering of RGD^[1]‐Terminated Nanocarriers Micellization and In‐Situ Docetaxel Encapsulation: An Atomistic Insight

Microfluidic Engineering of RGD^[1]‐Terminated Nanocarriers Micellization and In‐Situ Docetaxel Encapsulation: An Atomistic Insight