Unveiling the Interplay between Dopamine-like Molecules and Β-Amyloid Peptide: A Combined Molecular Dynamic and DFT Approach.

Aims: This study aims explore the impact of catechol, dopamine, and L-DOPA on the stability and toxicity of β-amyloid peptides, which play a key role in the neurodegenerative process of Alzheimer's disease, to assess their potential as therapeutic agents.

Background: Alzheimer's disease is marked by the aggregation of β-amyloid peptides, which contribute to neurodegeneration. Exploring how various compounds interact with β-amyloid peptides can offer valuable insights into potential therapeutic strategies.

Impact of surface-active ionic solutions on the structure and function of laccase from trametes versicolor: Insights from molecular dynamics simulations.

Many protein-ionic liquid investigations have examined laccase interactions. Laccases are a class of poly-copper oxidoreductases that retain significant biotechnological relevance owing to their notable oxidative capabilities and their application in the elimination of synthetic dyes, phenolic compounds, insecticides, and various other substances. This study investigates the impact of surface active ionic liquids (SAILs), namely, decyltrimethylammonium bromide [N][Br] and 1-decyl-3-methylimidazolium chloride [C][Cl] as cationic surfactant ionic liquids and cholinium decanoate [Chl][Dec], an anionic surfactant ionic liquid, on the structure and function of laccase from the fungus Trametes versicolor (TvL) by the molecular dynamics (MD) simulation method.

Modeling and characterization of lenalidomide-loaded tripolyphosphate-crosslinked chitosan nanoparticles for anticancer drug delivery.

Tripolyphosphate-crosslinked chitosan (TPPCS) nanoparticles were employed in the encapsulation of lenalidomide (LND) using a straightforward ionic cross-linking approach. The primary objectives of this technique were to enhance the bioavailability of LND and mitigate inadequate or overloading of hydrophobic and sparingly soluble drug towards cancer cells. In this context, a quantum chemical model was employed to elucidate the characteristics of TPPCS nanoparticles, aiming to assess the efficiency of these nanocarriers for the anticancer drug LND.

Investigating the combined effect of copper, zinc, and iron ions on truncated and full-length Aβ peptides: insights from molecular dynamics simulation.

The truncated Aβ1 - 16 peptide containing the metal-binding domain is frequently used in and experimental investigations because it is more soluble and thus more suitable for studies in solution and does not form amyloids. Several spectroscopic studies have shown that the metal binding of Aβ1 - 16 is very similar to that of the full-length Aβ1 - 42. However, since small changes can have a significant impact on aggregation, further experimental and theoretical are needed to elucidate the detailed structures of truncated and full-length Aβ.

Porphyrin-based ligand interaction with G-quadruplex: Metal cation effects.

The G-quadruplex planar-ligand complex is used to detect heavy metal cations such as Ag , Cu , Pb , Hg , organic molecules, nucleic acids, and proteins. The interaction of the three planar porphyrins (L1), 5,10,15,20-tetrakis (1-ethyl-1-λ -pyridine-4-yl) porphyrin (L2), and 5,10,15,20-tetrakis (1-methyl-1-λ -pyridine-4-yl) porphyrin (L3), coming from the porphyrin family, with G-quadruplex obtained from human DNA telomeres in the presence of lithium, sodium, potassium, rubidium, cesium, magnesium, and calcium ions was studied by molecular dynamics simulation. When G-quadruplex containing divalent ions of magnesium and calcium interacts with L1, L2, and L3 ligands, the hydrogen bonds of the lower G-quadruplex sheet are more affected by ligands and the distance between guanines in the lower tetrad increases.

A comprehensive computer simulation insight into inhibitory mechanisms of EGCG and NQTrp ligands on amyloid-beta assemblies as the Alzheimer's disease insignia.

Amyloid-β peptide with predominant presence in the senile plaques is the most common agent for Alzheimer's disease (AD) incidence. Assembly of the amyloid-β(1-42) (Aβ1-42) isoform is known as the main reason for the AD appearance. Epigallocatechin gallate (EGCG) and 1,4-naphthoquinone-2-yl-L-tryptophan (NQTrp) are two small molecules that inhibit the formation of the Aβ1-42 fibrils.

New hybrids based on benzimidazole and diazepine moieties: design, synthesis, characterization, molecular docking studies and their in vitro interactions with benzodiazepine receptors.

Benzodiazepines are one of the most widely prescribed pharmacologic agents in the world. They are employed for numerous indications, including anxiety, insomnia, muscle relaxation, relief from spasticity caused by central nervous system pathology and epilepsy. In this work, we have synthesized some new hybrids based on benzimidazole and diazepine scaffolds from the reaction of suitable benzimidazole derivatives with glycine.

Recent advances in computational methods for biosensor design.

Biosensors are analytical tools with a great application in healthcare, food quality control, and environmental monitoring. They are of considerable interest to be designed by using cost-effective and efficient approaches. Designing biosensors with improved functionality or application in new target detection has been converted to a fast-growing field of biomedicine and biotechnology branches.

Effects of the deglycosylation on the structure and activity of chloroperoxidase: Molecular dynamics simulation approach.

Chloroperoxidase (CPO) is a versatile fungal heme-thiolate protein that catalyzes a variety of one electron and two-electron oxidations. Chloroperoxidase is a versatile fungal heme-thiolate protein that catalyzes a variety of oxidations. CPO enzyme contains thirteen sugars, including five N-acetyl D-glucosamines (NAG) and eight mannoses (MAN), which are attached to the protein via the glycosidic bonds.

Application of response surface modeling and chemometrics methods for the determination of Atenolol, Metoprolol and Propranolol in blood sample using dispersive liquid-liquid microextraction combined with HPLC-DAD.

A novel dispersive liquid-liquid microextraction (DLLME) method using ionic liquids (ILs) followed by high-performance liquid chromatography-diode array detector (HPLC-DAD) has been devised to specify Atenolol, Atenolol, Metoprolol and Propranolol in blood real samples. Fourteen effective parameters in DLLME process, including pH of aqueous sample, volume of the dispersion and extraction solvents and ionic strength of donor phase, etc.; were screened using fractional factorial screening methodology (FFSM) based on Placket-Burman design (PBD) and subsequently were optimized by response surface methodology using central composite design (CCD).

The Effect of Temperature on the Interaction of Phenanthroline-based Ligands with G-quadruplex: In Silico Viewpoint.

Aim And Objective: The stability of the G-quadruplex structure can increase its activity in telomerase inhibiting cancer cells. In this study, a molecular dynamics simulation method was used to study the effect of three phenanthroline-based ligands on the structure of G-quadruplex at the temperatures of 20, 40, 60 and 80°C.

Materials And Methods: RMSD values and frequency of calculated RMSD in the presence and absence of ligands show that ligands cause the relative stability of the G-quadruplex, particularly at low temperatures.

Acetyl-11-keto-β-boswellic acid derivatives effects on 5-lipoxygenase: In silico viewpoint.

The 5-lipoxygenase enzyme is a proinflammatory enzyme and produces leukotrienes. Evidence has shown that inflammation contributes to Alzheimer's disease. On the other hand, boswellic acid derivatives have also been shown to be involved in Alzheimer's disease.

The investigation of the G-quadruplex aptamer selectivity to Pb ion: a joint molecular dynamics simulation and density functional theory study.

The aptamers with the ability to form a G-quadruplex structure can be stable in the presence of some ions. Hence, study of the interactions between such aptamers and ions can be beneficial to determine the highest selective aptamer toward an ion. In this article, molecular dynamics (MD) simulations and quantum mechanics (QM) calculations have been applied to investigate the selectivity of the T30695 aptamer toward Pb in comparison with some ions.

A simple paper-based aptasensor for ultrasensitive detection of lead (II) ion.

In this study, a simple paper-based aptasensor has been developed for the ultrasensitive detection of lead (Pb) ion within about 10 min. The aptasensor has been successfully designed by taking advantages of the Förster Resonance Energy Transfer (FRET) process and the super fluorescence quenching property of graphene oxide (GO) sheet. The sensing mechanism of the aptasensor is based on the conformational switch of the Pb-specific aptamer from a random coil to a G-quadruplex structure.

Study of alpha-amylase and gold nanoparticles interaction at two different temperatures through molecular dynamics.

The interaction of alpha-amylase with gold nanoparticles was studied at the two different temperatures of 25 and 75 °C through molecular dynamics simulation. To this end, 3-nm diameter spherical gold nanoparticles were designed. According to root mean square deviation results, at a high temperature, enzyme stability decreased in the absence of nanoparticles and increased in the presence of nanoparticles.

The effect of different alcohols on the Asp23-Lys28 and Asp23-Ala42 salt bridges of the most effective peptide in Alzheimer's disease: Molecular dynamics viewpoints.

The beta-amyloid peptide Aβ1-42 is the most effective peptide in the process of forming plaque and creating Alzheimer's. After the separation of Aβ1-42 from APP membrane protein, the membrane surface is transmitted to the extracellular environment, which is a crowded environment. On the other hand, stability of salt bridges Asp23-Lys28 and Lys28-Ala42 is important for monomer toxicity and fibrillation formation.

Simultaneous detection and determination of mercury (II) and lead (II) ions through the achievement of novel functional nucleic acid-based biosensors.

The serious threats of mercury (Hg) and lead (Pb) ions for the public health makes it important to achieve the detection methods of the ions with high affinity and specificity. Metal ions usually coexist in some environment and foodstuff or clinical samples. Therefore, it is very necessary to develop a fast and simple method for simultaneous monitoring the amount of metal ions, especially when Hg and Pb coexist.

Does high pressure have any effect on the structure of alpha amylase and its ability to binding to the oligosaccharides having 3-7 residues? Molecular dynamics study.

Studies have shown that deletion of amino acids from the C-terminus of amylase do not alter its amylolytic activity. Although high pressure is used to modify the structure and function of this enzyme, the effects of high pressures on the structures of the wild-type and truncated amylases have not yet been understood at the molecular level. Using molecular dynamic simulations and docking, we studied the structures of wild-type and truncated Taka-amylases at high pressures (1000-4000 bar).

Spectroscopic and DFT investigation of interactions between cyclophosphamide and aspirin with lysozyme as binary and ternary systems.

Multi-spectroscopic and density functional theory (DFT) calculations was used to study the interaction between cyclophosphamide (CYP) and aspirin (ASA) with lysozyme (LYS). The experimental results showed that fluorescence quenching of LYS by drug was a result of the formation of drug-LYS complex; static quenching was confirmed to result in fluorescence quenching. Modified Stern-Volmer plots of interaction between CYP and ASA with protein in the binary and ternary systems were used to determine the binding parameters.

Structure-activity relationship for Fe(III)-salen-like complexes as potent anticancer agents.

Quantitative structure activity relationship (QSAR) for the anticancer activity of Fe(III)-salen and salen-like complexes was studied. The methods of density function theory (B3LYP/LANL2DZ) were used to optimize the structures. A pool of descriptors was calculated: 1497 theoretical descriptors and quantum-chemical parameters, shielding NMR, and electronic descriptors.

How a protein can remain stable in a solvent with high content of urea: insights from molecular dynamics simulation of Candida antarctica lipase B in urea : choline chloride deep eutectic solvent.

Deep eutectic solvents (DESs) are utilized as green and inexpensive alternatives to classical ionic liquids. It has been known that some of DESs can be used as solvent in the enzymatic reactions to obtain very green chemical processes. DESs are quite poorly understood at the molecular level.

Investigation of the behavior of HSA upon binding to amlodipine and propranolol: Spectroscopic and molecular modeling approaches.

The interaction between human serum albumin (HSA) and two drugs - amlodipine and propranolol - was investigated using fluorescence, UV absorption and circular dichroism (CD) spectroscopy. In addition, the binding site was established by applying molecular modeling technique. Fluorescence data suggest that amlodipine will quench the intrinsic fluorescence of HSA; whereas propranolol enhances the fluorescence of HSA.