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

The truncated Aß1 - 16 peptide containing the metal-binding domain is frequently used in in silico 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 Aß1 - 16 is very similar to that of the full-length Aß1 - 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 Aß. In this research, the binding of copper ion to the Aß1 - 16 and Aß1 - 42 has been studied by molecular dynamics simulation method. To investigate the effect of copper ion on beta-amyloid peptide structure, the simulations were repeated in the copper and zinc ions, copper and iron binary system, and the copper, zinc and iron ions ternary system. The conformation factor was calculated to calculate the binding affinity of copper ion to beta-amyloid peptide residues. The results showed that the initial 16 residues of the beta-amyloid peptide have high binding affinity for copper ions, and histidine 13 and histidine 14 have significantly higher binding affinity for copper ions in all studied systems. Zinc and iron ions were found to reduce the conformational factor of peptide residues in binding to copper ions, and the aggregation tendency was lower in the truncated structure. The SASA results suggest that the side chains of peptide residues are more affected by shortening and the presence of ions.Communicated by Ramaswamy H. Sarma.

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. Fifteen configurations of TPPCS and LND (TPPCS /LND1-15) were optimized using B3LYP density functional level of theory and PCM model (H2O). AIM analysis revealed that the high drug loading capacity of TPPCS can be attributed to hydrogen bonds, as supported by the average binding energy (168 kJ mol-1). The encouraging theoretical results prompted us to fabricate this drug delivery system and characterize it using advanced analytical techniques. The encapsulation efficiency of LND within the TPPCS was remarkably high, reaching approximately 87 %. Cytotoxicity studies showed that TPPCS/LND nanoparticles are more effective than the LND drug. To sum up, TPPCS/LND nanoparticles improved bioavailability of poorly soluble LND through cancerous cell membrane. In light of this accomplishment, the novel drug delivery route enhances efficiency, allowing for lower therapy doses.

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+ , Cu2+ , Pb2+ , Hg2+ , organic molecules, nucleic acids, and proteins. The interaction of the three planar porphyrins (L1), 5,10,15,20-tetrakis (1-ethyl-1-λ4 -pyridine-4-yl) porphyrin (L2), and 5,10,15,20-tetrakis (1-methyl-1-λ4 -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. In the case of G-quadruplex interactions containing monovalent ions with ligands, the hydrogen bond between the sheets does not follow a specific trend. For example, in the presence of lithium ions, the upper and middle sheets are more affected by ligands, while they are less affected by ligands in the presence of sodium. The binding pocket and the binding energy of the three ligands to the G-quadruplex were also obtained in the various systems. The results show that ligands make the G-quadruplex more stable through the penetration between the sheets and the interaction with the loops. Among the ligands mentioned, the interaction level of the ligand L2 is greater than the others. Our calculations are consistent with the previous experimental observations so that it can help to understand the molecular mechanism of porphyrin interaction and its derivatives with the G-quadruplex.

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. NMR spectra, IR and mass as well as elemental analyses approved the structure of the title compounds. In vitro interactions of the title compounds were also examined on recombinant benzodiazepine receptors (αxß2/3γ2, x = 1-3, 5) expressed in HEK293 cells. The results indicated that the title compounds exhibited suitable affinity for α1ß2 γ2 subtype (Ki = 16-29 nM). To achieve deeper insight into their interactions with benzodiazepine receptors, molecular dynamics simulation was employed. According to the results obtained from the molecular dynamics simulation, Pro85, Leu103, Pro101, Gln102, Ile79, Ser80, Pro17, Leu82 and Val84 interact with the most potent ligand by hydrophobic interactions and Asp86 and Leu87 interact with the ligand by hydrogen bond interactions.Communicated by Ramaswamy H. Sarma.

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

Amyloid-ß peptide with predominant presence in the senile plaques is the most common agent for Alzheimer's disease (AD) incidence. Assembly of the amyloid-ß(1-42) (Aß1-42) 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 Aß1-42 fibrils. The present study provides molecular insight to clarify the inhibitory mechanisms of the EGCG and NQTrp ligands on the Aß1-42 assemblies by using molecular dynamics (MD) simulation. Hence, nine different Aß1-42-containing systems including the monomer, dimer, and hexamer of Aß1-42 considering each of them in a media with no ligands, in the presence of one EGCG ligand, and in the presence of one EGCG ligand were studied with a simulation time of 1 µs for each system. The precise investigation of the peptide-ligand distance, conformational factor (Pi), solvent accessible surface area (SASA), dictionary of secondary structure (DSSP), and Lys28-Ala42 salt bridge analyses confirmed that the hydroxyl-rich structure of the EGCG ligand applied its inhibitory effect on the aggregation of the peptides indirectly by involving water molecules. While the hydroxyl-free structure of the NQTrp ligand exposed its inhibitory effect through a direct interaction with the Aß1-42 peptides. Besides, reduced density gradient (RDG) analysis clarified the hydrogen bonding interactions as the dominant ones for the peptide-EGCG systems, and also, steric and van der Waals interactions for the peptide-NQTrp systems.Communicated by Ramaswamy H. Sarma.

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. Removal of the sugars from CPO leads to increase the hydrophobicity of the enzyme, as well as the reduction of the alkylation reactions. However, due to the lack of the proper force field for the sugars, they are ignored in the theoretical studies. The present study aims to assess the effects of the sugar segments on the structure and activity of CPO through the simulation of the halo structure and the structures without the sugar segment. Despite the difficulty of the process and being time-consuming, the suitable force field is introduced successfully for the sugars. According to molecular dynamics simulation (MD), seven channels and fifteen cavities are identified in the CPO structure. Two of the channels provide the substrate access to the active site. The MD simulation results reveal that the removal of NAG decreases the number of the cavities from fifteen to eleven. Besides, the removal of NAG is associated with removing the channel providing the substrate access. The number of the cavities decreases from fifteen to fourteen through the removal of MAN; however, channel providing the substrate access to the active site is partly preserved. The MD simulation results indicate that the structures without the sugar units are more compact in comparison with the halo structures. The removal of the sugar segments induces the significant changes in the flexibility of the residues that affect the catalytic activity of the enzyme. As a result, the enzyme activities, such as the oxidation, alkylation, halogenation, and epoxidation cannot occur when the sugar segments of the enzyme are removed.

Acetyl-11-keto-ß-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. In this study, the interaction of four different derivatives of boswellic acid with 5-lipoxygenase enzyme was investigated using molecular dynamics simulation. The simulation of the enzyme was also carried out alone. Calculation of Cα-RMSD indicates that the enzyme stability is slightly affected by boswellic acid derivatives. Calculating the radius of gyration of the enzyme also shows that the overall shape of the protein is not affected by ligands. The RMSF values of the enzyme residues were calculated in the presence of boswellic acid derivatives and it was compared with that in the absence of ligands. The results show that the flexibility of the enzyme residues is influenced by ligands. The residues, whose flexibility is reduced, are scattered throughout the enzyme. However, their number is great in the N-terminal residue. The binding affinity between boswellic acid derivatives and the enzyme residues was calculated using the measure of conformation factor. The results show that the residues interacting with ligands are in the area of the first domain of enzyme. The results obtained from molecular dynamics simulation are well-consistent with the experimental evidence related to the inhibitory effect of the mentioned compounds with 5-lipoxygenase.

The investigation of the G-quadruplex aptamer selectivity to Pb2+ 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 Pb2+ in comparison with some ions. The Free Energy Landscape (FEL) analysis indicates that Pb2+ has remained inside the aptamer during the MD simulation, while the other ions have left it. The Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) binding energies prove that the conformational stability of the aptamer is the highest in the presence of Pb2+. According to the compaction parameters, the greatest compressed ion-aptamer complex, and hence, the highest ion-aptamer interaction have been induced in the presence of Pb2+. The contact maps clarify the closer contacts between the nucleotides of the aptamer in the presence of Pb2+. The density functional theory (DFT) results show that Pb2+ forms the most stable complex with the aptamer, which is consistent with the MD results. The QM calculations reveal that the N-H bonds and the O…H distances are the longest and the shortest, respectively, in the presence of Pb2+. The obtained results verify that the strongest hydrogen bonds (HBs), and hence, the most compressed aptamer structure are induced by Pb2+. Besides, atoms in molecules (AIM) and natural bond orbital (NBO) analyses confirm the results.Communicated by Ramaswamy H. Sarma.

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). A mixture of IL (1-butyl-3-methyl imidazolium hexa fluoro phosphate) and disperser solvent (methanol) was quickly injected into the sample solution leading to the formation of the semi cloudy solution. Afterwards, HPLC-DAD was applied to examine the sedimented IL drop. The detection limits (LOD) for all analytes ranges were 0.00268-0.00300 µg L-1. The relative standard deviations (RSDs) for seven experiments were between 3.832% and 4.432% for three target analytes. The proposed method illustrated wide dynamic linear range (DLR, 0.009-1 µg L-1), desirable linearity (R2 ≈ 0.997), high enrichment factors (EF, 313-330) and good relative recoveries (RR, 96-104%). Clear separation and desirable chromatogram was quickly reached without the intervention of the matrix. Besides, a comparison of this method with previous methods indicated that the suggested method is a reproducible, quick and dependable sample pretreatment technique for extraction and determination of pharmaceuticals in blood sample.

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 (Pb2+) 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 Pb2+-specific aptamer from a random coil to a G-quadruplex structure. An injection of Pb2+ on the paper-based platform induces the release of the specific aptamer from the GO surface that recovers the fluorescence emission. Under the optimal experimental conditions, there is a good linear relationship between the fluorescence recovery and the Pb2+concentration in the ranges of 5-70 pM and 0.07-20 nM. Moreover, the aptasensing array exhibits a high sensitivity to Pb2+ with an ultra-low detection limit of 0.5 pM. The developed aptasensor has been successfully applied to determine Pb2+ in tap water, lake water, milk, and human blood serum. The paper-based aptasensor can be efficiently utilized to detect other metal ions and biological molecules by substituting target specific aptamer.

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. Root mean square fluctuation results obtained for alpha-amylase residues indicated that the flexibility of residues 150-160 was affected more by the temperature in the presence and absence of nanoparticles. In addition, loop and helix regions in the secondary structure were affected more by the temperature. Results of enzyme contact maps in the designed systems showed that, in the absence of nanoparticles, a great number of contacts between residues were removed at high temperatures. The radius of gyration showed that the contact between the residues of amylase were removed in the absence of nanoparticles due to the enzyme expansion. Also Molecular dynamics simulation of α-amylase was performed in the presence of fifty 3- to 7-carbon sugar molecules at 25 and 75 °C. The results showed that the structure of α-amylase beta sheets is not affected by sugars. Docking of 3- to 7-carbon sugars with amylase sampled from simulations revealed that the affinity of sugars to the enzyme decreased at high temperatures in the absence of nanoparticles, while the presence of nanoparticles increased the affinity. Docking also showed that van der Waals and hydrophobic interactions contributed more than hydrogen interactions to the sugars-amylase interactions.

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 Aß1-42 is the most effective peptide in the process of forming plaque and creating Alzheimer's. After the separation of Aß1-42 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. In this work, the effects of ethanol, propanol, butanol, pentanol, hexanol, heptanol and octanol on the Asp23-Lys28 and Lys28-Ala42 salt bridges of the Aß1-42 have been investigated by molecular dynamics simulation. The radial distribution function of the oxygen atoms of the water around the atoms Cγ-Asp23, Nξ-Lys28 and O-Ala42 was calculated in the presence of the alcohols. The results show that the peak height of the radial distribution function around the Cγ-Asp23 atom is larger than the other two atoms. Also, the numbering of water molecules in the interval corresponding to the first peak in the radial distribution function for all atoms involved in the two salt bridges Asp23-Lys28 and Lys28-Ala42 was calculated. The results show that the obtained coordinate numbers are within the range of experimental numbers reported for water. The results also show that the order of water molecules around the O-Ala42 is lower. The results of solvent accessible surface area of Aß1-42 show that the Lys28-Ala42 Salt bridge stability is more important for toxicity of monomer.

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 (Hg2+) and lead (Pb2+) 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 Hg2+ and Pb2+ coexist. DNAzyme-based biosensors and aptasensors have been highly regarded for this purpose as two main groups of the functional nucleic acid (FNA)-based biosensors. In this review, we summarize the recent achievements of functional nucleic acid-based biosensors for the simultaneous detection of Hg2+ and Pb2+ ions in two main optical and electrochemical groups. The tremendous interest in utilizing the various nanomaterials is also highlighted in the fabrication of the FNA-based biosensors. Finally, some results are presented based on the advantages and disadvantages of the studied FNA-based biosensors to compare their validation.

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). To construct the truncated Taka-amylase, 50 and 100 C-terminal residues were removed in two separate steps. Results of simulation showed that, although the overall shape partly agglomerates with rise in pressure, high pressure fails to modify the structure of the barrel-like region of the ß-sheet in the wild-type and truncated enzymes. A comparison of contact graphs revealed that the changes at the N-terminus were less extensive than those at the C-terminus. Further analysis showed that 10 regions of the secondary structures changed due to pressure change in wild-type amylase, of which 6 regions were associated with the loops and 4 with helix, while the structure of ß-sheets remained unchanged. The docking of maltotriose, maltotetraose, maltopentaose, maltohexaose, and maltoheptaose with the averaged structures obtained from different simulations was conducted to characterize the influence of pressure on the activities of the wild-type and truncated enzymes. The results showed that maltoheptaose made hydrophobic contacts with residues Tyr238-Asp117-Tyr82-Leu166-Leu232-Tyr155 and hydrogen contacts with residues Asp233-Gly234-Asp206-Arg204-His296-Glu230. Similar results were obtained for other malto-oligosaccharides.

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. Molecular distances between the donor (LYS) and acceptor (CYP and ASA) for all systems were estimated according to Forster's theory. The quantitative analysis obtained by CD spectra suggested that the presence of ASA and CYP decreased the α-helical content of LYS and induced the destabilizing of it. Theoretical studies on the interaction between LYS with ASA and CYP have been carried out using DFT at the B3LYP/6-31G level in the solvent phase. Binding energy of the mentioned complexes was calculated. It showed that tryptophan (Trp) 62 had the most affinity toward ASA and CYP. Analyzing the calculated results revealed that the five member ring of Trp has a key role in interaction of LYS with ASA and CYP.

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. Moreover, we do not know much about the enzyme microstructure in such systems. For example, how some hydrolase can remain active and stable in a deep eutectic solvent including 9 M of urea? In this study, the molecular dynamics of DESs as a liquid was simulated at the molecular level. Urea : choline chloride as a well-known eutectic mixture was chosen as a model DES. The behavior of the lipase as a biocatalyst was studied in this system. For comparison, the enzyme structure was also simulated in 8M urea. The thermal stability of the enzyme was also evaluated in DESs, water, and 8M urea. The enzyme showed very good conformational stability in the urea : choline chloride mixture with about 66% urea (9 M) even at high temperatures. The results are in good agreement with recent experimental observations. In contrast, complete enzyme denaturation occurred in 8M urea with only 12% urea in water. It was found that urea molecules denature the enzyme by interrupting the intra-chain hydrogen bonds in a "direct denaturation mechanism". However, in a urea : choline chloride deep eutectic solvent, as a result of hydrogen bonding with choline and chloride ions, urea molecules have a low diffusion coefficient and cannot reach the protein domains. Interestingly, urea, choline, and chloride ions form hydrogen bonds with the surface residues of the enzyme which, instead of lipase denaturation, leads to greater enzyme stability. To the best of our knowledge, this is the first study in which the microstructural properties of a macromolecule are examined in a deep eutectic solvent.

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. The binding constants for the interaction of amlodipine and propranolol with HSA were found to be 3.63×10(5)M(-1) and 2.29×10(4)M(-1), respectively. The percentage of secondary structure feature of each one of the HSA-bound drugs, i.e. the α-helix content, was estimated empirically by circular dichroism. The results indicated that amlodipine causes an increase, and that propranolol leads to a decrease in α-helix content of HSA. The spectroscopic analysis indicates that the binding mechanisms of the two drugs are different from each other. The data obtained by the molecular modeling study indicated that these drugs bind, with different affinity, to different sites located in subdomain IIA and IIIA.