A combined molecular dynamics and quantum mechanics study on the interaction of Fe3+ and human serum albumin relevant to iron overload disease

Metal-Metalloid Modified C36 Fullerene: A Dual Role in Drug Delivery and Sensing for Anticancer Chlormethine Explored through DFT and MD Simulations

Spurred by the latest developments and growing utilization of zero-dimensional (0D) drug delivery and drug sensors, this investigation examines the possibilities of the 0D C36 fullerene for drug delivery and the detection of the anticancer drug chlormethine (CHL), the overabundance of which poses a significant threat to living organisms. This study employs density functional theory and ab initio molecular dynamics (AIMD) simulations (AIMD) to evaluate and gain insights into the interaction mechanisms between pristine C36 fullerene, metal-metalloid (MM)-modified C36 fullerene (with Al, Fe, and B), and the anticancer drug CHL. It is observed that in the gas phase, the CHL drug molecule adsorbs onto the fullerenes in the following order: B-C36 > Fe-C36 > Al-C36 > C36. However, when considering the solvent effect, the adsorption energy of the CHL drug molecule on B-C36 increases, indicating chemisorption behavior. This implies that B-C36 could be a promising candidate for drug delivery applications, particularly for the CHL anticancer drug. In contrast, the adsorption energy of the CHL drug molecule on Fe-C36 decreases with the presence of the solvent, resulting in intermediate physisorption. Due to its minimal recovery time, excellent sensing response, intermediate physisorption, and shorter interatomic distance compared to C36 and Al-C36 fullerenes, Fe-C36 is well-suited as a drug sensor for CHL. AIMD simulations demonstrate that the B-C36/CHL and Fe-C36/CHL complexes are well-equilibrated and highly stable in the aqueous phase at 300 and 310 K respectively, with no evidence of bond breakage or formation. The structural stability observed, even with temperature fluctuations, indicates that the electrostatic interactions are robust enough to maintain cohesion of the fragments.

Size-Dependent Fullerenes for Enhanced Interaction of l-Leucine: A Combined DFT and MD Simulations Approach

Fullerene-based biosensors have received great attention due to their unique electronic properties that allow them to transduce electrical signals by accepting electrons from amino acids. Babies with MSUD (maple syrup urine disease) are unable to break down amino acids such as l-leucine, and excess levels of the l-leucine are harmful. Therefore, sensing of l-leucine is foremost required. We aim to investigate the interaction tendencies of size-variable fullerenes (CX; X = 24, 36, 50, and 70) toward l-leucine (LEU) using density functional theory (DFT-D3) and classical molecular dynamics (MD) simulation. The C24 fullerene shows the highest affinity of the LEU biomolecule in the gas phase. Smaller fullerenes (C24 and C36) show stronger interactions with leucine due to their higher curvature in water environments. Moreover, recovery times in the ranges of 1010 and 104 s make it a viable candidate for the isolation application of LEU from the biological system. Further, the interaction between LEU and fullerenes is in line with the natural bond order (NBO) analysis, Mulliken charge analysis, quantum theory atom in molecule (QTAIM) analysis, and reduced density gradient (RDG) analysis. At 310 K, employing the explicit water model in classical MD simulations, fullerenes C24 and C36 demonstrate notably elevated binding free energies (-24.946 kJ/mol) in relation to LEU, showcasing their potential as sensors for l-leucine. Here, we demonstrate that the smaller fullerene exhibits a higher potential for l-leucine sensors than the larger fullerene.

A theoretical and electrochemical impedance spectroscopy study of the adsorption and sensing of selected metal ions by 4-morpholino-7-nitrobenzofuran

The selectivity of a novel chemosensor, based on a modified nitrobenzofurazan referred to as NBD-Morph, has been investigated for the detection of heavy metal cations (Co2+, Pb2+, Mg2+, Ag+, Cu2+, Hg2+, Ni2+, and Zn2+). The ligand, 4-morpholino-7-nitrobenzofurazan (NBD-Morph), was characterized using spectroscopic techniques including FT-IR and 1H NMR. Vibrational frequencies obtained from FT-IR and proton NMR (1H) chemical shifts were accurately predicted employing the density functional theory (DFT) at the B3LYP level of theory. Furthermore, an examination of the structural, electronic, and quantum chemical properties was conducted and discussed. DFT calculations were employed to explore the complex formation ability of the NBD-Morph ligand with Co2+, Pb2+, Mg2+, Ag+, Cu2+, Hg2+, Ni2+, and Zn2+ metal cations. The comparison of adsorption energies for all possible conformations reveals that NBD-Morph exhibits sensitivity and selectivity towards metal ions, including Pb2+, Cu2+, Ag+, and Ni2+. However, an assessment of their reactivity using QTAIM topological parameters demonstrated the ligand's greater complexation ability toward Cu2+ or Ni2+ than those formed by Pb2+ or Ag+. Additionally, molecular electrostatic potential (MEP), Hirshfeld surfaces, and their associated 2D-fingerprint plots were applied to a detailed study of the inter-molecular interactions in NBD-Morph-X (X = Pb2+, Cu2+, Ag+, Ni2+) complexes. The electron localization function (ELF) and the localized-orbital locator (LOL) were generated to investigate the charge transfer and donor-acceptor interactions within the complexes. Electrochemical analysis further corroborates the theoretical findings, supporting the prediction of NBD-Morph's sensory ability towards Ni2+ metal cations. In conclusion, NBD-Morph stands out as a promising sensor for Ni2+.

Effects of serum proteins on corrosion rates and product bioabsorbability of biodegradable metals

Corrodible metals are the newest kind of biodegradable materials and raise a new problem of the corrosion products. However, the removal of the precipitated products has been unclear and even largely ignored in publications. Herein, we find that albumin, an abundant macromolecule in serum, enhances the solubility of corrosion products of iron in blood mimetic Hank's solution significantly. This is universal for other main biodegradable metals such as magnesium, zinc and polyester-coated iron. Albumin also influences corrosion rates in diverse trends in Hank's solution and normal saline. Based on quantitative study theoretically and experimentally, both the effects on corrosion rates and soluble fractions are interpreted by a unified mechanism, and the key factor leading to different corrosion behaviors in corrosion media is the interference of albumin to the Ca/P passivation layer on the metal surface. This work has illustrated that the interactions between metals and media macromolecules should be taken into consideration in the design of the next-generation metal-based biodegradable medical devices in the formulism of precision medicine. The improved Hank's solution in the presence of albumin and with a higher content of initial calcium salt is suggested to access biodegradable metals potentially for cardiovascular medical devices, where the content of calcium salt is calculated after consideration of chelating of calcium ions by albumin, resulting in the physiological concentration of free calcium ions.

On the potentials of sialic acid derivatives as inhibitors for the mumps virus: A molecular dynamics and quantum chemistry investigation

Mumps virus is an infectious pathogen causing major health problems for humans such as encephalitis, orchitis, and parotitis. Therefore, designing an inhibitor for this virus is of great medical and public health importance. With this goal in mind, we investigate the affinity of different sialic acid-based compounds (ligands) against the hemagglutinin-neuraminidase (HN) protein of the mumps virus, using a combination of molecular dynamics (MD) simulations and quantum chemistry calculations. Our MD simulation results indicate that the ligands form stable complexes with the HN protein through a combination of electrostatic, van der Waals (vdW), and hydrogen bond (H-bond) interactions, which the electrostatic interactions play a more important role in the complexation process. Based on the obtained results from the structural analysis Arg381, Arg291, and Arg49 play a key role in the binding site interactions with the different ligands, in comparison with other residues. There are some candidates such as Neu5Acα2-6Galβ1-4GlcNAcβ, Neu5Acα2-3Galβ1-3GlcNacβ1-3Galβ1-4Glc, and Neu5Acα2-6Galβ1-4GlcNAcβ1-3Galβ1-4Glc that form more stable complexes with the HN than the α2-3-Sialyllactose confirmed by the calculated Gibbs binding energies (-39.65, -46.93, and -36.49 kcal.mol^-1, respectively). To investigate the relationship between the molecular properties of the selected compounds and their affinity to the HN receptor, density functional theory dispersion corrected (DFT-D3) calculations were employed. According to our DFT-D3 results, neutral sialic acid-based compounds have lower reactivity to the mumps virus than the negativity charge structures. Moreover, by increasing the electronic chemical potential (μ) the vdW and H-bond interactions between drugs and the HN protein increase. In other words, by elevating the electron tendency of the selected ligands their affinity to the mumps virus increases. Our quantum chemistry calculations reveal that in addition to the structural features the molecular properties of the drugs can play important roles in their affinity and reactivity against the virus. The results of this study can provide useful details to design new compounds or improve their properties against the mumps virus.

High Dietary Organic Iron Supplementation Decreases Growth Performance and Induces Oxidative Stress in Broilers

Although Iron (Fe) is an essential nutrient that plays a vital role in respiratory processes, excessive Fe in the diet can affect the health of broilers. We investigated the effects of diet supplemented with high levels of iron chelates with lysine and glutamic acid (Fe−LG) on the growth performance, serum biochemical parameters, antioxidant status, and duodenal mRNA expression of Fe transporters in broilers. A total of 800 1-day-old male Arbor Acres broilers were assigned to 5 groups, with 8 replicates each. Broilers were fed a corn−soybean meal basal diet or basal diets supplemented with 40, 80, 400, or 800 mg Fe/kg as Fe−LG for 6 weeks. The body weight (BW) was increased in the 80 mg Fe/kg treatment group, but decreased in the 800 mg Fe/kg treatment group on day 21. During days 1−21, compared with the control group, the supplementation of the 80 mg Fe/kg increased the average daily gain (ADG) and average daily feed intake (ADFI); however, the supplementation of the 800 mg Fe/kg group decreased the ADG and increased the FCR in broilers (p < 0.05). The heart, liver, spleen, and kidney indices were reduced in the 800 mg Fe/kg treatment group (p < 0.05). The supplementation of the 800 mg Fe/kg group increased the serum aspartate aminotransferase activity and the levels of creatinine and urea nitrogen on day 42 (p < 0.05). The broilers had considerably low liver total superoxide dismutase activity and total antioxidant capacity in the 800 mg Fe/kg treatment group (p < 0.05). Serum and liver Fe concentrations were elevated in the 400 and 800 mg Fe/kg treatment groups, but were not affected in the 40 and 80 mg Fe/kg treatment groups. The duodenal Fe transporters divalent metal transporter 1 (DMT1) and ferroportin 1 (FPN1) were downregulated in the Fe−LG treatment groups (p < 0.05). We conclude that a high dietary supplement of 800 mg Fe/kg in broilers leads to detrimental health effects, causing kidney function injury and liver oxidative stress.

Hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) Simulation: A Tool for Structure-based Drug Design and Discovery

Quantum mechanics (QM) is physics based theory which explains the physical properties of nature at the level of atoms and sub-atoms. Molecular mechanics (MM) construct molecular systems through the use of classical mechanics. So, hybrid quantum mechanics and molecular mechanics (QM/MM) when combined together can act as computer-based methods which can be used to calculate structure and property data of molecular structures. Hybrid QM/MM combines the strengths of QM with accuracy and MM with speed. QM/MM simulation can also be applied for the study of chemical process in solutions as well as in the proteins, and has a great scope in structure-based drug design (CADD) and discovery. Hybrid QM/MM also applied to HTS, to derive QSAR models and due to availability of many protein crystal structures; it has a great role in computational chemistry, especially in structure- and fragment-based drug design. Fused QM/MM simulations have been developed as a widespread method to explore chemical reactions in condensed phases. In QM/MM simulations, the quantum chemistry theory is used to treat the space in which the chemical reactions occur; however the rest is defined through molecular mechanics force field (MMFF). In this review, we have extensively reviewed recent literature pertaining to the use and applications of hybrid QM/MM simulations for ligand and structure-based computational methods for the design and discovery of therapeutic agents.