Targeting Beta-Blocker Drug-Drug Interactions with Fibrinogen Blood Plasma Protein: A Computational and Experimental Study.

In this work, one of the most prevalent polypharmacology drug-drug interaction events that occurs between two widely used beta-blocker drugs-i.e., acebutolol and propranolol-with the most abundant blood plasma fibrinogen protein was evaluated. Towards that end, molecular docking and Density Functional Theory (DFT) calculations were used as complementary tools. A fibrinogen crystallographic validation for the three best ranked binding-sites shows 100% of conformationally favored residues with total absence of restricted flexibility. From those three sites, results on both the binding-site druggability and ligand transport analysis-based free energy trajectories pointed out the most preferred biophysical environment site for drug-drug interactions. Furthermore, the total affinity for the stabilization of the drug-drug complexes was mostly influenced by steric energy contributions, based mainly on multiple hydrophobic contacts with critical residues (THR22: P and SER50: Q) in such best-ranked site. Additionally, the DFT calculations revealed that the beta-blocker drug-drug complexes have a spontaneous thermodynamic stabilization following the same affinity order obtained in the docking simulations, without covalent-bond formation between both interacting beta-blockers in the best-ranked site. Lastly, experimental ultrasound density and velocity measurements were performed and allowed us to validate and corroborate the computational obtained results.

Influence of concentration and position of carboxyl groups on the electronic properties of single-walled carbon nanotubes.

The effects of attaching COOH groups at different sites and in various concentrations on electronic and structural properties of (8,0) single-walled carbon nanotubes (SWNT) were investigated using ab initio calculations. The binding energies and the charge transfers between the COOH functional groups and the tube were calculated for several configurations and a novel feature in the electronic structure of these groups was observed. The electronic character of these systems can be modulated by playing with the concentration and the position of the carboxyl groups bonded on the tube wall. The carboxyl groups bound to different carbon atom sub-lattices are more hybridized than those bound in the same one. These results suggested that SWNT-COOH systems are a playground for engineering electronic properties through a proper chemical functionalization which exploit both the attachment site and concentration of functional groups.

Formulation and characterization of amiodarone-methyl-beta-cyclodextrin inclusion complexes: A molecular modelling perspective.

This study aimed to develop immediate-release tablets containing amiodarone hydrochloride (AM). AM is a BCS class II compound, i.e., high permeable, and poorly soluble. The interactions between amiodarone and methyl-ß-cyclodextrin were DFT-based, theoretically measured, supporting the complexation of AM with cyclodextrin by using methyl-ß-cyclodextrin through a spray-drying process. Thus, increasing substantially the drug solubility to 93.31% and 87.14%, respectively. Solubility studies demonstrated the formation of the Drug-Methyl-ß-cyclodextrin inclusion complex with 1:1 stoichiometry. The complex formation was characterized by SBET, XRD, DSC, SEM, FTIR, and 1H NMR. Complementing, immediate-release tablets containing the inclusion complex were developed by direct compression, and in vitro dissolution studies were performed in gastrointestinal fluids using USP Pharmacopeia standard dissolution rate testing equipment. The dissolution rate of immediate-release tablets was substantially higher than the pristine drug in all mediums evaluated. These results confirm the application of methyl-ß-cyclodextrin as an effective excipient for incorporation in novel dosage forms to increase the solubility of poorly soluble drugs.

Interactions of iron-oxide filled carbon nanotubes with gas molecules.

This work presents a study on iron-oxide filled carbon nanotubes (CNTs) and their interaction with the surrounding atmosphere. Theoretical and experimental methods were employed to determine the interaction mechanism between the CNTs and some gases, such as O2 and N2. The electrical behavior of these CNTs under different atmospheric conditions was studied through resistance measurements, and for comparison, similar studies were conducted on non-filled carbon nanotubes. The iron-oxide filled CNTs were found to be more sensitive to the presence of O2 than the non-filled carbon nanotubes. This behavior was confirmed by the first-principles simulations based on density functional theory with local spin density approximations for CNTs filled with hematite and magnetite iron-oxides. The theoretical study on the interactions of iron-oxide filled CNTs with gas molecules demonstrated a physisorption regime between the nanotube and the surrounding atmosphere, resulting in modifications of the electronic properties of this material.

Computational Modeling on Binding Interactions of Cyclodextrin s with the Human Multidrug Resistance P-glycoprotein Toward Efficient Drug-delivery System Applications.

BACKGROUND: Herein, molecular docking approaches and DFT ab initio simulations were combined for the first time, to study the key interactions of cyclodextrins (CDs: α-CD, ß-CD, and γ-CD) family with potential pharmacological relevance and the multidrug resistance P-gp protein toward efficient drug-delivery applications. The treatment of neurological disorders and cancer therapy where the multiple drug-resistance phenomenon mediated by the P-gp protein constitutes the fundamental cause of unsuccessful therapies. OBJECTIVES: To understand more about the CD docking mechanism and the P-gp. METHODS: In order to achieve the main goal, the computational docking process was used. The observed docking-mechanism of the CDs on the P-gp was fundamentally based on hybrid backbone/side-chain hydrophobic interactions,and also hybrid electrostatic/side-chain interactions of the CD-ligands' OHmotifs with acceptor and donor characteristics, which might theoretically cause local perturbations in the TMD/P-gp inter-residues network, influencing ligand extrusion through the blood-brain barrier. P-gp residues were conformationally favored. Despite the structural differences, all the cyclodextrins exhibit very close Gibbs free binding energy values (or affinity) by the P-gp binding site (transmembrane domains - TMDs). RESULT: The obtained theoretical docking-mechanism of the CDs on the P-gp was fundamentally based on hybrid backbone/side-chain hydrophobic interactions, and also hybrid electrostatic/side-chain interactions of the OH-motifs of the CD-ligands with acceptor and donor properties which theoretically could induce allosteric local-perturbations in the TMDs-inter-residues network of P-gp modulating to the CD-ligand extrusion from the blood-brain-barrier (or cancer cells). CONCLUSION: Finally, these theoretical results open new horizons for evaluating new nanotherapeutic drugs with potential pharmacological relevance for efficient drug-delivery applications and precision nanomedicine.

Metal-doped carbon nanotubes interacting with vitamin C.

In this paper, the structural, electronic and magnetic properties of carbon nanotubes doped with Al, Fe, Mn and Ti atoms interacting with vitamin C molecules are studied through first principles simulations based on the density functional theory. The charge transfers are obtained from the vitamins into the tubes for adsorption and substitutional doping cases. The highest binding energies of vitamin C molecules are calculated for the Al substitutional and Ti adsorbed cases, with values of about 1.20 and 3.26 eV, respectively. The results demonstrated that, depending on doping, the spin polarizations and the conductance characters of the systems can change, which could be relevant to improve the molecule adsorption on carbon nanostructures.

Theoretical study of small aromatic molecules adsorbed in pristine and functionalised graphene.

Small aromatic molecules are precursors for several biological systems such as DNA, proteins, drugs, and are also present in several pollutants. The understanding of the interaction of these small aromatic molecules with pristine and functionalised graphene (fGr) can generate different applications. We performed ab initio simulations based on the density functional theory to evaluate the interaction between the aromatic compounds, benzene, benzoic acid, aniline and phenol, with pristine and fGr. The results show that the binding energy for all cases is less than 103.24 kJ/mol (1.07 eV) without substantial modification of the electronic properties, indicating that the interaction occurs through a physical adsorption regime. The results are promising because they suggest that pristine graphene and functionalised graphene are suitable for removing these pollutants, or for carrying molecules for biological applications influenced by π-π and H-bonds interaction.

Ab initio simulations of black and blue phosphorene functionalised with chemical groups for biomolecule anchoring.

Black and blue phosphorene (2D-dimensional allotropes of phosphorus) have shown fascinating electronic, optical, and magnetic properties, with promising technological applications. In this work, we studied the adsorption of amine, hydroxyl, amide, and carboxyl groups onto both black and blue phosphorenes, in order to analyse the effects of biomolecule anchoring on the structural and electronic properties of phosphenes, using density functional simulations. Analyses were carried out of six different configurations for each chemical group functionalised on black and blue phosphorene. We observed that the radicals interacted via a chemisorption regime with the nanostructures, with binding energies that varied from 1.42 to 3.78 eV. The electronic properties showed that the presence of the chemical groups altered the energy gaps for both black and blue phosphorenes, due to a presence of a half-filled level when a single radical was adsorbed. We were able to observe that functionalised two-dimensional phosphorene showed promising characteristics in terms of anchoring molecules, and particularly those of biological interest, due to its high surface area, strong coupling between phosphorene and chemical groups, and the possibility of chemically manipulating radicals.

Corrigendum to: Computational Modeling of Environmental Co-exposure on Oil-Derived Hydrocarbon Overload by Using Substrate-Specific Transport Protein (TodX) with Graphene Nanostructures.

Due to an oversight of the publisher, Page no 2310 was missing in the published paper and page no 2311 repeated twice in the article entitled "Computational Modeling of Environmental Co-exposure on Oil-Derived Hydrocarbon Overload by Using Substrate-Specific Transport Protein (TodX) with Graphene Nanostructures, 2020, 20(25), 2308-2325 [1]. The page no 2310 is added in the article and the repetition of page no 2311 is corrected. The original article can be found online at https://doi.org/10.2174/1568026620666200820145412.

Computational Modeling of Environmental Co-exposure on Oil-Derived Hydrocarbon Overload by Using Substrate-Specific Transport Protein (TodX) with Graphene Nanostructures.

BACKGROUND: Bioremediation is a biotechnology field that uses living organisms to remove contaminants from soil and water; therefore, they could be used to treat oil spills from the environment. METHODS: Herein, we present a new mechanistic approach combining Molecular Docking Simulation and Density Functional Theory to modeling the bioremediation-based nanointeractions of a heterogeneous mixture of oil-derived hydrocarbons by using pristine and oxidized graphene nanostructures and the substrate-specific transport protein (TodX) from Pseudomonas putida. RESULTS: The theoretical evidences pointing that the binding interactions are mainly based on noncovalent bonds characteristic of physical adsorption mechanism mimicking the "Trojan-horse effect". CONCLUSION: These results open new horizons to improve bioremediation strategies in over-saturation conditions against oil-spills and expanding the use of nanotechnologies in the context of environmental modeling health and safety.

Interactions of graphene derivatives with glutamate-neurotransmitter: A parallel first principles - Docking investigation.

Glutamate plays an important role in excitatory neurotransmission, learning, and memory processes, and under pathological conditions it is directly associated with several chronic neurological disorders, such as depression, epilepsy, schizophrenia, and Parkinson's. Therefore, the detection and quantification of Glutamate is important for the rapid diagnosis of these diseases. Using first principles and molecular docking simulations we have evaluated the energetic, structural, and binding properties of graphene derivatives, such as pristine graphene (pristine-Gr) and oxidized graphene with carboxylic (Gr-COOH), carbonyl (Gr-COH), hydroxyl (Gr-OH), and epoxy (-O-) groups interacting with the glutamate neurotransmitter. The calculated binding affinity free energies from the docking complexes (glutamate-graphene family) suggest higher oxidized graphene-based glutamate molecular recognition than the pristine-Gr, with the following order of oxidized graphene derivatives according to ab initio results: (Gr-O∼Gr-COOH ∼ Gr-COH > Gr-OH)>pristine-Gr. Herein, the ab initio binding energies found for the glutamate-graphene family complexes are in the range of 0.24-0.80 eV. The configurations studied showed a biophysical adsorption regime without significant changes in the physico-chemical properties of the adsorbed glutamate neurotransmitter, in accordance with the general acceptance criteria of the detection systems.

C59Si on the monohydride Si(100):H-(2 x 1) surface.

We propose the use of the Si atom in the experimentally observed C59Si molecule as a possible way to controllably anchor fullerene molecules on a Si surface, due to the formation of a strong bond to one of the Si surface atoms. All our results are based on ab initio total energy density functional theory, and we obtain that the binding energy is on the order of 2.1 eV, approximately 1.4 eV more stable than a C60 bonded in a similar situation. A possible route to obtain such adsorption via a (C59Si)2 dimer is examined, and we find the whole process to be exothermic by approximately 0.2 eV.

Carbon nanostructures interacting with vitamins A, B3 and C: ab initio simulations.

The energetic and structural properties of fullerenes, carbon nanotubes and graphene interacting with vitamins A, B3 and C were studied by first principles simulations. These vitamins, which have antioxidant activities, give support to the cellular metabolism, have biochemical, therapeutic and cosmetic functions, and when combined with carbon nanostructures may have their chemical instability controlled. In this work, the results illustrate that the strongest interaction is between vitamin A and graphene. The binding energies found for the interactions between carbon nanostructures and these vitamins range from 0.10 to 0.93 eV. For all the configurations studied, a physisorption regime is observed without significant changes in the chemical and physical properties of the adsorbed vitamins, which is relevant for a drug delivery system.

Nicotine adsorption on single wall carbon nanotubes.

This work reports a theoretical study of nicotine molecules interacting with single wall carbon nanotubes (SWCNTs) through ab initio calculations within the framework of density functional theory (DFT). Different adsorption sites for nicotine on the surface of pristine and defective (8,0) SWCNTs were analyzed and the total energy curves, as a function of molecular position relative to the SWCNT surface, were evaluated. The nicotine adsorption process is found to be energetically favorable and the molecule-nanotube interaction is intermediated by the tri-coordinated nitrogen atom from the nicotine. It is also predicted the possibility of a chemical bonding between nicotine and SWCNT through the di-coordinated nitrogen.