New ruthenium(II) complexes with cyclic thio- and semicarbazone: evaluation of cytotoxicity and effects on cell migration and apoptosis of lung cancer cells.

We describe the synthesis, physicochemical characterization, and in vitro antitumor assays of four novel analogous ruthenium(II) complexes with general formula cis-[RuII(N-L)(P-P)2]PF6, where P-P = bis(diphenylphosphine)methane (dppm, in complexes 1 and 2) or bis(diphenylphosphine)ethane (dppe, in complexes 3 and 4) and N-L = 5,6-diphenyl-4,5-dihydro-2H-[1,2,4]triazine-3-thione (Btsc, in complexes 1 and 3) or 5,6-diphenyltriazine-3-one (Bsc, in complexes 2 and 4). The data were consistent with cis arrangement of the biphosphine ligands. For the Btsc and Bsc ligands, the data pointed to monoanionic bidentate coordination to ruthenium(II) through N,S and N,O, respectively. Single-crystal X-ray diffraction showed that complex 1 crystallized in the monoclinic system, space group P21/c. Determination of the cytotoxicity profiles of complexes 1-4 gave SI values ranging from 1.19 to 3.50 against the human lung adenocarcinoma cell line A549 and the non-tumor lung cell line MRC-5. Although the molecular docking studies suggested that the interaction between DNA and complex 4 was energetically favorable, the experimental results showed that they interacted weakly. Overall, our results demonstrated that these novel ruthenium(II) complexes have interesting in vitro antitumor potential and this study may contribute to further studies in medicinal inorganic chemistry.

A computational study of the interface interaction between SARS-CoV-2 RBD and ACE2 from human, cat, dog, and ferret.

The total impact of the worldwide COVID-19 pandemic is still emerging, changing all relationships as a result, including those with pet animals. In the infection process, the use of angiotensin-converting enzyme 2 (ACE2) as a cellular receptor to the spike protein of the new coronavirus is a fundamental step. In this sense, understanding which residue plays what role in the interaction between SARS-CoV-2 spike glycoprotein and ACE2 from cats, dogs, and ferrets is an important guide for helping to choose which animal model can be used to study the pathology of COVID-19, and if there are differences between these interactions and those occurring in the human system. To help answer these questions, we performed classical molecular dynamics simulations to evaluate, from an atomistic point of view, the interactions in these systems. Our results show that there are significant differences in the interacting residues between the systems from different animal species, and the role of ACE2 key residues are different in each system, and can assist in the search for different inhibitors for each animal.

Immobilization and unbinding investigation of the antigen-antibody complex using theoretical and experimental techniques.

Experimental results for the antibody known as immunoglobulin G - IgG interacting with phenobarbital were obtained via atomic force microscopy (AFM) and thereafter investigated using computer simulation modeling tools. Using molecular dynamics simulation and docking calculations, the energetically stable configurations of an immobilized antibody over a silicon surface were searched. Six stable configurations of the immobilized antibody over the silicon nitride surface covered by linker molecules were found. Although, only three of them (P1, P2, P5) maintained the Fragment antigen binding available for antigen interaction. Therefore, these configurations were equilibrated after reaching 100 ns molecular dynamics trajectory. The average interaction energy between the surface and the immunoglobulin G - IgG antibody in the P1, P2 and P5 configurations were -62.4 ±â€¯2.4 kcal/mol; -54.3 ±â€¯5.7 kcal/mol, and -360.9 ±â€¯4.2 kcal/mol respectively. Phenobarbital was docked within the Fab domain of P1, P2, and P5 immobilized configurations and equilibrated with molecular dynamics for binding energy estimation. Then, steered molecular dynamics was performed to evaluate unbinding energy pathway between phenobarbital and IgG in each of the three-oriented IgG configurations. No significant differences were observed in the rupture force values (EP1 = 591 ±â€¯13 pN, EP2 = 605 ±â€¯18 pN, and EP5 = 610 ±â€¯45 pN). In comparison, the average AFM experimental results were (641.6 ±â€¯363.3 pN). Therefore, it is worth noting that P5 is the configuration with highest protein-surface interaction. Therefore, the force value calculated for the P5 orientation is statistically more favorable and it is the one to be compared to the experimental data. The agreement between experimental and theoretical results indicates a favorable presented for this study opening new perspectives for antigen-antibody evaluation.

Unbinding pathway energy of glyphosate from the EPSPs enzyme binding site characterized by Steered Molecular Dynamics and Potential of Mean Force.

The quantification of herbicides in the environment, like glyphosate, is extremely important to prevent contamination. Nanobiosensors stands out in the quantization process, because of the high selectivity, sensitivity and short response time of the method. In order to emulate the detection of glyphosate using a specific nanobiossensor through an Atomic Force Microscope (AFM), this work carried out Steered Molecular Dynamics simulations (SMD) in which the herbicide was unbinded from the active site of the enzyme 5- enolpyruvylshikimate 3 phosphate synthase (EPSPS) along three different directions.After the simulations, Potential of Mean Force calculations were carried, from a cumulant expansion of Jarzynski's equation to obtain the profile of free energy of interaction between the herbicide and the active site of the enzyme in the presence of shikimate-3 substrate phosphate (S3P). The set of values for external work, had a Gaussian distribution. The PMF values ranged according to the directions of the unbindong pahway of each simulation, displaying energy values of 10.7, 14.7 and 19.5KJmol-1. The results provide a theoretical support in order to assist the construction of a specific nanobiossensor to quantify the glyphosate herbicide.

Centrosymmetric resonance-assisted intermolecular hydrogen bonding chains in the enol form of ß-diketone: Crystal structure and theoretical study.

Isobenzofuran-1(3H)-ones (phtalides) are heterocycles that present a benzene ring fused to a γ-lactone functionality. This structural motif is found in several natural and synthetic compounds that present relevant biological activities. In the present investigation, the 3-(2-hydroxy-4,4-dimethyl-6-oxocyclohexen-1-yl)isobenzofuran-1(3H)-one was characterized by single-crystal X-ray analysis. In the crystal structure, there are two molecules per asymmetric unit. One of them exhibits resonance assisted hydrogen bonds (RAHBs). Semi-empirical and DFT calculations were performed to obtain electronic structure and π-delocalization parameters, in order to better understand the energy stabilization of RAHBs in the crystal packing of the studied molecule. The structural parameters showed good agreement between theoretical and experimental data. The theoretical investigation revealed that the RAHBs stabilization energy is directly related to the electronic delocalization of the enol form fragment. In addition, RAHBs significantly affected the HOMO and charge distribution around the conjugated system.

Modeling the coverage of an AFM tip by enzymes and its application in nanobiosensors.

A stochastic simulation of adsorption processes was developed to simulate the coverage of an atomic force microscope (AFM) tip with enzymes represented as rigid polyhedrons. From geometric considerations of the enzyme structure and AFM tip, we could estimate the average number of active sites available to interact with substrate molecules in the bulk. The procedure was exploited to determine the interaction force between acetyl-CoA carboxylase enzyme (ACC enzyme) and its substrate diclofop, for which steered molecular dynamics (SMD) was used. The theoretical force of (1.6±0.5) nN per enzyme led to a total force in remarkable agreement with the experimentally measured force with AFM, thus demonstrating the usefulness of the procedure proposed here to assist in the interpretation of nanobiosensors experiments.

Molecular modeling of enzyme attachment on AFM probes.

The immobilization of enzymes on atomic force microscope tip (AFM tip) surface is a crucial step in the development of nanobiosensors to be used in detection process. In this work, an atomistic modeling of the attachment of the acetyl coenzyme A carboxylase (ACC enzyme) on a functionalized AFM tip surface is proposed. Using electrostatic considerations, suitable enzyme-surface orientations with the active sites of the ACC enzyme available for interactions with bulk molecules were found. A 50 ns molecular dynamics trajectory in aqueous solution was obtained and surface contact area, hydrogen bonding and protein stability were analyzed. The enzyme-surface model proposed here with minor adjustment can be applied to study antigen-antibody interactions as well as enzyme immobilization on silica for chromatography applications.

Designing an enzyme-based nanobiosensor using molecular modeling techniques.

Nanobiosensors can be built via functionalization of atomic force microscopy (AFM) tips with biomolecules capable of interacting with the analyte on a substrate, and the detection being performed by measuring the force between the immobilized biomolecule and the analyte. The optimization of such sensors may require multiple experiments to determine suitable experimental conditions for the immobilization and detection. In this study we employ molecular modeling techniques to assist in the design of nanobiosensors to detect herbicides. As a proof of principle, the properties of acetyl co-enzyme A carboxylase (ACC) were obtained with molecular dynamics simulations, from which the dimeric form in an aqueous solution was found to be more suitable for immobilization owing to a smaller structural fluctuation than the monomeric form. Upon solving the nonlinear Poisson-Boltzmann equation using a finite-difference procedure, we found that the active sites of ACC exhibited a positive surface potential while the remainder of the ACC surface was negatively charged. Therefore, optimized biosensors should be prepared with electrostatic adsorption of ACC onto an AFM tip functionalized with positively charged groups, leaving the active sites exposed to the analyte. The preferential orientation for the herbicides diclofop and atrazine with the ACC active site was determined by molecular docking calculations which displayed an inhibition coefficient of 0.168 µM for diclofop, and 44.11 µM for atrazine. This binding selectivity for the herbicide family of diclofop was confirmed by semiempirical PM6 quantum chemical calculations which revealed that ACC interacts more strongly with the herbicide diclofop than with atrazine, showing binding energies of -119.04 and +8.40 kcal mol(-1), respectively. The initial measurements of the proposed nanobiosensor validated the theoretical calculations and displayed high selectivity for the family of the diclofop herbicides.

Chitosan molecular structure as a function of N-acetylation.

Molecular dynamics simulations have been carried out to characterize the structure and solubility of chitosan nanoparticle-like structures as a function of the deacetylation level (0, 40, 60, and 100%) and the spatial distribution of the N-acetyl groups in the particles. The polysaccharide chains of highly N-deacetylated particles where the N-acetyl groups are uniformly distributed present a high flexibility and preference for the relaxed two-fold helix and five-fold helix motifs. When these groups are confined to a given region of the particle, the chains adopt preferentially a two-fold helix with ϕ and ψ values close to crystalline chitin. Nanoparticles with up to 40% acetylation are moderately soluble, forming stable aggregates when the N-acetyl groups are unevenly distributed. Systems with 60% or higher N-acetylation levels are insoluble and present similar degrees of swelling regardless the distribution of their N-acetyl groups. Overall particle solvation is highly affected by electrostatic forces resulting from the degree of acetylation. The water mobility and orientation around the polysaccharide chains affects the stability of the intramolecular O3-HO3((n)) ···O5((n +) (1)) hydrogen bond, which in turn controls particle aggregation.

Characterization of Chitin and Chitosan Molecular Structure in Aqueous Solution.

Molecular dynamics simulations have been used to characterize the structure of single chitin and chitosan chains in aqueous solutions. Chitin chains, whether isolated or in the form of a ß-chitin nanoparticle, adopt the 2-fold helix with ϕ and φ values similar to its crystalline state. In solution, the intramolecular hydrogen bond HO3(n)···O5(n+1) responsible for the 2-fold helical motif in these polysaccharides is stabilized by hydrogen bonds with water molecules in a well-defined orientation. On the other hand, chitosan can adopt five distinct helical motifs, and its conformational equilibrium is highly dependent on pH. The hydrogen bond pattern and solvation around the O3 atom of insoluble chitosan (basic pH) are nearly identical to these quantities in chitin. Our findings suggest that the solubility and conformation of these polysaccharides are related to the stability of the intrachain HO3(n)···O5(n+1) hydrogen bond, which is affected by the water exchange around the O3-HO3 hydroxyl group.