Implementation of Three Gallium-Based Complexes in the "Trojan Horse" Antibacterial Strategy against A. baumannii: A DFT Approach.

Microorganisms of the ESKAPE group pose an enormous threat to human well-being, thus requiring a multidisciplinary approach for discovering novel drugs that are not only effective but utilize an innovative mechanism of action in order to decrease fast developing resistance. A promising but still hardly explored implementation in the "Trojan horse" antibacterial strategy has been recognized in gallium, an iron mimicry species with no known function but exerting a bacteriostatic/bactericidal effect against some representatives of the group. The study herewith focuses on the bacterium A. baumannii and its siderophore acinetobactin in its two isomeric forms depending on the acidity of the medium. By applying the powerful tools of the DFT approach, we aim to delineate those physicochemical characteristics that are of great importance for potentiating gallium's ability to compete with the native ferric cation for binding acinetobactin such as pH, solvent exposure (dielectric constant of the environment), different metal/siderophore ratios, and complex composition. Hence, the provided results not only furnish some explanation of the positive effect of three Ga3+-based anti-infectives in terms of metal cation competition but also shed light on reported in vitro and in vivo observations at a molecular level in regard to gallium's antibacterial effect against A. baumannii.

Carbonic Anhydrases: Different Active Sites, Same Metal Selectivity Rules.

Carbonic anhydrases are mononuclear metalloenzymes catalyzing the reversible hydration of carbon dioxide in organisms belonging to all three domains of life. Although the mechanism of the catalytic reaction is similar, different families of carbonic anhydrases do not have a common ancestor nor do they exhibit significant resemblance in the amino acid sequence or the structure and composition of the metal-binding sites. Little is known about the physical principles determining the metal affinity and selectivity of the catalytic centers, and how well the native metal is protected from being dislodged by other metal species from the local environment. Here, we endeavor to shed light on these issues by studying (via a combination of density functional theory calculations and polarizable continuum model computations) the thermodynamic outcome of the competition between the native metal cation and its noncognate competitor in various metal-binding sites. Typical representatives of the competing cations from the cellular environments of the respective classes of carbonic anhydrases are considered. The calculations reveal how the Gibbs energy of the metal competition changes when varying the metal type, structure, composition, and solvent exposure of the active center. Physical principles governing metal competition in different carbonic anhydrase metal-binding sites are delineated.

Naphthalimide-Based Amphiphiles: Synthesis and DFT Studies of the Aggregation and Interaction of a Simplified Model System with Water Molecules.

Systems containing amphiphilic/pathic molecules have the tremendous capacity to self-assemble under appropriate conditions to form morphologies with well-defined structural order (systematic arrangement), nanometer-scale dimensions, and unique properties. In this work, the synthesis of novel naphthalimide-based amphiphilic probes that have 1,8-naphthalimide as the fluorescence signal reporting group, octyl as hydrophobic head, and PEG as hydrophilic tail, is described. These designed molecules represent a new class of self-assembling structures with some promising features. The lack of literature data on the use of 1,8-naphthalimides with cyclic and acyclic hydrophilic PEG fragments as self-assembling structures gives us the opportunity to initiate a new field in materials science. The successful synthesis of such structures is fundamental to synthetic chemistry, and computational studies of the aggregation and binding of water molecules shed light on the ability of these new systems to function as membrane water channels. This study not only expands the list of 1,8-naphthalimide derivatives but may also serve as a new platform for the development of membrane additives based on PEG-functionalized naphthalimides.

Electrostatic interactions - key determinants of the metal selectivity in La3+ and Ca2+ binding proteins.

Nearly half of all known proteins contain metal co-factors. In the course of evolution two dozen metal cations (mostly monovalent and divalent species) have been selected to participate in processes of vital importance for living organisms. Trivalent metal cations have also been selected, although to a lesser extent as compared with their mono- and divalent counterparts. Notably, factors governing the metal selectivity in trivalent metal centers in proteins are less well understood than those in the respective divalent metal centers. Thus, the source of high La3+/Ca2+ selectivity in lanthanum-binding proteins, as compared with that of calcium-binding proteins (i.e., calmodulin), is still shrouded in mystery. The well-calibrated thermochemical calculations, performed here, reveal the dominating role of electrostatic interactions in shaping the metal selectivity in La3+-binding centers. The calculations also disclose other (second-order) determinants of metal selectivity in these systems, such as the rigidity and extent of solvent exposure of the binding site. All these factors are also implicated in shaping the metal selectivity in Ca2+-binding proteins.

Lanthanides as Calcium Mimetic Species in Calcium-Signaling/Buffering Proteins: The Effect of Lanthanide Type on the Ca2+/Ln3+ Competition.

Lanthanides, the 14 4f-block elements plus Lanthanum, have been extensively used to study the structure and biochemical properties of metalloproteins. The characteristics of lanthanides within the lanthanide series are similar, but not identical. The present research offers a systematic investigation of the ability of the entire Ln3+ series to substitute for Ca2+ in biological systems. A well-calibrated DFT/PCM protocol is employed in studying the factors that control the metal selectivity in biological systems by modeling typical calcium signaling/buffering binding sites and elucidating the thermodynamic outcome of the competition between the "alien" La3+/Ln3+ and "native" Ca2+, and La3+ - Ln3+ within the lanthanide series. The calculations performed reveal that the major determinant of the Ca2+/Ln3+ selectivity in calcium proteins is the net charge of the calcium binding pocket; the more negative the charge, the higher the competitiveness of the trivalent Ln3+ with respect to its Ca2+ contender. Solvent exposure of the binding site also influences the process; buried active centers with net charge of -4 or -3 are characterized by higher Ln3+ over Ca2+ selectivity, whereas it is the opposite for sites with overall charge of -1. Within the series, the competition between La3+ and its fellow lanthanides is determined by the balance between two competing effects: electronic (favoring heavier lanthanides) and solvation (generally favoring the lighter lanthanides).

Theoretical Assessment of the Ligand/Metal/Quadruplex Recognition in the Non-Canonical Nucleic Acids Structures.

Quadruplexes (GQs), peculiar DNA/RNA motifs concentrated in specific genomic regions, play a vital role in biological processes including telomere stability and, hence, represent promising targets for anticancer therapy. GQs are formed by folding guanine-rich sequences into square planar G-tetrads which stack onto one another. Metal cations, most often potassium, further stabilize the architecture by coordinating the lone electron pairs of the O atoms. The presence of additional nucleic acid bases, however, has been recently observed experimentally and contributes substantially to the structural heterogeneity of quadruplexes. Therefore, it is of paramount significance to understand the factors governing the underlying complex processes in these structures. The current study employs DFT calculations to model the interactions between metal cations (K+, Na+, Sr2+) and diverse tetrads composed of a guanine layer in combination with a guanine (G)-, adenine (A)-, cytosine (C)-, thymine (T)-, or uracil (U)-based tetrad layer. Moreover, the addition of 4-(3,4-dihydroisoquinolin-2-yl)-2-(quinolin-2-yl)quinazoline to the modeled quadruplexes as a possible mechanism of its well-exerted antitumor effect is assessed. The calculations imply that the metal cation competition and ligand complexation are influenced by the balance between electronic and implicit/explicit solvation effects, the composition of the tetrad layers, as well as by the solvent exposure to the surrounding environment expressed in terms of different dielectric constant values. The provided results significantly enhance our understanding of quadruplex diversity, ligand recognition, and the underlying mechanisms of stabilization at an atomic level.

Metal-Assisted Complexation of Fluorogenic Dyes by Cucurbit[7]uril and Cucurbit[8]uril: A DFT Evaluation of the Key Factors Governing the Host-Guest Recognition.

With the emergence of host-guest systems, a novel branch of complexation chemistry has found wide application in industries such as food, pharmacy, medicine, environmental protection and cosmetics. Along with the extensively studied cyclodextrins and calixarenes, the innovative cucurbiturils (CB) have enjoyed increased popularity among the scientific community as they possess even better qualities as cavitands as compared to the former molecules. Moreover, their complexation abilities could further be enhanced with the assistance of metal cations, which can interestingly exert a dual effect on the complexation process: either by competitively binding to the host entity or cooperatively associating with the CB@guest structures. In our previous work, two metal species (Mg2+ and Ga3+) have been found to bind to CB molecules in the strongest fashion upon the formation of host-guest complexes. The current study focuses on their role in the complex formation with three dye molecules: thiazole orange, neutral red, and thioflavin T. Various key factors influencing the process have been recognized, such as pH and the dielectric constant of the medium, the cavity size of the host, Mn+ charge, and the presence/absence of hydration shell around the metal cation. A well-calibrated DFT methodology, solidly based and validated and presented in the literature experimental data, is applied. The obtained results shed new light on several aspects of the cucurbituril complexation chemistry.

N-Methyl- and N-Phenylpiperazine Functionalized Styryl Dyes Inside Cucurbiturils: Theoretical Assessment of the Factors Governing the Host-Guest Recognition.

The family of cucurbiturils (CBs), the unique pumpkin-shaped macrocycles, has received great attention over the past four decades owing to their remarkable recognition properties. They have found diverse applications including biosensing and drug delivery technologies. The cucurbituril complexation of guest molecules can modulate their pKas, improve their solubility in aqueous solution, and reduce the adverse effects of the drugs, as well as enhance the stability and/or enable targeted delivery of the drug molecule. Employing twelve cationic styryl dyes with N-methyl- and N-phenylpiperazine functionality as probes, we attempted to understand the factors that govern the host-guest complexation of such molecules within CB[7] and CB[8] host systems. Various key factors determining the process were recognized, such as the pH and dielectric constant of the medium, the cavity size of the host, the chemical characteristics of the substituents in the guest entity, and the presence/absence of metal cations. The presented results add to our understanding (at the molecular level) of the mechanism of encapsulation of styryl dyes by cucurbiturils, thus shedding new light on various aspects of the intriguing complexation chemistry and the underlying recognition processes.

Theoretical Insight into the Phosphate-Targeted Silver's Antibacterial Action: Differentiation between Gram (+) and Gram (-) Bacteria.

Although silver is one of the first metals finding broad applications in everyday life, specific key points of the intimate mechanism of its bacteriostatic/bactericidal activity lack explanation. It is widely accepted that the antimicrobial potential of the silver cation depends on the composition and thickness of the bacterial external envelope: the outer membrane in Gram-negative bacteria is more prone to Ag+ attack than the cell wall in Gram-positive bacteria. The major cellular components able to interact strongly with Ag+ (teichoic acids, phospholipids, and lipopolysaccharides) contain mono/diesterified phosphate moieties. By applying a reliable DFT/SMD methodology, we modeled the reactions between the aforementioned constituents in typical Gram-positive and Gram-negative bacteria and hydrated Ag+ species, thus disclosing the factors that govern the process of metal-model ligand complexation. The conducted research indicates thermodynamically possible reactions in all cases but still a greater preference of the Ag+ toward the constituents in Gram-negative bacteria in comparison with their counterparts in Gram-positive bacteria. The observed tendencies shed light on the specific interactions of the silver cation with the modeled phosphate-containing units at the atomic level.

Complexation of trivalent metal cations (Al3+, Ga3+, In3+, La3+, Lu3+) to cucurbiturils: a DFT/SMD evaluation of the key factors governing the host-guest recognition.

Cucurbiturils (CBs), the pumpkin-shaped macrocycles, are suitable hosts for an array of neutral and cationic species. A plethora of host-guest complexes between CBs and a variety of guest molecules has been studied. However, much remains unknown, even in the complexation of very simple guests such as metal cations. In the computational study herein, DFT molecular modeling has been employed to investigate the interactions of a series of trivalent metal cations (Al3+, Ga3+, In3+, La3+, Lu3+) to cucurbit[n]urils and to evaluate the main factors controlling the host-guest complexation. The thermodynamic descriptors (Gibbs energies in the gas phase and in a water environment) of the corresponding complexation reactions have been estimated. This research is a logical continuation of an earlier study on the interaction between CB[n]s and a series of biologically essential mono- and divalent metal cations (Na+/K+ and Mg2+/Ca2+, respectively).

Self-Associated 1,8-Naphthalimide as a Selective Fluorescent Chemosensor for Detection of High pH in Aqueous Solutions and Their Hg2+ Contamination.

A novel diamino triazine based 1,8-naphthalimide (NI-DAT) has been designed and synthesized. Its photophysical properties have been investigated in different solvents and its sensory capability evaluated. The fluorescence emission of NI-DAT is significantly impacted by the solvent polarity due to its inherent intramolecular charge transfer character. Moreover, the fluorescence emission quenched at higher pH as a result of photo-induced electron transfer (PET) from triazine moiety to 1,8-naphthalimide after cleaving hydrogen bonds in the self-associated dimers. Furthermore, the new chemosensor exhibited a good selectivity and sensitivity towards Hg2+ among all the used various cations and anions in the aqueous solution of ethanol (5:1, v/v, pH = 7.2, Tampon buffer). NI-DAT emission at 540 nm was quenched remarkably only by Hg2+, even in the presence of other cations or anions as interfering analytes. Job's plot revealed a 2:1 stoichiometric ratio for NI-DAT/Hg2+ complex, respectively.

Gallium (III) Complexes with 5-Bromosalicylaldehyde Benzoylhydrazones: In Silico Studies and In Vitro Cytotoxic Activity.

Gallium (III) complexes with the ligands 5-bromosalicylaldehyde-4-hydroxybenzoylhydrazone and 5-bromosalicylaldehyde isonicotinoylhydrazone were synthesized to receive compounds with improved antiproliferative action. Compounds were characterized by elemental analysis, IR, and NMR spectroscopy. Density functional theory calculations with Becke's 3-parameter hybrid functional and 6-31+G(d,p) basis set were carried out to investigate the structural features of the ligands and Ga(III) complexes. Cytotoxic screening by MTT-dye reduction assay was carried out using cisplatin and melphalan as reference cytotoxic agents. A general formula [Ga(HL)2]NO3 for the complexes obtained was suggested. The complexes are mononuclear with the Ga(III) ions being surrounded by two ligands. The ligands acted as monoanionic tridentate (ONO) donor molecules. The analysis revealed coordination binding through deprotonated phenolic-oxygen, azomethine-nitrogen, and amide-oxygen atoms. The bioassay demonstrated that all compounds exhibited concentration-dependent antiproliferative activity at low micromolar concentrations against the acute myeloid leukemia HL-60 and T-cell leukemia SKW-3 cell lines. IC50 values of 5-bromo-derivative ligands and gallium (III) complexes are lower than those of cisplatin and much lower than these of melphalan. The coordination to gallium (III) additionally increased the cytotoxicity compared to the metal-free hydrazones.

Host-Guest Complexation of Cucurbit[7]Uril and Cucurbit[8]Uril with the Antineoplastic and Multiple Sclerosis Agent Mitoxantrone (Novantrone).

The nature of interactions between the neutral/protonated mitoxantrone and the cucurbit[n]uril (n = 7, 8) host system was analyzed by employing density functional theory calculations. A comparison between the inclusion complexes of CB[7] and CB[8] shows various subtle differences in the complexation thermodynamics, given as changes in the Gibbs energy. Doubly and quadruply charged mitoxantrone (MX) molecules spontaneously form complexes in a water solvent, which are modeled using the polarizable continuum model approach. Both CB[7] and CB[8] complexes are stable as the geometry of the cavity allows for electrostatic interactions between the charged MX arms and the rim of the CB cavity. CB[8] also forms a stable complex with two mitoxantrone molecules with their aromatic rings stacked inside the cavity. Both CB[7] and CB[8] show properties that can be utilized in drug delivery.

Zinc and Its Critical Role in Retinitis pigmentosa: Insights from DFT/SMD Calculations.

Metal cations are required for the proper function of a great amount of biological processes, as they are indispensable cofactors participating in up to 40% of the active sites of the proteins. In the case of some diseases, however, metal cations could exhibit a dual function. As an example, the role of the zinc cation in the development of Retinitis pigmentosa could be given. Experimental works indicate the loss of thermostability of the rhodopsin protein, subjected to the combination of-typical for the disease-mutations and increased quantity of Zn2+. Two structural networks in the intradiscal domain surrounding His100 and His195 are supposed to be susceptible to pathophysiological changes in trace metal concentrations. From a thermodynamic point of view, it is of particular interest to decipher the foundations of the observed outcome, as well as to closely characterize the intimate interactions between the "native" cation and the building amino acid residues of the studied centers. Therefore, the powerful, but fundamentally limited, tools of computational chemistry were applied on simplified models of rhodopsin metal centers in order to shed light on the following aspects: (1) what is the preferred geometry of the Zn2+-containing complexes with the amino acid ligands from the binding pockets; (2) what is the role of the mutations for the interactions between Zn2+ and the examined centers; (3) could other divalent cations such as Ca2+ and Cu2+ substitute for the native zinc; (4) how does the dielectric constant of the environment affect the processes? The obtained results illuminate some aspects of the zinc coordination to amino acid residues and zinc biochemistry related to the presumed pathogenesis of Retinitis pigmentosa.

Spectral Characteristics and Sensor Ability of a New 1,8-Naphthalimide and Its Copolymer with Styrene.

In this study, a novel 6-(allylamino)-2-(2-(dimethylamino)ethyl)-1H-benzo[de]isoquinoline-1,3(2H)-dione (NI3) was synthesized and characterized. Its copolymer with styrene was also obtained. The photophysical characteristics of NI3 were investigated in organic solvents and the results were compared with those of its structural analogue, 2-allyl-6-((2-(dimethylamino)ethyl)amino)-1H-benzo[de]isoquinoline-1,3(2H)-dione (NI4). The influences of the pH in the medium and different metal ions on the fluorescent intensity of monomers and polymers were also investigated. Computational tools (DFT and TDDFT calculations) were employed when studying the structure and properties of the 1,8-naphthalimide-based chromophores. Although the position of the N,N-dimethylaminoethylamine receptor fragment did not significantly impact proton detection, it was still important for detecting metal ion sensor ability, especially for monomeric 1,8-naphthalimide structures and their copolymers with styrene.

Water inside ß-cyclodextrin cavity: amount, stability and mechanism of binding.

Cyclodextrins (CDs) are native host systems with inherent ability to form inclusion complexes with various molecular entities, mostly hydrophobic substances. Host cyclodextrins are accommodative to water molecules as well and contain water in the native state. For ß-cyclodextrin (ß-CD), there is no consensus regarding the number of bound water molecules and the location of their coordination. A number of intriguing questions remain: (1) Which localities of the host's macrocycle are the strongest attractors for the guest water molecules? (2) What are the stabilizing factors for the water clusters in the interior of ß-CD and what type of interactions between water molecules and cavity walls or between the water molecules themselves are dominating the energetics of the ß-CD hydration? (3) What is the maximum number of water molecules inside the cavity of ß-CD? (4) How do the thermodynamic characteristics of ß-CD hydration compare with those of its smaller α-cyclodextrin (α-CD) counterpart? In this study, we address these questions by employing a combination of experimental (DSC/TG) and theoretical (DFT) approaches.

Host-guest interactions between p-sulfonatocalix[4]arene and p-sulfonatothiacalix[4]arene and group IA, IIA and f-block metal cations: a DFT/SMD study.

The molecular recognition in aqueous solution is extremely important because most biological processes occur in aqueous solution. Water-soluble members of the calix[n]arene family (e.g., p-sulfonato substituted) can serve as model systems for studying the nature and manner of interactions between biological receptors and small ions. The complex formation behavior of water-soluble p-sulfonatocalix[4]arene and thiacalix[4]arene and group IA, IIA and f-block metal cations has been investigated computationally by means of density functional theory computations in the gas phase and in aqueous environment. The calculated Gibbs free energy values of the complex formation reaction of these ligands with the bare metal cations suggest a spontaneous and energy-favorable process for all metal cations in the gas phase and only for Na+, Mg2+, Lu3+ cations in water environment. For one of the studied cations (La3+) a supramolecular approach with explicit solvent treatment has been applied in the study of the effect of metal hydration on the complexation process. The La3+ binding to the p-sulfonatocalix[4]arene host molecule (now in the metal's second coordination shell) is still exergonic as evidenced by the negative Gibbs free energy values (ΔG 1 and ΔG 78). The combination of implicit/explicit solvent treatment seems useful in the modeling of the p-sulfonatocalix[4]arene (and thiacalix[4]arene) complexes with metal cations and in the prediction of the thermodynamic parameters of the complex formation reactions.

Precious metal-free molecular machines for solar thermal energy storage.

Four benzothiazolium crown ether-containing styryl dyes were prepared through an optimized synthetic procedure. Two of the dyes (4b and 4d) having substituents in the 5-position of the benzothiazole ring are newly synthesized compounds. They demonstrated a higher degree of trans-cis photoisomerization and a longer life time of the higher energy forms in comparison with the known analogs. The chemical structures of all dyes in the series were characterized by NMR, UV-vis, IR spectroscopy and elemental analysis. The steady-state photophysical properties of the dyes were elucidated. The stability constants of metal complexes were determined and are in good agreement with the literature data for reference dyes. The temporal evolution of trans-to-cis isomerization was observed in a real-time regime. The dyes demonstrated a low intrinsic fluorescence of their Ba2+ complexes and high yield of E/Z photoisomerization with lifetimes of the higher energy form longer than 500 seconds. Density functional theory (DFT) calculations at the B3LYP/6-31+G(d,p) level were performed in order to predict the enthalpies (H) of the cis and trans isomers and the storage energies (ΔH) for the systems studied.

Protective effects of new antioxidant compositions of 4-methylcoumarins and related compounds with dl-α-tocopherol and l-ascorbic acid.

BACKGROUND: Coumarin derivatives possess a wide range of biological activities. By functionalization of the parent coumarin skeleton that has neither antioxidant nor biological activity, a series of new bio-antioxidants has been designed. RESULTS: New antioxidant compositions (equimolar binary and ternary mixtures) of eight 4-methylcoumarins and three related compounds have been tested and different effects between individual components have been observed: synergism (positive effect), additivism (summary effect) and antagonism (negative effect). Higher oxidative stability of the lipid substrate was obtained in the presence of the new antioxidant compositions of the studied compounds with dl-α-tocopherol and l-ascorbic acid. The role of each component in the antioxidant compositions of ternary mixtures has been identified by using new equations composed by the authors. CONCLUSION: All ternary mixtures demonstrate synergism as a result of continuous regeneration of dl-α-tocopherol from the studied antioxidants and l-ascorbic acid. Theoretical calculations have been probed as indicators of the expected effects between the individual components in a binary mixture. © 2018 Society of Chemical Industry.

Factors Governing the Host-Guest Interactions between IIA/IIB Group Metal Cations and α-Cyclodextrin: A DFT/CDM Study.

Cyclodextrins' unique molecular structure with hydrophilic exterior surface and nonpolar cavity interior is responsible for their specific complexation properties. Although a wealth of information about these molecules has been accumulated, many aspects of their coordination chemistry remain unknown. For example, there are no systematic studies on the key factors controlling the processes of metal binding and selectivity in these systems. In the computational study herein, DFT molecular modeling has been employed to study the interactions of either hydrated or nonhydrated IIA/IIB group metal cations (Be2+, Mg2+, Ca2+, Sr2+, Ba2+, Zn2+, Cd2+, Hg2+) with the host α-cyclodextrin molecules. The thermodynamic descriptors (Gibbs free energies in the gas phase and in water medium) of the metal binding to α-cyclodextrin have been evaluated, and the effect of various factors (metal's radius, electron configuration and coordination number, and host molecule flexibility and binding site locality) on the interactions between the two binding partners has been assessed. The results obtained shed light on the intimate mechanism of the metal binding to α-cyclodextrin and disclose the key factors governing the process.