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.

Density Functional Theory Prediction of Laser Dyes-Cucurbit[7]uril Binding Affinities.

Among a variety of diverse host molecules distinguished by specific characteristics, the cucurbit[n]uril (CB) family stands out, being widely known for the attractive properties of its representatives along with their increasingly expanding area of applications. The presented herewith density functional theory (DFT)-based study is inspired by some recent studies exploring CBs as a key component in multifunctional hydrogels with applications in materials science, thus considering CB-assisted supramolecular polymeric hydrogels (CB-SPHs), a new class of 3D cross-linked polymer materials. The research systematically investigates the inclusion process between the most applied representative of the cavitand family CB[7] and a series of laser dye molecules as guests, as well as the possible encapsulation of a model side chain from the photoanisotropic polymer PAZO and its sodium-containing salt. The obtained results shed light on the most significant factors that play a key role in the recognition process, such as binding mode, charge, and dielectric constant of the solvent. The observed findings provide valuable insights at a molecular level for the design of dye-CB[7] systems in various environments, with potential applications in intriguing and prosperous fields like photonics and material science.

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.

Deciphering the mechanism of γ-cyclodextrin's hydrophobic cavity hydration: an integrated experimental and theoretical study.

Cyclodextrins (CDs) are host systems with inherent capability for inclusion complex formation with various molecular entities, mostly hydrophobic substances. Host CDs are highly accommodative to water molecules as well and usually contain water in the native state. There is still an ongoing discussion on both the total number of water molecules and their preferred binding position inside the cavities of the CDs. To understand the hydration/dehydration properties of γ-CD (the largest of the three most abundant native CDs), the main experimental methods applied in this study were differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). By coupling these techniques with density functional theory (DFT) calculations we try to shed some light on the mechanism of the γ-CD hydration and to address some unanswered questions: (i) what are the preferable locations for water molecules in the macrocyclic cavity ("hot spots"); (ii) what are the major factors contributing to the stability of the water cluster in the CD interior; (iii) what type of interactions (i.e., water-water and/or water-CD walls) contribute to the stability of the water assemble; (iv) how does the mechanism of the γ-CD hydration compare with those of its α-CD and ß-CD counterparts.

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).

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).

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.

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.

Host-guest complexation of cucurbit[7]uril and cucurbit[8]uril with the antimuscarinic drugs tropicamide and atropine.

Cucurbiturils are useful excipients in eye drop formulations: they can increase the water solubility of the drug, enhance drug absorption into the eye, improve aqueous stability and reduce local irritation. Effective and safe drug delivery is, however, a challenge and the information on the host (CBs)/guest (tropicamide and atropine) interactions can help improving the existing treatments and develop novel therapies not limited only to eye diseases/conditions. Since this carrier system can easily modify the properties of the drug and ensure its delivery at the targeted ocular tissue, further insight into the intimate mechanism of the host-guest recognition is crucial. The present DFT/SMD study focuses on the role of numerous factors governing this process, namely the specific position of the guest molecule in the cavity of the cucurbituril, the ionization form (non/protonated) of the antimuscarinic drug, the dielectric constant of the medium, and the size of the cavitant pore. The obtained results are in line with experimental observations and shed light on the mechanism, at atomic resolution, of recognition between the CBs and the two parasympatholytic drugs.

Cu+/Ag+ Competition in Type I Copper Proteins (T1Cu).

Due to the similarity in the basic coordination behavior of their mono-charged cations, silver biochemistry is known to be linked to that of copper in biological systems. Still, Cu+/2+ is an essential micronutrient in many organisms, while no known biological process requires silver. In human cells, copper regulation and trafficking is strictly controlled by complex systems including many cytosolic copper chaperones, whereas some bacteria exploit the so-called "blue copper" proteins. Therefore, evaluating the controlling factors of the competition between these two metal cations is of enormous interest. By employing the tools of computational chemistry, we aim to delineate the extent to which Ag+ might be able to compete with the endogenous copper in its Type I (T1Cu) proteins, and where and if, alternatively, it is handled uniquely. The effect of the surrounding media (dielectric constant) and the type, number, and composition of amino acid residues are taken into account when modelling the reactions in the present study. The obtained results clearly indicate the susceptibility of the T1Cu proteins to a silver attack due to the favorable composition and geometry of the metal-binding centers, along with the similarity between the Ag+/Cu+-containing structures. Furthermore, by exploring intriguing questions of both metals' coordination chemistry, an important background for understanding the metabolism and biotransformation of silver in organisms is provided.

Competition between Ag+ and Ni2+ in nickel enzymes: Implications for the Ag+ antibacterial activity.

Silver's antimicrobial properties have been known for centuries, but exactly how it kills bacteria is still a mystery. Information on the competition between the native Ni2+ and abiogenic Ag+ cations in bacterial systems is also critically lacking. For example, urease, a famous nickel-containing enzyme that hydrolyzes urea into carbon dioxide and ammonia (a key step in the biogeochemical nitrogen cycle on Earth), is inhibited by Ag+ cations, but the molecular mechanism of silver's action is poorly understood. By employing density functional theory (DFT) calculations combined with the polarizable continuum model (PCM) computations we assess the susceptibility of the mono/binuclear Ni2+ binding sites in the nickel enzymatic centers to Ni2+→Ag+ substitution. The active centers in the mononuclear glyoxalase I and acireductone dioxygenase enzymes appear to be well protected against Ag+ attack and, presumably, stay functional even in its presence. On the other hand, the binuclear nickel binding site in urease appears vulnerable to silver attack - the results obtained are in line with available experimental data and give reason to assume a possible substitution of the essential Ni2+ cation from the urease metal center by Ag+.

Mini-Review on Structure-Reactivity Relationship for Aromatic Molecules: Recent Advances.

Recent advances in quantifying nucleophilic reactivities in chemical reactions and intermolecular interactions of aromatic molecules are reviewed. This survey covers experimental (IR frequency shifts induced by hydrogen bonding) and theoretical (modeling of potential energy surfaces, atomic charges, molecular electrostatic potential) approaches in characterizing chemical reactivity. Recent advances in software developments assisting the evaluation of the reactive sites for electrophilic aromatic substitution are briefly discussed.

Strontium Binding to α-Parvalbumin, a Canonical Calcium-Binding Protein of the "EF-Hand" Family.

Strontium salts are used for treatment of osteoporosis and bone cancer, but their impact on calcium-mediated physiological processes remains obscure. To explore Sr2+ interference with Ca2+ binding to proteins of the EF-hand family, we studied Sr2+/Ca2+ interaction with a canonical EF-hand protein, α-parvalbumin (α-PA). Evaluation of the equilibrium metal association constants for the active Ca2+ binding sites of recombinant human α-PA ('CD' and 'EF' sites) from fluorimetric titration experiments and isothermal titration calorimetry data gave 4 × 109 M-1 and 4 × 109 M-1 for Ca2+, and 2 × 107 M-1 and 2 × 106 M-1 for Sr2+. Inactivation of the EF site by homologous substitution of the Ca2+-coordinating Glu in position 12 of the EF-loop by Gln decreased Ca2+/Sr2+ affinity of the protein by an order of magnitude, whereas the analogous inactivation of the CD site induced much deeper suppression of the Ca2+/Sr2+ affinity. These results suggest that Sr2+ and Ca2+ bind to CD/EF sites of α-PA and the Ca2+/Sr2+ binding are sequential processes with the CD site being occupied first. Spectrofluorimetric Sr2+ titration of the Ca2+-loaded α-PA revealed presence of secondary Sr2+ binding site(s) with an apparent equilibrium association constant of 4 × 105 M-1. Fourier-transform infrared spectroscopy data evidence that Ca2+/Sr2+-loaded forms of α-PA exhibit similar states of their COO- groups. Near-UV circular dichroism (CD) data show that Ca2+/Sr2+ binding to α-PA induce similar changes in symmetry of microenvironment of its Phe residues. Far-UV CD experiments reveal that Ca2+/Sr2+ binding are accompanied by nearly identical changes in secondary structure of α-PA. Meanwhile, scanning calorimetry measurements show markedly lower Sr2+-induced increase in stability of tertiary structure of α-PA, compared to the Ca2+-induced effect. Theoretical modeling using Density Functional Theory computations with Polarizable Continuum Model calculations confirms that Ca2+-binding sites of α-PA are well protected against exchange of Ca2+ for Sr2+ regardless of coordination number of Sr2+, solvent exposure or rigidity of sites. The latter appears to be a key determinant of the Ca2+/Sr2+ selectivity. Overall, despite lowered affinity of α-PA to Sr2+, the latter competes with Ca2+ for the same EF-hands and induces similar structural rearrangements. The presence of a secondary Sr2+ binding site(s) could be a factor contributing to Sr2+ impact on the functional activity of proteins.

Complexation of biologically essential (mono- and divalent) metal cations to cucurbiturils: a DFT/SMD evaluation of the key factors governing the host-guest recognition.

Supramolecular complexes based on classical synthetic macrocyclic host molecules such as cyclodextrins and calixarenes have received much attention recently due to their broad applications as biological and chemical sensors, bioimaging agents, drug delivery carriers, light-emitting materials, etc. Cucurbit[n]urils comprise another group of cavitands known for their high affinity for various guest molecules. Nonetheless, some aspects of their coordination chemistry remain enigmatic. Although they are recognized as potential biomimetic scaffolds, they are still not tested as metalloenzyme models and not much is known about their metal-binding properties. Furthermore, there is no systematic study on the key factors controlling the processes of metal coordination to these systems. In the computational study herein, DFT molecular modeling has been employed in order to investigate the interactions of biologically essential (mono- and divalent) metal cations to cucurbit[n]urils and evaluate the major determinants shaping the process. The thermodynamic descriptors (Gibbs energies in the gas phase and in a water medium) of the corresponding complexation reactions have been estimated. The results obtained shed light on the mechanism of host-guest recognition and disclose which factors more specifically affect the metal binding process.