Topology of the Interactions Pattern in Pharmaceutically Relevant Polymorphs of Methylxanthines (Caffeine, Theobromine, and Theophiline): Combined Experimental (1H–14N Nuclear Quadrupole Double Resonance) and Computational (DFT and Hirshfeld-Based) Study

Anti-Butterfly Effect in Ribavirin Studied by Combined Experiment (PXRD/1H-14N NQR Cross-Relaxation Spectroscopy), Quantum Chemical Calculations, Molecular Docking, Molecular Dynamics Simulations, and Novel Structure-Binding Strength and Quadrupolar Indices

Ribavirin, 1-(β-D-Ribofuranosyl)-1H-1,2,4-triazole-3-carboxamide, which is included in the list of drugs recommended in the guidelines for the diagnosis and treatment of SARS-CoV-2 infection, has been the subject of experimental and theoretical investigation. The most thermodynamically stable polymorphic form was studied using 1H-14N NQR cross-relaxation, periodic DFT/QTAIM/RDS/3D Hirshfeld surfaces, and molecular docking. For the first time, a 1H-14N cross-relaxation spectrum of ribavirin was recorded and interpreted. Twelve resonance frequencies were assigned to four inequivalent nitrogen positions in the molecule using combined experimental techniques and solid-state quantum chemical calculations. The influence of the structural alteration on the NQR parameters was modeled using GGA/RPBE. The differences in the binding pattern of ribavirin, acadesine, inosine, guanosine, and favipiravir-ribofuranosyl in the solid state and the protein-ligand complex were assessed to elucidate the differences in the binding mechanism at the molecular level due to aglycone modification. The replacement of the carbon adjacent to the ribose with nitrogen, in conjunction with the absence of oxygen at the 2-position of the ring, resulted in an increased flexibility of the RBV structure in comparison to the favipiravir-ribofuranosyl structure. The present study identified the intramolecular hydrogen bond NH···N in RBV as playing a crucial role in the formation of a quasi-five-membered ring. However, this bond was proven to be too weak to force positioning of the amide group in the ring plane. The ribofuranosyl in RBV inhibits tautomerism and freezes the conformation of the amide group. The results of the molecular dynamics simulations demonstrated that RBV and favipiravir-ribofuranosyl incorporated into the RNA primer exhibited comparable stability within the protein binding region. The titular anti-butterfly (inverted butterfly) effect is associated with the consequences of both the changes in aglycone moiety and the neighborhood alteration. Seven structure-binding strength indices and six novel quadrupolar indices defined in this study have been proven to facilitate the evaluation of the similarity of binding motifs in the solid state and protein-ligand complex.

Analytical insight into caffeine extraction from typica coffee leaves based on crystallinity enhancement, optical phonon vibration upshift, and morphological evolution

Caffeine extracted from callus cultures by in vitro technique induced from typica coffee (Coffea arabica L. var. typica) leaves was successfully carried out by a simple Soxhlet method. Analysis of X-ray diffraction patterns showed an increase in crystallinity fraction from leaves (13.56%) to callus (14.46%) and then to caffeine (39.18%). Crystallite size also varied, with average sizes of 18 ± 6, 69 ± 51, and 32.5 ± 17 nm for leaves, callus, and caffeine, respectively. Fourier transmission infrared absorption data confirmed the presence of hydroxyl (OH) groups bound to carbon (C─COH), indicating caffeine content. The high stability of the C─COH is indicated by the broad optical phonon vibrationsΔ ( L O - T O ) $\Delta ( {LO - TO} )$ of the leaves: 247 cm-1 to caffeine: 963 cm-1. Quantitative analysis of dielectric function and electron loss function intensity peaks of each sample showed that leaves efficiently capture and store light energy while caffeine has less potency. Scanning electron microscopy analysis showed irregular shapes of leaves, oval round shapes for callus, and rectangular crystals for caffeine due to crystal orientation during transformation and had a strong correlation with crystallinity fraction. Finally, the structure-based identification, chemistry, optical-dielectric function, and micro-surface properties have been fully studied, thus unmasking the phenomenon of slow transformation from leaves to caffeine form. PRACTICAL APPLICATION: The result of this study can be applied to uncover new methodologies related to the classification, and biotechnological utilization of callus culture based on structural properties, optical-dielectric function, and micro-surface analysis. Methodologically, the resulting callus culture provides a sustainable and controllable supply of plant material for caffeine extraction, thereby reducing traditional methods involving field-grown plants and avoiding the use of pesticides.

Non-invasive caffeinated-nanovesicles as adipocytes-targeted therapy for cellulite and localized fats

Caffeine (CAF) is a non-selective adenosine A1 receptor antagonist which predominates in fat cells. When CAF binds to adenosine receptors, it increases cyclic adenosine monophosphate; inhibiting adipogenesis and inducing fat lipolysis. Resveratrol (RSV) is an antioxidant polyphenol possessing different anti-obesity mechanisms. Topical application of both hydrophilic CAF and lipophilic RSV is limited. This study aimed to develop novel caffeinated-resveratrol bilosomes (CRB) and caffeine-bilosomes (CB) that could non-invasively target and deposit in fat cells. RSV bilosomes (RB) were prepared as a non-targeted system for comparison. CRB showed nanosize (364.1 nm ±6.5 nm) and high entrapment for both active compounds. Rats treated topically with CRB revealed a significant decrease (P = 0.039) in body weight. Histological analysis of the excised skin demonstrated a reduction in the subcutaneous fatty layer thickness and a decrease in the size of connective tissue-imbedded fat cells. Kidney histological examination of RB-treated rats showed subcapsular tubular epithelial cells with cytoplasmic vacuolation. This reflects a systemic effect of RSV from the non-targeted RB compared to CRB, which had a targeting effect on the adipose tissue. In conclusion, CAF in CRB significantly enhanced RSV deposition in adipose tissue and assisted its local-acting effect for managing obesity and cellulite.

Elucidating the Role of Noncovalent Interactions in Favipiravir, a Drug Active against Various Human RNA Viruses; a 1H-14N NQDR/Periodic DFT/QTAIM/RDS/3D Hirshfeld Surfaces Combined Study

Favipiravir (6-fluoro-3-hydroxypyrazine-2-carboxamide, FPV), an active pharmaceutical component of the drug discovered and registered in March 2014 in Japan under the name Avigan, with an indication for pandemic influenza, has been studied. The study of this compound was prompted by the idea that effective processes of recognition and binding of FPV to the nucleic acid are affected predominantly by the propensity to form intra- and intermolecular interactions. Three nuclear quadrupole resonance experimental techniques, namely ¹H-¹⁴N cross-relaxation, multiple frequency sweeps, and two-frequency irradiation, followed by solid-state computational modelling (density functional theory supplemented by the quantum theory of atoms in molecules, 3D Hirshfeld Surfaces, and reduced density gradient) approaches were applied. The complete NQR spectrum consisting of nine lines indicating the presence of three chemically inequivalent nitrogen sites in the FPV molecule was detected, and the assignment of lines to particular sites was performed. The description of the nearest vicinity of all three nitrogen atoms was used to characterize the nature of the intermolecular interactions from the perspective of the local single atoms and to draw some conclusions on the nature of the interactions required for effective recognition and binding. The propensity to form the electrostatic N-H···O, N-H···N, and C-H···O intermolecular hydrogen bonds competitive with two intramolecular hydrogen bonds, strong O-H···O and very weak N-H···N, closing the 5-member ring and stiffening the structure, as well as π···π and F···F dispersive interactions, were analysed in detail. The hypothesis regarding the similarity of the interaction pattern in the solid and the RNA template was verified. It was discovered that the -NH₂ group in the crystal participates in intermolecular hydrogen bonds N-H···N and N-H···O, in the precatalytic state only in N-H···O, while in the active state in N-H···N and N-H···O hydrogen bonds, which is of importance to link FVP to the RNA template. Our study elucidates the binding modes of FVP (in crystal, precatalytic, and active forms) in detail and should guide the design of more potent analogues targeting SARS-CoV-2. Strong direct binding of FVP-RTP to both the active site and cofactor discovered by us suggests a possible alternative, allosteric mechanism of FVP action, which may explain the scattering of the results of clinical trials or the synergistic effect observed in combined treatment against SARS-CoV-2.

A Competition between Relative Stability and Binding Energy in Caffeine Phenyl-Glucose Aggregates: Implications in Biological Mechanisms

Hydrogen bonds and stacking interactions are pivotal in biological mechanisms, although their proper characterisation within a molecular complex remains a difficult task. We used quantum mechanical calculations to characterise the complex between caffeine and phenyl-β-D-glucopyranoside, in which several functional groups of the sugar derivative compete with each other to attract caffeine. Calculations at different levels of theory (M06-2X/6-311++G(d,p) and B3LYP-ED=GD3BJ/def2TZVP) agree to predict several structures similar in stability (relative energy) but with different affinity (binding energy). These computational results were experimentally verified by laser infrared spectroscopy, through which the caffeine·phenyl-β-D-glucopyranoside complex was identified in an isolated environment, produced under supersonic expansion conditions. The experimental observations correlate with the computational results. Caffeine shows intermolecular interaction preferences that combine both hydrogen bonding and stacking interactions. This dual behaviour had already been observed with phenol, and now with phenyl-β-D-glucopyranoside, it is confirmed and maximised. In fact, the size of the complex's counterparts affects the maximisation of the intermolecular bond strength because of the conformational adaptability given by the stacking interaction. Comparison with the binding of caffeine within the orthosteric site of the A2A adenosine receptor shows that the more strongly bound caffeine·phenyl-β-D-glucopyranoside conformer mimics the interactions occurring within the receptor.

Synthesis and Crystal Structure of Adamantylated 4,5,6,7-Tetrahalogeno-1H-benzimidazoles Novel Multi-Target Ligands (Potential CK2, M2 and SARS-CoV-2 Inhibitors); X-ray/DFT/QTAIM/Hirshfeld Surfaces/Molecular Docking Study

A series of new congeners, 1-[2-(1-adamantyl)ethyl]-1H-benzimidazole (AB) and 1-[2-(1-adamantyl)ethyl]-4,5,6,7-tetrahalogeno-1H-benzimidazole (Hal=Cl, Br, I; tClAB, tBrAB, tIAB), have been synthesized and studied. These novel multi-target ligands combine a benzimidazole ring known to show antitumor activity and an adamantyl moiety showing anti-influenza activity. Their crystal structures were determined by X-ray, while intermolecular interactions were studied using topological Bader's Quantum Theory of Atoms in Molecules, Hirshfeld Surfaces, CLP and PIXEL approaches. The newly synthesized compounds crystallize within two different space groups, P-1 (AB and tIAB) and P21/c (tClAB and tBrAB). A number of intramolecular hydrogen bonds, C-H⋯Hal (Hal=Cl, Br, I), were found in all halogen-containing congeners studied, but the intermolecular C-H⋯N hydrogen bond was detected only in AB and tIAB, while C-Hal⋯π only in tClAB and tBrAB. The interplay between C-H⋯N and C-H⋯Hal hydrogen bonds and a shift from the strong (C-H⋯Cl) to the very weak (C-H⋯I) attractive interactions upon Hal exchange, supplemented with Hal⋯Hal overlapping, determines the differences in the symmetry of crystalline packing and is crucial from the biological point of view. The hypothesis about the potential dual inhibitor role of the newly synthesized congeners was verified using molecular docking and the congeners were found to be pharmaceutically attractive as Human Casein Kinase 2, CK2, inhibitors, Membrane Matrix 2 Protein, M2, blockers and Severe Acute Respiratory Syndrome Coronavirus 2, SARS-CoV-2, inhibitors. The addition of adamantyl moiety seems to broaden and modify the therapeutic indices of the 4,5,6,7-tetrahalogeno-1H-benzimidazoles.

Experimental and Theoretical Study on Theobromine Solubility Enhancement in Binary Aqueous Solutions and Ternary Designed Solvents

The solubility of theobromine was studied both experimentally and theoretically. The solubility was determined spectrophotometrically at 25 °C in neat organic solvents, aqueous binary mixtures, Natural Deep Eutectic Solvents (NADES) and ternary NADES mixtures with water. It was found that addition of water in unimolar proportions with some organic solvents increases theobromine solubility compared to neat solvents. Additionally, using NADES results in a solubility increase of the studied compound not only in relation to water but also DMSO. The addition of water (0.2 molar fraction) to NADES is responsible for an even larger increase of solubility. The measured solubilities were interpreted in terms of three theoretical frameworks. The first one-belonging to the set of data reduction techniques-proved to be very efficient in quantitative back-computations of excess solubility of theobromine in all studied systems. The default approach utilizing the well-recognized COSMO-RS (Conductor-like Screening Model for Real Solvents) framework offered at most a qualitative solubility description. The extended search for possible contacts provided evidence for the existence of many intermolecular complexes that alter the electron density of the solute molecule, thus influencing solubility computations. Taking into account such intermolecular contacts by using the COSMO-RS-DARE (Conductor-like Screening Model for Realistic Solvation-Dimerization, Aggregation, and Reaction Extension) framework seriously increased the accuracy of solubility computations.

Valorization of Spent Coffee by Caffeine Extraction Using Aqueous Solutions of Cholinium-Based Ionic Liquids

Spent coffee grounds (SCGs) are a waste product with no relevant commercial value. However, SCGs are rich in extractable compounds with biological activity. To add value to this coffee byproduct, water and aqueous solutions of cholinium-based ionic liquids (ILs) were studied to extract caffeine from SCGs. In general, all IL aqueous solutions lead to higher extraction efficiencies of caffeine than pure water, with aqueous solutions of cholinium bicarbonate being the most efficient. A factorial planning was applied to optimize operational conditions. Aqueous solutions of cholinium bicarbonate, at a temperature of 80 °C for 30 min of extraction, a biomass–solvent weight ratio of 0.05 and at an IL concentration of 1.5 M, made it possible to extract 3.29 wt% of caffeine (against 1.50 wt% obtained at the best conditions obtained with pure water). Furthermore, to improve the sustainability of the process, the same IL aqueous solution was consecutively applied to extract caffeine from six samples of fresh biomass, where an increase in the extraction yield from 3.29 to 13.10 wt% was achieved. Finally, the cholinium bicarbonate was converted to cholinium chloride by titration with hydrochloric acid envisioning the direct application of the IL-caffeine extract in food, cosmetic and nutraceutical products. The results obtained prove that aqueous solutions of cholinium-based ILs are improved solvents for the extraction of caffeine from SCGs, paving the way for their use in the valorization of other waste rich in high-value compounds.

Impact of structural differences in carcinopreventive agents indole-3-carbinol and 3,3'-diindolylmethane on biological activity. An X-ray, ¹H-¹⁴N NQDR, ¹³C CP/MAS NMR, and periodic hybrid DFT study

Three experimental techniques (1)H-(14)N NQDR, (13)C CP/MAS NMR and X-ray and Density Functional Theory (GGA/BLYP with PBC) and Hirshfeld surfaces were applied for the structure-activity oriented studies of two phyto-antioxidants and anticarcinogens: indole-3-carbinol, I3C, and 3,3'-diindolylmethane, DIM, (its bioactive metabolite). One set of (14)N NQR frequencies for DIM (2.310, 2.200 and 0.110 MHz at 295K) and I3C (2.315, 1.985 and 0.330 MHz at 160K) was recorded. The multiplicity of NQR lines recorded at RT revealed high symmetry (chemical and physical equivalence) of both methyl indazole rings of DIM. Carbonyl (13)C CSA tensor components were calculated from the (13)C CP/MAS solid state NMR spectrum of I3C recorded under fast and slow spinning. At room temperature the crystal structure of I3C is orthorhombic: space group Pca21, Z=4, a=5.78922(16), b=15.6434(7) and c=8.4405(2)Å. The I3C molecules are aggregated into ribbons stacked along [001]. The oxygen atomsare disorderedbetween the two sites of different occupancy factors. It implies that the crystal is built of about 70% trans and 30% gauche conformers, and apart from the weak OH⋯O hydrogen bonds (O⋯O=3.106Å) the formation of alternative O'H⋯O bonds (O'⋯O=2.785Å) is possible within the 1D ribbons. The adjacent ribbons are further stabilised by O'H⋯O bonds (O'⋯O=2.951Å). The analysis of spectra and intermolecular interactions pattern by experimental techniques was supported by solid (periodic) DFT calculations. The knowledge of the topology and competition of the interactions in crystalline state shed some light on the preferred conformations of CH2OH in I3C and steric hindrance of methyl indole rings in DIM. A comparison of the local environment in gas phase and solid permitted drawing some conclusions on the nature of the interactions required for effective processes of recognition and binding of a given anticarcinogen to the protein or nucleic acid.