Mechanism of Ligand Binding to Theophylline RNA Aptamer.

Studying RNA-ligand interactions and quantifying their binding thermodynamics and kinetics are of particular relevance in the field of drug discovery. Here, we combined biochemical binding assays and accelerated molecular simulations to investigate ligand binding and dissociation in RNA using the theophylline-binding RNA as a model system. All-atom simulations using a Ligand Gaussian accelerated Molecular Dynamics method (LiGaMD) have captured repetitive binding and dissociation of theophylline and caffeine to RNA. Theophylline's binding free energy and kinetic rate constants align with our experimental data, while caffeine's binding affinity is over 10,000 times weaker, and its kinetics could not be determined. LiGaMD simulations allowed us to identify distinct low-energy conformations and multiple ligand binding pathways to RNA. Simulations revealed a "conformational selection" mechanism for ligand binding to the flexible RNA aptamer, which provides important mechanistic insights into ligand binding to the theophylline-binding model. Our findings suggest that compound docking using a structural ensemble of representative RNA conformations would be necessary for structure-based drug design of flexible RNA.

Production of 1-methylxanthine via the biodegradation of theophylline by an optimized Escherichia coli strain.

1-Methylxanthine is a high-value derivative of caffeine of limited natural availability with many potential pharmaceutical applications. Unfortunately, production of 1-methylxanthine through purely chemical methods of synthesis are unfavorable due to lengthy chemical processes and the requirement of hazardous chemicals, ultimately resulting in low yields. Here, we describe a novel biosynthetic process for the production of 1-methylxanthine from theophylline using engineered Escherichia coli whole-cell biocatalysts and reaction optimization. When scaled-up to 1590 mL, the simple biocatalytic reaction produced approximately 1188 mg 1-methylxanthine from 1444 mg theophylline, constituting gram-scale production of 1-methylxanthine in as little as 3 hours. Following HPLC purification and solvent evaporation, 1163 mg of dried 1-methylxanthine powder was collected, resulting in a 97.9 wt% product recovery at a purity of 97.8%. This is the first report of a biocatalytic process designed specifically for the production and purification of the high-value biochemical 1-methylxanthine from theophylline. This process is also the most robust methylxanthine N-demethylation process featuring engineered E. coli to date, capable of gram-scale production.

Glutathione-Mediated Neuroprotective Effect of Purine Derivatives.

Numerous basic studies have reported on the neuroprotective properties of several purine derivatives such as caffeine and uric acid (UA). Epidemiological studies have also shown the inverse association of appropriate caffeine intake or serum urate levels with neurodegenerative diseases such as Alzheimer disease (AD) and Parkinson's disease (PD). The well-established neuroprotective mechanisms of caffeine and UA involve adenosine A2A receptor antagonism and antioxidant activity, respectively. Our recent study found that another purine derivative, paraxanthine, has neuroprotective effects similar to those of caffeine and UA. These purine derivatives can promote neuronal cysteine uptake through excitatory amino acid carrier protein 1 (EAAC1) to increase neuronal glutathione (GSH) levels in the brain. This review summarizes the GSH-mediated neuroprotective effects of purine derivatives. Considering the fact that GSH depletion is a manifestation in the brains of AD and PD patients, administration of purine derivatives may be a new therapeutic approach to prevent or delay the onset of these neurodegenerative diseases.

Cross-Binding of Adenosine by Aptamers Selected Using Theophylline.

We recently reported that some adenosine binding aptamers can also bind caffeine and theophylline with around 20-fold lower affinities. This discovery led to the current work to examine the cross-binding of adenosine to theophylline aptamers. For the DNA aptamer for theophylline, cross-binding to adenosine was observed, and the affinity was 18 to 38-fold lower for adenosine based on assays using isothermal titration calorimetry and ThT fluorescence spectroscopy. The binding complexes were characterized using NMR spectroscopy, and both adenosine and theophylline showed an overall similar binding structure to the DNA theophylline aptamer, although small differences were also observed. In contrast, the RNA aptamer did not show binding to adenosine, although both aptamers have very similar relative selectivity for various methylxanthines including caffeine. After a negative selection, a few new aptamers with completely different primary sequences for theophylline were obtained and they did not show binding to adenosine. Thus, there are many ways for aptamers to bind theophylline and some can have cross-binding to adenosine. In biology, theophylline, caffeine, and adenosine can bind to the same protein receptors to regulate sleep, and their binding to the same DNA motifs may suggest an early role of nucleic acids in similar regulatory functions.

Coformer-Dependent Physical Stability in a Series of Naringenin-Based Coamorphous Materials with Caffeine, Theophylline, and Theobromine.

PURPOSE: To investigate the production and physical stability of coamorphous materials (CAM) of naringenin (NAR) and coformers-caffeine, theophylline or theobromine (CAF/THY/THE, respectively). We independently assessed the impact of moisture and temperature on the physical stability of CAMs, and transformation products after destabilization were examined. METHODS: Neat grinding, liquid assisted grinding and water slurry were selected to prepare multi-component materials with NAR and CAF, THY or THE. The physical stability of CAMs was investigated at 65°C/<10%RH, 21°C/85% RH and 21°C/<10% RH. Differential scanning calorimetry (DSC) and powder X-ray diffraction (PXRD) were employed to monitor for recrystallization during the stability studies. Glass forming ability of amorphous NAR was assessed to understand CAM formation and physical stability. RESULTS: NAR:THY and NAR:THE CAMs showed physical stability for approximately nine months, under 21°C/<10% RH while NAR:CAF CAMs destabilized in 2.5 weeks. All CAMs recrystallized within a week at 65°C/<10%RH, and the physical stability at 21°C/85% RH was in the order of - NAR:THY > NAR:THE > NAR:CAF. NAR:THY produced 1:1 cocrystal under all storage conditions, while NAR:CAF destabilized to a 1:1 cocrystal at high RH but a physical mixture at high temperature. NAR:THE was found to recrystallize as a physical mixture in all conditions. NAR was found to be strong glass, with moderate kinetic fragility and good glass forming ability. CONCLUSION: Five naringenin-based multi-component solids were generated in this study: 3 new CAMs, 1 new cocrystal, and 1 previously reported cocrystal. Destabilization of CAMs was found to be exposure specific and coformer dependent.

Experimental and theoretical approaches to interactions between DNA and purine metabolism products.

Deoxyribonucleic acid (DNA) is a significant target for small organic and inorganic drug molecules. Understanding the DNA interaction mechanism of these molecules is vital for new drug designs. In this work, interactions between xanthine (XT), theophylline (TP), and theobromine (TB) with calf-thymus double-strained DNA (dsDNA) were monitored via an experimental and theoretical approach. Experimentally, cyclic voltammetry (CV) and differential pulse voltammetry (DPV) techniques were used on the surface of the NiO/MWCNT/NNaM/PGE electrochemical platform in vitro. Kinetic parameters, including diffusion coefficients, surface concentrations, and standard heterogeneous rate constants, were measured in the absence and presence of DNA using scan rate studies. In the presence of DNA, kinetic parameters were observed to be reduced significantly. Thermodynamic parameters, such as DNA binding constants and standard free Gibbs energies, were calculated for each molecule using the CV and DPV techniques. Both techniques suggested a binding affinity order of XT > TB > TP. Theoretically, density functional theory was applied for geometry optimization, natural bond orbital analyses, and molecular orbital energies of XT, TP, and TB. Experimental and theoretical binding affinities confirm each other. The most energetically stable ligand-DNA complexes expressed that XT, TP, and TB interact with dsDNA via minor groove binding mode, using mostly hydrogen bonds.

Lanthanum vanadate-based carbon nanocomposite as an electrochemical probe for amperometric detection of theophylline in real food samples.

Theophylline (THP) is an emerging drug for chronic obstructive pulmonary disease whose side effects can be greatly affected by caffeine-containing real foods. Because an overdose of this substance can cause respiratory and neurological damage, producing a fast and accurate analytical procedure is critical. Based on a cutting-edge hybrid nanocomposite, this study was used to construct an electrochemical sensor for the accurate detection of THP. Spectroscopy and morphological investigation supported the easy synthesis of tetragonal-LaVO4 (t-LV) nanopellets and LV@CNF hybrid nanocomposite. To detect THP, a highly dispersed LV@CNF nanocomposite was modified on a glassy carbon electrode as a sensing substrate. By amperometric technique, the sensor shows a wide linear range of 0.01-1070 µM, low limit of detection (2.63 nM), and sensitivity (0.228 µA µM-1 cm-2). Finally, the current technique was successfully used to identify THP in real food samples (chocolate, coffee and black tea).

Analysis of Co-Crystallization Mechanism of Theophylline and Citric Acid from Raman Investigations in Pseudo Polymorphic Forms Obtained by Different Synthesis Methods.

Designing co-crystals can be considered as a commonly used strategy to improve the bioavailability of many low molecular weight drug candidates. The present study has revealed the existence of three pseudo polymorphic forms of theophylline-citric acid (TP-CA) co-crystal obtained via different routes of synthesis. These forms are characterized by different degrees of stability in relation with the strength of intermolecular forces responsible for the co-crystalline cohesion. Combining low- and high-frequency Raman investigations made it possible to identify anhydrous and hydrate forms of theophylline-citric acid co-crystals depending on the preparation method. It was shown that the easiest form to synthesize (form 1'), by milling one hydrate with an anhydrous reactant, is very metastable, and transforms into the anhydrous form 1 upon heating or into the hydrated form 2 when it is exposed to humidity. Raman investigations performed in situ during the co-crystallization of forms 1 and 2 have shown that two different types of H-bonding ensure the co-crystalline cohesion depending on the presence of water. In the hydrated form 2, the cohesive forces are related to strong O-H … O H-bonds between water molecules and the reactants. In the anhydrous form 1, the co-crystalline cohesion is ensured by very weak H-bonds between the two anhydrous reactants, interpreted as corresponding to π-H-bonding. The very weak strength of the cohesive forces in form 1 explains the difficulty to directly synthesize the anhydrous co-crystal.

Natural rubber blends for floating theophylline beads.

Natural rubber (NR)'s value has become increasingly important for human applications. This study prepared NR beads as floating drug delivery system by dripping NR latex into hardening solution to obtain spherical beads. Theophylline was loaded as a model drug. NR latex formed into harden beads suddenly after dripping droplets in acidic medium. These NR beads floated instantly and buoyant in HCl buffer for over 8 h with prolonged theophylline release. Their morphologies, crystallinity and thermal properties were observed using microscope, X-ray diffractometer, and thermogravimetry, respectively. Addition of 100 phr sodium bicarbonate increased drug release owing to liberation of carbon dioxide promoting porous NR matrix. Composite of 50 and 200 phr shellac in NR beads floated in HCl buffer for over 12 h. Moreover, 200 phr shellac efficiently retarded release of theophylline from NR composite beads (lower than 10 % in 8 h), whereby promoting theophylline release in phosphate buffer (pH 6.8) (approximately 80 % in 8 h). NR-shellac beads had greater water sorption (2.5 times) and erosion (4.9 times) in phosphate buffer than in HCl buffer. Thus, NR beads exhibited desirable attributes as floating drug delivery system. Both sodium bicarbonate and shellac modified matrix properties and drug release of NR beads.

[Preparation and in vitro evaluation of FDM 3D printed theophylline tablets with personalized dosage].

OBJECTIVE: To explore the feasibility of preparing different doses of tablets for personalized treatment by fused deposition modeling (FDM) 3D printing technology, and to evaluate the in vitro quality of the FDM 3D printed tablets. METHODS: Three different sizes of hollow tablets were prepared by fused deposition modeling 3D printing technology with polyvinyl alcohol (PVA) filaments. Theophylline was chosen as the model drug. In the study, 20 mg, 50 mg and 100 mg of theophylline was filled into the cavity of the tablets, respectively. The microscopic morphology of the tablets was observed by scanning electron microscopy (SEM). The weight variation of the tablets was investigated by weighing method. The hardness of the tablets was measured by tablet hardness tester. The contents of the drugs in the tablets were determined by ultraviolet and visible spectrophotometry (UV-Vis), and the dissolution apparatus was used to assay the in vitro drug release of the tablets. RESULTS: The prepared FDM 3D printed tablets were all in good shape without printing defects. And there was no leakage phenomenon. The diameter and thickness of the tablets were consistent with the design. The layers were tightly connected, and the fine structure of the formulation could be clearly observed without printing defects by scanning electron microscopy. The average weight of the three sizes of tablets was (150.5±2.3) mg, (293.6±2.6) mg and (456.2±5.6) mg, respectively. The weight variation of the three sizes of tablets were boss less than 5%, which met the requirements; The hardness of the tablets all exceeded 200 N; The contents of theophylline in the three tablets were 98.0%, 97.2% and 97.9% of the dosage (20 mg, 50 mg and 100 mg), and the relative standard deviation (RSD) was 1.06%, 1.15% and 0.63% respectively; The time for 80% drug released from the three dosage of tablets was within 30 min. CONCLUSION: Three different dosages of theophylline tablets were successfully prepared by FDM 3D printing technology in this study. The exploration may bring beneficial for the preparation of personalized dose preparations. We expect that with the development of 3D printing technology, FDM 3D printed personalized tablets can be used in the clinic as soon as possible to provide personalized treatment for patients.

Discovery of small molecules that target a tertiary-structured RNA.

There is growing interest in therapeutic intervention that targets disease-relevant RNAs using small molecules. While there have been some successes in RNA-targeted small-molecule discovery, a deeper understanding of structure-activity relationships in pursuing these targets has remained elusive. One of the best-studied tertiary-structured RNAs is the theophylline aptamer, which binds theophylline with high affinity and selectivity. Although not a drug target, this aptamer has had many applications, especially pertaining to genetic control circuits. Heretofore, no compound has been shown to bind the theophylline aptamer with greater affinity than theophylline itself. However, by carrying out a high-throughput screen of low-molecular-weight compounds, several unique hits were identified that are chemically distinct from theophylline and bind with up to 340-fold greater affinity. Multiple atomic-resolution X-ray crystal structures were determined to investigate the binding mode of theophylline and four of the best hits. These structures reveal both the rigidity of the theophylline aptamer binding pocket and the opportunity for other ligands to bind more tightly in this pocket by forming additional hydrogen-bonding interactions. These results give encouragement that the same approaches to drug discovery that have been applied so successfully to proteins can also be applied to RNAs.

A DNA Aptamer for Theophylline with Ultrahigh Selectivity Reminiscent of the Classic RNA Aptamer.

Since the report of the RNA aptamer for theophylline, theophylline has become a key molecule in chemical biology for designing RNA switches and riboswitches. In addition, theophylline is an important drug for treating airway diseases including asthma. The classic RNA aptamer with excellent selectivity for theophylline has been used to design biosensors, although DNA aptamers are more desirable for stability and cost considerations. In this work, we selected DNA aptamers for theophylline, and all the top sequences shared the same binding motifs. Binding was confirmed using isothermal titration calorimetry and a nuclease digestion assay, showing a dissociation constant (Kd) around 0.5 µM theophylline. The Theo2201 aptamer can be truncated down to 23-mer while still has a Kd of 9.8 µM. The selectivity for theophylline over caffeine is around 250,000-fold based on a strand-displacement assay, which was more than 20-fold higher compared to the classic RNA aptamer. For other tested analogs, the DNA aptamer also showed better selectivity. Using the structure-switching aptamer sensor design method, a detection limit of 17 nM theophylline was achieved in the selection buffer, and a detection limit of 31 nM was obtained in 10% serum.

Simultaneous quantification of caffeine and its main metabolites by gas chromatography mass spectrometry in horse urine.

Caffeine is a naturally occurring alkaloid and it is metabolized to paraxanthine, theophylline and theobromine. Analysis of caffeine and its metabolites is challenging since the metabolites theophylline and paraxanthine generate similar product and precursor ions. In this study, a new method was developed for the simultaneous analysis of caffeine, paraxanthine, theobromine and theophylline in horse urine using gas chromatography-mass spectrometry (GC-MS). Urine samples were treated using solid-phase extraction followed by the elution with dichloromethane-isopropanol (90:10) after the pH was adjusted to 6, and then derivatization with N-methyl-N-trimethylsilyl-trifluoroacetamide-1% trimethylchlorosilane before analysis with GC-MS. Sample preparation and derivatization steps were optimized and the method permitted elution all of these analytes within 13 min. The method was fully validated according to Commission Decision, 2002/657/EC guidelines. The calibration curves were linear with a correlation coefficient of >0.99. Precision and accuracy were well within the 15% acceptance range and the method was robust. The validation results demonstrated that the method is highly reproducible, easily applicable and selective. The method was applied to urine samples collected from racehorses to demonstrate its applicability.

EDTA salt modified carbon paste electrode for square wave voltammetric determination of theophylline in pharmaceutical tablet formulation.

In this study, a square wave voltammetric method for determination of theophylline in tablet formulation based on EDTA salt modified carbon paste electrode is presented. CV, FT-IR, and EIS results confirmed modification of the carbon paste with EDTA salt. In contrast to the unmodified carbon paste electrode, the modified carbon paste electrode showed irreversible oxidation of theophylline with considerable current enhancement. Investigation of the effect of scan rate on the Ip and Ep response of the modified electrode for theophylline revealed predominantly diffusion controlled oxidation kinetics. Under the optimized conditions, square wave oxidative peak current of theophylline in pH 7.0 PBS showed linear dependence on concentration in the range 10-200 µM with determination coefficient (R2), limit of detection, and limit of quantification of 0.99782, 0.0257 µM, and 0.0857 µM, respectively. Detection of an amount of theophylline in the analyzed tablet formulation with 1.85% error from its nominal content (120 mg/tablet) confirmed the accuracy of the developed method. Spike and interference recovery results of 98.59%, and 95.7-100%, respectively validated the applicability of the developed method for determination of theophylline content in tablet samples.

Dual genetic selection of the theophylline riboswitch with altered aptamer specificity for caffeine.

The aptamer domain of the theophylline riboswitch was randomized to generate a library containing millions of different variants. Dual genetic selection utilizing the cat-upp fusion gene was performed for the library, which successfully led to the identification of a caffeine-specific synthetic riboswitch. When a chloramphenicol-resistance gene was expressed under control of this riboswitch, E. coli cells showed chloramphenicol resistance only in the presence of caffeine. When inserted upstream of the gfpuv or lacZ gene, the caffeine riboswitch induced the expression of green fluorescent protein or ß-galactosidase in the presence of caffeine, respectively. When tested with various concentrations of caffeine, the ß-galactosidase activity was proportional to the amount of caffeine, clearly indicating the caffeine-dependent gene regulation by the caffeine riboswitch.

Synthesis, Identification, and Biological Study for Some Complexes of Azo Dye Having Theophylline.

This article includes the synthesis of heterocyclic azo dye of theophylline by coupling diazonium salt of 4-chloroaniline with theophylline which is, namely, 8-(1-(4-chlorophenyl)azo)theophylline (CPAT). The complexes of cobalt and nickel were prepared by reacting their ions with CPAT ligand in ethanol under 1 : 2 ratio metal-ligand. The CPAT ligand and its complexes were characterized by elemental analysis, infrared spectrometry, electronic absorption spectroscopy, molar conductivity, and magnetic moment. The cobalt and nickel complexes show octahedral geometry having general formula [M(CPAT)2Cl2]. This article addresses the properties of CPAT dye such as photochromic properties. The CPAT dye exhibited obvious and desired changes under irradiation with visible light (405 nm), high sensitive for pH changes which refer to its ability to be analysis indicator. CPAT dye exhibited solvatochromic properties presenting red shift with polar solvent. The CPAT and its complexes show interesting antibiological activities towards Staph. aureus and E. coli bacteria and Aspergillus fungi.

Injection-molded capsule bodies and caps based on polymer blends for controlled drug delivery.

A variety of polymer:polymer blends was used to prepare hot melt extrudates and empty capsules (bodies and caps) by injection-molding using a benchtop extruder (Babyplast). KollidonSR:inulin and Carbothane:inulin blends were investigated. The impact of the blend ratio on the water uptake and dry mass loss kinetics upon exposure to 0.1 MHCl, phosphate buffer pH6.8 and culture medium optionally inoculated with fecal samples from Inflammatory Bowel Disease (IBD) patients were studied. Hot melt extrudates were loaded with up to 60% theophylline, capsules were filled with drug powder. Increasing the inulin content led to increased water uptake and dry mass loss rates, resulting in accelerated drug release from the dosage forms, irrespective of the type of polymer blend. This can be attributed to the higher hydrophilicity/water-solubility of this polymer compared to KollidonSR and Carbothane. Interestingly, the presence of fecal samples in culture medium increased the water uptake and dry mass loss of hot melt extrudates to a certain extent, suggesting partial system degradation by bacterial enzymes. However, these phenomena did not translate into any noteworthy impact of the presence of colonic bacteria on theophylline release from the investigated extrudates or capsules. Hence, drug release can be expected to be independent of the location "small intestine vs. colon" from these dosage forms, which can be advantageous for long term release throughout the entire gastro intestinal tract.

Understanding the Metastability of Theophylline FIII by Means of Low-Frequency Vibrational Spectroscopy.

While theophylline has been extensively studied with multiple polymorphs discovered, there is still currently no conclusive structure for the metastable theophylline form III. In this present work, by combining more widely used techniques such as X-ray diffraction and thermogravimetric analysis with more emerging techniques like low-frequency Raman and terahertz time-domain spectroscopy, to analyze the structure and dynamics of a crystalline system, it was possible to provide further evidence that the form III structure has a theophylline monohydrate structure with the water molecules removed. Solid-state density functional theory simulations were paramount in proving that this proposed structure is correct and explain how vibrational modes within the crystal structures feature and govern polymorphic transitions and the metastable form III. Through the insight provided by both simulated and experimental results, it was possible to decisively conclude the elusive crystal structure of theophylline form III. It was also shown that the correct space group for theophylline monohydrate is not P21/n but, in fact, Pc.

Ultrasound-assisted theophylline polymorphic transformation: Selective polymorph nucleation, molecular mechanism and kinetics analysis.

In this paper, the ultrasound-assisted solvent-mediated polymorphic transformation of theophylline was explored in detail. The induction time and reconstruction time were significantly decreased by ultrasound, thereby decreasing the total transformation time and promoting the transformation process. The ultrasound-promoted efficiency of nucleation was different in three alcoholic solvents, which was difficult to explain by traditional kinetic effects. To resolve the above confusion, binding energies calculated by Density Functional Theory were applied to explore the relationship between the ultrasound-promoted efficiency of nucleation and solute-solvent interactions. Then, a possible molecular self-assembly nucleation pathway affected by ultrasound was proposed: the ultrasound could change and magnify the crucial effect of the specific sites of solute-solvent interactions in the nucleation process. Finally, the transformation kinetics with different effective ultrasonic energies was quantitatively analyzed by Avrami-Erofeev model, indicating that the dissolution element in the rate-limiting step was gradually eliminated by higher ultrasonic energy. Fortunately, the elusive crystal form V could be easily obtained by the ultrasound-assisted polymorph transformation. This proved to be a robust method to produce high purity form V of theophylline. The outcome of this study demonstrated that the proper ultrasonic irradiation had the potential to produce specific polymorphs selectively.

Solvent Screening for Solubility Enhancement of Theophylline in Neat, Binary and Ternary NADES Solvents: New Measurements and Ensemble Machine Learning.

Theophylline, a typical representative of active pharmaceutical ingredients, was selected to study the characteristics of experimental and theoretical solubility measured at 25 °C in a broad range of solvents, including neat, binary mixtures and ternary natural deep eutectics (NADES) prepared with choline chloride, polyols and water. There was a strong synergistic effect of organic solvents mixed with water, and among the experimentally studied binary systems, the one containing DMSO with water in unimolar proportions was found to be the most effective in theophylline dissolution. Likewise, for NADES, the addition of water (0.2 molar fraction) resulted in increased solubility compared to pure eutectics, with the highest solubilisation potential offered by the composition of choline chloride with glycerol. The ensemble of Statistica Automated Neural Networks (SANNs) developed using intermolecular interactions in pure systems has been found to be a very accurate model for solubility computations. This machine learning protocol was also applied as an extensive screening for potential solvents with higher solubility of theophylline. Such solvents were identified in all three subgroups, including neat solvents, binary mixtures and ternary NADES systems. Some methodological considerations of SANNs applications for future modelling were also provided. Although the developed protocol is focused exclusively on theophylline solubility, it also has general importance and can be used for the development of predictive models adequate for solvent screening of other compounds in a variety of systems. Formulation of such a model offers rational guidance for the selection of proper candidates as solubilisers in the designed solvents screening.