Opioid/Dopamine Receptor Binding Studies, NMR and Molecular Dynamics Simulation of LENART01 Chimera, an Opioid-Bombesin-like Peptide.

The design and development of hybrid compounds as a new class of drug candidates remains an excellent opportunity to improve the pharmacological properties of drugs (including enzymatic stability, efficacy and pharmacokinetic and pharmacodynamic profiles). In addition, considering various complex diseases and/or disorders, the conjugate chemistry approach is highly acceptable and justified. Opioids have long been recognized as the most potent analgesics and serve as the basic pharmacophore for potent hybrid compounds that may be useful in pain management. However, a risk of tolerance and physical dependence exists. Since dopamine receptors have been implicated in the aforementioned adverse effects of opioids, the construction of a hybrid with dual action at opioid and dopamine receptors is of interest. Herein, we present nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics simulation results for LENART01, an opioid-ranatensin hybrid peptide. Apart from molecular docking, protein-ligand interactions were also assessed in vitro using a receptor binding assay, which proved LENART01 to be bound to mu-opioid and dopamine receptors, respectively.

Density Functional Theory and Density Functional Tight Binding Studies of Thiamine Hydrochloride Hydrates.

Thiamine hydrochloride (THCL), also known as vitamin B1, is an active pharmaceutical ingredient (API), present on the list of essential medicines developed by the WHO, which proves its importance for public health. THCL is highly hygroscopic and can occur in the form of hydrates with varying degrees of hydration, depending on the air humidity. Although experimental characterization of the THCL hydrates has been described in the literature, the questions raised in previously published works suggest that additional research and in-depth analysis of THCL dehydration behavior are still needed. Therefore, the main aim of this study was to characterize, by means of quantum chemical calculations, the behavior of thiamine hydrates and explain the previously obtained results, including changes in the NMR spectra, at the molecular level. To achieve this goal, a series of DFT (CASTEP) and DFTB (DFTB+) calculations under periodic boundary conditions have been performed, including molecular dynamics simulations and GIPAW NMR calculations. The obtained results explain the differences in the relative stability of the studied forms and changes in the spectra observed for the samples of various degrees of hydration. This work highlights the application of periodic DFT calculations in the analysis of various solid forms of APIs.

The Reaction Mechanism of Loganic Acid Methyltransferase: A Molecular Dynamics Simulation and Quantum Mechanics Study.

In this work, the catalytic mechanism of loganic acid methyltransferase was characterized at the molecular level. This enzyme is responsible for the biosynthesis of loganin, which is a precursor for a wide range of biologically active compounds. Due to the lack of detailed knowledge about this process, the aim of this study was the analysis of the structure and activity of loganic acid methyltransferase. Using molecular dynamics (MD) simulations, the native structure of the complex was reconstructed, and the key interactions between the substrate and loganic acid methyltransferase were investigated. Subsequently, the structures obtained from the simulations were used for quantum chemical (QM) calculations. The QM calculations allowed for the exploration of the energetic aspects of the reaction and the characterization of its mechanism. The results obtained in this study suggest the existence of two patterns of interactions between loganic acid methyltransferase and the substrate. The role of residue Q38 in the binding and orientation of the substrate's carboxyl group was also demonstrated. By employing a combined MD and QM approach, the experimental reaction barrier was reproduced, and detailed insights into the enzymatic activity mechanism of loganic acid methyltransferase were revealed.

17-ß-Estradiol-ß-Cyclodextrin Complex as Solid: Synthesis, Structural and Physicochemical Characterization.

17-ß-estradiol (EST) is the most potent form of naturally occurring estrogens; therefore, it has found a wide pharmaceutical application. The major problem associated with the use of EST is its very low water solubility, resulting in poor oral bioavailability. To overcome this drawback, a complexation with cyclodextrins (CD) has been suggested as a solution. In this work, the host-guest inclusion complex between the ß-CD and EST has been prepared using four different methods. The obtained samples have been deeply characterized using 13C CP MAS solid state NMR, PXRD, FT-IR, TGA, DSC, and SEM. Using SCXRD, the crystal structure of the complex has been determined, being to the best of our knowledge the first solved crystal structure of an estrogen/CD complex. The periodic DFT calculations of NMR properties using GIPAW were found to be particularly helpful in the analysis of disorder in the solid state and interpretation of experimental NMR results. This work highlights the importance of a combined ssNMR/SCXRD approach to studying the structure of the inclusion complexes formed by cyclodextrins.

Solid state 13C NMR spectroscopy as a tool for identification of counterfeit Viagra tablets and guide for develop new identification approach of falsified product.

Counterfeit drugs are a global problem that is directly related to the safety and effectiveness of pharmacotherapy. The black market for counterfeit products is constantly growing and related to the wide availability through online shopping. Therefore, there is a constant need to develop analytical methods that would allow for the unambiguous identification of counterfeit products from the original ones. One of such techniques is solid-state NMR spectroscopy, which allows for direct registration and analysis of spectra of multicomponent solid forms of pharmaceutical formulations. The paper explores the possibility of using this technique in the identification of counterfeit Viagra tablets. In this study, solid-state NMR has been used to detect the non-pharmacopoeial cellulose present in the samples of counterfeit Viagra tablets. Besides, the NMR results allowed to develop a rapid dying technique that can be used to distinguish between the counterfeit and original drug. It has been shown that solid-state NMR spectroscopy allows for numerous analyses such as identification of counterfeit products, assessment of the composition of analyte, estimation of qualitative differences between the original and falsified product, and the development of simple analytical methods based on tablets composition differences.

Catalase Inhibition by Aminoalkanol Derivatives with Potential Anti-Cancer Activity-In Vitro and In Silico Studies Using Capillary Electrophoresis Method.

In this work, the investigation of type and inhibitory strength of catalase by two pairs of aminoalkanol derivatives (1,7 diEthyl- and 1,7-diMethyl-8,9-diphenyl-4-azatricyclo (5.2.1.02.6) dec-8-ene- 3,5,10-trione) has been presented. The obtained results allowed for the determination of all kinetic parameters (Km, Vmax, slope angles of Lineweaver-Burk plots, Ki and IC50) on the basis of which it was shown that all four aminoalkanol derivatives are competitive inhibitors of catalase. However, the strength of action of each of them depends on the type of substituents present in the main structure of the molecule. Subtle differences in the potency of individual derivatives were possible to detect thanks to the developed, sensitive method of capillary electrophoresis, which allowed simultaneous monitoring of the mutual changes in the concentrations of substrates and products of the reaction catalyzed by the enzyme. Detailed values of kinetic parameters showed that all derivatives are weak inhibitors of catalase, which in this case is a big advantage because each inhibition of catalase activity is associated with a greater amount of accumulated, harmful reactive oxygen species. The results of docking studies also show the convergence of the binding energies values of individual inhibitors with all kinetic parameters of the investigated catalase inhibition and thus additionally confirm the weak inhibitory strength of all four aminoalkanol derivatives.

13C CP MAS NMR and DFT Studies of 6-Chromanyl Ethereal Derivatives.

Vitamin E consists of a group of compounds including α- ß- γ- and δ-tocopherols and α- ß- γ- and δ-tocotrienols, containing the chroman-6-ol system. The recognition of the structural and dynamic properties of this system, present in all vitamers, seems to be important for the full explanation of the mechanism of the biological activity of vitamin E. This paper presents results of the structural analysis of the chosen 6-chromanyl ethereal derivatives using experimental (13 C NMR-in solution and solid state, as well as variable temperature experiments; single crystal X-ray diffraction) and theoretical (DFT) methods. For one of the studied compounds, 2,2,5,7,8-pentamethyl-6-((tetrahydro-2H-pyran-2-yl)oxy) chroman, the splitting of some signals was observed in the 13C dynamic NMR spectra. This observation was explained by the application of a conformational analysis and subsequent DFT optimization, followed by the calculation of NMR properties.

Kinetic Studies of Newly Patented Aminoalkanol Derivatives with Potential Anticancer Activity as Competitive Inhibitors of Prostate Acid Phosphatase.

BACKGROUND: Acid phosphatase and its regulation are important objects of biological and clinical research and play an important role in the development and treatment of prostate and bone diseases. The newly patented aminoalkanol (4-[2-hydroxy-3-(propan-2-ylamino)propyl]-1,7-dimethyl-8,9-diphenyl-4-azatricyclo[5.2.1.02,6]dec-8-ene-3,5,10-trione hydrochloride) (I) and (4-[3-(dimethylamino)-2-hydroxypropyl]-1,7-dimethyl-8,9-diphenyl-4-azatricyclo[5.2.1.02,6]dec-8-ene-3,5,10-trione hydrochloride) (II) derivatives have potential anticancer activity, and their influence on enzymatic activity can significantly impact the therapeutic effects of acid phosphatase against many diseases. Therefore, in this study, we investigated the action of compounds (I) and (II) on acid phosphatase. METHODS: Capillary electrophoresis was used to evaluate the inhibition of acid phosphatase. Lineweaver-Burk plots were constructed to compare the Km of this enzyme in the presence of inhibitors (I) or (II) with the Km in solutions without these inhibitors. RESULTS: Compound (I) showed a stronger competitive inhibition against acid phosphatase, whereas derivative (II) showed a weaker competitive type of inhibition. The detailed kinetic studies of these compounds showed that their type and strength of inhibition as well as affinity depend on the kind of substituent occurring in the main chemical molecule. CONCLUSIONS: This study is of great importance because the disclosed inhibition of acid phosphatase by compounds (I) and (II) raises the question of whether these compounds could have any effect on the treatment possibilities of prostate diseases.

Can We Predict the Isosymmetric Phase Transition? Application of DFT Calculations to Study the Pressure Induced Transformation of Chlorothiazide.

Isosymmetric structural phase transition (IPT, type 0), in which there are no changes in the occupation of Wyckoff positions, the number of atoms in the unit cell, and the space group symmetry, is relatively uncommon. Chlorothiazide, a diuretic agent with a secondary function as an antihypertensive, has been proven to undergo pressure-induced IPT of Form I to Form II at 4.2 GPa. For that reason, it has been chosen as a model compound in this study to determine if IPT can be predicted in silico using periodic DFT calculations. The transformation of Form II into Form I, occurring under decompression, was observed in geometry optimization calculations. However, the reverse transition was not detected, although the calculated differences in the DFT energies and thermodynamic parameters indicated that Form II should be more stable at increased pressure. Finally, the IPT was successfully simulated using ab initio molecular dynamics calculations.

A Review on Combination of Ab Initio Molecular Dynamics and NMR Parameters Calculations.

This review focuses on a combination of ab initio molecular dynamics (aiMD) and NMR parameters calculations using quantum mechanical methods. The advantages of such an approach in comparison to the commonly applied computations for the structures optimized at 0 K are presented. This article was designed as a convenient overview of the applied parameters such as the aiMD type, DFT functional, time step, or total simulation time, as well as examples of previously studied systems. From the analysis of the published works describing the applications of such combinations, it was concluded that including fast, small-amplitude motions through aiMD has a noticeable effect on the accuracy of NMR parameters calculations.

In Vitro and In Silico Kinetic Studies of Patented 1,7-diEthyl and 1,7-diMethyl Aminoalkanol Derivatives as New Inhibitors of Acetylcholinesterase.

Two aminoalkanol derivatives of 1,7-diEthyl-8,9-diphenyl-4azatricyclo (5.2.1.02.6) dec-8-ene-3,5,10-trione and two derivatives of 1,7-diMethyl-8,9-diphenyl-4-azatricyclo (5.2.1.02.6) dec-8-ene-3,5,10-trione were evaluated in vitro for their inhibition efficacy of acetylcholinesterase. The Km, Vmax, slope angles of Lineweaver-Burk plots, Ki and IC50 values showed that all four aminoalkanol derivatives are competitive inhibitors of acetylcholinesterase whose inhibitory potency depends, to a varying extent, on the nature of the four different substituents present in the main compound structure. Studies have shown that the most potent acetylcholinesterase inhibitors are derivatives containing isopropylamine and/or methyl substituents in their structure. In contrast, dimethylamine and/or ethyl substituents seem to have a weaker, albeit visible, effect on the inhibitory potency of acetylcholinesterase. Additionally, docking studies suggest that studied compounds binds with the peripheral anionic site and not enter into the catalytic pocket due to the presence of the sterically extended substituent.

Pharmaceutical Hydrates Analysis-Overview of Methods and Recent Advances.

This review discusses a set of instrumental and computational methods that are used to characterize hydrated forms of APIs (active pharmaceutical ingredients). The focus has been put on highlighting advantages as well as on presenting some limitations of the selected analytical approaches. This has been performed in order to facilitate the choice of an appropriate method depending on the type of the structural feature that is to be analyzed, that is, degree of hydration, crystal structure and dynamics, and (de)hydration kinetics. The presented techniques include X-ray diffraction (single crystal X-ray diffraction (SCXRD), powder X-ray diffraction (PXRD)), spectroscopic (solid state nuclear magnetic resonance spectroscopy (ssNMR), Fourier-transformed infrared spectroscopy (FT-IR), Raman spectroscopy), thermal (differential scanning calorimetry (DSC), thermogravimetric analysis (TGA)), gravimetric (dynamic vapour sorption (DVS)), and computational (molecular mechanics (MM), Quantum Mechanics (QM), molecular dynamics (MD)) methods. Further, the successful applications of the presented methods in the studies of hydrated APIs as well as studies on the excipients' influence on these processes have been described in many examples.

Application of Various Molecular Modelling Methods in the Study of Estrogens and Xenoestrogens.

In this review, applications of various molecular modelling methods in the study of estrogens and xenoestrogens are summarized. Selected biomolecules that are the most commonly chosen as molecular modelling objects in this field are presented. In most of the reviewed works, ligand docking using solely force field methods was performed, employing various molecular targets involved in metabolism and action of estrogens. Other molecular modelling methods such as molecular dynamics and combined quantum mechanics with molecular mechanics have also been successfully used to predict the properties of estrogens and xenoestrogens. Among published works, a great number also focused on the application of different types of quantitative structure-activity relationship (QSAR) analyses to examine estrogen's structures and activities. Although the interactions between estrogens and xenoestrogens with various proteins are the most commonly studied, other aspects such as penetration of estrogens through lipid bilayers or their ability to adsorb on different materials are also explored using theoretical calculations. Apart from molecular mechanics and statistical methods, quantum mechanics calculations are also employed in the studies of estrogens and xenoestrogens. Their applications include computation of spectroscopic properties, both vibrational and Nuclear Magnetic Resonance (NMR), and also in quantum molecular dynamics simulations and crystal structure prediction. The main aim of this review is to present the great potential and versatility of various molecular modelling methods in the studies on estrogens and xenoestrogens.

Periodic DFT Calculations-Review of Applications in the Pharmaceutical Sciences.

In the introduction to this review the complex chemistry of solid-state pharmaceutical compounds is summarized. It is also explained why the density functional theory (DFT) periodic calculations became recently so popular in studying the solid APIs (active pharmaceutical ingredients). Further, the most popular programs enabling DFT periodic calculations are presented and compared. Subsequently, on the large number of examples, the applications of such calculations in pharmaceutical sciences are discussed. The mentioned topics include, among others, validation of the experimentally obtained crystal structures and crystal structure prediction, insight into crystallization and solvation processes, development of new polymorph synthesis ways, and formulation techniques as well as application of the periodic DFT calculations in the drug analysis.

Can We Predict the Pressure Induced Phase Transition of Urea? Application of Quantum Molecular Dynamics.

Crystalline urea undergoes polymorphic phase transition induced by high pressure. Form I, which is the most stable form at normal conditions and Form IV, which is the most stable form at 3.10 GPa, not only crystallize in various crystal systems but also differ significantly in the unit cell dimensions. The aim of this study was to determine if it is possible to predict polymorphic phase transitions by optimizing Form I at high pressure and Form IV at low pressure. To achieve this aim, a large number of periodic density functional theory (DFT) calculations were performed using CASTEP. After geometry optimization of Form IV at 0 GPa Form I was obtained, performing energy minimization of Form I at high pressure did not result in Form IV. However, employing quantum molecular isothermal-isobaric (NPT) dynamics calculations enabled to accurately predict this high-pressure transformation. This study shows the potential of different approaches in predicting the polymorphic phase transition and points to the key factors that are necessary to achieve the success.

Application of combined solid-state NMR and DFT calculations for the study of piracetam polymorphism.

Piracetam, a popular nootropic drug, widely used in the treatment of age-associated mental decline and disorders of the nervous system such as Alzheimer's disease and dementia exists under normal pressure in three polymorphic forms (P1, P2 and P3) of different stability. In this work the relative stability of piracetam polymorphs depending on the temperature was studied using the ssNMR spectroscopy combined with ab initio DFT calculations. The ssNMR spectroscopy enabled the analysis of polymorphic phase transition in the case of pure active substance as well as polymorphic form identification in the analysis of the commercial solid dosage formulations. Quantum chemical calculations of phonon density of states were performed to obtain the temperature dependence of the enthalpy, entropy and free energy of the piracetam polymorphs in a quasi-harmonic approximation. GIPAW NMR calculations combined with molecular dynamics were performed to support the chemical shift assignment. The obtained results showed that DFT calculations can be used not only to obtain the NMR parameters but also to predict the influence of the temperature on the stability order of the polymorphic forms of molecular crystals.

Can we predict the structure and stability of molecular crystals under increased pressure? First-principles study of glycine phase transitions.

The aim of this study was to determine whether the periodic density functional theory (DFT) calculations can be used for accurate prediction of the influence of the increased pressure on crystal structure and stability of molecular solids. To achieve this goal a series of geometry optimization and thermodynamic parameters calculations were performed for γ-glycine and δ-glycine structures at different pressure values using CASTEP program. In order to perform most accurate geometry optimization various exchange-correlation functionals defined within generalized gradient approximation (GGA): PBE, PW91, RPBE, WC, PBESOL as well as defined within local density approximation (LDA), i.e. CAPZ, were tested. Geometry optimization was carried out using different dispersion correction methods (i.e. Grimme, TS, OBS) or without them. The linear response density functional perturbation theory (DFPT) was used to obtain the phonon dispersion curves and phonon density of states from which thermodynamic parameters, such as: free energy (ΔG), enthalpy (ΔH) and entropy (ΔS) were evaluated. The results of the geometry optimization depend strongly on the choice of the DFT functional. Calculated differences between the free energy of the studied polymorphic forms at the studied pressure values were consistent with experimental observations on their stability. The computations of thermodynamic properties not only confirmed the order of stability of two studied forms, but also enabled to predict the pressure at which this order is reversed. The results obtained in this study have proven that the plane-wave basis set first principles calculations under periodic conditions is suitable for accurate prediction of crystal structure and stability. © 2018 Wiley Periodicals, Inc.

Does the choice of the crystal structure influence the results of the periodic DFT calculations? A case of glycine alpha polymorph GIPAW NMR parameters computations.

Glycine is a common amino acid with relatively complex chemistry in solid state. Although several polymorphs (α, ß, δ, γ, ε) of crystalline glycine are known, for NMR spectroscopy the most important is a polymorph, which is used as a standard for calibration of spectrometer performance and therefore it is intensively studied by both experimental methods and theoretical computation. The great scientific interest in a glycine results in a large number of crystallographic information files (CIFs) deposited in Cambridge Structural Database (CSD). The aim of this study was to evaluate the influence of the chosen crystal structure of α glycine obtained in different crystallographic experimental conditions (temperature, pressure and source of radiation of α glycine) on the results of periodic DFT calculation. For this purpose the total of 136 GIPAW calculations of α glycine NMR parameters were performed, preceded by the four approaches ("SP", "only H", "full", "full+cell") of structure preparation. The analysis of the results of those computations performed on the representative group of 34 structures obtained at various experimental conditions revealed that though the structures were generally characterized by good accuracy (R < 0.05 for most of them) the results of the periodic DFT calculations performed using the unoptimized structures differed significantly. The values of the standard deviations of the studied NMR parameters were in most cases decreasing with the number of optimized parameters. The most accurate results (of the calculations) were in most cases obtained using the structures with solely hydrogen atoms positions optimized. © 2018 Wiley Periodicals, Inc.

Comparison of the analytical methods (solid state NMR, FT-IR, PXRD) in the analysis of the solid drug forms with low concentration of an active ingredient - 17-ß-estradiol case.

The application of various techniques (FT-IR, PXRD, ssNMR) in the analysis of solid dosage forms with low concentration of an API (17-ß-estradiol hemihydrate, EBHH) was tested. PXRD analysis of Estrofem Mite tablets (EMT) confirmed the presence of the main crystalline excipient, α-lactose monohydrate. In the PXRD pattern of EMT the strong background from polycrystalline excipients, i.e. hydroxypropylmethylcellulose and corn starch was observed. FT-IR spectra were characterized by the broad peaks in the 3000-3600cm-1 region of the OH stretching modes coming from multiple hydrogen bonds that are present in the structures of the excipients (α-lactose monohydrate, corn starch) and API. The only technique which unambiguously confirmed the presence of an API in the EMT was solid state NMR. Despite the tabletting process each of the EMT component retained its characteristic features like relaxation time and T1ρI. Due to the possibility of the manipulation in the experimental registration parameters like recycle delay (RD), evolution time (τ) and contact time (CT) it was possible to perform multiple experiments on the same sample of EMT. The most valuable were the inversion recovery CP experiments in which, by setting the proper values of τ, it was possible to selectively observe the signals of the chosen component of the drug formulation. In this study the great potential of solid state NMR in the analysis of solid dosage forms, as the unique technique that combines the possibility of selective observation of the chosen signals with the non destructive character that enables further analysis of the same sample, was confirmed.