Dual Piperidine-Based Histamine H3 and Sigma-1 Receptor Ligands in the Treatment of Nociceptive and Neuropathic Pain.

In search of new dual-acting histamine H3/sigma-1 receptor ligands, we designed a series of compounds structurally based on highly active in vivo ligands previously studied and described by our team. However, we kept in mind that within the previous series, a pair of closely related compounds, KSK67 and KSK68, differing only in the piperazine/piperidine moiety in the structural core showed a significantly different affinity at sigma-1 receptors (σ1Rs). Therefore, we first focused on an in-depth analysis of the protonation states of piperazine and piperidine derivatives in the studied compounds. In a series of 16 new ligands, mainly based on the piperidine core, we selected three lead structures (3, 7, and 12) for further biological evaluation. Compound 12 showed a broad spectrum of analgesic activity in both nociceptive and neuropathic pain models based on the novel molecular mechanism.

Development of in vivo HDX-MS with applications to a TonB-dependent transporter and other proteins.

Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is a powerful tool that monitors protein dynamics in solution. However, the reversible nature of HDX labels has largely limited the application to in vitro systems. Here, we describe a protocol for measuring HDX-MS in living Escherichia coli cells applied to BtuB, a TonB-dependent transporter found in outer membranes (OMs). BtuB is a convenient and biologically interesting system for testing in vivo HDX-MS due to its controllable HDX behavior and large structural rearrangements that occur during the B12 transport cycle. Our previous HDX-MS study in native OMs provided evidence for B12 binding and breaking of a salt bridge termed the Ionic Lock, an event that leads to the unfolding of the amino terminus. Although purified OMs provide a more native-like environment than reconstituted systems, disruption of the cell envelope during lysis perturbs the linkage between BtuB and the TonB complex that drives B12 transport. The in vivo HDX response of BtuB's plug domain (BtuBp) to B12 binding corroborates our previous in vitro findings that B12 alone is sufficient to break the Ionic Lock. In addition, we still find no evidence of B12 binding-induced unfolding in other regions of BtuBp that could enable B12 passage. Our protocol was successful in reporting on the HDX of several endogenous E. coli proteins measured in the same measurement. Our success in performing HDX in live cells opens the possibility for future HDX-MS studies in a native cellular environment. IMPORTANCE: We present a protocol for performing in vivo HDX-MS, focusing on BtuB, a protein whose native membrane environment is believed to be mechanistically important for B12 transport. The in vivo HDX-MS data corroborate the conclusions from our previous in vitro HDX-MS study of the allostery initiated by B12 binding. Our success with BtuB and other proteins opens the possibility for performing additional HDX-MS studies in a native cellular environment.

HDX-MS performed on BtuB in E. coli outer membranes delineates the luminal domain's allostery and unfolding upon B12 and TonB binding.

To import large metabolites across the outer membrane of gram-negative bacteria, TonB-dependent transporters (TBDTs) undergo significant conformational change. After substrate binding in BtuB, the Escherichia coli vitamin B12 TBDT, TonB binds and couples BtuB to the inner-membrane proton motive force that powers transport [N. Noinaj, M. Guillier, T. J. Barnard, S. K. Buchanan, Annu. Rev. Microbiol. 64, 43­60 (2010)]. However, the role of TonB in rearranging the plug domain of BtuB to form a putative pore remains enigmatic. Some studies focus on force-mediated unfolding [S. J. Hickman, R. E. M. Cooper, L. Bellucci, E. Paci, D. J. Brockwell, Nat. Commun. 8, 14804 (2017)], while others propose force-independent pore formation by TonB binding [T. D. Nilaweera, D. A. Nyenhuis, D. S. Cafiso, eLife 10, e68548 (2021)], leading to breakage of a salt bridge termed the "Ionic Lock." Our hydrogen­deuterium exchange/mass spectrometry (HDX-MS) measurements in E. coli outer membranes find that the region surrounding the Ionic Lock, far from the B12 site, is fully destabilized upon substrate binding. A comparison of the exchange between the B12-bound and the B12+TonB­bound complexes indicates that B12 binding is sufficient to unfold the Ionic Lock region, with the subsequent binding of a TonB fragment having much weaker effects. TonB binding accelerates exchange in the third substrate-binding loop, but pore formation does not obviously occur in this or any region. This study provides a detailed structural and energetic description of the early stages of B12 passage that provides support both for and against current models of the transport process.

International Regulatory Collaboration on the Analysis of Nitrosamines in Metformin-Containing Medicines.

Recalls of some batches of metformin have occurred due to the detection of N-nitrosodimethylamine (NDMA) in amounts above the acceptable intake (AI) of 96 ng per day. Prior to the recalls, an international regulatory laboratory network had been monitoring drugs for nitrosamine impurities with each laboratory independently developing and validating multiple analytical procedures to detect and measure nitrosamines in metformin drugs used in their jurisdictions. Here, we provide an overview of the analysis of metformin active pharmaceutical ingredients (APIs) and drug products with 1090 samples (875 finished dosage forms (FDFs) and 215 API samples) tested beginning in November of 2019 through July of 2020. Samples were obtained internationally by a variety of approaches, including purchased, received from firms via information requests or selected by regional regulatory authorities (either at wholesalers or during GMP inspections). Only one nitrosamine (NDMA) was detected and was only present in some batches of metformin products. For API samples, 213 out of 215 lots tested had no measurable level of NDMA. For FDF samples tested, the number of batches with NDMA above the AI amount for patient safety was 17.8% (156/875). Based on these data, although the presence of NDMA was of concern, 82.2% of the samples of metformin drug products tested met quality and safety standards for patients. Regulatory agencies continue to collaborate extensively and work with marketing authorization holders to understand root causes of nitrosamine formation and agree on corrective actions to mitigate the presence of NDMA in future metformin batches.

Separation of menaquinone-7 geometric isomers by semipreparative high-performance liquid chromatography with silver complexation and identification by nuclear magnetic resonance.

Dietary supplements containing vitamin K2 are often used to prevent osteoporosis, vascular calcification and coronary heart disease. It has been shown that some of these products contain a mixture of menaquinone-7 geometric isomers. Since the geometric shape may influence biological activity, there was a need for a semipreparative method to isolate single compounds for further studies. Here, we present an argentation chromatographic method for the separation of menaquinone-7 isomers and an nuclear magnetic resonance (NMR) methodology for the configuration assignment of isoprenoid side chain. The DFT calculations were performed to determine more energetically favorable complexes between the cis or trans menaquinone-7 isomers and the silver cation. Seventeen components were resolved, and fractions were collected and subjected to NMR study. Structures and chemical shifts for thirteen new compounds were assigned, and the identity of three known compounds was confirmed.

Synthesis of Oxidized 3ß,3'ß-Disteryl Ethers and Search after High-Temperature Treatment of Sterol-Rich Samples.

It was proven that sterols subjected to high-temperature treatment can be concatenated, which results in polymeric structures, e.g., 3ß,3'ß-disteryl ethers. However, it was also proven that due to increased temperature in oxygen-containing conditions, sterols can undergo various oxidation reactions. This study aimed to prove the existence and perform quantitative analysis of oxidized 3ß,3'ß-disteryl ethers, which could form during high-temperature treatment of sterol-rich samples. Samples were heated at 180, 200 and 220 °C for 0.5 to 4 h. Quantitative analyses of the oxidized 3ß,3'ß-disteryl ethers were performed with liquid extraction, solid-phase extraction and liquid chromatography coupled with mass spectrometry. Additionally, to perform this analysis, the appropriate standards of all oxidized 3ß,3'ß-disteryl ethers were prepared. Eighteen various oxidized 3ß,3'ß-disteryl ethers (derivatives of 3ß,3'ß-dicholesteryl ether, 3ß,3'ß-disitosteryl ether and 3ß,3'ß-distigmasteryl ether) were prepared. Additionally, the influence of metal compounds on the mechanism of ether formation at high temperatures was investigated.

N-Nitrosodimethylamine Contamination in the Metformin Finished Products.

A GC-MS/MS method with EI ionization was developed and validated to detect and quantify N-nitrosodimethylamine (NDMA) and seven other nitrosamines in 105 samples of metformin tablets from 13 different manufactures. Good linearity for each compound was demonstrated over the calibration range of 0.5-9.5 ng/mL. The assay for all substances was accurate and precise. NDMA was not detected in the acquired active pharmaceutical ingredient (API); however, NDMA was detected in 64 (85.3%) and 22 (91.7%) of the finished product and prolonged finished product samples, respectively. European Medicines Agency recommends the maximum allowed limit of 0.032 ppm in the metformin products. Hence, 28 finished products and 7 pronged dosage products were found to exceed the acceptable limit of daily intake of NDMA contamination. The implications of our findings for the testing of pharmaceutical products are discussed.

Synthesis and search for 3ß,3'ß-disteryl ethers after high-temperature treatment of sterol-rich samples.

It has been proven that at increased temperature, sterols can undergo various chemical reactions e.g., oxidation, dehydrogenation, dehydration and polymerisation. The objectives of this study are to prove the existence of dimers and to quantitatively analyse the dimers (3ß,3'ß-disteryl ethers). Sterol-rich samples were heated at 180 °C, 200 °C and 220 °C for 1 to 5 h. Quantitative analyses of the 3ß,3'ß-disteryl ethers were conducted using liquid extraction, solid-phase extraction and gas chromatography coupled with mass spectrometry. Additionally, for the analyses, suitable standards were synthetized from native sterols. To identify the mechanism of 3ß,3'ß-disteryl ether formation at high temperatures, an attempt was made to use the proposed synthesis method. Additionally, due to the association of sterols and sterol derivatives with atherosclerosis, preliminary studies with synthetized 3ß,3'ß-disteryl ethers on endothelial cells were conducted.

Commonly used FRET fluorophores promote collapse of an otherwise disordered protein.

The dimensions that unfolded proteins, including intrinsically disordered proteins (IDPs), adopt in the absence of denaturant remain controversial. We developed an analysis procedure for small-angle X-ray scattering (SAXS) profiles and used it to demonstrate that even relatively hydrophobic IDPs remain nearly as expanded in water as they are in high denaturant concentrations. In contrast, as demonstrated here, most fluorescence resonance energy transfer (FRET) measurements have indicated that relatively hydrophobic IDPs contract significantly in the absence of denaturant. We use two independent approaches to further explore this controversy. First, using SAXS we show that fluorophores employed in FRET can contribute to the observed discrepancy. Specifically, we find that addition of Alexa-488 to a normally expanded IDP causes contraction by an additional 15%, a value in reasonable accord with the contraction reported in FRET-based studies. Second, using our simulations and analysis procedure to accurately extract both the radius of gyration (Rg) and end-to-end distance (Ree) from SAXS profiles, we tested the recent suggestion that FRET and SAXS results can be reconciled if the Rg and Ree are "uncoupled" (i.e., no longer simply proportional), in contrast to the case for random walk homopolymers. We find, however, that even for unfolded proteins, these two measures of unfolded state dimensions remain proportional. Together, these results suggest that improved analysis procedures and a correction for significant, fluorophore-driven interactions are sufficient to reconcile prior SAXS and FRET studies, thus providing a unified picture of the nature of unfolded polypeptide chains in the absence of denaturant.

Oxysterols as a biomarker in diseases.

Cholesterol is one of the most important chemical substances as a structural element in human cells, and it is very susceptible to oxidation reactions that form oxysterol. Oxysterols exhibit almost the exact structure as cholesterol and a cholesterol precursor (7-dehydrocholesterol) with an additional hydroxyl, epoxy or ketone moiety. The oxidation reaction is performed via an enzymatic or non-enzymatic mechanism. The wide array of enzymatic oxysterols encountered in the human body varies in origin and function. Oxysterols establish a concentration equilibrium in human body fluids. Disease may alter the equilibrium, and oxysterols may be used as a diagnostic tool. The current review presents the possibility of using non-enzymatic oxysterols and disturbances in enzymatic oxysterol equilibrium in the human body as a potential biomarker for diagnosing and/or monitoring of the progression of various diseases.

Response to Comment on "Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water".

Best et al claim that we provide no convincing basis to assert that a discrepancy remains between FRET and SAXS results on the dimensions of disordered proteins under physiological conditions. We maintain that a clear discrepancy is apparent in our and other recent publications, including results shown in the Best et al comment. A plausible origin is fluorophore interactions in FRET experiments.

Analysis of Menaquinone-7 Content and Impurities in Oil and Non-Oil Dietary Supplements.

Rapid, global technological development has caused the food industry to use concentrated food component sources like dietary supplements ever more commonly as part of the human diet. This study analysed the menaquinone-7 (MK-7) content of dietary supplements in oil capsule and hard tablet forms. A novel method for separating and measuring geometric isomers of MK-7 in dietary supplements was developed and validated. Eleven different isomers of cis/trans- menaquinone-7 were identified. Identification of cis/trans isomers was performed by combination of HPLC, UPLC and HRMS-QTOF detection, whereas their quantities were determined by DAD detection. The content of menaquinone impurities was ascertained, including cis/trans- menaquinone-6 isomers (5.5⁻16.9 µg per tablet/capsule) and cis/trans-menaquinone-7 isomers (70.9⁻218.7 µg tablet/capsule), which were most likely formed during the chemical synthesis of the menaquinone-7. The all-trans MK-7 content was lower than the isomeric form and often lower than what the labels declared. A new method of quantification, developed and validated for menaquinones in oil capsules, provided on average 90% recovery and a limit of quantification (LOQ) of approximately 1 µg mL−1.

Gold-capped silicon for ultrasensitive SERS-biosensing: Towards human biofluids analysis.

Surface-enhanced Raman spectroscopy (SERS) has been widely used in a variety of biomedical, analytical, forensic and environmental investigations due to its chemical specificity, label-free nature combined with high sensitivity. Here, we report a simple method for the fabrication of reproducible and reliable, well-defined, stable SERS substrates with uniform and giant Raman enhancement suitable for routine trace chemical analysis and detection of biological compounds in complex biological fluids. We prepared porous silicone (PS) surface by a galvanostatic anodic etch of crystalline silicon wafers. The electrochemical process generates a specific layer of PS: the thickness and porosity of a given layer is controlled by the current density, the duration of the etch cycle, and the composition of the etchant solution. These substrates presented high sensitivity to p-mercaptobenzoic acid (p-MBA) at a low concentration of 10-6M and the enhancement factor of over 108 was achieved. Such high enhancement is attributed to semiconducting silicon-induced and stabilized hot spots. The uniform distribution of SERS-active 'hot-spots' on the Au/Si surface results in high reproducibility towards detecting p-MBA at 40 different, randomly selected positions on a single substrate (RSD=6.7%) and on twenty different SERS substrates prepared under identical conditions (RSD=8%). Designed substrates allow the ultrahigh sensitive and specific detection of human such biofluids as blood, urine and cerebrospinal fluid (CSF) in a reliable, label-free, and reproducible manner. The SERS spectra of these fluids are rich in patient-specific information and can be useful in many analytical and biomedical applications. We have shown that our developed SERS substrates allow the nanomolar detection of neopterin (bacterial infections' marker) in cerebrospinal fluid samples. In order to test the performance of our SERS method in term of low detection limit (LOD), the calibration curve i.e. plot of SERS intensity of the marker band at 695cm-1 versus the concentration of neopterin in CSF was constructed and used to calculate the neopterin concentration in clinical samples. The level of neopterin was significantly higher in CSF samples infected by Neisseria meningitidis, (54nmol/L), compared to normal (control) group, (4.3nmol/L). The high sensitivity, selectivity and stability of obtained SERS-active substrates combined with simple, low-cost, and easy method of producing offer a promising tool for SERS-based analysis in clinical trials.

Identification of cis/trans isomers of menaquinone-7 in food as exemplified by dietary supplements.

For the first time, the cis/trans isomer content of menaquinone-7 in food products has been identified and marked. A novel method of marking isomers of vitamin K2MK-7 in dietary supplements was developed and validated. Five different isomers of cis/trans vitamin K2MK-7 were identified. Identification of cis/trans isomers was performed by HRMS-QTOF, whereas their quantities were determined by using CAD and DAD detectors. In the majority of cases, the content of biologically active all trans vitamin K2MK-7 was below its declared content. The content of all trans K2MK-7 was in the range between 5.5 and 49 µg in pills. In one of the studied supplements, this vitamin was not found, regardless of the claim on the product label. The content of cis/trans isomers in certain dietary supplements exceeded the content of all trans K2MK-7 by up to 3.7 times.

Application of hydrophilic interaction liquid chromatography for the quantification of succinylcholine in Active Pharmaceutical Ingredient and medicinal product. Identification of new impurities of succinylcholine chloride.

A new method, using hydrophilic interaction chromatography (HILIC), for quantification of succinylcholine and impurities in Active Pharmaceutical Ingredient (API), as well as in the medicinal product, was developed. Additionally, the new impurities in API were discovered using ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-QTOF) technique. The substances were quantified with the application of a UV detector (λ = 214 nm). Chromatographic separation was performed isocratically with the application of 30% phosphate buffer (pH 4,0; 0.05 M) in ACN as a mobile phase. A major feature of the developed method is a very high resolution (Rs > 3), between succinylcholine and its main impurity - succinylmonocholine, whereas the width of peak bands does not exceed 0.7 min. A low value of limits of detection (LOD) were obtained for succinic acid, succinylmonocholine and for succinylcholine, which amounted to 2.4, 6.0 and 11.5 µg ml-1, respectively. Another feature of the developed method is linearity in a very wide range of concentrations: 7.3 µg ml-1 - 670 µg ml-1 amounting to R2 = 0.999. The recovery provided by this method at three different fortification levels for all analytes remained within the following range: 95.7 - 98.9 %. Intra-day and inter-day precision remained within the following range: 1.0 - 5.9 % coefficient of variation (CV), whereas accuracy within the range: -1.3 - 6.3. The developed method of hydrophilic interactions made it possible to quantify two new impurities, probably originating from the synthesis of an API: [2-(trimethylaminium)ethyl]-[2'-(trimethylaminium)vinyl] succinate and [2-(dimethylamino)etyl]-[2'-(trimethylaminium)etyl] succinate, which were identified and described for the first time. In addition, a physicochemical form of peak doublet described in the USP as impurities was studied and it was demonstrated that these peaks are the result of the specific physicochemical interactions in ion pair chromatography.

Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water.

A substantial fraction of the proteome is intrinsically disordered, and even well-folded proteins adopt non-native geometries during synthesis, folding, transport, and turnover. Characterization of intrinsically disordered proteins (IDPs) is challenging, in part because of a lack of accurate physical models and the difficulty of interpreting experimental results. We have developed a general method to extract the dimensions and solvent quality (self-interactions) of IDPs from a single small-angle x-ray scattering measurement. We applied this procedure to a variety of IDPs and found that even IDPs with low net charge and high hydrophobicity remain highly expanded in water, contrary to the general expectation that protein-like sequences collapse in water. Our results suggest that the unfolded state of most foldable sequences is expanded; we conjecture that this property was selected by evolution to minimize misfolding and aggregation.

Role of thiamine in Huntington's disease pathogenesis: In vitro studies.

BACKGROUND: Oxidative stress accompanies neurodegeneration and also causes abnormalities in thiaminedependent processes. These processes have been reported to be diminished in the brains of patients with several neurodegenerative diseases. OBJECTIVES: The aim of this work was to conduct a comparative analysis of the impact of supplemented thiamine on the viability of human B lymphocytes with CAG abnormal expanded huntingtin gene (mHTT) (GM13509) and control, B lymphocytes without mHTT (GM14467) through the following studies: determination of the supplemented thiamine concentrations, which are effective for cell growth stimulation after incubation in thiamine deficit conditions; determination of cell capability to intake the exogenous thiamine; evaluation of exogenous thiamine influence on the profile of the genes related to thiamine and energy metabolism; determination of ATP synthesis and activities of thiamine-dependent enzymes, KGDHC and BCKDHC in the intact cells and upon the exogenous thiamine. MATERIAL AND METHODS: The following methods were used: EZ4U test for cell growth analysis; HPLC for determination of thiamine intake and ATP synthesis, qRT-PCR for evaluation of the gene profiles and spectrophotometric method for KGDHC and BCKDHC activities determination. RESULTS: Maximal cell growth stimulation was observed at 2.5 mM in GM14467 up to 135% of the control culture and at 5.0 mM in GM13509 cells up to 165% of the control culture. Native levels of total ATP and KGDHC and BCKDHC activities in both cell types were comparable and did not changed upon thiamine deficit or supplementation. GM13509 cells showed more of an increase in growth stimulation upon thiamine supplementation than GM14467 cells and this effect was reflected in the increase of intracellular thiamine concentration. CONCLUSIONS: The above results and reported changes in expression of GAPDH, IDH1 and SLC19A3 genes observed upon thiamine deficit conditions suggest that intracellular thiamine status and energy metabolism can have a role in HD pathogenesis.

Current knowledge on the mechanism of atherosclerosis and pro-atherosclerotic properties of oxysterols.

Due to the fact that one of the main causes of worldwide deaths are directly related to atherosclerosis, scientists are constantly looking for atherosclerotic factors, in an attempt to reduce prevalence of this disease. The most important known pro-atherosclerotic factors include: elevated levels of LDL, low HDL levels, obesity and overweight, diabetes, family history of coronary heart disease and cigarette smoking. Since finding oxidized forms of cholesterol - oxysterols - in lesion in the arteries, it has also been presumed they possess pro-atherosclerotic properties. The formation of oxysterols in the atherosclerosis lesions, as a result of LDL oxidation due to the inflammatory response of cells to mechanical stress, is confirmed. However, it is still unknown, what exactly oxysterols cause in connection with atherosclerosis, after gaining entry to the human body e.g., with food containing high amounts of cholesterol, after being heated. The in vivo studies should provide data to finally prove or disprove the thesis regarding the pro-atherosclerotic prosperities of oxysterols, yet despite dozens of available in vivo research some studies confirm such properties, other disprove them. In this article we present the current knowledge about the mechanism of formation of atherosclerotic lesions and we summarize available data on in vivo studies, which investigated whether oxysterols have properties to cause the formation and accelerate the progress of the disease. Additionally we will try to discuss why such different results were obtained in all in vivo studies.

Structural Basis for Multi-specificity of MRG Domains.

Chromatin-binding proteins play vital roles in the assembly and recruitment of multi-subunit complexes harboring effector proteins to specific genomic loci. MRG15, a chromodomain-containing chromatin-binding protein, recruits diverse chromatin-associated complexes that regulate gene transcription, DNA repair, and RNA splicing. Previous studies with Pf1, another chromatin-binding subunit of the Sin3S/Rpd3S histone deacetylase complex, defined the sequence and structural requirements for interactions with the MRG15 MRG domain, a common target of diverse subunits in the aforementioned complexes. We now show that MRGBP, a member of the Tip60/NuA4 histone acetyltransferase complex, engages the same two surfaces of the MRG domain as Pf1. High-affinity interactions occur via a bipartite structural motif including an FxLP sequence motif. MRGBP shares little sequence and structural similarity with Pf1, yet targets similar pockets on the surface of the MRG domain, mimicking Pf1 in its interactions. Our studies shed light onto how MRG domains have evolved to bind diverse targets.