The NMR chemical shift pH measurement revisited: analysis of error and modeling of a pH dependent reference

The influence of pH on the adhesive performance of phosphoric ester monomers with zirconia

OBJECTIVE

Functional phosphoric ester monomers containing primers have been widely used in dental adhesives. This study aims to analyze the atomic-level interaction between zirconia and phosphoric ester monomers under different pH conditions (acidic or neutral).

METHODS

Solid-state 31P NMR spectroscopy was employed to investigate the binding interactions between two types of phosphoric ester monomers-glycerophosphate-dimethacrylate (GPDM) and 10-methacryloyloxydecyl dihydrogen phosphate (MDP)-with zirconia under varying pH conditions. Contact angles were measured on the zirconia surfaces with and without the application of phosphoric ester monomers. Additionally, tensile bond strength (TBS) tests were conducted to determine the effects of different phosphoric ester monomer-containing primers under different pH conditions on zirconia.

RESULTS

Solid-state 31P NMR spectroscopy revealed that both GPDM and MDP exhibited broadened peaks, positioned differently from their unreacted forms, indicating that the environment surrounding the phosphate groups in both GPDM and MDP changed upon adhesion to zirconia at the atomic level. Acidic MDP may form covalent bonds with zirconia through additional esterification on the zirconia surface. MDP-primed zirconia demonstrated a higher contact angle than GPDM-primed zirconia. The highest TBS was observed in the group of MDP reacted with zirconia under acidic conditions.

SIGNIFICANCE

These findings suggest that phosphoric ester monomers, particularly MDP in acidic conditions, can chemically bind to zirconia, contributing to enhanced adhesion behavior.

Investigation of pH-dependent 1H NMR urine metabolite profiles for diagnosis of obesity-related disordering

BACKGROUND

Human urine is highly favorable for 1H NMR metabolomics analyses of obesity-related diseases, such as non-alcoholic fatty liver, type 2 diabetes, and hyperlipidemia (HL), due to its non-invasiveness and ease of large-scale collection. However, the wide range of intrinsic urine pH (5.5-8.5) results in inevitably chemical shift and signal intensity modulations in the 1H NMR spectra. For patients where acidic urine pH is closely linked to obesity-related disease phenotypes, the pH-dependent modulations complicate the spectral analysis and deteriorate quantifications of urine metabolites.

METHODS

We characterized human urine metabolites by NMR at intrinsic urine pH, across urine pH 4.5 to 9.5, to account for pH-dependent modulations. A pH-dependent chemical shift database for quantifiable urine metabolites was generated and integrated into a "pH intelligence" program developed for quantifications of pH-dependent modulations at various pH. The 1H NMR spectra of urines collected from patients with Ob-HL and healthy controls were compared to uncover potential metabolic biomarkers of Ob-HL disease.

RESULTS

Three urine metabolites were unveiled by pH-dependent NMR approach, i.e., TMAO, glycine, and pyruvic acid, with VIP score >1.0 and significant q-value < 0.05, that represent as potential biomarkers for discriminating Ob-HL from healthy controls. Further ROC-AUC analyses revealed that TMAO alone achieved the highest diagnostic accuracy (AUC 0.902), surpassed to that obtained by neutralizing pH approach (AUC 0.549) and enabled better recovering potential urine metabolites from the Ob-HL disease phenotypes.

CONCLUSIONS

We concluded that 1H NMR-derived urine metabolite profile represents a snapshot that can reveal the physiological condition of humans in either a healthy or diseased state under intrinsic urine pH. We demonstrated a systematic analysis of pH-dependent modulations on the human urine metabolite signals and further developed software for quantification of urine metabolite profiles with high accuracy, enabling the uncovering of potential metabolite biomarkers in clinical diagnosis applications.

MetAssimulo 2.0: a web app for simulating realistic 1D and 2D metabolomic 1H NMR spectra

MOTIVATION

Metabolomics extensively utilizes nuclear magnetic resonance (NMR) spectroscopy due to its excellent reproducibility and high throughput. Both 1D and 2D NMR spectra provide crucial information for metabolite annotation and quantification, yet present complex overlapping patterns which may require sophisticated machine learning algorithms to decipher. Unfortunately, the limited availability of labeled spectra can hamper application of machine learning, especially deep learning algorithms which require large amounts of labeled data. In this context, simulation of spectral data becomes a tractable solution for algorithm development.

RESULTS

Here, we introduce MetAssimulo 2.0, a comprehensive upgrade of the MetAssimulo 1.b metabolomic 1H NMR simulation tool, reimplemented as a Python-based web application. Where MetAssimulo 1.0 only simulated 1D 1H spectra of human urine, MetAssimulo 2.0 expands functionality to urine, blood, and cerebral spinal fluid, enhancing the realism of blood spectra by incorporating a broad protein background. This enhancement enables a closer approximation to real blood spectra, achieving a Pearson correlation of approximately 0.82. Moreover, this tool now includes simulation capabilities for 2D J-resolved (J-Res) and Correlation Spectroscopy spectra, significantly broadening its utility in complex mixture analysis. MetAssimulo 2.0 simulates both single, and groups, of spectra with both discrete (case-control, e.g. heart transplant versus healthy) and continuous (e.g. body mass index) outcomes and includes inter-metabolite correlations. It thus supports a range of experimental designs and demonstrating associations between metabolite profiles and biomedical responses.By enhancing NMR spectral simulations, MetAssimulo 2.0 is well positioned to support and enhance research at the intersection of deep learning and metabolomics.

AVAILABILITY AND IMPLEMENTATION

The code and the detailed instruction/tutorial for MetAssimulo 2.0 is available at https://github.com/yanyan5420/MetAssimulo_2.git. The relevant NMR spectra for metabolites are deposited in MetaboLights with accession number MTBLS12081.

Determination of the pKa and Concentration of NMR-Invisible Molecules and Sites Using NMR Spectroscopy

NMR spectroscopy is a very powerful tool for measuring the dissociation constants (pKa) of molecules, requiring smaller quantities of samples of lower purity relative to potentiometric or conductometric methods. However, current approaches are generally limited to those molecules possessing favorable pH-dependent NMR properties. Typically, a series of 1D experiments at varying pH are performed, and the pKa is obtained by fitting the observed chemical shift of the analyte as a function of pH using nonlinear routines. However, the majority of polymers, biomolecules, and inorganic species do not present favorable NMR resonances. Either the resonances are not observable or too broad, or the unambiguous interpretation of the NMR data is impossible without resorting to complex 2D experiments due to spectral overlap. To overcome these fundamental limitations, we present a method to obtain the pKa values and concentrations of acidic species without their direct observation by NMR. We instead determine the quantity of acidic protons removed from the species along a concentration gradient of an organic base in a single 1H chemical shift imaging experiment that can be run under automation. The pKa values are determined via simple linear plots, avoiding complex and potentially unreliable nonlinear fitting routines.

Quantification of Residual Water in Pharmaceutical Frozen Solutions Via 1H Solid-State NMR

Freezing is essential for the stability of biological drug substances and products, particularly in frozen solution formulations and during the primary drying of lyophilized preparations. However, the unfrozen segment within the frozen matrix can alter solute concentration, ionic strength, and stabilizer crystallization, posing risks of increased biophysical instability and faster chemical degradation. While quantifying the unfrozen water content is important for designing stable biopharmaceuticals, there is a lack of analytical techniques for in situ quantitative measurements. In this study, we introduce a 1H magic angle spinning NMR technique to identify the freezing point (Tice) and quantify mobile water content in frozen biologics, applying this method to analyze the freezing of a commercial high-concentration drug product, Dupixent®. Our results demonstrate that water freezing is influenced by buffer salt properties and formulation composition, including the presence of sugar cryoprotectants and protein concentration. Additionally, the 1H chemical shift can probe pH in the unfrozen phase, potentially predicting the microenvironmental acidity in the frozen state. Our proposed methodology provides fresh insights into the analysis of freeze-concentrated solutions, enhancing our understanding of the stability of frozen and lyophilized biopharmaceuticals.

A pH-enhanced resolution in benchtop NMR spectroscopy

NMR spectroscopy is one of the most potent methods in analytical chemistry. NMR titration experiments are particularly useful since they measure molecular binding affinities and other concentration-dependent effects. These experiments, however, require a long series of measurements. An alternative to these serial measurements has recently been presented, exploiting a pH (or generally - a concentration) gradient along the NMR tube. The proposed experiment, although efficient, was based on the sensitivity- and hardware-demanding chemical shift imaging (CSI) method. Thus, it is practically limited to high-resolution NMR spectrometers. This paper proposes modifying and adapting the approach to the popular and cost-efficient benchtop NMR machines. Instead of CSI, we use a device that shifts the NMR tube vertically to measure the spectra of different sample volumes, which have different pH values due to the established gradient along the tube. We demonstrate the potential of the method on the test samples of L-tyrosine and 2,6-lutidine, and two real samples from the food industry - an infant formula and an energy drink. The proposed method boosts spectral resolution and allows for the sampling of a broader range of pH values when compared to the original approach.

Measurement of the pKa Values of Organic Molecules in Aqueous-Organic Solvent Mixtures by 1H NMR without External Calibrants

Aqueous-organic solvent mixtures are commonly used for reactions or analyses, where the components of a system are insoluble in pure water. The acid dissociation constant is an important property to measure in these media as it determines the charge state, solubility, and reactivity of a molecule. While NMR spectroscopy is an established tool for the measurement of pKa in water, its use in aqueous-organic solvents is greatly hindered by the requirement for external calibrants on which a working pH scale is set. Such calibrants include buffer solutions, "anchor" molecules with known pKa values, and pH electrodes that have undergone lengthy calibration procedures in the solvent mixture of interest. However, such calibrations are often inconvenient to perform, while literature pKa data covering the required range may not be available at the solvent composition or the temperature of interest. Here, we present a method to determine pKa in aqueous-organic solvents directly by NMR. We first determine pKa of an organic acid such as 2,6-dihydroxybenzoic acid (2,6-DHB) by measuring its 1H chemical shift as a function of concentration along a concentration gradient using chemical shift imaging (CSI). Using 2,6-DHB as a reference, we then determine pKa of less acidic molecules in single CSI experiments via the variation of their 1H chemical shifts along pH gradients. As proof of concept, we determine the pKa values of organic acids and bases up to pKa 10 in 50% (v/v) 1-propanol/water, 50% (v/v) dimethyl sulfoxide/water, and 30% (v/v) acetonitrile/water and obtain good agreement with the literature values.

In-cell NMR: Why and how?

NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.

Potential of multiparametric characterization of foodstuffs by nuclear magnetic resonance to better predict microbial behavior

Numerous predictive microbiology models have been proposed to describe bacterial population behaviors in foodstuffs. These models depict the growth kinetics of particular bacterial strains based on key physico-chemical parameters of food matrices and their storage temperature. In this context, there is a prominent issue to accurately characterize these parameters, notably pH, water activity (a_w ), and NaCl and organic acid concentrations. Usually, all these product features are determined using one destructive analysis per parameter at macroscale (>5 g). Such approach prevents an overall view of these characteristics on a single sample. Besides, it does not take into account the intra-product microlocal variability of these parameters within foods. Nuclear magnetic resonance (NMR) is a versatile non-invasive spectroscopic technique. Experiments can be recorded successively on a same collected sample without damaging it. In this work, we designed a dedicated NMR approach to characterize the microenvironment of foods using 10-mg samples. The multiparametric mesoscopic-scale approach was validated on four food matrices: a smear soft cheese, cooked peeled shrimps, cold-smoked salmon, and smoked ham. Its implementation in situ on salmon fillets enabled to observe the intra-product heterogeneity and to highlight the impact of process on the spatial distribution of pH, NaCl, and organic acids. This analytical development and its successful application can help address the shortcomings of monoparametric methods traditionally used for predictive microbiology purposes.

Efficient pKa Determination in a Nonaqueous Solvent Using Chemical Shift Imaging

pK_a is an important property of a molecule which impacts many fields, such as drug design, catalysis, reactivity, and environmental toxicity. It is often necessary to measure pK_a in nonaqueous media due to the poor solubility of an analyte in water, for example, many compounds of pharmaceutical interest. Although NMR methods to measure pK_a in water are well established, determining pK_a in organic solvents is laborious and problematic. We present an efficient one-shot method to determine the pK_a of an analyte in an organic solvent in a single measurement. Diffusion of an acid into a basic solution of the analyte and a set of pH indicators establishes a pH gradient in the NMR tube. The chemical shift of a pH sensitive resonance of the analyte and the pH of the solution are then determined simultaneously as a function of position along the pH gradient by recording a chemical shift image of the NMR tube. The pK_a of the analyte is then determined using the Henderson-Hasselbalch equation. The method can be implemented in any laboratory with a gradient equipped NMR high-field spectrometer and is demonstrated for a range of pharmaceutical compounds and inorganic phosphazene bases.

Influence of Electronic Modulation of Phenanthroline-Derived Ligands on Separation of Lanthanides and Actinides

The solvent extraction, complexing ability, and basicity of tetradentate N-donor 2,9-bis(5,5,8,8-tetramethyl-5,6,7,8-tetrahydro-1,2,4-benzotriazin-3-yl)-1,10-phenanthroline (CyMe4-BT- Phen) and its derivatives functionalized by Br, hydroxyphenyl, nitryl were discussed and compared. It was demonstrated that four BTPhen ligands are able to selectively extract Am(lll) over Eu(lll). It was notable that the distribution ratio of 5-nitryl-CyMe4-BTPhen for Eu(lll) was suppressed under 0.02, which was much lower compared to DEu(lll) = 1 by CyMe4-BTPhen. The analysis of the effect of the substituent on the affinity to lanthanides was conducted by UV/vis and fluorescence spectroscopic titration. The stability constants of various ligands with Eu(lll) were obtained by fitting titration curve. Additionally, the basicity of various ligands was determined to be 3.1 ± 0.1, 2.3 ± 0.2, 0.9 ± 0.2, 0.5 ± 0.1 by NMR in the media of CD3OD with the addition of DClO4. The basicity of ligands follows the order of L1 > L2 > L3 > L4, indicating the tendency of protonation decreases with the electron-withdrawing ability increase.

Convenient and accurate insight into solution-phase equilibria from FlowNMR titrations

Solution phase titrations are made easy by multi-nuclear FlowNMR spectroscopy with automated, continuous titre addition to give accurate insights into Brønsted acid/base, hydrogen bonding, Lewis acid/base and metal/ligand binding equilibria under native conditions.

Quantitative analysis of wine and other fermented beverages with benchtop NMR

We present a fully automated approach for quantitative compositional analysis of fermented beverages using benchtop nuclear magnetic resonance (NMR) spectroscopy. NMR spectroscopy, renowned for its applications in chemical structure elucidation, is gaining attention as a quantitative analytical technique due to its inherent linearity and the ability to obtain comprehensive quantitative information with a single simple experiment. Recently developed benchtop NMR spectrometers offer the quantitative capabilities of NMR to a wide range of potential users in industry, but their applicability has been limited by the reduced effective spectral resolution and the need for more advanced data processing. We address this problem with a model-based algorithm that hinges on the well-understood description of quantum mechanical phenomena in NMR spectroscopy. We demonstrate the effectiveness of our approach on a challenging problem of analysing the composition of wine and related fermented beverages - an important potential niche application of quantitative NMR. We successfully quantify more than 15 major components in the wine matrix and enable the quantification of species whose analysis is generally not possible with established methods. The average discrepancy of the obtained concentrations, when compared to the traditional methods of analysis, usually does not exceed 10% and is lower for the most abundant species (e.g. below 5% for ethanol).

Brain pH Imaging and its Applications

Acid-base homeostasis and pH regulation are critical for normal tissue metabolism and physiology, and brain tissue pH alters in many diseased states. Several noninvasive tissue pH Magnetic Resonance (MR) techniques have been developed over the past few decades to shed light on pH change during tissue function and dysfunction. Nevertheless, there are still challenges for mapping brain pH noninvasively at high spatiotemporal resolution. To address this unmet biomedical need, chemical exchange saturation transfer (CEST) MR techniques have been developed as a sensitive means for non-invasive pH mapping. This article briefly reviews the basic principles of different pH measurement techniques with a focus on CEST imaging of pH. Emerging pH imaging applications in the tumor are provided as examples throughout the narrative, and CEST pH imaging in acute stroke is discussed in the final section.

Probing Microenvironmental Acidity in Lyophilized Protein and Vaccine Formulations Using Solid-state NMR Spectroscopy

Biophysical and biochemical instability of therapeutic proteins in the solution state may necessitate the development of products in the solid form, due to their enhanced stability. Lyophilization is a widely used method to ensure dry state stabilization of biological products. A commonly encountered issue is the pH shifts that can occur due to undesired crystallization of a buffer component, resulting in loss of protein activities. However, it is technically challenging to noninvasively investigate the physicochemical environment in the lyophile matrix. In this work, we demonstrate an approach based on solid-state NMR to investigate the microenvironmental acidity in lyophilized protein formulations, using histidine, a commonly used buffer agent, as a molecular probe. The solid-state acidity in the lyophilized matrix can be assessed by monitoring the chemical shift changes of histidine. The protonation and tautomeric states of histidine lyophilized at a range of pH values from 4.5 to 11.0 were identified from full ¹³C and ¹⁵N resonance assignments in one-dimensional and two-dimensional NMR experiments. The results demonstrated a pH-dependence of histidine chemical shift in the amorphous state. Moreover, we successfully applied this protocol to investigate the microenvironmental pH in lyophilized formulations of the HPV vaccine and lactate dehydrogenase protein.

Integrated pH Measurement during Reaction Monitoring with Dual-Reception 1H-31P NMR Spectroscopy

Simultaneous detection of ¹H and ³¹P NMR signals through a dual-detection scheme with two receivers allows monitoring of both the signals of a molecule and the pH of the solution through the resonance of the inorganic phosphate. We evaluate here the method in terms of sensitivity and ease of implementation and show that the additional information obtained without any loss of information or increase in measuring time can be of practical importance in a number of biochemical systems.

Bayesian estimation of the number of protonation sites for urinary metabolites from NMR spectroscopic data

INTRODUCTION

To aid the development of better algorithms for [Formula: see text]H NMR data analysis, such as alignment or peak-fitting, it is important to characterise and model chemical shift changes caused by variation in pH. The number of protonation sites, a key parameter in the theoretical relationship between pH and chemical shift, is traditionally estimated from the molecular structure, which is often unknown in untargeted metabolomics applications.

OBJECTIVE

We aim to use observed NMR chemical shift titration data to estimate the number of protonation sites for a range of urinary metabolites.

METHODS

A pool of urine from healthy subjects was titrated in the range pH 2-12, standard [Formula: see text]H NMR spectra were acquired and positions of 51 peaks (corresponding to 32 identified metabolites) were recorded. A theoretical model of chemical shift was fit to the data using a Bayesian statistical framework, using model selection procedures in a Markov Chain Monte Carlo algorithm to estimate the number of protonation sites for each molecule.

RESULTS

The estimated number of protonation sites was found to be correct for 41 out of 51 peaks. In some cases, the number of sites was incorrectly estimated, due to very close pKa values or a limited amount of data in the required pH range.

CONCLUSIONS

Given appropriate data, it is possible to estimate the number of protonation sites for many metabolites typically observed in [Formula: see text]H NMR metabolomics without knowledge of the molecular structure. This approach may be a valuable resource for the development of future automated metabolite alignment, annotation and peak fitting algorithms.

Establishing upper limits on neuronal activity-evoked pH changes with APT-CEST MRI at 7 T

Purpose

To detect neuronal activity–evoked pH changes by amide proton transfer–chemical exchange saturation transfer (APT‐CEST) MRI at 7 T.

Methods

Three healthy subjects participated in the study. A low‐power 3‐dimensional APT‐CEST sequence was optimized through the Bloch‐McConnell equations. pH sensitivity of the sequence was estimated both in phantoms and in vivo. The feasibility of pH–functional MRI was tested in Bloch‐McConnell‐simulated data using the optimized sequence. In healthy subjects, the visual stimuli were used to evoke transient pH changes in the visual cortex, and a 3‐dimensional APT‐CEST volume was acquired at the pH‐sensitive frequency offset of 3.5 ppm every 12.6 s.

Results

In theory, a three‐component general linear model was capable of separating the effects of blood oxygenation level–dependent contrast and pH. The Bloch‐McConnell equations indicated that a change in pH of 0.03 should be measurable at the experimentally determined temporal signal‐to‐noise ratio of 108. However, only a blood oxygenation level–dependent effect in the visual cortex could be discerned during the visual stimuli experiments performed in the healthy subjects.

Conclusions

The results of this study suggest that if indeed there are any transient brain pH changes in response to visual stimuli, those are under 0.03 units pH change, which is extremely difficult to detect using the existent techniques. Magn Reson Med 80:126–136, 2018. © 2017 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

15N Hyperpolarization of Imidazole-15N2 for Magnetic Resonance pH Sensing via SABRE-SHEATH

¹⁵N nuclear spins of imidazole-¹⁵N₂ were hyperpolarized using NMR signal amplification by reversible exchange in shield enables alignment transfer to heteronuclei (SABRE-SHEATH). A ¹⁵N NMR signal enhancement of ∼2000-fold at 9.4 T is reported using parahydrogen gas (∼50% para-) and ∼0.1 M imidazole-¹⁵N₂ in methanol:aqueous buffer (∼1:1). Proton binding to a ¹⁵N site of imidazole occurs at physiological pH (pK_a ∼ 7.0), and the binding event changes the ¹⁵N isotropic chemical shift by ∼30 ppm. These properties are ideal for in vivo pH sensing. Additionally, imidazoles have low toxicity and are readily incorporated into a wide range of biomolecules. ¹⁵N-Imidazole SABRE-SHEATH hyperpolarization potentially enables pH sensing on scales ranging from peptide and protein molecules to living organisms.

Modelling the acid/base 1H NMR chemical shift limits of metabolites in human urine

INTRODUCTION

Despite the use of buffering agents the ¹H NMR spectra of biofluid samples in metabolic profiling investigations typically suffer from extensive peak frequency shifting between spectra. These chemical shift changes are mainly due to differences in pH and divalent metal ion concentrations between the samples. This frequency shifting results in a correspondence problem: it can be hard to register the same peak as belonging to the same molecule across multiple samples. The problem is especially acute for urine, which can have a wide range of ionic concentrations between different samples.

OBJECTIVES

To investigate the acid, base and metal ion dependent ¹H NMR chemical shift variations and limits of the main metabolites in a complex biological mixture.

METHODS

Urine samples from five different individuals were collected and pooled, and pre-treated with Chelex-100 ion exchange resin. Urine samples were either treated with either HCl or NaOH, or were supplemented with various concentrations of CaCl₂, MgCl₂, NaCl or KCl, and their ¹H NMR spectra were acquired.

RESULTS

Nonlinear fitting was used to derive acid dissociation constants and acid and base chemical shift limits for peaks from 33 identified metabolites. Peak pH titration curves for a further 65 unidentified peaks were also obtained for future reference. Furthermore, the peak variations induced by the main metal ions present in urine, Na⁺, K⁺, Ca²⁺ and Mg²⁺, were also measured.

CONCLUSION

These data will be a valuable resource for ¹H NMR metabolite profiling experiments and for the development of automated metabolite alignment and identification algorithms for ¹H NMR spectra.

Using solution state NMR spectroscopy to probe NMR invisible gelators

Supramolecular hydrogels are formed via the self-assembly of gelator molecules upon application of a suitable trigger. The exact nature of this self-assembly process has been widely investigated as a practical understanding is vital for the informed design of these materials. Solution-state NMR spectroscopy is an excellent non-invasive tool to follow the self-assembly of supramolecular hydrogels. However, in most cases the self-assembled aggregates are silent by conventional (1)H NMR spectroscopy due to the low mobility of the constituent molecules, limiting NMR spectroscopy to following only the initial assembly step(s). Here, we present a new solution-state NMR spectroscopic method which allows the entire self-assembly process of a dipeptide gelator to be followed. This gelator forms transparent hydrogels by a multi-stage assembly process when the pH of an initially alkaline solution is lowered via the hydrolysis of glucono-δ-lactone (GdL). Changes in the charge, hydrophobicity and relative arrangement of the supramolecular aggregates can be followed throughout the assembly process by measuring the residual quadrupolar couplings (RQCs) of various molecular probes (here, (14)NH4(+) and isopropanol-d8), along with the NMR relaxation rates of (23)Na(+). The initially-formed aggregates comprise negatively charged fibrils which gradually lose their charge and become increasingly hydrophobic as the pH falls, eventually resulting in a macroscopic contraction of the hydrogel. We also demonstrate that the in situ measurement of pH by NMR spectroscopy is both convenient and accurate, representing a useful tool for the characterisation of self-assembly processes by NMR.

Electrostatic Energetics of Bacillus subtilis Ribonuclease P Protein Determined by Nuclear Magnetic Resonance-Based Histidine pKa Measurements

The pKa values of ionizable groups in proteins report the free energy of site-specific proton binding and provide a direct means of studying pH-dependent stability. We measured histidine pKa values (H3, H22, and H105) in the unfolded (U), intermediate (I), and sulfate-bound folded (F) states of RNase P protein, using an efficient and accurate nuclear magnetic resonance-monitored titration approach that utilizes internal reference compounds and a parametric fitting method. The three histidines in the sulfate-bound folded protein have pKa values depressed by 0.21 ± 0.01, 0.49 ± 0.01, and 1.00 ± 0.01 units, respectively, relative to that of the model compound N-acetyl-l-histidine methylamide. In the unliganded and unfolded protein, the pKa values are depressed relative to that of the model compound by 0.73 ± 0.02, 0.45 ± 0.02, and 0.68 ± 0.02 units, respectively. Above pH 5.5, H22 displays a separate resonance, which we have assigned to I, whose apparent pKa value is depressed by 1.03 ± 0.25 units, which is ∼0.5 units more than in either U or F. The depressed pKa values we observe are consistent with repulsive interactions between protonated histidine side chains and the net positive charge of the protein. However, the pKa differences between F and U are small for all three histidines, and they have little ionic strength dependence in F. Taken together, these observations suggest that unfavorable electrostatics alone do not account for the fact that RNase P protein is intrinsically unfolded in the absence of ligand. Multiple factors encoded in the P protein sequence account for its IUP property, which may play an important role in its function.

In vivo ³¹P-nuclear magnetic resonance studies of glyphosate uptake, vacuolar sequestration, and tonoplast pump activity in glyphosate-resistant horseweed

Horseweed (Conyza canadensis) is considered a significant glyphosate-resistant (GR) weed in agriculture, spreading to 21 states in the United States and now found globally on five continents. This laboratory previously reported rapid vacuolar sequestration of glyphosate as the mechanism of resistance in GR horseweed. The observation of vacuole sequestration is consistent with the existence of a tonoplast-bound transporter. (31)P-Nuclear magnetic resonance experiments performed in vivo with GR horseweed leaf tissue show that glyphosate entry into the plant cell (cytosolic compartment) is (1) first order in extracellular glyphosate concentration, independent of pH and dependent upon ATP; (2) competitively inhibited by alternative substrates (aminomethyl phosphonate [AMPA] and N-methyl glyphosate [NMG]), which themselves enter the plant cell; and (3) blocked by vanadate, a known inhibitor/blocker of ATP-dependent transporters. Vacuole sequestration of glyphosate is (1) first order in cytosolic glyphosate concentration and dependent upon ATP; (2) competitively inhibited by alternative substrates (AMPA and NMG), which themselves enter the plant vacuole; and (3) saturable. (31)P-Nuclear magnetic resonance findings with GR horseweed are consistent with the active transport of glyphosate and alternative substrates (AMPA and NMG) across the plasma membrane and tonoplast in a manner characteristic of ATP-binding cassette transporters, similar to those that have been identified in mammalian cells.

Quantitative in vivo characterization of intracellular and extracellular pH profiles in heterogeneous tumors: a novel method enabling multiparametric pH analysis

Acid production and transport are currently being studied to identify new targets for efficient cancer treatment, as subpopulations of tumor cells frequently escape conventional therapy owing to their particularly acidic tumor microenvironment. Heterogeneity in intracellular and extracellular tumor pH (pHi, pHe) has been reported, but none of the methods currently available for measuring tissue pH provides quantitative parameters characterizing pH distribution profiles in tissues. To this intent, we present here a multiparametric, noninvasive approach based on in vivo (31)P nuclear magnetic resonance (NMR) spectroscopy and its application to mouse tumor xenografts. First, localized (31)P NMR spectrum signals of pHi and pHe reporter molecules [inorganic phosphate (Pi) and 3-aminopropylphosphonate (3-APP), respectively] were transformed into pH curves using established algorithms. Although Pi is an endogenous compound, 3-APP had to be injected intraperitoneally. Then, we developed algorithms for the calculation of six to eight quantitative pH parameters from the digital points of each pH curve obtained. For this purpose, each pH distribution profile was approximated as a histogram, and intensities were corrected for the nonlinearity between chemical-shift and pH.

pH-Sensitive MR Responses Induced by Dendron-Functionalized SPIONs

We report a series of investigations of the pH-sensitive magnetic resonance (MR) responses of various surface-functionalized SPIONs (superparamagnetic iron oxide nanoparticles). First, functionalization of ~12 nm highly monocrystalline SPION cores with three different generations of melamine-dendrons was optimized to give agents with high molar relaxivities (e.g. R2m ~300 mM-1·s-1 at 7 T and R1m ~20-30 mM-1·s-1 at 0.5 T) and excellent aqueous stabilities. Molar relaxivities were found to exhibit great sensitivity to pH at physiologically-relevant ionic strengths, with sharp inflections observed at pH values near the pKa of the melamine monomer. The strength of the effect was observed to grow with increasing dendron generation (with concomitant shift in the position of the main pH inflection). Opposing behavior in R2m and R2m * trends may be exploited to provide a ratiometric MR response to pH. Combined with TEM and corresponding MR measurements from solutions of varying ionic strengths, these results are consistent with the pH-sensitive behavior originating from transient, reversible SPION clustering modulated by an interplay between SPION surface charge density and solution ionic strength. Studies of SPION cellular uptake and MR response in HeLa cell cultures are also presented. Finally, comparisons with the MR responses of SPIONs with alternative functionalities-derivatives of nitrilotriacetic acid or poly(1-vinylimidazole)-indicate that these types of pH-sensitive MR responses can be highly dependent upon the chemical composition of the surface species (and thus amenable to modulation through rational design).

A novel technology for the imaging of acidic prostate tumors by positron emission tomography

Solid tumors often develop an acidic environment due to the Warburg effect. The effectiveness of diagnosis and therapy may therefore be enhanced by the design and use of pH-sensitive agents that target acidic tumors. Recently, a novel technology was introduced to target acidic tumors using pH low insertion peptide (pHLIP), a peptide that inserts across cell membranes as an alpha-helix when the extracellular pH (pH(e)) is acidic. In this study, we expanded the application of the pHLIP technology to include positron emission tomography imaging of the acidic environment in prostate tumors using (64)Cu conjugated to the pHLIP ((64)Cu-DOTA-pHLIP). Studies showed that this construct avidly accumulated in LNCaP and PC-3 tumors, with higher uptake and retention in the LNCaP tumors. Uptake correlated with differences in the bulk pH(e) of PC-3 and LNCaP tumors measured in magnetic resonance spectroscopy experiments by the (31)P chemical shift of the pH(e) marker 3-aminopropylphosphonate. This article introduces a novel class of noninvasive pH-selective positron emission tomography imaging agents and opens new research directions in the diagnosis of acidic solid tumors.

Defining the pHi-hyperthermia sensitivity relationship for the RIF-1 tumor in vivo: a 31P MR spectroscopy study

This study quantifies the enhancement of the therapeutic efficacy of hyperthermia resulting from an acutely acidified and accurately monitored intracellular pH (pHi) in a mouse tumor model in vivo. Metabolic manipulation of the physiology of RIF-1 tumor (subcutaneous, on the hind flanks of female C3H/HeJ mice) achieved by i.p. bolus injection of glucose (glycolytic tumor acidification) or 3-O-methylglucose (non-glycolytic tumor acidification) was monitored by 31P magnetic resonance (31P MR) prior to, during and up to 1 h after localized hyperthermia. The pre-hyperthermia 31P MR-observable metabolic parameter that correlates most strongly with thermal sensitivity is pHi. Thermal sensitivity increases linearly with decreasing pHi regardless of the mechanism (glycolytic or non-glycolytic) of metabolic manipulation. The quantitative relationship is described by log10(SF)/EQ43=0.0079 pHi,preHT -0.0606 (R=0.63, P<0.0001), where EQ43 is the thermal heat dose delivered to the tumor (in units of equivalent minutes at 42.5 degrees C), pHi,preHT is the intracellular pH immediately prior to hyperthermia, and SF is the surviving fraction. The therapeutic enhancement is not as dramatic as expected based upon previously reported in vitro studies but is generally consistent with other in vivo studies. The method still represents a viable strategy for enhancing the therapeutic efficacy of hyperthermia, especially when used in combination with other therapeutic modalities.

Therapeutic efficacy as predicted by quantitative assessment of murine RIF-1 tumour pH and phosphorous metabolite response during hyperthermia: an in vivo 31P NMR study

Described herein are the initial findings from an 'in-magnet' 31P NMR compatible hyperthermia system capable of concurrently heating and monitoring the metabolic response of murine tumours; the murine radiation induced fibrosarcoma (RIF-1) was employed for these studies. At thermal doses sufficient to raise tumour temperature to 41.5 and 43 degrees C for a period of 30 min, a marked and rapid decrease in nucleoside triphosphate concentration and in pH was observed during the heating period, while inorganic phosphate concentration increased significantly but more gradually. These 31P NMR determined metabolic indices remained depressed/elevated throughout a 1.5 h post-hyperthermia monitoring period. Importantly, these metabolic indices correlated significantly with specific growth delay. This suggests a possible role for NMR spectroscopy in early assessment, and perhaps control, of therapeutic response to hyperthermia.

Mobile lipid production after confluence and pH stress in perfused C6 cells

NMR-visible mobile lipid (ML) has been observed in aggressive tumors and also in in vitro tumor cell models subjected to growth-inhibiting conditions, such as confluence or low-pH stress. The aim of the present study was to determine if ML production after confluence or low pH stress in a cultured cell model of brain tumor is due to growth arrest alone. ML was observed in situ by one- and two-dimensional (1)H NMR in viable but growth-arrested C6 glioma cells superfused for a period of 48 h after harvesting. The rate of ML production in cells harvested at subconfluence was compared to the rate in cells confluent for one cell cycle and to the rate in subconfluent-harvested cells superfused at low pH (pH 6.1). Confluent-harvested cells produced ML at a markedly greater rate than that of cells harvested at subconfluence, suggesting the involvement of prior cell-cell contact rather than simple growth arrest. A high rate was also observed in subconfluent-harvested cells subjected to low pH, indicating that ML in pH-stressed cells also does not arise from growth arrest alone. Furthermore, two-dimensional data on the degree of unsaturation of the ML fatty acyl chains and one-dimensional (31)P and two-dimensional (1)H NMR data on the GPC content of the cells suggest distinct metabolic pathways for the production of ML following confluence and low-pH stress.

In vivo microdialysis of 2-deoxyglucose 6-phosphate into brain: a novel method for the measurement of interstitial pH using 31P-NMR

A unique method for simultaneously measuring interstitial (pHe) as well as intracellular (pHi) pH in the brains of lightly anesthetized rats is described. A 4-mm microdialysis probe was inserted acutely into the right frontal lobe in the center of the area sampled by a surface coil tuned for the collection of 31P-NMR spectra. 2-Deoxyglucose 6-phosphate (2-DG-6-P) was microdialyzed into the rat until a single NMR peak was detected in the phosphomonoester region of the 31P spectrum. pHe and pHi values were calculated from the chemical shift of 2-DG-6-P and inorganic phosphate, respectively, relative to the phosphocreatine peak. The average in vivo pHe was 7.24+/-0.01, whereas the average pHi was 7.05+/-0.01 (n = 7). The average pHe value and the average CSF bicarbonate value (23.5+/-0.1 mEq/L) were used to calculate an interstitial Pco2 of 55 mm Hg. Rats were then subjected to a 15-min period of either hypercapnia, by addition of CO2 (2.5, 5, or 10%) to the ventilator gases, or hypocapnia (PCO2 < 30 mm Hg), by increasing the ventilation rate and volume. pHe responded inversely to arterial Pco2 and was well described (r2 = 0.91) by the Henderson-Hasselbalch equation, assuming a pKa for the bicarbonate buffer system of 6.1 and a solubility coefficient for CO2 of 0.031. This confirms the view that the bicarbonate buffer system is dominant in the interstitial space. pHi responded inversely and linearly to arterial PCO2. The intracellular effect was muted as compared with pHe (slope = -0.0025, r2 = 0.60). pHe and pHi values were also monitored during the first 12 min of ischemia produced by cardiac arrest. pHe decreases more rapidly than pHi during the first 5 min of ischemia. After 12 min of ischemia, pHe and pHi values were not significantly different (6.44+/-0.02 and 6.44+/-0.03, respectively). The limitations, advantages, and future uses of the combined microdialysis/31P-NMR method for measurement of pHe and pHi are discussed.

A study of imidazole-based nuclear magnetic resonance probes of cellular pH

A number of imidazole-based compounds were tested for their utility as (1)H NMR molecular probes of intracellular pH. Imidazole, previously found useful as a probe of erythrocyte pH, reported a pH in perfused canine glioma cells that was more than 1 pH unit lower than that reported by inorganic phosphate, consistent with the known lysosomal compartmentation of the molecule. Imidazole acetate, also proposed as an NMR probe of cellular pH, was found not to enter the cells of this study. Histidine was found to be readily taken up by cells and reported a pH consistent with that reported by inorganic phosphate. Using the chemical shift of the histidine H2 proton in cells incubated with 10 mM histidine, cellular pH measurements could be obtained in less than 1 s. This compares quite favorably with the measurement time, typically several minutes, needed to assess in vivo pH by (31)P NMR. The use of histidine as a probe of pH is demonstrated in perfused canine and rat glioma cells subjected to ischemia or to low extracellular pH.

Homocarnosine and the measurement of neuronal pH in patients with epilepsy

Homocarnosine is a dipeptide of gamma-aminobutyric acid (GABA) and histidine found uniquely in the brain, most likely in a subclass of GABAergic neurons. By comparison of spectra from the occipital lobe of patients receiving a homocarnosine elevation drug to normal subjects we have assigned two elevated resonances in the short TE 1H MRS spectrum to homocarnosine. These resonances are partially resolved at 7.05 and 8.02 ppm in a short TE spectrum at 2.1 T when macromolecule resonances are removed by subtraction of a spectrum in which the metabolite resonances are nulled by inversion recovery. The chemical shift of both of these resonances is sensitive to pHi. By comparison with a titration curve the pHi was calculated from the downfield resonance to be 7.06 in the patient group which is similar to values reported using the P(i) resonance. Based on the in vivo results and theoretical considerations the potential sensitivity for using nonelevated homocarnosine to measure pH is similar to that of P(i) under physiological conditions.

Tumor 31P NMR pH measurements in vivo: a comparison of inorganic phosphate and intracellular 2-deoxyglucose-6-phosphate as pHnmr indicators in murine radiation-induced fibrosarcoma-1

Uncertainty regarding the intracellular/extracellular distribution of inorganic phosphate (P(i)) in tumors has raised concerns that pH calculated from the tumor P(i) chemical shift may not accurately represent the intracellular pH (pHin). This issue was addressed in subcutaneously transplanted murine radiation induced fibrosarcoma-1 by directly comparing pH measured via P(i) with pH measured via the in situ generated intracellular xenometabolite 2-deoxyglucose-6-phosphate (2DG6P). In 131 comparative measurements employing eight tumor-bearing mice under both control and hyperglycemic conditions (the latter to extend the range of tumor pH examined), the pH as derived from either 2DG6P or P(i) showed only a small, but statistically significant, difference (0.07 +/- 0.11 SD; P = 0.0001). Scatter in the comparative analysis over the pH range examined (ca. 5.5-7.5) was not uniform. Above pH 6.6, 2DG6P indicated a pH lower than that of P(i) by 0.088 +/- 0.105 SD (n = 107, P = 0.0001); below pH 6.6, 2DG6P indicated a pH essentially identical to and not statistically different from that of P(i) (mean difference 0.003 +/- 0.128 SD (n = 24, P = 0.92)). Evidence is presented in support of this differential arising from a systematic measurement error due to peak overlap between 2DG6P and endogenous phosphomonoester species. These results support the use of P(i) as a tumor 31P NMR pHin indicator, at least in RIF-1 tumors under control and hyperglycemic conditions.