Application of NMR metabolomics to search for human disease biomarkers

Since antiquity, humans have used body fluids like saliva, urine and sweat for the diagnosis of diseases. The amount, color and smell of body fluids are still used in many traditional medical practices to evaluate an illness and make a diagnosis. The development and application of analytical methods for the detailed analysis of body fluids has led to the discovery of numerous disease biomarkers. Recently, mass spectrometry (MS), nuclear magnetic resonance spectroscopy (NMR), and multivariate statistical techniques have been incorporated into a multidisciplinary approach to profile changes in small molecules associated with the onset and progression of human diseases. The goal of these efforts is to identify metabolites that are uniquely correlated with a specific human disease in order to accurately diagnose and treat the malady. In this review we will discuss recent developments in sample preparation, experimental techniques, the identification and quantification of metabolites, and the chemometric tools used to search for biomarkers of human diseases using NMR.     

Novel synthesis of desymmetrized resorcinol derivatives: aryl fluoride displacement on deactivated substrates

A short, high-yielding synthesis of differentially substituted resorcinol derivatives has been developed that utilizes 1,3-difluorobenzene as the starting material and employs sequential nucleophilic aromatic substitution (S(N)Ar) reactions to generate desymmetrized products. The scope and limitations of the second S(N)Ar reaction on the deactivated 1-alkoxy-3-fluorobenzene intermediates have been investigated. This methodology has also been employed in the synthesis of desymmetrized catechol derivatives from 1,2-difluorobenzene.     

Thermal reactions of 7-d- and 8-d-bicyclo[4.2.0]oct-2-enes

The gas phase thermal reactions exhibited by bicyclo[4.2.0]oct-2-ene and 7-d and 8-d analogues at 300 degrees C have been followed kinetically through GC and 2H NMR spectroscopic analyses. In contrast to the pattern of transformations exhibited by bicyclo[3.2.0]hept-2-ene and deuterium-labeled analogues, no reactions initiated by C1-C6 bond cleavage are seen, epimerization at C8 is much faster than [1,3] shifts leading to bicyclo[2.2.2]oct-2-ene, and the ratio of rate constants for [1,3] carbon migration with inversion versus migration with retention is approximately 1.4. Homolysis of C1-C8 to give a conformationally flexible diradical intermediate having a relatively long lifetime and multiple options for further reaction (re-formation of C1-C8 with or without net epimerization, fragmentation to 1,3-cyclohexadiene and ethylene, migration to the original C3 with inversion or retention) accords well with the observations. Clearly, orbital symmetry control does not govern stereochemistry for the [1,3] sigmatropic carbon shifts.     

Oxidative group transfer to a triiron complex to form a nucleophilic μ(3)-nitride, [Fe3(μ(3)-N)]-

Utilizing a hexadentate ligand platform, a high-spin trinuclear iron complex of the type ((tbs)L)Fe(3)(thf) was synthesized and characterized ([(tbs)L](6-) = [1,3,5-C(6)H(9)(NPh-o-NSi(t)BuMe(2))(3)](6-)). The silyl-amide groups only permit ligation of one solvent molecule to the tri-iron core, resulting in an asymmetric core wherein each iron ion exhibits a distinct local coordination environment. The triiron complex ((tbs)L)Fe(3)(thf) rapidly consumes inorganic azide ([N(3)]NBu(4)) to afford an anionic, trinuclear nitride complex [((tbs)L)Fe(3)(μ(3)-N)]NBu(4). The nearly C(3)-symmetric complex exhibits a highly pyramidalized nitride ligand that resides 1.205(3) ? above the mean triiron plane with short Fe-N (1.871(3) ?) distances and Fe-Fe separation (2.480(1) ?). The nucleophilic nitride can be readily alkylated via reaction with methyl iodide to afford the neutral, trinuclear methylimide complex ((tbs)L)Fe(3)(μ(3)-NCH(3)). Alkylation of the nitride maintains the approximate C(3)-symmetry in the imide complex, where the imide ligand resides 1.265(9) ? above the mean triiron plane featuring lengthened Fe-N(imide) bond distances (1.892(3) ?) with nearly equal Fe-Fe separation (2.483(1) ?).     

Quantification of patellofemoral joint contact area using magnetic resonance imaging

To describe a method for quantifying patellofemoral joint contact area using magnetic resonance imaging (MRI), we used a repeated measures design using cadaver specimens. The use of contact area obtained from cadaveric specimens for biomechanical modeling does not permit investigators to assess the inter-subject variability in contact area as a result of patellofemoral pathology or malalignment. Therefore, a method for measuring patellofemoral joint contact area in-vivo is necessary. Six fresh frozen unmatched human cadaver knees were thawed at room temperature and minimally dissected to permit insertion of a pressure sensitive film packet into the suprapatellar pouch. A custom loading apparatus was designed to apply a compressive load to the patellofemoral joint at 30 degrees of flexion. Simultaneous measurement of contact area was made using both the pressure sensitive film technique and MRI. The intraclass correlation coefficient (ICC) and coefficient of variation were used to compare the agreement between the two methods and to assess the repeatability of the MRI method. Good agreement was found between the MRI and pressure sensitive film techniques (ICC 0.91; CV 13%). The MRI technique also was found to be highly reproducible (ICC 0.98; CV 2.3%). MRI assessment of patellofemoral joint contact area was found to be comparable to the established pressure sensitive film technique. These results suggest that this method may be a valuable tool in quantifying patellofemoral joint contact area in-vivo. Quantification of the patellofemoral joint stress has been dependent on patellofemoral joint contact area obtained from cadaver specimens, thereby negating the potential influence of subject specific variability. Developing a non-invasive technique to evaluate contact area will assist researchers and/or clinicians in obtaining patient-specific contact area data to be used in biomechanical analyses and clinical decision making.     

Negative impact of noise on the principal component analysis of NMR data

Principal component analysis (PCA) is routinely applied to the study of NMR based metabolomic data. PCA is used to simplify the examination of complex metabolite mixtures obtained from biological samples that may be composed of hundreds or thousands of chemical components. PCA is primarily used to identify relative changes in the concentration of metabolites to identify trends or characteristics within the NMR data that permits discrimination between various samples that differ in their source or treatment. A common concern with PCA of NMR data is the potential over emphasis of small changes in high concentration metabolites that would over-shadow significant and large changes in low-concentration components that may lead to a skewed or irrelevant clustering of the NMR data. We have identified an additional concern, very small and random fluctuations within the noise of the NMR spectrum can also result in large and irrelevant variations in the PCA clustering. Alleviation of this problem is obtained by simply excluding the noise region from the PCA by a judicious choice of a threshold above the spectral noise.