Electrospray tandem mass spectrometry of alendronate analogues: fingerprints for characterization of new potential prodrugs

1-hydroxymethylene-1,1-bisphosphonic acids (HMBPs) are important drugs for the treatment of a variety of bone diseases. Since these compounds have no chromophore, their detection is challenging and mass spectrometry (MS) appears to be an appropriate sensitive tool. Our work deals with the analysis by electrospray ionization tandem mass spectrometry (ESI-MSn) of the well-known nitrogen-containing HMBP alendronate and of three analogues, considered as potential prodrugs. These four molecules share a common structure with different protecting groups on the phosphonic acid and on the amine functions. We describe the dissociation mechanisms of nitrogen-containing HMBPs in positive ion mode and we compare, in negative ion mode, our results with literature data. In both modes, the dissociations are essentially losses of ROH, and of phosphorus-containing species (HPO2, ROP(OH)2 and ROPO(OH)2), where R=H, C6H5, or CH3OC6H5. These fingerprints will be of great value for differentiating alendronate from its potential prodrugs in complex biological mixtures.     

Towards a universal product ion mass spectral library - reproducibility of product ion spectra across eleven different mass spectrometers

Product ion spectra produced by collision-induced dissociation (CID) in tandem mass spectrometry experiments can differ markedly between instruments. There have been a number of attempts to standardise the production of product ion spectra; however, a consensus on the most appropriate approach to the reproducible production of spectra has yet to be reached. We have previously reported the comparison of product ion spectra on a number of different types of instruments - a triple quadrupole, two ion traps and a Fourier transform ion cyclotron resonance mass spectrometer (Bristow AWT, Webb KS, Lubben AT, Halket JM. Rapid Commun. Mass Spectrom. 2004; 18: 1). The study showed that a high degree of reproducibility was achievable. The goal of this study was to improve the comparability and reproducibility of CID product ion mass spectra produced in different laboratories and using different instruments. This was carried out experimentally by defining a spectral calibration point on each mass spectrometer for product ion formation. The long-term goal is the development of a universal (instrument independent) product ion mass spectral library for the identification of unknowns.The spectra of 48 compounds have been recorded on eleven mass spectrometers: six ion traps, two triple quadrupoles, a hybrid triple quadrupole, and two quadrupole time-of-flight instruments. Initially, 4371 spectral comparisons were carried out using the data from eleven instruments and the degree of reproducibility was evaluated. A blind trial has also been carried out to assess the reproducibility of spectra obtained during LC/MS/MS.The results suggest a degree of reproducibility across all instrument types using the tuning point technique. The reproducibility of the product ion spectra is increased when comparing the tandem in time type instruments and the tandem in space instruments as two separate groups. This may allow the production of a more limited, yet useful, screening library for LC/MS/MS identification using instruments of the same type from different manufacturers.     

An in vitro comparison of microdialysis relative recovery of Met- and Leu-enkephalin using cyclodextrins and antibodies as affinity agents

Cyclodextrins and antibodies have been used as affinity agents to improve relative recovery during microdialysis sampling. Two neuropeptides, methionine-enkephalin (ME) and leucine-enkephalin (LE), were chosen to compare the use of cyclodextrins and antibodies as possible affinity agents for improving their relative recovery across polycarbonate and polyethersulfone membranes during in vitro sampling. Cyclodextrins (CD) including β-CD, 2-hydroxypropyl-β-cyclodextrin (2HPβ-CD), and γ-CD gave improvements of relative recovery for both peptides of less than 2-fold as compared to controls. Comparisons of relative recovery between tyrosine–glycine–glycine, tyrosine, and phenylalanine using different cyclodextrins in the perfusion fluid were also obtained. Inclusion of an antibody against met-enkephalin in the microdialysis perfusion fluid resulted in relative recovery increases of up to 2.5-fold. These results show that using antibodies as affinity agents during microdialysis sampling may be more effective agents to improve the relative recovery of these opioid neuropeptides.     

Generalised 2D-correlation NMR analysis of a wine fermentation

A wine fermentation has been monitored on a daily basis by (1)H NMR spectroscopy. Following data pre-processing that includes synthesis of the spectra to ensure all peaks are of constant half-width, the series of spectra were examined using generalised two-dimensional correlation techniques. Synchronous and asynchronous data maps have been generated and employed to interpret the changes in the fermentation process as a function of time. The results illustrate the potential of high resolution NMR with multivariate data analysis as a tool for process monitoring and the manner in which two-dimensional correlation mapping can aid in data interpretation.     

Coordination "oligomers" in self-assembly reactions of some "tritopic" picolinic dihydrazone ligands-mononuclear, dinuclear, hexanuclear, heptanuclear, and nonanuclear examples

"Tritopic" picolinic dihydrazone ligands with tridentate coordination pockets are designed to produce homoleptic [3 x 3] nonanuclear square grid complexes on reaction with transition-metal salts, and many structurally documented examples have been obtained with Mn(II), Cu(II), and Zn(II) ions. However, other oligomeric complexes with smaller nuclearities have also been discovered and identified structurally in some reactions involving Fe(II), Co(II), Ni(II), and Cu(II), with certain tritopic ligands. This illustrates the dynamic nature of the metal-ligand interaction and the conformationally flexible nature of the ligands and points to the possible involvement of some of these species as intermediates in the [3 x 3] grid formation process. Examples of mononuclear, dinuclear, hexanuclear, heptanuclear, and nonanuclear species involving Fe(II), Co(II), Ni(II), and Cu(II) salts with a series of potentially heptadentate picolinic dihydrazone ligands with pyrazine, pyrimidine, and pyridine end groups are described in the present study. Iron and cobalt complexation reactions are complicated by redox processes, which lead to mixed-oxidation-state Co(II)/Co(III) systems when starting with Co(II) salts, and reduction of Fe(III) to Fe(II) when starting with Fe(III). Magnetic exchange within the polynuclear structural frameworks is discussed and related to the structural features.     

Adiabatic and nonadiabatic dynamics in the CH3(CD3)+HCl reaction

The scattering dynamics leading to the formation of Cl (2P(3/2)) and Cl* (2P(1/2)) products of the CH(3)+HCl reaction (at a mean collision energy =22.3 kcal mol(-1)) and the Cl (2P(3/2)) products of the CD(3)+HCl reaction (at =19.4 kcal mol(-1)) have been investigated by using photodissociation of CH(3)I and CD(3)I as sources of translationally hot methyl radicals and velocity map imaging of the Cl atom products. Image analysis with a Legendre moment fitting procedure demonstrates that, in all three reactions, the Cl/Cl* products are mostly forward scattered with respect to the HCl in the center-of-mass (c.m.) frame but with a backward scattered component. The distributions of the fraction of the available energy released as translation peak at f(t)=0.31-0.33 for all the reactions, with average values that lie in the range =0.42-0.47. The detailed analysis indicates the importance of collision energy in facilitating the nonadiabatic transitions that lead to Cl* production. The similarities between the c.m.-frame scattering and kinetic energy release distributions for Cl and Cl* channels suggest that the nonadiabatic transitions to a low-lying excited potential energy surface (PES) correlating to Cl* products occur after passage through the transition state region on the ground-state PES. Branching fractions for Cl* are determined to be 0.14+/-0.02 for the CH(3)+HCl reaction and 0.20+/-0.03 for the CD(3)+HCl reaction. The difference cannot be accounted for by changes in collision energy, mass effects, or vibrational excitation of the photolytically generated methyl radical reagents and instead suggests that the low-frequency bending modes of the CD(3)H or CH(4) coproduct are important mediators of the nonadiabatic couplings occurring in this reaction system.     

Substrates and Cyclic Peptide Inhibitors of the Oligonucleotide-Activated Sirtuin 7**

The sirtuins are NAD⁺-dependent lysine deacylases, comprising seven isoforms (SIRT1–7) in humans, which are involved in the regulation of a plethora of biological processes, including gene expression and metabolism. The sirtuins share a common hydrolytic mechanism but display preferences for different ϵ-N-acyllysine substrates. SIRT7 deacetylates targets in nuclei and nucleoli but remains one of the lesser studied of the seven isoforms, in part due to a lack of chemical tools to specifically probe SIRT7 activity. Here we expressed SIRT7 and, using small-angle X-ray scattering, reveal SIRT7 to be a monomeric enzyme with a low degree of globular flexibility in solution. We developed a fluorogenic assay for investigation of the substrate preferences of SIRT7 and to evaluate compounds that modulate its activity. We report several mechanism-based SIRT7 inhibitors as well as de novo cyclic peptide inhibitors selected from mRNA-display library screening that exhibit selectivity for SIRT7 over other sirtuin isoforms, stabilize SIRT7 in cells, and cause an increase in the acetylation of H3 K18.     

Photophysics of reduced silicon tetraphenylporphyrin

The contrasting photophysical properties of two silicon (IV) tetraphenylporphyrins, Si(TPP)(py)2 and Si(TPP)Cl2, have been investigated using static absorption and fluorescence spectroscopy and ultrafast transient absorption measurements. The parent Si(TPP)Cl2, in which the porphyrin macrocycle has its normal 2- oxidation state, has a fluorescence yield of 0.027, and a lifetime of 1.8 ns for the lowest excited singlet state. In marked contrast, the reduced, anti-aromatic complex Si(TPP)(py)2, with the macrocycle in the 4- oxidation state, has an extremely low fluorescence yield (< or =0.0004) and a 750-fold shorter excited-state lifetime (2.4 ps) in the same solvent (pyridine). The rapid deactivation of photoexcited Si(TPP)(py)2 to the ground state is likely associated with its ruffled structure and the presence of low-energy excited states in its electronic manifold.     

Thermal degradation in a trimodal poly(dimethylsiloxane) network studied by (1)H multiple quantum NMR

Thermal degradation of a filled, cross-linked siloxane material synthesized from poly(dimethylsiloxane) chains of three different average molecular weights and with two different cross-linking species has been studied by (1)H multiple quantum (MQ) NMR methods. Multiple domains of polymer chains were detected by MQ NMR exhibiting residual dipolar coupling () values of 200 and 600 Hz, corresponding to chains with high average molecular weight between cross-links and chains with low average molecular weight between cross-links or near the multifunctional cross-linking sites. Characterization of the values and changes in distributions present in the material were studied as a function of time at 250 degrees C and indicate significant time-dependent degradation. For the domains with low , a broadening in the distribution was observed with aging time. For the domain with high , increases in both the mean and the width in were observed with increasing aging time. Isothermal thermal gravimetric analysis reveals a 3% decrease in weight over 20 h of aging at 250 degrees C. Degraded samples also were analyzed by traditional solid-state (1)H NMR techniques, and off-gassing products were identified by solid-phase microextraction followed by gas chromatography-mass spectrometry. The results, which will be discussed here, suggest that thermal degradation proceeds by complex competition between oxidative chain scissioning and postcuring cross-linking that both contribute to embrittlement.     

Oxygen as a paramagnetic probe of clustering and solvent exposure in folded and unfolded states of an SH3 domain

The N-terminal SH3 domain of the Drosophila modular protein Drk undergoes slow exchange between a folded (Fexch) and highly populated unfolded (Uexch) state under nondenaturing buffer conditions, enabling both Fexch and Uexch states to be simultaneously monitored. The addition of dissolved oxygen, equilibrated to a partial pressure of either 30 atm or 60 atm, provides the means to study solvent exposure with atomic resolution via 13C NMR paramagnetic shifts in 1H,13C HSQC (heteronuclear single quantum coherence) spectra. Absolute differences in these paramagnetic shifts between the Fexch and Uexch states allow the discrimination of regions of the protein which undergo change in solvent exposure upon unfolding. Contact with dissolved oxygen for both the Fexch and Uexch states could also be assessed through 13C paramagnetic shifts which were normalized based on the corresponding paramagnetic shifts seen in the free amino acids. In the Fexch state, the 13C nuclei belonging to the hydrophobic core of the protein exhibited very weak normalized paramagnetic shifts while those with greater solvent accessible surface area exhibited significantly larger normalized shifts. The Uexch state displayed less varied 13C paramagnetic shifts although distinct regions of protection from solvent exposure could be identified by a lack of such shifts. These regions, which included Phe9, Thr12, Ala13, Lys21, Thr22, Ile24, Ile27, and Arg38, overlapped with those found to have residual nativelike and non-native structures in previous studies and in some cases provided novel information. Thus, the paramagnetic shifts from dissolved oxygen are highly useful in the study of a transient structure or clustering in disordered systems, where conventional NMR measurements (couplings, chemical shift deviations from random coil values, and NOEs) may give little information.