"Texas-sized" molecular boxes: building blocks for the construction of anion-induced supramolecular species via self-assembly.

It was previously established that the flexible tetraimidazolium macrocycle cyclo[2](2,6-bis(1H-imidazol-1-yl)pyridine)[2](1,4-dimethylenebenzene) (1(4+)) is capable of stabilizing higher-order supramolecular structures via both anion and cation recognition. Described herein is a set of structurally related imidazolium macrocycles (2(4+)-4(4+)) that contain modified central cores. The flexible nature of these new constructs is highlighted by the isolation of several independent crystalline forms for the same basic structure. Each of the individual receptors was found to bind the 2,6-naphthalenedicarboxylate dianion and to stabilize the formation of self-associated structures. The observed binding modes and resulting supramolecular organizational forms were found to differ dramatically depending on the nature of the bridging group present in the imidazolium macrocycle. This finding was established by solution studies involving, inter alia, one- and two-dimensional ((1)H, (1)H-(1)H COSY, DOSY, and NOESY) NMR spectroscopy as well as electrospray ionization mass spectrometry. The new systems in this report serve to expand the available "tool box" for the construction of complex self-assembled materials while providing insights into the determinants that regulate the formation of specific supramolecular structures from flexible receptors capable of adopting multiple stable conformations.

Calcium/calmodulin stimulates the autophosphorylation of elongation factor 2 kinase on Thr-348 and Ser-500 to regulate its activity and calcium dependence.

Eukaryotic elongation factor 2 kinase (eEF-2K) is an atypical protein kinase regulated by Ca(2+) and calmodulin (CaM). Its only known substrate is eukaryotic elongation factor 2 (eEF-2), whose phosphorylation by eEF-2K impedes global protein synthesis. To date, the mechanism of eEF-2K autophosphorylation has not been fully elucidated. To investigate the mechanism of autophosphorylation, human eEF-2K was coexpressed with λ-phosphatase and purified from bacteria in a three-step protocol using a CaM affinity column. Purified eEF-2K was induced to autophosphorylate by incubation with Ca(2+)/CaM in the presence of MgATP. Analyzing tryptic or chymotryptic peptides by mass spectrometry monitored the autophosphorylation over 0-180 min. The following five major autophosphorylation sites were identified: Thr-348, Thr-353, Ser-445, Ser-474, and Ser-500. In the presence of Ca(2+)/CaM, robust phosphorylation of Thr-348 occurs within seconds of addition of MgATP. Mutagenesis studies suggest that phosphorylation of Thr-348 is required for substrate (eEF-2 or a peptide substrate) phosphorylation, but not self-phosphorylation. Phosphorylation of Ser-500 lags behind the phosphorylation of Thr-348 and is associated with the Ca(2+)-independent activity of eEF-2K. Mutation of Ser-500 to Asp, but not Ala, renders eEF-2K Ca(2+)-independent. Surprisingly, this Ca(2+)-independent activity requires the presence of CaM.

Neutral and anionic guests and their effect on the formation of pseudorotaxanes by using a flexible tetracationic imidazolium macrocycle.

The ability to control and direct molecular assembly has important implications in the design of environmentally responsive materials. Reported here is the use of competitive neutral- and anionic-guest recognition to control the formation, disruption, replacement-based construction and higher-order assembly properties of pseudorotaxane structures involving a large, cationic tetraimidazolium receptor. In particular, we showed that the chloride anion (as the tetrabutylammonium (TBA(+)) salt) serves to replace directly the 2,6-naphthalene dicarboxylate dianion from the preformed complex, involving this dianion. In contrast, the addition of the nitrate anion (as the TBA(+) salt) serves to effect displacement of a pre-bound 2,6-naphthalene dicarboxylate dianion in a stepwise manner allowing for stabilization of a so-called "outside"-binding mode under appropriate conditions. We have also found that by using biphenyl-3,4,3',4'-tetraamine as the guest, a 1D-donor-acceptor-donor coordination polymer can be stabilized, whereas the addition of 6-amino-naphthalene-2-sulfonate anion to the pre-formed complex between the tetraimidazolium receptor and the 2,6-naphthalene dicarboxylate dianion produces a new pseudorotaxane complex. This guest-based competition and subsequent molecular translocation is supported by solution-state NMR spectroscopic studies as well as solid-state single-crystal X-ray structural analyses. The results described herein provide initial evidence that guest competition can be used to control molecular "switching" and substrate binding within an appropriately designed anion receptor.

An integrated bioanalytical method development and validation approach: case studies.

We proposed an integrated bioanalytical method development and validation approach: (1) method screening based on analyte's physicochemical properties and metabolism information to determine the most appropriate extraction/analysis conditions; (2) preliminary stability evaluation using both quality control and incurred samples to establish sample collection, storage and processing conditions; (3) mock validation to examine method accuracy and precision and incurred sample reproducibility; and (4) method validation to confirm the results obtained during method development. This integrated approach was applied to the determination of compound I in rat plasma and compound II in rat and dog plasma. The effectiveness of the approach was demonstrated by the superior quality of three method validations: (1) a zero run failure rate; (2) >93% of quality control results within 10% of nominal values; and (3) 99% incurred sample within 9.2% of the original values. In addition, rat and dog plasma methods for compound II were successfully applied to analyze more than 900 plasma samples obtained from Investigational New Drug (IND) toxicology studies in rats and dogs with near perfect results: (1) a zero run failure rate; (2) excellent accuracy and precision for standards and quality controls; and (3) 98% incurred samples within 15% of the original values.

Environmentally responsive threading, dethreading, and fixation of anion-induced pseudorotaxanes.

The tetracationic macrocycle cyclo[2](2,6-di(1H-imidazol-1-yl)pyridine)[2](1,4-dimethylenebenzene) hexafluorophosphate (1(4+)·4PF(6)(-)) acts as a large, flexible "molecular box" that supports the formation of environmentally responsive anion-induced pseudorotaxanes, as well as other extended structures, including metal-linked supramolecular polyrotaxanes. Specifically, the combination of the tetracation 1(4+) and bis-carboxylate guests derived from 4,4'-biphenyldicarboxylic acid and 2,6-naphthalenedicarboxylic acid results in the formation of pseudorotaxanes that respond to changes in environmental stimuli, including pH and temperature. The resulting structures can be "locked into place" via the addition of a metal-linker in the form of Ag(I); this gives rise to an ordered metal-linked polyrotaxane. The interpenetrated constructs described in this article were characterized in solution and in the solid state by one- and two-dimensional ((1)H and NOESY) NMR spectroscopy, as well as by mass spectrometry (ESI-MS) and single-crystal X-ray diffraction methods.

Charge state-dependent fragmentation of oligonucleotide/metal complexes.

Collision-activated dissociation (CAD) has been employed to assess the gas-phase fragmentation behavior of a series of 1:1 oligodeoxynucleotide (ODN):metal complexes over a range of charge states, using several ten-residue ODNs and a wide array of alkali, alkaline earth, and transition metals. For parent species in low to intermediate charge states, complexation with Ca(+2), Sr(+2), or Ba(+2) altered the relative intensity of M-B species, promoting loss of cytosine over loss of guanine. The relative intensities of sequence ions were largely unaffected. This behavior was most prevalent for isomeric sequences with complementary residues at the 5'- and 3'-termini, suggesting that metal complexation may change the gas-phase conformation and/or conformational dynamics for some sequences. In higher charge states, some ODN/Ba(+2) complexes produced abundant fragment ions corresponding to metallated a(n)(-m) species, which are not commonly observed in CAD mass spectra for deprotonated ODNs. The formation of these ions was most favored for complexes between Ba(+2) and ODN sequences with a thymine residue at Position 6. Literature precedent exists for the formation of a(n)(-m) ions from sequences in which covalent modification generates one or more neutral sites along the phosphate backbone. ODN/metal adducts in high charge states possess only a few acidic protons, and the juxtaposition of these neutral phosphate groups near thymine residues and the bound Ba(+2) ion may direct formation of the metallated a(n)(-m) species.

Influence of initial charge state on fragmentation patterns for noncovalent drug/DNA duplex complexes.

The charge state-dependent dissociation of various DNA duplexes and drug/duplex complexes has been investigated using collisionally activated dissociation (CAD) in a quadrupole ion trap mass spectrometer (QIT-MS). Several non-self-complementary 14-residue oligonucleotides were employed, in addition to an array of known DNA-interactive ligands, including the intercalators daunomycin and nogalamycin, as well as the minor groove binding agents distamycin, netropsin, 4',6-diamidino-2-phenylindole, and Hoechst 33342. In general, the dissociation pathways exhibited by both the duplexes and the drug/duplex complexes were found to be markedly sensitive to initial charge state. Time- and activation voltage-independent duplex strand separation predominated for higher charge states, which was interpreted to be a result of internal Coulombic repulsion or partial unzipping in the interface, while time- and activation voltage-dependent covalent cleavage predominated for lower charge states. The identity of the drug and the sequence of the duplex were both found to affect the competition between different dissociation processes. The dissociation pathways for the lower charge state complexes are probably more reflective of specific drug-DNA interactions because Coulombic and/or conformational effects are less marked for these precursors.

Electrospray ionization of nucleic acid aptamer/small molecule complexes for screening aptamer selectivity.

Molecular recognition of small molecule ligands by the nucleic acid aptamers for tobramycin, ATP, and FMN has been examined using electrospray ionization mass spectrometry (ESI-MS). Mass spectrometric data for binding stoichiometry and relative binding affinity correlated well with solution data for tobramycin aptamer complexes, in which aptamer/ligand interactions are mediated by hydrogen bonds. For the ATP and FMN aptamers, where ligand interactions involve both hydrogen bonding and significant pi-stacking, the relative binding affinities determined by MS did not fully correlate with results obtained from solution experiments. Some high-affinity aptamer/ligand complexes appeared to be destabilized in the gas phase by internal Coulombic repulsion. In CAD experiments, complexes with a greater number of intermolecular hydrogen bonds exhibited greater gas-phase stability even in cases when solution binding affinities were equivalent. These results indicate that in at least some cases, mass spectrometric data on aptamer/ligand binding affinities should be used in conjunction with complementary techniques to fully assess aptamer molecular recognition properties.

Comparison of sustained off-resonance irradiation collisionally activated dissociation and multipole storage-assisted dissociation for top-down protein analysis.

Tandem mass spectrometric data acquired for small (8-18 kDa) intact proteins by sustained off-resonance irradiation collisionally activated dissociation (SORI-CAD) and multipole storage-assisted dissociation (MSAD) were compared, and the results indicate that the two activation methods do not always provide the same fragmentation patterns. In MSAD experiments, the charge state distribution made available by the ionization conditions may dictate the range of fragment ions that can be generated. In addition, conditions of high space charge within the hexapole impair transmission and/or trapping of high m/z species, which can result in loss of important precursor and product ions. Finally, the non-resonant nature of activation in MSAD can provide access to secondary dissociation processes that are not available by SORI. Because of these considerations, MSAD is less reliable than SORI for generating sequence tag data. However, it appears that MSAD samples 'preferred' cleavage processes (i.e. those occurring at D and P residues) just as well as SORI, which implies that MSAD data may be somewhat more compatible with search algorithms that utilize unprocessed fragment ion masses.

Collisionally activated dissociation and infrared multiphoton dissociation of oligonucleotides in a quadrupole ion trap.

Infrared multiphoton dissociation (IRMPD) of deprotonated and protonated oligonucleotides ranging from 5 to 40 residues has been performed in a quadrupole ion trap mass spectrometer at normal operating pressure and temperature. Only moderate exposure times and laser powers were required to achieve efficient dissociation. In general, IRMPD and collisionally activated dissociation (CAD) produce comparable sequencing information, indicating that IRMPD is a viable alternative to CAD for oligonucleotide analysis in the quadrupole ion trap. Two major characteristics distinguish CAD and IRMPD spectra for a given parent ion. First, structurally uninformative M-B ions that dominate CAD spectra are generally only low-intensity species in IRMPD spectra because nonresonant activation causes these species to dissociate to backbone cleavage products. Second, phosphate and nucleobase ions can be observed directly in IRMPD experiments because the low-mass cutoff can be set to trap small fragment ions. For this reason IRMPD can sometimes facilitate analysis of sequences containing modified bases.