Distinctive Nucleic Acid Recognition by Lysine-Embedded Phenanthridine Peptides.

Three new phenanthridine peptide derivatives (19, 22, and 23) were synthesized to explore their potential as spectrophotometric probes for DNA and RNA. UV/Vis and circular dichroism (CD) spectra, mass spectroscopy, and computational analysis confirmed the presence of intramolecular interactions in all three compounds. Computational analysis revealed that compounds alternate between bent and open conformations, highlighting the latter's crucial influence on successful polynucleotide recognition. Substituting one glycine with lysine in two regioisomers (22, 23) resulted in stronger binding interactions with DNA and RNA than for a compound containing two glycines (19), thus emphasizing the importance of lysine. The regioisomer with lysine closer to the phenanthridine ring (23) exhibited a dual and selective fluorimetric response with non-alternating AT and ATT polynucleotides and induction of triplex formation from the AT duplex. The best binding constant (K) with a value of 2.5 × 107 M-1 was obtained for the interaction with AT and ATT polynucleotides. Furthermore, apart from distinguishing between different types of ds-DNA and ds-RNA, the same compound could recognize GC-rich DNA through distinct induced CD signals.

The transformation from 2°-amine to 3°-amine of cyclam ring alters the fragmentation patterns of 1-tosylcytosine-cyclam conjugates.

The novel N-1-sulfonylcytosine-cyclam conjugates 1 and 2 conjugates are ionized by electrospray ionization mass spectrometry (ESI MS) in positive and negative modes (ES+ and ES- ) as singly protonated/deprotonated species or as singly or doubly charged metal complexes. Their structure and fragmentation behavior is examined by collision induced experiments. It was observed that the structure of the conjugate dictated the mode of the ionization: 1 was analyzed in ES- mode while 2 in positive mode. Complexation with metal ions did not have the influence on the ionization mode. Zn2+ and Cu2+ complexes with ligand 1 followed the similar fragmentation pattern in negative ionization mode. The transformation from 2°-amine in 1 to 3°-amine of cyclam ring in 2 leads to the different fragmentation patterns due to the modification of the protonation priority which changed the fragmentation channels within the conjugate itself. Cu2+ ions formed complexes practically immediately, and the priority had the cyclam portion of the ligand 2. The structure of the formed Zn2+ complexes with ligand 2 depended on the number of 3° amines within the cyclam portion of the conjugate and the ratio of the metal:ligand used. The cleavage of the cyclam ring of metal complexes is driven by the formation of the fragment that suited the coordinating demand of the metal ions and the collision energy applied. Finally, it was shown that the structure of the cyclam conjugate dictates the fragmentation reactions and not the metal ions.

C5-Morpholinomethylation of N1-sulfonylcytosines by a one-pot microwave assisted Mannich reaction.

A fast and efficient route for the introduction of a methylene bridged-amine (morpholinomethyl) functionality in the C5 position of the sulfonylated cytosine nucleobase has been developed. First, novel N1-sulfonylcytosine derivatives 3-6 were prepared by the condensation of silylated cytosine with selected sulfonyl chlorides. They were subsequently transformed to 5-morpholinomethyl-N1-sulfonylcytosine derivatives (8, 12-15) using microwave irradiation. As a result of cytosine ring opening in N1-tosylcytosine, depending on the reaction conditions, peculiar tosyl-urea derivative 9 has been isolated, which provided additional insight into the reaction pathway. The influence of the C5-substituent on the antiproliferative activity has been evaluated by performing the MTT test on U251, MCF-7 and MOLT-4 tumor cell-lines.

Quantification of free fatty acids in human stratum corneum using tandem mass spectrometry and surrogate analyte approach.

The free fatty acids (FFAs) are one of the major components of the lipids in the stratum corneum (SC), the uppermost layer of the skin. Relative composition of FFAs has been proposed as a biomarker of the skin barrier status in patients with atopic dermatitis (AD). Here, we developed an LC-ESI-MS/MS method for simultaneous quantification of a range of FFAs with long and very long chain length in the SC collected by adhesive tape (D-Squame). The method, based on derivatization with 2-bromo-1-methylpyridinium iodide and 3-carbinol-1-methylpyridinium iodide, allowed highly sensitive detection and quantification of FFAs using multiple reaction monitoring. For the quantification, we applied a surrogate analyte approach and internal standardization using isotope labeled derivatives of FFAs. Adhesive tapes showed the presence of several FFAs, which are also present in the SC, a problem encountered in previous studies. Therefore, the levels of FFAs in the SC were corrected using C12:0, which was present on the adhesive tape, but not detected in the SC. The method was applied to SC samples from patients with atopic dermatitis and healthy subjects. Quantification using multiple reaction monitoring allowed sufficient sensitivity to analyze FFAs of chain lengths C16-C28 in the SC collected on only one tape strip.

The Metal Effect on Self-Assembling of Oxalamide Gelators Explored by Mass Spectrometry and DFT Calculations.

Gels formed by self-assembly of small organic molecules are of wide interest as dynamic soft materials with numerous possible applications, especially in terms of nanotechnology for functional and responsive biomaterials, biosensors, and nanowires. Four bis-oxalamides were chosen to show if electrospray ionization mass spectrometry (ESI-MS) could be used as a prediction of a good gelator and also to shed light on the gelation processes. By inspecting the gelation of several solvent, we showed that bis(amino acid)oxalamide 1 proved to be the most efficient, also being able of forming the largest observable assemblies in the gas phase. The formation of singly charged assemblies holding from one up to six monomer units is the outcome of the strong intermolecular H-bonds, particularly among terminal carboxyl groups. The variation of solvents from polar aprotic towards polar protic did not have any significant effects on the size of the assemblies. The addition of a salt such as NaOAc or Mg(OAc)2, depending on the concentration, altered the assembling. Computational analysis at the DFT level aided in the interpretation of the observed trends and revealed that individual gelator molecules spontaneously assemble to higher aggregates, but the presence of the Na+ cation disrupts any gelator organization since it becomes significantly more favorable for gelator molecules to bind Na+ cations up to the 3:1 ratio than to self-assemble, being fully in line with experimental observations reported here. Graphical Abstract ᅟ.

ESI-MS studies of the non-covalent interactions between biologically important metal ions and N-sulfonylcytosine derivatives.

The aim of this report is to present the electrospray ionization mass spectrometry results of the non-covalent interaction of two biologically active ligands, N-1-(p-toluenesulfonyl)cytosine, 1-TsC, 1 and N-1-methanesulfonylcytosine, 1-MsC, 2 and their Cu(II) complexes Cu(1-TsC-N3)2 Cl2 , 3 and Cu(1-MsC-N3)2 Cl2 and 4 with biologically important cations: Na+ , K+ , Ca2+ , Mg2+ and Zn2+ . The formation of various complex metal ions was observed. The alkali metals Na+ and K+ formed clusters because of electrostatic interactions. Ca2+ and Mg2+ salts produced the tris ligand and mixed ligand complexes. The interaction of Zn2+ with 1-4 produced monometal and dimetal Zn2+ complexes as a result of the affinity of Zn2+ ions toward both O and N atoms. Copyright © 2016 John Wiley & Sons, Ltd.

Mass spectrometry and theoretical studies on N-C bond cleavages in the N-sulfonylamidino thymine derivatives.

The reactivity of new biologically active thymine derivatives substituted with 2-(arylsulfonamidino)ethyl group at N1 and N3 position was investigated in the gas phase using CID experiments (ESI-MS/MS) and by density functional theory (DFT) calculations. Both derivatives show similar chemistry in the negative mode with a retro-Michael addition (Path A(-)) being the most abundant reaction channel, which correlate well with the fluoride induced retro-Michael addition observed in solution. The difference in the fragmentation of N-3 substituted thymine 5 and N-1 substituted thymine 1 in the positive mode relates to the preferred cleavage of the sulfonyl group (m/z 155, Path B) in N-3 isomer and the formation of the acryl sulfonamidine 3 (m/z 309) via Path A in N-1 isomer. Mechanistic studies of the cleavage reaction conducted by DFT calculations give the trend of the calculated activation energies that agree well with the experimental observations. A mechanism of the retro-Michael reaction was interpreted as a McLafferty type of fragmentation, which includes Hß proton shift to one of the neighboring oxygen atoms in a 1,5-fashion inducing N1(N3)-Cα bond scission. This mechanism was found to be kinetically favorable over other tested mechanisms. Significant difference in the observed fragmentation pattern of N-1 and N-3 isomers proves the ESI-MS/MS technique as an excellent method for tracking the fate of similar sulfonamidine drugs. Also, the observed N-1 and/or N-3 thymine alkylation with in situ formed reactive acryl sulfonamidine 3 as a Michael acceptor may open interesting possibilities for the preparation of other N-3 substituted pyrimidines.

ESI-MS studies of palladium (II) complexes with 1-(p-toluenesulfonyl)cytosine/cytosinato ligands.

The mononuclear complex Pd(1-TosC-N3)(2)Cl(2) (2) containing 1-(p-toluenesulfonyl)cytosine (1) as a ligand, as well as dinuclear complexes Pd(2)(1-TosC(-)-N3,N4)(4) (3) and Pd(2)(1-TosC(-)-N3,N4)(2)DMSO(2)Cl(2) (4) containing the ligand anion (1-TosC(-)), was mass analyzed by electrospray ionization ion trap MS/MS and high resolution MS. Complexes 3 and 4 were obtained by recrystallization of 2 from DMF and DMSO, respectively. The behavior of complex 2 in different solutions was monitored by electrospray ionization mass spectrometry (ESI-MS). Under the applied ESI-MS conditions, complex 2 in methanol reorganized itself dominantly as new complex 3 and the solvent did not coordinate the formed species. In H(2)O/DMSO, CH(3)CN/DMSO and CH(3)OH/DMSO solutions, complex 2 formed several new species with solvent molecules involved in their structure, e.g. complex 4 was formed as the major product. The newly formed species were also examined by LC-MS-DAD, confirming the solvent induced reorganization and the solution instability of complex 2.

ESI-MS studies of mixed-ligand Fe(II) complexes containing 1,10-phenanthroline and 1,10-phenanthroline-5,6-dione as ligands.

In order to monitor the progression of the synthesis and the separation of novel mixed-ligand iron complexes containing 1,10-phenanthroline, 1,10-phenanthroline-5,6-dione, and NCS- as ligands all products were mass analyzed by electrospray ionization ion trap MS/MS. The spectra of methanol (MeOH), acetonitrile (ACN), water, and ethanol (EtOH) solutions were collected and the results were compared. It was detected under applied electrospray ionization mass spectrometry (ESI-MS) conditions that MeOH, water, and EtOH formed solvent clusters around the free or complexed 1,10-phenanthroline-5,6-dione. Owing to the solvent-ligand hydrogen-bond formation, the solvent-ligand clusters were formed in the polar protic solvents. The number of protic solvent molecules per complex ion in cluster depended on the number of 1,10-phenanthroline-5,6-dione ligands in the complex ion. Unlike MeOH, EtOH, or water, ACN was not involved in the formation of the solvent clusters with the iron complexes containing 1,10-phenanthroline-5,6-dione as ligand. We also showed that the NCS- group under certain solvent conditions served as a bidentate ligand.