New solid phase synthesis of distamycin analogues

A novel and straightforward solid phase synthesis of distamycin analogues containing benzene units has been developed.     

Monitoring the synthetic reaction of a polyamide/peptide conjugate using electrospray ionization mass spectrometry

Recently, the chemical structures of a series of monoimidazole/polyamine conjugates were studied in this laboratory using electrospray ionization mass spectrometry (ESI-MS) combined with tandem mass spectrometry (ESI-MS/MS). The method was found to be a powerful tool for the identification of this class of compounds. During the synthesis of targeted polyamide/peptide conjugates as derivatives or analogues of netropsin and distamycin, the method was applied to analyze and track the coupling reaction for the formation of the polyamide, which was difficult to achieve using thin layer chromatography (TLC). Characteristic fragmentation pathways for a nitro-monoimidazole conjugate, an amino-monoimidazole conjugate, and the final product (a nitro-diimidazole conjugate) were explored. The fragmentations of these conjugates were strongly affected by the presence of an amino group instead of a nitro group in the molecule, and led to the identification of the three compounds in the reacting solution or in the final reaction mixture. Consequently, the reaction could be monitored successfully and the synthetic route optimized.     

Programmable oligomers for minor groove DNA recognition

The four Watson-Crick base pairs of DNA can be distinguished in the minor groove by pairing side-by-side three five-membered aromatic carboxamides, imidazole (Im), pyrrole (Py), and hydroxypyrrole (Hp), four different ways. On the basis of the paradigm of unsymmetrical paired edges of aromatic rings for minor groove recognition, a second generation set of heterocycle pairs, imidazopyridine/pyrrole (Ip/Py) and hydroxybenzimidazole/pyrrole (Hz/Py), revealed that recognition elements not based on analogues of distamycin could be realized. A new set of end-cap heterocycle dimers, oxazole-hydroxybenzimidazole (No-Hz) and chlorothiophene-hydroxybenzimidazole (Ct-Hz), paired with Py-Py are shown to bind contiguous base pairs of DNA in the minor groove, specifically 5'-GT-3' and 5'-TT-3', with high affinity and selectivity. Utilizing this technology, we have developed a new class of oligomers for sequence-specific DNA minor groove recognition no longer based on the N-methyl pyrrole carboxamides of distamycin.     

Systematical Synthesis of Distamycin Analogues and Their Interaction with Herring Sperm DNA

A simple procedure for the systematical synthesis of eight distamycin analogues containing N‐methylpyrrole (Py) and N‐methylimidazole (Im) has been developed by a chloroform reaction and DCC coupling reaction without amino protection and deprotection, and the interaction of the analogues with Herring Sperm DNA was investigated by fluorescence spectroscopy.     

Electron ionisation induced fragmentation of fused norbornene analogues containing SiMe2 or GeMe2 and oxygen bridges. Migration of SiMe2 and GeMe2 groups

The main electron ionisation induced fragmentation processes of fused norbornene analogues containing SiMe2 or GeMe2 and oxygen bridges, as well as their dependence on substitution, were investigated using mass (MS) and tandem mass (MS/MS) spectrometric analysis. Formation of the rearrangement ions of m/z 176 in the mass spectra of fused norbornene analogues containing SiMe2 and m/z 222 in the mass spectrum of norbornene analogues containing GeMe2 provides firm evidence for the migration of a SiMe2 and GeMe2 bridge, respectively.     

Structural determination of sildenafil and its analogues in dietary supplements by fast‐atom bombardment collision‐induced dissociation tandem mass spectrometry

Sildenafil and its analogues, which are used as illegal additives in several dietary supplements, were isolated by liquid‐liquid extraction and column chromatography and analyzed by fast‐atom bombardment mass spectrometry (FAB‐MS). Structures of sildenafil and its derivatives were elucidated by FAB‐tandem mass spectrometry (MS/MS) with exact mass measurement in the positive‐ion mode. To find structurally diagnostic ions for the sildenafil analogues, authentic sildenafil was preferentially analyzed by high‐energy collision‐induced dissociation (CID)‐MS/MS. The CID‐MS/MS spectra of [M+H]⁺ precursor ions resulted in the formation of numerous characteristic ions via a series of dissociative processes. The product ions formed by CID provided important information on the modification of the piperazine ring, the phenylsulfonyl group and the pyrazolopyrimidine moiety of sildenafil. By interpreting their MS/MS spectra, the chemical structures of sildenafil analogues isolated from dietary supplements could be elucidated and fragmentation patterns were proposed. To clearly identify the sidenafil derivatives in dietary supplements, some of the derivatives such as acetildenafil, homosildenafil and hydroxyhomosildenafil which are not commercially available were synthesized and compared with their MS/MS spectra. In addition, high‐resolution mass measurements were conducted to obtain the elemental compositions of sildenafil and its analogues. Copyright © 2009 John Wiley & Sons, Ltd.     

Structural and thermodynamic studies of the interaction of distamycin A with the parallel quadruplex structure [d(TGGGGT)]4

The complex between distamycin A and the parallel DNA quadruplex [d(TGGGGT)]4 has been studied by 1H NMR spectroscopy and isothermal titration calorimetry (ITC). To unambiguously assert that distamycin A interacts with the grooves of the quadruplex [d(TGGGGT)]4, we have analyzed the NMR titration profile of a modified quadruplex, namely [d(TGGMeGGT)]4, and we have applied the recently developed differential frequency-saturation transfer difference (DF-STD) method, for assessing the ligand-DNA binding mode. The three-dimensional structure of the 4:1 distamycin A/[d(TGGGGT)]4 complex has been determined by an in-depth NMR study followed by dynamics and mechanics calculations. All results unequivocally indicate that distamycin molecules interact with [d(TGGGGT)]4 in a 4:1 binding mode, with two antiparallel distamycin dimers that bind simultaneously two opposite grooves of the quadruplex. The affinity between distamycin A and [d(TGGGGT)]4 enhances ( approximately 10-fold) when the ratio of distamycin A to the quadruplex is increased. In this paper we report the first three-dimensional structure of a groove-binder molecule complexed to a DNA quadruplex structure.     

Challenges in the identification process of phenidate analogues in LC‐ESI‐MS/MS analysis: Information enhancement by derivatization with isobutyl chloroformate

A new analytical technique for the structural elucidation of four representative phenidate analogues possessing a secondary amine residue, which leads to a major/single amine‐representative fragment/product ion at m/z 84 both in their GC‐EI‐MS and LC‐ESI‐MS/MS spectra, making their identification ambiguous, was developed. The method is based on “in vial” chemical derivatization with isobutyl chloroformate in both aqueous and organic solutions, followed by liquid chromatography‐electrospray ionization mass spectrometry (LC‐ESI‐MS/MS). The resulting carbamate derivatives promote rich fragmentation patterns with full coverage of all substructures of the molecule, enabling detailed structural elucidation and unambiguous identification of the original compounds at low ng/mL levels.     

Identification and separation of saxitoxins using hydrophilic interaction liquid chromatography coupled to traveling wave ion mobility‐mass spectrometry

The aim of this work was to develop a reliable and efficient analytical method to characterise and differentiate saxitoxin analogues (STX), including sulphated (gonyautoxins, GTX) and non‐sulphated analogues. For this purpose, hydrophilic interaction liquid chromatography (HILIC) was used to separate sulphated analogues. We also resorted to ion mobility spectrometry to differentiate the STX analogues because this technique adds a new dimension of separation based on ion gas phase conformation. Positive and negative ionisation modes were used for gonyautoxins while positive ionisation mode was used for non‐sulphated analogues. Subsequently, the coupling of these three complementary techniques, HILIC‐IM‐MS, permitted the separation and identification of STX analogues; isomer differentiation was achieved in HILIC dimension while non‐sulphated analogues were separated in the IM‐MS dimension. Additional structural characteristics concerning the conformation of STXs could be obtained using IM‐MS measurements. Thus, the collision cross sections (CCS) of STXs are reported for the first time in the positive ionisation mode. These experimental CCSs correlated well with the calculated CCS values using the trajectory method. Copyright © 2015 John Wiley & Sons, Ltd.     

Molecular dynamics simulation of the sliding of distamycin anticancer drug along DNA: interactions and sequence selectivity

Molecular dynamics simulations and umbrella sampling have been used to investigate the sliding of distamycin anticancer drug along the DNA minor groove. The potential energy surface calculated for the sliding of drug shows three minima. The global minimum corresponds to the binding of drug to the AT-rich region, which is the origin of sequence selectivity of distamycin. This selectivity originates from both structural factors and energy contributions. The analysis of energy contributions of binding was performed by the MM–PBSA method. The analysis of hydrogen bonds and van der Waals, electrostatic, and solvation interactions show that structural or steric factors are more important in the selectivity of distamycin than energetic factors. The results of this study can be applied in the design of new derivatives of distamycin anticancer drug with improved properties.     

ELISA and LC-MS/MS methods for determining cyanobacterial toxins in blue-green algae food supplements

The use of natural products as a diet supplement is increasing worldwide but sometimes is not followed by adequate sanitary controls and analyses. Twenty samples of pills and capsules of lyophilised cyanobacteria (blue-green algae), commercialised in Italy as dietary supplements, were found positive at the Vibrio fischeri bioassay. Further analyses with ELISA and LC-MS/MS methods revealed the presence of four microcystin (MC) analogues, MC-LR, -YR, -LA, -RR and two demethylated forms of MC-RR. The highest total microcystin content was 4.5 and 1.4 microg g-1 in pills and capsules, respectively. The ELISA measurements, compared to the LC-MS/MS analyses, showed significantly lower concentrations of microcystins in pills, this confirming a possible ELISA underestimate of mixed microcystins, due to different sensitivities for some toxic analogues.     

Analysis of streptolydigin degradation and conversion in cultural supernatants of <Emphasis Type="Italic">Streptomyces lydicus</Emphasis> AS 4.2501

A variety of structural analogues of streptolydigin exists in the cultural supernatants of Streptomyces lydicus AS 4.2501. The degradation of streptolydigin in cultural supernatants with different pH values kept at 25°C in a thermostatic bath was investigated using LC-MS/MS detection. Analysis of the alkaline supernatants (pH 9.50) provides evidence of degradation and conversion between streptolydigin and its structural analogues. Interestingly, a new streptolydigin analogue was detected by LC-MS and photo-diode array (PDA) detection in the process of alkaline degradation. After 48 h in a thermostatic bath, the degradation of streptolydigin and its two analogues at pH 9.50 approached pseudo-first order kinetics. Comparatively, the degradation of streptolydigin was much more rapid in the cultural supernatants with pH 3.05, only requiring 2 hours. Qualitative analysis of the degradation products by LC-MS/MS and PDA indicated that hydrolysis of the epoxy ether bond and acid amide bond was the major mechanism of degradation in acidic cultural supernatants. Two degradation products in the acid supernatant were assumed.     

Structural elucidation studies of erythromycins by electrospray tandem mass spectrometry

Erythromycin A (EryA) was studied by electrospray ionisation tandem mass spectrometry (ESI-MS/MS) with the aim of developing a methodology for the structural elucidation of novel erythromycins developed by biological synthetic methods. Skimmer dissociation along with sequential mass spectrometry studies (up to MS5) have been employed in this study. In the low-resolution MS/MS analysis of the polyketides, there are several fragment ions that are easily assigned to various neutral losses. These have all been confirmed by accurate-mass measurements. There is also a series of peaks due to ring opening and fragmentation that can only be assigned by high-resolution MSn analysis. Further experiments were performed in deuterated media (D2O/CD3OD 50%) which, along with the high-resolution MSn of erythromycin analogues, has enabled us to identify some of the steps in the ring fragmentation, particularly the loss of the polyketide starter acid. This is an essential step for determining structural alterations in the novel polyketides, but further labelling experiments and studies on more erythromycin analogues are required before the complete fragmentation pathway can be confirmed.     

Synthesis of distamycin A polyamides targeting G-quadruplex DNA

A number of amide-linked oligopyrroles based on distamycin molecules have been synthesized by solid-state methods, and their interactions with a human intramolecular G-quadruplex have been measured by a melting procedure. Several of these molecules show an enhanced ratio of quadruplex vs. duplex DNA binding compared to distamycin itself, including one with a 2,5-disubstituted pyrrole group. Quadruplex affinity increases with the number of pyrrole groups, and it is suggested that this is consistent with a mixed groove/G-quartet stacking binding mode.     

A Convenient Method for the Synthesis of Distamycin Analogue

A novel distamycin analogue was synthesized by chloroform reaction and DCC/HOBT coupling reaction without using amino protection and deprotection.     

Stereochemical differentiation of C‐7 hydroxyltaxane isomers by electrospray ionization mass spectrometry

In this study, different electrospray ionization mass spectrometric (ESI‐MS) methods were utilized to analyze several pairs of taxane stereoisomers including paclitaxel and 7‐epi‐paclitaxel. Both ESI‐MS and tandem mass spectrometry (MS/MS) techniques provided stereochemically dependent mass spectra in negative‐ion mode, and all studied stereoisomers could be easily distinguished based on their characteristic ions or distinct fragmentation patterns. MS/MS experiments for several taxane analogues at various collision energies were performed to elucidate potential dissociation pathways. The gas‐phase deprotonation potentials were also calculated to estimate the most thermodynamically favorable deprotonation site using DFT B3LYP/6‐31G(d). The results of the theoretical studies agreed well with the fragmentation patterns of paclitaxel and 7‐epi‐paclitaxel observed from MS/MS experiments. In addition, it was found that liquid chromatography (LC)/ESI‐MS was a useful and sensitive technique for assignment of C‐7 taxane stereoisomers from realistic samples. Copyright © 2009 John Wiley & Sons, Ltd.     

A total synthesis of distamycin a,an antiviral antibiotic

A new total synthesis of distamycin A (1) is described. The route followed passes through an intermediate acid (2a) which can serve as a convenient starting material for the synthesis of distamycin analogs.     

Product ion mass spectra of amphetamine-type substances, designer analogues, and ketamine using ultra-performance liquid chromatography/tandem mass spectrometry

This paper describes the application of ultra-performance liquid chromatography/tandem mass spectrometry (UPLC/MS/MS) technology to separate and identify amphetamine-type substances (amphetamine, methamphetamine), common and novel designer analogues (MDA, MDMA, PMA, 4-MTA, MBDB), and ketamine using Acquity UPLC/Micromass Quattro Micro API mass spectrometer instrumentation (Waters Corporation, USA). From injection of drug reference standards, it was demonstrated that these compounds can be identified by product ion mass spectra in less than 4 min total analysis time, indicating that the technological advancements associated with UPLC/MS/MS allow it to serve as a powerful analytical tool for high-throughput testing. In addition to demonstrating the separation and response of these drug compounds under the stated UPLC/MS/MS conditions, we believe the acquired product ion spectra will be a beneficial reference to laboratories interested in incorporating the use of this technology in the routine analysis of drugs of abuse.     

Synthesis of isochrysohermidin-distamycin hybrids

The synthesis of the alkylating subunit of the DNA cross-linking agent, isochrysohermidin (2), and its subsequent incorporation into conjugates with distamycin A (1) are described. The DNA binding properties of these agents were compared to that of distamycin A, using a fluorescence intercalator displacement (FID) assay.     

Combinatorial synthesis, reversed-phase and normal-phase high-performance liquid chromatography elution data and liquid chromatography/positive atmospheric pressure chemical ionization tandem mass spectra of methoxylated and glycosylated resveratrol analogues

Analyses of methoxylated and glycosylated stilbenes remain scarce in the literature because of the commercial unavailability of these compounds. Here a library of 22 compounds was synthesized by combinatorial chemistry. Their elution profiles were compared on three different columns (C18, C8, and silica) with those of seven commercial resveratrol analogues and two viniferins. The spectra recorded by liquid chromatography/positive atmospheric pressure chemical ionization tandem mass spectrometry (LC-APCI(+)-MS/MS) are discussed and recommendations made for easier identification of new stilbenes.