Dereplikace látek a de novo charakterizace malých molekul z hmotnostních spekter

We describe the molecular dereplication principles and de novo characterization of small molecules obtained from liquid-chromatography mass spectrometry and imaging mass spectrometry data sets. Our methodology aims at supporting chemists and computer programmers to understand the hidden computing algorithms used for metabolomics mass spectrometry data processing. The approaches have been made available in the open-source tool CycloBranch. The presented tutorial extends the interpretation of mass spectra portfolia described in a series of papers published in Chemicke Listy, issues 2/2020 and 3/2020.

Evaluating the Accuracy of the QCEIMS Approach for Computational Prediction of Electron Ionization Mass Spectra of Purines and Pyrimidines

Mass spectrometry is the most commonly used method for compound annotation in metabolomics. However, most mass spectra in untargeted assays cannot be annotated with specific compound structures because reference mass spectral libraries are far smaller than the complement of known molecules. Theoretically predicted mass spectra might be used as a substitute for experimental spectra especially for compounds that are not commercially available. For example, the Quantum Chemistry Electron Ionization Mass Spectra (QCEIMS) method can predict 70 eV electron ionization mass spectra from any given input molecular structure. In this work, we investigated the accuracy of QCEIMS predictions of electron ionization (EI) mass spectra for 80 purine and pyrimidine derivatives in comparison to experimental data in the NIST 17 database. Similarity scores between every pair of predicted and experimental spectra revealed that 45% of the compounds were found as the correct top hit when QCEIMS predicted spectra were matched against the NIST17 library of >267,000 EI spectra, and 74% of the compounds were found within the top 10 hits. We then investigated the impact of matching, missing, and additional fragment ions in predicted EI mass spectra versus ion abundances in MS similarity scores. We further include detailed studies of fragmentation pathways such as retro Diels–Alder reactions to predict neutral losses of (iso)cyanic acid, hydrogen cyanide, or cyanamide in the mass spectra of purines and pyrimidines. We describe how trends in prediction accuracy correlate with the chemistry of the input compounds to better understand how mechanisms of QCEIMS predictions could be improved in future developments. We conclude that QCEIMS is useful for generating large-scale predicted mass spectral libraries for identification of compounds that are absent from experimental libraries and that are not commercially available.

Nimesulide derivatives reduced cell proliferation against breast and ovarian cancer: synthesis, characterization, biological assessment, and crystal structure.

New nimesulide derivatives (A1-A6) were synthesized and investigated by IR, 1H NMR, 13C NMR, melting point, elemental analysis, mass spectra, and DSC analysis. Agent A3 single crystal was grown and solved in a monoclinic crystal system with Cc. Heat shock protein 27 (HSP27) and tubulin are essential cellular proteins for normal cell division and growth. In addition, these proteins are expressed highly in cancer cells. Breast cancer (SKBR3) and ovarian cancer (SKOV3) cell lines are our models for biological assessment. The data revealed that nimesulide analogs showed high cytotoxicity when treated with SKBR3 cell line ranges from 0.22 µM to 12.0 µM, while SKOV3 cell line from 0.1 µM to 16.0 µM. In-depth, structure-activity relationship applied on nimesulide lead structure highlights the importance of a bulk moiety on position two that reduces cell proliferation in both cell lines.

An efficient protocol for the synthesis of new camphor pyrimidine and camphor thiazole derivatives using conventional and microwave irradiation techniques and in vitro evaluation as potential antimicrobial agents

Background: A series of new pyrimidines and thiazoles containing camphor moiety were synthesized under both conventional and microwave irradiation techniques. Methods: The condensation of camphor either with aminoguanidine or thiosemicarbazide gives the camphor hydrazine carboximidiamide 2 and the camphor thiosemicarbazone 3, respectively. Refluxing of 3 with chloroacetonitrile afforded the camphor thiazol-4-imine 4. Compounds 2 and 4 were used as precursors for the synthesis of target products. Results: The reaction of 2 with different species such as arylidene malononitrile, acetylacetone, and ethyl acetoacetate gave the corresponding camphor pyrimidine derivatives 5a,b-7 while refluxing of compound 4 with different reagents e.g. aldehydes, isatin, ninhydrin, acetic anhydride, benzene sulphonyl chloride, and p-nitro-benzoyl chloride afforded the camphor thiazole derivatives 8a-d-13, respectively. Conclusion: A comparison between the conventional way and the eco-friendly microwave irradiation method occurred in the synthesis of the same compounds, which the latter was more efficient. The elemental analysis, FT-IR, 1H NMR, 13C NMR, and Mass spectra confirm the structures of the obtained new compounds. The potential use of some selected derivatives as antimicrobial agents was investigated and gave promising results

New soluble 4-(4-formyl-2,6-dimethoxyphenoxy) substituted phthalocyanines: Synthesis, characterization, photophysical and photochemical properties

This work describes the synthesis, spectral and fluorescence properties of bis 4-(4-formyl-2,6-dimethoxyphenoxy) substituted zinc (ZnPc) and magnesium (MgPc) phthalocyanines. The new compounds have been characterized by elemental analysis, UV-Vis, FT-IR, 1H-NMR and mass spectra. Afterward, the effects of including metal ion on the photophysicochemical properties of the complexes were studied in biocompatible solvent DMSO to analyze their potential to use as a photosensitizer in photodynamic therapy (PDT). The fluorescence and singlet oxygen quantum yields were calculated as 0.04–0.15 and 0.70–0.52 for ZnPc and MgPc, respectively. According to the results, MgPc has higher fluorescence quantum yield than ZnPc, while ZnPc has higher singlet oxygen quantum yield than MgPc. The results show that the synthesized complexes can have therapeutic outcomes for cancer treatment.

Validation of De Novo Peptide Sequences with Bottom-Up Tag Convolution

De novo sequencing is indispensable for the analysis of proteins from organisms with unknown genomes, novel splice variants, and antibodies. However, despite a variety of methods developed to this end, distinguishing between the correct interpretation of a mass spectrum and a number of incorrect alternatives often remains a challenge. Tag convolution is computed for a set of peptide sequence tags of a fixed length k generated from the input tandem mass spectra and can be viewed as a generalization of the well-known spectral convolution. We demonstrate its utility for validating de novo peptide sequences by using a set of those generated by the algorithm PepNovo+ from high-resolution bottom-up data sets for carbonic anhydrase 2 and the Fab region of alemtuzumab and indicate its further potential applications.