Determination of Alkaloids and Flavonoids in Sophora flavescens by UHPLC-Q-TOF/MS

This study is based on UHPLC-Q-TOF/MS and fragment ions to achieve classification and identification of alkaloids and flavonoids in Sophora flavescens. By reviewing the available and relevant literature, the mass fragmentation rules of alkaloids and flavonoids were summarized. 0.1% formic acid water (A) and acetonitrile (B) were used as mobile phases. 37 chemical constituents were identified, including 13 alkaloids and 24 flavonoids. This research method offers a complete strategy based on the fragmentation information of characteristic fragment ions and neutral loss obtained by MS/MS to characterize the chemical composition of Sophora flavescens.

“Molecular Anatomy”: a new multi-dimensional hierarchical scaffold analysis tool

The scaffold representation is widely employed to classify bioactive compounds on the basis of common core structures or correlate compound classes with specific biological activities. In this paper, we present a novel approach called “Molecular Anatomy” as a flexible and unbiased molecular scaffold-based metrics to cluster large set of compounds. We introduce a set of nine molecular representations at different abstraction levels, combined with fragmentation rules, to define a multi-dimensional network of hierarchically interconnected molecular frameworks. We demonstrate that the introduction of a flexible scaffold definition and multiple pruning rules is an effective method to identify relevant chemical moieties. This approach allows to cluster together active molecules belonging to different molecular classes, capturing most of the structure activity information, in particular when libraries containing a huge number of singletons are analyzed. We also propose a procedure to derive a network visualization that allows a full graphical representation of compounds dataset, permitting an efficient navigation in the scaffold’s space and significantly contributing to perform high quality SAR analysis. The protocol is freely available as a web interface at https://ma.exscalate.eu.

“Molecular Anatomy”: A New Multi-Dimensional Hierarchical Scaffold Analysis tool

The scaffold representation is widely employed to classify bioactive compounds on the basis of common core structures or correlate compound classes with specific biological activities.In this paper, we present a novel approach called “Molecular Anatomy” as a flexible and unbiased molecular scaffold-based metrics to cluster large set of compounds. We introduce a set of nine molecular representations at different abstraction levels, combined with fragmentation rules, to define a multi-dimensional network of hierarchically interconnected molecular frameworks. We demonstrate that the introduction of a flexible scaffold definition and multiple pruning rules is an effective method to identify relevant chemical moieties. This approach allows to cluster together different molecular species with similar biological activity, capturing most of the structure activity information, in particular when libraries containing a huge number of singletons are analyzed. We also propose a procedure to derive a network visualization that allows a full graphical representation of compounds dataset, permitting an efficient navigation in the scaffold’s space and significantly contributing to perform high quality SAR analysis.

“Molecular Anatomy”: A New Multi-Dimensional Hierarchical Scaffold Analysis tool

The scaffold representation is widely employed to classify bioactive compounds on the basis of common core structures or correlate compound classes with specific biological activities. In this paper, we present a novel approach called “Molecular Anatomy” as a flexible and unbiased molecular scaffold-based metrics to cluster large set of compounds. We introduce a set of nine molecular representations at different abstraction levels, combined with fragmentation rules, to define a multi-dimensional network of hierarchically interconnected molecular frameworks. We demonstrate that the introduction of a flexible scaffold definition and multiple pruning rules is an effective method to identify relevant chemical moieties. This approach allows to cluster together different molecular species with similar biological activity, capturing most of the structure activity information, in particular when libraries containing a huge number of singletons are analyzed. We also propose a procedure to derive a network visualization that allows a full graphical representation of compounds dataset, permitting an efficient navigation in the scaffold’s space and significantly contributing to perform high quality SAR analysis.

Analysis of Chemical Constituents of Guizhi Shaoyao Zhimu Granules by UPLC-Q-Orbitrap HRMS

Background: Guizhi Shaoyao Zhimu Granules (GSZG), which are derived from Guizhi Shaoyao Zhimu decoction in China, have good clinical efficacy in Rheumatoid arthritis(RA) especially. However, there is currently no reliable and systematic method to research the effective ingredients of the kind of prescription. Methods: Vanquish Ultra High Performance Liquid Chromatography Q Exactive IV Pole-electrostatic field orbital trap high resolution mass spectrometer (UPLC-Q-Orbitrap HRMS), a quick and systematic method was established and apply to analysis the chemical component of GSZG. According to using reference standards comparsion, fragmentation rules elucidation and available databases like mzCloud and the OTCML to identify the components of GSZG.Results: The results showed that it identified a total of 74 components, including 2 chromone, 23 flavonoids, 10 alkaloid, 9 phenolic acid, 8 nucleosides and nucleobases, and 22 other components, were characterized from GSZG. Conclusion: this was the first time to systematically report the compounds of GSZG, the chemical basis inquiry of this work would have a profound impact on mechanism exploration and providing certain reference for the preparation and quality control of GSZG developed by China independently.

Mining the NIST Mass Spectral Library Reveals the Extent of Sodium Assisted Inductive Cleavage in Collision-Induced Fragmentation

Interpretation and annotation of fragmentation mass spectra strongly depends on our knowledge of collision-induced fragmentation mechanisms. Computational methods for interpretation of fragmentation operate in the boundaries of recognized fragmentation rules. The prevalence of non-sodiated fragment ions in sodiated ion fragmentation spectra is not yet fully recognized by the mass spectrometry community. Here, we investigated the extent of “Sodium Assisted Inductive Cleavage” (SAIC), a charge migration fragmentation occurring in the fragmentation spectra of sodiated precursors. The NIST17 fragmentation library was mined for evidence of SAIC. A substantial amount of fragment ions in sodiated precursor spectra can be linked to SAIC. Thus, this fragmentation mechanism must be considered to allow for accurate interpretation of fragmentation spectra.

Mining the NIST Mass Spectral Library Reveals the Extent of Sodium Assisted Inductive Cleavage in Collision-Induced Fragmentation

Interpretation and annotation of fragmentation mass spectra strongly depends on our knowledge of collision-induced fragmentation mechanisms. Computational methods for interpretation of fragmentation operate in the boundaries of recognized fragmentation rules. The prevalence of non-sodiated fragment ions in sodiated ion fragmentation spectra is not yet fully recognized by the mass spectrometry community. Here, we investigated the extent of “Sodium Assisted Inductive Cleavage” (SAIC), a charge migration fragmentation occurring in the fragmentation spectra of sodiated precursors. The NIST17 fragmentation library was mined for evidence of SAIC. A substantial amount of fragment ions in sodiated precursor spectra can be linked to SAIC. Thus, this fragmentation mechanism must be considered to allow for accurate interpretation of fragmentation spectra.

A Comprehensive Review of the Structure Elucidation of Tannins from Terminalia Linn.

Objectives. Tannins with complex structures are important plant resources, which are abundant in the genus Terminalia. Various Terminalia species have been playing an important role in traditional medicine system. A systematic scoping review of Terminalia Linn. research literature for tannins was conducted to summarize the structures of tannins and analysis fragmentation pathway characteristics, which could provide references for the structural analysis of tannins from Terminalia Linn. Methods. After an update of the literature search up to September 2018, the terms of Terminalia in all publications were analyzed. Electronic searches were conducted in scifinder and PubMed, and the information from 197 articles in all with regard to the tannin structure study was extracted. Results. The compounds of 82 tannins from the genus Terminalia were reviewed. According to the structural differences, they can be divided into three categories, hydrolysable tannins, condensed tannins, and complex tannins, respectively. The fragmentation pathways of 46 identified tannins were analyzed, and the fragmentation rules of tannins were speculated according to different types. Conclusion. This review has attracted attention to the active substances in this species such as the tannins summarized in further study. How to improve the extraction and purification technology of tannins from genus Terminalia is an urgent problem to be solved.

Chemical Profiling of Xueshuan Xinmaining Tablet by HPLC and UPLC-ESI-Q-TOF/MS

Xueshuan Xinmaining Tablet (XXT) is a widely used traditional Chinese medicine for the treatment of stroke, chest pain, coronary heart disease, and angina pectoris caused by blood stasis. Having a multiple-component preparation, it is still far from meeting the requirements of modernization and standardization because its detailed chemical basis and action mechanism have not been clarified. In this work, the different batches of XXT samples were analyzed by HPLC and the typical sample was analyzed by UPLC-ESI-Q-TOF/MS to understand its chemical profiling. As a result, 77 chromatographic peaks were detected, among which 63 constituents were identified or tentatively characterized based on the comparison of retention time and UV spectra with authentic compounds as well as by summarized MS fragmentation rules and matching of empirical molecular formula with those of published components. This is the first systematic report on the chemical profiling of the commercial XXT products, which provides the sufficiently chemical evidence for the global quality evaluation of XXT products.