MS Visualization and Interpretation Software (MS‐VIS), a Tool for Visualizing Mass Spectra and Analyzing Mass Lists

Incorporating selenium metal bonded to the pyridine nucleus was achieved by the reaction of selenium metal with 2-chloropyridine carbonitrile 1 in the presence of sodium borohydride as reducing agent. The resulting non isolated selanyl sodium salt was subjected to react with various α-halogenated carbonyl compounds to afford the selenyl pyridine derivatives 3a-f which compounds 3a-d underwent Thorpe-Ziegler cyclization to give 1-amino-2-substitutedselenolo[2,3-b]pyridine compounds 4a-d, while the other compounds 3e,f failed to be cyclized. Basic hydrolysis of amino selenolo[2,3-b]pyridine carboxylate 4a followed by decarboxylation furnished the corresponding amino selenolopyridine compound 6 which was used as a versatile precursor for synthesis of other heterocyclic compound 7-16. All the newly synthesized compounds were established by elemental and spectral analysis (IR, 1H NMR) in addition to mass spectra for some of them hoping these compounds afforded high biological activity.

Download Full-text

Exploring the Active Compounds of Traditional Mongolian Medicine Agsirga in Intervention of Novel Coronavirus (2019-nCoV) Based on HPLC-Q-Exactive-MS/MS and Molecular Docking Method

10.26434/chemrxiv.11955273 ◽

2020 ◽

Author(s):

Jie Cheng ◽

Yuchen Tang ◽

Baoquan Bao ◽

Ping Zhang

Keyword(s):

Mass Spectrometry ◽

Molecular Docking ◽

High Resolution ◽

Mass Spectra ◽

High Resolution Mass Spectrometry ◽

Structural Formula ◽

Active Compounds ◽

High Resolution Mass ◽

Q Exactive ◽

Resolution Mass

<a></a><a></a><a></a><a>Objective</a>: To screen all compounds of Agsirga based on the HPLC-Q-Exactive high-resolution mass spectrometry and find potential inhibitors that can respond to 2019-nCoV from active compounds of Agsirga by molecular docking technology. Methods: HPLC-Q-Exactive high-resolution mass spectrometry was adopted to identify the complex components of Mongolian medicine Agsirga, and separated by the high-resolution mass spectrometry Q-Exactive detector. Then the Orbitrap detector was used in tandem high-resolution mass spectrometry, and the related molecular and structural formula were found by using the chemsipider database and related literature, combined with precise molecular formulas (errors ≤ 5 × 10−6) , retention time, primary mass spectra, and secondary mass spectra information, The fragmentation regularities of mass spectra of these compounds were deduced. Taking ACE2 as the receptor and deduced compounds as the ligand, all of them were pretreated by discover studio, autodock and Chem3D. The molecular docking between the active ingredients and the target protein was studied by using AutoDock molecular docking software. The interaction between ligand and receptor is applied to provide a choice for screening anti-2019-nCoV drugs. Result: Based on the fragmentation patterns of the reference compounds and consulting literature, a total of 96 major alkaloids and stilbenes were screened and identified in Agsirga by the HPLC-Q-Exactive-MS/MS method. Combining with molecular docking, a conclusion was got that there are potential active substances in Mongolian medicine Agsirga which can block the binding of ACE2 and 2019-nCoV at the molecular level.

Download Full-text

α-Methylene-β-Lactone Probe for Measuring Live-Cell Reactions of Small Molecules

10.26434/chemrxiv.12078582.v2 ◽

2020 ◽

Author(s):

Lei Wang ◽

Louis Riel ◽

Bekim Bajrami ◽

Bin Deng ◽

Amy Howell ◽

...

Keyword(s):

Mass Spectra ◽

Live Cell ◽

Live Cells ◽

The Novel ◽

Proteomics Analysis ◽

Chemical Proteomics ◽

Tandem Mass Spectra ◽

Modified Peptides ◽

Covalent Probes ◽

Ht 29

The novel use of the α-methylene-β-lactone (MeLac) moiety as a warhead of multiple electrophilic sites is reported. In this study, we demonstrate that a MeLac-alkyne is a competent covalent probe and reacts with diverse proteins in live cells. Proteomics analysis of affinity-enriched samples identifies probe-reacted proteins, resolves their modified peptides/residues, and thus characterizes probe-protein reactions. Unique methods are developed to evaluate confidence in the identification of the reacted proteins and modified peptides. Tandem mass spectra of the peptides reveal that MeLac reacts with nucleophilic cysteine, serine, lysine, threonine, and tyrosine residues, through either Michael addition or acyl addition. A peptide-centric proteomics platform, using MeLac-alkyne as the measurement probe, successfully analyzes the Orlistat selectivity in live HT-29 cells. MeLac is a versatile warhead demonstrating enormous potential to expedite the development of covalent probes and inhibitors in interrogating protein (re)activity. MeLac-empowered platforms in chemical proteomics are widely adaptable for measuring the live-cell action of reactive molecules.

Download Full-text

Structure Revision of Protoaculeine B, a Posttranslationally Modified N-Terminal Residue in the Peptide Toxin Aculeine B

10.26434/chemrxiv.13066082 ◽

2020 ◽

Author(s):

Raku Irie ◽

Kei Miyako ◽

Satoko Matsunaga ◽

Ryuichi Sakai ◽

Masato Oikawa

Keyword(s):

Mass Spectra ◽

Chemical Reactivity ◽

Model Compounds ◽

Structural Revision ◽

Structure Revision ◽

Peptide Toxin ◽

One Step ◽

Marine Peptide ◽

Synthetic Models ◽

Long Chain

<div>Here, we newly propose the structure of protoaculeine B, an N-terminal moiety of the marine peptide toxin aculeine B, as possessing the cis-disubstituted tetrahydro-beta-carboline framework. We prepared two truncated model compounds that lack long-chain polyamine by one-step Pictet-Spengler reaction of tryptophan, and compared the NMR and mass spectra and chemical reactivity with those of natural protoaculeine B. The synthetic models reproduced the profiles of the natural product well, which was conclusive for the structural revision.</div>

Download Full-text

Unrestrictive protein modification localization and quality control for open search of mass spectra

10.26434/chemrxiv.5797995 ◽

2018 ◽

Author(s):

Zhiwu An ◽

Fuzhou Gong ◽

Yan Fu

Keyword(s):

Mass Spectrometry ◽

Quality Control ◽

Tandem Mass Spectrometry ◽

Mass Spectra ◽

Protein Modification ◽

Software Tool ◽

Tandem Mass ◽

Simulation Data ◽

Post Translational Modifications

We have developed PTMiner, a first software tool for automated, confident filtering, localization and annotation of protein post-translational modifications identified by open (mass-tolerant) search of large tandem mass spectrometry datasets. The performance of the software was validated on carefully designed simulation data.

Download Full-text