MassChemSite for In-Depth Forced Degradation Analysis of PARP Inhibitors Olaparib, Rucaparib, and Niraparib

MassChemSite for In-Depth Forced Degradation Analysis of PARP Inhibitors Olaparib, Rucaparib, and Niraparib

February 2023

Stefano BonciarelliJenny DesantisSimone CerquigliniLaura Goracci 

 

Abstract

Drugs must satisfy several protocols and tests before being approved for the market. Among them, forced degradation studies aim to evaluate drug stability under stressful conditions in order to predict the formation of harmful degradation products (DPs). Recent advances in LC-MS instrumentation have facilitated the structure elucidation of degradants, although a comprehensive data analysis still represents a bottle-neck due to the massive amount of data that can be easily generated. MassChemSite has been recently described as a promising informatics solution for LC-MS/MS and UV data analysis of forced degradation experiments and for the automated structural identification of DPs. Here, we applied MassChemSite to investigate the forced degradation of three poly(ADP-ribose) polymerase inhibitors (olaparib, rucaparib, and niraparib) under basic, acidic, neutral, and oxidative stress conditions. Samples were analyzed by UHPLC with online DAD coupled to high-resolution mass spectrometry. The kinetic evolution of the reactions and the influence of solvent on the degradation process were also assessed. Our investigation confirmed the formation of three DPs of olaparib and the wide degradation of the drug under the basic condition. Intriguingly, base-catalyzed hydrolysis of olaparib was greater when the content of aprotic-dipolar solvent in the mixture decreased. For the other two compounds, whose stability has been much less studied previously, six new degradants of rucaparib were identified under oxidative degradation, while niraparib emerged as stable under all stress conditions tested.

 

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Guiding the choice of informatics software and tools for lipidomics research applications

Guiding the choice of informatics software and tools for lipidomics research applications

February 2023.

Zhixu Ni Michele WölkGeoff JukesKarla Mendivelso EspinosaRobert AhrendsLucila AimoJorge Alvarez-JarretaSimon AndrewsRobert AndrewsAlan BridgeGeremy C ClairMatthew J ConroyEoin FahyCaroline GaudLaura GoracciJürgen HartlerNils HoffmannDominik KopczyinkiAnsgar KorfAndrea F Lopez-ClavijoAdnan MalikJacobo Miranda AckermanMartijn R MolenaarClaire O’DonovanTomáš PluskalAndrej ShevchenkoDenise SlenterGary SiuzdakMartina KutmonHiroshi TsugawaEgon L WillighagenJianguo XiaValerie B O’DonnellMaria Fedorova

 

Abstract

Progress in mass spectrometry lipidomics has led to a rapid proliferation of studies across biology and biomedicine. These generate extremely large raw datasets requiring sophisticated solutions to support automated data processing. To address this, numerous software tools have been developed and tailored for specific tasks. However, for researchers, deciding which approach best suits their application relies on ad hoc testing, which is inefficient and time consuming. Here we first review the data processing pipeline, summarizing the scope of available tools. Next, to support researchers, LIPID MAPS provides an interactive online portal listing open-access tools with a graphical user interface. This guides users towards appropriate solutions within major areas in data processing, including (1) lipid-oriented databases, (2) mass spectrometry data repositories, (3) analysis of targeted lipidomics datasets, (4) lipid identification and (5) quantification from untargeted lipidomics datasets, (6) statistical analysis and visualization, and (7) data integration solutions. Detailed descriptions of functions and requirements are provided to guide customized data analysis workflows.

 

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A platelet lipidomics signature in patients with COVID-19

A platelet lipidomics signature in patients with COVID-19

December 2023.

Laura Goracci, Eleonora Petito, Alessandra Di Veroli, Emanuela Falcinelli, Caterina Bencivenga, Elisa Giglio, Cecilia Becattini, Edoardo De Robertis, Gaetano Vaudo, Paolo Gresele

Abstract

Ischemic cardiovascular and venous thromboembolic events are a frequent cause of death in severe COVID-19 patients. Platelet activation plays a key role in these complications, however platelet lipidomics have not been studied yet. The aim of our pilot investigation was to perform a preliminary study of platelet lipidomics in COVID-19 patients compared to healthy subjects. Lipid extraction and identification of ultrapurified platelets from eight hospitalized COVID-19 patients and eight age- and sex-matched healthy controls showed a lipidomic pattern almost completely separating COVID-19 patients from healthy controls. In particular, a significant decrease of ether phospholipids and increased levels of ganglioside GM3 were observed in platelets from COVID-19 patients. In conclusion, our study shows for the first time that platelets from COVID-19 patients display a different lipidomics signature distinguishing them from healthy controls, and suggests that altered platelet lipid metabolism may play a role in viral spreading and in the thrombotic complications of COVID-19.

Keywords: COVID-19; Platelet lipidomics.

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Analysis of Phosphatidylinositol Modifications by Reactive Nitrogen Species Using LC-MS: Coming to Grips with Their Nitroxidative Susceptibility

Analysis of Phosphatidylinositol Modifications by Reactive Nitrogen Species Using LC-MS: Coming to Grips with Their Nitroxidative Susceptibility

July 2023.

Stefano Bonciarelli, Bruna Neves, Pedro Domingues, Tânia Melo, Laura Goracci, Maria Rosário Domingues

Abstract

Phosphatidylinositols (PIs) are complex lipids that play a key role in cell signaling. Like other phospholipids, they are esterified with unsaturated fatty acyl residues (FAs), making them susceptible to modification by reactive oxygen and nitrogen species (RNS). Recent studies using mass spectrometry (MS)-based lipidomics approaches have revealed that lipid nitration results in a plethora of structurally and chemically modified lipids (epilipids), including nitrated and nitroxidized derivatives of phosphatidylcholines, phosphatidylethanolamines, phosphatidylserines, and cardiolipins. However, there is a notable lack of knowledge regarding the characterization of RNS-modified PI derivatives. In this study, we used C18 high-resolution liquid chromatography-tandem MS approaches to describe the fragmentation signature of nitrated and nitroxidized PIs, bearing different fatty acyl chains. Using this approach and accurate mass measurements, we were able to identify nitro- PI derivatives, dinitro- and nitrohydroxy- derivatives for a few PI species. The data showed the typical neutral loss of nitrous acid (HNO2) as well as the fragmentation patterns corresponding to modified fatty acyl chains (such as NOx-RCOO, [M – NOx-RCOOH – H] and [M – NOx-RCOOH – C6H10O5 – H]), making it possible to identify these epilipids. The susceptibility of PIs to nitration was also investigated, revealing that it depends exclusively on the chains of unsaturated FAs esterified in PI, showing a higher conversion rate for those with C18:1. Overall, the knowledge gathered in this study will contribute to the precise characterization of these epilipids in complex biological samples, offering new opportunities to unveil the pathophysiological roles of nitrated and nitroxidized PI derivatives at the cellular and tissue levels.

Keywords: LC-MS; lipidomics; nitration; nitrative stress; nitroxidative stress.

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