Automation of data analysis in High-Troughput Experimentation using WebChembase server application

Automation of data analysis in High-Troughput Experimentation using WebChembase server application

ESOC 2021. European Symposium on Organic Chemistry. Virtual Mini Symposium. July 2021

Elisabeth Ortega-Carrasco, Jenny Desantis, Stefano Bonciarelli, Laura Goracci, Ismael Zamora

Abstract

High-throughput experimentation is nowadays a well-known technique useful to design large arrays of experiments on microscale, accelerating the exploration of reaction conditions in order to find the most appropriate combination of reaction constituents efficiently.1

General HTE workflows include the use of HPLC and UPLC, frequently with MS detection to generate results quickly. Additional structural information provided by HRMS can be useful to properly identify reaction products.2 However, the large amount of data generated in HTE can be overwhelming if scientists do not have the appropriate software devoted to this task.

In the present work, an automatic workflow covering completely the HRMS processing and analysis steps using WebChembase application server will be shown. The complete workflow starts by processing HRMS data from a local (HRMS computer, scientist laptop, …) or remote (network drive, AWS Bucket, UNIFI server,…) folder using MassChemSite (Molecular Discovery, Ltd) 2 in background. Then, processing results will be loaded into WebChembase server and later automatically analyzed applying the conditions predefined by the user. Final results can be later summarized in a report generated once the experiment data is processed.

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Automation of Routine HRMS Analysis for stress testing: lansoprazole as case study

Automation of Routine HRMS Analysis for stress testing: lansoprazole as case study

August 2021. 61st Annual Land o’ Lakes Pharmaceutical Analysis Conference

Elisabeth Ortega-Carrasco, Luca Morettoni, Fabien Fontaine, Ismael Zamora

Abstract

Purpose:

The purpose of this work is to show the automation workflow that can be achieve by using software tools (MassChemSite\WebChembase) for unsupervised and fast data processing and analysis to identify the degradation products of lansoprazole under multiple stress conditions (acid, base, neutral and oxidative stress).

Methods:

Experimental data for the forced degradation study of lansoprazole was obtained following the ICH guidelines Q1A (R2). Lansoprazole was stressed under acidic (0.01 N HCl; room temperature; 60 min), basic (2N NaOH; 80 ⁰C; 72h), neutral (H2O/ACN 50:50, % v/v; 80 ⁰C; 48h) and oxidative (H2O2; room temperature; 60 min) stress conditions. Samples were analyzed via LC-HRMS using an Agilent Q-TOF 6450 coupled to an UV-Vis detector. Data processing was performed using the Derivatization workflow within the MassChemSite application (Molecular Discovery, Ltd). The processed data was consolidated by collecting all the samples for the same experimental condition and automatic comparison of the degradation products obtained in each sample.

Results:

The automatic approach provided to the researcher the structure of the different degradants found under the four mentioned conditions according to the m/z from the degradation reaction and the agreement between the structure of the degradation product and the MS/MS fragmentation. Moreover, kinetic parameters are also reported for the reactant compound degradation. Acidic stress condition resulted the most aggressive for lansoprazole drug being totally degraded in 60 minutes and generating lansoprazole sulfide as main degradant. For oxidative stress condition, the degradation reaction was stopped after 60 minutes, and lansoprazole was partially degraded to its oxidation product (lansoprazole sulphone). Under basic media, lansoprazole was almost unaltered. Last, under neutral conditions lansoprazole was totally degraded after 24h, generating two major degradants (the reduction product and a reorganization involving the loss of the sulfoxide group).

Conclusions:

The automatic workflow has been proved as a valuable tool for general chemistry by automatize structural elucidation of reaction products.

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Development, optimization and implementation of a centralized metabolic soft spot assay

Development, optimization and implementation of a centralized metabolic soft spot assay

April 2017

Anthony A PaivaCheryl KlakouskiShu LiBenjamin M JohnsonYue-Zhong ShuJonathan JosephsTatyana ZvyagaIsmael ZamoraWilson Z Shou

Abstract

Aim 

High clearance is a commonly encountered issue in drug discovery. Here we present a centralized metabolic soft spot identification assay with adequate capacity and turnaround time to support the metabolic optimization needs of an entire discovery organization.

Methodology

An integrated quan/qual approach utilizing both an orthogonal sample-pooling methodology and software-assisted structure elucidation was developed to enable the assay. Major metabolic soft spots in liver microsomes (rodent and human) were generated in a batch mode, along with kinetics of parent disappearance and metabolite formation, typically within 1 week of incubation.

Results & conclusion

A centralized metabolic soft spot identification assay has been developed and has successfully impacted discovery project teams in mitigating instability and establishing potential structure-metabolism relationships.

Keywords

Dual-concentration incubation; metabolic soft spot; metabolic stability; orthogonal sample pooling; software assisted data processing.

Automatic Identification of Lansoprazole Degradants under Stress Conditions by LC-HRMS with MassChemSite and WebChembase

Automatic Identification of Lansoprazole Degradants under Stress Conditions by LC-HRMS with MassChemSite and WebChembase

June 2021.

Stefano Bonciarelli, Jenny Desantis*, Laura Goracci, Lydia Siragusa, Ismael Zamora, Elisabeth Ortega-Carrasco*

Abstract

Stress testing is one of the most important parts of the drug development process, helping to foresee stability problems and to identify degradation products. One of the processes involving stress testing is represented by forced degradation studies, which can predict the impact of certain conditions of pH, moisture, heat, or other negative effects due to transportation or packaging issues on drug potency and purity, ensuring patient safety. Regulatory agencies have been working on a standardization of laboratory procedures since the past two decades. One of the results of those years of intensive research is the International Conference on Harmonization (ICH) guidelines, which clearly define which forced degradation studies should be performed on new drugs, which become a routine work in pharmaceutical laboratories. Since used techniques based on high-performance liquid chromatography coupled with high-resolution mass spectrometry have been developed years ago and are now mastered by pharmaceutical scientists, automation of data analysis, and thus data processing, is becoming a hot topic nowadays. In this work, we present MassChemSite and WebChembase as a tandem to automatize the routine analysis studies without missing information quality, using as a case study the degradation of lansoprazole under acidic, oxidative, basic, and neutral stress conditions.

Mass spectrometry imaging of phosphatidylcholine metabolism in lungs administered with therapeutic surfactants and isotopic tracers

Mass spectrometry imaging of phosphatidylcholine metabolism in lungs administered with therapeutic surfactants and isotopic tracers

January 2021.

Shane R. Ellis, Emily Hall, Madhuriben Panchal, Bryn Flinders, Jens Madsen, Grielof KosterRon.M.AHeeren, Howard W. Clark, Anthony D. Postle 

Abstract

Mass spectrometry imaging (MSI) visualizes molecular distributions throughout tissues but is blind to dynamic metabolic processes. Here, MSI with high mass resolution together with multiple stable isotope labelling provided spatial analyses of phosphatidylcholine (PC) metabolism in mouse lungs. 

Dysregulated surfactant metabolism is central to many respiratory diseases. Metabolism and turnover of therapeutic pulmonary surfactants were imaged from distributions of intact and metabolic products of an added tracer, universally 13C-labelled dipalmitoyl PC (U13C-DPPC). The parenchymal 

distributions of newly synthesized PC species were also imaged from incorporations of methyl-D9- choline. This dual labelling strategy demonstrated both lack of inhibition of endogenous PC synthesis by exogenous surfactant and location of acyl chain remodeling processes acting on the U13C-DPPClabelled surfactant, leading to formation of polyunsaturated PC lipids. This ability to visualize discrete metabolic events will greatly enhance our understanding of lipid metabolism in diverse tissues and has potential application to both clinical and experimental studies.