User story: Where Galaxy meets medicinal chemistry

Author(s) Julia Jakiela avatar Julia Jakiela
computational chemistry user story gtn

Posted on: 18 December 2023 purlPURL: https://gxy.io/GTN:N00065

As a medicinal chemistry student, I undertook a semester project on natural products isolation and derivatisation. One of the compounds my group was working on was piperine, extracted from black pepper. Inspired by literature findings, we found out that the derivatives of piperine can inhibit monoamine oxidase-B and thus can be possibly used in Parkinson’s disease. As a novelty element in our project, we came up with new structures of derivatives that could act as inhibitors.

Before synthesising any new molecules, it would make sense to check if they correctly dock into the active site. As an enthusiastic user and developer of Galaxy, the idea of using GTN came straight to my mind. Even though molecular docking was beyond the scope of our project, I knew that Galaxy and GTN give such an amazing opportunity to do it in the blink of an eye that I wouldn’t be myself if I hadn’t tried! Therefore, by using the tutorial on molecular docking, I identified the pocket, then I studied the binding of the approved drugs such as Safinamide and Zonisamide and finally I checked how our proposed molecule fits within the pocket. After that, we were ready to synthesise the derivative we came up with!

Picture of piperine derivative docking into MAO-B pocket.Open image in new tab

Figure 1: Piperine derivative as a potential inhibitor of MAO-B

This example shows how GTN and Galaxy can facilitate and accelerate the work of medicinal chemists before starting the synthesis. It is easy to follow the GTN tutorials, the results are reproducible, the datasets are stored in the history and can be easily shared with anyone on the team.


Recent News

See all news

GTN Video Library 2.0: 107 hours of learning across 154 videos

14 June 2024   gtn

Many GTN tutorials already have recordings. These recordings were made by members of the community for a variety of (online) training events. Up until now, this video library were part of the Gallantries Project. We have now integrated this video library directly into the GTN, and made it even easier to add video recordings to GTN tutorials or slide decks! Just use a Google Form to submit your video recordings!

Phylogenetics tutorial takes researchers back to basics!

13 June 2024   Phylogenetics Tutorial GTN Australian BioCommons

A new Galaxy Training Network tutorial has been created to take researchers back to basics to uncover the principles of phylogenetics and how tree-building methods work. A longstanding collaboration between Professor Michael Charleston from the University of Tasmania and Australian BioCommons has delivered this self-guided tutorial featuring videos and hands-on exercises. To maximise its impact, the resource was tailored specifically to be shared globally via the Galaxy Training Network, and will form the basis of an upcoming live training workshop.

From GTN Intern to Tutorial Author to Bioinformatician

13 June 2024   single-cell training education trajectory user contributor

With growing access and interest in sequencing data, Galaxy is a knight in shining armor for wet lab scientists hoping to analyze their own data. With long term intentions of increasing access to bioinformatic analyses, the Galaxy Training Network (GTN) creates a safe space where non-computer-scientists may analyze their own data and even learn to code: an invaluable skill in today’s scientific world. Galaxy introduced me to brand new skills as an undergraduate and ultimately changed the trajectory of my career. Here is my story as a biology undergraduate with no coding experience turned GTN contributor &, eventually, coding bioinformatician: thanks to Galaxy.