Data Management
Data management is an essential component of the drug discovery process. Without proper data management, it can be challenging to connect data across different disciplines, leading to missed information and lost opportunities. However, data management does more than just linking data. It can assist in optimising chemical reactions, library enumeration, compound design, and many other critical aspects of drug discovery.
By implementing data management techniques, drug discovery teams can streamline their workflows, reduce errors and improve decision-making. With the right data management tools and strategies, researchers can access, analyse, and share data across different teams and disciplines, ensuring that everyone is working towards the same goal.
This section will provide you worked examples and tools to implement data management into your drug discovery pipeline
KNIME: Reaction Enumeration
A tutorial on virtual synthesis using data-mining software KNIME.
Have you ever been overwhelmed by the vast array of reagents when trying to synthesise a collection of compounds? With this tutorial, you can now easily filter and narrow down your list of compounds using descriptors and compound properties.
In this tutorial, we will be working with amides synthesised from primary amines and carboxylic acids from commercial catalogues. The step-by-step guide will walk you through the entire process, from data preparation to filtering your list of compounds. Additionally, you will be able to search for your compounds in ChEMBL to see if your compounds are novel or already contain information against your drug target of interest.
This tutorial is a must for anyone who needs to synthesise a collection of compounds efficiently and effectively
KNIME: Reaction Customisation
This tutorial follows on from “Reaction Enumeration”. Now that you have established how to build a library of compounds from carboxylic acids and amines, “Reaction Customisation” will take you through how to change the workflow to allow for customised reactions using SMARTS.
This tutorial is a must for anyone wanting to synthesise a library of compounds using common reactions.
KNIME: Isosteric Replacement
A tutorial on how to apply isosteric replacements on a chemical structure using KNIME.
Isosterism – a known strategy in drug design – can be used to generate new chemical entities by replacing one functional group of the molecule by another with common electronic properties (isostere). Given the known number of possible isosteric replacements for some functional groups, this effort can be burdensome sometimes. What if you could easily enumerate the possible isosteric exchanges that can be applied on a molecule structure?
In this tutorial, we will be working with a known drug structure – Celecoxib – and, with a step-by-step guide, you will check which functional groups in the drug’s structure can be replaced by isosteres. You will be able to select which functional groups you want to see the suggestions for and get the enumerated list of possible compounds. In addition to that, you will be able to search for your enumerated compounds in ChEMBL to check for novelty.
This tutorial is recommended for anyone who wants to check quickly which isosteric replacements can be applied in compound of interest.