How Discngine enhanced building blocks data handling for Medicinal Chemists – Pharma success story
Easy access to available building blocks (BBs) is fundamental to medicinal chemistry programs. BBs are critical to project SAR and the properties of final compounds. Most pharmaceutical companies possess thousands of diverse BBs, and the important information about them is stored in databases. This requires proper management to ensure the correct usage of the BBs and the rapid synthesis of desired compounds.
However, due to the sheer number and diversity of the BBs, handling those databases can be challenging. BBs data mismanagement can thus unfavorably impact the efficiency of drug discovery projects.
Building blocks are the molecular reagents or fragments used to synthesize drug compounds.
This article will highlight how Discngine collaborated with its customer from one of the Top 5 Pharma Companies to develop a centralized and customized solution for efficient BBs data handling, as well as its real-life impact on drug discovery projects.
Issues with outdated BBs data management systems
Medicinal chemists within the company’s Drug Discovery group required access to adequate BB data daily. The main challenge they encountered while searching for available BBs came from the usage of legacy tools. These applications were numerous and varied in features and having to look for BBs in multiple tools was inefficient. Such circumstances created a major bottleneck for teams’ productivity and project advancement.
The companies’ activities related to the BBs usage with legacy tools:
Number of active projects: 30-35
Number of building block data points: around 750,000 (internal collections and external supplier building block data points)
Time needed to find the building block of interest with legacy tools: 30 minutes to 1 hour (longer for complex searches)
Number of users searching for building blocks: >100
With such an amount of data, the existing BB data management tools became slow with suboptimal performance. This was emphasized when enumerating and running predictive property computations on large numbers of compounds. Moreover, some redundant tools were being discontinued, and others were becoming bug-prone without dedicated IT support.
These issues triggered an urgent need for the development of a new, standalone, centralized tool for efficient BB data handling. This new, improved solution would address medicinal chemistry bottlenecks for singleton design, library design, compound synthesis and more.
First steps toward a tailored solution
After gathering detailed requirements from medicinal chemists involved in various projects, the company’s IT Research group and users from the Discovery teams determined a multiphase project with two key releases:
The primary objective of the initial release was to establish an efficient framework for storing and managing BB data.
For the second release, they envisioned the integration of the solution with internal tools and the broader internal IT ecosystem.
Overall, they aimed for a custom-made, flexible tool that could be continually expanded upon, making it useful for the entire medicinal chemistry community.
“Based on these requirements, the off-the-shelf software wasn’t a good fit since it didn’t allow the level of integration and flexibility necessary to fulfill our needs.”
Recognizing the need for a tailored solution, the company reached out to Discngine to collaborate on the development of this new standalone centralized tool for efficient BB data handling.
The decision to involve Discngine in this project was driven by the decade-long history of productive collaboration and successful scientific informatics projects. The mutual trust, long-term collaborations, and the Discngine team’s expertise seamlessly justified this choice.
Looking for a tailored solution for drug discovery research? Check out our custom services
The power of collaboration
Upon sharing the project vision, a dedicated Discngine team worked closely with the company’s IT Research group and users from the Discovery teams on the foundation of the tool. The Discngine team’s input was crucial as the team quickly understood requirements for the development of the tool and provided constructive advice in making critical software development decisions, such as how to:
Access data ingestion from in-house and external supplier sources from pre-existing tools.
Format structures (SMILES vs SMARTS vs InChIs vs InChIKeys) to be able to view listed structures.
Display results after various queries, including structure, substructure, and similarity searches.
Keep the flexibility to build on the tool in the future.
What the customer highlighted as a key metric for successful work together was Discngine’s complete dedication to the project. Regular mockup trials for users were conducted and feedback was implemented when needed and as often as necessary before deploying new features. This open back-and-forth communication with end users ensured a user-friendly interface and quick launch of the tool.
Additionally, Discngine’s IT team maintained a hyper-vigilant mode for any technical issues that might occur. They proactively looked to identify and address errors before users encountered them. In cases where bugs did emerge, their support was rapid and extensive.
“The tool developed by Discngine has been a huge shortcut that saves our medicinal chemists time for further cycles of analyses and studies.”
Project Outcomes
The medicinal chemists are very satisfied since, with this new application, their data are organized, easy to access, and always up to date. It allows them to operate faster. What they could achieve with the legacy tools in 30 minutes to 1 hour now takes only 10-20 minutes (even for large datasets). This application has been a huge shortcut that saves medicinal chemists time (especially when working with large BB datasets) for further cycles of analyses and studies.
Time needed to find building block of interest with new platform developed by Discngine is 3 times faster than with legacy tools
The overview of the usage of the BBs data handling platform developed by Discngine:
Number of users: 120, on-site and remote
Location: various sites
Frequency of usage: weekly basis
-
Average usage: 55 searches in a week / 9 distinct users
Type of projects: Medicinal Chemistry projects across therapeutic areas
Number of queries: around 3000 from Dec 2021 to Dec 2022
Stability of the tool in prod: standalone mode
After the application’s first launch in December 2021, around 120 medicinal chemists got onboarded and started using it regularly. It became a go-to platform for users at every career level - from interns to postdocs to experienced scientists, which confirms the simplicity of the tool. Moreover, the users have been located across multiple sister sites of the company, working on-site and remotely.
The success of the project is further confirmed by the fact that the platform has been used for numerous projects in the Discovery group across different therapeutic areas. It is now possible to export data from 1,000 to 200,000 building blocks.
The usage of the tool is on a weekly basis, with the total number of queries in production being around 3,000 searches in one year period (from December 2021 to December 2022) and an average of 55 searches/week from 9 distinct users.
After just one year, the tool is fully launched and very stable in production without any major bugs.
“Performance. Efficiency. Simplicity. That’s how I would describe the platform developed by Discngine”
Summary
The usage of contemporary applications for scientific data management, which account for data centralization, integrability, and flexibility, is an effective way of accelerating drug discovery projects. After collaborating with Discngine, this leading pharma company successfully implemented the much-needed application that replaced legacy tools for BBs data handling. The tool is centralized, easy to use and extendable, which saves project time for over 100 medicinal chemists at the company, who can focus more on critical decision-making rather than technology issues.
Designed with adaptability in mind, both companies plan to enrich the tool with additional features in the future, further streamlining the drug discovery process. The company will leverage the usage of this tailored solution across more projects and onboard more users. Therefore, this success story doesn’t end here since the solution is ready for further integrations, additions, and feature developments.