Expanding 3D structure portals with BioPharma

This biopharmaceutical company finds, creates, and markets advanced medications for patients with life-threatening conditions around the globe. The main focuses of the company's research and development initiatives include inflammatory and respiratory disorders, cardiovascular ailments, hematology, liver diseases, and oncology.

Challenge: A legacy research informatics database that did not meet scientists’ needs

The medicinal/computational chemists and modelers that make up the R&D project teams required flexible ways to view the three-dimensional structures of ligand-protein complexes.

The company had previously used BIOVIA Pipeline Pilot to create a database and application that could store and provide access to biological data, medicinal chemistry, and DMPK results.

This early initiative provided a tool to access relevant data and entry points into their 3D molecular visualization system and the Cambridge Structural Database (CSD). This permitted the scientists to compare 3D structural data of related molecules. This old system, however, could not accommodate all of the 3D modeling outputs.

Projects often included modeling unsynthesized structures, so they were unavailable in core workflow systems that tracked small molecule activity and registration. Team interactions were complex because their database could not contain these potential models.

Congested folders of files, emails, and PowerPoint slides resulted in poor communication between medicinal chemists and modelers. The company’s R&D division required a sustainable and comprehensive 3D Structure Portal to enhance and accelerate its expanding pipeline of investigational compounds.

Solutions: Improved 3D structure portal built with Biovia Pipeline Pilot

The company added structures to its new 3D Structure Portal, links to Protein Data Bank (PDB) files for proteins, and Ctab files for ligands using Pipeline Pilot. The new system tracks metadata such as views and perspectives for proteins and residues related to certain projects.

Naturally, the creators retained key functionality from the original Pipeline Pilot application, like 3D visualization and CSD integration.

Scientists can link compounds to things already registered in the system, browse by batch, and search by keywords, ligand names, and registered structures. They can track their preferred biochemical assays by project and view the available IC50 values to assess the substance's efficacy in inhibiting specific biochemical or biological functions.

They can also include editable comments and ratings to promote dialog among team members. The Structure Portal also automatically connects synthesized molecules to prospective structures when possible. If a 3D model is available for a registered substance, scientists can immediately tell by looking at it.

A scientific automation feature called BIOVIA Pipeline Pilot promotes research innovation, boosts operational effectiveness, and lowers expenses for both IT and research. The software provides data management, analysis, and reporting for textual, numerical, and complicated scientific data, such as chemical structures, biological sequences, and scientific imagery.

It also offers collections of scientific building blocks that researchers can drag and drop into digital workflows to enable quick data processing, retrieval, modification, computational analysis, filtering, displaying, and reporting.

Pipeline Pilot’s extensive chemistry features and powerful integration capabilities improve our ability to tie 3D models into our general research informatics infrastructure, ultimately bringing medicinal chemists closer to modelers and speeding therapeutics to people.

Director, Research Informatics, Leading Biopharmaceutical Company

The company used the same development environment, Pipeline Pilot, to build and roll out its legacy research database and application. It decided to continue to use Pipeline Pilot as the development environment for its upgraded 3D Structure Portal since it had already used it to create the central repository.

This enabled the company to reuse and improve the old system's existing code. The company's chemistry community also strongly supported Pipeline Pilot’s potent cheminformatics, ETL, and database integration capabilities.

The Pipeline Pilot Chemistry Collection was essential to the implementation of this improved Structure Portal. The collection enables scientists to manage and analyze the substances in their database through chemically intelligent filters and learning. The BIOVIA Direct Chemistry Cartridge, a high-performance data cartridge that lets users store and explore chemical structures and reactions in Oracle, is also a part of the collection.

Results: Closing the communication gap between medicinal chemists and modelers

The scientists at this company can document and replicate the steps needed to get specific outcomes by using Pipeline Pilot to compile, annotate, and version their organization's best practices.

To encourage cooperative development and information transfer, they then publish the resultant Pipeline Pilot protocols and make them available to others.

The scientists can make Pipeline Pilot protocols accessible via web interfaces like Pipeline Pilot Web Port, SharePoint, customized clients, and other deployment methods to make automated processes accessible to an even larger audience.

Using BIOVIA Pipeline Pilot’s powerful integration capabilities, this customer has tied 3D structure models into its general research informatics infrastructure for the first time.

The Pipeline Pilot-based 3D Structure Portal provides fully integrated chemistry capabilities, a user-friendly interface with structure search, automatic indexing/compound ID, flexible displays, dynamic pages, clear tiled controls (nodes), and various options for database and reporting connections.

Pipeline Pilot has considerably accelerated development time, a significant advantage since developers work through continuous Portal iterations while collaborating with end users to execute desired changes.

In addition to the innate benefits of an updated Structure Portal, the company’s research database/application has also enabled multiple enhancement opportunities as portal developers collaborate with end users to refine system requirements.

Anticipated pending work includes more sophisticated cataloging of targets, special polymerase features, fully embedding structures in the browser and continuing enhancements to performance and speed.

This company’s upgraded 3D Structure Portal, created using BIOVIA Pipeline Pilot, connects its medicinal chemists and modelers, enhancing communication and enabling more efficient collaboration with the same tools in a shared small molecule ecosystem.

The capacity to create mission-critical tools quickly is an essential competitive advantage for this biopharmaceutical company.

About BIOVIA, Dassault Systèmes

BIOVIA™ provides global, collaborative product lifecycle experiences to transform scientific innovation. Our solutions create an unmatched scientific management environment that can help science-based organizations create and connect biological, chemical and material innovations to improve the way we live.

The industry-leading BIOVIA portfolio integrates the diversity of science, experimental processes and information requirements, end-to-end, across research, development, QA/QC and manufacturing. Capabilities include Scientific Informatics, Molecular Modeling/Simulation, Data Science, Laboratory Informatics, Formulation Design, BioPharma Quality & Compliance and Manufacturing Analytics.

BIOVIA is committed to enhancing and speeding innovation, increasing productivity, improving quality and compliance, reducing costs and accelerating product development for customers in multiple industries.

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Last updated: Oct 11, 2022 at 9:40 AM


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