case-study

Case Study: Schrödinger Accelerates In Silico Discovery from Plasmid to Structure with Sapio Sciences

Executive Summary

Schrödinger, a leader in computational chemistry since 1990, has partnered with Sapio Sciences to augment and extend its proprietary computational platform. By implementing the Sapio laboratory informatics platform, Schrödinger has efficiently accelerated the in silico discovery of high-quality, novel molecules and enhanced its drug discovery capabilities. 

This collaboration transformed Schrödinger’s newly established internal wet lab from paper-based processes to a model of efficiency, adaptability, and value creation, achieving unified visibility across the entire drug discovery process and enabling real-time cost analysis and strategic resource allocation.

The Customer: Schrödinger

Company Overview

Schrödinger, founded in 1990, has approximately 900 employees globally and is a leader in computational chemistry, leveraging its physics-based platform to discover high-quality, novel molecules for materials science and drug development.

Schrödinger’s material science group has achieved breakthroughs in areas like organic light-emitting diodes (OLEDs), and its life science group is a multidisciplinary team of platform experts and scientists advancing proprietary programs in drug discovery and development and collaborating on programs in multiple disease areas.

The company maintains its proprietary drug discovery pipeline, alongside collaborations with major biopharmaceutical companies, including Bristol Myers Squibb and Novartis.

Background

Schrödinger, which historically focused on computational methods and utilized external CROs for lab work, decided to establish its internal wet lab to accelerate drug discovery. The CRO it acquired in 2021 utilized paper-based processes, which lacked the digitization, scalability, traceability, and efficiency needed to meet Schrödinger’s ambitious goals.

The Challenge: Digitizing and Scaling Wet Lab Operations

In 2022, Rajesh Kumar, Ph.D., joined Schrödinger as Senior Director of Drug Discovery. Specific challenges he faced included:

• Collecting, storing, and managing massive datasets, including complex images, in a searchable format.
• Establishing an end-to-end audit trail for lab processes.
• Ensuring adaptability for future technological and process needs.
• Demonstrating incremental value to secure continued leadership buy-in.

Dr. Kumar had previous experience with an ELN (Electronic Laboratory Notebook), which was good for documentation, and he knew a LIMS (Laboratory Information Management System) could be used to search large amounts of data. At Schrödinger, he wanted to “find a platform that would master both.”

The Solution: Sapio Sciences Lab Informatics Platform

Why Sapio Sciences Was Chosen

From the 6 to 8 vendors it evaluated, Schrödinger selected the Sapio Platform. The decision was based on its ability to integrate Sapio ELN and Sapio LIMS in one seamless environment. The decision was based on:

1. Unified Functionality: Seamless integration of ELN and LIMS to address Schrödinger’s present and future informatics needs.
2. Advanced Search and Traceability: Comprehensive data capture and audit trails for regulatory and operational insights.
3. Customization Capabilities: Tailored workflows to support specialized lab functions, developed collaboratively with the Sapio Consulting team.

Implementation Overview

Dr. Kumar executed a strategy to improve laboratory operations and simultaneously demonstrate the value of the improvements to Schrödinger’s leadership group through an iterative, multi-phase process:

• Customized Workflows: Unique workflows for plasmid expression, protein purification, binding studies, and structural biology were developed iteratively with Sapio, and weekly feedback sessions ensured alignment with lab needs.
• Automated Calculations: Features protein sequence automated calculations, accessed through webhooks, boosting efficiency.
• Instrument Integration: Initial deployment focused on plate readers, and future phases will integrate more instruments, aligning with Schrödinger’s “future-proof” vision.

The platform was tested for a month, refined, and fully deployed, with Sapio and Schrödinger teams maintaining close communication throughout.

Key Features

• Integrated Sapio ELN and Sapio LIMS: Provided a single, seamless environment for both electronic laboratory notebooks and laboratory information management.
• Proprietary Computational Platform Augmentation: Extended Schrödinger’s existing in silico discovery capabilities.
• Automated Calculations (via Webhooks): Enabled protein sequence automated calculations for efficiency.
• API-First Design (Implied by Instrument Integration): Facilitated smooth integration with laboratory instruments like plate readers.
• Comprehensive Data Capture and Audit Trails: Supported advanced search, traceability, regulatory, and operational insights.

• Customization Capabilities: Allowed for the development of specialized workflows (e.g., plasmid expression, protein purification, binding studies, structural biology).

The Results: Enhanced Efficiency, Traceability, and Strategic Insights

Schrödinger transformed its wet lab into a model of efficiency, adaptability, and value creation. Key outcomes of the Sapio Platform implementation include:

• Improved Operational Efficiency: Unified visibility across the entire drug discovery process (plasmid to structure) for all 25 lab team members; Automated tracking of resource consumption, such as media costs ($40 to $350 per liter depending on cell type), enabling real-time cost analysis and decision-making.
• Enhanced Traceability and Reporting: Comprehensive documentation of lab activities accelerates new drug filings and simplifies audit readiness; Leadership gains detailed insights into lab performance, justifying ongoing investments in lab expansion.
• Strategic Insights for Resource Allocation: Historical data enables predictive planning and budgeting for new projects; Metrics like resource consumption and project timelines are benchmarked for continuous improvement.

• Long-Term Knowledge Retention: Archival data supports future projects, ensuring scientists can easily access historical insights for decades to come.

Customer Quotes

“I wanted to find a platform that would master both [ELN and LIMS].” – Rajesh Kumar, Ph.D., Senior Director of Drug Discovery, Schrödinger

Lessons for Drug Discovery Leaders

Schrödinger’s journey offers critical insights for any organization seeking to transform its drug discovery operations:

• Strategic Internal Lab Establishment: Recognizing when to build internal wet lab capabilities can accelerate drug discovery, especially when external CROs’ processes are outdated.
• Unified Informatics is Key: Integrating ELN and LIMS into a single, seamless platform is crucial for overcoming data silos and enabling comprehensive search and traceability.
• Iterative Implementation Pays Off: Adopting a multi-phase, iterative implementation strategy with continuous feedback ensures alignment with lab needs and demonstrates value incrementally.
• Future-Proofing is Essential: Investing in a configurable and API-first platform ensures adaptability for future technological and process advancements.
• Data-Driven Justification: Leveraging automated data capture and reporting provides clear metrics to justify ongoing investments and expansions to leadership.

• Long-Term Knowledge Management: A robust informatics platform enables archival data retention, supporting future projects and ensuring decades of accessible historical insights.

Next Steps

The transparency and traceability provided by the Sapio Platform efficiently and effectively help Schrödinger progress from plasmid to the target structure and accelerate the drug discovery process to create value now. In addition, 5, 10, or even 20 years from now, scientists at Schrödinger can quickly and easily find key end-to-end archival data to understand past laboratory experiments and inform their own.

Conclusion

Schrödinger transformed its wet lab into a model of efficiency, adaptability, and value creation. This iterative, multiphase approach enhances current drug discovery workflows and establishes a robust foundation for future advancements, ensuring that Schrödinger remains at the forefront of innovation.

The value of the Sapio Informatics Platform to Schrödinger is end-to-end lab performance to automatically capture the cost of media, consumables, and other resources across multiple projects in their pipeline. They can determine which project is consuming the most resources and why. And they can quickly search and capture key metrics weekly, monthly, quarterly, and annually to create a constantly expanding timeline of key performance information.

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FAQ

Q: Why did Schrödinger choose Sapio?
A: For a unified LIMS and ELN solution that supports wet lab scalability, traceability, and strategic insights.

Q: What were the key implementation priorities?
A: Customized workflows, automated protein sequence calculations, and lab-wide integration with plate readers.

Q: What results were achieved?
A: Real-time cost analysis, audit-ready reporting, and accelerated internal drug discovery pipelines.

Q: What long-term benefits did Schrödinger realize?
A: Data traceability across decades and predictive planning capabilities from a centralized system.