Accelerating Drug Discovery From One Year to Less Than One Day – Featuring OMass Therapeutics

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Learn how YellowDog helped OMass Therapeutics accelerate their drug discovery process from one year to less than one day with a 162,120 core supercomputer, on demand.
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OMass Therapeutics are an Oxford biotechnology company spun out of Oxford University harnessing native mass spectrometry and other biophysical technologies to drive drug discovery in high definition. The company’s suite of proprietary technologies delivers superior resolution to traditional pharmacology assays enabling a clearer, more detailed picture of how a putative ligand engages a protein target, assessing binding and function in parallel. The company is building a pipeline of small molecule therapeutics to bring life-changing benefits to patients suffering from immunology and genetic disorders. OMass is backed by Syncona Ltd, Oxford Sciences Innovation and Oxford University.

Learn how YellowDog helped accelerate OMass Therapeutics’ virtual screening process from one year to less than one day, with their powerful multi-cloud workload management solution. 

The Potential of Using the Cloud for Drug Discovery

For today’s drug discovery processes, as with many of the life sciences, data is key. The size of a dataset and the number and quality of the analyses has a powerful influence on the potential success and efficacy of a given drug development programme. The larger the population of data points, the faster you can carry out the analyses, and the greater probability of success in identifying new chemical matter to targets of interest.

There is great potential for the cloud to aid the process of drug discovery as it offers companies the ability to dynamically scale their research and analyse more data than they would with their traditional on-premise infrastructure. Considering the commercial value of new drugs and therapeutics, any acceleration to the process can result in substantial commercial benefits.

Overcoming the Barriers to Cloud Adoption for Drug Discovery

Although the cloud can help biotechnology companies, such as OMass, a fear of uncontrolled costs can often hold companies back: with unpredictable variable costs, potential costs for failed tests, and traditional on-premise analysis applications licensed in such a way that doesn’t fit with the way the cloud works.

Then there’s the technical challenges of securely connecting to, and provisioning computing power in, the cloud. Finding the right compute and storage resources that meet the needs of the dynamic, compute hungry workload can be difficult. With over 25,000 individual cloud instances available today across the main public cloud providers, it’s not always easy to find the best source of compute – whether for price, performance or compliance requirements.

Utilising Intelligent Scheduling and Provisioning Strategies to Process Molecules in Record Time

Harvard University’s REAL database contains over 1.4 billion commercially available on-demand molecules. This database can be used by companies to find potential hit compounds for the development of new drugs and therapeutics.

OMass saw an opportunity to accelerate and expand their virtual screening capabilities by utilising this large compound database and YellowDog’s multi-cloud workload management solution. With access to an on-demand supercomputer, OMass were able to dock 500 times more virtual compounds, and significantly enrich the top 10% of compounds screened. This top-level analysis enabled OMass to focus their attention on the most likely active molecules for their specific drug target.

Based on an initial set of filters, OMass presented YellowDog with a refined list of 477 million molecules for virtual screening. To achieve this scale, YellowDog delivered:

  • YellowDog Sigma for fast provisioning and intelligent orchestration of 2,000 AWS spot instances, a total of 162,120 cores, across four regions.
  • Sigma also managed task distribution and re-distribution when spot instances were reclaimed by AWS to ensure job delivery.
  • YellowDog Sigma+ and the YellowDog Index to identify the Best Source of Compute for this workload; based on cost, processing power and availability.
  • Integration with AutoDock Vina, an Open Source application for molecular docking.
  • Secure storage and data retrieval using YellowDog Object Store.
Figure 1 – The blue circles in the above graph show the points at which spot instances were reclaimed by AWS and then reprovisioned by YellowDog's intelligent Scheduler Service; there is very little effect on productivity with the yellow line, showing running instances, closely mirroring the blue line, which shows the number of instances requested.

Significantly Accelerating Virtual Screening From One Year to Less Than One Day

The outcomes for OMass are outstanding:

  • The 477 million compounds were analysed and screened in a total of 22.5 hours. Using OMass’s existing setup, the same number of analyses would have taken one year.
  • By finding the Best Source of Compute, YellowDog Sigma+ delivers a cost saving of 56.9% on the cloud compute costs for the workload.
  • YellowDog Sigma is fast: provisioning the 2,000 cloud instances in AWS and getting them to process the workload took only 10 minutes. Using a standard scheduler or cloud provisioner would typically take 13 hours.
Figure 2 - A graph to show the time it took to provision 2,000 instances using AWS. The blue circle represents the point at which all instances were running: within 10 minutes.

Bringing Life-Changing Benefits to Patients

The radical order change in the number of molecular docking analyses that are able to be carried out at this early stage in the drug discovery process, coupled with the speed and cost effectiveness of YellowDog Sigma and Sigma+, will help to significantly accelerate the time it takes OMass to identify lead compounds and bring life-changing benefits to patients.
“The professional and timely manner of this collaboration has enabled OMass to rapidly screen a novel target and help the company in its’ ambition to build a pipeline of small molecule therapeutics. The scale and speed of the platform is something OMass would not be able to replicate internally and we look forward to working with YellowDog in the future to further develop this capability.” Giles Brown VP, Head of Medicinal Chemistry, OMass

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