Numerate and Takeda Enter Agreement to Generate Novel Clinical Candidates Using AI-Driven Drug Discovery

Numerate, Inc., a computational drug design company applying artificial intelligence (AI) at cloud scale to transform small molecule drug discovery, announced the formation of a multi-year agreement with Takeda Pharmaceutical Company Limited (TSE: 4502) under which Numerate will identify and deliver multiple clinical candidates.

Under the agreement, Numerate will drive discovery programs aimed at identifying clinical candidates for use in Takeda’s core therapeutic areas: oncology, gastroenterology, and central nervous system disorders. The projects will rely on Numerate leveraging its AI-driven platform, from hit finding and expansion through lead design/optimization and ADME (absorption, distribution, metabolism and excretion)/toxicity modeling.

“This is an ideal arrangement for Numerate because our team will be working largely independently while having the opportunity to leverage Takeda’s global experience, therapeutic area insights, and unique R&D capabilities,” said Guido Lanza, President and CEO of Numerate. “We expect to produce multiple clinical candidates, while also continuing to refine, validate and expand our proprietary AI-driven platform as we work across a broad range of target types and drug design challenges.”

Financial terms of the current agreement were not disclosed, but include a combination of milestone payments and royalties that reflect the value of the clinical candidates being delivered.

“We are excited to partner with Numerate. Numerate has established an impressive track record of leveraging their AI platform to overcome drug design challenges, both for its own pipeline and in pharma/biotech collaborations,” said David Weitz, Head of Takeda California and Global Research Externalization. “By having Numerate select projects that align with Takeda’s strategy we expect the partnership to yield multiple assets that Takeda can develop into truly transformative medicines for patients.”

Numerate and Servier Establish Collaboration to Advance First-in-Class Ryanodine Receptor 2 Candidates for Cardiovascular Diseases

Numerate, Inc., a computational drug design company applying artificial intelligence (AI) at cloud scale to transform small molecule drug discovery, and Servier, an independent international pharmaceutical company, today announced a collaboration to pursue the design of small molecule modulators of ryanodine receptor 2 (RyR2), a target identified as physiologically important in cardiovascular diseases, but whose drug-ability has proven highly challenging. This collaboration could lead to potential first-in-class therapies for cardiovascular diseases, including heart failure and arrhythmias.

Ryanodine receptor dysfunction is known to be involved in the defects in calcium handling associated with cardiovascular diseases. The design of novel ryanodine receptor modulators remains challenging to address with traditional drug discovery methods, largely because of the complexity of the underlying biology.

Numerate’s disruptive, proprietary algorithm-driven drug discovery platform has overcome these challenges to successfully identify a series of novel RyR2 modulators. This collaboration will include the modeling of all aspects of small molecule drug discovery, leveraging all available chemical and biological data and using Numerate’s AI-driven process to accelerate the path to the clinical phase.

“We are very pleased to be working with Servier, a global leader in cardiovascular medicine,” said Guido Lanza, President and CEO of Numerate. “Their long-standing appreciation for the complexity and the promise of this target made the power of our approach and the success we were having with our internal discovery program appealing. Our agreement forges an ideal combination of capabilities and expertise to advance these assets.”

“Numerate’s platform has literally cracked the code on rapidly identifying diverse, potent, and functionally active modulators of the ryanodine receptor,” said Dr. Isabelle Tupinon-Mathieu, Vice President of Research and Development and Head of Cardiovascular and Metabolism Therapeutic Innovation Poles. “This collaboration will also integrate with our ongoing and very productive partnership with Professor Andrew Marks and ARMGO, and accelerate the design of novel molecules to advance our cardiovascular program toward clinical development.”

Under the agreement, Servier has licensed Numerate’s RyR2 program including the novel compounds it identified. Numerate will also support efforts in assay development, lead design and optimization. Financial terms of the agreement were not disclosed.

About Servier

Servier is an international pharmaceutical company governed by a non-profit foundation with its headquarters based in Suresnes (France). With a strong international presence in 148 countries and a turnover of 4 billion euros in 2016, Servier employs 21,000 people worldwide. Corporate growth is driven by Servier’s constant search for innovation in five areas of excellence: cardiovascular diseases, diabetes, cancers, immune-inflammatory diseases, and neurodegenerative diseases, as well as by its activities in high-quality generic drugs. Being completely independent, the Group reinvests 25% of turnover (excluding generics) in research and development and uses all its profits for growth. A key player in cardiology and hypertension for the last 20 years, Servier has 12 major products on the market with a total turnover of more than 1.6 billion euro in 2016. Currently, there are 12 new fixed-dose combinations and 10 new molecular entities in research or development, mainly targeting heart failure. This portfolio of innovative treatments is being developed with partners worldwide. For more information, visit www.servier.com.

Forbes article by our CTO on what you need to know about AI

Scan today’s headlines and it seems that every business is adopting artificial intelligence (AI), or more accurately, machine learning. Everyone is being told that they need AI, but few know why — and even fewer know how to use it. The truth is, AI is complex in nature. As the CTO of a company with a foundation in AI, trust me when I tell you that it’s harder to implement than you might think.

AI and machine learning are not commonplace today because we still lack a few essential building blocks…

What You Need To Know Before Incorporating AI Into Your Business Model

Numerate licenses it’s ApoE4 program to stealth biotech company

Numerate and the Gladstone Institute have licensed their novel ApoE4 drug program to a stealth biotechnology company with whom they will continue to work to push the program forward.  Financial terms of the agreement were not disclosed.  As details are made public by the stealth biotech and its investors, we will update the story.

This is an example of what the Numerate platform can do to translate early stage programs with exciting emerging biology into valuable assets worth advancing, as quickly as possible, towards the clinic. Despite the intrinsic difficulty of designing structure correctors, we were able to generate valuable ApoE4 assets in a matter of months and with only the money from our Wellcome Trust contract. We are unaware of any other approach (computational or non) that could have produced these results.

Numerate Closes New Round of Financing

San Bruno, CA – June 24, 2014 – Numerate, Inc., a biotechnology company that is applying novel machine-learning algorithms at cloud scale to transform small molecule drug discovery, today announced that it has completed a $8 million financing round co-led by Atlas Venture and Lilly Ventures, with participation from existing investors. Concurrent with the financing, Bruce Booth, Ph.D, Partner at Atlas Venture, and Steve Hall, Ph.D., Venture Partner at Lilly Ventures, have joined the Numerate Board of Directors.

“We are pleased to have the support of Atlas Venture and Lilly Ventures,” said Guido Lanza, president and chief executive officer of Numerate. “Their investment recognizes the success of our novel drug design platform in solving key problems of small molecule drug discovery and will enable us to advance our lead programs in metabolic, cardiovascular and neurodegenerative diseases. In metabolic disease, we are targeting the free fatty acid receptors to address diabetes, obesity and related co-morbidities, while in cardiovascular disease we are targeting the Ryanodine receptor 2 to discover improved drugs for heart failure and arrhythmia.”

According to Bruce Booth, “Numerate has created an innovative platform for designing novel drug leads against targets previously addressed poorly by computer-aided drug design.”

“We are excited about the progress Numerate is making in its lead programs, which address major conditions that lack effective treatments today,” added Steve Hall.

Numerate is focused on making the drug design process more data-driven, efficient and predictable. Unlike structure-based approaches that rely on crystal structure data, Numerate’s drug design platform uses all relevant data (SAR, patents, phenotypic data, etc.) to design novel compounds in an iterative fashion. This platform is ideally suited to emerging targets where there is little known data or where traditional methods have been unable to generate lead compounds that meet all the criteria for a drug candidate.

About Numerate
Numerate is a privately held biotechnology company that applies novel machine-learning algorithms, at cloud scale, to overcome major challenges in small molecule drug discovery. Numerate’s drug design platform combines advances in computer science and statistics with traditional medicinal chemistry approaches to address, in parallel, the factors that determine the success and failure of a drug candidate. Numerate is using this proprietary platform to develop a pipeline of drug programs in the cardiovascular, metabolic and neurodegenerative disease areas, focused on targets not typically addressed by computer-aided drug discovery. For more information, visit www.numerate.com.

About Atlas Venture
Atlas Venture is an early-stage venture capital firm that invests in technology and life sciences businesses. Since inception, its partners have helped build more than 400 companies. Atlas is currently investing from its ninth fund and manages approximately $2B in committed capital. For more information, visit www.atlasventure.com.

About Lilly Ventures
Lilly Ventures, one of the venture capital funds associated with Eli Lilly and Company, manages $200 million in committed capital, investing in start-up biopharmaceutical and medical technology companies in early through expansion-stage investments. The primary goal of Lilly Ventures is to facilitate the success of companies with innovative technologies by providing both financial and intellectual resources to accelerate the management teams’ paths to success. For more information, visit www.lillyventures.com.

Numerate Collaborates with Sage Bionetworks and IBM to Help Researchers Create Better Models of the Cell

SAN BRUNO, CA – August 14, 2013 – Numerate, a pioneer in computational drug design, announced today that it has provided its cloud-based BitMill data analytics platform to support the DREAM Whole Cell Parameter Estimation Challenge, organized by Sage Bionetworks and sponsored by IBM.

The DREAM (Dialogue on Reverse Engineering Assessment and Methods) Whole Cell Parameter Estimation project is one of four big data open computational challenges taking place through the fall of 2013. These crowd-sourcing efforts offer a new approach to advancing biomedicine by enabling the rapid sharing and improvement of predictive models to better understand complex processes in systems biology.  The ultimate goal is to foster collaborations among researchers that will result in new solutions to critical problems in science and medicine. To date, over 100 academic research teams have registered to participate in the Whole Cell Challenge.

“The Whole Cell Parameter Challenge is fostering important research about cellular processes, which will likely help us to better understand key diseases, identify new drug targets, and predict the side effects of potential drugs,” said Brandon Allgood, co-founder and Chief Technology Officer of Numerate. “Predictive modeling like this requires a highly adept big data tool – and with the budgetary and time constraints of the medical research community – our cloud-based BitMill service provides the scalability and ease of use required, and is an ideal way for researchers to test various algorithms and conduct necessary analysis to formulate conclusions. In this challenge, modelers are being presented with a substantial leap in computational demands as they are working with a model that is orders of magnitude more complex than in previous DREAM runs. We are pleased to offer a tool that can provide the needed computational power, and are excited to see what the research reveals.”

BitMill: The Elasticity and Scalability of the Cloud with Minimal IT Requirements

Numerate’s BitMill platform is a cloud-based big data analytics service for scientists and life sciences companies that provides massive scalability of familiar software tools.  The current focus for BitMill is next generation sequencing (NGS) analysis.  By leveraging the power of the cloud, BitMill delivers performance and cost efficiency in an easy-to-use package:

  • Performance – The NGS tools offered by BitMill have been integrated into a highly parallelized and distributed computing infrastructure, allowing fast delivery of results while handling large amounts of data.
  • Cost – By taking advantage of the scale and centralized nature of the cloud, the cost of processing is much lower than running software locally, and the pay-as-you-go payment model means users pay only for resources they use.
  • Ease-of-use – BitMill delivers high-performance computational capabilities with a lower barrier to entry.

Numerate’s BitMill is currently a beta service based on its Numatix cloud platform. This platform has been continuously developed and deployed to run Numerate’s drug design projects, both internally and in collaboration with several major pharmaceutical companies, over the past 10 years. The BitMill service is a dataflow execution solution that allows users to run data analysis pipelines at large-scale in the cloud and can cost-effectively process extremely large sets of data in hours or minutes.  Numerate uses the platform in combination with proprietary machine learning and screening technologies to fuel its drug design programs.

“We are excited to collaborate with IBM and Sage Bionetworks to make this challenge possible,” said Guido Lanza, Chief Executive Officer of Numerate.  “It has always been a goal of ours to apply our underlying analytics technology to a wider set of problems and make it available to the external community of scientists and researchers.  Numerate is dedicated to empowering scientists to tackle tough problems like the Whole Cell Challenge.”

The DREAM Whole Cell Parameter Estimation Challenge launched on June 21, 2013, and will run through September 20, 2013, when the winning team will be invited to present their approach at the 6th Annual RECOMB/ISCB conference on Regulatory and Systems Genomics in Toronto, Canada.  In addition the winning team will be invited to submit a manuscript describing their methodology to PLoS Computational Biology, the leading computational biology journal. For more information about the challenge, visit https://www.synapse.org/#!Synapse:syn1876068.

About the DREAM Project

The Dialogue on Reverse Engineering Assessment and Methods Project (DREAM Project), founded in 2006 by Andrea Califano (Columbia University) and Gustavo Stolovitzky (IBM), was originally conceived as an initiative to advance the nascent field of network biology through the organization of Challenges on network reconstruction and pathway inference. Since the first set of network inference challenges of 2007 (DREAM2) the concept of using collaborative-competitions as a vehicle to carry on a meaningful dialogue in the computational biology community has evolved significantly. In 2012, the last DREAM7 project featured four powerful challenges of which one was on network biology and the other three dealt with three important problems in translational medicine. With the experience gathered by the launching of 24 successful challenges over the past five years, the “Challenge” concept has reached a status of legitimacy and maturity. The DREAM Challenges have brought rigor in the process of verification of computational methods, have enabled the democratization of different kinds of biological data, and have facilitated the collaboration of dozens of research teams. This success has triggered considerable interest by different government institutions and private organizations in working with DREAM to engage distributed teams to solve tough computational problems in biomedical research.

About Sage Bionetworks

Sage Bionetworks (www.sagebase.org) is a nonprofit biomedical research organization, founded in 2009, with a vision to promote innovations in personalized medicine by enabling a community based approach to scientific inquiries and discoveries. Sage Bionetworks strives to activate patients and to incentivize scientists, funders and researchers to work in fundamentally new ways in order to shape research, accelerate access to knowledge and transform human health. It is located on the campus of the Fred Hutchinson Cancer Research Center in Seattle, Washington and is supported through a portfolio of philanthropic donations, competitive research grants, and commercial partnerships. More information is available at www.sagebase.org.

Numerate joins the Google Cloud Platform Partner Program

We are pleased to announce that we have joined the Google Cloud Platform Partner Program as a Technology Partner. This step follows our successful early use of the Google Compute Engine and our participation in its recent launch. As a Technology Partner, we have been able to integrate our proprietary drug design platform with the Google Cloud Platform, which offers a broad set of application development, cloud storage, large scale computing and big data capabilities. As a result, we are able to easily and elastically scale to thousands of cores in response to our partners’ needs. We are now making Numatix, the distributed framework that powers our drug design platform and enables the deep and interactive analyses of large data sets, available to users in the life sciences and related fields.

Numerate’s Drug Design Platform Scales to 10,000+ Cores Using Spot Instances

We are excited to announce today that we have scaled our drug design platform to 10,000+ cores on Amazon Web Services’ Elastic Cloud Compute (AWS EC2) utilizing spot instances.  Spot instances are regular EC2 instances that are run on unutilized cloud hardware, allowing AWS to recoup the cost of idle hardware.  The spot instances are acquired through an auction.  Because the price can fluctuate, due to demand, spot instances may spin up and down at any time.  The Numerate drug design platform and the Numatix distributed framework on which it runs were both designed from the ground up to handle such ephemeralness with ease, allowing us to take full advantage of the cost savings of spot instances, which can be as low as a third of the on-demand price.

Numerate’s Drug Design Platform Scales to 10,000+ Cores Using Spot Instances;
Large-Scale Data Analyses Enabled by Numatix, Numerate’s Distributed Framework

SAN BRUNO, CA – June 10, 2012 – Numerate, Inc., a technology platform company that is leveraging proprietary algorithms and the power of cloud computing to transform the drug design process, announced today that its drug discovery platform, based on its open-source distributed framework, Numatix, has been shown to reliably and cost-effectively scale to 10,000+ cores using spot instances on Amazon Web Services’ Elastic Cloud Compute (AWS EC2). The 10,000+ cores were used to screen virtual compounds against predictive assay models in one of the company’s commercial partnerships.

Numatix is a dataflow processing platform developed by Numerate that enables great scalability and flexibility in distributed computing with minimal operational overhead. Combining online processing with detailed dataflows, Numatix allows for the deep and interactive analyses of large data sets. At Numerate, Numatix is used for the computational assessment of billions of molecules in the search for new drugs and for the development of complex systems biology models of drug behavior in various animals and humans.

“This level of scalability is essential for Numerate due to growing demand for our drug design services in the pharmaceutical and biotechnology industry,” said Nigel Duffy, Ph.D., Chief Technology Officer. “This achievement demonstrates the power of the Numatix platform and its ability to tackle large-scale computational problems cost effectively. We designed Numatix from the ground up to be extremely robust to all types of failures, allowing us to take full advantage of spot instances and their cost savings.”

“We were able to scale up to 10,000 nodes in the US-East zone of EC2,” stated Brandon Allgood, Ph.D., Director of Computational Science. “And because the Numatix platform uses spot instances, the cost was only 2.7¢ per core-hour, or $270 per hour for a 10,000-core cluster – just one-third of the on-demand cost. Moreover, we were able to reach this scale while handling spot instance ephemeralness and maintaining a high level of security.”

Allgood added, “The limiting factor on this run was our cloud provider-independent security layer. On less sensitive types of workloads, we expect that Numatix should be able to scale well beyond 10,000 cores.”