Numerate Enhances Platform Through Acquisition of DeepCrystal Technology

San Bruno, CA – Numerate, Inc., the world’s leading computational drug design company applying artificial intelligence (AI) at cloud scale to transform small molecule drug discovery has acquired DeepCrystal’s small molecule design platform. The platform is used to build models of compound activity and ADME based on advances in graph-valued deep-learning technology.  These methods will augment Numerate’s existing AI platform by compressing timelines to facilitate the discovery of next generation therapeutics.

As part of the acquisition, Patrick Hop, the Founder of DeepCrystal, will join Numerate as Principal Engineer of Deep Learning. At DeepCrystal, Mr. Hop was responsible for the development of its core technology and platform, as well as leading the company into strategic partnerships with top pharmaceutical companies to advance in-silico modeling. He holds a B.A in Applied Mathematics from UC Berkeley, and serves as a mentor to River Accelerator.

“We are excited to have Patrick join our team and bring his extensive experience in applying deep learning to drug discovery,” said Brandon Allgood, Ph.D., Chief Technology Officer at Numerate. “His research and insights combined with our expertise of applying AI to drug discovery will be synergistic.”

“I’m excited to begin working with the world-class engineering and scientific teams at Numerate,” said Mr. Hop. “Among the groups working in this space, I believe Numerate is the one striking the right balance of AI technology, and classical drug-discovery experience which, combined with the deep-learning technology from DeepCrystal, will help identify new therapies for patients faster and with less capital investment than ever before.”

CSO Report: Collaborating with academic investigators to unlock emerging biology

A most distinctive and valuable application of our AI platform is to rapidly advance small molecule therapeutic programs that exploit exciting insights as they emerge from basic biomedical research.  Our ability to learn accurate, scaffold-hopping predictive models from small, non-diverse and noisy training sets enables us to initiate and accelerate work against new targets from an early stage, e.g., from the point where an academic group has identified a small number of tool compounds having an activity of interest in a complex high-content/low-throughput assay that exists only in that laboratory.  Many promising projects that have the potential to address major unmet medical needs and opportunities languish at just this point because they cannot be adapted to traditional pharmaceutical screening and lead design processes.  We are able to unlock these projects, leveraging our AI to bootstrap the limited information content of initial training sets into models that we then use to screen large (107-109) compound libraries in silico to quickly (and with high laboratory-validated accuracy) expand the number and diversity of active compounds.  This sets the stage for AI-driven Hit-to-Lead and Lead Optimization.

We have published some of the results we have obtained in collaboration with leading academic laboratories.  With Prof. Chaitan Khosla and his group at Stanford, we demonstrated our ability to identify and improve upon new inhibitors of transglutaminase 2 (TG2).  Here, we built useful predictive models from a small training set comprising two very different chemotypes that were later found to bind to different binding sites on, and different conformational states of, TG2.  With Prof. Carl Nathan and his colleagues at Weill Cornell Medical College, we highlighted the scaffold-hopping capabilities of our models to identify structurally distinct new inhibitors of protein kinase R, including a potent, non-cytotoxic inhibitor suitable for use as a biological probe of PKR function.

More recently, we applied our AI to identify new stabilizers of the cardiac ryanodine receptor (RYR2), and licensed them to Servier.  Our work on this project benefitted from a very productive interaction with Prof. Wayne Chen at University of Calgary.  We also enjoyed a very productive collaboration with Prof. Robert Mahley of the J. David Gladstone Institutes where, with financial support from a Seeding Drug Discovery Award from the Wellcome Trust, we designed multiple series of ApoE4 structure correctors as potential leads for treating Alzheimer’s disease.  These became core assets for E-Scape, the founding and financing of which was recently announced.

Applying advanced AI in conjunction with cutting-edge biomedical science to produce scarce, first-in-class therapeutic assets sits at the core of Numerate’s business.  We believe that recognition of the value of translating insights into assets for compelling yet challenging targets, by Pharma partners and venture investors, has validated our strategy.  We look forward to continuing and expanding work with investigators from leading research institutions, as in our recently announced, NIH-funded collaboration with UCLA’s Cardiovascular Research Laboratory, where we are seeking to unlock an exciting new approach to preventing fatal heart arrhythmias.

National Institutes of Health Awards Innovation Research Grant to Numerate to Accelerate Discovery of Novel Antiarrhythmic Drug Candidates

Numerate and the UCLA Cardiovascular Research Laboratory will focus efforts on identifying therapy for the treatment and prevention of ventricular tachycardias and fibrillation (VT/VF)

San Bruno, CA – Numerate, Inc., a computational drug design company applying artificial intelligence (AI) at cloud scale to transform small molecule drug discovery, announced that the National Heart, Lung, and Blood Institute (NHLBI) of the National Institutes of Health (NIH) has awarded Numerate a Small Business Innovation Research (SBIR) Phase I grant.  Numerate, working with members of the UCLA Cardiovascular Research Laboratory (CVRL), will use the funds to initiate a drug discovery program targeting cardiac arrhythmias.

The project targets the discovery of small molecule drug candidates that address the need for a novel well-tolerated antiarrhythmic therapy for the treatment and prevention of ventricular tachycardias and fibrillation (VT/VF). Uwe Klein, Ph.D., Vice President, Biology at Numerate, will lead the discovery efforts and serve as Principal Investigator for the project titled, “Peripherally restricted α2/δ-1 subunit ligands that modulate CaV channel gating as novel antiarrhythmic drugs.” The project is funded under Grant Number 1R43HL139143-01.

The co-investigators include esteemed members of the UCLA Cardiovascular Research Laboratory, including:

  • Hrayr S. Karagueuzian, Ph.D., Professor of Medicine at the David Geffen School of Medicine at UCLA, Director of Translational Arrhythmias Research Section
  • Riccardo Olcese, Ph.D., Professor of Anesthesiology and Physiology at UCLA, Division of Molecular Medicine

“We are pleased to receive this award from the NIH and thrilled to be working with Drs. Karagueuzian and Olcese at the CVRL to build upon their existing work and discover an important new medicine for treatment of life-threatening arrhythmias,” said Dr. Klein.

John Griffin, Ph.D., Chief Scientific Officer of Numerate, added, “Our AI-based drug discovery platform has the potential to accelerate the rapid discovery and development of novel small molecule therapeutics and we are looking forward to collaborating with these two renowned cardiac pathobiology experts”.

“The NHLBI funding will expand upon our innovative research to manage cardiac arrhythmias with novel small molecule drugs that specifically block the arrhythmogenic late inward calcium current without altering other cardiac ionic currents,” said Dr. Karagueuzian. “I look forward to working with the scientists at Numerate who have developed highly sophisticated approaches using data driven machine learning and cloud computing to discover and develop a new antiarrhythmic drug therapy.”

“It’s a very exciting time for the fight against cardiac arrhythmias as my laboratory, which uses the quantitative rigor of biophysics to understand aberrant cardiac excitability, will benefit greatly from the application of artificial intelligence that Numerate brings to the table,” said Dr. Riccardo Olcese. “Numerate is the ideal partner to complement my laboratory’s expertise and with the generous support from the NHLBI, we are ready to evaluate the capabilities of rationally designed next-generation antiarrhythmics.”

About Cardiac Arrhythmias

According to the Mayo Clinic, more than 4 million Americans, most over age 60, experience heart arrhythmias (abnormal heart rhythms)[i]. Arrhythmias are caused by problems with the electrical system that regulates the steady heartbeat. The heart rate may be too slow or too fast; it may stay steady or become irregular and disorganized[ii]. The most serious and life-threatening arrhythmia is ventricular fibrillation (VF), which is an erratic disorganized firing of impulses in the lower chambers of the heart, called the ventricles. VF result in the heart being unable to pump blood, and is the most common cause of sudden cardiac death, claiming the lives of about 300,000 adults in the United States each year[iii].

AI Pharma Summit Meeting

Guido Lanza (CEO) and Brandon Allgood (CTO) attended the AI Pharma Summit in Boston last week.  The meeting brought together both large and small companies pushing the boundaries of AI in Pharma R&D.  Overall the discussions were productive, but there is a lot of work to be done and that is exciting! Below is the technical keynote given by Brandon at the meeting.

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

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

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

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