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Can We Predict Drug Efficacy with Artificial Intelligence?

Journal : Applied Clinical trial
Date of publication : 22 May 2017

The success of personalised medicine depends on the ability to identify patient sub-populations, which is only possible with accurate diagnostic tests based on biomarkers. Given the vast amount of genomics, proteomics or metabolomics data, identifying effective biomarkers is a complex task.

Large amounts of individual patient Omics data are being collected, unfortunately bioinformaticians lack sophisticated tools to extract information from the data. Big computing approaches such as machine learning, artificial intelligence (AI) and neural networks are still in their infancy in the pharmaceutical sector but with several AI companies rewriting the code for drug discovery, the implications in healthcare are likely to be far ranging in the coming years. In particular, newly founded start-ups offer some unprecedented solutions using machine learning and AI.

In a booming biomarkers market, which spans both diagnostics and drug discovery, there are, according to AngelList, 173 companies in the bioinformatics space, with only 15 in Europe. UK-based BenevolentAI is one leader in the use of artificial intelligence (AI) for the efficient diagnosis of diseases and discovery of drugs. The company was founded in 2013 with the idea that the drug discovery process required a complete turnaround. Their mission became to change the healthcare and biotechnology industry which they addressed using knowledge networks to reduce the time and cost of drug discovery and find new molecular targets.

Recently, BenevolentAI’s approach is unique as it uses data from scientific papers and abstracts to make connections and patterns, an aspect that pharmaceutical companies may not have exploited yet. It is therefore no surprise that Janssen, a J&J company, entered an exclusive license agreement with BenevolentAI for clinical stage drug candidates. As Ken Mulvany, Chairman of BenevolentAI, explained, “The data [from scientific articles] might show that a protein up regulates a particular gene which is not directly related, leading researchers to look for drugs in a completely different area.” This is how BenevolentAI is capable of finding novel targets with data mining.

In the United States, AtomWise, founded in 2012, has a slightly different value proposition. They have developed the AtomNet, “the first Deep Learning technology for novel small molecule discovery,” which can predict the bioactivity of small molecule drugs. Using this proprietary algorithm, AtomWise was able to screen 8.2 million molecules to discover a protein inhibitor for the treatment of multiple sclerosis that filled all the requirements for its target product profile: “blood-brain-barrier penetrant, orally available, and highly efficacious in animals.” In another example, the AtomNet algorithm discovered a drug with no previous antiviral properties that blocked Ebola infectivity across strains from different epidemics. With such results, AtomWise was able to partner with large corporations such as Merck and IBM and subsequently raise $6 million in seed funding in order to improve and develop their algorithm. It is certainly possible to envision what drug discovery could look like in the future with AI being an integral part of the pharmaceutical industry.

Currently thousands of candidate molecules are screened with such new approaches and no doubt this strategy is about to revolutionise the way pharmaceutical companies perform screening. First, it will significantly improve time to market. Second, as a result it will also significantly reduce drug development costs. For example, in 2014, the FDA estimated that just a 10% improvement in the ability to predict drug failures before clinical trials could save $100M in development costs per drug. With this method, predictability is expected to increase significantly. Third, after a promising candidate is identified, AI can be used to improve clinical trials from the design to the data analysis.

Computer assisted drug delivery (CADD) has been around since the 80s, particularly in the pharma sector where it was integrated in the drug discovery process. Although it has contributed to modern drug discovery, it hasn’t removed the need for biological data and it surely hasn’t revolutionised the drug discovery process. Big data computing approaches such as AI have the potential to do so but need to solve a couple of issues such as noise in data sets, which slow down the data training process. The other issue is to learn to deal with the complexity and variability found in biology. Once these hurdles are overcome, sophisticated mining processes are likely to increase the individualisation of the drugs lowering the cost of drug development, addressing two of the major problems in healthcare. At this stage the success depends on the wider adoption of these novel drug discovery methods within larger biotechnology and pharmaceutical companies as well as the development of novel data mining and big data analysis software.

Jeanne-Françoise Williamson D.Phil, CEO, Williamson Biotech Solutions and Pablo Lubroth, University of Cambridge, MPhil Bioscience Enterprise.

Reach for the BioStars! Meet the Top 3 Biotech Startups from Oxford

Journal :
Date of publication : 23/02/2017

A new round of this young startup competition is underway! What is this Oxford-based competition, and who competes? We talked to previous participants.

BioStars is a flagship startups booster run by a group of PhDs, MBA and post-docs, who dedicate their spare time to enabling bio-entrepreneurs to turn their scientific ideas into actual products. Brought together by Mina Bekheet and now known as Panacea Innovation, the team aims to bridge the gap between research and scientific innovation with the aim of creating an ecosystem to for scientists to translate academic research into companies.

“I’m now convinced that what really makes successful entrepreneurs is pure persistence. A true entrepreneur not only dreams big, but executes even bigger. So why do we do it? Because we could now clearly see how BioStars is filling in the gaps in between the academia/industry/investment triple-helix and maximising the translation of the undervalued assets, and since we are impact-driven, we decided to roll our sleeves-up and dive all in with our start-ups.”
Mina Bekheet, Panacea Innovation

In two years, Panacea is succeeding by making the most of the Oxford network in which it’s embedded. Forbes recognised Bekheet as one of its 30 Under 30 in Healthcare & Science and Dorm Room Founders after he drove Panacea Innovation from a student-led network to a hands-on multi-armed organisation.

This year’s round is in high gear, as teams prepare to submit business plans. The Grand Finale will take place at the end of next month, and a winner will be chosen. The lucky team will take home £30K (€35K) to further develop their concepts to the next stage. (If you’re interested in competing next year, applications will open next October!)

When I spoke to last year’s participants, most of whom have taken part in several accelerators competitions, they said what really set Biostars apart is the quality of the network and the mentoring available though the program. Mentors are well matched to teams, as many pairs continue to work together closely after a year. As a mentor, what I find most striking is the enthusiasm and dedication of these entrepreneurs.

Here’s what last year’s participants have to say about BioStars!

Last year’s winner, VisusNano, develops a drug-eluting intraocular lens for cataract replacements. Elodie Siney, COO and co-founder, says her team of 4 is grateful to BioStars for giving them the confidence in their ability to move from science to commercialisation. “The mentors were fantastic and the entrepreneurship courses we were able to attend as part of Biostars were the perfect complement for us novice entrepreneurs,” she says.

With the prize, the team set up the company, established a strategy and developed the prototype using laboratory space at Stevenage Biocatalyst (SBC) as another part of the BioStars prize. Validation work will soon be underway. The next step for VisusNano is early stage funding to take it to the next level and find industrial partners. For the VisusNano team, Biostars was the start of their entrepreneurial journey.

“I get my inspiration from the feeling of independence I get and the ability do to something that benefits human healthcare.”Elodie Siney, VisusNano.

For DJS Antibodies, Biostars People’s Choice Award winner, the main attraction BioStars was for the mentorship and networking, as the company had already been running for one year. The team developed a close relationship with its mentor at AstraZeneca, which is ongoing.

DJS Antibodies has developed a novel platform to isolate high-quality antibodies against proteins. David Llewellyn, CEO and co-founder, told us they secured seed funding for 12 months in September 2016 and took on board three discovery programs to validate their technology. The team of 2 is currently working hard on both lab work and business development, aiming for Series A fundraising later this year.

“I love coming up with ideas and then figuring out how to turn them into opportunities. It is great to be able to both set the agenda and take an active role in executing it.”David Llewellyn, DJS Antibodies

BioMe Oxford, who develops a small ingestible gut-sampling device that can sample any part of the intestines in a non-invasive manner, was a mature team when they embarked on BioStars. When it joined the programme, the team was looking for seed funding for the proof-of-concept and to widen their network.

Looking back, Søren Thomsen, CEO and co-founder of BioMe Oxford, reflects that the main benefit of the Biostars accelerator was the expansion their network. They have worked with their mentor, patent attorney from JA Kemp, to file the patent in September 2016. BioMe Oxford has also achieved raising seed funding of £50K (€59K) and is now preparing for Series A. The team of 6 is currently 3D printing the α-prototype and waiting to hear on their patent application in spring 2017.

“Working in academia, my entrepreneurial driving force is to know that we are developing a world-changing technology that would impact how things are done today.”Søren Thomsen, BioMe Oxford.

Watch the competition for new disruptive technologies in therapeutics, medtech, digital health, and diagnostics! The most promising teams from the first two editions will be able to participate in the BioStars Elevator program later to give them a leg up towards their next milestones. Stay Tuned!

Written by Jeanne-Françoise Williamson, a biotech facilitator who helps entrepreneurs take their businesses to the next level. Also a keen capoeirista, she helps them plan, develop and execute their next moves. Currently working with start-ups, research institutes, academics and SMEs in life sciences, Medtech, Bioinformatics and Pharma. In 2015, it launched BioStars as an accelerator program for young entrepreneurial scientists — this year marks the second edition!

Revolution in Personalised Medicine: First Time Approval of Drug for Cancer by the FDA Based on Biomarker


31 May 2017

The FDA’s announcement to approve pembrolizumab marketed as Keytruda (Merck) for treatment of solid tumors with a biomarker irrespective of its location in the body is a crucial milestone in the fast moving field of cancer immunotherapy and personalized medicine. It is the first time a drug is approved without a tumor specific context, highlighting a new way of defining and treating cancer based on their genetic mutations rather than on the organs where they spread or originated from.

The FDA’s announcement to approve pembrolizumab marketed as Keytruda (Merck) for treatment of solid tumors with a biomarker irrespective of its location in the body is a crucial milestone in the fast moving field of cancer immunotherapy and personalised medicine. It is the first time a drug is approved without a tumor specific context, highlighting a new way of defining and treating cancer based on their genetic mutations rather than on the organs where they spread or originated from.

Pembrolizumab activates the immune system to attack tumors by inhibiting the Programmed cell protein 1 (PD1) checkpoint regulator who guards the body against autoimmunity. It had already been approved for a range of specific cancers including bladder and lung cancer but now the drug is approved for patients whose tumors are MSI-H (microsatellite instability-high) or MMRd (mismatch repair deficiency), both of which are genetic mutation which increase the risk of cancer.

With huge efforts in the field on biomarker discovery exploiting artificial intelligence, novel data mining methods, easier routes for regulatory approval and significant clinical results, biomarker based cancer treatment is likely to pave the way to novel personalised medicine in the years to come

Read more about the financial and therapeutic implications.

Written as a post by Jeanne-Françoise Williamson, 31st May 2017.

Reach for the Biostars 2017


26 April 2017

BioStars, a young start-up accelerator brought by Panacea Innovation aims to bridge the gap between research and scientific innovation creating an ecosystem to for scientists to translate ideas into companies. Last years’s winners have all come a long way. With the second round of the competition completed last month, here is what impressed the jury this year. The judges were looking at projects addressing a real gap in the market or ideas that represent true innovation so don’t be surprised if their choices sounds a little unexpected.


Aberdeen-based EnteroBiotix is a patient-centered biotechnology company focused on using the body’s own microorganisms to prevent and treat infections and diseases of the intestinal tract. Biostars was a great opportunity for the team to showcase the Scottish company in the Golden Triangle but the real added value came from the mentors at GSK and JA Kemp who helped them strengthen their business plan and strategy. “The timing was perfect and the prize money will be put to excellent use furthering our business.” said James Mcilroy CEO of EnteroBiotix. The company is well advanced in plans to establish a GMP manufacturing facility to commercialise its pipeline of microbial therapeutics for use in a medical treatment called Faecal Microbiota Transplantation (FMT). The team is very busy working on an autologous FMT service, and computational models to match donors to patients. James, who is still a medical student, says that his driving force simple: “making a positive impact on society. With EnteroBiotix, I wake up every morning excited at the potential of making thousands of people‘s lives better with our product offering.”

The Uprising Biostar

The runner up was HyperC whose concept is to provide effective 13C compound labelling service for preclinical in vivo MRI (magnetic resonance imaging) research & diagnostics. This is particularly important for hyperpolarised MRI, a powerful new technique with the potential to revolutionize medical imaging. Their idea focuses on solving a real problem as CEO Dragana Savic, a PhD student at Oxford University, explains: “The supply of some C13 labelled compounds is slow (min 6 weeks) and often delayed forcing us to skip experiments. These large companies’ core business lies elsewhere. So we decided to make the 13C isotope labelled compounds ourselves”. Biostars was their first to evaluate the idea. But the team members aren’t novice-entrepreneurs but going into the regulated environment of medical imaging is a new adventure. Biostars’ mentors just gave them the confidence that they can do it. “It made me believe I can reach higher. If I can, I would like to change the world, even just a bit to make it a better place”.

The People’s Choice Award

Finally, it is no surprise that The People’s choice prize went to Natalie Price, Founder and CEO from Proximity Care . She definitely won the audience’s over by her soft and genuine pitch, showing why she wanted to help Dementia carer’s, like her mum, keep the people under her care safe from wandering. Her solution: The Proximity Button, a wearable for patients that alerts the carer’s phone when the patient is out of reach. “ The problem is close to my heart. I care about what I do. This makes it easier to remain motivated. My mum and the people around me are my inspiration” reveals Natalie. Currently the company is selling the button online and planning to launch 3 new products once funding is secured. For Natalie, meeting other young exciting entrepreneurs was very stimulating and acquiring new business skills was welcome. Her mentors were “fantastic, they made me realise what greater things we are onto with Proximity Care” explains Natalie. “The process was fun and the Finale was inspiring. I would recommend to it anyone with an idea”.

The next step for Panacea Innovation is to organise the Elevator, which should take place later in the year, where selected few teams from the first two cohorts will be de-risked and taken one step further. Contact me if you would like to find out more or get ready for next year.

Written as a post by Jeanne-Françoise Williamson, 16 April 2017.

“Jeanne was an exceptional mentor, and helped us solve some of our key business challenges. With her help we were able to identify our core value offering, adjusting the message to deliver the greatest impact.”

Ross Ward, CEO, Motus Innovations

“I would like to thank you for your professionalism. I am extremely glad to be working with you.”

Roberto Casalegno, Yobiminds

“We learnt a lot from you. Your suggestions for the pitch and the business plan have been extremely useful, and we are really grateful”

Pablo Lubroth, Founder, Hera Biotech

“We have greatly valued your advice, support and input over the entire programme. Your belief in us has been invaluable in creating the success of BioStars.”

Vinton Cheng, Biostars Programme Manager, Panacea Innovation

Scientific Publications

  • Williamson, J.F. (2008) Advances and perspectives in intracellular biomolecule delivery. Pharmaceutical Technology Europe, p. 43-46.
  • Roth J.F, Shikama N., Henzen C., Desbaillets I., Lutz W., Marino S., Wittwer J., Gassmann M. and Eckner R. (2003) Differential role of p300 and CBP acetyltransferase during myogenesis: p300 acts upstream of MyoD and Myf5. EMBO J. 22, 5186-5196
  • Shikama N., Lutz W., Kretzschmar R., Sauter N., Roth J.F., Marino S., Wittwer J., Scheidweiler A. and Eckner R. (2003) Essential function of p300 acetyltransferase activity in heart lung and small intestine formation. EMBO J. 22, 5175-5185
  • J.F. Roth. (2000) Ty Virus-like particles: a review. Yeast. 16, 785-795.
  • J.F. Roth, S.M. Kingsman, A.J. Kingsman, E. Martin-Rendon. (2000) Possible regulatory function of the Saccharomyces cerevisiae Ty1 retrotransposon core protein. Yeast 16, 921-932
  • P.T.F Williamson, J.F. Roth, T. Haddingham. A.Watts. (2000) Expression and purification of recombinant neurotensin in Escherichia coli. Prot. Expr. Purif. 19, 271-275.
  • A.Watts, J.M.G. Higgins, J.F. Roth, A. Ward.(1999) Weekly highlights, Invest. Drugs,32, 21-25.
  • H.AL-Khayat, D. Bhella, J.M. Kenney, J.F. Roth, A.J. Kingsman, E. Martin-Rendon, H.Saibil. (1999). The Yeast Ty retrotransposon assembles into virus-like particles, whose T-number depend on the C-terminal length of the capsid protein. J. Mol. Biol. 292, (1), 65-73.
  • S.J. Harris, J.F. Roth, N. Savage, S.A. Woodrow, I.K. Hemingway, G.F. Hoyne, J.R.Lamb and G.T.Layton. (1997). Prediction of murine MHC class I epitopes in a major house dust mite allergen and induction of T1-type CD8+ T cell responses. Int. Immunol. 9, 273-280.

Scientific Tranlations

Book Translation from German to English:

The Green Tree Python and Emerald Tree Boa (Kirschner & Seufer Verlag) ISB3-98008264-0-6

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