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Publications

Current Challenges in PIC design

Current Challenges in Small Molecule Proximity-Inducing Compound Development for Targeted Protein Degradation Using the Ubiquitin Proteasomal System

Bivalent proximity-inducing compounds represent a novel class of small molecule therapeutics with exciting potential and new challenges. The most prominent examples of such compounds are utilized in targeted protein degradation where E3 ligases are hijacked to recruit a substrate protein to the proteasome via ubiquitination. In this review we provide an overview of the current state of E3 ligases used in targeted protein degradation, their respective ligands as well as challenges and opportunities that present themselves with these compounds.
Read on MDPI (molecules)

Ternary Complex Prediction       

Bayesian Optimization for Ternary Complex Prediction (BOTCP)       

Proximity-inducing compounds (PICs) are an emergent drug technology through which a protein of interest (POI), often a drug target, is brought into the vicinity of a second protein which modifies the POI's function, abundance or localisation, giving rise to a therapeutic effect. One of the best-known examples for such compounds are heterobifunctional molecules known as proteolysis targeting chimeras (PROTACs). PROTACs reduce the abundance of the target protein by establishing proximity to an E3 ligase which targets the protein towards degradation via the ubiquitin-proteasomal pathway. Design of PROTACs in silico requires the computational prediction of the ternary complex consisting of POI, PROTAC molecule, and the E3 ligase. Here, we present a novel machine learning-based method for predicting PROTAC-mediated ternary complex structures using Bayesian optimization.
Read on bioRxiv

Protein-protein interactions

Protein-protein interaction prediction for targeted protein degradation

Recent developments in machine-learning-based molecular fragment linking have demonstrated the importance of Protein-protein interactions (PPIs) play a fundamental role in various biological functions; thus, detecting PPI sites is essential for understanding diseases and developing new drugs. PPI prediction is of particular relevance for the development of drugs employing targeted protein degradation, as their efficacy relies on the formation of a stable ternary complex involving two proteins. However, experimental methods to detect PPI sites are both costly and time-intensive. In recent years, computer-aided approaches have been developed as screening tools, but these tools are primarily based on sequence information and are therefore limited in their ability to address spatial requirements and have thus far not been applied to targeted protein degradation.
Read on IJMS

Linker Generation

Decoupled coordinates for machine learning-based molecular fragment linking

Recent developments in machine-learning-based molecular fragment linking have demonstrated the importance of informing the generation process with structural information specifying the relative orientation of the fragments to be linked. A significant impact on the quality of the generated linkers is demonstrated numerically. The amount of reliable information within the different types of degrees of freedom is investigated. Ablation studies and an information-theoretical analysis are performed. The presented benefits suggest the application of a complete and decoupled relative coordinate system as a standard good practice in linker design.
Read in IOPscience

Technology Overview

Identification of Drug-Target Interactions using Xanthos Match Maker™

In this short whitepaper, we have tried to explain our Xanthos Match Maker™ tool for DTI prediction and virtual screening. Our solution not only can achieve a significant performance on a benchmark dataset but also can provide a reasonable prediction on out-of-distribution data. Moreover, the Celeris One platform can cope with the low amount of input data and extract maximum information from sparse input data.
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Case Study

Identification of Novel West Nile Virus NS2B/NS3 Protease Warheads

In this whitepaper we showcase the utilities of Xanthos Match Maker™ in rapidly and accurately predicting biomolecular interactions between drug/target pairs. Based on a deep learning approach, the presented drug-repurposing case study has arguably demonstrated promising as well as competitive results.
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A Model for Structured Information Representation in Neural Networks of the Brain

eNeuro, 2020 Michael G. Müller, Christos H. Papadimitriou, Wolfgang Maass and Robert Legenstein
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Drug–excipient interactions in the solid state: The role of different stress factors

Molecular Pharmaceutics, 2017 Gressl C, Brunsteiner M, Davis A, Landis M, Pencheva K, Scrivens G, Sluggett G, Wood G, Gruber-Woelfler H, Khinast J, Paudel A 9
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Light-assisted small-molecule screening against protein kinases

Nature Chemical Biology, 2015 Álvaro Inglés-Prieto, Eva Reichhart, Markus K Muellner, Matthias Nowak, Sebastian M B Nijman, Michael Grusch & Harald Janovjak 38
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Prediction of drug-packaging interactions via molecular dynamics (MD) simulations

International Journal of Pharmaceutics, July 2012 Feenstra P, Brunsteiner M, Khinast J 13
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Dabigatran and Dabigatran Ethyl Ester: Potent Inhibitors of Ribosyldihydronicotinamide Dehydrogenase (NQO2)

Journal of Medicinal Chemistry, 2012 Simon Michaelis, Anett Marais, Anna K. Schrey, Olivia Y. Graebner, Cornelia Schaudt, Michael Sefkow, Friedrich Kroll, Mathias Dreger, Mirko Glinski, Hubert Koester, Rainer Metternich, and Jenny J. Fischer 10
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Global gene disruption in human cells to assign genes to phenotypes by deep sequencing

Nature Biotechnology, 2011 Jan E Carette, Carla P Guimaraes, Irene Wuethrich, Vincent A Blomen, Malini Varadarajan, Chong Sun, George Bell, Bingbing Yuan, Markus K Muellner, Sebastian M Nijman, Hidde L Ploegh & Thijn R Brummelkamp 178
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Rotation of the exo-Methylene Group of 2-Methyleneglutarate Catalyzed by Coenzyme B12-Dependent 2-Methyleneglutarate Mutase from Clostridium barkeri

Journal of the American Chemical Society, 1996 Christopher H. Edwards, Bernard T. Golding, Friedrich Kroll, Birgitta Beatrix, Gerd Bröker, and Wolfgang Buckel 10
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Rationalizing the diverse reactivity of [1.1.1]propellane through sigma-pi-delocalization

Chemical Science, 2020 Alistair J. Sterling, Alexander B. Dürr, Russell C. Smith, Edward A. Anderson and Fernanda Duarte
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Identification of Potential Off-target Toxicity Liabilities of Catechol-O-methyltransferase Inhibitors by Differential Competition Capture Compound Mass Spectrometry

Journal of Medicinal Chemistry, 2016 Lisa von Kleist, Simon Michaelis, Kathrin Bartho, Olivia Graebner, Marén Schlief, Mathias Dreger, Anna K Schrey, Michael Sefkow, Friedrich Kroll, Hubert Koester, Yan Luo 17
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Targeting a cell state common to triple-negative breast cancers

Molecular Systems Biology, 2015 Markus K Muellner, Barbara Mair, Yasir Ibrahim, Claudia Kerzendorfer, Hannelore Lechtermann, Claudia Trefzer, Freya Klepsch, , André C Müller, Ernestine Leitner, Sabine Macho-Maschler, Giulio Superti-Furga, Keiryn L Bennett, José Baselga, Uwe Rix, Stefan Kubicek, Jacques Colinge, Violeta Serra, Sebastian MB Nijman 19
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TOPS: A versatile software tool for statistical analysis and visualization of combinatorial gene-gene and gene-drug interaction screens

BMC Bioinformatics, 2014 Markus K Muellner, Gerhard Duernberger, Florian Ganglberger, Claudia Kerzendorfer, Iris Z Uras, Andreas Schoenegger, Klaudia Bagienski, Jacques Colinge & Sebastian MB Nijman %
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Capture Compound Mass Spectrometry Sheds Light on the Molecular Mechanisms of Liver Toxicity of Two Parkinson Drugs

Toxicological Sciences, 2010 Jenny J. Fischer, Simon Michaelis, Anna K. Schrey, Olivia Graebner nee Baessler, Mirko Glinski, Mathias Dreger, Friedrich Kroll, Hubert Koester
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Evidence for a Mechanism Involving Transient Fragmentation in Carbon Skeleton Rearrangements Dependent on Coenzyme B12

Angewandte Chemie International, 1995 Dr. Birgitta Beatrix,Dr. Oskar Zelder,Dr. Friedrich K. Kroll,Gissur Örlygsson,Prof. Dr. Bernard T. Golding,Prof. Dr. Wolfgang Buckel 74
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Synthesis and applications of highly functionalized 1-halo-3-substituted bicyclo[1.1.1]pentanes

Chemical Science, 2018 Dimitri F. J. Caputo, Carlos Arroniz, Alexander B. Dürr, James J. Mousseau, Antonia F. Stepan, Steven J. Mansfielda and Edward A. Anderson
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NOTCH1 activation in breast cancer confers sensitivity to inhibition of SUMOylation

Oncogene, 2015 M P Licciardello, M K Müllner, G Dürnberger, C Kerzendorfer, B Boidol, C Trefzer, S Sdelci, T Berg, T Penz, M Schuster, C Bock, R Kralovics, G Superti-Furga, J Colinge, S M Nijman & S Kubicek 33
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Structure based descriptors for the estimation of colloidal interactions and protein aggregation propensities

PLoS One, April 2013 Brunsteiner M, Flock M, Nidetzky B 9
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A chemical genetic screen reveals a resistance mechanism to PI3K inhibitors in cancer

Nature Chemical Biology, 2012 Markus K Muellner, Iris Z Uras, Bianca V Gapp, Claudia Kerzendorfer, Michal Smida, Hannelore Lechtermann, Nils Craig-Mueller, Jacques Colinge, Gerhard Duernberger, and Sebastian MB Nijman 173
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Design, synthesis, docking, and biological evaluation of novel diazide-containing isoxazole-and pyrazole-based histone deacetylase probes

Journal of Medicinal Chemistry, July 2011 Neelarapu R, Holzle D, Velaparthi D, Bai H, Brunsteiner M, Blond S, Petukhov P 67
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Are meaningful predictions of toxicological outcomes in clinical trials based on in vitro diagnostics of preclinical drug candidates possible?

Future Medicinal Chemistry, 2010 Friedrich Kroll, Mathias Dreger
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Alkyne(carbene) Complexes: Stabilization of an Intermediate of Carbene Annelation

Angewandte Chemie International, 1992 Prof. Dr. Karl Heinz Dötz, Dr. Thomas Schäfer, Friedrich Kroll, Klaus Harms 40
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Celeris Therapeutics, Inc.

585 Glenwood Ave
Menlo Park, CA 94025
USA
EIN: 30-1282444

 

Celeris Therapeutics GmbH

Schmiedlstraße 3, 8042 Graz, Austria

Company register: FN 550442z

UID: ATU76712158

IBAN: AT10 3800 0000 0082 1272 BIC: RZSTAT2G

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SAVE & ACCEPT

Dr. Peter Ho

Peter received his B.A. in biology from The Johns Hopkins University and his M.D. and Ph.D. (pharmacology) degrees from Yale University, then completed a pediatrics residency at The Children’s Hospital of Boston followed by clinical fellowships in pediatric hematology/oncology at the Dana-Farber Cancer Institute and in clinical oncology and regulatory sciences jointly through the U.S. FDA and the NCI.

He began his career in drug discovery and development at the Investigational Drug Branch of the Cancer Therapy Evaluation Program, NCI followed by positions of increasing responsibility at Novartis and DuPont Pharmaceuticals. He subsequently served as Senior VP of the Oncology Center of Excellence in Drug Discovery at GlaxoSmithKline and VP of Oncology Clinical Development at Johnson and Johnson.  In 2010, he co-founded BeiGene Ltd. and served as President. Most recently, he served as Chief Medical Officer at Epizyme Inc. and then at Boston Pharmaceuticals both of which are based in Cambridge, MA.  Over his career, he has been directly responsible for the first-time-in-human dosing of 19 anticancer agents and has overseen the development of over 60 hematology and oncology compounds in all phases of clinical trials.  His work has contributed to eleven NCE or biologics approvals to date:  Gleevec®; Arranon®; Tykerb®; Promacta®; Votrient®; Synribo®; Tafinlar®; Mekinist®; Sylvant®; and Rydap®, and Tazverik®.

DI Christopher Trummer

Christopher Trummer is CEO and Co-Founder of Celeris Therapeutics.

Through his professional experience, he has a strong network in the pharmaceutical and biotech industry.
He is responsible for the technical lead, at the intersection of tech and chemistry for all development processes as well as technology partnerships. He has been an invited speaker in AI for drug discovery conferences several times and is co-author of peer-reviewed publications in various journals.

Christopher holds a degree in molecular biology and biotechnology with honors from TU Graz and KFU Graz. Besides, he completed his Master’s degree in information systems at IU in Bad Honnef.

Petr Šrámek

Petr Sramek has been a serial entrepreneur in DeepTech for more than 30 years. Petr builds science, funding, and business infrastructure to support the faster adoption of technologies to improve health. Petr was Entrepreneur in Residence at Singularity University, Co-Founder of the Artificial Intelligence Platform at the Confederation of Industry, and Senator for the Czech Republic in the World Business Angels Investment Forum (WBAF).

Petr is also the founder of the AI Awards project. Petr was listed in the group of 28 AI leaders in the World Intellectual Property Organization’s flagship study alongside Nick Bostrom, Frank Chen, Martin Ford, Kai-Fu Lee, Andrew Ng, Ben Lorica, and others.

Petr is Co-Founder, Chairman of the Board, and Managing Partner of Longevitytech.fund, a Czech VC.

Noah Weber

Noah is the Chief Technology Officer of Celeris Therapeutics.
While graduating in applied mathematics and data science at the Technical University of Vienna, he became a Kaggle grandmaster proving excellence and discipline in global data science competitions.

With his extensive knowledge and experience in machine learning, from research to operations, he’s a lecturer at the Technical University of Vienna and the University of Applied Sciences Vienna.

Nick DeHaan

Nick is VP, Head of Partnerships at Celeris Therapeutics. He gained experience setting up computationally-enabled drug discovery collaborations and commercial agreements as a Partnering Executive at Atomwise. He also managed a commercialization grant program which included drug discovery and development efforts at the University of Michigan Medical School. He holds an MsE from the University of Michigan in Entrepreneurship, with a focus on bioinformatics.

Dr. Markus Müllner

Markus received his Ph.D. in Life Sciences in 2007 at the Institute of Medicinal Chemistry, University of Vienna. He then did his postdoc with BROAD Institute alumni Sebastian Nijman at the Center for Molecular Medicine (CeMM) in Vienna on functional genetic drug screening.

After several high-impact publications on cancer vulnerabilities, he switched from academia to Biotech, where he ultimately joined the leadership team at PhoreMost Ltd. in Cambridge, UK – starting as Assoc. Director R&D and ending at Chief Technology Officer (CTO). At PhoreMost, he hired, shaped, and directed the R&D team, set up the SiteSeeker screening technology, Targeted Degradation technology, and analysis pipeline (both wet lab and dry lab). He oversaw and managed internal and external projects (i.e., with Pharma partners & clients) covering cancer and other disease areas, fundraising, and business development.

Dr. Friedrich Kroll

Friedrich is our VP Drug Discovery and has more than 25 years of experience in medicinal and computational chemistry. He obtained his Ph.D. in 1992 at the Marburg University in organic chemistry and worked for small and big pharma and biotech companies, leading teams of up to 40 people, and already successfully brought a drug to the market. His vast experience covers all stages in drug discovery, including CRO activities, out-, and in-licensing.

Marius Swart

Marius Swart has over 20 years of innovation and financial investment experience. He is a co-founder, angel investor, and worked at Coca-Cola and Henkel in operating roles as well as investment partner for their early stage venture capital arms.

He is currently a board member on several start-ups, advising them on financing and growth strategies and also a member of the World Economic Forum’s Executive Group, Digital Platforms and Ecosystems.

From 2018 to Sept 2021, he worked at Henkel and managed the ±EUR100mm venture arm for the consumer facing businesses. Prior to Henkel, he worked at The Coca-Cola Company for 14 years where he held several positions in finance and operations including 4 years in M&A. During the last 7 years in venture, he has invested in ±40 start ups in several verticals.

Karel Kubias

Karel Kubias is an experienced leader in Life Sciences, chemical, and pharmaceutical businesses with more than 25 years of experience.

Karel studied chemistry at TH Merseburg, Germany, and holds an MBA from Auburn University.

He worked for five years as the CEO of Merck spol. s.r.o., Czech Republic, before becoming the Regional Head Eastern Europe, Middle East & Africa at Merck Millipore, division of Merck KGaA Darmstadt, for another five years.
Karel, Partner in the i&i Biotech Fund, joins the Board of Directors at Celeris Therapeutics.

Hosein Fooladi, MSc

Hosein Fooladi is Chief Data Scientist and one of the first employees of Celeris Therapeutics. He holds a degree in Biomedical Engineering. Hosein was honored by the Iranian Ministry of Science and Research as an exceptional talent after being ranked in the top 0.1% in the national licensing exams.
Since 2017, Hosein has worked at Cambridge Systems Biology Center as a Machine Learning Researcher in Drug Discovery. After this role, he became a Senior Data Scientist for cheminformatics at an in silico drug discovery and design company based in Cambridge.

Hosein is responsible for the intersections of chemistry, biology and machine learning research. Hosein gained our attention through his peer-reviewed publications on deep learning and drug discovery.

Jakob Hohenberger

Jakob has co-founded several tech companies over the past few years, covering a wide variety of areas from marketing, to sales, business management, and product development.
While he was active in various markets, high technology was always the common denominator, including artificial intelligence and natural language processing.
Before co-founding Celeris Therapeutics, he was Head of Sales of an international venture building company in Switzerland.

Jakob is responsible for finance, operations, investments, marketing, and sales.

Dr. Ronjon Nag

Ronjon Nag is a British-American inventor and entrepreneur specializing in the field of mobile technology. He co-founded the technology company Lexicus, which was acquired by Motorola in 1993. His later co-founded company Cellmania was acquired by Research in Motion in 2010. He later served as vice president at both Motorola and BlackBerry.

Ronjon is the founder and president of R42, a U.S. VC group. He was one of the early investors in Healx and Oxford Drug Design.

Assoc.-Prof. Dr. Johannes Kirchmair

Johannes Kirchmair is Associate Professor of cheminformatics at the Institute of Pharmaceutical Chemistry at the University of Vienna and Head of the Computational Drug Discovery and Design Group (COMP3D).
He is also a group leader at the Center for Bioinformatics (ZBH) at the University of Hamburg. After receiving his Ph.D. from the University of Innsbruck (2007), Johannes started his career as an application scientist at Inte:Ligand GmbH (Vienna) and as a university assistant at his alma mater. In 2010, he moved to BASF SE (Ludwigshafen) as a postdoctoral fellow. He then worked as a research associate at the University of Cambridge (2010-2013) and ETH Zurich (2013-2014). Johannes held an assistant professorship in applied bioinformatics at the University of Hamburg (2014 to 2018) and an associate professorship in bioinformatics at the University of Bergen (2018 to 2019).
He has been a visiting professor at the National Institute of Warangal (2016), at the University of Cagliari (2017), and the University of Vienna (2018). His main research interests include the development and application of computational methods to predict the biological activities, metabolic activities, and toxicity of small molecules (including natural products) in the context of drug discovery.

Assist.-Prof. Dr. Günter Klambauer

Günter Klambauer is Assistant Professor for Machine Learning in the field of drug discovery at the Institute for Machine Learning at JKU in Linz. He also leads the research group on AI and Drug Discovery.
His main research interests are self-normalizing neural networks, convolutional neural networks, recurrent neural networks and reinforcement learning, machine learning methods for drug discovery, and life science data analysis and bioinformatics. After his diploma studies in mathematics and biology and teaching positions at BORG Linz and BORG Bad Leonfelden, Günter pursued graduate studies in bioinformatics and did his doctoral thesis with Sepp Hochreiter at JKU.

Günter has received several awards for his scientific excellence, including the Austrian Life Science Award and the Award of Excellence of the Austrian Ministry of Science.

Prof. Dr. Ola Spjuth

Ola Spjuth is a professor at Uppsala University focusing on mathematical and statistical modeling, informatics, and quantitative analysis of pharmacological systems. He has developed methods, algorithms, and software to study and model pharmaceutical interactions.
A major focus of his group is how artificial intelligence and machine learning can aid the drug discovery process: for example, in drug screening and the study of drug toxicity, metabolism, and resistance.
His group combines in silico and in vitro experiments at the cellular level and has access to a robotic high-content imaging laboratory connected to a modern IT infrastructure to manage and analyze large amounts of data.

Prof. Dr. Jean-Louis Reymond

Jean-Louis Reymond is a Professor of Chemistry at the University of Bern, Switzerland. He studied chemistry and biochemistry at the ETH Zurich and received his Ph.D. from the University of Lausanne on the synthesis of natural products (1989).
After a post-doc and an assistant professorship at the Scripps Research Institute, he moved to the University of Bern (1997). His research focuses on the recognition and representation of the chemical space for small molecule drug discovery, the synthesis of new molecules from GDB (http://gdb.unibe.ch), and the design and synthesis of peptide dendrimers and polycyclic peptides as antimicrobial agents and for nucleic acid transport. He is the author of > 300 scientific publications and reviews (h = 62).

Dr. Siham Ceballos

Siham Ceballos is an international medical executive with more than 17 years of experience in biotech and pharma industry and VC-backed start-ups.

Among other achievements, Siham set up and led international medical organizations for several biotechs at their start-up stage in Europe, including Celgene, Alnylam, and Mayne Pharma. She more recently contributed to the inception and was the COO of Rejuveron Life Sciences.

Siham holds a Master in Cellular and Molecular Physiopathology and a Ph.D. in Cancer Cellular and Molecular Biology from the University of Pierre and Marie Curie, Paris. She earned an executive MBA in ESSEC Business School, Paris. 

FH-Prof. Dr. Stephan Winkler

Stephan Winkler is a FH-Professor and Program Director at the University of Applied Sciences Upper Austria in the field of Medical- and Bioinformatics. He is also Head of the Department of Medical- and Bioinformatics, and Data Science at University of Applied Sciences Upper Austria.

After receiving his doctorate from Johannes Kepler University (2008), Stephan started his career at University of Applied Sciences Upper Austria, as FH-Professor for Medical- and Bioinformatics. In the course of his work, he was awarded several times, among others as the best lecturer of the UAS Upper Austria.