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Publications

CADD to design PICs

Computer Aided Drug Design in the Development of Proteolysis Targeting Chimeras

Proteolysis targeting chimeras represent a class of drug molecules with a number of attractive properties, most notably a potential to work for targets that, so far, have been in-accessible for conventional small molecule inhibitors. Due to their different mechanism of action, and physico-chemical properties, many of the methods that have been designed and applied for computer aided design of traditional small molecule drugs are not applicable for proteolysis targeting chimeras. Here we review recent developments in this field focusing on three aspects: de-novo linker-design, estimation of absorption for beyond-rule-of-5 compounds, and the generation and ranking of ternary complex structures. In spite of this field still being young, we find that a good number of models and algorithms are available, with the potential to assist the design of such compounds in-silico, and accelerate applied pharmaceutical research.
Read in the Computational and Structural Biotechnology Journal (CSBJ)

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 Artificial Intelligence in the Life Sciences

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

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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Dr. Mark Whittaker

Mark Whittaker is a passionate and experienced researcher in drug discovery. He has a D.Phil. in chemistry from the University of York and undertook postdoctoral studies in Toronto and Oxford. He has worked for Evotec, a leading biotechnology company, for over 20 years, where he initially held the position of Director of Drug Discovery, leading integrated drug discovery collaborations within the CRO business. He moved in 2013 to the internal research business segment, where he held positions of SVP Head of Oncology and, latterly, SVP Head of Protein Homeostasis. During his time at Evotec, he was involved in several projects that aimed to develop novel drugs in various therapeutic areas, including oncology, diabetes, and neuroscience. Prior to joining Evotec, Mark spent 13 years at British Biotech, initially as a Group Leader in Medicinal Chemistry and subsequently, he became Head of Medicinal Chemistry and finally Director of Chemistry.

Dr. Chris Tame

Chris is a distinguished scientist in the field of drug discovery and development, renowned for his expertise in this area. He brings a wealth of experience across all preclinical phases, coupled with a diverse skill set encompassing AI and targeted protein degradation. Dr. Tame has held several key positions in the industry, including Head of Early Discovery Chemistry and Target Evaluation at Benevolent AI, and Protein Degradation Research Leader at GSK (in collaboration with Craig Crews’ group). His contributions to these organizations have been invaluable, and he continues to make significant strides in the field of drug discovery.

Dr. James Field

Dr. James Field is the Founder and Chief Executive Officer of LabGenius, a London-based biotech company that leverages the combined power of synthetic biology, robotic automation, and machine learning. This combination of technologies is used to develop a smart platform capable of intelligently developing therapeutic antibodies.

For decades, scientists, engineers, and technologists have dreamt of building ‘robot scientists’ capable of autonomously discovering new knowledge, technologies, and sophisticated real-world products.

For Dr. Field, this represents the most exciting opportunity of our generation, and he founded LabGenius with the dream of making this a reality.

In 2017, James was awarded the BBSRC Innovator of the Year award for early career impact. In 2018, he was featured on Forbes’ 30 Under 30 list for Science and Healthcare. He is also a fellow of the prestigious Synthetic Biology Leadership Excellence Accelerator Program (LEAP).

In addition to his company responsibilities, James is a recognized thought leader in his field. He has spoken at global events such as the Milken Global Conference, TEDMED, RAAIS and CogX, and works with The Ditchley Foundation to brief key policymakers in government on AI-enabled drug discovery.

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.

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.

DI Christopher Trummer

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

He is an accomplished biotech executive with expertise in bridging the fields of engineering and biotechnology, driving development processes and forging technology partnerships. As a board member of BIOTECH AUSTRIA, the biotechnology association in Austria, he contributes to shaping the industry landscape.

Christopher is regularly invited to share his insights at drug development conferences, particularly focusing on the intersection of artificial intelligence and pharmaceuticals. Additionally, he has co-authored peer-reviewed publications across 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.

Prof. Dr. Stefan Knapp

Prof. Dr. Stefan Knapp joined Frankfurt University (Germany) in 2015 as a Professor of Pharmaceutical Chemistry and the Buchmann Institute of Molecular Life Sciences. He is associated to the Structural Genomics Consortia (SGC) as a visiting Professor at Oxford and an adjunct Professor at George Washington University. Since 2017 he has been the CSO of the newly founded SGC node at the Goethe-University Frankfurt. His research interests are the rational design of selective inhibitors that target protein kinases and protein interactions.

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®.

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.

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.

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.

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).