Featuring Stefan Simic, PhD Student in the University of Graz

We are delighted to highlight Stefan Simic’s activity within the CLASSY project. He is a PhD Student at the University of Graz, Austria and he has contributed to the project by applying his knowledge to demonstrate how can enzymes and light be jointly useful. He made a great research on the power of biocatalysis in the development of cell-like molecular assembly lines. In this short interview, Stefan shares some insights into his work and experience as a doctoral researcher working within the CLASSY research and innovation action.

How did you get into this field of research?

I came from an organic chemistry background, which deals with the properties and preparation of small molecules. Of course, nature has been making small molecules long before humans and I was fascinated by the sophistication of nature’s synthetic machinery (enzymes). That’s why I decided to look for a PhD in a group that is well-established in the field of enzyme catalysis (biocatalysis) and this led me to the Elk Crew at the University of Graz.

Why did you apply for a researcher position with CLASSY?

I didn’t actually know any details about the position before the interview, but when I was told I would be working with a light-dependent enzyme in flow, that sounded quite exciting and new, and it was indeed.

What do you think you bring to the CLASSY team besides your expertise?

As I enjoy taking part in science communication events and presenting research to the public, I was happy to contribute to various dissemination activities of CLASSY.

What is the most important quality you consider a researcher should have?

I would say, to do good science it’s important to have excellent understanding of your topic and to be rigorous with experiments and data analysis. Doing research is a bit like having a conversation with nature, by doing experiments you ask questions and through data, nature provides the answers. It’s important to know how to ask the right questions and then to know how to decipher the answers.

What is your favorite memory during CLASSY so far?

That would probably be the kick-off meeting in Zurich. It was my very first contact with CLASSY, everything felt big, new and exciting and the meeting location (ETH Zurich) definitely contributed to it.

What are your aspirations for your research? (explain what you would like to do after your PhD)

What I would like to see as a follow-up of my research and understanding of the topic is the improvement of stability of the enzyme we studied and the discovery of more similar enzymes. However, I probably won’t be personally involved in these findings as I am looking for a new and different set of challenges in industrial/corporate settings.

Let’s leave science aside, what other hobbies do you have?

Having lived in Austria for around 4 years, I enjoy hiking in the Austrian Alps on a regular basis. I’ve also always enjoyed learning foreign languages (German being the most recent focus, of course). I also enjoy reading popular and not-so-popular psychology and recently I started giving dancing a try.

Featuring Miglė Jakštaitė, PhD Student in Radboud University Nijmegen

We are delighted to highlight Miglė Jakštaitė’s activity within the CLASSY project. She is a PhD Student at Radboud University, Nijmegen and she has brought key contributions to the project by applying her knowledge to demonstrate how to perform cell-free biosynthesis in flow while having control of enzymatic reactions. In this short interview she shares some insights into her work and experience as a doctoral researcher working within the CLASSY research and innovation action.

How did you get into this field of research?

I have gained prior knowledge of enzyme kinetics during my internship in the group of Prof. Wilhelm T.S. Huck, where I later decided to continue my PhD programme. During my PhD I expanded my expertises of enzymatic synthesis, microfluidics and enzyme immobilisation. Now I use all these fields daily in my research for CLASSY project. 

Why did you apply for a researcher position with CLASSY?

I imagined it would be a great opportunity to closely collaborate with researchers from various groups within the consortium and that would result in many challenging projects. And I was right! Also having discussions and getting advices from other experts in the field is a highly valuable experience.

What is the most important quality you consider a researcher should have?

Curiosity – a quality which pushes you forward and doesn’t let you give up when you don’t get the results you were hoping for.

What is your favorite memory during CLASSY so far?

Our kick-off meeting in Zurich was quite memorable as we all met there for the first time and we could learn more about each other’s research interests. Also, filming CLASSY video in the labs was fun as well!

What are your aspirations for your research? (explain what you would like to do after your PhD)

After my PhD I would like to apply my knowledge in industry where hopefully I could continue working on enzymatic reactions.

Let’s leave science aside, what other hobbies do you have?

Dancing, hiking and dog walking!

HIGHLIGHTS ON THE CLASSY INDUSTRY WORKSHOP: BRINGING BIOCATALYSTS TO MICROREACTORS IN FLOW

The CLASSY Industry Workshop was held online on Monday, 16 October 2023, attracting 70 participants from the industry and academia. The event, titled “Bioreactions in flow reactors: bringing out the potential applications for cell-free synthetic biology”, zoomed in on the hot topic of cell-free enzymatic pathways in flow through eight talks by ten experts in the field.

Guided by Prof. Wolfgang Kroutil (Universität Graz), the CLASSY partners and scientists in systems chemistry showcased the latest results of the project: Prof. Wilhelm Huck (Radboud University Nijmegen) kicked off with a talk titled “Optimal experimental design strategies for optimising immobilized enzymatic reaction networks”. Subsequently, Dr. Christoph K. Winkler (Universität Graz) showcased the challenges with light and enzymes in flow; and Dr. Elwin Vrouwe (Micronit) ended the project research results with the layout of a general-purpose perfusable microfluidic reactor array.

Giving way to the six guest industry experts in the field of biocatalysis who raised the presentations towards the industry: Dr. David Roura Padrosa (inSEIT Biotech), Dr. Mattia Lazzarotto and Dr. Stefan Payer (Enzyan Biocatalysis), Dr. Rob Schoevaart (ChiralVision), Dr.Javier Ibáñez (EnginZyme) and Dr. David Liese (Enzymicals), showcased their latest research on the topic and actively answered to all the questions from the attendees. To foster the knowledge exchange between the academic sector and industrial R&D departments, each presentation was followed by a dedicated Q&A session. The workshop ended with an interesting panel discussion with all the speakers, led by Prof. Wolfgang Kroutil and Prof. Wilhelm Huck, concerning the potential applications of the Innovations in the industry.

All these excellent lectures are highlighted in the workshop recording and come up with the fact that applying all these innovations into the industry will accelerate the development greately. The speakers pointed out that all of them will keep on pushing the flow chemistry and the enzymes (either in cascades or batch) to have more showcases from which all can learn and improve further for the future industrial applications of cell-free synthetic biology.

Did you miss (parts of) the event or want to know more than these key takeaways from the workshop? You can also watch the full video on the CLASSY YouTube channel.

CLASSY holds its 10th General Assembly in Graz

The 10th General Assembly meeting, hosted by the Graz University, took place in Graz on the 10-11th of October 2023. The meeting brought together 15 participants from all partners to discuss the progress towards the development of a new type of chemical reactor inspired by the way in which living systems manage to modulate catalytic activity.

The CLASSY partners pictured at the 10th General Assembly in October 2023 at Graz

Prof. Wolfgang Kroutil, Dr. Christoph K. Winkler, Dr. Mathias Pickl and Mr. Stefan Simic from University of Graz (UG) opened the meeting, welcoming all partners. To start with the programme of Day 1, Dr. Jeanette Muller (accelCH) presented the overall status of the project, leading a discussion between partners on how to address the next steps for research avenues to ensure the project’s progress until it’s final stage.

The rest of the morning was fully dedicated to research updates from all scientific work packages, starting with presentations from Prof. Gonen Ashkenasy (BGU), who presented his group’s progress on nucleic-acid-peptide chimeras and nucleopeptide replication networks, that were also released in two recent publications (Soft Matter, 2023, 19, 1940 and Cell Reports Physical Sciences, 2023, 4, 101594). Prof. Bartosz Lewandowski (ETH) contributed showing their collaboration with UAM, on the self-assembly and catalytic properties of peptide-nucleolipids and with BGU, on the recently started self-replicating assemblies for catalysis reactions. Still in showcasing their most recent publications, Prof. Andrés de la Escosura and Mr. Alonso Puente (UAM) made an update on the Syschem group’s latest progress including preliminary results in achieving controlled molecular assembly-disassembly with new techniques and informed that three papers will be published soon.

After the lunch break, Dr. Mathias Pickl and Mr. Stefan Simic (UG) presented and discussed their progress in bio- and organo-catalysis, followed by the intervention of Dr. Jonas Rackl (ETH), who presented their progress and new research avenues in chemoenzymatic cascade reactions. Subsequently, Ms. Miglė Jakštaitė and Wilhelm Huck (RU) presented their computational and lab-based approaches to cascade reactions, leading into an update on the latest microfluidic device prototypes by Elwin Vrouwe (MICRONIT). All these research progresses and collaboration highlights are available in the recently released joint CLASSY’s science slams video.

The consortium finished the first day full of presentations with several scientific discussion groups for more in-depth exchange between partners. Afterwards, an interactive brainstorming and discussion session on the project’s exploitation opportunities, led by Dr. Jeanette Muller and Ms. Miriam Frances (accelCH), was arranged with updated insights to be compiled in the innovation management system and lay the path for the upcoming exploitation activities, planned for the end of the project. The productive catch-up finished with a wrap-up on the upcoming CLASSY Industry Workshop that will take place on 16th October 2023 and with new ideas for upcoming conference participations and possibilities for the final CLASSY Scientific Symposium 2024.

On Day 2, all the partners had the chance to attend a guided lab tour through the laboratory facilities at the University of Graz, guided by Mr. Stefan Simic, gathering a better feel and understanding of how the Biocatalysis Research Group keep science in motion.

 

Registration is open for the online CLASSY Workshop

Join us online on 16th October 2023 from 13:00 – 15:30 CET for the CLASSY workshop Bioreactions in flow reactors: bringing out the potential applications for cell-free synthetic biology.

Are you working with enzymatic cell-free pathways in flow or are you using or developing (biocatalytic) flow chemistry technologies? Then you might be interested to join our workshop on the opportunities, technological challenges and bottlenecks for the application of immobilised enzymatic pathways! The CLASSY partners and scientists in systems chemistry will showcase the latest results of the project and several industry experts in the field of biocatalysis will participate in the event. Our invited guest speakers Dr. David Roura Padrosa (inSEIT Biotech), Dr. Mattia Lazzarotto and Dr. Stefan Payer (Enzyan Biocatalysis), Dr. Rob Schoevaart (ChiralVision), Dr.Javier Ibáñez (EnginZyme) and Dr. David Liese (Enzymicals), will present their latest research on the topic and will be available to answer questions.  
To foster the knowledge exchange between the academic sector and industrial R&D departments, each presentation will be followed by a dedicated Q&A session. The workshop will be closed with a panel discussion with all the speakers, lead by Prof. Wolfgang Kroutil (Universität Graz) and Prof. Wilhelm Huck (Radboud University Nijmegen), concerning the potential applications of the Innovations in the industry. The workshop is free and open to all audiences. Do you want to know more? Check out the programme and register today!

New CLASSY publication in PNAS

Exciting news from Andrés de la Escosura’s team at UAM and Gonen Ashkenasy’s team at BGU: their first CLASSY results have just been published in PNAS. Getting one step further towards understanding the processes at the origin of life, the published results reveal a successful attempt at replicating simple nucleopeptide chimeras. The authors identified mechanisms of selective replication processes that may be realted to those that led to the emergence of biological assemblies, such as ribosomes and viruses. Read all about their findings in: Anil Kumar Bandela, Nathaniel Wagner, Hava Sadihov, Sara Morales-Reina, Agata Chotera-Ouda, Kingshuk Basu, Rivka Cohen-Luria, Andrés de la Escosura, Gonen Ashkenasy. Primitive selection of the fittest emerging through functional synergy in nucleopeptide networks. PNAS. 2021, 118

First CLASSY publication is out

We are happy to announce that after just about half a year from the project start, the first results of the CLASSY project are now available from the Wennemers team at ETH. Read all about the latest developments in organocatalysis in: Jasper S. Möhler, Tobias Schnitzer, Helma Wennemers. Amine Catalysis with Substrates Bearing N-Heterocyclic Moieties Enabled by Control over the Enamine Pyramidalization Direction. Chem. Eur. J. 2020, 26, 15623 –15628 DOI: 10.1002/chem.202002966

CLASSY: what does the origin of life have to do with modern industry?

​Where, how and when did life originate? Or, more simply put, Where do we come from? Molecular synthesis, the series of reaction processes needed to build the simplest components of life, is at the basis of life itself. Yet, we still don’t know what type of reactions were responsible for the genesis of life’s first building blocks. Molecular synthesis is also at the foundation of many industrial sectors, from drug development in the pharmaceutical industry, agricultural and household product development in the chemical industry, aroma and scent creation in the food and perfume industries to many more. Yet state-of-the-art molecular synthesis used in today’s industries is unsustainable, as it requires many intermediate reaction steps, each producing vast amounts of waste products (e.g., 25-100 kg of waste for each kg of product for pharmaceutical drugs). Living cells can synthesize an enormous variety of complex products in a single ‘cell reactor’, overcoming the need for many intermediate steps.

An international, multidisciplinary consortium of researchers has set out to create, within the framework of the European Union’s Horizon 2020 Research and Innovation Programme, a new type of chemical reactor for molecular synthesis that mimics living cells. During the 4-year CLASSY project the team of researchers from five European countries aims to revolutionise molecular synthesis and develop a unique chemical reactor able to combine multiple biocatalysis, carrying out compartmentalized and programmable reactions in a similar way as living cells do, limiting the amount of waste generated. Achieving this will not only require high-tech microfluidic compartments and programmable reactions, but also significant developments in the fundamental understanding of molecular synthesis. Thus, CLASSY will bring benefits to modern industrial procedures, by developing a new technology that will constitute an important leap towards a limited-waste, sustainable, green factory of the future, alongside contributing significant advances in basic knowledge on the dynamics of molecular synthesis, likely to have exciting implications for furthering our understanding of the origin of life.

“The vision of having a dynamic cell-like system sounds almost like science fiction, but definitely something to strive for. Having an inspiring goal motivates our work and this end goal should be enough motivation to get the project going.” says a researcher from the CLASSY project. With this ambition and the enthusiasm to become game-changers in chemical synthesis, 18 members from the multidisciplinary consortium kicked off the CLASSY project on November 12-13th 2019 at ETH Zürich, Switzerland. The EU has committed 3.08 m euro in funding to the project’s budget.

Besides four leading research groups with expertise in systems chemistry, biocatalysis and microfluidics, the team also includes two companies specialized in microfluidic technology and project management, communication, dissemination and exploitation.

Project Partners:

  • Biohybrid Materials and Systems Chemistry Group, Universidad Autónoma de Madrid, ES (coordinator)
  • accelopment AG, CH
  • Laboratory for Systems Chemistry, Ben-Gurion University of the Negev, IL
  • Laboratory of Organic Chemistry and Chemical Biology, ETH Zürich, CH
  • Physical-Organic Chemistry Research Group, Radboud University Nijmegen, NL
  • Organic and Bioinorganic Chemistry Group, Universität Graz, AT
  • Micronit Microtechnologies B.V., NL
CLASSY team participants at the kick-off meeting in November 2019 at ETH Zürich.