"I have never dreamt of working with virtual reality, " says the Fulbright scholarship program graduate about her internship

You spent most of your time in the laboratory during your internship. What did you do?

I started in a synthetic laboratory where I focused on the synthesis of new cholinesterase reactivators. I spent approximately 3-4 months there. In the second phase of the internship, I worked in a biochemical laboratory and carried out different methodologies of biological (in vitro) evaluation. I already knew some of them, for example from previous stays abroad. But work in laboratories in the USA was performed at a higher level.

The next step included in silico testing, specifically molecular docking and measurement of some parameters for selected docked molecules and prepared complexes. I worked in a virtual reality (VR) program and docked the molecules designed by us into a specific binding site. I compared those molecules with another set that had been prepared earlier. I managed to present the results of this research at one of the greatest toxicological conferences in the USA - right in San Diego.

How did it feel to attend such a conference in the early days of your doctoral studies?

It was great! The results of our work came from in silico modeling and synthesis. Unfortunately, towards the end of my internship, we felt the need of having and devoting more time to ensure the sufficient purity of some synthesized substances. As the result, it wasn´t possible to subject the substances to biological testing. Nevertheless, I still evaluate the presented data as sufficient. That was my first scientific conference and I hope to visit such a great and carefully prepared conference again in the future.

How is one supposed to imagine "having molecules in virtual reality"? Did you have to draw or create them?

This is one possibility - we draw the molecules in computer programs and then we import them into the VR program. Molecules can also be modeled directly in the relevant VR program. Greater structures, such as proteins (enzymes) and others can be imported from the Internet. There is a so-called Protein Data Bank which is linked to a virtual reality program. Proteins are loaded from this bank.

How do they get to the bank?

From crystallographic measurements. It is one of the very important techniques of structural biology that focuses on the spatial arrangement of biomolecules. If we know the structure of a protein, for example, we can understand the way it works and deduce the necessary modifications that would affect it. Information obtained from crystallographic data helps us understand the principles of the functioning of an organism and it also leads us to new "ways" that show possibilities how to treat various diseases.

What awaits molecules modeled in this way?

The molecules then undergo further testing. We already know from in silico testing that our substances should be effective. This stage is followed by in vitro testing, or by testing on animals (in vivo) and then by clinical studies - but it´s still a long way to go 😊.

You already did an internship in San Diego as part of your doctoral studies. What will your dissertation focus on?

My dissertation deals with a research in small molecules with anti-aging properties. The work ahead of me includes work on synthesis and article writing. However, after some time I´d like to return to computer chemistry and molecular modeling because this specialization is the one of all have tried and enjoyed most of all. I also assume that in the future this specialization will be of a considerable importance in the development of new drugs.

What can we imagine under "small molecules" with anti-aging properties? Will we find them in our creams in the future?

The purpose is to limit the rate of aging in humans at the cellular level, so we target the structures and processes in the cell that affect the aging of the organism. The goal is to slow down aging and maintain better vitality even in advanced age. And as for the pharmaceutical form – the molecules  probably won't be found in cream, rather in a pill. 

Did the internship meet your expectations regarding the professional aspect?

Absolutely yes - my intention was to learn more about in silico modeling. I didn't even expect to work with virtual reality, so it was like a bite of the cherry. As part of my internship, I received one of the VR headsets from my mentor, Dr. Radić, and I´d like to exploit the work with VR here at our university. I think it's better for students or non professionals to actually see how chemistry "works" instead of having someone to describe it to you in an abstract way. The first mentioned way is definitely more enjoyable, visual and interactive.

Trying other methods was also beneficial. In chemistry, we mostly focus on a specific area – analytical or synthetic chemistry, molecular biology , etc. I'm glad that I tried a little bit of each, it's more advantageous to be multifunctional. I understand the whole process and individual phases of the drug development much better now.

Presenting a poster at SOT Meeting 2022

The internship teaches you openness

What was San Diego like as a city?

It was completely different from what we are used to in the Czech Republic. Getting from one side of the city to the other one was a major problem for me. I had to rely on public transport which was unfortunately not very convenient for me. Sometimes it was my friends who offered me to get to a certain place.

Where did you stay? In a dormitory?

I stayed with a family, an elderly couple. It was advantageous for me because I didn't have to furnish a room. Staying with a family was also more affordable than living on campus. And unfortunately, campus offered no housing opportunities for another one and a half years.

Was the place where you stayed far from the campus?

By the most direct way it didn´t seem to be far. I planned to get a bike and ride the bike to the campus. It was about 5-7 kilometers. But San Diego is not flat. I would have had to climb several steep climbs and canyons on my way and leave the house very early in the morning. I tried that once and it was really challenging. Then I decided to take a bus or go by car lent to me by my host family. Surprisingly, I got used to driving very quickly, even though the traffic there is a bit more chaotic. But people are more conscious when driving and respect one another. A trip on a multi-lane highway was a real challenge but everything turned out well in the end.

What is the cultural environment like in San Diego and on campus? Are there many foreigners there?

Apparently there are more foreigners than American students. There were about 8 of us in the lab, of which only 2 were Americans. I worked with Italians and French people. The atmosphere of the entire campus was more multicultural compared to universities in the Czech Republic.

What about the financial aspect of the internship? Did the scholarship cover your expenses?

Yes, it did. Since I tried not to waste too much money I saved some. I knew that the budget may be tight and I had to live on it for 8 months. For a young person, this is certainly a good experience too. Finally, I had some money left to travel - first I tried a Christmas road trip to Las Vegas, the Zion National Park, the Grand Canyon and Death Valley, and at the end of the internship I went on a road trip through Northern California to the Sequoia National Park, Yosemite National Park, San Francisco and on the way back along Highway 1 and the beautiful Big Sur coastline.

Have you noticed a difference between Czechs and Americans in terms of mindset?

It seemed to me that their (American) internal setting was much more optimistic. For example, when considering new ideas, they don't automatically focus on why something culdn´t work or be done. Moreover, they perceive failure as experience, not necessarily as something bad or condemnable. Unfortunately, Czech nature seems to be more pessimistic to me.

How would you encourage students who are considering similar experience but have not yet gathered the courage to apply for a scholarship?

I think the more you travel, the more insight you have. In addition, if you travel completely alone, similar experiences toughen you up and teach you to be open-minded, you establish new professional and informal contacts, you develop your soft skills, and learn to understand the mentality of people in a new environment. You gain experience from a foreign academic environment, you experience the differences in funding of science and education. The aim of similar scholarship stays is to establish international contacts, share values ​​of your country and the research you are engaged in. The world today needs to be more united, and sharing knowledge is one of the many ways to achieve such unity.

Are you already planning where to go next?

I´d like to go on Erasmus at least during my doctoral studies, preferably in Germany or Scandinavia.

Mgr. Veronika Skoupilová

Veronika graduated from the Bachelor´s Study Program in Toxicology and the Analysis of Pollutants followed by the Master´s Study Program in Chemistry – specialization in Bioorganic Chemistry at the Chemistry Department of the Faculty of Science, UHK. Currently, she is a PhD student of the Toxicology Study program at this department. Veronika also serves as the chairperson of the Student Chamber of the Academic Senate of the Faculty of Science of the University of Hradec Králové.

Photo source: Veronika Skoupilová