Hi. I’m Patrik Nikolić.
My scientific research and interest involve the following:
- drug discovery using computational chemistry with emphasis on high-throughput virtual screening protocols and molecular dynamics simulations
- drug development
- translational research
For further information and a formal introduction, please download my résumé or follow me on LinkedIn and GitHub.
Biomolecular Structure and Function Group
In 2013, as a medicinal chemistry student at the University of Rijeka Department of Biotechnology, I started working in Dr. Željko Svedružić’s Biomolecular Structure and Function Group and Group (BioSFGroup) on the development of mechanism-based inhibitors of human DNA methyltransferase Dnmt1. While I have primarily used GROMACS and PyMOL in my research, the group relied heavily on software for research and teaching and used several other packages. I obtained my master’s degree in medicinal chemistry in 2015 by defending the thesis titled In silico optimization of the first DNA-independent mechanism-based inhibitors of mammalian DNA methyltransferase Dnmt1. Resulting from this work, BioSFGroup later published the book chapter:
- Nikolić, P., Miletić, V., Odorčić, I. & Svedružić, Ž. M. Chapter 5 - In Silico Optimization of the First DNA-Independent Mechanism-Based Inhibitor of Mammalian DNA Methyltransferase DNMT1. in Epi-Informatics (ed. Medina-Franco, J. L.) 113–153 (Academic Press, 2016). doi:10.1016/B978-0-12-802808-7.00005-8.
The group also published the journal paper:
- Miletić, V., Odorčić, I., Nikolić, P. & Svedružić, Ž. M. In silico design of the first DNA-independent mechanism-based inhibitor of mammalian DNA methyltransferase Dnmt1. PLOS ONE 12(4), e0174410 (2017). doi:10.1371/journal.pone.0174410. PDF, PubMed
In 2019, Dr. Vedran Miletić returned from his postdoctoral research in computational biophysics at Heidelberg Institute for Theoretical Studies in Molecular Biomechanics (MBM) group to become a Senior Lecturer at the University of Rijeka Department of Informatics. We jointly started RxTx Research, where I entered as a translational research scientist. Our goal was to advance pharmaceutical drug research by improving the scientific software behind the scenes, most notably the high-throughput virtual screening engine RxDock. We also started using RDKit for data pre-processing at the same time.
By then, the computational resources became more available, drivers necessary for using those resources more mature, and research topics more complex. Thus, the volume of data comprising research inputs and outputs grew exponentially, so we have employed end-to-end data science solutions, specifically KNIME for workflow automation and data analysis.
We continued the collaboration with BioSFGroup and gave a conference presentation:
- Koren, R., Martinović, M., Nikolić, P., Odorčić, I., Ostojić, L., Visentin, D., Vrbnjak, K., Miletić, V. & Svedružić, Ž. M. Supercomputers as microscopes for the 21st century: substrate channeling, epigenetic regulation, and molecular basis of Alzheimer’s disease. in 27HSKIKI Book of Abstracts, Zagreb, Croatia (Croatian Chemical Society, 2021).
Dr. Vedran Miletić and I independently published another paper in collaboration with Dominik Kinkela:
- Miletić, V., Nikolić, P. & Kinkela, D. Structure-based Molecular Docking in the Identification of Novel Inhibitors Targeting SARS-CoV-2 Main Protease in 2021 44th International Convention on Information, Communication and Electronic Technology (MIPRO), 435–440 (2021). doi:10.23919/MIPRO52101.2021.9596660.
We also opened a number of new collaborations with other groups worldwide.
Group for Applications and Services on Exascale Research Infrastructure
In Q4 2021, Dr. Vedran Miletić was promoted to Assistant Professor at the Faculty of Informatics and Digital Technologies, University of Rijeka, and formed Group for Applications and Services on Exascale Research Infrastructure (GASERI). I continued the collaboration with GASERI as an external partner.
With the ever-increasing applications of artificial intelligence, machine learning, neural networks, and deep learning in computational biochemistry, I became increasingly aware that more than the methods applied in my previous and current research is needed. For example, Greg Landrum, the owner of T5 Informatics and the author of RDKit, has already been blogging about machine learning using RDKit for some years.
My goal is to bring medicinal chemistry know-how of applications of artificial intelligence methods to GASERI to stay relevant in the long term and be able to tackle any challenge that is interesting both to industry and academia.
The list of my thus far scientific publications can be found on Web of Science and Google Scholar.
My contribution is acknowledged in the following journal paper:
Saftić Martinović, L., Birkić, N., Miletić, V., Antolović, R., Štanfel, D. & Wittine, K. Antioxidant Activity, Stability in Aqueous Medium and Molecular Docking/Dynamics Study of 6-Amino- and N-Methyl-6-amino-L-ascorbic Acid. Int. J. Mol. Sci. 24(2), 1410 (2023). doi:10.3390/ijms24021410
We wish to thank Patrik Nikolić (BioRX Partners LLC) for help in the conceptualization of the in silico workflow.
Private Industry Career
Translational Research Scientist at Fidelta
A cornerstone of my career has been the scientist position at the Translational Research and Alliances Department at Fidelta Ltd.. With Fidelta being a pharmaceutical contract research organization (CRO), I had the opportunity to work on projects for a large number of originator pharmaceutical companies. My position was designed as a scientist with a high-level overview of all the projects Fidelta had at the time, where I provided support to the project management team in preparing, visualizing, and analyzing data on integrated drug discovery projects.
The experience and knowledge I gained with my mentor Vesna Eraković Haber, MD, Ph.D., MBA of the pharmaceutical industry as a whole proved invaluable. My duties included setting up, monitoring, and closing collaborations with clinical and academic institutions. The primary focus of development projects was in the oncology, pulmonology, and gastroenterology fields.
I also worked as a “regular” scientist in a wet lab, mainly on human tissue sample preparation and handling for further tests (ELISA, flow cytometry, immunohistochemistry).
An overview of my duties included:
- clinical study site visits, including qualification, initiation, monitoring, and close-out visits according to GCP, GDPR, and other relevant national legislation
- writing clinical study protocols with accompanying procedures and documents
- managing communication between Clinical Investigators, clients, local regulatory authorities, and research teams
- performing in vitro and ex vivo assays for drug development
Sales and Applications Specialist for Life Science at Biomedica dijagnostika
A new step in my career was an opportunity to develop and expand a research portfolio of AddLife Group. As a Sales and Application Specialist for the Life Science portfolio, I started working for the Croatian subsidiary Biomedica dijagnostika Ltd. of Biomedica Group. The main reason I took up this opportunity was the challenge of introducing new and cutting-edge technology in the competitive European market.
Nobody expected a global pandemic of that size and scope, and certainly not the size and scope of the disruption it caused on worldwide manufacturing and distribution chains. Furthermore, nobody expected industry-wide changes in how the business is being done. All those changes made that challenge and the goals I set even harder to achieve. Given my previous experience and know-how, coupled with the forward-looking team at Biomedica and AddLife, I’m happy to say that I achieved those goals and then some.
Similar to the position at Fidelta, my portfolio was diverse and included many manufacturers. The clients I worked with ranged from small academic groups across the public sector and private hospitals to pharmaceutical companies. A comprehensive overview of industry trends, setting up commercial contracts, and following up on successful sales projects is the most valuable experience I could gain in this industry. That was one of the goals I set myself up back when I was joining Biomedica.
An overview of my duties included:
- regular meetings with scientists, physicians, nurses, and other support members in the pharmaceutical industry, academia, public hospital systems, and private hospitals
- participation in and organization of congresses
- product demonstration and performing demonstrations for a selected portfolio