Patrik Nikolic | Curriculum Vitæ
Marcelji 97 – 51216 Viskovo – Croatia
H +385 (95) 880 5924 • T +385 (51) 257 704
B [email protected] / [email protected]
personal web page: www.nikoli.ch; Skype account: patrik.nikolic91
Research
1: Development of mechanism-based inhibitors of mammalian/human DNA methyltransferases
with IC50 values below 50 nM. The most successful inhibitors can be used for control of functional
organization of mammalian genome in research laboratories, biotechnology and, ultimately, in clinics
for treatment of pathogenic mechanisms related to epigenetic processes (i.e. tissue regeneration,
oncogenesis, psychiatric and neurological disorders, viral infections, immunological disorders).
Area of Expertise
Specialty: Enzymology: In silico approaches for studies of structure and function of biomolecules
Training: Molecular biology, physical biochemistry (i.e. biophysics), medicinal chemistry, biochemistry, cell biology
Expertise: Molecular mechanism in epigenetics; protein-protein and protein-ligand interactions;
drug-design based on enzyme structure-function principles
Work Experience
Department of Biotechnology, University of Rijeka
Student researcher
Rijeka
2013–Present
Student researcher on project "Development of human DNA methyltransferase 1 inhibitors" led by Zeljko
Svedruzic, Ph.D.
Detailed achievements:
{ Novel open source drug design pipeline was developed
{ Toxicity of current generation Dnmt1 inhibitors was characterized
{ Novel Dnmt1 inhibitors our team developed are currently being synthesized in Ruder Boskovic Institute,
Zagreb.
Department of Biotechnology, University of Rijeka
Student researcher
Rijeka
01/2015–04/2015
Student researcher on project of measuring Michaelis-Menten kinetics of novel drugs for pharmaceutical
company "Jiva Pharmaceuticals" under supervision of Zeljko Svedruzic, Ph.D.
Department of Biotechnology, University of Rijeka
Teaching Assistant
Rijeka
2014–2015
Student demonstrator on Chemoinformatics course.
Supervisor and course lecturer: Zeljko Svedruzic, Ph.D
Department of Biotechnology, University of Rijeka
Teaching Assistant
Student demonstrator on Computer Design Methods of Biologically Active Molecules course.
Supervisor and course lecturer: Zeljko Svedruzic, Ph.D
Rijeka
2014–2015
Department of Biotechnology, University of Rijeka
Teaching Assistant
Rijeka
2013–2014
Student demonstrator on Chemoinformatics course.
Supervisor and course lecturer: Zeljko Svedruzic, Ph.D
Jadran Galenski Laboratory d.o.o
Student intern
Rijeka
06/2013–07/2013
Summer internship position in Department of quality control at pharmaceutical company "Jadran Galenski
Laboratorij"
Education
Department of Biotechnology, University of Rijeka
Master degree in Medicinal chemistry, 4.8 of 5 (current)
Department of Biotechnology, University of Rijeka
Bachelor degree in biotechnology and drug research, 4.2 of 5
Rijeka
2013–Present
Rijeka
2010–2013
Master thesis
Title: In silico development of novel human DNA methyltransferase 1 inhibitors
Supervisor: Zeljko Svedruzic, Ph.D
Description: DNA methylation is a fundamental mechanism in functional organization of the
human genome. Accordingly, human DNA methyltransferase 1 (Dnmt1) has been unsuccessfully
targeted in different drug-design efforts for the last 30 years. Most of those failures can be attributed
to inadequate understanding of dynamic structural changes that regulate Dnmt1 activity. Using
a combination of different QM/MM/MD methods, I have identified and characterized several
novel mechanism-based inhibitors by exploiting dynamic structural changes that control interactions
between Dnmt1 and its substrates.
Languages
English: Fluent conversational English and excellent writing skills
Italian: Basic conversational Italian
German: Basic, passive knowledge of German
Awards
City of Viskovo scholarship
City of Viskovo scholarship
2006–Present
Recipient of city of Viskovo scholarship for outstanding academic track, special achievements and high school
grades
Austrian Association of Molecular Life Sciences and Biotechnology
OEGMBT fellowship recipient
Vienna
September 2014
OEGMBT fellowship recipient as presenter on 6th OEGMBT Annual Meeting
Presentations and posters
"Hydrogen bonding in biological systems"
Patrik Nikolic, Ivica Odorcic
April 2015
Workshop and lecture on "Open Day Festival" in organization of Department of Biotechnology, University of
Rijeka
"Open source formats in biomedical sciences"
Patrik Nikolic
March 2015
Lecture on Document Freedom Day, invited speaker
"Open source computational chemistry"
Patrik Nikolic, Vedran Miletic,
October 2014
Lecture on LKLK Conference of Linux users.
"Dna methyltransferase 1 Dnmt1: regional structure selectivity"
Patrik Nikolic, Vedran Miletic, Zeljko Svedruzic
th
Lecture and poster on 6
September 2014
OEGMBT Annual Meeting.
"Pulmonary surfactants"
Gala Grba, Martina Matesic, Patrik Nikolic, Ivica Odorcic, Ticijana Zornada
June 2014
Best student presentation award on seminars of Department of Biotechnology.
Mentor: Dusko Cakara, Ph.D
"Computers as a window into the world of molecules"
Patrik Nikolic
April 2014
Presentation on Open Day Festival at University of Rijeka.
Mentor: Zeljko Svedruzic, Ph.D
"Computational biology and drug research"
Zeljko Svedruzic, Patrik Nikolic
September 2013
Presentation and poster on Night of the Researchers Festival, Croatian national festival of science.
Computer skills
Generic: Outstanding knowledge of generic computer skills both in Windows and Linux OS
enviroment (fluency in both MS and Libre variants of Office suites)
Computational biology: Proficiency in range of chemoinformatics and molecular modeling program
suites such as GROMACS, Gamess-US, UCSF Chimera, Autodock Tools, VMD-NAMD, etc.
Proficent in range of numerical analysis software packages such as Tenua, SciDAvis, Copasi, etc.
Various: Proficiency of statistical analysis in R program suite and STATISTICA program suite
Basic knowledge of Python programming
Interests and hobbies
Music: Active member of "Spincici" Concert Band orchestra since 2002, being lead clarinet player
since 2008.
Finished "Ivan Matetic Ronjgov" elementary music school in 2005.
Traveling: Traveled and toured with orchestra in more than a dozen European countries since 2002.
References
Zeljko Svedruzic:
email: [email protected]
telephone number: +385 51 584 575
Assistant professor at Department of Biotechnology, University of Rijeka
Adjunct assistant professor at Faculty of Medicine, University of Rijeka
Karlo Wittine:
email:[email protected]
telephone number: +385 51 584 587
Assistant professor at Department of Biotechnology, University of Rijeka