Assoc. Prof. Andrej Perdih, PhD
National Institute of Chemistry Hajdrihova 19 Tel.: +386-1-4760-376 |
My research interests:
1. Application of structure-based and ligand-based drug design techniques in virtual screening experiments aimed at identifying novel hit molecules on a range of macromolecular therapeutic targets,
2. Molecular dynamics (MD) simulations of macromolecules to increase the understanding of the target protein molecules structure-function relationships and to gain insight into the molecular recognition process of the ligand-target interactions,
3, Modeling of organic and enyzmatic reaction mechanisms using quantum chemistry and multiscale QM/MM methods
Education
2004-2009 PhD in Medicinal Chemistry
Dynamical Model of the E. coli MurD enzyme and in silico design of novel inhibitors
University of Ljubljana, Slovenia
1999-2004 Undergraduate Studies of Pharmacy
University of Ljubljana, Slovenia
Research Positions
2017 - Senior Research Associate
National Institute of Chemistry, SI
2013-2017 Visiting Scholar (15 months)
University of Michigan, USA
2012-2017 Research Associate
National Institute of Chemistry
2012 - 2013 Visiting Scholar (14 months)
Freie Universität Berlin, Germany
2009-2012 Postdoctoral Researcher
National Institute of Chemistry, SI
2008 Visiting Scholar (4 months)
Inte:Ligand, Vienna, Austria
2004 - 2009 Junior Researcher (PhD student)
Teaching
2011- Associate Professor (Med. Chemistry)
University of Ljubljana
2011-2021 Assistant Professor (Med. Chemistry)
University of Ljubljana
2006-2011 Teaching assistant (Med. Chemistry)
Faculty of Pharmacy
Honors and Awards
2009 Krka prize for PhD. Thesis
2004 Krka prize for M. Pharm. Thesis
2004 Faculty of Pharmacy Award
Selected Publications
1. Computer-added drug design
a) Anticancer targets
1. BERGANT Kaja, JANEŽIČ Matej, ŠTAMPAR Martina, ŽEGURA Bojana, GOBEC Stanislav, FILIPIČ Metka, PERDIH Andrej. Substituted 4,5'-Bithiazoles as Catalytic Inhibitors of Human DNA Topoisomerase IIα, Journal of chemical information and modeling, 2020, vol 60, str. 3662–3678.
2. KUMP, Karson J., MIAO, Lei, MADY, Ahmed S.A., ANSARI, Nurul H., SHRESTHA, Uttar K., YANG, Yuting, PAL, Mohan, LIAO, Chenzhong, PERDIH, Andrej, ABULWERDI, Fardokht A., CHINNASWAMY, Krishnapriya, MEAGHER, Jennifer L., CARLSON, Jacob M., KHANNA, May, STUCKEY, Jeanne A., NIKOLOVSKA-COLESKA, Zaneta. Discovery and characterization of 2,5-substituted benzoic acid dual inhibitors of the anti-apoptotic Mcl-1 and Bfl-1 proteins. Journal of medicinal chemistry. 2020, 63, 2489-2510.
b) Antibacterial targets
1. PERDIH, Andrej, HRAST, Martina, BARRETEAU, Hélène, GOBEC, Stanislav, WOLBER, Gerhard, ŠOLMAJER, Tomaž. Inhibitor design strategy based on an enzyme structural flexibility : a case of bacterial MurD ligase.J. Chem. Inf. Model, 2014, 54, 1451-1466.
2. BRVAR, Matjaž, PERDIH, Andrej, RENKO, Miha, ANDERLUH, Gregor, TURK Dušan, ŠOLMAJER, Tomaž. Structure-based discovery of substituted 4,5’-bithiazoles as novel DNA gyrase inhibitors.J. Med. Chem.2012, 55, 6413−6426.
2. Studies of macromolecules using molecular simulations
1. PRAŠNIKAR Eva, PERDIH Andrej, BORIŠEK, Jure. All-Atom Simulations Reveal a Key Interaction Network in the HLA-E/NKG2A/CD94 Immune Complex Fine-Tuned by the Nonameric PeptideJournal of chemical information and modeling, 2021, vol 61, 3593–3603.
2. PINTAR, Sara, BORIŠEK, Jure, USENIK, Aleksandra, PERDIH, Andrej, TURK, Dušan. Domain sliding of two Staphylococcus aureus N-acetylglucosaminidases enables their substrate-binding prior to its catalysis.Communications biology. 2020, vol. 3,178-1-178-9.
3. Modeling of reaction mechanisms
a) Enzymatic reactions
1. BORIŠEK, Jure, PINTAR, Sara, OGRIZEK, Mitja, TURK, Dušan, PERDIH, Andrej, NOVIČ, Marjana. A water-assisted catalytic mechanism in glycoside hydrolases demonstrated on the Staphylococcus aureus autolysin E. ACS catalysis, 2018, 8, 4334-4345.
2. PERDIH, Andrej, HODOŠČEK, Milan, ŠOLMAJER, Tomaž. MurD ligase from E. coli: Tetrahedral intermediate formation study by hybrid quantum mechanical/molecular mechanical replica path method.Proteins2009, 74, 744-759.
b) Organic reactions
1. RIČKO, Sebastijan, SVETE, Jurij, ŠTEFANE, Bogdan, PERDIH, Andrej, GOLOBIČ, Amalija, MEDEN, Anže, GROŠELJ, Uroš. 1,3-diamine-derived bifunctional organocatalyst prepared from camphor.Advanced Synthesis & Catalysis, 2016, 358, 3786-3796
2. ŠTEFANE, Bogdan, PERDIH, Andrej, PEVEC, Andrej, ŠOLMAJER, Tomaž, KOČEVAR, Marijan. The participation of 2H-pyran-2-ones in [4+2] cycloadditions : an experimental and computational study. Eur. J. Org. Chem.2010, 30, 5870-5883.
4. Review articles
1. BERGANT, Kaja, JANEŽIČ, Matej, PERDIH, Andrej. Bioassays and in silico methods in the identification of human DNA topoisomerase IIa inhibitors. Curr. Med. Chem., 2018, 25, 3284-3316.
1. POGORELČNIK, Barbara, PERDIH, Andrej, ŠOLMAJER, Tomaž. Recent advances in the development of catalytic inhibitors of human DNA topoisomerase II[alpha] as novel anticancer agents. Curr. Med. Chem., 2013, 20, 694-709.
Reviewing activities
2011 - Reviewer for most of the established journals in the fields of Medicinal and Computational Chemistry
Journal of Medicinal Chemistry, Scientific Reports, ACS Medicinal Chemistry Letters, Drug Discovery Today, ChemMedChem, Bioorg. & Med. Chem., Journal of Chemical Information and Modeling, Chemical Biology & Drug Design,Current Medicinal Chemistry, European Journal of Medicinal Chemistry, RSC Advances, WIREs Computational Molecular Science etc.
2012 - Expert evaluator of grant proposals of several European reserach agencies