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Assoc. Prof. Andrej Perdih, PhD

National Institute of Chemistry Hajdrihova 19
SI-1000 Ljubljana
Slovenia

Tel.: +386-1-4760-376
E-mail: andrej.perdih(at)ki.si

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Bibiography (COBISS)

CV (full)

    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

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