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Departments

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

 

RESEACH INTERESTS

1. Computational molecular design

2. Molecular simulations of macromolecules

3. Modeling of organic and enyzmatic reaction mechanisms

 

LINKS

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ORCID

Web of Science

Scopus

Full CV

    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

    2021-           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

    2019                Publons award:Top peer reviewer  

    2009                Krka prize for PhD. Thesis

    2004                Krka prize for M. Pharm. Thesis

    2004                Faculty of Pharmacy Award

    SELECTED PUBLICATIONS

    1.  VIRTUAL SCREENING AND MOLECULAR DESIGN

    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, J. Chem. Inf. Model., 2020, 60, 3662–3678. Full text

    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. J. Med. Chem., 2020, 63, 2489-2510. Full text

    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. Full text

    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. Full text

    2. MOLECULAR SIMULATIONS OF BIOMOLECULES

    1. PAVLIN, Matic, HERLAH, Barbara, VALJAVEC, Katja, PERDIH, Andrej. Unveiling the interdomain dynamics of type II DNA topoisomerase through all-atom simulations : implications for understanding its catalytic cycle. Computational and Structural Biotechnology Journal. 2023, vol. 21, str. 3746-3759. Full text

    2. 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 Peptide. J. Chem. Inf. Model., 2021, vol 61, 3593–3603. Full text

    3.  MODELING OF REACTION MECHANISMS

    Enzymatic reactions

    1. OGRIZEK, Mitja, JANEŽIČ, Matej, VALJAVEC, Katja, PERDIH, Andrej. Catalytic mechanism of ATP hydrolysis in the ATPase domain of human DNA topoisomerase IIα  J. Chem. Inf. Model., 2022, 62, 3896–3909. Full text

    2. 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. Full text

    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.Adv. Synth. Catal,2016, 358, 3786-3796. Full text

    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. Full text

    4. SELECTED REVIEW ARTICLES

    1. PRAŠNIKAR Eva, BORIŠEK, Jure, PERDIH Andrej. Senescent cells as promising targets to tackle age-related diseases, Aging Research Reviews 2021, vol. 66, 101251. Full text

    2. 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. Full text

    REVIEWING ACTIVITIES

    2011 - Reviewer for most of the established journals in the fields of Medicinal and Computational Chemistry

    WIREs Computational Molecular Science, 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, etc.

    2012 - Expert evaluator of grant proposals of several European reserach agencies

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