Search results for: Andrej Perdih

Items from 1 to 20 out of 20 results

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Organocatalyzed Deracemization of Δ²‐Pyrrolin‐4‐ones

Sebastijan Ričko, Anže Meden, Anže Ivančič, Andrej Perdih, more

Advanced Synthesis & Catalysis > 359 > 13 > 2288 - 2296

Racemic pyrrolin‐4‐ones, accessible from α‐amino acids, undergo asymmetric stereoselective organocatalyzed 1,4‐additions to trans‐β‐nitrostyrenes (up to 98 % ee; dr up to 97:3). From a series of typical organocatalysts, the best performance was achieved using (+)‐camphor‐1,3‐diamine‐derived bifunctional organocatalysts. A broad substrate scope and some follow‐up modifications have been demonstrated...

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The CWB2 Cell Wall-Anchoring Module Is Revealed by the Crystal Structures of the Clostridium difficile Cell Wall Proteins Cwp8 and Cwp6

Aleksandra Usenik, Miha Renko, Marko Mihelič, Nataša Lindič, more

Structure > 2017 > 25 > 3 > 514-521

Bacterial cell wall proteins play crucial roles in cell survival, growth, and environmental interactions. In Gram-positive bacteria, cell wall proteins include several types that are non-covalently attached via cell wall binding domains. Of the two conserved surface-layer (S-layer)-anchoring modules composed of three tandem SLH or CWB2 domains, the latter have so far eluded structural insight. The...

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1,3‐Diamine‐Derived Bifunctional Organocatalyst Prepared from Camphor

Sebastijan Ričko, Jurij Svete, Bogdan Štefane, Andrej Perdih, more

Advanced Synthesis & Catalysis > 358 > 23 > 3786 - 3796

Chiral 1,2‐diamines are privileged structural motifs in organocatalysis, whereas efficient 1,3‐diamine‐derived organocatalysts are very rare. Herein we report a highly efficient camphor‐1,3‐diamine‐derived squaramide organocatalyst. Its catalytic activity in Michael additions of 1,3‐dicarbonyl nucleophiles to trans‐β‐nitrostyrene derivatives provides excellent enantioselectivities (up to >99% ee...

article

From carbohydrates to drug-like fragments: Rational development of novel α-amylase inhibitors

Jamil Al-Asri, Erika Fazekas, Gábor Lehoczki, Andrej Perdih, more

Bioorganic & Medicinal Chemistry > 2015 > 23 > 20 > 6725-6732

Starch catabolism leading to high glucose level in blood is highly problematic in chronic metabolic diseases, such as type II diabetes and obesity. α-Amylase catalyzes the hydrolysis of starch, increasing blood sugar concentration. Its inhibition represents a promising therapeutic approach to control hyperglycaemia. However, only few drug-like molecule inhibitors without sugar moieties have been discovered...

article

4,6-Substituted-1,3,5-triazin-2(1H)-ones as monocyclic catalytic inhibitors of human DNA topoisomerase IIα targeting the ATP binding site

Barbara Pogorelčnik, Matej Janežič, Izidor Sosič, Stanislav Gobec, more

Bioorganic & Medicinal Chemistry > 2015 > 23 > 15 > 4218-4229

Human DNA topoisomerase IIα (htIIα) is a validated target for the development of novel anticancer agents. Starting from our discovered 4-amino-1,3,5-triazine inhibitors of htIIα, we investigated a library of 2,4,6-trisubstituted-1,3,5-triazines for novel inhibitors that bind to the htIIα ATP binding site using a combination of structure-based and ligand-based pharmacophore models and molecular docking...

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Furan-based benzene mono- and dicarboxylic acid derivatives as multiple inhibitors of the bacterial Mur ligases (MurC–MurF): experimental and computational characterization

Andrej Perdih, Martina Hrast, Kaja Pureber, Hélène Barreteau, more

Journal of Computer-Aided Molecular Design > 2015 > 29 > 6 > 541-560

Bacterial resistance to the available antibiotic agents underlines an urgent need for the discovery of novel antibacterial agents. Members of the bacterial Mur ligase family MurC–MurF involved in the intracellular stages of the bacterial peptidoglycan biosynthesis have recently emerged as a collection of attractive targets for novel antibacterial drug design. In this study, we have first extended...

article

Monocyclic 4-amino-6-(phenylamino)-1,3,5-triazines as inhibitors of human DNA topoisomerase IIα

Barbara Pogorelčnik, Matjaž Brvar, Irena Zajc, Metka Filipič, more

Bioorganic & Medicinal Chemistry Letters > 2014 > 24 > 24 > 5762-5768

Human DNA topoisomerase IIα (htIIα) is a validated target for the development of anticancer agents. Starting from the available information about the binding of the purine-based htIIα inhibitors in the ATP binding site we designed a virtual screening campaign combining structure-based and ligand-based pharmacophores with a molecular docking calculation searching for compounds that would contain a...

article

Benzene-1,3-dicarboxylic acid 2,5-dimethylpyrrole derivatives as multiple inhibitors of bacterial Mur ligases (MurC–MurF)

Andrej Perdih, Martina Hrast, Hélène Barreteau, Stanislav Gobec, more

Bioorganic & Medicinal Chemistry > 2014 > 22 > 15 > 4124-4134

Enzymes catalyzing the biosynthesis of bacterial peptidoglycan represent traditionally a collection of highly selective targets for novel antibacterial drug design. Four members of the bacterial Mur ligase family—MurC, MurD, MurE and MurF—are involved in the intracellular steps of peptidoglycan biosynthesis, catalyzing the synthesis of the peptide moiety of the Park’s nucleotide. In our previous virtual...

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Structural elucidation of transmembrane transporter protein bilitranslocase: Conformational analysis of the second transmembrane region TM2 by molecular dynamics and NMR spectroscopy

Amrita Roy Choudhury, Andrej Perdih, Špela Župerl, Emilia Sikorska, more

BBA - Biomembranes > 2013 > 1828 > 11 > 2609-2619

Membrane proteins represent about a third of the gene products in most organisms, as revealed by the genome sequencing projects. They account for up to two thirds of known drugable targets, which emphasizes their critical pharmaceutical importance. Here we present a study on bilitranslocase (BTL) (TCDB 2.A.65), a membrane protein primarily involved in the transport of bilirubin from blood to liver...

article

Discovery of the first inhibitors of bacterial enzyme d-aspartate ligase from Enterococcus faecium (Aslfm)

Veronika Škedelj, Andrej Perdih, Matjaž Brvar, Ana Kroflič, more

European Journal of Medicinal Chemistry > 2013 > 67 > Complete > 208-220

The d-aspartate ligase of Enterococcus faecium (Asl _fm ) is an attractive target for the development of narrow-spectrum antibacterial agents that are active against multidrug-resistant E. faecium. Although there is currently little available information regarding the structural characteristics of Asl _fm , we exploited the knowledge that this enzyme belongs to the ATP-grasp superfamily...

article

Cluster‐based molecular docking study for in silico identification of novel 6‐fluoroquinolones as potential inhibitors against Mycobacterium tuberculosis

Nikola Minovski, Andrej Perdih, Marjana Novic, Tom Solmajer

Journal of Computational Chemistry > 34 > 9 > 790 - 801

A classical protein sequence alignment and homology modeling strategy were used for building three Mycobacterium tuberculosis‐DNA gyrase protein models using the available topoII‐DNA‐6FQ crystal structure complexes originating from different organisms. The recently determined M. tuberculosis‐DNA gyrase apoprotein structures and topoII‐DNA‐6FQ complexes were used for defining the 6‐fluoroquinolones...

article

Molecular dynamics simulation and linear interaction energy study of d-Glu-based inhibitors of the MurD ligase

Andrej Perdih, Gerhard Wolber, Tom Solmajer

Journal of Computer-Aided Molecular Design > 2013 > 27 > 8 > 723-738

The biosynthetic pathway of the bacterial peptidoglycan, where MurD is an enzyme involved at the intracellular stage of its construction, represents a collection of highly selective macromolecular targets for novel antibacterial drug design. In this study as part of our investigation of the MurD bacterial target two recently discovered classes of the MurD ligase inhibitors were investigated resulting...

article

In silico discovery and biophysical evaluation of novel 5-(2-hydroxybenzylidene) rhodanine inhibitors of DNA gyrase B

Matjaž Brvar, Andrej Perdih, Vesna Hodnik, Miha Renko, more

Bioorganic & Medicinal Chemistry > 2012 > 20 > 8 > 2572-2580

Bacterial DNA gyrase is an established and validated target for the development of novel antibacterials. In our previous work, we identified a novel series of bacterial gyrase inhibitors from the class of 4-(2,4-dihydroxyphenyl) thiazoles. Our ongoing effort was designated to search for synthetically more available compounds with possibility of hit to lead development. By using the virtual screening...

article

MurD ligase from Escherichia coli: C-terminal domain closing motion

Andrej Perdih, Tom Solmajer

Computational and Theoretical Chemistry > 2012 > 979 > Complete > 73-81

MurD (UDP-N-acetylmuramoyl-l-alanine:d-glutamate ligase), a three domain bacterial protein, catalyzes a highly specific incorporation of the d-glutamate into the cytoplasmic intermediate UDP-N-acetyl-muramoyl-l-alanine (UMA) utilizing ATP hydrolysis to ADP and P _i . This reaction is part of the biosynthetic pathway enabling bacterial peptidoglycan synthesis. During our previous investigations...

article

Combinatorially-generated library of 6-fluoroquinolone analogs as potential novel antitubercular agents: a chemometric and molecular modeling assessment

Nikola Minovski, Andrej Perdih, Tom Solmajer

Journal of Molecular Modeling > 2012 > 18 > 5 > 1735-1753

The virtual combinatorial chemistry approach as a methodology for generating chemical libraries of structurally-similar analogs in a virtual environment was employed for building a general mixed virtual combinatorial library with a total of 53.871 6-FQ structural analogs, introducing the real synthetic pathways of three well known 6-FQ inhibitors. The druggability properties of the generated combinatorial...

article

The Participation of 2H‐Pyran‐2‐ones in [4+2] Cycloadditions: An Experimental and Computational Study

Bogdan Štefane, Andrej Perdih, Andrej Pevec, Tomaž Šolmajer, more

European Journal of Organic Chemistry > 2010 > 30 > 5870 - 5883

Experimental and computational DFT studies of the Diels–Alder (DA) reaction mechanism for the series of 2H‐pyran‐2‐ones 1 and non‐symmetrically substituted alkynes 2, 10, and 11 were undertaken. Several 2H‐pyran‐2‐ones 1 were treated with N,N‐diethylpropynamine (2). The results point toward a polar and asynchronous two‐step mechanism that is in line with the characteristics of a polar Diels–Alder...

article

In silico discovery of 2-amino-4-(2,4-dihydroxyphenyl)thiazoles as novel inhibitors of DNA gyrase B

Matjaž Brvar, Andrej Perdih, Marko Oblak, Lucija Peterlin Mašič, more

Bioorganic & Medicinal Chemistry Letters > 2010 > 20 > 3 > 958-962

Cyclothialidines are a class of bacterial DNA gyrase B (GyrB) subunit inhibitors, targeting its ATP-binding site. Starting from the available structural information on cyclothialidine GR122222X (2), an in silico virtual screening campaign was designed combining molecular docking calculations with three-dimensional structure-based pharmacophore information. A novel class of 2-amino-4-(2,4-dihydroxyphenyl)thiazole...

article

Discovery of novel benzene 1,3-dicarboxylic acid inhibitors of bacterial MurD and MurE ligases by structure-based virtual screening approach

Andrej Perdih, Andreja Kovač, Gerhard Wolber, Didier Blanot, more

Bioorganic & Medicinal Chemistry Letters > 2009 > 19 > 10 > 2668-2673

The peptidoglycan biosynthetic pathway provides an array of potential targets for antibacterial drug design, attractive especially with respect to selective toxicity. Within this pathway, the members of the Mur ligase family are considered as promising emerging targets for novel antibacterial drug design. Based on the available MurD crystal structures co-crystallised with N-sulfonyl glutamic acid...

article

Binding free energy calculations of N-sulphonyl-glutamic acid inhibitors of MurD ligase

Andrej Perdih, Urban Bren, Tom Solmajer

Journal of Molecular Modeling > 2009 > 15 > 8 > 983-996

The increasing incidence of bacterial resistance to most available antibiotics has underlined the urgent need for the discovery of novel efficacious antibacterial agents. The biosynthesis of bacterial peptidoglycan, where the MurD enzyme is involved in the intracellular phase of UDP-MurNAc-pentapeptide formation, represents a collection of highly selective targets for novel antibacterial drug design...

article

Flavonoids and cinnamic acid esters as inhibitors of fungal 17β-hydroxysteroid dehydrogenase: A synthesis, QSAR and modelling study

Matej Sova, Andrej Perdih, Miha Kotnik, Katja Kristan, more

Bioorganic & Medicinal Chemistry > 2006 > 14 > 22 > 7404-7418

The 17β-hydroxysteroid dehydrogenases (17β-HSDs) modulate the biological potency of estrogens and androgens by interconversion of inactive 17-keto-steroids and their active 17β-hydroxy- counterparts. We have shown previously that flavonoids are potentially useful lead compounds for developing inhibitors of 17β-HSDs. In this paper, we describe the synthesis and biochemical evaluation of structurally...

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