OPEN Repository

Welcome to OPEN - the Repository of Open Scientific Publications, run by the Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, previously operating as the CeON Repository. The Repository enables Polish researchers from all fields to openly share their articles, books, conference materials, reports, doctoral theses, and other scientific texts.

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Recent Submissions

Cascade Transformation of the Ansamycin Benzoquinone Core into Benzoxazole Influencing Anticancer Activity and Selectivity
(American Chemical Society, 2023) Skrzypczak, Natalia; Pyta, Krystian; Bohusz, Wiktor; Leśniewska, Aleksandra; Gdaniec, Maria; Ruszkowski, Piotr; Schilf, Wojciech; Bartl, Franz; Przybylski, Piotr; Faculty of Chemistry, Adam Mickiewicz University, Poznań; Department of Pharmacology, Poznań University of Medical Sciences; Institute of Organic Chemistry, Polish Academy of Sciences; Lebenswissenschaftliche Fakultӓt, Institut fȕr Biologie, Biophysikalische Chemie Humboldt - Universitӓt zu Berlin
The metal-free cascade transformation of geldanamycin benzoquinone core is proposed at relatively mild conditions. This approach yields new benzoxazole ansamycin antibiotics and enables their functionalization in an atom-economic manner, irrespective of the type of amine used. The analysis of the heterocyclization course reveals the dependence of its rate on the nature of the para-substituent within the benzylamine moiety (EDG/EWG) and the strength of the base. The reduction of the ansamycin core enables an increase in anticancer potency and selectivity.
Carboxylated Pillar[6]arene Emulates Pillar[5]arene in the Host–Guest Crystal Complexes and Shows Conformational Flexibility in the Solution/Gas Phase
(American Chemical Society, 2023) Butkiewicz, Helena; Kosiorek, Sandra; Sashuk, Volodymyr; Zimnicka, Magdalena M.; Danylyuk, Oksana; Institute of Physical Chemistry, Polish Academy of Sciences; Institute of Organic Chemistry, Polish Academy of Sciences
Despite the thriving interest in the aqueous complexation properties of carboxylated pillar[6]arene, its solid state supramolecular chemistry has remained a mystery. Here, overcoming challenging crystallogenesis, we report the first crystallographic authentication of carboxylated pillar[6]arene in the form of two host–guest inclusion complexes with methyl viologen and pentamidine. The key to the successful crystallization of carboxylated pillar[6]arene is the mixed ionization state of its 12 carboxylic substituents. The deprotonation of several but not all substituents enables intermolecular hydrogen bonding and, as a result, “gluing” and crystallization of pillar[6]arene complexes with the aid of carboxylic-carboxylate, carboxylic-carboxylic, and amidinium-carboxylate supramolecular synthons. Single crystal X-ray diffraction analysis revealed that upon guest inclusion pillar[6]arene adopts a quasi-pentagonal shape rather than the expected hexagonal shape. The squeezed quasi-pentagonal conformation of the six-membered macrocycle is stabilized by two intramolecular hydrogen bonds between pillar[6]arene substituents. Moreover, the distinctive deviation of the macrocycle from hexagonal shape stays operative in the solution/gas phase as concluded from ion mobility mass spectrometry (IM-MS) studies and theoretical calculations. These results provide the first insight into how to gain control over the conformation of flexible pillar[6]arene with a view of solid state design of more advanced supramolecular host–guest structures.
Carboxylated Pillar[5]arene Meets Medicinal Biguanides: Host–Guest Complexes with Alexidine and Phenformin in the Crystal and Solution/Gas Phase
(American Chemical Society, 2023) Butkiewicz, Helena; Kosiorek, Sandra; Sashuk, Volodymyr; Zimnicka, Magdalena M.; Danylyuk, Oksana; Institute of Physical Chemistry, Polish Academy of Sciences; Institute of Organic Chemistry, Polish Academy of Sciences
Here, we discuss crystal and solution/gas-phase complexes of carboxylated pillar[5]arene with two cationic guests, alexidine and phenformin, revealing host–guest and assembly curiosities, the role of hydrogen bonding, and cavity inclusion versus exo-mode binding. We show that the combination of carboxylated pillar[5]arene with bis(biguanidinium) guest alexidine results in the crystallization of open-type supramolecular architecture. This is also the first crystal structure of alexidine ever reported. The crystallization of pillar[5]arene with biguanidinium drug phenformin affects a rare solid-state complex comprising two cavity inclusion modes within the same crystal lattice. The winner in the competition between ethanol molecules and an organic cation (phenformin) for access to the cavity of pillar[5]arene is undecided, visualized as a “snapshot” of these two inclusion possibilities in one crystal structure. Our results demonstrate that carboxylated pillar[n]arenes can be a useful addition to the macrocyclic toolkit for the facilitation of the crystallization of bio(macro)molecules. Moreover, the IM-MS analysis of the precrystallization solutions of pillar[5]arene host and biguanide guests has shown the presence of structures and conformations closely related to those observed in the crystal forms. The most intriguing results obtained for a pillar[5]arene–alexidine complex imply a conformational evolution of the complex over 24 h. The IM-MS analysis complemented by theoretical calculations may be applied to predict and examine the crystallization process of host–guest systems, complementing crystallographic studies.
Determination of the Dissociation Constant for Polyvalent Receptors Using ELISA: A Case of M13 Phages Displaying Troponin T-Specific Peptides
(American Chemical Society, 2023) Machera, Sebastian J.; Niedziółka-Jönsson, Joanna; Jönsson-Niedziółka, Martin; Szot-Karpińska, Katarzyna; Institute of Physical Chemistry, Polish Academy of Sciences
Phage-derived affinity peptides have become widespread thanks to their easy selection via phage display. Interactions between a target protein and its specific peptide are similar to those between antibodies and antigens. The strength of these non-covalent complexes may be described by the dissociation constant (Kd). In this paper, protein-specific peptides are exposed on the pIII protein present in the M13 bacteriophage virion with up to five copies. Therefore, one phage particle can bind from one to five ligands. Here, we discuss the dependences between phage-displayed peptides and their ligands in solution using a model system based on troponin T (TnT) binding phages. Moreover, a method of calculating Kd values from ELISA experiments was developed and is presented. The determined Kd values are in the picomolar range.
Investigation of Peptides for Molecular Recognition of C-Reactive Protein–Theoretical and Experimental Studies
(American Chemical Society, 2023) Szot-Karpińska, Katarzyna; Kudła, Patryk; Orzeł, Urszuła; Narajczyk, Magdalena; Jönsson-Niedziółka, Martin; Pałys, Barbara; Filipek, Sławomir; Ebner, Andreas; Niedziółka-Jönsson, Joanna; Institute of Physical Chemistry, Polish Academy of Sciences; University of Warsaw; University of Gdansk; Johannes Kepler University
We investigate the interactions between C-reactive protein (CRP) and new CRP-binding peptide materials using experimental (biological and physicochemical) methods with the support of theoretical simulations (computational modeling analysis). Three specific CRP-binding peptides (P2, P3, and P9) derived from an M13 bacteriophage have been identified using phage-display technology. The binding efficiency of the peptides exposed on phages toward the CRP protein was demonstrated via biological methods. Fibers of the selected phages/peptides interact differently due to different compositions of amino acid sequences on the exposed peptides, which was confirmed by transmission electron microscopy. Numerical and experimental studies consistently showed that the P3 peptide is the best CRP binder. A combination of theoretical and experimental methods demonstrates that identifying the best binder can be performed simply, cheaply, and fast. Such an approach has not been reported previously for peptide screening and demonstrates a new trend in science where calculations can replace or support laborious experimental techniques. Finally, the best CRP binder─the P3 peptide─was used for CRP recognition on silicate-modified indium tin oxide-coated glass electrodes. The obtained electrodes exhibit a wide range of operation (1.0–100 μg mL–1) with a detection limit (LOD = 3σ/S) of 0.34 μg mL–1. Moreover, the dissociation constant Kd of 4.2 ± 0.144 μg mL–1 (35 ± 1.2 nM) was evaluated from the change in the current. The selectivity of the obtained electrode was demonstrated in the presence of three interfering proteins. These results prove that the presented P3 peptide is a potential candidate as a receptor for CRP, which can replace specific antibodies.