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Department of Bioorganic Chemistry is one of 14 departments of Faculty of Chemistry, Wrocław University of Science and Technology. It is headed by Łukasz Berlicki and formed by 5 research groups of: prof. Paweł Kafarski, prof. Artur Mucha, prof. Łukasz Berlicki, Dr. Rafał Kowalczyk and Dr. Rafał Latajka. The main research areas are on a border of chemistry and biology.


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Recent papers

N-Benzyl Residues as the P1' Substituents in Phosphorus-Containing Extended Transition State Analog Inhibitors of Metalloaminopeptidases
Janiszewska, K.; Talma, M.; Oszywa, B.; Pawełczak, M.; Kafarski, P.; Mucha, A.,
Molecules 2020, 25, 4334
DOI: 10.3390/molecules25184334

Abstract
Peptidyl enzyme inhibitors containing an internal aminomethylphosphinic bond system (P(O)(OH)-CH2-NH) can be termed extended transition state analogs by similarity to the corresponding phosphonamidates (P(O)(OH)-NH). Phosphonamidate pseudopeptides are broadly recognized as competitive mechanism-based inhibitors of metalloenzymes, mainly hydrolases. Their practical use is, however, limited by hydrolytic instability, which is particularly restricting for dipeptide analogs. Extension of phosphonamidates by addition of the methylene group produces a P-C-N system fully resistant in water conditions. In the current work, we present a versatile synthetic approach to such modified dipeptides, based on the three-component phospha-Mannich condensation of phosphinic acids, formaldehyde, and N-benzylglycines. The last-mentioned component allowed for simple and versatile introduction of functionalized P1' residues located on the tertiary amino group. The products demonstrated moderate inhibitory activity towards porcine and plant metalloaminopeptidases, while selected derivatives appeared very potent with human alanyl aminopeptidase (Ki = 102 nM for 6a). Analysis of ligand-protein complexes obtained by molecular modelling revealed canonical modes of interactions for mono-metallic alanyl aminopeptidases, and distorted modes for di-metallic leucine aminopeptidases (with C-terminal carboxylate, not phosphinate, involved in metal coordination). In general, the method can be dedicated to examine P1'-S1' complementarity in searching for non-evident structures of specific residues as the key fragments of perspective ligands.

Recent papers

Systematic ‘foldamerization’ of peptide inhibiting p53-MDM2/X interactions by the incorporation of trans- or cis-2-aminocyclopentanecarboxylic acid residues
Fortuna, P.; Twarda-Clapa, A.; Skalniak, L.; Ożga, K.; Holak, T. A.; Berlicki, Ł.
Eur. J. Med. Chem. 2020, 208, 112814
DOI: 10.1016/j.ejmech.2020.112814

Abstract
A ‘foldamerization’ strategy for the discovery of biologically active peptide is evaluated using as an example the peptides that inhibit the p53-MDM2/X interactions. Application of a peptide scan with two constrained β-residue of trans and cis stereochemistry indicated a substitution pattern that leads to active molecules with enhanced conformational stability and high resistance to proteolysis. This procedure led to the discovery of a peptide that showed subnanomolar inhibition of the p53-MDM2 interaction (Ki = 0.4 nM) with resistance to proteolysis enhanced by ca. two orders of magnitude. Crystallographic analysis and molecular modelling allowed for understanding of these peptide-protein interactions at the molecular level.

Recent papers

Synthesis and Inhibitory Studies of Phosphonic Acid Analogues of Homophenylalanine and Phenylalanine towards Alanyl Aminopeptidases
Wanat, W. ; Talma, M.; Dziuk, B.; Kafarski, P
Biomolecules 2020, 10, 1
DOI: 10.3390/biom10091319

Abstract
A library of novel phosphonic acid analogues of homophenylalanine and phenylalanine, containing fluorine and bromine atoms in the phenyl ring, have been synthesized. Their inhibitory properties against two important alanine aminopeptidases, of human (hAPN, CD13) and porcine(pAPN) origin, were evaluated. Enzymatic studies and comparison with literature data indicated the higher inhibitory potential of the homophenylalanine over phenylalanine derivatives towards both enzymes. Their inhibition constants were in the submicromolar range for hAPN and the micromolar range for pAPN, with 1-amino-3-(3-fluorophenyl) propylphosphonic acid (compound 15c) being one of the best low-molecular inhibitors of both enzymes. To the best of our knowledge, P1 homophenylalanine analogues are the most active inhibitors of the APN among phosphonic and phosphinic derivatives described in the literature. Therefore, they constitute interesting building blocks for the further design of chemically more complex inhibitors. Based on molecular modeling simulations and SAR (structure-activity relationship) analysis, the optimal architecture of enzymeinhibitor complexes for hAPN and pAPN were determined.

Recent papers

Covalent and noncovalent constraints yield a figure eight-like conformation of a peptide inhibiting the menin-MLL interaction
Fortuna, P.; Linhares, B. M.; Purohit, T.; Pollock, J.; Cierpicki, T.; Grembecka, J.; Berlicki, Ł.
Eur. J. Med. Chem. 2020, 207, 112748
DOI: 10.1016/j.ejmech.2020.112748

Abstract
The interaction between menin and mixed lineage leukemia (MLL) was identified as an interesting target for treating some cancers including acute leukemia. On the basis of the known crystal structure of the MBM1-menin complex (MBM - menin binding motif), several cyclic peptides were designed. Elaboration of the effective cyclization strategy using a metathesis reaction allowed for a successfully large number of derivatives to be obtained. Subsequent optimization of the loop size, as well as N-terminal, central and C-terminal parts of the studied peptides resulted in structures exhibiting low nanomolar activities. A crystal structure of an inhibitor-menin complex revealed a compact conformation of the ligand molecule, which is stabilized not only by the introduction of a covalent linker but also three intramolecular hydrogen bonds. The inhibitor adopts a figure eight-like conformation, which perfectly fits the cleft of menin. We demonstrated that the development of compact, miniprotein-like structures is a highly effective approach for inhibition of protein-protein interactions.

Recent papers

Phosphonopeptides containing free phosphonic groups: recent advances
Kafarski, P.
RCS Adv. 2020, 10, 25898
DOI: 10.1039/d0ra04655h

Abstract
Phosphonopeptides are mimetics of peptides in which phosphonic acid or related (phosphinic, phosphonous etc.) group replaces either carboxylic acid group present at C-terminus, is located in the peptidyl side chain, or phosphonamidate or phosphinic acid mimics peptide bond. Acting as inhibitors of key enzymes related to variable pathological states they display interesting and useful physiologic activities with potential applications in medicine and agriculture. Since the synthesis and biological properties of peptides containing C-terminal diaryl phosphonates and those with phosphonic fragment replacing peptide bond were comprehensively reviewed, this review concentrate on peptides holding free, unsubstituted phosphonic acid moiety. There are two groups of such mimetics: (i) peptides in which aminophosphonic acid is located at C-terminus of the peptide chain with most of them (including antibiotics isolated from bacteria and fungi) exhibiting antimicrobial activity; (ii) non-hydrolysable analogues of phosphonoamino acids, which are useful tools to study physiologic effects of phosphorylations.

Recent papers

Nuclear immunophilin FKBP39 from Drosophila melanogaster drives spontaneous liquid-liquid phase separation.
Tarczewska, A.; Wycisk, K.; Orłowski, M.;Waligórska, A.; Dobrucki, J.; Drewniak-Świtalska, M.; Berlicki, Ł.; Ożyhar, A.
Int. J. Biol. Macromol. 2020, 163, 108
DOI: 10.1016/j.ijbiomac.2020.06.255
Abstract
The FKBP39 from Drosophila melanogaster is a multifunctional regulatory immunophilin. It contains two globular domains linked by a highly charged disordered region. The N-terminal domain shows homology to the nucleoplasmin core domain, and the C-terminal domain is characteristic for the family of the FKBP immunophilin ligand binding domain. The specific partially disordered structure of the protein inspired us to investigate whether FKBP39 can drive spontaneous liquid-liquid phase separation (LLPS). Preliminary analyses using CatGranule and Pi-Pi contact predictors suggested a propensity for LLPS. Microscopy observations revealed that FKBP39 can self-concentrate to form liquid condensates. We also found that FKBP39 can lead to LLPS in the presence of RNA and peptides containing Arg-rich linear motifs derived from selected nuclear and nucleolar proteins. These heterotypic interactions have a stronger propensity for driving LLPS when compared to the interactions mediated by self-associating FKBP39 molecules. To investigate whether FKBP39 can drive LLPS in the cellular environment, we analysed it in fusion with YFP in COS-7 cells. The specific distribution and diffusion kinetics of FKBP39 examined by FRAP experiments provided evidence that immunophilin is an important driver of phase separation. The ability of FKBP39 to go into heterotypic interaction may be fundamental for ribosome subunits assembly.

Recent papers

A novel approach for obtaining alpha,beta-diaminophosphonates bearing structurally diverseside chains and their interactions with transition metal ions studied by ITC
Lenartowicz, P.; Witkowska, D.; Żyszka-Haberecht, B.; Dziuk, B.; Ejsmont, K.; Świątek-Kozłowska, J.; Kafarski, P.
RSC Adv. 2020, 10, 24045
DOI: 10.1039/d0ra03764h

Abstract
Aminophosphonates are an important group of building blocks in medicinal and pharmaceutical chemistry.Novel representatives of this class of compounds containing nontypical side chains are still needed. The aza-Michael-type addition of amines to phosphonodehydroalanine derivatives provides a simple andeffective approach for synthesizingN0-substituteda,b-diaminoethylphosphonates and thus affordsgeneral access to aminophosphonates bearing structurally diverse side chains. Thermodynamic analysisof the chosen aminophosphonates at physiological pH proves that they serve as potent chelators forcopper(II) ions and moderate chelators for nickel(II) ions.

Recent papers

P1′ Residue-Oriented Virtual Screening for Potent and Selective Phosphinic (Dehydro) Dipeptide Inhibitors of Metallo-Aminopeptidases
Talma, M.; Mucha, A.
Biomolecules 2020, 10, 659
DOI: https://doi.org/10.3390/biom10040659
Abstract
Designing side chain substituents complementary to enzyme binding pockets is of great importance in the construction of potent and selective phosphinic dipeptide inhibitors of metallo-aminopeptidases. Proper structure selection makes inhibitor construction more economic, as the development process typically consists of multiple iterative preparation/bioassay steps. On the basis of these principles, using noncomplex computation and modeling methodologies, we comprehensively screened 900 commercial precursors of the P1′ residues of phosphinic dipeptide and dehydrodipeptide analogs to identify the most promising ligands of 52 metallo-dependent aminopeptidases with known crystal structures. The results revealed several nonproteinogenic

residues with an improved energy of binding compared with the best known inhibitors. The data are discussed taking into account the selectivity and stereochemical implications of the enzymes. Using this approach, we were able to identify nontrivial structural elements substituting the recognized

phosphinic peptidomimetic scaffold of metallo-aminopeptidase inhibitors.

Recent papers

New crystal structures of fluorinated α-aminophosphonic acid analogues of phenylglycine
Wanat, W.; Dziuk, B.; Kafarski, P.
Struct. Chem. 2020, 31, 1197
DOI: 10.1007/s11224-020-01508-w
Abstract
The four novel phosphonic acid analogues of phenylglycine with various substituents in phenyl ring (mostly fluorine atoms) have been synthesized by using procedure of amidoalkylation of phosphorus trichloride with aromatic aldehydes and acetamide. The NMR, ESI-MS spectroscopy, and single-crystal X-Ray diffraction methods were used to characterize unusual structures: the amino-(4-trifluoromethylbenzyl)-(1), amino-(3,4-difluorobenzyl)-(2), amino-(2,4,6-trifluorobenzyl)-(3), and amino-(2-fluoro-4-hydroxybenzyl)-(4) phosphonic acids. Since the α-aminophosphonates have a potential for biological activity and could be used as building blocks in medicinal chemistry, it is important to know their detail crystal structures and properties which, in turn, may extend the knowledge on their interaction with physiologic receptors.

Recent papers

Phosphonic Acid Analogs of Fluorophenylalanines as Inhibitors of Human and Porcine Aminopeptidases N: Validation of the Importance of the Substitution of the Aromatic Ring
Wanat, W.; Talma, M.; Dziuk, B.; Pirat, J.-L.; Kafarski, P.
Biomolecules 2020, 10, 1
DOI: 10.3390/biom10040579

Abstract
A library of phosphonic acid analogs of phenylalanine substituted with fluorine, chlorine and trifluoromethyl moieties on the aromatic ring was synthesized and evaluated for inhibitory activity against human (hAPN) and porcine (pAPN) aminopeptidases. Fluorogenic screening indicated that these analogs are micromolar or submicromolar inhibitors, both enzymes being more active against hAPN. In order to better understand the mode of the action of the most active compounds, molecular modeling was used. It confirmed that aminophosphonic portion of the enzyme is bound nearly identically in the case of all the studied compounds, whereas the difference in activity results from the placement of aromatic side chain of an inhibitor. Interestingly, both enantiomers of the individual compounds are usually bound quite similarly.