dr hab. Agnieszka Krakowiak

Adiunkt, Dział Chemii Bioorganicznej

Telefon: (+48) (42) 68 03 272

Email:

ORCID:  0000-0002-0273-2972

RG:  https://www.researchgate.net/profile/Agnieszka-Krakowiak

Scientific career:

1988  MSc in chemistry

Lodz University of Technology, Faculty of Chemistry, Institute of Organic Chemistry, Specialization: Chemistry and Technology of Drugs; Title of M.Sc. thesis: Trials of enzymatic cleavage of α-hydroxy-amino acids”

1987  Chemist, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences Department of Bioorganic Chemistry,  Lodz, Poland

1992  Research Assistant, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz

1998 (2 weeks)  Visitor, France,  Museum National d’Histoire Naturelle, CNRS-MNHN, INSERM, Paris,  prof. Claude Hélène group, interchangeable weeks program between PAS and CNRS; subject: New methods in measuring biomolecular interactions, including protein-protein interactions, small molecule/fragment-protein interactions, etc. based on surface plasmon resonance (SPR) – BiaCore.

1999  Ph.D. (Doctor degree) in chemistry at area chemistry; Specialization: biochemistry of nucleic acids; Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz; Title of Ph.D. thesis: “Studies on the influence of stereochemistry of phosphorothioate oligonucleotides on activity of RNase H and reverse transcriptase”. Thesis supervisor: Prof. Dr hab. Wojciech J. Stec

2002 – 2003   Postdoctoral Fellow, Kimmel Cancer Center, Thomas Jefferson University, Dept. of Microbiology and Immunology, Philadelphia, USA; prof. Charles Brenner group.

Studies of biochemistry of HIT proteins (Fhit, Hint1, Hint2, DcpS).

2003   Assistant Professor, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz

2006 (5 days) Visitor; Universita degli Studi di Firenze; Dipartamento di Scienze Neurologiche Psichiatriche; Dr Bendetta Nacmias, subject: „Silencing of L392V PS-1 in 4NOV mutant bearing fibroblasts”.

2018  D.Sc. (Habilitation degree), Centre of Molecular and Macromolecular Studies Polish Academy of Sciences, Lodz; Thesis: Phosphorothioate nucleotide analogs as substrates and inhibitors of Fhit and Hint1 enzymes, tumor suppressor  proteins from HIT superfamily.

Additional training

2009  Flow cytometry training (BD FACS Calibur) (CMMS PAS, Lodz).

2009   Training: Analysis of gene expression by DNA microarray technique” (MBS, Lodz)

2009   Workshop: „DNA Microarray  – analysis of results” (MBS, Warszawa)

2015    Training „11 Summer school of Stem Cells”- Department of Clinical Immunology, Collegium Medicum, Jagiellonian University (Krakow).

2016   Training: Microscale thermophoresis (MST) – technology and application (CMMS PAS, Lodz)

2016   Workshop „II Workshop of Confocal Raman Microscopy SERS, AFM, SNOM” (Institute of Applied Radiation Chemistry, Lodz University of Technology)

Awards

• 1998 – Award of Polish Biochemical Society honoured to Bolesław Skarżyński, for the best paper published in „Postępy Biochemii” .
• 2001 – Award of Polish Academy of Sciences, Branch in Lodz, and Society of Rectors of the State Universities for the scope of scientific achievements.

From 1995 to 2018 – investigator for 8 grants.

From 2005 to 2018 leader (Principal Investigator) for 3 grants:

• 2005-2008, grant MNISW nr 2 P04A 079 29; Title: Studies on the influence of Fhit protein inhibitors on the apoptosis induction.
• 2009-2012, grant MNSW/NCN nr N N204 130137; Title: Metabolism of thiophosphate drugs and prodrugs – identification of 5′-thiophosphate nucleosides binding proteins using the photocrosslink.
• 2014-2017, grant NCN (Opus5) nr DEC-2013/09/B/ST5/03612; Title: Transformation of 5′-O-monothiophosphate nucleoside to 5′-O-monophosphate in the cell – possible metabolism of phosphorothioate drugs and prodrugs.

Current research area:

• Expression and isolation of proteins in various bacterial systems (including enzymes that are very sensitive to deactivation).
• Biochemistry of proteins of HIT superfamily (e.g., Fhit, Hint1, Hint2, DcpS).
• Analogs of nucleotides and oligonucleotides as substrates or inhibitors for various enzymes.
• The usefulness of nucleotide and oligonucleotide analogs in cancer research.
• The influence of seleno-derivatives of nucleotides on redox homeostasis in cells.

References:

1. Szczupak P, Radzikowska-Cieciura E, Kulik K, Madaj R, Sierant M, Krakowiak A, Nawrot B.

“Escherichia coli tRNA 2-selenouridine synthase SelU selects its prenyl substrate to accomplish its enzymatic function.”

Bioorg. Chem. 122: 105739 (2022).

2. Krakowiak A, Czernek L, Pichlak M, Kaczmarek R.

“Intracellular HINT1-Assisted Hydrolysis of Nucleoside 5′-O-Selenophosphate Leads to the Release of Hydrogen Selenide That Exhibits Toxic Effects in Human Cervical Cancer Cells.”

Int. J. Mol. Sci. 23: 607 (2022).

3. Kolasa M, Galita G, Majsterek I, Kucharska E, Czerczak K, Wasko J, Becht A, Fraczyk J, Gajda A, Pietrzak L, Szymanski L, Krakowiak A, Draczynski Z, Kolesinska B.

“Screening of Self-Assembling of Collagen IV Fragments into Stable Structures Potentially Useful in Regenerative Medicine.”

Int. J. Mol. Sci. 22: 13584 (2021).

4. Dolot R, Krakowiak A, Kaczmarek R, Włodarczyk A, Pichlak M, Nawrot B.

“Biochemical, crystallographic and biophysical characterization of histidine triad nucleotide-binding protein 2 with different ligands including a non-hydrolyzable analog of Ap4A.”

Biochim. Biophys. Acta Gen. Subj. 1865: 129968 (2021).

5. Krakowiak A, Piotrzkowska D, Kocoń-Rębowska B, Kaczmarek R, Maciaszek A.

“The role of the Hint1 protein in the metabolism of phosphorothioate oligonucleotides drugs and prodrugs, and the release of H₂S under cellular conditions.”

Biochem. Pharmacol. 163: 250-259 (2019).

6. Frączek T, Kamiński R, Krakowiak A, Naessens E, Verhasselt B, Paneth P.

“Diaryl ethers with carboxymethoxyphenacyl motif as potent HIV-1 reverse transcriptase inhibitors with improved solubility.”

J Enzyme Inhib Med Chem. 33: 9-16 (2018).

7. Krakowiak A.*, Kocoń-Rębowska B., Dolot R., Piotrzkowska D.

“New interactions between tumor suppressor Fhit protein and a non-hydrolyzable analog of its Ap₄A substrate.”

FEBS Letters 591: 548-559 (2017)

8. Dolot R., Kaczmarek R., Sęda A., Krakowiak A., Baraniak B., Nawrot B.

“Crystallographic studies of the complex of human HINT1 protein with a non-hydrolyzable analog of Ap₄A.”

Int. J. Biol. Macromol. 87: 62–69 (2016)

9. Frączek T., Paneth A., Kamiński R., Krakowiak A., Paneth P.

„Searching for novel scaffold of triazole non-nucleoside inhibitors of HIV-1 reverse transcriptase.”

1. Enzyme Inhib. Med. Chem. 31: 481-489 (2016)
2. Kaczmarek R.*,#, Krakowiak A.#, Korczyński D., Baraniak J., Nawrot B. (#equal contribution)

Phosphorothioate analogs of P1,P3-di(nucleosid-5’-yl) triphosphates: synthesis, assignment of the absolute configuration at P-atoms and P-stereodependent recognition by Fhit hydrolase.

Bioorg. Med. Chem. 24: 5068–5075 (2016)

11. Maciaszek A., Krakowiak A., Janicka M., Tomaszewska-Antczak A., Sobczak M., Mikołajczyk B., Guga P.

“LNA units present in the (2′-OMe)-RNA strand stabilize parallel duplexes (2′-OMe)-RNA/[All-R_P-PS]-DNA and parallel triplexes (2′-OMe)-RNA/[All-R_P-PS]-DNA/RNA. An improved tool for the inhibition of reverse transcription.”

Org. Biomol. Chem. 13: 2375-84 (2015).

12. Krakowiak A.*, Pawłowska R., Kocoń-Rębowska B., Dolot R., Stec W.J.

Interactions of cellular histidine triad nucleotide binding protein 1 with nucleosides 5′-O-monophosphorothioate and their derivatives — Implication for desulfuration process in the cell.

Biochim. Biophys. Acta Gen. Subj, 1840: 3357–3366 (2014)

13. Baraniak J., Pietkiewicz A., Kaczmarek R., Radzikowska E., Kulik K., Królewska K., Cieślak M., Krakowiak A., Nawrot B.

”N-Acyl-phosphoramidates as potential novel form of gemcitabine prodrugs”

Bioorg. Med. Chem. 22: 2133-2140 (2014)

14. Krakowiak A.*, Fryc I.,

„Rodzina białek triady histydynowej (HIT) – aktywność enzymatyczna a funkcja biologiczna”

Postępy Biochem. 58: 302-313 (2012)

15. Dolot R., Ozga M., Wlodarczyk A., Krakowiak A., Nawrot B.

„A new crystal form of human histidine triad nucleotide-binding protein 1 (hHINT1) in complex with adenosine 5′-monophosphate at 1.38 A resolution”

Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 68: 883-888 Pt .8 (2012)

16. Dolot R., Ozga M., Krakowiak A., Nawrot B.

“High-resolution X-ray structure of the rabbit histidine triad nucleotide-binding protein 1 (rHINT1)-adenosine complex at 1.10 Å resolution.”

Acta Crystallogr. D Biol. Crystallogr. (2011) 67(Pt7): 601-7

17. Krakowiak A *, Pęcherzewska R, Kaczmarek R, Tomaszewska A, Nawrot B, Stec WJ.

“Evaluation of influence of Ap(4)A analogues on Fhit-positive HEK293T cells; cytotoxicity and ability to induce apoptosis.”

Bioorg. Med. Chem. (2011) 19: 5053-60

18. Ozga M, Dolot R, Janicka M, Kaczmarek R, Krakowiak A.*

“Histidine triad nucleotide-binding protein 1 (HINT-1) phosphoramidase transforms nucleoside 5′-O-phosphorothioates to nucleoside 5′-O-phosphates.”

1. Biol. Chem. 285, 40809-18 (2010)
2. Stec-Michalska K., Peczek L., Michalski B., Wisniewska-Jarosinska M., Krakowiak A., Nawrot B.

„Helicobacter pylori infection and family history of gastric cancer decrease expression of FHIT tumor suppressor gene in gastric mucosa of dyspeptic patients”.

Helicobacter, 14, 126-34 (2009).

20. Stec-Michalska K., Peczek L., Krakowiak A., Michalski B., Chojnacki J., Knopik-Dabrowicz A., Klupinska G., Nawrot B.

“Expression of somatostatin receptor subtype 3 in the gastric mucosa of dyspeptic patients in relation to Helicobacter pylori infection and a family history of gastric cancer”.

1. Gastroenterol. Hepatol., 23, 424-429 (2008).
2. Krakowiak A., Kaczmarek R., Baraniak J., Wieczorek M., Stec W.J.

Stereochemistry of rHint1 hydrolase assisted cleavage of P-N bond in nucleoside 5’-O-phosphoramidothioates.

Chem. Commun., 2163-2165 (2007).

22. Stec-Michalska K., Peczek Ł., Michalski B., Krakowiak A., Chojnacki J., Knopik-Dabrowicz A., Jarosińska-Wiśniewska M., Nawrot B.

“Somatostatin receptor subtype 3 (SSTR3) mRNA level in gastric mucosa of patients with dyspepsia”.

Pol. Merkur. Lekarski., 22, 341-345 (2007).

23. Stec-Michalska K., Pęczek Ł., Krakowiak A., Klupińska G., Chojnacki J., Michalski B., Nawrot B.

“Determination of the level of mRNA of fragile histidine triad (FHIT) protein in the gastric mucosa of cigarette smoking patients with nonulcear dyspepsia infected with Helicobacter pylori”.

Gastroenterologia Polska, 13, 259-263 (2006).

24. Krakowiak A., Pace H.C., Blackburn G.M., Adams M., Mekhalfia A., Kaczmarek R., Baraniak J., Stec W.J., Brenner C.

“Biochemical, crystallographic, and mutagenic characterization of Hint, the AMP-lysine hydrolase, with novel substrates and inhibitors”.

1. Biol. Chem. 279,18711-18716 (2004).
2. Kwasnicka D.A, Krakowiak A., Thacker C., Brenner C., Vincent S.R.

“Coordinate expression of NADPH-dependent flavin reductase, Fre-1, and Hint-related 7meGMP-directed hydrolase, DCS-1”.

1. Biol. Chem., 278, 39051-39058 (2003).
2. Trapasso F., Krakowiak A., Cesari R., Arkles J., Yendamuri S., Ishii H., Vecchione A., Kuroki T., Bieganowski P., Pace H.C., Huebner K., M.Croce C., Brenner C.

“Designed FHIT alleles establish that Fhit-induced apoptosis in cancer cells is limited by substrate binding.”

27. Krakowiak A., Owczarek A., Koziołkiewicz M., Stec W.J.

„Stereochemical course of Escherichia coli RNase H”

ChemBioChem, 3, 1242-1250 (2002).

28. Kobylańska A., Pluskota E., Świątkowska M., Wójcik M., Cierniewska-Cieślak A., Krakowiak A., Boczkowska M., Pawłowska Z., Okruszek A., Koziołkiewicz M., Cierniewski C.S., Stec W.J.

“Inhibition of plasminogen activator inhibitor release in endothelial cell cultures by antisense oligodeoxyribonucleotides with a 5`-end lipophilic modification.”

Acta Biochim. Pol., 46, 679-691 (1999).

29. Koziołkiewicz M., Krakowiak A., Owczarek A., Boczkowska M.

“Phosphorothioate oligonucleotides as aptamers of retroviral reverse transcriptases.”

W: RNA Biochemistry and Biotechnology, 1999, 315-324; eds: J. Barciszewski, B. Clark; Kluwer Academic Publ., printed in the Netherlands

30. Krakowiak A., Koziołkiewicz M.

“Oligonukleotydy o właściwościach aptamerycznych.”

Postępy Biochem., 44, 306-317 (1998).

31. Krakowiak A., Koziołkiewicz M.

“Influence of P-chirality of phosphorothioate oligonucleotides on the activity of AMV reverse transcriptase.”

Nucleosides and Nucleotides, 17, 1823-1834 (1998).

32. Misiura K., Wojcik M., Krakowiak A., Koziolkiewicz M., Pawlowska Z., Pluskota E., Cierniewski C.S., Stec W.J.;

“Synthesis, biochemical and biological studies on oligonucleotides bearing a lipophilic dimethoxytrityl group.”

Acta Biochim. Pol., 45: 27-32 (1998).

33. Koziołkiewicz M., Krakowiak A., Kwinkowski M., Boczkowska M., Stec W.J.

“Stereodifferentiation – The effect of P-chirality of oligo(nucleoside phosphorothioate)s on the activity of bacterial RNase H.”

Nucleic Acids Res., 23, 5000-5005 (1995).