Unit for Organic and Bioorganic Chemistry

(Roger Strömberg, RST)

Professor

Roger Strömberg

Phone: +46-(0)8-524 810 24
Organizational unit: Department of Biosciences and Nutrition (BioNut), H2
E-mail: Roger.Stromberg@ki.se

Nucleic acids and peptides in biotechnology and therapy

Research projects

Stabilised, Cell Penetrating and Target Seeking Oligonucleotides for Enhanced Therapy

Oligonucleotide therapy is typically limited by inefficient in vivo delivery. To address this, we are currently developing modifications, conjugates and methods to accomplish these.This involves a novel type of modified oligonucleotide with cell penetrating properties (cell penetrating oligonucleotide, CPO) that is taken up by cells. This also includes conjugates of CPOs to entities with further endosomal escape enhancing properties. We are also developing multiple conjugates of therapeutic oligonucleotides with additional tissue targeting entities, such as homing peptides. Conjugates may also carry localising signals for different cell types as well as for subcellular localisation (e.g. the nucleus). We have also started to develop an approach to enable microRNA targeting at all stages of their biogenesis by invading clamps that form both Watson-Crick duplexes and triplexes. A substantial part of the work involves linker and method development to enable synthesis of different modification, conjugates and more complex nano-constructs. Current diseases targeted include Huntingtons disease, Duchenne Muscular Dystrophy, metabolic diseases and infectious diseases.

Oligonucleotide Based Artificial Nucleases and PNAzymes

A main aim is to develop oligonucleotide based artificial nucleases (OBANs) to the state of becoming useful tools in molecular biology and biotechnology also in a cellular environment and to move closer to being able to use these artificial enzymes for disease therapy. These artificial enzymes, including peptide nucleic acid based “PNAzymes” are developed to the stage that these are highly sequence selective and give single site cleavage with turnover, i.e., these are artificial RNA restriction enzymes. These tailor-made RNases, are usable tools for molecular biology and is currently developed further to obtain artificial nucleases that allow use in therapy. Initial diseases targeted are Malaria and other infectious diseases as well as metabolic diseases,

Treatment of Infections through Substances that Induce Our Own Defense Against Microbes

Another goal is treatment of infections, in particular by multidrug resistant bacteria, through induction of body-own antimicrobial peptides. We have developed a novel class (aroylated phenylenediamines, APDs) of highly potent inducers of antimicrobial peptides in vitro and in vivo. Oral treatment of rabbits with shigellosis gave reduction of bacterial count, reinstatement of antimicrobial peptides and clinical recovery from the bacterial infection in four days. Future work involves further development of the compounds and evaluation in co-treatment with antibiotics of infections caused by multidrug resistant bacteria. We also expect to combine this approach with microRNA targeting to induce autophagy for treatment of infections.

Aβ-Peptide Ligands for Potential Treatment of Alzheimers Disease

We have developed ligands that stabilise the Aβ peptide in the native alfa-helical conformation. These prevent Aβ induced reduction of hippocampal γ-oscillations (that is connected to cognition and learning and reduced in patients with AD) and oral administration of ligands increase longevity and decrease locomotor dysfunction in a Drosophila model of AD. As the approach holds promise for treatment of AD we are developing improved ligands.

EU-network


MMBIO: http://www.bioc.cam.ac.uk/hollfelder/Research/mmbio/mmbiofront
 

IS3NA

International Society of Nucleoside, Nucleotides and Nucleic Acids:
http://www.is3na.org/

Group pictures

Link to past and present pictures from the Strömberg group

Other contacts in the group

Assistant professor

Dmytro Honcharenko

Organizational unit: Strömberg
E-mail: dmytro.honcharenko@ki.se

Senior researcher

Malgorzata Honcharenko

Phone: +46-(0)8-524 810 25
Organizational unit: Department of Biosciences and Nutrition (BioNut), H2
E-mail: Malgorzata.Honcharenko@ki.se

Assistant professor

Merita Murtola

Phone: +46-(0)8-524 810 19
Organizational unit: Strömberg
E-mail: Merita.Murtola@ki.se

Senior lab manager

Håkan Ottosson

Organizational unit: Others
E-mail: hakan.ottosson@ki.se

Selected publications

(roughly ordered by interconnection):

Milton S Honcharenko D Moreno P Rocha C Smith E, Strömberg R (2015) Nuclease resistant oligonucleotides with cell-penetrating properties Chem Comm 51, 4044; Milton S, Ander C, Honcharenko M, Honcharenko D, Yeheskiely E, Strömberg R (2013) Synthesis and stability of a 2’-O-(N-(aminoethyl)carbamoyl)-methyladenosine containing dinucleotide Eur J Org Chem 7184; Milton S Ander C Yeheskiely E Strömberg R (2012) Stability of a 2’-O-(carbamoylmethyl) adenosine containing dinucleotide Eur J Org Chem 539.

Jezowska M, Honcharenko D; Ghidini A; Strömberg R; Honcharenko M. (2016) Enabling Multiple Conjugation to Oligonucleotides Using “Click Cycles”. Bioconjugate Chem., 27, 2620; Wenska M, Alvira M, Steunenberg, P, Stenberg Å, Murtola, M and Strömberg R (2011) An Activated Triple Bond Linker Enables “Click” Attachment of Peptides to Oligonucleotides Nucl Acids Res., 39, 9047; Zaramella S, Yeheskiely E, Strömberg R (2004) A Method for Solid Phase Synthesis of Oligonucleotide 5’-Peptide Conjugates Using Acid Labile a-Amino Protection J Am Chem Soc, 126, 14029.

Ghidini A, Murtola M, Strömberg, R (2016) Influence of conjugation and other structural changes on the activity of Cu2+ based PNAzymes. Org Biomol Chem, 14, 2768; Ghidini A, Murtola M, Strömberg R. (2015) Oligonucleotide based artificial ribonucleases DNA in Supramolecular Chemistry and Nanotechnology, Wiley, Chapter 3.2; Murtola M, Wenska M, Strömberg R (2010) PNAzymes that are artificial RNA restriction enzymes J Am Chem Soc, 132, 8984; Murtola M, Strömberg R (2008) PNA Based Artificial Nucleases Displaying Catalysis with Turnover in Cleavage of a Leukemia related RNA model Org Biomol Chem 6, 3837; Åström H, Williams NH, Strömberg R (2003) Oligonucleotide based artificial nuclease (OBAN) systems. Bulge size dependence and positioning of catalytic group in cleavage of RNA bulges. Org Biomol Chem 1461

Honcharenko M; Bestas B; Jezowska M; Wojtczak BA; Moreno PMD; Romanowska J; Bächle SM; Darzynkiewicz E; Jemielity J; Smith CIE; Strömberg R. (2016) Synthetic m3G-CAP attachment necessitates a minimum trinucleotide constituent to be recognised as a Nuclear Import Signal. RSC Advances, 6, 51367; Honcharenko M; Romanowska J; Alvira M; Jezowska M; Kjellgren M; Smith CIE; Strömberg R (2012) Capping of oligonucleotides with "clickable" m3G-CAPs RSC Advances, 2, 12949; Moreno P, Wenska M, Lundin K, Wrange Ö, Strömberg R, Smith E (2009) A synthetic snRNA m3G-CAP enhances nuclear delivery of exogenous proteins and nucleic acids. Nucl. Acids Res, 37, 1925.

Ottosson H; Nylen F; Sarker P; Miraglia E; Bergman P; Gudmundsson GH; Raquib R; Agerberth B; Strömberg R. (2016) Potent Inducers of Endogenous Antimicrobial Peptides for host Directed Therapy of Infections. Sci Rep. 6:36692. DOI: 10.1038/srep36692.

Ghidini A; Bergquist H; Punga T; Zain R; Strömberg R. (2016) Clamping of RNA with PNA enables targeting of microRNA. Org Biomol Chem 14, 5210;

Ghidini A Ander C Winqvist A Strömberg R (2013) An RNA modification with remarkable resistance to RNase A. Chem Comm 49, 9036; Winqvist A Strömberg R. (2008) Nucleoside 3’-Deoxy-3’-C-Methylenephosphinates Part 3. An investigation on Condensing Agents for Phosphinate Ester Formation with Nucleoside 5’-Hydroxyl Functions. Eur J Org Chem, 1705; Winqvist A Strömberg R (2002) Reactions of 3’-C-Halomethyl and 3’-C-Sulfonylmethyl Uridines with Phosphinic Acid Derivatives. Synthesis of Building Blocks for Oligonucleotides Containing 3’-C-Methylenephosphonate Linkages Eur J Org Chem, 1509; Winqvist A, Strömberg R (2001) Stereoselectivity in the synthesis of 3'-deoxy-3'-C-(hydroxymethyl) uridines by hydroboration and conversion into a building block for various 3'-deoxy-3'-C-(methylene)uridine analogues Eur J Org Chem, 4305.

Maity J, Honcharenko D, Strömberg R. (2015) Synthesis of Triamino Acid Building Blocks with Different Lipophilicities. PLoS One, 10, e0124046; Honcharenko D; Bose PP; Maity J; Kurudenkandy FR; Juneja A; Flöistrup E; Henrik Biverstål H; Johansson J; Nilsson L; Fisahn A; Strömberg R. (2014) Synthesis and Evaluation of Antineurotoxicity Properties of an Amyloid-β Peptide Targeting Ligand Containing a Triamino Acid. Org. Biomol. Chem., 12, 6684-6693; Nerelius, C.; Sandegren, A.; Sargsyan, H.; Raunak, R.; Leijonmarck, H.; Chatterjee, U.; Fisahn, A.; Imarisio, S.; Lomas, D. A.; Crowther, D. C.; Strömberg, R.; Johansson, J. (2009) α-Helix targeting reduces amyloid-β peptide toxicity. Proc. Natl. Acad. Sci. USA, 106, 9191.

Murtola M, Zaramella S, Yeheskiely E, Strömberg R (2010) Cationic Peptides that Increase the Thermal Stability of 2’-O-MeRNA/RNA Duplexes, but that do not Affect DNA/DNA Melting ChemBioChem, 11, 2606; Sandbrink J, Ossipov D, Åström H, Strömberg R (2005), Investigation of Potential RNA-bulge Stabilising Elements, J Mol Recognition, 18, 318; Madder A, Ehrl R, Stromberg, R. (2003) Stabilisation of RNA Bulges by Oligonucleotide Complements Containing an Adenosine Analogue. ChemBioChem, 4, 1194.

Rozners E Katkevica D Strömberg R (2007) Oligoribonucleotide analogues containing a mixed backbone of phosphodiester and formacetal internucleoside linkages, together with vicinal 2'-O-methyl groups ChemBioChem 8, 537; Rozners, E., Katkevica, D., Bizdena, E. and Strömberg, R. (2003) Synthesis and Properties of RNA Analogues Having Amides as Interuridine Linkages at Selected Positions, J Am Chem Soc 125, 12125; Rozners E. Strömberg, R. (1997) Synthesis and properties of oligoribonucleotides having formacetal internucleoside linkages J Org Chem, 62, 1846.

Åström, H., Limen, E. and Strömberg, R. (2004) The Acidity of Secondary Hydroxyls in ATP and Adenosine Analogues, and the question of a 2’,3’ hydrogen bond in ribonucleosides, J Am Chem Soc 126, 14710; Sjögren, A-S., Pettersson, E., Sjöberg, B-M. & Strömberg, R. (1997) Metal ion interaction with cosubstrate in self-splicing of group I introns. Nucl Acids Res, 25, 648;

Almer, H., Stawinski, J. & Strömberg, R. (1996) Solid support synthesis of all-Rp-oligo(ribonucleoside phosphorothioate)s, Nucleic Acids Res., 24, 3811. Almer, H. & Strömberg, R. (1996) Base-catalysis and leaving group dependence in intramolecular alcoholysis of uridine 3'-(aryl phosphorothioate)s. J. Am. Chem. Soc., 118, 7921; Oivanen, M., Almer, H., Strömberg, R. & Lönnberg, H. (1995), Hydrolytic reactions of the diastereomeric phosphoromonothioate analogs of uridylyl(3',5')uridine: Kinetics and mechanisms for desulfurization, phosphoester hydrolysis and transesterification to the 2',5'-isomers. J. Org. Chem., 60, 5620.

Stawinski J, Strömberg R (2005) Di and Oligonucleotide Synthesis Using H-Phosphonate Chemistry. In Oligonucleotide synthesis: Methods and applications; Edited by Piet Herdewijn; Humana Press, Totowa New Jersey, 81; Sigurdsson S, Strömberg R. (2002) The H-Phosphonate Approach to Oligonucleotide Synthesis. An Investigation on the Mechanism of the Coupling Step. J. Chem Soc. Perkin Trans 2, 1682; Garegg PJ, Henrichson C, Lindh, I, Regberg T, Stawinski J, Strömberg R (1986) Nucleoside H-phosphonates. III. Chemical synthesis of oligodeoxy-ribonucleotides by the hydrogenphosphonate approach. Tetrahedron Lett. 27, 4051; Garegg PJ, Henrichson C, Lindh I, Regberg T, Stawinski J, Strömberg, R (1986) Nucleoside H-phosphonates IV. Automated solid phase synthesis of oligo-ribonucleotides by the hydrogenphosphonate approach. Tetrahedron Lett. 27, 4055; Garegg PJ, Regberg T, Stawinski J, Strömberg R (1986) Nucleoside hydrogenphosphonates in oligonucleotide synthesis Chemica Scripta 26, 59.; Garegg PJ, Regberg T, Stawinski J, Strömberg R. (1985) Formation of internucleotidic bonds via phosphonate intermediates Chemica Scripta 25, 280.

Westman E, Strömberg R. (1994) Removal of t-butyldimethylsilyl protection in RNA-synthesis. Triethylamine trihydrofluoride (TEAx3HF) is a more reliable alternative to tetrabutylammonium fluoride (TBAF). Nucl Acids Res, 22 , 2430; Rozners E, Westman E, Strömberg R. (1994) Evaluation of 2'-hydroxyl protection in RNA-synthesis using the H-phosphonate approach. Nucl Acids Res, 22, 94; Stawinski J, Strömberg R, Thelin M, Westman E (1988) Studies on the t-butyl-dimethylsilyl group as 2´-O-protection in oligoribonucleotide synthesis via the H-phosphonate approach. Nucl Acids Res, 16, 9285.

Lönnberg H, Strömberg R, Williams A (2004) Compelling Evidence for a Stepwise Mechanism of the Alkaline Cyclisation of Uridine 3’-phosphate Esters Org Biomol Chem 2165: Mikkola S, Stenman E, Nurmi K, Yousefi-Salakdeh E, Strömberg R, Lönnberg H (1999) The mechanism of the metal ion promoted cleavage of RNA phosphodiester bonds involves a general acid catalysis by the metal aquo ion on the departure of the leaving group.” J Chem Soc Perkin Trans 2, 1619; Kosonen M, Yousefi-Salakdeh E, Strömberg R, Lönnberg H, (1998) pH- and Buffer-independent Cleavage and Mutual Isomerization of Uridine 2’ and 3’-alkylphosphodiesters: Implications for the Buffer Catalyzed Cleavage of RNA J Chem Soc Perkin Trans 2, 1589; Kosonen M, Yousefi-Salakdeh E, Strömberg R, Lönnberg H. Mutual Isomerization of Uridine 2’ and 3’-alkylphosphates and Cleavage of a 2’,3’-cyclic Phosphate: The Efffect of the alkyl Group on the Hydronium- and Hydroxide-ion-catalyzed Reactions. J. Chem. Soc. Perkin Trans 2, 1997, 2661

Chandler AJ, Hollfelder F, Kirby AJ, O`Carroll F, Strömberg R (1994) Models for enzyme catalysed phosphate transfer: Comparisons of reactivity towards neighbouring hydroxyl for phosphodiester anions and acids. General base catalysis of the cyclisation of a hydroxyalkyl phosphate triester. J Chem Soc Perkin Trans II 327; Camilleri P, Jones RFD, Kirby AJ, Strömberg R (1994) Nucleophilic catalysis of glycoside hydrolysis. The hydrolysis of 4-nitrophenyl a and b-D-glucopyranoside tetraphosphates. J Chem Soc Perkin Trans II 2085.

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