Papers by Jacek Jemielity
Ethynyl, 2-Propynyl, and 3-Butynyl C-Phosphonate Analogues of Nucleoside Di- and Triphosphates: Synthesis and Reactivity in CuAAC
Organic Letters, 2015
The synthesis and reactivity of a novel class of clickable nucleotide analogues containing a C-ph... more The synthesis and reactivity of a novel class of clickable nucleotide analogues containing a C-phosphonate subunit that has an alkyne group at the terminal position of the oligophosphate chain are reported. The C-phosphonate subunits were prepared by simple one- or two-step procedures using commercially available reagents. Nucleotides were prepared by MgCl2-catalyzed coupling reactions and then subjected to CuAAC reactions with various azide compounds to afford 5'-γ-labeled nucleoside triphosphates in excellent yields.
Efficient and Rapid Synthesis of Nucleoside Diphosphate Sugars from Nucleoside Phosphorimidazolides
European Journal of Organic Chemistry
We describe a simple, efficient, and protecting-group-free, magnesium-chloride-promoted synthesis... more We describe a simple, efficient, and protecting-group-free, magnesium-chloride-promoted synthesis of nucleoside diphosphate sugars from the corresponding nucleoside 5′-phosphorimidazolides and sugar phosphates in DMF. After optimization, nine different nucleoside sugars were synthesized and isolated in 63–92 % yield, demonstrating the applicability of this method with different nucleosides (A, G, U) and sugar moieties (1-Glc, 6-Glc, 1-Gal, 5-Rib, 1-Fuc). The procedure worked well even when a small excess of phosphosugars over nucleotides was used, and at low reagent concentrations, which makes it useful for small-scale (micromolar) NDP-sugar preparations.
Biochemical and Biophysical Research Communications
The assembly of the ribosome on majority of eukaryotic mRNAs is initiated by the recruitment of e... more The assembly of the ribosome on majority of eukaryotic mRNAs is initiated by the recruitment of eIF4E protein to the mRNA 5′ end cap structure. Flowering plants use two eIF4E isoforms, named eIF4E and eIF(iso)4E, as canonical translation initiation factors and possess a homolog of mammalian 4EHP (or eIF4E-2) termed nCBP. Plants from Brassicaceae family additionally conserve a close paralog of eIF4E which in Arabidopsis thaliana has two copies named eIF4E1b and eIF4E1c. In order to assess the efficiency of plant non-canonical (eIF4E1b/1c and nCBP) and canonical (eIF4E and eIF(iso)4E) eIF4E proteins to bind mRNAs we utilized fluorescence titrations to determine accurate binding affinities of five A.thaliana eIF4E isoforms for a series of cap analogs. We found that eIF4E binds cap analogs from 4-fold to 10-fold stronger than eIF(iso)4E, while binding affinities of nCBP and eIF(iso)4E are comparable. Furthermore, eIF4E1c interacts similarly strongly with the cap as eIF4E, but eIF4E1b bi...
Future medicinal chemistry
Cap analogs are chemically modified derivatives of the unique cap structure present at the 5´ end... more Cap analogs are chemically modified derivatives of the unique cap structure present at the 5´ end of all eukaryotic mRNAs and several non-coding RNAs. Until recently, cap analogs have served primarily as tools in the study of RNA metabolism. Continuing advances in our understanding of cap biological functions (including RNA stabilization, pre-mRNA splicing, initiation of mRNA translation, as well as cellular transport of mRNAs and snRNAs) and the consequences of the disruption of these processes - resulting in serious medical disorders - have opened new possibilities for pharmaceutical applications of these compounds. In this review, the medicinal potential of cap analogs in areas, such as cancer treatment (including eIF4E targeting and mRNA-based immunotherapy), spinal muscular atrophy treatment, antiviral therapy and the improvement of the localization of nucleus-targeting drugs, are highlighted. Advances achieved to date, challenges, plausible solutions and prospects for the futu...
Hint2, the mitochondrial nucleoside 5'-phosphoramidate hydrolase; properties of the homogeneous protein from sheep (Ovis aries) liver
Acta biochimica Polonica
Adenosine 5'-phosphoramidate (NH2-pA) is a rare natural nucleotide and its biochemistry and b... more Adenosine 5'-phosphoramidate (NH2-pA) is a rare natural nucleotide and its biochemistry and biological functions are poorly recognized. All organisms have proteins that may be involved in the catabolism of NH2-pA. They are members of the HIT protein family and catalyze hydrolytic splitting of NH2-pA to 5'-AMP and ammonia. At least five HIT proteins have been identified in mammals; however, the enzymatic and molecular properties of only Fhit and Hint1 have been comprehensively studied. Our study focuses on the Hint2 protein purified by a simple procedure to homogeneity from sheep liver mitochondrial fraction (OaHint2). Hint1 protein was also prepared from sheep liver (OaHint1) and the molecular and kinetic properties of the two proteins compared. Both function as homodimers and behave as nucleoside 5'-phosphoramidate hydrolases. The molecular mass of the OaHint2 monomer is 16 kDa and that of the OaHint1 monomer 14.9 kDa. Among potential substrates studied, NH2-pA appeared...
FEBS Journal
Decapping scavenger (DcpS) assists in precluding inhibition of cap-binding proteins by hydrolyzin... more Decapping scavenger (DcpS) assists in precluding inhibition of cap-binding proteins by hydrolyzing cap species remaining after mRNA 3→5 degradation. Its significance was reported in splicing, translation initiation and microRNA turnover. Here we examine the structure and binding mode of DcpS from Caenorhabditis elegans (CeDcpS) using a large collection of chemically modified methylenebis(phosphonate), imidodiphosphate and phosphorothioate cap analogs. We determine that CeDcpS is a homodimer and propose high-accuracy structural models of apo- and m(7) GpppG-bound forms. The analysis of CeDcpS regioselectivity uncovers that the only site of hydrolysis is located between the β and γ phosphates. Structure-affinity relationship studies of cap analogs for CeDcpS reveal molecular determinants for efficient cap binding: a strong dependence on the type of substituents in the phosphate chain, and reduced binding affinity for either methylated hydroxyl groups of m(7) Guo or extended triphospha...
Synthesis of Fluorophosphate Nucleotide Analogs and Their Characterization as Tools for 19F NMR Studies
The Journal of organic chemistry, Jan 27, 2015
To broaden the scope of existing methods based on 19F nucleotide labeling, we developed a new met... more To broaden the scope of existing methods based on 19F nucleotide labeling, we developed a new method for the synthesis of fluorophosphate (oligo)nucleotide analogs containing an O to F substitution at the terminal position of the (oligo)phosphate moiety and evaluated them as tools for 19F NMR studies. Using three efficient and comprehensive synthetic approaches based on phosphorimidazolide chemistry and tetra-n-butylammonium fluoride, fluoromonophosphate or fluorophosphate imidazolide as fluorine sources, we prepared over 30 fluorophosphate-containing nucleotides, varying in nucleobase type (A, G, C, U, m7G), phosphate chain length (from mono- to tetra-) and presence of additional phosphate modifications (thio-, borano-, imido-, methylene-). Using fluorophosphate imidazolide as fluorophosphorylating reagent for 5'-phosphorylated oligos we also synthesized oligonucleotide 5'-(2-fluorodiphosphates), which are potentially useful as 19F NMR hybridization probes. The compounds we...
The first examples of mRNA cap analogs bearing boranophosphate modification
Nucleic Acids Symposium Series, 2008
The syntheses of mRNA cap analogs modified with boranophosphate moiety at either the alpha or bet... more The syntheses of mRNA cap analogs modified with boranophosphate moiety at either the alpha or beta-position of the 5', 5'-triphosphate bridge (m(7)Gppp(BH3)G, m(7)Gpp(BH3)pG and m(7)Gpp(BH3)pm(7)G) are described. The preliminary biological characterization of these compounds revealed that they have high affinity for translational factor eIF4E and high potency to inhibit cap-dependent translation in cell free system. The analogs modified at the beta-position were also found to be resistant to DcpS decapping pyrophosphatase.
Hint2, the mitochondrial nucleoside 5'-phosphoramidate hydrolase; properties of the homogeneous protein from sheep (Ovis aries) liver
Acta biochimica Polonica, 2013
Adenosine 5'-phosphoramidate (NH2-pA) is a rare natural nucleotide and its biochemistry and b... more Adenosine 5'-phosphoramidate (NH2-pA) is a rare natural nucleotide and its biochemistry and biological functions are poorly recognized. All organisms have proteins that may be involved in the catabolism of NH2-pA. They are members of the HIT protein family and catalyze hydrolytic splitting of NH2-pA to 5'-AMP and ammonia. At least five HIT proteins have been identified in mammals; however, the enzymatic and molecular properties of only Fhit and Hint1 have been comprehensively studied. Our study focuses on the Hint2 protein purified by a simple procedure to homogeneity from sheep liver mitochondrial fraction (OaHint2). Hint1 protein was also prepared from sheep liver (OaHint1) and the molecular and kinetic properties of the two proteins compared. Both function as homodimers and behave as nucleoside 5'-phosphoramidate hydrolases. The molecular mass of the OaHint2 monomer is 16 kDa and that of the OaHint1 monomer 14.9 kDa. Among potential substrates studied, NH2-pA appeared...
Decapping of mRNA containing the histone 3'-stem loop requires recruitment of stem loop binding protein (SLBP)
ADENOSINE TETRAPHOSPHAT IS THE STRONGEST NUCLEOTIDIC ENDOTHELIUM DERIVED VASOCONSTRICTOR-CHARACTERIZATION OF VASOACTIVE PROPERTIES OF STABLE ANALOGUES
Experimental physics' resources for studying biological macromolecules; deep insight into DcpS enzymatic hydrolysis of short capped mRNAs
Fluorescent quantification of Gibbs free energy of cap binding to DcpS reveals DcpS-cap interactions
Five eIF4E isoforms from Arabidopsis thaliana are characterized by distinct features of cap analogs binding
Biochemical and Biophysical Research Communications, 2015
The assembly of the ribosome on majority of eukaryotic mRNAs is initiated by the recruitment of e... more The assembly of the ribosome on majority of eukaryotic mRNAs is initiated by the recruitment of eIF4E protein to the mRNA 5' end cap structure. Flowering plants use two eIF4E isoforms, named eIF4E and eIF(iso)4E, as canonical translation initiation factors and possess a homolog of mammalian 4EHP (or eIF4E-2) termed nCBP. Plants from Brassicaceae family additionally conserve a close paralog of eIF4E which in Arabidopsis thaliana has two copies named eIF4E1b and eIF4E1c. In order to assess the efficiency of plant non-canonical (eIF4E1b/1c and nCBP) and canonical (eIF4E and eIF(iso)4E) eIF4E proteins to bind mRNAs we utilized fluorescence titrations to determine accurate binding affinities of five A.thaliana eIF4E isoforms for a series of cap analogs. We found that eIF4E binds cap analogs from 4-fold to 10-fold stronger than eIF(iso)4E, while binding affinities of nCBP and eIF(iso)4E are comparable. Furthermore, eIF4E1c interacts similarly strongly with the cap as eIF4E, but eIF4E1b binds cap analogs ca. 2-fold weaker than eIF4E1c, regardless of the 95% sequence identity between these two proteins. The use of differentially chemically modified cap analogs in binding studies and a detailed analysis of the obtained homology models gave us insight into the molecular characteristic of varying cap-binding abilities of Arabidopsis eIF4E isoforms.
Synthesis and biochemical studies of tetraphosphate 5' mRNA cap analogs bearing bisphosphonate modification
Nucleic Acids Symposium Series, 2008
Dinucleotide cap analogs containing tetraphosphate bridge modified by replacing one of the bridgi... more Dinucleotide cap analogs containing tetraphosphate bridge modified by replacing one of the bridging oxygen atoms with methylene group were synthesized. The analogs have been examined for their stability towards enzymatic hydrolysis by human DcpS and binding affinity for eIF4E. Their inhibitory properties in rabbit reticulocyte lysate (RRL) translational system were studied.
Gold-decorated polymer vessel structures as carriers of mRNA cap analogs
Polymer, 2015
ABSTRACT We report on a facile and reliable preparation of polypyrrole vessel structures modified... more ABSTRACT We report on a facile and reliable preparation of polypyrrole vessel structures modified with gold nanoparticles that are able to encapsulate organic molecules of biological importance. The polymer is coated onto the surface of aqueous droplets through photopolymerization of the monomer. When gold nanoparticles and/or biomolecules are contained in the droplets, these species become incorporated within the formed polymer microvessels. Herein, we provide thorough physicochemical characterization of the polymer structures including electron and optical microscopy, spectroscopy (steady state and time-resolved fluorescence, XPS, XRF) and other experimental techniques. Polymer microvessels are promising as smart drug carriers for new experimental therapies. As model drugs we use mRNA cap analogues which are nucleotide-derived compounds that have been shown to be potential anti-cancer agents. We demonstrate that embedding the metallic nanoparticles within the microvessels provides usefully high contrast in micro-computed tomography (microCT) which is promising from the standpoint of monitoring the fate of administered drug carriers inside the body. Moreover, our in vivo studies on rats demonstrate that intravenous administration of the microvessels does not evoke acute toxicity or death of the animals.
Histidine triad (HIT)-family proteins interact with different mono- and dinucleotides and catalyz... more Histidine triad (HIT)-family proteins interact with different mono- and dinucleotides and catalyze their hydrolysis. During a study of the substrate specificity of seven HIT-family proteins, we have shown that each can act as a sulfohydrolase, catalyzing the liberation of AMP from adenosine 5 0 -
SYNTHESIS AND ENZYMATIC CHARACTERIZATION OF METHYLENE ANALOGS OF ADENOSINE 5′-TETRAPHOSPHATE (P4A)
Nucleosides Nucleotides & Nucleic Acids, 2005
A new methodology for synthesis of biologically important nucleoside tri- and tetraphosphates con... more A new methodology for synthesis of biologically important nucleoside tri- and tetraphosphates containing a bisphosphonate moiety instead of the terminal pyrophosphate bond is described. The series consists of tri- and tetraphosphate analogs of adenosine, guanosine and 7-methylguanosine (characteristic for mRNA cap). We have adopted a two-step procedure that allowed us to insert a methylene bridge into the phosphate chain. Nucleoside
Synthetic analogs of the 5-terminal caps of eukaryotic mRNAs and snRNAs are used in elucidating s... more Synthetic analogs of the 5-terminal caps of eukaryotic mRNAs and snRNAs are used in elucidating such physiological processes as mRNA translation, pre-mRNA splicing, intracellular transport of mRNA and snRNAs, and mRNA turnover. Particularly useful are RNAs capped with synthetic analogs, which are produced by in vitro transcription of a DNA template using a bacteriophage RNA polymerase in the presence of ribonucleoside triphosphates and a cap dinucleotide such as m 7 Gp 3 G. Unfortunately, because of the presence of a 3-OH on both the m 7 Guo and Guo moieties, up to half of the mRNAs contain caps incorporated in the reverse orientation. Previously we designed and synthesized two "anti-reverse" cap analogs (ARCAs), m 7 3dGp 3 G and m 2 7,3-O Gp 3 G, that cannot be incorporated in the reverse orientation because of modifications at the C3 position of m 7 Guo. In the present study, we have synthesized seven new cap analogs modified in the C2 and C3 positions of m 7 Guo and in the number of phosphate residues, m 2 7,2-O Gp 3 G, m 7 2dGp 3 G, m 7 2dGp 4 G, m 2 7,2-O Gp 4 G, m 2 7,3-O Gp 4 G, m 7 Gp 5 G, and m 2 7,3-O Gp 5 G.
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Papers by Jacek Jemielity