Synthesis of New Chiral Building Blocks for Novel Peptide Nucleic Acids

IntroductionAbouttenyearsago ,PNA ,astructuralmimicofDNAinwhichthesugar phosphatebackboneisreplacedbyN (2 aminoethyl)glycine (aeg)linkageemergedasapotentialanti sensetherapeuticagent.1PNAhassomeadvantages:(1)itisstabletocellularnucleasesandproteases,(2 )ithybridizeswithcomplementaryDNAorRNA (cDNA/RNA)sequenceswithhighaffinity ,(3)ithaslownon specificinteractionwithcellularcontentsand (4 )itiseasilysynthesizedbyadoptionofsolidphasepeptidesynthesischemistry .However,thema jorlimitationo…     

A Photoreactive G‐Quadruplex Ligand Triggered by Green Light

A photoreactive molecular dye targeting the G‐quadruplex nucleic acid (G4) of the human telomeric sequence Tel22, and several mutated analogues, was activated by green light (λ=532 nm). Highly selective covalent modification of G4 versus single‐stranded and double‐stranded DNA was achieved with efficiency up to 64 %. The phenoxyl radical was generated and detected by laser‐flash photolysis as a reactive intermediate that targeted loop thymine residues. These insights may suggest a non‐invasive tool for selective nucleic acid tagging and “pull‐down” cellular applications.     

New approach to l'C‐modified riboside scaffold via stereoselective functionalization of D‐(+)‐ribonic‐y‐lactone

We describe the preparation and spectroscopic properties of a novel class of nucleoside analogues in which a phenyl sulfonyl methylene group is attached to the 1′‐carbon atom of P‐D‐ribofuranose. The glyco‐sylation of 5‐O‐(tert‐butyldiphenylsilyl)‐2,3‐O‐isopropylidene‐D‐ribofuranolactone lb with phenyl methyl‐lithium sulfone in THF at ?60° C afforded 5‐O‐(tert‐butyldiphenylsilyl)‐1′‐(benzenesulfonylmethylene)‐2′,3′‐O‐isopropylidene‐α‐D‐ribofuranose 2b . When subjected to deoxydative reaction conditions with boron trifluoride etherate in the presence of triethylsilane at ?45° C, lactol 2b was converted into 2′,3′‐O‐isopro‐pylidene‐1′‐deoxy‐1′‐(benzenesulfonylmethylene)‐β‐D‐ribofuranose 4b with excellent stereocontrol over the anomeric carbon in moderate yield. This method has the potential for the development of a wider array of useful probes derived from 1′‐deoxy‐β‐D‐ribofuranose for nucleic acid research and for antisense therapeutic agents through further functionalization of the coupled sulfonyl group.     

Second‐Generation Fluorescent Quadracyclic Adenine Analogues: Environment‐Responsive Probes with Enhanced Brightness

Fluorescent base analogues comprise a group of increasingly important molecules for the investigation of nucleic acid structure, dynamics, and interactions with other molecules. Herein, we report on the quantum chemical calculation aided design, synthesis, and characterization of four new putative quadracyclic adenine analogues. The compounds were efficiently synthesized from a common intermediate through a two‐step pathway with the Suzuki–Miyaura coupling as the key step. Two of the compounds, qAN1 and qAN4, display brightnesses (εΦ_F) of 1700 and 2300, respectively, in water and behave as wavelength‐ratiometric pH probes under acidic conditions. The other two, qAN2 and qAN3, display lower brightnesses but exhibit polarity‐sensitive dual‐band emissions that could prove useful to investigate DNA structural changes induced by DNA–protein or –drug interactions. The four qANs are very promising microenvironment‐sensitive fluorescent adenine analogues that display considerable brightness for such compounds.     

Synthesis and conformational analysis of efrapeptins

The efrapeptin family of peptide antibiotics produced by the fungus Tolypocladium niveum, and the neo‐efrapeptins from the fungus Geotrichum candidumare inhibitors of F₁‐ATPase with promising antitumor, antimalaria, and insecticidal activity. They are rich in C^α‐dialkyl amino acids (Aib, Iva, Acc) and contain one β‐alanine and several pipecolic acid residues. The C‐terminus bears an unusual heterocyclic cationic cap. The efrapeptins C–G and three analogues of efrapeptin C were synthesized using α‐azido carboxylic acids as masked amino acid derivatives. All compounds display inhibitory activity toward F₁‐ATPase. The conformation in solution of the peptides was investigated with electronic CD spectroscopy, FT‐IR spectroscopy, and VCD spectroscopy. All efrapeptins and most efrapeptin analogues were shown to adopt helical conformations in solution. In the case of efrapeptin C, VCD spectra proved that a 3₁₀‐helix prevails. In addition, efrapeptin C was conformationally studied in detail with NMR and molecular modeling. Besides NOE distance restraints, residual dipolar couplings (RDC) observed upon partial alignment with stretched PDMS gels were used for the conformational analysis and confirmed the 3₁₀‐helical conformation.     

C5–C10 Directly Bonded Tetrodotoxin Analogues: Possible Biosynthetic Precursors of Tetrodotoxin From Newts

The identification of novel tetrodotoxin (TTX, 1 ) analogues would significantly contribute to the elucidation of its biosynthetic pathway. In this study, the first C5–C10 directly bonded TTX analogues, 4,9‐anhydro‐10‐hemiketal‐5‐deoxyTTX ( 2 ) and 4,9‐anhydro‐8‐epi‐10‐hemiketal‐5,6,11‐trideoxyTTX ( 3 ), were found in the newt Cynops ensicauda popei by using a screening method involving HILIC‐LC–MS/MS focused on the fragment ions of TTX analogues, and their structures were elucidated by spectroscopic methods. Compound 2 was detected in a wide range of newt species, and the 2 and TTX contents of 22 newt specimens were correlated (r_s=0.88). Based on these results and its structural features, 2 was predicted to serve as a precursor of TTX that would be directly converted into 4,9‐anhydroTTX ( 4 ) by Baeyer–Villiger‐like oxidation or via 4,9‐anhydro‐5‐deoxyTTX formed by cleavage of the C5–C10 bond. The bicyclic carbon skeletons of 2 and 3 suggested a possible monoterpene origin for TTX.     

Synthesis and Taste Properties of 4,1′,4′,6′‐Tetrahalodeoxysucrose Analogues

The synthesis of a series of 1,4,6‐trideoxy‐1,4,6‐trihalo‐β‐d‐hexulofuranosyl 4‐deoxy‐4‐halo‐α‐d‐hexopyranosides is described. The 4‐chloro‐, 4‐bromo‐ and 4‐iodo‐4‐deoxy‐β‐d‐fructofuranosyl analogues were synthesized from a 3′,4′‐lyxo‐epoxide using the respective alkali metal halides. The corresponding 4‐halodeoxytagatofuranosyl analogues, on the other hand, were obtained by direct halide displacement of the 4′‐O‐trifluoromethanesulfonyl derivative, which was derived by regioselective sulfonylation of 1,6‐di‐O‐trityl‐β‐d‐fructofuranosyl 6‐O‐trityl‐α‐d‐glucopyranoside via its stannylene acetal. The sweetness intensities of these tetrahalodeoxy compounds strongly suggest that both size and configuration of the halogen substituents at C‐4 and C‐4′ are critical for sweetness enhancement.     

Synthesis and Antitumor Activity Evaluation of γ-Monofluorinated and γ,γ-Difluorinated Goniothalamin Analogues

A series of novel γ,γ‐difluorinated Goniothalamin analogues 4a – 4i and 6a – 6i were synthesized. The key steps included the construction of C‐5 stereocenter adjacent to gem‐difluoromethylene group by way of lipase AK catalyzed kinetic resolution, the introduction of aryl group via Stille coupling, and lactonization by 1,5‐oxidative cyclization. These γ,γ‐difluorinated Goniothalamin analogues 4a – 4i and their enantiomers 6a – 6i , together with several corresponding γ‐monofluorinated Goniothalamin analogues were biologically evaluated against four different cancer cell lines. Compound 7h showed a nearly equivalent potency as the parent (R)‐Goniothalamin in the micromolar range. The different fluorine effects between fluoromethylene and gem‐difluoromethylene on antitumor activity were discussed through the analysis of bioassay data.     

SDS‐PAGE procedure: Application for characterization of new entirely uncharged nucleic acids analogs

SDS‐PAGE is considered to be a universal method for size‐based separation and analysis of proteins. In this study, we applied the principle of SDS‐PAGE to the analysis of new entirely uncharged nucleic acid (NA) analogues, – phosphoryl guanidine oligonucleotides (PGOs). The procedure was also shown to be suitable for morpholino oligonucleotides (PMOs) and peptide nucleic acids (PNAs). It was demonstrated that SDS can establish hydrophobic interactions with these types of synthetic NAs, giving them a net negative charge and thus making these molecules mobile in polyacrylamide slab gels under the influence of an electric field.     

Delivering Structural Information on the Polar Face of Membrane‐Active Peptides: 19F‐NMR Labels with a Cationic Side Chain

Conformationally constrained non‐racemizing trifluoromethyl‐substituted lysine isosteres [(E)‐ and (Z)‐TCBLys] with charged side chains are presented as a new type of ¹⁹F‐NMR labels for peptide studies. Design of the labels, their synthesis, incorporation into peptides and experimental demonstration of their application for solid state NMR studies of membrane‐active peptides are described. A series of fluorine‐labeled analogues of the helical amphipathic antimicrobial peptide PGLa(Nle) was obtained, in which different lysine residues in the original peptide sequence were replaced, one at a time, by either (E)‐ or (Z)‐TCBLys. Antimicrobial activities of the synthesized analogues were practically the same as those of the parent peptide. The structural and orientational parameters of the helical PGLa(Nle) peptide in model bilayers, as determined using the novel labels confirmed and refined the previously known structure. (E)‐ and (Z)‐TCBLys, as a set of cationic ¹⁹F‐NMR labels, were shown to deliver structural information about the charged face of amphipathic peptides by solid state ¹⁹F‐NMR, previously inaccessible by this method.     

Facile Chemoenzymatic Strategies for the Synthesis and Utilization of S‐Adenosyl‐L‐Methionine Analogues

A chemoenzymatic platform for the synthesis of S‐adenosyl‐L ‐methionine (SAM) analogues compatible with downstream SAM‐utilizing enzymes is reported. Forty‐four non‐native S/Se‐alkylated Met analogues were synthesized and applied to probing the substrate specificity of five diverse methionine adenosyltransferases (MATs). Human MAT II was among the most permissive of the MATs analyzed and enabled the chemoenzymatic synthesis of 29 non‐native SAM analogues. As a proof of concept for the feasibility of natural product “alkylrandomization”, a small set of differentially‐alkylated indolocarbazole analogues was generated by using a coupled hMAT2–RebM system (RebM is the sugar C4′‐O‐methyltransferase that is involved in rebeccamycin biosynthesis). The ability to couple SAM synthesis and utilization in a single vessel circumvents issues associated with the rapid decomposition of SAM analogues and thereby opens the door for the further interrogation of a wide range of SAM utilizing enzymes.     

Influence of Sequential Modifications and Carbohydrate Variations in Synthetic AFGP Analogues on Conformation and Antifreeze Activity

Certain Arctic and Antarctic ectotherm species have developed strategies for survival under low temperature conditions that, among others, consist of antifreeze glycopeptides (AFGP). AFGP form a class of biological antifreeze agents that exhibit the ability to inhibit ice growth in vitro and in vivo and, hence, enable life at temperatures below the freezing point. AFGP usually consist of a varying number of (Ala‐Ala‐Thr)_n units (n=4–55) with the disaccharide β‐D ‐galactosyl‐(1→3)‐α‐N‐acetyl‐D ‐galactosamine glycosidically attached to every threonine side chain hydroxyl group. AFGP have been shown to adopt polyproline II helical conformation. Although this pattern is highly conserved among different species, microheterogeneity concerning the amino acid composition usually occurs; for example, alanine is occasionally replaced by proline in smaller AFGP. The influence of minor and major sequence mutations on conformation and antifreeze activity of AFGP analogues was investigated by replacement of alanine by proline and glycosylated threonine by glycosylated hydroxyproline. The target compounds were prepared by using microwave‐enhanced solid phase peptide synthesis. Furthermore, artificial analogues were obtained by copper‐catalyzed azide–alkyne cycloaddition (CuAAC): propargyl glycosides were treated with polyproline helix II‐forming peptides comprising (Pro‐Azp‐Pro)_n units (n=2–4) that contained 4‐azidoproline (Azp). The conformations of all analogues were examined by circular dichroism (CD). In addition, microphysical analysis was performed to provide information on their inhibitory effect on ice recrystallization.     

“Reduced” Coumarin Dyes with an O‐Phosphorylated 2,2‐Dimethyl‐4‐(hydroxymethyl)‐1,2,3,4‐tetrahydroquinoline Fragment: Synthesis,Spectra, and STED Microscopy

Large Stokes‐shift coumarin dyes with an O‐phosphorylated 4‐(hydroxymethyl)‐2,2‐dimethyl‐1,2,3,4‐tetrahydroquinoline fragment emitting in the blue, green, and red regions of the visible spectrum were synthesized. For this purpose, N‐substituted and O‐protected 1,2‐dihydro‐7‐hydroxy‐2,2,4‐trimethylquinoline was oxidized with SeO₂ to the corresponding α,β‐unsaturated aldehyde and then reduced with NaBH₄ in a “one‐pot” fashion to yield N‐substituted and 7‐O‐protected 4‐(hydroxymethyl)‐7‐hydroxy‐2,2‐dimethyl‐1,2,3,4‐tetrahydroquinoline as a common precursor to all the coumarin dyes reported here. The photophysical properties of the new dyes (“reduced coumarins”) and 1,2‐dihydroquinoline analogues (formal precursors) with a trisubstituted C=C bond were compared. The “reduced coumarins” were found to be more photoresistant and brighter than their 1,2‐dihydroquinoline counterparts. Free carboxylate analogues, as well as their antibody conjugates (obtained from N‐hydroxysuccinimidyl esters) were also prepared. All studied conjugates with secondary antibodies afforded high specificity and were suitable for fluorescence microscopy. The red‐emitting coumarin dye bearing a betaine fragment at the C‐3‐position showed excellent performance in stimulation emission depletion (STED) microscopy.     

Peptide‐Assisted Design of Precision Polymer Sequences: On the Relevance of the Side‐Chain Sequences and the Variability of the Backbone

Functional sequences of monodisperse, sequence‐defined oligo(amide‐urethane)s are designed based on a peptide sequence as blueprint. The translation of a discrete side‐chain functionality sequence from a known peptide‐based solubilizer of the photosensitizer meta‐tetra(hydroxyphenyl)‐chlorin, into a non‐peptidic precision polymer backbone is demonstrated. The resulting peptidomimetic precision polymers retain the functions of the parent peptide sequence, showing analogues sensitivity toward single monomer mutations/exchanges and even exceeding the parent peptide equivalent by reaching up to 69% higher payload capacities and more favored release kinetics.     

Design and stereoselective synthesis of four peptide nucleic acid monomers with cyclic structures in backbone

Four isomers of the monomer of peptide nucleic acid (PNA) were derived from (2S,4R)‐4‐hydroxyproline; they had different stereochemistries at the C² and C⁴ positions in the pyrrolidine ring. These different backbone conformations corresponding to four different stereochemistries were realized through a combination of inversions at the C² and the C⁴ positions in pyrrolidine ring. The obtained backbone frameworks were reacted with N‐benzoyl thymine to give the corresponding PNA monomers. Spectroscopic comparison of the resultant monomers confirmed their stereochemistries. J. Heterocyclic Chem., (2011).     

Synthesis and Anti‐tumor Evaluation of B‐ring Modified Caged Xanthone Analogues of Gambogic Acid

Gambogic acid (GA, 1 ), the most prominent member of Garcinia natural products, has been reported to be a promising anti‐tumor agent. Previous studies have suggested that the planar B ring and the unique 4‐oxa‐tricyclo[4.3.1.0^3,7]dec‐2‐one caged motif were essential for anti‐tumor activity. To further explore the structure‐activity relationship (SAR) of caged Garcinia xanthones, two new series of B‐ring modified caged GA analogues 13a – 13e and 15a – 15e were synthesized utilizing a Claisen/Diel‐Alder cascade reaction. Subsequently, these compounds were evaluated for their in vitro anti‐tumor activities against A549, MCF‐7, SMMC‐7721 and BGC‐823 cancer cell lines by MTT assay. Among them, 13b – 13e exhibited micromolar inhibition against several cancer cell lines, being approximately 2–4 fold less potent in comparison to GA. SAR analysis revealed that the peripheral gem‐dimethyl groups are essential for maintaining anti‐tumor activity and substituent group on C1 position of B‐ring has a significant effect on potency, while modifications at C‐2, C‐3 and C‐4 positions are relatively tolerated. These findings will enhance our understanding of the SAR of Garcinia xanthones and lead to the development of simplified analogues as potential anti‐tumor agents.     

Bis‐Lactam Peptide [i,i + 4]‐Stapling

Even though the bis‐lactam peptide stapling with the [i, i + 7] and the [i, i + 11] systems has been known to be able to afford % α‐helicity values up to 100% (25°C), the performance of the bis‐lactam peptide stapling with the [i, i + 4] system in current literature has been mediocre (% α‐helicity ≦40%, 25°C). In the current study, we found that high % α‐helicity is also obtainable with the bis‐lactam [i, i + 4]‐stapling by demonstrating with our model peptide sequence that the bis‐lactam [i, i + 4]‐stapling with N^ε‐para‐phenylenediacetyl‐lysine was able to afford a % α‐helicity value of ~64.1% (25°C). Therefore, the bis‐lactam [i, i + 4]‐stapling could also be an efficacious peptide stapling mode that can be employed for biomedical applications.     

Oligomers with Intercalating Cytosine–Cytosine+ Base Pairs and Peptide Backbone: DNA i-Motif Analogues

Alanyl peptide nucleic acids organize in a similar manner to the DNA structure motif by stabilizing two cytosine–cytosine⁺ pairing double strands by intercalation (i-motif). These analogues demonstrate that a tetrameric arrangement of nucleobases is necessary for C–C⁺ pairing (see diagram), whereas formation of the i-motif does not depend on the ribosyl–phosphodiester backbone.     

Asymmetric α‐Hydroxylation of a Lactone with Vinylogous Pyridone by Using a Guanidine–Urea Bifunctional Organocatalyst: Catalytic Enantioselective Synthesis of a Key Intermediate for (20S)‐Camptothecin Analogues

We have developed a catalytic asymmetric synthesis of (S)‐4‐ethyl‐6,6‐(ethylenedioxy)‐7,8‐dihydro‐4‐hydroxy‐1H‐pyrano[3,4‐f]indolizine‐3,10(4H)dione ( 5 a ), a synthetic intermediate for (20S)‐camptothecin analogues. A key step in this synthesis is an asymmetric α‐hydroxylation of a lactone with a vinylogous pyridone structure ( 8 a ) by using a guanidine–urea bifunctional organocatalyst. The present oxidation was successfully applied to the synthesis of C20‐modified derivatives of (+)‐C20‐desethylbenzylcamptothecin ( 13 ).     

Protective Effects of Resveratrol and its Analogues against Free Radical-Induced Oxidative Hemolysis of Red Blood Cells

ＩｎｔｒｏｄｕｃｔｉｏｎＲｅｓｖｅｒａｔｒｏｌ (3,5 ,4′ ｔｒｉｈｙｄｒｏｘｙ ｔｒａｎｓ ｓｔｉｌｂｅｎｅ ,1)ｉｓａｎａｔｕｒａｌｌｙｏｃｃｕｒｒｉｎｇｐｈｙｔｏａｌｅｘｉｎｐｒｅｓｅｎｔｉｎｇｒａｐｅｓａｎｄｏｔｈｅｒｐｌａｎｔｓ .ＩｔｓｐｒｅｓｅｎｃｅｉｎｒｅｄｗｉｎｅｈａｓｂｅｅｎｓｕｇｇｅｓｔｅｄｔｏｂｅｌｉｎｋｅｄｔｏｔｈｅｌｏｗｉｎｃｉｄｅｎｃｅｏｆｈｅａｒｔｄｉｓｅａｓｅｓｉｎｓｏｍｅｒｅｇｉｏｎｓｏｆＦｒａｎｃｅ ,ｔｈｅｓｏ ｃａｌｌｅｄ“Ｆｒｅｎｃｈｐａｒａｄｏｘ” ,ｉ .ｅ .,ｄ…