Flexizyme‐Mediated Genetic Reprogramming As a Tool for Noncanonical Peptide Synthesis and Drug Discovery

Noncanonical peptides occur frequently in Nature, and often display high bioactivity. However, the lack of tractable systems for the synthesis of diverse libraries of such peptides has thus far hampered their development as drugs. Genetic reprogramming techniques, in which noncanonical amino acids may be incorporated into peptides, have largely removed this limitation. This Concept article outlines the development of these techniques with an emphasis on drug discovery.     

Homogeneous Catalytic Hydrogenation of Amides to Amines

Hydrogenation of amides in the presence of [Ru(acac)₃] (acacH=2,4‐pentanedione), triphos [1,1,1‐tris‐ (diphenylphosphinomethyl)ethane] and methanesulfonic acid (MSA) produces secondary and tertiary amines with selectivities as high as 93 % provided that there is at least one aromatic ring on N. The system is also active for the synthesis of primary amines. In an attempt to probe the role of MSA and the mechanism of the reaction, a range of methanesulfonato complexes has been prepared from [Ru(acac)₃], triphos and MSA, or from reactions of [RuX(OAc)(triphos)] (X=H or OAc) or [RuH₂(CO)(triphos)] with MSA. Crystallographically characterised complexes include: [Ru(OAc‐κ¹O)₂(H₂O)(triphos)], [Ru(OAc‐κ²O,O′)(CH₃SO₃‐κ¹O)(triphos)], [Ru(CH₃SO₃‐κ¹O)₂(H₂O)(triphos)] and [Ru₂(μ‐CH₃SO₃)₃(triphos)₂][CH₃SO₃], whereas other complexes, such as [Ru(OAc‐κ¹O)(OAc‐κ²O,O′)(triphos)], [Ru(CH₃SO₃‐κ¹O)(CH₃SO₃‐κ²O,O′)(triphos)], H[Ru(CH₃SO₃‐κ¹O)₃(triphos)], [RuH(CH₃SO₃‐κ¹O)(CO)(triphos)] and [RuH(CH₃SO₃‐κ²O,O′)(triphos)] have been characterised spectroscopically. The interactions between these various complexes and their relevance to the catalytic reactions are discussed.     

Disilicon Complexes with Two Hexacoordinate Si Atoms: Paddlewheel‐Shaped Isomers with (ClN4)Si?Si(S4Cl) and (ClN2S2)Si?Si(S2N2Cl) Skeletons

The reaction of 1‐methyl‐3‐trimethylsilylimidazoline‐2‐thione with hexachlorodisilane proceeds toward substitution of four of the disilane Cl atoms during the formation of disilicon complexes with two neighboring hexacoordinate Si atoms. The N,S‐bidentate methimazolide moieties adopt a buttressing role, thus forming paddlewheel‐shaped complexes of the type ClSi(μ‐mt)₄SiCl (mt=methimazolyl). Most interestingly, three isomers (i.e., with (ClN₄)Si? Si(S₄Cl), (ClN₃S)Si? Si(S₃NCl), and (ClN₂S₂)Si? Si(S₂N₂Cl) skeletons as so‐called (4,0), (3,1), and cis‐(2,2) paddlewheels) were detected in solution by using ²⁹Si NMR spectroscopic analysis. Two of these isomers could be isolated as crystalline solids, thus allowing their molecular structures to be analyzed by using X‐ray diffraction studies. In accord with time‐dependent NMR spectroscopy, computational analyses proved the cis‐(2,2) isomer with a (ClN₂S₂)Si? Si(S₂N₂Cl) skeleton to be the most stable. The compounds presented herein are the first examples of crystallographically evidenced disilicon complexes with two Si? Si‐bonded octahedrally coordinated Si atoms and representatives of the still scarcely explored class of Si coordination compounds with sulfur donor atoms.     

Functionalization of Metal–Organic Frameworks through the Postsynthetic Transformation of Olefin Side Groups

For the first time, the adaptability of the C?C double bond as a versatile precursor for the postsynthetic modification (PSM) of microporous materials was extensively investigated and evaluated. Therefore, an olefin‐tagged 4,4′‐bipyridine linker was synthesized and successfully introduced as pillar linker within a 9,10‐triptycenedicarboxylate (TDC) zinc paddle‐wheel metal–organic framework (MOF) through microwave‐assisted synthesis. Different reactions, predominately used in organic chemistry, were tested, leading to the development of new postsynthetic reactions for the functionalization of solid materials. The postsynthetic oxidation of the olefin side groups applying osmium tetroxide (OsO₄) as a catalyst led to the formation of a microporous material with free vicinal diol functionalities. The epoxidation with dimethyldioxirane (DMDO) enabled the synthesis of epoxy‐functionalized MOFs. In addition to that, reaction procedures for a postsynthetic hydroboration with borane dimethyl sulfide as well as a photoinduced thiol–ene click reaction with ethyl mercaptan were developed. For all of these PSMs, yields of more than 90 % were obtained, entirely maintaining the crystallinity of the MOFs. Since the direct introduction of the corresponding groups by means of pre‐synthetic approaches is hardly possible, these new PSMs are useful tools for the functionalization of porous solids towards applications such as selective adsorption, separation, and catalysis.     

Synthesis and Properties of Isobicyclo‐DNA

We present the synthesis of the isobicyclo‐DNA building blocks with the nucleobases A, C, G and T, as well as biophysical and biological properties of oligonucleotides derived thereof. The synthesis of the sugar part was achieved in 5 steps starting from a known intermediate of the tricyclo‐DNA synthesis. Dodecamers containing single isobicyclo‐thymidine incorporations, fully modified A‐ and T‐containing sequences, and fully modified oligonucleotides containing all four bases were synthesized and characterized. Isobicyclo‐DNA forms stable duplexes with natural nucleic acids with a pronounced preference for DNA over RNA as complements. The most stable duplexes, however, arise by self‐pairing. Isobicyclo‐DNA forms preferentially B‐DNA‐like duplexes with DNA and A‐like duplexes with complementary RNA as determined by circular dichroism (CD) spectroscopy. Self‐paired duplexes show a yet unknown structure, as judged from CD spectroscopy. Biochemical tests revealed that isobicyclo‐DNA is stable in fetal bovine serum and does not elicit RNaseH activity.     

Exploiting Aggregation To Achieve Phase Separation in Macrocyclization

The aggregation properties of poly(ethylene glycol) (PEG) can be exploited in organic synthesis to control dilution effects. Through the use of solvent mixtures containing PEG₄₀₀/MeOH, macrocyclization by Glaser–Hay coupling can be conducted at high concentrations. The origin of the selectivity has been studied by using surface tension measurements, UV spectroscopy, and chemical tagging and demonstrates the dependence of the yield and selectivity on the aggregation of PEG₄₀₀ and its ability to preferentially solubilize organic substrates, resulting in a phase separation from the catalyst system.     

A PEGylated Fluorescent Turn‐On Sensor for Detecting Fluoride Ions in Totally Aqueous Media and Its Imaging in Live Cells

Owing to the considerable significance of fluoride anions for health and environmental issues, it is of great importance to develop methods that can rapidly, sensitively and selectively detect the fluoride anion in aqueous media and biological samples. Herein, we demonstrate a robust fluorescent turn‐on sensor for detecting the fluoride ion in a totally aqueous solution. In this study, a biocompatible hydrophilic polymer poly(ethylene glycol) (PEG) is incorporated into the sensing system to ensure water solubility and to enhance biocompatibility. tert‐Butyldiphenylsilyl (TBDPS) groups were then covalently introduced onto the fluorescein moiety, which effectively quenched the fluorescence of the sensor. Upon addition of fluoride ion, the selective fluoride‐mediated cleavage of the Si? O bond leads to the recovery of the fluorescein moiety, resulting in a dramatic increase in fluorescence intensity under visible light excitation. The sensor is responsive and highly selective for the fluoride anion over other common anions; it also exhibits a very low detection limit of 19 ppb. In addition, this sensor is operative in some real samples such as running water, urine, and serum and can accurately detect fluoride ions in these samples. The cytotoxicity of the sensor was determined to be Grade I toxicity according to United States Pharmacopoeia and ISO 10993‐5, suggesting the very low cytotoxicity of the sensor. Moreover, it was found that the senor could be readily internalized by both HeLa and L929 cells and the sensor could be utilized to track fluoride level changes inside the cells.     

Longitudinal Relaxation Enhancement in 1H NMR Spectroscopy of Tissue Metabolites via Spectrally Selective Excitation

Nuclear magnetic resonance spectroscopy is governed by longitudinal (T₁) relaxation. For protein and nucleic acid experiments in solutions, it is well established that apparent T₁ values can be enhanced by selective excitation of targeted resonances. The present study explores such longitudinal relaxation enhancement (LRE) effects for molecules residing in biological tissues. The longitudinal relaxation recovery of tissue resonances positioned both down‐ and upfield of the water peak were measured by spectrally selective excitation/refocusing pulses, and compared with conventional water‐suppressed, broadband‐excited counterparts at 9.4 T. Marked LRE effects with up to threefold reductions in apparent T₁ values were observed as expected for resonances in the 6–9 ppm region; remarkably, statistically significant LRE effects were also found for several non‐exchanging metabolite resonances in the 1–4 ppm region, encompassing 30–50 % decreases in apparent T₁ values. These LRE effects suggest a novel means of increasing the sensitivity of tissue‐oriented experiments, and open new vistas to investigate the nature of interactions among metabolites, water and macromolecules at a molecular level.     

Structure and Biosynthesis of Xenoamicins from Entomopathogenic Xenorhabdus

During the search for novel natural products from entomopathogenic Xenorhabdus doucetiae DSM17909 and X. mauleonii DSM17908 novel peptides named xenoamicins were identified in addition to the already known antibiotics xenocoumacin and xenorhabdin. Xenoamicins are acylated tridecadepsipeptides consisting of mainly hydrophobic amino acids. The main derivative xenoamicin A ( 1 ) was isolated from X. mauleonii DSM17908, and its structure elucidated by detailed 1 D and 2 D NMR experiments. Detailed MS experiments, also in combination with labeling experiments, confirmed the determined structure and allowed structure elucidation of additional derivatives. Moreover, the xenoamicin biosynthesis gene cluster was identified and analyzed in X. doucetiae DSM17909, and its participation in xenoamicin biosynthesis was confirmed by mutagenesis. Advanced Marfey’s analysis of 1 showed that the absolute configuration of the amino acids is in agreement with the predicted stereochemistry deduced from the nonribosomal peptide synthetase XabABCD. Biological testing revealed activity of 1 against Plasmodium falciparum and other neglected tropical diseases but no antibacterial activity.     

Syntheses of 2‐Keto‐3‐deoxy‐D‐xylonate and 2‐Keto‐3‐deoxy‐L‐arabinonate as Stereochemical Probes for Demonstrating the Metabolic Promiscuity of Sulfolobus solfataricus Towards D‐Xylose and L‐Arabinose

Practical syntheses of 2‐keto‐3‐deoxy‐D ‐xylonate (D ‐KDX) and 2‐keto‐3‐deoxy‐L ‐arabinonate (L ‐KDA) that rely on reaction of the anion of ethyl 2‐[(tert‐butyldimethylsilyl)oxy]‐2‐(dimethoxy phosphoryl) acetate with enantiopure glyceraldehyde acetonide, followed by global deprotection of the resultant O‐silyl‐enol esters, have been developed. This has enabled us to confirm that a 2‐keto‐3‐deoxy‐D ‐gluconate aldolase from the archaeon Sulfolobus solfataricus demonstrates good activity for catalysis of the retro‐aldol cleavage of both these enantiomers to afford pyruvate and glycolaldehyde. The stereochemical promiscuity of this aldolase towards these enantiomeric aldol substrates confirms that this organism employs a metabolically promiscuous pathway to catabolise the C5‐sugars D ‐xylose and L ‐arabinose.