Organic & Biomolecular Chemistry (v.14, #26)

Front cover (6137-6137).

Inside front cover (6138-6138).

Contents list (6139-6146).

Asymmetric organocatalysis often operates under near ambient conditions, which means it is air and moisture compatible. However, in many examples water is indeed necessary for achieving excellent catalytic results. Ranging from the addition of small amounts of water to a reaction, to complex catalytic systems in the presence of water as the only reaction medium, this review offers an illustrative classification of the uses of water in asymmetric organocatalysis.

Dual modification of biomolecules by Antoine Maruani; Daniel A. Richards; Vijay Chudasama (6165-6178).
With the advent of novel bioorthogonal reactions and “click” chemistry, an increasing number of strategies for the single labelling of proteins and oligonucleotides have emerged. Whilst several methods exist for the site-selective introduction of a single chemical moiety, site-selective and bioorthogonal dual modification of biomolecules remains a challenge. The introduction of multiple modules enables a plethora of permutations and combinations and can generate a variety of bioconjuguates with many potential applications. From de novo approaches on oligomers to the post-translational functionalisation of proteins, this review will highlight the main strategies to dually modify biomolecules.

Cellular thermal shift and clickable chemical probe assays for the determination of drug-target engagement in live cells by Hua Xu; Ariamala Gopalsamy; Erik C. Hett; Shores Salter; Ann Aulabaugh; Robert E. Kyne; Betsy Pierce; Lyn H. Jones (6179-6183).
Proof of drug-target engagement in physiologically-relevant contexts is a key pillar of successful therapeutic target validation. We developed two orthogonal technologies, the cellular thermal shift assay (CETSA) and a covalent chemical probe reporter approach (harnessing sulfonyl fluoride tyrosine labeling and subsequent click chemistry) to measure the occupancy of the mRNA-decapping scavenger enzyme DcpS by a small molecule inhibitor in live cells. Enzyme affinity determined using isothermal dose response fingerprinting (ITDRFCETSA) and the concentration required to occupy 50% of the enzyme (OC50) using the chemical probe reporter assay were very similar. In this case, the chemical probe method worked well due to the long offset kinetics of the reversible inhibitor (determined using a fluorescent dye-tagged probe). This work suggests that CETSA could become the first choice assay to determine in-cell target engagement due to its simplicity.

Synthesis and regioselective functionalization of perhalogenated BODIPYs by Ning Zhao; Sunting Xuan; Brandon Byrd; Frank R. Fronczek; Kevin M. Smith; M. Graça H. Vicente (6184-6188).
Three perhalogenated BODIPYs (1b–3b), bearing chloro and bromo groups at all carbon positions, were synthesized and characterized. The reactivity of BODIPY 3b was investigated under Stille cross-coupling reactions, and single crystal X-ray analysis was used to confirm the regioselectivity of the reactions. Further substitution at the boron atom produced nona-functionalized BODIPYs 7a,b, which show 676 and 739 nm emissions with 91 and 100 nm Stokes shifts, respectively.

Chemoenzymatic synthesis and utilization of a SAM analog with an isomorphic nucleobase by C. Vranken; A. Fin; P. Tufar; J. Hofkens; M. D. Burkart; Y. Tor (6189-6192).
SalL, an enzyme that catalyzes the synthesis of SAM from l-methionine and 5′-chloro-5′-deoxyoadenosine, is shown to accept 5′-chloro-5′-deoxythienoadenosine as a substrate and facilitate the synthesis of a synthetic SAM analog with an unnatural nucleobase. This synthetic cofactor is demonstrated to replace SAM in the DNA methylation reaction with M.TaqI.

A highly enantioselective addition of alcohols to cyclic trifluoromethyl ketimines is developed catalyzed by quinine-thiourea, giving biologically interesting N,O-ketals in up to 99% yield and 96% ee.

Scalable procedure for the fragmentation of hydroperoxides mediated by copper and iron tetrafluoroborate salts by David Huang; Alexander W. Schuppe; Michael Z. Liang; Timothy R. Newhouse (6197-6200).
An improved protocol for the formal elimination of propene from organic substrates is reported. This process entails the ozonolytic conversion of an alkene to a methoxy hydroperoxide which undergoes fragmentation mediated by copper and iron. The use of soluble Cu(BF4)2 and Fe(BF4)2 results in reproducible results up to a 100 gram scale.

A Rh(iii)-catalyzed C–H activation/cyclization of oximes and alkenes for facile and regioselective access to isoquinolines has been developed. This protocol features mild reaction conditions and easily accessible starting materials, and has been applied to the concise synthesis of moxaverine. A kinetic isotope effect study was conducted and a plausible mechanism was proposed.

Arginine side-chain modification that occurs during copper-catalysed azide–alkyne click reactions resembles an advanced glycation end product by Anne C. Conibear; Karine Farbiarz; Rupert L. Mayer; Maria Matveenko; Hanspeter Kählig; Christian F. W. Becker (6205-6211).
Dehydroascorbate is a by-product of copper-catalysed azide–alkyne click (CuAAC) reactions and also forms advanced glycation end products (AGEs) in tissues undergoing oxidative stress. Here we isolate and characterize an arginine–dehydroascorbate adduct formed during CuAAC reactions, investigate strategies for preventing its formation, and propose its biological relevance as an AGE.

Gold-catalyzed Hosomi–Sakurai type reaction for the total synthesis of herboxidiene by Barla Thirupathi; Debendra K. Mohapatra (6212-6224).
Total synthesis of herboxidiene/GEX1A/TAN-1609 has been accomplished in the 22 longest linear sequences starting from 2-butyne-1,4-diol following our recently developed gold-catalyzed Hosomi–Sakurai type of reaction on lactols with allyltrimethyl silane and Stille cross coupling to assemble the advanced fragment. The synthesis of the C10–C19 fragment was accomplished by means of Sharpless epoxidation and asymmetric alkylation reactions starting from (R)-methyl lactate.

The first synthesis of a labdane-type diterpenoid isolated from Isodon yuennanensis was achieved in fourteen steps from commercially available starting material, (+)-sclareolide. The synthesis features the Barton nitrite ester reaction to introduce an oxime at the angular methyl group and the Jones oxidation to construct the lactone segment. By comparison of the optical rotation of our synthetic sample and the natural sample, the absolute stereochemistry of the natural diterpenoid has been determined.

Synthesis and in vitro bone cell activity of analogues of the cyclohexapeptide dianthin G by Zaid Amso; Renata Kowalczyk; Young-Eun Park; Maureen Watson; Jian-ming Lin; David S. Musson; Jillian Cornish; Margaret A. Brimble (6231-6243).
The cyclohexapeptide natural product dianthin G promotes osteoblast (bone-forming cell) proliferation in vitro at nanomolar concentrations, and is therefore considered a promising candidate for the treatment of osteoporosis. An Nα-methyl amide bond scan of dianthin G was performed to probe the effect of modifying amide bonds on osteoblast proliferation. In addition, to provide greater structural diversity, a series of dicarba dianthin G analogues was synthesised using ring closing metathesis. Dianthin G and one novel dicarba analogue increased the number of human osteoblasts and importantly they did not increase osteoclast (bone-resorbing cell) differentiation in bone marrow cells.

Labelling of endogenous target protein via N–S acyl transfer-mediated activation of N-sulfanylethylanilide by Masaya Denda; Takuya Morisaki; Taiki Kohiki; Jun Yamamoto; Kohei Sato; Ikuko Sagawa; Tsubasa Inokuma; Youichi Sato; Aiko Yamauchi; Akira Shigenaga; Akira Otaka (6244-6251).
The ligand-dependent incorporation of a reporter molecule (e.g., fluorescence dye or biotin) onto a endogenous target protein has emerged as an important strategy for elucidating protein function using various affinity-based labelling reagents consisting of reporter, ligand and reactive units. Conventional labelling reagents generally use a weakly activated reactive unit, which can result in the non-specific labelling of proteins in a ligand-independent manner. In this context, the activation of a labelling reagent through a targeted protein–ligand interaction could potentially overcome the problems associated with conventional affinity-based labelling reagents. We hypothesized that this type of protein–ligand-interaction-mediated activation could be accomplished using N-sulfanylethylanilide (SEAlide) as the reactive unit in the labelling reagent. Electrophilically unreactive amide-type SEAlide can be activated by its conversion to the corresponding active thioester in the presence of a phosphate salt, which can act as an acid–base catalyst. It has been suggested that protein surfaces consisting of hydrophilic residues such as amino, carboxyl and imidazole groups could function as acid–base catalysts. We therefore envisioned that a SEAlide-based labelling reagent (SEAL) bearing SEAlide as a reactive unit could be activated through the binding of the SEAL with a target protein. Several SEALs were readily prepared in this study using standard 9-fluorenylmethyloxycarbonyl (Fmoc)-based solid-phase protocols. These SEAL systems were subsequently applied to the ligand-dependent labelling of human carbonic anhydrase (hCA) and cyclooxyganese 1. Although we have not yet obtained any direct evidence for the target protein-mediated activation of the SEAlide unit, our results for the reaction of these SEALs with hCA1 or butylamine indirectly support our hypothesis. The SEALs reported in this study represent valuable new entries to the field of affinity-based labelling reagents and are expected to show great utility in protein labelling.

UGT74B1 from Arabidopsis thaliana as a versatile biocatalyst for the synthesis of desulfoglycosinolates by Sami Marroun; Sabine Montaut; Stéphanie Marquès; Pierre Lafite; Gaël Coadou; Patrick Rollin; Guillaume Jousset; Marie Schuler; Arnaud Tatibouët; Hassan Oulyadi; Richard Daniellou (6252-6261).
Thioglycosides, even if rare in Nature, have gained increased interest for their biological properties. Chemical syntheses of this class of compounds have been largely studied but little has been reported on their biosynthesis. Herein, combining experiments from the different fields of enzymology, bioorganic chemistry and molecular modeling, we wish to demonstrate the versatility of the glucosyltransferase UGT74B1 and its synthetic potency for the preparation of a variety of natural and unnatural desulfoglycosinolates.

Chemoselective modifications for the traceless ligation of thioamide-containing peptides and proteins by Yanxin J. Wang; D. Miklos Szantai-Kis; E. James Petersson (6262-6269).
Thioamides are single-atom substitutions of canonical amide bonds, and have been proven to be versatile and minimally perturbing probes in protein folding studies. Previously, our group showed that thioamides can be incorporated into proteins by native chemical ligation (NCL) with Cys as a ligation handle. In this study, we report the expansion of this strategy into non-Cys ligation sites, utilizing radical initiated desulfurization to “erase” the side chain thiol after ligation. The reaction exhibited high chemoselectivity against thioamides, which can be further enhanced with thioacetamide as a sacrificial scavenger. As a proof-of-concept example, we demonstrated the incorporation of a thioamide probe into a 56 amino acid protein, the B1 domain of Protein G (GB1). Finally, we showed that the method can be extended to β-thiol amino acid analogs and selenocysteine.

The syntheses of β,β-diaryl aryl propiophenones have been realized via palladium-catalyzed domino reactions of dimethyl amino functionalized enaminones and aryl boronic acids. This is the first example of transition metal-catalyzed enaminone C–N bond conversion for the generation of a new C–C(aryl) structure.

Stable-isotope-labeled precursors were used to establish the biosynthetic pathway leading from β-alanine towards isoxazolin-5-one glucoside 1 and its 3-nitropropanoate (3-NPA) ester 2 in Chrysomelina larvae. Both structural elements originate from sequestered plant-derived β-alanine or from propanoyl-CoA that is derived from the degradation of some essential amino acids, e.g. valine. β-Alanine is converted into 3-NPA and isoxazolinone 5 by consecutive oxidations of the amino group of β-Ala. Substituting the diphospho group of α-UDP-glucose with 5 generates the isoxazolin-5-one glucoside 1, which serves in the circulating hemolymph of the larva as a platform for esterification with 3-nitropropanoyl-CoA. The pathway was validated with larvae of Phaedon cochleariae, Chrysomela populi as well as Gastrophysa viridula.

pH-Dependent membrane lysis by using melittin-inspired designed peptides by A. Kashiwada; M. Mizuno; J. Hashimoto (6281-6288).
We developed a membrane-lytic peptide (LP) having 26 amino acid residues composed of a helix-promoting hydrophobic segment (Leu–Ala repetitive sequence) and a cationic segment from melittin. In the presence of liposomes, LP interacts with liposomal surfaces to form a hydrophobic helix in the lipid bilayer in a wide pH range. In order to provide LP with a weakly acidic (endosomal) pH-controlled membrane-lytic activity, we have designed an LPE peptide series (a typical peptide, LPE3-1) with a hydrophobic segment in which Leu (L) residues are replaced by acidic Glu (E) residues. To analyze the pH-selective membrane-lytic activity of the designed peptides, both calcein leakage and membrane accessibility assays were performed. In the case of membrane disruption induced by the active pore formation, the incorporated calcein would leak from the liposomes and simultaneously the aqueous solution in the membrane surrounding would be accessible to the liposome interior at pH 5.0. The assays in the presence of LPE3-1 indicated no significant leakage or accessibility at pH 7.4, but a typical leakage and some accessibility to liposomes were positively observed at pH 5.0. In order to estimate whether the weakly acidic pH-controlled lytic activity is due to a secondary structural change of the hydrophobic segment of LPE3-1 in the liposome membrane, we have measured circular dichroism spectra. In the presence of liposomes, the minimum showing the characteristic helical structure was observed at 222 nm only under weakly acidic conditions. This pH dependence is in good agreement with the results from the leakage and accessibility assays. The pH-dependent membrane disruption properties of LPE3-1 may open a new avenue to gain insight into the interaction between peptides and lipids for the development of efficient drug/gene delivery systems.

Enhancement of the properties of a drug by mono-deuteriation: reduction of acid-catalysed formation of a gut-motilide enol ether from 8-deuterio-erythromycin B by Pranab K. Bhadra; Abdolreza Hassanzadeh; Biljana Arsic; David G. Allison; Gareth A. Morris; Jill Barber (6289-6296).
Erythromycin B is structurally very similar to erythromycin A, and also shares its clinically important antibacterial activity. Its potential advantage is that it is much more stable to acid. Both compounds are susceptible to 6–9-enol ether formation, involving loss of a proton from C-8. The enol ethers lack antibacterial activity and can give rise to unpleasant gut motilide side-effects. Our previous work on degradation kinetics revealed that the formation of erythromycin B enol ether from erythromycin B is subject to a large deuterium isotope effect. We therefore synthesized 8-d-erythromycin B (in 87% yield) in the hope that acid-catalysed enol ether formation would be reduced, relative to erythromycin B. In a range of microbiological and biochemical assays, deuteriation did not appear to compromise the efficacy of the drug. Degradation studies showed, however, that incorporation of deuterium into erythromycin B reduces (though does not completely suppress) enol ether formation, providing the possibility of using a facile mono-deuteriation to reduce the gut motilide side-effects of the drug.

An efficient copper-catalyzed reaction for the synthesis of benzisothiazol-3(2H)-ones has been developed, starting from easily available 2-halobenzamides and carbon disulfide, which gave the corresponding target products in 30–89% yield for 25 examples. The reaction proceeds via a consecutive process with S–C bond and S–N bond formation.

Quinolone-1-(2H)-ones as hedgehog signalling pathway inhibitors by Trieu N. Trinh; Eileen A. McLaughlin; Mohammed K. Abdel-Hamid; Christopher P. Gordon; Ilana R. Bernstein; Victoria Pye; Peter Cossar; Jennette A. Sakoff; Adam McCluskey (6304-6315).
A series of quinolone-2-(1H)-ones derived from the Ugi-Knoevenagel three- and four-component reaction were prepared exhibiting low micromolar cytotoxicity against a panel of eight human cancer cell lines known to possess the Hedgehog Signalling Pathway (HSP) components, as well as the seminoma TCAM-2 cell line. A focused SAR study was conducted and revealed core characteristics of the quinolone-2-(1H)-ones required for cytotoxicity. These requirements included a C3-tethered indole moiety, an indole C5-methyl moiety, an aliphatic tail or an ester, as well as an additional aromatic moiety. Further investigation in the SAG-activated Shh-LIGHT2 cell line with the most active analogues: 2-(3-cyano-2-oxo-4-phenylquinolin-1(2H)-yl)-2-(1-methyl-1H-indol-3-yl)-N-(pentan-2-yl)acetamide (5), 2-(3-cyano-2-oxo-4-phenylquinolin-1(2H)-yl)-2-(5-methyl-1H-indol-3-yl)-N-(pentan-2-yl)acetamide (23) and ethyl (2-(3-cyano-2-oxo-4-phenylquinolin-1(2H)-yl)-2-(5-methyl-1H-indol-3-yl)acetyl)glycinate (24) demonstrated a down regulation of the HSP via a reduction in Gli expression, and in the mRNA levels of Ptch1 and Gli2. Analogues 5, 23 and 24 returned in cell inhibition values of 11.6, 2.9 and 3.1 μM, respectively, making this new HSP-inhibitor pharmacophore amongst the most potent non-Smo targeted inhibitors thus far reported.

Substituted racemic lactols or cyclic hemiaminals were directly used as nucleophiles in enamine-based asymmetric amination reactions to access enantioenriched α-amino lactones or lactams via a one-pot sequence. The desired products, which are very important building blocks in organic synthesis but difficult to be prepared in the optically enriched form, could be afforded with two stereogenic centers in high yields with excellent enantioselectivities. Moreover, starting from the racemic precursors and catalyzed by the enantiomeric pair of the catalyst, all possible stereoisomeric products were discretely provided only after simple column chromatography. Additionally, this protocol provides facile access to several novel bicyclic carbamates, and such drug-like heterocyclic compounds should be potentially useful in medicinal chemistry.

A metal-free, TBHP-promoted economical route is developed via the sp2 C–H bond functionalization strategy for the synthesis of indenoquinolinones, 4-azafluorenones and fluorenones. Reactions provided excellent yield of the products under mild conditions. We have successfully synthesized 11H-indeno[1,2-b]quinolin-11-one, an antibacterial agent, in excellent yields.

Organocatalytic asymmetric Michael addition of α-alkylidene succinimides to nitrostyrenes by Bo-Liang Zhao; Dongxiang Zhang; Lei Liu; Da-Ming Du (6337-6345).
A bifunctional squaramide-catalyzed asymmetric Michael addition reaction of α-alkylidene succinimides with nitrostyrenes and a nitrodiene has been developed. This organocatalytic asymmetric reaction provides easy access to functionalized succinimides with two contiguous stereocenters with a broad substrate scope. The desired succinimide derivatives were obtained in good to excellent yields (up to 98%) with high to excellent diastereoselectivities (up to >99 : 1 dr) and excellent enantioselectivities (up to 99% ee). This protocol provides a straightforward entry to functionalized chiral succinimide derivatives from simple starting materials.

Functional lipids based on [12]aneN3 and naphthalimide as efficient non-viral gene vectors by Yong-Guang Gao; Uzair Alam; Quan Tang; You-Di Shi; Ying Zhang; Ruibing Wang; Zhong-Lin Lu (6346-6354).
Small organic non-viral gene vectors with the structural combinations of (aliphatic chain)–naphthalimide–[12]aneN3 (11a, b) and naphthalimide–(aliphatic chain)–[12]aneN3 (12a–c) were synthesized and fully characterized. Agarose gel electrophoresis experiments indicated that the first type of compounds, 11a and 11b, could completely retard DNA at the concentration of 5 μM in the presence of DOPE. Within the second type of compounds, 12c with the decane chain showed a complete retardation of DNA at the concentration of 20 μM, whereas 12a and 12b with the ethyl and hexyl chains could not retard DNA effectively. Dynamic light scattering measurements indicated that compounds 11a, 11b and 12b, 12c condensed DNA into nanoparticles with the size in the range of 60–160 nm. Due to the strong fluorescence of 11a and 11b, the distribution of lipids/DNA complexes and the process of DNA release from the lipids were clearly observed via cellular uptake experiments. On the other hand, the non-fluorescent 12a–c enabled the EB exclusion assay to afford the binding constants of 4.88 × 106 M−1 (12a), 4.18 × 106 M−1 (12b) and 3.39 × 106 M−1 (12c), respectively. The MTT assay revealed that both types of compounds have low cytotoxicity. Non-fluorescent 12c was successfully applied in the eGFP expression experiments in A549 cells and showed stronger green fluorescence emission than that of lipofectamine 2000. Quantitative transfection experiments through the luciferase assay further revealed that compounds 11a, 11b and 12c can act as non-viral gene vectors in different cell lines. Among them, 12c gave the highest transfection efficiency in HeLa cells, which was about 2 times that offered by lipofectamine 2000. This work clearly demonstrated that the right combination of different functional units and long aliphatic linkers will likely promote gene delivery and transfection efficiency.

Back cover (6355-6356).