Palladium(0)-Catalyzed Anti-Selective Addition-Cyclizations of Alkynyl Electrophiles.

Palladium(0)/monophosphine complexes catalyze anti-selective alkylative, arylative, and alkynylative cyclizations of alkynyl electrophiles with organometallic reagents. The remarkable anti-selectivity results from novel oxidative addition, that is, the nucleophilic attack of electron-rich palladium(0) on the electrophile across the alkyne followed by transmetalation and reductive elimination ("anti-Wacker"-type cyclization). With regard to 5-alkynals, triphenylphosphine (PPh3 )-ligated palladium(0) catalyzes the cyclization of terminal alkynes and conjugated alkenyl- or alkynyl-substituted ones to afford 2-cyclohexen-1-ol and 2-alkylidene-cyclopentanol derivatives, respectively. For 6-alkyl- or 6-aryl-5-alkynals, the cyclization does not proceed with the palladium/PPh3 catalyst; however, it does proceed with palladium/tricyclohexylphosphine (PCy3 ), to yield the former products predominantly. Remarkably, the latter catalyst completely switches the regioselectivity in the cyclization of the conjugated diyne-aldehydes. Notably, palladium/PPh3 -catalyzed cyclizations also proceed with other organometallics or even without them.

Palladium(0)-Catalyzed Anti-Selective Addition-Cyclizations of Alkynyl Electrophiles.

Invited for the cover of this issue is the group of Hirokazu Tsukamoto at Tohoku University (current affiliation: Yokohama University of Pharmacy). The image depicts anti-selective arylative cyclization reactions of alkynyl aldehydes with arylboronic acids under palladium catalysis in methanol to afford endo- and exo-cyclic products. Read the full text of the article at 10.1002/chem.202203068.

Scalable Total Syntheses and Structure-Activity Relationships of Haouamines†A, B, and Their Derivatives as Stable Formate Salts.

Haouamines A, B, and their derivatives were synthesized via Suzuki-Miyaura coupling and three key cyclization reactions as follows: the newly developed palladium(0)-catalyzed arylative cyclization of phenylalanine-derived alkyne-aldehydes with 2-bromoarylboronic acid (an "anti-Wacker"-type cyclization); BF3 ⋅OEt2 -promoted Friedel-Crafts-type cyclization of symmetrical electron-rich aromatic rings adjacent to a tertiary allylic alcohol leading to the indeno-tetrahydropyridine skeleton; and (cyanomethyl)trimethylphosphonium iodide-mediated macrocyclization of amino alcohols to afford aza-paracyclophane precursors. The palladium-catalyzed reduction of mono- and di-triflate intermediates in the later stages enabled the alteration of both the position and number of hydroxyl groups on the C-ring. The instability of haouamine B was dramatically improved by salt formation with formic acid. An unambiguous evaluation of the cytotoxicity of the prepared haouamine derivative formates with and without hydroxyl groups at different positions on the C-ring indicated that the catechol structure in haouamine B produced weak cytotoxicity.

Total Synthesis of Spiromamakone A and Structure Revision of Spiropreussione A.

Spiromamakone A is a racemic natural product having a naphthyl acetal group on a spiro[4,4]nonadiene skeleton. Its total synthesis was achieved by double oxa-Michael addition of 1,8-dihydroxynaphthalene to 2-(1-bromoalkylidene)-4-isopropoxy-4-cyclopentene-1,3-dione, which was prepared by palladium(II)-catalyzed ring expansion of 4-(1-alkynyl)-4-hydroxy-3-isopropoxy-2-cyclobuten-1-one, and a subsequent intramolecular aldol reaction. The synthesis using optically active intermediates enabled identification of the racemization step of spiromamakone A and revealed that spiromamakone A and spiropreussione A are identical; the latter had been reported as a constitutional isomer of the other.

Palladium(II)-Catalyzed Annulation of Alkynes with 2-(Cyanomethyl)phenylboronates Leading to 3,4-Disubstituted 2-Naphthalenamines.

1,2-Bis(diphenylphosphino)ethane (dppe)-ligated palladium(II) complexes catalyze the annulation of internal alkynes with 2-(cyanomethyl)phenylboronates to provide 3,4-disubstituted-2-naphthalenamines in good yields. The annulation reaction proceeds under mild and neutral conditions and requires methanol as an essential solvent. In addition to symmetrical alkynes, unsymmetrical alkynes substituted by aryl, alkyl, and alkynyl groups participate in the annulation to afford the corresponding 2-naphthalenamines with electron-withdrawing sp(2)- and sp-carbons preferentially located at the C-3 position. Substituents including an alkyl or alkoxy group on the cyanomethyl moiety and a halogen atom on the benzene ring in the boronates are compatible with the reaction conditions. The annulation proceeds through the transmetalation of the palladium(II) complexes with the boronates and alkyne insertion followed by nucleophilic addition of the generated alkenylpalladium(II) species to the intramolecular cyano group. Stoichiometric reactions revealed that the methanol solvent was effective for both transmetalation and catalyst regeneration.

Total Synthesis and Structure Determination of JBIR-108-A 2-Hydroxy-2-(1-hydroxyethyl)-2,3-dihydro-3(2H)-furanone Isolated from Streptomyces gramineus IR087Pi-4.

The planar and stereostructures of JBIR-108 isolated from Streptomyces gramineus IR087Pi-4 were determined partly by spectral analysis, and these structural assignments were confirmed and completed by the total synthesis of both 1-epimers. The key stereocenters in JBIR-108 were constructed via a Corey-Bakshi-Shibata (CBS) reduction (C-1), vinylogous Mukaiyama aldol reaction (C-7), and Brown crotylation (C-14 and C-15). Although it was difficult to determine the stereochemistries at the C-1 and C-7 positions in the natural product using the modified Mosher's method, the synthesis of two possible C-1 diastereomers enabled the identification of the configurations at the hitherto unknown stereocenters.

Detection of lipid-linked peptidoglycan precursors by exploiting an unexpected transpeptidase reaction.

Penicillin-binding proteins (PBPs) are involved in the synthesis and remodeling of bacterial peptidoglycan (PG). Staphylococcus aureus expresses four PBPs. Genetic studies in S. aureus have implicated PBP4 in the formation of highly cross-linked PG, but biochemical studies have not reached a consensus on its primary enzymatic activity. Using synthetic Lipid II, we show here that PBP4 preferentially acts as a transpeptidase (TP) in vitro. Moreover, it is the PBP primarily responsible for incorporating exogenous d-amino acids into cellular PG, implying that it also has TP activity in vivo. Notably, PBP4 efficiently exchanges d-amino acids not only into PG polymers but also into the PG monomers Lipid I and Lipid II. This is the first demonstration that any TP domain of a PBP can activate the PG monomer building blocks. Exploiting the promiscuous TP activity of PBP4, we developed a simple, highly sensitive assay to detect cellular pools of lipid-linked PG precursors, which are of notoriously low abundance. This method, which addresses a longstanding problem, is useful for assessing how genetic and pharmacological perturbations affect precursor levels, and may facilitate studies to elucidate antibiotic mechanism of action.

Reconstitution of peptidoglycan cross-linking leads to improved fluorescent probes of cell wall synthesis.

The peptidoglycan precursor, Lipid II, produced in the model Gram-positive bacterium Bacillus subtilis differs from Lipid II found in Gram-negative bacteria such as Escherichia coli by a single amidation on the peptide side chain. How this difference affects the cross-linking activity of penicillin-binding proteins (PBPs) that assemble peptidoglycan in cells has not been investigated because B. subtilis Lipid II was not previously available. Here we report the synthesis of B. subtilis Lipid II and its use by purified B. subtilis PBP1 and E. coli PBP1A. While enzymes from both organisms assembled B. subtilis Lipid II into glycan strands, only the B. subtilis enzyme cross-linked the strands. Furthermore, B. subtilis PBP1 catalyzed the exchange of both D-amino acids and D-amino carboxamides into nascent peptidoglycan, but the E. coli enzyme only exchanged D-amino acids. We exploited these observations to design a fluorescent D-amino carboxamide probe to label B. subtilis PG in vivo and found that this probe labels the cell wall dramatically better than existing reagents.

Hg2+-trapping beads: Hg2+-specific recognition through thymine-Hg(II)-thymine base pairing.

Mercury pollution poses a severe threat to human health. To remove Hg(2+) from contaminated water, we synthesized Hg(2+)-trapping beads that include oligo-thymidine functionalities that can form thymine-Hg(II)-thymine base pairs on the solid support. The beads can selectively trap Hg(2+) even in the presence of other metal cations. More interestingly, Hg(2+)-trapping efficiency was higher in the presence of the co-existing cations. Thus, the developed Hg(2+)-trapping beads can capture Hg(2+) without affecting the mineral balance of water so much. The Hg(2+)-trapping beads presented here show promise for removing Hg(2+) from environmental water.

Tuning the moenomycin pharmacophore to enable discovery of bacterial cell wall synthesis inhibitors.

New antibiotic drugs need to be identified to address rapidly developing resistance of bacterial pathogens to common antibiotics. The natural antibiotic moenomycin A is the prototype for compounds that bind to bacterial peptidoglycan glycosyltransferases (PGTs) and inhibit cell wall biosynthesis, but it cannot be used as a drug. Here we report the chemoenzymatic synthesis of a fluorescently labeled, truncated analogue of moenomycin based on the minimal pharmacophore. This probe, which has optimized enzyme binding properties compared to moenomycin, was designed to identify low-micromolar inhibitors that bind to conserved features in PGT active sites. We demonstrate its use in displacement assays using PGTs from S. aureus, E. faecalis, and E. coli. 110,000 compounds were screened against S. aureus SgtB, and we identified a non-carbohydrate based compound that binds to all PGTs tested. We also show that the compound inhibits in vitro formation of peptidoglycan chains by several different PGTs. Thus, this assay enables the identification of small molecules that target PGT active sites, and may provide lead compounds for development of new antibiotics.

Forming cross-linked peptidoglycan from synthetic gram-negative Lipid II.

The bacterial cell wall precursor, Lipid II, has a highly conserved structure among different organisms except for differences in the amino acid sequence of the peptide side chain. Here, we report an efficient and flexible synthesis of the canonical Lipid II precursor required for the assembly of Gram-negative peptidoglycan (PG). We use a rapid LC/MS assay to analyze PG glycosyltransfer (PGT) and transpeptidase (TP) activities of Escherichia coli penicillin binding proteins PBP1A and PBP1B and show that the native m-DAP residue in the peptide side chain of Lipid II is required in order for TP-catalyzed peptide cross-linking to occur in vitro. Comparison of PG produced from synthetic canonical E. coli Lipid II with PG isolated from E. coli cells demonstrates that we can produce PG in vitro that resembles native structure. This work provides the tools necessary for reconstituting cell wall synthesis, an essential cellular process and major antibiotic target, in a purified system.

Transpeptidase-mediated incorporation of D-amino acids into bacterial peptidoglycan.

The ß-lactams are the most important class of antibiotics in clinical use. Their lethal targets are the transpeptidase domains of penicillin binding proteins (PBPs), which catalyze the cross-linking of bacterial peptidoglycan (PG) during cell wall synthesis. The transpeptidation reaction occurs in two steps, the first being formation of a covalent enzyme intermediate and the second involving attack of an amine on this intermediate. Here we use defined PG substrates to dissect the individual steps catalyzed by a purified E. coli transpeptidase. We demonstrate that this transpeptidase accepts a set of structurally diverse D-amino acid substrates and incorporates them into PG fragments. These results provide new information on donor and acceptor requirements as well as a mechanistic basis for previous observations that noncanonical D-amino acids can be introduced into the bacterial cell wall.

Primer preactivation of peptidoglycan polymerases.

Peptidoglycan glycosyltransferases are highly conserved bacterial enzymes that catalyze glycan strand polymerization to build the cell wall. Because the cell wall is essential for bacterial cell survival, these glycosyltransferases are potential antibiotic targets, but a detailed understanding of their mechanisms is lacking. Here we show that a synthetic peptidoglycan fragment that mimics the elongating polymer chain activates peptidoglycan glycosyltransferases by bypassing the rate-limiting initiation step.

N-methylimidazolium chloride-catalyzed pyrophosphate formation: application to the synthesis of Lipid I and NDP-sugar donors.

N-Methylimidazolium chloride is found to catalyze a coupling reaction between monophosphates and activated phosphorous-nitrogen intermediates such as a phosphorimidazolide and phosphoromorpholidate to form biologically important unsymmetrical pyrophosphate diesters. The catalyst is much more active, cheaper, and less explosive than 1H-tetrazole, known as the best catalyst for the pyrophosphate formation over a decade. The mild and neutral reaction conditions are compatible with allylic pyrophosphate formation in Lipid I syntheisis. (31)P NMR experiments suggest that the catalyst acts not only as an acid but also as a nucleophile to form cationic and electrophilic phosphor-N-methylimidazolide intermediates in the pyrophosphate formation.

Modular synthesis of diphospholipid oligosaccharide fragments of the bacterial cell wall and their use to study the mechanism of moenomycin and other antibiotics.

We present a flexible, modular route to GlcNAc-MurNAc-oligosaccharides that can be readily converted into peptidoglycan (PG) fragments to serve as reagents for the study of bacterial enzymes that are targets for antibiotics. Demonstrating the utility of these synthetic PG substrates, we show that the tetrasaccharide substrate lipid IV (3), but not the disaccharide substrate lipid II (2), significantly increases the concentration of moenomycin A required to inhibit a prototypical PG-glycosyltransferase (PGT). These results imply that lipid IV and moenomycin A bind to the same site on the enzyme. We also show the moenomycin A inhibits the formation of elongated polysaccharide product but does not affect length distribution. We conclude that moenomycin A blocks PG-strand initiation rather than elongation or chain termination. Synthetic access to diphospholipid oligosaccharides will enable further studies of bacterial cell wall synthesis with the long-term goal of identifying novel antibiotics.

Palladium(0)-Lithium Iodide Cocatalyzed Asymmetric Hydroalkylation of Conjugated Enynes with Pronucleophiles Leading to 1,3-Disubstituted Allenes.

Axially chiral 1,3-disubstituted allenes were synthesized via hydroalkylation of alkyl- or aryl-substituted conjugated enynes (readily prepared via a Sonogashira reaction) with pronucleophiles such as dimethyl malonate under the cocatalysis of DTBM-SEGPHOS-ligated palladium and lithium iodide. Although the palladium catalyst ligated with (S)-DTBM-SEGPHOS prefers the formation of (R)-1,3-disubstituted allenes, lithium iodide recovers and increases the intrinsic selectivity producing (S)-allenes by promoting the isomerization of the exo-alkylidene-π-allylpalladium intermediate prior to the nucleophilic substitution step.

A new five-membered ring forming process based on palladium(0)-catalyzed arylative cyclization of allenyl enones.

A palladium(0)/monophosphine catalyst promotes a novel arylative cyclization reaction of C1-, C2-, and C3-tethered allenyl enones with arylboronic acids to produce five-membered ring containing products. The regioselectivity of the process, associated with aryl group introduction into the allene moiety, depends on the length of the tether. This finding suggests that the cyclization reaction does not proceed through a carbopalladation pathway but rather via a route involving palladacycle-forming or "anti-Wacker"-type oxidative addition to the Pd(0) catalyst.

Enantioselective arylative cyclization of allenyl aldehydes with arylboronic acids under Pd(II)-diphosphine catalysis.

A Pd(OAc)2-SEGPHOS combination catalyzes the first enantioselective arylative cyclization of allenyl aldehydes with arylboronic acids to provide cis-fused five- and six-membered cyclic homoallylic alcohols. The excellent diastereo- and enantioselectivity and the fact that the reaction proceeds at room temperature in the absence of any additives make the process highly practical.

Palladium(0)-catalyzed direct cross-coupling reaction of allylic alcohols with aryl- and alkenylboronic acids.

Allylic alcohols can be used directly for the palladium(0)-catalyzed allylation of aryl- and alkenylboronic acids with a wide variety of functional groups. A triphenylphosphine-ligated palladium catalyst turns out to be most effective for the cross-coupling reaction and its low loading (less than 1 mol%) leads to formation of the coupling product in high yield. The Lewis acidity of the organoboron reagents and poor leaving ability (high basicity) of the hydroxyl group are essential for the cross-coupling reaction. The reaction process is atom-economical and environmentally benign, because it needs neither preparation of allyl halides and esters nor addition of stoichiometric amounts of a base. Furthermore, allylic alcohols containing another unsaturated carbon-carbon bond undergo arylative cyclization reactions leading to cyclopentane formation.

Development of new palladium(0)-catalyzed reactions based on novel oxidative addition mode.

We have developed palladium(0)/monophosphine-catalyzed trans-selective arylative, alkenylative, alkylative, and alkynylative cyclization reactions of alkyne-aldehydes and -ketones with organoboron reagents. These reactions afford six-membered allylic alcohols with endo tri- or tetra-substituted olefin groups and/or five-membered counterparts with exo olefin groups. The ratios of these products are dramatically affected by alkyne substituents as well as the phosphine ligand. The remarkable trans selectivity of the process results from the novel reaction mechanism involving 'anti-Wacker'-type oxidative addition. Although the cyclization reactions are influenced by the length of the tether between the alkyne and carbonyl group, they can be applied to a multi-component synthesis of biologically important indenes bearing three substituent groups at 1, 2, 3-positions from available o-ethynylbenzaldehyde derivatives. A two-component coupling reaction in methanol provides 1H-indenols, while a three-component reaction involving secondary aliphatic amines as the third component in DMF affords 1H-indenamines. This method allows combinatorial preparation of unsymmetrically substituted 1H-indenes that cannot be prepared via previous synthetic routes. The same catalytic system can also transform allene-carbonyl compounds into 3-cyclohexenols and -cyclopentenols with alkyl, aryl, alkenyl, alkynyl, and boryl groups at C-3. Microwave irradiation efficiently increases not only the reaction rate but also the product yield by suppressing formation of hydroarylation byproducts. Cyclization of optically active 1,3-disubstituted allene-aldehyde reveals that the reaction proceeds through not carbopalladation but 'anti-Wacker'-type oxidative addition.