Synthetic studies with the brevicidine and laterocidine lipopeptide antibiotics including analogues with enhanced properties and in vivo efficacy

Brevicidine and laterocidine are two recently discovered lipopeptide antibiotics with promising antibacterial activity. Possessing a macrocyclic core, multiple positive charges, and a lipidated N-terminus, these lipopeptides exhibit potent and selective activity against Gram-negative pathogens, including polymyxin-resistant isolates. Given the low amounts of brevicidine and laterocidine accessible by fermentation of the producing microorganisms, synthetic routes to these lipopeptides present an attractive alternative. We here report the convenient solid-phase syntheses of both brevicidine and laterocidine and confirm their potent anti-Gram-negative activities. The synthetic routes developed also provide convenient access to novel structural analogues of both brevicidine and laterocidine that display improved hydrolytic stability while maintaining potent antibacterial activity in both in vitro assays and in vivo infection models.

Convenient solid-phase approaches are described for the synthesis of brevicidine and laterocidine. Also reported are novel analogues including a laterocidine variant with enhanced hydrolytic stability and potent in vivo antibacterial activity.     

Synthesis of unsymmetrically tetrasubstituted pyrroles and studies of AIEE in pyrrolo[1,2-a]pyrimidine derivatives

Pyrroles are among the most important heterocycles in pharmaceuticals and agrochemicals. Construction of pyrrole scaffolds with different substituents and a free NH group, however, is challenging. Herein, a metal-free method for the synthesis of unsymmetrically tetrasubstituted NH-pyrroles using a consecutive chemoselective double cyanation is reported. The desired pyrroles were obtained with yields up to 99% and good functional group tolerance. Mechanistic studies identified a reaction mechanism that features a subtle sequence of first cyano-addition and migration, followed by cyano-addition and aromatization to afford the pyrrole skeleton. Pyrrolo[1,2-a]pyrimidines are synthesized as the synthetic applications of NH-pyrroles, and these pyrrolo[1,2-a]pyrimidines exhibit unpredicted time-dependent aggregation-induced emission enhancement (AIEE) properties.

A novel method for the challenging synthesis of unsymmetrically tetrasubstituted NH-pyrroles from chalcone derivatives is reported. The pyrrolo[1,2-a]pyrimidine derivatives that were synthesized from NH-pyrroles exhibit AIE and AIEE property.     

Hypervalent iodine promoted the synthesis of cycloheptatrienes and cyclopropanes

A new strategy is reported for intramolecular Buchner-type reactions using PIDA as a promotor. Traditionally, the Buchner reaction is achieved via Rh-carbenoids derived from Rh^II catalysts with diazo compounds. Herein, the first metal-free Buchner-type reaction to construct highly strained cycloheptatriene- and cyclopropane-fused lactams is presented. The advantage of these transformations is in their mild reaction conditions, simple operation, broad functional group compatibility and rapid synthetic protocol. In addition, scaled-up experiments and a series of follow-up synthetic procedures were performed to clarify the flexibility and practicability of this method. DFT calculations were carried out to clarify the mechanism.

A new strategy is reported for intramolecular Buchner-type reactions using PIDA as a promotor.     

Skeletal remodeling of chalcone-based pyridinium salts to access isoindoline polycycles and their bridged derivatives

Simultaneous deconstructive ring-opening and skeletal reconstruction of an inert, aromatic pyridinium ring is of great importance in synthetic communities. However, research in this area is still in its infancy. Here, a skeletal re-modeling strategy was developed to transform chalcone-based pyridinium salts into structurally intriguing polycyclic isoindolines through a dearomative ring-opening/ring-closing sequence. Two distinct driving forces for the deconstruction of the pyridinium core were involved in these transformations. One was the unprecedented harnessing of the instability of in situ generated cyclic β-aminoketones, and the other was the instability of the resultant N,N-ketals. The desired isoindoline polycycles could undergo the Wittig reaction with various phosphorus ylides to achieve structural diversity and complexity. Notably, by tuning the Wittig conditions by addition of one equivalent of base, an additional bridged ring was introduced. A plausible mechanism was proposed on the basis of control experiments and theoretical calculations.

A novel skeletal remodeling strategy to transform chalcone-based pyridinium salts into structurally intriguing polycyclic isoindolines was achieved through a dearomative ring-opening/ring-closing sequence.     

Identification of a metastable uranium metal–organic framework isomer through non-equilibrium synthesis

Since the structure of supramolecular isomers determines their performance, rational synthesis of a specific isomer hinges on understanding the energetic relationships between isomeric possibilities. To this end, we have systematically interrogated a pair of uranium-based metal–organic framework topological isomers both synthetically and through density functional theory (DFT) energetic calculations. Although synthetic and energetic data initially appeared to mismatch, we assigned this phenomenon to the appearance of a metastable isomer, driven by levers defined by Le Châtelier''s principle. Identifying the relationship between structure and energetics in this study reveals how non-equilibrium synthetic conditions can be used as a strategy to target metastable MOFs. Additionally, this study demonstrates how defined MOF design rules may enable access to products within the energetic phase space which are more complex than conventional binary (e.g., kinetic vs. thermodynamic) products.

Identifying the relationship between structure and energetics in a uranium MOF isomer system reveals how non-equilibrium synthetic conditions can be used as a strategy to target metastable MOFs.     

Fast relaxing red and near-IR switchable azobenzenes with chalcogen and halogen substituents: periodic trends,tuneable thermal half-lives and chalcogen bonding

Molecular photoswitches operating in the red to near-IR region with controllable thermal relaxation rates are attractive components for photo-regulating biological processes. Herein, we report the synthesis of red-shifted azobenzenes functionalised with the heavier chalcogens and halogens that meet these requirements for biological application; namely fatigue-resistant photo-switching with red and near IR light and functional handles for further functionalisation for application. We report robust periodic trends for the chalcogen and halogen azobenzene series, and exploit intramolecular chalcogen bonding to tune and redshift the absorption maxima, supported by photo-physical measurements and solid-state structural analysis. Remarkably, the rate of the Z → E thermal isomerisation can be tuned over timescales spanning 10⁷ s by judicious choice of chalcogen and halogen substituents.

The synthesis of red-shifted azobenzenes functionalised with heavy chalcogen and halogen substituents is reported, enabling photo-switching with red and near IR light and Z → E thermal isomerization rates spanning seven orders of magnitude.     

Solvent-controlled photocatalytic divergent cyclization of alkynyl aldehydes: access to cyclopentenones and dihydropyranols

Divergent synthesis is a powerful strategy for the fast assembly of different molecular scaffolds from identical starting materials. We describe here a solvent-controlled photocatalytic divergent cyclization of alkynyl aldehydes with sulfonyl chlorides for the direct construction of highly functionalized cyclopentenones and dihydropyranols that widely exist in bioactive molecules and natural products. Density functional theory calculations suggest that a unique N,N-dimethylacetamide-assisted 1,2-hydrogen transfer of alkoxy radicals is responsible for the cyclopentenone formation, whereas a C–C cleavage accounts for the selective production of dihydropyranols in acetonitrile and water at 50 °C. Given the simple and mild reaction conditions, excellent functional group compatibility, forming up to four chemical bonds, and tunable selectivity, it may find wide applications in synthetic chemistry.

A solvent-controlled photocatalytic divergent cyclization of alkynyl aldehydes is developed, providing a facile access to sulfonylated cyclopentenones and dihydropyranols under mild conditions.     

A redox-enabled strategy for intramolecular hydroamination

Metal- or acid-catalyzed intramolecular hydroamination and Cope-type intramolecular hydroamination, a distinct concerted approach using hydroxylamines, typically suffer from significant synthetic limitations. Herein we report a process for intramolecular hydroamination that uses a redox-enabled strategy relying on efficient in situ generation of hydroxylamines by oxidation, followed by Cope-type hydroamination, then reduction of the resulting pyrrolidine N-oxide. The steps are performed sequentially in a single pot, no catalyst is required, the conditions are mild, the process is highly functional group tolerant, and no chromatography is generally required for isolation. A robustness screen and a gram-scale example further support the practicality of this approach.

A redox strategy enables hydroaminations: mild conditions allows efficient hydroxylamine formation & cyclization, then B₂(OH)₄ as reductant also facilitates isolation!     

An economical approach for peptide synthesis via regioselective C–N bond cleavage of lactams

An economical, solvent-free, and metal-free method for peptide synthesis via C–N bond cleavage using lactams has been developed. The method not only eliminates the need for condensation agents and their auxiliaries, which are essential for conventional peptide synthesis, but also exhibits high atom economy. The reaction is versatile because it can tolerate side chains bearing a range of functional groups, affording up to >99% yields of the corresponding peptides without racemisation or polymerisation. Moreover, the developed strategy enables peptide segment coupling, providing access to a hexapeptide that occurs as a repeat sequence in spider silk proteins.

An economical, solvent-free, and metal-free method for peptide synthesis via C–N bond cleavage using lactams has been developed.     

The dioxasilepanyl group as a versatile organometallic unit: studies on stability,reactivity, and utility

Organic synthesis is performed based on precise choices of functional groups and reactions employed. In a multistep synthesis, an ideal functional group should be compatible with various reaction conditions and unaltered until it is subjected to a selective conversion. The current study was set out to search for a silicon functionality that meets these criteria. Here we have established a new silicon-based synthetic methodology centred on a bulky 7-membered dialkoxysilyl group (2,4,4,7,7-pentamethyl-1,3,2-dioxasilepan-2-yl) that uniquely has both stability and on-demand reactivity. The exceptional stability of this functional group was corroborated by both experimental and computational studies which demonstrated that key factors for its stability were a 7-membered structure and steric hindrance. In turn, the dioxasilepanyl group was found to become reactive and to be easily transformed in the presence of appropriate activators. Combined with the development of easy and robust methods to introduce the dioxasilepanyl group onto aryl rings, these findings have allowed a shorter and more efficient synthesis of a bioactive molecule, thus demonstrating the potential utility of the easily accessible dioxasilepanyl group in organic synthesis.

A bulky 7-membered dioxasilepanyl group has been established as a new organometallic unit for multistep organic syntheses.     

Expanded porphyrins: functional photoacoustic imaging agents that operate in the NIR-II region

Photoacoustic imaging (PAI) relies on the use of contrast agents with high molar absorptivity in the NIR-I/NIR-II region. Expanded porphyrins, synthetic analogues of natural tetrapyrrolic pigments (e.g. heme and chlorophyll), constitute as potentially attractive platforms due to their NIR-II absorptivity and their ability to respond to stimuli. Here, we evaluate two expanded porphyrins, naphthorosarin (1) and octaphyrin (4), as stimuli responsive PA contrast agents for functional PAI. Both undergo proton-coupled electron transfer to produce species that absorb well in the NIR-II region. Octaphyrin (4) was successfully encapsulated into 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-poly(ethylene glycol) (DSPE-PEG₂₀₀₀) nanoparticles to afford OctaNPs. In combination with PAI, OctaNPs allowed changes in the acidic environment of the stomach to be visualized and cancerous versus healthy tissues to be discriminated.

In this study, two expanded porphyrins, octaphyrin and naphthorosarin were evaluated as potential PA agents. The nanoparticle encapsulation of octaphyrin successfully enabled the visualization of acidic environments and the discrimination between cancerous and healthy tissues.     

Molecular planting of a single organothiol into a “gap-site” of a 2D patterned adlayer in an electrochemical environment

The self-assembled inclusion of molecules into two-dimensional (2D) porous networks on surfaces has been extensively studied because 2D functional materials consisting of organic molecules have become an important research topic. However, the isolation of a single molecular thiol remains a challenging goal. Here, we report a method of planting and isolating organothiols onto a 2D patterned organic adlayer at an electrochemical interface. In situ scanning tunneling microscopy revealed that the phase transition of an ovalene adlayer is electrochemically induced and that the gap site created by three ovalene molecules serves as a 2D molecular template to isolate thiol molecules and to standardize the distance between them via the formation of precise selective open spaces, suggesting that electrochemical “molecular planting” opens applications for 2D patterns of isolated single organothiol molecules.

Gap sites electrochemically created in the ovalene adlayer can accept a single thiol.     

Palladium-catalyzed intramolecular Heck dearomative gem-difluorovinylation of indoles

A palladium-catalyzed dearomative reaction of indoles has been developed through a domino Heck/gem-difluorovinylation sequence. By taking advantage of a difluorocarbene precursor (ClCF₂COONa), the palladium difluorocarbene ([Pd] CF₂) species was formed smoothly. Then, a migratory insertion/β-H elimination process enabled access to polycyclic indolines containing 1,1-difluoroethylene units in acceptable yields with a broad substrate scope, which also showed dearomative gem-difluorovinylation for the first time. Remarkably, the superb diversified transformations allowed the product to install various functional groups.

Dearomative gem-difluorovinylation was reported for the first time and provided a new way to construct complex organofluorine compounds rapidly.     

Molecularly imprinted polymers outperform lectin counterparts and enable more precise cancer diagnosis

Accurately analysing the particular glycosylation status of protein biomarkers is of significant importance in the precise, early diagnosis of cancer. Existing methods mainly rely on the use of antibodies and lectins. However, due to the macroscopic and microscopic heterogeneity of glycans, precise analysis of glycosylation status still remains a challenge. Molecularly imprinted polymers (MIPs), as a synthetic alternative to antibodies or lectins, may provide new solutions but have not yet been explored. Herein, we report an appealing strategy called triple MIP-based plasmonic immunosandwich assay (triMIP-PISA) for precise cancer diagnosis in terms of the relative glycosylation expression of glycoprotein biomarkers. As proof of the principle, alpha fetoprotein (AFP), which has been used as a clinical biomarker for early detection of hepatocellular carcinoma (HCC), as well as its Lens culinaris agglutinin (LCA)-reactive fraction (AFP-L3), which is mainly composed of core-fucosylated glycans, were used as two target proteoforms to test in this study. Using two MIPs that can specifically recognize the peptide sequence of AFP as well as a fucose-imprinted MIP that can specifically recognize the AFP-L3 fraction, facile simultaneous plasmon-enhanced Raman detection of AFP and AFP-L3 in serum was achieved, which allowed HCC patients to be distinguished from healthy individuals. Due to the excellent recognition properties of the MIPs that are comparable to those of antibodies and superior to those of lectins, our triMIP-PISA method exhibited improved precision as compared with an antibody plus lectin-based immunofluorescence assay. Thus, this strategy opened a new avenue towards the precise diagnosis of cancer.

A triple molecularly imprinted polymer (MIP)-based plasmonic assay was developed for precise cancer diagnosis in terms of the relative glycosylation expression of glycoprotein biomarkers.     

Dual ligand approach increases functional group tolerance in the Pd-catalysed C–H arylation of N-heterocyclic pharmaceuticals

The excellent functional group tolerance of the Suzuki–Miyaura cross-coupling reactions has been decisive for their success in the pharmaceutical industry. Highly diversified (hetero)aromatic scaffolds can be effectively coupled in the final step(s) of a convergent synthetic route. In contrast, electrophilic Pd catalysts for non-directed C–H activation are particularly sensitive to inhibition by coordinating groups in pharmaceutical precursors. While C–H arylation enables the direct conversion of (hetero)aromatics without preinstalled functional or directing groups, its functional group tolerance should be increased to be viable in late-stage cross-couplings. In this work, we report on a dual ligand approach that combines a strongly coordinating phosphine ligand with a chelating 2-hydroxypyridine for the highly robust C–H coupling of bicyclic N-heteroaromatics with aryl bromide scaffolds. The catalyst speciation was studied via in situ XAS measurements, confirming the coordination of both ligands under the reaction conditions. The C–H activation catalyst was shown to be tolerant to a wide range of pharmaceutically relevant scaffolds, including examples of late-stage functionalization of known drug molecules.

Ligand combination of a 2-pyridone with traditional phosphines enables superior functional group tolerance in the C–H (hetero)arylation of pharmaceutically relevant N-heterocyclic scaffolds.     

Aryl diazonium intermediates enable mild DNA-compatible C–C bond formation for medicinally relevant combinatorial library synthesis

Forging carbon–carbon (C–C) linkage in DNA-encoded combinatorial library synthesis represents a fundamental task for drug discovery, especially with broad substrate scope and exquisite functional group tolerance. Here we reported the palladium-catalyzed Suzuki–Miyaura, Heck and Hiyama type cross-coupling via DNA-conjugated aryl diazonium intermediates for DNA-encoded chemical library (DEL) synthesis. Starting from commodity arylamines, this synthetic route facilely delivers vast chemical diversity at a mild temperature and pH, thus circumventing damage to fragile functional groups. Given its orthogonality with traditional aryl halide-based cross-coupling, the aryl diazonium-centered strategy expands the compatible synthesis of complex C–C bond-connected scaffolds. In addition, DNA-tethered pharmaceutical compounds (e.g., HDAC inhibitor) are constructed without decomposition of susceptible bioactive warheads (e.g., hydroxamic acid), emphasizing the superiority of the aryl diazonium-based approach. Together with the convenient transformation into an aryl azide photo-crosslinker, aryl diazonium''s DNA-compatible diversification synergistically demonstrated its competence to create medicinally relevant combinatorial libraries and investigate protein–ligand interactions in pharmaceutical research.

Taking advantage of aryl diazonium intermediates, this work reported a DNA-compatible C–C bond formation strategy, achieving broad substrate scope, exquisite functional group tolerance, and orthogonality to aryl halide-based coupling reactions.     

Easily accessible non-aromatic heterocycles with handles: 4-bromo-2,3-dihydrofurans from 1,2-dibromohomoallylic alcohols

The first general preparation of 4-bromo-2,3-dihydrofurans is reported. These non-aromatic heterocycles containing a useful coupling handle are accessed via Cu-catalyzed intramolecular cyclization of 1,2-dibromohomoallylic alcohols, which are themselves available in just two steps from aromatic and aliphatic aldehydes and ketones. Molecular dynamics simulations using the simple substrates and key geometric parameters provide a rationale for the selectivities observed. The synthetic utility of the 4-bromodihydrofurans is also demonstrated.

The first general preparation of 4-bromo-2,3-dihydrofurans is reported.     

Engineered modular heterocyclic-diamidines for sequence-specific recognition of mixed AT/GC base pairs at the DNA minor groove

This report describes a breakthrough in a project to design minor groove binders to recognize any sequence of DNA. A key goal is to invent synthetic chemistry for compound preparation to recognize an adjacent GG sequence that has been difficult to target. After trying several unsuccessful compound designs, an N-alkyl-benzodiimidazole structure was selected to provide two H-bond acceptors for the adjacent GG-NH groups. Flanking thiophenes provide a preorganized structure with strong affinity, DB2831, and the structure is terminated by phenyl-amidines. The binding experimental results for DB2831 with a target AAAGGTTT sequence were successful and include a high ΔT_m, biosensor SPR with a K_D of 4 nM, a similar K_D from fluorescence titrations and supporting competition mass spectrometry. MD analysis of DB2831 bound to an AAAGGTTT site reveals that the two unprotonated N of the benzodiimidazole group form strong H-bonds (based on distance) with the two central G-NH while the central –CH of the benzodiimidazole is close to the –C O of a C base. These three interactions account for the strong preference of DB2831 for a -GG- sequence. Surprisingly, a complex with one dynamic, interfacial water is favored with 75% occupancy.

This report describes a breakthrough in a project to design minor groove binders to recognize any sequence of DNA.     

Vessel effects in organic chemical reactions; a century-old,overlooked phenomenon

One of the most intriguing aspects of synthetic chemistry is the interplay of numerous dependent and independent variables en route to achieve a successful, high-yielding chemical transformation. The experienced synthetic chemist will probe many of these variables during reaction development and optimization, which will routinely involve investigation of reaction temperature, solvent, stoichiometry, concentration, time, choice of catalyst, addition sequence or quenching conditions just to name some commonly addressed variables. Remarkably, little attention is typically given to the choice of reaction vessel material as the surface of common laboratory borosilicate glassware is, incorrectly, assumed to be chemically inert. When reviewing the scientific literature, careful consideration of the vessel material is typically only given during the use of well-known glass-etching reagents such as HF, which is typically only handled in HF-resistant, polyfluorinated polymer vessels. However, there are examples of chemical transformations that do not involve such reagents but are still clearly influenced by the choice of reaction vessel material. In the following review, we wish to condense the most significant examples of vessel effects during chemical transformations as well as observations of container-dependent stability of certain molecules. While the primary focus is on synthetic organic chemistry, relevant examples from inorganic chemistry, polymerization reactions, atmospheric chemistry and prebiotic chemistry are also covered.

One of the most intriguing aspects of synthetic chemistry is the interplay of numerous dependent and independent variables en route to achieve a successful, high-yielding chemical transformation.     

Nickel-catalyzed arylative substitution of homoallylic alcohols

Direct coupling of unactivated alcohols remains a challenge in synthetic chemistry. Current approaches to cross-coupling of alcohol-derived electrophiles often involve activated alcohols such as tosylates or carbonates. We report the direct arylative substitution of homoallylic alcohols catalyzed by a nickel-bisphosphine complex as a facile method to generate allylic arenes. These reactions proceed via formation of an allylic alcohol intermediate. Subsequent allylic substitution with arylboroxine nucleophiles enables the formation of a variety of allylic arenes. The presence of p-methoxyphenylboronic acid is crucial to activate the allylic alcohol to achieve high product yields.

Arylative substitutions of homoallylic alcohols with arylboron nucleophiles demonstrate the utility of unactivated alcohols as coupling partners in transition metal-catalyzed cross-coupling chemistry.