Controlling (E/Z)-Stereoselectivity of -NHC=O Chlorination: Mechanism Principles for Wide Scope Applications.

Organic halogen compounds are cornerstones of applied chemical sciences. Halogen substitution is a smart molecular design strategy adopted to influence reactivity, membrane permeability and receptor interaction. Chiral bioreceptors may restrict the stereochemical requirements in the halo-ligand design. Straightforward (but expensive) catalyzed stereospecific halogenation has been reported. Historically, PCl5 served access to uncatalyzed stereoselective chlorination although the stereochemical outcomes were influenced by steric parameters. Nonetheless, stereochemical investigation of PCl5 reaction mechanism with carbamoyl (RCONHX) compounds has never been addressed. Herein, we provide the first comprehensive stereochemical mechanistic explanation outlining halogenation of carbamoyl compounds with PCl5; the key regioselectivity-limiting nitrilimine intermediate (8-Z.HCl); how substitution pattern influences regioselectivity; why oxadiazole byproduct (P1) is encountered; stereo-electronic factors influencing the hydrazonoyl chloride (P2) production; and discovery of two stereoselectivity-limiting parallel mechanisms (stepwise and concerted) of elimination of HCl and POCl3. DFT calculations, synthetic methodology optimization, X-ray evidence and experimental reaction kinetics study evidence all supported the suggested mechanism proposal (Scheme 2). Finally, we provide mechanism-inspired future recommendations for directing the reaction stereoselectivity toward elusive and stereochemically inaccessible (E)-bis-hydrazonoyl chlorides along with potentially pivotal applications of both (E/Z)-stereoisomers especially in medicinal chemistry and protein modification.

Highly regio- and stereoselective (3 + 2) annulation reaction of allenoates with 3-methyleneindolin-2-ones catalyzed by a planar chiral [2.2]paracyclophane-based bifunctional phosphine-phenol catalyst.

A planar chiral [2.2]paracyclophane-based phosphine-phenol catalyst catalyzed the (3 + 2) annulation reaction of ethyl 2,3-butadienoate with 3-methyleneindolin-2-ones to produce 2,5-disubstituted cyclopentene-fused C3-spirooxindoles in high yields with high regio-, diastereo-, and enantioselectivities. This catalyst was suitable for reactions of not only benzylideneindolinones but also alkylideneindolinones, the chiral phosphine-catalyzed reactions of which have not yet been reported. Density functional theory calculations suggested that the formation of hydrogen bonds between the phenolic OH group of the catalyst and the allenoate carbonyl group, rather than between the OH group and the carbonyl group of indolinone, contributed to the formation of an efficient reaction space at the enantiodetermining step.

Green/red light-sensing mechanism in the chromatic acclimation photosensor.

Certain cyanobacteria alter their photosynthetic light absorption between green and red, a phenomenon called complementary chromatic acclimation. The acclimation is regulated by a cyanobacteriochrome-class photosensor that reversibly photoconverts between green-absorbing (Pg) and red-absorbing (Pr) states. Here, we elucidated the structural basis of the green/red photocycle. In the Pg state, the bilin chromophore adopted the extended C15-Z,anti structure within a hydrophobic pocket. Upon photoconversion to the Pr state, the bilin is isomerized to the cyclic C15-E,syn structure, forming a water channel in the pocket. The solvation/desolvation of the bilin causes changes in the protonation state and the stability of π-conjugation at the B ring, leading to a large absorption shift. These results advance our understanding of the enormous spectral diversity of the phytochrome superfamily.

Brønsted acid-catalyzed synthesis of spirocyclobutanes via heteroannulation of vinyloxyphenylbicyclobutanes with water.

We report a perchloric acid-catalyzed heteroannulation for the synthesis of spirocyclobutanes using vinyloxyphenylbicyclobutanes with water. This metal-free reaction yields high product outputs and is consistent with the formation of a cyclobutene intermediate originating from an isomerization of a bicyclobutane.

Total Synthesis and Antibacterial Activity of Marine Tris-indole Alkaloid Tulongicin A.

Bis-indole alkaloids from marine sponges are an intriguing class of natural products with a variety of activities. However, only a preliminary biological study of tulongicin A (5), a related previously isolated marine tris-indole alkaloid, has been conducted. In this study, we accomplished the first asymmetric total synthesis of 5 via the construction of an imidazoline-linked bis-indolylmethane skeleton using a Friedel-Crafts-type reaction. Our synthesis enabled a detailed study of the antibacterial profile of 5. Compound 5 displayed bactericidal activity against Staphylococcus aureus, including methicillin-resistant S. aureus (MRSA) strains.

First atroposelective Chan-Lam coupling for the synthesis of C-N linked biaryls.

The first atroposelective Chan-Lam coupling for the synthesis of C-N axial enantiomers is reported with good yields and ee. MnO2 additive is crucial for the success of the coupling. The longstanding problem of the lack of enantioselective synthesis to make chiral C-N linked atropisomers is solved.

Mechanism of the extremely high duplex-forming ability of oligonucleotides modified with N-tert-butylguanidine- or N-tert-butyl-N'- methylguanidine-bridged nucleic acids.

Antisense oligonucleotides (ASOs) are becoming a promising class of drugs for treating various diseases. Over the past few decades, many modified nucleic acids have been developed for application to ASOs, aiming to enhance their duplex-forming ability toward cognate mRNA and improve their stability against enzymatic degradations. Modulating the sugar conformation of nucleic acids by substituting an electron-withdrawing group at the 2'-position or incorporating a 2',4'-bridging structure is a common approach for enhancing duplex-forming ability. Here, we report on incorporating an N-tert-butylguanidinium group at the 2',4'-bridging structure, which greatly enhances duplex-forming ability because of its interactions with the minor groove. Our results indicated that hydrophobic substituents fitting the grooves of duplexes also have great potential to increase duplex-forming ability.

Organic Phase-Soluble Nanomagnetically Cationic Phospholipid: Synthesis, Characterization, and In Vitro Transfection Activity.

The presented work describes the synthesis and characterization of a novel magnetic cationic phospholipid (MCP) system with a stable dopamine anchor as well as its transfection activity study. The synthesized architectural system increases the biocompatibility of iron oxide and promises applications of magnetic nanoparticles in living cells. The MCP system is soluble in organic solvents and can be easily adapted to prepare magnetic liposomes. We created complexes with liposomes containing MCP and other functional cationic lipids and pDNA as gene delivery tools, which possessed the ability to enhance the efficiency of transfection, particularly the process of interaction with cells by inducing a magnetic field. The MCP is able to create iron oxide nanoparticles and has the potential for the materials to prepare the system for site-specific gene delivery with the application of an external magnetic field.

Heteroannulation of bicyclobutane derivatives via Au-catalyzed hydration to enol ethers and intramolecular cyclization giving spirocyclobutanes.

We report the heteroannulations of bicyclobutane derivatives bearing enol ether groups in the presence of H2O under mild conditions. The reaction affords spirocyclobutanes with cyclic acetal groups via the Au-catalyzed hydration of the enol ether group and subsequent intramolecular cyclization.

Study on coffee quality improvement by self-induced anaerobic fermentation: Microbial diversity and enzymatic activity.

The postharvest fermentation process of coffee has rapidly advanced in the last few years due to the search for quality and diversity of sensorial profiles. A new type of fermentation, named self-induced-anaerobic fermentation (SIAF), is a promising process that has been increasingly used. This study aims to evaluate the sensorial improvement of coffee beverages during SIAF and the influence of microorganism's community and enzymatic activity. The SIAF process was conducted in Brazilian farms for up to 8 days. The sensorial quality of coffee was evaluated by Q-graders; the microbial community was identified by the high-throughput sequencing of 16S rRNA and ITS regions; and the enzymatic activity (invertase, polygalacturonase, and endo-ß-mannanase) was also investigated. SIAF increased up to 3.8 points in the total score of sensorial evaluation (compared to the non-fermented sample), in addition to presenting more flavor diversity (especially within the fruity and sweetness descriptors). The high-throughput sequencing identified 655 bacterial and 296 fungal species during the three processes. The bacteria Enterobacter sp., Lactobacillus sp., Pantoea sp., and the fungi Cladosporium sp. and Candida sp. were the predominant genera. Fungi that are potential producers of mycotoxin were identified throughout the process, which indicates a risk of contamination since some of them are not degraded in the roasting process. Thirty-one species of microorganisms were described for the first time in coffee fermentation. The microbial community was influenced by the place where the process was carried out, mainly in relation to the diversity of fungi. Washing the coffee fruits before fermenting led to a fast reduction of pH; a fast development of Lactobacillus sp. and a fast dominance of Candida sp.; a reduction of the fermentation time necessary to achieve the best sensorial score; an increase in the invertase activity in the seed; a more expressive invertase activity in the husk; and a decreasing trend in polygalacturonase activity in the coffee husk. The increase in endo-ß-mannanase activity suggests that coffee starts germinating during the process. SIAF has a huge potential to increase the quality and add value to coffee, but further studies must be conducted to access its safety. The study allowed a better knowledge of the spontaneous microbial community and the enzymes that were present in the fermentation process.

Radical-Based Route to Functionalized Tetralin: Formal Total Synthesis of (±)-Hamigeran B.

A formal synthetic route to hamigeran B, an antiviral marine natural product with a unique tricyclic molecular architecture, has been developed. The key chemical transformations in the present route include a novel zinc(II)porphyrin-catalyzed photoredox radical cascade cyclization to access a functionalized tetralin, a catalyst-free benzylic radical bromination with NBS by visible-light irradiation, and a samarium(II)-induced cyclization of brominated tetralone possibly via an orthoquinodimethane-like intermediate.

Double Ring Expansion Strategy for Fused 3-Benzazepines: Alternative Synthesis of the Dolby-Weinreb Enamine.

A double ring expansion strategy for constructing fused 3-benzazepines is described. The oxidative ring expansion of spiroamine compounds with N-chlorosuccinimide and subsequent ring expansion of the resulting ketiminium ion intermediates with trimethylsilyldiazomethane afforded fused 3-benzazepines in a one-pot operation. Importantly, the Dolby-Weinreb enamine, which is a key synthetic intermediate for harringtonine alkaloids, cephalotaxines, can be accessed from commercial materials in only two steps using our developed method.

Human antibody recognition and neutralization mode on the NTD and RBD domains of SARS-CoV-2 spike protein.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19). Variants of concern (VOCs) such as Delta and Omicron have developed, which continue to spread the pandemic. It has been reported that these VOCs reduce vaccine efficacy and evade many neutralizing monoclonal antibodies (mAbs) that target the receptor binding domain (RBD) of the glycosylated spike (S) protein, which consists of the S1 and S2 subunits. Therefore, identification of optimal target regions is required to obtain neutralizing antibodies that can counter VOCs. Such regions have not been identified to date. We obtained 2 mAbs, NIBIC-71 and 7G7, using peripheral blood mononuclear cells derived from volunteers who recovered from COVID-19. Both mAbs had neutralizing activity against wild-type SARS-CoV-2 and Delta, but not Omicron. NIBIC-71 binds to the RBD, whereas 7G7 recognizes the N-terminal domain of the S1. In particular, 7G7 inhibited S1/S2 cleavage but not the interaction between the S protein and angiotensin-converting enzyme 2; it suppressed viral entry. Thus, the efficacy of a neutralizing mAb targeting inhibition of S1/2 cleavage was demonstrated. These results suggest that neutralizing mAbs targeting blockade of S1/S2 cleavage are likely to be cross-reactive against various VOCs.

Synthesis, Duplex-Forming Ability, and Nuclease Resistance of Oligonucleotides Containing a Thymidine Derivative with a 1-Oxaspiro[4.5]decane Skeleton.

Chemically modified nucleic acids are essential for the therapeutic application of oligonucleotides. In this study, 6'-C-spiro-thymidine exhibiting a fixed torsion angle γ was designed, synthesized, and incorporated into oligonucleotides. The conformational analysis of the 6'-C-spiro-thymidine monomer revealed that its torsion angle γ was in the +synclinal range (approx. 60°), which is similar to that in a natural RNA duplex, as expected. On the other hand, the sugar conformation of the RNA duplex is known to be predominantly an N-type, whereas that of the synthesized monomer was an S-type. The results of the UV melting analysis demonstrated that the duplex-forming ability of 6'-C-spiro-thymidine was inferior to that of natural DNA. Contrarily, 6'-C-spiro-thymidine could enhance the stability of oligonucleotides toward nucleases. Particularly, the incorporation of 6'-C-spiro-thymidine on the 3'-ends of the oligonucleotides significantly increased the nuclease resistance of the oligonucleotides.

Nicotinonitrile-derived apoptotic inducers: Design, synthesis, X-ray crystal structure and Pim kinase inhibition.

Although a plethora of targeted anticancer small molecule drugs became available, the low response rate and drug resistance imply the continuous need for expanding the anticancer chemical space. In this study, a novel series of nicotinonitrile derivatives was designed, synthesized and evaluated for cytotoxic activities in HepG2 and MCF-7 cells. All derivatives showed high to moderate cytotoxic activity against both cell lines, with cell-type and chemotype-dependent cytotoxic potential. The normal HEK-293 T cells were ca. 50-fold less susceptible to the cytotoxic effect of the inhibitors. The in vitro enzyme inhibitory activity of selected active cytotoxic derivatives 8c, 8e, 9a, 9e and 12 showed that they have sub- to one digit micromolar 50 % inhibitory concentration (IC50) against the three Pim kinase isoforms, with 8e being the most potent (IC50 ≤ 0.28 µM against three Pim kinases), comparable to the pan kinase inhibitor, Staurosporine. In HepG2, 8e induced cell cycle arrest at the G2/M phase. Apoptotic mechanistic studies with 8c and 8e in HepG2 cells, indicated a significant upregulation in both P53 and caspase-3 relative gene expression, as well as increased Bax/Bcl-2 protein expression level. Further, docking studies combined with molecular dynamic simulation showed a stable complex with high binding affinity of 8e to Pim-1 kinase; exploiting a negative electrostatic potential surface interaction with the added dimethyl amino group in the new compounds. Moreover, in silico ADME profile prediction indicated that all compounds are orally bioavailable and most of them can penetrate the blood-brain barrier. This study presents novel nicotinonitrile derivatives as auspicious hits for further optimization as antiproliferative agents against liver cancer cells and promising pan Pim kinase inhibitors at submicromolar concentrations.

ZnCl2-mediated stereo- and chemoselective synthesis of vinylphosphonates.

A highly chemo- and stereoselective synthesis of diethyl (E)-2-(alkylidene)-2-phosphonoacetonitriles via the Knoevenagel condensation reaction of carbonyl compounds with diethyl cyanomethylphosphonate in the presence of zinc chloride has been achieved. By the presented method, various E-isomers of arylmethylidene phosphonates rather than Horner-Wadsworth-Emmons olefination products were obtained in good to excellent yields. Their E configurations were determined by X-ray diffraction and NMR analyses. In addition, DFT calculations provided insights into the chemo- and stereoselectivity of the reaction.

Design, Synthesis, and Monoamine Oxidase Inhibitory Activity of (+)-Cinchonaminone and Its Simplified Derivatives.

The absolute structure of an indole alkaloid (+)-cinchonaminone by total synthesis of both (+)-cinchonaminone and its enantiomer was determined. The main focus of the study was the enantioselective synthesis of both enantiomers of a chiral cis-3,4-disubstituted piperidine. We also evaluated monoamine oxidase (MAO) inhibitory activities of these enantiomers. Furthermore, its structurally simplified derivatives were synthesized that did not have any chiral center. Two of these derivatives showed stronger MAO inhibitory activities than that of (+)-cinchonaminone.

Synthesis and duplex-forming ability of oligonucleotides modified with 4'-C,5'-C-methylene-bridged nucleic acid (4',5'-BNA).

We describe herein the design and synthesis of 4'-C,5'-C-methylene-bridged nucleic acid (4',5'-BNA), a novel artificial nucleic acid with the torsion angle γ in a non-canonical +ac range. The 4',5'-BNA phosphoramidite bearing a thymine nucleobase was synthesized from a commercially available thymidine analog in 11 steps and successfully incorporated into oligonucleotides. The resulting oligonucleotides were evaluated for their duplex-forming ability toward single-stranded DNA and RNA.

Could London Dispersion Force Control Regioselective (2 + 2) Cyclodimerizations of Benzynes? YES: Application to the Synthesis of Helical Biphenylenes.

In recent years, London dispersion interactions, which are the attractive component of the van der Waals potential, have been found to play an important role in controlling the regio- and/or stereoselectivity of various reactions. Particularly, the dispersion interactions between substrates and catalysts (or ligands) are dominant in various selective catalyzes. In contrast, repulsive steric interactions, rather than the attractive dispersion interactions, between bulky substituents are predominant in most of the noncatalytic reactions. Herein, we demonstrate the first example of London dispersion-controlled noncatalytic (2 + 2) cyclodimerization of substituted benzynes to selectively afford proximal biphenylenes in high yields and regioselectivities, depending on the extent of dispersion interactions in the substituents. This method can be applied for the synthesis of novel helical biphenylenes, which would be fascinating for chemists as these compounds are potential skeletons for ligands, catalysts, and medicines.

How to Select Firefly Luciferin Analogues for In Vivo Imaging.

Bioluminescence reactions are widely applied in optical in vivo imaging in the life science and medical fields. Such reactions produce light upon the oxidation of a luciferin (substrate) catalyzed by a luciferase (enzyme), and this bioluminescence enables the quantification of tumor cells and gene expression in animal models. Many researchers have developed single-color or multicolor bioluminescence systems based on artificial luciferin analogues and/or luciferase mutants, for application in vivo bioluminescence imaging (BLI). In the current review, we focus on the characteristics of firefly BLI technology and discuss the development of luciferin analogues for high-resolution in vivo BLI. In addition, we discuss the novel luciferin analogues TokeOni and seMpai, which show potential as high-sensitivity in vivo BLI reagents.