Substitution-Induced Mechanistic Switching in SNAr-Warheads for Cysteine Proteases.

The aim of this study was to investigate the transition from non-covalent reversible over covalent reversible to covalent irreversible inhibition of cysteine proteases by making delicate structural changes to the warhead scaffold. To this end, dipeptidic rhodesain inhibitors with different N-terminal electrophilic arenes as warheads relying on the SNAr mechanism were synthesized and investigated. Strong structure-activity relationships of the inhibition potency, the degree of covalency, and the reversibility of binding on the arene substitution pattern were found. The studies were complemented and substantiated by molecular docking and quantum-mechanical calculations of model systems. Furthermore, the improvement in the membrane permeability of peptide esters in comparison to their corresponding carboxylic acids was exemplified.

Mechanistic investigations of polyaza[7]helicene in photoredox and energy transfer catalysis.

Organic photocatalysts frequently possess dual singlet and triplet photoreactivity and a thorough photochemical characterization is essential for efficient light-driven applications. In this article, the mode of action of a polyazahelicene catalyst (Aza-H) was investigated using laser flash photolysis (LFP). The study revealed that the chromophore can function as a singlet-state photoredox catalyst in the sulfonylation/arylation of styrenes and as a triplet sensitizer in energy transfer catalysis. The singlet lifetime is sufficiently long to exploit the exceptional excited state reduction potential for the activation of 4-cyanopyridine. Photoinduced electron transfer generating the radical cation was directly observed confirming the previously proposed mechanism of a three-component reaction. Several steps of the photoredox cycle were investigated separately, providing deep insights into the complex mechanism. The triplet-excited Aza-H, which was studied with quantitative LFP, is formed with a quantum yield of 0.34. The pronounced triplet formation was exploited for the isomerization reaction of (E)-stilbene to the Z-isomer and the cyclization of cinnamyl chloride. Catalyst degradation mainly occurs through the long-lived Aza-H triplet (28 µs), but the photostability is greatly increased when the triplet efficiently reacts in a catalytic cycle such that turnover numbers exceeding 4400 are achievable with this organocatalyst.

Solving a Mystery with Classical and Dual Photoredox Catalysis: Application of Nickel in the Synthesis of Ergot Alkaloids.

A short synthesis of the ergot alkaloid lysergene and a formal total synthesis of lysergic acid diethylamide (LSD) under the avoidance of palladium and including two nickel-catalyzed steps instead have been developed. A key intermediate of this approach has already been reported by Hendrickson et al. in 2004 (Hendrickson, J.B. et al. Org. Lett. 2004, 6, 3-5), yet the spectral data do not match, adding to doubts about the course of their route. While the final steps of the Hendrickson synthesis could not be reproduced, we were able to leverage the elusive intermediate.

Total Synthesis of (±)-Oxacyclododecindione.

Racemic total synthesis of the natural product oxacyclododecindione, isolated in 2008 as the first member of the oxacyclododecindione family, is reported. Studies toward this molecule commenced with a biomimetic late-stage C-H oxidation starting from 14-deoxyoxacyclododecindione as a known precursor. This provided insights into the reactivity of the macrolactone class but did not permit the synthesis of the target natural product. Based on these results, a synthetic strategy through intramolecular Friedel-Crafts acylation combined with Barton decarboxylation to introduce the tertiary alcohol, a major challenge in previous synthetic efforts, was envisioned. This resulted in an 11-step racemic total synthesis of (±)-oxacyclododecindione, renowned for its potent anti-inflammatory and antifibrotic activities.

Esterification of Cyclic N6-Threonylcarbamoyladenosine During RNA Sample Preparation.

The continuous deciphering of crucial biological roles of RNA modifications and their involvement in various pathological conditions, together with their key roles in the use of RNA-based therapeutics, has reignited interest in studying the occurrence and identity of non-canonical ribonucleoside structures during the past years. Discovery and structural elucidation of new modified structures is usually achieved by combination of liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) at the nucleoside level and stable isotope labeling experiments. This approach, however, has its pitfalls as demonstrated in the course of the present study: we structurally elucidated a new nucleoside structure that showed significant similarities to the family of (c)t6A modifications and was initially considered a genuine modification, but subsequently turned out to be an in vitro formed glycerol ester of t6A. This artifact is generated from ct6A during RNA hydrolysis upon addition of enzymes stored in glycerol containing buffers in a mildly alkaline milieu, and was moreover shown to undergo an intramolecular transesterification reaction. Our results demand for extra caution, not only in the discovery of new RNA modifications, but also with regard to the quantification of known modified structures, in particular chemically labile modifications, such as ct6A, that might suffer from exposure to putatively harmless reagents during the diverse steps of sample preparation.

Reversible oxidative dimerization of 4-thiouridines in tRNA isolates.

The occurrence of non-canonical nucleoside structures in RNA of biological or synthetic origin has encountered several recent boosts in attention, namely in the context of RNA modifications, and with an eye to RNA vaccines. New nucleoside structures introduce added functionality and function into biopolymers that are otherwise rather homogenous in their chemical structure. Here, we report the discovery of a presumed RNA modification that was identified by combination of liquid chromatography-tandem mass spectrometry (LC-MS/MS) with stable isotope labelling as a dimer of the known RNA modification 4-thiouridine (s4U). The disulfide-linked structure, which had previously been synthetically introduced into RNA, was here formed spontaneously in isolates of E. coli tRNA. Judicious application of stable isotope labelling suggested that this presumed new RNA modification was rather generated ex vivo by oxidation with ambient oxygen. These findings do not only underscore the need for caution in the discovery of new RNA modifications with respect to artifacts, but also raise awareness of an RNA vulnerability, especially to oxidative damage, during its transport or storage.

Total Synthesis, Structure Reassignment, and Biological Evaluation of the Anti-Inflammatory Macrolactone 13-Hydroxy-14-deoxyoxacyclododecindione.

Herein, the first total synthesis of natural 13-hydroxy-14-deoxyoxacyclododecindione along with the revision of the proposed configuration is reported. This natural product, initially discovered in 2018, belongs to the oxacyclododecindione family, renowned for their remarkable anti-inflammatory and antifibrotic activities. The synthetic route involves an esterification/Friedel-Crafts-acylation approach and uses various triol fragments. It allows the preparation of different stereoisomers, including the (revised) natural product, two threo-derivatives, and two Z-isomers of the endocyclic C═C double bond. Furthermore, a late-stage inversion of the C-13 stereocenter could transform the originally proposed structure into the revised natural product. With this comprehensive set of compounds and the previously prepared (13R,14S,15R)-isomer, deeper insights into their structural properties and biological activities were obtained. A detailed analysis of the final macrolactones using spectroscopy (NMR, IR, UV-vis) and X-ray crystallography gave new insights such as the significance of the optical rotation for the elucidation of their configuration and the light-induced E/Z double-bond photoisomerization. The pharmacological potential of the compounds was underlined by remarkably low IC50 values in biological assays addressing the inhibition of cellular inflammatory responses.

Pyrroloquinolones B-F: Five unusual alkaloids from Vernonia glabra (Steetz) Vatke (Asteraceae).

Five unusual alkaloids featuring a pyrrolo[1,2-a]quinolone skeleton (pyrroloquinolones B-F, 1-5) were isolated from the ethanol extract of the whole plant of Vernonia glabra (Steetz) Vatke, along with sixteen known compounds. Their structures were established by means of spectroscopic (1D and 2D NMR, UV, IR, and ECD) and high resolution mass spectrometric techniques as well as by comparison of their spectroscopic data with those reported in the literature. The ethanol extract and some isolated compounds were assessed for their antibacterial activity against four bacterial strains. The extract was significantly active against Staphylococcus aureus ATCC1026 and S. epidermidis ATCC35984 (MIC = 64 µg/mL). All the tested compounds showed moderate activity against S. epidermidis (16 ≤ MIC ≤ 64 µg/mL). Furthermore, this is the first report on tricyclic pyrrolo[1,2-a]quinolone alkaloids from a plant source. A biosynthetic pathway for the formation of these compounds is also proposed.

Discovery and characterisation of a broderol-like illudin, omphaderol in the mycelial extracts of Omphalotus mexicanus (Omphalotaceae) using UPLC-QTOF-MS and NMR spectroscopy.

INTRODUCTION: The genus Omphalotus, in particular the "Jack-O'Lantern mushrooms" Omphalotus illudens and Omphalotus olearius, are famous for the production of the DNA-alkylating illudins. A lesser-known species, Omphalotus mexicanus, native to Central America, also produces cytotoxic illudins S and M, but its minor secondary metabolites are yet to be investigated. OBJECTIVE: To identify, isolate, and elucidate the structure of novel secondary metabolites of the illudin family in mycelial extracts of O. mexicanus from submerse cultivation. METHODOLOGY: A fermentation of the fungus in 15 L stirred tank bioreactors is described. Mycelial extracts were separated using a combination of flash chromatography with preparative RP-C18 high-performance liquid chromatography (HPLC). Analysis of metabolites was done using an ultrahigh-performance liquid chromatography ultraviolet diode array detector (UPLC-UV-DAD) system coupled to an electrospray ionisation quadrupole time-of-flight (ESI-QTOF) mass spectrometer. Structures were elucidated using one-dimensional (1D) and two-dimensional (2D) nuclear magnetic resonance spectroscopy (NMR) techniques followed by comparison of experimental and simulated electronic circular dichroism (ECD) spectra to determine absolute configurations. RESULTS: Two novel illudin derivatives, for which we propose the names omphaderol (1) and illudaneol B (2), as well as illudaneol (3) and the unusual cyclobutylcyclopentane illudosin (4), were isolated from the mycelia and characterised. CONCLUSION: Particularly the illudaneol derivatives with their high titers may be potential building blocks for an alternative semisynthetic route to new illudin derivatives with improved medical properties. Additionally, the findings improve the knowledge of minor illudin compounds in the mycelial extract of this fungus and may be of significance for future biosynthetic studies of the illudins.

One-Pot Synthesis of Cereblon Proteolysis Targeting Chimeras via Photoinduced C(sp2)-C(sp3) Cross Coupling and Amide Formation for Proteolysis Targeting Chimera Library Synthesis.

In this study, a one-pot synthesis via photoinduced C(sp2)-C(sp3) coupling followed by amide formation to access proteolysis targeting chimeras (PROTACs) was developed. The described protocol was studied on cereblon (CRBN)-based E3-ligase binders and (+)-JQ-1, a bromodomain inhibitor, to generate BET (bromodomain and extra terminal domain) targeting protein degraders. The generated PROTACs were profiled in vitro and tested for their degradation ability with several potent candidates identified. Upfront, the individual reactions of the one-pot transformation were carefully optimized for CRBN binder functionalization and multiple heterobifunctional linker moieties were designed and synthesized. Separate scopes detailing the C(sp2)-C(sp3) coupling and one-pot PROTAC synthesis are described in this report as well as a library miniaturization study showing the high-throughput compatibility. Overall, the developed protocol provides rapid access to PROTACs in a single process, thereby allowing efficient generation of CRBN-based PROTAC libraries.

NMR and Docking Calculations Reveal Novel Atomistic Selectivity of a Synthetic High-Affinity Free Fatty Acid vs. Free Fatty Acids in Sudlow's Drug Binding Sites in Human Serum Albumin.

Saturation transfer difference (STD), inter-ligand NOEs (INPHARMA NMR), and docking calculations are reported for investigating specific binding sites of the high-affinity synthetic 7-nitrobenz-2-oxa-1,3-diazoyl-4-C12 fatty acid (NBD-C12 FA) with non-labeled human serum albumin (HSA) and in competition with the drugs warfarin and ibuprofen. A limited number of negative interligand NOEs between NBD-C12 FA and warfarin were interpreted in terms of a short-range allosteric competitive binding in the wide Sudlow's binding site II (FA7) of NBD-C12 FA with Ser-202, Lys-199, and Trp-214 and warfarin with Arg-218 and Arg-222. In contrast, the significant number of interligand NOEs between NBD-C12 FA and ibuprofen were interpreted in terms of a competitive binding mode in Sudlow's binding site I (FA3 and FA4) with Ser-342, Arg-348, Arg-485, Arg-410, and Tyr-411. NBD-C12 FA has the unique structural properties, compared to short-, medium-, and long-chain saturated and unsaturated natural free fatty acids, of interacting with well-defined structures with amino acids of both the internal and external polar anchor sites in Sudlow's binding site I and with amino acids in both FA3 and FA4 in Sudlow's binding site II. The NBD-C12 FA, therefore, interacts with novel structural characteristics in the drug binding sites I and II and can be regarded as a prototype molecule for drug development.

Short and Efficient Synthesis of the Antituberculosis Agent Pretomanid from (R)-Glycidol.

An efficient gram-scale synthesis of the antituberculosis agent pretomanid using straightforward chemistry, mild reaction conditions, and readily available starting materials is reported. Four different protecting groups on the glycidol moiety were investigated for their technical feasibility and ability to suppress side reactions. Starting from readily available protected (R)-glycidols and 2-bromo-4-nitro-1H-imidazole, pretomanid could be prepared in a linear three-step synthesis in up to 40% isolated yield. In contrast to most syntheses reported so far, deprotection and cyclization were performed in a one-pot fashion without any hazardous steps or starting materials.

Total synthesis of lamellarin G trimethyl ether through enaminone cyclocondensation.

A synthesis of pyrrolo[2,1-a]isoquinolines based on intramolecular condensation of an enaminone intermediate obtained by C-acylation of an N-alkylated 6,7-dimethoxy-1-methyl-3,4-dihydroisoquinolinium salt was developed. This methodology was further applied to the total synthesis of lamellarin G trimethyl ether from commercially available starting materials compatible with xylochemistry with an overall yield of 26% in 7 steps based on homoveratrylamine.

A new phenolic glycoside from the leaves of Flacourtia flavescens Willd.

Chemical study of the methanol extract from the leaves of Flacourtia flavescens led to the isolation of a new phenolic glucoside (1) along with fifteen known secondary metabolites namely shanzhiside methyl ester (2), aurantiamide acetate (3), caffeic acid methyl ester (4), caffeic acid (5), apigenin (6), luteolin (7), kaempferol (8), quercetin (9), gyrophoric acid (10), luteolin-7-O-ß-D-glucopyranoside (11), luteolin-4'-O-ß-D-glucopyranoside (12), kaempferol-7-O-α-L-rhamnopyranoside (13), kaempferol-3-O-ß-D-glucopyranosyl-(1→6)-O-α-L-rhamnopyranoside (14), kaempferol-3,7-O-α-L-dirhamnopyranoside (15) and (2S,3S,4R,8E)-2-((2'R)-2'-hydroxy-octadecanoylamino)-lignocerane-1,3,4-triol-8-ene (16). Their structures were elucidated by 1D and 2D NMR analysis and mass spectrometry. The extracts and the isolated compounds were evaluated for their antibacterial activities. The EtOAc extract was highly active (MIC = 32 and 64 µg/mL) against E. coli and E. faecalis, respectively. Compounds 1, 2, 2b, 5, 8, 9, and 12 (MIC = 16-32 µg/mL) were moderately active against some tested bacteria.

The macrocyclic lactone oxacyclododecindione reduces fibrosis progression.

Background: Renal fibrosis is one of the most important triggers of chronic kidney disease (CKD), and only a very limited number of therapeutic options are available to stop fibrosis progression. As fibrosis is characterized by inflammation, myofibroblast activation, and extracellular matrix (ECM) deposition, a drug that can address all these processes might be an interesting therapeutic option. Methods: We tested in vivo in an ischemia-reperfusion (I/R) model in C57BL/6 mice and in kidney tubular epithelial cells (TEC) (HK2 cell line and primary cells) whether the natural product oxacyclododecindione (Oxa) reduces fibrosis progression in kidney disease. This was evaluated by Western blot, mRNA expression, and mass spectrometry secretome analyses, as well as by immunohistochemistry. Results: Indeed, Oxa blocked the expression of epithelial-mesenchymal transition marker proteins and reduced renal damage, immune cell infiltration, and collagen expression and deposition, both in vivo and in vitro. Remarkably, the beneficial effects of Oxa were also detected when the natural product was administered at a time point of established fibrotic changes, a situation close to the clinical situation. Initial in vitro experiments demonstrated that a synthetic Oxa derivative possesses similar features. Conclusion: Although open questions such as possible side effects need to be investigated, our results indicate that the combination of anti-inflammatory and anti-fibrotic effects of Oxa make the substance a promising candidate for a new therapeutic approach in fibrosis treatment, and thus in the prevention of kidney disease progression.

Copper-Catalyzed Synthesis of Pyrrolo[1,2-c]quinazolines and Pyrrolo[2,1-a]isoquinolines and Antiplasmodial Evaluation.

Reactions involving C(sp3)-H bonds of azaarenes have been widely studied in recent years as they allow direct functionalization of these N-heterocycles without the use of harsh reaction conditions. In this work, we describe the C(sp3)-H functionalization of 4-methylquinazolines and 1-benzylisoquinolines, employing α-substituted ß-nitrostyrenes catalyzed by inexpensive copper acetate. Under the optimized condition, 21 pyrrolo[1,2-c]quinazolines, as well as an imidazo[1,2-c]quinazoline and 4 pyrrolo[2,1-a]isoquinolines, were obtained in moderate to good yields. Furthermore, the biological activity of the pyrrolo[1,2-c]quinazolines was evaluated against Plasmodium falciparum, and promising results were obtained.

An In Vitro Study of Local Oxygen Therapy as Adjunctive Antimicrobial Therapeutic Option for Patients with Periodontitis.

Periodontitis is a common global disease caused by bacterial dysbiosis leading to tissue destruction, and it is strongly associated with anaerobic bacterial colonization. Therapeutic strategies such as oxygen therapy have been developed to positively influence the dysbiotic microbiota, and the use of oxygen-releasing substances may offer an added benefit of avoiding systemic effects commonly associated with antibiotics taken orally or hyperbaric oxygen therapy. Therefore, the oxygen release of calcium peroxide (CaO2) was measured using a dissolved oxygen meter, and CaO2 solutions were prepared by dissolving autoclaved CaO2 in sterile filtered and deionized water. The effects of CaO2 on planktonic bacterial growth and metabolic activity, as well as on biofilms of Streptococcus oralis and Porphyromonas gingivalis, were investigated through experiments conducted under anaerobic conditions. The objective of this study was to investigate the potential of CaO2 as an antimicrobial agent for the treatment of periodontitis. Results showed that CaO2 selectively inhibited the growth and viability of P. gingivalis (p < 0.001) but had little effect on S. oralis (p < 0.01), indicating that CaO2 has the potential to selectively affect both planktonic bacteria and mono-species biofilms of P. gingivalis. The results of this study suggest that CaO2 could be a promising antimicrobial agent with selective activity for the treatment of periodontitis.

Structure elucidation and biological activities of perylenequinones from an Alternaria species.

The KEAP1-Nrf2/ARE pathway is a pivotal cytoprotective regulator against oxidative stress which plays an important role in the development of many inflammatory diseases and cancer. Activation of the Nrf2 transcription factor by oxidative stress or electrophiles regulates antioxidant response element (ARE)-dependent transcription of antioxidative, detoxifying, and anti-inflammatory proteins. Therefore, modulators of the KEAP1-Nrf2/ARE pathway have received considerable interest as therapeutics to protect against diseases where oxidative stress constitutes the underlying pathophysiology. In a search for fungal secondary metabolites affecting the Nrf2/ARE-dependent expression of a luciferase reporter gene in BEAS-2B cells, three new perylenequinones, compounds 1, 2, and 3, together with altertoxin-I (ATX-I), were isolated from fermentations of an Alternaria species. The structures of the compounds were elucidated by a combination of one- and two-dimensional NMR spectroscopy and mass spectrometry. Compound 1 and ATX-I exhibited strong cytotoxic effects with LC50-values of 3.8 µM and 6.43 µM, respectively, whereas compound 3 showed no cytotoxic effects up to 100 µM on BEAS-2B cells. ATX-I induced ARE-dependent luciferase expression approximately fivefold and compound 1 approximately 2.6-fold at a concentration of 3 µM in transiently transfected BEAS-2B cells. In addition, compound 1 and ATX-I exhibited strong oxidative effects, whereas compound 3 did not show significant oxidative properties. For compound 1 and ATX-I, a strong upregulation of heme oxygenase-1 could be observed on mRNA and protein level in treated BEAS-2B cells. Moreover, compound 3 significantly decreased sod3 mRNA levels after induction of oxidative stress with benzoquinone.

Substitution Effects on the Photophysical and Photoredox Properties of Tetraaza[7]helicenes.

A series of substituted derivatives of tetraaza[7]helicenes were synthesized and the influence of the substitution on their photophysical and photoredox-catalytic properties was studied. The combination of their high fluorescence quantum yields of up to 0.65 and their circularly polarized luminescence (CPL) activity results in CPL brightness values (BCPL ) that are among the highest recorded for [7]helicenes so far. A sulfonylation/hetarylation reaction using cyanopyridines as substrates for photoinduced electron transfer (PET) from the excited helicenes was conducted to test for viability in photoredox catalysis. DFT calculations predict the introduction of electron withdrawing substituents to yield more oxidizing catalysts.

Comparison of different density functional theory methods for the calculation of vibrational circular dichroism spectra.

The determination of the absolute configuration (AC) of an organic molecule is still a challenging task for which the combination of spectroscopic with quantum-mechanical methods has become a promising approach. In this study, we investigated the accuracy of DFT methods (480 overall combinations of 15 functionals, 16 basis sets, and 2 solvation models) to calculate the VCD spectra of six chiral organic molecules in order to benchmark their capability to facilitate the determination of the AC.