Epoxides: Developability as Active Pharmaceutical Ingredients and Biochemical Probes

Storage evolution in non-volatile and volatile lipid oxidation products of salted large yellow croaker based on targeted lipidomics and GC-MS analysis

The hydroxylation and epoxidation of lipids rich in polyunsaturated fatty acids (PUFAs) are significant processes that cannot be overlooked. In this study, the concentrations of non-volatile and volatile compounds derived from lipid oxidation significantly increased during storage of salted large yellow croaker. In which epoxy-fatty acids demonstrated greater stability and steadily accumulated throughout the entire process. The precursors for non-volatile lipid oxidation secondary products included linoleic acid, α-linolenic acid, arachidonic acid, eicosapentaenoic acid, and docosahexaenoic acid. Additionally, compounds such as 1-penten-3-one, decanal, etc., which belong to alcohol, aldehyde, hydrocarbon, ester, and ketone, were identified as key variables. Correlation analysis revealed that non-volatile compounds exhibited a positive correlation with esters and linear alcohols, while showing a negative correlation with aldehydes, ketones, and linear alcohols. These findings have profound implications for a deeper understanding of the complex oxidation processes involved in the storage of salted marine fish with high levels of PUFAs.

5,6-Dihydro-5,6-Epoxymultiplolide A, Cytosporone C, and Uridine Production by Diaporthe hongkongensis, an Endophytic Fungus from Minquartia guianensis

Endophytic fungi are valuable sources of bioactive secondary metabolites, with potential applications in pharmaceutical and agricultural fields. This study investigates the metabolic potential of Diaporthe hongkongensis, an endophytic fungus isolated from Minquartia guianensis. To date, no secondary metabolites have been identified from this species, highlighting the novelty of this research and its contribution to understanding the chemical diversity of endophytic fungi. The fungus was cultivated on parboiled rice under static and dark conditions for 28 days, leading to the isolation of the following three compounds: 5,6-dihydro-5,6-epoxymultiplolide A (1), cytosporone C (2), and uridine (3). Structural identification was carried out using nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry. The results revealed the metabolic versatility of D. hongkongensis, as demonstrated by its ability to produce structurally diverse substances with biological relevance. Hence, it describes the first isolation of secondary metabolites from the endophytic fungus D. hongkongensis, marking a significant step in understanding its chemical profile. The identification of a known antifungal compound and a lactone derivative underscores the biosynthetic potential of this endophytic fungus, while the isolation of a nucleoside expands the chemical repertoire of fungal metabolites, suggesting possible roles in cellular metabolism and stress adaptation. These findings highlight the role of endophytic fungi as prolific sources of structurally diverse and potentially bioactive natural products, supporting further exploration of their biotechnological applications.

Next-Generation Analogues of AC265347 as Positive Allosteric Modulators of the Calcium-Sensing Receptor: Pharmacological Investigation of Structural Modifications at the Stereogenic Centre

The calcium-sensing receptor (CaSR) is a validated therapeutic target in the treatment of hyperparathyroidism and related diseases. The CaSR ago-positive allosteric modulator (PAM), AC265347 (1), exhibits a chemically and pharmacologically unique profile compared to current approved CaSR PAM therapeutics. Herein, we report a series of 'next-generation' analogues of AC265347, investigating the impact of structural modifications at the stereogenic centre on CaSR PAM activity. Compounds 5 and 7b featuring the alcohol functional group showed ago-PAM profiles comparable to 1, whilst compounds 6, 7 and 9 devoid of this functionality were 'pure' PAMs with no intrinsic agonism. These novel chemical tools provide an opportunity to explore the therapeutic potential of AC265347-like PAMs as a function of affinity, cooperativity and intrinsic agonism.

Innovative design and potential applications of covalent strategy in drug discovery

Covalent inhibitors provide persistent inhibition while maintaining excellent selectivity and efficacy by creating stable covalent connections with specific amino acids in target proteins. This technique enables the precise inhibition of previously undruggable targets, lowering the frequency of administration and potentially bypassing drug resistance. Because of these advantages, covalent inhibitors have tremendous potential in treating cancer, inflammation, and infectious illnesses, making them extremely important in modern pharmacological research. Covalent inhibitors targeting EGFR, BTK, and KRAS (G12X), which overcome drug resistance and off-target, non-"medicinal" difficulties, as well as covalent inhibitors targeting SARS-CoV-2 Mpro, have paved the way for the development of new antiviral medicines. Furthermore, the use of covalent methods in drug discovery procedures, such as covalent PROTACs, covalent molecular gels, covalent probes, CoLDR, and Dual-targeted covalent inhibitors, preserves these tactics' inherent features while incorporating the advantages of covalent inhibitors. This synthesis opens up new therapeutic opportunities. This review comprehensively examines the use of covalent techniques in drug discovery, emphasizing their transformational potential for future drug development.

Ringing medicinal chemistry: The importance of 3-membered rings in drug discovery

Scaffold-based drug design has become increasingly prominent in the pharmaceutical field due to the systematic and effective approach through which it facilitates the development of novel drugs. The identification of key scaffolds provides medicinal chemists with a fundamental framework for subsequent research. With mounting evidence suggesting that increased aromaticity could impede the chances of developmental success for oral drug candidates, there is an imperative need for a more thorough exploration of alternative ring systems to mitigate attrition risks. The unique characteristics exhibited by three-membered rings have led to their application in medicinal chemistry. This review explores the use of cyclopropane-, aziridine-, thiirane-, and epoxide-containing compounds in drug discovery, focusing on their roles in approved medicines and drug candidates. Specifically, the importance of the three-membered ring systems in rending biological activity for each drug molecule was highlighted. The undeniable therapeutic value and intriguing features presented by these compounds suggest significant pharmacological potential, providing justification for their incorporation into the design of novel drug candidates.

Eco-sustainable Synthesis and Potential Efficiency of Some Novel N-containing Heterocyclic Derivatives as Insecticidal and Photosensitizing Agents Against Musca domestica L

The rising application of conventional synthetic insecticides develops resistant populations of houseflies; therefore, using new chemical agents with different modes of action is essential to overcome this problem. The mechanical grinding technique was used as a green method, to synthesize the tested compounds because it is a more facile work-up and high-yield economy, simplicity and solvent-free than conventional thermal technique. Various methods were employed to synthesize new heterocycles containing anthracene (a photosensitizing agent) from chalcone 3, a building block material such as the preparation of the pyrazole derivatives 4-7, isoxazole derivative 8, pyrimidines 9-11, and oxirane derivative 12. The novel synthesized compounds were analyzed by FT-IR, 1H-NMR, 13C-NMR spectra, and elemental analysis. Herein, the toxicity of the anthracene derivatives was assessed against Musca domestica larvae and adults in different conditions to demonstrate the effect of various inserted moieties on the efficiency of tested compounds. Furthermore, the influence of sunlight on the toxicity of anthracene was studied in dark and sunlight tests against adult houseflies. Moreover, these compounds diminished the total protein and lipids contents while significantly influencing the antioxidant enzymes activities of M. domestica adults. Structure-activity relationships demonstrated the role of each moiety on the toxicity of compounds.

Complementary Tandem Reaction Manifolds and "Switch Mechanisms" in the Reaction of Epoxides with Selectfluor

Tandem reactions are highly sought after transformations in organic synthesis as they accomplish multiple steps at once and can serve as golden keys unlocking mechanistic complexities. Reactions that operate through different mechanisms depending on the conditions ("switch mechanisms") are of intense interest to organic chemists as fonts of new reactivity. We report that Selectfluor can catalyze the rearrangement of 1,1-disubstituted epoxides, providing a new approach to benzylic fluorination. These results complement earlier work involving radical-cation-based ring opening of epoxides.

Evaluation of a Covalent Library of Diverse Warheads (CovLib) Binding to JNK3, USP7, or p53

Purpose

Over the last few years, covalent fragment-based drug discovery has gained significant importance. Thus, striving for more warhead diversity, we conceived a library consisting of 20 covalently reacting compounds. Our covalent fragment library (CovLib) contains four different warhead classes, including five α-cyanoacacrylamides/acrylates (CA), three epoxides (EO), four vinyl sulfones (VS), and eight electron-deficient heteroarenes with a leaving group (SNAr/SN).

Methods

After predicting the theoretical solubility of the fragments by LogP and LogS during the selection process, we determined their experimental solubility using a turbidimetric solubility assay. The reactivities of the different compounds were measured in a high-throughput 5,5'-dithiobis-(2-nitrobenzoic acid) DTNB assay, followed by a (glutathione) GSH stability assay. We employed the CovLib in a (differential scanning fluorimetry) DSF-based screening against different targets: c-Jun N-terminal kinase 3 (JNK3), ubiquitin-specific protease 7 (USP7), and the tumor suppressor p53. Finally, the covalent binding was confirmed by intact protein mass spectrometry (MS).

Results

In general, the purchased fragments turned out to be sufficiently soluble. Additionally, they covered a broad spectrum of reactivity. All investigated α-cyanoacrylamides/acrylates and all structurally confirmed epoxides turned out to be less reactive compounds, possibly due to steric hindrance and reversibility (for α-cyanoacrylamides/acrylates). The SNAr and vinyl sulfone fragments are either highly reactive or stable. DSF measurements with the different targets JNK3, USP7, and p53 identified reactive fragment hits causing a shift in the melting temperatures of the proteins. MS confirmed the covalent binding mode of all these fragments to USP7 and p53, while additionally identifying the SNAr-type electrophile SN002 as a mildly reactive covalent hit for p53.

Conclusion

The screening and target evaluation of the CovLib revealed first interesting hits. The highly cysteine-reactive fragments VS004, SN001, SN006, and SN007 covalently modify several target proteins and showed distinct shifts in the melting temperatures up to +5.1 °C and -9.1 °C.

High-electrophilic (SiO)2Nb(OH)(=O) sites confined in silanol defects over Nb-Beta zeolite for efficient cyclic alkene epoxidation reactions

Dealuminated Beta zeolite has a large amount of silanol defects on its interface, which provides an ideal place for embedding metal species and creating metal active sites in a confined microenvironment. The confined metal sites as well as their surroundings are closely related to the reactant activation and transient state achievement. Hence, unraveling the confined metal sites is of great significance for the catalytic reaction process. Herein, niobium species were incorporated into the silanol defects over dealuminated Beta zeolite with a facile dry impregnation method, co-grinding the niobium precursor with dealuminated Beta zeolite support. The successful incorporation of niobium into the silanol defects for 30Nb-Beta zeolite was verified by DRIFT, 1H MAS NMR, UV-Vis and UV-Raman characterizations. XAS characterization and DFT calculations further disclosed that the confined Nb species existed as (SiO)2Nb(OH)(=O), containing two Si-O-Nb bonds, one Nb=O bond as well as one Nb-OH bond. The synthesized 30Nb-Beta zeolite catalyst displayed a superior cyclohexene conversion of 51.1%, cyclohexene oxide selectivity of 83.1% as well as TOF value of 188.2 h-1 ascribed to the inherent electrophilicity of Nb(V) for confined (SiO)2Nb(OH)(=O) species as well as the low oxygen transfer energy barrier for NbV-OOH species. Furthermore, the prepared 30Nb-Beta zeolite can be effectively employed to other cyclic alkene epoxidation reactions.

Novel pyrazole and imidazolone compounds: synthesis, X-ray crystal structure with theoretical investigation of new pyrazole and imidazolone compounds anticipated insecticide's activities against targeting Plodia interpunctella and nilaparvata lugens

In this study, we synthesized (2-propoxyphenyl)(3-(p-tolyl)oxiran-2-yl)methanone through oxidizing the double bond of the respective chalcone via the Weitz-Scheffer epoxidation reaction. Additionally, the chalcone with an oxirane ring served as a fundamental building block for the synthesis of various pyrazole and imidazole derivatives, employing diverse nitrogen nucleophiles. All synthesized compounds were confirmed via analytical and spectroscopic analysis, such as FT-IR, 1H NMR, 13C NMR, and mass spectroscopy. Furthermore, all these nitrogen heterocycles were optimized via the DFT/B3LYP/6-31G(d,p) basis set and their physical descriptors were identified. Compound 11 was further confirmed using single-crystal X-ray diffraction with Hirshfeld analysis, and the results were correlated with the optimized structure by comparing their bond length and bond angle, which provided excellent correlation. Additionally, the insecticidal activities of the newly synthesized compounds were tested against P. interpunctella and Nilaparvata lugens. The heterocyclic compounds exhibited remarkable activity compared to the standard reference thiamethoxam. These findings were further confirmed through docking simulation with different proteins, namely PDBID 3aqy and 3wyw. The compounds interacted effectively within the protein pockets, displaying a higher binding energy with amino acids.

Valtrate, an iridoid compound in Valeriana, elicits anti-glioblastoma activity through inhibition of the PDGFRA/MEK/ERK signaling pathway

BACKGROUND

Valtrate, a natural compound isolated from the root of Valeriana, exhibits antitumor activity in many cancers through different mechanisms. However, its efficacy for the treatment of glioblastoma (GBM), a tumor type with a poor prognosis, has not yet been rigorously investigated.

METHODS

GBM cell lines were treated with valtrate and CCK-8, colony formation and EdU assays, flow cytometry, and transwell, 3D tumor spheroid invasion and GBM-brain organoid co-culture invasion assays were performed to assess properties of proliferation, viability, apoptosis and invasion/migration. RNA sequencing analysis on valtrate-treated cells was performed to identify putative target genes underlying the antitumor activity of the drug in GBM cells. Western blot analysis, immunofluorescence and immunohistochemistry were performed to evaluate protein levels in valtrate-treated cell lines and in samples obtained from orthotopic xenografts. A specific activator of extracellular signal-regulated kinase (ERK) was used to identify the pathways mediating the effect.

RESULTS

Valtrate significantly inhibited the proliferation of GBM cells in vitro by inducing mitochondrial apoptosis and suppressed invasion and migration of GBM cells by inhibiting levels of proteins associated with epithelial mesenchymal transition (EMT). RNA sequencing analysis of valtrate-treated GBM cells revealed platelet-derived growth factor receptor A (PDGFRA) as a potential target downregulated by the drug. Analysis of PDGFRA protein and downstream mediators demonstrated that valtrate inhibited PDGFRA/MEK/ERK signaling. Finally, treatment of tumor-bearing nude mice with valtrate led to decreased tumor volume (fivefold difference at day 28) and enhanced survival (day 27 vs day 36, control vs valtrate-treated) relative to controls.

CONCLUSIONS

Taken together, our study demonstrated that the natural product valtrate elicits antitumor activity in GBM cells through targeting PDGFRA and thus provides a candidate therapeutic compound for the treatment of GBM.

Sulfonic Acid-Grafted Hybrid Porous Polymer Based on Double-Decker Silsesquioxane as Highly Efficient Acidic Heterogeneous Catalysts for the Alcoholysis of Styrene Oxide

β-Alkoxyalcohols generated from epoxide ring-opening reactions are significant due to their enormous value as pharmaceutical intermediates and fine chemicals. Using a phenyl-substituted double-decker-type silsesquioxane as the precursor, a hybrid porous material (PCS-DDSQ) was synthesized through a Scholl coupling reaction with an AlCl₃ catalyst. Then, novel excellent Brønsted acid-derived silsesquioxane solid catalysts (PCS-DDSQ-SO₃H-x) were successfully obtained through an electrophilic aromatic substitution reaction of chlorosulfonic acid on phenyl rings of PCS-DDSQ, fully characterized by Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, scanning electron microscopy, energy-dispersive X-ray spectroscopy, powder X-ray diffraction, temperature-programmed desorption, water contact angle, Brunauer-Emmett-Teller model, thermogravimetric analysis, and solid-state ¹³C and ²⁹Si nuclear magnetic resonance techniques. The catalytic behavior of the PCS-DDSQ-SO₃H-x with different SO₃H loadings for the methanolysis of styrene oxide was compared and evaluated. The presence of SO₃H groups endows them with excellent catalytic abilities, achieving the highest values from PCS-DDSQ-SO₃H-1 (the acid site of its catalyst is 1.84 mmol/g) as 99% conversion and 100% selectivity for the methanolysis of styrene oxide in 30 min, which shows superior catalytic properties of low dosage and high efficiency. Furthermore, the PCS-DDSQ-SO₃H-1 catalyst can maintain high activity and selectivity after three cycles. This study provides a feasible method for the preparation of Brønsted solid acid catalysts with different acid loadings by introducing the sulfonic group into PCS-DDSQ.

Covalent Warheads Targeting Cysteine Residue: The Promising Approach in Drug Development

Cysteine is one of the least abundant amino acids in proteins of many organisms, which plays a crucial role in catalysis, signal transduction, and redox regulation of gene expression. The thiol group of cysteine possesses the ability to perform nucleophilic and redox-active functions that are not feasible for other natural amino acids. Cysteine is the most common covalent amino acid residue and has been shown to react with a variety of warheads, especially Michael receptors. These unique properties have led to widespread interest in this nucleophile, leading to the development of a variety of cysteine-targeting warheads with different chemical compositions. Herein, we summarized the various covalent warheads targeting cysteine residue and their application in drug development.

Mechanistic Details of the Sharpless Epoxidation of Allylic Alcohols—A Combined URVA and Local Mode Study

In this work, we investigated the catalytic effects of a Sharpless dimeric titanium (IV)–tartrate–diester catalyst on the epoxidation of allylalcohol with methyl–hydroperoxide considering four different orientations of the reacting species coordinated at the titanium atom (reactions R1–R4) as well as a model for the non-catalyzed reaction (reaction R0). As major analysis tools, we applied the URVA (Unified Reaction Valley Approach) and LMA (Local Mode Analysis), both being based on vibrational spectroscopy and complemented by a QTAIM analysis of the electron density calculated at the DFT level of theory. The energetics of each reaction were recalculated at the DLPNO-CCSD(T) level of theory. The URVA curvature profiles identified the important chemical events of all five reactions as peroxide OO bond cleavage taking place before the TS (i.e., accounting for the energy barrier) and epoxide CO bond formation together with rehybridization of the carbon atoms of the targeted CC double bond after the TS. The energy decomposition into reaction phase contribution phases showed that the major effect of the catalyst is the weakening of the OO bond to be broken and replacement of OH bond breakage in the non-catalyzed reaction by an energetically more favorable TiO bond breakage. LMA performed at all stationary points rounded up the investigation (i) quantifying OO bond weakening of the oxidizing peroxide upon coordination at the metal atom, (ii) showing that a more synchronous formation of the new CO epoxide bonds correlates with smaller bond strength differences between these bonds, and (iii) elucidating the different roles of the three TiO bonds formed between catalyst and reactants and their interplay as orchestrated by the Sharpless catalyst. We hope that this article will inspire the computational community to use URVA complemented with LMA in the future as an efficient mechanistic tool for the optimization and fine-tuning of current Sharpless catalysts and for the design new of catalysts for epoxidation reactions.