Epoxides: Developability as Active Pharmaceutical Ingredients and Biochemical Probes

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.