Recent advances in the synthesis of anticancer pyrazole derivatives using microwave, ultrasound, and mechanochemical techniques

Pyrazole and its derivatives have attracted considerable attention in pharmaceutical and medicinal chemistry, as reflected in their presence in numerous FDA-approved drugs and clinical candidates. This review presents a comprehensive analysis of articles published between 2014 and 2024, focusing on the microwave-, ultrasound-, and mechanochemical-assisted synthesis of pyrazole derivatives with anticancer activity. It explores synthetic methodologies, anticancer efficacy, and molecular docking studies, underscoring the significance of pyrazole derivatives in drug discovery and medicinal chemistry. Notably, microwave irradiation stands out as the most widely employed technique, providing high efficiency by significantly reducing reaction times while maintaining moderate temperatures. Ultrasound irradiation serves as a valuable alternative, particularly for processes that require milder conditions, whereas mechanochemical activation, though less frequently employed, offers distinct advantages in terms of sustainability.

Novel 5-(Trifluoromethyl)-1,2,4-oxadiazole-Based Pyrimidin-4-ether Histone Deacetylase Inhibitors for Controlling Rust Disease: Design, Synthesis, Activity, and Structure-Activity Relationship

Rust disease, an important plant pathogen, can lead to reduced crop or fruit production. Trifluoromethyloxadiazole (TFMO) is a class of histone deacetylase inhibitors (HDACs). Herein, a series of 5-(trifluoromethyl)-1,2,4-oxadiazole (TFMO)-based pyrimidin-4-ether derivatives were designed and synthesized. Antirust bioassay results of TFMOs showed that some of them possessed excellent activities against plant rust pathogens, such as Puccinia sorghi, Phakopsora pachyrhizi, and Puccinia rubigo. The most active compound, 3-(5-(((6-(difluoromethyl)pyrimidin-4-yl)oxy)methyl)thiophen-2-yl)-5-(trifluoromethyl)-1,2,4-oxadiazole (XII6), exhibited 50% control against P. pachyrhizi at 0.780 mg/L, which was significantly better than the commercial fungicide azoxystrobin (0%) at the same concentration. The field trial results indicated that the compound exhibited an excellent control effect against P. rubigo at 116 g a.i./ha. The acute toxic results indicated that compound XII6 has low toxicity. Furthermore, the enzyme activity results showed that compound XII6 is a strong, nonselective HDAC inhibitor. Finally, the structure-activity relationship was established, and the compound XII6-HDAC binding mode was carried out based on the crystal structure of hHDAC1, hHDAC4, and hHDAC6. This work provided an excellent fungicide against rust for further optimization.

Single Dose of a Small Molecule Leads to Complete Regressions of Large Breast Tumors in Mice

Patients with estrogen receptor α positive (ERα+) breast cancer typically undergo surgical resection, followed by 5-10 years of treatment with adjuvant endocrine therapy. This prolonged intervention is associated with a host of undesired side effects that reduce patient compliance, and ultimately therapeutic resistance and disease relapse/progression are common. An ideal anticancer therapy would be effective against recurrent and refractory disease with minimal dosing; however, there is little precedent for marked tumor regression with a single dose of a small molecule therapeutic. Herein we report ErSO-TFPy as a small molecule that induces quantitative or near-quantitative regression of tumors in multiple mouse models of breast cancer with a single dose. Importantly, this effect is robust and independent of tumor size with eradication of even very large tumors (500-1500 mm3) observed. Mechanistically, these tumor regressions are a consequence of rapid induction of necrotic cell death in the tumor and are immune cell independent. If successfully translated to human cancer patients, the benefits of such an anticancer drug that is effective with a single dose would be significant.

A mutation in RNA polymerase imparts resistance to β-lactams by preventing dysregulation of amino acid and nucleotide metabolism

Resistance to diverse antibiotics can result from mutations in RNA polymerase (RNAP), but the underlying mechanisms remain poorly understood. In this study, we compare two Bacillus subtilis RNAP mutations: one in β' (rpoC G1122D) that increases resistance to cefuroxime (CEF; a model β-lactam) and one in β (rpoB H482Y) that increases sensitivity. CEF resistance is mediated by a decrease in branched-chain amino acid (BCAA), methionine, and pyrimidine pathways. These same pathways are upregulated by CEF, and their derepression increases CEF sensitivity and antibiotic-induced production of reactive oxygen species. The CEF-resistant rpoC G1122D mutant evades these metabolic perturbations, and repression of the BCAA and pyrimidine pathways may function to restrict membrane biogenesis, which is beneficial when cell wall synthesis is impaired. These findings provide a vivid example of how RNAP mutations, which commonly arise in response to diverse selection conditions, can rewire cellular metabolism to enhance fitness.

Gold(I) N-heterocyclic carbene complexes show strong proapoptotic, antioxidant and anti-inflammatory effects in A2780 and endothelial cells

A series of eight gold(I) N-heterocyclic carbene (NHC) complexes [Au(IMes)(Ln)] based on 1,3-bis(2,4,6-trimethylphenyl)imidazole-2-ylidene (IMes) and 7-azaindole derivatives (HLn), where n = 1-8 for HL1 = 5-fluoro-7-azaindole, HL2 = 5-bromo-7-azaindole, HL3 = 3-chloro-7-azaindole, HL4 = 3-iodo-7-azaindole, HL5 = 5-bromo-3-chloro-7-azaindole, HL6 = 5-bromo-3-iodo-7-azaindole, HL7 = 4-chloro-2-methyl-7-azaindole and HL8 = 7-azaindole, was prepared, characterised and studied for their in vitro anti-cancer and anti-inflammatory effects. The complexes showed significant cytotoxicity on human ovarian cancer cell lines (A2780, IC50 ≈ 8-19 μM and A2780R, IC50 ≈ 8-19 μM) and lowered toxicity in normal HaCat and MRC-5 cells. Cellular effects of the selected complexes 1 and 7 were evaluated in A2780 cells using flow cytometry. Moreover, the time-dependent cellular uptake in A2780 cells, a shotgun proteomic analysis, an ESI-MS study of hydrolysis and interactions with l-cysteine and reduced glutathione (GSH) were performed. Complexes 1 and 7 revealed remarkable anti-inflammatory effects via inhibition of NF-κB activity in human endothelial cells.

Interaction of Avapritinib with Congo Red in Pancreatic Cancer Cells: Molecular Modeling and Biophysical Studies

Pancreatic cancer is a malignant tumor with one of the worst prognoses among solid tumors, characterized by resistance to treatment. Therefore, there is an urgent need for new methods of targeted therapy. Previous studies have shown that the overexpression of receptor tyrosine kinases such as c-KIT or PDGFR can increase proliferation, migration, and invasion of cancer cells. The aim of our study was to analyze aggregates between a supramolecular carrier (Congo red, CR) and a tyrosine kinase inhibitor (BLU-258) as well as to investigate the effect of the free inhibitor and its aggregate with Congo red (CR-BLU-258) on selected properties of pancreatic cells, including these cells' viability and three-dimensional cell spheroid cultures. To better understand the interactions between Congo red and BLU-258, we used molecular modeling in addition to biophysical methods. These attempts allowed us to determine the optimal molar ratio, which we used for in vitro studies on pancreatic cancer cell lines. A significantly greater decrease in the viability of the tested 3D cultures was observed after 48 h of incubation with CR-BLU-258, which resulted in a lower IC50 value for the tested co-aggregate compared with BLU-258 alone. Moreover, a higher resistance of PANC-1 and BxPC3 spheroid cells to the tested compounds was noted compared with the 2D culture model. A significantly lower response was observed in 3D cell cultures (BxPC3 and PANC-1) treated with BLU-258 alone compared with the 2D culture. Thus, our results showed that both BLU-258 (alone) and in its co-aggregate with Congo red exhibit anticancer activity, inhibiting the growth of pancreatic cancer cells and reducing their viability, survival, and migration. Both tested compounds also affected the phosphorylation of the selected signaling proteins. We conclude that the selected tyrosine kinase inhibitor (alone) and in its co-aggregate with Congo red exhibit anticancer activity and should be considered as a novel effective therapy against pancreatic cancer.

Survivin in cardiovascular diseases and its therapeutic potential

Aberrant changes in cell behaviors, such as proliferation, apoptosis, and migration, are some of the contributing factors to the development of various cardiovascular diseases (CVDs) and pathologies, including atherosclerosis, neointimal hyperplasia, and heart failure. In recent years, numerous studies have identified survivin, a key player in the anti-apoptotic pathway, to be extensively involved in modulating cellular functioning in cancer, with many reaching clinical trials. Though seemingly different, CVDs and cancer share abundant similarities regarding abnormal cell modifications and behaviors. This overlap has sparked growing interest in investigating survivin as a therapeutic target in the context of CVD. With new findings emerging rapidly, a comprehensive understanding of survivin's role in cardiovascular pathology is crucial to revealing its full therapeutic potential and translating these discoveries into effective treatments. This review discusses recent findings of survivin in CVDs and related pathologies, focusing on its dual role in promoting proliferation and inhibiting apoptosis, specifically in atherosclerosis, neointimal hyperplasia, stroke, hypertension, myocardial infarction, and heart failure. Across different cell types and pathological contexts, survivin plays a pivotal role throughout the disease progression-from the onset of disease development to the facilitation of compensatory mechanisms post-injury-primarily through its function in regulating cell proliferation and apoptosis. Furthermore, given the limited research on survivin as a therapeutic target for CVDs, potential clinical avenues, including YM155 (a survivin inhibitor) or adenoviral, adeno-associated, and lentiviral vectors, are also discussed. Overall, this review highlights survivin as a promising target for mitigating the detrimental effects of CVDs and to provide new perspectives to advance research on the intervention of CVDs and associated pathologies.

Synthetic Approaches to Novel DPP-IV Inhibitors-A Literature Review

Dipeptidyl peptidase IV (DPP-IV) is a serine protease whose inhibition has been an object of considerable interest in the context of developing novel treatments for type 2 diabetes mellitus. The development of novel DPP-IV inhibitors from natural or synthetic origin has seen a growing scientific interest in recent years, especially during the SARS-CoV-2 pandemic, when DPP-IV inhibitors were found to be of beneficial therapeutic value for COVID-19 patients. The present manuscript aims to summarize the most recent information on the synthesis of different DPP-IV inhibitors, emphasizing the various heterocyclic scaffolds that can be found in them. Special attention is devoted to DPP-IV inhibitors that are currently in clinical trials. Different synthetic approaches for the construction of DPP-IV inhibitors are discussed, as well as the most recent developments in the field.

Bleaching of Idesia polycarpa Maxim. Oil Using a Metal-Organic Framework-Based Adsorbent: Kinetics and Adsorption Isotherms

Idesia polycarpa Maxim. is a woody oil crop with great potential for edible oil production. While crude oil is rich in pigments, traditional bleaching methods have limited effectiveness in improving its color. In this study, a metal-organic framework (MOF) material, MIL-88B(Fe), was synthesized and used for the bleaching of Idesia polycarpa Maxim. oil. The adsorption selectivity of MIL-88B(Fe) and the adsorption process of carotenoids and chlorophyll were investigated. The results demonstrated that the synthesized MIL-88B(Fe) exhibited excellent bleaching capability, achieving a bleaching rate of 97.67% in 65 min. It showed a strong adsorption effect on pigments, particularly carotenoids. The content of lutein decreased from 118.27 mg/kg to 0.01 mg/kg after 65 min of bleaching. The squalene and phytosterol contents in the oil were minimally affected by the bleaching process, while the free fatty acid content slightly increased due to the high reaction temperature and the adsorbent properties. The adsorption process of MIL-88B(Fe) was best described by a pseudo-first-order kinetic model, indicating that the adsorption was a spontaneous and endothermic chemical process. Moreover, MIL-88B(Fe) demonstrated good safety and reusability, making it a promising novel adsorbent for the bleaching of Idesia polycarpa Maxim. oil and other oils with a high pigment content for the vegetable oil industry.

Design of Cell-Penetrating Domain Antibodies via a Genetically Encoded β-Lactam Amino Acid

Domain antibodies such as monobodies provide an attractive immunoglobin fold for evolving high-affinity protein binders targeting the intracellular proteins implicated in cell signalling. However, it remains a challenge to endow cell permeability to these small and versatile protein binders. Here, we report a streamlined approach combining orthogonal crosslinking afforded by a genetically encoded β-lactam-lysine (BeLaK) and genetic supercharging to generate cell-penetrating monobodies. When introduced to the N-terminal β-strand of a series of supercharged monobodies, BeLaK enabled efficient inter-strand crosslinking with the neighbouring lysine. Compared to its non-crosslinked counterpart, a BeLaK-crosslinked, +18-charged monobody exhibited enhanced thermostability and greater cellular uptake at 40 nM. Moreover, this structurally rigidified, supercharged monobody inhibited ERK1/2 phosphorylation in KYSE-520 esophageal cancer cell line at sub-micromolar concentration, indicating significant endosomal escape after endocytosis. Together, the discovery of this BeLaK-encoded, rigidified immunoglobin fold should facilitate the design of cell-penetrating monobodies targeting intracellular signalling proteins.

Investigations into the Efficiency of Computer-Aided Synthesis Planning

The efficiency of machine learning (ML) models is crucial to minimize inference times and reduce the carbon footprints of models deployed in production environments. Current models employed in retrosynthesis to generate a synthesis route from a target molecule to purchasable compounds are prohibitively slow. The model operates in a single-step fashion in a tree search algorithm by predicting reactant molecules given a product molecule as input. In this study, we investigate the ability of alternative transformer architectures, knowledge distillation (KD), and simple hyper-parameter optimization to decrease inference times of the Chemformer model. Initially, we assess the ability of closely related transformer architectures and conclude that these models under-performed when using KD. Additionally, we investigate the effects of feature-based and response-based KD together with hyper-parameters optimized based on inference sample time and model accuracy. We find that although reducing model size and improving single-step speed are important, our results indicate that multi-step search efficiency is more significantly influenced by the diversity and confidence of single-step models. Based on this work, further research should use KD in combination with other techniques, as multi-step speed continues to prevent proper integration of synthesis planning. However, in Monte Carlo-based (MC) multi-step retrosynthesis, other factors play a crucial role in balancing exploration and exploitation during the search process, often outweighing the direct impact of single-step model speed and carbon footprints.

Optimization of Structure-Guided Development of Chemical Probes for the Pseudoknot RNA of the Frameshift Element in SARS-CoV-2

Targeting the RNA genome of SARS-CoV-2 is a viable option for antiviral drug development. We explored three ligand binding sites of the core pseudoknot RNA of the SARS-CoV-2 frameshift element. We iteratively optimized ligands, based on improved affinities, targeting these binding sites and report on structural and dynamic properties of the three identified binding sites. Available experimental 3D structures of the pseudoknot element were compared to SAXS and NMR data to validate its dominant folding state in solution. In order to experimentally map in silico predicted binding sites, NMR assignments of the majority of nucleobases were achieved by segmental labeling of the pseudoknot RNA and isotope-filtered NMR experiments at 1.2 GHz, demonstrating the value of NMR spectroscopy to supplement modelling and docking data. Optimized ligands with enhanced affinity were shown to specifically inhibit frameshifting without affecting 0-frame translation in cell-free translation assays, establishing the frameshift element as target for drug-like ligands of low molecular weight.

Highly Functional Allyl-Bicyclo[1.1.1]pentane Synthesis by Radical-Initiated Three-Component Stereoselective Allylation

Rapid access to highly functional allylated BCP synthons can be achieved with good selectivity and yield through a radical, three-component reaction (3CR) regime using various combinations of radical precursors and vinyl-appended heterocycles acting as versatile and modular precursors. This practical process combines mild operating conditions, a wide scope of reaction partners, and the ability to diversify the functionalized allylic scaffolds further using the allyl and other functional groups as synthetic branching points. The developed protocol allows structural alteration and increases the molecular complexity through late-stage drug modifications and drug conjugation approaches. Mechanistic probes demonstrate that the 3CR process is initiated by a selective, light-promoted radical addition to [1.1.1]-propellane, followed by coupling with the vinyl-substituted heterocycle, which represents a formal decarboxylative radical addition/double bond relay/protonation sequence.

Potent and selective SETDB1 covalent negative allosteric modulator reduces methyltransferase activity in cells

A promising drug target, SETDB1, is a dual methyl-lysine (Kme) reader and methyltransferase implicated in cancer and neurodegenerative disease progression. To help understand the role of the triple Tudor domain (3TD) of SETDB1, its Kme reader, we first identify a low micromolar potency small molecule ligand, UNC6535, which occupies simultaneously both the TD2 and TD3 reader binding sites. Further optimization leads to the discovery of UNC10013, a covalent 3TD ligand targeting Cys385 of SETDB1. UNC10013 is potent with a kinact/KI of 1.0 × 106 M-1s-1 and demonstrates proteome-wide selectivity. In cells, negative allosteric modulation of SETDB1-mediated Akt methylation occurs after treatment with UNC10013. Therefore, UNC10013 is a potent, selective, and cell-active covalent ligand for the 3TD of SETDB1, demonstrating negative allosteric modulator properties and making it a promising tool to study the biological role of SETDB1 in disease progression.

Inflammation in cancer: therapeutic opportunities from new insights

As one part of the innate immune response to external stimuli, chronic inflammation increases the risk of various cancers, and tumor-promoting inflammation is considered one of the enabling characteristics of cancer development. Recently, there has been growing evidence on the role of anti-inflammation therapy in cancer prevention and treatment. And researchers have already achieved several noteworthy outcomes. In the review, we explored the underlying mechanisms by which inflammation affects the occurrence and development of cancer. The pro- or anti-tumor effects of these inflammatory factors such as interleukin, interferon, chemokine, inflammasome, and extracellular matrix are discussed. Since FDA-approved anti-inflammation drugs like aspirin show obvious anti-tumor effects, these drugs have unique advantages due to their relatively fewer side effects with long-term use compared to chemotherapy drugs. The characteristics make them promising candidates for cancer chemoprevention. Overall, this review discusses the role of these inflammatory molecules in carcinogenesis of cancer and new inflammation molecules-directed therapeutic opportunities, ranging from cytokine inhibitors/agonists, inflammasome inhibitors, some inhibitors that have already been or are expected to be applied in clinical practice, as well as recent discoveries of the anti-tumor effect of non-steroidal anti-inflammatory drugs and steroidal anti-inflammatory drugs. The advantages and disadvantages of their application in cancer chemoprevention are also discussed.

Potential of Technetium and Rhenium Theranostics

While theranostics has transformed the precision medicine landscape over the last decade, there is scope for the development of true theranostic pairs, e.g. diagnostic and therapeutic partners in which any physical, chemical, and biological differences are negligible to in vivo application. Although simple to state in theory, there are, in fact, limited options exhibiting optimal physical characteristics and wholly shared elements. Further compounding real-world application of the traditional theranostic method are additional barriers. The use of PET/CT as the cornerstone of the diagnostic pair in theranostics creates inequity of access and opportunity based on socioeconomic and geographic factors, and the growing demand for both 68Ga and 177Lu is straining production capabilities globally. Improving access to theranostics globally will require novel thinking and infrastructure investment to ensure that patients of all economic and social backgrounds have access to this transformative technology. An approach which is underdeveloped, but which may address gaps in health inequities and improve outcomes, is the application of the widely available generator-produced 99mTc for imaging and 188Re for therapy. Despite favourable and near identical radiochemistry, the search for the next generation of theranostic radionuclide pairs seldom references technetium or rhenium radionuclides. Advances in SPECT/CT instrumentation and radiochemistry provide an opportunity to deliver theranostics to communities not serviced by PET-based theranostics. The 188Re and 99mTc supply by daily elution of a generator affords significant convenience, flexibility and delayed biomolecule imaging. Low abundance gamma emissions of 188Re allow serial imaging and dosimetry calculations. 99mTc / 188Re theranostics could address inequity in access and opportunity to cutting edge theranostics.

Microwave-Assisted Synthesis of Morpholine-Based Chalcones as Reversible MAO-A Inhibitors in the Management of Mental Depression

Background: Depression is one of the most serious and common health problems among the youth population and is responsible for the initiation of many diseases. As per the World Health Organization, 3.8% of the population suffers from mental depression, globally. The monoamine oxidase-A (MAO-A) enzyme is responsible for the degradation of neurotransmitters leading to lower levels of neurotransmitters. Methods: Chalcones (C1-C15) were synthesized by reacting substituted acetophenone with various benzaldehydes in a basic ethanolic solvent at 80 °C under microwave irradiation conditions. To compare the reaction time and product yield, a conventional method of synthesis of chalcones was also performed. The synthesized chalcones (C1-C15) were spectroscopically characterized and screened initially for inhibitory activities against MAO-A and MAO-B. The best active compounds were undertaken for IC50 determination against MAO-A enzyme followed by the reversibility of inhibition analysis and the antioxidant assay. Moreover, in silico molecular docking and ADME pharmacokinetic investigations were accomplished. Results: Most of the compounds inhibited MAO-A, specifically, compounds C14 and C6 exhibited the highest inhibition at IC50 values of 7.91 ± 0.08 μM and 8.45 ± 0.19 μM, respectively. Both these compounds exhibited a reversible MAO-A inhibition displaying up to 60% recovery of enzymatic activity when diluted with substrate (Tyramine). The results of the in silico study indicated docking scores of -9.56 Kcal/mol (C14) and -9.45 Kcal/mol (C6) and exhibited a π-π stacking interaction with the crucial amino acid Trp-397. The compounds were determined to cross the blood-brain barrier (BBB) and displayed favorable gastrointestinal (GI) absorption. Further, the antioxidant assay results demonstrated that the synthesized compounds possess modest free radical scavenging potential. Conclusions: This study displayed the MAO-A inhibitory potential of morpholine-substituted chalcones as a promising pharmacophore for the development of novel antidepressant lead compounds.

Alternative Approach to Sequence-Specific Recognition of DNA: Cooperative Stacking of Dication Dimers─Sensitivity to Compound Curvature, Aromatic Structure, and DNA Sequence

With the growing number and diversity of known genome sequences, there is an increasing opportunity to regulate gene expression through synthetic, cell-permeable small molecules. Enhancing the DNA sequence recognition abilities of minor groove compounds has the potential to broaden their therapeutic applications with significant implications for areas such as modulating transcription factor activity. While various classes of minor groove binding agents can selectively identify pure AT and mixed AT and GC base pair(s) containing sequences, there remains a lack of compounds capable of distinguishing between different AT sequences. In this work, we report on the design compounds that exhibit selective binding to -TTAA- or -TATA- containing DNA minor groove sequences compared with other AT ones. Several studies have shown that the -AATT- and -TTAA- sequences have distinct physical and interaction properties, especially in terms of their different requirements for recognition in the minor groove. Achieving strong, selective minor groove binding at -TTAA- sequences has been challenging, but DB1003, a benzimidazole-furan-furan diamidine, has demonstrated cooperative dimeric binding activity at -TTAA-. It has significantly less binding preference for AATT. To better understand and modify the selectivity, we synthesized a set of rationally designed analogs of DB1003 by altering the position of the five-membered heterocyclic structure. Binding affinities and stoichiometries obtained from biosensor-surface plasmon resonance experiments show that DB1992, a benzimidazolefuran-thiophene diamidine, binds strongly to -TTAA- as a positive cooperative dimer with high cooperativity. The high-resolution crystal structure of the TTAA-DNA-DB1992 complex reveals that DB1992 binds as an antiparallel π-stacked dimer with numerous diverse contacts to the DNA minor groove. This distinctive binding arrangement and the properties of diamidines at the -TTAA- minor groove demonstrate that benzimidazole-furan-thiophene is a unique DNA binding pharmacophore. Competition mass spectroscopy and circular dichroism studies confirmed the binding stoichiometry and selectivity preference of the compounds for the -TTAA- sequence.

Identification of Key Amino Acids in the A Domains of Polymyxin Synthetase Responsible for 2,4-Diaminobutyric Acid Adenylation in Paenibacillus polymyxa NBRC3020 Strain

Developing novel nonribosomal peptides (NRPs) requires a comprehensive understanding of the enzymes involved in their biosynthesis, particularly the substrate amino acid recognition mechanisms in the adenylation (A) domain. This study focused on the A domain responsible for adenylating l-2,4-diaminobutyric acid (l-Dab) within the synthetase of polymyxin, an NRP produced by Paenibacillus polymyxa NBRC3020. To date, investigations into recombinant proteins that selectively adenylate l-Dab─exploring substrate specificity and enzymatic activity parameters─have been limited to reports on A domains found in enzymes synthesizing l-Dab homopolymers (pldA from S. celluloflavus USE31 and pddA from S. hindustanus NBRC15115), which remain exceedingly rare. The polymyxin synthetase in NBRC3020 contains five A domains specific to l-Dab, distributed across five distinct modules (modules 1, 3, 4, 5, 8, and 9). In this study, we successfully obtained soluble A domain proteins from modules 1, 5, 8, and 9 by preparing module-specific recombinant proteins. These proteins were expressed in E. coli BAP-1, purified via Ni-affinity chromatography, and demonstrated high specificity for l-Dab. Through sequence homology analysis, three-dimensional structural modeling, docking simulations to estimate substrate-binding sites, and functional validation using alanine mutants, we identified Glu281 and Asp344 as critical residues for recognizing the side chain amino group of l-Dab, and Asp238 as essential for recognizing its main chain amino group in the A domain. Notably, these key residues were conserved not only across the A domains in modules 1, 5, 8, and 9 of P. polymyxa NBRC3020 but also in those of the P. polymyxa PKB1 strain, as confirmed by sequence homology analysis. Interestingly, in pldA and pddA, the key residues involved in recognizing the side-chain amino group of l-Dab, which are conserved among polymyxin synthetases of NBRC3020 and PKB1 strain, were not observed. This suggests a potentially different mechanism for l-Dab recognition.

Unraveling aromaticity: the dual worlds of pyrazole, pyrazoline, and 3D carborane

A new series of o-carborane-fused pyrazoles has been recently successfully synthesized. This fusion was expected to create a hybrid 3D/2D aromatic system, combining the 3D aromaticity of o-carborane with the 2D aromaticity of pyrazole. However, while the boron cage retains its aromatic character, the pyrazole's aromaticity is lost. As a result, rather than forming o-carborane-fused pyrazoles, the synthesis yielded o-carborane-fused pyrazolines, which are non-aromatic. The limited overlap between the π molecular orbitals (MOs) of the planar heterocycle and the n + 1 MOs of the carborane prevents significant electronic delocalization between the two fused components. This contrasts with the fusion of pyrazole and benzene to form indazole, where both rings maintain their 2D aromaticity. Our findings demonstrate that the peripheral σ-aromaticity of carborane and the π-aromaticity of the heterocycle are orthogonal, making a true 3D/2D aromatic system unachievable. The carborane is highly aromatic, generating highly negative NICS values (-25 to -30 ppm). We have observed that these high NICS values extend to fused rings, leading to incorrect estimations of aromaticity. Therefore, relying solely on NICS can be misleading, and other computational indicators, along with experimental or structural data, should be used to accurately assess aromaticity.

Design, synthesis and biological evaluation of 2H-[1,4]oxazino-[2,3-f]quinazolin derivatives as potential EGFR inhibitors for non-small cell lung cancer

Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) have emerged as the first-line treatment for patients with EGFR-mutant non-small cell lung cancer (NSCLC). A series of 2H-[1,4]oxazino[2,3-f]quinazolin derivatives were synthesized and evaluated as irreversible EGFR-TKIs for the treatment of NSCLC. Most of the synthesized compounds demonstrated strong inhibitory activity against the EGFR kinase and the tested cancer cells. Notably, compound 4a exhibited considerable inhibitory effects against the EGFR kinase and the EGFRL858R/T790M mutant NCI-H1975 cancer cells. Compound 4a was found to suppress cell proliferation, colony formation, cell invasion, and migration, while also inducing G0/G1 phase arrest of the cell cycle in NCI-H1975 cells. Compound 4a was docked into the active pocket of the EGFR mutant to ascertain the probable binding conformation. Overall, compound 4a was identified as a promising irreversible EGFR-TKI for the treatment of NSCLC.

Effects of organic salts of virucidal and antiviral compounds from Nelumbo nucifera and Kaempferia parviflora against SARS-CoV-2

The present work investigates virucidal and antiviral compounds in the extracts of seed embryos of a lotus, Nelumbo nucifera, and a Thai ginseng, Kaempferia parviflora. Separation of the extracts led to the identification of antiviral compounds against SARS-CoV-2. Neferine (1) and nuciferine (3) from N. nucifera, as well as their respective HCl salts (2 and 4), exhibited virucidal and antiviral activities against SARS-CoV-2. Virucidal activity of neferine salt (2) (EC50 4.78 µM) was 7.5 times better than its free-base, neferine (1) (EC50 36.01 µM), and the salt (2) also improved the selectivity index (SI), showing less cytotoxicity than 1. This work demonstrates that organic salts have an impact on biological activities. A crude extract of K. parviflora rhizomes displayed virucidal activity (EC50 42.11 µg/mL) and antiviral activity (EC50 39.28 µg/mL). Isolation of a crude extract of K. parviflora rhizomes led to the identification of nine flavonoids (5-13). Among these flavonoids, only 5,7,4'-trimethoxyflavone (8) was found to show virucidal (EC50 437.90 µM) and antiviral (EC50 50.97 µM) activities against SARS-CoV-2. However, flavonoids (5-13) did not inhibit SARS-CoV-2 3CLpro enzyme at the concentrations of 10 µM and 100 µM. In conclusion, our data underscores the therapeutic potential of N. nucifera and K. parviflora derived bioactive compounds against SARS-CoV-2.

Pyrazolo[3,4-d]pyrimidine-based neplanocin analogues identified as potential de novo pharmacophores for dual-target HBV inhibition

The discovery of selective and potent inhibitors through de novo pathways is essential to combat drug resistance in chronic hepatitis B (CHB) infections. Recent studies have highlighted that neplanocin A (NepA) derivatives are biologically selective inhibitors of the hepatitis B virus (HBV). In this study, we designed, synthesized, and evaluated various pyrazolo[3,4-d]pyrimidine-based NepA analogues (4a-h) for their anti-HBV activity. Notably, analogue 4g demonstrated significant activity against HBV replication, with EC50 (HBV DNA) = 0.96 μM, CC50 > 100 μM and EC50 (HBsAg) = 0.82 μM, showing selective inhibition of HBsAg secretion. The SAR analysis concluded that replacing the polar 4-NH2 group with -CH3 also acted as a weak H-bonding donor, and the presence of 3-iodo was found to be desirable for the activity/toxicity profile. The nucleoside analogues exhibited a distinct mechanism of action compared to existing nucleoside analogues for the selective inhibition of HBsAg secretion. Based on these findings, compound 4g represents a promising lead molecule for the development of new anti-HBV agents with unique mechanisms of action.

An engineered cereblon optimized for high-throughput screening and molecular glue discovery

The majority of clinical degraders utilize an immunomodulatory imide drug (IMiD)-based derivative that directs their target to the E3 ligase receptor cereblon (CRBN); however, identification of IMiD molecular glue substrates has remained underexplored. To tackle this, we design human CRBN constructs, which retain all features for ternary complex formation, while allowing generation of homogenous and cost-efficient expression in E. coli. Extensive profiling of the construct shows it to be the "best of both worlds" in terms of binding activity and ease of production. We next designed the "Enamine focused IMiD library" and demonstrated applicability of the construct to high-throughput screening, identifying binders with high potency, ligand efficiency, and specificity. Finally, we adapt our construct for proof of principle glue screening approaches enabling IMiD cellular interactome determination. Coupled with our IMiD binding landscape the methods described here should serve as valuable tools to assist discovery of next generation CRBN glues.

Structural basis for broad-spectrum binding of AT-9010 to flaviviral methyltransferases

AT-9010 (2'-methyl-2'-fluoro guanosine triphosphate) is a GTP analog whose prodrug, AT-752 is under consideration in human medicine as a potential antiviral drug against certain flaviviruses. It was previously believed to inhibit viral replication by acting primarily as a chain terminator. However, it was discovered recently that it also binds the GTP binding site of the methyltransferase (MTase) domain of the orthoflavivirus polymerase, thus interfering with RNA capping. Here, we investigated the binding of AT-9010 to Ntaya and Zika virus MTases. Structural analysis using X-ray crystallography revealed similar interactions between the base and sugar moieties of AT-9010 and key residues in both MTases, although differences in hydrogen bonding were observed. Our analysis also suggested that the triphosphate part of AT-9010 is flexible. Despite minor variations, the overall binding mode of AT-9010 was found to be the same for all of the flaviviral MTases examined, suggesting a structural basis for the efficacy of AT-9010 against multiple orthoflavivirus MTases.

Anticancer Activity of Ether Derivatives of Chrysin

Chrysin, a naturally occurring flavonoid, exhibits a broad spectrum of biological activities, including showing anticancer properties. However, its clinical application is limited by poor bioavailability and low solubility. The introduction of an amine, amide, ester, or alkoxy group to a flavone skeleton influences the biological activity. This review also discusses hybrid compounds, such as the chrysin-porphyrin hybrid, which are characterized by higher biological activity and better bioavailability properties than single molecules. This review concentrates on the anticancer activity of chrysin and its derivatives against the most popular cancers, such as breast, lung, prostate, and gastrointestinal tumors.

Hemiphosphoindigos as a platform for chiroptical or water soluble photoswitching

Photoswitches are important molecular tools to precisely control the behavior of matter by using light irradiation. They have found application in virtually all applied chemical fields from chemical biology to material sciences. However, great challenges remain in advanced property design including tailored chiroptical responses or water solubility. Here, hemiphosphoindigo (HPI) photoswitches are presented as capable phosphorus-based photoswitches and a distinct addition to the established indigoid chromophore family. Phosphinate is embedded in the core indigoid chromophore and the resulting optimized photoswitches display high thermal stabilities, excellent fatigue resistance and high isomer enrichment. A series of planar, twisted and heterocyclic HPIs are investigated to probe design strategies for advantageous photophysical properties. The phosphinate provides a platform for easily accessible, water-soluble photoswitches, especially interesting for biological applications. Its chiral nature further allows light-induced modulation of chiroptical properties. HPIs therefore open up a distinct structural space for photoswitch generation and advanced light-responsive applications.

Photoinduced radical cyclization reaction of isocyanides with α-carbonyl bromides to access 11-alkyl-substituted 1,4-dibenzodiazepines

1,4-Dibenzodiazepines, an important component of nitrogen-containing heterocycles, are widely present in drugs. Herein, we developed a photochemical radical cascade cyclization reaction of isocyanides with α-carbonyl bromides under mild conditions. A sequence of 11-alkyl-substituted 1,4-dibenzodiazepines were produced in 53%-85% yields, demonstrating excellent tolerance towards various functional groups. Primary, secondary, and tertiary α-carbonyl bromides were effectively employed as alkyl reagents.

Recent Anti-KRASG12D Therapies: A "Possible Impossibility" for Pancreatic Ductal Adenocarcinoma

Background: Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer, able to thrive in a challenging tumor microenvironment. Current standard therapies, including surgery, radiation, chemotherapy, and chemoradiation, have shown a dismal survival prognosis, resulting in less than a year of life in the metastatic setting. Methods: The pressing need to find better therapeutic methods brought about the discovery of new targeted therapies against the infamous KRAS mutations, the major oncological drivers of PDAC. Results: The most common KRAS mutation is KRASG12D, which causes a conformational change in the protein that constitutively activates downstream signaling pathways driving cancer hallmarks. Novel anti-KRASG12D therapies have been developed for solid-organ tumors, including small compounds, pan-RAS inhibitors, protease inhibitors, chimeric T cell receptors, and therapeutic vaccines. Conclusions: This comprehensive review summarizes current knowledge on the biology of KRAS-driven PDAC, the latest therapeutic options that have been experimentally validated, and developments in ongoing clinical trials.

The Therapeutic Potential of Spirooxindoles in Cancer: A Focus on p53-MDM2 Modulation

The p53, often referred to as the "guardian of the genome", is a well-established tumor-suppressor protein that plays a critical role in regulating the cell cycle, DNA repair, differentiation, and apoptosis, with its activity primarily modulated by the MDM2 protein (murine double minute 2, also known as HDM2 in humans). Disrupting the protein-protein interaction between p53 and MDM2 represents a promising therapeutic strategy for developing anticancer agents. Recent studies have shown that several spirooxindole-containing compounds exhibit significant antitumor properties, primarily by inhibiting the p53-MDM2 interaction. This review provides an overview of structure-based spirooxindoles that could have therapeutic potential. It highlights findings from the past decade concerning their antiproliferative properties and implications for interfering with the p53-MDM2 interaction. The discussion includes various analogs of spirooxindoles as promising candidates for optimizing leads in drug discovery programs aimed at developing novel and clinically effective agents.

Enhancing the antimycobacterial efficacy of pyridine-4-carbohydrazide: linkage to additional antimicrobial agents via oxocarboxylic acids

This study evaluates the antimycobacterial potential of novel "mutual" bioactive amides, combining pyridine-4-carbohydrazide (isoniazid, INH) with various antimicrobial agents (sulphonamides, 4-aminosalicylic acid, thiosemicarbazide, diphenyl (thio)ethers) via oxocarboxylic acids. The aim was to enhance activity against both drug-susceptible and multidrug-resistant (MDR) Mycobacterium tuberculosis and non-tuberculous strains, while overcoming drug resistance through dual-action mechanisms. Many derivatives exhibited potent antimycobacterial activity, with minimum inhibitory concentrations (MICs) as low as ≤0.25 μM, outperforming INH, especially diphenyl (thio)ethers and biphenyl analogues. Additionally, the compounds were effective against M. kansasii (MICs ≤1 μM) and inhibited MDR strains at higher concentrations (≥8 μM). The cytotoxicity assay indicated a favourable safety profile, with no significant haemolysis at 125 μM, and some compounds were even protective. Selectivity for mycobacteria was confirmed by low inhibition of Gram-positive bacteria and inactivity against Gram-negative bacteria or fungi, highlighting the potential for further development as antimycobacterial agents.

Mechanistic understanding of pH as a driving force in cancer therapeutics

The development of pH-directed nanoparticles for tumor targeting represents a significant advancement in cancer biology and therapeutic strategies. These innovative materials have the ability to interact with the unique acidic microenvironment of tumors. They enhance drug delivery, increase therapeutic efficacy, and reduce systemic toxicity. The acidic conditions within tumors trigger the release of drugs from pH-responsive nanoparticles, ensuring targeted and controlled delivery directly to cancer cells while minimizing damage to healthy tissues. This review comprehensively explores the design, synthesis, and application of pH-stabilized nanoparticles in cancer therapy. It delves into the mechanisms of pH-responsive behavior, such as the use of pH-sensitive polymers and cleavable linkages that respond to the acidic tumor environment. Current strategies for nanoparticle stabilization, including surface coating, core-shell nanostructures, and hybrid nanoparticles, are discussed in detail, highlighting how these approaches enhance the stability and functionality of the nanoparticles in biological systems. Recent advancements in nanoparticle-based drug delivery systems are examined, showcasing multi-functional nanoparticles that combine therapeutic and diagnostic functions, as well as those designed for combination therapy to overcome drug resistance. This review identifies future directions in the field, such as the need for improved stability and biocompatibility, controlled and predictable drug release, and overcoming regulatory and manufacturing hurdles. Herein, we have highlighted the transformative potential of pH-stabilized nanoparticles in cancer therapy, offering a pathway towards more effective and targeted cancer treatments.

Toward target 2035: EUbOPEN - a public-private partnership to enable & unlock biology in the open

Target 2035 is a global initiative that seeks to identify a pharmacological modulator of most human proteins by the year 2035. As part of an ongoing series of annual updates of this initiative, we summarise here the efforts of the EUbOPEN project whose objectives and results are making a strong contribution to the goals of Target 2035. EUbOPEN is a public-private partnership with four pillars of activity: (1) chemogenomic library collections, (2) chemical probe discovery and technology development for hit-to-lead chemistry, (3) profiling of bioactive compounds in patient-derived disease assays, and (4) collection, storage and dissemination of project-wide data and reagents. The substantial outputs of this programme include a chemogenomic compound library covering one third of the druggable proteome, as well as 100 chemical probes, both profiled in patient derived assays, as well as hundreds of data sets deposited in existing public data repositories and a project-specific data resource for exploring EUbOPEN outputs.

FLIM-Phasor Analysis (FLIM-ϕ) of Aβ-Induced Membrane Order Alterations: Towards a Cell-Based Biosensor for Early Alzheimer's Disease Diagnosis

Alzheimer's disease (AD) is a progressive neurodegenerative disorder, and its early detection can be critical for a prompt intervention that can potentially slow down the disease progression and improve the patient's quality of life. However, a diagnosis based solely on clinical symptoms can be challenging, especially in the early stages, while the detection of specific biomarkers such as amyloid-β peptide (Aβ) and tau proteins can provide objective evidence for diagnosis. In this work, we explored the effects of Aβ peptide on cell membrane properties thanks to fluorescence lifetime imaging (FLIM) combined with the phasor analysis (FLIM-ϕ). The results showed that the membrane viscosity is altered by the presence of Aβ peptide and that cells experience this effect even at nanomolar concentrations of peptide. This considerable sensitivity opens up the possibility of envisioning a cell-based biosensor able to detect very low concentrations of Aβ in a biological fluid, thus enabling timely diagnosis and intervention.

Natural peptides and their synthetic congeners acting against Acinetobacter baumannii through the membrane and cell wall: latest progress

Acinetobacter baumannii is one of the deadliest Gram-negative bacteria (GNB), responsible for 2-10% of hospital-acquired infections. Several antibiotics are used to control the growth of A. baumannii. However, in recent decades, the abuse and misuse of antibiotics to treat non-microbial diseases have led to the emergence of multidrug-resistant A. baumannii strains. A. baumannii possesses a complex cell wall structure. Cell wall-targeting agents remain the center of antibiotic drug discovery. Notably, the antibacterial drug discovery intends to target the membrane of the bacteria, offering several advantages over antibiotics targeting intracellular systems, as membrane-targeting agents do not have to travel through the plasma membrane to reach the cytoplasmic targets. Microorganisms, insects, and mammals produce antimicrobial peptides as their first line of defense to protect themselves from pathogens and predators. Importantly, antimicrobial peptides are considered potential alternatives to antibiotics. This communication summarises the recently identified peptides of natural origin and their synthetic congeners acting against the A. baumannii membrane by cell wall disruption.

Dual ligand functionalized pH-sensitive liposomes for metastatic breast cancer treatment: in vitro and in vivo assessment

This research demonstrates the design and development of a novel dual-targeting, pH-sensitive liposomal (pSL) formulation of 5-Fluorouracil (5-FU), i.e., (5-FU-iRGD-FA-pSL) to manage breast cancer (BC). The motivation to explore this formulation is to overcome the challenges of systemic toxicity and non-specific targeting of 5-FU, a conventional chemotherapeutic agent. The proposed formulation also combines folic acid (FA) and iRGD peptides as targeting ligands to enhance tumor cell specificity and penetration, while the pH-sensitive liposomes ensure the controlled drug release in the acidic tumor microenvironment. The physicochemical characterization revealed that 5-FU-iRGD-FA-pSL possesses optimal size, low polydispersity index, and favorable zeta potential, enhancing its stability and targeting capabilities. In vitro studies demonstrated significantly enhanced cellular uptake, cytotoxicity, and inhibition of cell migration in MCF-7 BC cells compared to free 5-FU and non-targeted liposomal formulations. DAPI staining revealed significant apoptotic features, including chromatin condensation (CC) and nuclear fragmentation (NF), with 5-FU-iRGD-FA-pSL inducing more pronounced apoptosis compared to 5-FU-pSL. Furthermore, in vivo analysis in a BC rat model showed superior anti-tumor efficacy, reduced systemic toxicity, and improved safety profile of the 5-FU-iRGD-FA-pSL formulation. This dual-targeting pSL system presents a promising approach for enhancing the therapeutic index of 5-FU, offering a potential strategy for more effective BC treatment.

SIGMAP: an explainable artificial intelligence tool for SIGMA-1 receptor affinity prediction

Developing sigma-1 receptor (S1R) modulators is considered a valuable therapeutic strategy to counteract neurodegeneration, cancer progression, and viral infections, including COVID-19. In this context, in silico tools capable of accurately predicting S1R affinity are highly desirable. Herein, we present a panel of 25 classifiers trained on a curated dataset of high-quality bioactivity data of small molecules, experimentally tested as potential S1R modulators. All data were extracted from ChEMBL v33, and the models were built using five different fingerprints and machine-learning algorithms. Remarkably, most of the developed classifiers demonstrated good predictive performance. The best-performing model, which achieved an AUC of 0.90, was developed using the support vector machine algorithm with Morgan fingerprints. To provide additional, user-friendly information for medicinal chemists in the rational design of S1R modulators, two independent explainable artificial intelligence (XAI) approaches were employed, namely Shapley Additive exPlanations (SHAP) and Contrastive Explanation. The top-performing model is accessible through a user-friendly web platform, SIGMAP (https://www.ba.ic.cnr.it/softwareic/sigmap/), specifically developed for this purpose. With its intuitive interface, robust predictive power, and implemented XAI approaches, SIGMAP serves as a valuable tool for the rational design of new and more effective S1R modulators.

Design, Synthesis, and Mechanistic Anticancer Evaluation of New Pyrimidine-Tethered Compounds

Background: Despite recent breakthroughs in cancer treatment, non-small cell lung cancer (NSCLC) and breast cancer remain major causes of death from all malignancies. The epidermal growth factor receptor (EGFR) is an important mediator of the pathways involved in cell proliferation, apoptosis, and angiogenesis. Thus, its overexpression triggers several types of cancer, including NSCLC and breast cancer. Methods: In the current study, we synthesized new pyrimidine-tethered compounds (chalcone derivative (B-4), pyrazoline-carbothioamide (B-9), and pyrazoline-thiazole hybrids (BH1-7)). These compounds were then tested for cytotoxicity against A549 NSCLC and MCF-7 breast cancer cells. Results: Of these, B-4 displayed significant cytotoxicity against both cells (IC50 = 6.70 ± 1.02 µM for MCF-7; IC50 = 20.49 ± 2.7 µM for A549) compared to the standard agent lapatinib (IC50 = 9.71 ± 1.12 µM for MCF-7; IC50 = 18.21 ± 3.25 µM for A549). The anticancer potential of B-4 between Jurkat leukemic T cells and peripheral blood mononuclear cells (PBMCs) (healthy) was found to be selective. Mechanistically, 11.9% and 10.2% of A549 and MCF-7 cells treated with B-4, respectively, underwent apoptosis and B-4 produced 46% EGFR inhibition at a concentration of 10 μM. The B-4/EGFR complex obtained after induced fit docking was subjected to 300 ns of molecular dynamics simulation, which confirmed the stability of the complex in a mimicked biological environment. On the other hand, B-4 was shown to have drug-like properties by in silico pharmacokinetic estimation. Conclusions: B-4 is an EGFR inhibitor and apoptosis inducer for future NSCLC and breast cancer studies.

Transformative reactions in nitroarene chemistry: C-N bond cleavage, skeletal editing, and N-O bond utilization

Nitroarenes are highly versatile building blocks in organic synthesis, playing a pivotal role in various reactions. Common transformations involving nitroarenes include nucleophilic aromatic substitution (SNAr) reactions, where the nitro group functions both as a potent electron-withdrawing group that activates the aromatic ring and as a leaving group facilitating the substitution. Additionally, the direct transformation of nitro groups, such as reduction-driven syntheses of amines and carboxylic acids, as well as ipso-substitution SNAr reactions, have been extensively explored. Interactions between ortho-nitro groups and neighboring substituents also provide unique opportunities for selective transformations. However, beyond these well-established processes, direct transformations of nitro groups have been relatively limited. In recent years, significant advancements have been made in alternative methodologies for nitro group transformations. This review focuses on the latest progress in novel transformations of nitroarenes, with emphasis on three major categories: (i) functional group transformations involving C-N bond cleavage in nitroarenes, (ii) skeletal editing via nitrene intermediates generated by N-O bond cleavage, and (iii) the utilization of nitroarenes as an oxygen source through N-O bond cleavage. These developments under-score the expanding utility of nitroarenes in modern organic synthesis.

Short Synthesis of Structurally Diverse N-Acylhomoserine Lactone Analogs and Discovery of Novel Quorum Quenchers Against Gram-Negative Pathogens

Quorum quenchers are emerging as an alternative to conventional antimicrobials, since they hinder the development of virulence or resistance mechanisms but without killing the microorganisms, thus, reducing the risk of antimicrobial resistance. Many quorum quenchers are analogs of the natural quorum-sensing signaling molecules or autoinducers. Thus, different analogs of natural N-acylhomoserine lactones (AHLs) have been reported for controlling virulence or reducing the production of biofilms in Gram-negative pathogens. Herein we report the preparation of AHL analogs with a variety of N-substituents in just two steps from readily available N-substituted hydroxyproline esters. The substrates underwent an oxidative radical scission of the pyrrolidine ring. The resulting N-substituted β-aminoaldehyde underwent reduction and in situ cyclization to give a variety of homoserine lactones, with N- and N,N-substituted amino derivatives and with high optical purity. The libraries were screened for the inhibition of violacein production in Chromobacterium violaceum, a Gram-negative pathogen. For the first time, N,N-disubstituted AHL analogs were studied. Several N-sulfonyl derivatives, one carbamoyl, and one N-alkyl-N-sulfonyl homoserine lactone displayed a promising inhibitory activity. Moreover, they did not display microbicide action against S. aureus, C. jejuni, S. enterica, P. aeruginosa, and C. albicans, confirming a pure QQ activity. The determination of structure-activity relationships and in silico ADME studies are also reported, which are valuable for the design of next generations QQ agents.

Mass spectrometry methods and mathematical PK/PD model for decision tree-guided covalent drug development

Covalent drug discovery efforts are growing rapidly but have major unaddressed limitations. These include high false positive rates during hit-to-lead identification; the inherent uncoupling of covalent drug concentration and effect [i.e., uncoupling of pharmacokinetics (PK) and pharmacodynamics (PD)]; and a lack of bioanalytical and modeling methods for determining PK and PD parameters. We present a covalent drug discovery workflow that addresses these limitations. Our bioanalytical methods are based upon a mass spectrometry (MS) assay that can measure the percentage of drug-target protein conjugation (% target engagement) in biological matrices. Further we develop an intact protein PK/PD model (iPK/PD) that outputs PK parameters (absorption and distribution) as well as PD parameters (mechanism of action, protein metabolic half-lives, dose, regimen, effect) based on time-dependent target engagement data. Notably, the iPK/PD model is applicable to any measurement (e.g., bottom-up MS and other drug binding studies) that yields % of target engaged. A Decision Tree is presented to guide researchers through the covalent drug development process. Our bioanalytical methods and the Decision Tree are applied to two approved drugs (ibrutinib and sotorasib); the most common plasma off-target, human serum albumin; three protein targets (KRAS, BTK, SOD1), and to a promising SOD1-targeting ALS drug candidates.

Glutathiones' life in multi-cancers: especially their potential micropetides in liver hepatocellular carcinoma

BACKGROUND

Glutathione plays critical roles in detoxifying xenobiotics, cell signaling, cell death and the antioxidant defence in an emerging body of evidence, the most abundant intracellular low molecular weight thiol in tissues. However, all glutathione metabolism pertinent genes (GMPGs) expression and their diagnostic/prognostic/micropeptide potential analyses have not been investigated to perform in pan-cancers.

METHODS

We gained GMPGs from the MsigDB 7.2, 12,123 samples were used to reveal the differentially expressed genes (DEGs) and the survival analysis in 32 types of cancers from TCGA, GTEx, and GEO datasets for the first time. All statistical analyses were performed by R for bioinformatics, such as DEGs, prognostic, diagnostic analysis, ceRNA, micropeptide prediction and immune infiltration. In addition, we utilized siRNA technology to target knockdown the expression of the G6PD gene in Huh7 hepatocellular carcinoma cells.

RESULTS

G6PD was significantly expressed and poor prognosis in liver hepatocellular carcinoma (LIHC) and predicted RBM26-AS1 encoded micropeptide might target G6PD in LIHC. In vitro experiments show that G6PD knockout in Huh7 cells reduces their proliferation, migration, and invasion capabilities.

CONCLUSIONS

We confirmed that G6PD played a crucial role in the occurrence and progression of LIHC. G6PD is positively associated with Th2 cells in LIHC, regulating immune responses in the immune system. We considered that micropeptide RBM26-AS1 might be a new player involved in LIHC by interacting with G6PD, might perform a key function in liver cancer.

Mycobacterium abscessus subsp. massiliense: Biofilm Formation, Host Immune Response, and Therapeutic Strategies

Infection by Mycobacterium abscessus subsp. massiliense poses a growing public health threat, especially to immunocompromised individuals. The pathogenicity of this mycobacterium is directly linked to its ability to form biofilms, complex structures that confer resistance to antibiotics and the host immune response. The extracellular matrix of the biofilm acts as a physical barrier, hindering the penetration of drugs and the action of the immune system, while also inducing a slow-growth state that reduces susceptibility to antibiotics. Current therapies, which involve prolonged use of multiple antibiotics, are often ineffective and cause significant side effects. Therefore, it is essential to explore new strategies targeting bacterial resistance and biofilm destruction. This narrative review explores the biofilm-forming capacity of Mycobacterium abscessus subsp. massiliense and the potential of novel therapeutic strategies. Promising approaches include inhibiting biofilm formation, developing drugs with improved penetration of the extracellular matrix, combination therapies with agents that destabilize the biofilm structure, and modulating the host immune response. Investing in research and development of new therapeutic strategies is essential to combat this resistant bacterium and improve patient outcomes.

Nanomaterial-Based Strategies to Combat Antibiotic Resistance: Mechanisms and Applications

The rapid rise of antibiotic resistance has become a global health crisis, necessitating the development of innovative strategies to combat multidrug-resistant (MDR) pathogens. Nanomaterials have emerged as promising tools in this fight, offering unique physicochemical properties that enhance antibiotic efficacy, overcome resistance mechanisms, and provide alternative therapeutic approaches. This review explores the diverse nanomaterial-based strategies used to combat antibiotic resistance, focusing on their mechanisms of action and practical applications. Nanomaterials such as metal nanoparticles, carbon-based nanomaterials, and polymeric nanostructures exhibit antibacterial properties through various pathways, including the generation of reactive oxygen species (ROS), disruption of bacterial membranes, and enhancement of antibiotic delivery. Additionally, the ability of nanomaterials to bypass traditional resistance mechanisms, such as biofilm formation and efflux pumps, has been demonstrated in numerous studies. This review also discusses the synergistic effects observed when nanomaterials are combined with conventional antibiotics, leading to increased bacterial susceptibility and reduced required dosages. By highlighting the recent advancements and clinical applications of nanomaterial-antibiotic combinations, this paper provides a comprehensive overview of how nanomaterials are reshaping the future of antibacterial therapies. Future research directions and challenges, including toxicity and scalability, are also addressed to guide the development of safer, more effective nanomaterial-based antibacterial treatments.

The role of efferocytosis in inflammatory bowel disease

Efferocytosis is the process by which various phagocytes clear apoptotic cells. In recent years, an increasing body of evidence has emphasized the importance of efferocytosis in maintaining internal homeostasis. Intestinal macrophages play a crucial role in modulating intestinal inflammation and promoting tissue repair. Inflammatory bowel disease (IBD) is a chronic, progressive, and relapsing condition, primarily marked by the presence of ulcers in the digestive tract. The exact mechanisms underlying IBD are not yet fully understood, and current treatment approaches mainly aim at repairing the damaged intestinal mucosa and reducing inflammatory responses to ease symptoms.This article provides new perspectives on IBD treatment and clinical management by examining the expression of macrophage efferocytosis-related molecules, the effects of efferocytosis on IBD development, the various roles of macrophage efferocytosis in IBD, and treatment strategies for IBD that focus on efferocytosis.

Solvent-controlled silver catalyzed radical transformation of α-imino-oxy acids with cyclic aldimines

A silver-catalyzed cross coupling of cyclic aldimines and α-imino-oxy acids has been developed. The solvent-dependent reaction could selectively deliver either cyclic imine moiety retained nitriles or ring-opened oxonitriles in moderate yields. The mechanistic studies show that the reaction undergoes a radical pathway.

Probing the Protein Kinases' Cysteinome by Covalent Fragments

Protein kinases are important drug targets, yet specific inhibitors have been developed for only a fraction of the more than 500 human kinases. A major challenge in designing inhibitors for highly related kinases is selectivity. Unlike their non-covalent counterparts, covalent inhibitors offer the advantage of selectively targeting structurally similar kinases by modifying specific protein side chains, particularly non-conserved cysteines. Previously, covalent fragment screens yielded potent and selective inhibitors for individual kinases such as ERK1/2 but have not been applied to the broader kinome. Furthermore, many of the accessible cysteine positions have not been addressed so far. Here, we outline a generalizable approach to sample ATP-site cysteines with fragment-like covalent inhibitors. We present the development of a kinase-focused covalent fragment library and its systematic screening against a curated selection of 47 kinases, with 60 active site-proximal cysteines using LC/MS and differential scanning fluorimetry (DSF) assays, followed by hit validation through various complementary techniques. Our findings expand the repertoire of targetable cysteines within protein kinases, provide insight into unique binding modes identified from crystal structures and deliver isoform-specific hits with promising profiles as starting points for the development of highly potent and selective covalent inhibitors.

Difunctionalization of bicyclo[1.1.0]butanes enabled by merging C-C cleavage and ruthenium-catalysed remote C-H activation

The high fraction of sp 3-hybridized carbon atom (Fsp 3) character of cyclobutane derivatives renders them as highly promising bioisosteres for otherwise typically flat arenes. Here, to address the current needs in medicinal chemistry for Fsp 3-rich molecules, we disclose a distinct strategy that exploits the merger of C-C scission in bicyclo[1.1.0]butanes (BCBs) with ruthenium-catalysed remote C-H functionalization of heteroarenes, affording densely substituted cyclobutanes in a chemo-controlled manner. This approach enabled the rapid and efficient synthesis of versatile tri- and tetrasubstituted cyclobutanes by coupling a wide range of mono- or disubstituted BCBs with heteroarenes and alkyl halides under mild reaction conditions, featuring ample substrate scope. The C-C/C-H functionalization was ensured by a multifunctional ruthenium(II) catalyst that enabled ruthenacycle-mediated halogen-atom transfer (Ru-XAT), as well as the selective functionalization of BCBs by strain release. Experimental and computational mechanistic studies unravelled a multi-catalysis manifold, while the C-H/C-C functionalization strategy allowed for telescoping late-stage modification.

Peptide design to control protein-protein interactions

Targeting of protein-protein interactions has become of huge interest in every aspect of medicinal and biological sciences. The control of protein interactions selectively offers the opportunity to control biological processes while limiting off target effects. This interest has massively increased with the development of cryo-EM and protein structure prediction with tools such as RosettaFold and AlphaFold. When designing molecules to control protein interactions, either inhibition or stabilisation, a starting point is commonly peptide design. This tutorial review describes that process, highlighting the selection of an initial sequence with and without structural information. Subsequently, methods for how the sequence can be analysed for key residues and how this information can be used to optimise the ligand efficiency are highlighted. Finally a discussion on how peptides can be further modified to increase their affinity and cell permeability, improving their drug-like properties, is presented.

Selective Recognition of Oncogene Promoter C-Myc G-Quadruplex: Design, Synthesis, and In Vitro Evaluation of Naphthalimide and Imidazo[1,2-a]pyrazines for Their Anticancer Activity

c-Myc is a transcription factor that is overexpressed in most human cancers. Despite its challenging nature, we have developed a series of naphthalimide-imidazopyrazine conjugates to target c-Myc. The library of synthesized derivatives was tested for their anticancer activity against a nine-panel of cancer cell lines. Compound 8eb showed excellent cytotoxicity against all the tested cancer cell lines, with the range of growth inhibition from -98.79% to 96.62% at a single-dose concentration of 10-5 M. Further, 8eb was employed for a 5-dose assay against the same cancer cell lines, which showed efficacy at varying concentrations with an MG-MID GI50 value of 2.61 μM. Biophysical studies were performed to explore the interaction of 8eb with c-Myc Pu27 over ct-DNA, oncogene promotor Pu22, and human telomere, with a binding constant value of 1.3 × 107 M-1. Additionally, experiments were performed to get insights into the interaction mechanism between 8eb and the c-Myc oncogene promoter. A molecular docking study unveiled the stacking of the compound with G4 DNA through groove binding, where very few reports are available, with a favorable binding energy of -9.2 kcal/mol. Moreover, the pharmacokinetic study and HOMO-LUMO energy gap analysis underscored the potency of the active candidate. The compound's binding ability toward HSA was also assessed, where results suggested effective binding of the compound to HSA, revealing its potential for easy delivery to the target site. The above findings suggested that these newly synthesized candidates with potent anticancer activity offer a promising avenue as G4 DNA c-Myc stabilizers.