Cobalt-Catalyzed Carbon-Heteroatom Transfer Enables Regioselective Tricomponent 1,4-Carboamination.

Tricomponent cobalt(salen)-catalyzed carbofunctionalization of unsaturated substrates by radical-polar crossover has the potential to streamline access to broad classes of heteroatom-functionalized synthetic targets, yet the reaction platform has remained elusive, despite the well-developed analogous hydrofunctionalizations mediated by high-valent alkylcobalt intermediates. We report herein the development of a cobalt(salen) catalytic system that enables carbofunctionalization. The reaction entails a tricomponent decarboxylative 1,4-carboamination of dienes and provides a direct route to aromatic allylic amines by obviating preformed allylation reagents and protection of oxidation-sensitive aromatic amines. The catalytic system merges acridine photocatalysis with cobalt(salen)-catalyzed regioselective 1,4-carbofunctionalization that facilitates the crossover of the radical and polar phases of the tricomponent coupling process, revealing critical roles of the reactants, as well as ligand effects and the nature of the formal high-valent alkylcobalt species on the chemo- and regioselectivity.

Integrating bulk and single-cell sequencing data to construct a Scissor+ dendritic cells prognostic model for predicting prognosis and immune responses in ESCC.

Esophageal squamous cell carcinoma (ESCC) is characterized by molecular heterogeneity with various immune cell infiltration patterns, which have been associated with therapeutic sensitivity and resistance. In particular, dendritic cells (DCs) are recently discovered to be associated with prognosis and survival in cancer. However, how DCs differ among ESCC patients has not been fully comprehended. Recently, the advance of single-cell RNA sequencing (scRNA-seq) enables us to profile the cell types, states, and lineages in the heterogeneous ESCC tissues. Here, we dissect the ESCC tumor microenvironment at high resolution by integrating 192,078 single cells from 60 patients, including 4379 DCs. We then used Scissor, a method that identifies cell subpopulations from single-cell data that are associated bulk samples with genomic and clinical information, to stratify DCs into Scissorhi and Scissorlow subtypes. We applied the Scissorhi gene signature to stratify ESCC scRNAseq patient, and we found that PD-L1, TIGIT, PVR and IL6 ligand-receptor-mediated cell interactions existed mainly in Scissorhi patients. Finally, based on the Scissor results, we successfully developed a validated prognostic risk model for ESCC and further validated the reliability of the risk prediction model by recruiting 40 ESCC clinical patients. This information highlights the importance of these genes in assessing patient prognosis and may help in the development of targeted or personalized therapies for ESCC.

Gold-Catalyzed Oxidative Rearrangement Strategy to Yield 2-Hydroxycyclohepta-1,3-diene-1-carbonyl Compounds.

A gold-catalyzed oxidative rearrangement of propargyl alcohols, derived from commercially available cyclohex-2-en-1-ones and alkynes, was successfully developed for the efficient synthesis of seven-membered rings. Thorough investigations were conducted to optimize the reaction conditions and evaluate its compatibility with various functional groups. Additionally, this methodology was applied to the formal total synthesis of guanacastepene A, demonstrating its practical utility in complex natural product synthesis. This versatile and efficient approach opens up new possibilities for the construction of diverse seven-membered ring systems, providing valuable building blocks for further exploration in drug discovery and the synthesis of intricate molecules.

Syntheses of Tetracyclic Indoline Derivatives Via Gold(I)-Catalyzed Hydroamination/Cycloisomerization Cascade of 2-Ethynyltryptamides.

A gold(I)-catalyzed hydroamination/cycloisomerization cascade reaction was developed to yield indolizino[8,7-b]indole and indolo[2,3-a]-quinolizine derivatives from 2-ethynyltryptamides. The optimal conditions were determined by condition screening, and the functional group tolerances of these reactions were explored based on synthetic substrates. An insight into the explanation on the selectivity of the ring closure was obtained by density functional theory calculations. A plausible mechanism for the cascade reactions was proposed. Derivatization of the indolizino[8,7-b]indole and total synthesis of nauclefidine demonstrated the practicality of this strategy.

Docking Score ML: Target-Specific Machine Learning Models Improving Docking-Based Virtual Screening in 155 Targets.

In drug discovery, molecular docking methods face challenges in accurately predicting energy. Scoring functions used in molecular docking often fail to simulate complex protein-ligand interactions fully and accurately leading to biases and inaccuracies in virtual screening and target predictions. We introduce the "Docking Score ML", developed from an analysis of over 200,000 docked complexes from 155 known targets for cancer treatments. The scoring functions used are founded on bioactivity data sourced from ChEMBL and have been fine-tuned using both supervised machine learning and deep learning techniques. We validated our approach extensively using multiple data sets such as validation of selectivity mechanism, the DUDE, DUD-AD, and LIT-PCBA data sets, and performed a multitarget analysis on drugs like sunitinib. To enhance prediction accuracy, feature fusion techniques were explored. By merging the capabilities of the Graph Convolutional Network (GCN) with multiple docking functions, our results indicated a clear superiority of our methodologies over conventional approaches. These advantages demonstrate that Docking Score ML is an efficient and accurate tool for virtual screening and reverse docking.

Discovery of non-sulfonamide carbonic anhydrase IX inhibitors through structure-based virtual screening.

Carbonic anhydrase IX (CA IX) is a subtype of the human carbonic anhydrase (hCA) family and exhibits high expression in various solid tumors, rendering it a promising target for tumor therapy. Currently, marketed carbonic anhydrase inhibitors (CAIs) are primarily composed of sulfonamides derivatives, which may have impeded their potential for further expansion. Therefore, we have developed a structure-based virtual screening approach to explore novel CAIs exhibiting distinctive structures and anti-tumor potential in the FDA database. In vitro experiments demonstrated that 3-pyridinemethanol (0.42 µM), procodazole (8.35 µM) and pamidronic acid (8.51 µM) exhibited inhibitory effects on CA IX activity. The binding stability and interaction mode between the CA IX and the hit compounds are further investigated through molecular dynamics simulations and binding free energy calculations. Furthermore, the ADME/Tox prediction results indicated that these compounds exhibited favorable pharmacological properties and minimal toxic side effects. Our study successfully applied computational strategies to discover three non-sulfonamide inhibitors of carbonic anhydrase IX (CA IX) that demonstrate inhibitory activity in vitro. These findings have significant implications for the development of CA IX inhibitors and anti-tumor drugs, contributing to their progress in the field.

Application of molecular dynamics-based pharmacophore and machine learning approaches to identify novel Mcl1 inhibitors through drug repurposing and mechanics research.

Myeloid cell leukemia 1 (Mcl1), a critical protein that regulates apoptosis, has been considered as a promising target for antitumor drugs. The conventional pharmacophore screening approach has limitations in conformation sampling and data mining. Here, we offered an innovative solution to identify Mcl1 inhibitors with molecular dynamics-refined pharmacophore and machine learning methods. Considering the safety and druggability of FDA-approved drugs, virtual screening of the database was performed to discover Mcl1 inhibitors, and the hit was subsequently validated via TR-FRET, cytotoxicity, and flow cytometry assays. To reveal the binding characteristics shared by the hit and a typical Mcl1 selective inhibitor, we employed quantum mechanics and molecular mechanics (QM/MM) calculations, umbrella sampling, and metadynamics in this work. The combined studies suggested that fluvastatin had promising cell inhibitory potency and was suitable for further investigation. We believe that this research will shed light on the discovery of novel Mcl1 inhibitors that can be used as a supplemental treatment against leukemia and provide a possible method to improve the accuracy of drug repurposing with limited computational resources while balancing the costs of experimentation well.

Bioisosteric replacement strategy leads to novel DNA gyrase B inhibitors with improved potencies and properties.

The identification of novel 4-hydroxy-2-quinolone-3-carboxamide antibacterials with improved properties is of great value for the control of antibiotic resistance. In this study, a series of N-heteroaryl-substituted 4-hydroxy-2-quinolone-3-carboxamides were developed using the bioisosteric replacement strategy. As a result of our research, we discovered the two most potent GyrB inhibitors (WBX7 and WBX18), with IC50 values of 0.816 µM and 0.137 µM, respectively. Additional antibacterial activity screening indicated that WBX18 possesses the best antibacterial activity against MRSA, VISA, and VRE strains, with MIC values rangingbetween0.5and 2 µg/mL, which was 2 to over 32 times more potent than that of vancomycin. In vitro safety and metabolic stability, as well as in vivo pharmacokinetics assessments revealed that WBX18 is non-toxic to HUVEC and HepG2, metabolically stable in plasma and liver microsomes (mouse), and displays favorable in vivo pharmacokinetic properties. Finally, docking studies combined with molecular dynamic simulation showed that WBX18 could stably fit in the active site cavity of GyrB.

Potential oral VEGFR2 inhibitors: Treatment of wet age-related macular degeneration.

Wet age-related macular degeneration (w-AMD) is one of the leading causes of vision loss in industrialized countries. A large body of evidence suggests that inhibitors targeting VEGFR2 may be effective in the treatment of w-AMD. The identification of an oral VEGFR2 inhibitor for the treatment of w-AMD provides an opportunity for a route of administration other than intravitreal injection. While screening potent VEGFR2 inhibitors at the enzyme and cellular levels, ensuring the safety of the compounds was our primary strategy for screening optimal compounds. Finally, compound 16 was identified, exhibiting enhanced inhibition of VEGFR2 enzyme and proliferation of BaF3-TEL-VEGFR2 cells compared to Vorolanib. Compound 16 had a weak inhibitory effect on human Ether-a-go-go-related gene (hERG) channel currents, showing a cardiac safety profile similar to Vorolanib. Compound 16 showed no significant toxicity to human liver cell LX-2, indicating a liver safety profile similar to Vorolanib. The water solubility of compound 16 was found to be higher than that of Vorolanib when tested at pH = 7.4. In addition, compound 16 was found to inhibit VEGFR2 phosphorylation in human umbilical vein endothelial cells (HUVECs) in a dose-dependent manner by WB assay. Furthermore, the in vitro preliminary evaluation of the drug-like properties of compound 16 showed remarkable plasma stability and moderate liver microsomal stability. Based on in vivo pharmacokinetic studies in ICR mice, compound 16 exhibited acceptable oral bioavailability (F = 20.2 %). Overall, these findings provide evidence that compound 16 is a leading potential oral drug candidate for w-AMD.

Discovery of novel CDK9 inhibitor with tridentate ligand: Design, synthesis and biological evaluation.

Cyclin-dependent kinase 9 (CDK9) plays a role in transcriptional regulation, which had become an attractive target for discovery of antitumor agent. In this work, beyond traditional CDK9 inhibitor with bidentate ligands in ATP binding domain, a series of novel CDK9 inhibitor with tridentate ligand were designed and synthesized. Surprisingly, this unique tridentate ligand structure endows better CDK9 inhibition selectivity compared to other CDK subtypes, and the lead candidate compound Z4-7a showed effective proliferation inhibition in HCT116 cells with acceptable pharmacokinetic properties. Research on the mechanism indicated that Z4-7a could induce apoptosis in the HCT116 cell line by inhibiting phosphorylation of RNA polymerase II at Ser2, which resulted in the inhibition of apoptosis-related genes and proteins expression. In brief, introduction of tridentate ligand might work as a promising strategy for the development of novel selective CDK9 inhibitor.

Design and synthesis of hemicyanine-based NIRF probe for detecting Aß aggregates in Alzheimer's disease.

Alzheimer's disease (AD), a progressive neurodegenerative disorder, has garnered increased attention due to its substantial economic burden and the escalating global aging phenomenon. Amyloid-ß deposition is a key pathogenic marker observed in the brains of Alzheimer's sufferers. Based on real-time, safe, low-cost, and commonly used, near-infrared fluorescence (NIRF) imaging technology have become an essential technique for the detection of AD in recent years. In this work, NIRF probes with hemicyanine structure were designed, synthesized and evaluated for imaging Aß aggregates in the brain. We use the hemicyanine structure as the parent nucleus to enhance the probe's optical properties. The introduction of PEG chain is to improve the probe's brain dynamice properties, and the alkyl chain on the N atom is to enhance the fluorescence intensity of the probe after binding to the Aß aggregates as much as possible. Among these probes, Z2, Z3, Z6, X3, X6 and T1 showed excellent optical properties and high affinity to Aß aggregates (Kd = 24.31 âˆ¼ 59.60 nM). In vitro brain section staining and in vivo NIRF imaging demonstrated that X6 exhibited superior discrimination between Tg mice and WT mice, and X6 has the best brain clearance rate. As a result, X6 was identified as the optimal probe. Furthermore, the docking theory calculation results aided in describing X6's binding behavior with Aß aggregates. As a high-affinity, high-selectivity, safe and effective probe of targeting Aß aggregates, X6 is a promising NIRF probe for in vivo detection of Aß aggregates in the AD brain.

Nanoprobiotics for Remolding the Pro-inflammatory Microenvironment and Microbiome in the Treatment of Colitis.

Despite the great progress of current bacterially based biotherapeutics, their unsatisfying efficacy and underlying safety problems have limited their clinical application. Herein, inspired by probiotic Escherichia coli strain Nissle 1917, probiotic-derived outer membrane vesicles (OMVs) are found to serve as an effective therapeutic platform for the treatment of inflammatory bowel disease (IBD). To further enhance the therapeutic effect, the probiotic-derived OMV-encapsulating manganese dioxide nanozymes are constructed, named nanoprobiotics, which can adhere to inflamed colonic epithelium and eliminate intestinal excess reactive oxygen species in the murine IBD model. Moreover, combined with the anti-inflammatory medicine metformin, nanoprobiotics could further remold the pro-inflammatory microenvironment, improve the overall richness and diversity of the gut microbiota, and exhibit better therapeutic efficacy than commercial IBD chemotherapeutics. Importantly, insignificant overt systemic toxicity in this treatment was observed. By integrating cytokine storm calm with biotherapy, we develop a safe and effective bionanoplatform for the effective treatment of inflammation-mediated intestinal diseases.

Synthesis and Antitumor Activity Evaluation of Novel Echinatin Derivatives with a 1,3,4-Oxadiazole Moiety.

A series of novel echinatin derivatives with 1,3,4-oxadiazole moieties were designed and synthesized. Most of the newly synthesized compounds exhibited moderate antiproliferative activity against the four cancer cell lines. Notably, Compound T4 demonstrated the most potent activity, with IC50 values ranging from 1.71 µM to 8.60 µM against the four cancer cell lines. Cell colony formation and wound healing assays demonstrated that T4 significantly inhibited cell proliferation and inhibited migration. We discovered that T4 exhibited moderate binding affinity with the c-KIT protein through reverse docking. The results were effectively validated through subsequent molecular docking and c-KIT enzyme activity assays. In addition, Western blot analysis revealed that T4 inhibits the phosphorylation of downstream proteins of c-KIT. The results provide valuable inspiration for exploring novel insights into the design of echinatin-related hybrids as well as their potential application as c-KIT inhibitors to enhance the efficacy of candidates.

Methodological Development and Applications of Tryptamine-Ynamide Cyclizations in Synthesizing Core Skeletons of Indole Alkaloids.

Over the past two decades, synthetic strategies for synthesizing the skeletons of various indole alkaloids based on tryptamine-ynamide have been continuously developed and applied to the total syntheses or formal total syntheses of related molecules. In this synopsis, we summarized the cyclization pathways of tryptamine-ynamide under different catalytic conditions, emphasizing the reaction mechanism and applications in the syntheses of indole alkaloids.

Collective Syntheses of 8-Oxoprotoberberines via Sequential In(OTf)3-Catalyzed Cyclization and Pd(OAc)2-Catalyzed Heck Coupling.

Six 8-oxoprotoberberines were synthesized collectively in four steps with acceptable yields (14-19%), of which the products 8-oxopalmatine, 8-oxopseudopalmatine, 8-oxoberberine, and 8-oxopseudoberberine come from nature. The synthetic route was featured with the In(OTf)3-catalyzed cyclization and Heck coupling. Moreover, the syntheses of the natural products berberine, canadine, and iambertine were achieved via various reductions from 8-oxoberberine, which provided a concise approach to the syntheses of this kind of alkaloids.

Gold(I)-Catalyzed Substitution-Controlled Syntheses of Spiro[indoline-3,3'-pyrrolidine] and Spiro[indoline-3,3'-piperidine] Derivatives.

Spiro[indoline-3,3'-pyrrolidine] and spiro[indoline-3,3'-piperidine] derivatives were synthesized in a substitution-controlled manner under the catalysis of cationic gold(I) species in the presence of Hantzsch ester (HEH). The optimal reaction condition was determined by screening, and the functional group tolerances of these two pathways were examined by readily synthetic substrates. The endo and exo selectivities of these cyclizations were elucidated by density functional theory calculations, and a plausible mechanism for these transformations was proposed.

Quantum Mechanical Prediction and Experimental Verification of Au(I)-Catalyzed Substitution-Controlled Syntheses of 1H-Pyrido[4,3-b]indole and Spiro[indoline-3,3'-pyridine] Derivatives.

Density functional theory calculations were applied to predict the pathways of gold(I)-catalyzed cycloisomerization of the indole substrates with 1,6-enynes, which were consistent with the ensuing experimental results. The substitution-controlled synthesis led to the formation of 1H-pyrido[4,3-b]indole and spiro[indoline-3,3'-pyridine] derivatives in a tunable way. The reactions had good functional group tolerances, and a possible mechanism was proposed based on the computational and experimental results.

Identification and in silicon binding study of a novel NR2B selective NMDAR antagonist.

Alzheimer's disease (AD) is a major group of diseases that threaten human health, and the search for drugs and treatments for it has never stopped. Research and development of NMDA receptor antagonists as potential therapeutic targets have also been ongoing. Our group designed and synthesized 22 new tetrahydropyrrolo[2,1-b]quinazolines based on NR2B-NMDARs targets and evaluated them for their neuroprotective activity against NMDA-induced cytotoxicity in vitro, A21 exhibited excellent neuroprotective activity. Subsequently, the structure-activity relationships and inhibitor binding modes of the tetrahydropyrrolo[2,1-b]quinazolines were further analyzed by molecular docking, molecular dynamics (MD) simulations and binding free energy calculations. The results showed that A21 could match the two binding pockets of NR2B-NMDARs. The research results of this project will lay a certain foundation for the research of novel NR2B-NMDA receptor antagonists and also provide new ideas for the subsequent research and development of this target.

Computational insight into gold(I)-catalyzed intramolecular regioselectivity of tryptamine-ynamide cycloisomerizations.

The regioselectivity for gold(I)-catalyzed intramolecular cycloisomerizations of tryptamine-ynamides has long been elusive despite various synthetic examples of similar substrates being available. Computational studies were carried out to provide insight into the mechanisms and the origin of the substrate-dependent regioselectivity of these transformations. Based on the analyses of non-covalent interactions, distortion/interaction, and energy decomposition on the interactions between the terminal substituent of alkynes and the gold(I) catalytic ligand, the electrostatic effect was determined to be the key factor for α-position selectivity while the dispersion effect was determined to be the key factor for ß-position selectivity. Our computational results were consistent with the experimental observations. This study provides useful guidance for understanding other similar gold(I)-catalyzed asymmetric alkyne cyclization reactions.

Novel Ziyuglycoside II derivatives inhibit MCF-7 cell proliferation via inducing apoptosis and autophagy.

A series of novel ziyuglycoside II derivatives were synthesized based on the classical 1,2,3-triazole moiety. Among the tested derivatives (Z-1 - Z-15), the compound Z-15 demonstrated the most potent antiproliferative effect on K562, MCF-7 and MV411 cell lines. Moreover, Z-15 did not show obvious cytotoxicity on MCF-10A cell, a human normal mammary epithelial cell. The cell colony formation assay showed that, compared to ziyuglycoside II and 5-fluorouracil, Z-15 could inhibit cell proliferation more robustly. Wound healing assays indicated that Z-15 could significantly inhibit MCF-7 cell migration. Further mechanistic research revealed that Z-15 induced mitochondrial-mediated apoptosis and autophagy in MCF-7 cell line in a dose-dependent manner.