Indenone derivatives as inhibitor of human DNA dealkylation repair enzyme AlkBH3

Radical Rearrangement Reaction of Propargyl Ethers to α,β-Unsaturated Aldehydes via Photoredox and Ni Catalysis

Aryl migration, especially 1,4-aryl migration, is one of the most important reactions in radical rearrangement. Over the past decades, 1,4-aryl migration by the addition of a radical to alkynes has become a simple and efficient method in the difunctionalization reactions of alkynes. Radical-based 1,4-aryl migration of aryl alkynoates has been well-explored; however, the 1,4-aryl migration of aryl propynyl ethers is rarely studied. Herein, we first described radical 1,4-aryl migration of propargyl ether to valuable α,β-unsaturated aldehydes via photoredox and Ni catalysis. This method features redox-neutral conditions, readily available starting materials, broad substrate scope, good functional group compatibility, and diverse transformations. Mechanistic studies suggest that this reaction proceeds through a radical-involved pathway.

Methylation modifications in tRNA and associated disorders: Current research and potential therapeutic targets

High-throughput sequencing has sparked increased research interest in RNA modifications, particularly tRNA methylation, and its connection to various diseases. However, the precise mechanisms underpinning the development of these diseases remain largely elusive. This review sheds light on the roles of several tRNA methylations (m1A, m3C, m5C, m1G, m2G, m7G, m5U, and Nm) in diverse biological functions, including metabolic processing, stability, protein interactions, and mitochondrial activities. It further outlines diseases linked to aberrant tRNA modifications, related enzymes, and potential underlying mechanisms. Moreover, disruptions in tRNA regulation and abnormalities in tRNA-derived small RNAs (tsRNAs) contribute to disease pathogenesis, highlighting their potential as biomarkers for disease diagnosis. The review also delves into the exploration of drugs development targeting tRNA methylation enzymes, emphasizing the therapeutic prospects of modulating these processes. Continued research is imperative for a comprehensive comprehension and integration of these molecular mechanisms in disease diagnosis and treatment.

A HMPA-H2O mediated oxygenative carbocyclization of 2-alkynylphenyl-substituted p-quinone methides to indenones

Herein, we report a transition-metal and base-free protocol to access a wide range of functionalized indenone derivatives through a HMPA-H2O-mediated oxygenative annulation of 2-alkynylphenyl-substituted p-quinone methides. This method worked effectively for most of the p-QMs investigated and the corresponding indenone derivatives were obtained in moderate to good yields. This methodology was further extended to the formal synthesis of one of the resveratrol based natural products, (±)-isopaucifloral F.

Demethylation-activated light-up dual-color RNA aptamersensor for label-free detection of multiple demethylases in lung tissues

Methylation is one of the most prevalent epigenetic modifications in natural organisms, and the processes of methylation and demethylation are closely associated with cell growth, differentiation, gene transcription and expression. Abnormal methylation may lead to various human diseases including cancers. Simultaneous analysis of multiple DNA demethylases remains a huge challenge due to the requirement of diverse substrate probes and scarcity of proper signal transduction strategies. Herein, we propose a sensitive and label-free method for simultaneous monitoring of multiple DNA demethylases on the basis of demethylation-activated light-up dual-color RNA aptamers. The presence of targets AlkB homologue-3 (ALKBH3) and fat mass and obesity-associated enzyme (FTO) erases the methyl group in DNA substrate probes, activating the ligation-mediate bidirectional transcription amplification reaction to produce enormous Spinach and Mango aptamers. The resulting RNA aptamers (i.e., Spinach and Mango aptamers) can bind with their cognate nonfluorescent fluorogens (DFHBI and TO1-biotin) to significantly improve the fluorescence signals. This aptamersensor shows high specificity and sensitivity with a limit of detection (LOD) of 8.50 × 10-14 M for ALKBH3 and 6.80 × 10-14 M for FTO, and it can apply to screen DNA demethylase inhibitors, evaluate DNA demethylase kinetic parameters, and simultaneously measure multiple endogenous DNA demethylases in a single cell. Importantly, this aptamersensor can accurately discriminate the expressions of ALKBH3 and FTO between healthy tissues and non-small cell lung cancer (NSCLC) patient tissues, offering a powerful platform for clinical diagnosis and drug discovery.

Synthesis of 2-amidoindenone derivatives through an ynamide carbosilylation/Houben-Hoesch cyclization 2-step sequence

Herein we report the efficient and selective two-step synthesis of various 3-silyl-2-amidoindenones from easily accessible ynamides. This sequence involves a regio- and stereo-selective silylcyanation followed by a Houben-Hoesch type cyclization. Thanks to post-transformations, various 3-substituted 2-amidoindenones could be obtained.

Carbonyl Olefin Metathesis and Dehydrogenative Cyclization of Aromatic Ketones and gem-Difluoroalkenes

The beauty of one-pot cascade reaction lies in the efficient disconnection and construction of several bonds in a single reaction flask, without the isolation of any intermediates. Herein, we report the first photoinduced thermally promoted cascade reactions of readily available aromatic ketones and aromatic gem-difluoroalkenes for the synthesis of phenanthrenes which possess potential utility in drug design and materials science. The reaction combines carbonyl-olefin metathesis (cascade photoinduced [2+2] cyclization and thermally controlled retro [2+2] cyclization) and dehydrogenative cyclization (cascade photoinduced conrotatory 6π electrocyclization and collidine-promoted dehydrogenative aromatization) together in one pot. The oxidant-free, acid-free and metal-free reaction shows broad substrate scope and wide functional group tolerance.

RNA modification: mechanisms and therapeutic targets

RNA modifications are dynamic and reversible chemical modifications on substrate RNA that are regulated by specific modifying enzymes. They play important roles in the regulation of many biological processes in various diseases, such as the development of cancer and other diseases. With the help of advanced sequencing technologies, the role of RNA modifications has caught increasing attention in human diseases in scientific research. In this review, we briefly summarized the basic mechanisms of several common RNA modifications, including m6A, m5C, m1A, m7G, Ψ, A-to-I editing and ac4C. Importantly, we discussed their potential functions in human diseases, including cancer, neurological disorders, cardiovascular diseases, metabolic diseases, genetic and developmental diseases, as well as immune disorders. Through the "writing-erasing-reading" mechanisms, RNA modifications regulate the stability, translation, and localization of pivotal disease-related mRNAs to manipulate disease development. Moreover, we also highlighted in this review all currently available RNA-modifier-targeting small molecular inhibitors or activators, most of which are designed against m6A-related enzymes, such as METTL3, FTO and ALKBH5. This review provides clues for potential clinical therapy as well as future study directions in the RNA modification field. More in-depth studies on RNA modifications, their roles in human diseases and further development of their inhibitors or activators are needed for a thorough understanding of epitranscriptomics as well as diagnosis, treatment, and prognosis of human diseases.

Antioxidative Indenone and Benzophenone Derivatives from the Mangrove-Derived Fungus Cytospora heveae NSHSJ-2

Seven new polyketides, including four indenone derivatives, cytoindenones A–C (1, 3–4), 3′-methoxycytoindenone A (2), a benzophenone derivative, cytorhizophin J (6), and a pair of tetralone enantiomers, (±)-4,6-dihydroxy-5-methoxy-α-tetralone (7), together with a known compound (5) were obtained from the endophytic fungus Cytospora heveae NSHSJ-2 isolated from the fresh stem of the mangrove plant Sonneratia caseolaris. Compound 3 represented the first natural indenone monomer substituted by two benzene moieties at C-2 and C-3. Their structures were determined by the analysis of 1D and 2D NMR, as well as mass spectroscopic data, and the absolute configurations of (±)-7 were determined on the basis of the observed specific rotation value compared with those of the tetralone derivatives previously reported. In bioactivity assays, compounds 1, 4–6 showed potent DPPH· scavenging activities, with EC50 values ranging from 9.5 to 16.6 µM, better than the positive control ascorbic acid (21.9 µM); compounds 2–3 also exhibited DPPH· scavenging activities comparable to ascorbic acid.

Solvent controlled synthesis of 2,3-diarylepoxy indenones and α-hydroxy diarylindanones and their evaluation as inhibitors of DNA alkylation repair

Herein, we report a novel and unexpected metal-free oxygenation of 2,3-diphenyl-1-indenones, under an oxygen atmosphere (air), to either 2,3-epoxy-2,3-diphenyl-1-indenone or 2-hydroxy-2,3-diphenyl-1-indanone, depending on the conditions. Several bioactive epoxy indenones and one-pot α-hydroxy indanones (α-acyloin) were synthesized from 2,3-diaryl dihydroindanone and 2,3-diarylindenone, respectively. A plausible reaction mechanism is also proposed, where oxygenation would take place at the α-position and further proton abstraction from the β-position leads to epoxy indenone derivatives. A one-pot cis-hydroxy indanone protocol is also achieved directly from biaryl indenone via reduction, epimerization, and oxygenation. The synthesized compounds were evaluated for inhibitory activity against the DNA repair protein AlkB. Among the screened (17 tested) compounds, one epoxide derivative was found to be a specific inhibitor of AlkB enzyme function.

Rhodium(iii)-catalyzed successive C(sp2)–H and C(sp2)–C(sp2) bond activation of aryl oximes: synthetic and mechanistic studies

A rhodium(iii)-catalyzed redox-neutral reaction of aryl oximes and internal alkynes to generate novel N-(2-cyanoaryl) indanone imines.

Demethylation of m1A assisted degradation of the signal probe for rapid electrochemical detection of ALKBH3 activity with practical applications

ALKBH3 is an important marker for early diagnosis and histopathological grading of prostate cancer. However, the lack of a rapid and sensitive method to quantify the enzyme's activity in the current time necessitates the development of a new quantitative assay. Herein, we first tried to quantitative assay for ALKBH3 activity using an electrochemical method based on the degradation of the signal probe due to alkyl group of the m1A removal by ALKBH3. A strong electrochemical signal can be obtained when the ferrocene (Fc) labeled dsDNAs with 1-methyladenine are immobilized on the electrode. In the presence of ALKBH3, the 3' blunt of DNA can be formed because of the removal of alkyl group of the Fc-DNA probe, which can be recognized and degraded by Exonuclease III (Exo III). As a result, the electrochemical signal produced by Fc greatly decreases, and the activity of ALKBH3 can be easily detected via changes in electrochemical signal. Quantitative analysis of ALKBH3 activity showed a wide detection range (0.1 and 20 ng/mL) and low detection limit (0.04 ng/mL). Furthermore, the method can be applied to detect 1-methyladenine through ALKBH3 in cell lysates and tissue samples, providing a new method for clinical detection of prostate cancer.

Inhibition of AlkB Nucleic Acid Demethylases: Promising New Epigenetic Targets

The AlkB family of nucleic acid demethylases is currently of intense chemical, biological, and medical interest because of its critical roles in several key cellular processes, including epigenetic gene regulation, RNA metabolism, and DNA repair. Emerging evidence suggests that dysregulation of AlkB demethylases may underlie the pathogenesis of several human diseases, particularly obesity, diabetes, and cancer. Hence there is strong interest in developing selective inhibitors for these enzymes to facilitate their mechanistic and functional studies and to validate their therapeutic potential. Herein we review the remarkable advances made over the past 20 years in AlkB demethylase inhibition research. We discuss the rational design of reported inhibitors, their mode-of-binding, selectivity, cellular activity, and therapeutic opportunities. We further discuss unexplored structural elements of the AlkB subfamilies and propose potential strategies to enable subfamily selectivity. It is hoped that this perspective will inspire novel inhibitor design and advance drug discovery research in this field.

DNA Methylation on N6-Adenine Regulates the Hyphal Development during Dimorphism in the Early-Diverging Fungus Mucor lusitanicus

The epigenetic modifications control the pathogenicity of human pathogenic fungi, which have been poorly studied in Mucorales, causative agents of mucormycosis. This order belongs to a group referred to as early-diverging fungi that are characterized by high levels of N6-methyldeoxy adenine (6mA) in their genome with dense 6mA clusters associated with actively expressed genes. AlkB enzymes can act as demethylases of 6mA in DNA, with the most remarkable eukaryotic examples being mammalian ALKBH1 and Caenorhabditis elegans NMAD-1. The Mucor lusitanicus (formerly M. circinelloides f. lusitanicus) genome contains one gene, dmt1, and two genes, dmt2 and dmt3, encoding proteins similar to C. elegans NMAD-1 and ALKBH1, respectively. The function of these three genes was analyzed by the generation of single and double deletion mutants for each gene. Multiple processes were studied in the mutants, but defects were only found in single and double deletion mutants for dmt1. In contrast to the wild-type strain, dmt1 mutants showed an increase in 6mA levels during the dimorphic transition, suggesting that 6mA is associated with dimorphism in M. lusitanicus. Furthermore, the spores of dmt1 mutants challenged with macrophages underwent a reduction in polar growth, suggesting that 6mA also has a role during the spore–macrophage interaction that could be important in the infection process.

Synthesis of 2-Chloro-3-amino indenone derivatives and their evaluation as inhibitors of DNA dealkylation repair

DNA alkylation damage, emanating from the exposure to environmental alkylating agents or produced by certain endogenous metabolic processes, affects cell viability and genomic stability. Fe(II)/2-oxoglutarate-dependent dioxygenase enzymes, such as Escherichia coli AlkB, are involved in protecting DNA from alkylation damage. Inspired by the natural product indenone derivatives reported to inhibit this class of enzymes, and a set of 2-chloro-3-amino indenone derivatives was synthesized and screened for their inhibitory properties against AlkB. The synthesis of 2-chloro-3-amino indenone derivatives was achieved from 2,3-dichloro indenones through addition-elimination method using alkyl/aryl amines under catalyst-free conditions. Using an in vitro reconstituted DNA repair assay, we have identified a 2-chloro-3-amino indenone compound 3o to be an inhibitor of AlkB. We have determined the binding affinity, mode of interaction, and kinetic parameters of inhibition of 3o and tested its ability to sensitize cells to methyl methanesulfonate that mainly produce DNA alkylation damage. This study established the potential of indenone-derived compounds as inhibitors of Fe(II)/2-oxoglutarate-dependent dioxygenase AlkB.

Hypoxia-Driven Effects in Cancer: Characterization, Mechanisms, and Therapeutic Implications

Hypoxia, a common feature of solid tumors, greatly hinders the efficacy of conventional cancer treatments such as chemo-, radio-, and immunotherapy. The depletion of oxygen in proliferating and advanced tumors causes an array of genetic, transcriptional, and metabolic adaptations that promote survival, metastasis, and a clinically malignant phenotype. At the nexus of these interconnected pathways are hypoxia-inducible factors (HIFs) which orchestrate transcriptional responses under hypoxia. The following review summarizes current literature regarding effects of hypoxia on DNA repair, metastasis, epithelial-to-mesenchymal transition, the cancer stem cell phenotype, and therapy resistance. We also discuss mechanisms and pathways, such as HIF signaling, mitochondrial dynamics, exosomes, and the unfolded protein response, that contribute to hypoxia-induced phenotypic changes. Finally, novel therapeutics that target the hypoxic tumor microenvironment or interfere with hypoxia-induced pathways are reviewed.

A novel indenone derivative selectively induces senescence in MDA-MB-231 (breast adenocarcinoma) cells

Triple-negative breast cancer is the most aggressive form of breast cancer with limited intervention options. Moreover, a number of belligerent therapeutic strategies adopted to treat such aggressive forms of cancer have demonstrated detrimental side effects. This necessitates exploration of targeted chemotherapeutics. We assessed the efficacy of a novel indenone derivative (nID) [(±)-N-(2-(-5-methoxy-1-oxo-3-(2-oxo-2-phenylethyl)-2,3-dihydro-1H-inden-2-yl)ethyl)-4-methylbenzenesulfonamide], synthesized by a novel internal nucleophile-assisted palladium-catalyzed hydration-olefin insertion cascade; against triple-negative breast cancer cells (MDA-MB-231). On 24 h treatment, the nID caused decline in the viability of MDA-MB-231 and MDA-MB-468 cells, but did not significantly (P < 0.05) affect WRL-68 (epithelial-like) cells. In fact, the nID demonstrated augmentation of p53 expression, and consequent p53-dependent senescence in both MDA-MB-231 and MDA-MB-468 cells, but not in WRL-68 cells. The breast cancer cells also exhibited reduced proliferation, downregulated p65/NF-κB and survivin, along with augmented p21Cip1/WAF1 expression, on treatment with the nID. This ensued cell cycle arrest at G1 stage, which might have driven the MDA-MB-231 cells to senescence. We observed a selectivity of the nID to target MDA-MB-231 cells, whereas WRL-68 cells did not show any considerable effect. The results underscored that the nID has potential to be developed into a cancer therapeutic.

Therapeutic potential of ALKB homologs for cardiovascular disease

Cardiovascular diseases (CVDs) are the leading causes of human death. Recently, ALKB homologs, including ALKBH1-8 and FTO, have been found to have a variety of biological functions, such as histone demethylation, RNA demethylation, and DNA demethylation. These functions may regulate the physiological and pathological processes of CVDs, including inflammation, oxidative stress, cell apoptosis, and mitochondrial, endothelial, and fat metabolism dysfunction. In the present review, we summarize the biological functions of ALKB homologs and the relationship between the ALKB homologs and CVDs. Importantly, we discuss the roles of ALKB homologs in the regulation of oxidative stress, inflammation, autophagy, and DNA damage in CVDs, as well as the practical applications of ALKB homologs inhibitors or agonists in treating CVDs. In conclusion, the ALKBH family might be a promising target for CVDs therapy.

T-type calcium channel antagonist, TTA-A2 exhibits anti-cancer properties in 3D spheroids of A549, a lung adenocarcinoma cell line

AIMS

Despite the advanced cancer treatments, there is increased resistance to chemotherapy and subsequent mortality. In lack of reliable data in monolayer cultures and animal models, researchers are shifting to 3D cancer spheroids, which represents the in vivo robust tumour morphology. Calcium is essential in cell signalling and proliferation. It is found that T-type calcium channels (TTCCs) are overexpressed in various cancer cells, supporting their increased proliferation. Many of the TTCCs blockers available could target other channels besides TTCCs, which can cause adverse effects. Therefore, we hypothesise that TTA-A2, a highly selective blocker towards TTCCs, can inhibit the growth of cancer spheroids, and provide an anti-cancer and an adjuvant role in cancer therapy.

METHODS

We studied TTA-A2 and paclitaxel (PTX-control drug) in lung adenocarcinoma cell line- A549, cancer cells and human embryonic kidney cell line- HEK 293, control cell, in their monolayer and spheroids forms for viability, proliferation, morphology change, migration, and invasion-after 48-96 h of treatment.

KEY FINDINGS

Though the results varied between the monolayer and spheroids studies, we found both anti-cancer as well as adjuvant effect of TTA-A2 in both the studies. TTA-A2 was able to inhibit the growth, viability, and metastasis of the cancer cells and spheroids. Differences in the results of two modes might explain that why drugs tested successfully in monolayer culture fail in clinical trials.

SIGNIFICANCE

This study establishes the role of TTA-A2, a potent TTCC blocker as an anti-cancer and adjuvant drug in reducing the viability and metastasis of the cancer cells.

Selective Inhibitors of AlkB Family of Nucleic Acid Demethylases

The α-ketoglutarate-dependent (AlkB) superfamily of Fe^II/2-oxoglutarate (2-OG)-dependent dioxygenases consists of a unique class of nucleic acid repair enzymes that reversibly remove alkyl substituents from nucleobases through oxidative dealkylation. Recent studies have verified the involvement of AlkB dioxygenases in a variety of human diseases. However, the development of small organic molecules that can function as enzyme inhibitors to block the action of oxidative dealkylation is still in its infancy. These purposeful chemical motifs, if capable of influencing the dealkylation activity, would have a potential clinical value by controlling genetic information expression. In this Perspective, we will summarize some of the most updated inhibitors of AlkB family demethylases and hope to provide a thought for the follow-up screening optimization.

Multiple Molecular Targets Associated with Genomic Instability in Lung Cancer

Lung cancer (LC) is the first cause of cancer-related deaths worldwide. Elucidating the pathogenesis of LC will give information on key elements of tumor initiation and development while helping to design novel targeted therapies. LC is an heterogeneous disease that has the second highest mutation rate surpassed only by melanoma, since 90% of LC occurs in tobacco smokers. However, only a small percent of smokers develops LC, indicating an inherent genomic instability. Additionally, LC in never smokers suggests other molecular mechanisms not causally linked to tobacco carcinogens. This review presents a current outlook of the connection between LC and genomic instability at the molecular and clinical level summarizing its implications for diagnosis, therapy, and prognosis. The genomic landscape of LC shows widespread alterations such as DNA methylation, point mutations, copy number variation, chromosomal translocations, and aneuploidy. Genome maintenance mechanisms including cell cycle control, DNA repair, and mitotic checkpoints open a window to translational research for finding novel diagnostic biomarkers and targeted therapies in LC.

On-chip anticancer drug screening - Recent progress in microfluidic platforms to address challenges in chemotherapy

There is an increasing need for advanced and inexpensive preclinical models to accelerate the development of anticancer drugs. While costly animal models fail to predict human clinical outcomes, in vitro models such as microfluidic chips ('tumor-on-chip') are showing tremendous promise at predicting and providing meaningful preclinical drug screening outcomes. Research on 'tumor-on-chips' has grown enormously worldwide and is being widely accepted by pharmaceutical companies as a drug development tool. In light of this shift in philosophy, it is important to review the recent literature on microfluidic devices to determine how rapidly the technology has progressed as a promising model for drug screening and aiding cancer therapy. We review the past five years of successful developments and capabilities in microdevice technology (cancer models) for use in anticancer drug screening. Microfluidic devices that are being designed to address current challenges in chemotherapy, such as drug resistance, combinatorial drug therapy, personalized medicine, and cancer metastasis are also reviewed in detail. We provide a perspective on how personalized 'tumor-on-chip', as well as high-throughput microfluidic platforms based on patient-specific tumor cells, can potentially replace the more expensive and 'non-human' animal models in preclinical anticancer drug development.

Metal-free cascade rearrangement/radical addition/oxidative C–H annulation of propargyl alcohols with sodium sulfinates: access to 2-sulfenylindenones

A facile protocol for the construction of 2-sulfenylindenones via one-pot cascade rearrangement/radical addition/oxidative C–H cyclization of propargyl alcohols with sodium sulfinates has been developed.