Diverse Molecules Research Articles

Origin and characterization of cyclodepsipeptides: Comprehensive structural approaches with focus on mass spectrometry analysis of alkali-cationized molecular species.

Cyclodepsipeptides (CDPs) represent a huge family of chemically and structurally diverse molecules with a wide ability for molecular interactions. CDPs are cyclic peptide-related natural products made up of both proteinogenic and nonproteinogenic amino acids linked by amide and ester bonds. The combined use of different analytical methods is required to accurately determine their integral structures including stereochemistry, thus allowing deeper insights into their often-intriguing bioactivities and their possible usefulness. Our goal is to present the various methods developed to accurately characterize CDPs. Presently, Marfey's method and NMR (nuclear magnetic resonance) are still considered the best for characterizing CDP configuration. Nevertheless, electrospray-high resolution tandem mass spectrometry (ESI-HRMS/MS) is of great value for efficiently resolving CDP's composition and sequences. For instance, recent data shows that the fragmentation of cationized CDPs (e.g., [M + Li]+ and [M + Na]+) leads to selective cleavage of ester bonds and specific cationized product ions (b series) useful to get unprecedented sequence information. Thus, after a brief presentation of their structure, biological functions, and biosynthesis, we also provide a historic overview of these various analytical approaches as well as their advantages and limitations with a special emphasis on the emergence of methods based on HRMS/MS through recent fundamental works and applications.

Benchmarking Quantum Mechanical Levels of Theory for Valence Parametrization in Force Fields.

A wide range of density functional methods and basis sets are available to derive the electronic structure and properties of molecules. Quantum mechanical calculations are too computationally intensive for routine simulation of molecules in the condensed phase, prompting the development of computationally efficient force fields based on quantum mechanical data. Parametrizing general force fields, which cover a vast chemical space, necessitates the generation of sizable quantum mechanical data sets with optimized geometries and torsion scans. To achieve this efficiently, choosing a quantum mechanical method that balances computational cost and accuracy is crucial. In this study, we seek to assess the accuracy of quantum mechanical theory for specific properties such as conformer energies and torsion energetics. To comprehensively evaluate various methods, we focus on a representative set of 59 diverse small molecules, comparing approximately 25 combinations of functional and basis sets against the reference level coupled cluster calculations at the complete basis set limit.

Multiplexed Nanoscopy via Buffer Exchange.

Understanding cellular functions, particularly in their intricate complexity, can greatly benefit from the spatial mapping of diverse molecules through multitarget single-molecule localization microscopy (SMLM). Existing methodologies, primarily restricting the encoding dimensions to color and lifetime or requiring cyclic staining, often involve broad chromatic detection, specialized optical configurations, or sophisticated labeling techniques. Here, we propose a simple approach called buffer-exchange stochastic optical reconstruction microscopy (beSTORM), which introduces an additional dimension to differentiate between single molecules irrespective of their spectral properties. This method leverages the distinguishable photoblinking responses to distinct buffer conditions, offering a straightforward yet effective means of fluorophore discrimination. Through buffer exchanges, beSTORM achieves multitarget SMLM imaging with minimal crosstalk. Direct integration with expansion microscopy (ExM) demonstrates its capability to resolve up to six proteins at the molecular level within a single emission color without chromatic aberration. Overall, beSTORM presents a highly compatible imaging platform, promising significant advancements in highly multiplexed nanoscopy for exploring multiple targets in biological systems with nanoscale precision.

The Liebeskind-Srogl Cross-Coupling Reaction as a Crucial Step in the Synthesis of New Squaramide-Based Antituberculosis Agents.

The synthesis of an extensive series of new squaramides with high potential in treating drug-resistant tuberculosis employing the Liebeskind-Srogl cross-coupling reaction is presented. Using the protocol given and various substrates, we assessed the scope and limitations of our methodology and prepared an extensive range of desired compounds. Moreover, 1H NMR spectra in solution show the presence of two rotational conformers (rotamers) in special cases. The results of antimycobacterial activity demonstrate the highly selective substrate specificity of the tested squaramides, requiring an efficient and widely applicable synthetic approach needed for the discovery of lead compounds. Our synthetic strategy confirms the versatility of squaramides that can be easily transformed into diverse functionalized molecules.

Diverse biological communities promote SOM molecular diversity and compositional transformations during natural fallow stage in paddy fields

Monoculture cultivation patterns in agro-ecosystems only provide less varied soil organic matter (SOM) molecules of plant origin. Whether and how the natural fallow stage between cultivation seasons facilitates the restoration of SOM molecular diversity and mitigates the adverse impacts of constant cropping pattern is elusive. Here, we utilized FT-ICR-MS, UHPLC-MS/MS, and high-throughput sequencing to investigate the biological change processes in SOM molecular composition under cultivation and fallow status in a long-farmed paddy field. Our study showed that SOM molecular diversity increased by 45.70%–85.36% in fallow stage compared to rice cultivation season. SOM molecular diversity was positively correlated with bacterial diversity and root exudate molecular diversity, and negatively correlated with fungal diversity. Notably, root exudate molecular diversity accounted for 48.48% of the variation in SOM molecular diversity. The increased SOM molecular diversity in fallow stage was attributed more to the diverse plant-produced molecules than the microbe-consumed molecules. Plant species turnover resulted in the conversion of root exudate components to Organoheterocyclic compounds and Organic acids/derivatives from rice planting stage to fallow stage. Recruited microbes were dominated by Basidiomycita, Ascomycota, Acidobacteria, Chloroflexi and Proteobacteria, resulting in the transformation from carbohydrates, lipid-like SOM molecules to lipid-like and lignin-like SOM molecules. Both field and microcosm experiments confirmed that root exudates are the main source of SOM molecules, and are influenced by the soil microbial community. This study provides solid evidence that fallow status in agro-ecosystems provides explosion of biodiversity and counteracts the negative effects of long-term monoculture cultivation on SOM diversity.Graphical

Surface engineering of metal-organic framework nanoparticles-based miRNA carrier: Boosting RNA stability, intracellular delivery and synergistic therapy

MicroRNAs (miRNAs) are small noncoding RNAs that are critical for the regulation of multiple physiological and pathological processes, thus holding great clinical potential. However, the therapeutic applications of miRNAs are severely limited by their biological instability and poor intracellular delivery. Herein, we describe a dual-layers surface engineering strategy to design an efficient miRNA delivery nanosystem based on metal–organic frameworks (MOFs) incorporating lipid coating. The resulting nanoparticle system was demonstrated to protect miRNA from ribonuclease degradation, enhance cellular uptake and facilitate lysosomal escape. These ensured effective miRNA mediated gene therapy, which synergized with MOF-specific photodynamic therapy and pre-encapsulated doxorubicin (Dox) chemotherapy to provide a multifunctional with therapeutic effectiveness against cencer cells The mechanisms of miRNA binding and Dox loading were revealed, demonstrating the potential of the present MOFs surface-engineered strategy to overcome their inherent pore-size restriction for macromolecular miRNA carrying, enableefficient co-delivery. In vitro studies revealed the potential of our multifunctional system for miRNA delivery and the demonstrated the therapeutic effectiveness against cancer cells, thereby providing a versatile all-in-one MOFs strategy for delivery of nucleic acids and diverse therapeutic molecules in synergistic therapy.

Orthogonal bioconjugation targeting cysteine-containing peptides and proteins using alkyl thianthrenium salts

Late-stage specific and selective diversifications of peptides and proteins performed at target residues under ambient conditions are recognized to be the most facile route to various and abundant conjugates. Herein, we report an orthogonal modification of cysteine residues using alkyl thianthreium salts, which proceeds with excellent chemoselectivity and compatibility under mild conditions, introducing a diverse array of functional structures. Crucially, multifaceted bioconjugation is achieved through clickable handles to incorporate structurally diverse functional molecules. This “two steps, one pot” bioconjugation method is successfully applied to label bovine serum albumin. Therefore, our technique is a versatile and powerful tool for late-stage orthogonal bioconjugation.

Nanoparticle-Based Drug Delivery Systems in Inhaled Therapy: Improving Respiratory Medicine.

Inhaled nanoparticle (NP) therapy poses intricate challenges in clinical and pharmacodynamic realms. Recent strides have revolutionized NP technology by enabling the incorporation of diverse molecules, thus circumventing systemic clearance mechanisms and enhancing drug effectiveness while mitigating systemic side effects. Despite the established success of systemic NP delivery in oncology and other disciplines, the exploration of inhaled NP therapies remains relatively nascent. NPs loaded with bronchodilators or anti-inflammatory agents exhibit promising potential for precise distribution throughout the bronchial tree, offering targeted treatment for respiratory diseases. This article conducts a comprehensive review of NP applications in respiratory medicine, highlighting their merits, ranging from heightened stability to exacting lung-specific delivery. It also explores cutting-edge technologies optimizing NP-loaded aerosol systems, complemented by insights gleaned from clinical trials. Furthermore, the review examines the current challenges and future prospects in NP-based therapies. By synthesizing current data and perspectives, the article underscores the transformative promise of NP-mediated drug delivery in addressing chronic conditions such as chronic obstructive pulmonary disease, a pressing global health concern ranked third in mortality rates. This overview illuminates the evolving landscape of NP inhalation therapies, presenting optimistic avenues for advancing respiratory medicine and improving patient outcomes.

(Invited) Stabilizing Graphite Anode in Electrolytes with Micelle-Like Nanostructures for High-Rate Lithium Storage

Graphite stands out as the preferred anode material in commercial lithium-ion batteries (LIBs). However, its limited compatibility with diverse solvent molecules poses a significant challenge in selecting electrolyte solvents for LIBs. The issue arises from the co-intercalation of solvent molecules into the graphite layer alongside Li ions, resulting in layer exfoliation. This constraint has left few alternatives, primarily relying on ethylene carbonate (EC)-based mixed solvents. Consequently, the translation of electrolyte advancements from the past three decades into practical LIBs has been hindered. In this study, we present electrolytes exhibiting a micelle-like structure designed at nanoscale to impede the liquid-phase exfoliation of the graphite layer. The micelle-like electrolyte structure, derived from concentrated long-chain lithium salts, effectively segregates Li ions from free diethylene carbonate (DOL) solvent molecules. This segregation mitigates interactions between graphite particles and free solvent molecules during Li intercalation. Our proposed mechanism provides refreshed insights, highlighting the significance of the concentrated long-chain lithium salts (LiTFSI) for the graphite stability rather than the widely accepted Li coordination structure or solid electrolyte interphase. These findings offer a pivotal guideline for enhancing LIB performance by overcoming electrolyte limitations on graphite anodes.

Assembly of Selenadiazine Scaffolds via Rh(III)-Catalyzed Amidine-Directed Cascade C-H Selenylation/[5 + 1] Annulation with Elemental Selenium.

By employing elemental selenium as the selenium source, we have realized the amidine-directed Rh(III)-catalyzed cascade C-H selenylation/[5 + 1] annulation for the direct construction of structurally novel selenadiazine, benzoselenadiazine, and benzoselenazol-3-amine frameworks with specific site selectivity and good functional group tolerance. Besides, the obtained products can serve as fundamental platforms for subsequent chemical transformations, and thus, the feasible SeNEx reaction, SeNEx/Michael addition, and simple conversion of the selenadiazine product into diverse other organoselenium molecules were demonstrated accordingly. Taken together, the developed methodology efficiently expands the chemical space of organoselenium species.

Unlocking the Therapeutic Potential of Oral Cancer Stem Cell-Derived Exosomes.

Oral cancer (OC) presents a significant global health burden with rising incidence rates. Despite advancements in diagnosis and treatments, the survival rate for OC patients, particularly those with advanced or recurrent disease, remains low at approximately 20%. This poor prognosis is often due to a small population of cancer stem cells (CSCs) that are capable of self-renewal and immune evasion, playing pivotal roles in proliferation, tumor initiation, progression, metastasis, and therapy resistance. Exosomes, which are nano-sized extracellular vesicles (EVs), have emerged as crucial mediators of cell-to-cell communication within the tumor microenvironment (TME). These vesicles carry diverse molecules such as DNA, RNA, proteins, lipids, and metabolites, influencing various cellular processes. Emerging evidence suggests that CSC-derived EVs significantly promote tumor progression and metastasis and maintain the balance between CSCs and non-CSCs, which is vital for intracellular communication within the TME of oral cancer. Recent reports indicate that oral cancer stem cell-derived EVs (OCSC-EVs) influence stemness, immune evasion, metastasis, angiogenesis, tumor reoccurrence, and drug resistance. Understanding OCSC-EVs could significantly improve oral cancer diagnosis, prognosis, and therapy. In this mini-review, we explore OCSC-derived exosomes in oral cancer, examining their potential as diagnostic and prognostic biomarkers that reflect CSC characteristics, and delve into their therapeutic implications, emphasizing their roles in tumor progression and therapy resistance. However, despite their promising potential, several challenges remain, including the need to standardize isolation and characterization methods and to elucidate exosome-mediated mechanisms. Thus, a comprehensive understanding of OCSC-EVs could pave the way for innovative therapeutic strategies that have the potential to improve clinical outcomes for OC patients.

Genome and Compound Analysis of Sioxanthin-Producing Marine Actinobacterium Micromonospora sp. nov. Strain SH-82 Isolated from Sponge Scopalina hapalia.

Pigments and other secondary metabolites originating from marine microbes have been a promising natural colorants and drugs for multifaceted applications. However, marine actinobacteria producing such natural molecules are least investigated in terms of their taxonomy, chemical diversity and applications in biomedical, textile, and food industries. In this study, sioxanthin pigment-producing Gram-positive actinobacteria, Micromonospora sp. strain SH-82 was isolated from a marine sponge, Scopalina hapalia, and its whole genome was analyzed. Strain SH-82is a prolific producer of diverse chemical molecules as it produced more compounds on A1 medium with different culture conditions. The genome size of SH-82 is 6.24Mb (6,246,890bp) carrying 23 identified biosynthetic gene clusters. A total of 5415 CDS, 60 tRNA, 9 rRNA, and 1 tmRNA are identified from SH-82 genome. The GC content (%) of whole genome was 71.6%. Strain SH-82 harbors genes encoding type I, type II, and type III polyketide synthases. Based on the multi-locus sequence analysis and fatty acid methyl ester (FAME) composition, strain SH-82 is confirmed as a novel species. The genetic information of Micromonospora sp. SH-82 has been deposited to NCBI under the BioProject ID PRJNA1087320, with corresponding identifiers in the Sequence Read Archive (SRA) as SAMN40439676 and the Genome accession as CP148049.

Recent Advances in Aptamer‐Based Sensors for In Vitro Detection of Small Molecules

AbstractSensitive and accurate detection of small molecules from complex matrix has aroused increasing interest in many fields, yet remains an open challenge. Recent years have witnessed a considerable advance of aptasensors for diagnostic assay development towards diverse small molecules because aptamer is one of the most powerful classes of molecular receptors with advanced affinity and specificity. Herein, we reviewed the small‐molecule aptasensors in the past five years, focusing on the principles to specific applications in clinical diagnosis, food safety, and environmental monitoring. The first introductory section on the development of aptasensors in historical view and its analytical features contextualizes essential health‐related small molecules. The second part highlights the basic components of aptasensor and the detection principles of different sensors based on signal output modes. The subsequent part systematically discusses various small‐molecule sensing platforms by interfacing aptamers with diverse signal amplification strategies. Finally, challenges and perspectives for improving the aptasensor performance are also discussed. By describing biochemical and analytical procedures, this review highlights the optimal use of aptamers in the detection, quantification, and imaging of important health‐related small molecules and presents new insights, technical advances, and engineering strategies for practical applications.

DNA Nanotechnology Targeting Mitochondria: From Subcellular Molecular Imaging to Tailor-Made Therapeutics.

Mitochondria, one of the most important organelles, represent a crucial subcellular target for fundamental research and biomedical applications. Despite significant advances in the design of DNA nanotechnologies for a variety of bio-applications, the dearth of strategies that enable mitochondria targeting for subcellular molecular imaging and therapy remains an outstanding challenge in this field. In this Minireview, we summarize the recent progresses on the emerging design and application of DNA nanotechnology for mitochondria-targeted molecular imaging and tumor treatment. We first highlight the engineering of mitochondria-localized DNA nanosensors for in situ detection and imaging of diverse key molecules that are essential to maintain mitochondrial functions, including mitochondrial DNA and microRNA, enzymes, small molecules, and metal ions. Then, we compile the developments of DNA nanotechnologies for mitochondria-targeted anti-tumor therapy, including modularly designed DNA nanodevices for subcellular delivery of therapeutic agents, and programmed DNA assembly for mitochondrial interference. We will place an emphasis on clarification of the chemical principles of how DNA nanobiotechnology can be designed to target mitochondria for various biomedical applications. Finally, the remaining challenges and future directions in this emerging field will be discussed, hoping to inspire further development of advanced DNA toolkits for both academic and clinical research regarding mitochondria.

DNA Nanotechnology Targeting Mitochondria: From Subcellular Molecular Imaging to Tailor‐Made Therapeutics

AbstractMitochondria, one of the most important organelles, represent a crucial subcellular target for fundamental research and biomedical applications. Despite significant advances in the design of DNA nanotechnologies for a variety of bio‐applications, the dearth of strategies that enable mitochondria targeting for subcellular molecular imaging and therapy remains an outstanding challenge in this field. In this Minireview, we summarize the recent progresses on the emerging design and application of DNA nanotechnology for mitochondria‐targeted molecular imaging and tumor treatment. We first highlight the engineering of mitochondria‐localized DNA nanosensors for in situ detection and imaging of diverse key molecules that are essential to maintain mitochondrial functions, including mitochondrial DNA and microRNA, enzymes, small molecules, and metal ions. Then, we compile the developments of DNA nanotechnologies for mitochondria‐targeted anti‐tumor therapy, including modularly designed DNA nanodevices for subcellular delivery of therapeutic agents, and programmed DNA assembly for mitochondrial interference. We will place an emphasis on clarification of the chemical principles of how DNA nanobiotechnology can be designed to target mitochondria for various biomedical applications. Finally, the remaining challenges and future directions in this emerging field will be discussed, hoping to inspire further development of advanced DNA toolkits for both academic and clinical research regarding mitochondria.

A duplexed high-throughput mass spectrometry assay for bifunctional POLB polymerase and lyase activity

Polymerase β (POLB), with dual functionality as a lyase and polymerase, plays a critical role in the base excision repair (BER) pathway to maintain genomic stability. POLB knockout and rescue studies in BRCA1/2-mutant cancer cell lines revealed that inhibition of lyase and polymerase activity is required for the synthetic lethal interaction observed with PARP inhibitors, highlighting POLB as a valuable therapeutic target. Traditional biochemical assays to screen for enzyme inhibitors focus on a single substrate to product relationship and limit the comprehensive analysis of enzymes such as POLB that utilize multiple substrates or catalyze a multi-step reaction. This report describes the first high-throughput mass spectrometry-based screen to measure the two distinct biochemical activities of POLB in a single assay using a duplexed self-assembled monolayer desorption ionization (SAMDI) mass spectrometry methodology. A multiplexed assay for POLB dual enzymatic activities was developed optimizing for kinetically balanced conditions and a collection of 200,000 diverse small molecules was screened in the duplexed format. Small molecule modulators identified in the screen were confirmed in a traditional fluorescence-based polymerase strand-displacement assay and an orthogonal label-free binding assay using SAMDI affinity selection mass spectrometry (ASMS). This work demonstrates the flexibility of high-throughput mass spectrometry approaches in drug discovery and highlights a novel application of SAMDI technology that opens new avenues for multiplexed high-throughput screening.

Frustrated Lewis pairs on hollow flower-liked carbon nitride by phosphorous and tungsten co-doping to enhance photocatalytic performance

Frustrated Lewis pairs (FLPs) exhibit a distinctive “push-pull” effect that efficiently triggers the activation of diverse molecules, leading to unforeseen catalytic capabilities. In this study, phosphotungstic acid (PTA) is introduced into graphitic carbon nitride (g-C3N4). Here, phosphorus (P) as the Lewis acid (LA) site, while the electron-rich N-active site neighboring tungsten (W) assumes the role of the Lewis base (LB) site, giving g-C3N4 a FLPs-like property. The formation of FLPs creates a robust “pull-push” effect, thereby improving the separation of photogenerated carriers. This prepared CNW-20 sample demonstrates effective photocatalytic capabilities for hydrogen (H2) evolution and for degrading organic pollutants. Production levels of H2 reached up to 1044.36 μmol h−1·g−1, surpassing the bulk g-C3N4 by a factor of 14. Concurrently, the efficiency of CNW-20 sample in degrading tetracycline hydrochloride (TC) reached 83.40 %. This study introduces a novel approach for the systematic design of FLP sites on metal-doped photocatalysts, aiming to enhance the efficiency of H2 generation and the degradation of pollutants.

Transition-Metal-Catalyzed Directed C-H Bond Functionalization with Iodonium Ylides: A Review of the Last 5 Years.

Transition-metal-catalyzed directed C-H functionalization with various carbene precursors has been widely employed for constructing a wide range of complex and diverse active molecules through metal carbene migratory insertion processes. Among various carbene precursors, iodonium ylides serve as a novel and emerging carbene precursor with features including easy accessibility, thermal stability and high activity, which have attracted great attention from organic chemists and have achieved tremendous success in organic transformation. In this review, recent progress on the application of iodonium ylides with multifunctional coupling characteristics in C-H bond activation reactions is summarized, and the potential of iodonium ylides is discussed.

Supramolecular Modulator Assisted Cryo-Engineered Porous Cu-DNA Nano-Vehicles for Versatile Theranostic Agent Delivery.

DNA nanotechnology combines structural design with therapeutic functions via programmable DNA motifs, but faces challenges in drug loading capacity. Herein a pore-engineering strategy is reported to develop a highly porous, universal DNA nano-vehicle through coordination self-assembly, cryo-engineering, and supramolecular chemistry, adapting to diverse cargo loading with desired theranostic agents. Thus, the complex synthesis and compatibility challenges typically associated with switching between different drug carriers are avoided. To this end, Cu2+ and nucleic acid therapeutic G3139 self-assemble into a prefabricated solid nanostructure, which subsequently undergoes ultrafast freezing and sublimation to introduce porosity, forming highly porous Cu-G3139 nanoparticles (CG NPs). The porous CG NPs efficiently accommodate diverse therapeutic molecules, from chemotherapeutics to non-chemotherapeutic agents, facilitated by positively-charged cyclodextrin. As a proof-of-concept, the photosensitizer indocyanine green (ICG) is loaded and coated with tannic acid (TA) to form CICG@TA, enabling remarkable photothermal and fluorescence imaging-guided synergistic tumor ablation. This work represents the first demonstration of sublimation-induced pore formation in metal-DNA hybrid nanoparticles without chemical etching, offering a scalable "plug-and-play" platform for personalized cancer therapy without redesign. This versatile pore-engineering strategy, merging supramolecular chemistry with cryo-engineered porosity, opens up new avenues for efficient, customized multidrug delivery for diverse tumor theranostic applications.

Photoinduced Lignin C α -C β Bond Cleavage and Chemodivergent Functionalization via Iron Catalysis.

The photocatalytic conversion of lignin into value-added chemicals especially those functionalized molecules represent one of the most important strategies for sustainable and environmental-friendly development. Cleavage of C-C bonds in lignin under mild photocatalytic conditions for refining lignin into useful molecules is meaningful but challenging. Meanwhile, the assembly of diverse functional groups into active lignin fragments during the depolymerization is of great challenging. Herein, using cheap iron catalysts under visible light irradiation, the highly selective and efficient cleavage of Cα-Cβ bond in lignin is realized via ligand-to-metal charge transfer (LMCT) and hydrogen atom transfer (HAT) processes. The subsequent divergent functionalization of generated lignin fragment-based radical intermediates enables an efficient formation of diverse functionalized molecules. This method is also effective for cleavage of Cα-Cβ bond in native lignin, yielding two identified benzaldehyde monomers in a total yield of 8.7 wt%.