jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Monica G. Kamel | Farid M. Sroor | Khaled Mahmoud | Heba I. Shafey | Hamdi M. Hassaneen | Laure Vendier
Source: RSC Advances (article, 2025-01-01)
Field: Chemistry — Organic Chemistry

Utility of 6-aza-2-thiothymine in the synthesis of novel [1,2,4]triazolo[4,3-<i>b</i>][1,2,4]triazin-7-one derivatives: synthesis, structure elucidation, molecular docking and <i>in vitro</i> anti-lung cancer activity Using 6-aza-2-thiothymine (ATT) as a suitable precursor, a novel series of [1,2,4]triazolo[4,3-<i>b</i>][1,2,4]triazin-7-one derivatives (7a-j) was prepared by refluxing 6-methyl-3-thioxo-3,4-dihydro-1,2,4-triazin-5(2<i>H</i>)-one (3) with hydrazonoyl halides (1a-j) in chloroform in the presence of triethylamine. The structures of the newly synthesized compounds 7a-j were confirmed using spectral data, elemental analyses, and single-crystal X-ray diffraction results. All the synthesized triazolotriazin-7-one derivatives (7a-j) were evaluated as <i>in vitro</i> anti-cancer agents against PC3 (prostate cell line), A549 (lung carcinoma), PACA2 (pancreatic cancer cell line) and BJ1 (normal skin fibroblast) cell lines using MTT assay. Compounds 7a and 7g showed greater efficacy and low IC<sub>50</sub> values (36.6 and 40.1 μM, respectively) compared to the reference drug, which exhibited an IC<sub>50</sub> value of 43.8 μM on the lung cell line, and demonstrated safe mortality effect on the normal cell line (BJ1) with cytotoxicity percentages of 3.5% and 2.8%, respectively. These compounds (7a and 7g) were the most active compounds of the synthesized triazolotriazin-7-one derivatives (7a-j). They were further investigated to ascertain their mechanism of action using DNA fragmentation, DNA damage and gene expression (BCL-2, BAX, and p53 genes). Results indicated a significant increase in the expression levels of BCL-2 and a reduction in the expression of p53 and BAX genes in negative lung cancer cell lines. However, the treatment of negative cell lines with 7g improved the expression of the tested genes to a greater extent than that with 7a. Additionally, the DNA damage and DNA fragmentation levels were significantly elevated in the lung cancer cell line samples treated with 7a much more than 7g. Molecular docking was employed to explore the potential interactions between the most active compounds (7a and 7g) and two key enzymes, human 3-phosphoglycerate dehydrogenase (PHGDH) and phosphoserine aminotransferase (PSAT1), which play vital roles in the progression of lung cancer. Chemistry ; Stereochemistry ; Docking (animal) ; Combinatorial chemistry ; DNA ; Molecular model ; A549 cell ; In vitro ; Biochemistry Synthesis and Characterization of Heterocyclic Compounds ; Click Chemistry and Applications ; Synthesis and biological activity
Authors: Bryn Reimer | Ernest Awoonor‐Williams | Andrei A. Golosov | Viktor Horn̆ák
Source: Journal of Chemical Information and Modeling (article, 2025-01-09)
Field: Chemistry — Organic Chemistry

CovCysPredictor: Predicting Selective Covalently Modifiable Cysteines Using Protein Structure and Interpretable Machine Learning Targeted covalent inhibition is a powerful therapeutic modality in the drug discoverer's toolbox. Recent advances in covalent drug discovery, in particular, targeting cysteines, have led to significant breakthroughs for traditionally challenging targets such as mutant KRAS, which is implicated in diverse human cancers. However, identifying cysteines for targeted covalent inhibition is a difficult task, as experimental and in silico tools have shown limited accuracy. Using the recently released CovPDB and CovBinderInPDB databases, we have trained and tested interpretable machine learning (ML) models to identify cysteines that are liable to be covalently modified (i.e., "ligandable" cysteines). We explored myriad physicochemical features (p<i>K</i><sub>a</sub>, solvent exposure, residue electrostatics, etc.) and protein-ligand pocket descriptors in our ML models. Our final logistic regression model achieved a median F<sub>1</sub> score of 0.73 on held-out test sets. When tested on a small sample of <i>holo</i> proteins, our model also showed reasonable performance, accurately predicting the most ligandable cysteine in most cases. Taken together, these results indicate that we can accurately predict potential ligandable cysteines for targeted covalent drug discovery, privileging cysteines that are more likely to be selective rather than purely reactive. We release this tool to the scientific community as CovCysPredictor. In silico ; Drug discovery ; Covalent bond ; Computational biology ; Cysteine ; Toolbox ; Chemistry ; Machine learning ; Artificial intelligence ; Computer science ; Biochemistry ; Biology Click Chemistry and Applications ; Computational Drug Discovery Methods ; Chemical Synthesis and Analysis
Authors: Eric A. Chen | Yingkai Zhang
Source: Journal of Chemical Information and Modeling (article, 2025-04-01)
Field: Chemistry — Spectroscopy

Can Deep Learning Blind Docking Methods be Used to Predict Allosteric Compounds? Allosteric compounds offer an alternative mode of inhibition to orthosteric compounds with opportunities for selectivity and noncompetition. Structure-based drug design (SBDD) of allosteric compounds introduces complications compared to their orthosteric counterparts; multiple binding sites of interest are considered, and often allosteric binding is only observed in particular protein conformations. Blind docking methods show potential in virtual screening allosteric ligands, and deep learning methods, such as DiffDock, achieve state-of-the-art performance on protein-ligand complex prediction benchmarks compared to traditional docking methods such as Vina and Lin_F9. To this aim, we explore the utility of a data-driven platform called the minimum distance matrix representation (MDMR) to retrospectively predict recently discovered allosteric inhibitors complexed with Cyclin-Dependent Kinase (CDK) 2. In contrast to other protein complex representations, it uses the minimum residue-residue (or residue-ligand) distance as a feature that prioritizes the formation of interactions. Analysis of this representation highlights the variety of protein conformations and ligand binding modes, and we identify an intermediate protein conformation that other heuristic-based kinase conformation classification methods do not distinguish. Next, we design self- and cross-docking benchmarks to assess whether docking methods can predict both orthosteric and allosteric binding modes and if prospective success is conditional on the selection of the protein receptor conformation, respectively. We find that a combined method, DiffDock followed by Lin_F9 Local Re-Docking (DiffDock + LRD), can predict both orthosteric and allosteric binding modes, and the intermediate conformation must be selected to predict the allosteric pose. In summary, this work highlights the value of a data-driven method to explore protein conformations and ligand binding modes and outlines the challenges of SBDD of allosteric compounds. Docking (animal) ; Allosteric regulation ; Artificial intelligence ; Computer science ; Computational biology ; Machine learning ; Chemistry ; Biology ; Biochemistry ; Medicine ; Receptor Analytical Chemistry and Chromatography ; Computational Drug Discovery Methods ; Metabolomics and Mass Spectrometry Studies
Authors: Jyotirmoy Ghosh | R. Graham Cooks
Source: Chemical Science (article, 2025-01-01)
Field: Chemistry — Organic Chemistry

Accelerated click reactions using boronic acids for heterocyclic synthesis in microdroplets Click chemistry is important for its simplicity and versatility, however, condensation-based click reactions are limited by the general requirement of high temperatures and catalysts. Here, we report accelerated click reactions using boronic acids in microdroplets under ambient conditions without a catalyst. The reaction between 2-formyl phenylboronic acid (2-FPBA) and substituted amines leads to the formation of multi-step click products, including iminoboronates, boroxines, thiazolidines, and diazaborines, depending on the selected amine. The reactions occur during microdroplet flight and are three orders of magnitude faster than the corresponding bulk reactions. MS and NMR spectral analysis confirmed the nature of the products. We suggest that the air-liquid interface of microdroplets serves both as a superacid and as a drying surface, facilitating dehydration by its superacidicity to access these products. We also demonstrate the application of these accelerated reactions as a late-stage functionalization (LSF) tool to access a range of antihistamine drug derivatives. Chemistry ; Click chemistry ; Combinatorial chemistry ; Organic chemistry Click Chemistry and Applications ; Chemical Synthesis and Analysis ; Innovative Microfluidic and Catalytic Techniques Innovation
Authors: Bohdan Kozibroda | Jean‐Marie Lehn | Andrey S. Klymchenko
Source: Angewandte Chemie International Edition (article, 2025-01-14)
Field: Chemistry — Spectroscopy

Fluorescent Artificial Receptor for Dopamine based on Molecular Recognition‐driven Dynamic Covalent Chemistry in a Lipid Nanoreactor Molecular recognition and detection of small bioactive molecules, like neurotransmitters, remain a challenge for chemists, whereas nature found an elegant solution in the form of protein receptors. Here, we introduce a concept of a dynamic artificial receptor that synergically combines molecular recognition with dynamic imine bond formation inside a lipid nanoreactor, inducing a fluorescence response. The designed supramolecular system combines a lipophilic recognition ligand derived from a boronic acid, a fluorescent aldehyde based on push-pull styryl pyridine and a phenol-based catalyst. The recognition ligand specifically captures dopamine inside lipid nanodroplets and thus triggers imine bond formation with the aldehyde, producing the emission color change. The rational design of the fluorescent aldehyde, the catalyst, and the recognition ligand allows dramatic acceleration of the imine bond formation required for rapid sensing of dopamine. The nanoprobe enables dopamine detection with micromolar sensitivity and singe-nanoprobe imaging of dopamine gradients through its robust two-color ratiometric response. It displays remarkable selectivity without the interference of competing biogenic primary amines and biological media: blood serum, plasma, urine and cell lysate. The proposed concept of a dynamic artificial receptor offers a solution to the long-standing problem of molecular recognition and sensing of small molecules in complex biological media. Chemistry ; Molecular recognition ; Imine ; Dynamic covalent chemistry ; Covalent bond ; Fluorescence ; Nanoreactor ; Ligand (biochemistry) ; Combinatorial chemistry ; Supramolecular chemistry ; Molecule ; Biochemistry ; Receptor ; Catalysis ; Organic chemistry Molecular Sensors and Ion Detection ; Supramolecular Self-Assembly in Materials ; Luminescence and Fluorescent Materials
Authors: Araz Taravati | Ahmad Poursattar Marjani | Sepideh Bibak | Hamideh Sarreshtehdar Aslaheh
Source: Scientific Reports (article, 2025-10-21)
Field: Chemistry — Organic Chemistry

One-pot synthesized g-C3N4/Fe3O4/CuO magnetic photocatalyst for one-pot synthesis of 2-amino-4H-benzochromenes and methylene blue photodegradation This article presents the synthesis, characterization, and dual-functional applications of a g-C<sub>3</sub>N<sub>4</sub>/Fe<sub>3</sub>O<sub>4</sub>/CuO photocatalyst in both environmental remediation and organic synthesis. This study integrated a composite of visible-light-responsive graphitic carbon nitride, narrow-bandgap copper oxide, and magnetically recoverable iron oxide into one synergistic photocatalyst system through a facile solvothermal method. Complete characterizations were made by Fourier Transform Infrared Spectroscopy (FTIR), X-ray Diffraction (XRD), Scanning Electron Microscopy (SEM), and Transmission Electron Microscopy (TEM), Energy-Dispersive X-ray Spectroscopy (EDS), Thermogravimetric Analysis/Differential Thermal Analysis (TGA/DTA), Brunauer-Emmett-Teller (BET), Point of Zero Charge (PZC), Vibrating Sample Magnetometry (VSM), Ultraviolet-Visible Diffuse Reflectance Spectroscopy (UV-Vis DRS), and Cyclic Voltammetry (CV). The photocatalyst exhibited the best degradation efficiency for methylene blue, achieving over 90% removal within 60 min under UV light irradiation. At pH = 9, the catalyst exhibited optimum performance, which was explained by enhanced radical generation and surface interactions. CV confirmed efficient electron transfer within the catalyst, hence its suitability for redox reactions. The composite proved very efficient for the one-pot synthesis of 2-amino-4H-benzochromenes, yielding products higher than 89% under neutral and mild conditions. This composite was stable, maintaining over 80% activity after six runs. These results bring g-C<sub>3</sub>N<sub>4</sub>/Fe<sub>3</sub>O<sub>4</sub>/CuO photocatalysts into the spotlight as efficient, robust, and green material applications in wastewater treatment and green organic synthesis. The high catalytic efficiency, structural robustness, and magnetic recoverability make these candidates potentially active for industrial and environmental applications. Photocatalysis ; Thermogravimetric analysis ; Photodegradation ; Diffuse reflectance infrared fourier transform ; Fourier transform infrared spectroscopy ; Scanning electron microscope ; Catalysis ; Methylene blue ; Cyclic voltammetry Nanomaterials for catalytic reactions ; Multicomponent Synthesis of Heterocycles ; Advanced Nanomaterials in Catalysis
Authors: Gabriela Pereira Parchen | Marion Quaillet | Rilton Alves de Freitas | Hervé Hillaireau
Source: RSC Pharmaceutics (article, 2025-01-01)
Field: Materials Science — Biomaterials

Chitosan-based nano-objects for drug delivery: a review of their chemical modifications, supramolecular organization and biological fate Chitosan is a widely applied polysaccharide in drug delivery. This review covers its main chemical modifications, the types of supramolecular assemblies as drug nanocarriers and their bioditribition and toxicology. Supramolecular chemistry ; Chitosan ; Drug delivery ; Nanotechnology ; Nano- ; Chemistry ; Materials science ; Engineering ; Chemical engineering ; Organic chemistry ; Molecule Nanoparticle-Based Drug Delivery ; Advanced Drug Delivery Systems
Authors: Anamarija Nikoletić | Evangelos Natsaridis | Timon Flathmann | Daiane P. C. de Quadros | Nubia Gogniat | Oya Tagit
Source: Advanced Healthcare Materials (review, 2025-06-11)
Field: Materials Science — Biomaterials

Soft Nanocarriers as Antimicrobial Co‐Delivery Systems to Combat Resistant Infections The rise of antimicrobial resistance (AMR) poses a global health challenge, driving the need for innovative solutions to effective treatment and prevention. The advancing field of nanotechnology has facilitated the development of nanocarriers based on polymer and lipid excipients with precisely controlled compositions, release mechanisms, and targeted biological interactions. These "soft" nanocarriers can be tailored to deliver multiple antimicrobial drugs with complementary mechanisms of action, offering an effective strategy to prevent and combat AMR. This review highlights the design and applications of nanocarriers as co-delivery systems, emphasizing their potential for optimized drug loading, spatio-temporal control of release, and pathogen-specific targeting. The unique benefits of diverse nanocarrier types, including lipid-based, polymer-based, and hybrid systems, are covered with a comprehensive set of examples from recent literature in multidrug encapsulation and synergistic antimicrobial therapies. The review also delves into the key challenges in achieving precise control over the sequence and rate of release, ensuring pathogen specificity, and overcoming biological barriers such as biofilms, and provides perspectives on future research efforts to advance nanocarrier engineering and optimization strategies to develop robust, targeted treatments capable of addressing the urgent threat of resistant infections. Nanocarriers ; Antimicrobial ; Drug delivery ; Medicine ; Nanotechnology ; Anti-Infective Agents ; Microbiology ; Materials science ; Biology Nanoparticle-Based Drug Delivery ; Graphene and Nanomaterials Applications ; Nanoplatforms for cancer theranostics
Authors: Widya Lestari | Nining Irfanita | Muhammad Salahuddin Haris | Galvin Sim Siang Lin | Irwandi Jaswir | Deny Susanti Darnis | Nurul Ruziantee | Nurzafirah Mazlan | Erik Idrus | Lisa Amir | Anis Fadhlina | Hassan I. Sheikh | Mohd Hafiz Arzmi
Source: Odontology (review, 2025-07-17)
Field: Materials Science — Biomaterials

Advancements and applications of gelatin-based scaffolds in dental engineering: a narrative review Gelatin-based scaffolds have garnered significant attention in dental tissue engineering due to their biocompatibility, biodegradability, and resemblance to the extracellular matrix (ECM). This narrative review highlights recent advancements and applications of gelatin-based scaffolds for oral tissue regeneration. Various scaffold types, including hydrogels, electrospun nanofibers, hybrid composites, crosslinked matrices, and microspheres, are discussed in terms of their physicochemical characteristics, fabrication techniques, and regenerative potential. Gelatin methacryloyl (GelMA) hydrogels, for instance, exhibit favorable hydration and mechanical properties for endodontic regeneration, while electrospun nanofibers support enhanced cellular attachment and proliferation. Hybrid scaffolds incorporating ceramics, such as hydroxyapatite or β-tricalcium phosphate (β-TCP), improve mechanical strength, making them suitable for alveolar bone regeneration. Key parameters influencing scaffold performance, including gelatin concentration, crosslinking density, pore size, and biofunctionalization, are also examined. Applications span dentin-pulp complex regeneration, periodontal therapy, and bone defect repair. Despite their promise, limitations, such as rapid degradation and mechanical weakness, necessitate optimization either through chemical modification or composite formation. The integration of emerging technologies, including bioprinting and smart biomaterials, may further enhance scaffold functionality. This review underscores gelatin's versatility and its pivotal role in shaping next-generation strategies for functional and biomimetic dental tissue restoration. Gelatin ; Scaffold ; Tissue engineering ; Regeneration (biology) ; Materials science ; Biocompatibility ; Self-healing hydrogels ; Biomedical engineering ; Nanofiber ; Extracellular matrix ; Nanotechnology ; Chemistry ; Polymer chemistry Electrospun Nanofibers in Biomedical Applications ; Bone Tissue Engineering Materials ; Periodontal Regeneration and Treatments
Authors: Xue Lou | Lei Zhan | Binbin Chen
Source: Inorganics (article, 2025-07-31)
Field: Materials Science — Materials Chemistry

Recent Progress of Carbon Dots in Fluorescence Sensing Carbon dots (CDs) have attracted much attention as new types of luminescent carbon nanomaterials in recent years because of their tunable fluorescence, good biocompatibility, high stability, and low cost. In this review, the classification of CDs is overviewed based on their differences in structure. Subsequently, the latest research progress of CDs in fluorescence sensing is systematically summarized and various sensing principles are elucidated in detail, including fluorescence resonance energy transfer, aggregation-induced emission, aggregation-caused quenching, electron transfer, and the inner filter effect. Finally, the challenges and future direction of CD fluorescent probes are discussed in detail. The purpose of this review is to stimulate the design of advanced CD fluorescent probes and achieve the accurate and reliable measurement of analytes in complex samples. Fluorescence ; Nanotechnology ; Carbon fibers ; Materials science ; Optics ; Physics ; Composite material Carbon and Quantum Dots Applications ; Nanocluster Synthesis and Applications ; Mercury impact and mitigation studies
Authors: Nimeet Desai | Helen Colley | Yamini Krishna | Lucy A. Bosworth | Victoria Kearns
Source: Drug Delivery and Translational Research (article, 2025-06-25)
Field: Materials Science — Biomaterials

Mucoadhesive nanofibers for ocular drug delivery: mechanisms, design strategies, and applications Delivering drugs effectively to the ocular surface is challenging due to rapid clearance mechanisms, including blinking, tear turnover, and protective barriers of the conjunctival and corneal epithelium. As a result, conventional options such as eye drops often fail to provide sustained therapeutic effects and require frequent dosing, leading to reduced patient compliance. Mucoadhesive nanofiber systems offer a promising solution by enhancing drug retention and enabling controlled release at the ocular surface. These nanofibers, produced primarily through electrospinning, provide a high surface area, tunable mechanical properties, and compatibility with mucoadhesive polymers, collectively improving drug bioavailability, extending residence times, and minimizing systemic side effects. This review comprehensively explores the fundamentals of mucoadhesion, including the structural and compositional characteristics of ocular mucosal surfaces and the molecular interactions essential for optimized drug delivery. It examines advanced strategies for incorporating mucoadhesive features into nanofibers, such as polymer blending, surface modification, and molecular imprinting, and assesses their influence on therapeutic outcomes. Finally, recent advancements and their potential for clinical translation are discussed. By presenting a thorough analysis of current techniques and emerging innovations, this review aims to guide researchers in developing next-generation mucoadhesive nanofiber platforms that improve therapeutic efficacy and patient compliance in ocular drug delivery. Mucoadhesion ; Drug delivery ; Nanotechnology ; Nanofiber ; Patient compliance ; Materials science ; Biomedical engineering ; Medicine ; Drug carrier Electrospun Nanofibers in Biomedical Applications ; Ocular Disorders and Treatments ; Advanced Drug Delivery Systems