jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Angelina Jocic | Tom Wickenhäuser | Sebastian Lindenthal | Wen‐Shan Zhang | Jana Zaumseil | Rasmus R. Schröder | R. Klingeler | Milan Kivala
Source: Chemical Science (article, 2024-01-01)
Field: Materials Science — Polymers and Plastics

Redox-active, photoluminescent porous polymers based on spirofluorene-bridged <i>N</i>-heterotriangulenes and their feasibility as organic cathode materials Novel microporous polymers were synthesized through Yamamoto polymerization of selectively brominated spirofluorene-bridged <i>N</i>-heterotriangulenes. Extensive characterization, including combustion analysis, ToF-SIMS, IR, and Raman spectroscopy, confirmed the elemental composition and integrity of the polymers. The amorphous polymers, observed by scanning electron microscopy as globular particles aggregating into larger structures, exhibited remarkable thermal stability (decomposition temperatures > 400 °C) and BET surface areas up to 690 m<sup>2</sup> g<sup>-1</sup>. Dispersions of the <i>tert</i>-butyl-substituted polymer in different solvents displayed bathochromically shifted emission with remarkable solvatochromism. The polymer is reversibly oxidized at +3.81 V (<i>vs.</i> Li/Li<sup>+</sup>) in composite electrodes with carbon black and reaches specific capacities up to 26 mA h g<sup>-1</sup> and excellent cycling stability when implemented as cathode material in lithium-ion batteries. Our results highlight the potential of spirofluorene-bridged <i>N</i>-heterotriangulenes as versatile building blocks for the development of functional redox-active porous polymers. Cathode ; Photoluminescence ; Polymer ; Porosity ; Redox ; Materials science ; Chemical engineering ; Nanotechnology ; Porous medium ; Chemistry ; Optoelectronics ; Composite material ; Metallurgy ; Physical chemistry ; Engineering Conducting polymers and applications ; Synthesis and Properties of Aromatic Compounds ; Organic Electronics and Photovoltaics
Authors: Ming Hou | Yuanrui Wang | Hefei Yang | Jiajun Zhang | Xiao‐Feng Wu
Source: Chemistry - A European Journal (article, 2024-12-04)
Field: Chemistry — Organic Chemistry

Carbon Monoxide and Alkoxycarbonyl Radical Enabled Migration Strategy for the Carbonylative Functionalization of Unactivated Alkenes Herein we report a "carbonylative migration" strategy for the acylation-esterification type double functionalization of unactivated alkenes using alkyloxalkyl chlorides and CO as the reagents. The transformation is proceeded by the alkoxycarbonyl radical addition to unactivated alkenes, followed by the insertion of carbon monoxide to induce intramolecular migration of heteroaryl groups, which is different from the traditional reaction modes. The reaction conditions were mild and well tolerated with varieties of functional groups. A variety of 1,4-dicarbonyl compounds with different ester groups were produced easily which has high potential applications in biology, medicine, and other fields. Surface modification ; Reagent ; Carbon monoxide ; Chemistry ; Intramolecular force ; Acylation ; Carbonylation ; Functional group ; Monoxide ; Combinatorial chemistry ; Alkene ; Organic chemistry ; Catalysis ; Polymer Radical Photochemical Reactions ; Catalytic C–H Functionalization Methods ; Oxidative Organic Chemistry Reactions
Authors: Diego Rodríguez | Kelly Johanna Lipez | Elena E. Stashenko | Iván Díaz | Justo Cobo | Alirio Palma
Source: RSC Advances (article, 2024-01-01)
Field: Chemistry — Organic Chemistry

Alternative and efficient one-pot three-component synthesis of substituted 2-aryl-4-styrylquinazolines/4-styrylquinazolines from synthetically available 1-(2-aminophenyl)-3-arylprop-2-en-1-ones: characterization and evaluation of their antiproliferative activities In this study, an alternative and efficient one-pot three-component synthesis approach to develop a new series of (<i>E</i>)-2-aryl-4-styrylquinazolines and (<i>E</i>)-4-styrylquinazolines is described. According to this approach, the target compounds were synthesized straightforward in high yields and in short reaction times from substituted 1-(2-aminophenyl)-3-arylprop-2-en-1-ones <i>via</i> its well-Cu(OAc)<sub>2</sub>-mediated cyclocondensation reactions with aromatic aldehydes or its well-catalyst-free cyclocondensation reactions with trimethoxy methane (trimethyl orthoformate), and ammonium acetate under aerobic conditions. This is an operationally simple, valuable, and direct method to synthesize 2-aryl- and non-C2-substituted quinazolines containing a styryl framework at C4 position from cheap and synthetically available starting materials. All the synthesized compounds were submitted to the US National Cancer Institute for <i>in vitro</i> screening. The bromo- and chloro-substituted quinazolines 5c and 5d displayed a potent antitumor activity against all the tested subpanel tumor cell lines with IC<sub>50</sub> (MG-MID) values of 5.25 and 5.50 μM, and a low cytotoxic effect with LC<sub>50</sub> (MG-MID) values of 91.20 and 84.67 μM, respectively, indicating a low toxicity of these compounds to normal human cell lines, as required for potential antitumor agents. Ammonium acetate ; Triethyl orthoformate ; Aryl ; Component (thermodynamics) ; Catalysis ; Chemistry ; Characterization (materials science) ; One-pot synthesis ; Organic chemistry ; Combinatorial chemistry ; Materials science ; Nanotechnology ; High-performance liquid chromatography Quinazolinone synthesis and applications ; Multicomponent Synthesis of Heterocycles ; Synthesis and biological activity
Authors: Xiaojie Ren | Haokun Li | Hui Peng | Yang Yang | Su Hang | Chen Huang | Xuan Wang | Jie Zhang | Zhiyang Liu | Wenyu Wei | Ke Cheng | Tianyang Zhu | Zhenpin Lu | Zhengqiu Li | Q. Zhao | Ben Zhong Tang | Shao Q. Yao | Xiangzhi Song | Hongyan Sun
Source: Advanced Science (article, 2024-06-19)
Field: Chemistry — Organic Chemistry

Reactivity‐Tunable Fluorescent Platform for Selective and Biocompatible Modification of Cysteine or Lysine Chemoselective modification of specific residues within a given protein poses a significant challenge, as the microenvironment of amino acid residues in proteins is variable. Developing a universal molecular platform with tunable chemical warheads can provide powerful tools for precisely labeling specific amino acids in proteins. Cysteine and lysine are hot targets for chemoselective modification, but current cysteine/lysine-selective warheads face challenges due to cross-reactivity and unstable reaction products. In this study, a versatile fluorescent platform is developed for highly selective modification of cysteine/lysine under biocompatible conditions. Chloro- or phenoxy-substituted NBSe derivatives effectively labeled cysteine residues in the cellular proteome with high specificity. This finding also led to the development of phenoxy-NBSe phototheragnostic for the diagnosis and activatable photodynamic therapy of GSH-overexpressed cancer cells. Conversely, alkoxy-NBSe derivatives are engineered to selectively react with lysine residues in the cellular environment, exhibiting excellent anti-interfering ability against thiols. Leveraging a proximity-driven approach, alkoxy-NBSe probes are successfully designed to demonstrate their utility in bioimaging of lysine deacetylase activity. This study also achieves integrating a small photosensitizer into lysine residues of proteins in a regioselective manner, achieving photoablation of cancer cells activated by overexpressed proteins. Lysine ; Cysteine ; Chemistry ; Amino acid ; Combinatorial chemistry ; Chemical modification ; Biochemistry ; Bioconjugation ; Biocompatible material ; Fluorescence ; Photosensitizer ; Organic chemistry ; Enzyme Click Chemistry and Applications ; Nanoplatforms for cancer theranostics ; Peptidase Inhibition and Analysis
Authors: Prajisha Jayaprakash | Twahira Begum | Mohan Lal
Source: In Silico Pharmacology (article, 2024-12-24)
Field: Chemistry — Organic Chemistry

Network pharmacology-integrated molecular modeling analysis of Aquilaria malaccensis L. (agarwood) essential oil phytocompounds Agarwood ; Docking (animal) ; Computational biology ; Chemistry ; Pharmacology ; Biology ; Biochemistry ; Medicine Wood and Agarwood Research ; Computational Drug Discovery Methods ; Plant biochemistry and biosynthesis
Authors: Oliver M. Crook | Nathan Gittens | Chun‐wa Chung | Charlotte M. Deane
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2024-04-13)
Field: Chemistry — Spectroscopy

Inferring residue level hydrogen deuterium exchange with ReX Abstract Hydrogen-Deuterium Exchange Mass-Spectrometry (HDX-MS) has emerged as a powerful technique to explore the conformational dynamics of proteins and protein complexes in solution. The bottom-up approach to MS uses peptides to represent an average of residues, leading to reduced resolution of deuterium exchange and complicates the interpretation of the data. Here, we introduce ReX, a method to infer residue-level uptake patterns leveraging the overlap in peptides, the temporal component of the data and the correlation along the sequence dimension. This approach infers statistical significance for individual residues by treating HDX-MS as a multiple change-point problem. By fitting our model in a Bayesian non-parametric framework, we perform parameter number inference, differential HDX confidence assessments, and uncertainty estimation for temporal kinetics. Benchmarking against existing methods using a three-way proteolytic digestion experiment shows our method’s superior performance at predicting unseen HDX data. Moreover, it aligns HDX-MS with the reporting standards of other structural methods by providing global and local resolution metrics. Using ReX, we analyze the differential flexibility of BRD4’s two Bromodomains in the presence of I-BET151 and quantify the conformational variations induced by a panel of seventeen small molecules on LXR α . Our analysis reveals distinct residue-level HDX signatures for ligands with varied functional outcomes, highlighting the potential of this characterisation to inform mode of action analysis. Residue (chemistry) ; Deuterium ; Hydrogen–deuterium exchange ; Hydrogen ; Chemistry ; Nuclear physics ; Physics ; Organic chemistry Mass Spectrometry Techniques and Applications ; RNA and protein synthesis mechanisms ; Chemical Synthesis and Analysis
Authors: António Gomes da Costa | Gonçalo Lopes | João F. G. Rodrigues | Isabel C. Santos | Dulce Simão | Elsa B. Lopes | Laura C. J. Pereira | Nolwenn Le Breton | Sylvie Choua | Stéphane A. Baudron | Manuel Almeida | Sandra Rabaça
Source: Crystals (article, 2024-05-17)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Cobalt and Iron Cyano Benzene Bis(Dithiolene) Complexes New iron and cobalt bis(dithiolene) complexes [M(3cbdt)2] (3cbdt = 3-cyanobenzene-1,2-dithiolate) were prepared as tetraphenylphosphonium (Ph4P+) salts for Fe in the monoanionic state and for Co in both the dianionic and monoanionic states: (Ph4P)2[Fe(III)(3cbdt)2]2 (1); (Ph4P)2[Co(III)(3cbdt)2]2 (2); (Ph4P)2[Co(II)(3cbdt)2] (3). These compounds were characterized by single-crystal X-ray diffraction, cyclic voltammetry, EPR, and static magnetic susceptibility. Their properties are discussed in comparison with the corresponding complexes based on the isomer ligand 4-cyanobenzene-1,2-dithiolate (4cbdt) and 4,5-cyanobenzene-1,2-dithiolate (dcbdt), previously described by us. The Fe(III) and the Co(III) compounds (1 and 2) are isostructural, crystallizing in the triclinic P1¯ space group, with cis [M(III)(3cbdt)2] complexes dimerized in a trans fashion, and the transition metal (M = Fe, Co) has a distorted 4+1 square pyramidal coordination geometry. The Co(II) compound (3) crystallizes in the triclinic P1¯ space group, with the unit cell containing one cis and three trans inequivalent [Co(II)(3cbdt)2] complexes with the transition metal (Co) and having a square planar coordination geometry. The Fe(III) complex (1) is EPR-silent, and the static magnetic susceptibility shows a temperature dependence typical of dimers of antiferromagnetically coupled S = 3/2 spins with −J/kB = 233.6 K and g = 1.8. Static magnetic susceptibility measurements of compound (3) show that this Co(II) complex is paramagnetic, corresponding to an S = ½ state with g = 2, in agreement with EPR spectra showing in solid state a hyperfine structure typical of the I(59Co) = 7/2. Static susceptibility measurements of Co(III) complex (2) showed an increase in the paramagnetic susceptibility upon warming above 100 K, which is consistent with strong AFM coupling between dimerized S = 1 units with a constant −J/kB ~1286 K. Triclinic crystal system ; Isostructural ; Crystallography ; Chemistry ; Electron paramagnetic resonance ; Cobalt ; Magnetic susceptibility ; Paramagnetism ; Coordination geometry ; Ligand (biochemistry) ; Square pyramidal molecular geometry ; Transition metal ; Metal ; Crystal structure ; Stereochemistry ; Inorganic chemistry ; Nuclear magnetic resonance ; Molecule ; Catalysis ; Hydrogen bond ; Condensed matter physics ; Physics Magnetism in coordination complexes ; Organic and Molecular Conductors Research ; Metal-Organic Frameworks: Synthesis and Applications
Authors: Kaouthar Louati | Amina Maalej | Fatma Kolsi | Rim Kallel | Yassine Gdoura | Mahdi Borni | Leila Sellami Hakim | Rania Zribi | Sirine Choura | Sami Sayadi | Mohamed Chamkha | Basma Mnif | Zouheir Khemakhem | Tahya Sellami Boudawara | Mohamed Zaher Boudawara | Abderrahman Bouraoui | Jamil Kraı̈em | Fathi Safta
Source: Journal of Proteome Research (article, 2024-11-18)
Field: Chemistry — Spectroscopy

A Shotgun Proteomic-Based Approach with a Q-Exactive Hybrid Quadrupole-Orbitrap High-Resolution Mass Spectrometer for the Assessment of Pesticide Mixture-Induced Neurotoxicity on a 3D-Developed Neurospheroid Model from Human Brain Meningiomas: Identification of Trityl-Post-Translational Modification The widespread use of pesticides, particularly in combinations, has resulted in enhanced hazardous health effects. However, little is known about their molecular mechanism of interactions. The aim of this study was to assess the neurotoxicity effect of pesticides in mixtures by adopting a 3D in vitro developed neurospheroid model, followed by treatment by increased concentrations of pesticides for 24 h and analysis by a shotgun proteomic-based approach with high-resolution tandem mass spectrometry. Three proteins, namely, glyceraldehyde-3-phosphate-dehydrogenase (GAPDH), α-enolase, and phosphoglycerate-kinase-1, were selected as key targets in the metabolic process. Only high doses of pesticides mitigated cell-density proliferation with the occurrence of apoptotic cells, which unlikely makes any neurological alterations in environmental regulatory exposures. The proteomic analysis showed that majority of altered proteins were implicated in cell metabolism. De novo peptide sequencing revealed ion losses and adduct formation, namely, a trityl-post-translational modification in the active site of 201-GAPDH protein. The study also highlights the plausible role of pyrethroids to be implicated in the deleterious effects of pesticides in a mixture. To the best of our knowledge, our finding is the first in toxicoproteomics to deeply elucidate pesticides' molecular interactions and their ability to adduct proteins as a pivotal role in the neurotoxicity mechanism. Orbitrap ; Chemistry ; Neurotoxicity ; Pesticide ; Mass spectrometry ; Tandem mass spectrometry ; Sarin ; Shotgun ; Biochemistry ; Shotgun proteomics ; Computational biology ; Proteomics ; Biology ; Chromatography ; Toxicity ; Gene ; Enzyme Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Paromita Islam | Ahmed Abosalha | Sabrina Schaly | Jacqueline L. Boyajian | Madison Santos | Stephanie Makhlouf | Editha Renesteen | Amal Kassab | Cedrique Shum-Tim | Dominique Shum‐Tim | Satya Prakash
Source: ACS Pharmacology & Translational Science (article, 2024-10-25)
Field: Materials Science — Biomaterials

Baculovirus Expressing Tumor Growth Factor-β1 (TGFβ1) Nanoshuttle Augments Therapeutic Effects for Vascular Wound Healing: Design and In Vitro Analysis One of the major challenges in vascular tissue regeneration is effective wound healing that can be resolved by an innovative targeted nanoshuttle that delivers growth factors to blood vessels. This study investigates the production and efficacy of transforming growth factor-β1 (TGFβ1) gene delivery using poly(lactic-<i>co</i>-glycolic acid) (PLGA) baculovirus (BV) nanoshuttles (NSs). They exhibited an encapsulation efficiency of 86.23% ± 0.65% and a negative zeta potential of -29.57 ± 1.27 mV. In vitro studies in human umbilical vein endothelial cells (HUVECs) revealed that a 12 h incubation period optimized virus transduction. The safety and superior intracellular uptake of NSs and BVs in HUVECs were observed. The NSs carrying 100 and 400 MOI exhibited the highest cell proliferation rates in HUVECs. These sustained-release NSs significantly improved vascular cell migration and wound closure compared to free TGFβ1 carrying BV and can be a groundbreaking find in regenerative medicine, cardiovascular diseases, and chronic ulcer conditions. Wound healing ; Transforming growth factor ; In vitro ; Growth factor ; Cancer research ; Immunology ; Medicine ; Cell biology ; Biology ; Internal medicine ; Receptor Electrospun Nanofibers in Biomedical Applications ; 3D Printing in Biomedical Research ; Silk-based biomaterials and applications
Authors: Zi‐Qi Li | Turki M. Alturaifi | Yilin Cao | Matthew V. Joannou | Peng Liu | Keary M. Engle
Source: Angewandte Chemie (article, 2024-09-02)
Field: Chemistry — Organic Chemistry

Hemilabile and Redox‐Active Quinone Ligands Unlock sp<sup>3</sup>‐Rich Couplings in Nickel‐Catalyzed Olefin Carbosulfenylation Abstract A three‐component coupling approach toward structurally complex dialkylsulfides is described via the nickel‐catalyzed 1,2‐carbosulfenylation of unactivated alkenes with organoboron nucleophiles and alkylsulfenamide (N−S) electrophiles. Efficient catalytic turnover is facilitated using a tailored N−S electrophile containing an N ‐methyl methanesulfonamide leaving group, allowing catalyst loadings as low as 1 mol %. Regioselectivity is controlled by a collection of monodentate, weakly coordinating native directing groups, including sulfonamides, amides, sulfinamides, phosphoramides, and carbamates. Key to the development of this transformation is the identification of quinones as a family of hemilabile and redox‐active ligands that tune the steric and electronic properties of the metal throughout the catalytic cycle. Density functional theory (DFT) results show that the duroquinone (DQ) ligand adopts different coordination modes in different stages of the Ni‐catalyzed 1,2‐carbosulfenylation‐binding as an η 6 capping ligand to stabilize the precatalyst/resting state and prevent catalyst decomposition, binding as an X‐type redox‐active durosemiquinone radical anion to promote alkene migratory insertion with a less distorted square planar Ni(II) center, and binding as an L‐type ligand to promote N−S oxidative addition at a relatively more electron‐rich Ni(I) center. Olefin fiber ; Catalysis ; Chemistry ; Nickel ; Redox ; Quinone ; Photochemistry ; Combinatorial chemistry ; Organic chemistry Sulfur-Based Synthesis Techniques ; Catalytic C–H Functionalization Methods ; Synthesis and Catalytic Reactions
Authors: Lindsey D. Ulmer | Daniele Canzani | Christopher N. Woods | Natalie L. Stone | Maria K. Janowska | Rachel E. Klevit | Matthew F. Bush
Source: Journal of Proteome Research (article, 2024-07-05)
Field: Chemistry — Spectroscopy

High-Performance Workflow for Identifying Site-Specific Crosslinks Originating from a Genetically Incorporated, Photoreactive Amino Acid In conventional crosslinking mass spectrometry, proteins are crosslinked using a highly selective, bifunctional chemical reagent, which limits crosslinks to residues that are accessible and reactive to the reagent. Genetically incorporating a photoreactive amino acid offers two key advantages: any site can be targeted, including those that are inaccessible to conventional crosslinking reagents, and photoreactive amino acids can potentially react with a broad range of interaction partners. However, broad reactivity imposes additional challenges for crosslink identification. In this study, we incorporate benzoylphenylalanine (BPA), a photoreactive amino acid, at selected sites in an intrinsically disordered region of the human protein HSPB5. We report and characterize a workflow for identifying and visualizing residue-level interactions originating from BPA. We routinely identify 30 to 300 crosslinked peptide spectral matches with this workflow, which is up to ten times more than existing tools for residue-level BPA crosslink identification. Most identified crosslinks are assigned to a precision of one or two residues, which is supported by a high degree of overlap between replicate analyses. Based on these results, we anticipate that this workflow will support the more general use of genetically incorporated, photoreactive amino acids for characterizing the structures of proteins that have resisted high-resolution characterization. Workflow ; Chemistry ; Computational biology ; Biochemistry ; Genetically engineered ; Computer science ; Biology ; Database ; Gene Advanced Proteomics Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; RNA and protein synthesis mechanisms
Authors: Farah Haidar | Monther Faisal Mahdi | Ayad Kareem Khan
Source: Al Mustansiriyah Journal of Pharmaceutical Sciences (article, 2024-01-14)
Field: Chemistry — Organic Chemistry

Synthesis, Molecular Docking, Characterization, and Preliminary Evaluation of Some New 1, 3-Diazetidin-2-One Derivatives as Anticancer Agents A series of novel 1,3-diazetidin-2-one derivatives were designed, synthesized, and evaluated preliminary (In Vitro) for their cytotoxic activity against the lung (A549) cancer cell line. GOLD software (version 2021.2.0) was used to conduct a molecular docking study; the tested derivatives demonstrated significant anticancer activity compared to the reference drug (erlotinib). PLP-fitness values for the final compounds are 79.81, 80.80, and 81.57, respectively, whereas the reference ligand, erlotinib, had a value of 76.20. The synthesized compounds were identified and characterized using physicochemical parameters (melting points and Rf values), FTIR, 1H-NMR, and 13C-NMR spectroscopy. According to the IC50 values for the synthesized derivatives, compounds N4a and N4b exhibit outstanding anti-proliferative activity with IC50 value of (7.51, 7.68) µM against A549 cell line, compared to erlotinib, which has an IC50 value of (11.5) µM. Combinatorial chemistry ; Chemistry ; Docking (animal) ; Characterization (materials science) ; Stereochemistry ; Computational biology ; Nanotechnology ; Materials science ; Biology ; Medicine Synthesis of β-Lactam Compounds ; Click Chemistry and Applications ; Synthesis and biological activity