jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Sabrina Ninck | Thomas Klaus | Tatiana V. Kochetkova | Sarah P. Esser | Leonard Sewald | Farnusch Kaschani | Christopher Bräsen | Alexander J. Probst | Ilya V. Kublanov | Bettina Siebers | Markus Kaiser
Source: Environmental Microbiome (article, 2024-06-03)
Field: Chemistry — Spectroscopy

Environmental activity-based protein profiling for function-driven enzyme discovery from natural communities By reporting enzyme activities within an ecosystem in their native state, we anticipate that eABPP will not only advance current methodological approaches to sequence homology-guided enzyme discovery from environmental ecosystems for subsequent biocatalyst development but also contributes to the ecological investigation of microbial community interactions by dissecting their underlying molecular mechanisms. Metagenomics ; Computational biology ; Biology ; Metaproteomics ; Bioprospecting ; Proteome ; Proteomics ; Function (biology) ; Ecology ; Evolutionary biology ; Bioinformatics ; Genetics ; Gene Advanced Proteomics Techniques and Applications ; Click Chemistry and Applications ; Enzyme Structure and Function
Authors: Elena Bombonato | Valerio Fasano | Daniel Pecorari | Luca Fornasari | Francesco Castagnini | Massimo Marcaccio | Paolo Ronchi
Source: ACS Omega (article, 2024-03-04)
Field: Chemistry — Organic Chemistry

Electrochemical Synthesis of Unnatural Amino Acids Embedding 5- and 6-Membered Heteroaromatics Using a commercially available potentiostat, the electrochemical synthesis of unnatural amino acids bearing heteroaromatics on the lateral chain has been accomplished. This strategy exploits the side-chain decarboxylative arylation of aspartic/glutamic acid, a reaction that becomes challenging with electron-rich coupling partners such as 5- and 6-membered heteroaromatics. These rings are underrepresented in unnatural amino acids, therefore allowing a wider exploration of the chemical space, given the abundance of the aryl bromides employable in this reaction. Amino acid ; Chemistry ; Electrochemistry ; Combinatorial chemistry ; Chemical space ; Aryl ; Decarboxylation ; Side chain ; Organic chemistry ; Drug discovery ; Biochemistry ; Catalysis ; Alkyl Radical Photochemical Reactions ; Sulfur-Based Synthesis Techniques ; Catalytic C–H Functionalization Methods
Authors: Nguyễn Ngọc Sơn | Vu Minh Thanh | Nguyen Thi Huong
Source: RSC Advances (article, 2024-01-01)
Field: Materials Science — Biomaterials

Synthesis of F127-GA@ZnO nanogel as a cisplatin drug delivery pH-sensitive system In this study, a novel drug delivery system based on zinc oxide nanoparticles (ZnO NPs) was developed for the enhanced delivery of cisplatin (CPT) to improve cancer treatment. The ZnO NPs were synthesized from guava leaf extract and then surface-functionalized with gallic acid (GA) to improve their biocompatibility and drug loading capacity. Pluronic F127, a biocompatible polymer, was then conjugated to the GA-modified ZnO NPs to further enhance their stability and cellular uptake. The resulting NPs were characterized by various techniques, including FT-IR, UV-Vis, SEM, TEM, <sup>1</sup>H NMR, and DLS. The drug loading and release profiles of CPT from the NPs were investigated, showing high CPT loading capacity and pH-dependent release behavior. The <i>in vitro</i> cytotoxicity of the NPs was evaluated against various cancer cell lines, demonstrating enhanced cytotoxicity compared to free CPT. Overall, this study highlights the potential of GA and Pluronic-modified ZnO NPs as a promising drug delivery system for enhanced CPT delivery and improved cancer therapy. Nanogel ; Cisplatin ; Drug delivery ; Drug ; Zinc ; Nanoparticle ; Nanotechnology ; Chemistry ; Delivery system ; Combinatorial chemistry ; Materials science ; Pharmacology ; Organic chemistry ; Chemotherapy ; Medicine Nanoparticle-Based Drug Delivery ; Nanoplatforms for cancer theranostics ; Graphene and Nanomaterials Applications
Authors: Maria Christina Prihatiningsih | Chaidir Pratama | Noor Anis Kundari | Kartini Megasari | Dhita Ariyanti | Andri Saputra | Hersandy Dayu Kusuma | Puji Astuti
Source: RSC Advances (article, 2024-01-01)
Field: Materials Science — Materials Chemistry

Rifampicin adsorption and release study using Santa Barbara amorphous-16 modified Al (SBA-16-Al) for a drug delivery system In this study, the surface modification of Santa Barbara Amorphous-16 (SBA-16) with aluminum (SBA-16-Al) was carried out as a rifampicin matrix for the treatment of tuberculosis. Surface modification of SBA-16 was achieved using the direct-synthesis grafting method. Then, the adsorption and release properties of rifampicin from the SBA-16-Al matrix have been studied in batches. In addition, the SBA-16-Al has been characterized using Fourier-Transform Infrared Spectroscopy (FTIR), X-ray diffraction analysis (XRD), transmission electron microscopy (TEM), and Surface Area Analysis (SAA) Brunaur, Emmett and Teller (SAA-BET). The results show that the mesoporous material, the SBA-16-Al has a specific surface area of 843.5 m<sup>2</sup> g<sup>-1</sup> and 624.3 m<sup>2</sup> g<sup>-1</sup> for SBA-16, nanometer-sized pore diameters, and an amorphous crystal lattice. The FTIR spectra showed the Al-O bond at 802 cm<sup>-1</sup> which indicates the Al group has been successfully added into SBA-16. The adsorption isotherm of rifampicin in SBA-16-Al follows the Freundlich model which illustrates the adsorption is heterogeneous and forms a multilayer. The adsorption of rifampicin is chemisorption which occurs non-spontaneously and is quite stable. The release kinetics of rifampicin in the drug delivery system followed the Higuchi model with <i>k</i><sub>1</sub> 0.5472 mg 0.5/hour pH 1.5 and <i>k</i><sub>2</sub> mg 0.5/hour pH 6.5. Adsorption ; Amorphous solid ; Fourier transform infrared spectroscopy ; Mesoporous material ; Chemisorption ; Freundlich equation ; Nuclear chemistry ; Materials science ; Chemical engineering ; Chemistry ; Organic chemistry ; Catalysis Mesoporous Materials and Catalysis ; Nanoparticle-Based Drug Delivery ; Nanomaterials for catalytic reactions
Authors: Alex De Salvo | Raffaella Mancuso | Xiao‐Feng Wu
Source: Beilstein Journal of Organic Chemistry (article, 2024-04-30)
Field: Chemistry — Organic Chemistry

Carbonylative synthesis and functionalization of indoles Carbonylation processes have become widely recognized as a versatile, convenient, and low-cost method for the synthesis of high-value compounds. Given the great importance of heterocyclic compounds, the carbonylative approach has become increasingly important for their synthesis. In this mini-review, as a class of benzo-fused nitrogen-containing heterocyclic compounds, we summarized and discussed the recent achievements on the synthesis and functionalization of indole derivatives via carbonylative approaches. Chemistry ; Carbonylation ; Surface modification ; Combinatorial chemistry ; Indole test ; Organic chemistry ; Nanotechnology ; Catalysis ; Carbon monoxide Catalytic C–H Functionalization Methods ; Synthesis of Indole Derivatives ; Synthesis and Catalytic Reactions
Authors: Diego López Barreiro | Klaartje Houben | Olaf Schouten | Gijsje H. Koenderink | Jens Thies | Cees M. J. Sagt
Source: ACS Applied Materials & Interfaces (article, 2024-12-16)
Field: Materials Science — Biomaterials

Order–Disorder Balance in Silk-Elastin-like Polypeptides Determines Their Self-Assembly into Hydrogel Networks The biofabrication of recombinant structural proteins with a range of mechanical or structural features usually relies on the generation of protein libraries displaying variations in terms of amino acid composition, block structure, molecular weight, or physical/chemical cross-linking sites. This approach, while highly successful in generating a wealth of knowledge regarding the links between design features and material properties, has some inherent limitations related to its low throughput. This slows down the pace of the development of <i>de novo</i> recombinant structural proteins. Here, we propose an approach to tune the viscoelastic properties of temperature-responsive hydrogels made of silk-elastin-like polypeptides (SELPs) without modifying their sequence. To do so, we subject purified SELPs to two different postprocessing methods─water annealing or EtOH annealing─that alter the topology of highly disordered SELP networks via the formation of ordered intermolecular β-sheet physical cross-links. Combining different analytical techniques, we connect the order/disorder balance in SELPs with their gelling behavior. Furthermore, we show that introducing a functional block (in this case, a biomineralizing peptide) in the sequence of SELPs can disrupt its self-assembly and that such disruption can only be overcome by EtOH annealing. Our results suggest that postprocessing of as-purified SELPs might be a simple approach to tune the self-assembly of SELPs into biomaterials with bespoke viscoelastic properties beyond the traditional approach of developing SELP libraries via genetic engineering. Self-healing hydrogels ; Molecular self-assembly ; Materials science ; Self-assembly ; Elastin ; Simulated annealing ; Nanotechnology ; Computer science ; Biology ; Algorithm Silk-based biomaterials and applications ; Cellular Mechanics and Interactions ; Advanced Materials and Mechanics
Authors: Esther Imperlini | Luisa Di Marzio | Armando Cevenini | Michele Costanzo | Nicola d’Avanzo | Massimo Fresta | Stefania Orrù | Christian Celia | Francesco Salvatore
Source: Nanoscale Advances (article, 2024-01-01)
Field: Materials Science — Biomaterials

Unraveling the impact of different liposomal formulations on the plasma protein corona composition might give hints on the targeting capability of nanoparticles Nanoparticles (NPs) interact with biological fluids after being injected into the bloodstream. The interactions between NPs and plasma proteins at the nano-bio interface affect their biopharmaceutical properties and distribution in the organ and tissues due to protein corona (PrC) composition, and in turn, modification of the resulting targeting capability. Moreover, lipid and polymer NPs, at their interface, affect the composition of PrC and the relative adsorption and abundance of specific proteins. To investigate this latter aspect, we synthesized and characterized different liposomal formulations (LFs) with lipids and polymer-conjugated lipids at different molar ratios, having different sizes, size distributions and surface charges. The PrC composition of various designed LFs was evaluated <i>ex vivo</i> in human plasma by label-free quantitative proteomics. We also correlated the relative abundance of identified specific proteins in the coronas of the different LFs with their physicochemical properties (size, PDI, zeta potential). The evaluation of outputs from different bioinformatic tools discovered protein clusters allowing to highlight: (i) common as well as the unique species for the various formulations; (ii) correlation between each identified PrC and the physicochemical properties of LFs; (iii) some preferential binding determined by physicochemical properties of LFs; (iv) occurrence of formulation-specific protein patterns in PrC. Investigating specific clusters in PrC will help decode the multivalent roles of the protein pattern components in the drug delivery process, taking advantage of the bio-nanoscale recognition and identification for significant advances in nanomedicine. Nanoparticle ; Liposome ; Composition (language) ; Corona (planetary geology) ; Plasma ; Nanotechnology ; Chemistry ; Materials science ; Physics ; Astrobiology ; Art Nanoparticle-Based Drug Delivery ; Gold and Silver Nanoparticles Synthesis and Applications ; Protein Interaction Studies and Fluorescence Analysis
Authors: Oleksii Zhelavskyi | S. Parikh | Yin‐Jia Jhang | Richard J. Staples | Paul M. Zimmerman | Pavel Nagorny
Source: Angewandte Chemie International Edition (article, 2024-01-25)
Field: Chemistry — Organic Chemistry

Green Light Promoted Iridium(III)/Copper(I)‐Catalyzed Addition of Alkynes to Aziridinoquinoxalines Through the Intermediacy of Azomethine Ylides This manuscript describes the development of alkyne addition to the aziridine moiety of aziridinoquinoxalines using dual Ir(III)/Cu(I) catalytic system under green light-emitting diode (LED) photolysis (λ<sub>max</sub> =525 nm). This mild method features high levels of chemo- and regioselectivity and was used to generate 30 highly functionalized substituted dihydroquinoxalines in 36-98 % yield. This transformation was also carried asymmetrically using phthalazinamine-based chiral ligand to provide 9 chiral addition products in 96 : 4 to 86 : 14 e.r. The experimental and quantum chemical explorations of this reaction suggest a mechanism that involves Ir(III)-catalyzed triplet energy transfer followed by a ring-opening reaction ultimately leading to the formation of azomethine ylide intermediates. These azomethine intermediates undergo sequential protonation/copper(I) acetylide addition to provide the products. Iridium ; Catalysis ; Copper ; Chemistry ; Photochemistry ; Organic chemistry Synthesis and Catalytic Reactions ; Catalytic C–H Functionalization Methods ; Asymmetric Hydrogenation and Catalysis
Authors: Musfra Khursheed
Source: ReiDoCrea Revista electrónica de investigación Docencia Creativa (article, 2024-01-03)
Field: Chemistry — Organic Chemistry

Chromatographic Techniques for the Detection and Identification of Olive Oil Adulteration Olive oil stands out as one of the most beneficial oils for human health, offering preventive measures against a spectrum of health issues, including cardiovascular problems, cancer, osteoporosis, and various chronic diseases.However, the surging demand for olive oil has led to its susceptibility to adulteration with cheaper oils, such as soybean, peanut, hazelnut, and sunflower oil.Notably, extra virgin olive oil (EVOO), commanding a premium price, is particularly prone to adulteration with lower-cost alternatives.This adulteration poses a significant risk to health, necessitating the development of methods to detect and separate these impurities, thereby ensuring the quality and safety of olive oil.In order to address this concern, chromatographic techniques have emerged as pivotal tools in the purification and detection of adulterants in olive oil.Commonly employed methods include Thin Layer Chromatography (TLC), Gas Chromatography (GC), Liquid Chromatography (LC), and High-Performance Liquid Chromatography (HPLC).These techniques play a crucial role in differentiating between pure and impure olive oil in the market.This article focuses on the most prospective chromatographic methods for the detection and identification adulteration in olive oil.The outcomes of this research have the potential to pave the way for new directions in food security research, contributing to overall sustainability.Moreover, the insights gained from this study can be valuable for young students, serving as a concise reference for analytical methods in this field. Olive oil ; Chromatography ; Identification (biology) ; Chemistry ; Food science ; Biology ; Botany Edible Oils Quality and Analysis ; Spectroscopy and Chemometric Analyses
Authors: Alejandro Gran‐Scheuch | Hein J. Wijma | Nikolas Capra | Hugo L. van Beek | Miloš Trajković | Kai Baldenius | Michael Breuer | A.M.W.H. Thunnissen | Dick B. Janssen
Source: ACS Catalysis (article, 2024-12-30)
Field: Materials Science — Materials Chemistry

Bioinformatics and Computationally Supported Redesign of Aspartase for β-Alanine Synthesis by Acrylic Acid Hydroamination Aspartate ammonia lyases catalyze the reversible amination of fumarate to l-aspartate. Recent studies demonstrate that the thermostable enzyme from <i>Bacillus</i> sp. YM55-1 (AspB) can be engineered for the enantioselective production of substituted β-amino acids. This reaction would be attractive for the conversion of acrylic acid to β-alanine, which is an important building block for the preparation of bioactive compounds. Here we describe a bioinformatics and computational approach aimed at introducing the β-alanine synthesis activity. Three strategies were used: First, we redesigned the α-carboxylate binding pocket of AspB to introduce activity with the acrylic acid. Next, different template enzymes were identified by genome mining, equipped with a redesigned α-carboxylate pocket, and investigated for β-alanine synthesis, which yielded variants with better activity. Third, interactions of the SS-loop that covers the active site and harbors a catalytic serine were computationally redesigned using energy calculations to stabilize reactive conformations and thereby further increase the desired β-alanine synthesis activity. Different improved enzymes were obtained and the best variants showed <i>k</i> <sub>cat</sub> values with acrylic acid of at least 0.6-1.5 s<sup>-1</sup> with <i>K</i> <sub>M</sub> values in the high mM range. Since the β-alanine production of wild-type enzyme was below the detection limit, this suggests that the <i>k</i> <sub>cat</sub>/<i>K</i> <sub>m</sub> was improved by at least 1000-fold. Crystal structures of the 6-fold mutant of redesigned AspB and the similarly engineered aspartase from <i>Caenibacillus caldisaponilyticus</i> revealed that their ligand-free structures have the SS-loop in a closed (reactive) conformation, which for wild-type AspB is only observed in the substrate-bound enzyme. AlphaFold-generated models suggest that other aspartase variants redesigned for acrylic acid hydroamination also prefer a 3D structure with the loop in a closed conformation. The combination of binding pocket redesign, genome mining, and enhanced active-site loop closure thus created effective β-alanine synthesizing variants of aspartase. Hydroamination ; Chemistry ; Acrylic acid ; Catalysis ; Alanine ; Organic chemistry ; Biochemistry ; Amino acid ; Copolymer Enzyme Structure and Function ; Biochemical and Molecular Research ; Diet, Metabolism, and Disease
Authors: Sergi Betkhoshvili | Ibério de P. R. Moreira | Jordi Poater | Josep María Bofill
Source: The Journal of Physical Chemistry Letters (article, 2024-05-08)
Field: Chemistry — Organic Chemistry

Pathway to Polyradicals: A Planar and Fully π-Conjugated Organic Tetraradical(oid) In this work, we provide a general strategy to stabilize the ground state of polyradical(oid)s and make higher spin states thermally accessible. As a proof of concept, we propose to merge two planar fully π-conjugated diradical(oid)s to obtain a planar and cross-conjugated tetraradical(oid). Using multireference quantum chemistry methods, we show that the designed tetraradical(oid) is stabilized by aromaticity and delozalization in the π-system and has six thermally accessible spin states within 1.72 kcal/mol. Analysis of the electronic structure of these six states of the tetraradical(oid) shows that its frontier π-system consists of two weakly interacting subsystems: aromatic cycles and four unpaired electrons. Conjugation between unpaired electrons, which favors closed-shell structures, is mitigated by delocalization and the aromaticity of the bridging groups, leading to the synergistic cross-coupling between two diradical(oid) subunits to stabilize the tetraradical(oid) electronic structure. Diradical ; Delocalized electron ; Unpaired electron ; Conjugated system ; Aromaticity ; Chemistry ; Electronic structure ; Planar ; Computational chemistry ; Chemical physics ; Photochemistry ; Radical ; Molecule ; Atomic physics ; Organic chemistry ; Polymer ; Physics ; Computer science Synthesis and Properties of Aromatic Compounds ; Fullerene Chemistry and Applications ; Axial and Atropisomeric Chirality Synthesis
Authors: Christiana Tourapi | Eleni Christoforou | Susana P. Gaudêncio | Marlen I. Vasquez
Source: Marine Drugs (review, 2024-09-20)
Field: Materials Science — Biomaterials

Aquatic Biomaterial Repositories: Comprehensive Guidelines, Recommendations, and Best Practices for Their Development, Establishment, and Sustainable Operation The alarming pace of species extinction severely threatens terrestrial and aquatic ecosystems, undermining the crucial ecological services vital for environmental sustainability and human well-being. Anthropogenic activities, such as urbanization, agriculture, industrialization, and those inducing climate change, intensify these risks, further imperiling biodiversity. Of particular importance are aquatic organisms, pivotal in biodiscovery and biotechnology. They contribute significantly to natural product chemistry, drug development, and various biotechnological applications. To safeguard these invaluable resources, establishing and maintaining aquatic biomaterial repositories (ABRs) is imperative. This review explores the complex landscape of ABRs, emphasizing the need for standardized procedures from collection to distribution. It identifies key legislative and regulatory frameworks, such as the Nagoya Protocol and EU directives, essential for ensuring responsible and equitable biorepository operations. Drawing on extensive literature and database searches, this study compiles existing recommendations and practices into a cohesive framework with which to guide the establishment and sustainable management of ABRs. Through collaborative efforts and adherence to best practices, ABRs can play a transformative role in the future of marine biotechnology and environmental conservation. Biomaterial ; Best practice ; Business ; Engineering ; Environmental resource management ; Environmental planning ; Biotechnology ; Biochemical engineering ; Environmental science ; Biology ; Biomedical engineering ; Management Diatoms and Algae Research ; Freshwater macroinvertebrate diversity and ecology ; Environmental DNA in Biodiversity Studies
Authors: Zi‐Qi Li | Turki M. Alturaifi | Yilin Cao | Matthew V. Joannou | Peng Liu | Keary M. Engle
Source: Angewandte Chemie International Edition (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 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<sup>6</sup> 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. Chemistry ; Electrophile ; Nucleophile ; Steric effects ; Ligand (biochemistry) ; Catalytic cycle ; Catalysis ; Denticity ; Stereochemistry ; Nickel ; Regioselectivity ; Redox ; Medicinal chemistry ; Combinatorial chemistry ; Metal ; Organic chemistry Sulfur-Based Synthesis Techniques ; Chemical Synthesis and Reactions ; Catalytic C–H Functionalization Methods