jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Alexander van Teijlingen | Melissa C. Smith | Tell Tuttle
Source: Accounts of Chemical Research (article, 2023-03-03)
Field: Materials Science — Biomaterials

Short Peptide Self-Assembly in the Martini Coarse-Grain Force Field Family Pivotal to the success of any computational experiment is the ability to make reliable predictions about the system under study and the time required to yield these results. Biomolecular interactions is one area of research that sits in every camp of resolution vs the time required, from the quantum mechanical level to <i>in vivo</i> studies. At an approximate midpoint, there is coarse-grained molecular dynamics, for which the Martini force fields have become the most widely used, fast enough to simulate the entire membrane of a mitochondrion though lacking atom-specific precision. While many force fields have been parametrized to account for a specific system under study, the Martini force field has aimed at casting a wider net with more generalized bead types that have demonstrated suitability for broad use and reuse in applications from protein-graphene oxide coassembly to polysaccharides interactions.In this Account, the progressive (Martini versions 1 through 3) and peripheral (Sour Martini, constant pH, Martini Straight, Dry Martini, etc.) developmental trajectory of the Martini force field will be analyzed in terms of self-assembling systems with a focus on short (two to three amino acids) peptide self-assembly in aqueous environments. In particular, this will focus on the effects of the Martini solvent model and compare how changes in bead definitions and mapping have effects on different systems. Considerable effort in the development of Martini has been expended to reduce the "stickiness" of amino acids to better simulate proteins in bilayers. We have included in this Account a short study of dipeptide self-assembly in water, using all mainstream Martini force fields, to examine their ability to reproduce this behavior. The three most recently released versions of Martini and variations in their solvents are used to simulate in triplicate all 400 dipeptides of the 20 gene-encoded amino acids. The ability of the force fields to model the self-assembly of the dipeptides in aqueoues environments is determined by the measurement of the aggregation propensity, and additional descriptors are used to gain further insight into the dipeptide aggregates. Molecular dynamics ; Force field (fiction) ; Peptide ; Computer science ; Chemistry ; Nanotechnology ; Biological system ; Materials science ; Computational chemistry ; Biology ; Biochemistry Supramolecular Self-Assembly in Materials ; Lipid Membrane Structure and Behavior ; Advanced biosensing and bioanalysis techniques
Authors: Marie-Lise Dubernet | C. Boursier | Otoniel Denis‐Alpizar | Yaye Awa Ba | Nicolas Moreau | Carlo Maria Zwölf | Mohamed Amine Ben Amor | Dmitri Babikov | N. Balakrishnan | Christian Balança | M. Ben Khalifa | Astrid Bergeat | Cheikh T Bop | Lisán David Cabrera‐González | Carlos Cárdenas | A Chefai | Paul J. Dagdigian | F. Dayou | S. Demes | Benjamin Desrousseaux | F. Dumouchel | Alexandre Faure | Robert C. Forrey | Jan Franz | Ricardo Manuel García‐Vázquez | F. A. Gianturco | Amélie Godard Palluet | Lola González‐Sánchez | Gerrit C. Groenenboom | P. Halvick | K. Hammami | F Khadri | Yulia N. Kalugina | I. Kleiner | Jacek Kłos | François Lique | Jérôme Loreau | Bikramaditya Mandal | Barry P. Mant | Sarantos Marinakis | D. Ndaw | P. Pirlot Jankowiak | T. Price | Ernesto Quintas‐Sánchez | R. Ramachandran | E. Sahnoun | Carlos Carmona Santander | P. C. Stancil | Thierry Stoecklin | Jonathan Tennyson | Francesca Tonolo | Rodrigo Urzúa-Leiva | Benhui Yang | E. Yurtsever | Michał Żółtowski
Source: Astronomy and Astrophysics (article, 2023-12-18)
Field: Chemistry — Spectroscopy

BASECOL2023 scientific content Context . The global context of making numerous data produced by researchers available requires collecting and organising the data, assigning meaningful metadata, and presenting the data in a meaningful and homogeneous way. The BASECOL database, which collects inelastic rate coefficients for application to the interstellar medium and to circumstellar and cometary atmospheres, meets those requirements. Aims . We aim to present the scientific content of the BASECOL2023 edition. Methods . While the previous versions relied on finding rate coefficients in the literature, the current version is populated with published results sent by the producers of data. The paper presents the database, the type of data that can be found, the type of metadata that are used, and the Virtual Atomic and Molecular Data Centre (VAMDC) standards that are used for the metadata. Finally, we present the different datasets species by species. Results . As the BASECOL database, interconnected with the VAMDC e-infrastructure, uses the VAMDC standards, the collisional data can be extracted with tools using VAMDC standards and can be associated with spectroscopic data extracted from other VAMDC connected databases such as the Cologne database for molecular spectroscopy (CDMS), the jet propulsion laboratory molecular spectroscopy database (JPL), and the high-resolution transmission molecular absorption database (HITRAN). Metadata ; HITRAN ; Context (archaeology) ; Database ; Physics ; Chemical database ; Computer science ; Information retrieval ; Astrophysics ; Spectroscopy ; World Wide Web ; Astronomy ; Bioinformatics Molecular Spectroscopy and Structure ; Atmospheric Ozone and Climate ; Spectroscopy and Laser Applications
Authors: Aiva Plotniece | Arkadij Sobolev | Claudiu T. Supuran | Fabrizio Carta | Fredrik Björkling | Henrik Franzyk | Jari Yli‐Kauhaluoma | Koen Augustyns | Paul Cos | Linda De Vooght | Matthias Govaerts | Juliana Aizawa | Päivi Tammela | Raivis Žalubovskis
Source: Journal of Enzyme Inhibition and Medicinal Chemistry (review, 2023-01-11)
Field: Materials Science — Materials Chemistry

Selected strategies to fight pathogenic bacteria Natural products and analogues are a source of antibacterial drug discovery. Considering drug resistance levels emerging for antibiotics, identification of bacterial metalloenzymes and the synthesis of selective inhibitors are interesting for antibacterial agent development. Peptide nucleic acids are attractive antisense and antigene agents representing a novel strategy to target pathogens due to their unique mechanism of action. Antisense inhibition and development of antisense peptide nucleic acids is a new approach to antibacterial agents. Due to the increased resistance of biofilms to antibiotics, alternative therapeutic options are necessary. To develop antimicrobial strategies, optimised <i>in vitro</i> and <i>in vivo</i> models are needed. In vivo models to study biofilm-related respiratory infections, device-related infections: ventilator-associated pneumonia, tissue-related infections: chronic infection models based on alginate or agar beads, methods to battle biofilm-related infections are discussed. Drug delivery in case of antibacterials often is a serious issue therefore this review includes overview of drug delivery nanosystems. Pathogenic bacteria ; Bacteria ; Microbiology ; Biology ; Political science ; Genetics Nanoparticles: synthesis and applications ; Bacterial biofilms and quorum sensing ; Legionella and Acanthamoeba research
Authors: Arafa Musa | Hamada S. Abulkhair | Ateyatallah Aljuhani | Nadjet Rezki | Mohamed A. Abdelgawad | Khaled Shalaby | Ahmed H. El‐Ghorab | Mohamed Reda Aouad
Source: Pharmaceuticals (article, 2023-03-20)
Field: Chemistry — Organic Chemistry

Phenylpyrazolone-1,2,3-triazole Hybrids as Potent Antiviral Agents with Promising SARS-CoV-2 Main Protease Inhibition Potential COVID-19 infection is now considered one of the leading causes of human death. As an attempt towards the discovery of novel medications for the COVID-19 pandemic, nineteen novel compounds containing 1,2,3-triazole side chains linked to phenylpyrazolone scaffold and terminal lipophilic aryl parts with prominent substituent functionalities were designed and synthesized via a click reaction based on our previous work. The novel compounds were assessed using an in vitro effect on the growth of SARS-CoV-2 virus-infested Vero cells with different compound concentrations: 1 and 10 μM. The data revealed that most of these derivatives showed potent cellular anti-COVID-19 activity and inhibited viral replication by more than 50% with no or weak cytotoxic effect on harboring cells. In addition, in vitro assay employing the SARS-CoV-2-Main protease inhibition assay was done to test the inhibitors' ability to block the common primary protease of the SARS-CoV-2 virus as a mode of action. The obtained results show that the one non-linker analog <b>6h</b> and two amide-based linkers <b>6i</b> and <b>6q</b> were the most active compounds with IC<sub>50</sub> values of 5.08, 3.16, and 7.55 μM, respectively, against the viral protease in comparison to data of the selective antiviral agent GC-376. Molecular modeling studies were done for compound placement within the binding pocket of protease which reveal conserved residues hydrogen bonding and non-hydrogen interactions of <b>6i</b> analog fragments: triazole scaffold, aryl part, and linker. Moreover, the stability of compounds and their interactions with the target pocket were also studied and analyzed by molecular dynamic simulations. The physicochemical and toxicity profiles were predicted, and the results show that compounds behave as an antiviral activity with low or no cellular or organ toxicity. All research results point to the potential usage of new chemotype potent derivatives as promising leads to be explored in vivo that might open the door to rational drug development of SARS-CoV-2 Main protease potent medicines. Protease ; Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ; Coronavirus disease 2019 (COVID-19) ; Virology ; Triazole ; 2019-20 coronavirus outbreak ; Pharmacology ; Chemistry ; Medicine ; Enzyme ; Biochemistry ; Infectious disease (medical specialty) Synthesis and biological activity ; Computational Drug Discovery Methods ; Click Chemistry and Applications
Authors: Linawati Sutrisno | Katsuhiko Ariga
Source: NPG Asia Materials (article, 2023-03-31)
Field: Materials Science — Biomaterials

Pore-engineered nanoarchitectonics for cancer therapy Abstract Nanoarchitectonics describes the integration of nanotechnology with other fields as a postnanotechnology concept that elevates it to material science. Based on this fundamental principle, we address pore-engineered nanoarchitectonics with application targets for cancer therapy by combining basic descriptions and exemplifying therapy applications in this review. The initial two sections briefly summarize pore-engineered nanoarchitectonics basics according to classification based on (i) material porosity and (ii) material composition. Afterward, the main application-oriented section—designing mesoporous material for cancer therapy—is presented. Various types of drug delivery systems, including mesoporous nanoparticles as nanocarriers, endogenous stimuli-responsive drug delivery, exogenous stimuli-responsive drug delivery, and targeted drug delivery, are described. Importantly, the clinical translation of mesoporous materials is further discussed. Mesoporous materials are unique nanoparticles that offer a network of cavities as vehicles for drug nanocarriers. Regarding the developments that allow mesoporous nanoparticles to be broadly used in clinical settings, there are several challenges that should be solved for their clinical application. From a clinical perspective, there are tremendous processes in the development of mesoporous materials. Nanocarriers ; Nanotechnology ; Drug delivery ; Mesoporous material ; Materials science ; Cancer therapy ; Targeted drug delivery ; Cancer ; Medicine ; Chemistry Nanoparticle-Based Drug Delivery ; Nanoplatforms for cancer theranostics ; Mesoporous Materials and Catalysis
Authors: Bhaskar C. Das | C. Parthiban | Pavithra Masilamani | Srushti Shukla | Sasmita Das
Source: International Journal of Molecular Sciences (review, 2023-02-01)
Field: Materials Science — Materials Chemistry

Stimuli-Responsive Boron-Based Materials in Drug Delivery Drug delivery systems, which use components at the nanoscale level as diagnostic tools or to release therapeutic drugs to particular target areas in a regulated manner, are a fast-evolving field of science. The active pharmaceutical substance can be released via the drug delivery system to produce the desired therapeutic effect. The poor bioavailability and irregular plasma drug levels of conventional drug delivery systems (tablets, capsules, syrups, etc.) prevent them from achieving sustained delivery. The entire therapy process may be ineffective without a reliable delivery system. To achieve optimal safety and effectiveness, the drug must also be administered at a precision-controlled rate and the targeted spot. The issues with traditional drug delivery are overcome by the development of stimuli-responsive controlled drug release. Over the past decades, regulated drug delivery has evolved considerably, progressing from large- and nanoscale to smart-controlled drug delivery for several diseases. The current review provides an updated overview of recent developments in the field of stimuli-responsive boron-based materials in drug delivery for various diseases. Boron-containing compounds such as boron nitride, boronic acid, and boron dipyrromethene have been developed as a moving field of research in drug delivery. Due to their ability to achieve precise control over drug release through the response to particular stimuli (pH, light, glutathione, glucose or temperature), stimuli-responsive nanoscale drug delivery systems are attracting a lot of attention. The potential of developing their capabilities to a wide range of nanoscale systems, such as nanoparticles, nanosheets/nanospheres, nanotubes, nanocarriers, microneedles, nanocapsules, hydrogel, nanoassembly, etc., is also addressed and examined. This review also provides overall design principles to include stimuli-responsive boron nanomaterial-based drug delivery systems, which might inspire new concepts and applications. Drug delivery ; Nanotechnology ; Nanocarriers ; Drug ; Nanocapsules ; Boron nitride ; Targeted drug delivery ; Controlled release ; Materials science ; Bioavailability ; Pharmacology ; Medicine ; Nanoparticle Luminescence and Fluorescent Materials ; Boron Compounds in Chemistry ; Dendrimers and Hyperbranched Polymers
Authors: Angela Punzi | Yasi Dai | Carlo Nazareno Dibenedetto | Ernesto Mesto | Emanuela Schingaro | Tobias Ullrich | Marinella Striccoli | Dirk M. Guldi | Fabrizia Negri | Gianluca M. Farinola | Davide Blasi
Source: Journal of the American Chemical Society (article, 2023-09-06)
Field: Materials Science — Materials Chemistry

Dark State of the Thiele Hydrocarbon: Efficient Solvatochromic Emission from a Nonpolar Centrosymmetric Singlet Diradicaloid In this work, a comprehensive investigation of the photoinduced processes and mechanisms linked to the luminescence of a novel nonperchlorinated Thiele hydrocarbon (<b>TTH</b>) is presented. Despite the comparable diradical character of <b>TTH</b> (<i>y</i><sub>0</sub> = 0.32-0.44) and the unsubstituted Thiele hydrocarbon (<b>TH</b>) (<i>y</i><sub>0</sub> = 0.30), the polyhalogenated species is inert and photostable, showing an intense deep-red/near-infrared (NIR) fluorescence (photoluminescence quantum yield (PLQY) = 0.84 in toluene) even at room temperature and in the solid state (PLQY = 0.19). <b>TTH</b> displays a large Stokes shift (307 nm in benzonitrile) and solvatochromic behavior, which is unusual for a centrosymmetric, nonpolar, and low-conjugated species. These outstanding emission features are interpreted through quantum-chemical calculations, indicating that its fluorescence arises from the low-lying dark doubly excited zwitterionic state, typically found at low excitation energies in diradicaloids, acquiring dipole moment and intensity by state mixing <i>via</i> twisting around the strongly elongated exocyclic CC bonds of the excited <i>p</i>-quinodimethane (<i>p</i>QDM) core, with a mechanism similar to sudden polarization occurring in olefins. Such a mechanism is derived from ns and fs transient absorption measurements. Chemistry ; Solvatochromism ; Photochemistry ; Excited state ; Bathochromic shift ; Quantum yield ; Stokes shift ; Benzonitrile ; Photoluminescence ; Photoexcitation ; Luminescence ; Singlet state ; Fluorescence ; Molecule ; Atomic physics ; Organic chemistry Luminescence and Fluorescent Materials ; Synthesis and Properties of Aromatic Compounds ; Photochemistry and Electron Transfer Studies
Authors: Qiong Huang | Zerun Liu | Yunrong Yang | Yuqi Yang | Ting Huang | Ying Hong | Jinping Zhang | Qiaohui Chen | Tianjiao Zhao | Zuoxiu Xiao | Xuejun Gong | Yitian Jiang | Jiang Peng | Yayun Nan | Kelong Ai
Source: Advanced Science (article, 2023-04-21)
Field: Materials Science — Materials Chemistry

Selenium Nanodots (SENDs) as Antioxidants and Antioxidant‐Prodrugs to Rescue Islet <i>β</i> Cells in Type 2 Diabetes Mellitus by Restoring Mitophagy and Alleviating Endoplasmic Reticulum Stress Preventing islet β-cells death is crucial for treating type 2 diabetes mellitus (T2DM). Currently, clinical drugs are being developed to improve the quality of T2DM care and self-care, but drugs focused on reducing islets β-cell death are lacking. Given that β-cell death in T2DM is dominated ultimately by excessive reactive oxygen species (ROS), eliminating excessive ROS in β-cells is a highly promising therapeutic strategy. Nevertheless, no antioxidants have been approved for T2DM therapy because most of them cannot meet the long-term and stable elimination of ROS in β-cells without eliciting toxic side-effects. Here, it is proposed to restore the endogenous antioxidant capacity of β-cells to efficiently prevent β-cell death using selenium nanodots (SENDs), a prodrug of the antioxidant enzyme glutathione peroxidase 1 (GPX1). SENDs not only scavenge ROS effectively, but also "send" selenium precisely to β-cells with ROS response to greatly enhance the antioxidant capacity of β-cells by increasing GPX1 expression. Therefore, SENDs greatly rescue β-cells by restoring mitophagy and alleviating endoplasmic reticulum stress (ERS), and demonstrate much stronger efficacy than the first-line drug metformin for T2DM treatment. Overall, this strategy highlights the great clinical application prospects of SENDs, offering a paradigm for an antioxidant enzyme prodrug for T2DM treatment. Mitophagy ; Antioxidant ; Reactive oxygen species ; Pharmacology ; Programmed cell death ; Oxidative stress ; Type 2 Diabetes Mellitus ; Endoplasmic reticulum ; Chemistry ; Cell biology ; Apoptosis ; Medicine ; Autophagy ; Biology ; Biochemistry ; Diabetes mellitus ; Endocrinology Carbon and Quantum Dots Applications ; Pancreatic function and diabetes ; Adenosine and Purinergic Signaling
Authors: Yixiu Luo | Luchao Sun | Jiemin Wang | Tiefeng Du | Cui Zhou | Jie Zhang | Jingyang Wang
Source: Nature Communications (article, 2023-03-07)
Field: Materials Science — Materials Chemistry

Phase formation capability and compositional design of β-phase multiple rare-earth principal component disilicates A key strategy to design environmental barrier coatings focuses on doping multiple rare-earth principal components into β-type rare-earth disilicates (RE<sub>2</sub>Si<sub>2</sub>O<sub>7</sub>) to achieve versatile property optimization. However, controlling the phase formation capability of (nRE<sub>xi</sub>)<sub>2</sub>Si<sub>2</sub>O<sub>7</sub> remains a crucial challenge, due to the complex polymorphic phase competitions and evolutions led by different RE<sup>3+</sup> combination. Herein, by fabricating twenty-one model (RE<sup>I</sup><sub>0.25</sub>RE<sup>II</sup><sub>0.25</sub>RE<sup>III</sup><sub>0.25</sub>RE<sup>IV</sup><sub>0.25</sub>)<sub>2</sub>Si<sub>2</sub>O<sub>7</sub> compounds, we find that their formation capability can be evaluated by the ability to accommodate configurational randomness of multiple RE<sup>3+</sup> cations in β-type lattice while preventing the β-to-γ polymorphic transformation. The phase formation and stabilization are controlled by the average RE<sup>3+</sup> radius and the deviations of different RE<sup>3+</sup> combinations. Subsequently, based on high-throughput density-functional-theory calculations, we propose that the configurational entropy of mixing is a reliable descriptor to predict the phase formation of β-type (nRE<sub>xi</sub>)<sub>2</sub>Si<sub>2</sub>O<sub>7</sub>. The results may accelerate the design of (nRE<sub>xi</sub>)<sub>2</sub>Si<sub>2</sub>O<sub>7</sub> materials with tailored compositions and controlled polymorphic phases. Rare earth ; Randomness ; Materials science ; Density functional theory ; Principal component analysis ; Phase (matter) ; Entropy (arrow of time) ; Chemical physics ; Biological system ; Computer science ; Chemistry ; Thermodynamics ; Physics ; Computational chemistry ; Mathematics ; Biology Nuclear materials and radiation effects ; Luminescence Properties of Advanced Materials ; Glass properties and applications
Authors: Sha Tian | Dongdong Zhan | Ying Yu | Yunzhi Wang | Mingwei Liu | Subei Tan | Yan Li | Lei Song | Zhaoyu Qin | Xianju Li | Yang Liu | Yao Li | Shuhui Ji | Shanshan Wang | Qing‐Yu He | Xingfeng Yin | Lunzhi Dai | Haiteng Deng | Chao Peng | Ping Wu | Minjia Tan | Jing Jiang | Yaoyang Zhang | Yunxia Li | Wenqin Liu | Wei Chen | Rui Wang | Jin Zi | Qidan Li | Mingzhou Bai | Zeng Wang | Zhanlong Mei | Zhongyi Cheng | Jun Zhu | Xuemei Wu | Xing Yang | Yue Zhou | Pengfei Zheng | Fuchu He | Jun Qin | Chen Ding
Source: Genome biology (article, 2023-09-06)
Field: Chemistry — Spectroscopy

Quartet protein reference materials and datasets for multi-platform assessment of label-free proteomics Abstract Background Quantitative proteomics is an indispensable tool in life science research. However, there is a lack of reference materials for evaluating the reproducibility of label-free liquid chromatography-tandem mass spectrometry (LC–MS/MS)-based measurements among different instruments and laboratories. Results Here, we develop the Quartet standard as a proteome reference material with built-in truths, and distribute the same aliquots to 15 laboratories with nine conventional LC–MS/MS platforms across six cities in China. Relative abundance of over 12,000 proteins on 816 mass spectrometry files are obtained and compared for reproducibility among the instruments and laboratories to ultimately generate proteomics benchmark datasets. There is a wide dynamic range of proteomes spanning about 7 orders of magnitude, and the injection order has marked effects on quantitative instead of qualitative characteristics. Conclusion Overall, the Quartet offers valuable standard materials and data resources for improving the quality control of proteomic analyses as well as the reproducibility and reliability of research findings. Reproducibility ; Proteomics ; Proteome ; Quantitative proteomics ; Mass spectrometry ; Label-free quantification ; Computational biology ; Chromatography ; Computer science ; Biology ; Bioinformatics ; Chemistry ; Biochemistry Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies