jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Maryan Lelyukh | Yuliia Matiichuk | Vadym Flud | Ihor Chaban | В. В. Огурцов | A Tripathi | S Gupta | G Fatima | P Sonar | A Verma | S Saraf | S Manjal | R Kaur | R Bhatia | K Kumar | V Singh | R Shankar | R Rawal | N Agrawal | V Patil | K Tilekar | S Mehendale-Munj | R Mohan | C Ramaa | M Iqbal | A Husain | O Alam | S Khan | A Ahmad | M Haider | M Alam | Design | A Tre | M Ergl | A Altun | Kkgzel | X.-F Liu | C.-J Zheng | L.-P Sun | X.-K Liu | H.-R Piao | N Patel | M Patel | S Pandey | P Pandey | S Gautam | J Singh | C Nitsche | V Schreier | M Behnam | A Kumar | R Bartenschlager | C Klein | Apaydin | B Loy | A V; Stevaert | L Naesens | R Rohini | M Manjunath | D Havrylyuk | B Zimenkovsky | O Karpenko | P Grellier | R Lesyk | B Yang | H Si | H Zhai | S El-Karim | H Mohamed | M Abdelhameed | A Amr | G Almehizia | A Nossier | E Design | K Abdellatif | M Abdelgawad | H Elshemy | S Alsayed | J Choi | Y Ko | H Le | Y Park | Y Yang | S Yoon | R Kumar | N Dogra | A Yadav | M Kumar | V Carbone | M Giglio | R Chung | T Huyton | J Adams | R Maccari | R Ottana
Source: Biointerface Research in Applied Chemistry (article, 2021-11-20)
Field: Chemistry — Organic Chemistry

Synthesis and Antioxidant Properties of Novel 2-(2,4-Dioxothiazolidin-5-ylidene)-Acetamides Containing 1,3,4-Thia/Oxadiazole Moieties A series of novel 1,3,4-thia(oxa)diazole substituted 2-(2,4-dioxothiazolidine-5-ylidene)-acetamides 3a-c, 4 and 5a-k have been synthesized following the acylation reaction of 2-amino-5-aryl-1,3,4-oxadiazoles, 5-amino-1,3,4-thiadiazole-2-thiol and it’s S-alkylated derivatives with 2-(2,4-dioxothiazolidine-5-ylidene)acetyl chloride in dioxane medium. The functionalization of compounds 3b, 3c, 5d and 5e was carried out on their N3 position under N-alkylation conditions with N-aryl-2-chloroacetamides in DMF/ethanol medium yielded the corresponding 2,4-dioxothiazolidine-3,5-diacetic acid diamides 6a-e and 7a-b. The structures of target compounds were confirmed by using 1H NMR spectroscopy and elemental analysis. The antioxidant activity evaluation in vitro of the synthesized compounds was performed by the method of scavenging effect on 2,2-diphenyl-1-picrylhydrazyl (DPPH) radicals. As a result, the highly active compound 4, namely 2-(2,4-dioxothiazolidin-5-ylidene)-N-(5-mercapto-[1,3,4]thiadiazol-2-yl)acetamide was found to be the most efficient candidate among all compounds with a radical scavenging ability of 88.9%, which was comparable that for ascorbic acid (92.7%). The experimentally calculated IC50 value of 43.1 µM for compound 4 was lower than for ascorbic acid (50.5 µM). Chemistry ; Acetamide ; Ascorbic acid ; DPPH ; Acylation ; Alkylation ; Antioxidant ; Aryl ; Organic chemistry ; Medicinal chemistry ; Oxadiazole ; Catalysis Synthesis and biological activity ; Synthesis and Characterization of Heterocyclic Compounds ; Synthesis and Reactivity of Sulfur-Containing Compounds
Authors: Yi Li | Kexin Wang | Yupeng Chen | Jieqi Cai | Xuemei Qin | Aiping Lü | Daogang Guan | Genggeng Qin | Weiguo Chen
Source: Frontiers in Pharmacology (article, 2021-11-16)
Field: Chemistry — Analytical Chemistry

A System Pharmacology Model for Decoding the Synergistic Mechanisms of Compound Kushen Injection in Treating Breast Cancer Breast cancer (BC) is one of the most common malignant tumors among women worldwide and can be treated using various methods; however, side effects of these treatments cannot be ignored. Increasing evidence indicates that compound kushen injection (CKI) can be used to treat BC. However, traditional Chinese medicine (TCM) is characterized by "multi-components" and "multi-targets", which make it challenging to clarify the potential therapeutic mechanisms of CKI on BC. Herein, we designed a novel system pharmacology strategy using differentially expressed gene analysis, pharmacokinetics synthesis screening, target identification, network analysis, and docking validation to construct the synergy contribution degree (SCD) and therapeutic response index (TRI) model to capture the critical components responding to synergistic mechanisms of CKI in BC. Through our designed mathematical models, we defined 24 components as a high contribution group of synergistic components (HCGSC) from 113 potentially active components of CKI based on ADME parameters. Pathway enrichment analysis of HCGSC targets indicated that <i>Rhizoma Heterosmilacis</i> and <i>Radix Sophorae Flavescentis</i> could synergistically target the PI3K-Akt signaling pathway and the cAMP signaling pathway to treat BC. Additionally, TRI analysis showed that the average affinity of HCGSC and targets involved in the key pathways reached -6.47 kcal/mmol, while <i>in vitro</i> experiments proved that two of the three high TRI-scored components in the HCGSC showed significant inhibitory effects on breast cancer cell proliferation and migration. These results demonstrate the accuracy and reliability of the proposed strategy. ADME ; PI3K/AKT/mTOR pathway ; Pharmacology ; Breast cancer ; Computational biology ; Active compound ; Pharmacokinetics ; Chemistry ; Medicine ; Cancer ; Signal transduction ; Biology ; Biochemistry ; Stereochemistry ; Internal medicine Chromatography in Natural Products ; Bioactive natural compounds ; Natural product bioactivities and synthesis
Authors: Victor Masip | Ángel Lirio | Albert Sánchez-López | Ana B. Cuenca | Raimon Puig de la Bellacasa | Pau Abrisqueta | Jordi Teixidó | José I. Borrell | Albert Gibert | Roger Estrada‐Tejedor
Source: Pharmaceuticals (article, 2021-12-15)
Field: Chemistry — Organic Chemistry

Expanding the Diversity at the C-4 Position of Pyrido[2,3-d]pyrimidin-7(8H)-ones to Achieve Biological Activity against ZAP-70 Pyrido[2,3-<i>d</i>]pyrimidin-7(8<i>H</i>)-ones have attracted widespread interest due to their similarity with nitrogenous bases found in DNA and RNA and their potential applicability as tyrosine kinase inhibitors. Such structures, presenting up to five diversity centers, have allowed the synthesis of a wide range of differently substituted compounds; however, the diversity at the C4 position has mostly been limited to a few substituents. In this paper, a general synthetic methodology for the synthesis of 4-substituted-2-(phenylamino)-5,6-dihydropyrido[2,3-<i>d</i>]pyrimidin-7(8<i>H</i>)-ones is described. By using cross-coupling reactions, such as Ullmann, Buchwald-Hartwig, Suzuki-Miyaura, or Sonogashira reactions, catalyzed by Cu or Pd, we were able to describe new potential biologically active compounds. The resulting pyrido[2,3-<i>d</i>]pyrimidin-7(8<i>H</i>)-ones include <i>N</i>-alkyl, <i>N</i>-aryl, <i>O</i>-aryl, <i>S</i>-aryl, aryl, and arylethynyl substituents at C4, which have never been explored in connection with the biological activity of such heterocycles as tyrosine kinase inhibitors, in particular as ZAP-70 inhibitors. Position (finance) ; Diversity (politics) ; Computational biology ; Computer science ; Biology ; Business ; Political science ; Law Synthesis and Reactivity of Heterocycles ; Chemical Synthesis and Analysis ; Synthesis and biological activity
Authors: Nguyễn Thị Thanh Hải | Thanh Q. Bui | Tran Thi Ai My | Huynh Thi Phuong Loan | Trần Thái Hòa | Phan Tứ Quý | Nguyễn Thị Thu Thủy | Dang Thanh Nhan | Nguyen Thi Ai Nhung
Source: Journal of Chemistry (article, 2021-12-30)
Field: Chemistry — Organic Chemistry

In Silico Inhibitability of Copper Carbenes and Silylenes against Rhizoctonia solani and Magnaporthe oryzae Copper lighter tetrylenes are promising for inhibition towards Rhizoctonia solani-based protein PDB-4G9M and Magnaporthe oryzae-based PDB-6JBR in rice. Quantum properties of four hypothetic copper complexes of carbenes and silylenes (Cu-NHC1, Cu-NHC2, Cu-NHSi1, and Cu-NHSi2) were examined using the density functional theory. Their inhibitability towards the targeted proteins was evaluated using molecular docking simulation. Quantum analysis predicts the stability of the investigated complexes and thus their practical existability and practicable synthesisability. Their electronic configurations are justified as highly conducive to intermolecular interaction. Regarding ligand-protein as carbenes/silylenes-4G9M inhibitory structures, the stability is estimated in the order [Cu-NHC2]-4G9M (DS −12.9 kcal⋅mol−1) &gt; [Cu-NHSi1]-4G9M (DS −11.8 kcal⋅mol−1) = [Cu-NHSi2]-4G9M (DS −11.7 kcal⋅mol−1) &gt; [Cu-NHC1]-4G9M (DS –11.4 kcal⋅mol−1). In contrast, the corresponding order for the carbenes/silylenes-6JBR systems is [Cu-NHSi2]-6JBR (DS –13.4 kcal⋅mol−1) &gt; [Cu-NHC2]-6JBR (DS −13.0 kcal⋅mol−1) = [Cu-NHSi1]-6JBR (DS −12.6 kcal⋅mol−1) &gt; [Cu-NHC1]-6JBR (DS −12.3 kcal⋅mol−1). In theory, this study suggests a potentiality of copper lighter tetrylenes and their derivatives against the infection of fungi Rhizoctonia solani and Magnaporthe oryzae, thus encouraging attempts for experimental developments. Protein Data Bank (RCSB PDB) ; Copper ; Rhizoctonia solani ; Chemistry ; Natural bond orbital ; Rhizoctonia ; Crystallography ; Intermolecular force ; Density functional theory ; Stereochemistry ; Computational chemistry ; Molecule ; Organic chemistry ; Biology ; Botany N-Heterocyclic Carbenes in Organic and Inorganic Chemistry ; Synthesis and Biological Evaluation ; Ferrocene Chemistry and Applications
Authors: R Singh | K K Verma | Abhilasha Choudhary | S Veena
Source: SAMRIDDHI A Journal of Physical Sciences Engineering and Technology (article, 2021-12-31)
Field: Chemistry — Organic Chemistry

Screening of Heartwood of Tectona Grandis Linn for Antifungal Activity AB S T R A C T Medicinal plants have always been a subject of interest for the human being from ancient times due to health benefits. Researchers found that people in different regions of the world used the same or similar plants for health benefits. Medicinal plant research includes many fields like drug discovery, ethnobotany, traditional and indigenous medicines. During the corona pandemic, we realised that there are no effective therapies available for new and remerging infectious diseases. Public health is badly affected due to drug- resistant microorganisms and the appearance of new disease- causing microbes. Due to the increasing side effects of synthetic drugs and uncontrolled infectious diseases, researchers have taken interest in natural sources of medicines and have screened a large number of plants for new bioactive compounds. Natural products have been a well-known source of various molecules in the process of drug discovery and many bioactive natural product derivatives. Stereochemical and structural properties of natural products are characteristics that are responsible for exploring novel molecular diversity. One of the successful strategies for the investigation of new medicinal agents from plants includes the screening of plant extract, fractions followed by the purification of the constituents. Several plants and their products have been evaluated for their antimicrobial and antioxidant activity. In the present study, the ethanolic extract of the heartwood of Tectona grandis Linn. was screened for antifungal activity Tectona ; Antimicrobial ; Traditional medicine ; Medicinal plants ; Antifungal ; Drug discovery ; Biology ; Natural product ; Biotechnology ; Medicine ; Botany ; Microbiology ; Biochemistry Plant-Derived Bioactive Compounds ; Biological Stains and Phytochemicals
Authors: Zhanggao Le | Zhiyu Hu | Xuehua Chen | Liyuan Yan | Yishuai Liu | Zongbo Xie
Source: Chinese Journal of Organic Chemistry (article, 2021-01-01)
Field: Chemistry — Organic Chemistry

Synthesis of Triarylmethane Derivatives by Baeyer Condensation in a Deep Eutectic Solvent Triarylmethane derivatives and their syntheses are of great interest owing to their broad applicability in areas from textiles to medicine. In this study, the green solvent [ChCl][ZnCl2] synergistically promoted Baeyer condensation between benzaldehyde and N-substituted aniline to efficiently synthesize triarylmethane derivatives with high para-selectivity. The employed deep eutectic solvent acted as both a catalyst and green reaction medium for the reaction. Moreover, the deep eutectic solvent was reused several times in this procedure without significant loss of activity. Chemistry ; Deep eutectic solvent ; Eutectic system ; Condensation ; Solvent ; Organic chemistry ; Combinatorial chemistry ; Thermodynamics Synthesis of Indole Derivatives ; Ionic liquids properties and applications ; Chemical Synthesis and Reactions
Authors: Aleksandra Dymek | Tomasz Mroczek
Source: Current Issues in Pharmacy and Medical Sciences (article, 2021-06-01)
Field: Chemistry — Organic Chemistry

Methods of isolation and bioactivity of alkaloids obtained from selected species belonging to the Amaryllidaceae and Lycopodiaceae families Abstract Alkaloids obtained from plants belonging to the Amaryllidaceae and Lycopodiaceae families are of great interest due to their numerous properties. They play a very important role mainly due to their strong antioxidant, anxiolytic and anticholinesterase activities. The bioactive compounds obtained from these two families, especially galanthamine and huperzine A, have found application in the treatment of the common and incurable dementia-like Alzheimer’s disease. Thanks to this discovery, there has been a breakthrough in its treatment by significantly improving the patient’s quality of life and slowing down disease symptoms – albeit with no chance of a complete cure. Therefore, a continuous search for new compounds with potent anti-AChE activity is needed in modern medicine. In obtaining new therapeutic bioactive phytochemicals from plant material, the isolation process and its efficiency are crucial. Many techniques are known for isolating bioactive compounds and determining their amounts in complex samples. The most commonly utilized methods are extraction using different variants of organic solvents allied with chromatographic and spectrometric techniques. Optimization of these methods and modification of their procedures potentially allows researchers to obtain the expected results. The aim of this paper is to present known techniques for the isolation of alkaloids, especially from three species Narcissus, Lycopodium and Huperzia that are a rich source of AChE inhibitors. In addition, innovative combinations of chromatographic and spectrometric methods and novel TLC-bioautography will be presented to enable researchers to better study the bioactivity of alkaloids. Huperzine A ; Amaryllidaceae Alkaloids ; Isolation (microbiology) ; Amaryllidaceae ; Traditional medicine ; Medicine ; Biology ; Botany ; Acetylcholinesterase ; Biochemistry ; Bioinformatics Chemical synthesis and alkaloids ; Cholinesterase and Neurodegenerative Diseases ; Psychedelics and Drug Studies
Authors: Alexander Petrillo | Alexander Hoffmann | Jonathan Becker | Sonja Herres‐Pawlis | Siegfried Schindler
Source: European Journal of Inorganic Chemistry (article, 2021-12-14)
Field: Chemistry — Inorganic Chemistry

Copper Mediated Intramolecular vs. Intermolecular Oxygenations: The Spacer makes the Difference! Abstract Copper complexes in combination with dioxygen are important as potential catalytic systems for regio‐ and stereoselective aerobic oxygenations of aromatic and aliphatic C−H bonds at ambient temperatures. In that context we herein describe a copper(I) complex with an imine ligand derived from (+)‐camphor and 2‐(2‐aminoethyl)pyridine that forms a bis( μ ‐hydroxido) dicopper complex upon reaction with dioxygen at room temperature. It is detectable by UV‐vis for several hours up to a few days, depending on the solvent and could be structurally characterized. In contrast to previous observations this complex rather oxygenates acetone or thioanisole as external substrates instead of undergoing an intramolecular ligand hydroxylation. Chemistry ; Intramolecular force ; Ligand (biochemistry) ; Hydroxylation ; Copper ; Photochemistry ; Stereochemistry ; Stereoselectivity ; Imine ; Medicinal chemistry ; Polymer chemistry ; Catalysis ; Organic chemistry Metal-Catalyzed Oxygenation Mechanisms ; Oxidative Organic Chemistry Reactions ; Synthesis and Catalytic Reactions
Authors: Michiaki Sakamoto | Itsuo Hanasaki
Source: Physical review. E (article, 2021-08-31)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Derivation of coarse-grained force fields for buckling-induced topological defects of liquid crystals Microscopic details of buckling-induced topological defects are required for molecular design of smectic liquid crystals to control buckling instability of the layers. In this study, we present a multiobjective optimization method to derive the coarse-grained (CG) force fields with sufficiently precise buckling characteristics including the molecular details for molecular dynamics (MD) simulations. We perform CGMD simulations of buckling deformation at sample points in the CG force field parameter space, from which the response surfaces of objective functions such as the scalar orientational order parameters, critical angles of layer collapse, and radial distribution functions are estimated. Since not all objective functions can be optimized simultaneously, we use a genetic algorithm to calculate the Pareto set of optimal solutions. We select the models with different molecular head-tail symmetries to study buckling deformation. The extracted CG model successfully reproduces the buckling deformation in terms of the collapse of smectic layers through the generation of dislocations with dipole disclinations. We also find that the molecular symmetry is a dominant factor to control the class of the buckling-induced dislocations. Buckling ; Materials science ; Topological defect ; Instability ; Deformation (meteorology) ; Molecular dynamics ; Dipole ; Scalar (mathematics) ; Homogeneous space ; Physics ; Geometry ; Mechanics ; Condensed matter physics ; Mathematics ; Composite material Liquid Crystal Research Advancements ; Block Copolymer Self-Assembly ; Material Dynamics and Properties
Authors: Julian Breidenbach | Carina Lemke | Thanigaimalai Pillaiyar | Laura Schäkel | Ghazl Al Hamwi | Miriam Diett | Robin Gedschold | Nina Geiger | Vittoria Lopez | Salahuddin Mirza | Vigneshwaran Namasivayam | Anke C. Schiedel | Katharina Sylvester | Dominik Thimm | Christin Vielmuth | Lan Phuong Vu | Maria Zyulina | Jochen Bodem | Michael Gütschow | Christa E. Müller
Source: Angewandte Chemie (article, 2021-03-03)
Field: Chemistry — Organic Chemistry

Die Hauptprotease von SARS‐CoV‐2 als Zielstruktur: Von der Etablierung eines Hochdurchsatz‐Screenings zum Design maßgeschneiderter Inhibitoren Abstract Die Hauptprotease von SARS‐CoV‐2 (M pro ), dem Auslöser von COVID‐19, ist ein wichtiges Arzneistoff‐Target. Ein neues fluorogenes Substrat, das kinetisch mit einem intern gequenchten fluoreszierenden Peptid verglichen wurde, erwies sich als ideal geeignet für ein Hochdurchsatz‐Screening mit rekombinant exprimierter M pro . Zwei Klassen von Protease‐Inhibitoren, Azanitrile und Pyridylester, wurden identifiziert, optimiert und biochemisch charakterisiert. Maßgeschneiderte Peptide mit einer reaktiven Azanitril‐Kopfgruppe zeigten eine duale Inhibition von M pro und Cathepsin L, einer Protease, welche die virale Zellinvasion befördert. Zur Optimierung der Pyridylindolester wurde ein Positions‐Scanning durchgeführt. Unser fokussierter Ansatz zur Entwicklung von M pro ‐Inhibitoren erwies sich dem virtuellen Screening als überlegen. Mit den beiden irreversiblen Inhibitoren Azanitril 8 (k inac /K i =37 500 m −1 s −1 , K i =24.0 n m ) und Pyridylester 17 (k inac /K i =29 100 m −1 s −1 , K i =10.0 n m ) wurden vielversprechende Kandidaten für die zukünftige Arzneistoffentwicklung entdeckt. Molecular biology ; Chemistry ; Physics ; Biology Click Chemistry and Applications ; Computational Drug Discovery Methods ; Antimicrobial Peptides and Activities
Authors: Fabio Le Piane | Matteo Baldoni | Mauro Gáspari | Francesco Mercuri
Source: arXiv (Cornell University) (preprint, 2021-11-03)
Field: Materials Science — Materials Chemistry

Introducing MAMBO: Materials And Molecules Basic Ontology Recent advances in computational and experimental technologies applied to the design and development of novel materials have brought out the need for systematic, rational and efficient methods for the organization of knowledge in the field. In this work, we present the initial steps carried out in the development of MAMBO - an ontology focused on the organization of concepts and knowledge in the field of materials based on molecules and targeted to applications. Our approach is guided by the needs of the communities involved in the development of novel molecular materials with functional properties at the nanoscale. As such, MAMBO aims at bridging the gaps of ongoing efforts in the development of ontologies in the materials science domain. By extending current work in the field, the modular nature of MAMBO also allows straightforward extension of concepts and relations to neighboring domains. Our work is expected to enable the systematic integration of computational and experimental data in specific domains of interest (nanomaterials, molecular materials, organic an polymeric materials, supramolecular and bio-organic systems, etc.). Moreover, MAMBO can be applied to the development of data-driven integrated predictive frameworks for the design of novel materials with tailored functional properties. Computer science ; Bridging (networking) ; Modular design ; Ontology ; Field (mathematics) ; Nanotechnology ; Data science ; Systems engineering ; Materials science ; Engineering ; Epistemology ; Programming language Machine Learning in Materials Science ; Computational Drug Discovery Methods ; History and advancements in chemistry
Authors: Tong‐Yi Zhang
Source: Journal of Materials Informatics (article, 2021-01-01)
Field: Materials Science — Materials Chemistry

New tool in the box Journal of Materials Informatics (JMI) is an international peer-reviewed, open access journal. The journal provides a platform for presentation, publication, and exchange of materials informatics research, seeking to break down barriers among materials science and engineering, data science and engineering, and artificial intelligence. The journal also provides a venue for presenting innovative approaches to overcome the difficulties in unraveling the complexity of data associated with numerous factors including noise, uncertainty, and small amount, to achieve the quantum jump from data to knowledge. Informatics ; Data science ; Presentation (obstetrics) ; Computer science ; Science and engineering ; Engineering ethics ; Engineering Machine Learning in Materials Science ; Advanced Materials Characterization Techniques
Authors: Hassna El‐Bousiydy | Teo Lombardo | Emiliano N. Primo | Marc Duquesnoy | Mathieu Morcrette | Patrik Johansson | Patrice Simon | Alexis Grimaud | Alejandro A. Franco
Source: Batteries & Supercaps (article, 2021-04-21)
Field: Materials Science — Materials Chemistry

What Can Text Mining Tell Us About Lithium‐Ion Battery Researchers’ Habits? Abstract Invited for this month's cover picture is an effort run by the group of Alejandro A. Franco and made in collaboration with Mathieu Morcrette, Patrik Johansson, Patrice Simon and Alexis Grimaud. The Front Cover illustrates an ideal scientific literature, in which all the data are systematically disclosed and available for researchers, together with artificial intelligence algorithms bringing new light on battery research and researchers. Read the full text of the Concept at 10.1002/batt.202000288 . Cover (algebra) ; Front cover ; Ideal (ethics) ; Lithium (medication) ; Battery (electricity) ; Computer science ; Front (military) ; Data science ; Psychology ; Engineering ; Epistemology ; Philosophy ; Physics ; Mechanical engineering Machine Learning in Materials Science ; Topic Modeling ; Advanced Text Analysis Techniques