jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Eman Sabry | Sherifa M. Abu‐Bakr | Maha D. Khidre | Hanem M. Awad | Ashraf A. Sediek
Source: Egyptian Journal of Chemistry (article, 2024-02-08)
Field: Chemistry — Organic Chemistry

Synthesis, Characterization and Antitumor Activity of Benzimidazole Phosphonate Derivatives A series of Benzimidazole derivatives were obtained via reaction of 2-chloro-1H-benzo[d]imidazole (1) with morpholine, which produce benzo[d]imidazol-yl-morpholine 2 that react with chloroacetonitrile to give (benzo[d]imidazol-yl)acetonitrile 3, by its next reaction with hydrazine hydrate afforded the key intermediate 4, that afford thiadiazole derivatives 5 by its reaction with carbon disulfide via cyclization reaction. Alkylation of compound 5 with ethyl bromoacetate, afforded benzo[d]imidazolo derivative 6, that react with thioglycolic acid to give thiazolidine compound in suitable conditions. Also Benzimidazole 1 reacted with various Wittig Horner reagents in DMF to afford phosphoryl and phosphonates derivatives 12a-e in moderate yields. On the other hand, 1 react with trialkyl phosphites to yield the known phosphonates derivatives 14a-c in high yields, also we obtained the same products by reacting 1 with dialkyl phosphites. In addition, hexaalkyltriamidophosphites were applied to 1 in ethanol to afford phosphonic diamide derivatives 17a-c in high yields through addition-elimination reaction. Antitumor activity of the newly synthesized compounds were tested on three cell lines of breast (MCF7) and liver (HepG2) carcinoma cell lines and HCT-116 cancer cells together with human healthy cell line (BJ-1) using the MTT assay. Most compounds suppressed three cancer cells (HCT-116, HepG2 and MCF-7) and exhibited considerable anticancer properties in a dose-dependent manner Benzimidazole ; Phosphonate ; Chemistry ; Characterization (materials science) ; Combinatorial chemistry ; Stereochemistry ; Nanotechnology ; Biochemistry ; Organic chemistry ; Materials science Organophosphorus compounds synthesis ; Synthesis and Reactivity of Sulfur-Containing Compounds ; Synthesis and Characterization of Heterocyclic Compounds
Authors: Matthew J. McLeod | Sarah Barwell | Todd Holyoak | Robert Thorne
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2024-08-23)
Field: Materials Science — Materials Chemistry

A structural perspective on the temperature-dependent activity of enzymes Enzymes are biomolecular catalysts whose activity varies with temperature. Unlike for small-molecule catalysts, the structural ensembles of enzymes can vary substantially with temperature, and it is in general unclear how this modulates the temperature dependence of activity. Here multi-temperature X-ray crystallography was used to record structural changes from -20°C to 40°C for a mesophilic enzyme in complex with inhibitors mimicking substrate-, intermediate-, and product-bound states, representative of major complexes underlying the kinetic constant <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msub><mml:mrow><mml:mi>k</mml:mi></mml:mrow> <mml:mrow><mml:mi>c</mml:mi> <mml:mi>a</mml:mi> <mml:mi>t</mml:mi></mml:mrow> </mml:msub> </mml:math> . Both inhibitors, substrates and catalytically relevant loop motifs increasingly populate catalytically competent conformations as temperature increases. These changes occur even in temperature ranges where kinetic measurements show roughly linear Arrhenius/Eyring behavior where parameters characterizing the system are assumed to be temperature independent. Simple analysis shows that linear Arrhenius/Eyring behavior can still be observed when the underlying activation energy / enthalpy values vary with temperature, e.g., due to structural changes, and that the underlying thermodynamic parameters can be far from values derived from Arrhenius/Eyring model fits. Our results indicate a critical role for temperature-dependent atomic-resolution structural data in interpreting temperature-dependent kinetic data from enzymatic systems. Perspective (graphical) ; Enzyme ; Chemistry ; Business ; Biochemistry ; Computer science ; Artificial intelligence Enzyme Structure and Function ; Protein Structure and Dynamics ; Microbial Metabolic Engineering and Bioproduction
Authors: Manoel T. Rodrigues | Aline Silva Barroso de Oliveira | Ralph da Costa Gomes | Amanda S. Hirata | Lucas A. Zeoly | Hugo Santos | João Arantes | Catarina Sofia Mateus Reis-Silva | João Agostinho Machado‐Neto | Letícia V. Costa‐Lotufo | Fernando Coelho
Source:  (preprint, 2024-01-03)
Field: Chemistry — Organic Chemistry

Bismuth(III) Triflate: An Economical and Environmentally Friendly Catalyst for the Nazarov Reaction We describe the use of bismuth (III) triflate as an efficient and environmentally friendly catalyst for the Nazarov reaction of aryl vinyl ketones, leading to the synthesis of 3-aryl-2-carboethoxy-1-indanones and 3-aryl-1-indanones. By changing the temperature and reaction time, it was possible to modulate the reactivity, allowing the synthesis of two different products in good to excellent yields (3-aryl-2-carboethoxy-1-indanones and 3-aryl-2-carbethoxy-1-indanones). The reaction does not need additives and is insensitive to both air and moisture. The preliminary biological evaluation of some indanones show a promissory profile against some human cancer line cells. Aryl ; Trifluoromethanesulfonate ; Bismuth ; Catalysis ; Environmentally friendly ; Chemistry ; Organic chemistry ; Halide ; Combinatorial chemistry ; Reaction conditions Quinazolinone synthesis and applications ; Synthesis and Reactions of Organic Compounds ; Microwave-Assisted Synthesis and Applications
Authors: Stoyan P. Gramatikov | Petko St. Petkov | Zhendong Wang | Weimin Yang | Georgi N. Vayssilov
Source: Nanomaterials (article, 2024-01-11)
Field: Chemistry — Inorganic Chemistry

Variation of the Orientations of Organic Structure-Directing Agents inside the Channels of SCM-14 and SCM-15 Germanosilicates Obtained by Ab Initio Molecular Dynamic Simulations We report ab initio molecular dynamic simulations of the organic structure-directing agent (OSDA) in the channels of SCM-14 and SCM-15 germanosilicates for models with different germanium distribution. Since OSDA was free to move inside the channels, independent of its initial orientation after the simulations in all structures the OSDA, protonated 4-pyrrolidinopyridine, is positioned almost perpendicular to the large channels of SCM-14. The structures obtained from the dynamic simulation are more stable by 157 to 331 kJ/mol than the structures obtained by initial geometry optimization. After simulations, the average distance between the N atom of the pyridine moiety of the OSDA and O from Ge-O-Ge is shorter by 0.2 Å than the same distance obtained from initial optimization. The stretching N-H frequencies in the IR spectra of the OSDA and other calculated vibrational frequencies are not characteristic of the orientation of the molecule and cannot be used to detect it. Materials science ; Molecular dynamics ; Ab initio ; Perpendicular ; Atom (system on chip) ; Crystallography ; Molecule ; Orientation (vector space) ; Molecular physics ; Computational chemistry ; Geometry ; Chemistry Zeolite Catalysis and Synthesis ; Mesoporous Materials and Catalysis ; Glass properties and applications
Authors: Nishita Nagpure | Harshal Raut | Deepak Askar | Neha Narange | Shrutika Bhurse | Rahul Kasliwal
Source:  (article, 2024-01-01)
Field: Chemistry — Analytical Chemistry

Navigating The N-Nitrosamine Impurities Challenge: Comprehensive Strategies For Ensuring Paracetamol Purity Through Analytical Advances, Control Measures, And Emerging Mitigation Trends The presence of N-nitrosamine impurities in paracetamol, a widely utilized analgesic and antipyretic, has raised significant safety concerns over their potential carcinogenicity. This abstract explores the regulatory landscape surrounding these impurities, focusing on international collaboration among health authorities to establish comprehensive guidelines. N-nitrosamines can form during the manufacturing process when nitrous acid interacts with secondary amines, influenced by factors such as pH and temperature. Regulatory bodies, including the European Medicines Agency (EMA) and the U.S. Food and Drug Administration (FDA), have implemented stringent testing requirements to mitigate risks associated with these impurities. Key initiatives include revising pharmacopoeial standards and enhancing analytical methodologies, such as liquid chromatography-tandem mass spectrometry (LC-MS/MS) and gas chromatography-mass spectrometry (GC-MS), for effective detection of nitrosamines in pharmaceutical products. The paper highlights the challenges faced by manufacturers in adhering to these guidelines, including communication gaps with regulatory authorities and the complexity of testing protocols. Furthermore, the impact of N-nitrosamine contamination extends beyond regulatory compliance, affecting public health through drug recalls and potential loss of patient trust in medications. Continuous monitoring and proactive risk management strategies are essential to ensure the safety of paracetamol and similar pharmaceuticals. In conclusion, addressing N-nitrosamine impurities requires a coordinated international effort to enhance safety measures, improve manufacturing practices, and maintain public confidence in pharmaceutical products. This collaboration is vital for safeguarding public health while ensuring the efficacy of essential medications like paracetamol. Safeguarding ; Agency (philosophy) ; Pharmaceutical manufacturing ; Public health ; Process (computing) ; SAFER ; Control (management) ; Risk management ; Food safety ; Pharmaceutical industry Analytical Methods in Pharmaceuticals ; Sulfur Compounds in Biology
Authors: Lei Chen | Xinyi Zhang | Wei Zhang | Yuwei Liu
Source: Journal of Experimental and Clinical Application of Chinese Medicine (article, 2024-04-23)
Field: Chemistry — Analytical Chemistry

Exploring the Potential of Lotus Leaf and Its Bioactive Compounds for Anti-obesity Interventions The complex syndrome of obesity is a complex syndrome associated with various metabolic disorders, poses significant threats to human health. Many weight loss medications have the potential to rapidly treat obesity, however their toxicity and adverse effects may compromise patients' physiological and psychological well-being. In China, the concept of drug and food homology has been utilized for thousands of years, with lotus leaves serving as a representative example. The lotus leaves have been traditionally used for heat-clearing and lipid-lowering purposes, as well as for cooling the blood and promoting hemostasis, since ancient times. This review represents the first attempt to qualitatively investigate the anti-obesity properties of lotus leaves by integrating gene-disease association databases and drug-target databases for analysis. Additionally, it summarizes the identified monomers in lotus leaves that have been reported to possess functions associated with anti-obesity. The aim of this study is to provide a comprehensive review of the research progress on anti-obesity drugs derived from lotus leaves, and to facilitate further research and development in the field of anti-obesity medication targeting adiposity. Lotus ; Obesity ; Medicine ; Metabolic syndrome ; Lotus effect ; Psychological intervention ; Biology ; Internal medicine ; Psychiatry Chromatography in Natural Products ; Ginseng Biological Effects and Applications ; Phytochemistry and biological activity of medicinal plants
Authors: Sahil | Sunil Kumar | Snehlata Yadav | Nirmala Kumari Yadav
Source: African Journal of Biomedical Research (article, 2024-12-27)
Field: Chemistry — Analytical Chemistry

Antibacterial Activity &amp;Phytochemical Screening of Chenopodium Album Leaves Against Listeria Monocytogene and Yersinia Enterocolitica The increasing incident of multidrug-resistant bacterial strains has promote a search of natural alternatives with excellent antibacterial activities. Chenopodium album, commonly known as lamb’s quarters is a medicinal plant with traditional uses in many disease. This review examine the antibacterial activity and phytochemical composition of Chenopodium album leaves and its effect on Listeria monocytogenes and Yersinia enterocolitica, two important foodborne pathogens connect with severe infection. Phytochemical analysis of Chenopodium album has identified the presence of bioactive compounds such as flavonoids, alkaloids, saponins, tannins and phenolic acids which all have antimicrobial activity. These compound are responsible for their antibacterial activity and also able to damage bacterial membranes, disrupt metabolism and inhibit enzyme activity. Verification from studies using agar diffusion, minimum inhibitory concentration (MIC) tests and bioassay-guided fractionation indicate that Chenopodium album is effective against these pathogens. This review has also presented the proposed mechanisms by which Chenopodium album have antibacterial activity including disruption of bacterial cell walls and inhibition of quorum sensing. To summarize, Chenopodium album is a natural antibacterial candidate which target the Listeria monocytogenes and Yersinia enterocolitica. Future investigation can include clinical trials for CNB formulation to potentially fight against multidrug-resistant bacterial infections. Phytochemical ; Yersinia enterocolitica ; Chenopodium ; Traditional medicine ; Biology ; Listeria ; Listeria monocytogenes ; Antibacterial activity ; Microbiology ; Botany ; Medicine ; Bacteria ; Weed Heavy Metals in Plants ; Seed and Plant Biochemistry
Authors: Rui Pan | Shengya He | Sili Qiu
Source: Research Square (preprint, 2024-02-13)
Field: Chemistry — Spectroscopy

Dependence of micro-structure regularity on the degree of molecular asymmetry in polynorbornene derivatives Abstract Although the correlation between the regularity of micro-structures and the length of side chains has been widely reported, experiments still require precursors of polynorbornene derivatives due to the complex inter-and intra-chain interplay. This research utilizes hydrogen bonding between amide groups to design molecular models of polynorbornene derivatives (PNbs). The PNbs are abbreviated as Pm-8, where “m” indicates the amount of methylene groups as spacers in the side chain, and “8” refers to the oxyoctyl tail. The aim is to obtain a gradual variation of inter-and intra-chain interplay for further elucidation. Based on an analysis of spatial descriptors, mean square displacement (MSD), and radial distribution function (RDF) by using molecular mechanics (MM) and molecular dynamics (MD) methods, it is found that the asymmetry of side chains plays a more significant role in determining micro-structural regularity than the length. Highly asymmetric side chains are favorable for forming inter-chain hydrogen bonding, promoting interdigitation, and creating a larger scale of regularity in P8-8 and P10-8 molecules. In contrast, the relatively symmetric side chains tend to form intra-chain bonding, resulting in limited regularity within P2-8 and P4-8 molecules. Therefore, unlike regular structures that usually require symmetrical molecules, polynorbornene derivatives with asymmetric side chains have achieved highly ordered orthorhombic lattices in experiments. This study aims to offer an alternative approach to screening effective precursors of long-side chain polymers by means of semi-quantitative geometric parameters, providing a fresh perspective on the subject. Asymmetry ; Degree (music) ; Mathematics ; Materials science ; Statistical physics ; Physics ; Particle physics Analytical Chemistry and Chromatography ; Synthesis and properties of polymers ; Synthesis and Properties of Aromatic Compounds
Authors: Fernando Baquero | Rafael Cantón | Ana Elena Pérez‐Cobas | Teresa M. Coque | Bruce R. Levin | Jeronimo Rodríguez-Beltrán
Source:  (preprint, 2024-12-16)
Field: Chemistry — Physical and Theoretical Chemistry

Antechodynamics and Antechokinetics: Dynamics and Kinetics of Antibiotic Resistance Molecules Pharmacology of antimicrobial drugs comprises pharmacodynamics (PD) and pharmacokinetics (PK). PD refers to studying drugs' mode of action at different concentrations on their molecular targets and the resulting effect(s). PK refers to studying the way(s) by which drugs enter and are distributed to reach their targets in different compartments (such as tissues in the body) and how the local drug concentrations are modified in time, as by metabolism or excretion. PD and PK constitute pivotal knowledge to establish breakpoints used to identify the appropriate antimicrobial agents in therapy of infections. Antibiotic resistance is the biological force opposing antimicrobial pharmacological effects. However, we do not have a term similar to pharmacology for microbial resistance reactions. Here, we propose the new scientific field of Antechology (from classic Greek antechó, resistance) studying the dynamics and kinetics of antibiotic resistance molecules, opposing the effect of antimicrobial drugs. Antechodynamics (AD) refers to the study of the molecular mechanisms by which antibiotic molecules are chemically modified or degraded by particular bacterial resistance enzymes (primary effectors), or drive the modification of the antibiotic target inhibition sites by molecules released by the antibiotic action on the microorganism (secondary effectors). Antechokinetics (AK) refers to the study of the processes leading to bacterial spatial cellular (subcellular, pericellular, extracellular) localizations of the molecules involved in antibiotic detoxifying mechanisms. Molecules' local concentrations change over time due to their production, degradation, and, eventually, excretion rates. The AD and AK for the different antimicrobial families, and the relation PD/PK and AD/AK is examined here Antimicrobial ; Antibiotic resistance ; Antibiotics ; Effector ; Pharmacokinetics ; Chemistry ; Pharmacology ; Pharmacodynamics ; Drug resistance ; Biology ; Biochemistry ; Microbiology thermodynamics and calorimetric analyses ; Antibiotics Pharmacokinetics and Efficacy ; Antibiotic Resistance in Bacteria
Authors: H.A. Arwa | S.J. Alyaa | Bashir Ali | H. Al-jubori Muna | Anjali Basil
Source: Лабораторная диагностика Восточная Европа (article, 2024-05-31)
Field: Materials Science — Materials Chemistry

Assessment of Antioxidant, Anticancer and Antimicrobial Activities of Silver Nanoparticles N-Acetylcysteine in Sarcoma Male Rat Induction by 7,12 Dimethylbenz[a] Anthracene Introduction.Multiple sclerosis (MS) is one of chronic autoimmune and neurological illness of the central nervous system (CNS).Young age peoples are the most common age grope of the onset of MS.Purpose.To estimate the immunity and pathogenesis of MS relationship with chemokines (CCL2, CCL5, and CXCL10) in sera of patients with MS. Materials and methods.This is case-control study, was conducted in Multiple Sclerosis Center in Basrah city at period from November 2021 to May 2022.All investigations of the measurement of CCL2, CCL5 and CXCL10 levels were done by using ELISA.Results.The age of subjects ranged between 15-55 years.There was a predominant female gender (72.10%).The concentration of CCL2, CCL5 and CXCL10 chemokines showed greater levels among MS patients when compared with control group (P<0.0001). Conclusion.Young age groups and female gender are prevalent in MS.The concentration of chemokines (CCL2, CCL5 and CXCL10) are at higher levels in multiple sclerosis.There is a positive association between CCL5 chemokine and age groups of normal persons. Antimicrobial ; Antioxidant ; Acetylcysteine ; Chemistry ; 7,12-Dimethylbenz[a]anthracene ; Sarcoma ; Pharmacology ; Traditional medicine ; Medicine ; Biochemistry ; DMBA ; Organic chemistry ; Pathology ; Gene Nanoparticles: synthesis and applications ; Graphene and Nanomaterials Applications ; Nanoparticle-Based Drug Delivery
Authors: Praveen Kumar Bandaru | Satya Kameswara Rao Nidasanametla | P. Shyamala
Source: Asian Journal of Chemistry (article, 2024-11-30)
Field: Chemistry — Organic Chemistry

Novel Pyrrolo-Pyrimidine Derivatives Bearing Amide Functionality as Potential Anticancer Agents: Synthesis and Molecular Docking Studies Current investigation presents the synthesis, molecular docking and anticancer evaluation of novel pyrrolo-pyrimidine derivatives designed to target Janus kinase 1 (JAK1), Janus kinase 2 (JAK2) and cyclin-dependent kinase 4 (CDK4). The synthesis route commenced with 2-amino-4,6-dichloropyrimidine-5-carbaldehyde, proceeding through sequential steps involving intermediate formations and coupling reactions to yield a diverse array of pyrrolo-pyrimidine derivatives. Characterization using spectroscopic techniques (1H NMR, 13C NMR and HRMS) confirmed the chemical structures of the synthesized compounds. Molecular docking studies against JAK1, JAK2 and CDK4 demonstrated substantial binding affinities, remarkably compounds 7k, 7l and 7d, which displayed promising interactions within the active sites of the proteins. Anticancer evaluation against breast cancer (MCF-7), chronic myeloid leukemia (SET-2), colorectal carcinoma (HCT-116) and HEK-293 cell lines revealed diverse cytotoxic profiles. Specifically, compounds 7k and 7f exhibited potent activity against breast cancer (MCF-7), 7k and 7f showed efficacy against chronic myeloid leukemia (SET-2) and compounds 7k and 7l demonstrated effectiveness against colorectal carcinoma (HCT-116). These findings underscore the potential of these pyrrolo-pyrimidine derivatives as selective and effective anticancer agents, prompting further exploration for therapeutic development. Chemistry ; Pyrimidine ; Docking (animal) ; Amide ; Combinatorial chemistry ; Stereochemistry ; Biochemistry Multicomponent Synthesis of Heterocycles ; Synthesis and biological activity ; Synthesis and Biological Evaluation
Authors: Kalle Gehring | Véronique Sauvé | Eric Stefan | Nathalie Croteau | Thomas Goiran | Rayan Fakih | Nupur Bansal | Adelajda Hadzipasic | Jing Fang | Edward A. Fon | Warren D. Hirst | Laura Silvian | Jean‐François Trempe
Source: Research Square (preprint, 2024-03-19)
Field: Chemistry — Organic Chemistry

Mechanism of Ubiquitin Ligase Activation of Parkin by a Small Molecule Molecular Glue Parkin ; Ubiquitin ligase ; Mechanism (biology) ; DNA ligase ; Ubiquitin ; GLUE ; Chemistry ; Cell biology ; Biophysics ; Biology ; Biochemistry ; Materials science ; Medicine ; Physics ; DNA ; Gene Click Chemistry and Applications ; Histone Deacetylase Inhibitors Research
Authors: Kenji Takahashi | Tomoya Tanaka | Atsushi Ishihara | Toshio Ohta
Source: Discover Oncology (article, 2024-05-20)
Field: Chemistry — Organic Chemistry

Strobilurin X acts as an anticancer drug by inhibiting protein synthesis and suppressing mitochondrial respiratory chain activity Strobilurin X induced cytotoxicity by blocking the mitochondrial respiratory chain and suppressing protein synthesis. These findings may aid in the development of novel anticancer drugs using strobilurins. Mitochondrial respiratory chain ; Respiratory chain ; Drug ; Strobilurin ; Pharmacology ; Respiratory system ; Mitochondrion ; Chemistry ; Chain (unit) ; Coenzyme Q – cytochrome c reductase ; Biochemistry ; Medicine ; Biology ; Internal medicine ; Cytochrome c ; Physics ; Fungicide Synthesis and Biological Evaluation ; Cancer therapeutics and mechanisms ; Plant Disease Resistance and Genetics
Authors: An‐Xin Wu
Source: Research Square (preprint, 2024-07-09)
Field: Chemistry — Organic Chemistry

From an Azaarene to the Spine of Fused Bicyclics: Cycloaddition-Induced Scaffold Hopping of 5-Hydroxypyrazoles SPINE (molecular biology) ; Scaffold ; Cycloaddition ; Chemistry ; Materials science ; Business ; Computer science ; Biology ; Bioinformatics ; Organic chemistry ; Programming language Organic Chemistry Cycloaddition Reactions ; Cyclopropane Reaction Mechanisms ; Catalytic Alkyne Reactions