jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Xiuzheng Zhuang | Jianguo Liu | Shurong Zhong | Longlong Ma
Source: ChemRxiv (preprint, 2021-06-15)
Field: Chemistry — Organic Chemistry

Selective Catalysis for the Reductive Amination of Furfural Towards Furfurylamine by the Graphene-Co-Shelled Cobalt Nanoparticles &lt;p&gt;Amines with functional groups are widely used in the manufacture of pharmaceuticals, agricultural chemicals, polymers, and surfactants; so far, amines are mostly produced via petrochemical routes, which &lt;a&gt;&lt;/a&gt;&lt;a&gt;motivates the sustainable production of amines from renewable resources&lt;/a&gt;, such as biomass. Unfortunately, the reductive amination of biomass-derived platforms is now suffering from challenges, e.g. poor &lt;a&gt;&lt;/a&gt;&lt;a&gt;selectivity &lt;/a&gt;and carbon balances, because of the restriction of homogenous catalyst. For this reason, we developed an eco-friendly, simplified, and highly effective procedure for the preparation of non-toxic heterogeneous catalyst based on the earth-abundant metals (i.e., cobalt), whose catalytic activity on furfural or other biomass-derived platforms were proved to be broadly available. The corresponding conversion rate and few of side products were also determined so as to optimized the reaction conditions, suggesting that the prepared cobalt-supported catalyst enables easy substitution of –NH&lt;sub&gt;2 &lt;/sub&gt;moiety towards functionalized and structurally diverse molecules, even under very mild industrially viable and scalable conditions. More surprisingly, the cobalt-supported catalyst could also be expediently recycled by magnetic bar and still remained the excellent catalytic activity after reusing up to eight times; on another hands, the gram-scale reductive amination catalyzed by the same catalyst exhibited the similar yield of target products in comparison to its smaller scale, which was comparable to the reported heterogeneous noble-based catalysts. And also, results from a series of analytic technologies involving XRD, XPS, TEM/Mapping and &lt;i&gt;in-suit&lt;/i&gt; FTIR revealed that the structural features of catalyst are closely in relation to its catalytic mechanisms; in simple terms, &lt;a&gt;&lt;/a&gt;&lt;a&gt;the outer graphitic shell is activated by the electronic interaction between the inner &lt;/a&gt;&lt;a&gt;&lt;/a&gt;&lt;a&gt;metallic &lt;/a&gt;nanoparticles and the carbon layer as well as the induced charge redistribution. In conclusion, this newly developed catalysts enable the synthesis of amines from biomass-derived platforms with satisfied selectivity and carbon balance, providing a cost-effective and sustainable access to the widely application of reductive amination.&lt;/p&gt; Cobalt ; Furfural ; Catalysis ; Reductive amination ; Chemistry ; Amination ; Petrochemical ; Organic chemistry ; Combinatorial chemistry Nanomaterials for catalytic reactions ; Asymmetric Hydrogenation and Catalysis ; Catalysis for Biomass Conversion
Authors: Sailaja Rani Talupur | KP Satheesh | Kothapalli Bannoth Chandrasekhar
Source: International Journal of Applied Research (article, 2021-06-01)
Field: Chemistry — Organic Chemistry

Synthesis, characterization, antimicrobial evaluation and docking studies of 3-(5-(2-oxido)-(4-substituted phenoxy)-benzo[d]dioxaphosphole-tetrazol-thiophene-2-carboxamides 3-(5-(2-oxido)-(4-substitudedphenoxy)-benzo[d][1,3,2]dioxaphosphol-5-yl)-1H-tetrazol-1-yl)thiophene-2-carboxamides(9a-g) were synthesized by condensing 3-(5-(3,4-dihydroxyphenyl)-1H-tetrazol-1-yl)thiophene-2-carboxamide (7) with 4-substituted phenyl phosphoro dichloridates (8a-g). The synthon (7) was synthesized by hydrolysis of 3-(5-(3,4-dimethoxyphenyl)-1H-tetrazol-1-yl)thiophene-2-carboxamide (6). The intermediate (6) was synthesized by condensing 3-((3,4-dimethoxy benzylidine)amino)thiophene-2-carboxamide (5) with sodium azide in Tetrahydrofuron. The synthon (5) was synthesized by reaction between 3-aminothiophene-2-caroxamide (3) and 3,4-dimethoxybenzaldehyde (4). Starting intermediate (3) was synthesized by condensation reaction between 2-cyano acetamide (1) and 1,4-dithiane-2,5-diol (2). The reagents and conditions were shown in a, b, c, d and e. The synthetic route was shown in Scheme-I. The target molecules (9a-g) were characterized by IR, 1HNMR, 13C-NMR, Mass and elemental analysis. The target molecules were subjected to biological evaluation and molecular docking studies. The results observed in the present investigation were reported in this present research article. Synthon ; Thiophene ; Chemistry ; Carboxamide ; Sodium azide ; Molecule ; Acetamide ; Stereochemistry ; Reagent ; Docking (animal) ; Medicinal chemistry ; Combinatorial chemistry ; Organic chemistry Synthesis and Characterization of Heterocyclic Compounds ; Synthesis of Tetrazole Derivatives ; Synthesis and biological activity
Authors: Manish Chaudhary | Deepali Gupta | Saumik Chaudhury | Paranjeet Kaur
Source: Asian Pacific Journal of Health Sciences (article, 2021-12-31)
Field: Chemistry — Organic Chemistry

Emerging Heterocyclic Compounds for the Management of Prostate Cancer Background: This review is an overview of emerging heterocyclic compound classes that might give a safe and effective treatment for prostate cancer.Main body: Most heterocyclic compounds or heterocyclic fragments present in most of the anticancer pharmaceuticals presently in market and are versatile with unique physicochemical properties. Most of anticancer research is being capitalized on the intrinsic versatility and dynamic core of heterocyclic compounds. In this review we shall focus on moieties that are suitable for prostate cancer therapy along with addressing their biochemical modes of action, biological targets, structure-activity relationship and intrinsic drawbacks in the use of these compoundsConclusion: These classes and their derivatives discussed here might provide a novel drug therapy for cancer treatment. Prostate cancer ; Cancer ; Combinatorial chemistry ; Prostate ; Anticancer drug ; Chemistry ; Drug ; Cancer therapy ; Computational biology ; Pharmacology ; Medicine ; Nanotechnology ; Biology ; Materials science ; Internal medicine Synthesis and biological activity ; Computational Drug Discovery Methods ; Synthesis of β-Lactam Compounds
Authors: Naceur Hamdi | Hamida Jellali | Ibrahim S. Al Nasr | Walid Coco | Tariq A. Khan | Eric Deniou | Mathieu Sauthier
Source: Research Square (preprint, 2021-03-13)
Field: Chemistry — Organic Chemistry

In Vitro Bioactivities&amp;nbsp;of Isoindolin-1-3-Phosophonate Compounds In vitro ; Chemistry ; Pharmacology ; Computational biology ; Combinatorial chemistry ; Biochemistry ; Medicine ; Biology Synthesis and pharmacology of benzodiazepine derivatives ; Synthesis and Reactivity of Heterocycles ; Biochemical and Molecular Research
Authors: Aytekin Köse
Source: Iğdır Üniversitesi Fen Bilimleri Enstitüsü Dergisi (article, 2021-12-11)
Field: Chemistry — Organic Chemistry

4-((3-(Triflorometil)piridin-2-il)oksi)benzohidrazit Birimi İçeren Yeni Hidrazon Türevlerinin Sentezi Bu çalışmada, 4-((3-(triflorometil)piridin-2-il)oksi)benzohidrazit birimi bulunduran yedi yeni hidrazon türevlerinin sentezi gerçekleştirildi. Başlangıç bileşiği olarak kullanılan 4-hidroksibenzoik asit metanol içerisinde katalitik miktarda sülfürik asit ile metil esterine dönüştürüldü. Ester bileşiği, 2-bromo-3(triflorometil)piridin ile reaksiyona sokularak 4-((3-(triflorometil)piridin-2-il)oksi)benzoikasit metil esteri elde edildi. Daha sonra Ester bileşiği hidrazin hidrat ile hidrazitine dönüştürüldü. Hidrazit bileşiği seçilmiş sübstitüe aldehitler ile katılma-eliminasyon reaksiyonuna maruz bırakılarak hedef hidrazon türevleri sentezlendi. Sentezlenen bileşiklerin yapıları 1H, 13C NMR ve HRMS spektroskopileri ile aydınlatıldı. Toplamda dört kademe organik sentez, basit kimyasal modifikasyonlar, yüksek skalada sentezlenebilme, ucuz kimyasal reaktifler ve kısa sentez süreleri bu çalışmanın avantajları olarak belirlendi. Chemistry ; Hydrazone ; Stereochemistry ; Medicinal chemistry Synthesis and biological activity ; Synthesis and Biological Evaluation ; Multicomponent Synthesis of Heterocycles
Authors: Y. Aparna | N Subhashini | L. N. Sharada
Source: International Journal of Advanced Chemistry Research (article, 2021-01-01)
Field: Chemistry — Organic Chemistry

Cytotoxic activity, corrosion inhibition activity and molecular docking studies of Imidazolone scaffolds-A review Several imidazole-based clinical drugs play imperious site in handling numerous diseases. Novel imidazoles with therapeutic values are being belligerently subjugated worldwide. Imidazoles exist in tautomeric forms and bind with receptors through vanderwaals forces, hydrogen bonding, dipole-dipole and π bonding interactions thereby exhibiting broad bioactivities and therapeutic action. Molecular docking studies of these compounds unravel the mode of interaction with bacterial enzymes and antifungal action. This article aims to review the work reported on the cytotoxic activities and molecular docking studies of imidazole derivatives. Docking (animal) ; Imidazole ; Hydrogen bond ; Chemistry ; Combinatorial chemistry ; Stereochemistry ; Pharmacology ; Computational biology ; Biology ; Medicine ; Molecule ; Organic chemistry Synthesis and biological activity ; Synthesis and Characterization of Heterocyclic Compounds ; Synthesis of heterocyclic compounds
Authors: Donglei Yu | Xiong Yuan | Li Huang | Chin Ho Chen | K.H. Lee
Source: UNC Libraries (article, 2021-10-29)
Field: Chemistry — Organic Chemistry

Mechanism of action and resistant profile of anti-HIV-1 coumarin derivatives Dicamphanoyl khellactone (DCK) is a coumarin derivative that can potently inhibit HIV-1 replication. DCK does not inhibit RNA-dependent DNA synthesis. However, an HIV reverse transcriptase (RT) inhibitor-resistant strain, HIV-1/RTMDR1, is resistant to DCK. Thus, it is possible that HIV-1 RT is the target of DCK. To test this possibility, DCK-resistant viruses were selected in the presence of DCK. Our results indicate that a single amino acid mutation, E138K in HIV-1 RT, is sufficient to confer DCK resistance. Interestingly, a DCK derivative, 3'R,4'R-Di-O-(-)-camphanoyl-2-ethyl-2',2'-dimethyldihydropyrano[2,3-f]chromo ne (DCP8), is effective against HIV-1/RTMDR1. However, the DCK-escape virus carrying the E138K mutation remains resistant to DCP8. Since DCK did not inhibit the RNA-dependent DNA polymerase activity of HIV-1 RT when using poly-rA or poly-rC as template, we evaluated the effect of DCK on the DNA-dependent DNA polymerase activity of HIV-1 RT. Our results indicate that DCK can inhibit the DNA-dependent DNA polymerase activity of HIV-1 RT. In conclusion, DCK is a unique HIV-1 RT inhibitor that inhibits the DNA-dependent DNA polymerase activity. In contrast, DCK did not significantly affect the RNA-dependent DNA polymerase activity when poly-rA or poly-rC was used as templates. An E138K mutation in the non-nucleoside RT inhibitors (NNRTIs) binding pocket of HIV-1 RT confers resistance to DCK and its chromone derivative, DCP8. Coumarin ; Mechanism (biology) ; Mechanism of action ; Human immunodeficiency virus (HIV) ; Action (physics) ; Chemistry ; Medicine ; Virology ; Biochemistry ; Physics ; In vitro ; Organic chemistry ; Philosophy ; Epistemology Synthesis and biological activity ; Analytical Chemistry and Chromatography
Authors: Takeshi Terabayashi | Katsuhiro Hanada | Shigeru Matsuoka | Takako Sasaki | Akira Katoh | Takahiro Akamine | Toshimasa Ishizaki
Source: Research Square (preprint, 2021-03-15)
Field: Materials Science — Biomaterials

Timosaponin Aiii Disrupts Morphological Plasticity and Migration of Breast Adenocarcinoma Through Inhibition of Integrin Internalisation Integrin ; Cell biology ; Plasticity ; Cancer research ; Chemistry ; Biology ; Cell ; Biochemistry ; Materials science Phytochemistry and Bioactive Compounds ; Phytochemical Studies and Bioactivities ; Marine Sponges and Natural Products
Authors: Tankam Rajeswari | Panga Siva Sankar | Kayathi Narendra Babu | Adivireddy Padmaja | V. Padmavathi
Source: Research Square (preprint, 2021-09-28)
Field: Chemistry — Organic Chemistry

Synthesis of thiophenylazolyl pyrrolylsulfamoyl acetamides as potential antimicrobial agents Antimicrobial ; Microbiology ; Biology Synthesis and Characterization of Pyrroles ; Synthesis and Biological Evaluation ; Synthesis and Catalytic Reactions
Authors: Anastasia A. Fesenko | Anatoly D. Shutalev
Source:  (article, 2021-11-14)
Field: Chemistry — Organic Chemistry

Reaction of N-(tosylmethyl)ureas with NaCN: Synthetic and Mechanistic Aspects The reaction of NaCN with N-(tosylmethyl)ureas, prepared by condensation of urea with aldehydes and p-toluenesulfinic acid, was studied. Generally, this reaction afforded the corresponding -ureido nitriles. Some mechanistic aspects of cyanide-anion amidoalkylation with N-(tosylmethyl)ureas were discussed based on DFT calculations. Chemistry ; Cyanide ; Urea ; Condensation ; Medicinal chemistry ; Organic chemistry Chemical Reaction Mechanisms ; Asymmetric Synthesis and Catalysis ; Organic and Inorganic Chemical Reactions
Authors: Mónica Gutiérrez-Salazar | Eduardo Santamaría‐Aranda | Louise Schaar | Jesús Salgado | Diego Sampedro | V. Lorenz
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2021-03-10)
Field: Materials Science — Materials Chemistry

A photoswitchable helical peptide with light-controllable interface / transmembrane topology in lipidic membranes Abstract According to the three-step model, the spontaneous insertion and folding of helical transmembrane (TM) polypeptides into lipid bilayers is driven by three sequential equilibria: solution-to-membrane interface (MI) partition, unstructured-to-helical folding, and MI-to-TM helix insertion. However, understanding these three steps with molecular detail has been challenged by the lack of suitable experimental approaches to rapidly and reversibly perturb membrane-bound hydrophobic polypeptides out of equilibrium. Here, we report on a 24-residues-long hydrophobic α-helical polypeptide, covalently coupled to an azobenzene photoswitch (KCALP-azo), which displays a light-controllable TM/MI equilibrium in hydrated lipid bilayers. FTIR spectroscopy shows that dark-adapted KCALP-azo ( trans azobenzene) folds as a TM α-helix, with its central TM region displaying an average tilt of 36 ± 4° with the membrane normal (TM topology). After trans -to- cis photoisomerization of the azobenzene moiety with UV light (reversed with blue light), spectral changes by FTIR spectroscopy indicate that the helical structure of KCALP-azo is maintained but the peptide experiences a more polar environment. Interestingly, pH changes induced similar spectral alterations in the helical peptide LAH 4 , with a well-characterized pH-dependent TM/MI equilibrium. Polarized experiments confirmed that the membrane topology of KCALP-azo is altered by light, with its helix tilt changing reversibly from 32 ± 5° (TM topology, blue light) to 79 ± 8° (MI topology, UV light). Further analysis indicates that, while the trans isomer of KCALP-azo is ~100% TM, the cis isomer exists in a ~90% TM and ~10% MI mixture. Strategies to further increase the perturbation of the TM/MI equilibrium with the light are briefly discussed. Azobenzene ; Photoisomerization ; Chemistry ; Crystallography ; Membrane ; Helix (gastropod) ; Transmembrane protein ; Transmembrane domain ; Topology (electrical circuits) ; Folding (DSP implementation) ; Peptide ; Molecule ; Isomerization ; Organic chemistry Photochromic and Fluorescence Chemistry ; Photoreceptor and optogenetics research ; Supramolecular Self-Assembly in Materials
Authors: Orion Dollar | Nisarg Joshi | David A. C. Beck | Jim Pfaendtner
Source: ChemRxiv (preprint, 2021-02-08)
Field: Materials Science — Materials Chemistry

Giving Attention to Generative VAE Models for De Novo Molecular Design We explore the impact of adding attention to generative VAE models for molecular design. Four model types are compared: a simple recurrent VAE (RNN), a recurrent VAE with an added attention layer (RNNAttn), a transformer VAE (TransVAE) and the previous state-of-the-art (MosesVAE). The models are assessed based on their effect on the organization of the latent space (i.e. latent memory) and their ability to generate samples that are valid and novel. Additionally, the Shannon information entropy is used to measure the complexity of the latent memory in an information bottleneck theoretical framework and we define a novel metric to assess the extent to which models explore chemical phase space. All three models are trained on millions of molecules from either the ZINC or PubChem datasets. We find that both RNNAttn and TransVAE models perform substantially better when tasked with accurately reconstructing input SMILES strings than the MosesVAE or RNN models, particularly for larger molecules up to ~700 Da. The TransVAE learns a complex “molecular grammar” that includes detailed molecular substructures and high-level structural and atomic relationships. The RNNAttn models learn the most efficient compression of the input data while still maintaining good performance. The complexity of the compressed representation learned by each model type increases in the order of MosesVAE < RNNAttn < RNN < TransVAE. We find that there is an unavoidable tradeoff between model exploration and validity that is a function of the complexity of the latent memory. However, novel sampling schemes may be used that optimize this tradeoff and allow us to utilize the information-dense representations learned by the transformer in spite of their complexity. Computer science ; Information bottleneck method ; Generative model ; Artificial intelligence ; Generative grammar ; Machine learning ; Theoretical computer science ; Mutual information Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Protein Structure and Dynamics
Authors: David Winkler
Source: La Trobe University (article, 2021-01-01)
Field: Materials Science — Materials Chemistry

Use of artificial intelligence and machine learning for discovery of drugs for neglected tropical diseases Neglected tropical diseases continue to create high levels of morbidity and mortality in a sizeable fraction of the world’s population, despite ongoing research into new treatments. Some of the most important technological developments that have accelerated drug discovery for diseases of affluent countries have not flowed down to neglected tropical disease drug discovery. Pharmaceutical development business models, cost of developing new drug treatments and subsequent costs to patients, and accessibility of technologies to scientists in most of the affected countries are some of the reasons for this low uptake and slow development relative to that for common diseases in developed countries. Computational methods are starting to make significant inroads into discovery of drugs for neglected tropical diseases due to the increasing availability of large databases that can be used to train ML models, increasing accuracy of these methods, lower entry barrier for researchers, and widespread availability of public domain machine learning codes. Here, the application of artificial intelligence, largely the subset called machine learning, to modelling and prediction of biological activities and discovery of new drugs for neglected tropical diseases is summarized. The pathways for the development of machine learning methods in the short to medium term and the use of other artificial intelligence methods for drug discovery is discussed. The current roadblocks to, and likely impacts of, synergistic new technological developments on the use of ML methods for neglected tropical disease drug discovery in the future are also discussed. Drug discovery ; Neglected tropical diseases ; Tropical disease ; Domain (mathematical analysis) ; Disease ; Developing country ; Drug development Machine Learning in Materials Science ; vaccines and immunoinformatics approaches ; Genetics, Bioinformatics, and Biomedical Research
Authors: Md. Dipu Ahmed | Kazi M Maraz | Shahirin Shahida | Ruhania Tarannum | Ruhul A. Khan
Source: Zenodo (CERN European Organization for Nuclear Research) (review, 2021-08-30)
Field: Materials Science — Biomaterials

A review on the synthesis, surface modification and drug delivery of nanoparticles Over the past few years, the evolution of nanotechnology has extended into a wide range of applications. Nanotechnology has now become a multidisciplinary science that applies to electronics, materials science, biomedical engineering, microbiology, etc. Recently, nanotechnology is being used in biomedical and pharmaceutical science. Among them drug delivery is set to spread rapidly. Application of nanotechnology in health sector also created a potential impact such as in the fields of immunology, cardiology, endocrinology, ophthalmology, and oncology. Nanoparticles are unique because of their large surface area and it has the potential to change the properties of a bulk number of materials. The surface of nanoparticles can be modified with the help of various polymers, organic and inorganic substances according to the specific application and their use. Nanoparticles are also utilized as nano shells in drug delivery systems and cancer therapy. Nano shells can recognize the cancer cells when they are injected into the cancer area. The heat generated by the light absorbing nano shells due to the application of the near infrared light successfully kills tumour cells leaving the noncarcinogenic cells intact. In this review article, nanoparticles, the health implication of nanoparticles and their synthesis are discussed. Surface modification ; Drug delivery ; Nanoparticle ; Nanotechnology ; Drug ; Materials science ; Chemical engineering ; Medicine ; Pharmacology ; Engineering Nanoparticle-Based Drug Delivery
Source: Angewandte Chemie International Edition (article, 2021-09-20)
Field: Chemistry — Organic Chemistry

Graphical Abstract: Angew. Chem. Int. Ed. 40/2021 SARS-CoV-2In their Communication on page 21662, Xinjing Tang et al. report the efficient inhibition of SARS-CoV-2 using chimeric antisense oligonucleotides through RNase La ctivation. Citation ; INT ; Computer science ; Library science ; Information retrieval ; Programming language Click Chemistry and Applications ; Fluorine in Organic Chemistry ; Radical Photochemical Reactions