scholarly journals Primary Target Prediction of Bioactive Molecules from Chemical Structure

2018 ◽  
Author(s):  
Abed Forouzesh ◽  
Sadegh Samadi Foroushani ◽  
Fatemeh Forouzesh ◽  
Eskandar Zand
Keyword(s):  
Molecular Structure ◽  
Chemical Structure ◽  
Target Prediction ◽  
Bioactive Molecules ◽  
Unknown Primary ◽  
Complex Nature ◽  
Primary Target ◽  
Innovative Method ◽  
Digital Material ◽  
Machine Readable

AbstractThere are various tools for computational target prediction of bioactive molecules from a chemical structure in a machine-readable material but these tools can’t distinguish a primary target from other targets. Also, due to the complex nature of bioactive molecules, there has not been a method to predict a target and or a primary target from a chemical structure in a non-digital material (for example printed or hand-written documents) yet. In this study, an attempt to simplify primary target prediction from a chemical structure was resulted in developing an innovative method based on the minimum structure which can be used in both formats of non-digital and machine-readable materials. A minimum structure does not represent a real molecule or a real association of functional groups, but is a part of a molecular structure which is necessary to ensure the primary target prediction of bioactive molecules. Structurally related bioactive molecules with the minimum structure were considered as neighbor molecules of the query molecule. The known primary target of the neighbor molecule is used as a reference for predicting the primary target of the neighbor molecule with an unknown primary target. In results, we confirmed the usefulness of our proposed method for primary target prediction in 548 drugs and pesticides involved in four primary targets by eight minimum structures.

scholarly journals The Triple Jags of Dietary Fibers in Cereals: How Biotechnology Is Longing for High FiberGrains

2021 ◽  
Vol 12 ◽  
Author(s):  
Ermelinda Botticella ◽  
Daniel Valentin Savatin ◽  
Francesco Sestili
Keyword(s):  
Human Health ◽  
Cell Walls ◽  
Chemical Structure ◽  
Bioactive Molecules ◽  
Whole Grain ◽  
Grain Products ◽  
Macro And Micronutrients ◽  
Main Components ◽  
Grain Foods ◽  
Significant Health

Cereals represent an important source of beneficial compounds for human health, such as macro- and micronutrients, vitamins, and bioactive molecules. Generally, the consumption of whole-grain products is associated with significant health benefits, due to the elevated amount of dietary fiber (DF). However, the consumption of whole-grain foods is still modest compared to more refined products. In this sense, it is worth focusing on the increase of DF fractions inside the inner compartment of the seed, the endosperm, which represents the main part of the derived flour. The main components of the grain fiber are arabinoxylan (AX), β-glucan (βG), and resistant starch (RS). These three components are differently distributed in grains, however, all of them are represented in the endosperm. AX and βG, classified as non-starch polysaccharides (NSP), are in cell walls, whereas, RS is in the endosperm, being a starch fraction. As the chemical structure of DFs influences their digestibility, the identification of key actors involved in their metabolism can pave the way to improve their function in human health. Here, we reviewed the main achievements of plant biotechnologies in DFs manipulation in cereals, highlighting new genetic targets to be exploited, and main issues to face to increase the potential of cereals in fighting malnutrition.

scholarly journals Demystifying and Unravelling the Factual Molecular Structure of the Biopolymer Sporopollenin

2019 ◽  
Author(s):  
Abanoub Mikhael ◽  
Kristina Jurcic ◽  
Celine Schneider ◽  
David carr ◽  
Gregory L. Fisher ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Nuclear Magnetic Resonance ◽  
Chemical Structure ◽  
Pollen Grains ◽  
Outer Wall ◽  
Mass Spectrometric ◽  
Chemical Degradation ◽  
Ionization Mass ◽  
Soft Ionization ◽  
Biochemical Pathways

<p></p><p>Sporopollenin is a natural, highly cross-linked biopolymer composed of carbon, hydrogen, and oxygen, which forms the outer wall of pollen grains. Sporopollenin is resilient to chemical degradation.<sup> </sup>Because of this stability, its exact chemical structure and the biochemical pathways involved in its biosynthesis remains a mystery and unresolved.<sup> </sup></p> <p>We have identified and characterized the molecular structure of the clean, intact sporopollenin using soft ionization mass spectrometric and nuclear magnetic resonance techniques. These analyses showed that sporopollenin contained a poly(hydroxyacid) dendrimer-like network, which accounted for the sporopollenin empirical formula. In addition, the identified hydroxy acid monomers contained a beta diketone moiety, which most probably accounts for the known antioxidant activity of sporopollenin. Moreover, our elucidation studies allowed us to identify a unique circular polyhydroxylated tetraketide polymer. This polymer acted as the rigid backbone on which the poly(hydroxyacid) network can be built, forming the scaffold of the spherical sporopollenin exine.</p><br><p></p>

scholarly journals TOXICOLOGICAL AND HYGIENIC CHARACTERISTICS OF MYCOTOXIN STERIGMATOCYSTIN AND METHODS FOR ITS DETERMINATION IN FOOD PRODUCTS

2019 ◽  
Vol 98 (1) ◽  
pp. 105-117 ◽  
Author(s):  
Irina B. Sedova ◽  
M. G. Kiseleva ◽  
L. P. Zakharova ◽  
V. A. Tutelyan
Keyword(s):  
Chemical Structure ◽  
Web Of Science ◽  
Food Products ◽  
International Agency ◽  
Primary Target ◽  
Teratogenic Effects ◽  
Similar Chemical ◽  
Food And Feed ◽  
International Data ◽  
Almost All

The present issue reviews literature and own research data and gives toxicological and hygienic characteristic of sterigmatocystin. This mycotoxin is produced by fungi of Aspergillus, Bipolaris, Chaetomium, Emiricella species, and is found in cereals, food products (bread, cheese, spices, coffee, dietary supplements) and feed. Sterigmatocystin being a biogenic precursor of aflatoxin B1, has similar chemical structure and exhibits the same toxicological properties, but its toxicity is ten times lower. However, these toxins are rarely detected together. A. versicolor and A. nidulans do not have enzymes necessary for the conversion of sterigmatocystin into aflatoxins, on the contrary, A. flavus and А. parasiticus transform almost all STC into aflatoxins. Sterigmatocystin has been recognized by International Agency for Research on Cancer (IARC) as a 2B carcinogen (possibly carcinogenic to humans). The primary target organ for both mycotoxins is liver. Sterigmatocystin shows mutagenic, toxic and teratogenic effects in animals. Up to date national and international data on sterigmatocystin occurrence in different products is summarized, analytical methods of the determination are reviewed, hygienic assessment of the STC as a priority pollutant is given in the present paper. Also information on STC exposure assessment with regard to different kinds of foodstuff in different countries is being reported, available data on maximum levels of STC in food and feed is discussed. However, data on toxin’s occurrence in food is insufficient for elaboration of hygienic regulations on allowable mycotoxin’s concentration in priority products. Databases Web of Science, PubMed, E-library, CyberLeninka were used when searching the literature.

scholarly journals Ubiquitin-Proteasome Modulating Dolabellanes and Secosteroids from Soft Coral Clavularia flava

Marine Drugs ◽  
2020 ◽  
Vol 18 (1) ◽  
pp. 39
Author(s):  
Che-Yen Chiu ◽  
Xue-Hua Ling ◽  
Shang-Kwei Wang ◽  
Chang-Yih Duh
Keyword(s):  
Inhibitory Activity ◽  
Structure Elucidation ◽  
Chemical Structure ◽  
Soft Coral ◽  
Proteasome Inhibitors ◽  
Proteasome Inhibition ◽  
Structural Elucidation ◽  
Bioactive Molecules ◽  
High Content Screening ◽  
Ubiquitin Proteasome

We performed a high-content screening (HCS) assay aiming to discover bioactive molecules with proteasome inhibitory activity. By structural elucidation, we identified six compounds purified from soft coral Clavularia flava, which potentiates proteasome inhibition. Chemical structure elucidation revealed they are dolabellane- and secosteroid-based compounds including a new dolabellane, clavinflol C (1), three known dolabellanes, stolonidiol (2), stolonidiol-17-acetate (3), and clavinflol B (4) as well as two new secosteroids, 3β,11-dihydroxy-24-methyl-9,11-secocholest-5-en-9,23-dione (5) and 3β,11-dihydroxy-24-methylene-9,11-secocholest-5-en-9,23-dione (6). All six compounds show less cytotoxicity than those of known proteasome inhibitors, bortezomib and MG132. In summary, the high-content measurements of control inhibitors, bortezomib and MG132, manifest the highest ratio >2 in high-content measurement. Of the isolated compounds, 2 and 5 showed higher activity, followed by 3 and 6, and then 1 and 4 exhibited moderate inhibition.

PharmKG: a dedicated knowledge graph benchmark for bomedical data mining

2020 ◽  
Author(s):  
Shuangjia Zheng ◽  
Jiahua Rao ◽  
Ying Song ◽  
Jixian Zhang ◽  
Xianglu Xiao ◽  
...  
Keyword(s):  
Chemical Structure ◽  
State Of The Art ◽  
Critical Role ◽  
Global Network ◽  
Evaluation Metrics ◽  
Complex Nature ◽  
Specific Information ◽  
Biomedical Knowledge ◽  
Domain Specific ◽  
Modeling Methods

Abstract Biomedical knowledge graphs (KGs), which can help with the understanding of complex biological systems and pathologies, have begun to play a critical role in medical practice and research. However, challenges remain in their embedding and use due to their complex nature and the specific demands of their construction. Existing studies often suffer from problems such as sparse and noisy datasets, insufficient modeling methods and non-uniform evaluation metrics. In this work, we established a comprehensive KG system for the biomedical field in an attempt to bridge the gap. Here, we introduced PharmKG, a multi-relational, attributed biomedical KG, composed of more than 500 000 individual interconnections between genes, drugs and diseases, with 29 relation types over a vocabulary of ~8000 disambiguated entities. Each entity in PharmKG is attached with heterogeneous, domain-specific information obtained from multi-omics data, i.e. gene expression, chemical structure and disease word embedding, while preserving the semantic and biomedical features. For baselines, we offered nine state-of-the-art KG embedding (KGE) approaches and a new biological, intuitive, graph neural network-based KGE method that uses a combination of both global network structure and heterogeneous domain features. Based on the proposed benchmark, we conducted extensive experiments to assess these KGE models using multiple evaluation metrics. Finally, we discussed our observations across various downstream biological tasks and provide insights and guidelines for how to use a KG in biomedicine. We hope that the unprecedented quality and diversity of PharmKG will lead to advances in biomedical KG construction, embedding and application.

The effect of molecular structure on the anticancer drug release rate from prodrug nanoparticles

2015 ◽  
Vol 51 (64) ◽  
pp. 12835-12838 ◽  
Author(s):  
Yoshikazu Ikuta ◽  
Yoshitaka Koseki ◽  
Tsunenobu Onodera ◽  
Hidetoshi Oikawa ◽  
Hitoshi Kasai
Keyword(s):  
Molecular Structure ◽  
Controlled Release ◽  
Drug Release ◽  
Anticancer Drug ◽  
Release Rate ◽  
Chemical Structure ◽  
Anticancer Agent ◽  
Drug Release Rate ◽  
Drug Nanoparticles

The controlled release of an anticancer agent from drug nanoparticles could be successfully achieved by optimizing the chemical structure of dimeric compounds as prodrug.

scholarly journals Molecular Descriptors of Nanotube, Oxide, Silicate, and Triangulene Networks

2017 ◽  
Vol 2017 ◽  
pp. 1-10 ◽  
Author(s):  
Wei Gao ◽  
Muhammad Kamran Siddiqui
Keyword(s):  
Molecular Structure ◽  
Carbon Nanotube ◽  
Interconnection Networks ◽  
Chemical Structure ◽  
Chemical Reactivity ◽  
Hexagonal Lattice ◽  
Zagreb Index ◽  
Chemical Graph Theory ◽  
Vertex Degrees ◽  
Carbon Nanotube Networks

A topological index is a real number associated with chemical constitution purporting for correlation of chemical structure with various physical properties, chemical reactivity, or biological activity. The concept of hyper Zagreb index, first multiple Zagreb index, second multiple Zagreb index, and Zagreb polynomials was established in chemical graph theory based on vertex degrees. It is reported that these indices are useful in the study of anti-inflammatory activities of certain chemical networks. In this paper, we study carbon nanotube networks which are motivated by molecular structure of regular hexagonal lattice and also studied interconnection networks which are motivated by molecular structure of a chemical compound SiO4. We determine hyper Zagreb index, first multiple Zagreb index, second multiple Zagreb index, and Zagreb polynomials for some important class of carbon nanotube networks, dominating oxide network, dominating silicate network, and regular triangulene oxide network.

scholarly journals Composition and Structure of Coal Organic Mass. Analytical Review

2009 ◽  
Vol 3 (4) ◽  
pp. 315-319
Author(s):  
Vadim Barsky ◽  
◽  
Vitaly Gulyaev ◽  
Andriy Rudnitsky ◽  
◽  
...  
Keyword(s):  
Molecular Structure ◽  
Chemical Structure ◽  
Chemical Potential ◽  
Solid Fuels ◽  
Organic Mass ◽  
Coal Structure ◽  
Critical Comparison ◽  
Composition And Structure ◽  
Analytical Review

The research works dedicated to the formation regularities of solid fuels chemical structure were analyzed. Modern conceptions of coals chemical structure, which are becoming deeper owing to tooling growth and facts accumulation, were examined by means of critical comparison of different hypothetical models of solid fuels “molecular” structure. The most general points of the respective theories were formulated, according to which “soft” influence on coal structure primary elements bonds system allows bringing its chemical potential to the maximum.

scholarly journals Bioactive Synthetic Peptides for Oral Tissues Regeneration

2021 ◽  
Vol 8 ◽  
Author(s):  
Mercedes Bermúdez ◽  
Lía Hoz ◽  
Gonzalo Montoya ◽  
Mikado Nidome ◽  
Adriana Pérez-Soria ◽  
...  
Keyword(s):  
Tissue Regeneration ◽  
Synthetic Peptides ◽  
Alveolar Bone ◽  
Biological Effects ◽  
The Body ◽  
Bioactive Molecules ◽  
Tissue Loss ◽  
Complex Nature ◽  
Major Health Problem

Regenerative therapy in oral tissues has gained relevance since tissue loss due to congenital or acquired diseases as well as trauma is a major health problem worldwide. Regeneration depends on the natural capacity of the body and the use of biomaterials and bioactive molecules that can module the processes to replace lost or damaged tissues and restore function. The combined use of scaffolds, cells, and bioactive molecules such as peptides is considered the best approach to achieve tissue regeneration. These peptides can induce diverse cellular processes as they can influence cell behavior and also can modify scaffold properties, giving as a result the enhancement of cell adhesion, proliferation, migration, differentiation, and biomineralization that are required given the complex nature of oral tissues. Specifically, synthetic peptides (SP) have a positive influence on scaffold biocompatibility since in many cases they can mimic the function of a natural peptide or a full-length protein. Besides, they are bioactive molecules easy to produce, process, and modify, and they can be prepared under well-defined and controlled conditions. This review aims to compile the most relevant information regarding advances in SP for dental and periodontal tissue regeneration, their biological effects, and their clinical implications. Even though most of the SP are still under investigation, some of them have been studied in vitro and in vivo with promising results that may lead to preclinical studies. Besides there are SP that have shown their efficacy in clinical trials such as P11-4 for enamel regeneration or caries prevention and ABM/P-15 for cementum, periodontal ligament (PDL), and alveolar bone on a previously calculus- and biofilm-contaminated zone. Also, some SP are commercially available such as PTH1-34 and PepGen P-15 which are used for bone defects treatment.

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