scholarly journals Predicting biological pathways of chemical compounds with a profile-inspired aproach

2021 ◽  
Author(s):  
Javier Lopez-Ibañez ◽  
Florencio Pazos ◽  
Monica Chagoyen
Keyword(s):  
Protein Sequence ◽  
Chemical Compounds ◽  
Biological Pathways ◽  
Biological Pathway ◽  
Molecular Fragments ◽  
New Members ◽  
Chemical Structures ◽  
Functional Features ◽  
Sequence Profiles ◽  
The Relationship

AbstractAssignment of chemical compounds to biological pathways is a crucial step to understand the relationship between the chemical repertory of an organism and its biology. Protein sequence profiles are very successful in capturing the main structural and functional features of a protein family, and can be used to assign new members to it based on matching of their sequences against these profiles. In this work, we extend this idea to chemical compounds, constructing a profile-inspired model for a set of related metabolites (those in the same biological pathway), based on a fragment-based vectorial representation of their chemical structures. We use this representation to predict the biological pathway of a chemical compound with good overall accuracy (AUC 0.74-0.90 depending on the database tested), and analyzed some factors that affect performance. The approach, which is compared with equivalent methods, can in addition detect those molecular fragments characteristic of a pathway. The method is available as a graphical interactive web server http://csbg.cnb.csic.es/iFragMent

scholarly journals Predicting biological pathways of chemical compounds with a profile-inspired approach

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Javier Lopez-Ibañez ◽  
Florencio Pazos ◽  
Monica Chagoyen
Keyword(s):  
Protein Sequence ◽  
Chemical Compounds ◽  
Biological Pathways ◽  
Biological Pathway ◽  
Molecular Fragments ◽  
New Members ◽  
Chemical Structures ◽  
Functional Features ◽  
Sequence Profiles ◽  
The Relationship

Abstract Background Assignment of chemical compounds to biological pathways is a crucial step to understand the relationship between the chemical repertory of an organism and its biology. Protein sequence profiles are very successful in capturing the main structural and functional features of a protein family, and can be used to assign new members to it based on matching of their sequences against these profiles. In this work, we extend this idea to chemical compounds, constructing a profile-inspired model for a set of related metabolites (those in the same biological pathway), based on a fragment-based vectorial representation of their chemical structures. Results We use this representation to predict the biological pathway of a chemical compound with good overall accuracy (AUC 0.74–0.90 depending on the database tested), and analyzed some factors that affect performance. The approach, which is compared with equivalent methods, can in addition detect those molecular fragments characteristic of a pathway. Conclusions The method is available as a graphical interactive web server http://csbg.cnb.csic.es/iFragMent.

scholarly journals Maximum Common Property: A New Approach for Molecular Similarity

2020 ◽  
Author(s):  
Gonzalo Cerruela-García ◽  
Aurelio Antelo Collado ◽  
Ramón Carrasco-Velar ◽  
Nicolás García-Pedrajas
Keyword(s):  
Common Property ◽  
Antimalarial Activity ◽  
Biological Response ◽  
Chemical Compounds ◽  
Molecular Fragments ◽  
Property A ◽  
New Approach ◽  
Chemical Structures ◽  
Common Substructure ◽  
State Index

Abstract The maximum common property similarity (MCPhd) method is presented using descriptors as a new approach to determine the similarity between two chemical compounds or molecular graphs. This method uses the concept of maximum common property arising from the concept of maximum common substructure and is based on the electrotopographic state index for atoms. A new algorithm to quantify the similarity values of chemical structures based on the presented maximum common property concept is also developed in this paper. To verify the validity of this approach, the similarity of a sample of compounds with antimalarial activity is calculated and compared with the results obtained by the small molecule subgraph detector (SMSD) method. The results obtained by the MCPhd method differ significantly from those obtained by the SMSD method, improving the quantification of the similarity. A major advantage of the proposed method is that it helps to understand the analogy or proximity between physicochemical properties of the molecular fragments or subgraphs compared with the biological response or biological activity. In this new approach, more than one property can be potentially used. The method can be considered a hybrid procedure because it combines descriptor and the fragment approaches.

Therapeutic Properties of Several Chemical Compounds from Salvia officinalis L. in Alzheimer’s Disease

2020 ◽  
Vol 21 ◽  
Author(s):  
Georgiana Uță ◽  
Denisa Ștefania Manolescu ◽  
Speranța Avram
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Side Effects ◽  
Chemical Compounds ◽  
Natural Compounds ◽  
Salvia Officinalis ◽  
Chemical Structures ◽  
In Silico Studies ◽  
Wide Range ◽  
Salvia Officinalis L

Background.: Currently, the pharmacological management in Alzheimer's disease is based on several chemical structures, represented by acetylcholinesterase and N-methyl-D-aspartate (NMDA) receptor ligands, with still unclear molecular mechanisms, but severe side effects. For this reason, a challenge for Alzheimer's disease treatment remains to identify new drugs with reduced side effects. Recently, the natural compounds, in particular certain chemical compounds identified in the essential oil of peppermint, sage, grapes, sea buckthorn, have increased interest as possible therapeutics. Objectives.: In this paper, we have summarized data from the recent literature, on several chemical compounds extracted from Salvia officinalis L., with therapeutic potential in Alzheimer's disease. Methods.: In addition to the wide range of experimental methods performed in vivo and in vitro, also we presented some in silico studies of medicinal compounds. Results. Through this mini-review, we present the latest information regarding the therapeutic characteristics of natural compounds isolated from Salvia officinalis L. in Alzheimer's disease. Conclusion.: Thus, based on the information presented, we can say that phytotherapy is a reliable therapeutic method in a neurodegenerative disease.

Structure-properties relationship for energy storage redox polymers: a review

2020 ◽  
Vol 40 (5) ◽  
pp. 373-393 ◽  
Author(s):  
Narendra Singh Chundawat ◽  
Nishigandh Pande ◽  
Ghasem Sargazi ◽  
Mazaher Gholipourmalekabadi ◽  
Narendra Pal Singh Chauhan
Keyword(s):  
Energy Storage ◽  
Cost Efficiency ◽  
Energy Storage Materials ◽  
High Scale ◽  
Chemical Structures ◽  
Redox Active ◽  
Potential Applications ◽  
Intelligent Clothing ◽  
The Relationship ◽  
Structure Properties

AbstractRedox-active polymers among the energy storage materials (ESMs) are very attractive due to their exceptional advantages such as high stability and processability as well as their simple manufacturing. Their applications are found to useful in electric vehicle, ultraright computers, intelligent electric gadgets, mobile sensor systems, and portable intelligent clothing. They are found to be more efficient and advantageous in terms of superior processing capacity, quick loading unloading, stronger security, lengthy life cycle, versatility, adjustment to various scales, excellent fabrication process capabilities, light weight, flexible, most significantly cost efficiency, and non-toxicity in order to satisfy the requirement for the usage of these potential applications. The redox-active polymers are produced through organic synthesis, which allows the design and free modification of chemical constructions, which allow for the structure of organic compounds. The redox-active polymers can be finely tuned for the desired ESMs applications with their chemical structures and electrochemical properties. The redox-active polymers synthesis also offers the benefits of high-scale, relatively low reaction, and a low demand for energy. In this review we discussed the relationship between structural properties of different polymers for solar energy and their energy storage applications.

Topological characterization of dendrimer, benzenoid, and nanocone

2018 ◽  
Vol 74 (1-2) ◽  
pp. 35-43
Author(s):  
Wei Gao ◽  
Muhammad Kamran Siddiqui ◽  
Najma Abdul Rehman ◽  
Mehwish Hussain Muhammad
Keyword(s):  
Chemical Properties ◽  
Chemical Compounds ◽  
Topological Indices ◽  
Zagreb Index ◽  
Topological Characterization ◽  
Complex Molecules ◽  
Chemical Structures ◽  
Physico Chemical ◽  
Quantitative Structure Activity Relationships

Abstract Dendrimers are large and complex molecules with very well defined chemical structures. More importantly, dendrimers are highly branched organic macromolecules with successive layers or generations of branch units surrounding a central core. Topological indices are numbers associated with molecular graphs for the purpose of allowing quantitative structure-activity relationships. These topological indices correlate certain physico-chemical properties such as the boiling point, stability, strain energy, and others, of chemical compounds. In this article, we determine hyper-Zagreb index, first multiple Zagreb index, second multiple Zagreb index, and Zagreb polynomials for hetrofunctional dendrimers, triangular benzenoids, and nanocones.

Studying how genetic variants affect mechanism in biological systems

2018 ◽  
Vol 62 (4) ◽  
pp. 575-582
Author(s):  
Francesco Raimondi ◽  
Robert B. Russell
Keyword(s):  
Genetic Variation ◽  
Molecular Mechanism ◽  
Genetic Variants ◽  
Biological Function ◽  
Biological Systems ◽  
Protein Structures ◽  
Clinical Applications ◽  
Biological Pathways ◽  
The Relationship

Genetic variants are currently a major component of system-wide investigations into biological function or disease. Approaches to select variants (often out of thousands of candidates) that are responsible for a particular phenomenon have many clinical applications and can help illuminate differences between individuals. Selecting meaningful variants is greatly aided by integration with information about molecular mechanism, whether known from protein structures or interactions or biological pathways. In this review we discuss the nature of genetic variants, and recent studies highlighting what is currently known about the relationship between genetic variation, biomolecular function, and disease.

Organizational Conditions Affecting Withdrawal Intentions and Decisions as Moderated by Work Experience

1980 ◽  
Vol 46 (3_suppl) ◽  
pp. 1223-1231 ◽  
Author(s):  
James M. La Rocco ◽  
Allan P. Jones
Keyword(s):  
Work Experience ◽  
Active Duty ◽  
New Members ◽  
Organizational Conditions ◽  
Situational Characteristics ◽  
Initial Expectation ◽  
Withdrawal Decision ◽  
One Year ◽  
The Impact ◽  
The Relationship

Numerous studies of withdrawal from work organizations have considered demographic and other personal history characteristics of leavers. Relatively few of these studies have incorporated dynamic situational characteristics in their designs. In the present effort, the relationship between perceived characteristics of the work environment and stated intentions to reenlist were examined for two groups of first-term Navy enlistees: 198 with less than one year of active duty and less than six months of sea duty, and 516 personnel with more than one year of active duty and more than six months of sea time. It was hypothesized that: (a) the relationship between organizational conditions and intent to reenlist would be weaker for new members than for experienced men, (b) that new personnel would be most likely to change their intentions over time, and (c) that new personnel would quickly assimilate the beliefs, values, and perspectives of their more experienced co-workers. Hypothesis 1 was not supported although the pattern of relationships was in the predicted direction. Hypotheses 2 and 3 were supported. The authors discuss the need for research which emphasizes the impact of initial expectation and organizational socialization on the withdrawal decision process.

scholarly journals Pharmaceutical properties of 'sucupira' (Pterodon spp.)

2010 ◽  
Vol 46 (4) ◽  
pp. 607-616 ◽  
Author(s):  
Daiane Hansen ◽  
Mitsue Haraguchi ◽  
Antonio Alonso
Keyword(s):  
Biological Effects ◽  
Chemical Compounds ◽  
Experimental Models ◽  
Popular Medicine ◽  
Isolation And Characterization ◽  
Pharmaceutical Properties ◽  
The Relationship

The plant of the genus Pterodon (Fabaceae, Leguminosae), commonly known as 'sucupira' or 'faveira', are disseminated throughout the central region of Brazil and has frequently been used in popular medicine for its anti-rheumatic, analgesic, and anti-inflammatory properties. In recent years, interest in these plants has increased considerably. The biological effects of different phytoextracts and pure metabolites have been investigated in several experimental models in vivo and in vitro. The literature describes flavonoids, triterpene and steroids, while one paper presented studies with proteins isolated from the genus. This review provides an overview of phytochemical and pharmacological research in Pterodon, showing the main chemical compounds studied to date, and focusing on the relationship between these molecules and their biological activity. Furthermore, this study paves the way for more in-depth investigation, isolation and characterization of the molecules of this plant genus.

scholarly journals Ethnobotanical, phytochemical and pharmacological aspects of Bengal Pogostemon (Pogostemon benghalensis)

2020 ◽  
Vol 9 (4) ◽  
pp. 318-327
Author(s):  
Sangeeta Dahiya ◽  
Daizy R. Batish ◽  
Harminader Pal Singh
Keyword(s):  
Molecular Level ◽  
Antioxidant Activities ◽  
Chemical Compounds ◽  
Biologically Active ◽  
Pharmacological Activities ◽  
Plant Parts ◽  
Chemical Structures ◽  
Traditional Uses ◽  
Traditional Remedies ◽  
Pharmacological Studies

Pogostemon benghalensis (Burm.f.) Kuntze (Lamiaceae) is an important aromatic plant. Multiple classes of phytochemicals such as flavonoids, phenols, phytosteroids, carbohydrates, fatty acids, glycosides, sterols, terpenoids, tannins, essential oil, and alkaloids have been isolated from the title species. Different plant parts have been used as traditional remedies for various ailments. The present review aims to update and coherent the fragmented information on botanical aspects, phytochemistry, traditional uses, and pharmacological activities. An extensive review of the literature was carried out by using various search engines like PubMed, Scopus, Science Direct, Google Scholar, Google, Scifinder for information. The articles were searched using the keywords "Pogostemon", "Parviflorus’, "benghalensis". Chemical structures of the chemical compounds were drawn using software Chem Draw ultra 8.0. Most of the plant parts have been used for the treatment of various ailments. Phytochemistry reveals that the plant is a rich source of various biologically active compounds. Pogostemon extracts exhibited numerous pharmacological effects like anticancer, anti-inflammatory, antimicrobial and antioxidant activities. In sum, P. benghalensis is a promising aromatic and medicinal plant as depicted by its various traditional uses and pharmacological studies. Bioactive compounds, responsible for its various pharmacological activities at the molecular level, need further detailed investigations. Future clinical studies are also required to validate the various traditional uses of P. benghalensis.

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