Topological properties of Sierpinski network and its application

2021 ◽  
Vol 24 ◽  
Author(s):  
Juanyan Fang ◽  
Muhammad Rafiullah ◽  
Hafiz Muhammad Afzal Siddiqui
Keyword(s):  
Biological Activity ◽  
Thermodynamic Properties ◽  
Physicochemical Properties ◽  
Graphical Representation ◽  
Standard Procedure ◽  
Topological Descriptors ◽  
Fractal Nature ◽  
Eccentric Connectivity Index ◽  
Chemical Structures ◽  
3D Graphical Representation

Background: Sierpinski graphs S(n,k) are largely studied because of their fractal nature with applications in topology, chemistry, mathematics of Tower of Hanoi, and computer sciences. Applications of molecular structure descriptors are a standard procedure that are used to correlate the biological activity of molecules with their chemical structures and thus can be helpful in the field of pharmacology. Objective: The aim of this article is to establish analytically closed computing formulae for eccentricity-based descriptors of Sierpinski networks and their regularizations. These computing formulae are useful to determine a large number of properties like thermodynamic properties, physicochemical properties, chemical and biological activity of chemical graphs. Methods: At first, vertex sets have been partitioned on the basis of their degrees, eccentricities, and frequencies of occurrence. Then these partitions are used to compute the eccentricity-based indices with the aid of some combinatorics. Results: The total eccentric index and eccentric-connectivity index have been computed. We also compute some eccentricity-based Zagreb indices of the Sierpinski networks. Moreover, a comparison has also been presented in the form of graphs. Conclusion: These computations will help the readers to estimate the thermodynamic properties, physicochemical properties of chemical structures, which are of fractal nature and can not be dealt with easily. A 3D graphical representation is also presented to understand the dynamics of the aforementioned topological descriptors.

scholarly journals Position Impact of Hydroxy Groups on Spectral, Acid–Base Profiles and DNA Interactions of Several Monohydroxy Flavanones

Molecules ◽  
2019 ◽  
Vol 24 (17) ◽  
pp. 3049 ◽  
Author(s):  
Elżbieta Łodyga-Chruścińska ◽  
Agnieszka Kowalska-Baron ◽  
Paulina Błazińska ◽  
Maria Pilo ◽  
Antonio Zucca ◽  
...  
Keyword(s):  
Antioxidant Activity ◽  
Cyclic Voltammetry ◽  
Biological Activity ◽  
Physicochemical Properties ◽  
Biological Activities ◽  
Dna Interactions ◽  
Acid Base ◽  
Chemical Structures ◽  
Vis Spectroscopy ◽  
Spectral Profiles

Structure-related biological activities of flavanones are still considered largely unexplored. Since they exhibit various medicinal activities, it is intriguing to enter deeper into their chemical structures, electronic transitions or interactions with some biomolecules in order to find properties that allow us to better understand their effects. Little information is available on biological activity of flavanone and its monohydroxy derivatives in relation to their physicochemical properties as spectral profiles, existence of protonated/deprotonated species under pH changes or interaction with Calf Thymus DNA. We devoted this work to research demonstrating differences in the physicochemical properties of the four flavanones: flavanone, 2′-hydroxyflavanone, 6-hydroxyflavanone and 7-hydroxyflavanone and linking them to their biological activity. Potentiometric titration, UV–Vis spectroscopy were used to investigate influence of pH on acid–base and spectral profiles and to propose the mode of interaction with DNA. Cyclic voltammetry was applied to evaluate antioxidant potentiality and additionally, theoretical DFT(B3LYP) method to disclose electronic structure and properties of the compounds. Molecular geometries, proton affinities and pKa values have been determined. According to computational and cyclic voltammetry results we could predict higher antioxidant activity of 6-hydroxyflavanone with respect to other compounds. The values of Kb intrinsic binding constants of the flavanones indicated weak interactions with DNA. Structure–activity relationships observed for antioxidant activity and DNA interactions suggest that 6-hydroxyflavanone can protect DNA against oxidative damage most effectively than flavanone, 2′-hydroxyflavanone or 7-hydroxyflavanone.

ANALYSIS OF SIMILARITY/DISSIMILARITY OF DNA SEQUENCES BY A NEW 3D GRAPHICAL REPRESENTATION

2007 ◽  
Vol 15 (03) ◽  
pp. 287-297 ◽  
Author(s):  
JIE SONG
Keyword(s):  
Dna Sequences ◽  
Chemical Structure ◽  
Graphical Representation ◽  
Globin Gene ◽  
Coding Sequences ◽  
Chemical Structures ◽  
Numerical Characterization ◽  
Analysis Of Similarity ◽  
3D Graphical Representation ◽  
3D Representations

A new 3D graphical representation of DNA sequences according to chemical structures of the bases is proposed, reflecting the distribution of bases with different chemical structure, preserving information on sequential adjacency of bases, avoiding loss of information accompanying alternative 3D representations in which the curve standing for DNA overlaps and intersects itself. Based on this representation, a numerical characterization approach is presented by constructing a six-component vector whose components are the normalized leading eigenvalues of the L/L matrices associated with the DNA sequences. The examination of similarities among the coding sequences of the first exon of β-globin gene of different species illustrates the utility of the approach.

Quantitative Structure- Property Relationship (QSPR) Investigation of Camptothecin Drugs Derivatives

2018 ◽  
Vol 21 (7) ◽  
pp. 533-542 ◽  
Author(s):  
Neda Ahmadinejad ◽  
Fatemeh Shafiei ◽  
Tahereh Momeni Isfahani
Keyword(s):  
Thermodynamic Properties ◽  
Predictive Ability ◽  
Total Sample ◽  
Basis Sets ◽  
Quantitative Structure ◽  
Structure Property ◽  
Quantitative Structure Property Relationship ◽  
Chemical Structures ◽  
Property Relationship ◽  
Structure Property Relationship

Aim and Objective: Quantitative Structure- Property Relationship (QSPR) has been widely developed to derive a correlation between chemical structures of molecules to their known properties. In this study, QSPR models have been developed for modeling and predicting thermodynamic properties of 76 camptothecin derivatives using molecular descriptors. Materials and Methods: Thermodynamic properties of camptothecin such as the thermal energy, entropy and heat capacity were calculated at Hartree–Fock level of theory and 3-21G basis sets by Gaussian 09. Results: The appropriate descriptors for the studied properties are computed and optimized by the genetic algorithms (GA) and multiple linear regressions (MLR) method among the descriptors derived from the Dragon software. Leave-One-Out Cross-Validation (LOOCV) is used to evaluate predictive models by partitioning the total sample into training and test sets. Conclusion: The predictive ability of the models was found to be satisfactory and could be used for predicting thermodynamic properties of camptothecin derivatives.

scholarly journals New Haloterpenes from the Marine Red Alga Laurencia papillosa: Structure Elucidation and Biological Activity

Marine Drugs ◽  
2021 ◽  
Vol 19 (1) ◽  
pp. 35
Author(s):  
Mohamed Shaaban ◽  
Ghada S. E. Abou-El-Wafa ◽  
Christopher Golz ◽  
Hartmut Laatsch
Keyword(s):  
Biological Activity ◽  
Crude Extract ◽  
Structure Elucidation ◽  
Antimicrobial Activities ◽  
Red Alga ◽  
Spectroscopic Methods ◽  
X Ray Diffraction ◽  
X Ray ◽  
Chemical Structures ◽  
Terpene Derivatives

Analysis of the air-dried marine red alga Laurencia papillosa, collected near Ras-Bakr at the Suez gulf (Red Sea) in Egypt delivered five new halogenated terpene derivatives: aplysiolic acid (1), 7-acetyl-aplysiol (2), aplysiol-7-one (3), 11,14-dihydroaplysia-5,11,14,15-tetrol (5a), and a new maneonene derivative 6, named 5-epi-maneolactone. The chemical structures of these metabolites were characterized employing spectroscopic methods, and the relative and absolute configurations were determined by comparison of experimental and ab initio-calculated NMR, NOE, ECD, and ORD data, and by X-ray diffraction of 2 and 6. The antimicrobial activities of the crude extract and compounds 1–3, 5a and 6 were studied.

scholarly journals Synthetic auxin-based double salt ionic liquids as herbicides with improved physicochemical properties and biological activity

2021 ◽  
pp. 116452
Author(s):  
Tomasz Rzemieniecki ◽  
Marta Wojcieszak ◽  
Katarzyna Materna ◽  
Tadeusz Praczyk ◽  
Juliusz Pernak
Keyword(s):  
Biological Activity ◽  
Ionic Liquids ◽  
Physicochemical Properties ◽  
Double Salt ◽  
Synthetic Auxin

On eccentricity-based topological descriptors of water-soluble dendrimers

2018 ◽  
Vol 74 (1-2) ◽  
pp. 25-33 ◽  
Author(s):  
Zahid Iqbal ◽  
Muhammad Ishaq ◽  
Adnan Aslam ◽  
Wei Gao
Keyword(s):  
Molecular Structure ◽  
Chemical Properties ◽  
Topological Indices ◽  
Water Soluble ◽  
Connectivity Index ◽  
Topological Descriptors ◽  
Physical And Chemical Properties ◽  
Eccentric Connectivity Index ◽  
Physical And Chemical ◽  
And Chemical Properties

AbstractPrevious studies show that certain physical and chemical properties of chemical compounds are closely related with their molecular structure. As a theoretical basis, it provides a new way of thinking by analyzing the molecular structure of the compounds to understand their physical and chemical properties. The molecular topological indices are numerical invariants of a molecular graph and are useful to predict their bioactivity. Among these topological indices, the eccentric-connectivity index has a prominent place, because of its high degree of predictability of pharmaceutical properties. In this article, we compute the closed formulae of eccentric-connectivity–based indices and its corresponding polynomial for water-soluble perylenediimides-cored polyglycerol dendrimers. Furthermore, the edge version of eccentric-connectivity index for a new class of dendrimers is determined. The conclusions we obtained in this article illustrate the promising application prospects in the field of bioinformatics and nanomaterial engineering.

scholarly journals A Computational Approach on Acetaminophen Drug using Degree-Based Topological Indices and M-Polynomials

2021 ◽  
Vol 12 (6) ◽  
pp. 7249-7266
Keyword(s):  
Biological Activity ◽  
Physicochemical Properties ◽  
Chemical Structure ◽  
Topological Index ◽  
Chemical Reactivity ◽  
Chemical Compounds ◽  
Computational Approach ◽  
Topological Indices ◽  
Numerical Representation ◽  
Essential Drug

Topological index is a numerical representation of a chemical structure. Based on these indices, physicochemical properties, thermodynamic behavior, chemical reactivity, and biological activity of chemical compounds are calculated. Acetaminophen is an essential drug to prevent/treat various types of viral fever, including malaria, flu, dengue, SARS, and even COVID-19. This paper computes the sum and multiplicative version of various topological indices such as General Zagreb, General Randić, General OGA, AG, ISI, SDD, Forgotten indices M-polynomials of Acetaminophen. To the best of our knowledge, for the Acetaminophen drugs, these indices have not been computed previously.

scholarly journals MeFSAT: A curated natural product database specific to secondary metabolites of medicinal fungi

2020 ◽  
Author(s):  
R.P. Vivek-Ananth ◽  
Ajaya Kumar Sahoo ◽  
Kavyaa Kumaravel ◽  
Karthikeyan Mohanraj ◽  
Areejit Samal
Keyword(s):  
Secondary Metabolites ◽  
Physicochemical Properties ◽  
Natural Product ◽  
Chemical Space ◽  
Chemical Structures ◽  
Therapeutic Uses ◽  
Natural Product Library ◽  
Medicinal Fungi ◽  
Similarity Networks ◽  
Shape Complexity

AbstractFungi are a rich source of secondary metabolites which constitutes a valuable and diverse chemical space of natural products. Medicinal fungi have been used in traditional medicine to treat human ailments for centuries. To date, there is no devoted resource on secondary metabolites and therapeutic uses of medicinal fungi. Such a dedicated resource compiling dispersed information on medicinal fungi across published literature will facilitate ongoing efforts towards natural product based drug discovery. Here, we present the first comprehensive manually curated database on Medicinal Fungi Secondary metabolites And Therapeutics (MeFSAT) that compiles information on 184 medicinal fungi, 1830 secondary metabolites and 149 therapeutics uses. Importantly, MeFSAT contains a non-redundant in silico natural product library of 1830 secondary metabolites along with information on their chemical structures, computed physicochemical properties, drug-likeness properties, predicted ADMET properties, molecular descriptors and predicted human target proteins. By comparing the physicochemical properties of secondary metabolites in MeFSAT with other small molecules collections, we find that fungal secondary metabolites have high stereochemical complexity and shape complexity similar to other natural product libraries. Based on multiple scoring schemes, we have filtered a subset of 228 drug-like secondary metabolites in MeFSAT database. By constructing and analyzing chemical similarity networks, we show that the chemical space of secondary metabolites in MeFSAT is highly diverse. The compiled information in MeFSAT database is openly accessible at: https://cb.imsc.res.in/mefsat/.

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