{"title":"On topological characterizations and computational analysis of benzenoid networks for drug discovery and development","authors":"Pradeepa A , Arathi P","doi":"10.1016/j.jmgm.2025.108957","DOIUrl":null,"url":null,"abstract":"<div><div>Topological indices are numerical invariants that provide key insights into the structural properties of molecular graphs and are crucial in predicting physio-chemical and biological activities. This paper applies established computational methodologies for analyzing benzenoid networks and their application to polycyclic aromatic hydrocarbons (PAHs) through degree-based topological indices computed via M-polynomial and NM-polynomial approaches. By examining tessellations, including linear chain, hexagonal, rhomboidal, and triangular configurations alongside their line graphs, this work highlights the influence of molecular topology on biological activity. Notably, the line graph of hexagonal tessellations resembling Kagome structures exhibits the highest potential bioactivity, revealing additional connectivity patterns that offer a structured framework for early-stage drug discovery and potentially enhance the understanding of molecular interactions. These findings underscore the value of topological indices in identifying key structural features, reducing attrition rates in drug development, and improving screening technologies, contributing to efficient drug design.</div></div>","PeriodicalId":16361,"journal":{"name":"Journal of molecular graphics & modelling","volume":"136 ","pages":"Article 108957"},"PeriodicalIF":2.7000,"publicationDate":"2025-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of molecular graphics & modelling","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1093326325000178","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
引用次数: 0
Abstract
Topological indices are numerical invariants that provide key insights into the structural properties of molecular graphs and are crucial in predicting physio-chemical and biological activities. This paper applies established computational methodologies for analyzing benzenoid networks and their application to polycyclic aromatic hydrocarbons (PAHs) through degree-based topological indices computed via M-polynomial and NM-polynomial approaches. By examining tessellations, including linear chain, hexagonal, rhomboidal, and triangular configurations alongside their line graphs, this work highlights the influence of molecular topology on biological activity. Notably, the line graph of hexagonal tessellations resembling Kagome structures exhibits the highest potential bioactivity, revealing additional connectivity patterns that offer a structured framework for early-stage drug discovery and potentially enhance the understanding of molecular interactions. These findings underscore the value of topological indices in identifying key structural features, reducing attrition rates in drug development, and improving screening technologies, contributing to efficient drug design.
期刊介绍:
The Journal of Molecular Graphics and Modelling is devoted to the publication of papers on the uses of computers in theoretical investigations of molecular structure, function, interaction, and design. The scope of the journal includes all aspects of molecular modeling and computational chemistry, including, for instance, the study of molecular shape and properties, molecular simulations, protein and polymer engineering, drug design, materials design, structure-activity and structure-property relationships, database mining, and compound library design.
As a primary research journal, JMGM seeks to bring new knowledge to the attention of our readers. As such, submissions to the journal need to not only report results, but must draw conclusions and explore implications of the work presented. Authors are strongly encouraged to bear this in mind when preparing manuscripts. Routine applications of standard modelling approaches, providing only very limited new scientific insight, will not meet our criteria for publication. Reproducibility of reported calculations is an important issue. Wherever possible, we urge authors to enhance their papers with Supplementary Data, for example, in QSAR studies machine-readable versions of molecular datasets or in the development of new force-field parameters versions of the topology and force field parameter files. Routine applications of existing methods that do not lead to genuinely new insight will not be considered.