Chemical similarity methods for analyzing secondary metabolite structures

Abstract

The relation that exists between the structure of a compound and its function is an integral part of chemoinformatics. The similarity principle states that “structurally similar molecules tend to have similar properties and similar molecules exert similar biological activities”. The similarity of the molecules can either be studied at the structure level or at the descriptor level (properties level). Generally, the objective of chemical similarity measures is to enhance prediction of the biological activities of molecules. In this article, an overview of various methods used to compare the similarity between metabolite structures has been provided, including two-dimensional (2D) and three-dimensional (3D) approaches. The focus has been on methods description; e.g. fingerprint-based similarity in which the molecules under study are first fragmented and their fingerprints are computed, 2D structural similarity by comparing the Tanimoto coefficients and Euclidean distances, as well as the use of physiochemical properties descriptor-based similarity methods. The similarity between molecules could also be measured by using data mining (clustering) techniques, e.g. by using virtual screening (VS)-based similarity methods. In this approach, the molecules with the desired descriptors or /and structures are screened from large databases. Lastly, SMILES-based chemical similarity search is an important method for studying the exact structure search, substructure search and also descriptor similarity. The use of a particular method depends upon the requirements of the researcher.

Interpretable molecular encodings and representations for machine learning tasks

“…The efficient use of molecular fingerprints relies on the “similar property principle”, i.e., structurally similar molecules tend to have similar properties and similar molecules exert similar biological activities [3] , [4] , [5] . At its core, the principle implies that molecules with analogous structural features often interact with biological systems or physical environments in comparable ways.…”

MetChem: a new pipeline to explore structural similarity across metabolite modules

“…During both biological activity and preanalytical procedures, non-enzymatic reactions can also muddle the structure and concentration of metabolites that either belong to the same chemical class or harbor specific functional groups ( Cacciatore et al , 2013 , 2017a ). Metabolites with a similar chemical structure tend to share similar properties and biological activity ( Ekaney et al , 2021 ; Menikarachchi et al , 2013 ).…”