Molecular representations have essential roles in bio-cheminformatics as they facilitate the growth of machine learning applications in numerous sub-domains of biology and chemistry, especially drug discovery. These representations transform the structural and chemical information of molecules into machine-readable formats that can be efficiently processed by computer programs. In this paper, we present a comprehensive review, providing readers with diverse perspectives on the strengths and weaknesses of well-known molecular representations, along with their respective categories and implementation sources. Moreover, we provide a summary of the applicability of these representations in de novo molecular design, molecular property prediction, and chemical reactions. Besides, representations for macromolecules are discussed with highlighted pros and cons. By addressing these aspects, we aim to offer a valuable resource on the significant role of molecular representations in advancing bio-cheminformatics and its related domains.

Tartrazine (E102, FD&C Yellow 5) is a vibrant yellow azo dye added to many processed foods. The safety of this ubiquitous chemical has not been fully elucidated, and it has been linked to allergic reactions and ADHD in some individuals. In our study, bacterial species isolated from human stool decolourised tartrazine and, upon exposure to air, a purple compound formed. Tartrazine is known to undergo reduction in the gut to sulfanilic acid and 4-amino-3-carboxy-5-hydroxy-1-(4-sulfophenyl)pyrazole (SCAP). These metabolites and their derivatives are relevant to the toxicology of tartrazine. The toxicity of sulfanilic acid has been studied before, but the oxidative instability of SCAP has previously prevented full characterisation. We have verified the chemical identity of SCAP and confirmed that the purple-coloured oxidation derivative is 4-(3-carboxy-5-hydroxy-1-(4-sulfophenyl)-1H-pyrazol-4-yl)imino-5-oxo-1-(4-sulfophenyl)-4,5-dihydro-1H-pyrazole-3-carboxylic acid (purpurazoic acid, PPA), as proposed by Westöö in 1965. A yellow derivative of SCAP is proposed to be the hydrolysed oxidation product, 4,5-dioxo-1-(4-sulfophenyl)-4,5-dihydro-1H-pyrazole-3-carboxylic acid. SCAP and PPA are moderately toxic to human cells (IC₅₀ 89 and 78 μM against HEK-293, respectively), but had no apparent effect on Escherichia coli and Bacillus subtilis bacteria. These results prompt further analyses of the toxicology of tartrazine and its derivatives.

gem-Dibromocyclopropane 1, prepared from tri-O-benzyl-D-glucal, undergoes thermal and silver-promoted ring expansion in the presence of alcohols to give substituted oxepines. With further heating, ring contraction to highly substituted tetrahydrofurans follows. These represent C-furanosides, potentially useful as precursors to C-nucleosides and other carbohydrate mimics.

Addition of a carbene to a glycal is the prominent method for the synthesis of 1,2-cyclopropyl carbohydrates. This incorporation of a cyclopropane into a carbohydrate scaffold enables divergent reactivity, with the two main classes being ring expansion and cleavage to 2-C-branched carbohydrates. A wide variety of products are obtained depending on the functionality attached to the cyclopropane (none or ester or halogens) and the promoter (Lewis acid, Brønsted acid, halophile or base) used in the reaction. This article reviews progress in the synthesis and reactions of 1,2-cyclopropyl carbohydrates since 2000 and discloses efforts by our group in the area.

Peloruside A is a macrocyclic natural product from a New Zealand marine sponge Mycale hentscheli. It has attracted significant attention in the synthetic chemistry, cellular and structural biology communities due to its complex structure and potent anticancer activity. Several natural congeners have since been isolated and synthetic analogues have been prepared. This review describes in detail the published syntheses of peloruside analogues and discusses the structure–activity relationships available to date.