Venom Mass Fingerprints for Species Delimitation, Reloaded: A Test Case with Italian Scorpions (Euscorpius)

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  Venom Mass Fingerprints for Species Delimitation, Reloaded: A Test Case with Italian Scorpions (Euscorpius) Abstract Scorpion venoms are complex mixtures of bioactive compounds including proteins, peptides and enzymes. Although venoms exhibit substantial intraspecific variation, some compounds appear to be species-specific, highlighting their potential as chemotaxonomic markers. Venom mass fingerprints (MFPs) derived from Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF) Mass Spectrometry (MS) have been proposed as a means of delimiting species. However, their utility for species delimitation has rarely been evaluated against independent sources of taxonomic evidence. In the present study, the performance of MALDI-TOF MS-based venom peptide barcoding (mass ranges of m/z 800‒4500 and m/z 3000‒10,000) was assessed in 52 populations of eight Italian species of the scorpion genus Euscorpius Thorell, 1876, representing different levels of evolutionary divergenc...

A Structure-Informed Atlas of Venom-Derived Peptides Reveals the Organization of Chemical Space

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A Structure-Informed Atlas of Venom-Derived Peptides Reveals the Organization of Chemical Space

Abstract

Venom-derived peptides are structurally diverse bioactive scaffolds with growing relevance for computational discovery and molecular design. However, their organization within chemical space remains poorly characterized in integrated frameworks. Here, we present a curated, structure-informed venom peptide atlas supported by an integrated descriptor-based framework combining sequence- and structure-derived features across 3,423 peptides. High-confidence AlphaFold models were integrated with physicochemical and structural descriptors to generate a unified molecular representation. Multivariate analyses reveal that venom peptides occupy constrained and interpretable regions of chemical space shaped by disulfide-mediated stabilization, structural compactness, and electrostatic–hydrophobic balance. Functional classes show clear separation, whereas taxonomic origin explains less variance, supporting convergent design principles. This atlas provides a reference resource for comparative analyses, scaffold prioritization, and hypothesis generation in peptide science.

Gonçalves, T. C., Toral Cortez, E. H., & Amaral, D. T. (2026). A Structure-Informed Atlas of Venom-Derived Peptides Reveals the Organization of Chemical Space. Molecular Informatics, 45(5), e70039. https://doi.org/10.1002/minf.70039