Computational Venomics: Atomistic Simulations of Snake Venom Toxins
Published in Physics
Speakers
- Prof. Pedro Alexandrino Fernandes — Universidade do Porto
Abstract
This lecture will highlight recent advances in our research on enzymatic catalysis using molecular simulations, with applications spanning both environmental and biomedical systems.
Our group has been actively investigating two fields: the molecular mechanisms of enzymes involved in plastic biodegradation, such as PETase, MHETase, and SP1-3[1, 2], as well as emerging systems targeting more recalcitrant polymers; and the mechanisms of action and origins of toxicity of key enzymatic toxins in snake venoms[3].
This talk will focus on the latter by discussing the enzymatic mechanisms and the origin of toxicity of the key venom toxins phospholipases A₂[4] and hyaluronidases[5]. Using molecular dynamics and hybrid quantum mechanics/molecular mechanics methods [6], we investigate their catalytic pathways and interactions with biological targets, including cell membranes, coagulation factors, and extracellular matrix components. Emphasis will be placed on the mechanistic basis of toxicity, including the role of C-terminal peptides derived from PLA₂-like proteins in membrane disruption and systemic effects[7].
By providing an atomistic perspective on enzyme reactivity, this work contributes to a deeper understanding of venom-induced pathology and supports the rational design of next-generation antivenoms. At the same time, it illustrates how common mechanistic principles underlie enzymatic adaptation to both biological and synthetic substrates, bridging challenges in health and sustainability.
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