Interfacial activation of snake venom phospholipases A2 (svPLA2) probed by molecular dynamics simulations

Characterization of a novel acidic phospholipase A2 isolated from the venom of Bothrops mattogrossensis: From purification to structural modeling

Phospholipases A2 (PLA2s) are highly prevalent in Bothrops snake venom and play a crucial role in inflammatory responses and immune cell activation during envenomation. Despite their significance, the specific role of PLA2s from Bothrops mattogrossensis venom (BmV) in inflammation is not fully understood. This study sought to isolate and characterize a novel acidic PLA2 from BmV, designated BmPLA2-A, and to evaluate its effects on human umbilical vein endothelial cells (HUVECs), with a specific focus on cytotoxicity, adhesion, and detachment. BmPLA2-A was isolated through a multi-step chromatographic procedure, involving cation exchange (CM-Sepharose), hydrophobic interaction (n-butyl-Sepharose-HP), and reversed-phase (C-18) chromatography. SDS-PAGE analysis revealed a single protein band of approximately 15 kDa. The primary structure of BmPLA2-A was determined by LC-MS/MS, while its tertiary structure was modeled using AlphaFold. Enzymatic activity was verified with the synthetic substrate 4N3OBA. Molecular dynamics simulations were conducted to further investigate the catalytic mechanism of BmPLA2-A at the molecular level. In vitro assays on HUVECs revealed that BmPLA2-A neither induce cytokine release (IL-6, IL-8, IL-1β, TNF) nor affected cell viability, adhesion, or detachment. The characteristics of BmPLA2-A are consistent with those of acidic Asp-49 PLA2 enzymes, highlighting its potential involvement in the cytotoxic and inflammatory effects of the venom.

Computational Studies of Snake Venom Toxins

Most snake venom toxins are proteins, and participate to envenomation through a diverse array of bioactivities, such as bleeding, inflammation, and pain, cytotoxic, cardiotoxic or neurotoxic effects. The venom of a single snake species contains hundreds of toxins, and the venoms of the 725 species of venomous snakes represent a large pool of potentially bioactive proteins. Despite considerable discovery efforts, most of the snake venom toxins are still uncharacterized. Modern bioinformatics tools have been recently developed to mine snake venoms, helping focus experimental research on the most potentially interesting toxins. Some computational techniques predict toxin molecular targets, and the binding mode to these targets. This review gives an overview of current knowledge on the ~2200 sequences, and more than 400 three-dimensional structures of snake toxins deposited in public repositories, as well as of molecular modeling studies of the interaction between these toxins and their molecular targets. We also describe how modern bioinformatics have been used to study the snake venom protein phospholipase A2, the small basic myotoxin Crotamine, and the three-finger peptide Mambalgin.

Structural Insight into Binding Mode of 9-Hydroxy Aristolochic Acid, Diclofenac and Indomethacin to PLA2

Phospholipase A₂ (PLA₂) catalyzes the hydrolysis of phospholipids into arachidonic acid and lysophospholipids. Arachidonic acid is modified by cyclooxygenases into active compounds called eicosanoids that act as signaling molecules in a number of physiological processes. Excessive production of eicosanoids leads to several pathological conditions such as inflammation. In order to block the inflammatory effect of these compounds, upstream enzymes such as PLA₂ are valid targets. In the present contribution, molecular dynamic analysis was performed to evaluate the binding of diclofenac, 9-hydroxy aristolochic acid (9-HAA) and indomethacin to PLA₂. Obtained results revealed that 9-HAA could form a more stable complex with PLA₂ when compared to diclofenac and indomethacin. Furthermore, analysis of intermolecular binding energy components indicated that hydrophobic interactions were dominant in binding process. On the basis of obtained data, inhibitors bearing fused rings with hydrogen acceptor/donor substituent(s) interacted with His48 and Asp49 residues of the active site. More affinity toward PLA₂ might be envisaged through negatively charged moieties via interaction with Trp31, Lys34 and Lys69.