In Silico Structural Analysis of a Putative Class IA Phospholipase A2 from the Brazilian Coral Snake, Micrurus corallinus

Introduction: The venom of the coral snake species Micrurus corallinus is highly potent and exerts neurotoxic effects through presynaptic enzymes such as class IA phospholipases. However, due to the difficulty in obtaining the venom and the fact that most collected venom is used for antivenom production in Brazil, pharmacological studies of these toxins are scarce. Previous studies have already characterized the primary structure of M. corallinus PLA2. With the advent of tools like AlphaFold2 and recent improvements in tools like CHARMM-GUI, in silico studies of these molecules have become more accessible and accurate. This study proposes the in silico characterization of M. corallinus PLA2, comparing its structure with other characterized elapid PLA2s, evaluating both catalytic and presynaptic toxicity-related residues. Methods: The alignment of primary structures of PLA2s from Micrurus altirostris (F5CPF0), Micrurus nigrocinctus (P81166), Naja atra (P00598), and Pseudechis australis (P04056 and P04057) was performed using ClustalW. The three-dimensional structure of M. corallinus PLA2 was modeled using AlphaFold2. The interactions of the enzyme with its substrates (phospholipid or tridecanoic acid) were analyzed using the CHARMM-GUI web interface and the PPM 2.0 server. All molecular representations were created using the PyMOL molecular graphics software package. Results: Micrurus corallinus PLA2 presents all residues necessary for catalytic action: CCXXH48D49XC in the active site and GCY28CG30X32GXG in the Ca²⁺ binding loop. Both catalytic mechanisms, the single-water mechanism and the assisted-water mechanism, were evaluated, with the latter being more likely due to the large distance observed between His48 and the Ca²⁺ ion. Conclusion: The results indicate that M. corallinus PLA2 possesses all the necessary residues to exert its catalytic effects, supporting the possibility that this toxin is responsible for the presynaptic action observed in M. corallinus venom.