Design of specific peptide inhibitors of phospholipase A₂: structure of a complex formed between Russell's viper phospholipase A₂and a designed peptide Leu-Ala-Ile-Tyr-Ser (LAIYS)

Abstract

Phospholipase A2 (EC 3.1.1.4) is a key enzyme of the cascade mechanism involved in the production of proinflammatory compounds known as eicosanoids. The binding of phospholipase A2 to membrane surfaces and the hydrolysis of phospholipids are thought to involve the formation of a hydrophobic channel into which a single substrate molecule diffuses before cleavage. In order to regulate the production of proinflammatory compounds, a specific peptide inhibitor of PLA2, Leu‐Ala‐Ile‐Tyr‐Ser, has been designed. Phospholipase A2 from Daboia russelli pulchella (DPLA2) and peptide Leu‐Ala‐Ile‐Tyr‐Ser (LAIYS) have been co‐crystallized. The structure of the complex has been determined and refined to 2.0 Å resolution. The structure contains two crystallographically independent molecules of DPLA2, with one molecule of peptide specifically bound to one of them. The overall conformations of the two molecules are essentially similar except in three regions; namely, the calcium‐binding loop including Trp31 (residues 25–34), the β‐wing consisting of two antiparallel β‐strands (residues 74–85) and the C‐terminal region (residues 119–133). Of these, the most striking difference pertains to the orientation of Trp31 in the two molecules. The conformation of Trp31 in molecule A was suitable to allow the binding of peptide LAIYS, while that in molecule B prevented the entry of the ligand into the hydrophobic channel. The structure of the complex clearly showed that the OH group of Tyr of the inhibitor formed hydrogen bonds with both His48 Nδ1 and Asp49 Oδ1, while OγH of Ser was involved in a hydrogen bond with Trp31. Other peptide backbone atoms interact with protein through water molecules, while Leu, Ala and Ile form strong hydrophobic interactions with the residues of the hydrophobic channel.

Simultaneous inhibition of anti‐coagulation and inflammation: crystal structure of phospholipase A2 complexed with indomethacin at 1.4 Å resolution reveals the presence of the new common ligand‐binding site

“…There have also been extensive investigations to understand their (www.interscience.wiley.com) DOI:10.1002/jmr.960 catalytic actions and various ligands have also been designed to inhibit their enzymatic function. The structures of several complexes of PLA 2 with natural compounds (Chandra et al, 2002a(Chandra et al, , 2002dSingh et al, 2006a), substrate analogues (Scott et al, 1990;Thunnissen et al, 1990;Scott et al, 1991;Sekar et al, 1997;Epstein et al, 2001;Pan et al, 2001;Hansford et al, 2003) and with other designed synthetic compounds (Schevitz et al, 1995;Chandra et al, 2002bChandra et al, , 2002cSingh et al, 2003) have also been reported. The anti-inflammatory response of non-steroidal anti-inflammatory drugs (NSAIDs) has been attributed to their binding to PLA 2 (Singh et al, , 2006bJabeen et al, 2005) and COX enzymes Gierse et al, 1999).…”

Phytochemical analysis, molecular docking and molecular dynamics simulations of selected phytoconstituents from four herbs as anti-dotes for snake bites

“…The venom PLA 2 does not have calcium ion coordination in the native and complex form. Calcium ion coordination can acquire only when it reacts with aggregated substrates [15,16]. The compounds, which are inhibiting PLA 2 , can be potent anti-inflammatory agents.…”

Structural Elements of Ligand Recognition Site in Secretory Phospholipase A2 and Structure-Based Design of Specific Inhibitors

“…The structures of several complexes of PLA 2 with natural compounds [29][30][31], substrate analogues [17,32], indole derivatives [37][38], non-steroidal anti-inflammatory drugs (NSAIDs) [33][34][35] and with designed peptides [39][40] have been investigated. The substrate-binding site in PLA 2 is a part of the hydrophobic channel.…”

“…Several structures of PLA 2 complexes with natural compounds [29][30][31], substrate analogues [17,32], nonsteroidal anti-inflammatory drugs (NSAIDs) [33][34][35] and other designed synthetic compounds including peptides [36,[39][40] have been reported. These studies have led to a complete identification of the structural elements of ligand recognition in the hydrophobic channel of PLA 2 , thus paving the way to further improving the quality of inhibitors using structure-based design approach.…”