High-Resolution Crystal Structure of the Snake Venom Metalloproteinase BaP1 Complexed with a Peptidomimetic: Insight into Inhibitor Binding

Abstract

BaP1, a zinc-dependent endopeptidase belonging to the P-I class of snake venom metalloproteinases, exerts multiple tissue-damaging activities, leading to hemorrhage, myonecrosis, dermonecrosis, blistering, and edema. Interestingly, this metalloproteinase shows a high degree of structural homology with the catalytic domain of human adamalysins and matrix metalloproteinases, especially at the strictly conserved zinc binding motif and the so-called Met turn. This highlights BaP1 as an interesting model concerning inhibitor design for several medicinally important metalloproteinases, such as tumor necrosis factor alpha converting enzyme. Here, we report the first crystal structure of BaP1 complexed with a peptidomimetic inhibitor. Suitable crystals were obtained at four different pH values (4.6, 6.5, 7.5, and 8.0), and four high-resolution structures (1.46, 1.14, 1.08, and 1.05 A) were established. These structures and the detailed analysis of the structure-activity relationship of the bound inhibitor form a basis for the design of potent BaP1 inhibitors. The latter can be used for the treatment of local pathological effects caused by snake bites, mainly due to metalloproteinases such as BaP1. Besides, the high-resolution structure is an excellent starting point for the rational development of inhibitors for human metalloproteinases. The finding of a flexible loop region may have a great impact on further studies as to date little is known about the structural dependencies of the hemorrhagic activity of snake venom metalloproteinases.

Backbone Flexibility Controls the Activity and Specificity of a Protein−Protein Interface: Specificity in Snake Venom Metalloproteases

“…The first hint that dynamics may play a crucial role for this protein-protein interaction site already emerged from the X-ray structure of BaP1. 72 Parts of a loop (residues 159-163) were found to exist in two clearly distinguishable conformations.…”

“…[73][74][75] Two of them exert hemorrhagic activity, while the other two do not induce this effect. The active ones are BaP1 from Bothrops asper 72 and acutolysin-A from Agkistrodon acutus, 76 and the inactive ones are leucurolysin-A from Bothrops leucurus 77 and H2-proteinase from Trimeresurus flaVoViridis, 78 respectively. In a pairwise sequence alignment, BaP1 and leucurolysin-A exhibit the same type of amino acid side chains in 78% of all residues ( Figure 1).…”

Cross-recognition of a pit viper (Crotalinae) polyspecific antivenom explored through high-density peptide microarray epitope mapping

“…Metalloprotease-domains: P83512 from B . asper mapped to RCSB entry: 2w15 [40]; J3SDW8 from C . adamanteus homology model based on RCSB entry 2ERQ [41].…”

Metalloproteases Affecting Blood Coagulation, Fibrinolysis and Platelet Aggregation from Snake Venoms: Definition and Nomenclature of Interaction Sites

“…One of the exceptions is kaouthiagin-like protease from Naja atra , which adopts a more elongated conformation due to the absence of a 17-residue segment and to a different disulfide bond pattern in the D domain [22] (Figure 3B). Other than variations in the peripheral loops, the structures of M domain among P-III [18,19,20,21,22,23], P-I [24,25,26,27,28,29,30,31,32,33,34] and P-II [35] enzymes are similar. M domains are folded as a five-stranded β-sheet interspersed with five α-helices into two subdomains flanking the catalytic cleft in which a zinc ion is localized.…”