Interactions between Triterpenes and a P-I Type Snake Venom Metalloproteinase: Molecular Simulations and Experiments

Abstract

Small molecule inhibitors of snake venom metalloproteinases (SVMPs) could provide a means to rapidly halt the progression of local tissue damage following viperid snake envenomations. In this study, we examine the ability of candidate compounds based on a pentacyclic triterpene skeleton to inhibit SVMPs. We leverage molecular dynamics simulations to estimate the free energies of the candidate compounds for binding to BaP1, a P-I type SVMP, and compare these results with experimental assays of proteolytic activity inhibition in a homologous enzyme (Batx-I). Both simulation and experiment suggest that betulinic acid is the most active candidate, with the simulations predicting a standard binding free energy of ΔG∘=−11.0±1.4 kcal/mol. The simulations also reveal the atomic interactions that underlie binding between the triterpenic acids and BaP1, most notably the electrostatic interaction between carboxylate groups of the compounds and the zinc cofactor of BaP1. Together, our simulations and experiments suggest that occlusion of the S1′ subsite is essential for inhibition of proteolytic activity. While all active compounds make hydrophobic contacts in the S1′ site, β-boswellic acid, with its distinct carboxylate position, does not occlude the S1′ site in simulation and exhibits negligible activity in experiment.

Cyano Enone-Bearing Triterpenoid Soloxolone Methyl Inhibits Epithelial-Mesenchymal Transition of Human Lung Adenocarcinoma Cells In Vitro and Metastasis of Murine Melanoma In Vivo

“…Moreover, molecular simulations performed by Negi et al demonstrated that ursolic acid can snugly fit into the active site of JNK1 [ 92 ]. In the case of matrix metalloproteinases-2/-9, primary effects of triterpenoids on their activity, as far as we know, have not been yet published, however, recently, Preciado et al reported that betulinic, oleanolic and ursolic acids can bind to catalytic site of snake venom metalloproteinases, being similar to those in human matrix metalloproteinases, and significantly inhibit their enzymatic and biological activities [ 93 , 94 ]. Furthermore, CDDO-Me and its analog RTA408 were found to decrease expression of MMP-9 in various models, including tumor necrosis factor α- (TNF-α-), receptor activator of nuclear factor kappa-B ligand- (RANKL-) and interleukin 1β- (IL-1β)-stimulated chronic myelogenous leukemia KBM-5 cells, RAW264.7 macrophages and rat brain astrocytes [ 72 , 95 , 96 ], respectively, as well as primary mammary tumor cells, isolated from polyoma middle T mice [ 97 ], which is consistent with revealed ability of SM to inhibit expression of MMP-9 in metastatic foci in lungs of B16 melanoma-bearing mice ( Figure 8 E).…”

Toxinology in Colombia: Contributions of Programa De Ofidismo/Escorpionismo and Other Research Groups

“…Also, the authors suggested that glycolic acid chelated the cofactor Zn 2+ employing fluorescence studies, chelation assays, and molecular docking. Other natural products tested against the same SVMP were triterpenic acids (65,66), which inhibited the enzymatic activity of the enzyme, and they were characterized as competitive inhibitors. Moreover, these compounds inhibited the hemorrhagic, myotoxic, and edema-forming activities provoked by this toxin.…”