title: Free energy calculations on snake venom metalloproteinase BaP1.
abstract: BaP1 is a snake venom metalloproteinase from the venom of Bothrops asper, showing high structural homology with the catalytic domain of human adamalysins and matrix metalloproteinases. It induces the release of cytokines, like interleukin-1 and tumor necrosis factor alpha. Recently, the high-resolution crystal structure of BaP1 with a bound inhibitor became available, representing an interesting model concerning inhibitor design for medicinally important metalloproteinases such as tumor necrosis factor alpha-converting enzyme and MMP13. We here use computational modeling to gain a better understanding about the binding properties of various ligands to BaP1, with a focus on computing ligand binding free energies. The obtained results should be of general significance for future research on medicinally important metalloproteinases. We have investigated the binding of the original inhibitor in detail and calculated its binding strength using MMP/GBSA free energy calculations. Additionally, the binding strengths of alternative ligands have been computed, and two of them are predicted and experimentally verified to strongly inhibit the enzyme. A suggestion for chemical modifications of BaP1 inhibitors could be made to guide future synthesis efforts. Furthermore, a contribution to the proteolytic reaction mechanism of metzincins is given. The pK value of the catalytically active glutamic acid residue 143 has been found to be significantly raised when compared with a free glutamate side chain. Calculations on other matrix metalloproteinases confirmed that this is not confined to BaP1, but seems to be a common feature of metzincins.
authors.affiliation: Department of Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, Freiburg University, Stefan-Meier Str. 19, 79104 Freiburg, Germany.
authors.forename: Torsten
authors.initials: T
authors.lastname: Lingott
authors.forename: Irmgard
authors.initials: I
authors.lastname: Merfort
authors.forename: Thomas
authors.initials: T
authors.lastname: Steinbrecher
mesh_terms: D000818:Animals; D001665:Binding Sites; D017837:Bothrops / Q000378:metabolism*; D020134:Catalytic Domain; D006860:Hydrogen Bonding; D007700:Kinetics; D008024:Ligands; D053509:Matrix Metalloproteinase 13 / Q000737:chemistry / Q000378:metabolism; D008666:Metalloendopeptidases / Q000037:antagonists & inhibitors* / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D012910:Snake Venoms / Q000201:enzymology; D013816:Thermodynamics; D014409:Tumor Necrosis Factor-alpha / Q000737:chemistry / Q000378:metabolism
chemical_list: D008024:Ligands; D012910:Snake Venoms; D014409:Tumor Necrosis Factor-alpha; C104933:BaP1 metalloproteinase; D053509:Matrix Metalloproteinase 13; D008666:Metalloendopeptidases