Combining in silico tools and NMR data to validate protein-ligand structural models: application to matrix metalloproteinases.
A combination of in silico tools and experimental NMR data is proposed for relatively fast determination of protein-ligand structural models and demonstrated from known inhibitors of matrix metalloproteinases (MMP). The 15N 1H heteronuclear single quantum coherence (HSQC) spectral assignment and the 3D structure, either X-ray or NMR, are needed. In this method, the HSQC spectrum with or without the ligand is used to determine the interaction region of the ligand. Docking calculations are then performed to obtain a set of structural models. From the latter, the nuclear Overhauser effects (NOEs) between the ligand and the protein can be predicted. Guided by these predictions, a number of NOEs can be detected and assigned through a HSQC NOESY experiment. These data are used as structural restraints to reject/refine the initial structural models through further in silico work. For a test protein (MMP-12, human macrophage metalloelastase), a final structure of a protein-ligand adduct was obtained that matches well with the full structural determination. A number of structural predictions were then made for adducts of a similar protein (MMP-1, human fibroblast collagenase) with the same and different ligands. The quality of the final results depended on the type and number of experimental NOEs, but in all cases, a well-defined ligand conformation in the protein binding site was obtained. This protocol is proposed as a viable alternative to the many approaches described in the literature.
Bertini
Ivano
I
Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy. bertini@cerm.unifi.it
Fragai
Marco
M
Giachetti
Andrea
A
Luchinat
Claudio
C
Maletta
Massimiliano
M
Parigi
Giacomo
G
Yeo
Kwon Joo
KJ
D000409:Alanine / Q000031:analogs & derivatives / Q000737:chemistry; D001665:Binding Sites; D004151:Dipeptides / Q000737:chemistry; D005998:Glycine / Q000031:analogs & derivatives; D006801:Humans; D006877:Hydroxamic Acids / Q000737:chemistry; D008024:Ligands; D009682:Magnetic Resonance Spectroscopy; D020781:Matrix Metalloproteinase 1 / Q000737:chemistry; D053508:Matrix Metalloproteinase 12; D061965:Matrix Metalloproteinase Inhibitors; D020782:Matrix Metalloproteinases / Q000737:chemistry*; D008666:Metalloendopeptidases / Q000737:chemistry; D008958:Models, Molecular; D008968:Molecular Conformation; D011392:Proline / Q000031:analogs & derivatives / Q000737:chemistry
D004151:Dipeptides; D006877:Hydroxamic Acids; D008024:Ligands; D061965:Matrix Metalloproteinase Inhibitors; C078131:N-(2(R)-2-(hydroxamidocarbonylmethyl)-4-methylpentanoyl)-L-tryptophan methylamide; D011392:Proline; D020782:Matrix Metalloproteinases; D008666:Metalloendopeptidases; C507122:MMP12 protein, human; D053508:Matrix Metalloproteinase 12; D020781:Matrix Metalloproteinase 1; D000409:Alanine; C010531:actinonin; D005998:Glycine