title: Combined spectroscopy and molecular modeling studies on the binding of galbanic acid and MMP9.
abstract: The molecular mechanism of galbanic acid (GBA) binding to matrix metalloproteinase 9 (MMP9) was investigated by fluorescence quenching, absorption spectroscopy, FT-IR, molecular docking and molecular dynamics (MD) simulation procedures. The fluorescence emission of MMP9 was quenched by GBA. The titration of MMP9 by various amount of GBA was also followed by UV-Vis absorption spectroscopy. The results revealed that GBA, as a biologically active sesquiterpene coumarin derivative, has an ability to bind strongly to MMP9. Molecular docking results indicated that the main active binding site for GBA has been located in a hydrophobic cavity in the vicinity of Zn atom. Moreover, MD simulation results suggested that GBA as a coumarin derivative can interact with MMP9, without affecting the secondary structure of MMP9. MD simulations, molecular docking as computational methods from one hand and experimental data from other hand reciprocally supported each other.
authors.affiliation: Department of Toxicology and pharmacology, Kermanshah University of Medical Sciences, Kermanshah, Iran.
authors.forename: Amir
authors.initials: A
authors.lastname: Kiani
authors.affiliation: Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran.
authors.forename: Khadijeh
authors.initials: K
authors.lastname: Almasi
authors.affiliation: Pharmaceutical Sciences Research Center, School of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Iran.
authors.forename: Yalda
authors.initials: Y
authors.lastname: Shokoohinia
authors.affiliation: Pharmaceutical Sciences Research Center, School of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Iran.
authors.forename: Komail
authors.initials: K
authors.lastname: Sadrjavadi
authors.affiliation: Nano Drug Delivery Research Center, School of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Iran.
authors.forename: Amin
authors.initials: A
authors.lastname: Nowroozi
authors.affiliation: Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran. Electronic address: mohsenshahlaei@yahoo.com.
authors.forename: Mohsen
authors.initials: M
authors.lastname: Shahlaei
mesh_terms: D001665:Binding Sites; D020134:Catalytic Domain; D003374:Coumarins / Q000737:chemistry* / Q000378:metabolism; D008024:Ligands; D020780:Matrix Metalloproteinase 9 / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D008968:Molecular Conformation; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D017550:Spectroscopy, Fourier Transform Infrared; D013057:Spectrum Analysis / Q000379:methods; D013329:Structure-Activity Relationship
chemical_list: D003374:Coumarins; D008024:Ligands; C048972:galbanic acid; D020780:Matrix Metalloproteinase 9
keywords: Coumarin derivatives; Ligand–protein interaction; Matrix metalloproteinase