title: Biofragments: an approach towards predicting protein function using biologically related fragments and its application to Mycobacterium tuberculosis CYP126.
abstract: We present a novel fragment-based approach that tackles some of the challenges for chemical biology of predicting protein function. The general approach, which we have termed biofragments, comprises two key stages. First, a biologically relevant fragment library (biofragment library) can be designed and constructed from known sets of substrate-like ligands for a protein class of interest. Second, the library can be screened for binding to a novel putative ligand-binding protein from the same or similar class, and the characterization of hits provides insight into the basis of ligand recognition, selectivity, and function at the substrate level. As a proof-of-concept, we applied the biofragments approach to the functionally uncharacterized Mycobacterium tuberculosis (Mtb) cytochrome P450 isoform, CYP126. This led to the development of a tailored CYP biofragment library with notable 3D characteristics and a significantly higher screening hit rate (14%) than standard drug-like fragment libraries screened previously against Mtb CYP121 and 125 (4% and 1%, respectively). Biofragment hits were identified that make both substrate-like type-I and inhibitor-like type-II interactions with CYP126. A chemical-fingerprint-based substrate model was built from the hits and used to search a virtual TB metabolome, which led to the discovery that CYP126 has a strong preference for the recognition of aromatics and substrate-like type-I binding of chlorophenol moieties within the active site near the heme. Future catalytic analyses will be focused on assessing CYP126 for potential substrate oxidative dehalogenation.
authors.forename: Sean A
authors.initials: SA
authors.lastname: Hudson
authors.forename: Ellene H
authors.initials: EH
authors.lastname: Mashalidis
authors.forename: Andreas
authors.initials: A
authors.lastname: Bender
authors.forename: Kirsty J
authors.initials: KJ
authors.lastname: McLean
authors.forename: Andrew W
authors.initials: AW
authors.lastname: Munro
authors.forename: Chris
authors.initials: C
authors.lastname: Abell
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism*; D003577:Cytochrome P-450 Enzyme System / Q000737:chemistry / Q000378:metabolism*; D008024:Ligands; D009169:Mycobacterium tuberculosis / Q000378:metabolism*; D011485:Protein Binding; D054852:Small Molecule Libraries / Q000737:chemistry; D013379:Substrate Specificity
chemical_list: D001426:Bacterial Proteins; D008024:Ligands; D054852:Small Molecule Libraries; D003577:Cytochrome P-450 Enzyme System