TY - JOUR
T1 - Biofragments: an approach towards predicting protein function using biologically related fragments and its application to Mycobacterium tuberculosis CYP126
AU - Hudson, Sean A
AU - Mashalidis, Ellene A
AU - Bender, Andreas
AU - Mclean, Kirsty
AU - Munro, Andrew W
AU - Abell, Chris
N1 - We acknowledge funding from the EC (as part of the NM4TB project) and the BBSRC (grants BB/I019227/1 to C.A. and BB/I019669/1 to A.W.M.). S.A.H. was supported by a Sir Mark Oliphant Cambridge Australia Scholarship awarded by the Cambridge Trusts. E.H.M. was supported by the NIH-Oxford-Cambridge Scholars Program. This research was supported in part by the Intramural Research Program of the NIH, NIAID. A.B. thanks Unilever for funding.
PY - 2014/3/3
Y1 - 2014/3/3
N2 - 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.
AB - 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.
KW - biofragments, cytochrome P450, ligand binding, protein models, tuberculosis
U2 - 10.1002/cbic.201300697
DO - 10.1002/cbic.201300697
M3 - Article
SN - 1439-7633
VL - 15
SP - 549
EP - 555
JO - CHEMBIOCHEM
JF - CHEMBIOCHEM
IS - 4
ER -