TY - JOUR
T1 - Spectroscopic and Computational Investigations of Ligand Binding to IspH
T2 - Discovery of Non-diphosphate Inhibitors
AU - O'Dowd, Bing
AU - Williams, Sarah
AU - Wang, Hongxin
AU - No, Joo Hwan
AU - Rao, Guodong
AU - Wang, Weixue
AU - McCammon, J. Andrew
AU - Cramer, Stephen P.
AU - Oldfield, Eric
N1 - Funding Information:
This work was supported by the National Institutes of Health (NIH; grants GM065307 to E.O. and GM-65440 to S.P.C.) and by the Department of Energy (DOE) Office of Biological and Environmental Research (S.P.C.). NRVS measurements were performed at the Advanced Photon Source (APS) (proposals 39192/ 43032) and at SPring-8 (2015B1134). The APS is supported by the DOE Office of Basic Energy Sciences. The EPR instrumentation was supported by NIH grants S10-RR15878 and S10-RR025438. Work at University of California San Diego (UCSD) was supported by NIH, National Science Foundation (NSF), Howard Hughes Medical Institute (HHMI), National Biomedical Computation Resource (NBCR), and San Diego Supercomputer Center (SDSC). W.W. was supported by a Predoctoral Fellowship from the American Heart Association, Midwest Affiliate (award 10PRE4430022). We would like to thank Drs. Jiyong Zhao, Michael Hu and Esen E. Alp at APS for assistance with the NRVS measurements, and Mark J. Nilges for assistance with the EPR measurements.
Publisher Copyright:
© 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
PY - 2017/5/18
Y1 - 2017/5/18
N2 - Isoprenoid biosynthesis is an important area for anti-infective drug development. One isoprenoid target is (E)-1-hydroxy-2-methyl-but-2-enyl 4-diphosphate (HMBPP) reductase (IspH), which forms isopentenyl diphosphate and dimethylallyl diphosphate from HMBPP in a 2H+/2e− reduction. IspH contains a 4 Fe−4 S cluster, and in this work, we first investigated how small molecules bound to the cluster by using HYSCORE and NRVS spectroscopies. The results of these, as well as other structural and spectroscopic investigations, led to the conclusion that, in most cases, ligands bound to IspH 4 Fe−4 S clusters by η1 coordination, forming tetrahedral geometries at the unique fourth Fe, ligand side chains preventing further ligand (e.g., H2O, O2) binding. Based on these ideas, we used in silico methods to find drug-like inhibitors that might occupy the HMBPP substrate binding pocket and bind to Fe, leading to the discovery of a barbituric acid analogue with a Ki value of ≈500 nm against Pseudomonas aeruginosa IspH.
AB - Isoprenoid biosynthesis is an important area for anti-infective drug development. One isoprenoid target is (E)-1-hydroxy-2-methyl-but-2-enyl 4-diphosphate (HMBPP) reductase (IspH), which forms isopentenyl diphosphate and dimethylallyl diphosphate from HMBPP in a 2H+/2e− reduction. IspH contains a 4 Fe−4 S cluster, and in this work, we first investigated how small molecules bound to the cluster by using HYSCORE and NRVS spectroscopies. The results of these, as well as other structural and spectroscopic investigations, led to the conclusion that, in most cases, ligands bound to IspH 4 Fe−4 S clusters by η1 coordination, forming tetrahedral geometries at the unique fourth Fe, ligand side chains preventing further ligand (e.g., H2O, O2) binding. Based on these ideas, we used in silico methods to find drug-like inhibitors that might occupy the HMBPP substrate binding pocket and bind to Fe, leading to the discovery of a barbituric acid analogue with a Ki value of ≈500 nm against Pseudomonas aeruginosa IspH.
KW - HYSCORE
KW - IspH
KW - NRVS
KW - in silico
KW - isoprenoid
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U2 - 10.1002/cbic.201700052
DO - 10.1002/cbic.201700052
M3 - Article
C2 - 28253432
AN - SCOPUS:85017616325
VL - 18
SP - 914
EP - 920
JO - ChemBioChem
JF - ChemBioChem
SN - 1439-4227
IS - 10
ER -