title: A novel cofactor-binding mode in bacterial IMP dehydrogenases explains inhibitor selectivity.
abstract: The steadily rising frequency of emerging diseases and antibiotic resistance creates an urgent need for new drugs and targets. Inosine 5'-monophosphate dehydrogenase (IMP dehydrogenase or IMPDH) is a promising target for the development of new antimicrobial agents. IMPDH catalyzes the oxidation of IMP to XMP with the concomitant reduction of NAD(+), which is the pivotal step in the biosynthesis of guanine nucleotides. Potent inhibitors of bacterial IMPDHs have been identified that bind in a structurally distinct pocket that is absent in eukaryotic IMPDHs. The physiological role of this pocket was not understood. Here, we report the structures of complexes with different classes of inhibitors of Bacillus anthracis, Campylobacter jejuni, and Clostridium perfringens IMPDHs. These structures in combination with inhibition studies provide important insights into the interactions that modulate selectivity and potency. We also present two structures of the Vibrio cholerae IMPDH in complex with IMP/NAD(+) and XMP/NAD(+). In both structures, the cofactor assumes a dramatically different conformation than reported previously for eukaryotic IMPDHs and other dehydrogenases, with the major change observed for the position of the NAD(+) adenosine moiety. More importantly, this new NAD(+)-binding site involves the same pocket that is utilized by the inhibitors. Thus, the bacterial IMPDH-specific NAD(+)-binding mode helps to rationalize the conformation adopted by several classes of prokaryotic IMPDH inhibitors. These findings offer a potential strategy for further ligand optimization.
authors.affiliation: From the Center for Structural Genomics of Infectious Diseases, Computational Institute, University of Chicago, Chicago, Illinois 60637.
authors.forename: Magdalena
authors.initials: M
authors.lastname: Makowska-Grzyska
authors.affiliation: From the Center for Structural Genomics of Infectious Diseases, the Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois 60439, and Computational Institute, University of Chicago, Chicago, Illinois 60637.
authors.forename: Youngchang
authors.initials: Y
authors.lastname: Kim
authors.affiliation: From the Center for Structural Genomics of Infectious Diseases, Computational Institute, University of Chicago, Chicago, Illinois 60637.
authors.forename: Natalia
authors.initials: N
authors.lastname: Maltseva
authors.affiliation: From the Center for Structural Genomics of Infectious Diseases, the Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois 60439, and Computational Institute, University of Chicago, Chicago, Illinois 60637.
authors.forename: Jerzy
authors.initials: J
authors.lastname: Osipiuk
authors.affiliation: From the Center for Structural Genomics of Infectious Diseases, Computational Institute, University of Chicago, Chicago, Illinois 60637.
authors.forename: Minyi
authors.initials: M
authors.lastname: Gu
authors.affiliation: the Departments of Biology and.
authors.forename: Minjia
authors.initials: M
authors.lastname: Zhang
authors.affiliation: the Departments of Biology and.
authors.forename: Kavitha
authors.initials: K
authors.lastname: Mandapati
authors.affiliation: the Departments of Biology and.
authors.forename: Deviprasad R
authors.initials: DR
authors.lastname: Gollapalli
authors.affiliation: the Departments of Biology and.
authors.forename: Suresh Kumar
authors.initials: SK
authors.lastname: Gorla
authors.affiliation: the Departments of Biology and Chemistry, Brandeis University, Waltham, Massachusetts 024549110 hedstrom@brandeis.edu.
authors.forename: Lizbeth
authors.initials: L
authors.lastname: Hedstrom
authors.affiliation: From the Center for Structural Genomics of Infectious Diseases, the Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois 60439, and Computational Institute, University of Chicago, Chicago, Illinois 60637, andrzejj@anl.gov.
authors.forename: Andrzej
authors.initials: A
authors.lastname: Joachimiak
mesh_terms: D000595:Amino Acid Sequence; D000890:Anti-Infective Agents / Q000737:chemistry / Q000494:pharmacology*; D001408:Bacillus anthracis / Q000187:drug effects / Q000201:enzymology / Q000235:genetics; D001426:Bacterial Proteins / Q000037:antagonists & inhibitors* / Q000235:genetics / Q000378:metabolism; D016123:Campylobacter jejuni / Q000187:drug effects / Q000201:enzymology / Q000235:genetics; D003016:Clostridium perfringens / Q000187:drug effects / Q000201:enzymology / Q000235:genetics; D018360:Crystallography, X-Ray; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000494:pharmacology*; D007168:IMP Dehydrogenase / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000235:genetics; D007700:Kinetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D009154:Mutation; D011485:Protein Binding / Q000187:drug effects; D017434:Protein Structure, Tertiary; D017386:Sequence Homology, Amino Acid
chemical_list: D000890:Anti-Infective Agents; D001426:Bacterial Proteins; D004791:Enzyme Inhibitors; D007168:IMP Dehydrogenase
keywords: Antibacterial; Antibiotic Resistance; Cofactor-binding Site; Cryptosporidium parvum-selective Inhibitors; Enzyme Inhibitor; Inosine 5′-Monophosphate Dehydrogenase; Ligand-binding Protein; Microbial Pathogenesis; Nicotinamide Adenine Dinucleotide (NAD)