Center for Structural Genomics of Infectious Diseases

Chicago Ridge, IL, United States

Center for Structural Genomics of Infectious Diseases

Chicago Ridge, IL, United States
Time filter
Source Type

News Article | April 25, 2017

CHICAGO --- An international team of scientists, led by Northwestern University Feinberg School of Medicine, has determined the 3-D atomic structure of more than 1,000 proteins that are potential drug and vaccine targets, to combat some of the world's most dangerous emerging and re-emerging infectious diseases. These experimentally determined structures have been deposited into the World-Wide Protein Data Bank, an archive supported by the National Institutes of Health (NIH), and are freely available to the scientific community. The 3-D structures help expedite drug and vaccine research and advance the understanding of pathogens and organisms causing infectious disease. "Almost 50 percent of the structures that we have deposited in the Protein Data Bank are proteins that were requested by scientific investigators from around the world," said Feinberg's Wayne Anderson, PhD, director of the project. "The NIH has also requested us to work on proteins for potential drug targets or vaccine candidates for many diseases, such as the Ebola virus, the Zika virus and antibiotic-resistant bacteria. We have determined several key structures from these priority organisms and published the results in high-impact journals such as Nature and Cell." This milestone effort, funded by two five-year contracts from the National Institute of Allergy and Infectious Diseases (NIAID), totaling a budget of $57.7 million, represents a decade of work by the Center for Structural Genomics of Infectious Diseases (CSGID) at Feinberg, led by Anderson in partnership with these institutions: Before work begins on a targeted protein, a board appointed by the NIH examines each request. Once approved, the protein must be cloned, expressed and crystallized, and then X-ray diffraction data is collected at the Advanced Photon Source at Argonne National Laboratory. This data defines the location of each of the hundreds or even thousands of atoms to generate 3-D models of the structures that can be analyzed with graphics software. Each institution in the Center has an area of expertise it contributes to the project, working in parallel on many requests at once. Until recently the process of determining the 3-D structure of a protein took many months or even years to complete, but advances in technology, such as the Advanced Photon Source, and upgrades to computational hardware and software has dramatically accelerated the process. The Seattle Structural Genomics Center for Infectious Disease, a similar center funded by NIAID, is also on track to complete 1,000 3-D protein structures soon. Browse all of the structures deposited by the CSGID. Anyone in the scientific community interested in requesting the determination of structures of proteins from pathogens in the NIAID Category A-C priority lists or organisms causing emerging and re-emerging infectious diseases, can submit requests to the Center's web portal. As part of the services offered to the scientific community, the CSGID can also provide expression clones and purified proteins, free of charge. This project has been supported by federal funds from the NIAID, NIH, Department of Health and Human Services, under contract numbers HHSN272200700058C and HHSN272201200026C

Smith J.M.,Johns Hopkins University | Warrington N.V.,Northern Arizona University | Vierling R.J.,Johns Hopkins University | Kuhn M.L.,Center for Structural Genomics of Infectious Diseases | And 3 more authors.
Journal of Antibiotics | Year: 2014

The unique methylerythritol phosphate pathway for isoprenoid biosynthesis is essential in most bacterial pathogens. The first enzyme in this pathway, 1-deoxy-D-xylulose 5-phosphate (DXP) synthase, catalyzes a distinct thiamin diphosphate (ThDP)-dependent reaction to form DXP from D-glyceraldehyde 3-phosphate (D-GAP) and pyruvate and represents a potential anti-infective drug target. We have previously demonstrated that the unnatural bisubstrate analog, butylacetylphosphonate (BAP), exhibits selective inhibition of Escherichia coli DXP synthase over mammalian ThDP-dependent enzymes. Here, we report the selective inhibition by BAP against recombinant DXP synthase homologs from Mycobacterium tuberculosis, Yersinia pestis and Salmonella enterica. We also demonstrate antimicrobial activity of BAP against both Gram-negative and Gram-positive strains (including E. coli, S. enterica and Bacillus anthracis), and several clinically isolated pathogens. Our results suggest a mechanism of action involving inhibition of DXP synthase and show that BAP acts synergistically with established antimicrobial agents, highlighting a potential strategy to combat emerging resistance in bacterial pathogens. © 2014 Japan Antibiotics Research Association.

Meziane-Cherif D.,Institute Pasteur Paris | Stogios P.J.,University of Toronto | Stogios P.J.,Center for Structural Genomics of Infectious Diseases | Evdokimova E.,University of Toronto | And 6 more authors.
mBio | Year: 2015

Vancomycin resistance in Gram-positive bacteria results from the replacement of the D-alanyl–D-alanine target of peptidoglycan precursors with D-alanyl–D-lactate or D-alanyl–D-serine (D-Ala-D-Ser), to which vancomycin has low binding affinity. VanT is one of the proteins required for the production of D-Ala-D-Ser-terminating precursors by converting L-Ser to D-Ser. VanT is composed of two domains, an N-terminal membrane-bound domain, likely involved in L-Ser uptake, and a C-terminal cytoplasmic catalytic domain which is related to bacterial alanine racemases. To gain insight into the molecular function of VanT, the crystal structure of the catalytic domain of VanTG from VanG-type resistant Enterococcus faecalis BM4518 was determined. The structure showed significant similarity to type III pyridoxal 5=-phosphate (PLP)-dependent alanine racemases, which are essential for peptidoglycan synthesis. Comparative structural analysis between VanTG and alanine racemases as well as site-directed mutagenesis identified three specific active site positions centered around Asn696 which are responsible for the L-amino acid specificity. This analysis also suggested that VanT racemases evolved from regular alanine racemases by acquiring additional selectivity toward serine while preserving that for alanine. The 4-fold-lower relative catalytic efficiency of VanTG against L-Ser versus L-Ala implied that this enzyme relies on its membrane-bound domain for L-Ser transport to increase the overall rate of D-Ser production. These findings illustrate how vancomycin pressure selected for molecular adaptation of a housekeeping enzyme to a bifunctional enzyme to allow for peptidoglycan remodeling, a strategy increasingly observed in antibiotic-resistant bacteria. IMPORTANCE Vancomycin is one of the drugs of last resort against Gram-positive antibiotic-resistant pathogens. However, bacteria have evolved a sophisticated mechanism which remodels the drug target, the D-alanine ending precursors in cell wall synthesis, into precursors terminating with D-lactate or D-serine, to which vancomycin has less affinity. D-Ser is synthesized by VanT serine racemase, which has two unusual characteristics: (i) it is one of the few serine racemases identified in bacteria and (ii) it contains a membrane-bound domain involved in L-Ser uptake. The structure of the catalytic domain of VanTG showed high similarity to alanine racemases, and we identified three specific active site substitutions responsible for L-Ser specificity. The data provide the molecular basis for VanT evolution to a bifunctional enzyme coordinating both transport and racemization. Our findings also illustrate the evolution of the essential alanine racemase into a vancomycin resistance enzyme in response to antibiotic pressure. © 2015 Meziane-Cherif et al.

Cox G.,McMaster University | Stogios P.J.,University of Toronto | Stogios P.J.,Center for Structural Genomics of Infectious Diseases | Savchenko A.,University of Toronto | And 2 more authors.
mBio | Year: 2015

The aminoglycosides are highly effective broad-spectrum antimicrobial agents. However, their efficacy is diminished due to enzyme-mediated covalent modification, which reduces affinity of the drug for the target ribosome. One of the most prevalent aminoglycoside resistance enzymes in Gram-negative pathogens is the adenylyltransferase ANT(2″)-Ia, which confers resistance to gentamicin, tobramycin, and kanamycin. Despite the importance of this enzyme in drug resistance, its structure and molecular mechanism have been elusive. This study describes the structural and mechanistic basis for adenylylation of aminoglycosides by the ANT(2″)-Ia enzyme. ANT(2″)-Ia confers resistance by magnesium-dependent transfer of a nucleoside monophosphate (AMP) to the 2″-hydroxyl of aminoglycoside substrates containing a 2-deoxystreptamine core. The catalyzed reaction follows a direct AMP transfer mechanism from ATP to the substrate antibiotic. Central to catalysis is the coordination of two Mg2″ ions, positioning of the modifiable substrate ring, and the presence of a catalytic base (Asp86). Comparative structural analysis revealed that ANT(2″)-Ia has a two-domain structure with an N-terminal active-site architecture that is conserved among other antibiotic nucleotidyltransferases, including Lnu(A), LinB, ANT(4=)-Ia, ANT(4″)-Ib, and ANT(6)-Ia. There is also similarity between the nucleotidyltransferase fold of ANT(2″)-Ia and DNA polymerase β. This similarity is consistent with evolution from a common ancestor, with the nucleotidyltransferase fold having adapted for activity against chemically distinct molecules. IMPORTANCE To successfully manage the threat associated with multidrug-resistant infectious diseases, innovative therapeutic strategies need to be developed. One such approach involves the enhancement or potentiation of existing antibiotics against resistant strains of bacteria. The reduction in clinical usefulness of the aminoglycosides is a particular problem among Gramnegative human pathogens, since there are very few therapeutic options for infections caused by these organisms. In order to successfully circumvent or inhibit the activity of aminoglycoside-modifying enzymes, and to thus rejuvenate the activity of the aminoglycoside antibiotics against Gram-negative pathogens, structural and mechanistic information is crucial. This study reveals the structure of a clinically prevalent aminoglycoside resistance enzyme [ANT(2″)-Ia] and depicts the molecular basis underlying modification of antibiotic substrates. Combined, these findings provide the groundwork for the development of broadspectrum inhibitors against antibiotic nucleotidyltransferases. © 2015 Cox et al.

Wlodawer A.,NCI Inc | Minor W.,University of Virginia | Minor W.,Midwest Center for Structural Genomics | Minor W.,Center for Structural Genomics of Infectious Diseases | And 2 more authors.
FEBS Journal | Year: 2013

The number of macromolecular structures deposited in the Protein Data Bank now approaches 100 000, with the vast majority of them determined by crystallographic methods. Thousands of papers describing such structures have been published in the scientific literature, and 20 Nobel Prizes in chemistry or medicine have been awarded for discoveries based on macromolecular crystallography. New hardware and software tools have made crystallography appear to be an almost routine (but still far from being analytical) technique and many structures are now being determined by scientists with very limited experience in the practical aspects of the field. However, this apparent ease is sometimes illusory and proper procedures need to be followed to maintain high standards of structure quality. In addition, many noncrystallographers may have problems with the critical evaluation and interpretation of structural results published in the scientific literature. The present review provides an outline of the technical aspects of crystallography for less experienced practitioners, as well as information that might be useful for users of macromolecular structures, aiming to show them how to interpret (but not overinterpret) the information present in the coordinate files and in their description. A discussion of the extent of information that can be gleaned from the atomic coordinates of structures solved at different resolution is provided, as well as problems and pitfalls encountered in structure determination and interpretation. This review, addressed to the less experienced macromolecular crystallographers and to users of biological structures, provides an outline of the technical aspects of crystallography, and discusses common problems and pitfalls encountered during structure determination and interpretation. It includes tips on how to interpret, but not overinterpret, the information present in the coordinate files and in their description. © 2013 FEBS.

Chruszcz M.,University of Virginia | Chruszcz M.,Center for Structural Genomics of Infectious Diseases | Chruszcz M.,Midwest Center for Structural Genomics | Domagalski M.,University of Virginia | And 9 more authors.
Current Opinion in Structural Biology | Year: 2010

Structural genomics (SG) programs have developed during the last decade many novel methodologies for faster and more accurate structure determination. These new tools and approaches led to the determination of thousands of protein structures. The generation of enormous amounts of experimental data resulted in significant improvements in the understanding of many biological processes at molecular levels. However, the amount of data collected so far is so large that traditional analysis methods are limiting the rate of extraction of biological and biochemical information from 3D models. This situation has prompted us to review the challenges that remain unmet by SG, as well as the areas in which the potential impact of SG could exceed what has been achieved so far. © 2010 Elsevier Ltd.

Kuhn M.L.,Center for Structural Genomics of Infectious Diseases | Majorek K.A.,University of Virginia | Minor W.,University of Virginia | Anderson W.F.,Center for Structural Genomics of Infectious Diseases
Protein Science | Year: 2013

Due to a combination of efforts from individual laboratories and structural genomics centers, there has been a surge in the number of members of the Gcn5-related acetyltransferasesuperfamily that have been structurally determined within the past decade. Although the number of three-dimensional structures is increasing steadily, we know little about the individual functions of these enzymes. Part of the difficulty in assigning functions for members of this superfamily is the lack of information regarding how substrates bind to the active site of the protein. The majority of the structures do not show ligand bound in the active site, and since the substrate-binding domain is not strictly conserved, it is difficult to predict the function based on structure alone. Additionally, the enzymes are capable of acetylating a wide variety of metabolites and many may exhibit promiscuity regarding their ability to acetylate multiple classes of substrates, possibly having multiple functions for the same enzyme. Herein, we present an approach to identify potential substrates for previously uncharacterized members of the Gcn5-related acetyltransferase superfamily using a variety of metabolites including polyamines, amino acids, antibiotics, peptides, vitamins, catecholamines, and other metabolites. We have identified potential substrates for eight bacterial enzymes of this superfamily. This information will be used to further structurally and functionally characterize them. © 2012 The Protein Society.

News Article | November 2, 2015

Tuberculosis, caused by Mycobacterium tuberculosis bacteria, has proved incredibly stubborn even in the age of powerful antibiotics, infecting about one third of all people worldwide. Treatment can take up to nine months. It has stealth properties that protect it from antibiotics; it can hide inside human cells, avoiding the body's immune system while it waits for the opportune moment to multiply; and it's very resourceful at acquiring resistance. "What we have now may not work in a few years," said Andrzej Joachimiak, an Argonne Distinguished Fellow, head of the Structural Biology Center, co-principal investigator at the Center for Structural Genomics of Infectious Diseases and a corresponding author on the new study. In order to make new drugs, researchers need to search through the thousands of proteins in the bacterial world to find one that does something so important the bacterium can't live without it—and then make a little block to match. One such entry point might be IMPDH (inosine-5?-monophosphate dehydrogenase), which is part of a cellular process that controls the making of guanine nucleotides, one of the building blocks for DNA and RNA. It's so essential that virtually all living organisms, including human and bacterial pathogens, have versions of it. "What we discovered earlier this year is that the human and bacterial versions bind molecules differently," Joachimiak said. "This is very important for finding a molecule to build a drug around—you don't want to inhibit a human enzyme, just the pathogen one." Researchers have been interested in the mycobacterium IMPDH enzyme as a drug target for years, Joachimiak said, but haven't been able to produce it well enough to study it. The team observed that one part of the enzyme's structure was particularly wobbly, so they engineered a version without it using resources at the Advanced Protein Characterization Facility and then then determined the structure employing synchrotron protein crystallography at the Advanced Photon Source, a DOE Office of Science User Facility (both at Argonne). The modified version functions very similarly to the original, Joachimiak said, but is much easier to purify and crystallize for study. Brandeis University professor Lizbeth Hedstrom and University of Minnesota professor Courtney Aldrich, two of the study's other research collaborators, had identified several inhibitor molecules that bind to IMPDH, and thus might be a starting point for a drug—but they couldn't be imaged while interacting with the enzyme. The new engineered enzyme allowed them to capture the structures of Hedstrom's and Aldrich's inhibitors in action, locked with IMPDH. Helena Boshoff at the National Institute of Allergies and Infectious Diseases performed complementary studies showing that these inhibitors do in fact efficiently block mycobacterium growth. The new structures were deposited into the Protein Data Bank for continued study. Explore further: Cancer drug target is promising lead for new TB treatments More information: Magdalena Makowska-Grzyska et al. Mycobacterium tuberculosis IMPDH in Complexes with Substrates, Products and Antitubercular Compounds, PLOS ONE (2015). DOI: 10.1371/journal.pone.0138976

Light S.H.,Center for Structural Genomics of Infectious Diseases | Light S.H.,Northwestern University | Minasov G.,Center for Structural Genomics of Infectious Diseases | Minasov G.,Northwestern University | And 4 more authors.
Acta Crystallographica Section D: Biological Crystallography | Year: 2014

The Bürgi-Dunitz angle (αBD) describes the trajectory of approach of a nucleophile to an electrophile. The adoption of a stereoelectronically favorable αBD can necessitate significant reactive-group repositioning over the course of bond formation. In the context of enzyme catalysis, interactions with the protein constrain substrate rotation, which could necessitate structural transformations during bond formation. To probe this theoretical framework vis-à-vis biocatalysis, Schiff-base formation was analysed in Francisella tularensis trans-aldolase (TAL). Crystal structures of wild-type and Lys→Met mutant TAL in covalent and noncovalent complexes with fructose 6-phosphate and sedoheptulose 7-phosphate clarify the mechanism of catalysis and reveal that substrate keto moieties undergo significant conformational changes during Schiff-base formation. Structural changes compelled by the trajectory considerations discussed here bear relevance to bond formation in a variety of constrained enzymic/engineered systems and can inform the design of covalent therapeutics. © 2014 International Union of Crystallography.

Shakya T.,McMaster University | Stogios P.J.,University of Toronto | Stogios P.J.,Center for Structural Genomics of Infectious Diseases | Waglechner N.,McMaster University | And 8 more authors.
Chemistry and Biology | Year: 2011

Kinase-mediated resistance to antibiotics is a significant clinical challenge. These enzymes share a common protein fold characteristic of Ser/Thr/Tyr protein kinases. We screened 14 antibiotic resistance kinases against 80 chemically diverse protein kinase inhibitors to map resistance kinase chemical space. The screens identified molecules with both broad and narrow inhibition profiles, proving that protein kinase inhibitors offer privileged chemical matter with the potential to block antibiotic resistance. One example is the flavonol quercetin, which inhibited a number of resistance kinases in vitro and in vivo. This activity was rationalized by determination of the crystal structure of the aminoglycoside kinase APH(2″)-IVa in complex with quercetin and its antibiotic substrate kanamycin. Our data demonstrate that protein kinase inhibitors offer chemical scaffolds that can block antibiotic resistance, providing leads for co-drug design. © 2011 Elsevier Ltd. All Rights Reserved.

Loading Center for Structural Genomics of Infectious Diseases collaborators
Loading Center for Structural Genomics of Infectious Diseases collaborators