1
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Rodríguez-Hernández D, Fenwick MK, Zigweid R, Sankaran B, Myler PJ, Sunnerhagen P, Kaushansky A, Staker BL, Grøtli M. Exploring Subsite Selectivity within Plasmodium vivax N-Myristoyltransferase Using Pyrazole-Derived Inhibitors. J Med Chem 2024; 67:7312-7329. [PMID: 38680035 PMCID: PMC11089503 DOI: 10.1021/acs.jmedchem.4c00168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/09/2024] [Accepted: 04/19/2024] [Indexed: 05/01/2024]
Abstract
N-myristoyltransferase (NMT) is a promising antimalarial drug target. Despite biochemical similarities between Plasmodium vivax and human NMTs, our recent research demonstrated that high selectivity is achievable. Herein, we report PvNMT-inhibiting compounds aimed at identifying novel mechanisms of selectivity. Various functional groups are appended to a pyrazole moiety in the inhibitor to target a pocket formed beneath the peptide binding cleft. The inhibitor core group polarity, lipophilicity, and size are also varied to probe the water structure near a channel. Selectivity index values range from 0.8 to 125.3. Cocrystal structures of two selective compounds, determined at 1.97 and 2.43 Å, show that extensions bind the targeted pocket but with different stabilities. A bulky naphthalene moiety introduced into the core binds next to instead of displacing protein-bound waters, causing a shift in the inhibitor position and expanding the binding site. Our structure-activity data provide a conceptual foundation for guiding future inhibitor optimizations.
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Affiliation(s)
- Diego Rodríguez-Hernández
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, S-405 30 Gothenburg, Sweden
- Department
of Structural and Functional Biology, Synthetic Biology Laboratory,
Institute of Biology, University of Campinas, Campinas, SP 13083-862, Brazil
| | - Michael K. Fenwick
- Seattle
Structural Genomics Center for Infectious Disease, Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | - Rachael Zigweid
- Seattle
Structural Genomics Center for Infectious Disease, Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | - Banumathi Sankaran
- Molecular
Biophysics and Integrated Bioimaging, Berkeley Center for Structural
Biology, Advanced Light Source, Berkeley
National Laboratory, Berkeley, California 94720, United States
| | - Peter J. Myler
- Seattle
Structural Genomics Center for Infectious Disease, Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
- Department
of Pediatrics, University of Washington, Seattle, Washington 98195, United States
| | - Per Sunnerhagen
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, S-405 30 Gothenburg, Sweden
| | - Alexis Kaushansky
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
- Department
of Pediatrics, University of Washington, Seattle, Washington 98195, United States
| | - Bart L. Staker
- Seattle
Structural Genomics Center for Infectious Disease, Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | - Morten Grøtli
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, S-405 30 Gothenburg, Sweden
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2
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Ran X, Parikh P, Abendroth J, Arakaki TL, Clifton MC, Edwards TE, Lorimer DD, Mayclin S, Staker BL, Myler P, McLaughlin KJ. Structural and functional characterization of FabG4 from Mycolicibacterium smegmatis. Acta Crystallogr F Struct Biol Commun 2024; 80:82-91. [PMID: 38656226 PMCID: PMC11058512 DOI: 10.1107/s2053230x2400356x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 04/19/2024] [Indexed: 04/26/2024] Open
Abstract
The rise in antimicrobial resistance is a global health crisis and necessitates the development of novel strategies to treat infections. For example, in 2022 tuberculosis (TB) was the second leading infectious killer after COVID-19, with multi-drug-resistant strains of TB having an ∼40% fatality rate. Targeting essential biosynthetic pathways in pathogens has proven to be successful for the development of novel antimicrobial treatments. Fatty-acid synthesis (FAS) in bacteria proceeds via the type II pathway, which is substantially different from the type I pathway utilized in animals. This makes bacterial fatty-acid biosynthesis (Fab) enzymes appealing as drug targets. FabG is an essential FASII enzyme, and some bacteria, such as Mycobacterium tuberculosis, the causative agent of TB, harbor multiple homologs. FabG4 is a conserved, high-molecular-weight FabG (HMwFabG) that was first identified in M. tuberculosis and is distinct from the canonical low-molecular-weight FabG. Here, structural and functional analyses of Mycolicibacterium smegmatis FabG4, the third HMwFabG studied to date, are reported. Crystal structures of NAD+ and apo MsFabG4, along with kinetic analyses, show that MsFabG4 preferentially binds and uses NADH when reducing CoA substrates. As M. smegmatis is often used as a model organism for M. tuberculosis, these studies may aid the development of drugs to treat TB and add to the growing body of research that distinguish HMwFabGs from the archetypal low-molecular-weight FabG.
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Affiliation(s)
- Xinping Ran
- Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA
| | - Prashit Parikh
- Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), 307 Westlake Avenue North, Seattle, WA 98109, USA
- Beryllium Discovery Corporation, 7869 Day Road West, Bainbridge Island, WA 98110, USA
| | | | - Matthew C. Clifton
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), 307 Westlake Avenue North, Seattle, WA 98109, USA
- Beryllium Discovery Corporation, 7869 Day Road West, Bainbridge Island, WA 98110, USA
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), 307 Westlake Avenue North, Seattle, WA 98109, USA
- Beryllium Discovery Corporation, 7869 Day Road West, Bainbridge Island, WA 98110, USA
| | - Donald D. Lorimer
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), 307 Westlake Avenue North, Seattle, WA 98109, USA
- UCB Pharma, Bedford, Massachusetts, USA
| | | | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), 307 Westlake Avenue North, Seattle, WA 98109, USA
- Seattle Children’s Research Institute, University of Washington, Seattle, Washington, USA
| | - Peter Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), 307 Westlake Avenue North, Seattle, WA 98109, USA
- Seattle Children’s Research Institute, University of Washington, Seattle, Washington, USA
| | - Krystle J. McLaughlin
- Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA
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3
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Gilleran JA, Ashraf K, Delvillar M, Eck T, Fondekar R, Miller EB, Hutchinson A, Dong A, Seitova A, De Souza ML, Augeri D, Halabelian L, Siekierka J, Rotella DP, Gordon J, Childers WE, Grier MC, Staker BL, Roberge JY, Bhanot P. Structure-Activity Relationship of a Pyrrole Based Series of PfPKG Inhibitors as Anti-Malarials. J Med Chem 2024; 67:3467-3503. [PMID: 38372781 DOI: 10.1021/acs.jmedchem.3c01795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Controlling malaria requires new drugs against Plasmodium falciparum. The P. falciparum cGMP-dependent protein kinase (PfPKG) is a validated target whose inhibitors could block multiple steps of the parasite's life cycle. We defined the structure-activity relationship (SAR) of a pyrrole series for PfPKG inhibition. Key pharmacophores were modified to enable full exploration of chemical diversity and to gain knowledge about an ideal core scaffold. In vitro potency against recombinant PfPKG and human PKG were used to determine compound selectivity for the parasite enzyme. P. berghei sporozoites and P. falciparum asexual blood stages were used to assay multistage antiparasitic activity. Cellular specificity of compounds was evaluated using transgenic parasites expressing PfPKG carrying a substituted "gatekeeper" residue. The structure of PfPKG bound to an inhibitor was solved, and modeling using this structure together with computational tools was utilized to understand SAR and establish a rational strategy for subsequent lead optimization.
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Affiliation(s)
- John A Gilleran
- Rutgers Molecular Design and Synthesis Core, Office for Research, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Kutub Ashraf
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, 225 Warren Street, Newark, New Jersey 07103, United States
| | - Melvin Delvillar
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, 225 Warren Street, Newark, New Jersey 07103, United States
| | - Tyler Eck
- Department of Chemistry and Biochemistry and Sokol Institute of Pharmaceutical Life Sciences, Montclair State University, Montclair, New Jersey 07043, United States
| | - Raheel Fondekar
- Rutgers Molecular Design and Synthesis Core, Office for Research, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States
- Rutgers School of Pharmacy, 160 Frelinghuysen Road, Piscataway, New Jersey 08854, United States
| | - Edward B Miller
- Schrödinger, Inc., 1540 Broadway, 24th Floor, New York, New York 10036, United States
| | - Ashley Hutchinson
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Aiping Dong
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Alma Seitova
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Mariana Laureano De Souza
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, 225 Warren Street, Newark, New Jersey 07103, United States
| | - David Augeri
- Rutgers Molecular Design and Synthesis Core, Office for Research, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States
- Schrödinger, Inc., 1540 Broadway, 24th Floor, New York, New York 10036, United States
| | - Levon Halabelian
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - John Siekierka
- Department of Chemistry and Biochemistry and Sokol Institute of Pharmaceutical Life Sciences, Montclair State University, Montclair, New Jersey 07043, United States
| | - David P Rotella
- Department of Chemistry and Biochemistry and Sokol Institute of Pharmaceutical Life Sciences, Montclair State University, Montclair, New Jersey 07043, United States
| | - John Gordon
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, Pennsylvania 19140, United States
| | - Wayne E Childers
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, Pennsylvania 19140, United States
| | - Mark C Grier
- Rutgers Molecular Design and Synthesis Core, Office for Research, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington 98109, United States
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington 98109, United States
| | - Jacques Y Roberge
- Rutgers Molecular Design and Synthesis Core, Office for Research, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Purnima Bhanot
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, 225 Warren Street, Newark, New Jersey 07103, United States
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4
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Fenwick M, Reers AR, Liu Y, Zigweid R, Sankaran B, Shin J, Hulverson MA, Hammerson B, Fernández Álvaro E, Myler PJ, Kaushansky A, Van Voorhis WC, Fan E, Staker BL. Identification of and Structural Insights into Hit Compounds Targeting N-Myristoyltransferase for Cryptosporidium Drug Development. ACS Infect Dis 2023; 9:1821-1833. [PMID: 37722671 PMCID: PMC10580320 DOI: 10.1021/acsinfecdis.3c00151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Indexed: 09/20/2023]
Abstract
Each year, approximately 50,000 children under 5 die as a result of diarrhea caused by Cryptosporidium parvum, a protozoan parasite. There are currently no effective drugs or vaccines available to cure or prevent Cryptosporidium infection, and there are limited tools for identifying and validating targets for drug or vaccine development. We previously reported a high throughput screening (HTS) of a large compound library against Plasmodium N-myristoyltransferase (NMT), a validated drug target in multiple protozoan parasite species. To identify molecules that could be effective against Cryptosporidium, we counter-screened hits from the Plasmodium NMT HTS against Cryptosporidium NMT. We identified two potential hit compounds and validated them against CpNMT to determine if NMT might be an attractive drug target also for Cryptosporidium. We tested the compounds against Cryptosporidium using both cell-based and NMT enzymatic assays. We then determined the crystal structure of CpNMT bound to Myristoyl-Coenzyme A (MyrCoA) and structures of ternary complexes with MyrCoA and the hit compounds to identify the ligand binding modes. The binding site architectures display different conformational states in the presence of the two inhibitors and provide a basis for rational design of selective inhibitors.
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Affiliation(s)
- Michael
K. Fenwick
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
| | - Alexandra R. Reers
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | - Yi Liu
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Rachael Zigweid
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | - Banumathi Sankaran
- Berkeley
Center for Structural Biology, Advanced Light Source, Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Janis Shin
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | - Matthew A. Hulverson
- Center
for Emerging and Re-emerging Infectious Diseases, Division of Allergy
and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington 98109, United States
| | - Bradley Hammerson
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | | | - Peter J. Myler
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
- Department
of Global Health, University of Washington, Seattle, Washington 98195, United States
- Department
of Pediatrics, University of Washington, Seattle, Washington 98195, United States
| | - Alexis Kaushansky
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
- Center
for Emerging and Re-emerging Infectious Diseases, Division of Allergy
and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington 98109, United States
- Department
of Global Health, University of Washington, Seattle, Washington 98195, United States
| | - Wesley C. Van Voorhis
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Emerging and Re-emerging Infectious Diseases, Division of Allergy
and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington 98109, United States
| | - Erkang Fan
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Bart L. Staker
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
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5
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Moorefield J, Konuk Y, Norman JO, Abendroth J, Edwards TE, Lorimer DD, Mayclin SJ, Staker BL, Craig JK, Barett KF, Barrett LK, Van Voorhis WC, Myler PJ, McLaughlin KJ. Characterization of a family I inorganic pyrophosphatase from Legionella pneumophila Philadelphia 1. Acta Crystallogr F Struct Biol Commun 2023; 79:257-266. [PMID: 37728609 PMCID: PMC10565794 DOI: 10.1107/s2053230x23008002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/13/2023] [Indexed: 09/21/2023] Open
Abstract
Inorganic pyrophosphate (PPi) is generated as an intermediate or byproduct of many fundamental metabolic pathways, including DNA/RNA synthesis. The intracellular concentration of PPi must be regulated as buildup can inhibit many critical cellular processes. Inorganic pyrophosphatases (PPases) hydrolyze PPi into two orthophosphates (Pi), preventing the toxic accumulation of the PPi byproduct in cells and making Pi available for use in biosynthetic pathways. Here, the crystal structure of a family I inorganic pyrophosphatase from Legionella pneumophila is reported at 2.0 Å resolution. L. pneumophila PPase (LpPPase) adopts a homohexameric assembly and shares the oligonucleotide/oligosaccharide-binding (OB) β-barrel core fold common to many other bacterial family I PPases. LpPPase demonstrated hydrolytic activity against a general substrate, with Mg2+ being the preferred metal cofactor for catalysis. Legionnaires' disease is a severe respiratory infection caused primarily by L. pneumophila, and thus increased characterization of the L. pneumophila proteome is of interest.
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Affiliation(s)
- Julia Moorefield
- Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA
| | - Yagmur Konuk
- Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA
| | - Jordan O. Norman
- Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- UCB Biosciences, 7869 Day Road West, Bainbridge Island, WA 98110, USA
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- UCB Biosciences, 7869 Day Road West, Bainbridge Island, WA 98110, USA
| | - Donald D. Lorimer
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- UCB Biosciences, 7869 Day Road West, Bainbridge Island, WA 98110, USA
| | - Stephen J. Mayclin
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- UCB Biosciences, 7869 Day Road West, Bainbridge Island, WA 98110, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Seattle Children’s Research Institute, University of Washington, Seattle, Washington, USA
| | - Justin K. Craig
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Kayleigh F. Barett
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Lynn K. Barrett
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Wesley C. Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Seattle Children’s Research Institute, University of Washington, Seattle, Washington, USA
| | - Krystle J. McLaughlin
- Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA
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6
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Rodríguez-Hernández D, Vijayan K, Zigweid R, Fenwick MK, Sankaran B, Roobsoong W, Sattabongkot J, Glennon EKK, Myler PJ, Sunnerhagen P, Staker BL, Kaushansky A, Grøtli M. Identification of potent and selective N-myristoyltransferase inhibitors of Plasmodium vivax liver stage hypnozoites and schizonts. Nat Commun 2023; 14:5408. [PMID: 37669940 PMCID: PMC10480161 DOI: 10.1038/s41467-023-41119-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 08/22/2023] [Indexed: 09/07/2023] Open
Abstract
Drugs targeting multiple stages of the Plasmodium vivax life cycle are needed to reduce the health and economic burdens caused by malaria worldwide. N-myristoyltransferase (NMT) is an essential eukaryotic enzyme and a validated drug target for combating malaria. However, previous PvNMT inhibitors have failed due to their low selectivity over human NMTs. Herein, we apply a structure-guided hybridization approach combining chemical moieties of previously reported NMT inhibitors to develop the next generation of PvNMT inhibitors. A high-resolution crystal structure of PvNMT bound to a representative selective hybrid compound reveals a unique binding site architecture that includes a selective conformation of a key tyrosine residue. The hybridized compounds significantly decrease P. falciparum blood-stage parasite load and consistently exhibit dose-dependent inhibition of P. vivax liver stage schizonts and hypnozoites. Our data demonstrate that hybridized NMT inhibitors can be multistage antimalarials, targeting dormant and developing forms of liver and blood stage.
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Affiliation(s)
- Diego Rodríguez-Hernández
- Department of Chemistry and Molecular Biology, University of Gothenburg; S-405 30, Gothenburg, Sweden
- Department of Chemistry, University of Bergen, Allegaten 41, NO-5007, Bergen, Norway
| | - Kamalakannan Vijayan
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, 98109, USA
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, 695551, India
| | - Rachael Zigweid
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, 98109, USA
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, 98109, USA
| | - Michael K Fenwick
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, 98109, USA
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, 98109, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Advanced Light Source; Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Wanlapa Roobsoong
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Elizabeth K K Glennon
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, 98109, USA
| | - Peter J Myler
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, 98109, USA
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, 98109, USA
- Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA
| | - Per Sunnerhagen
- Department of Chemistry and Molecular Biology, University of Gothenburg; S-405 30, Gothenburg, Sweden
| | - Bart L Staker
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, 98109, USA
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, 98109, USA
| | - Alexis Kaushansky
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, 98109, USA.
- Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA.
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg; S-405 30, Gothenburg, Sweden.
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7
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Gu Y, Liu M, Staker BL, Buchko GW, Quinn RJ. Drug-Repurposing Screening Identifies a Gallic Acid Binding Site on SARS-CoV-2 Non-structural Protein 7. ACS Pharmacol Transl Sci 2023; 6:578-586. [PMID: 37082753 PMCID: PMC10111621 DOI: 10.1021/acsptsci.2c00225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Indexed: 03/09/2023]
Abstract
SARS-CoV-2 is the agent responsible for acute respiratory disease COVID-19 and the global pandemic initiated in early 2020. While the record-breaking development of vaccines has assisted the control of COVID-19, there is still a pressing global demand for antiviral drugs to halt the destructive impact of this disease. Repurposing clinically approved drugs provides an opportunity to expediate SARS-CoV-2 treatments into the clinic. In an effort to facilitate drug repurposing, an FDA-approved drug library containing 2400 compounds was screened against the SARS-CoV-2 non-structural protein 7 (nsp7) using a native mass spectrometry-based assay. Nsp7 is one of the components of the SARS-CoV-2 replication/transcription complex essential for optimal viral replication, perhaps serving to off-load RNA from nsp8. From this library, gallic acid was identified as a compound that bound tightly to nsp7, with an estimated K d of 15 μM. NMR chemical shift perturbation experiments were used to map the ligand-binding surface of gallic acid on nsp7, indicating that the compound bound to a surface pocket centered on one of the protein's four α-helices (α2). The identification of the gallic acid-binding site on nsp7 may allow development of a SARS-CoV-2 therapeutic via artificial-intelligence-based virtual docking and other strategies.
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Affiliation(s)
- Yushu Gu
- Griffith
Institute for Drug Discovery, Griffith University, Brisbane 4111, Australia
| | - Miaomiao Liu
- Griffith
Institute for Drug Discovery, Griffith University, Brisbane 4111, Australia
| | - Bart L. Staker
- Seattle
Children’s Research Institute, Seattle, Washington 98101, United States
| | - Garry W. Buchko
- Earth
and Biological Sciences Directorate, Pacific
Northwest National Laboratory, Richland, Washington 99354, United States
- School of
Molecular Biosciences, Washington State
University, Pullman, Washington 99164, United States
| | - Ronald J. Quinn
- Griffith
Institute for Drug Discovery, Griffith University, Brisbane 4111, Australia
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8
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Gihaz S, Gareiss P, Choi JY, Renard I, Pal AC, Surovsteva Y, Chiu JE, Thekkiniath J, Plummer M, Hungerford W, Montgomery ML, Hosford A, Adams EM, Lightfoot JD, Fox D, Ojo KK, Staker BL, Fuller K, Ben Mamoun C. High-resolution crystal structure and chemical screening reveal pantothenate kinase as a new target for antifungal development. Structure 2022; 30:1494-1507.e6. [PMID: 36167065 PMCID: PMC10042587 DOI: 10.1016/j.str.2022.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 07/28/2022] [Accepted: 09/01/2022] [Indexed: 01/22/2023]
Abstract
Fungal infections are the leading cause of mortality by eukaryotic pathogens, with an estimated 150 million severe life-threatening cases and 1.7 million deaths reported annually. The rapid emergence of multidrug-resistant fungal isolates highlights the urgent need for new drugs with new mechanisms of action. In fungi, pantothenate phosphorylation, catalyzed by PanK enzyme, is the first step in the utilization of pantothenic acid and coenzyme A biosynthesis. In all fungi sequenced so far, this enzyme is encoded by a single PanK gene. Here, we report the crystal structure of a fungal PanK alone as well as with high-affinity inhibitors from a single chemotype identified through a high-throughput chemical screen. Structural, biochemical, and functional analyses revealed mechanisms governing substrate and ligand binding, dimerization, and catalysis and helped identify new compounds that inhibit the growth of several Candida species. The data validate PanK as a promising target for antifungal drug development.
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Affiliation(s)
- Shalev Gihaz
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Peter Gareiss
- Yale Center for Molecular Discovery, Yale West Campus, West Haven, CT 06516, USA
| | - Jae-Yeon Choi
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Isaline Renard
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Anasuya Chattopadhyay Pal
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yulia Surovsteva
- Yale Center for Molecular Discovery, Yale West Campus, West Haven, CT 06516, USA
| | - Joy E Chiu
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jose Thekkiniath
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Mark Plummer
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - William Hungerford
- Yale Center for Molecular Discovery, Yale West Campus, West Haven, CT 06516, USA
| | - Micaela L Montgomery
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Alanah Hosford
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Emily M Adams
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Jorge D Lightfoot
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - David Fox
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA; UCB Pharma, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Kayode K Ojo
- Center for Emerging & Re-emerging Infectious Disease, Division of Allergy & Infectious Disease, Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Kevin Fuller
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Choukri Ben Mamoun
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA.
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9
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Xie B, Maker A, Priest AV, Dranow DM, Phan JN, Edwards TE, Staker BL, Myler PJ, Gumbiner BM, Sivasankar S. Molecular mechanism for strengthening E-cadherin adhesion using a monoclonal antibody. Proc Natl Acad Sci U S A 2022; 119:e2204473119. [PMID: 35921442 PMCID: PMC9371698 DOI: 10.1073/pnas.2204473119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 07/07/2022] [Indexed: 12/14/2022] Open
Abstract
E-cadherin (Ecad) is an essential cell-cell adhesion protein with tumor suppression properties. The adhesive state of Ecad can be modified by the monoclonal antibody 19A11, which has potential applications in reducing cancer metastasis. Using X-ray crystallography, we determine the structure of 19A11 Fab bound to Ecad and show that the antibody binds to the first extracellular domain of Ecad near its primary adhesive motif: the strand-swap dimer interface. Molecular dynamics simulations and single-molecule atomic force microscopy demonstrate that 19A11 interacts with Ecad in two distinct modes: one that strengthens the strand-swap dimer and one that does not alter adhesion. We show that adhesion is strengthened by the formation of a salt bridge between 19A11 and Ecad, which in turn stabilizes the swapped β-strand and its complementary binding pocket. Our results identify mechanistic principles for engineering antibodies to enhance Ecad adhesion.
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Affiliation(s)
- Bin Xie
- Biophysics Graduate Group, University of California, Davis, CA, 95616
- Department of Biomedical Engineering, University of California, Davis, CA, 95616
| | - Allison Maker
- Seattle Children’s Research Institute, Center for Developmental Biology and Regenerative Medicine, Seattle, WA, 98101
- Department of Biochemistry, University of Washington, Seattle, WA, 98195
| | - Andrew V. Priest
- Department of Biomedical Engineering, University of California, Davis, CA, 95616
| | - David M. Dranow
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, 98109
- UCB Pharma, Bainbridge Island, WA, 98110
| | - Jenny N. Phan
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, 98109
- UCB Pharma, Bainbridge Island, WA, 98110
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, 98109
- UCB Pharma, Bainbridge Island, WA, 98110
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, 98109
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, 98109
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, 98109
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, 98109
- Department of Pediatrics, University of Washington, Seattle, WA, 98195
| | - Barry M. Gumbiner
- Seattle Children’s Research Institute, Center for Developmental Biology and Regenerative Medicine, Seattle, WA, 98101
- Department of Biochemistry, University of Washington, Seattle, WA, 98195
- Department of Pediatrics, University of Washington, Seattle, WA, 98195
| | - Sanjeevi Sivasankar
- Biophysics Graduate Group, University of California, Davis, CA, 95616
- Department of Biomedical Engineering, University of California, Davis, CA, 95616
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10
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Gihaz S, Gareiss P, Choi J, Renard I, Chattopadhyay Pal A, Surovsteva Y, Chiu JE, Thekkiniath J, Plummer M, Hungerford W, Montgomery ML, Hosford A, Adams EM, Lightfoot JD, Fox D, Ojo KK, Staker BL, Fuller K, Ben Mamoun C. Targeting Pantothenate Kinase as an Effective Strategy for Antifungal Drug Development. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.l7671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Shalev Gihaz
- Section of Infectious Diseases‐ Department of Internal MedicineYale University School of MedicineNew HavenCT
| | | | - Jae‐Yeon Choi
- Section of Infectious Diseases‐ Department of Internal MedicineYale University School of MedicineNew HavenCT
| | - Isaline Renard
- Section of Infectious Diseases‐ Department of Internal MedicineYale University School of MedicineNew HavenCT
| | - Anasuya Chattopadhyay Pal
- Section of Infectious Diseases‐ Department of Internal MedicineYale University School of MedicineNew HavenCT
| | | | - Joy E. Chiu
- Section of Infectious Diseases‐ Department of Internal MedicineYale University School of MedicineNew HavenCT
| | - Jose Thekkiniath
- Section of Infectious Diseases‐ Department of Internal MedicineYale University School of MedicineNew HavenCT
| | | | | | - Micaela L. Montgomery
- Department of Microbiology and ImmunologyUniversity of Oklahoma Health Sciences Center‐ Department of Microbiology and ImmunologyOklahoma CityOK
| | - Alanah Hosford
- Department of Microbiology and ImmunologyUniversity of Oklahoma Health Sciences Center‐ Department of Microbiology and ImmunologyOklahoma CityOK
- Department of OphthalmologyUniversity of Oklahoma Health Sciences Center‐ Department of Microbiology and ImmunologyOklahoma CityOK
| | - Emily M. Adams
- Department of Microbiology and ImmunologyUniversity of Oklahoma Health Sciences Center‐ Department of Microbiology and ImmunologyOklahoma CityOK
- Department of OphthalmologyUniversity of Oklahoma Health Sciences Center‐ Department of Microbiology and ImmunologyOklahoma CityOK
| | - Jorge D. Lightfoot
- Department of Microbiology and ImmunologyUniversity of Oklahoma Health Sciences Center‐ Department of Microbiology and ImmunologyOklahoma CityOK
- Department of OphthalmologyUniversity of Oklahoma Health Sciences Center‐ Department of Microbiology and ImmunologyOklahoma CityOK
| | - David Fox
- Seattle Structural Genomics Center for Infectious DiseaseSeattleWA
- Center for Global Infectious Disease ResearchSeattle Structural Genomics Center for Infectious DiseaseSeattleWA
| | - Kayode K. Ojo
- Department of MedicineUniversity of WashingtonSeattleWA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious DiseaseSeattleWA
- Center for Global Infectious Disease ResearchSeattle Structural Genomics Center for Infectious DiseaseSeattleWA
| | - Kevin Fuller
- Department of Microbiology and ImmunologyUniversity of Oklahoma Health Sciences Center‐ Department of Microbiology and ImmunologyOklahoma CityOK
- Department of OphthalmologyUniversity of Oklahoma Health Sciences Center‐ Department of Microbiology and ImmunologyOklahoma CityOK
| | - Choukri Ben Mamoun
- Section of Infectious Diseases‐ Department of Internal MedicineYale University School of MedicineNew HavenCT
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11
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Maddy J, Staker BL, Subramanian S, Abendroth J, Edwards TE, Myler PJ, Hybiske K, Asojo OA. Crystal structure of an inorganic pyrophosphatase from Chlamydia trachomatis D/UW-3/Cx. Acta Crystallogr F Struct Biol Commun 2022; 78:135-142. [PMID: 35234139 PMCID: PMC8900733 DOI: 10.1107/s2053230x22002138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/23/2022] [Indexed: 11/11/2022] Open
Abstract
Chlamydia trachomatis is the leading cause of bacterial sexually transmitted infections globally and is one of the most commonly reported infections in the United States. There is a need to develop new therapeutics due to drug resistance and the failure of current treatments to clear persistent infections. Structures of potential C. trachomatis rational drug-discovery targets, including C. trachomatis inorganic pyrophosphatase (CtPPase), have been determined by the Seattle Structural Genomics Center for Infectious Disease. Inorganic pyrophosphatase hydrolyzes inorganic pyrophosphate during metabolism. Furthermore, bacterial inorganic pyrophosphatases have shown promise for therapeutic discovery. Here, a 2.2 Å resolution X-ray structure of CtPPase is reported. The crystal structure of CtPPase reveals shared structural features that may facilitate the repurposing of inhibitors identified for bacterial inorganic pyrophosphatases as starting points for new therapeutics for C. trachomatis.
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12
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Davidson J, Nicholas K, Young J, Conrady DG, Mayclin S, Subramanian S, Staker BL, Myler PJ, Asojo OA. Crystal structure of a putative short-chain dehydrogenase/reductase from Paraburkholderia xenovorans. Acta Crystallogr F Struct Biol Commun 2022; 78:25-30. [PMID: 34981772 PMCID: PMC8725002 DOI: 10.1107/s2053230x21012632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/28/2021] [Indexed: 11/22/2022] Open
Abstract
Paraburkholderia xenovorans degrades organic wastes, including polychlorinated biphenyls. The atomic structure of a putative dehydrogenase/reductase (SDR) from P. xenovorans (PxSDR) was determined in space group P21 at a resolution of 1.45 Å. PxSDR shares less than 37% sequence identity with any known structure and assembles as a prototypical SDR tetramer. As expected, there is some conformational flexibility and difference in the substrate-binding cavity, which explains the substrate specificity. Uniquely, the cofactor-binding cavity of PxSDR is not well conserved and differs from those of other SDRs. PxSDR has an additional seven amino acids that form an additional unique loop within the cofactor-binding cavity. Further studies are required to determine how these differences affect the enzymatic functions of the SDR.
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Affiliation(s)
- Jaysón Davidson
- Department of Chemistry and Biochemistry, Hampton University, 200 William R. Harvey Way, Hampton, VA 23668, USA
| | - Kyndall Nicholas
- Department of Chemistry and Biochemistry, Hampton University, 200 William R. Harvey Way, Hampton, VA 23668, USA
| | - Jeremy Young
- Department of Chemistry and Biochemistry, Hampton University, 200 William R. Harvey Way, Hampton, VA 23668, USA
| | - Deborah G. Conrady
- UCB Pharma, Bedford, Massachusetts, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Stephen Mayclin
- UCB Pharma, Bedford, Massachusetts, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Sandhya Subramanian
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, 307 Westlake Avenue North Suite 500, Seattle, WA 98109, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, 307 Westlake Avenue North Suite 500, Seattle, WA 98109, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, 307 Westlake Avenue North Suite 500, Seattle, WA 98109, USA
| | - Oluwatoyin A. Asojo
- Department of Chemistry and Biochemistry, Hampton University, 200 William R. Harvey Way, Hampton, VA 23668, USA
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13
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Porter I, Neal T, Walker Z, Hayes D, Fowler K, Billups N, Rhoades A, Smith C, Smith K, Staker BL, Dranow DM, Mayclin SJ, Subramanian S, Edwards TE, Myler PJ, Asojo OA. Crystal structures of FolM alternative dihydrofolate reductase 1 from Brucella suis and Brucella canis. Acta Crystallogr F Struct Biol Commun 2022; 78:31-38. [PMID: 34981773 PMCID: PMC8725004 DOI: 10.1107/s2053230x21013078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/08/2021] [Indexed: 11/06/2023] Open
Abstract
Members of the bacterial genus Brucella cause brucellosis, a zoonotic disease that affects both livestock and wildlife. Brucella are category B infectious agents that can be aerosolized for biological warfare. As part of the structural genomics studies at the Seattle Structural Genomics Center for Infectious Disease (SSGCID), FolM alternative dihydrofolate reductases 1 from Brucella suis and Brucella canis were produced and their structures are reported. The enzymes share ∼95% sequence identity but have less than 33% sequence identity to other homologues with known structure. The structures are prototypical NADPH-dependent short-chain reductases that share their highest tertiary-structural similarity with protozoan pteridine reductases, which are being investigated for rational therapeutic development.
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Affiliation(s)
- Imani Porter
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Trinity Neal
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Zion Walker
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Dylan Hayes
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Kayla Fowler
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Nyah Billups
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Anais Rhoades
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Christian Smith
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Kaelyn Smith
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - David M Dranow
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Stephen J Mayclin
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Sandhya Subramanian
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Oluwatoyin A Asojo
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
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14
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Rodarte JV, Abendroth J, Edwards TE, Lorimer DD, Staker BL, Zhang S, Myler PJ, McLaughlin KJ. Crystal structure of acetoacetyl-CoA reductase from Rickettsia felis. Acta Crystallogr F Struct Biol Commun 2021; 77:54-60. [PMID: 33620038 PMCID: PMC7900926 DOI: 10.1107/s2053230x21001497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/08/2021] [Indexed: 11/10/2022] Open
Abstract
Rickettsia felis, a Gram-negative bacterium that causes spotted fever, is of increasing interest as an emerging human pathogen. R. felis and several other Rickettsia strains are classed as National Institute of Allergy and Infectious Diseases priority pathogens. In recent years, R. felis has been shown to be adaptable to a wide range of hosts, and many fevers of unknown origin are now being attributed to this infectious agent. Here, the structure of acetoacetyl-CoA reductase from R. felis is reported at a resolution of 2.0 Å. While R. felis acetoacetyl-CoA reductase shares less than 50% sequence identity with its closest homologs, it adopts a fold common to other short-chain dehydrogenase/reductase (SDR) family members, such as the fatty-acid synthesis II enzyme FabG from the prominent pathogens Staphylococcus aureus and Bacillus anthracis. Continued characterization of the Rickettsia proteome may prove to be an effective means of finding new avenues of treatment through comparative structural studies.
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Affiliation(s)
- Justas V. Rodarte
- Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, New York, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- UCB Biosciences Inc., 7869 Day Road West, Bainbridge Island, Washington, USA
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- UCB Biosciences Inc., 7869 Day Road West, Bainbridge Island, Washington, USA
| | - Donald D. Lorimer
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- UCB Biosciences Inc., 7869 Day Road West, Bainbridge Island, Washington, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Seattle Children’s Research Institute, University of Washington, Seattle, Washington, USA
| | - Sunny Zhang
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Seattle Children’s Research Institute, University of Washington, Seattle, Washington, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Seattle Children’s Research Institute, University of Washington, Seattle, Washington, USA
| | - Krystle J. McLaughlin
- Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, New York, USA
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15
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Riboldi GP, Zigweid R, Myler PJ, Mayclin SJ, Couñago RM, Staker BL. Identification of P218 as a potent inhibitor of Mycobacterium ulcerans DHFR. RSC Med Chem 2021; 12:103-109. [PMID: 34046602 PMCID: PMC8130613 DOI: 10.1039/d0md00303d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/07/2020] [Indexed: 11/21/2022] Open
Abstract
Mycobacterium ulcerans is the causative agent of Buruli ulcer, a debilitating chronic disease that mainly affects the skin. Current treatments for Buruli ulcer are efficacious, but rely on the use of antibiotics with severe side effects. The enzyme dihydrofolate reductase (DHFR) plays a critical role in the de novo biosynthesis of folate species and is a validated target for several antimicrobials. Here we describe the biochemical and structural characterization of M. ulcerans DHFR and identified P218, a safe antifolate compound in clinical evaluation for malaria, as a potent inhibitor of this enzyme. We expect our results to advance M. ulcerans DHFR as a target for future structure-based drug discovery campaigns.
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Affiliation(s)
- Gustavo P Riboldi
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP) Campinas SP 13083-875 Brazil
- Structural Genomics Consortium, Departamento de Genética e Evolução, Instituto de Biologia, UNICAMP Campinas SP 13083-886 Brazil
| | - Rachael Zigweid
- Center for Infectious Disease Research, Seattle Children's Research Institute Seattle Washington 98109 USA
| | - Peter J Myler
- Center for Infectious Disease Research, Seattle Children's Research Institute Seattle Washington 98109 USA
- Department of Pediatrics, University of Washington Seattle Washington 91895 USA
| | - Stephen J Mayclin
- Seattle Structural Genomics Center for Infectious Disease (SSGCID) Seattle Washington 98109 USA
- UCB Bainbridge Island Washington 98110 USA
| | - Rafael M Couñago
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP) Campinas SP 13083-875 Brazil
- Structural Genomics Consortium, Departamento de Genética e Evolução, Instituto de Biologia, UNICAMP Campinas SP 13083-886 Brazil
| | - Bart L Staker
- Center for Infectious Disease Research, Seattle Children's Research Institute Seattle Washington 98109 USA
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16
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Santos JC, Vieira ML, Abendroth J, Lin T, Staker BL, Myler PJ, Nascimento ALTO. Structural analysis of CACHE domain of the McpA chemoreceptor from Leptospira interrogans. Biochem Biophys Res Commun 2020; 533:1323-1329. [PMID: 33097187 DOI: 10.1016/j.bbrc.2020.10.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 10/07/2020] [Indexed: 11/26/2022]
Abstract
Leptospira is a genus of spirochete bacteria highly motile that includes pathogenic species responsible to cause leptospirosis disease. Chemotaxis and motility are required for Leptospira infectivity, pathogenesis, and invasion of bacteria into the host. In prokaryotes, the most common chemoreceptors are methyl-accepting chemotaxis proteins that have a role play to detect the chemical signals and move to a favorable environment for its survival. Here, we report the first crystal structure of CACHE domain of the methyl-accepting chemotaxis protein (McpA) of L. interrogans. The structural analysis showed that McpA adopts similar α/β architecture of several other bacteria chemoreceptors. We also found a typical dimerization interface that appears to be functionally crucial for signal transmission and chemotaxis. In addition to McpA structural analyses, we have identified homologous proteins and conservative functional regions using bioinformatics techniques. These results improve our understanding the relationship between chemoreceptor structures and functions of Leptospira species.
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Affiliation(s)
- Jademilson C Santos
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brasil, 1500, 05503-900, São Paulo, SP, Brazil.
| | - Mônica L Vieira
- Departamento de Microbiologia, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Jan Abendroth
- UCB Pharma SA, 7869 NE Day Road West, Bainbridge Island, WA, 98110, USA; Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, 98109, United States
| | - Tao Lin
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, United States
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, 98109, United States; Seattle Children's Research Institute, Seattle, WA, 98109, United States
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, 98109, United States; Seattle Children's Research Institute, Seattle, WA, 98109, United States; Department of Pediatrics, Department of Biomedical Informatics & Health Education and Department of Global Health, University of Washington, Seattle, WA 98105, USA
| | - Ana Lucia T O Nascimento
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, Avenida Vital Brasil, 1500, 05503-900, São Paulo, SP, Brazil
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17
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Harupa A, De Las Heras L, Colmenarejo G, Lyons-Abbott S, Reers A, Caballero Hernandez I, Chung CW, Charter D, Myler PJ, Fernández-Menéndez RM, Calderón F, Palomo S, Rodríguez B, Berlanga M, Herreros-Avilés E, Staker BL, Fernández Álvaro E, Kaushansky A. Identification of Selective Inhibitors of Plasmodium N-Myristoyltransferase by High-Throughput Screening. J Med Chem 2019; 63:591-600. [DOI: 10.1021/acs.jmedchem.9b01343] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anke Harupa
- Center for Infectious Disease Research, Seattle, Washington 98109, United States
- GlaxoSmithKline, Tres Cantos, Madrid 28760, Spain
- Novartis Institute for Biomedical Research, Emeryville, California 94608, United States
| | | | | | - Sally Lyons-Abbott
- Center for Infectious Disease Research, Seattle, Washington 98109, United States
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington 98109, United States
| | - Alexandra Reers
- Center for Infectious Disease Research, Seattle, Washington 98109, United States
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington 98109, United States
- Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | | | | | | | - Peter J. Myler
- Center for Infectious Disease Research, Seattle, Washington 98109, United States
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington 98109, United States
- Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | | | | | - Sara Palomo
- GlaxoSmithKline, Tres Cantos, Madrid 28760, Spain
| | | | | | | | - Bart L. Staker
- Center for Infectious Disease Research, Seattle, Washington 98109, United States
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington 98109, United States
- Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | | | - Alexis Kaushansky
- Center for Infectious Disease Research, Seattle, Washington 98109, United States
- Seattle Children’s Research Institute, Seattle, Washington 98109, United States
- Department of Global Health, University of Washington, Seattle, Washington 98195, United States
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18
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Schlott AC, Mayclin S, Reers AR, Coburn-Flynn O, Bell AS, Green J, Knuepfer E, Charter D, Bonnert R, Campo B, Burrows J, Lyons-Abbott S, Staker BL, Chung CW, Myler PJ, Fidock DA, Tate EW, Holder AA. Structure-Guided Identification of Resistance Breaking Antimalarial N‑Myristoyltransferase Inhibitors. Cell Chem Biol 2019; 26:991-1000.e7. [PMID: 31080074 PMCID: PMC6658617 DOI: 10.1016/j.chembiol.2019.03.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 02/25/2019] [Accepted: 03/25/2019] [Indexed: 01/26/2023]
Abstract
The attachment of myristate to the N-terminal glycine of certain proteins is largely a co-translational modification catalyzed by N-myristoyltransferase (NMT), and involved in protein membrane-localization. Pathogen NMT is a validated therapeutic target in numerous infectious diseases including malaria. In Plasmodium falciparum, NMT substrates are important in essential processes including parasite gliding motility and host cell invasion. Here, we generated parasites resistant to a particular NMT inhibitor series and show that resistance in an in vitro parasite growth assay is mediated by a single amino acid substitution in the NMT substrate-binding pocket. The basis of resistance was validated and analyzed with a structure-guided approach using crystallography, in combination with enzyme activity, stability, and surface plasmon resonance assays, allowing identification of another inhibitor series unaffected by this substitution. We suggest that resistance studies incorporated early in the drug development process help selection of drug combinations to impede rapid evolution of parasite resistance.
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Affiliation(s)
- Anja C Schlott
- Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Molecular Sciences Research Hub, Imperial College, White City Campus Wood Lane, London W12 0BZ, UK.
| | - Stephen Mayclin
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA; UCB Pharma, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Alexandra R Reers
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, USA
| | - Olivia Coburn-Flynn
- Department of Microbiology & Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Andrew S Bell
- Molecular Sciences Research Hub, Imperial College, White City Campus Wood Lane, London W12 0BZ, UK
| | - Judith Green
- Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ellen Knuepfer
- Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - David Charter
- Structural and Biophysical Sciences, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Roger Bonnert
- Medicines for Malaria Venture, Route de Pré-Bois 20, Post Box 1826, 1215 Geneva 15, Switzerland
| | - Brice Campo
- Medicines for Malaria Venture, Route de Pré-Bois 20, Post Box 1826, 1215 Geneva 15, Switzerland
| | - Jeremy Burrows
- Medicines for Malaria Venture, Route de Pré-Bois 20, Post Box 1826, 1215 Geneva 15, Switzerland
| | - Sally Lyons-Abbott
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, USA
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, USA
| | - Chun-Wa Chung
- Structural and Biophysical Sciences, GlaxoSmithKline, Stevenage, Hertfordshire, UK; Crick-GSK Biomedical LinkLabs, GSK Medicines Research Centre, Stevenage, UK
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, USA; Department of Biomedical Informatics & Medical Education, University of Washington, Seattle, USA; Department of Global Health, University of Washington, Seattle, USA
| | - David A Fidock
- Department of Microbiology & Immunology, Columbia University Medical Center, New York, NY 10032, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Edward W Tate
- Molecular Sciences Research Hub, Imperial College, White City Campus Wood Lane, London W12 0BZ, UK.
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19
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Dumais M, Davies DR, Lin T, Staker BL, Myler PJ, Van Voorhis WC. Structure and analysis of nucleoside diphosphate kinase from Borrelia burgdorferi prepared in a transition-state complex with ADP and vanadate moieties. Acta Crystallogr F Struct Biol Commun 2018; 74:373-384. [PMID: 29870023 PMCID: PMC5987747 DOI: 10.1107/s2053230x18007392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 05/16/2018] [Indexed: 01/13/2023] Open
Abstract
Nucleoside diphosphate kinases (NDKs) are implicated in a wide variety of cellular functions owing to their enzymatic conversion of NDP to NTP. NDK from Borrelia burgdorferi (BbNDK) was selected for functional and structural analysis to determine whether its activity is required for infection and to assess its potential for therapeutic inhibition. The Seattle Structural Genomics Center for Infectious Diseases (SSGCID) expressed recombinant BbNDK protein. The protein was crystallized and structures were solved of both the apoenzyme and a liganded form with ADP and vanadate ligands. This provided two structures and allowed the elucidation of changes between the apo and ligand-bound enzymes. Infectivity studies with ndk transposon mutants demonstrated that NDK function was important for establishing a robust infection in mice, and provided a rationale for therapeutic targeting of BbNDK. The protein structure was compared with other NDK structures found in the Protein Data Bank and was found to have similar primary, secondary, tertiary and quaternary structures, with conserved residues acting as the catalytic pocket, primarily using His132 as the phosphohistidine-transfer residue. Vanadate and ADP complexes model the transition state of this phosphoryl-transfer reaction, demonstrating that the pocket closes when bound to ADP, while allowing the addition or removal of a γ-phosphate. This analysis provides a framework for the design of potential therapeutics targeting BbNDK inhibition.
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Affiliation(s)
- Mitchell Dumais
- Department of Allergy and Infectious Disease, University of Washington, Seattle, Washington, USA
| | | | - Tao Lin
- Department of Pathology and Laboratory Medicine, McGovern Medical School at UTHealth, Houston, Texas, USA
| | - Bart L. Staker
- Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute) , Seattle, Washington, USA
| | - Peter J. Myler
- Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute) , Seattle, Washington, USA
- Department of Biomedical Informatics and Health Education, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Wesley C. Van Voorhis
- Department of Allergy and Infectious Disease, University of Washington, Seattle, Washington, USA
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20
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Helgren TR, Seven ES, Chen C, Edwards TE, Staker BL, Abendroth J, Myler PJ, Horn JR, Hagen TJ. The identification of inhibitory compounds of Rickettsia prowazekii methionine aminopeptidase for antibacterial applications. Bioorg Med Chem Lett 2018; 28:1376-1380. [PMID: 29551481 PMCID: PMC5908248 DOI: 10.1016/j.bmcl.2018.03.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 02/28/2018] [Accepted: 03/01/2018] [Indexed: 11/25/2022]
Abstract
Methionine aminopeptidase (MetAP) is a dinuclear metalloprotease responsible for the cleavage of methionine initiator residues from nascent proteins. MetAP activity is necessary for bacterial proliferation and is therefore a projected novel antibacterial target. A compound library consisting of 294 members containing metal-binding functional groups was screened against Rickettsia prowazekii MetAP to determine potential inhibitory motifs. The compounds were first screened against the target at a concentration of 10 µM and potential hits were determined to be those exhibiting greater than 50% inhibition of enzymatic activity. These hit compounds were then rescreened against the target in 8-point dose-response curves and 11 compounds were found to inhibit enzymatic activity with IC50 values of less than 10 µM. Finally, compounds (1-5) were docked against RpMetAP with AutoDock to determine potential binding mechanisms and the results were compared with crystal structures deposited within the PDB.
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Affiliation(s)
- Travis R Helgren
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115, USA
| | - Elif S Seven
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115, USA
| | - Congling Chen
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115, USA
| | - Thomas E Edwards
- Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA; Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA; Center for Infectious Disease Research, Formerly Seattle Biomedical Research Institute, 307 Westlake Avenue N., Seattle, WA 98109, USA
| | - Jan Abendroth
- Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA; Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA; Center for Infectious Disease Research, Formerly Seattle Biomedical Research Institute, 307 Westlake Avenue N., Seattle, WA 98109, USA
| | - James R Horn
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115, USA
| | - Timothy J Hagen
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115, USA.
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21
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Abendroth J, Frando A, Phan IQ, Staker BL, Myler PJ, Edwards TE, Grundner C. Mycobacterium tuberculosis Rv3651 is a triple sensor-domain protein. Protein Sci 2017; 27:568-572. [PMID: 29119630 DOI: 10.1002/pro.3343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 11/03/2017] [Accepted: 11/06/2017] [Indexed: 01/27/2023]
Abstract
The genome of the human pathogen Mycobacterium tuberculosis (Mtb) encodes ∼4,400 proteins, but one third of them have unknown functions. We solved the crystal structure of Rv3651, a hypothetical protein with no discernible similarity to proteins with known function. Rv3651 has a three-domain architecture that combines one cGMP-specific phosphodiesterases, adenylyl cyclases and FhlA (GAF) domain and two Per-ARNT-Sim (PAS) domains. GAF and PAS domains are sensor domains that are typically linked to signaling effector molecules. Unlike these sensor-effector proteins, Rv3651 is an unusual sensor domain-only protein with highly divergent sequence. The structure suggests that Rv3651 integrates multiple different signals and serves as a scaffold to facilitate signal transfer.
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Affiliation(s)
- Jan Abendroth
- Beryllium Discovery, Bainbridge Island, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - Andrew Frando
- Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, Washington.,Department of Global Health, University of Washington, Seattle, Washington
| | - Isabelle Q Phan
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, Washington
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, Washington
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, Washington.,Department of Global Health, University of Washington, Seattle, Washington.,Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington
| | - Thomas E Edwards
- Beryllium Discovery, Bainbridge Island, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - Christoph Grundner
- Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, Washington.,Department of Global Health, University of Washington, Seattle, Washington
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22
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Moen SO, Edwards TE, Dranow DM, Clifton MC, Sankaran B, Van Voorhis WC, Sharma A, Manoil C, Staker BL, Myler PJ, Lorimer DD. Ligand co-crystallization of aminoacyl-tRNA synthetases from infectious disease organisms. Sci Rep 2017; 7:223. [PMID: 28303005 PMCID: PMC5428304 DOI: 10.1038/s41598-017-00367-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 02/20/2017] [Indexed: 12/15/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) charge tRNAs with their cognate amino acid, an essential precursor step to loading of charged tRNAs onto the ribosome and addition of the amino acid to the growing polypeptide chain during protein synthesis. Because of this important biological function, aminoacyl-tRNA synthetases have been the focus of anti-infective drug development efforts and two aaRS inhibitors have been approved as drugs. Several researchers in the scientific community requested aminoacyl-tRNA synthetases to be targeted in the Seattle Structural Genomics Center for Infectious Disease (SSGCID) structure determination pipeline. Here we investigate thirty-one aminoacyl-tRNA synthetases from infectious disease organisms by co-crystallization in the presence of their cognate amino acid, ATP, and/or inhibitors. Crystal structures were determined for a CysRS from Borrelia burgdorferi bound to AMP, GluRS from Borrelia burgdorferi and Burkholderia thailandensis bound to glutamic acid, a TrpRS from the eukaryotic pathogen Encephalitozoon cuniculi bound to tryptophan, a HisRS from Burkholderia thailandensis bound to histidine, and a LysRS from Burkholderia thailandensis bound to lysine. Thus, the presence of ligands may promote aaRS crystallization and structure determination. Comparison with homologous structures shows conformational flexibility that appears to be a recurring theme with this enzyme class.
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Affiliation(s)
- Spencer O Moen
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA.,Beryllium Discovery Corp, Bainbridge Island, WA, 98110, USA
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA. .,Beryllium Discovery Corp, Bainbridge Island, WA, 98110, USA.
| | - David M Dranow
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA.,Beryllium Discovery Corp, Bainbridge Island, WA, 98110, USA
| | - Matthew C Clifton
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA.,Beryllium Discovery Corp, Bainbridge Island, WA, 98110, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Advanced Light Source, Berkeley, CA, 94720, USA
| | - Wesley C Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA.,University of Washington, Seattle, WA, 98195-6423, USA
| | - Amit Sharma
- International Center for Genetic Engineering and Biotechnology, New Delhi, 110 067, India
| | - Colin Manoil
- University of Washington, Department of Genome Sciences, Seattle, WA, 98195-5065, USA
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA.,Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, WA, 98109, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA.,Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, WA, 98109, USA.,University of Washington, Department of Medical Education and Biomedical Informatics & Department of Global Health, Seattle, WA, 98195, USA
| | - Donald D Lorimer
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA.,Beryllium Discovery Corp, Bainbridge Island, WA, 98110, USA
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23
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Dubey R, Staker BL, Foe IT, Bogyo M, Myler PJ, Ngô HM, Gubbels MJ. Membrane skeletal association and post-translational allosteric regulation of Toxoplasma gondii GAPDH1. Mol Microbiol 2017; 103:618-634. [PMID: 27859784 PMCID: PMC5296235 DOI: 10.1111/mmi.13577] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2016] [Indexed: 01/07/2023]
Abstract
When Toxoplasma gondii egresses from the host cell, glyceraldehyde-3-phosphate dehydrogenase 1 (GAPDH1), which is primary a glycolysis enzyme but actually a quintessential multifunctional protein, translocates to the unique cortical membrane skeleton. Here, we report the 2.25 Å resolution crystal structure of the GAPDH1 holoenzyme in a quaternary complex providing the basis for the molecular dissection of GAPDH1 structure-function relationships Knockdown of GAPDH1 expression and catalytic site disruption validate the essentiality of GAPDH1 in intracellular replication but we confirmed that glycolysis is not strictly essential. We identify, for the first time, S-loop phosphorylation as a novel, critical regulator of enzymatic activity that is consistent with the notion that the S-loop is critical for cofactor binding, allosteric activation and oligomerization. We show that neither enzymatic activity nor phosphorylation state correlate with the ability to translocate to the cortex. However, we demonstrate that association of GAPDH1 with the cortex is mediated by the N-terminus, likely palmitoylation. Overall, glycolysis and cortical translocation are functionally decoupled by post-translational modifications.
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Affiliation(s)
- Rashmi Dubey
- Department of Biology, Boston College, MA 02467, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA 98109, USA,The Center for Infectious Disease Research, Seattle (formerly Seattle BioMed), WA 98109, USA
| | - Ian T. Foe
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 55324, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 55324, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA 98109, USA,The Center for Infectious Disease Research, Seattle (formerly Seattle BioMed), WA 98109, USA,Department of Global Health and Department of Biomedical Informatics & Medical Education, University of Washington, Seattle, WA 98195, USA
| | - Huân M. Ngô
- Center for Structural Genomics of Infectious Disease, Northwestern University, Chicago, IL 60611, USA,BrainMicro LLC, New Haven, CT 06511, USA,Corresponding authors: Huân Ngô and Marc-Jan Gubbels
| | - Marc-Jan Gubbels
- Department of Biology, Boston College, MA 02467, USA,Corresponding authors: Huân Ngô and Marc-Jan Gubbels
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24
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Haft DH, Pierce PG, Mayclin SJ, Sullivan A, Gardberg AS, Abendroth J, Begley DW, Phan IQ, Staker BL, Myler PJ, Marathias VM, Lorimer DD, Edwards TE. Mycofactocin-associated mycobacterial dehydrogenases with non-exchangeable NAD cofactors. Sci Rep 2017; 7:41074. [PMID: 28120876 PMCID: PMC5264612 DOI: 10.1038/srep41074] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 12/12/2016] [Indexed: 01/08/2023] Open
Abstract
During human infection, Mycobacterium tuberculosis (Mtb) survives the normally bacteriocidal phagosome of macrophages. Mtb and related species may be able to combat this harsh acidic environment which contains reactive oxygen species due to the mycobacterial genomes encoding a large number of dehydrogenases. Typically, dehydrogenase cofactor binding sites are open to solvent, which allows NAD/NADH exchange to support multiple turnover. Interestingly, mycobacterial short chain dehydrogenases/reductases (SDRs) within family TIGR03971 contain an insertion at the NAD binding site. Here we present crystal structures of 9 mycobacterial SDRs in which the insertion buries the NAD cofactor except for a small portion of the nicotinamide ring. Line broadening and STD-NMR experiments did not show NAD or NADH exchange on the NMR timescale. STD-NMR demonstrated binding of the potential substrate carveol, the potential product carvone, the inhibitor tricyclazol, and an external redox partner 2,6-dichloroindophenol (DCIP). Therefore, these SDRs appear to contain a non-exchangeable NAD cofactor and may rely on an external redox partner, rather than cofactor exchange, for multiple turnover. Incidentally, these genes always appear in conjunction with the mftA gene, which encodes the short peptide MftA, and with other genes proposed to convert MftA into the external redox partner mycofactocin.
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Affiliation(s)
- Daniel H Haft
- National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Phillip G Pierce
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Stephen J Mayclin
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Amy Sullivan
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Anna S Gardberg
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Darren W Begley
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Isabelle Q Phan
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Avenue North, Seattle WA 98109, USA
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Avenue North, Seattle WA 98109, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Avenue North, Seattle WA 98109, USA.,University of Washington, Department of Medical Education and Biomedical Informatics &Department of Global Health, Seattle WA 98195, USA
| | - Vasilios M Marathias
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Donald D Lorimer
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
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25
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Cala AR, Nadeau MT, Abendroth J, Staker BL, Reers AR, Weatherhead AW, Dobson RCJ, Myler PJ, Hudson AO. The crystal structure of dihydrodipicolinate reductase from the human-pathogenic bacterium Bartonella henselae strain Houston-1 at 2.3 Å resolution. Acta Crystallogr F Struct Biol Commun 2016; 72:885-891. [PMID: 27917836 PMCID: PMC5137465 DOI: 10.1107/s2053230x16018525] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 11/19/2016] [Indexed: 11/10/2022] Open
Abstract
In bacteria, the second committed step in the diaminopimelate/lysine anabolic pathways is catalyzed by the enzyme dihydrodipicolinate reductase (DapB). DapB catalyzes the reduction of dihydrodipicolinate to yield tetrahydrodipicolinate. Here, the cloning, expression, purification, crystallization and X-ray diffraction analysis of DapB from the human-pathogenic bacterium Bartonella henselae, the causative bacterium of cat-scratch disease, are reported. Protein crystals were grown in conditions consisting of 5%(w/v) PEG 4000, 200 mM sodium acetate, 100 mM sodium citrate tribasic pH 5.5 and were shown to diffract to ∼2.3 Å resolution. They belonged to space group P4322, with unit-cell parameters a = 109.38, b = 109.38, c = 176.95 Å. Rr.i.m. was 0.11, Rwork was 0.177 and Rfree was 0.208. The three-dimensional structural features of the enzymes show that DapB from B. henselae is a tetramer consisting of four identical polypeptides. In addition, the substrate NADP+ was found to be bound to one monomer, which resulted in a closed conformational change in the N-terminal domain.
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Affiliation(s)
- Ali R. Cala
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, USA
| | - Maria T. Nadeau
- School of Chemistry and Materials Science, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, USA
| | - Jan Abendroth
- Beryllium Discovery Inc., Bainbridge Island, WA 98110, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease, USA
- Center for Infectious Disease Research, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
| | - Alexandra R. Reers
- Seattle Structural Genomics Center for Infectious Disease, USA
- Center for Infectious Disease Research, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
| | - Anthony W. Weatherhead
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, USA
- Center for Infectious Disease Research, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
- Department of Biomedical Informatics and Health Education, University of Washington, Seattle, WA 98195, USA
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, USA
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Helgren TR, Chen C, Wangtrakuldee P, Edwards TE, Staker BL, Abendroth J, Sankaran B, Housley NA, Myler PJ, Audia JP, Horn JR, Hagen TJ. Rickettsia prowazekii methionine aminopeptidase as a promising target for the development of antibacterial agents. Bioorg Med Chem 2016; 25:813-824. [PMID: 28089350 DOI: 10.1016/j.bmc.2016.11.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/06/2016] [Accepted: 11/08/2016] [Indexed: 01/07/2023]
Abstract
Methionine aminopeptidase (MetAP) is a class of ubiquitous enzymes essential for the survival of numerous bacterial species. These enzymes are responsible for the cleavage of N-terminal formyl-methionine initiators from nascent proteins to initiate post-translational modifications that are often essential to proper protein function. Thus, inhibition of MetAP activity has been implicated as a novel antibacterial target. We tested this idea in the present study by targeting the MetAP enzyme in the obligate intracellular pathogen Rickettsia prowazekii. We first identified potent RpMetAP inhibitory species by employing an in vitro enzymatic activity assay. The molecular docking program AutoDock was then utilized to compare published crystal structures of inhibited MetAP species to docked poses of RpMetAP. Based on these in silico and in vitro screens, a subset of 17 compounds was tested for inhibition of R. prowazekii growth in a pulmonary vascular endothelial cell (EC) culture infection model system. All compounds were tested over concentration ranges that were determined to be non-toxic to the ECs and 8 of the 17 compounds displayed substantial inhibition of R. prowazekii growth. These data highlight the therapeutic potential for inhibiting RpMetAP as a novel antimicrobial strategy and set the stage for future studies in pre-clinical animal models of infection.
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Affiliation(s)
- Travis R Helgren
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115, USA
| | - Congling Chen
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115, USA
| | - Phumvadee Wangtrakuldee
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115, USA
| | - Thomas E Edwards
- Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA; Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA
| | - Bart L Staker
- Center for Infectious Disease Research, Formerly Seattle Biomedical Research Institute, 307 Westlake Avenue N., Seattle, WA 98109, USA; Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA
| | - Jan Abendroth
- Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA; Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nicole A Housley
- Department of Microbiology and Immunology and The Center for Lung Biology, University of South Alabama College of Medicine, Laboratory of Infectious Diseases, 307 North University Blvd, Mobile, AL 36688, USA
| | - Peter J Myler
- Center for Infectious Disease Research, Formerly Seattle Biomedical Research Institute, 307 Westlake Avenue N., Seattle, WA 98109, USA; Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA; Department of Global Health and Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA 98195, USA
| | - Jonathon P Audia
- Department of Microbiology and Immunology and The Center for Lung Biology, University of South Alabama College of Medicine, Laboratory of Infectious Diseases, 307 North University Blvd, Mobile, AL 36688, USA
| | - James R Horn
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115, USA
| | - Timothy J Hagen
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115, USA.
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Staker BL, Buchko GW, Myler PJ. Recent contributions of structure-based drug design to the development of antibacterial compounds. Curr Opin Microbiol 2016; 27:133-8. [PMID: 26458180 DOI: 10.1016/j.mib.2015.09.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/09/2015] [Accepted: 09/23/2015] [Indexed: 11/28/2022]
Abstract
According to a Pew Research study published in February 2015, there are 37 antibacterial programs currently in clinical trials in the United States. Protein structure-based methods for guiding small molecule design were used in at least 34 of these programs. Typically, this occurred at an early stage (drug discovery and/or lead optimization) prior to an Investigational New Drug (IND) application, although sometimes in retrospective studies to rationalize biological activity. Recognizing that structure-based methods are resource-intensive and often require specialized equipment and training, the NIAID has funded two Structural Genomics Centers to determine structures of infectious disease species proteins with the aim of supporting individual investigators' research programs with structural biology methods.
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Affiliation(s)
- Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease, United States; Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States.
| | - Garry W Buchko
- Seattle Structural Genomics Center for Infectious Disease, United States; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease, United States; Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States; Department of Global Health, University of Washington, Seattle, WA 98195, United States; Department of Biomedical Informatics and Health Education, University of Washington, Seattle, WA 98195, United States
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Naqvi KF, Staker BL, Dobson RCJ, Serbzhinskiy D, Sankaran B, Myler PJ, Hudson AO. Cloning, expression, purification, crystallization and X-ray diffraction analysis of dihydrodipicolinate synthase from the human pathogenic bacterium Bartonella henselae strain Houston-1 at 2.1 Å resolution. Acta Crystallogr F Struct Biol Commun 2016; 72:2-9. [PMID: 26750477 PMCID: PMC4708043 DOI: 10.1107/s2053230x15023213] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 12/02/2015] [Indexed: 11/10/2022] Open
Abstract
The enzyme dihydrodipicolinate synthase catalyzes the committed step in the synthesis of diaminopimelate and lysine to facilitate peptidoglycan and protein synthesis. Dihydrodipicolinate synthase catalyzes the condensation of L-aspartate 4-semialdehyde and pyruvate to synthesize L-2,3-dihydrodipicolinate. Here, the cloning, expression, purification, crystallization and X-ray diffraction analysis of dihydrodipicolinate synthase from the pathogenic bacterium Bartonella henselae, the causative bacterium of cat-scratch disease, are presented. Protein crystals were grown in conditions consisting of 20%(w/v) PEG 4000, 100 mM sodium citrate tribasic pH 5.5 and were shown to diffract to ∼2.10 Å resolution. They belonged to space group P212121, with unit-cell parameters a = 79.96, b = 106.33, c = 136.25 Å. The final R values were Rr.i.m. = 0.098, Rwork = 0.183, Rfree = 0.233.
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Affiliation(s)
- Kubra F. Naqvi
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease, USA
- Center for Infectious Disease Research, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
| | - Renwick C. J. Dobson
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Dmitry Serbzhinskiy
- Seattle Structural Genomics Center for Infectious Disease, USA
- Center for Infectious Disease Research, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Ernest Orlando Lawrence Berkeley National Laboratory, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, USA
- Center for Infectious Disease Research, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109, USA
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
- Department of Biomedical Informatics and Health Education, University of Washington, Seattle, WA 98195, USA
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, USA
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R. Helgren T, Wangtrakuldee P, L. Staker B, J. Hagen T. Advances in Bacterial Methionine Aminopeptidase Inhibition. Curr Top Med Chem 2015; 16:397-414. [DOI: 10.2174/1568026615666150813145410] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 05/11/2015] [Accepted: 05/12/2015] [Indexed: 11/22/2022]
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Serbzhinskiy DA, Clifton MC, Sankaran B, Staker BL, Edwards TE, Myler PJ. Structure of an ADP-ribosylation factor, ARF1, from Entamoeba histolytica bound to Mg(2+)-GDP. Acta Crystallogr F Struct Biol Commun 2015; 71:594-9. [PMID: 25945714 PMCID: PMC4427170 DOI: 10.1107/s2053230x15004677] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/06/2015] [Indexed: 01/21/2023] Open
Abstract
Entamoeba histolytica is the etiological agent of amebiasis, a diarrheal disease which causes amoebic liver abscesses and amoebic colitis. Approximately 50 million people are infected worldwide with E. histolytica. With only 10% of infected people developing symptomatic amebiasis, there are still an estimated 100,000 deaths each year. Because of the emergence of resistant strains of the parasite, it is necessary to find a treatment which would be a proper response to this challenge. ADP-ribosylation factor (ARF) is a member of the ARF family of GTP-binding proteins. These proteins are ubiquitous in eukaryotic cells; they generally associate with cell membranes and regulate vesicular traffic and intracellular signalling. The crystal structure of ARF1 from E. histolytica has been determined bound to magnesium and GDP at 1.8 Å resolution. Comparison with other structures of eukaryotic ARF proteins shows a highly conserved structure and supports the interswitch toggle mechanism of communicating the conformational state to partner proteins.
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Affiliation(s)
- Dmitry A. Serbzhinskiy
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Seattle Biomedical Research Institute, Seattle, WA 98109, USA
| | - Matthew C. Clifton
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Beryllium West Coast Operations, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Seattle Biomedical Research Institute, Seattle, WA 98109, USA
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Beryllium West Coast Operations, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA
- Seattle Biomedical Research Institute, Seattle, WA 98109, USA
- Departments of Global Health and Medical Education and Biomedical Informatics, University of Washington, Seattle, WA 98195, USA
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Buchko GW, Abendroth J, Clifton MC, Robinson H, Zhang Y, Hewitt SN, Staker BL, Edwards TE, Van Voorhis WC, Myler PJ. Structure of a CutA1 divalent-cation tolerance protein from Cryptosporidium parvum, the protozoal parasite responsible for cryptosporidiosis. Acta Crystallogr F Struct Biol Commun 2015; 71:522-30. [PMID: 25945704 PMCID: PMC4427160 DOI: 10.1107/s2053230x14028210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 12/29/2014] [Indexed: 11/11/2022] Open
Abstract
Cryptosporidiosis is an infectious disease caused by protozoan parasites of the Cryptosporidium genus. Infection is associated with mild to severe diarrhea that usually resolves spontaneously in healthy human adults, but may lead to severe complications in young children and in immunocompromised patients. The genome of C. parvum contains a gene, CUTA_CRYPI, that may play a role in regulating the intracellular concentration of copper, which is a toxic element in excess. Here, the crystal structure of this CutA1 protein, Cp-CutA1, is reported at 2.0 Å resolution. As observed for other CutA1 structures, the 117-residue protein is a trimer with a core ferrodoxin-like fold. Circular dichroism spectroscopy shows little, in any, unfolding of Cp-CutA1 up to 353 K. This robustness is corroborated by (1)H-(15)N HSQC spectra at 333 K, which are characteristic of a folded protein, suggesting that NMR spectroscopy may be a useful tool to further probe the function of the CutA1 proteins. While robust, Cp-CutA1 is not as stable as the homologous protein from a hyperthermophile, perhaps owing to a wide β-bulge in β2 that protrudes Pro48 and Ser49 outside the β-sheet.
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Affiliation(s)
- Garry W. Buchko
- Seattle Structural Genomics Center for Infectious Disease, USA
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, USA
- Beryllium, Bainbridge Island, Washington, USA
| | - Matthew C. Clifton
- Seattle Structural Genomics Center for Infectious Disease, USA
- Beryllium, Bainbridge Island, Washington, USA
| | - Howard Robinson
- Biology Department, Brookhaven National Laboratory, Upton, New York, USA
| | - Yanfeng Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Stephen N. Hewitt
- Seattle Structural Genomics Center for Infectious Disease, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease, USA
- Seattle Biomedical Research Institute, Seattle, Washington, USA
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease, USA
- Beryllium, Bainbridge Island, Washington, USA
| | - Wesley C. Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, USA
- Seattle Biomedical Research Institute, Seattle, Washington, USA
- Department of Medical Education and Biomedical Informatics and Department of Global Health, University of Washington, Seattle, Washington, USA
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Lorimer DD, Choi R, Abramov A, Nakazawa Hewitt S, Gardberg AS, Van Voorhis WC, Staker BL, Myler PJ, Edwards TE. Structures of a histidine triad family protein from Entamoeba histolytica bound to sulfate, AMP and GMP. Acta Crystallogr F Struct Biol Commun 2015; 71:572-6. [PMID: 25945711 PMCID: PMC4427167 DOI: 10.1107/s2053230x1500237x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 02/04/2015] [Indexed: 11/10/2022] Open
Abstract
Three structures of the histidine triad family protein from Entamoeba histolytica, the causative agent of amoebic dysentery, were solved at high resolution within the Seattle Structural Genomics Center for Infectious Disease (SSGCID). The structures have sulfate (PDB entry 3oj7), AMP (PDB entry 3omf) or GMP (PDB entry 3oxk) bound in the active site, with sulfate occupying the same space as the α-phosphate of the two nucleotides. The C(α) backbones of the three structures are nearly superimposable, with pairwise r.m.s.d.s ranging from 0.06 to 0.13 Å.
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Affiliation(s)
- Donald D. Lorimer
- Seattle Structural Genomics Center for Infectious Disease, USA
- Beryllium, Bainbridge Island, WA 98110, USA
| | - Ryan Choi
- Seattle Structural Genomics Center for Infectious Disease, USA
- CERID, University of Washington, Seattle, WA 98109, USA
| | - Ariel Abramov
- Seattle Structural Genomics Center for Infectious Disease, USA
- Seattle Biomedical Research Institute, Seattle, WA 98109, USA
| | - Stephen Nakazawa Hewitt
- Seattle Structural Genomics Center for Infectious Disease, USA
- CERID, University of Washington, Seattle, WA 98109, USA
| | - Anna S. Gardberg
- Seattle Structural Genomics Center for Infectious Disease, USA
- Beryllium, Bainbridge Island, WA 98110, USA
| | - Wesley C. Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease, USA
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease, USA
- Seattle Biomedical Research Institute, Seattle, WA 98109, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, USA
- Seattle Biomedical Research Institute, Seattle, WA 98109, USA
- Department of Global Health and Medical Education and Biomedical Bioinformatics, University of Washington, Seattle, WA 98109, USA
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease, USA
- Beryllium, Bainbridge Island, WA 98110, USA
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Moen SO, Fairman JW, Barnes SR, Sullivan A, Nakazawa-Hewitt S, Van Voorhis WC, Staker BL, Lorimer DD, Myler PJ, Edwards TE. Structures of prostaglandin F synthase from the protozoa Leishmania major and Trypanosoma cruzi with NADP. Acta Crystallogr F Struct Biol Commun 2015; 71:609-14. [PMID: 25945716 PMCID: PMC4427172 DOI: 10.1107/s2053230x15006883] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/06/2015] [Indexed: 11/10/2022] Open
Abstract
The crystal structures of prostaglandin F synthase (PGF) from both Leishmania major and Trypanosoma cruzi with and without their cofactor NADP have been determined to resolutions of 2.6 Å for T. cruzi PGF, 1.25 Å for T. cruzi PGF with NADP, 1.6 Å for L. major PGF and 1.8 Å for L. major PGF with NADP. These structures were determined by molecular replacement to a final R factor of less than 18.6% (Rfree of less than 22.9%). PGF in the infectious protozoa L. major and T. cruzi is a potential therapeutic target.
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Affiliation(s)
- Spencer O. Moen
- Seattle Structural Genomics Center for Infectious Disease, USA
- Beryllium, Bainbridge Island, WA 98110, USA
| | - James W. Fairman
- Seattle Structural Genomics Center for Infectious Disease, USA
- Beryllium, Bainbridge Island, WA 98110, USA
| | - Steve R. Barnes
- Seattle Structural Genomics Center for Infectious Disease, USA
- Beryllium, Bainbridge Island, WA 98110, USA
| | - Amy Sullivan
- Seattle Structural Genomics Center for Infectious Disease, USA
- Beryllium, Bainbridge Island, WA 98110, USA
| | - Stephen Nakazawa-Hewitt
- Seattle Structural Genomics Center for Infectious Disease, USA
- CERID, University of Washington, Seattle, WA 98109, USA
| | - Wesley C. Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease, USA
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease, USA
- Seattle Biomedical Research Institute, Seattle, WA 98109, USA
| | - Donald D. Lorimer
- Seattle Structural Genomics Center for Infectious Disease, USA
- Beryllium, Bainbridge Island, WA 98110, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, USA
- Seattle Biomedical Research Institute, Seattle, WA 98109, USA
- Department of Global Health and Medical Education and Biomedical Bioinformatics, University of Washington, Seattle, WA 98109, USA
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease, USA
- Beryllium, Bainbridge Island, WA 98110, USA
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Edwards TE, Gardberg AS, Phan IQH, Zhang Y, Staker BL, Myler PJ, Lorimer DD. Structure of uridine diphosphate N-acetylglucosamine pyrophosphorylase from Entamoeba histolytica. Acta Crystallogr F Struct Biol Commun 2015; 71:560-5. [PMID: 25945709 PMCID: PMC4427165 DOI: 10.1107/s2053230x1500179x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 01/27/2015] [Indexed: 11/10/2022] Open
Abstract
Uridine diphosphate N-acetylglucosamine pyrophosphorylase (UAP) catalyzes the final step in the synthesis of UDP-GlcNAc, which is involved in cell-wall biogenesis in plants and fungi and in protein glycosylation. Small-molecule inhibitors have been developed against UAP from Trypanosoma brucei that target an allosteric pocket to provide selectivity over the human enzyme. A 1.8 Å resolution crystal structure was determined of UAP from Entamoeba histolytica, an anaerobic parasitic protozoan that causes amoebic dysentery. Although E. histolytica UAP exhibits the same three-domain global architecture as other UAPs, it appears to lack three α-helices at the N-terminus and contains two amino acids in the allosteric pocket that make it appear more like the enzyme from the human host than that from the other parasite T. brucei. Thus, allosteric inhibitors of T. brucei UAP are unlikely to target Entamoeba UAPs.
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Affiliation(s)
- Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease, USA
- Beryllium, Bainbridge Island, WA 98110, USA
| | - Anna S. Gardberg
- Seattle Structural Genomics Center for Infectious Disease, USA
- Beryllium, Bainbridge Island, WA 98110, USA
| | - Isabelle Q. H. Phan
- Seattle Structural Genomics Center for Infectious Disease, USA
- Seattle Biomedical Research Institute, Seattle, WA 98109, USA
| | - Yang Zhang
- Seattle Structural Genomics Center for Infectious Disease, USA
- Seattle Biomedical Research Institute, Seattle, WA 98109, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease, USA
- Seattle Biomedical Research Institute, Seattle, WA 98109, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, USA
- Seattle Biomedical Research Institute, Seattle, WA 98109, USA
- Departments of Global Health and Medical Education and Biomedical Informatics, University of Washington, Seattle, WA 98195, USA
| | - Donald D. Lorimer
- Seattle Structural Genomics Center for Infectious Disease, USA
- Beryllium, Bainbridge Island, WA 98110, USA
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Abendroth J, Choi R, Wall A, Clifton MC, Lukacs CM, Staker BL, Van Voorhis W, Myler P, Lorimer DD, Edwards TE. Structures of aspartate aminotransferases from Trypanosoma brucei, Leishmania major and Giardia lamblia. Acta Crystallogr F Struct Biol Commun 2015; 71:566-71. [PMID: 25945710 PMCID: PMC4427166 DOI: 10.1107/s2053230x15001831] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 01/27/2015] [Indexed: 11/10/2022] Open
Abstract
The structures of three aspartate aminotransferases (AATs) from eukaryotic pathogens were solved within the Seattle Structural Genomics Center for Infectious Disease (SSGCID). Both the open and closed conformations of AAT were observed. Pyridoxal phosphate was bound to the active site via a Schiff base to a conserved lysine. An active-site mutant showed that Trypanosoma brucei AAT still binds pyridoxal phosphate even in the absence of the tethering lysine. The structures highlight the challenges for the structure-based design of inhibitors targeting the active site, while showing options for inhibitor design targeting the N-terminal arm.
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Affiliation(s)
- Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
- Beryllium Inc., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Ryan Choi
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
- Department of Medicine, Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Box 356423, Seattle, WA 98195, USA
| | - Abigail Wall
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
- Beryllium Inc., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Matthew C. Clifton
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
- Beryllium Inc., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Christine M. Lukacs
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
- Beryllium Inc., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
- Seattle BioMed, 307 Westlake Avenure North, Seattle, WA 98109, USA
| | - Wesley Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
- Department of Medicine, Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Box 356423, Seattle, WA 98195, USA
| | - Peter Myler
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
- Seattle BioMed, 307 Westlake Avenure North, Seattle, WA 98109, USA
| | - Don D. Lorimer
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
- Beryllium Inc., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
- Beryllium Inc., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
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Baugh L, Phan I, Begley DW, Clifton MC, Armour B, Dranow DM, Taylor BM, Muruthi MM, Abendroth J, Fairman JW, Fox D, Dieterich SH, Staker BL, Gardberg AS, Choi R, Hewitt SN, Napuli AJ, Myers J, Barrett LK, Zhang Y, Ferrell M, Mundt E, Thompkins K, Tran N, Lyons-Abbott S, Abramov A, Sekar A, Serbzhinskiy D, Lorimer D, Buchko GW, Stacy R, Stewart LJ, Edwards TE, Van Voorhis WC, Myler PJ. Increasing the structural coverage of tuberculosis drug targets. Tuberculosis (Edinb) 2014; 95:142-8. [PMID: 25613812 DOI: 10.1016/j.tube.2014.12.003] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 12/10/2014] [Indexed: 01/31/2023]
Abstract
High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus "homolog-rescue" strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. Of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structures would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Cα RMSD <1 Å, >85% side chain identity, and ≥80% PSAPF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases.
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Affiliation(s)
- Loren Baugh
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Isabelle Phan
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Darren W Begley
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Matthew C Clifton
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Brianna Armour
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - David M Dranow
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Brandy M Taylor
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Marvin M Muruthi
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - James W Fairman
- Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - David Fox
- Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Shellie H Dieterich
- Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Anna S Gardberg
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States; EMD Serono Research & Development Institute, Inc., 45A Middlesex Turnpike, Billerica, MA 01821, United States
| | - Ryan Choi
- Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States
| | - Stephen N Hewitt
- Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States
| | - Alberto J Napuli
- Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States
| | - Janette Myers
- Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States
| | - Lynn K Barrett
- Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States
| | - Yang Zhang
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Micah Ferrell
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Elizabeth Mundt
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Katie Thompkins
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Ngoc Tran
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Sally Lyons-Abbott
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Ariel Abramov
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Aarthi Sekar
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Dmitri Serbzhinskiy
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Don Lorimer
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Garry W Buchko
- Seattle Structural Genomics Center for Infectious Disease, United States; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Robin Stacy
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Lance J Stewart
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States; Institute for Protein Design, University of Washington, Box 357350, Seattle, WA 98195, United States
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Wesley C Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States; Department of Global Health, University of Washington, Box 359931, Seattle, WA, 98195, United States; Department of Microbiology, University of Washington, Box 357735, Seattle, WA 98195, United States
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States; Department of Global Health, University of Washington, Box 359931, Seattle, WA, 98195, United States; Department of Biomedical Informatics and Medical Education, University of Washington, Box 358047, Seattle, WA 98195, United States.
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Linford AS, Jiang NM, Edwards TE, Sherman NE, Van Voorhis WC, Stewart LJ, Myler PJ, Staker BL, Petri WA. Crystal structure and putative substrate identification for the Entamoeba histolytica low molecular weight tyrosine phosphatase. Mol Biochem Parasitol 2014; 193:33-44. [PMID: 24548880 DOI: 10.1016/j.molbiopara.2014.01.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Revised: 01/12/2014] [Accepted: 01/22/2014] [Indexed: 11/28/2022]
Abstract
Entamoeba histolytica is a eukaryotic intestinal parasite of humans, and is endemic in developing countries. We have characterized the E. histolytica putative low molecular weight protein tyrosine phosphatase (LMW-PTP). The structure for this amebic tyrosine phosphatase was solved, showing the ligand-induced conformational changes necessary for binding of substrate. In amebae, it was expressed at low but detectable levels as detected by immunoprecipitation followed by immunoblotting. A mutant LMW-PTP protein in which the catalytic cysteine in the active site was replaced with a serine lacked phosphatase activity, and was used to identify a number of trapped putative substrate proteins via mass spectrometry analysis. Seven of these putative substrate protein genes were cloned with an epitope tag and overexpressed in amebae. Five of these seven putative substrate proteins were demonstrated to interact specifically with the mutant LMW-PTP. This is the first biochemical study of a small tyrosine phosphatase in Entamoeba, and sets the stage for understanding its role in amebic biology and pathogenesis.
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Affiliation(s)
- Alicia S Linford
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, USA.
| | - Nona M Jiang
- Division of Infectious Diseases and International Health, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA; Emerald Bio, Bainbridge Island, WA 98110, USA
| | - Nicholas E Sherman
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA 22908, USA
| | - Wesley C Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA; Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Lance J Stewart
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA; Emerald Bio, Bainbridge Island, WA 98110, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA; Seattle Biomedical Research Institute, Seattle, WA 98109, USA; Departments of Global Health and Medical Education & Biomedical Informatics, University of Washington, Seattle, WA 98195, USA
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA; Emerald Bio, Bainbridge Island, WA 98110, USA
| | - William A Petri
- Division of Infectious Diseases and International Health, University of Virginia Health System, Charlottesville, VA 22908, USA; Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA; Department of Pathology, University of Virginia, Charlottesville, VA 22908, USA.
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Abendroth J, Ollodart A, Andrews ESV, Myler PJ, Staker BL, Edwards TE, Arcus VL, Grundner C. Mycobacterium tuberculosis Rv2179c protein establishes a new exoribonuclease family with broad phylogenetic distribution. J Biol Chem 2013; 289:2139-47. [PMID: 24311791 DOI: 10.1074/jbc.m113.525683] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Ribonucleases (RNases) maintain the cellular RNA pool by RNA processing and degradation. In many bacteria, including the human pathogen Mycobacterium tuberculosis (Mtb), the enzymes mediating several central RNA processing functions are still unknown. Here, we identify the hypothetical Mtb protein Rv2179c as a highly divergent exoribonuclease. Although the primary sequence of Rv2179c has no detectable similarity to any known RNase, the Rv2179c crystal structure reveals an RNase fold. Active site residues are equivalent to those in the DEDD family of RNases, and Rv2179c has close structural homology to Escherichia coli RNase T. Consistent with the DEDD fold, Rv2179c has exoribonuclease activity, cleaving the 3' single-strand overhangs of duplex RNA. Functional orthologs of Rv2179c are prevalent in actinobacteria and found in bacteria as phylogenetically distant as proteobacteria. Thus, Rv2179c is the founding member of a new, large RNase family with hundreds of members across the bacterial kingdom.
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Affiliation(s)
- Jan Abendroth
- From Emerald Bio, Bainbridge Island, Washington 98110
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Zhang Z, Jakkaraju S, Blain J, Gogol K, Zhao L, Hartley RC, Karlsson CA, Staker BL, Edwards TE, Stewart LJ, Myler PJ, Clare M, Begley DW, Horn JR, Hagen TJ. Cytidine derivatives as IspF inhibitors of Burkolderia pseudomallei. Bioorg Med Chem Lett 2013; 23:6860-3. [PMID: 24157367 DOI: 10.1016/j.bmcl.2013.09.101] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Revised: 09/30/2013] [Accepted: 09/30/2013] [Indexed: 11/17/2022]
Abstract
Published biological data suggest that the methyl erythritol phosphate (MEP) pathway, a non-mevalonate isoprenoid biosynthetic pathway, is essential for certain bacteria and other infectious disease organisms. One highly conserved enzyme in the MEP pathway is 2C-methyl-d-erythritol 2,4-cyclodiphosphate synthase (IspF). Fragment-bound complexes of IspF from Burkholderia pseudomallei were used to design and synthesize a series of molecules linking the cytidine moiety to different zinc pocket fragment binders. Testing by surface plasmon resonance (SPR) found one molecule in the series to possess binding affinity equal to that of cytidine diphosphate, despite lacking any metal-coordinating phosphate groups. Close inspection of the SPR data suggest different binding stoichiometries between IspF and test compounds. Crystallographic analysis shows important variations between the binding mode of one synthesized compound and the pose of the bound fragment from which it was designed. The binding modes of these molecules add to our structural knowledge base for IspF and suggest future refinements in this compound series.
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Affiliation(s)
- Zheng Zhang
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL, USA
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Armour BL, Barnes SR, Moen SO, Smith E, Raymond AC, Fairman JW, Stewart LJ, Staker BL, Begley DW, Edwards TE, Lorimer DD. Multi-target parallel processing approach for gene-to-structure determination of the influenza polymerase PB2 subunit. J Vis Exp 2013. [PMID: 23851357 PMCID: PMC3747311 DOI: 10.3791/4225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Pandemic outbreaks of highly virulent influenza strains can cause widespread morbidity and mortality in human populations worldwide. In the United States alone, an average of 41,400 deaths and 1.86 million hospitalizations are caused by influenza virus infection each year 1. Point mutations in the polymerase basic protein 2 subunit (PB2) have been linked to the adaptation of the viral infection in humans 2. Findings from such studies have revealed the biological significance of PB2 as a virulence factor, thus highlighting its potential as an antiviral drug target. The structural genomics program put forth by the National Institute of Allergy and Infectious Disease (NIAID) provides funding to Emerald Bio and three other Pacific Northwest institutions that together make up the Seattle Structural Genomics Center for Infectious Disease (SSGCID). The SSGCID is dedicated to providing the scientific community with three-dimensional protein structures of NIAID category A-C pathogens. Making such structural information available to the scientific community serves to accelerate structure-based drug design. Structure-based drug design plays an important role in drug development. Pursuing multiple targets in parallel greatly increases the chance of success for new lead discovery by targeting a pathway or an entire protein family. Emerald Bio has developed a high-throughput, multi-target parallel processing pipeline (MTPP) for gene-to-structure determination to support the consortium. Here we describe the protocols used to determine the structure of the PB2 subunit from four different influenza A strains.
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Baugh L, Gallagher LA, Patrapuvich R, Clifton MC, Gardberg AS, Edwards TE, Armour B, Begley DW, Dieterich SH, Dranow DM, Abendroth J, Fairman JW, Fox D, Staker BL, Phan I, Gillespie A, Choi R, Nakazawa-Hewitt S, Nguyen MT, Napuli A, Barrett L, Buchko GW, Stacy R, Myler PJ, Stewart LJ, Manoil C, Van Voorhis WC. Combining functional and structural genomics to sample the essential Burkholderia structome. PLoS One 2013; 8:e53851. [PMID: 23382856 PMCID: PMC3561365 DOI: 10.1371/journal.pone.0053851] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 12/05/2012] [Indexed: 11/19/2022] Open
Abstract
Background The genus Burkholderia includes pathogenic gram-negative bacteria that cause melioidosis, glanders, and pulmonary infections of patients with cancer and cystic fibrosis. Drug resistance has made development of new antimicrobials critical. Many approaches to discovering new antimicrobials, such as structure-based drug design and whole cell phenotypic screens followed by lead refinement, require high-resolution structures of proteins essential to the parasite. Methodology/Principal Findings We experimentally identified 406 putative essential genes in B. thailandensis, a low-virulence species phylogenetically similar to B. pseudomallei, the causative agent of melioidosis, using saturation-level transposon mutagenesis and next-generation sequencing (Tn-seq). We selected 315 protein products of these genes based on structure-determination criteria, such as excluding very large and/or integral membrane proteins, and entered them into the Seattle Structural Genomics Center for Infection Disease (SSGCID) structure determination pipeline. To maximize structural coverage of these targets, we applied an “ortholog rescue” strategy for those producing insoluble or difficult to crystallize proteins, resulting in the addition of 387 orthologs (or paralogs) from seven other Burkholderia species into the SSGCID pipeline. This structural genomics approach yielded structures from 31 putative essential targets from B. thailandensis, and 25 orthologs from other Burkholderia species, yielding an overall structural coverage for 49 of the 406 essential gene families, with a total of 88 depositions into the Protein Data Bank. Of these, 25 proteins have properties of a potential antimicrobial drug target i.e., no close human homolog, part of an essential metabolic pathway, and a deep binding pocket. We describe the structures of several potential drug targets in detail. Conclusions/Significance This collection of structures, solubility and experimental essentiality data provides a resource for development of drugs against infections and diseases caused by Burkholderia. All expression clones and proteins created in this study are freely available by request.
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Affiliation(s)
- Loren Baugh
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Larry A. Gallagher
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Rapatbhorn Patrapuvich
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Matthew C. Clifton
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Anna S. Gardberg
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Brianna Armour
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Darren W. Begley
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | | | - David M. Dranow
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - James W. Fairman
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - David Fox
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Isabelle Phan
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Angela Gillespie
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
| | - Ryan Choi
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
| | - Steve Nakazawa-Hewitt
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
| | - Mary Trang Nguyen
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
| | - Alberto Napuli
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
| | - Lynn Barrett
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
| | - Garry W. Buchko
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Robin Stacy
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Medical Education and Biomedical Informatics, University of Washington, Seattle, Washington
| | - Lance J. Stewart
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Colin Manoil
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Wesley C. Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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Edwards TE, Abramov AB, Smith ER, Baydo RO, Leonard JT, Leibly DJ, Thompkins KB, Clifton MC, Gardberg AS, Staker BL, Van Voorhis WC, Myler PJ, Stewart LJ. Structural characterization of a ribose-5-phosphate isomerase B from the pathogenic fungus Coccidioides immitis. BMC Struct Biol 2011; 11:39. [PMID: 21995815 PMCID: PMC3212906 DOI: 10.1186/1472-6807-11-39] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 10/13/2011] [Indexed: 01/01/2023]
Abstract
BACKGROUND Ribose-5-phosphate isomerase is an enzyme that catalyzes the interconversion of ribose-5-phosphate and ribulose-5-phosphate. This family of enzymes naturally occurs in two distinct classes, RpiA and RpiB, which play an important role in the pentose phosphate pathway and nucleotide and co-factor biogenesis. RESULTS Although RpiB occurs predominantly in bacteria, here we report crystal structures of a putative RpiB from the pathogenic fungus Coccidioides immitis. A 1.9 Å resolution apo structure was solved by combined molecular replacement and single wavelength anomalous dispersion (SAD) phasing using a crystal soaked briefly in a solution containing a high concentration of iodide ions. RpiB from C. immitis contains modest sequence and high structural homology to other known RpiB structures. A 1.8 Å resolution phosphate-bound structure demonstrates phosphate recognition and charge stabilization by a single positively charged residue whereas other members of this family use up to five positively charged residues to contact the phosphate of ribose-5-phosphate. A 1.7 Å resolution structure was obtained in which the catalytic base of C. immitis RpiB, Cys76, appears to form a weakly covalent bond with the central carbon of malonic acid with a bond distance of 2.2 Å. This interaction may mimic that formed by the suicide inhibitor iodoacetic acid with RpiB. CONCLUSION The C. immitis RpiB contains the same fold and similar features as other members of this class of enzymes such as a highly reactive active site cysteine residue, but utilizes a divergent phosphate recognition strategy and may recognize a different substrate altogether.
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Affiliation(s)
- Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA.
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Buchko GW, Edwards TE, Abendroth J, Arakaki TL, Law L, Napuli AJ, Hewitt SN, Van Voorhis WC, Stewart LJ, Staker BL, Myler PJ. Structure of a Nudix hydrolase (MutT) in the Mg(2+)-bound state from Bartonella henselae, the bacterium responsible for cat scratch fever. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1078-83. [PMID: 21904053 PMCID: PMC3169405 DOI: 10.1107/s1744309111011559] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Accepted: 03/28/2011] [Indexed: 05/31/2023]
Abstract
Cat scratch fever (also known as cat scratch disease and bartonellosis) is an infectious disease caused by the proteobacterium Bartonella henselae following a cat scratch. Although the infection usually resolves spontaneously without treatment in healthy adults, bartonellosis may lead to severe complications in young children and immunocompromised patients, and there is new evidence suggesting that B. henselae may be associated with a broader range of clinical symptoms then previously believed. The genome of B. henselae contains genes for two putative Nudix hydrolases, BH02020 and BH01640 (KEGG). Nudix proteins play an important role in regulating the intracellular concentration of nucleotide cofactors and signaling molecules. The amino-acid sequence of BH02020 is similar to that of the prototypical member of the Nudix superfamily, Escherichia coli MutT, a protein that is best known for its ability to neutralize the promutagenic compound 7,8-dihydro-8-oxoguanosine triphosphate. Here, the crystal structure of BH02020 (Bh-MutT) in the Mg(2+)-bound state was determined at 2.1 Å resolution (PDB entry 3hhj). As observed in all Nudix hydrolase structures, the α-helix of the highly conserved `Nudix box' in Bh-MutT is one of two helices that sandwich a four-stranded mixed β-sheet with the central two β-strands parallel to each other. The catalytically essential divalent cation observed in the Bh-MutT structure, Mg(2+), is coordinated to the side chains of Glu57 and Glu61. The structure is not especially robust; a temperature melt obtained using circular dichroism spectroscopy shows that Bh-MutT irreversibly unfolds and precipitates out of solution upon heating, with a T(m) of 333 K.
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Affiliation(s)
- Garry W. Buchko
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
- Emerald BioStructures, Bainbridge Island, Washington, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
- Emerald BioStructures, Bainbridge Island, Washington, USA
| | - Tracy L. Arakaki
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
- Emerald BioStructures, Bainbridge Island, Washington, USA
| | - Laura Law
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
- Emerald BioStructures, Bainbridge Island, Washington, USA
| | - Alberto J. Napuli
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Stephen N. Hewitt
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Wesley C. Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Lance J. Stewart
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
- Emerald BioStructures, Bainbridge Island, Washington, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
- Emerald BioStructures, Bainbridge Island, Washington, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
- Seattle Biomedical Research Institute, Seattle, Washington, USA
- Department of Medical Education and Biomedical Informatics and Department of Global Health, University of Washington, Seattle, Washington, USA
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44
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Smith ER, Begley DW, Anderson V, Raymond AC, Haffner TE, Robinson JI, Edwards TE, Duncan N, Gerdts CJ, Mixon MB, Nollert P, Staker BL, Stewart LJ. The Protein Maker: an automated system for high-throughput parallel purification. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1015-21. [PMID: 21904043 PMCID: PMC3169395 DOI: 10.1107/s1744309111028776] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Accepted: 07/17/2011] [Indexed: 12/03/2022]
Abstract
The Protein Maker is an automated purification system developed by Emerald BioSystems for high-throughput parallel purification of proteins and antibodies. This instrument allows multiple load, wash and elution buffers to be used in parallel along independent lines for up to 24 individual samples. To demonstrate its utility, its use in the purification of five recombinant PB2 C-terminal domains from various subtypes of the influenza A virus is described. Three of these constructs crystallized and one diffracted X-rays to sufficient resolution for structure determination and deposition in the Protein Data Bank. Methods for screening lysis buffers for a cytochrome P450 from a pathogenic fungus prior to upscaling expression and purification are also described. The Protein Maker has become a valuable asset within the Seattle Structural Genomics Center for Infectious Disease (SSGCID) and hence is a potentially valuable tool for a variety of high-throughput protein-purification applications.
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Affiliation(s)
- Eric R. Smith
- Seattle Structural Genomics Center for Infectious Disease (http://www.ssgcid.org), USA
- Emerald BioStructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Darren W. Begley
- Seattle Structural Genomics Center for Infectious Disease (http://www.ssgcid.org), USA
- Emerald BioStructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Vanessa Anderson
- Seattle Structural Genomics Center for Infectious Disease (http://www.ssgcid.org), USA
- Emerald BioStructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Amy C. Raymond
- Seattle Structural Genomics Center for Infectious Disease (http://www.ssgcid.org), USA
- Emerald BioStructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Taryn E. Haffner
- Seattle Structural Genomics Center for Infectious Disease (http://www.ssgcid.org), USA
- Emerald BioStructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - John I. Robinson
- Emerald BioStructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease (http://www.ssgcid.org), USA
- Emerald BioStructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Natalie Duncan
- Emerald BioSystems, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Cory J. Gerdts
- Emerald BioSystems, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Mark B. Mixon
- Seattle Structural Genomics Center for Infectious Disease (http://www.ssgcid.org), USA
- Emerald BioStructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Peter Nollert
- Emerald BioStructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease (http://www.ssgcid.org), USA
- Emerald BioStructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Lance J. Stewart
- Seattle Structural Genomics Center for Infectious Disease (http://www.ssgcid.org), USA
- Emerald BioStructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
- Emerald BioSystems, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
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45
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Clifton MC, Abendroth J, Edwards TE, Leibly DJ, Gillespie AK, Ferrell M, Dieterich SH, Exley I, Staker BL, Myler PJ, Van Voorhis WC, Stewart LJ. Structure of the cystathionine γ-synthase MetB from Mycobacterium ulcerans. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1154-8. [PMID: 21904066 PMCID: PMC3169418 DOI: 10.1107/s1744309111029575] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 07/21/2011] [Indexed: 11/27/2022]
Abstract
Cystathionine γ-synthase (CGS) is a transulfurication enzyme that catalyzes the first specific step in L-methionine biosynthesis by the reaction of O(4)-succinyl-L-homoserine and L-cysteine to produce L-cystathionine and succinate. Controlling the first step in L-methionine biosythesis, CGS is an excellent potential drug target. Mycobacterium ulcerans is a slow-growing mycobacterium that is the third most common form of mycobacterial infection, mainly infecting people in Africa, Australia and Southeast Asia. Infected patients display a variety of skin ailments ranging from indolent non-ulcerated lesions as well as ulcerated lesions. Here, the crystal structure of CGS from M. ulcerans covalently linked to the cofactor pyridoxal phosphate (PLP) is reported at 1.9 Å resolution. A second structure contains PLP as well as a highly ordered HEPES molecule in the active site acting as a pseudo-ligand. These results present the first structure of a CGS from a mycobacterium and allow comparison with other CGS enzymes. This is also the first structure reported from the pathogen M. ulcerans.
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Affiliation(s)
- Matthew C Clifton
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA.
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46
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Davies DR, Staker BL, Abendroth JA, Edwards TE, Hartley R, Leonard J, Kim H, Rychel AL, Hewitt SN, Myler PJ, Stewart LJ. An ensemble of structures of Burkholderia pseudomallei 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1044-50. [PMID: 21904048 PMCID: PMC3169400 DOI: 10.1107/s1744309111030405] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2011] [Accepted: 07/28/2011] [Indexed: 11/29/2022]
Abstract
Burkholderia pseudomallei is a soil-dwelling bacterium endemic to Southeast Asia and Northern Australia. Burkholderia is responsible for melioidosis, a serious infection of the skin. The enzyme 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase (PGAM) catalyzes the interconversion of 3-phosphoglycerate and 2-phosphoglycerate, a key step in the glycolytic pathway. As such it is an extensively studied enzyme and X-ray crystal structures of PGAM enzymes from multiple species have been elucidated. Vanadate is a phosphate mimic that is a powerful tool for studying enzymatic mechanisms in phosphoryl-transfer enzymes such as phosphoglycerate mutase. However, to date no X-ray crystal structures of phosphoglycerate mutase have been solved with vanadate acting as a substrate mimic. Here, two vanadate complexes together with an ensemble of substrate and fragment-bound structures that provide a comprehensive picture of the function of the Burkholderia enzyme are reported.
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Affiliation(s)
- Douglas R Davies
- Seattle Structural Genomics Center for Infectious Disease (http://www.ssgcid.org), USA.
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47
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Begley DW, Davies DR, Hartley RC, Hewitt SN, Rychel AL, Myler PJ, Van Voorhis WC, Staker BL, Stewart LJ. Probing conformational states of glutaryl-CoA dehydrogenase by fragment screening. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1060-9. [PMID: 21904051 PMCID: PMC3169403 DOI: 10.1107/s1744309111014436] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Accepted: 04/17/2011] [Indexed: 11/10/2022]
Abstract
Glutaric acidemia type 1 is an inherited metabolic disorder which can cause macrocephaly, muscular rigidity, spastic paralysis and other progressive movement disorders in humans. The defects in glutaryl-CoA dehydrogenase (GCDH) associated with this disease are thought to increase holoenzyme instability and reduce cofactor binding. Here, the first structural analysis of a GCDH enzyme in the absence of the cofactor flavin adenine dinucleotide (FAD) is reported. The apo structure of GCDH from Burkholderia pseudomallei reveals a loss of secondary structure and increased disorder in the FAD-binding pocket relative to the ternary complex of the highly homologous human GCDH. After conducting a fragment-based screen, four small molecules were identified which bind to GCDH from B. pseudomallei. Complex structures were determined for these fragments, which cause backbone and side-chain perturbations to key active-site residues. Structural insights from this investigation highlight differences from apo GCDH and the utility of small-molecular fragments as chemical probes for capturing alternative conformational states of preformed protein crystals.
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Affiliation(s)
- Darren W Begley
- Seattle Structural Genomics Center for Infectious Disease (http://www.ssgcid.org), USA.
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48
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Edwards TE, Bryan CM, Leibly DJ, Dieterich SH, Abendroth J, Sankaran B, Sivam D, Staker BL, Van Voorhis WC, Myler PJ, Stewart LJ. Structures of a putative ζ-class glutathione S-transferase from the pathogenic fungus Coccidioides immitis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1038-43. [PMID: 21904047 PMCID: PMC3169399 DOI: 10.1107/s1744309111009493] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Accepted: 03/12/2011] [Indexed: 11/25/2022]
Abstract
Coccidioides immitis is a pathogenic fungus populating the southwestern United States and is a causative agent of coccidioidomycosis, sometimes referred to as Valley Fever. Although the genome of this fungus has been sequenced, many operons are not properly annotated. Crystal structures are presented for a putative uncharacterized protein that shares sequence similarity with ζ-class glutathione S-transferases (GSTs) in both apo and glutathione-bound forms. The apo structure reveals a nonsymmetric homodimer with each protomer comprising two subdomains: a C-terminal helical domain and an N-terminal thioredoxin-like domain that is common to all GSTs. Half-site binding is observed in the glutathione-bound form. Considerable movement of some components of the active site relative to the glutathione-free form was observed, indicating an induced-fit mechanism for cofactor binding. The sequence homology, structure and half-site occupancy imply that the protein is a ζ-class glutathione S-transferase, a maleylacetoacetate isomerase (MAAI).
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49
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Ferrell M, Abendroth J, Zhang Y, Sankaran B, Edwards TE, Staker BL, Van Voorhis WC, Stewart LJ, Myler PJ. Structure of aldose reductase from Giardia lamblia. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1113-7. [PMID: 21904059 PMCID: PMC3169411 DOI: 10.1107/s1744309111030879] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 08/01/2011] [Indexed: 12/02/2022]
Abstract
Giardia lamblia is an anaerobic aerotolerant eukaryotic parasite of the intestines. It is believed to have diverged early from eukarya during evolution and is thus lacking in many of the typical eukaryotic organelles and biochemical pathways. Most conspicuously, mitochondria and the associated machinery of oxidative phosphorylation are absent; instead, energy is derived from substrate-level phosphorylation. Here, the 1.75 Å resolution crystal structure of G. lamblia aldose reductase heterologously expressed in Escherichia coli is reported. As in other oxidoreductases, G. lamblia aldose reductase adopts a TIM-barrel conformation with the NADP(+)-binding site located within the eight β-strands of the interior.
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Affiliation(s)
- M Ferrell
- Seattle Structural Genomics Center for Infectious Disease, USA.
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50
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Subramanian S, Abendroth J, Phan IQH, Olsen C, Staker BL, Napuli A, Van Voorhis WC, Stacy R, Myler PJ. Structure of 3-ketoacyl-(acyl-carrier-protein) reductase from Rickettsia prowazekii at 2.25 Å resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1118-22. [PMID: 21904060 PMCID: PMC3169412 DOI: 10.1107/s1744309111030673] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 07/29/2011] [Indexed: 11/29/2022]
Abstract
Rickettsia prowazekii, a parasitic Gram-negative bacterium, is in the second-highest biodefense category of pathogens of the National Institute of Allergy and Infectious Diseases, but only a handful of structures have been deposited in the PDB for this bacterium; to date, all of these have been solved by the SSGCID. Owing to its small genome (about 800 protein-coding genes), it relies on the host for many basic biosynthetic processes, hindering the identification of potential antipathogenic drug targets. However, like many bacteria and plants, its metabolism does depend upon the type II fatty-acid synthesis (FAS) pathway for lipogenesis, whereas the predominant form of fatty-acid biosynthesis in humans is via the type I pathway. Here, the structure of the third enzyme in the FAS pathway, 3-ketoacyl-(acyl-carrier-protein) reductase, is reported at a resolution of 2.25 Å. Its fold is highly similar to those of the existing structures from some well characterized pathogens, such as Mycobacterium tuberculosis and Burkholderia pseudomallei, but differs significantly from the analogous mammalian structure. Hence, drugs known to target the enzymes of pathogenic bacteria may serve as potential leads against Rickettsia, which is responsible for spotted fever and typhus and is found throughout the world.
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