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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:S2053230X2400356X. [PMID: 38656226 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] [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
| | | | - Matthew C Clifton
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), 307 Westlake Avenue North, Seattle, WA 98109, USA
| | - Thomas E Edwards
- 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
| | | | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), 307 Westlake Avenue North, Seattle, WA 98109, USA
| | - Peter Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), 307 Westlake Avenue North, Seattle, WA 98109, USA
| | - Krystle J McLaughlin
- Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA
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2
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De Vitto H, Belfon KKJ, Sharma N, Toay S, Abendroth J, Dranow DM, Lukacs CM, Choi R, Udell HS, Willis S, Barrera G, Beyer O, Li TD, Hicks KA, Torelli AT, French JB. Characterization of an Acinetobacter baumannii Monofunctional Phosphomethylpyrimidine Kinase That Is Inhibited by Pyridoxal Phosphate. Biochemistry 2024. [PMID: 38306231 DOI: 10.1021/acs.biochem.3c00640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2024]
Abstract
Thiamin and its phosphate derivatives are ubiquitous molecules involved as essential cofactors in many cellular processes. The de novo biosynthesis of thiamin employs the parallel synthesis of 4-methyl-5-(2-hydroxyethyl)thiazole (THZ-P) and 4-amino-2-methyl-5(diphosphooxymethyl) pyrimidine (HMP) pyrophosphate (HMP-PP), which are coupled to generate thiamin phosphate. Most organisms that can biosynthesize thiamin employ a kinase (HMPK or ThiD) to generate HMP-PP. In nearly all cases, this enzyme is bifunctional and can also salvage free HMP, producing HMP-P, the monophosphate precursor of HMP-PP. Here we present high-resolution crystal structures of an HMPK from Acinetobacter baumannii (AbHMPK), both unliganded and with pyridoxal 5-phosphate (PLP) noncovalently bound. Despite the similarity between HMPK and pyridoxal kinase enzymes, our kinetics analysis indicates that AbHMPK accepts HMP exclusively as a substrate and cannot turn over pyridoxal, pyridoxamine, or pyridoxine nor does it display phosphatase activity. PLP does, however, act as a weak inhibitor of AbHMPK with an IC50 of 768 μM. Surprisingly, unlike other HMPKs, AbHMPK catalyzes only the phosphorylation of HMP and does not generate the diphosphate HMP-PP. This suggests that an additional kinase is present in A. baumannii, or an alternative mechanism is in operation to complete the biosynthesis of thiamin.
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Affiliation(s)
- Humberto De Vitto
- The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, United States
| | - Kafi K J Belfon
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11790, United States
| | - Nandini Sharma
- The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, United States
| | - Sarah Toay
- Department of Biological Chemistry, Grinnell College, Grinnell, Iowa 50112, United States
| | - Jan Abendroth
- UCB BioSciences, Bainbridge Island, Washington 98110, United States
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98104, United States
| | - David M Dranow
- UCB BioSciences, Bainbridge Island, Washington 98110, United States
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98104, United States
| | - Christine M Lukacs
- UCB BioSciences, Bainbridge Island, Washington 98110, United States
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98104, United States
| | - Ryan Choi
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98104, United States
| | - Hannah S Udell
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98104, United States
| | - Sydney Willis
- Department of Chemistry, Rollins College, Winter Park, Florida 32789, United States
| | - George Barrera
- Department of Chemistry and Biochemistry, Weber State University, Ogden, Utah 84408, United States
| | - Olive Beyer
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
| | - Teng Da Li
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11790, United States
| | - Katherine A Hicks
- Chemistry Department, State University of New York at Cortland, Cortland, New York 13045, United States
| | - Andrew T Torelli
- Department of Chemistry, Ithaca College, Ithaca, New York 14850, United States
| | - Jarrod B French
- The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, United States
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3
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Milanes JE, Yan VC, Pham CD, Muller F, Kwain S, Rees KC, Dominy BN, Whitehead DC, Millward SW, Bolejack M, Abendroth J, Phan IQ, Staker B, Moseman EA, Zhang X, Ma X, Jebet A, Yin X, Morris JC. Enolase inhibitors as therapeutic leads for Naegleria fowleri infection. bioRxiv 2024:2024.01.16.575558. [PMID: 38293107 PMCID: PMC10827119 DOI: 10.1101/2024.01.16.575558] [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] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Infections with the pathogenic free-living amoebae Naegleria fowleri can lead to life-threatening illnesses including catastrophic primary amebic meningoencephalitis (PAM). Efficacious treatment options for these infections are lacking and the mortality rate remains >95% in the US. Glycolysis is very important for the infectious trophozoite lifecycle stage and inhibitors of glucose metabolism have been found to be toxic to the pathogen. Recently, human enolase 2 (ENO2) phosphonate inhibitors have been developed as lead agents to treat glioblastoma multiforme (GBM). These compounds, which cure GBM in a rodent model, are well-tolerated in mammals because enolase 1 (ENO1) is the predominant isoform used systemically. Here, we describe findings that demonstrate that these agents are potent inhibitors of N. fowleri ENO ( Nf ENO) and are lethal to amoebae. In particular, (1-hydroxy-2-oxopiperidin-3-yl) phosphonic acid (HEX) was a potent enzyme inhibitor (IC 50 value of 0.14 ± 0.04 µM) that was toxic to trophozoites (EC 50 value of 0.21 ± 0.02 µM) while the reported CC 50 was >300 µM. Molecular docking simulation revealed that HEX binds strongly to the active site of Nf ENO with a binding affinity of -8.6 kcal/mol. Metabolomic studies of parasites treated with HEX revealed a 4.5 to 78-fold accumulation of glycolytic intermediates upstream of Nf ENO. Last, nasal instillation of HEX increased longevity of amoebae-infected rodents. Two days after infection, animals were treated for 10 days with 3 mg/kg HEX, followed by one week of observation. At the conclusion of the experiment, eight of 12 HEX-treated animals remained alive (resulting in an indeterminable median survival time) while one of 12 vehicle-treated rodents remained, yielding a median survival time of 10.9 days. Brains of six of the eight survivors were positive for amoebae, suggesting the agent at the tested dose suppressed, but did not eliminate, infection. These findings suggest that HEX is a promising lead for the treatment of PAM.
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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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5
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DeBouver ND, Bolejack MJ, Esan TE, Krysan DJ, Hagen TJ, Abendroth J. Bacterial structural genomics target enabled by a recently discovered potent fungal acetyl-CoA synthetase inhibitor. Acta Crystallogr F Struct Biol Commun 2023; 79:137-143. [PMID: 37223974 DOI: 10.1107/s2053230x23003801] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/27/2023] [Indexed: 05/25/2023] Open
Abstract
The compound ethyl-adenosyl monophosphate ester (ethyl-AMP) has been shown to effectively inhibit acetyl-CoA synthetase (ACS) enzymes and to facilitate the crystallization of fungal ACS enzymes in various contexts. In this study, the addition of ethyl-AMP to a bacterial ACS from Legionella pneumophila resulted in the determination of a co-crystal structure of this previously elusive structural genomics target. The dual functionality of ethyl-AMP in both inhibiting ACS enzymes and promoting crystallization establishes its significance as a valuable resource for advancing structural investigations of this class of proteins.
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Affiliation(s)
| | | | - Taiwo E Esan
- Department of Chemistry and Biochemistry, Northern Illinois University, 1426 Lincoln Highway, DeKalb, IL 60115, USA
| | - Damian J Krysan
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Timothy J Hagen
- Department of Chemistry and Biochemistry, Northern Illinois University, 1426 Lincoln Highway, DeKalb, IL 60115, USA
| | - Jan Abendroth
- UCB Pharma, 7869 NE Day Road West, Bainbridge Island, WA 98102, USA
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6
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Ghafoori SM, Petersen GF, Conrady DG, Calhoun BM, Stigliano MZZ, Baydo RO, Grice R, Abendroth J, Lorimer DD, Edwards TE, Forwood JK. Structural characterisation of hemagglutinin from seven Influenza A H1N1 strains reveal diversity in the C05 antibody recognition site. Sci Rep 2023; 13:6940. [PMID: 37117205 PMCID: PMC10140725 DOI: 10.1038/s41598-023-33529-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/14/2023] [Indexed: 04/30/2023] Open
Abstract
Influenza virus (IV) causes several outbreaks of the flu each year resulting in an economic burden to the healthcare system in the billions of dollars. Several influenza pandemics have occurred during the last century and estimated to have caused 100 million deaths. There are four genera of IV, A (IVA), B (IVB), C (IVC), and D (IVD), with IVA being the most virulent to the human population. Hemagglutinin (HA) is an IVA surface protein that allows the virus to attach to host cell receptors and enter the cell. Here we have characterised the high-resolution structures of seven IVA HAs, with one in complex with the anti-influenza head-binding antibody C05. Our analysis revealed conserved receptor binding residues in all structures, as seen in previously characterised IV HAs. Amino acid conservation is more prevalent on the stalk than the receptor binding domain (RBD; also called the head domain), allowing the virus to escape from antibodies targeting the RBD. The equivalent site of C05 antibody binding to A/Denver/57 HA appears hypervariable in the other H1N1 IV HAs. Modifications within this region appear to disrupt binding of the C05 antibody, as these HAs no longer bind the C05 antibody by analytical SEC. Our study brings new insights into the structural and functional recognition of IV HA proteins and can contribute to further development of anti-influenza vaccines.
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Affiliation(s)
- Seyed Mohammad Ghafoori
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2650, Australia
| | - Gayle F Petersen
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2650, Australia
| | - Deborah G Conrady
- UCB BioSciences, Bainbridge Island, WA, 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, 98109, USA
| | - Brandy M Calhoun
- UCB BioSciences, Bainbridge Island, WA, 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, 98109, USA
| | - Matthew Z Z Stigliano
- UCB BioSciences, Bainbridge Island, WA, 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, 98109, USA
| | - Ruth O Baydo
- UCB BioSciences, Bainbridge Island, WA, 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, 98109, USA
| | - Rena Grice
- UCB BioSciences, Bainbridge Island, WA, 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, 98109, USA
| | - Jan Abendroth
- UCB BioSciences, Bainbridge Island, WA, 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, 98109, USA
| | - Donald D Lorimer
- UCB BioSciences, Bainbridge Island, WA, 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, 98109, USA
| | - Thomas E Edwards
- UCB BioSciences, Bainbridge Island, WA, 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, 98109, USA
| | - Jade K Forwood
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2650, Australia.
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Roquet-Banères F, Alcaraz M, Hamela C, Abendroth J, Edwards TE, Kremer L. In Vitro and In Vivo Efficacy of NITD-916 against Mycobacterium fortuitum. Antimicrob Agents Chemother 2023; 67:e0160722. [PMID: 36920188 PMCID: PMC10112203 DOI: 10.1128/aac.01607-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 12/01/2022] [Accepted: 02/16/2023] [Indexed: 03/16/2023] Open
Abstract
Mycobacterium fortuitum represents one of the most clinically relevant rapid-growing mycobacterial species. Treatments are complex due to antibiotic resistance and to severe side effects of effective drugs, prolonged time of treatment, and co-infection with other pathogens. Herein, we explored the activity of NITD-916, a direct inhibitor of the enoyl-ACP reductase InhA of the type II fatty acid synthase in Mycobacterium tuberculosis. We found that this compound displayed very low MIC values against a panel of M. fortuitum clinical strains and exerted potent antimicrobial activity against M. fortuitum in macrophages. Remarkably, the compound was also highly efficacious in a zebrafish model of infection. Short duration treatments were sufficient to significantly protect the infected larvae from M. fortuitum-induced killing, which correlated with reduced bacterial burdens and abscesses. Biochemical analyses demonstrated an inhibition of de novo synthesis of mycolic acids. Resolving the crystal structure of the InhAMFO in complex with NAD and NITD-916 confirmed that NITD-916 is a direct inhibitor of InhAMFO. Importantly, single nucleotide polymorphism leading to a G96S substitution in InhAMFO conferred high resistance levels to NITD-916, thus resolving its target in M. fortuitum. Overall, these findings indicate that NITD-916 is highly active against M. fortuitum both in vitro and in vivo and should be considered in future preclinical evaluations for the treatment of M. fortuitum pulmonary diseases.
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Affiliation(s)
- Françoise Roquet-Banères
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
| | - Matthéo Alcaraz
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
| | - Claire Hamela
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
| | - Jan Abendroth
- UCB BioSciences, Bainbridge Island, Washington, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Thomas E. Edwards
- UCB BioSciences, Bainbridge Island, Washington, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Laurent Kremer
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
- INSERM, IRIM, Montpellier, France
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8
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Alcaraz M, Roquet-Banères F, Leon-Icaza SA, Abendroth J, Boudehen YM, Cougoule C, Edwards TE, Kremer L. Efficacy and Mode of Action of a Direct Inhibitor of Mycobacterium abscessus InhA. ACS Infect Dis 2022; 8:2171-2186. [PMID: 36107992 DOI: 10.1021/acsinfecdis.2c00314] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
There is an unmet medical need for effective treatments against Mycobacterium abscessus pulmonary infections, to which cystic fibrosis (CF) patients are particularly vulnerable. Recent studies showed that the antitubercular drug isoniazid is inactive against M. abscessus due to the incapacity of the catalase-peroxidase to convert the pro-drug into a reactive metabolite that inhibits the enoyl-ACP reductase InhA. To validate InhAMAB as a druggable target in M. abscessus, we assayed the activity of NITD-916, a 4-hydroxy-2-pyridone lead candidate initially described as a direct inhibitor of InhA that bypasses KatG bioactivation in Mycobacterium tuberculosis. The compound displayed low MIC values against rough and smooth clinical isolates in vitro and significantly reduced the bacterial burden inside human macrophages. Moreover, treatment with NITD-916 reduced the number and size of intracellular mycobacterial cords, regarded as markers of the severity of the infection. Importantly, NITD-916 significantly lowered the M. abscessus burden in CF-derived lung airway organoids. From a mechanistic perspective, NITD-916 abrogated de novo synthesis of mycolic acids and NITD-916-resistant spontaneous mutants harbored point mutations in InhAMAB at residue 96. That NITD-916 targets InhAMAB directly without activation requirements was confirmed genetically and by resolving the crystal structure of the protein in complex with NADH and NITD-916. These findings collectively indicate that InhAMAB is an attractive target to be exploited for future chemotherapeutic developments against this difficult-to-treat mycobacterium and highlight the potential of NITD-916 derivatives for further evaluation in preclinical settings.
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Affiliation(s)
- Matthéo Alcaraz
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Françoise Roquet-Banères
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Stephen Adonai Leon-Icaza
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, 31400 Toulouse, France
| | - Jan Abendroth
- UCB BioSciences, Bainbridge Island, Washington 98109, United States.,Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
| | - Yves-Marie Boudehen
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Céline Cougoule
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, 31400 Toulouse, France
| | - Thomas E Edwards
- UCB BioSciences, Bainbridge Island, Washington 98109, United States.,Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
| | - Laurent Kremer
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293 Montpellier, France.,INSERM, IRIM, 34293 Montpellier, France
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9
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Lowe MA, Cardenas A, Valentin JP, Zhu Z, Abendroth J, Castro JL, Class R, Delaunois A, Fleurance R, Gerets H, Gryshkova V, King L, Lorimer DD, MacCoss M, Rowley JH, Rosseels ML, Royer L, Taylor RD, Wong M, Zaccheo O, Chavan VP, Ghule GA, Tapkir BK, Burrows JN, Duffey M, Rottmann M, Wittlin S, Angulo-Barturen I, Jiménez-Díaz MB, Striepen J, Fairhurst KJ, Yeo T, Fidock DA, Cowman AF, Favuzza P, Crespo-Fernandez B, Gamo FJ, Goldberg DE, Soldati-Favre D, Laleu B, de Haro T. Discovery and Characterization of Potent, Efficacious, Orally Available Antimalarial Plasmepsin X Inhibitors and Preclinical Safety Assessment of UCB7362. J Med Chem 2022; 65:14121-14143. [PMID: 36216349 DOI: 10.1021/acs.jmedchem.2c01336] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Plasmepsin X (PMX) is an essential aspartyl protease controlling malaria parasite egress and invasion of erythrocytes, development of functional liver merozoites (prophylactic activity), and blocking transmission to mosquitoes, making it a potential multistage drug target. We report the optimization of an aspartyl protease binding scaffold and the discovery of potent, orally active PMX inhibitors with in vivo antimalarial efficacy. Incorporation of safety evaluation early in the characterization of PMX inhibitors precluded compounds with a long human half-life (t1/2) to be developed. Optimization focused on improving the off-target safety profile led to the identification of UCB7362 that had an improved in vitro and in vivo safety profile but a shorter predicted human t1/2. UCB7362 is estimated to achieve 9 log 10 unit reduction in asexual blood-stage parasites with once-daily dosing of 50 mg for 7 days. This work demonstrates the potential to deliver PMX inhibitors with in vivo efficacy to treat malaria.
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Affiliation(s)
| | | | | | - Zhaoning Zhu
- UCB, 216 Bath Road, Slough SL1 3WE, United Kingdom
| | - Jan Abendroth
- UCB, 7869 NE Day Road West, Bainbridge Island, Washington 98110, United States
| | | | - Reiner Class
- UCB, Chem. du Foriest 1, 1420 Braine-l'Alleud, Belgium
| | | | | | - Helga Gerets
- UCB, Chem. du Foriest 1, 1420 Braine-l'Alleud, Belgium
| | | | - Lloyd King
- UCB, 216 Bath Road, Slough SL1 3WE, United Kingdom
| | - Donald D Lorimer
- UCB, 7869 NE Day Road West, Bainbridge Island, Washington 98110, United States
| | - Malcolm MacCoss
- Bohicket Pharma Consulting LLC, 2556 Seabrook Island Road, Seabrook Island, South Carolina 29455, United States
| | | | | | - Leandro Royer
- UCB, Chem. du Foriest 1, 1420 Braine-l'Alleud, Belgium
| | | | - Melanie Wong
- UCB, 216 Bath Road, Slough SL1 3WE, United Kingdom
| | | | - Vishal P Chavan
- Sai Life Sciences Limited, Plot DS-7, IKP Knowledge Park, Genome Valley, Turkapally, Hyderabad 500078, Telangana, India
| | - Gokul A Ghule
- Sai Life Sciences Limited, Plot DS-7, IKP Knowledge Park, Genome Valley, Turkapally, Hyderabad 500078, Telangana, India
| | - Bapusaheb K Tapkir
- Sai Life Sciences Limited, Plot DS-7, IKP Knowledge Park, Genome Valley, Turkapally, Hyderabad 500078, Telangana, India
| | - Jeremy N Burrows
- Medicines for Malaria Venture, ICC, Route de Pré-Bois 20, 1215 Geneva, Switzerland
| | - Maëlle Duffey
- Medicines for Malaria Venture, ICC, Route de Pré-Bois 20, 1215 Geneva, Switzerland
| | - Matthias Rottmann
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, CH-4123 Allschwil, Switzerland.,University of Basel, 4002 Basel, Switzerland
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, CH-4123 Allschwil, Switzerland.,University of Basel, 4002 Basel, Switzerland
| | - Iñigo Angulo-Barturen
- The Art of Discovery, SL Biscay Science and Technology Park, Astondo Bidea, BIC Bizkaia Building, no. 612, Derio 48160, Bizkaia, Basque Country, Spain
| | - María Belén Jiménez-Díaz
- The Art of Discovery, SL Biscay Science and Technology Park, Astondo Bidea, BIC Bizkaia Building, no. 612, Derio 48160, Bizkaia, Basque Country, Spain
| | - Josefine Striepen
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Kate J Fairhurst
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Tomas Yeo
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - David A Fidock
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States.,Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Alan F Cowman
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Paola Favuzza
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | | | | | - Daniel E Goldberg
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8051, St. Louis, Missouri 63110, United States
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, CMU, 1 rue Michel-Servet, CH-1211 Genève 4, Switzerland
| | - Benoît Laleu
- Medicines for Malaria Venture, ICC, Route de Pré-Bois 20, 1215 Geneva, Switzerland
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10
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Deshmukh A, Kesari P, Pahelkar N, Suryawanshi A, Rathore I, Mishra V, Dupuis J, Xiao H, Gustchina A, Abendroth J, Labaied M, Yada R, Wlodawer A, Edwards T, Lorimer D, Bhaumik P. Structural insights of plasmepsin X from Plasmodium falciparum uncovering a novel inactivation mechanism of zymogen. Acta Cryst Sect A 2022. [DOI: 10.1107/s2053273322093470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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11
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Maker A, Bolejack M, Schecterson L, Hammerson B, Abendroth J, Edwards TE, Staker B, Myler PJ, Gumbiner BM. Regulation of multiple dimeric states of E-cadherin by adhesion activating antibodies revealed through Cryo-EM and X-ray crystallography. PNAS Nexus 2022; 1:pgac163. [PMID: 36157596 PMCID: PMC9491697 DOI: 10.1093/pnasnexus/pgac163] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/15/2022] [Indexed: 01/29/2023]
Abstract
E-cadherin adhesion is regulated at the cell surface, a process that can be replicated by activating antibodies. We use cryo-electron microscopy (EM) and X-ray crystallography to examine functional states of the cadherin adhesive dimer. This dimer is mediated by N-terminal beta strand-swapping involving Trp2, and forms via a different transient X-dimer intermediate. X-dimers are observed in cryo-EM along with monomers and strand-swap dimers, indicating that X-dimers form stable interactions. A novel EC4-mediated dimer was also observed. Activating Fab binding caused no gross structural changes in E-cadherin monomers, but can facilitate strand swapping. Moreover, activating Fab binding is incompatible with the formation of the X-dimer. Both cryo-EM and X-ray crystallography reveal a distinctive twisted strand-swap dimer conformation caused by an outward shift in the N-terminal beta strand that may represent a strengthened state. Thus, regulation of adhesion involves changes in cadherin dimer configurations.
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Affiliation(s)
- Allison Maker
- Department of Biochemistry, University of Washington, USA,Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, USA
| | - Madison Bolejack
- UCB Pharma, Bainbridge, WA, USA,Seattle Structural Genomics Center for Infectious Disease, USA
| | - Leslayann Schecterson
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, USA
| | - Brad Hammerson
- Seattle Structural Genomics Center for Infectious Disease, USA,Center for Global Infectious Disease Research, Seattle Children's Research Institute, USA
| | - Jan Abendroth
- UCB Pharma, Bainbridge, WA, USA,Seattle Structural Genomics Center for Infectious Disease, USA
| | - Thomas E Edwards
- UCB Pharma, Bainbridge, WA, USA,Seattle Structural Genomics Center for Infectious Disease, USA
| | - Bart Staker
- Seattle Structural Genomics Center for Infectious Disease, USA,Center for Global Infectious Disease Research, Seattle Children's Research Institute, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease, USA,Center for Global Infectious Disease Research, Seattle Children's Research Institute, USA,Department of Pediatrics, University of Washington, USA,Department of Biomedical Informatics and Medical Education, University of Washington, USA
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12
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Fox D, DeBouver N, Jezewski A, Alden K, Esan T, Abendroth J, Bullen J, Calhoun B, Potts K, Murante D, Hagen T, Krysan D. Structural characterization and mechanistic insights into pathogenic fungal acetyl-CoA synthetases. Acta Crystallogr A Found Adv 2022. [DOI: 10.1107/s2053273322097212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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13
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Hall A, Abendroth J, Bolejack MJ, Ceska T, Dell’Aiera S, Ellis V, Fox D, François C, Muruthi MM, Prével C, Poullennec K, Romanov S, Valade A, Vanbellinghen A, Yano J, Geraerts M. Discovery and Characterization of a Novel Series of Chloropyrimidines as Covalent Inhibitors of the Kinase MSK1. ACS Med Chem Lett 2022; 13:1099-1108. [PMID: 35859861 PMCID: PMC9290008 DOI: 10.1021/acsmedchemlett.2c00134] [Citation(s) in RCA: 1] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
![]()
We describe the identification and
characterization of a series
of covalent inhibitors of the C-terminal kinase domain (CTKD) of MSK1.
The initial hit was identified via a high-throughput screening and
represents a rare example of a covalent inhibitor which acts via an
SNAr reaction of a 2,5-dichloropyrimidine with a
cysteine residue (Cys440). The covalent mechanism of action was supported
by in vitro biochemical experiments and was confirmed
by mass spectrometry. Ultimately, the displacement of the 2-chloro
moiety was confirmed by crystallization of an inhibitor with the CTKD.
We also disclose the crystal structures of three compounds from this
series bound to the CTKD of MSK1, in addition to the crystal structures
of two unrelated RSK2 covalent inhibitors bound to the CTKD of MSK1.
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Affiliation(s)
- Adrian Hall
- UCB, Avenue de l’Industrie, Braine-L’Alleud 1420, Belgium
| | - Jan Abendroth
- UCB Seattle, 7869 NE Day Road West, Bainbridge Island, Washington 98110, United States
| | - Madison J. Bolejack
- UCB Seattle, 7869 NE Day Road West, Bainbridge Island, Washington 98110, United States
| | - Tom Ceska
- UCB, 216 Bath Road, Slough SL1 3WE, U.K
| | | | | | - David Fox
- UCB Seattle, 7869 NE Day Road West, Bainbridge Island, Washington 98110, United States
| | - Cyril François
- NovAliX, Avenue de l’Industrie, Braine-L’Alleud 1420, Belgium
| | - Muigai M. Muruthi
- UCB Seattle, 7869 NE Day Road West, Bainbridge Island, Washington 98110, United States
| | - Camille Prével
- UCB, Avenue de l’Industrie, Braine-L’Alleud 1420, Belgium
| | | | - Sergei Romanov
- NANOSYN, 3100 Central Expressway, Santa Clara, California 95051, United States
| | - Anne Valade
- UCB, Avenue de l’Industrie, Braine-L’Alleud 1420, Belgium
| | | | - Jason Yano
- UCB Boston, 87 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
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14
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Milanes JE, Suryadi J, Monaghan NP, Harding EM, Morris CS, Rozema SD, Khalifa MM, Golden JE, Phan IQ, Zigweid R, Abendroth J, Rice CA, McCord HT, Wilson S, Fenwick MK, Morris JC. Characterization of Glucokinases from Pathogenic Free-Living Amoebae. Antimicrob Agents Chemother 2022; 66:e0237321. [PMID: 35604214 PMCID: PMC9211422 DOI: 10.1128/aac.02373-21] [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: 12/16/2021] [Accepted: 04/27/2022] [Indexed: 11/20/2022] Open
Abstract
Infection with pathogenic free-living amoebae, including Naegleria fowleri, Acanthamoeba spp., and Balamuthia mandrillaris, can lead to life-threatening illnesses, primarily because of catastrophic central nervous system involvement. Efficacious treatment options for these infections are lacking, and the mortality rate due to infection is high. Previously, we evaluated the N. fowleri glucokinase (NfGlck) as a potential target for therapeutic intervention, as glucose metabolism is critical for in vitro viability. Here, we extended these studies to the glucokinases from two other pathogenic free-living amoebae, including Acanthamoeba castellanii (AcGlck) and B. mandrillaris (BmGlck). While these enzymes are similar (49.3% identical at the amino acid level), they have distinct kinetic properties that distinguish them from each other. For ATP, AcGlck and BmGlck have apparent Km values of 472.5 and 41.0 μM, while Homo sapiens Glck (HsGlck) has a value of 310 μM. Both parasite enzymes also have a higher apparent affinity for glucose than the human counterpart, with apparent Km values of 45.9 μM (AcGlck) and 124 μM (BmGlck) compared to ~8 mM for HsGlck. Additionally, AcGlck and BmGlck differ from each other and other Glcks in their sensitivity to small molecule inhibitors, suggesting that inhibitors with pan-amoebic activity could be challenging to generate.
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Affiliation(s)
- Jillian E. Milanes
- Eukaryotic Pathogens Innovation Center, Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
| | - Jimmy Suryadi
- Eukaryotic Pathogens Innovation Center, Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
| | - Neil P. Monaghan
- Eukaryotic Pathogens Innovation Center, Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
| | - Elijah M. Harding
- Eukaryotic Pathogens Innovation Center, Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
| | - Corbin S. Morris
- Eukaryotic Pathogens Innovation Center, Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
| | - Soren D. Rozema
- School of Pharmacy, Pharmaceutical Sciences Division, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Muhammad M. Khalifa
- School of Pharmacy, Pharmaceutical Sciences Division, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Jennifer E. Golden
- School of Pharmacy, Pharmaceutical Sciences Division, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Isabelle Q. Phan
- Seattle Structural Genomics Center for Infectious Disease, Center for Global Infection Disease Research, Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Rachael Zigweid
- Seattle Structural Genomics Center for Infectious Disease, Center for Global Infection Disease Research, Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, Center for Global Infection Disease Research, Seattle Children’s Research Institute, Seattle, Washington, USA
- UCB BioSciences, Bainbridge Island, Washington, USA
| | - Christopher A. Rice
- Pharmaceutical and Biomedical Sciences, Center for Drug Discovery, College of Pharmacy, University of Georgia, Athens, Georgia, USA
| | - Hayden T. McCord
- Pharmaceutical and Biomedical Sciences, Center for Drug Discovery, College of Pharmacy, University of Georgia, Athens, Georgia, USA
| | - Stevin Wilson
- Eukaryotic Pathogens Innovation Center, Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
- Genomics and Bioinformatics Facility, Clemson University, Clemson, South Carolina, USA
| | - Michael K. Fenwick
- Seattle Structural Genomics Center for Infectious Disease, Center for Global Infection Disease Research, Seattle Children’s Research Institute, Seattle, Washington, USA
| | - James C. Morris
- Eukaryotic Pathogens Innovation Center, Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
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15
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Mandel C, Yang H, Buchko GW, Abendroth J, Grieshaber N, Chiarelli T, Grieshaber S, Omsland A. Expression and structure of the Chlamydia trachomatis DksA ortholog. Pathog Dis 2022; 80:6564600. [PMID: 35388904 PMCID: PMC9126822 DOI: 10.1093/femspd/ftac007] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 02/15/2022] [Accepted: 04/04/2022] [Indexed: 11/14/2022] Open
Abstract
Chlamydia trachomatis is a bacterial obligate intracellular parasite and a significant cause of human disease, including sexually transmitted infections and trachoma. The bacterial RNA polymerase-binding protein DksA is a transcription factor integral to the multicomponent bacterial stress response pathway known as the stringent response. The genome of C. trachomatis encodes a DksA ortholog (DksACt) that is maximally expressed at 15–20 h post infection, a time frame correlating with the onset of transition between the replicative reticulate body (RB) and infectious elementary body (EB) forms of the pathogen. Ectopic overexpression of DksACt in C. trachomatis prior to RB–EB transitions during infection of HeLa cells resulted in a 39.3% reduction in overall replication (yield) and a 49.6% reduction in recovered EBs. While the overall domain organization of DksACt is similar to the DksA ortholog of Escherichia coli (DksAEc), DksACt did not functionally complement DksAEc. Transcription of dksACt is regulated by tandem promoters, one of which also controls expression of nrdR, encoding a negative regulator of deoxyribonucleotide biosynthesis. The phenotype resulting from ectopic expression of DksACt and the correlation between dksACt and nrdR expression is consistent with a role for DksACt in the C. trachomatis developmental cycle.
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Affiliation(s)
- Cameron Mandel
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA 99164, USA
| | - Hong Yang
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA 99164, USA
| | - Garry W Buchko
- School of Molecular Biosciences, Washington State University, Pullman WA 99164, USA.,Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA.,Seattle Structural Genomics Center for Infectious Disease, WA, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, WA, USA.,UCB, Bainbridge Island, WA 98110, USA
| | - Nicole Grieshaber
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Travis Chiarelli
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Scott Grieshaber
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Anders Omsland
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA 99164, USA
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16
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Kesari P, Deshmukh A, Pahelkar N, Suryawanshi AB, Rathore I, Mishra V, Dupuis JH, Xiao H, Gustchina A, Abendroth J, Labaied M, Yada RY, Wlodawer A, Edwards TE, Lorimer DD, Bhaumik P. Structures of plasmepsin X from Plasmodium falciparum reveal a novel inactivation mechanism of the zymogen and molecular basis for binding of inhibitors in mature enzyme. Protein Sci 2022; 31:882-899. [PMID: 35048450 PMCID: PMC8927862 DOI: 10.1002/pro.4279] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/05/2022] [Accepted: 01/14/2022] [Indexed: 11/06/2022]
Abstract
Plasmodium falciparum plasmepsin X (PfPMX), involved in the invasion and egress of this deadliest malarial parasite, is essential for its survival and hence considered as an important drug target. We report the first crystal structure of PfPMX zymogen containing a novel fold of its prosegment. A unique twisted loop from the prosegment and arginine 244 from the mature enzyme is involved in zymogen inactivation; such mechanism, not previously reported, might be common for apicomplexan proteases similar to PfPMX. The maturation of PfPMX zymogen occurs through cleavage of its prosegment at multiple sites. Our data provide thorough insights into the mode of binding of a substrate and a potent inhibitor 49c to PfPMX. We present molecular details of inactivation, maturation, and inhibition of PfPMX that should aid in the development of potent inhibitors against pepsin-like aspartic proteases from apicomplexan parasites.
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Affiliation(s)
- Pooja Kesari
- Department of Biosciences and BioengineeringIndian Institute of Technology BombayMumbaiIndia
| | - Anuradha Deshmukh
- Department of Biosciences and BioengineeringIndian Institute of Technology BombayMumbaiIndia
| | - Nikhil Pahelkar
- Department of Biosciences and BioengineeringIndian Institute of Technology BombayMumbaiIndia
| | - Abhishek B. Suryawanshi
- Department of Biosciences and BioengineeringIndian Institute of Technology BombayMumbaiIndia
| | - Ishan Rathore
- Department of Biosciences and BioengineeringIndian Institute of Technology BombayMumbaiIndia
| | - Vandana Mishra
- Department of Biosciences and BioengineeringIndian Institute of Technology BombayMumbaiIndia
| | - John H. Dupuis
- Food, Nutrition, and Health Program, Faculty of Land and Food SystemsUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Huogen Xiao
- Summerland Research and Development CenterAgriculture and Agri‐Food CanadaSummerlandBritish ColumbiaCanada
| | - Alla Gustchina
- Protein Structure Section, Center for Structural BiologyNational Cancer InstituteFrederickMarylandUSA
| | - Jan Abendroth
- UCB PharmaBainbridge IslandWashingtonUSA
- Seattle Structural Genomics Center for Infectious DiseaseSeattleWashingtonUSA
| | - Mehdi Labaied
- UCB PharmaBainbridge IslandWashingtonUSA
- Seattle Structural Genomics Center for Infectious DiseaseSeattleWashingtonUSA
| | - Rickey Y. Yada
- Food, Nutrition, and Health Program, Faculty of Land and Food SystemsUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Alexander Wlodawer
- Protein Structure Section, Center for Structural BiologyNational Cancer InstituteFrederickMarylandUSA
| | - Thomas E. Edwards
- UCB PharmaBainbridge IslandWashingtonUSA
- Seattle Structural Genomics Center for Infectious DiseaseSeattleWashingtonUSA
| | - Donald D. Lorimer
- UCB PharmaBainbridge IslandWashingtonUSA
- Seattle Structural Genomics Center for Infectious DiseaseSeattleWashingtonUSA
| | - Prasenjit Bhaumik
- Department of Biosciences and BioengineeringIndian Institute of Technology BombayMumbaiIndia
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17
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Abstract
The ammonia-oxidizing bacterium Nitrosomonas europaea expresses two cytochromes in the P460 superfamily that are predicted to be structurally similar. In one, cytochrome (cyt) P460, the substrate hydroxylamine (NH2OH) is converted to nitric oxide (NO) and nitrous oxide (N2O) requiring a unique heme-lysyl cross-link in the catalytic cofactor. In the second, cyt c'β-Met, the cross-link is absent, and the cytochrome instead binds H2O2 forming a ferryl species similar to compound II of peroxidases. Here, we report the 1.80 Å crystal structure of cyt c'β-Met─a well-expressed protein in N. europaea with a lysine to a methionine replacement at the cross-linking position. The structure of cyt c'β-Met is characterized by a large β-sheet typical of P460 members; however, several localized structural differences render cyt c'β-Met distinct. This includes a large lasso-like loop at the "top" of the cytochrome that is not observed in other structurally characterized members. Active site variation is also observed, especially in comparison to its closest homologue cyt c'β from the methane-oxidizing Methylococcus capsulatus Bath, which also lacks the cross-link. The phenylalanine "cap" which is presumed to control small ligand access to the distal heme iron is replaced with an arginine, reminiscent of the strictly conserved distal arginine in peroxidases and to the NH2OH-oxidizing cytochromes P460. A critical proton-transferring glutamate residue required for NH2OH oxidation is nevertheless missing in the active site. This in part explains the inability of cyt c'β-Met to oxidize NH2OH. Our structure also rationalizes the absence of a methionyl cross-link, although the side chain's spatial position in the structure does not eliminate the possibility that it could form under certain conditions.
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Affiliation(s)
- Jan Abendroth
- Seattle Structural Genomics Center for Infectious Diseases, Seattle, Washington 98105, United States.,UCB Biosciences, Bainbridge Island, Washington 98110, United States
| | - Garry W Buchko
- Seattle Structural Genomics Center for Infectious Diseases, Seattle, Washington 98105, United States.,Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 98354, United States.,School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, United States
| | - Fong Ning Liew
- Division of Physical Sciences, Chemistry, University of Washington-Bothell, Bothell, Washington 98011, United States
| | - Joline N Nguyen
- Division of Physical Sciences, Chemistry, University of Washington-Bothell, Bothell, Washington 98011, United States
| | - Hyung J Kim
- Division of Physical Sciences, Chemistry, University of Washington-Bothell, Bothell, Washington 98011, United States
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18
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Beard DK, Bristol S, Cosby K, Davis A, Manning C, Perry L, Snapp L, Toy A, Wheeler K, Young J, Staker B, Arakaki TL, Abendroth J, Subramanian S, Edwards TE, Myler PJ, Asojo OA. Crystal structure of a hypothetical protein from Giardia lamblia. Corrigendum. Acta Crystallogr F Struct Biol Commun 2022; 78:143. [PMID: 35234140 PMCID: PMC8900735 DOI: 10.1107/s2053230x22001704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The article by Beard et al. [(2022), Acta Cryst. F78, 59–65] is corrected. The name of one of the authors in Beard et al. [(2022), Acta Cryst. F78, 59–65] is corrected.
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19
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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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20
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Beard DK, Bristol S, Cosby K, Davis A, Manning C, Perry L, Snapp L, Toy A, Wheeler K, Young J, Staker B, Arakaki TL, Abendroth J, Subrahamanian S, Edwards TE, Myler PJ, Asojo OA. Crystal structure of a hypothetical protein from Giardia lamblia. Acta Crystallogr F Struct Biol Commun 2022; 78:59-65. [PMID: 35102894 PMCID: PMC8805217 DOI: 10.1107/s2053230x21013595] [Citation(s) in RCA: 1] [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: 10/13/2021] [Accepted: 12/23/2021] [Indexed: 11/17/2022] Open
Abstract
Giardiasis is the most prevalent diarrheal disease globally and affects humans and animals. It is a significant problem in developing countries, the number one cause of travelers' diarrhea and affects children and immunocompromised individuals, especially HIV-infected individuals. Giardiasis is treated with antibiotics (tinidazole and metronidazole) that are also used for other infections such as trichomoniasis. The ongoing search for new therapeutics for giardiasis includes characterizing the structure and function of proteins from the causative protozoan Giardia lamblia. These proteins include hypothetical proteins that share 30% sequence identity or less with proteins of known structure. Here, the atomic resolution structure of a 15.6 kDa protein was determined by molecular replacement. The structure has the two-layer αβ-sandwich topology observed in the prototypical endoribonucleases L-PSPs (liver perchloric acid-soluble proteins) with conserved allosteric active sites containing small molecules from the crystallization solution. This article is an educational collaboration between Hampton University and the Seattle Structural Genomics Center for Infectious Disease.
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Affiliation(s)
- Dylan K. Beard
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Seonna Bristol
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Kayla Cosby
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Amber Davis
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Courtney Manning
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Lionel Perry
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Lauren Snapp
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Arian Toy
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Kayla Wheeler
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Jeremy Young
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Bart Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Center for Infectious Disease Research, formerly Seattle Biomedical Research Institute, 307 Westlake Avenue North Suite 500, Seattle, WA 98109, USA
| | | | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Sandhya Subrahamanian
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Center for Infectious Disease Research, formerly Seattle Biomedical Research Institute, 307 Westlake Avenue North Suite 500, Seattle, WA 98109, USA
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Center for Infectious Disease Research, formerly Seattle Biomedical Research Institute, 307 Westlake Avenue North Suite 500, Seattle, WA 98109, USA
| | - Peter J. Myler
- Center for Infectious Disease Research, formerly Seattle Biomedical Research Institute, 307 Westlake Avenue North Suite 500, Seattle, WA 98109, USA
| | - Oluwatoyin A. Asojo
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
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21
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Beard DK, Subramanian S, Abendroth J, Dranow DM, Edwards TE, Myler PJ, Asojo OA. Crystal structure of betaine aldehyde dehydrogenase from Burkholderia pseudomallei. Acta Crystallogr F Struct Biol Commun 2022; 78:45-51. [PMID: 35102892 PMCID: PMC8805214 DOI: 10.1107/s2053230x21013455] [Citation(s) in RCA: 1] [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: 11/01/2021] [Accepted: 12/19/2021] [Indexed: 11/10/2022] Open
Abstract
Burkholderia pseudomallei infection causes melioidosis, which is often fatal if untreated. There is a need to develop new and more effective treatments for melioidosis. This study reports apo and cofactor-bound crystal structures of the potential drug target betaine aldehyde dehydrogenase (BADH) from B. pseudomallei. A structural comparison identified similarities to BADH from Pseudomonas aeruginosa which is inhibited by the drug disulfiram. This preliminary analysis could facilitate drug-repurposing studies for B. pseudomallei.
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Affiliation(s)
- Dylan K Beard
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Sandhya Subramanian
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Avenue North Suite 500, Seattle, WA 98109, USA
| | - Jan Abendroth
- 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
- 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, 100 William R. Harvey Way, Hampton, VA 23668, USA
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22
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Iwasaki J, Lorimer DD, Vivoli-Vega M, Kibble EA, Peacock CS, Abendroth J, Mayclin SJ, Dranow DM, Pierce PG, Fox D, Lewis M, Bzdyl NM, Kristensen SS, Inglis TJJ, Kahler CM, Bond CS, Hasenkopf A, Seufert F, Schmitz J, Marshall LE, Scott AE, Norville IH, Myler PJ, Holzgrabe U, Harmer NJ, Sarkar-Tyson M. OUP accepted manuscript. J Antimicrob Chemother 2022; 77:1625-1634. [PMID: 35245364 PMCID: PMC9155639 DOI: 10.1093/jac/dkac065] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 02/23/2022] [Indexed: 11/12/2022] Open
Affiliation(s)
- Jua Iwasaki
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, 6008, Australia
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Nedlands, Western Australia, 6008, Australia
- Centre for Child Health Research, University of Western Australia, Perth, Western Australia, 6008, Australia
| | - Donald D. Lorimer
- Seattle Structural Genomics Center for Infectious Disease, 307 Westlake Avenue North, Seattle, WA, 98109, USA
- Beryllium, Inc., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Mirella Vivoli-Vega
- Department of Biosciences, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
- Living Systems Institute, Stocker Road, Exeter, EX4 4QD, UK
| | - Emily A. Kibble
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, 6008, Australia
- School of Veterinary and Life Sciences, Murdoch University, Perth, WA, Australia
- DMTC Limited, Level 2, 24 Wakefield St, Hawthorn, VIC 3122, Australia
| | - Christopher S. Peacock
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, 6008, Australia
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, 307 Westlake Avenue North, Seattle, WA, 98109, USA
- Beryllium, Inc., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Stephen J. Mayclin
- Seattle Structural Genomics Center for Infectious Disease, 307 Westlake Avenue North, Seattle, WA, 98109, USA
- Beryllium, Inc., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - David M. Dranow
- Seattle Structural Genomics Center for Infectious Disease, 307 Westlake Avenue North, Seattle, WA, 98109, USA
- Beryllium, Inc., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Phillip G. Pierce
- Seattle Structural Genomics Center for Infectious Disease, 307 Westlake Avenue North, Seattle, WA, 98109, USA
- Beryllium, Inc., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - David Fox
- Seattle Structural Genomics Center for Infectious Disease, 307 Westlake Avenue North, Seattle, WA, 98109, USA
- Beryllium, Inc., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Maria Lewis
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, 6008, Australia
| | - Nicole M. Bzdyl
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, 6008, Australia
| | - Sofie S. Kristensen
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, 6008, Australia
| | - Timothy J. J. Inglis
- Department of Microbiology, PathWest Laboratory Medicine, Nedlands, WA 6009, Australia
- Medical School, University of Western Australia, Nedlands, WA 6009, Australia
| | - Charlene M. Kahler
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, 6008, Australia
| | - Charles S. Bond
- School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, 6009, Australia
| | - Anja Hasenkopf
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Florian Seufert
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Jens Schmitz
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Laura E. Marshall
- Defence Science and Technology Laboratory, Porton Down, Salisbury, UK
| | - Andrew E. Scott
- Defence Science and Technology Laboratory, Porton Down, Salisbury, UK
| | | | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, 307 Westlake Avenue North, Seattle, WA, 98109, USA
| | - Ulrike Holzgrabe
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Nicholas J. Harmer
- Department of Biosciences, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
- Living Systems Institute, Stocker Road, Exeter, EX4 4QD, UK
| | - Mitali Sarkar-Tyson
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, 6008, Australia
- Corresponding author. E-mail:
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23
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Demars A, Vitali A, Comein A, Carlier E, Azouz A, Goriely S, Smout J, Flamand V, Van Gysel M, Wouters J, Abendroth J, Edwards TE, Machelart A, Hoffmann E, Brodin P, De Bolle X, Muraille E. Aconitate decarboxylase 1 participates in the control of pulmonary Brucella infection in mice. PLoS Pathog 2021; 17:e1009887. [PMID: 34525130 PMCID: PMC8443048 DOI: 10.1371/journal.ppat.1009887] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 02/21/2021] [Accepted: 08/12/2021] [Indexed: 12/15/2022] Open
Abstract
Brucellosis is one of the most widespread bacterial zoonoses worldwide. Here, our aim was to identify the effector mechanisms controlling the early stages of intranasal infection with Brucella in C57BL/6 mice. During the first 48 hours of infection, alveolar macrophages (AMs) are the main cells infected in the lungs. Using RNA sequencing, we identified the aconitate decarboxylase 1 gene (Acod1; also known as Immune responsive gene 1), as one of the genes most upregulated in murine AMs in response to B. melitensis infection at 24 hours post-infection. Upregulation of Acod1 was confirmed by RT-qPCR in lungs infected with B. melitensis and B. abortus. We observed that Acod1-/- C57BL/6 mice display a higher bacterial load in their lungs than wild-type (wt) mice following B. melitensis or B. abortus infection, demonstrating that Acod1 participates in the control of pulmonary Brucella infection. The ACOD1 enzyme is mostly produced in mitochondria of macrophages, and converts cis-aconitate, a metabolite in the Krebs cycle, into itaconate. Dimethyl itaconate (DMI), a chemically-modified membrane permeable form of itaconate, has a dose-dependent inhibitory effect on Brucella growth in vitro. Interestingly, structural analysis suggests the binding of itaconate into the binding site of B. abortus isocitrate lyase. DMI does not inhibit multiplication of the isocitrate lyase deletion mutant ΔaceA B. abortus in vitro. Finally, we observed that, unlike the wt strain, the ΔaceA B. abortus strain multiplies similarly in wt and Acod1-/- C57BL/6 mice. These data suggest that bacterial isocitrate lyase might be a target of itaconate in AMs.
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Affiliation(s)
- Aurore Demars
- Unité de Recherche en Biologie des Microorganismes (URBM), NARILIS, University of Namur, Namur, Belgium
| | - Armelle Vitali
- Unité de Recherche en Biologie des Microorganismes (URBM), NARILIS, University of Namur, Namur, Belgium
| | - Audrey Comein
- Unité de Recherche en Biologie des Microorganismes (URBM), NARILIS, University of Namur, Namur, Belgium
| | - Elodie Carlier
- Unité de Recherche en Biologie des Microorganismes (URBM), NARILIS, University of Namur, Namur, Belgium
| | - Abdulkader Azouz
- Université Libre de Bruxelles, Institute for Medical Immunology, and ULB Center for Research in Immunology (U-CRI), Gosselies, Belgium
| | - Stanislas Goriely
- Université Libre de Bruxelles, Institute for Medical Immunology, and ULB Center for Research in Immunology (U-CRI), Gosselies, Belgium
| | - Justine Smout
- Université Libre de Bruxelles, Institute for Medical Immunology, and ULB Center for Research in Immunology (U-CRI), Gosselies, Belgium
| | - Véronique Flamand
- Université Libre de Bruxelles, Institute for Medical Immunology, and ULB Center for Research in Immunology (U-CRI), Gosselies, Belgium
| | - Mégane Van Gysel
- Namur Medicine and Drug Innovation Center (NAMEDIC), Namur Research Institute for Life Sciences (Narilis), Department of Chemistry, Laboratoire de Chimie Biologique Structurale (CBS), Namur, Belgium
| | - Johan Wouters
- Namur Medicine and Drug Innovation Center (NAMEDIC), Namur Research Institute for Life Sciences (Narilis), Department of Chemistry, Laboratoire de Chimie Biologique Structurale (CBS), Namur, Belgium
| | - Jan Abendroth
- UCB BioSciences, 7869 NE Day Road West Bainbridge Island, WA 98110 USA and Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
| | - Thomas E. Edwards
- UCB BioSciences, 7869 NE Day Road West Bainbridge Island, WA 98110 USA and Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
| | - Arnaud Machelart
- Université de Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019—UMR 9017—CIIL—Center for Infection and Immunity of Lille, Lille, France
| | - Eik Hoffmann
- Université de Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019—UMR 9017—CIIL—Center for Infection and Immunity of Lille, Lille, France
| | - Priscille Brodin
- Université de Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019—UMR 9017—CIIL—Center for Infection and Immunity of Lille, Lille, France
| | - Xavier De Bolle
- Unité de Recherche en Biologie des Microorganismes (URBM), NARILIS, University of Namur, Namur, Belgium
| | - Eric Muraille
- Unité de Recherche en Biologie des Microorganismes (URBM), NARILIS, University of Namur, Namur, Belgium
- Université Libre de Bruxelles, Laboratoire de Parasitologie, and ULB Center for Research in Immunology (U-CRI), Gosselies, Belgium
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24
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Jezewski A, Alden KM, Esan TE, DeBouver ND, Abendroth J, Bullen JC, Calhoun BM, Potts KT, Murante DM, Hagen TJ, Fox D, Krysan DJ. Structural Characterization of the Reaction and Substrate Specificity Mechanisms of Pathogenic Fungal Acetyl-CoA Synthetases. ACS Chem Biol 2021; 16:1587-1599. [PMID: 34369755 PMCID: PMC8383264 DOI: 10.1021/acschembio.1c00484] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 06/24/2021] [Accepted: 07/29/2021] [Indexed: 11/28/2022]
Abstract
Acetyl CoA synthetases (ACSs) are Acyl-CoA/NRPS/Luciferase (ANL) superfamily enzymes that couple acetate with CoA to generate acetyl CoA, a key component of central carbon metabolism in eukaryotes and prokaryotes. Normal mammalian cells are not dependent on ACSs, while tumor cells, fungi, and parasites rely on acetate as a precursor for acetyl CoA. Consequently, ACSs have emerged as a potential drug target. As part of a program to develop antifungal ACS inhibitors, we characterized fungal ACSs from five diverse human fungal pathogens using biochemical and structural studies. ACSs catalyze a two-step reaction involving adenylation of acetate followed by thioesterification with CoA. Our structural studies captured each step of these two half-reactions including the acetyl-adenylate intermediate of the first half-reaction in both the adenylation conformation and the thioesterification conformation and thus provide a detailed picture of the reaction mechanism. We also used a systematic series of increasingly larger alkyl adenosine esters as chemical probes to characterize the structural basis of the exquisite ACS specificity for acetate over larger carboxylic acid substrates. Consistent with previous biochemical and genetic data for other enzymes, structures of fungal ACSs with these probes bound show that a key tryptophan residue limits the size of the alkyl binding site and forces larger alkyl chains to adopt high energy conformers, disfavoring their efficient binding. Together, our analysis provides highly detailed structural models for both the reaction mechanism and substrate specificity that should be useful in designing selective inhibitors of eukaryotic ACSs as potential anticancer, antifungal, and antiparasitic drugs.
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Affiliation(s)
- Andrew
J. Jezewski
- Department
of Pediatrics Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, United States
| | - Katy M. Alden
- Department
of Pediatrics Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, United States
| | - Taiwo E. Esan
- Department
of Chemistry and Biochemistry, Northern
Illinois University, DeKalb, Illinois 60115, United States
| | - Nicholas D. DeBouver
- UCB
Pharma, 7869 NE Day Road West, Bainbridge Island, Washington 98110, United States
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
| | - Jan Abendroth
- UCB
Pharma, 7869 NE Day Road West, Bainbridge Island, Washington 98110, United States
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
| | - Jameson C. Bullen
- UCB
Pharma, 7869 NE Day Road West, Bainbridge Island, Washington 98110, United States
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
| | - Brandy M. Calhoun
- UCB
Pharma, 7869 NE Day Road West, Bainbridge Island, Washington 98110, United States
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
| | - Kristy T. Potts
- UCB
Pharma, 7869 NE Day Road West, Bainbridge Island, Washington 98110, United States
- Beryllium
Discovery Corp., 7869
NE Day Road West, Bainbridge Island, Washington 98110, United States
| | - Daniel M. Murante
- Department
of Pediatrics Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, United States
| | - Timothy J. Hagen
- Department
of Chemistry and Biochemistry, Northern
Illinois University, DeKalb, Illinois 60115, United States
| | - David Fox
- UCB
Pharma, 7869 NE Day Road West, Bainbridge Island, Washington 98110, United States
- Beryllium
Discovery Corp., 7869
NE Day Road West, Bainbridge Island, Washington 98110, United States
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
| | - Damian J. Krysan
- Department
of Pediatrics Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, United States
- Microbiology/Immunology,
Carver College of Medicine, University of
Iowa, Iowa City, Iowa 52242, United States
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25
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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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26
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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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27
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Melgar K, Walker MM, Jones LM, Bolanos LC, Hueneman K, Wunderlich M, Jiang JK, Wilson KM, Zhang X, Sutter P, Wang A, Xu X, Choi K, Tawa G, Lorimer D, Abendroth J, O'Brien E, Hoyt SB, Berman E, Famulare CA, Mulloy JC, Levine RL, Perentesis JP, Thomas CJ, Starczynowski DT. Overcoming adaptive therapy resistance in AML by targeting immune response pathways. Sci Transl Med 2020; 11:11/508/eaaw8828. [PMID: 31484791 DOI: 10.1126/scitranslmed.aaw8828] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 07/24/2019] [Indexed: 12/17/2022]
Abstract
Targeted inhibitors to oncogenic kinases demonstrate encouraging clinical responses early in the treatment course; however, most patients will relapse because of target-dependent mechanisms that mitigate enzyme-inhibitor binding or through target-independent mechanisms, such as alternate activation of survival and proliferation pathways, known as adaptive resistance. Here, we describe mechanisms of adaptive resistance in FMS-like receptor tyrosine kinase (FLT3)-mutant acute myeloid leukemia (AML) by examining integrative in-cell kinase and gene regulatory network responses after oncogenic signaling blockade by FLT3 inhibitors (FLT3i). We identified activation of innate immune stress response pathways after treatment of FLT3-mutant AML cells with FLT3i and showed that innate immune pathway activation via the interleukin-1 receptor-associated kinase 1 and 4 (IRAK1/4) complex contributes to adaptive resistance in FLT3-mutant AML cells. To overcome this adaptive resistance mechanism, we developed a small molecule that simultaneously inhibits FLT3 and IRAK1/4 kinases. The multikinase FLT3-IRAK1/4 inhibitor eliminated adaptively resistant FLT3-mutant AML cells in vitro and in vivo and displayed superior efficacy as compared to current targeted FLT3 therapies. These findings uncover a polypharmacologic strategy for overcoming adaptive resistance to therapy in AML by targeting immune stress response pathways.
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Affiliation(s)
- Katelyn Melgar
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Immunology Graduate Program, Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Morgan M Walker
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Lyndsey C Bolanos
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Kathleen Hueneman
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Mark Wunderlich
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Jian-Kang Jiang
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kelli M Wilson
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiaohu Zhang
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Patrick Sutter
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy Wang
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xin Xu
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kwangmin Choi
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Gregory Tawa
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | - Eric O'Brien
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Scott B Hoyt
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ellin Berman
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Christopher A Famulare
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - James C Mulloy
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Ross L Levine
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - John P Perentesis
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Craig J Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA. .,Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20829, USA
| | - Daniel T Starczynowski
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA. .,Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
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28
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Ghosh S, Padalia J, Ngobeni R, Abendroth J, Farr L, Shirley DA, Edwards T, Moonah S. Targeting Parasite-Produced Macrophage Migration Inhibitory Factor as an Antivirulence Strategy With Antibiotic-Antibody Combination to Reduce Tissue Damage. J Infect Dis 2020; 221:1185-1193. [PMID: 31677380 PMCID: PMC7325720 DOI: 10.1093/infdis/jiz579] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 10/14/2019] [Accepted: 11/01/2019] [Indexed: 12/13/2022] Open
Abstract
Targeting virulence factors represents a promising alternative approach to antimicrobial therapy, through the inhibition of pathogenic pathways that result in host tissue damage. Yet, virulence inhibition remains an understudied area in parasitology. Several medically important protozoan parasites such as Plasmodium, Entamoeba, Toxoplasma, and Leishmania secrete an inflammatory macrophage migration inhibitory factor (MIF) cytokine homolog, a virulence factor linked to severe disease. The aim of this study was to investigate the effectiveness of targeting parasite-produced MIF as combination therapy with standard antibiotics to reduce disease severity. Here, we used Entamoeba histolytica as the model MIF-secreting protozoan, and a mouse model that mirrors severe human infection. We found that intestinal inflammation and tissue damage were significantly reduced in mice treated with metronidazole when combined with anti-E. histolytica MIF antibodies, compared to metronidazole alone. Thus, this preclinical study provides proof-of-concept that combining antiparasite MIF-blocking antibodies with current standard-of-care antibiotics might improve outcomes in severe protozoan infections.
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Affiliation(s)
- Swagata Ghosh
- Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA
| | - Jay Padalia
- Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA
| | - Renay Ngobeni
- Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, USA
| | - Laura Farr
- Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA
| | - Debbie-Ann Shirley
- Department of Pediatrics, University of Virginia Health System, Charlottesville, Virginia, USA
| | - Thomas Edwards
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, USA
| | - Shannon Moonah
- Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA
- Correspondence: Shannon Moonah, MD, ScM, Division of Infectious Diseases, Department of Medicine, University of Virginia Health System, 345 Crispell Dr, Charlottesville, VA 22908 ()
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29
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Barrett KF, Dranow DM, Phan IQ, Michaels SA, Shaheen S, Navaluna ED, Craig JK, Tillery LM, Choi R, Edwards TE, Conrady DG, Abendroth J, Horanyi PS, Lorimer DD, Van Voorhis WC, Zhang Z, Barrett LK, Subramanian S, Staker B, Fan E, Myler PJ, Soge OO, Hybiske K, Ojo KK. Structures of glyceraldehyde 3-phosphate dehydrogenase in Neisseria gonorrhoeae and Chlamydia trachomatis. Protein Sci 2020; 29:768-778. [PMID: 31930578 DOI: 10.1002/pro.3824] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 11/02/2019] [Revised: 01/05/2020] [Accepted: 01/08/2020] [Indexed: 12/12/2022]
Abstract
Neisseria gonorrhoeae (Ng) and Chlamydia trachomatis (Ct) are the most commonly reported sexually transmitted bacteria worldwide and usually present as co-infections. Increasing resistance of Ng to currently recommended dual therapy of azithromycin and ceftriaxone presents therapeutic challenges for syndromic management of Ng-Ct co-infections. Development of a safe, effective, and inexpensive dual therapy for Ng-Ct co-infections is an effective strategy for the global control and prevention of these two most prevalent bacterial sexually transmitted infections. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a validated drug target with two approved drugs for indications other than antibacterials. Nonetheless, any new drugs targeting GAPDH in Ng and Ct must be specific inhibitors of bacterial GAPDH that do not inhibit human GAPDH, and structural information of Ng and Ct GAPDH will aid in finding such selective inhibitors. Here, we report the X-ray crystal structures of Ng and Ct GAPDH. Analysis of the structures demonstrates significant differences in amino acid residues in the active sites of human GAPDH from those of the two bacterial enzymes suggesting design of compounds to selectively inhibit Ng and Ct is possible. We also describe an efficient in vitro assay of recombinant GAPDH enzyme activity amenable to high-throughput drug screening to aid in identifying inhibitory compounds and begin to address selectivity.
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Affiliation(s)
- Kayleigh F Barrett
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - David M Dranow
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bainbridge Island, Washington
| | - Isabelle Q Phan
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Seattle Children's Research Institute, Seattle, Washington
| | - Samantha A Michaels
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington
| | - Shareef Shaheen
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington
| | - Edelmar D Navaluna
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington
| | - Justin K Craig
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - Logan M Tillery
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington
| | - Ryan Choi
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bainbridge Island, Washington
| | - Deborah G Conrady
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bedford, Massachusetts
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bainbridge Island, Washington
| | - Peter S Horanyi
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bedford, Massachusetts
| | - Donald D Lorimer
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bainbridge Island, Washington
| | - Wesley C Van Voorhis
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Department of Global Health, University of Washington, Seattle, Washington
| | - Zhongsheng Zhang
- Department of Biochemistry, University of Washington, Seattle, Washington
| | - Lynn K Barrett
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - Sandhya Subramanian
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Seattle Children's Research Institute, Seattle, Washington
| | - Bart Staker
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Seattle Children's Research Institute, Seattle, Washington
| | - Erkang Fan
- Department of Biochemistry, University of Washington, Seattle, Washington
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Seattle Children's Research Institute, Seattle, Washington.,Department of Global Health, University of Washington, Seattle, Washington.,Department of Biomedical Informatics & Medical Education
| | - Olusegun O Soge
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington.,Department of Global Health, University of Washington, Seattle, Washington
| | - Kevin Hybiske
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington.,Department of Global Health, University of Washington, Seattle, Washington
| | - Kayode K Ojo
- Department of Medicine, Division of Allergy and Infectious Diseases, Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington, Seattle, Washington
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30
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Abendroth J, Klement A. [Perioperative management of polymedication in geriatric patients: risk reduction and coordination with the family practitioner]. Chirurg 2020; 91:115-120. [PMID: 31940066 DOI: 10.1007/s00104-019-01094-6] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The increasing proportion of older and polymorbid people in the population also means an increase in polymedication and its risks. This places new and complex demands on the interdisciplinary and transsectoral collaboration. The preoperative, perioperative and postoperative management of polymedication is described in the article with respect to frequent risks and the chances of a systematic exchange of information. The establishment of an interdisciplinary admission routine in departments of surgery and communication with the family practitioner is crucial for patient safety.
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Affiliation(s)
- J Abendroth
- Institut für Allgemeinmedizin, Universität Halle-Wittenberg, Magdeburger Str. 8, 06112, Halle (Saale), Deutschland
| | - A Klement
- Institut für Allgemeinmedizin, Universität Halle-Wittenberg, Magdeburger Str. 8, 06112, Halle (Saale), Deutschland.
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31
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Tillery LM, Barrett KF, Dranow DM, Craig J, Shek R, Chun I, Barrett LK, Phan IQ, Subramanian S, Abendroth J, Lorimer DD, Edwards TE, Van Voorhis WC. Toward a structome of Acinetobacter baumannii drug targets. Protein Sci 2020; 29:789-802. [PMID: 31930600 DOI: 10.1002/pro.3826] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 10/01/2019] [Revised: 01/06/2020] [Accepted: 01/08/2020] [Indexed: 12/13/2022]
Abstract
Acinetobacter baumannii is well known for causing hospital-associated infections due in part to its intrinsic antibiotic resistance as well as its ability to remain viable on surfaces and resist cleaning agents. In a previous publication, A. baumannii strain AB5075 was studied by transposon mutagenesis and 438 essential gene candidates for growth on rich-medium were identified. The Seattle Structural Genomics Center for Infectious Disease entered 342 of these candidate essential genes into our pipeline for structure determination, in which 306 were successfully cloned into expression vectors, 192 were detectably expressed, 165 screened as soluble, 121 were purified, 52 crystalized, 30 provided diffraction data, and 29 structures were deposited in the Protein Data Bank. Here, we report these structures, compare them with human orthologs where applicable, and discuss their potential as drug targets for antibiotic development against A. baumannii.
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Affiliation(s)
- Logan M Tillery
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - Kayleigh F Barrett
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - David M Dranow
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bainbridge Island, Washington
| | - Justin Craig
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - Roger Shek
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - Ian Chun
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - Lynn K Barrett
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
| | - Isabelle Q Phan
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Seattle Children's Research Institute, Seattle, Washington
| | - Sandhya Subramanian
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Seattle Children's Research Institute, Seattle, Washington
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bainbridge Island, Washington
| | - Donald D Lorimer
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bainbridge Island, Washington
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Pharma, Bainbridge Island, Washington
| | - Wesley C Van Voorhis
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease (CERID), University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington
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32
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Escamilla Y, Hughes CA, Abendroth J, Dranow DM, Balboa S, Dean FB, Bullard JM. Glutaminyl-tRNA Synthetase from Pseudomonas aeruginosa: Characterization, structure, and development as a screening platform. Protein Sci 2019; 29:905-918. [PMID: 31833153 DOI: 10.1002/pro.3800] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/08/2019] [Accepted: 12/09/2019] [Indexed: 11/12/2022]
Abstract
Pseudomonas aeruginosa has a high potential for developing resistance to multiple antibiotics. The gene (glnS) encoding glutaminyl-tRNA synthetase (GlnRS) from P. aeruginosa was cloned and the resulting protein characterized. GlnRS was kinetically evaluated and the KM and kcat obs , governing interactions with tRNA, were 1.0 μM and 0.15 s-1 , respectively. The crystal structure of the α2 form of P. aeruginosa GlnRS was solved to 1.9 Å resolution. The amino acid sequence and structure of P. aeruginosa GlnRS were analyzed and compared to that of GlnRS from Escherichia coli. Amino acids that interact with ATP, glutamine, and tRNA are well conserved and structure overlays indicate that both GlnRS proteins conform to a similar three-dimensional structure. GlnRS was developed into a screening platform using scintillation proximity assay technology and used to screen ~2,000 chemical compounds. Three inhibitory compounds were identified and analyzed for enzymatic inhibition as well as minimum inhibitory concentrations against clinically relevant bacterial strains. Two of the compounds, BM02E04 and BM04H03, were selected for further studies. These compounds displayed broad-spectrum antibacterial activity and exhibited moderate inhibitory activity against mutant efflux deficient strains of P. aeruginosa and E. coli. Growth of wild-type strains was unaffected, indicating that efflux was likely responsible for the lack of sensitivity. The global mode of action was determined using time-kill kinetics. BM04H03 did not inhibit the growth of human cell cultures at any concentration and BM02E04 only inhibit cultures at the highest concentration tested (400 μg/ml). In conclusion, GlnRS from P. aeruginosa is shown to have a structure similar to that of E. coli GlnRS and two natural product compounds were identified as inhibitors of P. aeruginosa GlnRS with the potential for utility as lead candidates in antibacterial drug development in a time of increased antibiotic resistance.
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Affiliation(s)
| | | | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Biosciences, Bainbridge Island, Washington
| | - David M Dranow
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB Biosciences, Bainbridge Island, Washington
| | | | - Frank B Dean
- University of Texas Rio Grande Valley, Edinburg, Texas
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33
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Buchko GW, Abendroth J, Robinson JI, Phan IQ, Myler PJ, Edwards TE. Structural diversity in the Mycobacteria DUF3349 superfamily. Protein Sci 2019; 29:670-685. [PMID: 31658388 DOI: 10.1002/pro.3758] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/17/2019] [Accepted: 10/21/2019] [Indexed: 11/11/2022]
Abstract
A protein superfamily with a "Domain of Unknown Function,", DUF3349 (PF11829), is present predominately in Mycobacterium and Rhodococcus bacterial species suggesting that these proteins may have a biological function unique to these bacteria. We previously reported the inaugural structure of a DUF3349 superfamily member, Mycobacterium tuberculosis Rv0543c. Here, we report the structures determined for three additional DUF3349 proteins: Mycobacterium smegmatis MSMEG_1063 and MSMEG_1066 and Mycobacterium abscessus MAB_3403c. Like Rv0543c, the NMR solution structure of MSMEG_1063 revealed a monomeric five α-helix bundle with a similar overall topology. Conversely, the crystal structure of MSMEG_1066 revealed a five α-helix protein with a strikingly different topology and a tetrameric quaternary structure that was confirmed by size exclusion chromatography. The NMR solution structure of a fourth member of the DUF3349 superfamily, MAB_3403c, with 18 residues missing at the N-terminus, revealed a monomeric α-helical protein with a folding topology similar to the three C-terminal helices in the protomer of the MSMEG_1066 tetramer. These structures, together with a GREMLIN-based bioinformatics analysis of the DUF3349 primary amino acid sequences, suggest two subfamilies within the DUF3349 family. The division of the DUF3349 into two distinct subfamilies would have been lost if structure solution had stopped with the first structure in the DUF3349 family, highlighting the insights generated by solving multiple structures within a protein superfamily. Future studies will determine if the structural diversity at the tertiary and quaternary levels in the DUF3349 protein superfamily have functional roles in Mycobacteria and Rhodococcus species with potential implications for structure-based drug discovery.
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Affiliation(s)
- Garry W Buchko
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington.,School of Molecular Biosciences, Washington State University, Pullman, Washington
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB, Bainbridge Island, Washington
| | - John I Robinson
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB, Bainbridge Island, Washington
| | - Isabelle Q Phan
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Center for Global Infectious Disease Research, Seattle Children's Hospital, Seattle, Washington
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,Center for Global Infectious Disease Research, Seattle Children's Hospital, Seattle, Washington.,Department of Medical Education and Biomedical Informatics, University of Washington, Seattle, Washington.,Department of Global Health, University of Washington, Seattle, Washington
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington.,UCB, Bainbridge Island, Washington
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34
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Abendroth J. Strong translational NCS leads to space group ambiguity, or how close inspection of data can rescue structures. Two examples from SSGCID. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s0108767319095588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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35
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Patterson EI, Nanson JD, Abendroth J, Bryan C, Sankaran B, Myler PJ, Forwood JK. Structural characterization of β-ketoacyl ACP synthase I bound to platencin and fragment screening molecules at two substrate binding sites. Proteins 2019; 88:47-56. [PMID: 31237717 DOI: 10.1002/prot.25765] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 03/18/2019] [Revised: 05/30/2019] [Accepted: 06/07/2019] [Indexed: 11/08/2022]
Abstract
The bacterial fatty acid pathway is essential for membrane synthesis and a range of other metabolic and cellular functions. The β-ketoacyl-ACP synthases carry out the initial elongation reaction of this pathway, utilizing acetyl-CoA as a primer to elongate malonyl-ACP by two carbons, and subsequent elongation of the fatty acyl-ACP substrate by two carbons. Here we describe the structures of the β-ketoacyl-ACP synthase I from Brucella melitensis in complex with platencin, 7-hydroxycoumarin, and (5-thiophen-2-ylisoxazol-3-yl)methanol. The enzyme is a dimer and based on structural and sequence conservation, harbors the same active site configuration as other β-ketoacyl-ACP synthases. The platencin binding site overlaps with the fatty acyl compound supplied by ACP, while 7-hydroxyl-coumarin and (5-thiophen-2-ylisoxazol-3-yl)methanol bind at the secondary fatty acyl binding site. These high-resolution structures, ranging between 1.25 and 1.70 å resolution, provide a basis for in silico inhibitor screening and optimization, and can aid in rational drug design by revealing the high-resolution binding interfaces of molecules at the malonyl-ACP and acyl-ACP active sites.
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Affiliation(s)
- Edward I Patterson
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas
| | - Jeffrey D Nanson
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia.,The Institute for Molecular Biosciences (IMB), University of Queensland, Brisbane, QLD, Australia
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington.,UCB Beryllium Discovery Corp, Bainbridge Island, Washington
| | - Cassie Bryan
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington.,Institute for Protein Design, University of Washington, Seattle, Washington
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
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Sullivan AH, Dranow DM, Horanyi PS, Lorimer DD, Edwards TE, Abendroth J. Crystal structures of thiamine monophosphate kinase from Acinetobacter baumannii in complex with substrates and products. Sci Rep 2019; 9:4392. [PMID: 30867460 PMCID: PMC6416309 DOI: 10.1038/s41598-019-40558-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 10/12/2018] [Accepted: 02/19/2019] [Indexed: 11/08/2022] Open
Abstract
Thiamine monophosphate kinase (ThiL) catalyzes the last step of thiamine pyrophosphate (TPP) synthesis, the ATP-dependent phosphorylation of thiamine monophosphate (TMP) to thiamine pyrophosphate. We solved the structure of ThiL from the human pathogen A. baumanii in complex with a pair of substrates TMP and a non-hydrolyzable adenosine triphosphate analog, and in complex with a pair of products TPP and adenosine diphosphate. High resolution of the data and anomalous diffraction allows for a detailed description of the binding mode of substrates and products, and their metal environment. The structures further support a previously proposed in-line attack reaction mechanism and show a distinct variability of metal content of the active site.
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Affiliation(s)
- Amy H Sullivan
- UCB/Beryllium Discovery, 98110, 7869 NE Day Road West, Bainbridge Island, WA, USA
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, USA
| | - David M Dranow
- UCB/Beryllium Discovery, 98110, 7869 NE Day Road West, Bainbridge Island, WA, USA
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, USA
| | - Peter S Horanyi
- UCB/Beryllium Discovery, 98110, 7869 NE Day Road West, Bainbridge Island, WA, USA
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, USA
| | - Donald D Lorimer
- UCB/Beryllium Discovery, 98110, 7869 NE Day Road West, Bainbridge Island, WA, USA
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, USA
| | - Thomas E Edwards
- UCB/Beryllium Discovery, 98110, 7869 NE Day Road West, Bainbridge Island, WA, USA
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, USA
| | - Jan Abendroth
- UCB/Beryllium Discovery, 98110, 7869 NE Day Road West, Bainbridge Island, WA, USA.
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, USA.
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37
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Abendroth J, Sankaran B, Myler PJ, Lorimer DD, Edwards TE. Ab initio structure solution of a proteolytic fragment using ARCIMBOLDO. Acta Crystallogr F Struct Biol Commun 2018; 74:530-535. [PMID: 30198884 PMCID: PMC6130419 DOI: 10.1107/s2053230x18010063] [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: 05/15/2018] [Accepted: 07/12/2018] [Indexed: 11/10/2022] Open
Abstract
Crystal structure determination requires solving the phase problem. This can be accomplished using ab initio direct methods for small molecules and macromolecules at resolutions higher than 1.2 Å, whereas macromolecular structure determination at lower resolution requires either molecular replacement using a homologous structure or experimental phases using a derivative such as covalent labeling (for example selenomethionine or mercury derivatization) or heavy-atom soaking (for example iodide ions). Here, a case is presented in which crystals were obtained from a 30.8 kDa protein sample and yielded a 1.6 Å resolution data set with a unit cell that could accommodate approximately 8 kDa of protein. Thus, it was unclear what had been crystallized. Molecular replacement with pieces of homologous proteins and attempts at iodide ion soaking failed to yield a solution. The crystals could not be reproduced. Sequence-independent molecular replacement using the structures available in the Protein Data Bank also failed to yield a solution. Ultimately, ab initio structure solution proved successful using the program ARCIMBOLDO, which identified two α-helical elements and yielded interpretable maps. The structure was the C-terminal dimerization domain of the intended target from Mycobacterium smegmatis. This structure is presented as a user-friendly test case in which an unknown protein fragment could be determined using ARCIMBOLDO.
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Affiliation(s)
- Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Beryllium Discovery Corporation, Bainbridge Island, WA 98110, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Center for Infectious Disease Research, formerly Seattle Biomedical Research Institute, 307 Westlake Avenue North Suite 500, Seattle, WA 98109, USA
| | - Donald D. Lorimer
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Beryllium Discovery Corporation, Bainbridge Island, WA 98110, USA
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Beryllium Discovery Corporation, Bainbridge Island, WA 98110, USA
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38
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Abendroth J, Mayclin SJ, Lorimer DD, Horanyi PS, Edwards TE. Molecular replacement at SSGCID. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s0108767318095715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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39
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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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40
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Asojo OA, Subramanian S, Abendroth J, Exley I, Lorimer DD, Edwards TE, Myler PJ. Crystal structure of chorismate mutase from Burkholderia phymatum. Acta Crystallogr F Struct Biol Commun 2018; 74:187-192. [PMID: 29633965 PMCID: PMC5894103 DOI: 10.1107/s2053230x18002868] [Citation(s) in RCA: 2] [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: 10/05/2017] [Accepted: 02/18/2018] [Indexed: 11/10/2022] Open
Abstract
The bacterium Burkholderia phymatum is a promiscuous symbiotic nitrogen-fixating bacterium that belongs to one of the largest groups of Betaproteobacteria. Other Burkholderia species are known to cause disease in plants and animals, and some are potential agents for biological warfare. Structural genomics efforts include characterizing the structures of enzymes from pathways that can be targeted for drug development. As part of these efforts, chorismate mutase from B. phymatum was produced and crystallized, and a 1.95 Å resolution structure is reported. This enzyme shares less than 33% sequence identity with other homologs of known structure. There are two classes of chorismate mutase: AroQ and AroH. The bacterial subclass AroQγ has reported roles in virulence. Chorismate mutase from B. phymatum has the prototypical AroQγ topology and retains the characteristic chorismate mutase active site. This suggests that substrate-based chorismate mutase inhibitors will not be specific and are likely to affect beneficial bacteria such as B. phymatum.
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Affiliation(s)
- Oluwatoyin A. Asojo
- National School of Tropical Medicine, Baylor College of Medicine, 1102 Bates Avenue Suite 550, Mail Stop BCM320, Houston, TX 77030-3411, USA
| | - Sandhya Subramanian
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Center for Infectious Disease Research, 307 Westlake Avenue North Suite 500, Seattle, WA 98109, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Beryllium Discovery Corporation, Bainbridge Island, WA 98110, USA
| | - Ilyssa Exley
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Donald D. Lorimer
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Beryllium Discovery Corporation, Bainbridge Island, WA 98110, USA
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Beryllium Discovery Corporation, Bainbridge Island, WA 98110, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Center for Infectious Disease Research, 307 Westlake Avenue North Suite 500, Seattle, WA 98109, USA
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41
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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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42
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Varela-Ramirez A, Abendroth J, Mejia AA, Phan IQ, Lorimer DD, Edwards TE, Aguilera RJ. Structure of acid deoxyribonuclease. Nucleic Acids Res 2017; 45:6217-6227. [PMID: 28369538 PMCID: PMC5449587 DOI: 10.1093/nar/gkx222] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [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: 02/16/2017] [Accepted: 03/23/2017] [Indexed: 01/06/2023] Open
Abstract
Deoxyribonuclease II (DNase II) is also known as acid deoxyribonuclease because it has optimal activity at the low pH environment of lysosomes where it is typically found in higher eukaryotes. Interestingly, DNase II has also been identified in a few genera of bacteria and is believed to have arisen via horizontal transfer. Here, we demonstrate that recombinant Burkholderia thailandensis DNase II is highly active at low pH in the absence of divalent metal ions, similar to eukaryotic DNase II. The crystal structure of B. thailandensis DNase II shows a dimeric quaternary structure which appears capable of binding double-stranded DNA. Each monomer of B. thailandensis DNase II exhibits a similar overall fold as phospholipase D (PLD), phosphatidylserine synthase (PSS) and tyrosyl-DNA phosphodiesterase (TDP), and conserved catalytic residues imply a similar mechanism. The structural and biochemical data presented here provide insights into the atomic structure and catalytic mechanism of DNase II.
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Affiliation(s)
- Armando Varela-Ramirez
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98110, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Adrian A Mejia
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968, USA
| | - Isabelle Q Phan
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98110, USA.,Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Ave N, Seattle, WA 98109, USA
| | - Donald D Lorimer
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98110, 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 98110, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Renato J Aguilera
- Department of Biological Sciences, Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968, USA
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43
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Abendroth J, Varela-Ramirez A, Mejia AA, Phan IQ, Lorimer DD, Aguilera RJ, Edwards TE. Crystal structure of acid deoxyribonuclease. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s010876731709763x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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44
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Sullivan AH, Dranow DM, Horanyi PS, Lorimer DD, Edwards TE, Abendroth J. Crystal structures of thiamine monophosphate kinase from Acinetobacter baumannii in complex with substrates and products. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s0108767317098713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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45
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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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McKary MG, Abendroth J, Edwards TE, Johnson RJ. Structural Basis for the Strict Substrate Selectivity of the Mycobacterial Hydrolase LipW. Biochemistry 2016; 55:7099-7111. [PMID: 27936614 DOI: 10.1021/acs.biochem.6b01057] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The complex life cycle of Mycobacterium tuberculosis requires diverse energy mobilization and utilization strategies facilitated by a battery of lipid metabolism enzymes. Among lipid metabolism enzymes, the Lip family of mycobacterial serine hydrolases is essential to lipid scavenging, metabolic cycles, and reactivation from dormancy. On the basis of the homologous rescue strategy for mycobacterial drug targets, we have characterized the three-dimensional structure of full length LipW from Mycobacterium marinum, the first structure of a catalytically active Lip family member. LipW contains a deep, expansive substrate-binding pocket with only a narrow, restrictive active site, suggesting tight substrate selectivity for short, unbranched esters. Structural alignment reinforced this strict substrate selectivity of LipW, as the binding pocket of LipW aligned most closely with the bacterial acyl esterase superfamily. Detailed kinetic analysis of two different LipW homologues confirmed this strict substrate selectivity, as each homologue selected for unbranched propionyl ester substrates, irrespective of the alcohol portion of the ester. Using comprehensive substitutional analysis across the binding pocket, the strict substrate selectivity of LipW for propionyl esters was assigned to a narrow funnel in the acyl-binding pocket capped by a key hydrophobic valine residue. The polar, negatively charged alcohol-binding pocket also contributed to substrate orientation and stabilization of rotameric states in the catalytic serine. Together, the structural, enzymatic, and substitutional analyses of LipW provide a connection between the structure and metabolic properties of a Lip family hydrolase that refines its biological function in active and dormant tuberculosis infection.
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Affiliation(s)
- Magy G McKary
- Department of Chemistry, Butler University , 4600 Sunset Avenue, Indianapolis, Indiana 46208, United States
| | - Jan Abendroth
- Beryllium Discovery Corporation, Seattle Structural Genomics Center for Infectious Disease (SSGCID) , 7869 Northeast Day Road West, Bainbridge Island, Washington 98110, United States
| | - Thomas E Edwards
- Beryllium Discovery Corporation, Seattle Structural Genomics Center for Infectious Disease (SSGCID) , 7869 Northeast Day Road West, Bainbridge Island, Washington 98110, United States
| | - R Jeremy Johnson
- Department of Chemistry, Butler University , 4600 Sunset Avenue, Indianapolis, Indiana 46208, United States
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47
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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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48
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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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49
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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 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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 01/27/2015] [Indexed: 11/10/2022]
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
| | - Ryan Choi
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
| | - Abigail Wall
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
| | - Matthew C Clifton
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
| | - Christine M Lukacs
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
| | - Wesley Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
| | - Peter Myler
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
| | - Don D Lorimer
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease, http://www.ssgcid.org, USA
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50
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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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