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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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Pierce PG, Hartnett BE, Laughlin TM, Blain JM, Mayclin SJ, Bolejack MJ, Myers JB, Higgins TW, Dranow DM, Sullivan A, Lorimer DD, Edwards TE, Hagen TJ, Horn JR, Myler PJ. Crystal structure and biophysical characterization of IspD from Burkholderia thailandensis and Mycobacterium paratuberculosis. Acta Crystallogr F Struct Biol Commun 2024; 80:43-51. [PMID: 38305785 PMCID: PMC10836425 DOI: 10.1107/s2053230x24000621] [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: 08/09/2023] [Accepted: 01/17/2024] [Indexed: 02/03/2024] Open
Abstract
The methylerythritol phosphate (MEP) pathway is a metabolic pathway that produces the isoprenoids isopentyl pyrophosphate and dimethylallyl pyrophosphate. Notably, the MEP pathway is present in bacteria and not in mammals, which makes the enzymes of the MEP pathway attractive targets for discovering new anti-infective agents due to the reduced chances of off-target interactions leading to side effects. There are seven enzymes in the MEP pathway, the third of which is IspD. Two crystal structures of Burkholderia thailandensis IspD (BtIspD) were determined: an apo structure and that of a complex with cytidine triphosphate (CTP). Comparison of the CTP-bound BtIspD structure with the apo structure revealed that CTP binding stabilizes the loop composed of residues 13-19. The apo structure of Mycobacterium paratuberculosis IspD (MpIspD) is also reported. The melting temperatures of MpIspD and BtIspD were evaluated by circular dichroism. The moderate Tm values suggest that a thermal shift assay may be feasible for future inhibitor screening. Finally, the binding affinity of CTP for BtIspD was evaluated by isothermal titration calorimetry. These structural and biophysical data will aid in the discovery of IspD inhibitors.
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Affiliation(s)
- Phillip G Pierce
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA
| | - Brian E Hartnett
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 Lincoln Highway, DeKalb, IL 60115, USA
| | - Tosha M Laughlin
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 Lincoln Highway, DeKalb, IL 60115, USA
| | - Joy M Blain
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 Lincoln Highway, DeKalb, IL 60115, USA
| | | | | | - Janette B Myers
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA
| | - Tate W Higgins
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA
| | - David M Dranow
- UCB Pharma, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Amy Sullivan
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA
| | - Donald D Lorimer
- UCB Pharma, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Thomas E Edwards
- UCB Pharma, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Timothy J Hagen
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 Lincoln Highway, DeKalb, IL 60115, USA
| | - James R Horn
- Department of Chemistry and Biochemistry, Northern Illinois University, 1425 Lincoln Highway, DeKalb, IL 60115, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA
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Xie B, Maker A, Priest AV, Dranow DM, Phan JN, Edwards TE, Staker BL, Myler PJ, Gumbiner BM, Sivasankar S. Molecular mechanism for strengthening E-cadherin adhesion using a monoclonal antibody. Proc Natl Acad Sci U S A 2022; 119:e2204473119. [PMID: 35921442 PMCID: PMC9371698 DOI: 10.1073/pnas.2204473119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 07/07/2022] [Indexed: 12/14/2022] Open
Abstract
E-cadherin (Ecad) is an essential cell-cell adhesion protein with tumor suppression properties. The adhesive state of Ecad can be modified by the monoclonal antibody 19A11, which has potential applications in reducing cancer metastasis. Using X-ray crystallography, we determine the structure of 19A11 Fab bound to Ecad and show that the antibody binds to the first extracellular domain of Ecad near its primary adhesive motif: the strand-swap dimer interface. Molecular dynamics simulations and single-molecule atomic force microscopy demonstrate that 19A11 interacts with Ecad in two distinct modes: one that strengthens the strand-swap dimer and one that does not alter adhesion. We show that adhesion is strengthened by the formation of a salt bridge between 19A11 and Ecad, which in turn stabilizes the swapped β-strand and its complementary binding pocket. Our results identify mechanistic principles for engineering antibodies to enhance Ecad adhesion.
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Affiliation(s)
- Bin Xie
- Biophysics Graduate Group, University of California, Davis, CA, 95616
- Department of Biomedical Engineering, University of California, Davis, CA, 95616
| | - Allison Maker
- Seattle Children’s Research Institute, Center for Developmental Biology and Regenerative Medicine, Seattle, WA, 98101
- Department of Biochemistry, University of Washington, Seattle, WA, 98195
| | - Andrew V. Priest
- Department of Biomedical Engineering, University of California, Davis, CA, 95616
| | - David M. Dranow
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, 98109
- UCB Pharma, Bainbridge Island, WA, 98110
| | - Jenny N. Phan
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, 98109
- UCB Pharma, Bainbridge Island, WA, 98110
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, 98109
- UCB Pharma, Bainbridge Island, WA, 98110
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, 98109
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, 98109
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, 98109
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, 98109
- Department of Pediatrics, University of Washington, Seattle, WA, 98195
| | - Barry M. Gumbiner
- Seattle Children’s Research Institute, Center for Developmental Biology and Regenerative Medicine, Seattle, WA, 98101
- Department of Biochemistry, University of Washington, Seattle, WA, 98195
- Department of Pediatrics, University of Washington, Seattle, WA, 98195
| | - Sanjeevi Sivasankar
- Biophysics Graduate Group, University of California, Davis, CA, 95616
- Department of Biomedical Engineering, University of California, Davis, CA, 95616
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Brooks L, Subramanian S, Dranow DM, Mayclin SJ, Myler PJ, Asojo OA. Crystal structures of glutamyl-tRNA synthetase from Elizabethkingia anopheles and E. meningosepticum. Acta Crystallogr F Struct Biol Commun 2022; 78:306-312. [PMID: 35924598 PMCID: PMC9350836 DOI: 10.1107/s2053230x22007555] [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: 05/26/2022] [Accepted: 07/25/2022] [Indexed: 11/24/2022] Open
Abstract
Elizabethkingia bacteria cause opportunistic infections in neonates, the elderly and the immunocompromised with mortality rates of up to 40%. The high-resolution structures of glutamyl-tRNA synthetase (GluRS) from E. meningosepticum and E. anopheles reveal similarities to bacterial GluRSs that can be exploited to accelerate rational drug discovery for these globally important emerging infectious Gram-negative bacteria. Elizabethkingia bacteria are globally emerging pathogens that cause opportunistic and nosocomial infections, with up to 40% mortality among the immunocompromised. Elizabethkingia species are in the pipeline of organisms for high-throughput structural analysis at the Seattle Structural Genomics Center for Infectious Disease (SSGCID). These efforts include the structure–function analysis of potential therapeutic targets. Glutamyl-tRNA synthetase (GluRS) is essential for tRNA aminoacylation and is under investigation as a bacterial drug target. The SSGCID produced, crystallized and determined high-resolution structures of GluRS from E. meningosepticum (EmGluRS) and E. anopheles (EaGluRS). EmGluRS was co-crystallized with glutamate, while EaGluRS is an apo structure. EmGluRS shares ∼97% sequence identity with EaGluRS but less than 39% sequence identity with any other structure in the Protein Data Bank. EmGluRS and EaGluRS have the prototypical bacterial GluRS topology. EmGluRS and EaGluRS have similar binding sites and tertiary structures to other bacterial GluRSs that are promising drug targets. These structural similarities can be exploited for drug discovery.
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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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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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Porter I, Neal T, Walker Z, Hayes D, Fowler K, Billups N, Rhoades A, Smith C, Smith K, Staker BL, Dranow DM, Mayclin SJ, Subramanian S, Edwards TE, Myler PJ, Asojo OA. Crystal structures of FolM alternative dihydrofolate reductase 1 from Brucella suis and Brucella canis. Acta Crystallogr F Struct Biol Commun 2022; 78:31-38. [PMID: 34981773 PMCID: PMC8725004 DOI: 10.1107/s2053230x21013078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/08/2021] [Indexed: 11/06/2023] Open
Abstract
Members of the bacterial genus Brucella cause brucellosis, a zoonotic disease that affects both livestock and wildlife. Brucella are category B infectious agents that can be aerosolized for biological warfare. As part of the structural genomics studies at the Seattle Structural Genomics Center for Infectious Disease (SSGCID), FolM alternative dihydrofolate reductases 1 from Brucella suis and Brucella canis were produced and their structures are reported. The enzymes share ∼95% sequence identity but have less than 33% sequence identity to other homologues with known structure. The structures are prototypical NADPH-dependent short-chain reductases that share their highest tertiary-structural similarity with protozoan pteridine reductases, which are being investigated for rational therapeutic development.
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Affiliation(s)
- Imani Porter
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Trinity Neal
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Zion Walker
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Dylan Hayes
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Kayla Fowler
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Nyah Billups
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Anais Rhoades
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Christian Smith
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Kaelyn Smith
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - David M Dranow
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Stephen J Mayclin
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Sandhya Subramanian
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Oluwatoyin A Asojo
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
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8
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Ghafoori SM, Robles AM, Arada AM, Shirmast P, Dranow DM, Mayclin SJ, Lorimer DD, Myler PJ, Edwards TE, Kuhn ML, Forwood JK. Structural characterization of a Type B chloramphenicol acetyltransferase from the emerging pathogen Elizabethkingia anophelis NUHP1. Sci Rep 2021; 11:9453. [PMID: 33947893 PMCID: PMC8096840 DOI: 10.1038/s41598-021-88672-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/24/2021] [Indexed: 02/02/2023] Open
Abstract
Elizabethkingia anophelis is an emerging multidrug resistant pathogen that has caused several global outbreaks. E. anophelis belongs to the large family of Flavobacteriaceae, which contains many bacteria that are plant, bird, fish, and human pathogens. Several antibiotic resistance genes are found within the E. anophelis genome, including a chloramphenicol acetyltransferase (CAT). CATs play important roles in antibiotic resistance and can be transferred in genetic mobile elements. They catalyse the acetylation of the antibiotic chloramphenicol, thereby reducing its effectiveness as a viable drug for therapy. Here, we determined the high-resolution crystal structure of a CAT protein from the E. anophelis NUHP1 strain that caused a Singaporean outbreak. Its structure does not resemble that of the classical Type A CATs but rather exhibits significant similarity to other previously characterized Type B (CatB) proteins from Pseudomonas aeruginosa, Vibrio cholerae and Vibrio vulnificus, which adopt a hexapeptide repeat fold. Moreover, the CAT protein from E. anophelis displayed high sequence similarity to other clinically validated chloramphenicol resistance genes, indicating it may also play a role in resistance to this antibiotic. Our work expands the very limited structural and functional coverage of proteins from Flavobacteriaceae pathogens which are becoming increasingly more problematic.
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Affiliation(s)
| | - Alyssa M Robles
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, USA
| | - Angelika M Arada
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, USA
| | - Paniz Shirmast
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2650, Australia
| | - David M Dranow
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, USA
- UCB Pharma, Bainbridge Island, WA, USA
| | - Stephen J Mayclin
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, USA
- UCB Pharma, Bainbridge Island, WA, USA
| | - Donald D Lorimer
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, USA
- UCB Pharma, Bainbridge Island, WA, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, USA
- Seattle Children's Research Institute, University of Washington, Seattle, WA, USA
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, USA
- UCB Pharma, Bainbridge Island, WA, USA
| | - Misty L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, USA
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2650, Australia.
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9
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Rai G, Urban DJ, Mott BT, Hu X, Yang SM, Benavides GA, Johnson MS, Squadrito GL, Brimacombe KR, Lee TD, Cheff DM, Zhu H, Henderson MJ, Pohida K, Sulikowski GA, Dranow DM, Kabir M, Shah P, Padilha E, Tao D, Fang Y, Christov PP, Kim K, Jana S, Muttil P, Anderson T, Kunda NK, Hathaway HJ, Kusewitt DF, Oshima N, Cherukuri M, Davies DR, Norenberg JP, Sklar LA, Moore WJ, Dang CV, Stott GM, Neckers L, Flint AJ, Darley-Usmar VM, Simeonov A, Waterson AG, Jadhav A, Hall MD, Maloney DJ. Pyrazole-Based Lactate Dehydrogenase Inhibitors with Optimized Cell Activity and Pharmacokinetic Properties. J Med Chem 2020; 63:10984-11011. [PMID: 32902275 DOI: 10.1021/acs.jmedchem.0c00916] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Lactate dehydrogenase (LDH) catalyzes the conversion of pyruvate to lactate, with concomitant oxidation of reduced nicotinamide adenine dinucleotide as the final step in the glycolytic pathway. Glycolysis plays an important role in the metabolic plasticity of cancer cells and has long been recognized as a potential therapeutic target. Thus, potent, selective inhibitors of LDH represent an attractive therapeutic approach. However, to date, pharmacological agents have failed to achieve significant target engagement in vivo, possibly because the protein is present in cells at very high concentrations. We report herein a lead optimization campaign focused on a pyrazole-based series of compounds, using structure-based design concepts, coupled with optimization of cellular potency, in vitro drug-target residence times, and in vivo PK properties, to identify first-in-class inhibitors that demonstrate LDH inhibition in vivo. The lead compounds, named NCATS-SM1440 (43) and NCATS-SM1441 (52), possess desirable attributes for further studying the effect of in vivo LDH inhibition.
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Affiliation(s)
- Ganesha Rai
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Daniel J Urban
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Bryan T Mott
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Xin Hu
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Shyh-Ming Yang
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Gloria A Benavides
- Mitochondrial Medicine Laboratory, Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Michelle S Johnson
- Mitochondrial Medicine Laboratory, Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Giuseppe L Squadrito
- Mitochondrial Medicine Laboratory, Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Kyle R Brimacombe
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Tobie D Lee
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Dorian M Cheff
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Hu Zhu
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Mark J Henderson
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Katherine Pohida
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Gary A Sulikowski
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - David M Dranow
- Beryllium Discovery Corp., 7869 Day Road West, Bainbridge Island, Washington 98110, United States
| | - Md Kabir
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Pranav Shah
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Elias Padilha
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Dingyin Tao
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Yuhong Fang
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Plamen P Christov
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Kwangho Kim
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Somnath Jana
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Pavan Muttil
- College of Pharmacy, University of New Mexico Health Sciences Center, Albuquerque, New Mexico 87131, United States
| | - Tamara Anderson
- College of Pharmacy, University of New Mexico Health Sciences Center, Albuquerque, New Mexico 87131, United States
| | - Nitesh K Kunda
- College of Pharmacy, University of New Mexico Health Sciences Center, Albuquerque, New Mexico 87131, United States
| | - Helen J Hathaway
- College of Pharmacy, University of New Mexico Health Sciences Center, Albuquerque, New Mexico 87131, United States
| | - Donna F Kusewitt
- Dept of Pathology, University of New Mexico Cancer Center, Albuquerque, New Mexico 87131, United States
| | - Nobu Oshima
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Murali Cherukuri
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Douglas R Davies
- Beryllium Discovery Corp., 7869 Day Road West, Bainbridge Island, Washington 98110, United States
| | - Jeffrey P Norenberg
- College of Pharmacy, University of New Mexico Health Sciences Center, Albuquerque, New Mexico 87131, United States
| | - Larry A Sklar
- Dept of Pathology, University of New Mexico Cancer Center, Albuquerque, New Mexico 87131, United States
| | - William J Moore
- NExT Program Support, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Chi V Dang
- Abramson Cancer Center, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.,Ludwig Institute for Cancer Research, New York, New York 10017, United States
| | - Gordon M Stott
- NExT Program Support, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Leonard Neckers
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Andrew J Flint
- NExT Program Support, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Victor M Darley-Usmar
- Mitochondrial Medicine Laboratory, Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Alex G Waterson
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - David J Maloney
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
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10
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Plewe MB, Sokolova NV, Gantla VR, Brown ER, Naik S, Fetsko A, Lorimer DD, Dranow DM, Smutney H, Bullen J, Sidhu R, Master A, Wang J, Kallel EA, Zhang L, Kalveram B, Freiberg AN, Henkel G, McCormack K. Discovery of Adamantane Carboxamides as Ebola Virus Cell Entry and Glycoprotein Inhibitors. ACS Med Chem Lett 2020; 11:1160-1167. [PMID: 32550996 DOI: 10.1021/acsmedchemlett.0c00025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/21/2020] [Indexed: 12/24/2022] Open
Abstract
We identified and explored the structure-activity-relationship (SAR) of an adamantane carboxamide chemical series of Ebola virus (EBOV) inhibitors. Selected analogs exhibited half-maximal inhibitory concentrations (EC50 values) of ∼10-15 nM in vesicular stomatitis virus (VSV) pseudotyped EBOV (pEBOV) infectivity assays, low hundred nanomolar EC50 activity against wild type EBOV, aqueous solubility >20 mg/mL, and attractive metabolic stability in human and nonhuman liver microsomes. X-ray cocrystallographic characterizations of a lead compound with the EBOV glycoprotein (GP) established the EBOV GP as a target for direct compound inhibitory activity and further provided relevant structural models that may assist in identifying optimized therapeutic candidates.
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Affiliation(s)
- Michael B. Plewe
- Arisan Therapeutics, 11189 Sorrento Valley Road, Suite 104, San Diego, California 92121, United States
| | - Nadezda V. Sokolova
- Arisan Therapeutics, 11189 Sorrento Valley Road, Suite 104, San Diego, California 92121, United States
| | - Vidyasagar Reddy Gantla
- Arisan Therapeutics, 11189 Sorrento Valley Road, Suite 104, San Diego, California 92121, United States
| | - Eric R. Brown
- Arisan Therapeutics, 11189 Sorrento Valley Road, Suite 104, San Diego, California 92121, United States
| | - Shibani Naik
- Arisan Therapeutics, 11189 Sorrento Valley Road, Suite 104, San Diego, California 92121, United States
| | - Alexandra Fetsko
- Arisan Therapeutics, 11189 Sorrento Valley Road, Suite 104, San Diego, California 92121, United States
| | - Donald D. Lorimer
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98105, United States
- UCB Pharma, 7869 NE Day Road West, Bainbridge Island, Washington 98110, United States
| | - David M. Dranow
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98105, United States
- UCB Pharma, 7869 NE Day Road West, Bainbridge Island, Washington 98110, United States
| | - Hayden Smutney
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98105, United States
- UCB Pharma, 3 Preston Court, Bedford, Massachusetts 01730, United States
| | - Jameson Bullen
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98105, United States
- UCB Pharma, 7869 NE Day Road West, Bainbridge Island, Washington 98110, United States
| | - Rana Sidhu
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98105, United States
- UCB Pharma, 3 Preston Court, Bedford, Massachusetts 01730, United States
| | - Arshil Master
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98105, United States
- UCB Pharma, 3 Preston Court, Bedford, Massachusetts 01730, United States
| | - Junru Wang
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98105, United States
- UCB Pharma, 3 Preston Court, Bedford, Massachusetts 01730, United States
| | - E. Adam Kallel
- Victrix, 12631 Bendito Drive, San Diego, California 92128, United States
| | | | | | | | - Greg Henkel
- Arisan Therapeutics, 11189 Sorrento Valley Road, Suite 104, San Diego, California 92121, United States
| | - Ken McCormack
- Arisan Therapeutics, 11189 Sorrento Valley Road, Suite 104, San Diego, California 92121, United States
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11
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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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12
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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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13
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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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14
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Pena N, Dranow DM, Hu Y, Escamilla Y, Bullard JM. Characterization and structure determination of prolyl-tRNA synthetase from Pseudomonas aeruginosa and development as a screening platform. Protein Sci 2019; 28:727-737. [PMID: 30666738 PMCID: PMC6423717 DOI: 10.1002/pro.3579] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 01/17/2019] [Indexed: 11/09/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic multi-drug resistant pathogen implicated as a causative agent in nosocomial and community acquired bacterial infections. The gene encoding prolyl-tRNA synthetase (ProRS) from P. aeruginosa was overexpressed in Escherichia coli and the resulting protein was characterized. ProRS was kinetically evaluated and the KM values for interactions with ATP, proline, and tRNA were 154, 122, and 5.5 μM, respectively. The turn-over numbers, kcatobs , for interactions with these substrates were calculated to be 5.5, 6.3, and 0.2 s-1 , respectively. The crystal structure of the α2 form of P. aeruginosa ProRS was solved to 2.60 Å resolution. The amino acid sequence and X-ray crystal structure of P. aeruginosa ProRS was analyzed and compared with homologs in which the crystal structures have been solved. The amino acids that interact with ATP and proline are well conserved in the active site region and overlay of the crystal structure with ProRS homologs conforms to a similar overall three-dimensional structure. ProRS was developed into a screening platform using scintillation proximity assay (SPA) technology and used to screen 890 chemical compounds, resulting in the identification of two inhibitory compounds, BT06A02 and BT07H05. This work confirms the utility of a screening system based on the functionality of ProRS from P. aeruginosa.
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Affiliation(s)
- Noah Pena
- The University of Texas – RGVEdinburgTexas 78541
| | - David M. Dranow
- Seattle Structural Genomics Center for Infectious DiseaseSeattleWA 98109
- Beryllium Discovery CorpBainbridge IslandWA 98110
| | - Yanmei Hu
- The University of Texas – RGVEdinburgTexas 78541
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15
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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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16
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Asojo OA, Dranow DM, Serbzhinskiy D, Subramanian S, Staker B, Edwards TE, Myler PJ. Crystal structure of chorismate mutase from Burkholderia thailandensis. Acta Crystallogr F Struct Biol Commun 2018; 74:294-299. [PMID: 29717997 PMCID: PMC5931142 DOI: 10.1107/s2053230x1800506x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 03/28/2018] [Indexed: 11/10/2022] Open
Abstract
Burkholderia thailandensis is often used as a model for more virulent members of this genus of proteobacteria that are highly antibiotic-resistant and are potential agents of biological warfare that are infective by inhalation. As part of ongoing efforts to identify potential targets for the development of rational therapeutics, the structures of enzymes that are absent in humans, including that of chorismate mutase from B. thailandensis, have been determined by the Seattle Structural Genomics Center for Infectious Disease. The high-resolution structure of chorismate mutase from B. thailandensis was determined in the monoclinic space group P21 with three homodimers per asymmetric unit. The overall structure of each protomer has the prototypical AroQγ topology and shares conserved binding-cavity residues with other chorismate mutases, including those with which it has no appreciable sequence identity.
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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
| | - David M. Dranow
- Beryllium Discovery Corporation, Bainbridge Island, WA 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Dmitry Serbzhinskiy
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Sandhya Subramanian
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Center for Infectious Disease Research, 307 Westlake Avenue North Suite 500, Seattle, WA 98109, USA
| | - Bart Staker
- 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
| | - Thomas E. Edwards
- Beryllium Discovery Corporation, Bainbridge Island, WA 98110, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Center for Infectious Disease Research, 307 Westlake Avenue North Suite 500, Seattle, WA 98109, USA
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17
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Rai G, Brimacombe KR, Mott BT, Urban DJ, Hu X, Yang SM, Lee TD, Cheff DM, Kouznetsova J, Benavides GA, Pohida K, Kuenstner EJ, Luci DK, Lukacs CM, Davies DR, Dranow DM, Zhu H, Sulikowski G, Moore WJ, Stott GM, Flint AJ, Hall MD, Darley-Usmar VM, Neckers LM, Dang CV, Waterson AG, Simeonov A, Jadhav A, Maloney DJ. Discovery and Optimization of Potent, Cell-Active Pyrazole-Based Inhibitors of Lactate Dehydrogenase (LDH). J Med Chem 2017; 60:9184-9204. [PMID: 29120638 PMCID: PMC5894102 DOI: 10.1021/acs.jmedchem.7b00941] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We report the discovery and medicinal chemistry optimization of a novel series of pyrazole-based inhibitors of human lactate dehydrogenase (LDH). Utilization of a quantitative high-throughput screening paradigm facilitated hit identification, while structure-based design and multiparameter optimization enabled the development of compounds with potent enzymatic and cell-based inhibition of LDH enzymatic activity. Lead compounds such as 63 exhibit low nM inhibition of both LDHA and LDHB, submicromolar inhibition of lactate production, and inhibition of glycolysis in MiaPaCa2 pancreatic cancer and A673 sarcoma cells. Moreover, robust target engagement of LDHA by lead compounds was demonstrated using the cellular thermal shift assay (CETSA), and drug-target residence time was determined via SPR. Analysis of these data suggests that drug-target residence time (off-rate) may be an important attribute to consider for obtaining potent cell-based inhibition of this cancer metabolism target.
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Affiliation(s)
- Ganesha Rai
- National Center for Advancing Translational Sciences, National Institutes of Health , 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Kyle R Brimacombe
- National Center for Advancing Translational Sciences, National Institutes of Health , 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Bryan T Mott
- National Center for Advancing Translational Sciences, National Institutes of Health , 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Daniel J Urban
- National Center for Advancing Translational Sciences, National Institutes of Health , 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Xin Hu
- National Center for Advancing Translational Sciences, National Institutes of Health , 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Shyh-Ming Yang
- National Center for Advancing Translational Sciences, National Institutes of Health , 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Tobie D Lee
- National Center for Advancing Translational Sciences, National Institutes of Health , 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Dorian M Cheff
- National Center for Advancing Translational Sciences, National Institutes of Health , 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Jennifer Kouznetsova
- National Center for Advancing Translational Sciences, National Institutes of Health , 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Gloria A Benavides
- Mitochondrial Medicine Laboratory, Department of Pathology, University of Alabama at Birmingham , Birmingham, Alabama 35294, United States
| | - Katie Pohida
- National Center for Advancing Translational Sciences, National Institutes of Health , 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Eric J Kuenstner
- National Center for Advancing Translational Sciences, National Institutes of Health , 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Diane K Luci
- National Center for Advancing Translational Sciences, National Institutes of Health , 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Christine M Lukacs
- Beryllium Discovery Corp. , 7869 Day Road West, Bainbridge Island, Washington 98110, United States
| | - Douglas R Davies
- Beryllium Discovery Corp. , 7869 Day Road West, Bainbridge Island, Washington 98110, United States
| | - David M Dranow
- Beryllium Discovery Corp. , 7869 Day Road West, Bainbridge Island, Washington 98110, United States
| | - Hu Zhu
- National Center for Advancing Translational Sciences, National Institutes of Health , 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Gary Sulikowski
- Vanderbilt Institute of Chemical Biology, Vanderbilt University , Nashville, Tennessee 37232, United States
| | - William J Moore
- NExT Program Support, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research , Frederick, Maryland 21702, United States
| | - Gordon M Stott
- NExT Program Support, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research , Frederick, Maryland 21702, United States
| | - Andrew J Flint
- NExT Program Support, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research , Frederick, Maryland 21702, United States
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health , 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Victor M Darley-Usmar
- Mitochondrial Medicine Laboratory, Department of Pathology, University of Alabama at Birmingham , Birmingham, Alabama 35294, United States
| | - Leonard M Neckers
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute , 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Chi V Dang
- Abramson Cancer Center, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania , Philadephia, Pennsylvania 19104, United States
| | - Alex G Waterson
- Vanderbilt Institute of Chemical Biology, Vanderbilt University , Nashville, Tennessee 37232, United States
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health , 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institutes of Health , 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - David J Maloney
- National Center for Advancing Translational Sciences, National Institutes of Health , 9800 Medical Center Drive, Rockville, Maryland 20850, United States
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18
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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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19
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Moen SO, Edwards TE, Dranow DM, Clifton MC, Sankaran B, Van Voorhis WC, Sharma A, Manoil C, Staker BL, Myler PJ, Lorimer DD. Ligand co-crystallization of aminoacyl-tRNA synthetases from infectious disease organisms. Sci Rep 2017; 7:223. [PMID: 28303005 PMCID: PMC5428304 DOI: 10.1038/s41598-017-00367-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 02/20/2017] [Indexed: 12/15/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) charge tRNAs with their cognate amino acid, an essential precursor step to loading of charged tRNAs onto the ribosome and addition of the amino acid to the growing polypeptide chain during protein synthesis. Because of this important biological function, aminoacyl-tRNA synthetases have been the focus of anti-infective drug development efforts and two aaRS inhibitors have been approved as drugs. Several researchers in the scientific community requested aminoacyl-tRNA synthetases to be targeted in the Seattle Structural Genomics Center for Infectious Disease (SSGCID) structure determination pipeline. Here we investigate thirty-one aminoacyl-tRNA synthetases from infectious disease organisms by co-crystallization in the presence of their cognate amino acid, ATP, and/or inhibitors. Crystal structures were determined for a CysRS from Borrelia burgdorferi bound to AMP, GluRS from Borrelia burgdorferi and Burkholderia thailandensis bound to glutamic acid, a TrpRS from the eukaryotic pathogen Encephalitozoon cuniculi bound to tryptophan, a HisRS from Burkholderia thailandensis bound to histidine, and a LysRS from Burkholderia thailandensis bound to lysine. Thus, the presence of ligands may promote aaRS crystallization and structure determination. Comparison with homologous structures shows conformational flexibility that appears to be a recurring theme with this enzyme class.
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Affiliation(s)
- Spencer O Moen
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA.,Beryllium Discovery Corp, Bainbridge Island, WA, 98110, USA
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA. .,Beryllium Discovery Corp, Bainbridge Island, WA, 98110, USA.
| | - David M Dranow
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA.,Beryllium Discovery Corp, Bainbridge Island, WA, 98110, USA
| | - Matthew C Clifton
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA.,Beryllium Discovery Corp, Bainbridge Island, WA, 98110, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Advanced Light Source, Berkeley, CA, 94720, USA
| | - Wesley C Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA.,University of Washington, Seattle, WA, 98195-6423, USA
| | - Amit Sharma
- International Center for Genetic Engineering and Biotechnology, New Delhi, 110 067, India
| | - Colin Manoil
- University of Washington, Department of Genome Sciences, Seattle, WA, 98195-5065, USA
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA.,Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, WA, 98109, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA.,Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, WA, 98109, USA.,University of Washington, Department of Medical Education and Biomedical Informatics & Department of Global Health, Seattle, WA, 98195, USA
| | - Donald D Lorimer
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA.,Beryllium Discovery Corp, Bainbridge Island, WA, 98110, USA
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20
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Hewitt SN, Dranow DM, Horst BG, Abendroth JA, Forte B, Hallyburton I, Jansen C, Baragaña B, Choi R, Rivas KL, Hulverson MA, Dumais M, Edwards TE, Lorimer DD, Fairlamb AH, Gray DW, Read KD, Lehane AM, Kirk K, Myler PJ, Wernimont A, Walpole C, Stacy R, Barrett LK, Gilbert IH, Van Voorhis WC. Biochemical and Structural Characterization of Selective Allosteric Inhibitors of the Plasmodium falciparum Drug Target, Prolyl-tRNA-synthetase. ACS Infect Dis 2017; 3:34-44. [PMID: 27798837 PMCID: PMC5241706 DOI: 10.1021/acsinfecdis.6b00078] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [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] [Indexed: 12/12/2022]
Abstract
Plasmodium falciparum (Pf) prolyl-tRNA synthetase (ProRS) is one of the few chemical-genetically validated drug targets for malaria, yet highly selective inhibitors have not been described. In this paper, approximately 40,000 compounds were screened to identify compounds that selectively inhibit PfProRS enzyme activity versus Homo sapiens (Hs) ProRS. X-ray crystallography structures were solved for apo, as well as substrate- and inhibitor-bound forms of PfProRS. We identified two new inhibitors of PfProRS that bind outside the active site. These two allosteric inhibitors showed >100 times specificity for PfProRS compared to HsProRS, demonstrating this class of compounds could overcome the toxicity related to HsProRS inhibition by halofuginone and its analogues. Initial medicinal chemistry was performed on one of the two compounds, guided by the cocrystallography of the compound with PfProRS, and the results can instruct future medicinal chemistry work to optimize these promising new leads for drug development against malaria.
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Affiliation(s)
- Stephen Nakazawa Hewitt
- Center for Emerging
and Reemerging Infectious Disease (CERID), University of Washington, 750 Republican Street, Seattle, Washington 98109, United States
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
| | - David M. Dranow
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Beryllium Discovery Corporation, 7869 N.E. Day Road West, Bainbridge Island, Washington 98110, United States
| | - Benjamin G. Horst
- Center for Emerging
and Reemerging Infectious Disease (CERID), University of Washington, 750 Republican Street, Seattle, Washington 98109, United States
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
| | - Jan A. Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Beryllium Discovery Corporation, 7869 N.E. Day Road West, Bainbridge Island, Washington 98110, United States
| | - Barbara Forte
- Drug Discovery Unit (DDU), Division of Biological Chemistry and Drug
Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Irene Hallyburton
- Drug Discovery Unit (DDU), Division of Biological Chemistry and Drug
Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Chimed Jansen
- Drug Discovery Unit (DDU), Division of Biological Chemistry and Drug
Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Beatriz Baragaña
- Drug Discovery Unit (DDU), Division of Biological Chemistry and Drug
Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Ryan Choi
- Center for Emerging
and Reemerging Infectious Disease (CERID), University of Washington, 750 Republican Street, Seattle, Washington 98109, United States
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
| | - Kasey L. Rivas
- Center for Emerging
and Reemerging Infectious Disease (CERID), University of Washington, 750 Republican Street, Seattle, Washington 98109, United States
| | - Matthew A. Hulverson
- Center for Emerging
and Reemerging Infectious Disease (CERID), University of Washington, 750 Republican Street, Seattle, Washington 98109, United States
| | - Mitchell Dumais
- Center for Emerging
and Reemerging Infectious Disease (CERID), University of Washington, 750 Republican Street, Seattle, Washington 98109, United States
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Beryllium Discovery Corporation, 7869 N.E. Day Road West, Bainbridge Island, Washington 98110, United States
| | - Donald D. Lorimer
- Beryllium Discovery Corporation, 7869 N.E. Day Road West, Bainbridge Island, Washington 98110, United States
| | - Alan H. Fairlamb
- Drug Discovery Unit (DDU), Division of Biological Chemistry and Drug
Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - David W. Gray
- Drug Discovery Unit (DDU), Division of Biological Chemistry and Drug
Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Kevin D. Read
- Drug Discovery Unit (DDU), Division of Biological Chemistry and Drug
Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Adele M. Lehane
- Research School of Biology, The Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Kiaran Kirk
- Research School of Biology, The Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center for Infectious Disease Research, 307 Westlake Avenue North, Suite 500, Seattle, Washington 98109, United States
- Departments of Global Health and Biomedical
Informatics and Medical Education, University of Washington, Seattle, Washington 98195, United States
| | - Amy Wernimont
- Structure-guided Drug Discovery Coalition (SDDC), Structural Genomic Consortium, 101 College Street, MaRS South Tower, Suite 700, Toronto, Ontario M5G 1L7, Canada
| | - Chris Walpole
- Structure-guided Drug Discovery Coalition (SDDC), Structural Genomic Consortium, 101 College Street, MaRS South Tower, Suite 700, Toronto, Ontario M5G 1L7, Canada
| | - Robin Stacy
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center for Infectious Disease Research, 307 Westlake Avenue North, Suite 500, Seattle, Washington 98109, United States
| | - Lynn K. Barrett
- Center for Emerging
and Reemerging Infectious Disease (CERID), University of Washington, 750 Republican Street, Seattle, Washington 98109, United States
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
| | - Ian H. Gilbert
- Drug Discovery Unit (DDU), Division of Biological Chemistry and Drug
Discovery, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Wesley C. Van Voorhis
- Center for Emerging
and Reemerging Infectious Disease (CERID), University of Washington, 750 Republican Street, Seattle, Washington 98109, United States
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
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21
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Stanger FV, de Beer TAP, Dranow DM, Schirmer T, Phan I, Dehio C. The BID Domain of Type IV Secretion Substrates Forms a Conserved Four-Helix Bundle Topped with a Hook. Structure 2016; 25:203-211. [PMID: 27889208 DOI: 10.1016/j.str.2016.10.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [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: 08/08/2016] [Revised: 10/07/2016] [Accepted: 10/25/2016] [Indexed: 10/20/2022]
Abstract
The BID (Bep intracellular delivery) domain functions as secretion signal in a subfamily of protein substrates of bacterial type IV secretion (T4S) systems. It mediates transfer of (1) relaxases and the attached DNA during bacterial conjugation, and (2) numerous Bartonella effector proteins (Beps) during protein transfer into host cells infected by pathogenic Bartonella species. Furthermore, BID domains of Beps have often evolved secondary effector functions within host cells. Here, we provide crystal structures for three representative BID domains and describe a novel conserved fold characterized by a compact, antiparallel four-helix bundle topped with a hook. The conserved hydrophobic core provides a rigid scaffold to a surface that, despite a few conserved exposed residues and similarities in charge distribution, displays significant variability. We propose that the genuine function of BID domains as T4S signal may primarily depend on their rigid structure, while the plasticity of their surface may facilitate adaptation to secondary effector functions.
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Affiliation(s)
- Frédéric V Stanger
- Focal Area Infection Biology, Biozentrum University of Basel, 4056 Basel, Switzerland; Focal Area Structural Biology and Biophysics, Biozentrum University of Basel, 4056 Basel, Switzerland
| | - Tjaart A P de Beer
- Focal Area Infection Biology, Biozentrum University of Basel, 4056 Basel, Switzerland
| | - David M Dranow
- Seattle Structural Genomics Center for Infectious Disease, The Center for Infectious Disease Research, Seattle, WA 98109, USA; Beryllium Discovery Corp., Bainbridge Island, WA 98110, USA
| | - Tilman Schirmer
- Focal Area Structural Biology and Biophysics, Biozentrum University of Basel, 4056 Basel, Switzerland.
| | - Isabelle Phan
- Seattle Structural Genomics Center for Infectious Disease, The Center for Infectious Disease Research, Seattle, WA 98109, USA
| | - Christoph Dehio
- Focal Area Infection Biology, Biozentrum University of Basel, 4056 Basel, Switzerland.
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22
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Ojo KK, Ranade RM, Zhang Z, Dranow DM, Myers JB, Choi R, Nakazawa Hewitt S, Edwards TE, Davies DR, Lorimer D, Boyle SM, Barrett LK, Buckner FS, Fan E, Van Voorhis WC. Correction: Brucella melitensis Methionyl-tRNA-Synthetase (MetRS), a Potential Drug Target for Brucellosis. PLoS One 2016; 11:e0163641. [PMID: 27658298 PMCID: PMC5033446 DOI: 10.1371/journal.pone.0163641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0160350.].
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23
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Ojo KK, Ranade RM, Zhang Z, Dranow DM, Myers JB, Choi R, Nakazawa Hewitt S, Edwards TE, Davies DR, Lorimer D, Boyle SM, Barrett LK, Buckner FS, Fan E, Van Voorhis WC. Brucella melitensis Methionyl-tRNA-Synthetase (MetRS), a Potential Drug Target for Brucellosis. PLoS One 2016; 11:e0160350. [PMID: 27500735 PMCID: PMC4976878 DOI: 10.1371/journal.pone.0160350] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [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: 04/04/2016] [Accepted: 07/18/2016] [Indexed: 12/22/2022] Open
Abstract
We investigated Brucella melitensis methionyl-tRNA-synthetase (BmMetRS) with molecular, structural and phenotypic methods to learn if BmMetRS is a promising target for brucellosis drug development. Recombinant BmMetRS was expressed, purified from wild type Brucella melitensis biovar Abortus 2308 strain ATCC/CRP #DD-156 and screened by a thermal melt assay against a focused library of one hundred previously classified methionyl-tRNA-synthetase inhibitors of the blood stage form of Trypanosoma brucei. Three compounds showed appreciable shift of denaturation temperature and were selected for further studies on inhibition of the recombinant enzyme activity and cell viability against wild type B. melitensis strain 16M. BmMetRS protein complexed with these three inhibitors resolved into three-dimensional crystal structures and was analyzed. All three selected methionyl-tRNA-synthetase compounds inhibit recombinant BmMetRS enzymatic functions in an aminoacylation assay at varying concentrations. Furthermore, growth inhibition of B. melitensis strain 16M by the compounds was shown. Inhibitor-BmMetRS crystal structure models were used to illustrate the molecular basis of the enzyme inhibition. Our current data suggests that BmMetRS is a promising target for brucellosis drug development. However, further studies are needed to optimize lead compound potency, efficacy and safety as well as determine the pharmacokinetics, optimal dosage, and duration for effective treatment.
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Affiliation(s)
- Kayode K. Ojo
- Center for Emerging and Re-emerging Infectious Diseases (CERID), Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Ranae M. Ranade
- Center for Emerging and Re-emerging Infectious Diseases (CERID), Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Zhongsheng Zhang
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - David M. Dranow
- Beryllium, Bainbridge Island, Washington, United States of America
| | - Janette B. Myers
- Center for Emerging and Re-emerging Infectious Diseases (CERID), Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Ryan Choi
- Center for Emerging and Re-emerging Infectious Diseases (CERID), Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Steve Nakazawa Hewitt
- Center for Emerging and Re-emerging Infectious Diseases (CERID), Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | | | | | - Donald Lorimer
- Beryllium, Bainbridge Island, Washington, United States of America
| | - Stephen M. Boyle
- Center for Molecular Medicine and Infectious Diseases, Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Lynn K. Barrett
- Center for Emerging and Re-emerging Infectious Diseases (CERID), Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Frederick S. Buckner
- Center for Emerging and Re-emerging Infectious Diseases (CERID), Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Erkang Fan
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Wesley C. Van Voorhis
- Center for Emerging and Re-emerging Infectious Diseases (CERID), Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
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Clifton MC, Dranow DM, Leed A, Fulroth B, Fairman JW, Abendroth J, Atkins KA, Wallace E, Fan D, Xu G, Ni ZJ, Daniels D, Van Drie J, Wei G, Burgin AB, Golub TR, Hubbard BK, Serrano-Wu MH. A Maltose-Binding Protein Fusion Construct Yields a Robust Crystallography Platform for MCL1. PLoS One 2015; 10:e0125010. [PMID: 25909780 PMCID: PMC4409056 DOI: 10.1371/journal.pone.0125010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 03/06/2015] [Indexed: 01/26/2023] Open
Abstract
Crystallization of a maltose-binding protein MCL1 fusion has yielded a robust crystallography platform that generated the first apo MCL1 crystal structure, as well as five ligand-bound structures. The ability to obtain fragment-bound structures advances structure-based drug design efforts that, despite considerable effort, had previously been intractable by crystallography. In the ligand-independent crystal form we identify inhibitor binding modes not observed in earlier crystallographic systems. This MBP-MCL1 construct dramatically improves the structural understanding of well-validated MCL1 ligands, and will likely catalyze the structure-based optimization of high affinity MCL1 inhibitors.
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Affiliation(s)
- Matthew C. Clifton
- Beryllium, Bedford, Massachusetts, United States of America
- * E-mail: (MS-W); (MCC)
| | | | - Alison Leed
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Ben Fulroth
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | | | - Jan Abendroth
- Beryllium, Bedford, Massachusetts, United States of America
| | | | - Ellen Wallace
- Beryllium, Bedford, Massachusetts, United States of America
| | - Dazhong Fan
- Acme Bioscience, Palo Alto, California, United States of America
| | - Guoping Xu
- Acme Bioscience, Palo Alto, California, United States of America
| | - Z. J. Ni
- Acme Bioscience, Palo Alto, California, United States of America
| | - Doug Daniels
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - John Van Drie
- Van Drie Research, North Andover, Massachusetts, United States of America
| | - Guo Wei
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Alex B. Burgin
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Todd R. Golub
- The Broad Institute, Cambridge, Massachusetts, United States of America
- Dana-Farber Cancer Institute and Howard Hughes Medical Institute, Boston, Massachusetts, United States of America
| | - Brian K. Hubbard
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Michael H. Serrano-Wu
- The Broad Institute, Cambridge, Massachusetts, United States of America
- * E-mail: (MS-W); (MCC)
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25
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Baugh L, Phan I, Begley DW, Clifton MC, Armour B, Dranow DM, Taylor BM, Muruthi MM, Abendroth J, Fairman JW, Fox D, Dieterich SH, Staker BL, Gardberg AS, Choi R, Hewitt SN, Napuli AJ, Myers J, Barrett LK, Zhang Y, Ferrell M, Mundt E, Thompkins K, Tran N, Lyons-Abbott S, Abramov A, Sekar A, Serbzhinskiy D, Lorimer D, Buchko GW, Stacy R, Stewart LJ, Edwards TE, Van Voorhis WC, Myler PJ. Increasing the structural coverage of tuberculosis drug targets. Tuberculosis (Edinb) 2014; 95:142-8. [PMID: 25613812 DOI: 10.1016/j.tube.2014.12.003] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 12/10/2014] [Indexed: 01/31/2023]
Abstract
High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus "homolog-rescue" strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. Of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structures would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Cα RMSD <1 Å, >85% side chain identity, and ≥80% PSAPF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases.
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Affiliation(s)
- Loren Baugh
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Isabelle Phan
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Darren W Begley
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Matthew C Clifton
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Brianna Armour
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - David M Dranow
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Brandy M Taylor
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Marvin M Muruthi
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - James W Fairman
- Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - David Fox
- Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Shellie H Dieterich
- Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Anna S Gardberg
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States; EMD Serono Research & Development Institute, Inc., 45A Middlesex Turnpike, Billerica, MA 01821, United States
| | - Ryan Choi
- Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States
| | - Stephen N Hewitt
- Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States
| | - Alberto J Napuli
- Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States
| | - Janette Myers
- Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States
| | - Lynn K Barrett
- Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States
| | - Yang Zhang
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Micah Ferrell
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Elizabeth Mundt
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Katie Thompkins
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Ngoc Tran
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Sally Lyons-Abbott
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Ariel Abramov
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Aarthi Sekar
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Dmitri Serbzhinskiy
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Don Lorimer
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Garry W Buchko
- Seattle Structural Genomics Center for Infectious Disease, United States; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Robin Stacy
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States
| | - Lance J Stewart
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States; Institute for Protein Design, University of Washington, Box 357350, Seattle, WA 98195, United States
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States
| | - Wesley C Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States; Department of Global Health, University of Washington, Box 359931, Seattle, WA, 98195, United States; Department of Microbiology, University of Washington, Box 357735, Seattle, WA 98195, United States
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States; Department of Global Health, University of Washington, Box 359931, Seattle, WA, 98195, United States; Department of Biomedical Informatics and Medical Education, University of Washington, Box 358047, Seattle, WA 98195, United States.
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26
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Baugh L, Gallagher LA, Patrapuvich R, Clifton MC, Gardberg AS, Edwards TE, Armour B, Begley DW, Dieterich SH, Dranow DM, Abendroth J, Fairman JW, Fox D, Staker BL, Phan I, Gillespie A, Choi R, Nakazawa-Hewitt S, Nguyen MT, Napuli A, Barrett L, Buchko GW, Stacy R, Myler PJ, Stewart LJ, Manoil C, Van Voorhis WC. Combining functional and structural genomics to sample the essential Burkholderia structome. PLoS One 2013; 8:e53851. [PMID: 23382856 PMCID: PMC3561365 DOI: 10.1371/journal.pone.0053851] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 12/05/2012] [Indexed: 11/19/2022] Open
Abstract
Background The genus Burkholderia includes pathogenic gram-negative bacteria that cause melioidosis, glanders, and pulmonary infections of patients with cancer and cystic fibrosis. Drug resistance has made development of new antimicrobials critical. Many approaches to discovering new antimicrobials, such as structure-based drug design and whole cell phenotypic screens followed by lead refinement, require high-resolution structures of proteins essential to the parasite. Methodology/Principal Findings We experimentally identified 406 putative essential genes in B. thailandensis, a low-virulence species phylogenetically similar to B. pseudomallei, the causative agent of melioidosis, using saturation-level transposon mutagenesis and next-generation sequencing (Tn-seq). We selected 315 protein products of these genes based on structure-determination criteria, such as excluding very large and/or integral membrane proteins, and entered them into the Seattle Structural Genomics Center for Infection Disease (SSGCID) structure determination pipeline. To maximize structural coverage of these targets, we applied an “ortholog rescue” strategy for those producing insoluble or difficult to crystallize proteins, resulting in the addition of 387 orthologs (or paralogs) from seven other Burkholderia species into the SSGCID pipeline. This structural genomics approach yielded structures from 31 putative essential targets from B. thailandensis, and 25 orthologs from other Burkholderia species, yielding an overall structural coverage for 49 of the 406 essential gene families, with a total of 88 depositions into the Protein Data Bank. Of these, 25 proteins have properties of a potential antimicrobial drug target i.e., no close human homolog, part of an essential metabolic pathway, and a deep binding pocket. We describe the structures of several potential drug targets in detail. Conclusions/Significance This collection of structures, solubility and experimental essentiality data provides a resource for development of drugs against infections and diseases caused by Burkholderia. All expression clones and proteins created in this study are freely available by request.
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Affiliation(s)
- Loren Baugh
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Larry A. Gallagher
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Rapatbhorn Patrapuvich
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Matthew C. Clifton
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Anna S. Gardberg
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Brianna Armour
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Darren W. Begley
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | | | - David M. Dranow
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - James W. Fairman
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - David Fox
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Isabelle Phan
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Angela Gillespie
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
| | - Ryan Choi
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
| | - Steve Nakazawa-Hewitt
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
| | - Mary Trang Nguyen
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
| | - Alberto Napuli
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
| | - Lynn Barrett
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
| | - Garry W. Buchko
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Robin Stacy
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Medical Education and Biomedical Informatics, University of Washington, Seattle, Washington
| | - Lance J. Stewart
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Emerald BioStructures, Bainbridge Island, Washington, United States of America
| | - Colin Manoil
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Wesley C. Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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